title: polyA plus RNA-seq from GM18498 (ENCSR398UQG)

summary:
GM18498 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21297 (ENCSR398IOH)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR398FYY)


title: total RNA-seq from GM21509 (ENCSR397EUF)


title: snATAC-seq from HepG2 (ENCSR398OHC)

type: Genome binding/occupancy profiling by high throughput sequencing


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR397FKH)


title: long read RNA-seq from kidney (ENCSR397AFD)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR396TZQ)


title: total RNA-seq from GM21335 (ENCSR396RWR)


title: total RNA-seq from GM19374 (ENCSR395XGU)


title: total RNA-seq from inflammatory macrophage (ENCSR395TPM)


title: long read RNA-seq from heart (ENCSR394MBR)


title: total RNA-seq from GM18505 (ENCSR392YTM)


title: total RNA-seq from HG03520 (ENCSR391DEQ)


title: snATAC-seq from lower lobe of left lung (ENCSR391BWM)


title: RhoA in postnatal spinal motoneuron is essential for peripheral myelination

status: Public on Jul 30 2026

city: Guangzhou

first: YE

last: HE

address: 1023-1063 shatai South Road, Baiyun District

country: China

institute: Southern medicial unversity

summary: Peripheral myelination requires precise axon-glia communication, yet the neuronal intrinsic machinery that governs the release of axonal signals remains incompletely understood. Here, we discover that RhoA, a classic cytoskeletal regulator, is highly expressed in postnatal spinal motoneurons and unexpectedly governs this axon-glia communication. RhoA conditional knockout in postnatal motoneurons causes profound peripheral hypomyelination without affecting neuronal survival, dendrites, or axonal caliber. Mechanistically, RhoA deficiency in postnatal spinal motoneurons attenuates ROCK2/p-Erk/SP1/BACE1 signaling and NRG1-III secretion, then disrupts Schwann cell’s differentiation, lipid biosynthesis, and myelin formation. Together, this study reveals a novel, non-cell-autonomous role for RhoA, and provides new insights into the complexity of neuronal control over peripheral myelination.

overall_design: RNA-seq profiling of sciatic nerve lysate from RhoAfl/fl (flox) and  RhoAfl/fl ChATCreERT2+ (icKO) mice at postnatal day 14.

first: Jiasong

last: Guo

first: Ye

last: He

first: Shuyi

last: Xu


title: total RNA-seq from HG03265 (ENCSR390WJQ)


title: long read RNA-seq from renal pelvis (ENCSR390AHP)


title: total RNA-seq from HG03436 (ENCSR390OCZ)


title: total RNA-seq from HG03162 (ENCSR389UOP)


title: total RNA-seq from GM19324 (ENCSR388XWZ)


title: total RNA-seq from GM21339 (ENCSR388XYJ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR388BAM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR387QNB)


title: total RNA-seq from GM21597 (ENCSR387DCM)


title: total RNA-seq from GM18864 (ENCSR386MVA)


title: total RNA-seq from GM19397 (ENCSR385YME)


title: snATAC-seq from mucosa of descending colon (ENCSR384AYS)

summary:
scATAC-seq on human mucosa of descending colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from spinal cord (ENCSR383POI)


title: total RNA-seq from T follicular helper cell (ENCSR383IYX)


title: long read RNA-seq from renal pelvis (ENCSR382JPG)


title: snATAC-seq from bile duct (ENCSR381NFT)


title: total RNA-seq from HG02968 (ENCSR381HHP)


title: total RNA-seq from GM21770 (ENCSR380MGB)


title: total RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR380UXM)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCSR378SSX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR380HRM)


title: total RNA-seq from HG02977 (ENCSR378HSG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR377DQZ)


title: snATAC-seq from heart (ENCSR376OIU)


title: snATAC-seq from colonic mucosa (ENCSR375XCZ)

summary:
scATAC-seq on human colonic mucosa

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21614 (ENCSR374LLP)


title: total RNA-seq from GM21716 (ENCSR374DLH)


title: total RNA-seq from activated effector memory CD4-positive, alpha-beta T cell (ENCSR375TBP)


title: total RNA-seq from GM21379 (ENCSR374DHS)


title: total RNA-seq from HG03121 (ENCSR373KYU)


title: long read RNA-seq from right lung (ENCSR373VQC)


title: total RNA-seq from T-cell (ENCSR371BHW)


title: snATAC-seq from GM12878 (ENCSR371ZNU)

summary:
scATAC-seq on human cell line GM12878

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR370ORE)


title: total RNA-seq from HG03511 (ENCSR371ANC)


title: total RNA-seq from HG03066 (ENCSR367JCF)


title: total RNA-seq from T-cell (ENCSR368ZJO)


title: total RNA-seq from GM19377 (ENCSR367CJH)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR366ANX)


title: total RNA-seq from HG02888 (ENCSR365RUM)


title: total RNA-seq from HG03088 (ENCSR360IYN)


title: snATAC-seq from spleen (ENCSR363EAJ)

summary:
scATAC-seq on human spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03583 (ENCSR360GOQ)


title: snATAC-seq from right lobe of liver (ENCSR364FHN)

summary:
scATAC-seq on human right lobe of liver

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM19438 (ENCSR359VLP)


title: total RNA-seq from GM21599 (ENCSR358ZQT)


title: total RNA-seq from suppressor macrophage (ENCSR358IQT)


title: total RNA-seq from GM21449 (ENCSR357YYW)


title: total RNA-seq from GM18924 (ENCSR356LOW)


title: Pandion PT-101 single-cell RNA-seq of CD122+ non-myeloid cells following IL-2 mutein treatment

city: Seattle

first: Laura

last: Cooeny

state: WA

address: 1201 9th Ave

department: University of Michigan

institute: Immune Tolerance Network

summary: This study uses samples from the Pandion Phase 1a IL-2 mutein (PT-101) trial to investigate the mechanism of action of IL-2 mutein therapy. IL-2 mutein is engineered for increased affinity for CD25 and decreased affinity for CD122, selectively activating regulatory T cells (Tregs) while limiting stimulation of CD122-expressing effector populations (NK cells, ILCs, and CD122+ T cells). This dataset addresses whether the highest tested dose (10mg) induces an undesirable, off-target transcriptional signature in CD122+ non-myeloid cells. Single-cell RNA-seq (10x Genomics Chromium) was performed on FACS-sorted CD122+ cells from PBMC of 4 subjects in the 10mg dose cohort, at baseline (pre-treatment) and Day 8 post-dose, to assess treatment-induced changes in cell cluster composition and gene expression at single-cell resolution.

overall_design: PBMC from 4 subjects who received the 10mg IL-2 mutein dose (Cohort 3) in the Pandion PT-101 Phase 1a trial were collected at baseline (pre-treatment) and Day 8 post-dose. CD122+ non-myeloid cells (including NK cells, ILCs, and CD122+ T cells) were FACS-sorted from each PBMC sample and processed using the 10x Genomics Chromium Next GEM Single Cell 3' v3.1 (dual index) platform to generate single-cell gene expression libraries, which were sequenced on an Illumina NextSeq 2000.

first: Kristina

last: Harris

first: Dan

last: Campbell

last: Cooney

first: Alice

last: Long


title: total RNA-seq from HG03095 (ENCSR359NAG)


title: total RNA-seq from HG02810 (ENCSR360BWE)


title: long read RNA-seq from large intestine (ENCSR354MMF)


title: total RNA-seq from suppressor macrophage (ENCSR353EHP)


title: total RNA-seq from HG02642 (ENCSR356ESQ)


title: total RNA-seq from HG03515 (ENCSR353BNA)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR358DGI)


title: total RNA-seq from CD14-positive monocyte (ENCSR351BFL)


title: total RNA-seq from HG02851 (ENCSR348CLS)


title: long read RNA-seq from adrenal gland (ENCSR348TSX)


title: polyA plus RNA-seq from GM19239 (ENCSR350PLV)

summary:
GM19239 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR345WTX)


title: total RNA-seq from GM19027 (ENCSR347PFE)


title: snATAC-seq from posterior vena cava (ENCSR352RMS)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR716VLR).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from heart (ENCSR351AFA)


title: total RNA-seq from GM21356 (ENCSR345DTP)


title: polyA plus RNA-seq from GM07037 (ENCSR345CKK)

summary:
GM07037 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from left ventricle myocardium inferior (ENCSR541CKC)

summary:
scATAC-seq on human left ventricle myocardium inferior

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03367 (ENCSR342EIB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR341NVL)


title: snATAC-seq from MCF-7 (ENCSR341TTX)


title: total RNA-seq from inflammatory macrophage (ENCSR341MGP)


title: total RNA-seq from HG02896 (ENCSR340WCM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR342HIN)


title: total RNA-seq from GM21740 (ENCSR339YKD)


title: total RNA-seq from HG03175 (ENCSR339SAH)


title: total RNA-seq from T-cell (ENCSR337PXJ)


title: total RNA-seq from HG03514 (ENCSR337UDT)


title: total RNA-seq from inflammatory macrophage (ENCSR338VRX)


title: long read RNA-seq from kidney (ENCSR337PJI)


title: total RNA-seq from GM18871 (ENCSR336KOK)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR339FTN)


title: snATAC-seq from gastrocnemius (ENCSR334WIT)


title: total RNA-seq from HG03291 (ENCSR335AIJ)


title: snATAC-seq from PC-9 (ENCSR338KBR)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR337CAN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR334JVS)


title: long read RNA-seq from kidney (ENCSR332ZOH)


title: total RNA-seq from GM21768 (ENCSR335GZY)


title: snATAC-seq from psoas muscle (ENCSR332XEW)

summary:
scATAC on human psoas muscle. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR005TCL).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from K562 (ENCSR332SXG)

summary:
scATAC-seq on human cell line K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR330KBN)


title: total RNA-seq from GM21420 (ENCSR328VZB)


title: long read RNA-seq from muscle of back (ENCSR325LUL)


title: total RNA-seq from GM21649 (ENCSR329BWL)


title: long read RNA-seq from right lung (ENCSR328GKH)


title: total RNA-seq from GM21510 (ENCSR330IHF)


