title: T083_B_BAL_TB

description: Library name: T083_B


title: T082_B_BAL_TB

status: Public on May 01 2026

type: SRA

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

description: Library name: T082_B

library_source: transcriptomic

data_processing:
nf-core/rnaseq pipeline v3.16.1; default parameters
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: csv of DESeq2 normalised expression values

molecule: total RNA

organism: Homo sapiens

source_name: Bronchoalveolar lavage

extract_protocol:
Cell suspensions containing 0.5 x 106 live cells were pelleted by centrifuging at 400 x G for 5 minutes at 4oC and pellets suspended in TRI reagent (Sigma-Aldrich). Samples were vortexed at high speed for around 20 seconds before storage at -80oC until RNA extraction. RNA extraction was performed using the DirectZol RNA Microprep kit (Zymo Technologies), as per manufacturer’s instructions, including on-column DNase I digestion.
Extracted RNA from whole BAL cell pellets was subjected to Agilent TapeStation quality control analysis and RNA integrity (RIN) values determine to be ≥7.4 and ≤9.9, except for one sample (T219_1, from active TB patient #219), which had a RIN value of 4.1. 200 ng of total RNA was used for library preparation using the RNA library prep kit with Polaris ribosomal RNA depletion (Watchmaker Genomics). Approximately 2.5 x107 100 base pair paired end reads were obtained per sample using an Illumina NovaSeq X sequencer.

tag: tissue

value: Bronchoalveolar lavage

tag: sample status

value: TB


title: T067_B_BAL_TB

description: Library name: T067_B


title: T043_B_BAL_TB

description: Library name: T043_B


title: T048_B_BAL_IGRApos_PETpos

description: Library name: T048_B


title: T020_B_BAL_TB

description: Library name: T020_B


title: T044_B_BAL_TB

description: Library name: T044_B


title: T004_B_BAL_TB

description: Library name: T004_B


title: T017_B_BAL_TB

description: Library name: T017_B


title: P164_T_BAL_Post-treatment

description: Library name: P164_T

value: Post-treatment


title: T001_B_BAL_TB

description: Library name: T001_B


title: P122_P_BAL_Progressor

description: Library name: P122_P

value: Progressor


title: P077_P_BAL_Progressor

description: Library name: P077_P


title: P074_P_BAL_Progressor

description: Library name: P074_P


title: P026_P_BAL_Progressor

description: Library name: P026_P


title: P103_P_BAL_Progressor

description: Library name: P103_P


title: P013_P_BAL_Progressor

description: Library name: P013_P


title: C239_B_BAL_IGRApos_PETpos

description: Library name: C239_B


title: C233_B_BAL_IGRApos_PETpos

description: Library name: C233_B


title: C231_B_BAL_IGRAneg

description: Library name: C231_B

value: IGRAneg


title: C225_F_BAL_Progressor

description: Library name: C225_F


title: C224_F_BAL_IGRAneg_PETpos

description: Library name: C224_F


title: C224_B_BAL_IGRAneg_PETpos

description: Library name: C224_B


title: C222_B_BAL_Progressor

description: Library name: C222_B


title: C223_B_BAL_IGRApos_PETneg

description: Library name: C223_B


title: C211_F_BAL_IGRApos_PETpos

description: Library name: C211_F


title: C220_B_BAL_IGRAneg

description: Library name: C220_B


title: C211_B_BAL_IGRApos_PETpos

description: Library name: C211_B


title: C189_B_BAL_IGRAneg_PETpos

description: Library name: C189_B


title: C164_P_BAL_Progressor

description: Library name: C164_P


title: C182_B_BAL_IGRApos_PETpos

description: Library name: C182_B


title: C157_B_BAL_IGRAneg

description: Library name: C157_B


title: C155_F_BAL_IGRApos_PETneg

description: Library name: C155_F


title: C155_B_BAL_IGRApos_PETneg

description: Library name: C155_B


title: C154_B_BAL_IGRAneg

description: Library name: C154_B


title: C157_F_BAL_IGRApos_PETneg

description: Library name: C157_F


title: C142_B_BAL_IGRAneg

description: Library name: C142_B


title: C141_B_BAL_IGRAneg_PETpos

description: Library name: C141_B


title: C141_F_BAL_IGRApos_PETpos

description: Library name: C141_F


title: C140_F_BAL_IGRApos_PETpos

description: Library name: C140_F


title: C136_B_BAL_IGRAneg

description: Library name: C136_B


title: C140_B_BAL_IGRApos_PETpos

description: Library name: C140_B


title: C135_F_BAL_IGRAneg

description: Library name: C135_F


title: C131_B_BAL_IGRAneg

description: Library name: C131_B


title: C128_B_BAL_IGRAneg

description: Library name: C128_B


title: C122_B_BAL_IGRAneg_PETpos

description: Library name: C122_B


title: C118_B_BAL_IGRAneg

description: Library name: C118_B


title: C134_B_BAL_IGRAneg

description: Library name: C134_B


title: C110_B_BAL_IGRAneg

description: Library name: C110_B


title: C115_B_BAL_IGRAneg

description: Library name: C115_B


title: C106_B_BAL_IGRApos_PETpos

description: Library name: C106_B


title: C107_F_BAL_IGRApos_PETneg

description: Library name: C107_F


title: C106_F_BAL_IGRApos_PETpos

description: Library name: C106_F


title: C107_B_BAL_IGRApos_PETneg

description: Library name: C107_B


title: C103_B_BAL_IGRAneg_PETpos

description: Library name: C103_B


title: C097_B_BAL_IGRAneg

description: Library name: C097_B


title: C098_B_BAL_IGRAneg

description: Library name: C098_B


title: C091_F_BAL_IGRAneg

description: Library name: C091_F


title: C093_F_BAL_IGRAneg

description: Library name: C093_F


title: C103_F_BAL_IGRApos_PETpos

description: Library name: C103_F


title: C090_F_BAL_IGRApos_PETneg

description: Library name: C090_F


title: C090_B_BAL_IGRApos_PETneg

description: Library name: C090_B


title: C077_F_BAL_IGRApos_PETpos

description: Library name: C077_F


title: C077_B_BAL_IGRApos_PETpos

description: Library name: C077_B


title: C079_F_BAL_IGRApos_PETpos

description: Library name: C079_F


title: C079_B_BAL_IGRAneg_PETpos

description: Library name: C079_B


title: C089_B_BAL_IGRAneg

description: Library name: C089_B


title: C075_P_BAL_Progressor

description: Library name: C075_P


title: C078_P_BAL_Progressor

description: Library name: C078_P


title: C075_B_BAL_IGRApos_PETpos

description: Library name: C075_B


title: C075_F_BAL_Progressor

description: Library name: C075_F


title: C074_F_BAL_Progressor

description: Library name: C074_F


title: C074_B_BAL_IGRApos_PETpos

description: Library name: C074_B


title: C071_B_BAL_IGRAneg

description: Library name: C071_B


title: C073_B_BAL_IGRAneg

description: Library name: C073_B


title: C070_F_BAL_IGRAneg_PETpos

description: Library name: C070_F


title: C069_B_BAL_IGRApos_PETpos

description: Library name: C069_B


title: C068_B_BAL_IGRAneg

description: Library name: C068_B


title: C070_B_BAL_IGRAneg_PETpos

description: Library name: C070_B


title: C058_B_BAL_IGRApos_PETneg

description: Library name: C058_B


title: C056_F_BAL_IGRApos_PETpos

description: Library name: C056_F


title: C058_F_BAL_IGRApos_PETpos

description: Library name: C058_F


title: UPN827 cells, TN1695 TrailNet 3or6 month T1D plasma

status: Public on Jun 01 2026

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: UPN827 cells stimulated with TN1695 TrailNet 3or6 month T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet 3 or 6 month


title: C047_B_BAL_IGRAneg

description: Library name: C047_B


title: C052_F_BAL_IGRApos_PETneg

description: Library name: C052_F


title: C052_B_BAL_IGRApos_PETneg

description: Library name: C052_B


title: Cochlear outer sulcus , Euthyroid rep3

city: Shanghai

first: zhifang

last: xie

address: 1665 Kongjiang Road

department: Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health

country: China

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke(V1.5.2) by removing reads containing adaptors, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, removing reads whose unknown base ratio is more than 5%.
The clean reads were mapped to the reference genome (Mus musculus, GCF_000001635.26_GRCm38.p6) with HISAT2 (v2.0.4) program and aligned to reference coding gene set with Bowtie2 (v2.2.5).
Expression levels of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel files include read counts and FPKM, tpm, read count values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Cochlear outer sulcus

extract_protocol:
Articular cartilage total RNA was extracted from bilateral femoral heads of each mouse at P22 using Trizol combined with Qiagen RNeasy Micro kit.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Timed-pregnant C57BL/6J mice were treated with either antithyroid agents (0.05% methimazole, 1.0% sodium perchlorate monohydrate, and 5.0% sucrose in drinking water) or vehicle from embryonic day 17. The treatment was continued during lactation and stopped at P10.

