title: sh3_MINUS-WT_1

description: Library name: AM16_08_JS13_S8


title: R_PLUS-CTRL_1

status: Public on Feb 27 2026

type: SRA

city: Manchester

first: Martin

middle: James

last: Baker

state: England

address: 555 Wilmslow Rd

department: Division of Cancer Sciences

country: United Kingdom

institute: University of Manchester

description: Library name: AM16_03_JS6_S3

library_source: transcriptomic

data_processing:
Reads were quality-checked using FastQC and adapters were trimmed, reads were aligned to the human genome (GRCh38) using STAR aligner, and read counts generated using feature Counts with Ensemble GTF annotation (Homo_sapiens.GRCh38.75.gtf).
Assembly: Homo_sapiens.GRCh38.75.gtf
Supplementary files format and content: counts.tsv [Count file][.tsv]

molecule: polyA RNA

organism: Homo sapiens

source_name: H358 LUAD

growth_protocol: Cells cultured in RPMI 1640 growth medium with 5% Fetal bovine serum (FBS).

extract_protocol:
and RNA extracted using the RNeasy Mini kit (Qiagen) with sample homogenisation by QIAshredder (Qiagen) as per manufacturer’s protocols.
libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI (Lexogen) on a Bravo NGS Workstation Option B (Agilent Technologies). ). Single read 100bp sequencing was performed by loading 220pM pooled libraries on a NovaSeq 6000 sequencer (Illumina) with standard loading.

treatment_protocol: Pretreated with -/+ 10ng/ml doxycycline for 72 hours prior to seeding at equal low density with fresh media and -/+ 10ng/ml doxyclcine. Fresh media -/+ doxycycline added at 7 days. At 10 days, media removed, cells washed with PBS.

tag: cell line

value: H358 LUAD

tag: genotype

value: KD

tag: treatment


title: sh2_MINUS-WT_1

description: Library name: AM16_06_JS15_S6

value: WT


title: sh2_PLUS-KD_1

description: Library name: AM16_07_JS2_S7

value: CTRL


title: R_MINUS-CTRL_1

description: Library name: AM16_01_JS10_S1


title: DE_MEKi.d2_RNA_Rep2

status: Public on Feb 26 2026

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Library name: DE_MEKi_d2_RNA_r2

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: hg38 + dm6
Supplementary files format and content: Excel file containing read counts per human genes. Columns names matche with sample titles.

source_name: Definitive Endoderm

growth_protocol: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW) were obtained from the CCHMC Pluripotent Stem Cell Facility (PSCF) and cultured under feeder-free condition in mTeSR1 medium (85850, StemCell Technologies) on plates coated with either hESC-qualified Matrigel (354277, Corning) or Cultrex Stem Cell Qualified Reduced Growth Factor Basement Membrane Extract (3434-010-02, Biotechne). hPSCs were cultured in a humidified incubator at 37℃ with 5% CO2.

extract_protocol:
1.0x106 cultured cells were dissociated into single cells using Accutase and were mixed with 100,000 Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were lysed with Aurum Total RNA Lysis Solution (7326802, BioRad). Total RNA was extracted using Aurum™ Total RNA Mini Kit (7326820, BioRad).
The sequencing libraries were prepared by Novogene or Plasmidsaurus

treatment_protocol:
For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.
For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.
For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for one or two days during differentiation from hPSC into NE, ME, and DE.
For inducing MTase-TKD/CRISPRi, cells were cultured with 2 uM doxycycline (D9891-5G, Sigma-Aldrich) for 3 days.

value: Definitive Endoderm

value: MEKi inhibitor


title: DE_MEKi.d2_RNA_Rep1

description: Library name: DE_MEKi_d2_RNA_r1


title: NE_MEKi.d2_ChIP_Input_Rep2

description: Library name: NED2_MEKiD2_Input_Rep2_Lib639

library_source: genomic

data_processing:
Sequencing reads were aligned to combined genome of hg38 and dm6 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
BigWig files were generated using reads aligned to hg38 using bedtools and UCSC toolkit in a RPM scale (*.rpm.bw). For ChIP samples, additional bigwig files were generated by normalizing by spike-in counts, i.e. read per 0.1 million spike-in count (*.rpsm.bw).
Assembly: hg38 + dm6
Supplementary files format and content: bigwig in RPM scale (*.rpm.bw); bigwig in spike-in normalized scale (*.rpsm.bw)

molecule: genomic DNA

source_name: Neuroectoderm

extract_protocol:
Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was quenched by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 x g for 5 min at 4°C, and the supernatant was removed. The cell pellet was washed with ice-cold 1x PBS, centrifuged again at 600 x g for 5 min at 4°C, and the supernatant was aspirated. This wash step was repeated once more. The final cell pellet was frozen on dry ice and stored at -80°C until use.  Crosslinked human cells were resuspended in Lysis Buffer1 (10 mM Tris-HCl [pH 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. For Drosophila S2 spike-in controls, crosslinked S2 cells were resuspended in 100 uL Lysis Buffer1 at a final concentration of 2.0x105 or 4.0x105 cells/uL, and 25% of the S2 cells were mixed with human cells. The mixed cell suspension was centrifuged at 665 x g for 5 min at 4℃, and the supernatant was removed. The cell pellet was then resuspended in Lysis Buffer2 (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA-free) and incubated on ice for 10 min. The cell lysate was then diluted in IP Dilution Buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA-free) and transferred to a milliTUBE ATA Fiber (Covaris). Chromatin was sonicated using a Covaris S220 (Covaris) for 5.5 min. Insoluble debris was removed by centrifugation at 12,000 x g for 5 min at 4℃. The supernatant containing sonicated chromatin was transferred to a new tube and stored at -80℃ until use.  Dynabeads Protein-G (10004D, Thermo Fisher Scientific) (25 - 80 uL) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). The desired amounts of H3K9me3 (ab8898, Abcam) antibodies were conjugated to washed Dynabeads by incubating for 2 to 6 hours at 4°C with rotation. Meanwhile, frozen sonicated chromatin was thawed on ice. A desired amount of chromatin (Table S3, based on DNA quantity) was diluted with IP dilution buffer at a 4:1 ratio. Antibody-conjugated Dynabeads were washed twice with IP Dilution Buffer (without protease inhibitor), resuspended in the diluted chromatin, and incubated overnight at 4°C with rotation. The next day, ChIPed beads were washed four times using the following washing buffers: (1) FA Lysis Buffer (50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA-free); (2) NaCl Buffer (50 mM HEPES-KOH [pH 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); (3) LiCl Buffer (100 mM Tris-HCl [pH 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); (4) 10 mM Tris-HCl [pH 8.0]. Following washing steps, chromatin was eluted with TES buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1,000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse-crosslinked by adding NaCl to a final concentration of 200 mM and incubating for 8 hours at 65°C. Samples were then treated with 50 ng/uL RNaseA (EN0531, ThermoFisher Scientific) for 30 min at 37°C, followed by treatment with 0.2 mg/mL Protease K (03115828001, Roche) for 2 hours at 37°C. DNA was purified using phenol-chloroform extraction, followed by ethanol precipitation. DNA concentration was measured using Quantus fluorometer (Promega).
Multiplexed libraries were prepared from ChIP and Input samples (two replicates) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB), following the manufacturer’s protocol with the following modifications. After adaptor ligation, cleanup was performed using AMPure XP Beads (A63880, Beckman Coulter), MagBind Magnetic Beads (M1378-01, Omega), or homemade Sera-mag beads (Rohland et al., Genome Res. 2012) without size selection. After RCR enrichment of the adaptor-ligated library, two rounds of size selection were performed using the AMPure XP Beads or MagBind Magnetic Beads.

treatment_protocol:
For definitive endoderm (DE) differentiation, hPSCs were plated on Matrigel- or Culturex SCQ-coated plates (dilution factor as per hPSC culture) one day before induction. For ME induction, hPSCs were cultured in CDM2 medium supplemented with 100 ng/ml ActivinA, 2 uM CHIR99021, and 50 nM PI103 (SML0559-5MG, Sigma-Aldrich) for 24 hours. For subsequent DE differentiation, ME cells were briefly washed with DMEM/F12 and cultured in CDM2 medium supplemented with 100 ng/ml ActivinA and 250 nM LDN193189 for 24 hours.
For neuroectoderm (NE) differentiation, hPSCs were plated on Matrigel- (1:50 dilution) or Culturex SCQ-coated cell culture plates one day before differentiation. NE was induced by E6 medium (A1516401, Thermo Fisher Scientific) supplemented with 500 nM LDN193189 (SML0559-5MG, Sigma-Aldrich), 10 uM, SB431542 (S4317-5MG, Sigma-Aldrich), and 5 uM XAV931 (X3004-5MG, Sigma-Aldrich). Cells were cultured in this medium for 48 hours with daily media changes.
For inhibiting MEK/ERK signaling, cells were treated with 1 uM of PD0325901 (MEK inhibitor; 72182, STEMCELL Technologies) or DMSO (vehicle control) for one or two days during differentiation from hPSC into NE, ME, and DE.

value: Neuroectoderm


title: DE_MEKi.d2_ChIP_Input_Rep2

description: Library name: DE_MEKiD2_Input_Rep2_Lib643

source_name: Definitive endoderm

value: Definitive endoderm


title: DE_MEKi.d2_ChIP_Input_Rep1

description: Library name: DE_MEKiD2_Input_Rep1_Lib642


title: Pre-tumor p53 proficient 3

status: Public on Mar 18 2026

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: 9268_RH_PanINPM_DP
10x_v2

library_source: transcriptomic single cell

data_processing:
All scRNA-seq datasets were demultiplexed, barcode-corrected, aligned and UMI-corrected with SEQC using mouse genome mm10 and default parameters.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with our custom pipeline SEQC (v0.2.8) are deposited in the Matrix Market format for sparse matrix representation. Cell barcodes in processed data files are encoded using the DNA3Bit class of the SEQC package.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our KPLOH model (GFP, rtTA3-IRES-mKate2, shRen) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

growth_protocol: Mice were generated by 8-cell injection of KPLOH (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt; TRE-GFP-shRen.713) ESCs.

