详细内容（前10条）

1. ⭐ GSE329811 使用 Visium HD 对小鼠正常胰腺 (N)、胰腺炎 (P) 和 PDAC 福尔马林固定石蜡包埋 (FFPE) 样本进行单细胞空间转录组学分析。

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、spatial、Visium、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Giulia Biffi ; Wenlong Li ; Muntadher Jihad ; Alwin Koonan-LonappanSeries Type : OtherOrganism : Mus musculusWe investigated the single-cell spatial transcriptomics of murine normal pancreas (N), pancreatitis (P) and PDAC formalin-fixed paraffin-embedded (FFPE) samples using Visium HD.
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2. GSE337245 SCRMP 敲除和对照 NCI-H69 小细胞肺癌细胞的转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、transcriptome
• 📝 描述：Contributors : Yuli Chen ; Qinnan Chen ; Jiahao Guo ; Peng Huang ; Ming Sun ; Fengqi Nie ; Xianghua LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis series contains RNA-seq data from NCI-H69 small cell lung cancer cells with CRISPR/Cas9-mediated SCRMP knockout and corresponding negative control cells. SCRMP is a microprotein encoded by MIR7-3HG that promotes cisplatin resistance and DNA damage repair in SCLC. The experiment was designed to identify gene expression changes caused by SCRMP depletion and to explore pathways involved in DNA damage repair and homologous recombination.
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3. GSE337244：CSNK2B敲低后小细胞肺癌细胞中RBBP4和P300的ChIP-seq分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ChIP-seq
• 📝 描述：Contributors : Yuli Chen ; Qinnan Chen ; Jiahao Guo ; Ziwei Li ; Shaokun Yu ; Peng Huang ; Ming SunSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis ChIP-seq dataset profiles genome-wide occupancy of RBBP4 and P300 in NCI-H69 human small cell lung cancer cells after siRNA-mediated CSNK2B knockdown. The study was designed to investigate how the CSNK2B/RBBP4/P300 complex regulates chromatin occupancy and downstream transcriptional programs involved in DNA damage repair and cisplatin resistance.
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4. GSE329148 IL-2/CD25融合蛋白增强抗原特异性CD8⁺ T细胞扩增以抑制肝细胞癌

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、antigen
• 📝 描述：Contributor : Nan XuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigated how IL-2/CD25 change the Immune microenvironment of hepatocelluar carcinoma
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5. GSE299033 鉴定 PEG10 为 DICER1 相关肿瘤易感综合征的生物标志物 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNA-seq
• 📝 描述：Contributor : Mona WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground: MicroRNAs (miRNAs) are short non-coding RNA molecules that downregulate messenger RNA (mRNA) expression. Mature miRNAs (designated -5p or -3p) are produced by the endonuclease DICER1. Mature miRNAs are loaded into the AGO2-containing RNA-Induced Silencing Complex where they target mRNAs via a seed sequence in the mRNA’s 3’ untranslated region (3’ UTR). Children with pathogenic variants of DICER1 have a highly elevated risk of cancers in many different organs– recognized as DICER1-related tumour predisposition (DRTP). These tumours/lesions have one inactivated copy and one “hotspot” mutated copy of DICER1. All “hotspot” DICER1 mutations impair 5p miRNA production. DICER1 DNA sequencing has become the diagnostic standard but an immunohistochemical (IHC) diagnostic method may improve patient care via faster return of results. Methods: Using AGO2 miR-eCLIP and RNAseq data of a mouse cell model of DRTP (E1705K) I identified paternally expressed gene 10 (Peg10) as a diagnostic candidate. Validation of cell overexpression (mRNA and protein) and de-repression of Peg10 3’ UTR was assessed. Dependence on Peg10 for cell viability was measured (post 72-hour siRNA-mediated knockdown). IHC staining of two tumour microarrays (TMAs) was performed and scored (H-score) to evaluate its use in the clinic (Area Under Curve, AUC). Results: In E1705K, Peg10 displayed elevated RNA and protein levels as well as de-repression of its 3’ UTR. Peg10 knockdown does not impact cell viability. TMA1 (41 female samples) had an AUC of 0.80 (considered of good clinical utility) while TMA2 (95 male and female samples) had an AUC was 0.71 (fair clinical utility). Conclusion: E1705K identified Peg10 as a biomarker that is elevated in DRTP tumours from both sexes bearing a variety of DICER1 hotspot variants. Elevated Peg10 mRNA levels are in part due to lack of 5p-mediated interactions with its 3’ UTR.
