title: E15.5 embryonic BAT, replicate 2

description: Library name: E15.5_2


title: Donor 3, Day 4, NKAR

status: Public on Dec 20 2025

type: SRA

city: Providence

first: Jacob

middle: Andrew

last: Myers

state: RI

address: 171 Meeting St.

country: USA

institute: Brown University

description: Library name: Day_4_D3_X_S166

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the human reference genome (GRCh38 p13) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed between WT and conditional KO and skeletal site were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: GRCh38
Supplementary files format and content: pbNK_NKAR_rawcounts.txt and KLF2_Nkar_rawcounts.txt

molecule: polyA RNA

organism: Homo sapiens

source_name: Natural Killer cells

growth_protocol: See SERIES summary or associated publication

extract_protocol:
Qiagen Rneasy Plus Universal
TruSeq Stranded mRNA

tag: tissue

value: Natural Killer cells

tag: condition

value: NKAR

tag: time point

value: Day 4


title: Donor 1, Day 4, NKAR

description: Library name: Day_4_D1_X_S165

treatment_protocol: See SERIES summary or associated publication


title: Donor 14, Day 4, Isotype control

description: Library name: Day_4_D14_iso_S164

value: Isotype control


title: X184_RY_T_RNA

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

description: Library name: X184_RY_T_RNA

data_processing:
Workflow: Nextflow: 22.04.0,  nf-core/rnaseq: 3.8.1
Read trimming: trimgalore: 0.6.7
Transcript expression quantification: salmon: 1.5.2
Summarize expression to genes: bioconductor-tximeta: 1.8.0,  r-base: 4.0.3
Assembly: GRCh38
Supplementary files format and content: tab separated value (TSV) files with gene read counts and TPM from Salmon

molecule: total RNA

source_name: CRC sample

extract_protocol:
RNA was extracted from the intervening sections using the RNAeasy kit (Qiagen, Netherlands) and itsÕ quality and quantity controlled using a tape station (Agilent, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat reagents (Illumina, San Diego, USA). Following quality assessment on the Fragment Analyzer (Agilent, Santa Clara, USA), libraries were 100nt paired-end sequenced to a target of 50 million clusters per library on the Illumina NovaSeq 6000 (Illumina, San Diego, USA).

treatment_protocol: Cryosections of the fresh frozen blocks were cut and the first and last sections stained using standard techniques and the tumor content verified by a trained pathologist. Only samples with a tumor cell content of more than 30% were used for further analysis

value: Colon/Rectum

tag: disease state

value: colorectal cancer


title: Donor 10, Day 4, NKAR

description: Library name: Day_4_D10_X_S168


title: E15.5 embryonic BAT, replicate 1

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

description: Library name: E15.5_1

data_processing:
Reads were pseudoaligned to the mouse genome (GRCm39), and transcript abundances were quantified using kallisto v0.46.2 with default parameters.
RNA abundances were converted to counts using tximport with the “lengthScaledTPM” option.
Assembly: GRCm39
Supplementary files format and content: CSV file containing estimated counts for each gene, as converted from kallisto-computed abundances using tximport with the "lengthScaledTPM" option.

organism: Mus musculus

source_name: Brown adipose tissue

extract_protocol:
Tissues were lysed in TRIzol (Invitrogen #15596018) using a TissueLyser II (QIAGEN) for 4 minutes at 24 Hz in pre-chilled tube adapters. Total RNA of BAT from E15.5-E18.5 embryos and P0.5 neonates was isolated using TRIzol and purified using PureLink RNA Mini columns (Invitrogen #12183025).
Library preparation with poly(A) selection and Illumina sequencing were completed by Azenta/GENEWIZ.

value: Brown adipose tissue

tag: age

tag: genotype

value: wild-type

tag: batch


title: Donor 14, Day 4, NKAR

description: Library name: Day_4_D14_X_S171


title: Liver, Untreated Control [snRNA-Seq]

city: New York

first: Scott

last: Friedman

state: NY

address: 1425 Madison Ave

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Untreated Control
10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced files from each independent sample were processed through 10X Genomics Space Ranger software to generate a count matrix.
Assembly: Mouse mm10
Supplementary files format and content: Tab and Comma-Separated Value Files

molecule: nuclear RNA

source_name: liver

extract_protocol:
40 to 60 mg of total liver tissue (pooled from 3 mice per condition) were chopped on ice in 1 mL of 0.03% TST buffer [146 mM NaCl, 10 mM Tris-HCl (pH 7.5), 1 mM CaCl2, and 21 mM MgCl2 with freshly added 0.03% Tween 20, 0.01% BSA, and RiboLock RNase Inhibitor (0.4 U/mL; Thermo Fisher Scientific, FEREO0382)] with Tungsten Noyes Spring Scissors (FST, 15514-12) following our previously published procedures. The resulting nuclei suspension was then filtered through 40μm cell strainers (Thermo Fisher Scientific, 352340) into a fresh 50-mL conical tube on ice. One more milliliter of 0.03% TST was used to rinse the cell strainer, and 3 mL of ST buffer were added to the nuclei suspension, followed by briefly mixing by gentle flicking. The nuclei suspensions were spun at 500xg for 5 min at 4°C in a swing-bucket centrifuge. The final nuclei pellet was suspended in 200μL of 0.4% BSA in PBS by pipetting 30 times with a regular p1000 tip. The resulting pellet was resuspended by pipetting 30 times in 200µL of 0.4% BSA/PBS, and nuclei were visually inspected using a 1:1 trypan blue solution under a light microscope. Samples were transferred to the Mount Sinai Genomics CoRE for counting, quality control and sequencing.
Nuclei preparations were processed by the Chromium 3′ Gene Expression V2 Kit according to the manufacturer’s guidelines.

value: liver


title: Donor 4, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D4_iso_g_S174

value: Day 10


title: Donor 4, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D4_iso_c_S181

value: Isotype control, continuous IL-15


title: Donor 4, Day 10, NKAR, continuous IL-15

description: Library name: Day_10_D4_X_c_S193

value: NKAR, continuous IL-15


title: Liver, 6wk FAT-MASH Regression [snRNA-Seq]

description:
Library name: 6wk FAT
10X Genomics


title: Donor 3, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D3_iso_g_S173


title: Liver, 2wk FAT-MASH Regression [snRNA-Seq]

description:
Library name: 2wk FAT
10X Genomics


title: Donor 11, Day 4, Isotype control

description: Library name: Day_4_D11_iso_S162


title: Liver, 6wk CCl4 Regression - Spatial Transcriptomics

description:
Library name: 6wk CCl4
Fresh Frozen Spatial Transcriptomic Sequencing

data_processing:
To generate a count matrix, the sequenced files from each sample were processed through 10X Genomics Space Ranger software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-Separated Value Files
Library strategy: Spatial Transcriptomics

extract_protocol:
Cryosections were prepared from liver samples that were harvested and stored directly on OCT. Two sections were placed on each slide and samples were sent to the Mount Sinai Genomics CoRE for library preparation and sequencing.
Standard 10X Visium protocol for fresh frozen tissue was used.


title: Donor 13, Day 4, NKAR

description: Library name: Day_4_D13_X_S170


title: X180_ZE_T_RNA

description: Library name: X180_ZE_T_RNA


title: Donor 10, Day 4, Isotype control

description: Library name: Day_4_D10_iso_S161


title: Donor 3, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D3_iso_c_S180


title: X174_JO_T_RNA

description: Library name: X174_JO_T_RNA


title: Liver, Peak CCl4 Fibrosis - Spatial Transcriptomics

description:
Library name: Peak CCl4
Fresh Frozen Spatial Transcriptomic Sequencing


title: X174_JA_T_RNA

description: Library name: X174_JA_T_RNA


title: X172_AU_T_RNA

description: Library name: X172_AU_T_RNA


title: Donor 1, Day 10, NKAR, discontinuous ("gapped") IL-15

description: Library name: Day_10_D1_X_g_S186

value: NKAR, discontinuous ("gapped") IL-15


title: X178_SC_T_RNA

description: Library name: X178_SC_T_RNA


title: Donor 14, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D14_iso_g_S178


title: X171_VE_T_RNA

description: Library name: X171_VE_T_RNA


title: X177_BR_T_RNA

description: Library name: X177_BR_T_RNA


title: X184_HU_T_RNA

description: Library name: X184_HU_T_RNA


title: Donor 14, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D14_iso_c_S185


title: Donor 14, Day 10, NKAR, discontinuous ("gapped") IL-15

description: Library name: Day_10_D14_X_g_S190


title: Liver, Peak CCl4 Fibrosis [snRNA-Seq]

description:
Library name: Peak CCl4
10X Genomics


title: Liver, Peak FAT-MASH Regression [snRNA-Seq]

description:
Library name: Peak FAT
10X Genomics


title: Donor 14, Day 10, NKAR, continuous IL-15

description: Library name: Day_10_D14_X_c_S195


title: Donor 13, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D13_iso_c_S184