extract_protocol:
Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) or immune cells (marked as mKate2-negative, CD45-positive and DAPI-negative) were sorted using Aria3 or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS). Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).
Cells were resuspended in 1X PBS and BSA (0.04%) and checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II). All sequencing experiments were performed on samples with a minimum of 80% viable cells. Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2 or v3). For pre-tumor p53 deficient samples, we spiked-in CD45+ cells to the cell suspension to allow visualization of cell pellets during sample preparation prior to encapsulation. Each sample loaded onto the cartridge contained approximately 5,000 cells (non-hashed samples) or 15,000 cells (hashed samples) at a final dilution of ~500 cells μl-1. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina sequencer (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads per cell) at MSK’s Integrated Genomics Operation Core Facility.

treatment_protocol: GFP was induced by treatment of the resulting mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age.

tag: tissue

value: Pancreas

tag: cell type

value: Epithelial

value: mKate2+/GFP+ (p53 proficient)

value: Dox

tag: batch


title: NE_MEKi.d2_ChIP_Input_Rep1

description: Library name: NED2_MEKiD2_Input_Rep1_Lib638


title: DE_MEKi.d2_ChIP_H3K9me3_Rep2

description: Library name: DE_MEKiD2_H3K9me3_Rep2_Lib649


title: DE_MEKi.d2_ChIP_H3K9me3_Rep1

description: Library name: DE_MEKiD2_H3K9me3_Rep1_Lib648


title: Muscle,Intermittent_fasting,Male,rep6

city: Melbourne

first: Yibo

last: Fan

state: VIC

address: Science Dr, Bundoora VIC 3083

country: Australia

institute: La Trobe University

description: Library name: MIF14

data_processing:
Base Calling,CASAVA base recognition
Data Filtering,Remove reads with adapter contamination.Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Alignment,HISAT2
Assembly: mm39
Supplementary files format and content: txt file includes raw counts for each sample

source_name: Muscle

extract_protocol:
RNA was extracted using TRIzol Reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: Muscle

tag: Sex

value: male

tag: diet

value: IF


title: NE_MEKi.d2_ChIP_H3K9me3_Rep2

description: Library name: NED2_MEKiD2_H3K9me3_Rep2_Lib645


title: NE_MEKi.d2_ChIP_H3K9me3_Rep1

description: Library name: NED2_MEKiD2_H3K9me3_Rep1_Lib644


title: NE_Ctrl_RNA_Rep3

description: Library name: D2_iNE_3

value: Ctrl


title: Muscle,Intermittent_fasting,Male,rep2

description: Library name: MIF10


title: NE_Ctrl_ChIP_Input_Rep2

description: Library name: NEd2_ChIP_Input_R2


title: NE_Ctrl_RNA_Rep1

description: Library name: D2_iNE_1


title: NE_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: NEd2_ChIP_H3K9me3_R2


title: NE_Ctrl_ChIP_Input_Rep1

description: Library name: NEd2_ChIP_Input_R1


title: NE_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: NEd2_ChIP_H3K9me3_R1


title: DE_Ctrl_ChIP_Input_Rep2

description: Library name: DE_Ctrl_ChIP_Input_CloneH5


title: DE_Ctrl_ChIP_Input_Rep1

description: Library name: DE_Ctrl_ChIP_Input_CloneA6


title: 25mM glucose, H3K27Ac (CUT&Tag), replicate 2

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Library name: H3K27Ac_25mM_rep2

data_processing:
H3K18La CUT&Tag fastq files were processed using nf-core/cutandrun v3.1 to GRCm38 assembly. MACS peaks, filtered for qValue > 6, present in at least two biological replicates were used as consensus peaks for each experimental grouping.
Annotation of consensus peaks was performed in R with ChipSeeker v1.34.1 using Ensembl v102 annotation.
Peak quantitation was performed on merged consensus peaks using CSAW v1.32.0. Normalization was performed using windowCounts function in CSAW with 10,000 base windows. Differential peak analysis was performed using gene wise negative binomial generalized linear models with quasi-likelihood tests using edgeR v3.40.2.
Assembly: GRCm38/Ensembl v102
Supplementary files format and content: bigWig of alignment data
Supplementary files format and content: xlsx files of annotated concensus peaks for each condition
Supplementary files format and content: tsv files of CUT&Tag peak quantitation and differential binding results
Library strategy: CUT&Tag

source_name: retina explant

extract_protocol:
CUT&Tag protocol was performed using CUT&Tag-IT® Assay Kit – Tissue (Active Motif) with slight modifications. In brief, explanted retinas were dissected and cells were dissociated in a 5 ml polypropylene round-bottom tube with a papain dissociation protocol adapted from previous study {Fadl, 2020 #16} . After dissociation the cells were washed using 1X wash buffer provided in the kit at 200g for 5 minutes. CUT&Tag was performed using 500,000 cells per experiment following kit protocol. Antibodies against H3K18La (Rabbit, cat.no. PTM1406), and H3K9me3 (Rabbit, cat.no. ab6002, Abcam, Cambridge, UK) were used at a concentration of 1:100 in 100 μl and pA-MNase conjugated to protein A (generous gift of Dr. Steven Henikoff, Howard Hughes Medical Institute, Washington, USA) used at a concentration of 700 ng/ml. Total RNA from explant retinae was extracted using TRIzol® (Invitrogen, Carlsbad, CA), treated with DNase and cleaned up using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions. Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification. Paired-end sequencing of 101 bases were obtained using the NextSeq 2000 (Illumina, San Diego, CA).
CUT&Tag-IT® Assay Kit – Tissue (Active Motif)

treatment_protocol: Wild-type, P28 C57BL/6J mice used for retinal explant cultures were euthanized by CO2 asphyxiation and freshly dissected in 1X Hank's Balanced Salt Solution (HBSS) To avoid variability due to circadian effects, retinas were dissected 2 hours after lights are turned ON in the facility for all experiments. Extraocular tissue was trimmed off and the cornea and iris were carefully removed. Sclera along with the RPE was gently removed to get the clean retina tissue. The dissected retinas were incubated in Neurobasal-A media supplemented with 5 mM glucose/25 mM glucose or 5 mM glucose with different concentration of 2DG (10mM and 15mM), 0.2% B27 supplement, 0.1% N2 supplement, 0.1%   and penicillin/streptomycin (Thermofisher Scientific) with 5% CO2 at 37°C for 48 hours times as described in previous reports {Chinchore, 2017 #9}. At the end of incubation period, the retinas were rinsed with prewarmed Krebs’ Ringers medium and were further incubated in 0.3 mL Krebs’ Ringers medium for 1hr in 37°C incubator. The supernatant and retinas were rapidly frozen separately at the end of the experiment for lactate assay and western blot respectively. For CUT&Tag and RNAseq retinas were processed immediately.

value: retina explant

value: 25mM glucose


title: DE_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: DE_Ctrl_ChIP_H3K9me3_CloneH5


title: 25mM glucose, H3K27Ac (CUT&Tag), replicate 1

description: Library name: H3K27Ac_25mM_rep1


title: DE_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: DE_Ctrl_ChIP_H3K9me3_CloneA6


title: hPSC_Ctrl_ChIP_Input__Rep2

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_Input_Clone11

source_name: hPSC

value: hPSC


title: 5mM glucose, H3K27Ac (CUT&Tag), replicate 2

description: Library name: H3K27Ac_5mM_rep2

value: 5mM glucose


title: 5mM glucose, H3K27Ac (CUT&Tag), replicate 1

description: Library name: H3K27Ac_5mM_rep1


title: hPSC_Ctrl_ChIP_Input_Rep1

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_Input_Clone10


title: hPSC_Ctrl_ChIP_H3K9me3_Rep2

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_H3K9me3_Clone11


title: hPSC_Ctrl_ChIP_H3K9me3_Rep1

description: Library name: hPSC_Ctl_OCT4CRISPRi_ChIP_H3K9me3_Clone10


title: Lung airway epithelium, IPF9

status: Public on Feb 20 2026

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

description: IPF, Sex: M, Age 50

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the GRChg38 transcriptome
All subsequent analyses were performed in R v.3.6.0  using the Seurat (v3) package
Assembly: GRCh38
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Lung airway epithelium

growth_protocol: Not applicable

extract_protocol:
Enzymatic dissociation with collagenase D from Clostridium histolyticum (Roche) and 0.1mg/ml DNase I from bovine pancreas (Roche). Incubation for 1 hour at 37oC. Dissociated cells passed through passed through a 70μm filter, centrifuged (1200rpm, 5mins, 4oC) and the resulting cell pellet resuspended in HBSS with 0.04% UltraPure BSA (Invitrogen).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: Not applicable

value: Lung airway epithelium

tag: disease state

value: IPF

value: Epithelial cells, immune cells

value: M

tag: age


title: Lung airway epithelium, IPF7

description: IPF, Sex: M, Age 66


title: Lung airway epithelium, IPF8

description: IPF, Sex: M, Age 74


title: Lung airway epithelium, IPF6

description: IPF, Sex: M, Age 79


title: Lung airway epithelium, IPF5

description: IPF, Sex: M, Age 65


title: Lung airway epithelium, IPF4

description: IPF, Sex: M, Age 84


title: Lung airway epithelium, IPF3

description: IPF, Sex: M, Age 71


title: Lung airway epithelium, IPF2

description: IPF, Sex: M, Age 61


title: Lung airway epithelium, IPF1

description: IPF, Sex: M, Age 73


title: Lung airway epithelium, H7

description: Healthy, Sex: M, Age: 44

value: Healthy


title: Lung airway epithelium, H5

description: Healthy, Sex: F, Age: 50

value: F


title: Lung airway epithelium, H6

description: Healthy, Sex: F, Age: 55


title: Lung airway epithelium, H4

description: Healthy, Sex: F, Age: 47


title: Lung airway epithelium, H3

description: Healthy, Sex: M, Age: 51


title: Lung airway epithelium, H2

description: Healthy, Sex: F, Age: 26


title: Br2421

status: Public on Feb 16 2026

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: Br2421-V13F27-336_D1

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: brain (dorsolateral prefrontal cortex)