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6. GSE337447 对小鼠骨髓纤维化脾脏进行全面的空间分析，揭示了可靶向的免疫-基质相互作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、spatial
• 📝 描述：Contributors : Bérénice Dugué ; Pia Wanner ; Mayra Ruiz Tejada Segura ; Mohamed Saad ; Lucas Greven ; Katrin Gotz ; Carmen Schalla ; Stijn Fuchs ; Gerjanne Vroeg in de wei ; Hélène Gleitz ; Anna Katharina Galyga ; Jessica Ellen Pritchard ; Tobias Schlangen ; Niklas Lutterbach ; Salim Atakhanov ; Lina Schmidt ; Marie Parrens ; Armelle Peyrat ; Damien Luque Paz ; Marie-Christine Copin ; Alexandre Guy ; Victor-Emmanuel Brett ; Olivier Mansier ; Susanne Schmitz ; Paul Wanek ; Bella Banjanin ; Stephani Schmitz ; Martina Crysandt ; Marian Clahsen-van Groningen ; Konnie Hebeda ; Sascha Dietrich ; Harald Voehringer ; Matthias Meyer-Bender ; Kristin Séré ; Chloé James ; Adam Benabid ; Ivan Costa ; Charles Dussiau ; Rebekka SchneiderSeries Type : OtherOrganism : Mus musculusSplenomegaly is a defining feature of myelofibrosis, yet the contribution of splenic mesenchymal stroma to disease progression remains unclear. We perferomed spatial transcriptomics of murine spleens to map extramedullary hematopoiesis niches. Activated red pulp reticular cells localize near hematopoietic stem and progenitor cells, and early disease shows marginal zone disruption with lymphoid depletion preceding stromal remodeling. Trajectory analyses reveal a shift of reticular cells from hematopoiesis-supportive to inflammatory and pro-fibrotic states driven by macrophage- and megakaryocyte-derived signals that activate complement and induce TNFα, TGF-β, extracellular matrix, and Thbs1 programs. Stromal deletion or pharmacological inhibition of complement component C3 suppresses these pathways, restores splenic architecture, and reduces splenomegaly and bone marrow fibrosis. These findings identify complement-dependent stromal reprogramming as a mechanism governing hematopoietic niches and a targetable axis in myelofibrosis.
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7. GSE318657 整合单细胞、蛋白质组学和组织水平分析揭示腹膜假性黏液瘤中与癌症相关的成纤维细胞程序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell
• 📝 描述：Contributors : Felix De Vuyst ; Olivier De WeverSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPseudomyxoma peritonei (PMP) is an ultra-rare mucinous neoplasm with extensive stromal remodeling, yet the role of cancer-associated fibroblasts (CAFs) remains poorly defined. CAF are abundantly present in fibrous septae containing the mucin and regions of inflammation. We established PMP-derived CAF cultures and characterized them through multiple omics and phenotypic assays. Single-cell transcriptomic profiling revealed two distinct CAF populations: fibroblast-derived CAFs enriched for characteristic CAF functionalities and mesothelial-derived CAFs expressing mesothelial markers and pathways linked to metabolism and motility, consistent with mesothelial-to-mesenchymal transition. PMP CAFs exhibit baseline invasive and contractile properties and acquire an inflammatory CAF-like phenotype upon TNF-α/IL-1β stimulation, accompanied by altered proteomic and secretome profiles. Conditioned media from PMP CAFs further promoted macrophage polarization, highlighting their role in shaping the immune microenvironment. In conclusion, our findings reveal a previously uncharacterized role for CAF in PMP, highlighting their contribution to immune modulation in this extremely scarce peritoneal malignancy.