title: Donor 1, Day 10, NKAR, continuous IL-15

description: Library name: Day_10_D1_X_c_S191


title: Liver, 2wk CCl4 Regression [snRNA-Seq]

description:
Library name: 2wk CCl4
10X Genomics


title: Liver, 6wk CCl4 Regression [snRNA-Seq]

description:
Library name: 6wk CCl4
10X Genomics


title: Donor 1, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D1_iso_g_S172


title: Liver, 2wk FAT-MASH Regression

description:
Library name: 2wk FAT
10X Genomics

data_processing:
10X Genomics Cell Ranger software v6 was used to generate a count matrix from the sequenced files from each sample.
Assembly: Mouse mm10
Supplementary files format and content: Tab and Comma-Separated Value Files

extract_protocol:
40mg of liver tissue each from 5 mice were pooled and stored in RPMI (Corning, 15-040-CM) + 10% fetal bovine serum (FBS; Invitrogen, 10082147) on ice overnight. The following morning, livers were injected with digestion buffer consisting of RPMI with 10% FBS, 0.25mL Collagenase IV (Sigma, C5138), and 0.1mg/mL DNase I (Sigma, D5025). For digestion, samples were initially minced and incubated at 37°C for 1 hour under slow agitation (80rpm), and then mechanically digested using 16G needles, before being filtered through 100uM and 70uM strainers. Thereafter, for gradient separation, samples were centrifuged (500xg, 4°C, 10 min), resuspended in 25% Percoll, and layered atop 70% Percoll (Cytiva, 17-0891-02), and centrifuged again (500xg, 20°C, 25 min, no acceleration/brake). Non-parenchymal cells (NPCs) were collected at the meeting point of the Percoll layers. NPCs were rinsed with 1XHBSS (no ions; Corning, 21-022-CV) and subjected to RBC lysis (Fisher, A1049201). A fraction of cells from this suspension was transferred to the Mount Sinai Genomics CoRE for counting, quality control and sequencing.
Nuclei preparations were processed by the Chromium 3′ Single Cell 3’ Reagent Kit according to the manufacturer’s guidelines.


title: X155_RU_RNA_T2

description: Library name: X155_RU_RNA_T2


title: Donor 11, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D11_iso_g_S176


title: Donor 11, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D11_iso_c_S183


title: Donor 3, Day 10, NKAR, continuous IL-15

description: Library name: Day_10_D3_X_c_S192


title: Donor 13, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D13_iso_g_S177


title: Liver, 6wk FAT-MASH Regression

description:
Library name: 6wk FAT
10X Genomics


title: X168_ST_T_RNA

description: Library name: X168_ST_T_RNA


title: X155_RU_T_RNA

description: Library name: X155_RU_T_RNA


title: Donor 1, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D1_iso_c_S179


title: Donor 13, Day 10, NKAR, discontinuous ("gapped") IL-15

description: Library name: Day_10_D13_X_g_S189


title: Donor 13, Day 10, NKAR, continuous IL-15

description: Library name: Day_10_D13_X_c_S194


title: Liver, 2wk CCl4 Regression

description:
Library name: 2wk CCl4
10X Genomics


title: Liver, Peak FAT-MASH Regression

description:
Library name: Peak FAT
10X Genomics


title: X152_PA_T_RNA

description: Library name: X152_PA_T_RNA


title: A_Cpa_153, Aging

city: Halle (Saale)

first: Ferdinand

last: Krannich

address: Ernst Grube Street 40

department: Department of Internal Medicine I

country: Germany

institute: Martin Luther University Halle-Wittenberg, University Medicine Halle (Saale)

description:
Library name: A_Cpa_153
aging_cohort_FPKM.csv

data_processing:
Adapter sequences as well as low quality read ends were clipped off using Cutadapt. The processed sequencing reads were aligned to the mouse reference genome (UCSC mm10) using HiSat2. Samtools was used to extract primary alignments and to index the resulting BAM files. FeatureCounts was used for summarizing gene-mapped reads, using ENSEMBL GRCm 38.100 as annotation basis.
Assembly: mm10
Supplementary files format and content: FPKM values for each sample at early ages (.csv) and in the aging cohort (.csv).

source_name: pancreas

extract_protocol:
Total RNA was isolated from pancreatic tissue (proximal to duodenum) using a combination of QIAzol lysis reagent (Qiagen, ID.79306) and chloroform-based (Serva, 39553.01) phase separation, followed by purification with the RNeasy Mini Kit (Qiagen, ID.74106), according to the manufacturer’s protocol. Approximately 2–3 mm³ of snap-frozen tissue was transferred into 200 µL of ice-cold QIAzol containing 1% β-mercaptoethanol (final concentration; Sigma Aldrich, M6250). Samples were immediately frozen in liquid nitrogen and stored at –80°C until further processing. For homogenization, a sterile, RNase-free stainless steel bead was added, and 1.3 mL of additional ice-cold QIAzol was added while maintaining the samples on dry ice to prevent thawing. Tissue homogenization was performed using a pre-cooled Qiagen TissueLyser II at 30 Hz for 20 minutes at 4°C. Lysates were centrifuged at 13,000 × g for 5 minutes at 4°C, and the supernatant was carefully transferred to a fresh tube, avoiding residual tissue fragments. Phase separation was performed by adding 300 µL of ice-cold chloroform, followed by vigorous vortexing for 10 seconds. After centrifugation at 13,000 × g for 5 minutes at 4°C, the upper aqueous phase (∼600 µL) was carefully collected, avoiding contamination from the interphase, and mixed with an equal volume of isopropanol (Fisher Scientific, BP2618-500). RNA purification was completed using the RNeasy Mini Kit, including on-column DNase I digestion (Macherey-Nagel, 740963) to eliminate residual genomic DNA.
Library construction was performed by Novogene (Cambridge, UK).

value: pancreas

value: 51 weeks


title: Liver, 6wk CCl4 Regression

description:
Library name: 6wk CCl4
10X Genomics


title: X169_RO_T_RNA

description: Library name: X169_RO_T_RNA


title: Donor 11, Day 10, NKAR, discontinuous ("gapped") IL-15

description: Library name: Day_10_D11_X_g_S188


title: X155_RU_RNA_T1

description: Library name: X155_RU_RNA_T1


title: Donor 10, Day 10, Isotype control, discontinuous ("gapped") IL-15

description: Library name: Day_10_D10_iso_g_S175


title: Donor 10, Day 10, NKAR, discontinuous ("gapped") IL-15

description: Library name: Day_10_D10_X_g_S187


title: X155_LI_T_RNA

description: Library name: X155_LI_T_RNA


title: Donor 10, Day 10, Isotype control, continuous IL-15

description: Library name: Day_10_D10_iso_c_S182


title: X145_TR_T_RNA

description: Library name: X145_TR_T_RNA


title: A_Cpa_177, Aging

description:
Library name: A_Cpa_177
aging_cohort_FPKM.csv


title: X144_BE_T_RNA_2

description: Library name: X144_BE_T_RNA_2


title: A_Cpa_3, Aging

description:
Library name: A_Cpa_3
aging_cohort_FPKM.csv

value: 52 weeks


title: Liver, Peak CCl4 Fibrosis

description:
Library name: Peak CCl4
10X Genomics


title: X153_PI_T_RNA

description: Library name: X153_PI_T_RNA


title: A_Cpa_858, Aging

description:
Library name: A_Cpa_858
aging_cohort_FPKM.csv


title: X144_BE_T_RNA_1

description: Library name: X144_BE_T_RNA_1


title: X151_VA_T_RNA

description: Library name: X151_VA_T_RNA


title: X144_BE_T_RNA

description: Library name: X144_BE_T_RNA


title: A_Cpa_913, Aging

description:
Library name: A_Cpa_913
aging_cohort_FPKM.csv

value: 39 weeks


title: A_Cpa_979, Aging

description:
Library name: A_Cpa_979
aging_cohort_FPKM.csv


title: Patient 4 T-VD3DC

type: RNA

city: Newcastle upon Tyne

first: Catharien

middle: MU

last: Hilkens

state: Tyne & Wear

address: Framlington Place

department: Translational and Clinical Research

country: United Kingdom

institute: Newcastle University

description: 100ng of RNA was analysed by Nanostring nCounter, using the immune exhaustion panel.

hyb_protocol: The NanoString nCounter system hybridizes RNA targets using a direct, enzyme-free, solution-based reaction with two target-specific DNA probes: a reporter probe and a capture probe. Hybridisation protocol was carried out according to the nCounter protocol: https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

scan_protocol: nCounter data are scanned by an automated fluorescence microscope within the nCounter Digital Analyzer instrument, which takes images of immobilized, fluorescently-labeled molecular barcodes.

data_processing: The data was normalised in two steps using positive spike-in controls and geNorm-selected housekeeping genes. Removal of any outlier samples was performed based on different QC flags as recommended in NanoString® Gene Expression Data Analysis Guidelines.