extract_protocol:
DLPFC tissue blocks were dissected from fresh-frozen postmortem human brain tissue slabs. Coronal cryosections (10 µm thick) were mounted onto 10x Genomics Visium Spatial Transcriptomics arrays (v1, 3’ Gene Expression based on 3’ poly(A) capture-based chemistry). Sections were immunostained for nuclei (DAPI), neurons (NeuN), perineuronal nets (WFA), and vasculature (Claudin-5), and subsequently processed for spatial transcriptomics. Tissue permeabilization and cDNA synthesis incorporating positional barcodes were performed according to the manufacturer’s instructions (CG000239 Rev F).
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions (CG000239 Rev F)

value: brain (dorsolateral prefrontal cortex)


title: Lung airway epithelium, H1

description: Healthy, Sex: M, Age: 47


title: Br1923

description: Library name: Br1923-V13F27-336_C1


title: Br8218

description: Library name: Br8218-V13F27-336_A1


title: Br1204

description: Library name: Br1204-V13F27-336_B1


title: Br6369

description: Library name: Br6369-V13M06-344_B1


title: Br6496

description: Library name: Br6496-V13M06-344_A1


title: Br5228

description: Library name: Br5228-V13M06-344_D1


title: Br1214

description: Library name: Br1214-V13M06-344_C1


title: Br5973

description: Library name: Br5973-V13M06-343_D1


title: Br8492

description: Library name: Br8492-V13M06-343_B1


title: Br5573

description: Library name: Br5573-V13M06-343_C1


title: mix_JHH357CoOrg

status: Public on Apr 01 2026

first: Jacquelyn

middle: W

last: Zimmerman

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

description:
Library name: mix_JHH357CoOrg
Orgnanoid Patient 357, Coculture

data_processing:
Salmon v.1.9.0
Alignment was performed utilizing Salmon v1.9.0 on the Joint High-Performance Computing Exchange (JHPCE). “salmon_partial_sa_index__default.tgz” was used as the index for alignment for the HG38 genome, which was premade and available on refgenie (http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). Salmon quantification, [salmon quant], was completed in mapping-based mode (--validateMappings) with automatic library detection. Salmon quantifications were the imported into R using tximport v1.20.0, with the use of the “tgMap.tsv” file also provided in the HG38 refgenie repository for accurate gene-level summarization.
We evaluated sample quality from the distribution of reads as visualized in a boxplot of log counts. We observed no samples with zero median expression, reflective of a low read count, so samples were not of low quality. We used principal component analysis (PCA) of the variance stabilization transform (vst) RNA-seq data to evaluate sample clustering. Projection of the discovered CoGAPS Pattern 7 onto the VST data was completed using ProjectR (V1.8.0). The bulk-seq normalized data and CoGAPs feature loadings were run through the projectR function of the package(14). The projection results were combined with the bulk-seq metadata and plotted using ggplot2 (V3.3.5) and paired t-test results added using ggpubr (V0.4.0)(14).
Analysis completed using DESeq2
Assembly: HG38
Supplementary files format and content: tab-separated values

source_name: pancreas

extract_protocol:
Cells that were coculture were sorted by FACS and immediately underwent RNA extraction (Qiagen RNeasy kit 74004) per manufacturers protocol. RNA was quantified at 260nm using NanoDrop1000 (Thermo Fisher Scientific) and 200ug of RNA was sent to Novogene Corporation Inc. RNA integrity (RIN) was measured at Novogene with Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN > 6.8 and ranged from 7.2 to 10.0.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: pancreas

value: Patient-derived organoid

value: epithelium

value: coculture


title: Br8667

description: Library name: Br8667-V13M06-342_D1


title: Br5276

description: Library name: Br5276-V13M06-343_A1


title: Br8433

description: Library name: Br8433-V13M06-342_C1


title: Br8207

description: Library name: Br8207-V13M06-342_B1


title: Br5224

description: Library name: Br5224-V13M06-342_A1


title: Br2470

description: Library name: Br2470-V13M06-340_D1


title: Br1682

description: Library name: Br1682-V13M06-340_C1


title: Br8406

description: Library name: Br8406-V13M06-340_B1


title: Br6389

description: Library name: Br6389-V13F27-296_D1


title: Br1753

description: Library name: Br1753-V13F27-296_C1


title: Br5931

description: Library name: Br5931-V13M06-340_A1


title: Br1139

description: Library name: Br1139-V13F27-296_A1


title: Br1578

description: Library name: Br1578-V13F27-296_B1


title: Br8772

description: Library name: Br8772-V13F27-295_D1


title: Br2627

description: Library name: Br2627-V13F27-295_C1


title: NE_Ctrl_RNA_Rep2

description: Library name: D2_iNE_2

value: Neuroectoderm


title: Br8325

description: Library name: Br8325-V13F27-295_B1


title: Br1092

description: Library name: Br1092-V13F27-295_A1


title: Br5639

description: Library name: Br5639-V13F27-294_D1


title: Br6032

description: Library name: Br6032-V13F27-293_D1


title: Br5588

description: Library name: Br5588-V13F27-293_C1


title: Br5314

description: Library name: Br5314-V13F27-294_C1


title: Br5746

description: Library name: Br5746-V13F27-294_A1


title: Br5599

description: Library name: Br5599-V13F27-293_B1


title: Br5928

description: Library name: Br5928-V13F27-294_B1


title: Br5622

description: Library name: Br5622-V13F27-293_A1


title: Br5436

description: Library name: Br5436-V13M06-282_D1


title: Br6437

description: Library name: Br6437-V13M06-282_B1


title: Br6560

description: Library name: Br6560-V13M06-282_A1


title: Br2242

description: Library name: Br2242-V13M06-281_C1


title: Br6297

description: Library name: Br6297-V13M06-282_C1


title: Br5888

description: Library name: Br5888-V13M06-281_D1


title: Br5395

description: Library name: Br5395-V13M06-281_B1


title: Br5400

description: Library name: Br5400-V13M06-281_A1


title: Br2720

description: Library name: Br2720-V13M06-280_C1


title: Br5636

description: Library name: Br5636-V13M06-280_B1


title: Br6257

description: Library name: Br6257-V13M06-280_D1


title: Br5590

description: Library name: Br5590-V13M06-280_A1


title: Br8514

description: Library name: Br8514-V13M06-279_D1


title: Br8537

description: Library name: Br8537-V13M06-279_C1


title: Br1113

description: Library name: Br1113-V13M06-279_A1


title: Br5789

description: Library name: Br5789-V12D07-334_C1


title: Br8042

description: Library name: Br8042-V13M06-279_B1


title: Br6432

description: Library name: Br6432-V12D07-334_D1


title: Br5472

description: Library name: Br5472-V12D07-334_B1


title: Br5373

description: Library name: Br5373-V12D07-334_A1


title: Br2378

description: Library name: Br2378-V12F14-057_D1


title: Br1958

description: Library name: Br1958-V12F14-057_B1


title: Br5367

description: Library name: Br5367-V12F14-053_D1


title: Br2039

description: Library name: Br2039-V12F14-057_C1


title: Br1526

description: Library name: Br1526-V12F14-057_A1


title: Br2719

description: Library name: Br2719-V12F14-053_A1


title: Br5182

description: Library name: Br5182-V12F14-053_C1


title: Ribo_hSLFN14_K219N_+Dox

status: Public on Feb 09 2026

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

department: Division of Nutritional Sciences

institute: Cornell University

description:
Library name: Sample_4
shift_Asite_hSLFN14_K219N_+Dox_hSLFN14_K219N_-Dox.csv

library_source: other

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including codon subsequence abundance shift for each codon.
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
WT or K219N SLFN14-inducible 293T cells were seeded in 6-well plates and left untreated or induced with doxycycline (2 μg/mL) for 24 h. The 6-well plates were pre-coated with poly-D-lysine (Gibco) for 5 min at room temperature to enhance the cell attachment. Following treatment, cells were washed once with ice-cold PBS and lysed in polysome lysis buffer (10 mM HEPES, pH 7.4, 5 mM MgCl₂, 100 mM KCl, 1% Triton X-100, 100 μg/mL cycloheximide). Lysates were clarified by centrifugation at maximum speed (≥ 13,000 × g) for 15 min at 4 °C, and the supernatant was collected for downstream ribo-seq analysis.
Ribo-seq libraries were constructed by modifying the Ezra-seq method, as previously described. In brief, the whole cell lysates were digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by agitation at 4°C for 1 h. RNAs were extracted using Trizol LS reagent (Invitrogen) followed by isopropanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In (Invitrogen)) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by isopropanol precipitation. 4 μl RNAs (10~200 ng) were mixed with 1 nmol ATP, 1 μl T4 PNK (NEB), 20 U SUPERase·In, 1 μl Poly(A) Polymerase (NEB), and 1 μl homemade Ezra enzyme in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 70 °C for 10 min. Then ligation was performed for 90 min at 25 °C by mixing with a 10 μl reaction mixture (1 pmol biotinylated 5’ end adaptor, 1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 12.5% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). The ligated RNA samples were pulled down after incubation with 20 uL pre-washed streptavidin magnetic beads (NEB) at room temperature for 10 min. After washing once with 100 uL 2 × SSC (Invitrogen), beads were resuspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (1 poml RT primer, 1 × first strand buffer, 100 nmol DTT, 1 nmol dNTP, 20 U SUPERase·In and 100 ng m-MLV) followed by incubation at 50 °C for 20 min. After washing once with 2 × SSC, beads were resuspended in 20 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 67 °C, 15 s; 72 °C, 20 s) for 13 cycles; 72 °C, 2 min. PCR products were separated on an 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 170 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). After quantification by Qubit 4 Fluorometer (Invitrogen), equal amounts of barcoded samples were pooled and sequenced using MiniSeq (Illumina).