value: Cochlear outer sulcus

tag: age

tag: strain

tag: treatment

value: Euthyroid


title: C046_B_BAL_IGRAneg

description: Library name: C046_B


title: C040_B_BAL_IGRApos_PETneg

description: Library name: C040_B


title: C042_B_BAL_IGRAneg

description: Library name: C042_B


title: C039_B_BAL_IGRAneg_PETpos

description: Library name: C039_B


title: C038_B_BAL_IGRAneg

description: Library name: C038_B


title: C039_F_BAL_IGRApos_PETpos

description: Library name: C039_F


title: C037_B_BAL_IGRAneg

description: Library name: C037_B


title: C026_B_BAL_IGRApos_PETpos

description: Library name: C026_B


title: C034_F_BAL_IGRAneg

description: Library name: C034_F


title: C030_B_BAL_IGRAneg

description: Library name: C030_B


title: C031_B_BAL_IGRAneg

description: Library name: C031_B


title: C018_F_BAL_IGRApos_PETpos

description: Library name: C018_F


title: C012_B_BAL_IGRApos_PETneg

description: Library name: C012_B


title: C011_F_BAL_IGRApos_PETneg

description: Library name: C011_F


title: C013_B_BAL_IGRApos_PETpos

description: Library name: C013_B


title: C018_B_BAL_IGRApos_PETpos

description: Library name: C018_B


title: C011_B_BAL_IGRApos_PETneg

description: Library name: C011_B


title: C233_F

description: Library name: BRA6403A15

library_source: transcriptomic single cell

data_processing:
CellRanger v7.0.1 was used to demultiplex samples and generate raw matrices for input into CellBender v0.3.2, using force-cells to specify a lower limit for cell number per sample. Samples T017_B, C090_B, C074_F, C070_F were not multiplexed. The barcode and number of cells forced for each sample can be found in the demultiplexing_barcodes.csv file.
Scripts for analysis available at github.com/ogarralab/branchett_human_bal_tb_2026
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: CellBender filtered matrices per sample
Supplementary files format and content: Data slot from anndata object integrated across all samples

extract_protocol:
All sample processing, flow cytometry staining and preservation of samples for subsequent 525 analyses was performed on the day of bronchoscopy. Samples were filtered to remove mucus and debris by pipetting through 70 um 529 cell strainers, before pelleting by centrifugation at 500 x G for 7 minutes at 4oC and transferring 530 supernatants in aliquots to storage at -80oC for subsequent processing. All cell pellets were 531 briefly suspended in ammonium chloride potassium (ACK) lysing buffer (Thermo Fisher 532 Scientific) to lyse erythrocytes, before washing with RPMI 1640 supplemented with 10% foetal 533 bovine serum and 5% penicillin and streptomycin (all Thermo Fisher Scientific) and 534 centrifuging at 400 x G for 5 minutes at 4oC and suspending in supplemented RPMI.
Cell pellets containing 0.5-1 x 106 live cells were fixed and permeabilized using the Chromium 576 Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics), as per 577 manufacturer’s instructions. Briefly, cell pellets were suspended in 0.04% Ultrapure BSA 578 (Thermo Fisher Scientific) in 1X PBS (Corning), then centrifuged at 400 x G for 5 minutes at 579  17 4oC, before suspending in 10X Genomics Fixation and Permeabilization buffer, supplemented 580 with 4% molecular biology grade formaldehyde, and fixing at 4 oC for 22 hours. Fixed cells 581 were pelleted by centrifugation at 900 x G for 5 minutes, suspended in 10X Genomics Quench 582 buffer and supplemented with 10X Genomics Enhancer solution and 50% molecular biology 583 grade glycerol (Sigma-Aldrich), to a final glycerol concentration of 10%, before storing at -584 80oC until subsequent batch processing. Sample were stored for between 7 and 574 days 585 before running scRNA-seq. Fixed samples were processed in pooled scRNA-seq runs of up 586 to 10 samples using the Chromium Fixed RNA Profiling Kits for Multiplexed Samples, splitting 587 each sample over one to three barcoded probe sets, to maximise cells recovered per sample 588 where input cell number was sufficient for splitting over multiple barcoded probe sets.

tag: barcoding

value: Multiplex sample

tag: library type

value: mRNA

tag: kit

value: 10X Flex Gene


title: C222_B, C224_F, C225_F

description: Library name: BRA6403A14


title: C189_B, P164_T

description: Library name: BRA6403A13


title: T185_B, T219_B, T218_B, C231_B

description: Library name: BRA6403A12


title: C036_B_BAL_IGRAneg_PETpos

description: Library name: C036_B


title: C220_B, C224_B, C223_B, C239_B, C233_B, P074_P, T196_B , T202_B

description: Library name: BRA6403A7


title: C140_B , T132_B, C134_B, C154_B, C103_F, C157_F, P103_P, C075_P

description: Library name: BRA6403A6


title: C182_B, T212_B, C211_B, C211_F

description: Library name: BRA6403A11


title: T146_B, T123_B, C155_B, C155_F, C106_F

description: Library name: BRA6403A5


title: C052_F, C093_B, C107_F, C118_B, C131_B, C135_B, C141_B, C141_F, T173_B

description: Library name: BRA6403A4


title: T147_B, T127_B, T156_B

description: Library name: BRA6403A10


title: P013_P, C034_B, C039_F, T096_B, C110_B, T137_B, P077_P, T158_B, C164_P, T166_B

description: Library name: BRA6403A3


title: C089_B, C079_F, C075_F, C090_F, C128_B, C142_B, C091_B, C122_B

description: Library name: BRA6403A2


title: T094_B, C077_F, T095_B, C098_B, T105_B ,C106_B, C107_B, C115_B

description: Library name: BRA6403A1


title: C070_F

description: Library name: BRA5853A4

value: Single sample


title: C074_F

description: Library name: BRA5853A3


title: C090_B

description: Library name: BRA5853A2


title: T017_B

description: Library name: BRA5853A1


title: mT23-2D, JQ1, BRD2

status: Public on Apr 29 2026

city: Davis

first: Chang-il

last: Hwang

state: CA

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California Davis

description: Library name: Sample 9

library_source: genomic

data_processing:
All analyses were performed on the Galaxy platform. Raw reads were quality-trimmed with Trim Galore! (Galaxy Version 0.6.10+galaxy0) to remove adapter sequences and low-quality bases. Trimmed reads were aligned to the Mus musculus mm9 reference genome using Bowtie2 (Galaxy Version 2.5.3+galaxy1), then filtered with SAMtools (Galaxy Version 2.5.2+galaxy3) to retain only properly paired reads with a mapping quality ≥ 30 while excluding mitochondrial reads (chrM). PCR and optical duplicates were removed with MarkDuplicates (Galaxy Version 3.1.1.0), and coverage tracks (BigWig files) were generated from the resulting unique, high-quality reads using bamCoverage (Galaxy Version 3.5.4+galaxy0).
Assembly: mm9
Supplementary files format and content: BigWig file for each sample except input

molecule: genomic DNA

growth_protocol: All cells (mT3-2D, mT23-2D) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
For ChIP-seq, approximately 1 × 10⁷ cells were harvested per sample using TrypLE Express Enzyme (Gibco, 12605028) and resuspended in PBS to generate a single-cell suspension. Chromatin immunoprecipitation was carried out using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, #9003) according to the manufacturer’s protocol with minor modifications. Briefly, cells were fixed in 1% formaldehyde at room temperature for 10 minutes to crosslink protein-DNA interactions. Crosslinking was quenched with glycine (final concentration 125 mM) for 5 minutes at room temperature. Cells were then washed twice with ice-cold PBS and lysed in lysis buffer to isolate nuclei. Chromatin was enzymatically digested with 1 µl of micrococcal nuclease (MNase) at 37°C for 20 minutes to achieve partial digestion, followed by mechanical shearing using a Bioruptor (Diagenode) set to high power for 3 rounds of 10 cycles (30 seconds on, 30 seconds off). Shearing was performed in 1.5 ml TPX microtubes (Diagenode, C30010010) to generate DNA fragments ranging from 150 to 500 bp. DNA fragmentation was verified by 1.8-2% agarose gel electrophoresis. For immunoprecipitation, 10 µl of antibody was used per reaction: BRD2 (Cell Signaling Technology, 5848S) or BRD4 (Bethyl Laboratories, A301-985A100). Chromatin and protein G magnetic beads were incubated overnight at 4°C with antibodies under constant agitation using a tube rotator to promote optimal antigen-antibody interaction. Beads were then washed sequentially with low salt, high salt, and LiCl wash buffers, followed by TE buffer. Crosslinks were reversed by incubating with Proteinase K at 65°C for 2 hours. DNA was purified using spin columns included in the kit according to the manufacturer’s instructions (Cell Signaling Technology, 14209S).
Library preparation and sequencing for ChIP-seq was carried out by Novogene Co., LTD. Sample quality was assessed prior to library construction. DNA fragments were end-repaired, A-tailed, and ligated to Illumina adapters, followed by size selection, PCR amplification, and quantification.

treatment_protocol: Cells (mT3-2D, mT23-2D) were treated with JQ1 (1 µM; MedChemExpress, Cat. No. HY-13030) or DMSO for 24 hours prior to ChIP-seq preparation.