source_name: CD4+ T cells

label_protocol: Not applicable

growth_protocol: Cryopreserved PBMC from early arthritis patients were thawed and labelled with CellTrace™ as above and co-cultured with freshly generated allogeneic healthy donor monocyte-derived DC at a 1:10 DC:PBMC ratio (1x105 DC and 1x106 PBMC/well) in a 24-well plate in RF10 at 37°C, 5% CO2. On day 6, the cells were harvested and stained for fluorescence activated cell sorting (FACS) using viability dye Zombie NIR™ and the following mouse anti-human antibodies: CD3-BUV395 (UCHT1), CD4-PE-Cy7 (RPA-T4), CD11c-PE/Dazzle™ 594 (BU15) and CD14-FITC (M5E2) in staining buffer supplemented with human IgG (Hizentra®). Cells were strained through a 35μm cell strainer and acquired at 4°C on the BD FACSAria™ II using a 70μm nozzle. Events were gated sequentially as follows: cells, single cells, live cells (Zombie NIR-), proliferated cells (CellTrace-), CD11c-, CD14- and CD3+CD4+. Approximately 3 x 10⁵ cells were sorted into cold RF10 per sample.

extract_protocol: Approximately 3 x 10⁵ CD4+ T cells cells were sorted into cold RF10 per sample. Sorted CD4+ T cells that had proliferated in response to matDC (T-MatDC), DexVD3DC (T-DexVD3DC) or VD3DC (T-VD3DC) were lysed in RLT buffer containing 1% β-mercaptoethanol, passed through a QIAshredder column (Qiagen, Hilden, Germany) and stored at -80°C. Total RNA was extracted using the RNeasy® Micro Kit (Qiagen) according to manufacturer’s instruction. RNA concentration was determined using Qubit (Invitrogen) and 100ng RNA per sample was analysed on the NanoString nCounter® platform using the Immune Exhaustion panel.

treatment_protocol: PBMC were co-cutured with allogeneic mature DC or DexVD3DC or VD3DC

tag: disease

value: Rheumatoid arthritis

tag: stage of disease

value: Early

tag: treatment

value: drug-naïve

tag: Sex

value: female

tag: rheumatoid factor

value: positive

tag: anti-cyclic citrullinated peptide (acpa)

value: negative


title: Patient 4 T-DexVD3DC


title: X143_GE_T_RNA

description: Library name: X143_GE_T_RNA

value: Colon/Rectum

value: colorectal cancer


title: Patient 4 T-MatDC


title: Patient 3 T-VD3DC


title: A_Cpa_982, Aging

description:
Library name: A_Cpa_982
aging_cohort_FPKM.csv


title: Patient 3 T-DexVD3DC


title: Patient 3 T-MatDC


title: A_Cpa_7, Aging

description:
Library name: A_Cpa_7
aging_cohort_FPKM.csv


title: The second replicate for untreated A375 melanoma cells

city: Chengdu

first: Bei

last: Zhao

address: No.32, Western 2nd Section, 1st Ring Rd, Qingyang District

country: China

institute: University of Electronic Science and Technology Hospital

description: The RNA was identified via Affymetrix GeneChip

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: Biotin

source_name: melanoma A375 cell lines, untreated control, 48 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: All cell lines were cultured using RPMI-1640 medium

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

treatment_protocol: For Group A375+T-AIII, A375 cells treated with 8 μmol/L Timosaponin AIII for 48 hours.

tag: cell type

value: Melanoma cell


title: Patient 2 T-VD3DC


title: Patient 2 T-DexVD3DC


title: The second replicate for normal human melanocytes

source_name: human melanocytes, untreated control, 48 h

value: Melanocyte


title: X143_DE_T_RNA

description: Library name: X143_DE_T_RNA


title: The second replicate for A375 cells treated with 8 μmol/L Timosaponin AIII

source_name: melanoma A375 cell lines, treated with 8 μmol/L Timosaponin AIII, 48 h


title: The third replicate for untreated A375 melanoma cells


title: X138_DU_T_RNA

description: Library name: X138_DU_T_RNA


title: The first replicate for normal human melanocytes


title: The first replicate for A375 cells treated with 8 μmol/L Timosaponin AIII


title: A_Cpa_9, Aging

description:
Library name: A_Cpa_9
aging_cohort_FPKM.csv


title: The third replicate for normal human melanocytes


title: The first replicate for untreated A375 melanoma cells


title: X137_FA_T_RNA

description: Library name: X137_FA_T_RNA


title: A_Cre_305, Aging

description:
Library name: A_Cre_305
aging_cohort_FPKM.csv

value: Cre

value: 53 weeks


title: Patient 2 T-MatDC


title: h-nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A whi5::hphMX6 cells,EMM+auxine-nitrogen24h,biorep2

city: Salamanca

first: Sergio

last: Moreno

email: smo@usal.es, ibfg_smp@usal.es

state: Salamanca

address: Zacarias Gonzalez 2

department: IBFG

country: Spain

institute: Institute of Functional Biology and Genomics (IBFG) (CSIC)

description: Library name: Sample 20

data_processing:
Sequencing quality was check with FastQC (v 0.11.8, Babraham Bioinformatics).
Adaptors were trimmed using Trimmomatic (v 0.38) (Bolger et al. 2014) .
Alignment was performed with HISAT2 v 2.1.0 (CCB in John Hopkins University) (Kim et al. 2015)
Read counts were obtained with featureCounts (Subread package v 1.6.3, Walter+Eliza Hall Bioinformatics) (Liao et al.2014) .
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text files include normalized counts after Deseq2 analysisis

organism: Schizosaccharomyces pombe

source_name: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  whi5::hphMX6

growth_protocol: Cells were grown to mid-exponential phase in supplemented yeast extract medium (YES) and minimal medium (MM).

extract_protocol:
Cells were washed with 1 ml of cold water, and frozen in dry ice. Total RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was checked by electrophoresis, and RNA concentration was measured with a Nanodrop microspectrophotometer.
library preparation and subsequent NGS analysis were performed by Novogene. Libraries were prepared from total RNA using polyA enrichment of the mRNA.

treatment_protocol:
Wild type and whi5 knockdown cells were centrifuged and washed three times in MM-N, and cultured in MM-N at 25ºC. 2x10E8 cells were harvested at times 0,10 and 24 hours.
Cells overexpressing whi5 + from the nmt1 + promoter were grown in minimal medium with thiamine (promoter OFF), washed three times with minimal medium without thiamine, and then inoculated into the same medium (promoter ON). Then cells cells were centrifuged and washed three times in MM-N, and cultured in MM-N at 25ºC. 2x10E8 cells were harvested at times 0 and 24 hours
To induce Nrm1 degradation in Nrm1:3xsAID cells, 100 nM 5-adamantyl-IAA was added to minimal medium from a 1 mM stock solution (Tokyo Chemical Industry, A3390). Then cells cells were centrifuged and washed three times in MM-N, and cultured in MM-N at 25ºC. 2x10E8 cells were harvested at times 0 and 24 hours

tag: cell line

value: nrm1 depletion whi5 knockdown

value: Minimal medium without nitrogen 24 hours


title: The third replicate for A375 cells treated with 8 μmol/L Timosaponin AIII


title: Patient 1 T-DexVD3DC


title: X135_VA_T_RNA

description: Library name: X135_VA_T_RNA


title: Patient 1 T-MatDC


title: A_Cre_470, Aging

description:
Library name: A_Cre_470
aging_cohort_FPKM.csv

value: pancreas

value: 51 weeks


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  whi5::hphMX6 cells, nrm1depletionmutant,whi5mutant, EMM+auxine, biorep2

description: Library name: Sample 18

value: Minimal medium


title: Patient 1 T-VD3DC

value: Rheumatoid arthritis


title: X135_SC_T_RNA

description: Library name: X135_SC_T_RNA


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  whi5::hphMX6 cells, nrm1depletionmutant, whi5mutant, EMM+auxine, biorep1

description: Library name: Sample 17


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  cells, nrm1 depletion mutant, EMM +auxine  -nitrogen 24h, bio rep 2

description: Library name: Sample 16

value: nrm1 depletion


title: A_Cre_476, Aging

description:
Library name: A_Cre_476
aging_cohort_FPKM.csv


title: X135_CU_T_RNA

description: Library name: X135_CU_T_RNA


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  cells, nrm1 depletionmutant, EMM+auxine -nitrogen 24h, biorep 1

description: Library name: Sample 15


title: A_Cre_487_b, Aging

description:
Library name: A_Cre_487_b
aging_cohort_FPKM.csv


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  cells, nrm1 depletion mutant, minimal medium with auxine, bio rep 2

description: Library name: Sample 14


title: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A cells, nrm1 depletionmutant, minimal medium with auxine, bio rep 1