title: long read RNA-seq from brain (ENCSR327TOR)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR721NBI)


title: long read RNA-seq from left kidney (ENCSR324XFA)


title: total RNA-seq from HG02763 (ENCSR324GJH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR324GEQ)


title: total RNA-seq from HG03082 (ENCSR323KRN)


title: snATAC-seq from ovary (ENCSR322LEY)


title: total RNA-seq from HG02643 (ENCSR321NYJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR321JCI)


title: snATAC-seq from gastrocnemius (ENCSR322HGX)


title: snATAC-seq from heart left ventricle (ENCSR321AHR)


title: long read RNA-seq from renal cortex interstitium (ENCSR321AWD)


title: snATAC-seq from heart left ventricle (ENCSR320QOP)


title: long read RNA-seq from stomach (ENCSR319ZJH)


title: total RNA-seq from HG03118 (ENCSR319FNG)


title: total RNA-seq from GM19360 (ENCSR318SAZ)


title: total RNA-seq from GM21573 (ENCSR318HAQ)


title: snATAC-seq from heart left ventricle (ENCSR318ERF)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR405YKM).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG02922 (ENCSR316MUV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR316GRL)


title: total RNA-seq from HG03470 (ENCSR318BOT)


title: snATAC-seq from OCI-LY7 (ENCSR314WGW)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR313MPK)


title: total RNA-seq from activated gamma-delta T cell (ENCSR314ZXO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR310TTV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR310GKZ)


title: long read RNA-seq from adrenal gland (ENCSR309URD)


title: snATAC-seq from K562 (ENCSR308ZGJ)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR308QRZ)


title: total RNA-seq from HG03189 (ENCSR308AAU)


title: total RNA-seq from HG03049 (ENCSR307SKY)


title: long read RNA-seq from brain (ENCSR307SHM)


title: long read RNA-seq from right lung (ENCSR307QHG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR307EHG)


title: total RNA-seq from HG03271 (ENCSR306XSI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR306KPQ)


title: snATAC-seq from ovary (ENCSR305VES)


title: total RNA-seq from GM19390 (ENCSR305RZD)


title: snATAC-seq from heart left ventricle (ENCSR305KUV)


title: total RNA-seq from T-cell (ENCSR303LFR)


title: long read RNA-seq from renal cortex interstitium (ENCSR302UOZ)


title: total RNA-seq from GM21737 (ENCSR301GDF)


title: total RNA-seq from T-helper 17 cell (ENCSR302SSR)


title: total RNA-seq from HG03473 (ENCSR714QUV)


title: total RNA-seq from GM19314 (ENCSR717BWR)


title: snATAC-seq from heart (ENCSR300TZG)


title: snATAC-seq from adrenal gland (ENCSR713FPX)


title: snATAC-seq from heart left ventricle (ENCSR718YPN)


title: snATAC-seq from heart (ENCSR714PLQ)


title: total RNA-seq from GM21738 (ENCSR300UGR)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR711IBG)


title: long read RNA-seq from left kidney (ENCSR300AUI)


title: total RNA-seq from GM19430 (ENCSR297TFS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR298QSD)


title: long read RNA-seq from left lung (ENCSR296JRY)


title: total RNA-seq from HG03172 (ENCSR296IPK)


title: total RNA-seq from HG02970 (ENCSR296FVA)


title: total RNA-seq from HG03313 (ENCSR292FRI)


title: long read RNA-seq from adrenal gland (ENCSR294LJB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR294VVV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR292CVA)


title: total RNA-seq from HG02721 (ENCSR291GAN)


title: total RNA-seq from GM21776 (ENCSR291JPP)


title: total RNA-seq from HG03565 (ENCSR290OZK)


title: polyA plus RNA-seq from GM11920 (ENCSR289AAO)

summary:
GM11920 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM18519 (ENCSR287BGD)


title: snATAC-seq from heart left ventricle (ENCSR288RQI)

summary:
scATAC-seq on human heart left ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from GM23338 (ENCSR290IUT)

summary:
scATAC-seq on human cell line PGP1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from right lung (ENCSR287XKO)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from GM12286 (ENCSR289KIV)

summary:
GM12286 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from activated CD4-positive, alpha-beta memory T cell (ENCSR287GYJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR286GSC)


title: total RNA-seq from HG03472 (ENCSR287KOI)


title: total RNA-seq from GM18861 (ENCSR284UWJ)


title: total RNA-seq from GM21405 (ENCSR286VXU)


title: total RNA-seq from GM18507 (ENCSR284QGB)


title: total RNA-seq from T-cell (ENCSR287FLI)


title: total RNA-seq from HG03464 (ENCSR283BQG)


title: long read RNA-seq from spinal cord (ENCSR285JMB)


title: total RNA-seq from HG02973 (ENCSR283KGT)


title: total RNA-seq from GM21785 (ENCSR282JJL)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR282KBZ)


title: long read RNA-seq from kidney (ENCSR281RTT)


title: Cellular context restricts IDR plasticity to a single essential effector interface for m6A-dependent mRNA turnover [Chan_RNA-seq_experiment 2]

status: Public on Jul 29 2026

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: N6-methyladenosine (m6A) is a conserved mRNA modification that regulates transcript stability, yet how m6A reader proteins engage effectors remains poorly understood. Using yeast meiosis as a model, we investigated how the YTH-domain protein Pho92 promotes decay of m6A-modified transcripts through its intrinsically disordered region (IDR). In vitro, the Pho92 IDR makes multiple contacts with the Ccr4-NOT deadenylase complex and drives tethered reporter decay in the absence of any single subunit. Yet in meiosis, turnover of endogenous m6A-modified transcripts strictly depends on a single interface: direct binding of the Pho92 IDR to Caf40. A single hydrophobic residue substitution is sufficient to abolish Caf40 binding and halt transcript decay. Human YTHDF proteins can functionally substitute for Pho92, but require multiple hydrophobic patches within the IDR for decay activity. Thus, the cellular context of meiosis dictates which IDR-mediated contacts are functional for m6A turnover, adding a layer of specificity in post-transcriptional gene regulation.

overall_design: CUP induced expression Pho92 IDR mutants

first: Wei

last: Chan

first: Duncan

last: Berger

first: James

last: Booth


title: long read RNA-seq from left kidney (ENCSR281BDV)


title: total RNA-seq from HG03280 (ENCSR280NHG)


title: total RNA-seq from HG02944 (ENCSR279XCC)


title: snATAC-seq from heart left ventricle (ENCSR280RVT)


title: snATAC-seq from heart left ventricle (ENCSR277LDY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR276BWA)


title: total RNA-seq from GM21622 (ENCSR277HKQ)


title: snATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR278XIZ)


title: snATAC-seq from pancreas (ENCSR275TWX)

summary:
scATAC-seq on human pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from large intestine (ENCSR273NIW)


title: snATAC-seq from heart left ventricle (ENCSR273DAC)


title: total RNA-seq from GM21596 (ENCSR273BGW)


title: total RNA-seq from HG02891 (ENCSR273CUX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR273HGA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR271OTY)


title: snATAC-seq from heart left ventricle (ENCSR270CUT)


title: TF ChIP-seq from K562 (ENCSR269ZGG)

summary:
CEBPB ChIP-seq on K562 cells treated with shRNA targeting GATA1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from renal pelvis (ENCSR267ZNP)


title: total RNA-seq from GM18487 (ENCSR267HYR)


title: snATAC-seq from left cerebral cortex (ENCSR265XVL)


title: total RNA-seq from GM19332 (ENCSR264HRG)


title: total RNA-seq from HG02678 (ENCSR263KTR)


title: long read RNA-seq from renal cortex interstitium (ENCSR261AYY)


title: total RNA-seq from GM19372 (ENCSR262DEI)


title: long read RNA-seq from right kidney (ENCSR260VXZ)


title: total RNA-seq from GM21769 (ENCSR261LTY)


title: long read RNA-seq from muscle of arm (ENCSR257NKC)


title: total RNA-seq from GM21615 (ENCSR257XFI)


title: total RNA-seq from HG03351 (ENCSR256ODN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR255UHN)


title: total RNA-seq from HG02923 (ENCSR255EMJ)


title: total RNA-seq from HG03303 (ENCSR255NTN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR254ZLS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR254TFM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR252PFT)


title: total RNA-seq from CD14-positive monocyte (ENCSR252NGG)


title: long read RNA-seq from left kidney (ENCSR247GVU)


title: total RNA-seq from GM19461 (ENCSR247BNP)


title: long read RNA-seq from spinal cord (ENCSR246BOF)


title: long read RNA-seq from lung (ENCSR246OTF)


title: total RNA-seq from HG03363 (ENCSR245LXH)


title: total RNA-seq from HG03124 (ENCSR244TCU)


title: total RNA-seq from HG03157 (ENCSR251NJW)


title: long read RNA-seq from muscle of leg (ENCSR243FLD)


title: total RNA-seq from GM19334 (ENCSR243MXR)


title: Hippocampal small RNAs from patients with schizophrenia induce specific cognitive and neural phenotypes in mice [mouse]

city: Barcelona

first: Marcos

last: Galán-Ganga

address: C/ Casanova, 143.

department: Biomedicine

country: Spain

institute: University of Barcelona

summary: Schizophrenia is a neuropsychiatric syndrome characterized by the presence of psychotic, negative and cognitive symptoms. Cognitive deficits can appear even before the onset of the first psychotic episode and their severity has been recently associated with altered levels of small RNAs (sRNAs), including microRNAs. Nevertheless, how the dysregulation of sRNAs can lead to cognitive impairments and their role in the onset and pathophysiology of the disorder are still unknown. In our research, we hypothesized that hippocampal sRNAs generated in patients with schizophrenia could contribute to the impairment of specific cognitive domains that are altered in the disease. Through deep sequencing, we identified novel dysregulated sRNAs (including microRNAs and tRNA derived fragments) in the hippocampus of patients with schizophrenia. Furthermore, when injected in the hippocampus of wild-type mice, animals exhibited an impairment in spatial short-term memory accompanied by a reduction in spine density of CA1 pyramidal neurons. RNA-sequencing of the hippocampus of injected mice revealed changes in key pathways related to neurotransmission. Specifically, we found higher levels of the presynaptic marker for Parvalbumin interneurons synaptotagmin II (Syt2), mirroring observations made in the brain of schizophrenia patients. We also detected subtle morphological changes in mouse hippocampal microglia in response to sRNAs from affected individuals. Our results point out that sRNAs can contribute to cognitive symptoms in schizophrenia through synaptic alterations, highlighting these molecules as promising novel therapeutic targets for the disorder.