tag: cell line

tag: cell type

value: Pancreatic cancer cells

tag: chip antibody


title: mT23-2D, JQ1, BRD4

description: Library name: Sample 10


title: mT23-2D, DMSO, BRD4

description: Library name: Sample 8

value: DMSO


title: mT23-2D, Input

description: Library name: Sample 6


title: mT3-2D, JQ1, BRD4

description: Library name: Sample 5


title: mT3-2D, JQ1, BRD2

description: Library name: Sample 4


title: mT3-2D, DMSO, BRD4

description: Library name: Sample 3


title: mT3-2D, DMSO, BRD2

description: Library name: Sample 2


title: mT23-2D, DMSO, BRD2

description: Library name: Sample 7


title: mT3-2D, Input

description: Library name: Sample 1


title: OV_GSKJ4_72h reps 1 and 2

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using STAR
Gene count tables were generated using the --quantMode GeneCounts argument in STAR
DESeq2 was used to identify significant differential expression between control and experimental samples
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including per sample: Ensembl gene ID, total counts

source_name: OVCAR-3 cell line

growth_protocol: OVCAR-3, CAOV3 and SKOV3 cells were grown in 12-well TC plates using RMPI 1640, DMEM/F12 and McCoys media respectively (Life Scientific)

extract_protocol:
Following 48h and 72h of JMJD3/UTX inhibition, total RNA samples were extracted using the Qiagen Rneasy mini kit (74106)
cDNA libraries were prepared at Novogene (Eukaryotic RNA-Seq, cDNA library)

treatment_protocol: OVCAR-3, CAOV3 and SKOV3 cells were treated with GSK-J5 (control) and GSK-J4 (Stripped media, 2.5uM) for 48h and 72h prior to RNA extraction

tag: treatment length


title: mT23-2D, JQ1

description: Library name: Sample 6

data_processing:
Raw reads were quality-trimmed with Trim Galore! (Galaxy Version 0.6.7+galaxy0) to remove adapter sequences and low-quality bases. Clean reads were aligned to the Mus musculus mm9 reference genome using HISAT2 (Galaxy Version 2.2.1+galaxy1), and gene-level counts were obtained with featureCounts (Galaxy Version 2.0.3+galaxy2). Normalizationanalysis was performed with DESeq2 (Galaxy Version 2.11.40.8+galaxy0).
Assembly: mm9
Supplementary files format and content: Tabular file includes normalized counts for each sample
Supplementary files format and content: Tabular files include raw counts for each sample

growth_protocol: All cells (mT3-2D, mT19-2D, mT23-2D) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were lysed in 1 ml of TRIzol reagent (Thermo Fisher Scientific, 15596026) at room temperature for 5 minutes with gentle agitation, followed by the addition of 200 µl of chloroform (Reagents, C755N59), according to the manufacturer’s protocol. RNA was extracted using the PureLink RNA Mini Kit (Invitrogen, 12183018A) and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific) prior to sequencing submission.
Library preparation and sequencing for RNA-seq was carried out by Novogene Co., LTD. Total RNA quality was assessed using 1% agarose gel electrophoresis, NanoDrop spectrophotometry (for RNA quantity and purity), and an Agilent 2100 Bioanalyzer (for RNA Integrity Number, RIN). Poly(A) mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to synthesize first-strand cDNA with random primers. Second-strand cDNA synthesis was performed using a dUTP-incorporation protocol to maintain strand specificity. The resulting double-stranded cDNA was end-repaired, A-tailed, and ligated to Illumina adapters, followed by size selection and PCR amplification. Libraries were quantified and quality-checked prior to sequencing.

treatment_protocol: Cells (mT3-2D, mT19-2D, mT23-2D) were treated with JQ1 (1 µM; MedChemExpress, Cat. No. HY-13030) or DMSO for 24 hours prior to RNA extraction.


title: UPN827 cells, TN1667 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1667 TrailNet 3or6 month T1D plasma


title: mT23-2D, DMSO

description: Library name: Sample 5


title: mT3-2D, JQ1

description: Library name: Sample 2


title: mT3-2D, DMSO

description: Library name: Sample 1


title: mT19-2D, JQ1

description: Library name: Sample 4


title: Ribo_HEK293_Arg_-Arg

status: Public on Apr 20 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_7

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.
Assembly: GRCh39.p13
Supplementary files format and content: tab-delimited text files including normalized read counts per codon on individual mRNAs for Ribo-seq.
Supplementary files format and content: comma-delimited text files including read counts mapped to each position on reporter mRNA Ribo-seq.
Library strategy: Ribo-Seq

extract_protocol:
For mRNA reporters, 8 μg of mRNA was transfected into HEK293-Kb cells (~80% confluence) in 10 cm dishes for 8 h. For plasmid reporters, 1 μg plasmid was transfected into 35 mm dishes for 24 h. Cells were washed with cold PBS and lysed in polysome lysis buffer (10 mM HEPES, pH 7.4; 100 mM KCl; 5 mM MgCl₂; 100 μg/mL cycloheximide; 1% Triton X-100). Lysates were cleared by centrifugation at 20,000 × g for 10 min at 4 °C and digested with RNase I (Ambion, 750 U per 100 A₂₆₀ units) at 4 °C for 1 h. Total RNA was extracted using TRIzol LS (Invitrogen) for cDNA library construction.
Ribosome-protected fragments (25–35 nt) or disome footprints (40-60 nt) were resolved on a 15% polyacrylamide TBE–urea gel (Invitrogen) and visualized with SYBR Gold. Excised RNA fragments were eluted overnight in RNA elution buffer (300 mM sodium acetate, pH 5.2; 1 mM EDTA; 0.1 U/μL SUPERase·In), cleared through Spin-X columns, and ethanol-precipitated. cDNA libraries were constructed using T4 PNK, Poly(A) polymerase, and custom Ezra enzyme, followed by ligation of 5' adapters, streptavidin bead-based purification, and reverse transcription following the previous study [28]. Final cDNA was amplified with barcoded primers, size-selected (180 bp), quantified, pooled, and sequenced on an Illumina MiniSeq or NextSeq 500.

tag: genotype

value: WT


title: Ribo_HEK293_control_rep3

description: Library name: Sample_3


title: mT19-2D, DMSO

description: Library name: Sample 3


title: Ribo_SAMD9_Dox

description: Library name: Sample_5


title: Ribo_SAMD9_Con

description: Library name: Sample_4


title: Ribo_HEK293_Arg

description: Library name: Sample_6


title: Ribo_HEK293_control_rep2

description: Library name: Sample_2


title: Ribo_HEK293_control_rep1

description: Library name: Sample_1


title: Ribo_miRFP-D-EGFP

description: Library name: Sample_87


title: Ribo_miRFP-P-EGFP

description: Library name: Sample_86


title: Disome_Q-P_mix

description: Library name: Sample_85


title: Disome_Asp_GAT-GAC

description: Library name: Sample_84


title: Disome_K-A

description: Library name: Sample_83


title: Disome_A-K

description: Library name: Sample_82


title: Disome_Arg_CGCCGC-CGGCGG

description: Library name: Sample_81


title: Disome_Asp_GAC

description: Library name: Sample_80


title: Disome_Arg_IV

description: Library name: Sample_78


title: Disome_Val

description: Library name: Sample_77


title: Disome_Tyr

description: Library name: Sample_76


title: Disome_Trp

description: Library name: Sample_75


title: Disome_Thr

description: Library name: Sample_74


title: Disome_Ser

description: Library name: Sample_73


title: Disome_Phe

description: Library name: Sample_72


title: Disome_Met

description: Library name: Sample_71


title: Disome_Lys

description: Library name: Sample_70


title: Disome_Arg_AGC

description: Library name: Sample_79


title: Disome_Ile

description: Library name: Sample_68


title: Disome_Leu

description: Library name: Sample_69


title: Disome_His

description: Library name: Sample_67


title: Sham Gastroc 1

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

description: Library name: Sample Gastroc 5

data_processing:
Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Assembly: Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Supplementary files format and content: CSV file including PFKM values for each sample

organism: Rattus norvegicus

source_name: skeletal muscle

extract_protocol:
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using a divalent cation buffer at elevated temperatures.
The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: sham and hindlimb ischemia

value: skeletal muscle

value: Sprague Dawley

value: Sham


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 2, unsorted cells

city: Vancouver

first: Arman

middle: Foyez

last: Adel

state: British Columbia

address: 6088 University Boulevard

department: The School of Biomedical Engineering

country: Canada

institute: the University of British Columbia

description:
Library name: mESC-Unsort-Rep2_S2_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

data_processing:
miRNA targets were extracted and counted from raw reads using a whitelist of cgRNA targets (mmuSequences.csv) and a modified version of the barcode counting script (cgLibV2_BC_counter.ipynb) from Joung et al., Cell, 2023 (PMID 36608654).
miRNA target counts were then paired to their corresponding miRNA target names and samples were ordered in a matrix using the mmuSequences.csv file and either multiClonal_cgRNA_matrix.ipynb script for the multi-clonal mESC screen or the SMC_cgRNA_matrix.ipynb for the clonal mESC, SMC differentiation Day 3, SMC differentiation Day 6 and cumulative recording screens.
All analysis scripts and associated files to generate process counts data can be found at https://github.com/yachielab
Assembly: miRbase v22
Supplementary files format and content: raw counts for each sample labelled in the columns and the miRNA target named in the rows
Supplementary files format and content: miRNA target seqeunce and subsequent raw read count for each target for each sample
Library strategy: CRISPR Screen

source_name: Mouse ES cells differentiated to smooth muscle cells

growth_protocol: mESCs were grown in DMEM low-glucose (Thermo Fisher #11885084) supplemented with 15% FBS (Thermo Fisher #A5256501), 1% Glutamax (Gibco #35050061), 1% Non-essential amino acids (Gibco #11140050), 1% Sodium Pyruvate (Gibco #11360070), 20µM 2-Mercaptoethanol (Sigma-Aldrich #M6250-100ML), 3µM of GSK-3 inhibitor CHIR99021 (Sigma-Aldrich # SML1046-5MG), 1µM MEK1 and MEK2 inhibitor PD0325901 (Sigma-Aldrich # PZ0162-5MG), 10^3 U LIF (Biotechnie R&D Systems # 8878-LF-500/CF) and 200µg/ml of Geneticin (G418 Sulfate) (Gibco #10131035). Prior to transduction, media was supplemented with 10µg/ml of polybrene (Sigma-Aldrich# H9268-5G). 24 hours after the transduction of the cgRNA library, the media was further supplemented with 3µg/ml of Puromycin (Thermo Fisher #A1113803).