description: Library name: Sample 13


title: h- natMX6:P41nmt1:whi5 cells, whi5 overexpression, minimal medium without nitrogen 24 hours, bio rep 1

description: Library name: Sample 11

source_name: h- natMX6:P41nmt1:whi5

value: h- natMX6:P41nmt1:whi5

value: whi5 overexpression


title: A_Cre_489_b, Aging

description:
Library name: A_Cre_489_b
aging_cohort_FPKM.csv


title: h- natMX6:P41nmt1:whi5 cells, whi5 overexpression, minimal medium without nitrogen 24 hours, bio rep 2

description: Library name: Sample 12


title: A_Cre_619_b, Aging

description:
Library name: A_Cre_619_b
aging_cohort_FPKM.csv


title: h- natMX6:P41nmt1:whi5 cells, whi5 overexpression, minimal medium, bio rep 2

description: Library name: Sample 10


title: X130_WI_T_RNA

description: Library name: X130_WI_T_RNA


title: h- natMX6:P41nmt1:whi5 cells, whi5 overexpression, minimal medium, bio rep 1

description: Library name: Sample 9


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium without nitrogen 24 hours, bio rep 2

description: Library name: Sample 8

source_name: h- whi5::hphMX6

value: h- whi5::hphMX6

value: whi5 knockdown


title: A_Cre_620_b, Aging

description:
Library name: A_Cre_620_b
aging_cohort_FPKM.csv


title: X128_CA_T_RNA

description: Library name: X128_CA_T_RNA

value: Colon/Rectum


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium, bio rep 2

description: Library name: Sample 6


title: A_Cre_328, Aging

description:
Library name: A_Cre_328
aging_cohort_FPKM.csv

value: 52 weeks


title: h-nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A whi5::hphMX6 cells,EMM+auxine-nitrogen24h,biorep1

description: Library name: Sample 19

value: h- nrm1:3xsAID:KanMX6 ura4+::Padh1-osTIR1-F74A  whi5::hphMX6


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium without nitrogen 24 hours, bio rep 1

description: Library name: Sample 7


title: A_KCCpa_11, Aging

description:
Library name: A_KCCpa_11
aging_cohort_FPKM.csv

value: 37 weeks


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium, bio rep 1

description: Library name: Sample 5


title: X127_MO_T_RNA

description: Library name: X127_MO_T_RNA

value: colorectal cancer


title: A_KCCpa_17, Aging

description:
Library name: A_KCCpa_17
aging_cohort_FPKM.csv

value: 20 weeks


title: h- 972 cells, wild type, minimal medium without nitrogen 24 hours, bio rep 1

description: Library name: Sample 3

value: WT


title: h- 972 cells, wild type, minimal medium, bio rep 2

description: Library name: Sample 2


title: h- 972 cells, wild type, minimal medium without nitrogen 24 hours, bio rep 2

description: Library name: Sample 4

value: Minimal medium without nitrogen 24 hours


title: X125_CA_T_RNA

description: Library name: X125_CA_T_RNA


title: X119_TR_T_RNA

description: Library name: X119_TR_T_RNA


title: A_KCCpa_4, Aging

description:
Library name: A_KCCpa_4
aging_cohort_FPKM.csv

value: pancreas


description:
Library name: Sample 11
whi_1_24

extract_protocol:
Cells were washed with 1 ml of cold water, and frozen in dry ice. Total RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was checked by electrophoresis, and RNA concentration was measured with a Nanodrop microspectrophotometer.
Library preparation and subsequent NGS analysis were performed by Novogene. Libraries were prepared from total RNA using polyA enrichment of the mRNA.

treatment_protocol: Wild type and whi5 knockdown cells were centrifuged and washed three times in MM-N, and cultured in MM-N at 25ºC. 2x10E8 cells were harvested at times 0,10 and 24 hours.


title: X132_VO_T_RNA

description: Library name: X132_VO_T_RNA


title: h- 972 cells, wild type, minimal medium, bio rep 1

description: Library name: Sample 1


title: A_KCCpa_859, Aging

description:
Library name: A_KCCpa_859
aging_cohort_FPKM.csv

value: 43 weeks


description:
Library name: Sample 12
whi_2_24


title: X132_CU_T_RNA

description: Library name: X132_CU_T_RNA


title: X117_GA_T_RNA

description: Library name: X117_GA_T_RNA


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium without nitrogen 10 hours, bio rep 2

description:
Library name: Sample 10
whi_2_10

value: Minimal medium without nitrogen 10 hours


title: A_KCCpa_901, Aging

description:
Library name: A_KCCpa_901
aging_cohort_FPKM.csv


title: h- whi5::hphMX6 cells, whi5 mutant, minimal medium without nitrogen 10 hours, bio rep 1

description:
Library name: Sample 9
whi_1_10


title: X114_FU_T_RNA

description: Library name: X114_FU_T_RNA


title: X113_FO_T_RNA

description: Library name: X113_FO_T_RNA


description:
Library name: Sample 7
whi_1_0

value: Minimal medium


description:
Library name: Sample 8
whi_2_0


description:
Library name: Sample 6
wt_2_24


title: X112_PE_T_RNA

description: Library name: X112_PE_T_RNA


description:
Library name: Sample 5
wt_1_24


title: A_KCCpa_978, Aging

description:
Library name: A_KCCpa_978
aging_cohort_FPKM.csv

value: 17 weeks


title: A_KCCpa_984, Aging

description:
Library name: A_KCCpa_984
aging_cohort_FPKM.csv


title: X110_FA_2_2_0

description: Library name: X110_FA_2_2_0


title: h- 972 cells, wild type, minimal medium without nitrogen 10 hours, bio rep 1

description:
Library name: Sample 3
wt_1_10


description:
Library name: Sample 2
wt_2_0


description:
Library name: Sample 1
wt_1_0


title: CTC (LM2) - 5541-5

city: Houston

first: Bree

last: Lege

state: TX

address: one baylor plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description: Library name: 5541-5

data_processing:
aligned with STAR v2.7.10a
normalized with DESeq2 v1.42.1
removed sample columns for CTCs excluded from analysis
removed gene rows with rowMeans=0
output expression matrix
Assembly: GRCh38 (Gencode v38)
Supplementary files format and content: Normalized expression matrix

source_name: Breast cancer - CTC

extract_protocol:
Single cells were visualized in chamber slides coated with polyHEMA for isolation and deposited in tubes via Rarecyte aspirating needle in 400-600nL PBS. Individual tubes containing deposited cells were processed using SMARTseq2 protocol as previously described23 with several modifications. Shortly, 2uL of lysis buffer was added to each tube, consisting of Triton, RNase inhibitor, dNTPs, and Oligo dT, and incubated first at room temp for 5min, then at 72°C for 5min. Reverse transcription mix was added (3uL), containing 5x first strand buffer, RNase inhibitor, DTT, MgCl2, Betaine, TSO, and Smart scribe reagent. Samples were incubated at 42°C for 90min, then at 70°C for 5min. Amplification cycle number was determined for each set of cells using iTaq SYBR green reagent and run for 40 cycles. Amplification mix, containing IS PCR primer, KAPA HiFi hotstart, and Lambda exonuclease, was added (7.5uL) and amplification was run at ~28-35 cycles depending on the single cell.
Libraries were prepared for sequencing from amplified cDNA using tagmentation via Nextera XT library prep kit (library kit FC-131-1096, index kit FC-131-1001) and standard kit protocol. Libraries were pooled and sequenced on a NextSeq550 platform. Data was demultiplexed using Basespace BCL Convert v1.2.1.

value: Breast cancer - CTC

value: CTC

value: Breast cancer


title: X109_BO_T_RNA

description: Library name: X109_BO_T_RNA


title: A_KCCpa_985, Aging

description:
Library name: A_KCCpa_985
aging_cohort_FPKM.csv

value: 29 weeks


title: A_KC_327, Aging

description:
Library name: A_KC_327
aging_cohort_FPKM.csv

value: KC

value: 49 weeks


title: CTC (LM2) - 5541-1

description: Library name: 5541-1


title: X108_JA_T_RNA

description: Library name: X108_JA_T_RNA

value: Colon/Rectum


title: CTC (LM2) - 5549-7

description:
Library name: 5549-7
excluded proc data


title: CTC (LM2) - 5549-6

description: Library name: 5549-6


title: CTC (LM2) - 5549-5

description: Library name: 5549-5


title: CTC (LM2) - 5549-3

description: Library name: 5549-3


title: A_KC_483, Aging

description:
Library name: A_KC_483
aging_cohort_FPKM.csv

value: 51 weeks


title: X106_DO_T_RNA

description: Library name: X106_DO_T_RNA

value: colorectal cancer


title: A_KC_472, Aging

description:
Library name: A_KC_472
aging_cohort_FPKM.csv


title: X106_CH_T_RNA

description: Library name: X106_CH_T_RNA


title: A_KCCpa_902, Aging

description:
Library name: A_KCCpa_902
aging_cohort_FPKM.csv

value: 41 weeks


title: CTC (LM2) - 5549-2

description: Library name: 5549-2


title: A_KC_488, Aging

description:
Library name: A_KC_488
aging_cohort_FPKM.csv


title: X104_MA_T_RNA

description: Library name: X104_MA_T_RNA


title: h- 972 cells, wild type, minimal medium without nitrogen 10 hours, bio rep 2