overall_design: Bulk RNA-seq profiling of mouse hippocampal CA1 tissue following stereotaxic infusion of pooled human hippocampal small RNAs. Experimental groups included mice injected with sRNAs pooled from control individuals (Pool Control), sRNAs pooled from two independent cohorts of patients with schizophrenia (Pool 1 and Pool 2), and vehicle control (artificial cerebrospinal fluid). Samples were collected 24 hours after the last behavioural test for transcriptomic analysis.

first: Anna

last: Guisado-Corcoll

last: Sancho-Balsells

first: Marina

last: Herrero-Lorenzo

first: Ivan

last: Ballasch

first: Lisa

last: Patterer

first: Jordi

last: Alberch

first: Belén

last: Arranz

first: Albert

last: Giralt

first: Eulàlia

last: Martí


title: snATAC-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR242VMQ)

first: ENCODE

last: DCC


title: total RNA-seq from GM21368 (ENCSR240OYY)


title: total RNA-seq from HG03160 (ENCSR240BDA)


title: total RNA-seq from GM19035 (ENCSR237TRX)


title: total RNA-seq from HG02947 (ENCSR238AZV)


title: total RNA-seq from GM21303 (ENCSR237NBV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR237SUT)


title: total RNA-seq from GM19403 (ENCSR295MME)


title: snATAC-seq from A549 (ENCSR237BTV)

summary:
scATAC-seq on human cell line A549

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03099 (ENCSR236JKN)


title: total RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR234TAQ)


title: total RNA-seq from GM21402 (ENCSR232AIN)


title: snATAC-seq from heart left ventricle (ENCSR233KYH)


title: total RNA-seq from HG02854 (ENCSR231JEO)


title: snATAC-seq from mesothelial cell of epicardium (ENCSR231GXD)


title: total RNA-seq from HG02952 (ENCSR231FVM)


title: long read RNA-seq from left lung (ENCSR228HRA)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR228YDZ)


title: snATAC-seq from pancreas (ENCSR229VVY)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR472RRP).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from kidney (ENCSR227LUE)


title: total RNA-seq from HG02667 (ENCSR227KXJ)


title: total RNA-seq from GM21388 (ENCSR226WFV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR225VEP)


title: total RNA-seq from HG02798 (ENCSR225QLT)


title: total RNA-seq from HG03460 (ENCSR223JWC)


title: long read RNA-seq from small intestine (ENCSR222RWQ)


title: total RNA-seq from GM19475 (ENCSR221NQI)


title: total RNA-seq from GM21491 (ENCSR219KEH)


title: long read RNA-seq from renal cortex interstitium (ENCSR219CXA)


title: total RNA-seq from GM19318 (ENCSR218GPO)


title: total RNA-seq from HG03258 (ENCSR217LLB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR216POR)


title: total RNA-seq from HG03558 (ENCSR213ZST)


title: long read RNA-seq from muscle of back (ENCSR213OVS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR213LIB)


title: total RNA-seq from HG03410 (ENCSR212TVA)


title: total RNA-seq from HG03241 (ENCSR212UYG)


title: total RNA-seq from HG03538 (ENCSR212SSB)


title: total RNA-seq from GM21453 (ENCSR211VEI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR211PUA)


title: long read RNA-seq from muscle of trunk (ENCSR210ICG)


title: snATAC-seq from placenta (ENCSR207ABL)


title: total RNA-seq from GM19323 (ENCSR208KSN)


title: snATAC-seq from adrenal gland (ENCSR205VFW)

summary:
scATAC-seq on human adrenal gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR205XKX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR205GOW)


title: total RNA-seq from GM19239 (ENCSR203WRA)


title: total RNA-seq from GM21360 (ENCSR203HJG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR203CWA)


title: total RNA-seq from HG03108 (ENCSR202FZX)


title: total RNA-seq from T-cell (ENCSR201NVJ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR198YAQ)


title: snATAC-seq from HepG2 (ENCSR198TTU)

summary:
scATAC-seq on human cell line HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03120 (ENCSR197QHM)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR197OZY)


title: snATAC-seq from ovary (ENCSR197GLE)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR938CZJ).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21344 (ENCSR196SAS)


title: total RNA-seq from GM19038 (ENCSR195NKT)


title: polyA plus RNA-seq from GM11993 (ENCSR195LZH)

summary:
GM11993 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from muscle of back (ENCSR194VUL)


title: snATAC-seq from adrenal gland (ENCSR194KHA)

summary:
scATAC on human adrenal gland. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR726IPC).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR194GTV)

summary:
Input for K562 cells treated with sgRNA targeting CEBPB

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR207HVA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR193WWA)


title: long read RNA-seq from spleen (ENCSR193BFC)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR191MTW)


title: total RNA-seq from HG03354 (ENCSR190VMF)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR190JAK)


title: total RNA-seq from HG02882 (ENCSR190BVW)


title: total RNA-seq from T-cell (ENCSR189ADQ)


title: snATAC-seq from spleen (ENCSR188TJX)

summary:
scATAC-seq on human spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG02562 (ENCSR272DJF)


title: long read RNA-seq from thymus (ENCSR641JDY)


title: total RNA-seq from GM21617 (ENCSR272BGX)


title: long read RNA-seq from left kidney (ENCSR270XWF)


title: total RNA-seq from HG02568 (ENCSR188QRH)


title: snATAC-seq from pancreas (ENCSR268LMV)


title: total RNA-seq from HG03091 (ENCSR269JGO)


title: total RNA-seq from GM21318 (ENCSR195DEV)


title: total RNA-seq from GM21722 (ENCSR195EDC)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR188FWR)


title: total RNA-seq from HG03432 (ENCSR185YKL)


title: long read RNA-seq from left lung (ENCSR186JQU)


title: snATAC-seq from heart left ventricle (ENCSR185NXG)


title: total RNA-seq from GM19347 (ENCSR186FEP)


title: total RNA-seq from T-cell (ENCSR184SAB)


title: total RNA-seq from GM19385 (ENCSR183UYO)


title: total RNA-seq from GM18877 (ENCSR183JRL)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR183GSI)


title: total RNA-seq from HG03111 (ENCSR182ZQT)


title: total RNA-seq from GM19310 (ENCSR182MKX)


title: snATAC-seq from mucosa of descending colon (ENCSR181TLD)

summary:
scATAC-seq on human mucosa of descending colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM19031 (ENCSR179JFX)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR181BTV)


title: long read RNA-seq from stomach (ENCSR179EYZ)


title: total RNA-seq from GM19456 cell (ENCSR178XBV)


title: snATAC-seq from B cell (ENCSR177OXQ)


title: long read RNA-seq from renal cortex interstitium (ENCSR176MGF)


title: snATAC-seq from MCF-7 (ENCSR176EJL)

summary:
scATAC-seq on human cell line MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from heart left ventricle (ENCSR175JHG)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from muscle of leg (ENCSR174AAK)


title: total RNA-seq from GM21741 (ENCSR173BSI)


title: total RNA-seq from HG02610 (ENCSR174DGO)


title: snATAC-seq from heart left ventricle (ENCSR173UUN)


title: long read RNA-seq from muscle of arm (ENCSR170QUW)


title: total RNA-seq from HG03202 (ENCSR170LYC)


title: snATAC-seq from heart right ventricle (ENCSR169BCG)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR426PDU).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR168QRY)


title: total RNA-seq from HG03079 (ENCSR167QJU)


title: total RNA-seq from GM18876 (ENCSR167QKJ)


title: total RNA-seq from HG02624 (ENCSR166RJP)


title: long read RNA-seq from muscle of arm (ENCSR617WTI)


title: long read RNA-seq from heart (ENCSR165CWR)


title: total RNA-seq from GM21423 (ENCSR164PHT)


title: total RNA-seq from GM21357 (ENCSR163ELK)


title: snATAC-seq from heart left ventricle (ENCSR161IHV)


title: total RNA-seq from suppressor macrophage (ENCSR160SIL)


title: snATAC-seq from SK-N-SH (ENCSR161GPE)

summary:
scATAC-seq on human cell line SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG02860 (ENCSR160KZU)


title: total RNA-seq from GM19436 (ENCSR160EEU)


title: total RNA-seq from GM21521 (ENCSR159HCQ)


title: long read RNA-seq from placenta (ENCSR158RZR)


title: total RNA-seq from CD14-positive monocyte (ENCSR158GGH)


title: total RNA-seq from GM18498 (ENCSR157QJQ)


title: total RNA-seq from HG03458 (ENCSR156IFC)


title: snATAC-seq from activated CD8-positive, alpha-beta T cell (ENCSR154JHG)


title: total RNA-seq from technical sample (ENCSR154RVC)

summary:
LRGASP_mix

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD14-positive monocyte (ENCSR154CBP)


title: polyA plus RNA-seq from GM20787 (ENCSR150XQV)

summary:
GM20787 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03063 (ENCSR150EPG)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR148XTC)


title: total RNA-seq from HG02768 (ENCSR147SNS)


title: snATAC-seq from osteocyte (ENCSR146VJA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR146SOA)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR146QDU)


title: total RNA-seq from GM18873 (ENCSR146NXN)


title: total RNA-seq from T-cell (ENCSR144LNR)


title: total RNA-seq from HG03457 (ENCSR144CGD)


title: total RNA-seq from T-cell (ENCSR142YRS)


title: long read RNA-seq from small intestine (ENCSR166KWG)


title: total RNA-seq from T-cell (ENCSR142OOS)


title: Control ChIP-seq from HepG2 (ENCSR142JFU)

summary:
Input for HepG2 cells treated with shRNA targeting FOXA3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM19394 (ENCSR140MWC)