extract_protocol:
The genomic DNA of cells that were either taken from the population or EGFP+ FACS sorted cells were extracted using Monarch® Spin gDNA Extraction Kit (T3010S) as per the manufacturers protocols.
miRNA targets were then amplified from the extracted gDNA using a two step PCR process where in the first process, targets were amplified with primers containing partial Truseq adapter seqeunces. In the second PCR, the rest of the Truseq adapters and subsequent index and flow-cell adapter sequences were added on to the first round PCR product.

treatment_protocol: Differentiation of mESCs to SMCs was carried out in DMEM-F12 (Gibco # 11320033) supplemented with 10% FBS (Gibco #A5256701), 1mM Glutamax (Gibco #35050061), 0.1mM Non-essential amino acids (Gibco #11140050), 0.1 mM Sodium Pyruvate (Gibco #11360070), 0.2µM 2-Mercaptoethanol (Sigma-Aldrich #M6250-100ML), 10µM RA (Stem Cell Technologies #100-1045) and 200µg/ml of Geneticin (G418 Sulfate) (Gibco #10131035). Prior to transduction, media was supplemented with 10µg/ml of polybrene (Sigma-Aldrich# H9268-5G). 24 hours after the transduction of the cgRNA library, the media was further supplemented with 3µg/ml of Puromycin (Thermo Fisher #A1113803).

value: Transduction of Clone # 7 mESCs with cgRNA library,unsorted cells


title: Disome_Gly

description: Library name: Sample_66


title: Disome_Glu

description: Library name: Sample_65


title: Disome_Gln

description: Library name: Sample_64


title: Disome_Asp

description: Library name: Sample_62


title: Disome_Asn

description: Library name: Sample_61


title: Disome_Ala

description: Library name: Sample_60


title: Disome_Pro

description: Library name: Sample_59


title: Disome_Cys

description: Library name: Sample_63


title: Disome_Arg

description: Library name: Sample_58


title: cArg_AGC

description: Library name: Sample_55


title: cArg_20-80

description: Library name: Sample_57


title: cQ-P_mix

description: Library name: Sample_56


title: cK-A

description: Library name: Sample_54


title: cA-K

description: Library name: Sample_53


title: cArg_CGT

description: Library name: Sample_52


title: cAsp_GAT-GAC

description: Library name: Sample_50


title: Ribo_cPro_eIF5A_KD

description: Library name: Sample_48


title: cArg_CGG

description: Library name: Sample_51


title: cPhe_SAMD9_-Dox_rep2

description: Library name: Sample_46


title: cPhe_SAMD9_+Dox_rep2

description: Library name: Sample_47


title: Ribo_cPro_scramble

description: Library name: Sample_49


title: cArg_CGCCGC-CGGCGG

description: Library name: Sample_44


title: cArg_IV_rep2

description: Library name: Sample_43


title: cAsp_GAC

description: Library name: Sample_45


title: cArg_rep6

description: Library name: Sample_41


title: Ribo_cPro_GC7

description: Library name: Sample_42


title: cArg_rep4

description: Library name: Sample_39


title: cArg_rep5

description: Library name: Sample_40


title: cArg_rep3

description: Library name: Sample_38


title: cPhe_SAMD9_+Dox_rep1

description: Library name: Sample_37


title: cPhe_SAMD9_-Dox_rep1

description: Library name: Sample_36


title: cLys_-Lys

description: Library name: Sample_35


title: cLeu_-Leu

description: Library name: Sample_34


title: cPhe_-Phe

description: Library name: Sample_33


title: cMet_-Met

description: Library name: Sample_32


title: cArg_-Arg

description: Library name: Sample_31


title: cCys_-Cys

description: Library name: Sample_30


title: cArg_IV_rep1

description: Library name: Sample_29


title: cArg_rep2

description: Library name: Sample_28


title: Sham Gastroc 3

description: Library name: Sample Gastroc 3


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark15_4

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Library name: snRNAseq_mouse_models_Mitopark15_4
15d

data_processing:
We generated the count matrix from the sequencing data for each sample (fastq) using the software commercialized by 10x Genomics Cellranger (10x Genomics Cell Ranger v7.1.0)
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix_<filename>.h5, sparse matrix of gene expression counts. Rows = Genes (Features), Columns = Cell Barcodes (IDs) and Expression Counts

source_name: Brain

extract_protocol:
Striatum from one hemisphere of 19 brains was collected for nuclei isolation. Brain tissue was placed into a tube together with lysis buffer (10?mM Tris-HCl, 10?nM NaCl, 3?nM MgCl2, 0.1% Nonidet P40 Substitute 0.1%, 1?mM DTT, 1U/µl RNAse inhibitor and Nuclease free water), homogenized by pestle homogenization in a tissue grinder tube and incubated on ice for 5?min. The nuclei were extracted by following 10x Genomics protocol for Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC?+?Gene Expression Sequencing (User Guide, CG000375 Rev A). Each sample was filtered through a 70?µm cell strainer, sorted and permeabilized nuclei were pelleted at 500?×?g for 5?min at 4?°C, and resuspended in 1 ml PBS 1x, 1% BSA + 1 U/?l RNase inhibitor, for two times. After the second centrifuge nuclei were stained with 7-AAD Ready Made Solution (SML 633-1ML) 0.01% for FACS sorting.
The nuclei were processed according to the 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) protocol (User Guide CG000315 Rev C). For each sample, we aimed to recover between 2,000 and 7,000 nuclei. Libraries were constructed for sequencing in accordance with the protocol and manufacturer's recommendations. Sequencing was performed using an Illumina NextSeq 2000, targeting a depth of 300 to 400 million reads per sample. The sequencing read lengths were as follows: Read 1, 28 cycles; i7 and i5 index, 10 cycles each; Read 2, 90 cycles.

treatment_protocol: Mild Neurotoxin Model (6-OHDA): Adult wild-type mice received unilateral injections of 6-hydroxydopamine (6-OHDA) at a low dose (0.6 µg/µL) into the medial forebrain bundle (MFB), selectively damaging nigrostriatal dopaminergic neurons and inducing mild Parkinsonian pathology. Untreated wild-type mice served as controls.  Progressive Genetic Model (MitoPark): The MitoPark model (Slc6a3-cre; Tfam^flx/flx) induces mitochondrial dysfunction specifically in dopaminergic neurons, leading to progressive neurodegeneration. Samples were collected at two timepoints:

value: Brain

value: no cell line

value: all cells

value: +/DAT-cre, TfamloxP/TfamloxP

value: transgenic animals


title: Ribo_Gly

description: Library name: Sample_27


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_Pol2-NTD

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 46

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER (v2) with following configuration: For ChIP-seq of HIRA and SPT6, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For S5P-Pol II, S2P-Pol II, and CDK9, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. For H3K27ac, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all ChIP-Seq data.
Paired-end reads of RNA-seq were aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Assembly: mm9
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

growth_protocol: Mouse 3T3-L1 white preadipocytes were maintained in growth (DMEM +10%BS) medium

extract_protocol:
Total RNA was subjected to rRNA depletion using theNEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads (NEB, E7405L) before using Click-iT™ Nascent RNA Capture Kit (C10365) to capture nascent RNA.
Isolated nascent RNAs were reverse-transcribed into cDNA using  SuperScript™ VILO™ cDNA Synthesis Kit (Thermo, 11754050) and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol: For the adipogenesis assay, cells were plated in growth medium (DMEM plus 10% BS) 4 days before the induction and were induced with 10 μg/mL insulin, 0.5 mM IBMX and 1 μM DEX in FBS medium (DMEM plus 10% FBS) for 2 days. After 2 days of induction, the culture medium was changed to DMEM supplemented with FBS and insulin only.

value: Differentiating preadipocytes

value: HIRA depleted

value: adipogenic differentiation

tag: time

value: day 4

value: Anti-Rbp1 NTD(D8L4Y) (14958, Cell Signaling Technology)


title: Ribo_Gln

description: Library name: Sample_26


title: PAD Soleus 1

description: Library name: Sample Soleus 10

value: hindlimb ischemia


title: WT Sal_Recovery_NO rIL10_B

city: San Jose

first: Eleana

middle: Stephanie

last: Guardado

address: 3166 Kimlee Dr

institute: Stanford

description: Mouse 14

scan_protocol: Chip was imaged and quantified by a nCounter Sprint profiler.

data_processing: All samples passed the NanoString system quality control (QC) test. Data were analyzed using nSolver 4.0 and by performing a NanoString Advanced analysis. The following housekeeping genes showing the strongest correlation with each other were used for normalization of gene expression: Acad9, Cnot10, Mtmr14, Nol7, Nubp1, Pgk1, Ppia, and Rplp0. The agglomerative analysis on nSolver was used to generate heatmaps. Per NanoString’s recommendation, 50 transcript counts was taken as the “count threshold”. The 20 most upregulated genes among all treatments were identified by the differential expression analysis. The STRING database (https://string-db.org) was used to explore protein-protein interactions among differentially regulated genes from NanoString that were statistically significant based on the unadjusted p-values [20].

source_name: RNA from lung tissue

growth_protocol: Male C57BL/6J and B6.129P2-Lcn2tm1Aade/AkiJ mice 8-13 weeks of age were received from The Jackson Laboratory (Bar Harbor, ME, USA) and housed in micro-isolator cages (five per cage) at the University of California, Riverside animal barrier facilities. Mice were allowed unrestricted access to food and water, monitored for any behavioral or physiological changes, and weighed weekly. All experiments and procedures were approved by the University of California River-side Institutional Animal Care and Use Committee.