description:
Library name: Sample 4
wt_2_10

value: WT


title: A_KC_618, Aging

description:
Library name: A_KC_618
aging_cohort_FPKM.csv

value: 28 weeks


title: X104_BE_T_RNA

description: Library name: X104_BE_T_RNA


title: CTC (LM2) - 5545-18

description: Library name: 5545-18


title: CTC (LM2) - 5545-11

description: Library name: 5545-11


title: CTC (LM2) - 5545-12

description: Library name: 5545-12


title: X099_BU_T_RNA

description: Library name: X099_BU_T_RNA


title: A_KC_645, Aging

description:
Library name: A_KC_645
aging_cohort_FPKM.csv

value: pancreas

value: 52 weeks


title: CTC (LM2) - 5545-14

description:
Library name: 5545-14
excluded proc data


title: CTC (LM2) - 5545-10

description: Library name: 5545-10


title: C108, 8 weeks

description:
Library name: C108
early_ages_FPKM.csv

value: Cre

value: 8 weeks


title: X098_GR_T_RNA

description: Library name: X098_GR_T_RNA


title: CTC (LM2) - 5545-6

description: Library name: 5545-6


title: CTC (LM2) - 5545-7

description: Library name: 5545-7


title: X097_CI_T_RNA

description: Library name: X097_CI_T_RNA


title: CTC (LM2) - 5545-4

description: Library name: 5545-4


title: CTC (LM2) - 5545-3

description: Library name: 5545-3


title: C138, 8 weeks

description:
Library name: C138
early_ages_FPKM.csv


title: CTC (LM2) - 5545-1

description: Library name: 5545-1


title: X094_BE_T_RNA

description: Library name: X094_BE_T_RNA


title: CTC (LM2) - 5542-8

description: Library name: 5542-8


title: C412, 2 weeks

description:
Library name: C412
early_ages_FPKM.csv

value: 2 weeks


title: CTC (LM2) - 5545-15

description: Library name: 5545-15

value: Breast cancer - CTC


title: X088_CA_T_RNA

description: Library name: X088_CA_T_RNA


title: CTC (LM2) - 5542-2

description: Library name: 5542-2

value: CTC


title: C482, 2 weeks

description:
Library name: C482
early_ages_FPKM.csv


title: X091_GA_T_RNA

description: Library name: X091_GA_T_RNA


title: CTC (LM2) - 5542-1

description: Library name: 5542-1

value: Breast cancer


title: CTC (LM2) - 5542-4

description: Library name: 5542-4


city: Headington

first: Toby

last: Brown

state: Oxfordshire

address: Nuffield Department of Medicine, Roosevelt Dr

institute: Centre for Human Genetics

description: Library name: CD4 Donor 1 Input Control H3K27ac ChIP-seq

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the GRCh38 genome with bowtie2. Duplicate reads were filtered out to remove PCR duplicates. Count-per-million input-normalised coverage tracks were generated with deepTools and visualised in IGV Genome Browser. Raw data from the input control is available at SRR32651972.
Assembly: GRCh38
Supplementary files format and content: .bigwig files containing counts-per-million input control-normalised tracks.

molecule: genomic DNA

source_name: Peripheral blood-derived CD4+ T cells

extract_protocol:
The MAGnify Chromatin Immunoprecipitation System was used in accordance with the manufacturer's instructions.
2µl of antibody [total rabbit IgG or anti-H3K27ac (Abcam ab472)] was used for immunoprecipitation, with sonicated but untreated lysates used as input controls.

treatment_protocol: Cells were treated for 48 hours with 50 g/ml OxLDL or similar volume of buffer solution.

value: Peripheral blood-derived CD4+ T cells

value: CD4+ T cells

value: Input Control


title: X083_SC_T_RNA

description: Library name: X083_SC_T_RNA

value: Colon/Rectum


title: X082_ZE_T_RNA

description: Library name: X082_ZE_T_RNA


title: CD4 Donor 1 Buffer H3K27ac ChIP-seq

description:
Library name: CD4 Donor 1 Buffer H3K27ac ChIP-seq
CB1

value: Buffer


title: C492, 2 weeks

description:
Library name: C492
early_ages_FPKM.csv


title: CD4 Donor 1 oxLDL H3K27ac ChIP-seq

description:
Library name: CD4 Donor 1 oxLDL H3K27ac ChIP-seq
CO1

value: oxLDL


title: C634, 4 weeks

description:
Library name: C634
early_ages_FPKM.csv

value: 4 weeks


title: CTC (LM2) - 5546-c9

description: Library name: 5546-c9


title: CTC (LM2) - 5546-c10

description: Library name: 5546-c10


title: C644, 4 weeks

description:
Library name: C644
early_ages_FPKM.csv


title: CTC (LM2) - 5546-c8

description: Library name: 5546-c8


title: C664, 4 weeks

description:
Library name: C664
early_ages_FPKM.csv


title: C118, 8 weeks

description:
Library name: C118
early_ages_FPKM.csv


title: X077_DI_T_RNA

description: Library name: X077_DI_T_RNA

value: colorectal cancer


title: CD4 Donor 2 oxLDL RNA-seq

description:
Library name: CD4 Donor 2 oxLDL RNA-seq
CO2

data_processing:
Raw reads were aligned to the human hg38 genome using STAR. Reads overlapping features were counted with the FeatureCounts package from Rsubread.
Assembly: GRCh38
Supplementary files format and content: .RDS file containing count matrix for 6 samples.

extract_protocol:
RNA was extracted following the manufacturers instructions with TRIzol and the PureLink RNA mini kit from Invitrogen.
Illumina reverse-stranded TruSeq library preparation with polyA selection was performed prior to sequencing.


title: CTC (LM2) - 5546-c6

description: Library name: 5546-c6


title: C834, 4 weeks

description:
Library name: C834
early_ages_FPKM.csv


title: X069_TH_T_RNA

description: Library name: X069_TH_T_RNA


title: C882, 2 weeks

description:
Library name: C882
early_ages_FPKM.csv


title: X067_MO_T_RNA

description: Library name: X067_MO_T_RNA


title: CD4 Donor 1 oxLDL RNA-seq

description:
Library name: CD4 Donor 1 oxLDL RNA-seq
CO1


title: X067_QU_T_RNA

description: Library name: X067_QU_T_RNA


title: CTC (LM2) - 5546-c5

description: Library name: 5546-c5


title: CTC (LM2) - 5546-c4

description: Library name: 5546-c4


title: C888, 8 weeks

description:
Library name: C888
early_ages_FPKM.csv


title: CD4 Donor 3 Buffer RNA-seq

description:
Library name: CD4 Donor 3 Buffer RNA-seq
CB3


title: X057_RA_T_RNA

description: Library name: X057_RA_T_RNA


title: CTC (LM2) - 5546-c3

description:
Library name: 5546-c3
excluded proc data


title: C892, 2 weeks

description:
Library name: C892
early_ages_FPKM.csv


title: CD4 Donor 2 Buffer RNA-seq

description:
Library name: CD4 Donor 2 Buffer RNA-seq
CB2


title: X078_TI_T_RNA

description: Library name: X078_TI_T_RNA


title: X051_SP_T_RNA

description: Library name: X051_SP_T_RNA


title: CTC (LM2) - 5546-c2

description: Library name: 5546-c2


title: CD4 Donor 2 oxLDL ATAC-seq

description:
Library name: CD4 Donor 2 oxLDL ATAC-seq
CO2_shifted

data_processing:
ATAC-sequencing reads were trimmed for adapter content with NGmerge, before both ChIP- and ATAC-reads were aligned to the GRCh38 genome with bowtie2. Duplicate reads were filtered from ATAC experiments, and reads aligning to the mitochondrial genome were filtered from ATAC-sequencing alignments. ATAC-seq alignments were shifted using a +4/-5 bp to represent the centre of the Tn5 transposition. Count-per-million normalised coverage tracks were generated with deepTools and visualised in IGV Genome Browser. Consensus peak sets were generated for ATAC-sequencing using MACS3. Differential accessibility analysis for ATAC-sequencing was performed with FeatureCounts, csaw and edgeR.
Assembly: GRCh38
Supplementary files format and content: .RDS file with peak matrix for 6 ATAC-sequencing samples. Peak coordinates are specified in the annotations component of the .rds file.
Supplementary files format and content: .bigwig files containing counts-per-million normalised tracks.