value: WT

value: Dox


title: Ribo_hSLFN14_K219N_-Dox

description:
Library name: Sample_3
shift_Asite_hSLFN14_K219N_+Dox_hSLFN14_K219N_-Dox.csv


title: Ribo_hSLFN14_WT_+Dox

description:
Library name: Sample_2
shift_Asite_hSLFN14_WT_+Dox_hSLFN14_WT_-Dox.csv


title: pooled input Rep.1

status: Public on Feb 02 2026

city: Houston

first: Nourhan

last: Abdelfattah

state: TX

address: 6670 Bertner Avenue, HMRI R11-330.17

institute: Houston Methodist Research Institute

data_processing:
The 75-nt single-end (SE75) sequence reads were mapped to the mouse mm9 genome using the BWA algorithm (RRID:SCR_010910) with default settings.  Duplicate reads were removed, and only uniquely mapped reads (mapping quality ≥25) were used for further analysis. Known motifs were identified with the findMotifsGenome program in HOMER (v4.11; RRID:SCR_010881) using default parameters
Assembly: mm9
Supplementary files format and content: BigWig and NarrowPeak

source_name: MB

extract_protocol:
Flash frozen fSMO;GFAP-cre MB tissues from males and females were sent to Active Motif (Carlsbad, CA) for ChIP-Seq analysis, using a previously ChIP validated anti-YAP1 antibody (US Biological, Salem, MA; # Y1200-01D- RRID:AB_2927438).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 instrument.

value: MB

value: Female


title: Ribo_hSLFN14_WT_-Dox

description:
Library name: Sample_1
shift_Asite_hSLFN14_WT_+Dox_hSLFN14_WT_-Dox.csv


title: pooled input Rep.2

value: Male


title: SGf Rep.2

description: 2_08MK_012BHMRI_Fsmo-MB-Female_YAP1_mm_i86


title: SGf Rep.1


title: SGm Rep.1


title: SGm Rep.2

description: 1_08MJ_012BHMRI_Fsmo-MB-Male_YAP1_mm_i85


title: EP.YSGr [Yun.Yp.9]

data_processing:
Bulk RNA-seq analysis was carried out using the in-house pipeline at The Jackson Laboratory. Trimmomatic (version 0.33) was used to remove adapters and also leading and trailing low quality bases. Reads fewer than 36 bases long were discarded. Reads with more than 50% low-quality bases overall were filtered out, and the remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (v1.2.12 RRID:SCR_013027). RSEM uses bowtie2 (RRID:SCR_016368) as an aligner to align the mapped reads against the mm10 reference genome. Data quality control was performed using Picard (v1.95- RRID:SCR_006525) and bamtools (RRID:SCR_015987) to obtain general alignment statistics from the BAM file. The read counts estimated for each gene by RSEM were given as input to the R package edgeR (v3.30.3-RRID:SCR_012802) for differential expression analysis.
Assembly: mm10
Supplementary files format and content: comma separated file containig the log2CPM values for all samples

extract_protocol:
RNA was isolated  from tumor tissue using the standard Triazol protocol.
Whole RNA was sent to BGI for library prep and sequencing on the BGISEQ-500 platform


title: EP.YSGr [Yun.Yp.11]


title: EP.YSGr [Yun.Yp.12]


title: EP.YSGr [Yun.Yp.8]


title: EP.YSGr [Yun.Yp.10]


title: EP.YSGr [Yun.Yp.7]


title: EP.SG [Yun.Yp.6]


title: EP.SG [Yun.Yp.4]


title: EP.SG [Yun.Yp.5]


title: FFPE NSCLC patient (L8) sample profiled with the Xenium Prime 5K gene panel

status: Public on Mar 27 2026

type: RNA

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

country: Switzerland

institute: Lausanne University Hospital

description: Lung cancer tissues analyzed with Xenium human Prime 5k gene panel

scan_protocol: https://cdn.10xgenomics.com/image/upload/v1670350987/user-guides-pdfs/CG000601_XeniumInSituGeneExpression_ProtocolPlanner_RevB.pdf Post-Xenium multiplex immunofluorescence-stained slides were imaged using fluorescence microscopy or whole-slide fluorescence scanning. Fluorescence channels corresponding to DAPI, CD8, and pan-cytokeratin were acquired.

label: Xenium probe set

source_name: primary NSCLC

label_protocol: Xenium probe set

value: primary NSCLC

tag: tissue preservation method

value: FFPE

value: Sq. cell carcinoma, keratinizing, NOS


title: EP.SG [Yun.Yp.2]


title: EP.SG [Yun.Yp.3]


title: EP.SG [Yun.Yp.1]


title: YSGnr.3

description:
KY16-22-GT16-02753
AllP8_BulkRNAseq.log2CPM.csv

data_processing:
Bulk RNA-seq analysis was carried out using the in-house pipeline at The Jackson Laboratory. Trimmomatic was used to remove adapters and also leading and trailing low quality bases. Reads fewer than 36 bases long were discarded. Reads with more than 50% low-quality bases overall were filtered out, and the remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM . RSEM uses bowtie2 as an aligner to align the mapped reads against the mm10 reference genome. Data quality control was performed using Picard and bamtools  to obtain general alignment statistics from the BAM file. The read counts estimated for each gene by RSEM were given as input to the R package edgeR  for differential expression analysis.
Assembly: mm10
Supplementary files format and content: comma separated file containig the log2CPM values for all samples

extract_protocol:
RNA was isolated  from tumor tissue using the standard Triazol protocol.
Whole RNA was sent to BGI for library prep and sequencing on the DNBseq platform


title: YSGnr.2

description:
KY16-21-GT16-02752
AllP8_BulkRNAseq.log2CPM.csv


title: YSGnr.1

description:
KY16-20-GT16-02751
AllP8_BulkRNAseq.log2CPM.csv


title: YSGr.3

description:
KY16-18-GT16-02749
AllP8_BulkRNAseq.log2CPM.csv


title: YSGr.2

description:
KY16-17-GT16-02748
AllP8_BulkRNAseq.log2CPM.csv


title: SG.3

description:
KY16-15-GT16-02746
AllP8_BulkRNAseq.log2CPM.csv


title: SG.2

description:
KY16-14-GT16-02745
AllP8_BulkRNAseq.log2CPM.csv


title: YSGr.1

description:
KY16-16-GT16-02747
AllP8_BulkRNAseq.log2CPM.csv


title: SG.1

description:
KY16-13-GT16-02744
AllP8_BulkRNAseq.log2CPM.csv


title: SGm

data_processing:
Raw sequencing reads  were aligned to mm10 genome (mouse) using Cell Ranger
Assembly: mm10
Supplementary files format and content: Filtered Barcodes,features and matrix files /Output of Cell Ranger

extract_protocol:
Fresh tumor tissues were dissociated and captured using 10X Genomics Chromium system following the 10X Genomics 3' Transcriptomics kit V3
Following 10X Genomics 3' Transcriptomics kit V3, Sequenced at BGI using DNBseq.


title: Gut_TCR_KO_rep6

status: Public on Jan 21 2026

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.15.1 (https://nf-co.re/rnaseq/3.15.1/) with the STAR /RSEM option against mouse genome assembly GRCm38 and Ensembl release 95 transcript annotations. Other options were left as default.
Gene-level RSEM abundance estimates were imported into R using the Bioconductor package tximport’s tximport function for further analysis using DESeq2
Normalisation factors were calculated per gene using the default DESeq2 function, correcting for library size and feature length.
Variance-stabilised abundance estimates were calculated using the VST function. PCA analysis was performed on the variance stabilised values using all available genes
Assembly: mm10
Supplementary files format and content: RSEM normalised counts, in .genes.results files output from nf-core/rnaseq pipeline run

source_name: Gut IEL (Vγ7+) γδ T cells

growth_protocol: Mouse colony

extract_protocol:
RNA extraction using RNeasy® Plus Micro Kit - QIAGEN
NEBNext_Low_Input_w_NEB_Ultra_II_FS

treatment_protocol: Tamoxifen

value: Gut

tag: strain of_mouse

value: TCR KO


title: Gut_TCR_KO_rep5


title: YSGf


title: SGf


title: YSGm


title: Gut_TCR_KO_rep2


title: Gut_TCR_KO_rep4


title: Gut_TCR_KO_rep1


title: Gut_TCR_KO_rep3


title: Gut_WT_rep3


title: Gut_WT_rep2


title: Dermis_TCR_KO_rep4

source_name: Dermal (Vγ4+ & Vγ6+) γδ T cells

value: Dermis


title: Gut_WT_rep1


title: Dermis_TCR_KO_rep3


title: Dermis_TCR_KO_rep1


title: Dermis_WT_rep4


title: Dermis_WT_rep2


title: Dermis_TCR_KO_rep2


title: Epidermis_TCR_KO_rep4

source_name: DETC (Vγ5+) γδ T cells

value: Epidermis


title: Dermis_WT_rep1


title: Epidermis_TCR_KO_rep2


title: Epidermis_TCR_KO_rep3


title: Epidermis_WT_rep4


title: Epidermis_WT_rep2


title: WT_Gut_REP3

data_processing:
Reads were processed using the publicly available nf-core atacseq pipeline v1.2.1  (https://nf-co.re/atacseq/2.1.2) against the mouse genome assembly GRCm38
using Nextflow v22.04.0 and Singularity v3.6.4, with the following settings:
--deseq2_vst, --min_reps_consensus ,--macs_gsize 2600000000
A peak was only considered to be genuine if present in at least 3 biological replicates for each treatment group.
A consensus peak set was then constructed by combining the peak calls from the individual genotype x organ groups into a set of non-overlapping intervals.
Assembly: Mm10 / GRCm38 (release 95)
Supplementary files format and content: bigWig files, output from nf-core/atacseq pipeline

extract_protocol:
Tn5 Tagmentation was performed using ATAC-Seq Kit from Active Motif
ATAC-Seq Kit from Active Motif


title: HET_Gut_REP4


title: HET_Gut_REP5


title: HET_Gut_REP2_b


title: HET_Gut_REP3


title: HET_Gut_REP1


title: HET_Gut_REP2_a


title: WT_Gut_REP2_b


title: WT_Gut_REP2_a


title: WT_Gut_REP1_b


title: WT_Gut_REP1_a


title: HET_Skin_REP4


title: HET_Skin_REP3


title: HET_Skin_REP2


title: HET_Skin_REP1


title: WT_Skin_REP3


title: WT_Skin_REP2


title: WT_Skin_REP1


title: siCT1 2 INPUT

status: Public on Jan 07 2026

city: Boston

first: Kashish

last: Chetal

state: MA

address: 55 Fruit St

department: Molecular biology

institute: MGH

description: Library name: siCT1_2_INPUT

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID: 20080505). Alignments were filtered for uniquely mapped reads and duplicates were removed.
ChIP over Input ratio coverage tracks were generated using deepTools (PMID: 27079975).
Peaks were called using HOMER (PMID: 20513432) with default parameters.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: RPE

extract_protocol:
Cells were fixed with 1% formaldehyde for 13 minutes. After quenching and cell lysis, chromatin was sonicated using a Q800R3 sonicator (QSonica).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit Set A and B with associated index barcode adapters. 1 ng or 30µL of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity D1000 DNA Kit.