title: long read RNA-seq from left lung (ENCSR141JSO)


title: total RNA-seq from GM21438 (ENCSR194AHO)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR140GZF)


title: total RNA-seq from HG03388 (ENCSR140FBG)


title: total RNA-seq from GM19384 (ENCSR159NRB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR137ZAT)


title: total RNA-seq from HG02594 (ENCSR139WHO)


title: snATAC-seq from left lobe of liver (ENCSR139ATR)

summary:
scATAC on left lobe of liver Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR369UFT).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: snATAC-seq from pancreas (ENCSR137FPX)

summary:
scATAC-seq on human pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21575 (ENCSR192PWG)


title: long read RNA-seq from lung (ENCSR137VJX)


title: total RNA-seq from HG03123 (ENCSR156VTP)


title: long read RNA-seq from renal cortex interstitium (ENCSR137BTX)


title: total RNA-seq from GM19023 (ENCSR137BGK)


title: long read RNA-seq from muscle of leg (ENCSR136VYG)


title: total RNA-seq from HG03352 (ENCSR136MBP)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR134COS)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR133IAE)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR131HNT)


title: total RNA-seq from inflammatory macrophage (ENCSR129JAM)


title: total RNA-seq from suppressor macrophage (ENCSR127IQP)


title: snATAC-seq from heart left ventricle (ENCSR131DKN)

summary:
scATAC on human heart left ventricle. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR481QQR)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21528 (ENCSR126XIL)


title: total RNA-seq from GM21421 (ENCSR125SOW)


title: long read RNA-seq from muscle of leg (ENCSR125GHJ)


title: total RNA-seq from HG03270 (ENCSR189EAL)


title: total RNA-seq from HG03382 (ENCSR124OEJ)


title: long read RNA-seq from stomach (ENCSR122FHJ)


title: total RNA-seq from inflammatory macrophage (ENCSR123GNM)


title: total RNA-seq from GM19019 (ENCSR122LSS)


title: total RNA-seq from T-helper 1 cell (ENCSR124FVF)


title: total RNA-seq from GM21678 (ENCSR121IJT)


title: total RNA-seq from GM19025 (ENCSR121CVF)


title: total RNA-seq from HG03109 (ENCSR120DWY)


title: total RNA-seq from inflammatory macrophage (ENCSR121CEH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR119OKW)


title: total RNA-seq from HG02769 (ENCSR119EFB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR118GLJ)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR117NBV)


title: total RNA-seq from T-cell (ENCSR116HHQ)


title: total RNA-seq from GM19468 (ENCSR117BGR)


title: snATAC-seq from right lobe of liver (ENCSR114OKU)

summary:
scATAC-seq on human right lobe of liver

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM19440 (ENCSR113JEX)


title: total RNA-seq from HG03449 (ENCSR116LRD)


title: polyA plus RNA-seq from GM12889 (ENCSR113EAE)

summary:
GM12889 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG02571 (ENCSR112ZML)


title: snATAC-seq from right lobe of liver (ENCSR112UBQ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR111UMO)


title: total RNA-seq from GM21826 (ENCSR111VVJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR110EAN)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR108VOF)


title: total RNA-seq from GM21308 (ENCSR108RIM)


title: total RNA-seq from HG03366 (ENCSR108MUL)


title: snATAC-seq from ovary (ENCSR180GUX)

summary:
scATAC-seq on human ovary

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21515 (ENCSR106YRC)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR182HSC)


title: total RNA-seq from HG03485 (ENCSR111FCV)


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCSR108HJO)


title: snATAC-seq from ovary (ENCSR105VKN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR104XPI)


title: total RNA-seq from GM19338 (ENCSR103VZI)


title: snATAC-seq from CD4-positive, alpha-beta T cell (ENCSR102QKY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR099JHK)


title: snATAC-seq from heart left ventricle (ENCSR101LQQ)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR098KNC)


title: total RNA-seq from inflammatory macrophage (ENCSR097FKR)


title: total RNA-seq from HG02702 (ENCSR097JPR)


title: long read RNA-seq from large intestine (ENCSR098FNB)


title: snATAC-seq from SK-N-SH (ENCSR095KCD)

summary:
scATAC-seq on human cell line SK-N-SH (RA treated)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21650 (ENCSR096XEJ)


title: total RNA-seq from GM21304 (ENCSR095WQC)


title: total RNA-seq from HG03168 (ENCSR097IXN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR171AEU)


title: total RNA-seq from HG02982 (ENCSR095BUO)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR094IXV)


title: total RNA-seq from GM18907 (ENCSR094BAF)


title: total RNA-seq from HG03199 (ENCSR093TPC)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR093FXB)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR092ZRN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR092TIL)


title: total RNA-seq from T-helper 9 cell (ENCSR092PHJ)


title: long read RNA-seq from renal cortex interstitium (ENCSR091MZX)


title: total RNA-seq from HG03572 (ENCSR090UCN)


title: total RNA-seq from HG03055 (ENCSR090IOW)


title: total RNA-seq from HG02836 (ENCSR089IOS)


title: long read RNA-seq from muscle of trunk (ENCSR091GMV)


title: snATAC-seq from heart left ventricle (ENCSR088ZOL)


title: total RNA-seq from HG03437 (ENCSR538GET)


title: long read RNA-seq from adrenal gland (ENCSR539XOD)


title: total RNA-seq from HG03247 (ENCSR087SMP)


title: snATAC-seq from upper lobe of right lung (ENCSR086LCZ)

summary:
scATAC-seq on human upper lobe of right lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG03114 (ENCSR264ICG)


title: total RNA-seq from HG02890 (ENCSR085NEA)


title: long read RNA-seq from large intestine (ENCSR085CHJ)


title: total RNA-seq from GM21635 (ENCSR085SBJ)


title: total RNA-seq from HG02620 (ENCSR085ZNJ)


title: snATAC-seq from heart left ventricle (ENCSR084DVM)


title: snATAC-seq from lung (ENCSR083HFN)

summary:
scATAC on human lung Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR225OII)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HG02983 (ENCSR083WME)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR083GNI)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR256UBZ)


title: total RNA-seq from HG02971 (ENCSR082TWO)


title: long read RNA-seq from small intestine (ENCSR081FFD)


title: snATAC-seq from heart left ventricle (ENCSR080TZR)

summary:
scATAC-seq on human heart left ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR080BPH)


title: total RNA-seq from GM18865 (ENCSR079VGX)


title: snATAC-seq from heart left ventricle (ENCSR079TCC)


title: total RNA-seq from HG02946 (ENCSR079FJT)


title: total RNA-seq from HG03575 (ENCSR076ZTH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR075FPQ)


title: snATAC-seq from HCT116 (ENCSR076QTT)


title: TF ChIP-seq from K562 (ENCSR075FCS)

summary:
TEAD4 ChIP-seq on K562 cells treated with shRNA targeting MAFF

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM19448 (ENCSR080ZWV)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21520 (ENCSR074IYA)


title: snATAC-seq from ovary (ENCSR075FKI)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR074DPH)


title: total RNA-seq from HG02974 (ENCSR088NYJ)


title: total RNA-seq from HG03556 (ENCSR074UEU)


title: total RNA-seq from HG02461 (ENCSR073YWU)


title: total RNA-seq from GM18523 (ENCSR073PJT)


title: total RNA-seq from inflammatory macrophage (ENCSR072XZF)


title: long read RNA-seq from left lung (ENCSR245XMK)


title: long read RNA-seq from stomach (ENCSR071XIZ)


title: total RNA-seq from CD14-positive monocyte (ENCSR072WBA)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR068SXL)


title: total RNA-seq from HG03084 (ENCSR068IPN)


title: total RNA-seq from HG03380 (ENCSR065ZHU)


title: total RNA-seq from GM21451 (ENCSR065DHQ)


title: total RNA-seq from HG02879 (ENCSR065HUM)


title: total RNA-seq from GM19319 (ENCSR068RYG)


title: long read RNA-seq from thymus (ENCSR063MJL)


title: total RNA-seq from GM21341 (ENCSR063GUM)


title: total RNA-seq from HG03212 (ENCSR063HLA)


title: total RNA-seq from GM21522 (ENCSR061IMG)


title: total RNA-seq from HG03578 (ENCSR060KDT)


title: total RNA-seq from HG02573 (ENCSR064ABZ)


title: snATAC-seq from heart left ventricle (ENCSR061BEN)


title: total RNA-seq from HG03073 (ENCSR059RCN)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR058NWZ)


title: total RNA-seq from GM19439 (ENCSR060QQK)


title: snATAC-seq from HCT116 (ENCSR058GOM)


title: total RNA-seq from HG02813 (ENCSR058EMK)


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR056RVQ)


title: long read RNA-seq from renal cortex interstitium (ENCSR057UZA)


title: total RNA-seq from HG03452 (ENCSR055TOH)


title: total RNA-seq from HG02645 (ENCSR055PWN)


title: TF ChIP-seq from HepG2 (ENCSR054ZMK)

summary:
NR2F2 ChIP-seq on HepG2 cells treated with shRNA targeting FOXA3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from right kidney (ENCSR054SPN)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR053ZUQ)


title: total RNA-seq from T-cell (ENCSR051QDS)


title: total RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR049VKA)


title: total RNA-seq from HG02887 (ENCSR046SVK)


title: long read RNA-seq from small intestine (ENCSR047HDL)


title: snATAC-seq from heart left ventricle (ENCSR051ECW)


title: total RNA-seq from GM18486 (ENCSR045PFH)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR044ICH)


title: total RNA-seq from T-cell (ENCSR225DON)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR043DGB)


title: long read RNA-seq from large intestine (ENCSR042HCJ)


title: snATAC-seq from pancreas (ENCSR042RUW)


title: total RNA-seq from suppressor macrophage (ENCSR040ZFV)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR040XOI)


title: total RNA-seq from effector CD4-positive, alpha-beta T cell (ENCSR039LCP)


title: total RNA-seq from GM19346 (ENCSR039KCN)


title: total RNA-seq from GM21517 (ENCSR038YSS)


title: long read RNA-seq from muscle of leg (ENCSR032UWN)


title: total RNA-seq from GM18489 (ENCSR038NUI)


title: total RNA-seq from HG02820 (ENCSR038ZQK)


title: total RNA-seq from GM21443 (ENCSR029OEU)


title: snATAC-seq from heart left ventricle (ENCSR033ENA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR030BLB)