extract_protocol: Animals were euthanized with isoflurane and collection of bronchoalveolar lavage fluid (BALF) and lung tissue was performed as described below. For BALF collection, a cannula was first inserted into the trachea and secured by tying a knot with a suture around the trachea. A syringe was used to rinse/wash the whole lung with 1 ml of sterile 1X PBS, which was collected in a separate tube to prevent over-dilution in subsequent enzyme-linked immunoassays (ELISAs). The lungs were washed two additional times with 1 ml PBS, and combined in a second tube for downstream cellular analyses. After BALF collection, the left lung lobe was tied off, excised and frozen in RNAlater to be used for NanoString analyses.

treatment_protocol: WT and LCN-2 KO mice were repetitively exposed to DE prepared from dusts collected from swine confinement facilities or their saline vehicle control. An aqueous solution of dust extract was prepared as described above and published previously and administered to mice as a 50 l intranasal instillation (IN) of 12.5% DE or saline under light isoflurane anesthesia. Male mice of 8-13 weeks old were given IN instillations in the mornings for 15 weekdays.  For this work, we evaluated two time points after repetitive DE exposure: 1) five hours after last IN (no recovery period), and 2) 72 hours after last IN (recovery period). For studies that included IL-10 administration, 1 ug of recombinant mouse IL-10 per 25 g mouse body weight was administered to LCN-2 KO animals on the day of the final DE IN and at 48 hr post final DE IN.

tag: gender

value: Male

value: Lung


title: Ribo_Asp

description: Library name: Sample_24

value: WT


title: Ribo_Phe

description: Library name: Sample_22


title: Ribo_Cys

description: Library name: Sample_25


title: Ribo_His

description: Library name: Sample_23


title: Ribo_Arg_rep1

description: Library name: Sample_21


title: UPN827 cells, TN1603RH TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1603RH TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: Ribo_Tyr

description: Library name: Sample_19


title: Ribo_Asn

description: Library name: Sample_17


title: Ribo_Thr

description: Library name: Sample_20


title: Ribo_Glu

description: Library name: Sample_15


title: Ribo_Lys

description: Library name: Sample_16


title: Ribo_Ser

description: Library name: Sample_12


title: Ribo_Pro

description: Library name: Sample_13


title: Ribo_Ile

description: Library name: Sample_11


title: R3, responder 3

status: Public on Apr 17 2026

first: Kristi

last: Briggs

address: 10 Center Drive

institute: NIDDK

description:
Library name: Sample 6_R3
10X Genomics

data_processing:
Gene counting was done using CellRanger software
Assembly: Homo Sapien GRCh38
Supplementary files format and content: tab seperated matrix and values files

source_name: sigmoid colon

extract_protocol:
Cryopreserved tissue was thawed at 37 °C and immediately washed and placed in solution of RPMI and 5% fetal bovine serum (FBS) with the addition of and disassociated using DNAse 1 and Collagenase P at 37 °C for 40 minutes. Digestion was stopped with 100 mM EDTA. Cells were filtered through a 70-µm pore size filter to obtain a single-cell suspension and washed with solution of RPMI + 5% FBS + 2 mM EDTA. Cells were spun down and resuspended in phosphate-buffered saline (PBS) to count. Cells were then stained with Live/Dead Fixable Aqua (Thermo Fisher Scientific) for 20 minutes. Cells were then washed and stained with CD45 (BV510; BD), CD3 (APC; BD), and EpCAM (BV605; BioLegend) with the addition of human Fc block and Brilliant buffer plus (BD). CD45+ and CD3+ cells (T cells) and CD45− and EpCAM+ (epithelial cells) were sorted on the BD FACSAria II and collected into tubes with PBS + 1% bovine serum albumin. Cells were then stained with trypan blue and manually counted with a hemocytometer and resuspended with the desired concentration of 1000 cells/µL. Any cell population with <10 000 cells were combined with another population. Cells were then sent to the Johns Hopkins Sidney Kimmell Comprehensive Cancer Center Experimental and Computational Genetics Core for library preparation and sequencing.  output.
The single-cell 5′ V(D)J and 5′ digital gene expression kits (10x Genomics) were used with an emulsion-based protocol provided by the manufacturer. Cells and barcoded gel beads were partitioned into nanoliter-scale droplets using the 10x Genomics Chromium platform to partition up to 10 000 cells per sample (when possible) followed by RNA capture and cell-barcoded complementary DNA synthesis using the manufacturer’s standard protocols. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2 × 150-bp paired end sequencing. The 5′ VDJ libraries were sequenced to a depth of ∼5000 reads per cell and the 5′ differential gene expression libraries were sequenced to a target depth of ∼50 000 reads per cell. Cell Ranger (v9.0; 10x Genomics) was used to align reads to reference (GRCh38-3.0.0) and generate feature-barcodematrices from the Chromium scRNAseq

tag: tissue

value: sigmoid colon

tag: phenotype

value: responder


title: NR3, non-responder 3

description:
Library name: Sample 4_NR3
10X Genomics

value: non-responder


title: Ribo_Ala

description: Library name: Sample_8


title: NR1, non-responder 1

description:
Library name: Sample 1_NR1
10X Genomics


title: NR2, non-responder 2

description:
Library name: Sample 2_NR2
10X Genomics


title: delta_HNS_MicroC_biol_rep2

status: Public on Apr 16 2026

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description: Library name: gav28

data_processing:
The raw reads were processed with distiller-nf pipeline using NC_000913.3 E.coli reference genome and BWA as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: cooler (.cool, a contact matrix) file for each sample

organism: Escherichia coli

growth_protocol: E. coli K-12 MG1655 strain was grown in Luria-Bertani broth at 37 °C and 200 rpm until reaching an OD600 of ~ 0.6.

extract_protocol:
Cells were resuspended in 250 µL TE (10 mM Tris pH 8.0, 1 mM EDTA) supplemented with 1× protease inhibitors (Bimake) followed by adding lysozyme (Sigma L6876) to 4 µg/mL and incubating for 30 min at 37 °C with shaking at 1000 rpm. The sample was pelleted for 5 min at 16100 g and room temperature and resuspended in an appropriate volume of MNase buffer (10 mM Tris pH 7.5, 1 mM CaCl2) followed by adding MNase (ThermoFisher EN0181, used as 5 U/µL stock solution) to 10 U/mL and incubating for 25 min at 37 °C with shaking at 1000 rpm. The volume of MNase buffer ranged from 475 to 1160 µL for different samples; it was determined individually for each sample to obtain the fragment distribution from ~ 75 to 1000 bp. DNA digestion was terminated by adding EGTA to 5 mM followed by centrifugation for 5 min at 16100 g and room temperature.
The libraries were prepared following a modified Micro-C protocol

treatment_protocol: For heat shock treatment, cells were incubated at 44 °C for 10 min. For transcription inhibition, cells were treated with 25 or 750 µg/mL rifampicin for 40 min. For antibiotic treatment cells were treated with the indicated concentration of the drug for 40 min.

value: bacteria

value: delta HNS


title: delta_HNS_MicroC_biol_rep1

description: Library name: gav27


title: Variation_MPRA_Barcode_Association

status: Public on Apr 02 2026

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: Variation_MPRA_Barcode_Association

library_source: other

data_processing:
Adapters were trimmed from sequencing during demuxing using bcl2fastq --use-bases-mask=N15Y136,Y15,I10,N15Y136
The barcode association dictionary was generated using MPRAflow for each size present in the design (219bp, 218bp, 216bp, 214bp, 212bp, 210bp, 208bp) using ---mapq 0 and a cigar score flag for the length of the oligo to require an exact match (ex: --cigar 219M) dictionaries were converted to tsvs, combined, and repeat barcodes were removed.
Assembly: hg38
Supplementary files format and content: The barcode association dictionary is a tsv file of barcodes and oligo names.
Supplementary files format and content: The design file is the fasta file sent to Twist biosciences to generate the oligo pool.

molecule: other

source_name: NEB 10-beta electrocompetent cells

extract_protocol:
Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: NEB 10-beta electrocompetent cells