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown

value: Chromatin


title: siCT1 1 INPUT

description: Library name: siCT1_1_INPUT


title: siCT1 2 H3K4me3

description: Library name: siCT1_2_H3K4me3


title: siKDM5A 36 INPUT

description: Library name: siKDM5A_36_INPUT


title: siKDM5A 34 INPUT

description: Library name: siKDM5A_34_INPUT


title: siCT1 1 H3K4me3

description: Library name: siCT1_1_H3K4me3


title: siKDM5A 34 H3K4me3

description: Library name: siKDM5A_34_H3K4me3


title: siKDM5A 36 H3K4me3

description: Library name: siKDM5A_36_H3K4me3


title: SiNC_2

status: Public on Jan 06 2026

city: Hefei

first: Hongfeng

last: Chang

state: Anhui

address: jixi road number 218

country: China

institute: The First Affiliated Hospital of Anhui Medical University

description:
Library name: Sample6
siRNA-control

data_processing:
Illumina HiSeq 4000 software was used for basecaling.
After acquiring raw sequencing data, quality control procedures were implemented, including removal of low-quality reads and adapter sequences. Filtered clean reads were aligned to reference genome sequences. Principal component analysis was performed using R software (v.3.2.0) to evaluate biological replicates. Transcript assembly and quantification were executed, with read counts per gene/transcript reflecting expression levels. Transcript expression was quantified in fragments per kilobase of exon per million mapped fragments. Reads were mapped to the transcriptome for quantification of transcript-overlapping reads, and this was followed by differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: epidermis cell culture

growth_protocol: Human immortalized keratinocytes were maintained in RPMI-1640 suppledmented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using SparkZol RNA Extraction Reagent (AC0101, SparkJade Science, Shandong, China). One microgram of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing standard.

treatment_protocol: Human immortalized keratinocytes within passages P21–P33 were maintained in customized RPMI-1640 medium containing 5.5 mM glucose (L210KJ, Yuanpei Biology, Shanghai, China), supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. For RNA sequencing, the glucose concentration was adjusted to 35 mM. Cells were exposed to high-glucose conditions for 96 h and transfected with siETV4 or siNC for 48 h.

tag: group

value: siNC

tag: biological replicate

value: Human immortalized keratinocytes

value: HaCaT

tag: passage range

tag: basal medium

value: Customized RPMI-1640 medium (L210KJ, Yuanpei Biology, Shanghai, China), supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin

tag: basal glucose concentration

tag: experimental glucose condition

value: High glucose, 35 mM

tag: high-glucose exposure duration

tag: transfection duration

tag: osmotic-control status

value: Normal-glucose and mannitol osmotic-control samples were not included in the RNA-sequencing dataset


title: SiNC_4

description:
Library name: Sample8
siRNA-control

tag: cell type

tag: cell line

tag: treatment


title: SiNC_3

description:
Library name: Sample7
siRNA-control


title: SiNC_1

description:
Library name: Sample5
siRNA-control


title: SiETV4_2

description:
Library name: Sample2
siRNA ETV4


title: SiETV4_4

description:
Library name: Sample4
siRNA ETV4


title: SiETV4_3

description:
Library name: Sample3
siRNA ETV4


title: SiETV4_1

description:
Library name: Sample1
siRNA ETV4


title: cell pellet array

status: Public on Dec 31 2025

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences

description: Library name: SAM009165_LIB009655

data_processing:
Illumina Fastq files were aligned to 10x Visium human transcriptome probe set v2.0_GRCh38-2020-A using Spaceranger-3.0.1
Count data were merged in R using the Seurat package and normalized using SCTransform
Cell-type estimation was performed using RCTD from spacexr version 2.2.1
Assembly: hg38
Supplementary files format and content: compressed Seurat R data objects
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
10X Visium FFPE Kit
FFPE sections of 5µm thickness were prepared using a Leica RM2255 microtome and placed on Superfrost Plus glass slides (Epredia, Cat#22-042-941), as per guidance outlined in 10X Genomics Visium CytAssist Tissue preparation guide (CG000518). Slides were subjected to H&E staining as outlined in guidance provided by 10X Genomics (CG000518). Following H&E staining, slides were imaged using Aperio AT2 DX scanner (Leica Biosystems, Cat#23AT2100) at 40X magnification. Following imaging, coverslips were removed, and tissues were decrosslinked. Library construction was conducted as described in 10X Genomics, CG000495. Post library construction QC was performed on the 2100 Bioanalyzer Instrument (Agilent) with the High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626). Library concentrations were measured using the Qubit dsDNA High Sensitive Assay Kit (Invitrogen, Cat#Q32854). Sequencing was performed on the Illumina NovaSeq6000, following the guidance outlined in the 10X Genomics Visium CytAssist Spatial Gene Expression User Guide (CG000495). Sequencing was performed to meet a targeted sequencing depth of 50,000 read pairs per tissue-covered spot.

tag: tissue

value: Liver

value: PLC/PRF/5, PHH

value: HCC, Primary Human hepatocyte


title: PPCM LV rep2

status: Public on Dec 22 2025

city: Torrance

first: Michelle

middle: L

last: Matter

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

description:
Library name: PPCM Sample 2
PPCM_200507

data_processing:
DNBSEQ-T7 Platform (Human) and Illumina NextSeq 500 sequence platform (mouse)
For Human samples: Raw data contained reads of low quality, reads with adaptor sequence and reads with high level of N base. Those reads were filtered and cleaned by cutadapt (version 1.9) and paired end were produced. Bowtie2 was used to align clean reads to reference genes and HISAT was used to align clean reads to reference genome. For mouse: Data Files were uploaded to Partek flow, contaminants were removed using Bowtie2 (version 2.2.5) and unaligned reads were aligned to STAR (version 2.7.8a) using mouse genome as reference.
Assembly: Human:GCF_000001405.39_GRCh38.p13; Mouse: Mus_musculus.GRCm38.dna
Supplementary files format and content: csv files include FPKMs for all human data and csv files include TPMs for all mouse data

source_name: Human LV heart

extract_protocol:
Total RNA (human and mouse) was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
Human: RNA libraries for RNAseq were prepared with MGIEasy RNA library Prep Set (Proprietary for DNBSEQ platforms). Mouse: RNA libraries for RNAseq were prepared with  Illumina Stranded Total RNA prep with Ribo-Zero Plus according to manufacturer’s instructions.

value: Human LV heart

tag: genotype

value: Knockout


title: PPCM LV rep1

description:
Library name: PPCM Sample 1
PPCM_180107


title: Donor LV rep3

description:
Library name: NORMAL Sample 3
NORMAL_42G

value: wildtype


title: PPCM LV rep3

description:
Library name: PPCM Sample 3
PPCM_210324


title: Donor LV rep1

description:
Library name: NORMAL Sample 1
NORMAL_412m


title: Donor LV rep2

description:
Library name: NORMAL Sample 2
NORMAL_4163


title: Combo

city: Kensington

first: Holly

last: Holliday

address: Lowy Cancer Research Centre

institute: Children's Cancer Institute

description: Multimodal Cell Segmentation

hyb_protocol: Priming oligos were hybridized to the target RNA, followed by site-specific cleavage using RNase treatment to release the RNA strand from the hybridized oligo. The 5000-gene panel was then added to the sections to hybridize with the RNA, followed by ligation to generate circular DNA probes, which were subsequently amplified via rolling circle amplification.

scan_protocol: Xenium In Situ Analyzer

data_processing: Xenium output from the four treatment conditions were merged into a single Seurat object (Seurat v5.2.1). Cells with transcript counts <10 and above the 98th percentile were filtered, and data were normalized with the median transcript count.  The Seurat object was down sampled (25,000 cells per sample) using SketchData and LeverageScore to retain rare cell populations for subsequent scaling and clustering. From the subsetted data, variable features (n = 2000 genes) were identified using FindVariableFeatures, data were scaled using ScaleData and Dimensionality reduction performed using RunPCA. Batch correction was performed using Harmony Integration, followed by UMAP projection and clustering in Harmony space. Clustering was then projected to all cells.

label: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel

source_name: mouse brain, CBL0137 and JQ1 treated

growth_protocol: 5-7 weeks old female C57BL6 mice were intracranially injected into the brainstem with IUE 24B7 cells that harbor H3.3K27M mutation generated in (doi: 10.1093/neuonc/noz197 and 10.1093/noajnl/vdac079). The timing of treatment initiation was 18 days post intracranial surgery.

extract_protocol: Brain samples were collected on the final day of treatment and fixed in a 10% formalin neutral buffered solution then embedded in paraffin wax (FFPE)

treatment_protocol: The drug treatments were as follows: CBL0137 - dissolved in 5% dextrose, CBL0137 was administered intravenously at a dosage of 40 mg/kg/day. The treatment was given once every four days for a total of three weeks. JQ1 - dissolved in DMSO and subsequently in a solution containing 0.9% saline with 5% PEG400 and 5% TWEEN-80, JQ1 was administered at a dosage of 50 mg/kg/day intraperitoneally. The treatment was given five days a week over three weeks.