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCSR029MBZ)


title: snATAC-seq from placenta (ENCSR029KFQ)


title: total RNA-seq from GM21352 (ENCSR028PMB)


title: snATAC-seq from adrenal gland (ENCSR028JGT)

summary:
scATAC-seq on human adrenal gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR028HEK)

summary:
TEAD4 ChIP-seq on HepG2 cells treated with shRNA targeting FOXA3

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR025QHQ)


title: total RNA-seq from GM21363 (ENCSR025LOD)


title: snATAC-seq from adrenal gland (ENCSR024LKR)


title: long read RNA-seq from renal pelvis (ENCSR024CQN)


title: total RNA-seq from GM21476 (ENCSR022CXD)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR022BIB)


title: snATAC-seq from layer of hippocampus (ENCSR021UQR)


title: snATAC-seq from heart left ventricle (ENCSR020FAW)


title: total RNA-seq from GM21719 (ENCSR022BLY)


title: total RNA-seq from suppressor macrophage (ENCSR019RPZ)


title: total RNA-seq from HG03040 (ENCSR019NBI)


title: total RNA-seq from HG03139 (ENCSR018OWO)


title: total RNA-seq from HG03343 (ENCSR016KCQ)


title: long read RNA-seq from muscle of leg (ENCSR017XQY)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR014SGQ)


title: total RNA-seq from HG03517 (ENCSR014QPI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR015AOP)


title: snATAC-seq from gastrocnemius (ENCSR012QUJ)


title: total RNA-seq from GM21524 (ENCSR011CTI)


title: long read RNA-seq from adrenal gland (ENCSR014HNT)


title: snATAC-seq from CD14-positive monocyte (ENCSR009WQK)


title: total RNA-seq from HG03521 (ENCSR009PIF)


title: total RNA-seq from HG02629 (ENCSR059GHC)


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR008FVJ)


title: total RNA-seq from T-helper 1 cell (ENCSR008FFS)


title: long read RNA-seq from heart (ENCSR008AXU)


title: total RNA-seq from HG03372 (ENCSR008AAJ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR007YPV)


title: total RNA-seq from HG02613 (ENCSR007NUY)


title: polyA plus RNA-seq from GM18505 (ENCSR006SBQ)

summary:
GM18505 RNA Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM21351 (ENCSR006WEQ)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR006DUH)


title: long read RNA-seq from renal pelvis (ENCSR005ESF)


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR053TWA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR051IEG)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR003JNT)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR004XRD)


title: total RNA-seq from GM21410 (ENCSR004YFS)


title: snATAC-seq from heart left ventricle (ENCSR003DSI)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR045PKU)


title: total RNA-seq from GM18915 (ENCSR001WWO)


title: total RNA-seq from HG03081 (ENCSR000VUK)


title: snATAC-seq from psoas muscle (ENCSR000XQD)

summary:
Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR471YTA).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: long read RNA-seq from small intestine (ENCSR000OEW)


title: Taxus cuspidata extract attenuates allergic airway inflammation, and its constituent taxinine targets the IL-17/TNF program in mast cells

city: Gangneung si

first: Wook-Bin

last: Lee

state: Gangwon do

address: 679 Saimdang-ro

department: Natural Product Efficacy Optimization Research Center

country: South Korea

institute: Korea Institute of Science and Technology

summary: Mast cells are central effectors of IgE-mediated allergic inflammation. To define, transcriptome-wide, how the Taxus cuspidata-derived diterpenoid taxinine modulates mast-cell activation, we profiled bone-marrow-derived mast cells (BMMCs) from C57BL/6 mice in three conditions: untreated control, IgE-sensitized cells stimulated with DNP-BSA (BSA), and DNP-BSA-stimulated cells treated with taxinine. Differential expression, functional enrichment, and gene-set enrichment analysis showed that IgE/antigen stimulation induced a strong inflammatory signature that taxinine partially attenuated, with the IL-17 and TNF signaling programs enriched by stimulation and reciprocally suppressed by taxinine.

overall_design: BMMCs (C57BL/6) profiled by paired-end mRNA sequencing in three groups - untreated Control, IgE-sensitized + DNP-BSA-stimulated (BSA), and BSA + taxinine - with n=3 biological replicates per group (9 samples total). Libraries: TruSeq Stranded mRNA; sequenced on Illumina NovaSeq 6000 (paired-end, 2x101 bp).

first: Tae Kyeom

last: Kang

first: Myungsuk

last: Kim

first: Sang Hoon

last: Jung


title: Single-cell RNA sequencing of human CAR-NK cells before infusion and after tumor cells challenge in mice model

city: Houston

first: DONGHAI

last: XIONG

state: TX

address: 6565 MD Anderson Blvd,

institute: The University of Texas MD Anderson Cancer Center

summary: We profiled the transcriptomes of human CD5 CAR-NK cells at the single-cell level to compare the pre-infusion state with the post-challenge state.

overall_design: Two samples were subjected to scRNA-seq. The first sample is the human CD5 CAR-NK cells product before being injected to the mouse model ('PreInfusion_NK'). The second sample is prepared as follows: The human CD5 CAR-NK cells were injected into the mouse model with CD5+ CCRF tumor cells, 100 days later rechallenged with tumor cells; then the sample was collected 4 weeks after tumor rechallenge. Both samples were processed with the 10x Genomics Chromium Single Cell 3' v3.1 assay and sequenced on Illumina NovaSeq 6000 sequencer. The second sample contained sequencing reads from contaminated mouse monocytes and tumor cells, which were removed in the downstream bioinformatic analyses. Only CAR-NK cells in the second sample (called 'PostChallenge_NK') were retained to be compared to the pure CAR-NK cells in the first sample ('PreInfusion_NK'). Each sample was sequenced across two lanes (L001, L002).

first: May

last: Daher

first: Nadima

last: Uprety

first: Ana Karen

last: Nunez Cortes

first: Emily

last: Ensley

first: Rejeena

last: Shrestha

first: Donghai

last: Xiong

first: Francia

last: Reyes Silva

first: Elif

last: Gokdemir

first: Madison

last: Moore

first: Silvia

last: Tiberti

first: Huihui

last: Fan

first: Andre

last: Nguyen

first: Cameron

middle: L

last: Gardner

first: Elizabeth

last: Wood

first: Mayra

last: Shanley

first: Sunil

last: Acharya

first: Amina

last: Nurmammadova

first: Luis

last: Muniz-Feliciano

first: Ye

last: Li

first: Michael

last: Wang

first: Vivian

last: Jiang

first: Merve

last: Dede

first: Vakul

last: Mohanty

first: Pinaki

middle: P

last: Banerjee

first: Bin

last: Liu

first: Enli

first: Ken

last: Chen

middle: J

last: Shpall

first: Katayoun

last: Rezvani

first: Rafet

last: Basar


title: Impaired synthesis of both telomere strands and adaptive TERT reduction in RTEL1 ATPase-dead cells

city: Boulder

first: Mingfeng

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

summary: Regulator of Telomere Elongation Helicase 1 (RTEL1) plays a critical role in telomere replication by disassembling DNA secondary structures such as G-quadruplexes and telomeric loops (T-loops). However, its precise mechanism remains unclear. Previously, we generated HeLa cells homozygous for ATPase-dead RTEL1. Here, we found that these cells have a 50-60% reduction in the synthesis of both telomere strands, indicating that RTEL1 ATPase activity is essential for replicating both leading and lagging telomeric DNA. Surprisingly, these cells also showed a substantial reduction in Telomerase Reverse Transcriptase (TERT) mRNA levels and a 60-80% reduction in telomerase activity, without activating alternative lengthening of telomeres (ALT). Forced TERT overexpression suppressed proliferation and caused late S/G2 accumulation, implying that the natural TERT reduction provides adaptive resistance. Expressing wild-type (WT) RTEL1 at levels close to physiological levels failed to rescue growth defects, suggesting a dominant-negative effect. These results reveal unexpected interactions between RTEL1 and telomerase and show how cancer cells compensate for RTEL1 dysfunction by decreasing TERT expression.

overall_design: RNA-seq profiling of wild-type HaloTag-RTEL1 HeLa cell lines (clones 1 and 15) and ATPase-dead (K48R) HaloTag-RTEL1 HeLa cell lines (clones 17 and 19). Each condition was run in triplicate. These cell lines were generated using CRISPR genome editing (see the NAR paper “Rapid dynamics allow the low-abundance RTEL1 helicase to promote telomere replication; doi: 10.1093/nar/gkaf177.” for more details).

first: Guanhui

last: Wu

first: Arthur

last: Zaug

first: John

last: Rinn

first: Thomas

middle: R

last: Cech


title: Lentiviral hTERT overexpression extends the lifespan of primary human epidermal melanocytes and reshapes transcriptional programs

city: Kunming

first: Li

middle: Qiao

last: hua

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

summary: Lentiviral hTERT overexpression can generate expandable epidermal melanocyte models that preserve closer global similarity to primary melanocytes than melanoma cell lines. Nevertheless, hTERT overexpression and subsequent clonal selection induced broad remodeling of genes and pathways associated with cell-cycle progression, telomere regulation, antiviral immune response, extracellular matrix organization, cell adhesion, dendrite-associated structures, and pigmentation. These findings indicate that lentiviral hTERT overexpression extends the lifespan of human epidermal melanocytes but is not functionally neutral. Instead, this process promotes dedifferentiation and compromises key melanocytic functions. Moreover, single-cell cloning appears to impose additional selection pressure and may further drive model drift. hTERT-extended melanocytes should therefore be used cautiously in studies involving pigmentation, adhesion, differentiation, and normal melanocyte physiology.

overall_design: mRNA-seq was used to compare primary human epidermal melanocytes, hTERT-overexpressing melanocytes, single-cell-derived hTERT-overexpressing clones, and melanoma cell line comparators, with three biological replicates per group.