extract_protocol:
samples were repeatedly centrifuged before nuclear pellets were suspended in a transposition reaction mix (25 µl 2x TD buffer (from Illumina DNA sample preparation kit), 2.5 µl hyperactive Tn5 transposase (from Illumina DNA sample preparation kit), and 22.5 µl nuclease-free water) and incubated for 30 minutes at 37◦C.
Transposed DNA was purified with the Qiagen MinElute kit and amplified by PCR.


title: C994, 4 weeks

description:
Library name: C994
early_ages_FPKM.csv


title: CD4 Donor 3 oxLDL RNA-seq

description:
Library name: CD4 Donor 3 oxLDL RNA-seq
CO3


title: C988, 8 weeks

description:
Library name: C988
early_ages_FPKM.csv


title: CTC (LM2) - 5546-s9

description: Library name: 5546-s9


title: X055_RO_T_RNA

description: Library name: X055_RO_T_RNA


title: CD4 Donor 1 oxLDL ATAC-seq

description:
Library name: CD4 Donor 1 oxLDL ATAC-seq
CO1_shifted


title: CTC (LM2) - 5546-c1

description: Library name: 5546-c1


title: X051_BU_T_RNA

description: Library name: X051_BU_T_RNA


title: CD4 Donor 3 oxLDL ATAC-seq

description:
Library name: CD4 Donor 3 oxLDL ATAC-seq
CO3_shifted


title: CD4 Donor 1 Buffer RNA-seq

description:
Library name: CD4 Donor 1 Buffer RNA-seq
CB1


title: CTC (LM2) - 5546-c7

description: Library name: 5546-c7


title: CPA142, 2 weeks

description:
Library name: CPA142
early_ages_FPKM.csv


title: CD4 Donor 3 Buffer ATAC-seq

description:
Library name: CD4 Donor 3 Buffer ATAC-seq
CB3_shifted


title: CPA092, 2 weeks

description:
Library name: CPA092
early_ages_FPKM.csv


title: CD4 Donor 2 Buffer ATAC-seq

description:
Library name: CD4 Donor 2 Buffer ATAC-seq
CB2_shifted


title: X044_HE_T_RNA

description: Library name: X044_HE_T_RNA


title: CPA152, 2 weeks

description:
Library name: CPA152
early_ages_FPKM.csv


title: CPA374, 4 weeks

description:
Library name: CPA374
early_ages_FPKM.csv


title: CD4 Donor 1 Buffer ATAC-seq

description:
Library name: CD4 Donor 1 Buffer ATAC-seq
CB1_shifted


title: X042_AR_T_RNA

description: Library name: X042_AR_T_RNA


title: CTC (LM2) - 5546-s6

description: Library name: 5546-s6


title: CPA184, 4 weeks

description:
Library name: CPA184
early_ages_FPKM.csv


title: CTC (LM2) - 5546-s7

description: Library name: 5546-s7


title: CTC (LM2) - 5546-s5

description: Library name: 5546-s5


title: X036_SA_T_RNA

description: Library name: X036_SA_T_RNA


title: X036_KU_T_RNA

description: Library name: X036_KU_T_RNA


title: CTC (LM2) - 5546-s8

description: Library name: 5546-s8


title: CPA454, 4 weeks

description:
Library name: CPA454
early_ages_FPKM.csv


title: CPA56210, 10 weeks

description:
Library name: CPA56210
early_ages_FPKM.csv

value: 10 weeks


title: DON1

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
Library name: sample5
DON1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Danio rerio

source_name: AB

growth_protocol: Adult zebrafish (wild type, AB series, purchased from the National Zebrafish Resource Center) were bred and kept in our laboratory in a zebrafish breeding system. The system automatically adjusts the pH value to 7.2-7.6, conductivity to 450-550 μ S/cm, indoor lighting for 10:14 hours with alternating brightness and darkness, and water temperature of 28 ± 2 ℃,. Feed fresh prawns twice a day, and the prawns will hatch themselves in the laboratory.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The DONs were dissolved in Dimethyl sulfoxide (DMSO) to prepare a stock solution of 0.5 M, which was stored at −20 ◦C. The stock solution was further diluted to prepare a working solution.

tag: strain

value: AB

value: DON


title: X031_AB_T_RNA

description: Library name: X031_AB_T_RNA


title: CTC (LM2) - 5546-s3

description:
Library name: 5546-s3
excluded proc data


title: X036_CO_T_RNA

description: Library name: X036_CO_T_RNA


title: X041_GE_T_RNA

description: Library name: X041_GE_T_RNA


title: CPA57010, 10 weeks

description:
Library name: CPA57010
early_ages_FPKM.csv

value: pancreas


title: CT2

description:
Library name: sample2
CT2

value: DMSO


title: CPA56510, 10 weeks

description:
Library name: CPA56510
early_ages_FPKM.csv


title: CTC (LM2) - 5546-s2

description: Library name: 5546-s2


title: X029_BI_T_RNA

description: Library name: X029_BI_T_RNA


title: CPA5728, 8 weeks

description:
Library name: CPA5728
early_ages_FPKM.csv

value: 8 weeks


title: CT1

description:
Library name: sample1
CT1


title: CPA60310, 10 weeks

description:
Library name: CPA60310
early_ages_FPKM.csv


title: X021_CH_T_RNA

description: Library name: X021_CH_T_RNA


title: X021_JE_T_RNA

description: Library name: X021_JE_T_RNA


title: Cell culture single cells (LM2) - LM-P3

description: Library name: LM-P3

source_name: Breast cancer - cell culture

value: Breast cancer - cell culture

value: cell culture


title: Cell culture single cells (LM2) - LM-10

description: Library name: LM-10

value: Breast cancer


title: CPA60410, 10 weeks

description:
Library name: CPA60410
early_ages_FPKM.csv


title: CTC (LM2) - 5546-s4

description: Library name: 5546-s4

value: Breast cancer - CTC

value: CTC


title: X021_AD_T_RNA

description: Library name: X021_AD_T_RNA


title: DON2

description:
Library name: sample6
DON2


title: CPA6308, 8 weeks

description:
Library name: CPA6308
early_ages_FPKM.csv


title: X015_CE_T_RNA

description: Library name: X015_CE_T_RNA


title: CTC (LM2) - 5546-s1

description: Library name: 5546-s1


title: Cell culture single cells (LM2) - LM-3

description: Library name: LM-3


title: X013_AM_T_RNA

description: Library name: X013_AM_T_RNA


title: Cell culture single cells (LM2) - LM-2

description: Library name: LM-2


title: Cheetah liver female 7y

type: genomic

city: 15600 San Pasqual Valley Rd

first: Michelle

last: Ysrael

state: CA

address: 15600 San Pasqual Valley Rd

institute: San Diego Zoo Wildlife Alliance

description: Cheetah liver DNA, female 7y

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3, Cy5

organism: Acinonyx jubatus

label_protocol: Standard Illumina Protocol

extract_protocol:
Monarch
DNA was exctracted using either Qiagen Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA; Cat.T3010S) or DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA; Cat. No. / ID: 69504 ) with the following modifications for the DNeasy kit: 40 uL Proteinase K was used instead of the 20 uL suggested in the manual.

value: liver


title: Cell culture single cells (LM2) - LM-P4

description: Library name: LM-P4


title: CPA6678, 8 weeks

description:
Library name: CPA6678
early_ages_FPKM.csv


title: Cell culture single cells (LM2) - LM-1

description: Library name: LM-1


title: Cheetah blood male 10y

description: Cheetah blood DNA, male 10y

source_name: blood

value: blood


title: X011_BR_T_RNA

description: Library name: X011_BR_T_RNA

value: Colon/Rectum


title: CPA6718, 8 weeks

description:
Library name: CPA6718
early_ages_FPKM.csv


title: CPA792, 2 weeks

description:
Library name: CPA792
early_ages_FPKM.csv

value: 2 weeks


title: X010_CO_T_RNA

description: Library name: X010_CO_T_RNA


title: CPALL2, 2 weeks

description:
Library name: CPALL2
early_ages_FPKM.csv


title: X007_LO_T_RNA

description: Library name: X007_LO_T_RNA


title: Cheetah blood male 9y

description: Cheetah blood DNA, male 9y


title: X014_MO_T_RNA

description: Library name: X014_MO_T_RNA


title: Input_for_H3K27ac

first: Julian

last: Pulecio

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Input_for_H3K27ac
Input for H3K27ac experiments

data_processing:
Paired-end reads were mapped to hg19 reference genome with bowtie2(Langmead and Salzberg, 2012) using default parameters.
Peaks were called using macs2 (Model-based Analysis of ChIP-Seq (MACS) (Zhang et al., 2008)), with the options to filter duplicates using –keepdup auto with the permissive P-value threshold of 0.01.
Peaks were further filtered down using irreproducible discovery ratio (IDR) (Li et al., 2011) filter of 0.01.
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

source_name: Embryonic Stem Cells

growth_protocol: hESCs were cultured in Essential 8 (E8) medium (Thermo Fisher Scientific, A1517001) on vitronectin (VTN) (Thermo Fisher Scientific, A14700) pre-coated plates at 37 °C with 5% CO2. Medium was changed every day. Cells were passaged every 4-5 days at a ratio 1:15-20 using 0.5 mM EDTA (KD Medical, RGE-3130) or TrypLE Select (Gibco, 12563029) to dissociate cells. 5 μM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the E8 media when passaging or thawing hESCs.