tag: age

value: 5-7 weeks

tag: gender

value: Female

tag: strain

tag: glioma cell line


title: JQ1

description: Multimodal Cell Segmentation

source_name: mouse brain, JQ1 treated

label_protocol: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel


title: Vehicle

description: Multimodal Cell Segmentation

source_name: mouse brain, vehicle treated

value: Vehicle (0.9% saline, 5% PEG400 and 5% TWEEN-80)


title: CBL0137

description: Multimodal Cell Segmentation

source_name: mouse brain, CBL0137 treated


title: PDAC, Human Tumor, sample129

status: Public on Dec 18 2025

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

description: Library name: Bulk129

data_processing:
Raw base call (BCL) files were converted to fastq files using bcl2fastq2 (v2.19.0).
RefSeq assembly (GCF_000001405.40) of the human reference genome GRCh38.p14 was used as the reference for gene quantification by Salmon 1.9.064 ("-- gcBias -- seqBias").
The total expected read counts per gene were normalized to transcripts per million (TPM).
Assembly: GENCODE Release 38 (GrCh38.p14)
Supplementary files format and content: comma-separated file containing Bulk RNAseq gene expression normalized TPM for all samples
Supplementary files format and content: comma-separated file containing Bulk RNAseq total expected read counts

source_name: Primary PDAC

extract_protocol:
Total RNA was extracted from tissues using the AllPrep DNA/RNA Kit (Qiagen, 80204). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
RNA expression libraries were generated for flash frozen samples or FFPE samples, with TruSeq Stranded mRNA kits or with KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions.