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8. GSE301594 单细胞测序揭示了 ETV6::RUNX1 融合阳性 B 细胞急性淋巴细胞白血病 (B-ALL) 儿童复发的原因

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Guotao Guan ; Xiuxiu Wang ; Xiuxin Li ; Qi Wang ; Xiuli Li ; Xiaojun Sun ; Liying Liu ; Yunfeng Lu ; Bingju Liu ; Xinyu Li ; Ping Zhao ; Fei Gao ; Lijun Chen ; Lihua Zhao ; Yunpeng DaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensObjective: The ETV6::RUNX1 fusion is the most common genetic abnormality in childhood B-cell acute lymphoblastic leukemia (B-ALL), yet nearly 50% of relapses occur in patients initially classified as low-risk with this alteration. This study aimed to unravel the underlying pathways driving relapse in ETV6::RUNX1 positive B-ALL. Methods: Single-cell RNA sequencing (scRNA-seq) was performed on a cohort of four B-ALL patients with the ETV6::RUNX1 fusion (three newly diagnosed and one relapsed case, selected from 25 patients). Results: we discovered that relapsed samples exhibited a decline in T cell populations, an increase in CD8 Tex cells and B cells, and a higher proportion of malignant cells. Gene enrichment analysis demonstrated that IFN-γ response signaling pathways and inflammatory responses were significantly enriched in newly diagnosed samples. Conversely, the relapsed samples showed enrichment in the oxidative phosphorylation and glycolysis pathways. Additionally, analysis of cellular interactions revealed that malignant B cells could interact with T cells through LGALS9-HAVCR2, potentially leading to the exhaustion of effector T cells. Moreover, NPDC1, LEF1, and ERG exhibited higher activity levels in malignant B cells from relapsed patients, highlighting their roles in the progression and maintenance of leukemia. Conclusion: In summary, our study provides valuable insights into the potential causes of relapse in B-ALL patients with ETV6::RUNX1, providing a foundation for the identification of prospective therapeutic targets.
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9. GSE329665 将 Smad4 WT 或 Smad4 KO 胰腺导管腺癌 (PDAC) KPC (即 KrasG12D；p53 突变体) 类器官原位移植到 C57BL/6J 小鼠体内，对由此产生的小鼠胰腺肿瘤进行单核 RNA 测序 (snRNA-seq)。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：Contributors : Giulia Biffi ; Wenlong Li ; Muntadher JihadSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe investigated the impact of SMAD4 loss in PDAC tumors from orthotopically grafted organoid-derived mouse models using snRNA-sequencing.
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10. GSE329640 对从与小鼠胰腺炎 (P) 衍生类器官、PDAC 类器官或与 P 类器官初始共培养后 PDAC 类器官（即 P 到 PDAC 或顺序）的共培养物中分离的多基质流式分选进行批量 RNA 测序分析。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：Contributors : Giulia Biffi ; Wenlong Li ; Muntadher JihadSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe investigated the transcriptomic differences of multi-stroma flow-sorted from cocultures with murine pancreatitis (P)-derived organoids, PDAC organoids, or PDAC organoids following initial coculture with P organoids (ie P-to-PDAC or sequential).
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1. 纳米孔直接RNA测序拓展了我们对转录组的认识。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、transcriptome
• 📝 描述：RNA sequencing using nanopore direct RNA sequencing enables simultaneous analysis of native RNA molecules, transcript isoforms, RNA modifications, and poly(A) tails for comprehensive transcriptome… The post Nanopore direct RNA sequencing expands the view of the transcriptome appeared first on RNA-Seq Blog.
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2. 罗氏宣布推出AXELIOS 1，这是一款变革性的下一代测序平台。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing capabilities are expanding with Roche’s AXELIOS 1 platform, offering faster, scalable sequencing to support genomics research, single-cell studies, and future clinical applications… The post Roche announces the launch of AXELIOS 1, a transformative next-generation sequencing platform appeared first on RNA-Seq Blog.