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Libraries were generated by the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S). Samples were QC on a Bioanalyzer(Agilent) and sequenced on an Illumina Next Gen sequencer by the Integrated Genomic Operation(IGO) Core Facility at the MSKCC.

treatment_protocol: For FOXA2 expression in hESCs, 2x105 iSAM hESCs were transduced with two lentiviral gRNAS targeting the promoter region of the endogenous FOXA2 locus. After one day of recovery cells were cultured in E8 medium and treated with puromycin for three days. Doxycycline was added for an additional day ( no Doxycycline for the NODOX conditions)

value: Embryonic Stem Cells

value: WildType

tag: chip antibody

value: Input Control


title: Input_for_TFs

description:
Library name: Input_for_TFs
Input for pluripotent TF ChIP

tag: tissue


title: Input_for_FOXA2

description:
Library name: Input_for_FOXA2
Input for FOXA2 experiments


title: CPA6658, 8 weeks

description:
Library name: CPA6658
early_ages_FPKM.csv


title: CPAR4, 4 weeks

description:
Library name: CPAR4
early_ages_FPKM.csv

value: 4 weeks


title: X004_BE_T_RNA

description: Library name: X004_BE_T_RNA

source_name: CRC sample

extract_protocol:
RNA was extracted from the intervening sections using the RNAeasy kit (Qiagen, Netherlands) and itsÕ quality and quantity controlled using a tape station (Agilent, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat reagents (Illumina, San Diego, USA). Following quality assessment on the Fragment Analyzer (Agilent, Santa Clara, USA), libraries were 100nt paired-end sequenced to a target of 50 million clusters per library on the Illumina NovaSeq 6000 (Illumina, San Diego, USA).

value: colorectal cancer


title: CPARL4, 4 weeks

description:
Library name: CPARL4
early_ages_FPKM.csv

value: pancreas


title: KC018, 8 weeks

description:
Library name: KC018
early_ages_FPKM.csv

value: KC


title: X000_RO_T_RNA_2

description: Library name: X000_RO_T_RNA_2


title: KC038, 8 weeks

description:
Library name: KC038
early_ages_FPKM.csv

value: 8 weeks


title: Cheetah blood female 10y

description: Cheetah blood DNA, female 10y


title: X000_RO_T_RNA_1

description: Library name: X000_RO_T_RNA_1


title: KC048, 8 weeks

description:
Library name: KC048
early_ages_FPKM.csv


title: DMSO1_3

description:
Library name: sample12
DMSO1_3

source_name: Jurkat

growth_protocol: Human T lymphocyte cell line Jurkat T were purchased from American Type Culture Collection (ATCC). Jurkat cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 (Thermo Scientific) complete medium with 10% (vol/vol) fetal bovine serum (FBS, Thermo Scientific, Cat: 10270106, New York, NY, USA) and 1%(vol/vol) penicillin/streptomycin (P/S,Thermo Scientific, Cat: 15140122, New York, NY, USA).

treatment_protocol: The DONs were dissolved in Dimethyl sulfoxide (DMSO) to prepare a stock solution of 5 mM, which was stored at −20 ◦C.The stock solution was further diluted 1000−fold to prepare a working solution, which was subsequently diluted 2-fold to prepare DONs ranging from 0 to 5000 nM.

value: Jurkat

value: Human T lymphocyte cell line Jurkat T

value: DMSO


title: DMSO1_2

description:
Library name: sample11
DMSO1_2


title: KC058, 8 weeks

description:
Library name: KC058
early_ages_FPKM.csv


title: KC212, 2 weeks

description:
Library name: KC212
early_ages_FPKM.csv


title: X002_KU_T_RNA

description: Library name: X002_KU_T_RNA


title: Cheetah blood m 10y

description: Cheetah blood DNA, male 10y


title: Cheetah blood female 8y

description: Cheetah blood DNA, female 8y


title: DMSO1_1

description:
Library name: sample10
DMSO1_1


title: NIV1_3

description:
Library name: sample9
NIV1_3

value: NIV


title: Cheetah liver female 3y

description: Cheetah liver DNA, female 3y

source_name: liver


title: KC232, 2 weeks

description:
Library name: KC232
early_ages_FPKM.csv

source_name: pancreas


title: KC272, 2 weeks

description:
Library name: KC272
early_ages_FPKM.csv


title: Cheetah blood male 14y

description: Cheetah blood DNA, male 14y


title: Cheetah skin female 9y

description: Cheetah skin DNA, female 9y

source_name: skin

value: skin


title: P5_ex vivo

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

description:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Ex vivo culture protocol: Freshly isolated mammary gland tissues were cultured ex vivo for 48 hours in 3D mammosphere culture, with or without 5uM LPA stimulation. The composition of the mammosphere media is detailed in Shackleton M et al., 2006, Nature 439(7072):84-8. doi: 10.1038/nature04372. P4 and P5 cells were isolated using the above mentioned FACS sorting protocol.

hyb_protocol: Each cy5 labeled testing sample was mixed with equal amount cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit),  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0).

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and linear Lowess normalization.

source_name: Subpopulation P5 (CD24+CD29lo) from virgin wild type C57BL6 mice in 3D mammosphere culture

label_protocol: The testing RNA samples and universal mouse reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: mg condition

value: Virgin

tag: subpopulation

value: Luminal progenitor

tag: condition

value: 3D ex vivo

value: Vehicle control

source_name: Universal Mouse Reference RNA

value: Mix of 11 mouse cell lines


title: Cheetah liver male 4y

description: Cheetah liver DNA, male 4y

value: liver


title: Cheetah skin male 4y

description: Cheetah skin DNA, male 4y


title: Cheetah skin female 3y

description: Cheetah skin DNA, female 3y


title: KC222, 2 weeks

description:
Library name: KC222
early_ages_FPKM.csv

tag: age

value: 2 weeks


title: P5+LPA_ex vivo

source_name: Subpopulation P5 (CD24+CD29lo) from virgin wild type C57BL6 mice in 3D mammosphere culture, treated with LPA

value: LPA


title: P4+LPA_ex vivo

source_name: Subpopulation P4 (CD24+CD29hi) from virgin wild type C57BL6 mice in 3D mammosphere culture, treated with LPA

value: MaSC


title: Cheetah liver female 9y

description: Cheetah liver DNA, female 9y


title: NIV1_1

description:
Library name: sample7
NIV1_1

tag: genotype


title: Cheetah liver male 14.8y

description: Cheetah liver DNA, male 14.8y

extract_protocol:
Qiagen
DNA was exctracted using either Qiagen Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA; Cat.T3010S) or DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA; Cat. No. / ID: 69504 ) with the following modifications for the DNeasy kit: 40 uL Proteinase K was used instead of the 20 uL suggested in the manual.


title: Cheetah skin female 12.2y

description: Cheetah skin DNA, female 12.2y


title: P4_ex vivo

source_name: Subpopulation P4 (CD24+CD29hi) from virgin wild type C57BL6 mice in 3D mammosphere culture


title: Cheetah liver female 12.2y

description: Cheetah liver DNA, female 12.2y


title: Cheetah blood male 13y

description: Cheetah blood DNA, male 13y

value: blood


title: NIV1_2

description:
Library name: sample8
NIV1_2


title: KC302, 2 weeks

description:
Library name: KC302
early_ages_FPKM.csv

value: pancreas

value: KC


title: DON1_3

description:
Library name: sample6
DON1_3

value: Jurkat

value: DON


title: KO_P5_replicate3

source_name: Subpopulation P5 (CD24+CD29lo) from virgin Plpp1 KO mice in C57BL6 background, replicate 3

value: in vivo


title: KO_P5_replicate2

source_name: Subpopulation P5 (CD24+CD29lo) from virgin Plpp1 KO mice in C57BL6 background, replicate 2


title: Cheetah skin male 14.3y

description: Cheetah skin DNA, male 14.3y


title: KC424, 4 weeks

description:
Library name: KC424
early_ages_FPKM.csv

value: 4 weeks


title: KO_P5_replicate1

source_name: Subpopulation P5 (CD24+CD29lo) from virgin Plpp1 KO mice in C57BL6 background, replicate 1


title: KC434, 4 weeks

description:
Library name: KC434
early_ages_FPKM.csv


title: WT_P5_replicate3

source_name: Subpopulation P5 (CD24+CD29lo) from virgin wild type C57BL6 mice, replicate 3