first: Hong

last: Shi

first: Qiaohua

first: Shaoxuan


title: The N-Terminal Tail of H2A.Z Modulates the Magnitude of Transcriptional Response to Abscisic Acid in Arabidopsis thaliana

city: Atlanta

first: Roger

last: Deal

state: GA

address: 1510 Clifton Rd NE, Room 2006

department: Biology

institute: Emory University

summary: The role of the highly histone variant H2A.Z remains engimatic, in part because of its context-dependent effects on modulating transcription. Here, we investigate the role of the H2A.Z N-terminal tail in regulating transcriptional responses to the stress hormone abscisic acid (ABA) in Arabidopsis thaliana. In WT plants, treatment with ABA induces hundreds of transcripts to be rapidly up- and downregulated. Using h2a.z null mutant plants expressing either an H2A.Z missing the entire N-temrinal tail (Delta28), or carrying lysine to arginine mutations in either a single lysine (K>R 3) or all nine N-terminal lysines (K>R 1-9), we find that the H2A.Z N-terminus is surprisingly dispensable for the intiation of the ABA response program, but plays an important role in fine-tuning the magnitude of response. Interestingly, distinct subsets of genes exhibit altered response magnitude in each mutant, with limited overlap between genotypes. The most significantly dysregulated of these in the mutants compared to WT are associated with chromatin context: genes upregulated by ABA are enriched for gene-body H2A.Z (gbH2A.Z) at baseline, and show increased expression in mutants primarily under mock (non-ABA) conditions. Meanwhile, ABA-repressed genes tend to be enriched for transcription start site (TSS)-localized H2A.Z at baseline, and exhibit enhanced repression in mutants upon ABA treatment. Notably, the K>R 1-9 mutant produces more differentially expressed genes (DEGs) compared to WT in both mock and ABA-treated conditions that does complete removal of the tail, indiciating that loss of modifiability is not equivalent to loss of the N-terminus. Together, our results support a model in which the major regulatory functions of H2A.Z reside in the highly conserved histone fold domain, while the more evolutionarily variable N-terminal tail acts as a bidirectional buffer to fine-tune transcirptional output. While dispensable for the broad execution of transcriptional programs, this fine-tuning capacity is critical for maintaining transcriptional precision during stress responses, with implications for organismal fitness.

overall_design: Three week old Arabidopsis thaliana leaf tissue from four different genotypes - WT, Delta28 (h2a.z null background, expressing HTA11 lacking the first 28 amino acids), K>R 1-9 (h2a.z null background, expressing HTA11 with all 9 lysines in the N-terminus altered to arginine), and K>R 3 (h2a.z null background, expressing  HTA11 with only the third lysine, residue 13, altered to arginine). Tissue was subjected to either 4 hours of treatment with 10 uM ABA solution applied exogenously to the leaf, or a mock solution of DMSO in water, and flash frozen before being used for RNA-seq using 500 ng a sample as input ito the Lexogen QuantSeq FWD 3’ mRNA-Seq V2 Library Prep Kit with UDI. Each genotype/condition combination was done in biological triplicate.

first: Brianna

middle: D

last: Silver

middle: B


title: Peri-weaning, diet-induced activation of an IFNγ-mediated regulatory circuit promotes cDC1 maturation and CD8+ T Cells differentiation

city: Planegg

first: Barbara

last: Schraml

address: Großhaderner Strasse 9

country: Germany

institute: LMU Munich

summary: Maintaining a balanced immunity between pathogen defense and allergen tolerance in neonates is essential for survival and the establishment of life-long immune homeostasis. Instructed by environmental signals, type 1 conventional dendritic cells (cDC1) contribute to both processes but how the balance may be achieved is unclear. Here we uncover an interferon (IFN)γ-driven regulatory circuit in early life that relays dietary cues to spleen cDC1. Loss-of-function demonstrates that IFNγ-mediated STAT1 signaling induces an immunogenic maturation program in spleen cDC1 that instructs cDC1 to expand effector memory CD8⁺ T cells. This cDC1 program emerges during weaning when IFNγ production from lymphocytes rises, occurs in germ-free mice, and remains operative to dietary intervention in adult mice. During the transition from breastfeeding to solid food at weaning, this IFNγ signal relays dietary information to spleen cDC1 to shape the effector phenotype of food antigen- specific CD8+ T cells in a feedforward manner, allowing cDC1 to recalibrate the T cell pool at the time of weaning.

overall_design:
1. CD11c+MHCII+ Dendritic cells were isolated and sort purified from spleens of 1-week, 3-week, 4-week and 6-week-old mice and subjected to scRNAseq via 10x Genomics platform.
2. CD11c+MHCII+ Dendritic cells and CD90+ Lymphocytes were isolated and sort purified from spleens of 3-week-old Clec9a-cre Stat1-flox/flox mice and Stat1-flox/flox littermate controls and subjected to scRNAseq via 10x Genomics platform.

first: Ramin

last: Shakiba

first: Doğuş

last: Altunöz

first: Nikos

middle: E

last: Papaioannou

middle: U


title: ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

summary: To investigate the epigenetic landscape of tumor-reactive exhausted CD8+ T cells, ATAC-seq was performed on fluorescence-activated cell sorted CD8+ T cell subsets isolated from Lag3^iCreERT2^ Rosa26^LSL-tdTomato^ mice bearing B16-F10 melanoma tumors. Chromatin accessibility profiles were generated for lineage-traced LAG3^+tdTomato^+, LAG3^-tdTomato^+, and corresponding control CD8+ T cell populations isolated from tumors and draining lymphoid tissues. These data were used to characterize chromatin accessibility changes associated with exhausted, progenitor-like, and memory-like CD8+ T cell states and to define epigenetic relationships among lineage-traced T cell populations.

overall_design: B16-F10 melanoma cells were implanted subcutaneously into Lag3^iCreERT2^ Rosa26^LSL-tdTomato^ mice. Tamoxifen was administered on days 8–10 after tumor implantation to permanently label Lag3-expressing cells. On day 19, single-cell suspensions were prepared from tumors, draining lymph nodes (DLN), and non-draining lymph nodes (NDLN). CD8+ T cell subsets were isolated by fluorescence-activated cell sorting based on tdTomato and LAG3 expression, including LAG3^-tdTomato^- (DN), LAG3^+tdTomato^+ (DP), and LAG3^-tdTomato^+ (SP) populations. Bulk ATAC-seq libraries were generated from sorted populations to assess chromatin accessibility associated with exhausted and memory-like CD8+ T cell differentiation.

first: Vaishali

last: Aggarwal

first: Creg

last: Workman

first: Dario

last: A A Vignali


title: Tumor-specific memory-like progenitor exhausted CD8+ T cell subsets diverge into terminally exhausted cells and long-lived memory T cells

summary: Chronic antigen stimulation induces CD8+ T cell exhaustion (TEX) in tumors. To investigate the developmental fate and heterogeneity of exhausted T cells, we generated an inducible Lag3^iCreERT2 Rosa26^LSL-tdTomato lineage-tracing mouse model and profiled lineage-traced CD8+ T cells isolated from tumors and peripheral lymphoid tissues at multiple time points following B16-F10 melanoma challenge. Single-cell RNA sequencing, paired TCR sequencing, and ATAC-seq were performed to characterize transcriptional, clonal, and epigenetic states of LAG3^+tdTomato^+, LAG3^-tdTomato^+, and corresponding control CD8+ T cell populations. These datasets provide a resource for studying the differentiation trajectories, clonal relationships, and chromatin remodeling underlying exhausted and memory-like tumor-reactive CD8+ T cells.

overall_design: CD8+ T cell subsets were sorted from B16-F10 tumor-bearing Lag3^iCreERT2 Rosa26^LSL-tdTomato mice after tamoxifen-induced lineage tracing of Lag3-expressing cells. Tumor and peripheral lymphoid tissues were collected at day 11 and day 19 after tumor inoculation. Sorted populations included intratumoral LAG3^-tdT^-, LAG3^+tdT^+, and LAG3^-tdT^+ CD8+ T cells, together with peripheral CD44^+tdT^- and CD44^+tdT^+ CD8+ T cells. Single-cell RNA-seq was performed together with paired TCR-seq to profile transcriptional states and clonal relationships among lineage-traced exhausted and memory-like CD8+ T cell populations. CITE-seq antibody-derived tag data were generated in parallel to quantify surface protein expression and support phenotypic annotation of the sorted CD8+ T cell subsets.

first: Gracie

last: Liu

last: A Vignali


title: Narrow-wavelength red LED lighting enhances growth and aroma of hydroponic leafy fennel (Foeniculum vulgare Mill.)

city: Blacksburg

first: Jingsi

address: 360 Duck Pond Drive

department: Food Science and Technology

institute: Virginia Tech

summary: Fennel (Foeniculum vulgare Mill.) is an aromatic herb cultivated worldwide. Narrow-wavelength red LED light can potentially regulate the accumulation of secondary metabolites such as aroma compounds for crops, but its impact on fennel aroma remains unclear. This study investigated supplemental red LED effects on fennel aroma using nutrient film hydroponic systems, comparing natural greenhouse light (control) with supplemental red LED (100 μmol·m-2·s-1, 14h·d-1). GC-MS-O characterized aroma compounds in fresh fennel while RNA-seq analyzed gene expression. Supplemental red LED was found to enhance growth (height, fresh biomass) and significantly increase aroma-active compounds in leaves, particularly phenylpropanoids like (E)-anethole and estragole. RNA-seq revealed 1958 upregulated and 278 downregulated genes. Under supplemental red light conditions, several phenylpropanoid biosynthesis genes were regulated, including eugenol synthase and isoeugenol synthase; related transcripts were also identified as differentially expressed. Results demonstrated the potential application of LED lighting for enhancing culinary herb quality in controlled environments and providing some molecular insights for fennel aroma biosynthesis.

overall_design: RNA-seq of fennel leaf tissue under two lighting conditions: ambient sunlight (control) and ambient sunlight supplemented with narrow-wavelength red LED light. Three biological replicates were sequenced per treatment (6 libraries total).