title: JHH390CAF

status: Public on Apr 01 2026

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

description:
Library name: JHH390CAF
CAF Patient 390, Monoculture

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: CAF

value: monoculture


title: mix_JHH390CoCAF

description:
Library name: mix_JHH390CoCAF
CAF Patient 390, Coculture

value: coculture


title: mix_JHH387CoCAF

description:
Library name: mix_JHH387CoCAF
CAF Patient 387, Coculture


title: JHH387Org

description:
Library name: JHH387Org
Orgnanoid Patient 387, Monoculture

value: epithelium


title: JHH387CoOrg

description:
Library name: JHH387CoOrg
Orgnanoid Patient 387, Coculture


title: JHH383CAF

description:
Library name: JHH383CAF
CAF Patient 383, Monoculture


title: mix_JHH383CoCAF

description:
Library name: mix_JHH383CoCAF
CAF Patient 383, Coculture


title: mix_JHH383Org

description:
Library name: mix_JHH383Org
Orgnanoid Patient 383, Monoculture


title: mix_JHH383CoOrg

description:
Library name: mix_JHH383CoOrg
Orgnanoid Patient 383, Coculture


title: JHH372CAF

description:
Library name: JHH372CAF
CAF Patient 372, Monoculture


title: JHH372CoCAF

description:
Library name: JHH372CoCAF
CAF Patient 372, Coculture


title: JHH372Org

description:
Library name: JHH372Org
Orgnanoid Patient 372, Monoculture


title: mix_JHH369CoOrg

description:
Library name: mix_JHH369CoOrg
Orgnanoid Patient 369, Coculture


title: JHH369CoCAF

description:
Library name: JHH369CoCAF
CAF Patient 369 Coculture


title: JHH369Org

description:
Library name: JHH369Org
Orgnanoid Patient 369, Monoculture


title: JHH369CAF

description:
Library name: JHH369CAF
CAF Patient 369, Monoculture


title: JHH368CAF

description:
Library name: JHH368CAF
CAF Patient 368, Monoculture


title: mix_JHH368CoOrg

description:
Library name: mix_JHH368CoOrg
Orgnanoid Patient 368, Coculture


title: JHH357CoCAF

description:
Library name: JHH357CoCAF
CAF Patient 357, Coculture


title: mix_JHH368Org

description:
Library name: mix_JHH368Org
Orgnanoid Patient 368, Monoculture


title: JHH357CAF

description:
Library name: JHH357CAF
CAF Patient 357, Monoculture


title: JHH352CoCAF

description:
Library name: JHH352CoCAF
CAF Patient 352, Coculture


title: mix_JHH357Org

description:
Library name: mix_JHH357Org
Orgnanoid Patient 357, Monoculture


title: mix_JHH352CoOrg

description:
Library name: mix_JHH352CoOrg
Orgnanoid Patient 352, Coculture


title: JHH380CoCAF

description:
Library name: JHH380CoCAF
CAF Patient 380, Coculture


title: JHH380CAF

description:
Library name: JHH380CAF
CAF Patient 380, Monoculture


title: JHH352Org

description:
Library name: JHH352Org
Orgnanoid Patient 352, Monoculture


title: JHH352CAF

description:
Library name: JHH352CAF
CAF Patient 352, Monoculture


title: JHH362CAF

description:
Library name: JHH362CAF
CAF Patient 362, Monoculture


title: JHH348CoCAF

description:
Library name: JHH348CoCAF
CAF Patient 348, Coculture


title: JHH362CoCAF

description:
Library name: JHH362CoCAF
CAF Patient 362, Coculture


title: PRC1-CD_FGO_Rep2

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description:
Library name: Sample13
PRC1-CD rep2

data_processing:
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1). For allele-specific analysis of BDF1 x JF1 F1 hybrid embryos, The SNPs in BDF1 and JF1 were masked as ‘N’ in the reference genome (GRCm38) by the ‘Dual strain mode’ in SNPsplit_genome_preparation of SNPsplit (version 0.3.4). Then reads were aligned to the N-masked genome by STAR (version 2.7.6) with specific setting of parameters ‘--alignEndsType EndToEnd --outSAMattributes NH HI NM MD’. By filtering the alignment records with the ‘NH:i:1’ tag, uniquely aligned reads were assigned to its parental origins. SNPsplit was used to assign the SNP-containing reads to maternal and paternal genome. The number of allelic reads of each gene were calculated by featureCounts (version 1.6.0) to calculate the RPKM values.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include RPKM value for each sample
Supplementary files format and content: bigWig files for FGO sample

source_name: embryo

extract_protocol:
For bulk RNA-seq of PRC1-WT and -CD FGOs, ten oocytes were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
For RNA-seq, libraries were prepared as previously described (Inoue et al., Genes Dev. 2018). Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacture's instructions. Two hundreds picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacture's instructions.

value: embryo

tag: developmental stage

value: Full-grown oocyte

value: PRC1 catalytic dead


title: Human_Pancreas_FFPE_1

status: Public on Mar 31 2026

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Xenium Analyzer

hyb_protocol: A pre-designed Xenium probe panel targeting 377 genes (human multi-tissue), along with an additional 100 custom target genes, was hybridized to RNA in situ, followed by fluorescent labeling, imaging, and decoding using the Xenium Analyzer (v1.7.6.0).

scan_protocol: not provided

data_processing: Data were processed using the Xenium analysis pipeline (version xenium-1.7.1.0), which included signal segmentation, transcript decoding, quality score assignment, and spatial mapping of transcripts to x/y coordinates.

source_name: FFPE spatial transcriptomic

extract_protocol: No RNA extraction was performed. FFPE tissue sections from human pancreas were cut at 5 µm thickness and mounted onto Xenium slides. After deparaffinization and decrosslinking, we performed probe hybridization, ligation, and amplification according to the 10x Genomics Xenium FFPE Tissue Preparation Guide

value: Pancreas


title: FFPE breast cancer patient (B1) sample (2) profiled with the Xenium human breast gene panel

status: Public on Mar 27 2026

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: Breast cancer tissues analyzed with Xenium human breast 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 breast cancer

label_protocol: Xenium probe set

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: primary breast cancer

tag: tissue preservation method

value: FFPE

value: Apocrine adenocarcinoma


title: FFPE breast cancer patient (B1) sample (3) profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B5) sample profiled with the Xenium human breast gene panel

value: Carcinoma, NOS


title: FFPE breast cancer patient (B3) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B6) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B1) sample (1) profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B8) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B9) sample profiled with the Xenium human breast gene panel

value: Infiltrating duct carcinoma, NOS


title: FFPE breast cancer patient (B4) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B10) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B12) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B2) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B14) sample profiled with the Xenium human breast gene panel

value: Infiltr. duct mixed with other types of carcinoma


title: FFPE breast cancer patient (B16) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B17) sample profiled with the Xenium human breast gene panel


title: FFPE NSCLC patient (L7) sample profiled with the Xenium human lung gene panel

description: Lung cancer tissues analyzed with Xenium human lung gene panel

source_name: primary NSCLC

value: primary NSCLC

value: Adenocarcinoma, NOS


title: FFPE NSCLC patient (L8) sample profiled with the Xenium human lung gene panel

value: Sq. cell carcinoma, keratinizing, NOS


title: FFPE NSCLC patient (L10) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L5) sample profiled with the Xenium human lung gene panel

value: Acinar cell carcinoma


title: FFPE NSCLC patient (L4) sample profiled with the Xenium human lung gene panel


title: mix_JHH372CoOrg

description:
Library name: mix_JHH372CoOrg
Orgnanoid Patient 372, Coculture

value: pancreas

value: Patient-derived organoid


title: FFPE NSCLC patient (L3) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L2) sample (2) profiled with the Xenium human lung gene panel

value: Adenocarcinoma with mixed subtypes


title: FFPE NSCLC patient (L2) sample (1) profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L9) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L1) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L3) sample profiled with the custom immunooncology gene panel

description: Lung cancer tissues analyzed with a custom Xenium immunooncology 340 gene panel


title: FFPE NSCLC patient (L2) sample profiled with the custom immunooncology gene panel


title: FFPE NSCLC patient (L4) sample profiled with the custom immunooncology gene panel


title: FFPE NSCLC patient (L1) sample (1) profiled with the custom immunooncology gene panel


title: FFPE NSCLC patient (L7) sample profiled with the Xenium Prime 5K gene panel

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


title: FFPE NSCLC patient (L6) sample profiled with the Xenium Prime 5K gene panel


title: FFPE NSCLC patient (L1) sample profiled with the Xenium Prime 5K gene panel


title: FFPE NSCLC patient (L3) sample profiled with the Xenium Prime 5K gene panel


title: Control

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

data_processing:
Raw sequencing data were processed using Cell Ranger v7.2.0 (10x Genomics). The steps included:
Demultiplexing: Sequencing reads were demultiplexed based on sample indices.
Alignment: Reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner integrated within Cell Ranger.
Barcode and UMI Processing: Cellular barcodes and unique molecular identifiers (UMIs) were extracted to generate count matrices.
Alignment: Reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner integrated within Cell Ranger.
Barcode and UMI Processing: Cellular barcodes and unique molecular identifiers (UMIs) were extracted to generate count matrices.
Gene Expression Quantification: UMI counts were aggregated to quantify gene expression levels for each cell.
Quality Control: Cells with mitochondrial gene content exceeding 50% or ribosomal gene content exceeding 40% were excluded. Cells expressing fewer than 200 genes and genes expressed in fewer than three cells were also filtered out.
Ambient RNA Correction: SoupX v1.6.0 was used to correct for ambient RNA contamination.
Doublet Detection: Potential doublets were identified and removed using scDblFinder v3.19.
Assembly: The genome build used for read alignment was the GRCm39 (Genome Reference Consortium Mouse Build 39) mouse genome assembly.
Supplementary files format and content: The processed data files are provided in standard formats compatible with common single-cell analysis tools

source_name: Kidney

extract_protocol:
Kidney tissues from control, AKI, and CKD phase mice were harvested and immediately processed to obtain single-cell suspensions. The kidneys were minced into small fragments and enzymatically digested using a cocktail of enzymes, including collagenase type IV and DNase I, at 37°C with gentle agitation for 30 minutes. The resulting cell suspension was filtered through a 40 μm cell strainer to remove debris and obtain a uniform single-cell suspension. Cells were then washed with PBS containing 0.04% BSA and counted using a hemocytometer to ensure viability above 85% before proceeding to library preparation.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics) according to the manufacturer's protocol.
The library strategy employed was single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform.

value: Kidney

value: Wild-Type


title: K2_MRTX1133_cell_hash

status: Public on Mar 18 2026

description:
Library name: JR-2281_Krasi_caer_epi_HTO
10x_v3

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.