value: Primary PDAC

value: Gemcitabine


title: PDAC, Human Tumor, sample128

description: Library name: Bulk128

value: FOLFIRINOX


title: PDAC, Human Tumor, sample127

description: Library name: Bulk127


title: PDAC, Human Tumor, sample126

description: Library name: Bulk126


title: PDAC, Human Tumor, sample124

description: Library name: Bulk124


title: PDAC, Human Tumor, sample122

description: Library name: Bulk122


title: PDAC, Human Tumor, sample123

description: Library name: Bulk123


title: PDAC, Human Tumor, sample120

description: Library name: Bulk120


title: PDAC, Human Tumor, sample119

description: Library name: Bulk119


title: PDAC, Human Tumor, sample121

description: Library name: Bulk121


title: PDAC, Human Tumor, sample11

description: Library name: Bulk011

value: Untreated


title: PDAC, Human Tumor, sample7

description: Library name: Bulk007


title: Epidermis_TCR_KO_rep1

value: Epidermis

tag: strain of_mouse

value: TCR KO


title: PDAC, Human Tumor, sample53

description: Library name: Bulk053


title: PDAC, Human Tumor, sample125

description: Library name: Bulk125


title: PDAC, Human Tumor, sample118

description: Library name: Bulk118


title: PDAC, Human Tumor, sample117

description: Library name: Bulk117


title: Epidermis_WT_rep1

value: WT


title: PDAC, Human Tumor, sample116

description: Library name: Bulk116

value: Combination


title: PDAC, Human Tumor, sample114

description: Library name: Bulk114


title: PDAC, Human Tumor, sample113

description: Library name: Bulk113


title: PDAC, Human Tumor, sample115

description: Library name: Bulk115


title: PDAC, Human Tumor, sample112

description: Library name: Bulk112


title: PDAC, Human Tumor, sample110

description: Library name: Bulk110


title: PDAC, Human Tumor, sample111

description: Library name: Bulk111


title: PDAC, Human Tumor, sample108

description: Library name: Bulk108


title: PDAC, Human Tumor, sample107

description: Library name: Bulk107


title: PDAC, Human Tumor, sample106

description: Library name: Bulk106


title: PDAC, Human Tumor, sample109

description: Library name: Bulk109


title: PDAC, Human Tumor, sample105

description: Library name: Bulk105


title: PDAC, Human Tumor, sample104

description: Library name: Bulk104


title: PDAC, Human Tumor, sample103

description: Library name: Bulk103


title: PDAC, Human Tumor, sample101

description: Library name: Bulk101


title: PDAC, Human Tumor, sample100

description: Library name: Bulk100


title: PDAC, Human Tumor, sample102

description: Library name: Bulk102


title: PDAC, Human Tumor, sample98

description: Library name: Bulk098


title: PDAC, Human Tumor, sample99

description: Library name: Bulk099


title: PDAC, Human Tumor, sample96

description: Library name: Bulk096


title: PDAC, Human Tumor, sample97

description: Library name: Bulk097

value: XRT Alone


title: PDAC, Human Tumor, sample94

description: Library name: Bulk094


title: PDAC, Human Tumor, sample95

description: Library name: Bulk095


title: PDAC, Human Tumor, sample93

description: Library name: Bulk093


title: PDAC, Human Tumor, sample91

description: Library name: Bulk091


title: PDAC, Human Tumor, sample92

description: Library name: Bulk092


title: PDAC, Human Tumor, sample89

description: Library name: Bulk089


title: PDAC, Human Tumor, sample90

description: Library name: Bulk090


title: PDAC, Human Tumor, sample88

description: Library name: Bulk088


title: PDAC, Human Tumor, sample87

description: Library name: Bulk087


title: PDAC, Human Tumor, sample86

description: Library name: Bulk086


title: PDAC, Human Tumor, sample84

description: Library name: Bulk084


title: PDAC, Human Tumor, sample83

description: Library name: Bulk083


title: PDAC, Human Tumor, sample82

description: Library name: Bulk082


title: PDAC, Human Tumor, sample81

description: Library name: Bulk081

value: Chemo/RT


title: PDAC, Human Tumor, sample79

description: Library name: Bulk079


title: PDAC, Human Tumor, sample80

description: Library name: Bulk080


title: PDAC, Human Tumor, sample78

description: Library name: Bulk078


title: PDAC, Human Tumor, sample76

description: Library name: Bulk076


title: PDAC, Human Tumor, sample75

description: Library name: Bulk075


title: PDAC, Human Tumor, sample77

description: Library name: Bulk077


title: PDAC, Human Tumor, sample73

description: Library name: Bulk073


title: PDAC, Human Tumor, sample74

description: Library name: Bulk074


title: PDAC, Human Tumor, sample71

description: Library name: Bulk071


title: PDAC, Human Tumor, sample72

description: Library name: Bulk072


title: PDAC, Human Tumor, sample68

description: Library name: Bulk068


title: PDAC, Human Tumor, sample67

description: Library name: Bulk067


title: PDAC, Human Tumor, sample66

description: Library name: Bulk066


title: PDAC, Human Tumor, sample65

description: Library name: Bulk065


title: PDAC, Human Tumor, sample64

description: Library name: Bulk064


title: PDAC, Human Tumor, sample61

description: Library name: Bulk061


title: PDAC, Human Tumor, sample63

description: Library name: Bulk063


title: PDAC, Human Tumor, sample60

description: Library name: Bulk060


title: PDAC, Human Tumor, sample59

description: Library name: Bulk059


title: PDAC, Human Tumor, sample57

description: Library name: Bulk057


title: PDAC, Human Tumor, sample58

description: Library name: Bulk058


title: PDAC, Human Tumor, sample55

description: Library name: Bulk055


title: PDAC, Human Tumor, sample56

description: Library name: Bulk056


title: PDAC, Human Tumor, sample54

description: Library name: Bulk054


title: PDAC, Human Tumor, sample52

description: Library name: Bulk052


title: PDAC, Human Tumor, sample49

description: Library name: Bulk049


title: PDAC, Human Tumor, sample50

description: Library name: Bulk050

value: FOLFIRINOX with XRT


title: PDAC, Human Tumor, sample48

description: Library name: Bulk048


title: PDAC, Human Tumor, sample47

description: Library name: Bulk047


title: PDAC, Human Tumor, sample45

description: Library name: Bulk045


title: PDAC, Human Tumor, sample46

description: Library name: Bulk046

value: FOLFOX


title: PDAC, Human Tumor, sample44

description: Library name: Bulk044


title: PDAC, Human Tumor, sample43

description: Library name: Bulk043


title: PDAC, Human Tumor, sample41

description: Library name: Bulk041


title: PDAC, Human Tumor, sample42

description: Library name: Bulk042


title: PDAC, Human Tumor, sample40

description: Library name: Bulk040


title: PDAC, Human Tumor, sample35

description: Library name: Bulk035


title: PDAC, Human Tumor, sample39

description: Library name: Bulk039


title: PDAC, Human Tumor, sample36

description: Library name: Bulk036


title: PDAC, Human Tumor, sample38

description: Library name: Bulk038


title: PDAC, Human Tumor, sample37

description: Library name: Bulk037


title: PDAC, Human Tumor, sample34

description: Library name: Bulk034


title: PDAC, Human Tumor, sample33

description: Library name: Bulk033


title: PDAC, Human Tumor, sample30

description: Library name: Bulk030


title: PDAC, Human Tumor, sample31

description: Library name: Bulk031


title: PDAC, Human Tumor, sample29

description: Library name: Bulk029


title: PDAC, Human Tumor, sample26

description: Library name: Bulk026

value: Gemcitabine with XRT


title: PDAC, Human Tumor, sample27

description: Library name: Bulk027


title: PDAC, Human Tumor, sample28

description: Library name: Bulk028


title: PDAC, Human Tumor, sample85

description: Library name: Bulk085


title: PDAC, Human Tumor, sample32

description: Library name: Bulk032


title: PDAC, Human Tumor, sample24

description: Library name: Bulk024


title: PDAC, Human Tumor, sample23

description: Library name: Bulk023


title: PDAC, Human Tumor, sample21

description: Library name: Bulk021


title: PDAC, Human Tumor, sample22

description: Library name: Bulk022


title: PDAC, Human Tumor, sample19

description: Library name: Bulk019


title: PDAC, Human Tumor, sample18

description: Library name: Bulk018


title: PDAC, Human Tumor, sample20

description: Library name: Bulk020


title: PDAC, Human Tumor, sample69

description: Library name: Bulk069


title: PDAC, Human Tumor, sample70

description: Library name: Bulk070


title: PDAC, Human Tumor, sample16

description: Library name: Bulk016


title: PDAC, Human Tumor, sample17

description: Library name: Bulk017


title: PDAC, Human Tumor, sample15

description: Library name: Bulk015


title: PDAC, Human Tumor, sample13

description: Library name: Bulk013


title: PDAC, Human Tumor, sample12

description: Library name: Bulk012


title: PDAC, Human Tumor, sample9

description: Library name: Bulk009


title: PDAC, Human Tumor, sample62

description: Library name: Bulk062


title: PDAC, Human Tumor, sample10

description: Library name: Bulk010


title: PDAC, Human Tumor, sample8

description: Library name: Bulk008


title: PDAC, Human Tumor, sample6

description: Library name: Bulk006


title: PDAC, Human Tumor, sample5

description: Library name: Bulk005

value: FOLFIRI


title: PDAC, Human Tumor, sample3

description: Library name: Bulk003


title: PDAC, Human Tumor, sample2

description: Library name: Bulk002


title: PDAC, Human Tumor, sample1

description: Library name: Bulk001


title: PDAC, Human Tumor, sample4

description: Library name: Bulk004


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep6

status: Public on Dec 12 2025

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

description: Library name: 3UTR.control.post.6

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38

source_name: kidney

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA

value: kidney

value: human embryonic kidney cells

value: ISOMPRA Library Transfection


title: PDAC, Human Tumor, sample51

description: Library name: Bulk051

value: Primary PDAC


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep5

description: Library name: 3UTR.control.post.5


title: PDAC, Human Tumor, sample14

description: Library name: Bulk014


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep3

description: Library name: 3UTR.control.post.3


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep4

description: Library name: 3UTR.control.post.4


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep2

description: Library name: 3UTR.control.post.2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep1

description: Library name: 3UTR.control.post.1


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep6

description: Library name: 3UTR.control.pre.6


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep5

description: Library name: 3UTR.control.pre.5


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep3

description: Library name: 3UTR.control.pre.3


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep2

description: Library name: 3UTR.control.pre.2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep4

description: Library name: 3UTR.control.pre.4


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep1

description: Library name: 3UTR.control.pre.1


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep4

description: Library name: 3UTR.control.DNA.4

organism: Escherichia coli

source_name: Escherichia coli

value: Escherichia coli

value: ISOMPRA Library DNA from Plasmid


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep2

description: Library name: 3UTR.control.DNA.2


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep1

description: Library name: 3UTR.control.DNA.1


title: Ribo_sh-ABCE1_3

status: Public on Dec 11 2025

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.
Supplementary files format and content: comma-delimited text files including normalized read density around stop codons for each sample.

extract_protocol:
For MRPA, fractions of 500 μl corresponding to monosome or polysome were collected for RNA extraction using TRIzol LS. RNA was purified using RNA Clean & Concentrator and eluted with 11 μl of nuclease-free water.  For Ribo-seq, RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
For  Ribo-seq, 14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). For MPRA, The purified RNA was reverse transcribed using SuperScript III and gene-specific primers. In brief, RNA samples were mixed with 1 μl of 10 mM dNTP, 2 pmol reverse primer and incubated at 65 °C for 5 min, then immediately placed on ice for 1 min. The reverse transcription was carried out by incubating with the 7 μl reaction mixture (5 × first strand buffer, 0.1 M DTT, RNaseOUT and SuperScript III) at 50 °C for 60 min followed by heating at 70 °C for 15 minutes. The products were then amplified with Illumina-based sequencing primers with barcode. PCR were performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. The PCR was initiated at 98 °C, 30 s; then (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. The PCR products with the expected size 190 bp were excised from a 8% polyacrylamide TBE gel. The DNA products were recovered from DNA elution buffer.


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep3

description: Library name: 3UTR.control.DNA.3


title: Ribo_sh-ABCE1_2


title: Ribo_sh-ABCE1_1


title: RNA_9N_heavy


title: RNA_9N_mono


title: RNA_9N_light


title: RNA_9N-TAGT_light


title: RNA_9N-TAGT_mono


title: RNA_9N-TAGT_heavy


title: Ribo_eRF1IP_+CHX


title: Ribo_eRF1IP_-CHX


title: Ribo_input_+CHX


title: Ribo_input_-CHX


title: PDAC, Human Tumor, sample25

description: Library name: Bulk025

value: Untreated


title: Ribo_Rps26-OE1

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCm39.106
Supplementary files format and content: comma-delimited text files including normalized read density around start codons for each sample.

extract_protocol:
RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).


title: Ribo_vector2


title: Ribo_vector1


title: Ribo_Rps26-OE2


title: Ribo_sh-Scram


title: Ribo_sh-Rps26


title: Ribo_18SrRNA_WT-OE


title: Ribo_heart

source_name: heart

value: heart


title: Ribo_18SrRNA_mut2-OE


title: Ribo_brain

source_name: brain

value: brain


title: Ribo_18SrRNA_mut1-OE

value: WT


title: Ribo_kidney


title: Ribo_testis

source_name: testis

value: testis


title: Ribo_liver

source_name: liver

value: liver


title: scRNASeq Mouse Thymus (hAPC): Wild type, P10, Bio Rep 2, Batch C

status: Public on Dec 05 2025

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

description:
Library name: P10_WT_2_C
P10_WT_2_C

data_processing:
FASTQ files were processed with Cellranger v 6.0.1 to derive filtered feature count matrices. Reads were aligned against mm10 and filtered feature matrices were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger: barcodes, features, and count matrices

source_name: Thymus

extract_protocol:
To sort hAPCs for scRNA-sequencing, thymi were harvested and enzymatically digested with an enzymatic solution comprising LiberaseTM (Roche) and DNAse I in PBS at 37°C. Isolated cells were centrifuged and immunostained with a panel of fluorescently-labeled antibodies prior to resuspension in FWB+ EDTA  + propidium iodide (Enzo). HAPCs were FACS purified as MHCII lo to + CD45+ Thy1.2- non-thymic epithelial cells (Epcam+CD11c-). Purified hAPCs  were then centrifuged and resuspended in FWB without EDTA, counted and resuspended at a concentration of 700-1200 cells/µL prior to submission to the University of Texas Genomic Sequencing and Analysis Facility.
Cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics). Libraries were examined for size and quality using the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche).

value: Thymus

value: Antigen Presenting Cells

tag: age (days)

tag: batch

value: C


title: scRNASeq Mouse Thymus (hAPC): Wild type, P10, Bio Rep 1, Batch C

description:
Library name: P10_WT_1_C
P10_WT_1_C


title: scRNASeq Mouse Thymus (hAPC): Wild type, P14, Bio Rep 2, Batch D

description:
Library name: P14_WT_2_D
P14_WT_2_D

value: D


title: scRNASeq Mouse Thymus (hAPC): Wild type, P07, Bio Rep 2, Batch F

description:
Library name: P07_WT_2_F
P07_WT_2_F

value: F


title: scRNASeq Mouse Thymus (hAPC): Wild type, P14, Bio Rep 1, Batch D

description:
Library name: P14_WT_1_D
P14_WT_1_D


title: scRNASeq Mouse Thymus (hAPC): Wild type, P07, Bio Rep 1, Batch F

description:
Library name: P07_WT_1_F
P07_WT_1_F


title: scRNASeq Mouse Thymus (hAPC): Wild type, P03, Bio Rep 1, Batch D

description:
Library name: P03_WT_1_D
P03_WT_1_D


title: scRNASeq Mouse Thymus (hAPC): Wild type, P03, Bio Rep 2, Batch D

description:
Library name: P03_WT_2_D
P03_WT_2_D


title: scRNASeq Mouse Thymus (hAPC): Wild type, P00, Bio Rep 2, Batch E

description:
Library name: P00_WT_2_E
P00_WT_2_E

value: E


title: scRNASeq Mouse Thymus (hAPC): Wild type, P00, Bio Rep 1, Batch D

description:
Library name: P00_WT_1_D
P00_WT_1_D


title: mRNA_60min_rep2

status: Public on Dec 04 2025

description: Library name: Sample_11

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including read counts mapped to each transcript.

extract_protocol:
From polysome profiling samples, an aliquot of ribosome fractions representing monosome and polysome were collected followed by digestion with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 ºC for 1 h. RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 µL RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/µL SUPERase·In) at 4 ºC for overnight. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. To enrich capped small RNAs, 50 μg of total cellular RNA was fractionated using the RNA Clean & Concentrator kit (Zymo research). Briefly, adjusted RNA Binding Buffer was prepared by mixing an equal volume of buffer and 100% ethanol. Total RNA sample were mixed with 2 volumes of the adjusted buffer and transferred to the column. The mix was then centrifuged at 16,000 g for 30 s, and the flow-through was collected. 1 volume of ethanol were mixed with flow-through and transferred to a new column. The mix were centrifuged at 16,000 g for 30 s, and the flow-through was discarded. The column was washed by RNA Prep Buffer and Wash buffer, and the bound RNA was eluted with 50 μl DNase/RNase-Free water.  The eluted RNAs were dephosphorylated with 50 U of CIP (NEB) in a 100 μl reaction containing 1 × rCutSmart Buffer and 0.5 U/μl SUPERase·In at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. Three-fourths of resulting RNAs were decapped with 0.75 μl of 5 U/μl Cap-Clip Acid Pyrophosphatase (Cellscript) in 1 × Cap-Clip Acid Pyrophosphatase Buffer at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The remaining one-fourth RNAs were phosphorylated with 20 U of T4 PNK in a 20 μl reaction containing 0.5 U/μl SUPERase·In, 2 mM ATP and 1 × T4 PNK Buffer at 37 °C for 1 h, followed by ethanol precipitation.
10~200 ng RNAs were mixed with 10 U T4 PNK (NEB), 1 µL homemade Ezra enzyme, 5 U Poly(A) Polymerase (NEB), and 20 U SUPERase·In in Ezra buffer and incubated at 37 ºC for 30 min followed by 70 ºC for 10 min. Ligation was performed for 60 min at 25 ºC by adding a 10 µL reaction mixture (0.5 μM biotinylated 5’ end adaptor, 1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 10 U T4 RNA ligase 2 truncated KQ (NEB)). The ligated RNA sample was mixed with 10 µL of pre-washed streptavidin beads (NEB) and incubated at room temperature for 10 min. After washing once with 2 × SSC, beads were re-suspended in 12 µL nuclease-free water and mixed with 8 µL cDNA synthesis mixture (5 μM reverse transcription primer, 5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, SuperScript III) followed by incubation at 50 ºC for 30 min. After washing once with 2 × SSC, the cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 ºC, 30 s; (98 ºC, 5 s; 68 ºC, 15 s; 72 ºC, 20 s) for 14 cycles; 72 ºC, 2 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size around 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled and sequenced using NextSeq 500 (Illumina).