first: Adam

last: Sumner

first: Alex

last: Harris

first: Song

last: Li

first: Bastiaan

last: Bargmann

first: David

last: Haak

first: Yun

last: Yin


title: Therapy Induced Senescence Promotes Immunogenicity in Acute Myeloid Leukemia through Reduced EZH2 Activity (Cut&Tag Taz)

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Chemotherapy resistance and disease relapse are major determinants of treatment failure in acute myeloid leukemia (AML). Therapy-induced senescence (TIS) is one outcome of chemotherapy, but its immunological consequences in AML remain unclear. Here we show that ex vivo chemotherapy induces senescence in a subset of therapy-naïve AML samples. TIS is marked by elevated interferon signaling, upregulation of human leukocyte antigen (HLA) class I and II molecules, and increased presentation of leukemia- and senescence-associated peptides, conferring AML cells antigen-presenting cell-like features. These changes enhance autologous CD4+ and CD8+ T cell responses against AML, both ex vivo and in patient-derived xenograft models. TIS also restores AML sensitivity to immune checkpoint blockade therapy. Mechanistically, we identify reduced Polycomb Repressive Complex 2 (PRC2) activity as central to TIS induction and its immunogenicity. PRC2 inhibition reactivates senescence-related genes and HLA expression in non-senescent AML cells, enabling T cell activation. These findings uncover a senescence-driven immune mechanism with potential to improve therapy outcomes in AML.

overall_design: Patient-derived AML samples left untreated or treated ex-vivo with Tazemetostat

first: Simona

last: Fusco

first: Tatiana

last: Volpari

first: Giacomo

last: Farina

first: Teresa

last: Tavella


title: Cardiomyocyte-intrinsic somatic mtDNA mutations induce an OXPHOS-dependent immune response and promote progressive heart failure

city: Solna

first: Nils-Göran

last: Larsson

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Mitochondrial DNA (mtDNA) mutations accumulate with age, but their mechanistic contribution to ageing remains unclear. The classical mtDNA mutator mouse expresses a proofreading-deficient mtDNA polymerase (POLGD257A) and accumulates mtDNA mutations across all tissues leading to premature ageing. However, this model cannot resolve whether the ageing phenotype results from systemic dysfunction or cell-intrinsic effects of somatic mtDNA mutations. To overcome this limitation, we generated PolgiMut mice allowing spatial and temporal control of POLGD257A expression. We demonstrate here that mtDNA mutations induced in cardiomyocytes cause progressive contractile dysfunction and respiratory chain deficiency in the heart without accompanying systemic pathology. Proteomic analyses link cardiac mosaic OXPHOS dysfunction to a progressive immune response, characterized by upregulation of antigen-processing proteins and immune cell infiltration. In contrast, longevity-associated pathways are suppressed and uncoupled from mitochondrial and immune alterations, indicating distinct regulatory mechanisms. These findings demonstrate that mtDNA mutations can drive cardiac dysfunction and reveal a mechanistic link between mitochondrial dysfunction, immune responses and ageing.

overall_design: Bulk RNA-seq was performed on heart tissue samples collected from 12–16-month-old control and hMut mice to compare transcriptomic profiles between genotypes.

first: Kristina

last: Bubb


title: snATAC-seq from MCF 10A (ENCSR037XNN)

first: ENCODE

last: DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A roadmap for enriching rare cell populations from human post-mortem brain, demonstrated by 100% microglial purity (scRNA-Seq)

first: Nathan

last: Skene

address: 80 Wood Lane

department: Brain Sciences

institute: Imperial College London

summary: This submission contains processed single-nucleus RNA-seq feature-barcode matrices generated to validate fluorescence-activated nuclei sorting (FANS) strategies for enrichment of microglia from frozen human post-mortem brain. Nuclei were isolated from neurologically unaffected donor tissue from parietal cortex, occipital cortex, and cerebellum, then sorted using panels based on NeuN, OLIG2, IRF8, PU.1, and SOX9. The study benchmarks single-marker and multi-marker nuclear sorting strategies, including IRF8-positive enrichment, PU.1-positive enrichment, SOX9-positive astrocyte sorting, SOX9 dump-channel exclusion, and an extended four-channel panel enabling parallel recovery of neurons, oligodendrocytes, microglia, astrocytes, and an all-negative population. Initial validation experiments used 10x Genomics Chromium Single Cell 3' v3.1 chemistry. Subsequent validation used Illumina Single Cell 3' RNA Prep, T2, based on PIP-seq chemistry, as a lower-cost orthogonal workflow for routine sort-quality assessment.

overall_design:
Frozen human post-mortem brain nuclei from parietal cortex, occipital cortex, and cerebellum were fluorescence-sorted using NeuN, OLIG2, IRF8, PU.1, and SOX9 marker combinations. Sorted nuclear populations were profiled by single-nucleus RNA sequencing using 10x Genomics Chromium Single Cell 3' v3.1 or Illumina Single Cell 3' RNA Prep, T2 chemistry, followed by generation of feature-barcode matrices for cell-type composition and microglial enrichment assessment.

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Raw data not provided due to patient privacy concerns
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first: Isidora

last: Gocmanac

first: Hiranyamaya

last: Dash

first: Maria

last: Weinert

first: Alexi

last: Nott

first: Elina

last: Nagaeva


title: Oncogenic Modulation of MAPK Signaling in Leukemia via SPNS2-Mediated Sphingosine Metabolism Rewiring

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Lipid metabolism rewiring is an essential determinant of cancer transformation and progression, yet metabolic checkpoints that act as key switches in this process remain poorly defined. Using functional genomics in a mouse model of acute myeloid leukemia (AML), we identified the sphingosine-1-phosphate transporter SPNS2 as a sphingolipid checkpoint protein critical for leukemia development. SPNS2 expression is regulated by MYC and progressively decreases with AML differentiation, highlighting its tumor-suppressive role in a subset of Core Binding Factor AMLs. Integrating lipidomic profiling, RNA-seq, flow cytometry, and microscopy with gain- and loss-of-function approaches, we showed that SPNS2 modulation rewires sphingolipid metabolism by altering sphingomyelin levels, thereby affecting membrane nanodomain formation, active RAS localization and MAPK signaling. Exogenous reintroduction of SPNS2 decreases sphingomyelin levels, disrupts nanodomain organization, and limits leukemic progression in AML mouse models. Our data revealed an unrecognized mechanism by which sphingolipid transport dynamics intersect with oncogenic signaling to control cancer progression.

overall_design: ME-1 cells were transduced either with control empty vector or a vector allowing overexpression of SPNS2. After infected cells selection RNA was extracted and RNAseq was performed.

first: Gaetano

last: Sodaro

first: Khansa

last: Saadallah

first: Alexandre

last: Puissant


title: A multi-omics characterization of the human lumbar spinal cord and motor cortex reveals non-overlapping molecular signatures in ALS

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease characterized by the loss of upper and lower motor neurons in the motor cortex (MTC) and spinal cord (SC), respectively, leading to muscle atrophy and ultimately respiratory failure. While motor neurons (MNs) are the selectively vulnerable cell type, their interactions with glia contribute to the progression of ALS pathology. However, it remains unclear whether the molecular alterations underlying MN and glial dysfunction in ALS are the same in the MTC and lumbar SC (LSC). To address this, we constructed spatially-resolved gene expression maps of the MTC and LSC by combining spatial and single-nucleus transcriptomic profiles from a cohort of non-neurological controls and ALS patients clinically stratified by site of symptom onset. In the ventral horn of the LSC, we see a decrease in genes associated with MNs and synaptic signaling in ALS patients. We also identify region-specific alterations in endothelial- and glial-related functions. Notably, the severity of these MN deficits and endothelial-related functions is influenced by the site of symptom onset, whereas alterations in glial function largely are not. In the MTC, we observe layer-specific increases in synaptic signaling in ALS patients. Comparing the molecular and cellular changes within the LSC and MTC in ALS indicates that they are predominantly non-overlapping, and have different molecular signatures.

overall_design: 320 10x Visium spatial transcriptomic libraries generated from 35 human donor lumbar spinal cords and from 50 human donor motor cortexes, across a range of non-neuropathological sudden-death controls and ALS patients

first: Natalie

last: Barretto

first: Aidan

last: Daly

first: Hemali

last: Phatnani


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [stability]

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: In most plants, germination begins with the reactivation of metabolism during water uptake by the desiccated seed. Notably, Pol II transcription is hypothesised not to be required for early germination, as seeds appear to initially rely on stored mRNAs produced during their maturation. Here, we show that efficient blocking of Pol II transcription completely stops germination in Arabidopsis seeds. Pol II activity is initiated early and is widespread, following expression and Pol II binding patterns established during seed drying. Our findings suggest that the earliest transcriptional phase relies on pre-existing protein factors. The transcriptional programme initiated during water uptake is robust across diverse imbibition conditions and in seeds matured at different temperatures, and is conserved in rapeseed (Brassica napus). Only after the successful completion of this initial phase and the passing of the translation-dependent checkpoint do seeds activate genes that lead to germination. Our results redefine the role of transcription in seed germination and highlight a conserved pattern of early transcriptional activation.

overall_design: Time course of Arabidopsis seeds imbibition in the presence of alpha-amanitin or cycloheximide and alpha-amanitin analysed using 3'RNA-seq.

first: Szymon

last: Swiezewski


title: A multi-omics characterization of the human lumbar spinal cord and motor cortex reveals non-overlapping molecular signatures in ALS [snRNA-Seq; snATAC-Seq]

overall_design: 44 10x Multiomics (snRNAseq & snATACseq) libraries generated from 20 human donor lumbar spinal cords and from 24 human donor motor cortexes, across a range of non-neuropathological sudden-death controls and ALS patients


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [spike]

overall_design: mRNAs were labelled with 4-SU during 1h, 3h or 6h seed imbibition. Both positive and negative spike-ins were added to samples before enrichment. 3' RNA-seq was performed on enriched labelled and input samples.


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [puromycin]

overall_design: mRNAs were labelled with 4-SU during 6h seed imbibition in the presence of cycloheximide, purpmycin or mock. 3'RNA-seq was performed for enriched labelled and input samples.