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. For every sample that would be subjected to cell hashing, we used DNAse-free buffers following digestion. Samples were resuspended in 1 mL ACK-lysis buffer and incubated for 5 min at room temperature to deplete red blood cells, and washed the ACK lysis buffer with 20 mL HBSS. We blocked samples with TruStain Fc block Plus (Biolegend, 156603; clone S17011E, 1:100) for 7 min at 4°C, followed by incubation with a sample-specific TotalSeq cell hashing antibody (Biolegend, 155832, 155833, 155835, 155837, 155839, 155841; clones M1/42; 30-F11). We incubated cell hashing antibodies at a 1:50 dilution for 30 min. We washed samples 3 times with DNAse-free FACS buffer + STI, followed by filtering through a 40-μm strainer and FACS-based isolation of mKate2+/GFP+ cells (KrasG12D+ pancreatic epithelial cells expressing shp53 or shCtrl). To prepare cells for scRNA-seq, we pooled samples from the same experimental conditions into the same tube, and resuspended cells at a 1000 cells μL-1.
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’ v3). Each sample loaded onto the cartridge contained approximately 15,000 cells 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 4 weeks of age. At 5 weeks of age, mice were subjected to eight-hourly intraperitoneal injections of 80 μg kg-1 of caerulein (Bachem) for two consecutive days (16 injections total). In addition,  mice were treated with MRTX1133 (30mg/kg) or vehicle concurrently with caerulein treatment, euthanizing mice within 4 h of the last MRTX1133 or vehicle dose (fifth dose, 2 days after the first dose).

value: Epithelial

value: KPLOH (p53 proficient)


title: K2_vehicle_cell_hash

description:
Library name: JR-2281_Ctrl_caer_epi_HTO
10x_v3

value: Pancreas

value: vehicle


title: K2_MRTX1133

description:
Library name: JR-2281_Krasi_caer_epi
10x_v3


title: K2_vehicle

description:
Library name: JR-2281_Ctrl_caer_epi
10x_v3


title: p489c_shRen_caer_multiome_2_ATAC

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_2_ATAC
10x_RNA_ATAC_multiome

data_processing:
All multiome datasets were processed using cellranger-arc-2.0.0 with default parameters, using the mm10 mouse annotation as reference.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing are deposited in the Matrix Market format for sparse matrix representation.
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 mouse models 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.

growth_protocol: Mice were generated by 8-cell injection of KCshRen (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shRen.713 or TRE-GFP-shp53.1224) ESCs, or through breeding KPfC (Ptf1a-Cre; LSL-KrasG12D;  Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt)

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. For every sample that would be subjected to cell hashing, we used DNAse-free buffers following digestion. Samples were resuspended in 1 mL ACK-lysis buffer and incubated for 5 min at room temperature to deplete red blood cells, and washed the ACK lysis buffer with 20 mL HBSS. Samples  were washed 3 times with DNAse-free FACS buffer + STI, followed by filtering through a 40-μm strainer and FACS-based isolation of mKate2+/GFP+ or mKate2+ cells (KrasG12D+ pancreatic epithelial cells). 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).
ATAC and gene expression libraries were prepared according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, following 10x Genomics guidelines for ATAC, gene expression, and sequencing preparation. Cells were pelleted (300 g, 5 min, 4°C), permeabilized in chilled lysis buffer, incubated on ice for 5 min, and washed in chilled buffer containing RNase inhibitor (Protector, Roche). After centrifugation (500 g, 5 min, 4°C), nuclei were resuspended in Nuclei Buffer (10x Genomics), counted, and adjusted to 3,000 nuclei/µL.  For each reaction, up to 15,400 nuclei were diluted in isotonic Tagmentation Buffer with RNase inhibitor and mixed with ATAC Buffer B and ATAC Enzyme B (10x Genomics) for transposition (37°C, 60 min). Samples were loaded onto a Chromium Next GEM Chip J with barcoding reagents, gel beads, and partitioning oil (10x Genomics) and processed on the Chromium Controller to generate GEMs. Reverse transcription and barcoding proceeded at 37°C for 45 min and 25°C for 30 min. Later, GEMs were broken, and the aqueous phase was purified using Dynabeads MyOne SILANE (10x Genomics) and SPRIselect magnetic bead cleanups (Beckman Coulter). Barcoded ATAC and cDNA fragments were pre-amplified and purified with SPRIselect.  ATAC libraries were constructed using sample indexing PCR with 10x Genomics reagents, followed by dual-sided SPRI size selection. cDNA was amplified, cleaned, fragmented, end-repaired, A-tailed, and ligated using 10x Genomics reagents, with SPRI-based purifications throughout. Final gene expression libraries were indexed using 10x Genomics dual-index reagents and purified with SPRIselect. Sequencing was performed according to 10x Genomics recommendations on an Illumina NovaSeq 6000.

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

value: KCshRen

value: Dox

tag: batch


title: DACE657_mKate2_multiome_ATAC

description:
Library name: DACE657_mKate2_multiome_ATAC
10x_RNA_ATAC_multiome

value: KPfC (p53 flox/wt)


title: DACE657_mKate2

description:
Library name: DACE657_mKate2_multiome
10x_RNA_ATAC_multiome


title: p489c_shRen_caer_multiome_2

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_2
10x_RNA_ATAC_multiome


title: p489c_shRen_caer_multiome_1_ATAC

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_1_ATAC
10x_RNA_ATAC_multiome


title: p489c_shRen_caer_multiome_1

description:
Library name: JR-1497_p489c_shRen_caer_48h_multiome_1
10x_RNA_ATAC_multiome


title: K3_shCtrl_batch3_cellHash

description:
Library name: p489c_shRen_p53exp_caer_3weeks_cellHash
10x_v3

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 mouse models (GFP, rtTA3-IRES-mKate2, shRen, shp53) 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.

growth_protocol: Mice were generated by 8-cell injection of KCshRen or KCshp53 (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shRen.713 or TRE-GFP-shp53.1224) ESCs.

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.


title: K3_shp53_batch3_cellHash

description:
Library name: p489c_shp53_caer_3weeks_cellHash
10x_v3


title: FFPE NSCLC patient (L5) sample profiled with the Xenium Prime 5K gene panel

value: FFPE


title: K3_shCtrl_batch5

description:
Library name: shRen_caer_3weeks_repeat
10x_v3


title: K3_shp53_batch5

description:
Library name: shp53_caer_3weeks_repeat
10x_v3


title: K3_shCtrl_batch3

description:
Library name: p489c_shRen_p53exp_caer_3weeks
10x_v3


title: Ribo_Trp

description: Library name: Sample_18

value: WT


title: K3_shp53_batch3

description:
Library name: p489c_shp53_caer_3weeks
10x_v3


title: K3_FLEX

description:
Library name: K3_shp53_ctrl_FLEX
10x GEMX FLEX

data_processing:
Raw BCL files were processed with Cell Ranger (9.0.0), and the resulting FASTQ files were quantified using a custom probe set reference for the mouse genome (GRCm39) within the Cell Ranger pipeline.
Assembly: GRCm39
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with Cell Ranger (9.0.0) are deposited in the Matrix Market format for sparse matrix representation.
Supplementary files format and content: FLEX_cells_per_tag.json contains results from cell hashing assignment to individual biological repllicates.

growth_protocol: Mice were generated by 8-cell injection of KCshp53 (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shp53.1224) ESCs.

extract_protocol:
Collected tissue was fixed in 10% neutral buffered formalin (Richard-Allan Scientific), and embedded in paraffin. Single cells were extracted from FFPE blocks. GEM encapsulation was performed following the 10x Genomics Flex GEM-X (PN-1000782) protocol, using their guidelines for cell and reagent volumes per well based on the desired cell recovery. After loading the Chip FX and running it on the Chromium X, GEMs were recovered and processed according to the manufacturer’s instructions.
Following GEM processing, the resulting product was pre-amplified and indexed to generate the sequencing library. All libraries were sequenced on an Illumina NovaSeq X+ (R1 – 28 cycles, i5 – 10 cycles, i7 – 10 cycles, R2 – 90 cycles) using standard dual indexing and demultiplexing.

treatment_protocol: shp53 was induced by treatment of two mice mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age. Another set of two mice were left in normal chow as negative controls.

value: on or off dox


title: Ribo_Leu

description: Library name: Sample_14

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.
Assembly: GRCh39.p13
Supplementary files format and content: tab-delimited text files including normalized read counts per codon on individual mRNAs for Ribo-seq.
Supplementary files format and content: comma-delimited text files including read counts mapped to each position on reporter mRNA Ribo-seq.
Library strategy: Ribo-Seq


title: Ribo_Val

description: Library name: Sample_9


title: Ribo_Met

description: Library name: Sample_10


title: R1, responder 1

description:
Library name: Sample 3_R1
10X Genomics

value: sigmoid colon

value: responder


title: Tumor p53 deficient 8

description:
Library name: 9268_PHLH_PDAC_SP
10x_v2

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.