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• GSE327286 Kv8.2基因敲除小鼠视网膜RNA测序
• GSE267711 利用人类转录因子对核小体进行全基因组旋转和平移相位分析
• GSE266494 利用人类转录因子对核小体进行全基因组旋转和平移相位分析
• GSE153235 TLR3抑制剂对沙眼衣原体感染的T24/83细胞转录组的影响
• GSE336668 水凝胶递送凋亡中性粒细胞可调节伤口愈合过程中巨噬细胞的血管生成和炎症反应
• GSE327277 LPS 或 TNF-α 刺激的 THP-1 细胞中 Delta-like 4 (Dll4) 敲低的批量 RNA-seq 分析
• GSE299299 鉴定出 PEG10 作为 DICER1 相关肿瘤易感综合征的生物标志物
• GSE269111 胶质血管相互作用在血管病理学和阿尔茨海默病中的作用
• GSE268803 炎症对3D培养的人类星形胶质细胞的影响
• GSE268780 纤连蛋白通过抑制稳态胶质血管串扰介导血管病理与阿尔茨海默病之间的相互作用
• GSE266547 人类基因组中核小体的平移和旋转设置
• GSE266495 利用人类转录因子对核小体进行全基因组旋转和平移相位分析 [ChIP-exo]
• GSE196618 合成转录因子可克服持续存在的抑制性染色质标记 [RNA-seq]
• GSE196617 合成转录因子可克服持续存在的抑制性染色质标记 [ChIP-seq]
• GSE337334 ARHGAP29缺失的人类胚胎腭间充质细胞转录组分析
• GSE336958 表型 CRISPR 筛选鉴定出 ZBTB10 是人类滋养层分化的新型调节因子 [RNA-Seq BeWo]
• GSE336955 表型 CRISPR 筛选鉴定出 ZBTB10 是人类滋养层分化的新型调节因子 [ChIP-Seq]
• GSE336823 胸腺-卵巢轴失调促进虚拟记忆T细胞极化，从而加重多囊卵巢综合征的病理 [scRNAseq-human]
• GSE336822 胸腺-卵巢轴失调促进虚拟记忆T细胞极化，从而加重多囊卵巢综合征的病理 [scRNAseq-mouse]
• GSE319517 皮下MC38结直肠癌的生长引发轻度恶病质
• GSE301833 脑渗透性血液蛋白图谱将神经保护与阿尔茨海默病风险基因联系起来
• GSE301832 脑渗透性血液蛋白图谱将神经保护与阿尔茨海默病风险基因联系起来 [snRNAseq_microglia]
• GSE301830 脑渗透性血液蛋白图谱将神经保护与阿尔茨海默病风险基因联系起来 [snRNAseq_astrocyte]
• GSE301828 脑渗透性血液蛋白图谱将神经保护与阿尔茨海默病风险基因联系起来 [bulk_RNAseq_astroocyte]
• GSE301825 脑渗透性血液蛋白图谱将神经保护与阿尔茨海默病风险基因联系起来 [bulk_RNAseq_astroocyte_AD]
• GSE294325 甲状腺癌相关的 EZH1 Q571R 突变驱动染色质致密化和 H3K27me3 入侵活性染色质
• GSE294323 甲状腺癌相关的 EZH1 Q571R 突变驱动染色质致密化和 H3K27me3 入侵活性染色质
• GSE294321 甲状腺癌相关的 EZH1 Q571R 突变驱动染色质致密化和 H3K27me3 入侵活性染色质
• GSE294320 甲状腺癌相关的 EZH1 Q571R 突变驱动染色质致密化和 H3K27me3 入侵活性染色质
• GSE326162 RNA-seq 分析高糖条件下过表达 ATF7 的 HaCaT 角质形成细胞
• GSE312869 纤维蛋白介导的2’-O-甲基化作用抑制无帽肠道病毒RNA的翻译
• GSE308872 ILC2 在胰腺的稳态、炎症和肿瘤条件下调控 Pi16+Dpp4+Ly6c+ 成纤维细胞祖细胞微环境（Dpp4CreERT2 谱系追踪 scRNA-seq）
• GSE305709 无体外转录、计算机合成的蛋白质编码RNA寡核苷酸，用于快速生产个性化癌症疫苗
• GSE248386 ILC2 调控胰腺中的 Pi16+ 成纤维细胞祖细胞微环境（急性胰腺炎 scRNA-seq）
• GSE248385 ILC2 调控胰腺中的 Pi16+ 成纤维细胞祖细胞微环境（原始 ILC2 scRNA-seq）
• GSE248384 ILC2 在胰腺稳态和炎症条件下调控 Pi16+ 成纤维细胞祖细胞微环境（ILC2 批量 RNA 测序）
• GSE248383 ILC2 在胰腺稳态和炎症条件下调控 Pi16+ 成纤维细胞祖细胞微环境（共培养批量 RNA 测序）