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR029LAA)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC


title: total RNA-seq from HG03078 (ENCSR029GJS)


title: Transcriptional regulation of the embryonic ζ-globin gene [human]

city: Oxford

first: Siyu

last: Liu

state: England

address: John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: Reactivating the embryonic ζ-globin expression is a promising prospect for treating severe forms of α-thalassaemia. Here, we address the mechnisms underlying the transcriptional regulation of the ζ-globin gene.

overall_design: We have identified the key cis-regulatory elements that silence the ζ-globin gene in definitive erythroid cells and demonstrated that combined disruption of the two identified elements (Double Mutant, DM) can restore ζ-globin expression to therapeutically meaningful levels. This approach has been tested in WT HUDEP-2 cells, as well as a BHFS HUDEP-2 cell model homozygous for the most prevalent α-thalassaemia Southeast Asian (SEA) deletion. Clonal HUDEP-2 cell models were differentiated to erythroid cells and were assessed by ATAC-seq and ChIPmentation for GATA1.


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [conversion]

overall_design: mRNAs were labelled with 4-SU during 3h seed imbibition. 3' RNA-seq was performed on 4-SU-to-C converted total RNA and biotin-enriched samples. Unconverted total samples were used to estimate RNA-seq error rates.


title: Sam68 stimulates Theta-Mediated End-Joining by suppressing poison exon inclusion in Polq mRNA

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: DNA polymerase Theta-Mediated End-Joining (TMEJ) is a stand-alone mutagenic DNA double-strand break (DSB) repair pathway that becomes critical when high-fidelity repair is compromised. Although the enzymatic mechanism of TMEJ has been extensively studied in recent years, its regulation remains poorly understood. Here, we identify and characterize the RNA-binding protein Sam68 (also known as Khdrbs1) as a key modulator of TMEJ in mammalian cells. We demonstrate that Sam68 is required for proper expression of Polq, the gene encoding polymerase theta (Polθ), the central factor in TMEJ. Loss of Sam68 results in reduced TMEJ at CRISPR-induced DSBs and increased sensitivity to ionizing radiation. Mechanistically, Sam68 promotes correct splicing of Polq mRNA by suppressing the inclusion of a conserved poison exon that introduces a premature termination codon in the transcript. This function depends on the RNA-binding domain of Sam68. Genetic deletion of the poison exon restores Polq expression and rescues TMEJ activity in Sam68-depleted cells. Together, these findings establish alternative splicing as a direct mechanism controlling TMEJ capacity and reveal a conserved regulatory mechanism that tunes mutagenic DSB repair through modulation of Polθ abundance.

overall_design: To study differences in RNA production and splicing in the presence or absence of Khdrbs1, we performed RNA-sequencing in mES cells, either wild type or knockout for Khdrbs1

first: Marloes

last: van Wezel

first: Hanneke

last: Kool

first: Diana

last: van den Heuvel

first: Robin

last: van Schendel

first: Marco

last: Barazas

middle: S

first: Marcel

last: Tijsterman

first: Joost

last: Schimmel


title: Transcriptional regulation of the main olfactory epithelium by environmental olfactory exposures

city: Rochester

first: Regina

middle: K

last: Rowe

address: 601 Elmwood Ave, Box 850

institute: University of Rochester

summary: The main olfactory epithelium (MOE) is a highly heterogeneous tissue, comprised of many cell types including but not limited to olfactory sensory neurons, support cells, and immune cells. In this study, we investigated how environmental olfactory exposures impact cell-type specific transcriptional responses in the mouse MOE. We performed single-cell RNA sequencing (scRNA-seq) of the MOE following controlled environmental exposure to both well-known odorants (soiled bedding, amyl acetate) and an aeroallergen (house dust mite). We identified major cell types and subtypes within the MOE and identified transcriptional changes in response to the olfactory exposures.

overall_design: Wild-type C57BL/6J mice aged 6 weeks were solo housed for 7 days followed by environmental olfactory exposure for 7 days with: water (negative control), soiled bedding, amyl acetate, or house dust mite extract (HDM). On day 7, the olfactory epithelium was isolated by dissection and dissociated into a single cell suspension. Samples were barcoded and pooled, single cell captures performed using the 10x Genomics Chromium platform and analyzed using single cell RNA sequencing. The experiment was performed in duplicate for a total of 16 animals (8 male, 8 female, 4 per condition). In addition to the 16 exposed mice, 2 male mice were taken directly from the cage (i.e. homeostasis) which were processed similarly and used only for cell clustering and not for differential gene analysis.

first: Varun

last: Haran

first: Chinyi

last: Chu

first: Ryan

last: Owens

first: Thomas

last: Mariani

first: Julian

last: Meeks


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [pulse]

first: Michal

last: Krzyszton

overall_design: mRNAs were labelled with 4-SU during a 30 min incubation of embryos following 2.5 or 5.5 h of seed imbibition. 3' RNA-seq was performed on enriched labelled and input samples.

first: Szymon

last: Swiezewski


title: Engineered bacteria as exogenous organelle mimics restore PTEN and p53 tumor suppressor functions for cancer therapy

city: qingdao

first: shijie

last: bi

address: No. 23, Hong Kong East Road

institute: ouc

summary: This work establishes a novel paradigm for using engineered intracellular bacteria asexogenous organelle-like systems to restore tumor suppressor functions and offers a promising strategy for cancer therapy

overall_design: Transcriptomic analysis was conducted on tumor tissues from B16F10 subcutaneous xenograft mice that received different treatments(PBS, VPE-WT, VPE-PTEN, RG-NPs, VPE-PTEN+RG-NPs, VPE-PTEN@RG-NPs).

first: Shijie

last: Bi

first: Maoqin

last: Wang

first: Qing

last: Guan

first: Yaxin

first: Runchang

last: Liu

first: Jiaying

last: Zhang

first: Meng

last: Li

first: Quan

first: Peng

first: Youming

first: Jun

last: Fu

first: Ruijuan


title: Transcriptional regulation of the embryonic ζ-globin gene [mouse]

first: Siyu

overall_design: To localise the cis-regulatory elements responsible for ζ-globin silencing, we generated a mouse model in which a 4.4 kb segment containing the entire ζ-globin (Hba-x) gene is replaced with a 2.3 kb fragment containing a modified α-globin (termed Hba-alt) gene that encodes 20 naturally occurring single nucleotide polymorphisms (SNPs) into the primary RNA transcript, enabling us to distinguish Hba-alt transcripts from the endogenous Hba-a1/2 transcripts. This engineered mouse line was named Deleted Zeta Inserted Alpha (DZIA). To assess gene therapy approaches in vivo, we generated a pre-clinical mouse model harbouring a deletion equivalent to the human Southeast Asian (SEA) deletion. Erythroid cells from these models were assessed by ATAC-seq in biological replicates.


title: A Pan-Cancer Single-Cell Atlas to Evaluate Tumor Identity, Cell Line Concordance, and Dependency Mapping

first: James

middle: Paul

last: Agolia

address: 257 Campus Dr West

department: Surgery

institute: Stanford University

summary: Bulk RNA sequencing enables pan-cancer transcriptional analyses, but obscures cancer cell-specific programs due to admixture with nonmalignant cells, limiting direct comparison between experimental models and human tumors. Single-cell RNA sequencing (scRNA-seq) overcomes these limitations, yet biological interpretability of public datasets is often compromised by variable data quality, inconsistent annotation, and atlas-scale aggregation strategies that favor data volume over biological coherence. We therefore developed a stringent integration framework that prioritizes representative malignant transcriptional states. Using Mahalanobis distance-based selection in batch-corrected latent space, we constructed a pan-cancer atlas of 135,441 high-quality malignant cells from 494 samples spanning 36 adult and pediatric cancer types. Atlas-derived signatures were used to assess tumor–cell line concordance and project ElasticNet models trained on DepMap CRISPR screens to infer cancer-specific gene dependencies. Together, the scTumor Atlas provides a scalable framework for tumor identity inference, cancer cell line benchmarking, and systematic identification of genetic vulnerabilities.

overall_design:
At the time of tumor resection, a sample of the resected tumor was collected. The specimen was transported on ice in Miltenyi MACS tissue storage solution to Retro Bio and carried through to 10x Genomics library preparation 10x Genomics Single Cell 5' PE chemistry. FASTQs were aligned to GRCh38-2020-A using  cellranger-7.1.0.

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We are not able to release FASTQs or BAM files due to patient privacy concerns.
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first: Rosyli

middle: F

last: Reveron-Thornton

first: Daniel

last: Delitto


title: Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

city: Baltimore

first: Jeff

last: Coller

state: MD

address: 725 N Wolfe St

institute: Johns Hopkins University

summary: Ribosome dynamics during mRNA translation elongation regulate mRNA stability. Yet, known regulators of ribosome transit, such as codon usage, cannot fully explain transcriptome-wide decay rates. Here, we demonstrate that nascent polypeptide folding status modulates elongation rates, with Zuotin (Zuo1) serving as an essential mediator, and this also influences mRNA stability. Using reporter constructs encoding co-translationally unstructured proteins and RNA sequencing under proteotoxic stress, we show that Zuo1 is required for the selective destabilization of transcripts whose nascent peptides fail to fold properly. This process is independent of codon optimality but relies on the co-translational mRNA decay factor Not5, which detects slowed ribosomes. 35S labeling indicates that nascent peptide folding defects correlate with reduced elongation rates in a Zuo1-dependent manner, and ribosome profiling reveals that global protein misfolding induces Zuo1-dependent ribosome pausing. These findings position Zuo1 as a key mediator linking nascent peptide folding status to ribosome dynamics and mRNA stability. Furthermore, this work suggests an expanded role for Not5 beyond codon optimality sensing.

overall_design: Ribosome profiling of wild-type and zuo1 S288C yeast grown at room temperature, treated with, treated with MG132 or MG132 + L-azetidine-2-carboxylic acid (AZC) for 45 minutes.

first: Suhee

last: Chang

first: Ryan

last: Kawalerski

first: Sophie

last: Martin