title: mRNA_360min_rep2

description: Library name: Sample_12


title: mRNA_0min_rep2

description: Library name: Sample_10


title: RPF_360min_rep2

description: Library name: Sample_9

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including read counts mapped to each transcript.
Library strategy: Ribo-Seq


title: RPF_60min_rep2

description: Library name: Sample_8


title: mRNA_360min_rep1

description: Library name: Sample_6


title: RPF_0min_rep2

description: Library name: Sample_7


title: mRNA_60min_rep1

description: Library name: Sample_5


title: RPF_360min_rep1

description: Library name: Sample_3


title: mRNA_0min_rep1

description: Library name: Sample_4


title: RPF_60min_rep1

description: Library name: Sample_2


title: RPF_0min_rep1

description: Library name: Sample_1


title: VAS7564A91

status: Public on Nov 20 2025

description:
Library name: VAS7564A91
C5deltaVav_male_ileum_IEL_time_6_weeks_2

data_processing:
Trim adapters with Trimmomatic v0.39
Align reads to mm10 with STAR 2.7.11b
Count reads with Salmon 1.10.3
Variance-stabilised counts with DESeq2 (vst)
Assembly: GRCm38 release-95
Supplementary files format and content: csv format – vst normalized data

source_name: IEL

extract_protocol:
Small intestines were cut into small pieces digested and isolated following the instructions provided in Miltenyi Biotec Lamina propria dissociation kit protocol, 130-097-410. lamina propria and intraepithelial cells were resuspended in FACS buffer after centrifugation. Single cell suspensions were stained with lineage exclusion antibodies against CD19, CD3, NK1.1, Ly6G and gated in CD45+, CD11b+, CD64+ then, FACS sorted on an Aria Fusion (BD) with a 100um nozzle.
RNA-seq libraries were made using total RNA made with KAPA RNA HyperPrep with RiboErase following manufacturer’s instructions (Roche, 08098131702). SMART‑Seq libraries were pooled and sequenced on an Illumina NovaSeq 6000 (2 × 100 bp) (Illumina).

value: IEL

value: KO


title: VAS7564A94

description:
Library name: VAS7564A94
C5HetVav_male_ileum_IEL_time_6_weeks_2

value: CTRL


title: VAS7564A93

description:
Library name: VAS7564A93
C5HetVav_male_ileum_IEL_time_6_weeks_1


title: VAS7564A92

description:
Library name: VAS7564A92
C5HetVav_female_ileum_IEL_time_6_weeks_1


title: VAS7564A90

description:
Library name: VAS7564A90
C5deltaVav_male_ileum_IEL_time_6_weeks_1


title: VAS7564A9

description:
Library name: VAS7564A9
C5HetVav_female_ileum_IEL_time_8_weeks_1


title: VAS7564A88

description:
Library name: VAS7564A88
C5deltaVav_female_ileum_IEL_time_6_weeks_1


title: VAS7564A86

description:
Library name: VAS7564A86
C5HetVav_male_ileum_LP_time_6_weeks_2

source_name: LP

value: LP


title: VAS7564A89

description:
Library name: VAS7564A89
C5deltaVav_female_ileum_IEL_time_6_weeks_2


title: VAS7564A84

description:
Library name: VAS7564A84
C5HetVav_female_ileum_LP_time_6_weeks_1


title: VAS7564A85

description:
Library name: VAS7564A85
C5HetVav_male_ileum_LP_time_6_weeks_1


title: VAS7564A83

description:
Library name: VAS7564A83
C5deltaVav_male_ileum_LP_time_6_weeks_2


title: VAS7564A82

description:
Library name: VAS7564A82
C5deltaVav_male_ileum_LP_time_6_weeks_1


title: VAS7564A81

description:
Library name: VAS7564A81
C5deltaVav_female_ileum_LP_time_6_weeks_2


title: VAS7564A80

description:
Library name: VAS7564A80
C5deltaVav_female_ileum_LP_time_6_weeks_1


title: VAS7564A78

description:
Library name: VAS7564A78
C5HetVav_male_colon_LP_time_6_weeks_2


title: VAS7564A75

description:
Library name: VAS7564A75
C5deltaVav_male_colon_LP_time_6_weeks_2


title: VAS7564A76

description:
Library name: VAS7564A76
C5HetVav_female_colon_LP_time_6_weeks_1


title: VAS7564A77

description:
Library name: VAS7564A77
C5HetVav_male_colon_LP_time_6_weeks_1


title: VAS7564A74

description:
Library name: VAS7564A74
C5deltaVav_male_colon_LP_time_6_weeks_1


title: VAS7564A73

description:
Library name: VAS7564A73
C5deltaVav_female_colon_LP_time_6_weeks_2


title: VAS7564A71

description:
Library name: VAS7564A71
C5HetVav_male_ileum_IEL_time_4_weeks_2


title: VAS7564A70

description:
Library name: VAS7564A70
C5HetVav_male_ileum_IEL_time_4_weeks_1


title: VAS7564A72

description:
Library name: VAS7564A72
C5deltaVav_female_colon_LP_time_6_weeks_1


title: VAS7564A69

description:
Library name: VAS7564A69
C5HetVav_female_ileum_IEL_time_4_weeks_2


title: VAS7564A68

description:
Library name: VAS7564A68
C5HetVav_female_ileum_IEL_time_4_weeks_1


title: VAS7564A67

description:
Library name: VAS7564A67
C5deltaVav_male_ileum_IEL_time_4_weeks_2


title: VAS7564A66

description:
Library name: VAS7564A66
C5deltaVav_male_ileum_IEL_time_4_weeks_1


title: VAS7564A65

description:
Library name: VAS7564A65
C5deltaVav_female_ileum_IEL_time_4_weeks_2


title: VAS7564A64

description:
Library name: VAS7564A64
C5deltaVav_female_ileum_IEL_time_4_weeks_1


title: VAS7564A61

description:
Library name: VAS7564A61
C5HetVav_female_ileum_LP_time_4_weeks_2


title: VAS7564A62

description:
Library name: VAS7564A62
C5HetVav_male_ileum_LP_time_4_weeks_1


title: VAS7564A60

description:
Library name: VAS7564A60
C5HetVav_female_ileum_LP_time_4_weeks_1


title: VAS7564A58

description:
Library name: VAS7564A58
C5deltaVav_male_ileum_LP_time_4_weeks_1


title: VAS7564A6

description:
Library name: VAS7564A6
C5deltaVav_female_ileum_LP_time_8_weeks_2


title: VAS7564A57

description:
Library name: VAS7564A57
C5deltaVav_female_ileum_LP_time_4_weeks_2


title: VAS7564A56

description:
Library name: VAS7564A56
C5deltaVav_female_ileum_LP_time_4_weeks_1


title: VAS7564A59

description:
Library name: VAS7564A59
C5deltaVav_male_ileum_LP_time_4_weeks_2


title: VAS7564A63

description:
Library name: VAS7564A63
C5HetVav_male_ileum_LP_time_4_weeks_2


title: VAS7564A54

description:
Library name: VAS7564A54
C5HetVav_male_colon_LP_time_4_weeks_1


title: VAS7564A55

description:
Library name: VAS7564A55
C5HetVav_male_colon_LP_time_4_weeks_2


title: VAS7564A53

description:
Library name: VAS7564A53
C5HetVav_female_colon_LP_time_4_weeks_2


title: VAS7564A52

description:
Library name: VAS7564A52
C5HetVav_female_colon_LP_time_4_weeks_1


title: VAS7564A51

description:
Library name: VAS7564A51
C5deltaVav_male_colon_LP_time_4_weeks_2


title: VAS7564A5

description:
Library name: VAS7564A5
C5deltaVav_female_ileum_LP_time_8_weeks_1


title: VAS7564A49

description:
Library name: VAS7564A49
C5deltaVav_female_colon_LP_time_4_weeks_2


title: VAS7564A50

description:
Library name: VAS7564A50
C5deltaVav_male_colon_LP_time_4_weeks_1


title: VAS7564A48

description:
Library name: VAS7564A48
C5deltaVav_female_colon_LP_time_4_weeks_1


title: VAS7564A47

description:
Library name: VAS7564A47
C5deltaVav_male_colon_LP_time_8_weeks_2


title: VAS7564A46

description:
Library name: VAS7564A46
C5deltaVav_male_colon_LP_time_8_weeks_1


title: VAS7564A43

description:
Library name: VAS7564A43
C5HetVav_male_ileum_LP_time_8_weeks_1


title: VAS7564A41

description:
Library name: VAS7564A41
C5deltaVav_male_ileum_LP_time_8_weeks_1


title: VAS7564A42

description:
Library name: VAS7564A42
C5deltaVav_male_ileum_LP_time_8_weeks_2


title: VAS7564A4

description:
Library name: VAS7564A4
C5HetVav_male_ileum_LP_time_8_weeks_2


title: VAS7564A39

description:
Library name: VAS7564A39
C5deltaVav_male_ileum_IEL_time_8_weeks_2


title: VAS7564A45

description:
Library name: VAS7564A45
C5HetVav_male_colon_LP_time_8_weeks_1


title: VAS7564A38

description:
Library name: VAS7564A38
C5deltaVav_male_ileum_IEL_time_8_weeks_1