value: mKate2+/GFP- (p53 deficient)


title: R2, responder 2

description:
Library name: Sample 5_R2
10X Genomics


title: Tumor p53 deficient 6

description:
Library name: PDAC-SP3
10x_v2


title: Tumor p53 deficient 7

description:
Library name: 53_LHRH_PDACreg_KATE
10x_v2


title: Tumor p53 proficient 8

description:
Library name: 9268_PHLH_PDAC_DP
10x_v2

value: mKate2+/GFP+ (p53 proficient)


title: Tumor p53 proficient 12

description:
Library name: 53_LHRH_PanINreg_GFPh
10x_v2


title: Tumor p53 proficient 7

description:
Library name: 53_LHRH_PDACreg_GFPh
10x_v2


title: Tumor p53 proficient 6

description:
Library name: PDAC-DP
10x_v2


title: JHH387CAF

description:
Library name: JHH387CAF
CAF Patient 387, Monoculture

value: pancreas

value: Patient-derived organoid

value: CAF

value: monoculture


title: Pre-tumor p53 deficient 5

description:
Library name: pre_sp_2
10x_v3

value: Epithelial


title: Pre-tumor p53 deficient 4

description:
Library name: Preclinical_SP_batch1
10x_v3

value: Pancreas


title: Pre-tumor p53 deficient 2

description:
Library name: 254_RH_PanINPM_Kate_CD45_1_4
10x_v2


title: mix_JHH390Org

description:
Library name: mix_JHH390Org
Orgnanoid Patient 390, Monoculture

value: epithelium


title: Pre-tumor p53 deficient 1

description:
Library name: 254_2RH_PanINPM_Kate_CD45_1_31
10x_v2


title: Pre-tumor p53 proficient 4

description:
Library name: Preclinical_DP_batch1
10x_v3


title: Pre-tumor p53 proficient 5

description:
Library name: pre_dp_2
10x_v3


title: Pre-tumor p53 proficient 2

description:
Library name: 254_RH_PanINPM_GFPh
10x_v2


title: Pre-tumor p53 proficient 0

description:
Library name: 53_NH_PanINPM_GFPh
10x_v2


title: Pre-tumor p53 proficient 1

description:
Library name: 254_2RH_PanINPM_GFPh
10x_v2


title: Muscle,Intermittent_fasting,Male,rep7

city: Melbourne

first: Yibo

last: Fan

state: VIC

address: Science Dr, Bundoora VIC 3083

country: Australia

institute: La Trobe University

description: Library name: MIF15

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: Muscle,Intermittent_fasting,Male,rep8

description: Library name: MIF16


title: Muscle,Intermittent_fasting,Male,rep5

description: Library name: MIF13


title: Muscle,Intermittent_fasting,Male,rep3

description: Library name: MIF11


title: Muscle,Intermittent_fasting,Male,rep4

description: Library name: MIF12


title: Muscle,Intermittent_fasting,Male,rep1

description: Library name: MIF9


title: Muscle,Ad_libtum,Male,rep7

description: Library name: MAL7

value: AL


title: Muscle,Ad_libtum,Male,rep8

description: Library name: MAL8


title: Muscle,Ad_libtum,Male,rep6

description: Library name: MAL6


title: Muscle,Ad_libtum,Male,rep5

description: Library name: MAL5


title: Muscle,Ad_libtum,Male,rep4

description: Library name: MAL4


title: Muscle,Ad_libtum,Male,rep2

description: Library name: MAL2


title: Muscle,Ad_libtum,Male,rep3

description: Library name: MAL3


title: Muscle,Ad_libtum,Male,rep1

description: Library name: MAL1


title: Liver,Intermittent_fasting,Male,rep8

description: Library name: LIF16

source_name: Liver

value: Liver


title: Liver,Intermittent_fasting,Male,rep7

description: Library name: LIF15


title: Liver,Intermittent_fasting,Male,rep6

description: Library name: LIF14


title: Liver,Intermittent_fasting,Male,rep5

description: Library name: LIF13


title: Liver,Intermittent_fasting,Male,rep3

description: Library name: LIF11


title: Liver,Intermittent_fasting,Male,rep2

description: Library name: LIF10


title: Liver,Ad_libtum,Male,rep8

description: Library name: LAL8


title: Liver,Ad_libtum,Male,rep6

description: Library name: LAL6


title: Liver,Ad_libtum,Male,rep7

description: Library name: LAL7


title: Liver,Ad_libtum,Male,rep5

description: Library name: LAL5


title: Liver,Ad_libtum,Male,rep4

description: Library name: LAL4


title: Liver,Ad_libtum,Male,rep2

description: Library name: LAL2


title: Liver,Ad_libtum,Male,rep1

description: Library name: LAL1


title: Cortex,Intermittent_fasting,Male,rep8

description: Library name: CIF16

source_name: Cortex

value: Cortex


title: Cortex,Intermittent_fasting,Male,rep7

description: Library name: CIF15


title: 0042724_Region_3

description:
Spatial Transcriptomics
Xenium Analyzer
FFPE spatial transcriptomic

data_processing:
Data were processed using the Xenium analysis pipeline (version xenium-1.7.1.0), which included signal segmentation, transcript decoding, quality score assignment, and spatial mapping of transcripts to x/y coordinates.
mm10
Gene expression matrix (HDF5), Transcript table (CSV), Metadata files (CSV)

extract_protocol:
No RNA extraction was performed. FFPE tissue sections from human pancreas were cut at 5 µm thickness and mounted onto Xenium slides. After deparaffinization and decrosslinking, we performed probe hybridization, ligation, and amplification according to the 10x Genomics Xenium FFPE Tissue Preparation Guide
No sequencing library was constructed. A custom Xenium probe panel targeting 480 genes was hybridized to RNA in situ, followed by fluorescent labeling, imaging, and decoding using the Xenium Analyzer (v1.7.6.0).

tag: condition


title: Cortex,Intermittent_fasting,Male,rep6

description: Library name: CIF14


title: 0042724_Region_2


title: Cortex,Intermittent_fasting,Male,rep5

description: Library name: CIF13


title: 0042724_Region_1


title: Cortex,Intermittent_fasting,Male,rep4

description: Library name: CIF12


title: 0042536_Region_2


title: Cortex,Intermittent_fasting,Male,rep3

description: Library name: CIF11


title: 0042536_Region_1


title: Cortex,Intermittent_fasting,Male,rep2

description: Library name: CIF10


title: 0042569_Region_3


title: Cortex,Intermittent_fasting,Male,rep1

description: Library name: CIF9


title: 0028094_Region_2


title: Liver,Intermittent_fasting,Male,rep4

description: Library name: LIF12


title: Cortex,Ad_libtum,Male,rep8

description: Library name: CAL8


title: 0028094_Region_1


title: Liver,Intermittent_fasting,Male,rep1

description: Library name: LIF9


title: Cortex,Ad_libtum,Male,rep7

description: Library name: CAL7


title: 0011181_Region_2


title: Cortex,Ad_libtum,Male,rep6

description: Library name: CAL6


title: Cortex,Ad_libtum,Male,rep5

description: Library name: CAL5


title: 0011181_Region_1


title: 0011178_Region_2


title: Liver,Ad_libtum,Male,rep3

description: Library name: LAL3


title: Cortex,Ad_libtum,Male,rep4

description: Library name: CAL4


title: 0011178_Region_1


title: Cortex,Ad_libtum,Male,rep3

description: Library name: CAL3


title: Cortex,Ad_libtum,Male,rep2

description: Library name: CAL2


title: 0027846_Region_2


title: 0027846_Region_3


title: K3_shCtrl_batch5_cellHash

description:
Library name: shRen_caer_3weeks_repeat_cellHash
10x_v3

value: KCshRen

tag: treatment

value: Dox


title: K3_shp53_batch5_cellHash

description:
Library name: shp53_caer_3weeks_repeat_cellHash
10x_v3


title: Cortex,Ad_libtum,Male,rep1

description: Library name: CAL1


title: 0027845_Region_3


title: 0027846_Region_1


title: 0027845_Region_2


title: 0027845_Region_1


title: 0015410_Region_4


title: 0015410_Region_1


title: 0015410_Region_2


title: 0015410_Region_3


title: 0015409_Region_5


title: 0015409_Region_4


title: 0015409_Region_3


title: 0015409_Region_2


title: 0015409_Region_1


title: 0004329_Region_3


title: 0004329_Region_2


title: 0004329_Region_1


title: 0004279_Region_3


title: 0004279_Region_2


title: 0004279_Region_1


title: Sox9iresGFP XX pups genomic landscape

status: Public on Mar 16 2026

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

description:
Library name: YFPpos_ATAC_XX
10X Genomics

library_source: genomic single cell

data_processing:
All subsequent analyses were performed in R v.4.4.1 using the Seurat (v5) package.
Assembly: mm10
Supplementary files format and content: tab-delimited text containing output files from CellRanger ARC version 2.0.0

source_name: Pituitary

extract_protocol:
Ilumina 10X genomics nuclei extraction protocol
Ilumina 10X genomics expression and atac protocol

value: Pituitary

value: Stem cell

tag: library type

value: ATAC


title: Sox9iresGFP XX pups transcriptome

description:
Library name: YFPpos_RNA_XX
10X Genomics

value: RNA


title: Sox9iresGFP XY pups transcriptome

description:
Library name: YFPpos_RNA_XY
10X Genomics

value: female


title: Sox9iresGFP XY pups genomic landscape

description:
Library name: YFPpos_ATAC_XY
10X Genomics


title: sh3_PLUS-KD_3

status: Public on Feb 27 2026

city: Manchester

first: Martin

middle: James

last: Baker

state: England

address: 555 Wilmslow Rd

department: Division of Cancer Sciences

institute: University of Manchester

description: Library name: AM16_30_JS14_S30

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]

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

value: KD


title: sh3_MINUS-WT_3

description: Library name: AM16_28_JS7_S28

value: WT


title: sh2_PLUS-KD_3

description: Library name: AM16_25_JS22_S25


title: R_PLUS-CTRL_3

description: Library name: AM16_21_JS1_S21

value: CTRL


title: sh3_PLUS-KD_2

description: Library name: AM16_18_JS24_S18


title: sh2_MINUS-WT_3

description: Library name: AM16_23_JS16_S23


title: R_MINUS-CTRL_3

description: Library name: AM16_20_JS18_S20


title: sh3_MINUS-WT_2

description: Library name: AM16_16_JS23_S16


title: sh2_PLUS-KD_2

description: Library name: AM16_14_JS5_S14


title: sh2_MINUS-WT_2

description: Library name: AM16_13_JS17_S13


title: R_PLUS-CTRL_2

description: Library name: AM16_12_JS9_S12


title: R_MINUS-CTRL_2

description: Library name: AM16_11_JS8_S11


title: sh3_PLUS-KD_1

description: Library name: AM16_09_JS21_S9