title: DON1_2

description:
Library name: sample5
DON1_2

value: Human T lymphocyte cell line Jurkat T


title: DON1_1

description:
Library name: sample4
DON1_1


title: WT_P5_replicate2

source_name: Subpopulation P5 (CD24+CD29lo) from virgin wild type C57BL6 mice, replicate 2

value: Virgin


title: KC464, 4 weeks

description:
Library name: KC464
early_ages_FPKM.csv


title: Cheetah liver female 7.0y

description: Cheetah liver DNA, female 7.0y


title: WT_P5_replicate1

source_name: Subpopulation P5 (CD24+CD29lo) from virgin wild type C57BL6 mice, replicate 1

value: Luminal progenitor


title: Ac15DON1_3

description:
Library name: sample3
Ac15DON1_3


title: Ac15DON1_2

description:
Library name: sample2
Ac15DON1_2


title: KCCPA10004, 4 weeks

description:
Library name: KCCPA10004
early_ages_FPKM.csv


title: KCCPA132, 2 weeks

description:
Library name: KCCPA132
early_ages_FPKM.csv


title: Ac15DON1_1

description:
Library name: sample1
Ac15DON1_1


title: Cheetah liver male 5.1y

description: Cheetah liver DNA, male 5.1y


title: KCCPA34, 4 weeks

description:
Library name: KCCPA34
early_ages_FPKM.csv


title: M2_DMSO3

description:
Library name: sample12
M2_DMSO3

source_name: Human monocytic THP-1 cell

growth_protocol: Human monocytic THP-1 cell were purchased from American Type Culture Collection (ATCC). THP-1 cell were cultured in Roswell Park Memorial Institute (RPMI) 1640 (Thermo Scientific) complete medium with 10% (vol/vol) fetal bovine serum (FBS, Thermo Scientific, Cat: 10270106, New York, NY, USA) and 1%(vol/vol) penicillin/streptomycin (P/S,Thermo Scientific, Cat: 15140122, New York, NY, USA).

value: Human monocytic THP-1 cell

value: M2 macrophage

value: DMSO


title: KCCPA382, 2 weeks

description:
Library name: KCCPA382
early_ages_FPKM.csv


title: KCCPA392, 2 weeks

description:
Library name: KCCPA392
early_ages_FPKM.csv


title: M2_DMSO1

description:
Library name: sample10
M2_DMSO1


title: Cheetah liver female 9.4y

description: Cheetah liver DNA, female 9.4y

value: liver


title: KCCPA43910, 10 weeks

description:
Library name: KCCPA43910
early_ages_FPKM.csv

value: 10 weeks


title: M2_NIV3

description:
Library name: sample9
M2_NIV3

value: NIV


title: KCCPA44110, 10 weeks

description:
Library name: KCCPA44110
early_ages_FPKM.csv


title: Cheetah liver male 14.5y

description: Cheetah liver DNA, male 14.5y


title: M2_NIV2

description:
Library name: sample8
M2_NIV2


title: M2_DMSO2

description:
Library name: sample11
M2_DMSO2


title: KCCPA44, 4 weeks

description:
Library name: KCCPA44
early_ages_FPKM.csv


title: KO_P4_replicate2

source_name: Subpopulation P4 (CD24+CD29hi) from virgin Plpp1 KO mice in C57BL6 background, replicate 2

value: MaSC

value: Mix of 11 mouse cell lines


title: Cheetah liver female 6.7y

description: Cheetah liver DNA, female 6.7y


title: Cheetah liver male 13.4y

description: Cheetah liver DNA, male 13.4y


title: KO_P4_replicate1

source_name: Subpopulation P4 (CD24+CD29hi) from virgin Plpp1 KO mice in C57BL6 background, replicate 1


title: Kidney_Colistin_rep4

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

country: Japan

institute: National Institute of Health Sciences

description: Gene expression in kidney of rat-treated with colistin

hyb_protocol: 3 ug of Cy3-labelled SPIA cDNA was fragmented at 60°C for 30 minutes using Gene Expression Hybridazation Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, 2x GE Hybridization Buffer HI-PRM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (G2519) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028282_D_F_20140723) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: 30 mg/kg colistin, day 28

label_protocol: Cyanine-3 (Cy3) labeled SPIA cDNA was prepared using theSureTag DNA labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).

extract_protocol: total RNA was prepared using the RNeasy Micro Kit  (Qiagen, GmbH, Hilden, Germany) following the manufacturer's recommendations.

value: Kidney

tag: gender

value: Male


title: Cheetah liver female 3.7y

description: Cheetah liver DNA, female 3.7y

source_name: liver


title: KO_P4_replicate3

source_name: Subpopulation P4 (CD24+CD29hi) from virgin Plpp1 KO mice in C57BL6 background, replicate 3


title: Cheetah liver female 10.4y

description: Cheetah liver DNA, female 10.4y


title: WT_P4_replicate2

source_name: Subpopulation P4 (CD24+CD29hi) from virgin wild type C57BL6 mice, replicate 2


title: M2_NIV1

description:
Library name: sample7
M2_NIV1


title: KCCPA47910, 10 weeks

description:
Library name: KCCPA47910
early_ages_FPKM.csv

source_name: pancreas

value: pancreas


title: Kidney_Colistin_rep3


title: Kidney_Saline Control_rep4

description: Gene expression in control rat kidney

source_name: Saline, day 28


title: Cheetah liver male 0.1y 2

description: Cheetah liver DNA, male 0.1y


title: Cheetah liver male 7.4y

description: Cheetah liver DNA, male 7.4y


title: Kidney_Colistin_rep2


title: WT_P4_replicate3

source_name: Subpopulation P4 (CD24+CD29hi) from virgin wild type C57BL6 mice, replicate 3

source_name: Universal Mouse Reference RNA


title: KCCPA48210, 10 weeks

description:
Library name: KCCPA48210
early_ages_FPKM.csv


title: M2_DON3

description:
Library name: sample6
M2_DON3

value: DON


title: Cheetah liver male 0.0y 3

description: Cheetah liver DNA, male 0.0y


title: Cheetah liver male 12.3y

description: Cheetah liver DNA, male 12.3y


title: Cheetah liver female 0.0y 5

description: Cheetah liver DNA, female 0.0y


title: M2_DON2

description:
Library name: sample5
M2_DON2


title: KCCPA54, 4 weeks

description:
Library name: KCCPA54
early_ages_FPKM.csv


title: WT_P4_replicate1

source_name: Subpopulation P4 (CD24+CD29hi) from virgin wild type C57BL6 mice, replicate 1

value: in vivo


title: Cheetah liver male 10.6y

description: Cheetah liver DNA, male 10.6y


title: M2_DON1

description:
Library name: sample4
M2_DON1


title: Veh_Spn_5

city: South San Francisco

first: Jerome

last: Bouquet

address: 121 oyster point blvd

department: integrated Bioanalysis

institute: AstraZeneca

data_processing:
Bulk RNAseq analysis managed by python toolkit bcbio-nextgen 1.1.6.
Aligned using hisat2 2.1.0 against GRCm38 (mm10) genome assembly.
Gene level transcript counts using cufflinks 2.2.1.
multiQC using fastqc 0.11.8, qualimap 2.2.2c, samtools 1.9, salmon 0.14.1.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: annotated_combined.counts.txt: Matrix table file of Ensembl IDs FPKM values for all samples.

source_name: precision cut lung slice

growth_protocol: Lung slices were cultured in 0.5-mL small airway epithelial cell growth medium (SAGM, CC-3118, Lonza) at 37°C, 5% CO2, and 95% humidity in a 24-well cell culture plate.

extract_protocol:
After treatment, lung slices were washed once and pooled in 1.0-mL QIAzol lysis buffer (QIAGEN) with one 5-mm stainless steel bead (Qiagen) in 2.0-mL Eppendorf tubes, followed by homogenization using a TissueLyser homogenizer (Qiagen) at a setting of oscillation frequency 30 Hz and two 2 min with flipping orientation. The homogenate was transferred to a Phasemaker tube (Invitrogen) and incubated for 5 min at RT, followed by mixing vigorously by hand for 15 s and incubation for 5 min at RT with 0.2-mL chloroform. After centrifuged for 5 min at 16,000 × g at 4°C, the aqueous phase was transferred to a new Eppendorf tube and mixed with an equal volume of 70% ethanol and passed through a RNeasy spin column according to the manufacturer’s instructions (Qiagen). Total RNA was then dissolved in RNase-free water and eluted from spin columns after on-column DNase digestion. RNA concentration and integrity were measured and evaluated using a 5300 Fragment Analyzer System (Advanced Analytical Technologies).
Total RNA (450 ng, RNA Quality Number ≥ 7) was used to prepare cDNA libraries using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Tagged and fragmented libraries were assessed and quantitated with the Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies). Libraries were normalized, pooled and then sequenced across 4 lanes of a NextSeq 500 platform using a High Output Kit v2.5 (150 Cycles, paired-end) (Illumina).

treatment_protocol: After wash with media, lung slices were pre-treated with 0.1, 1 and 10 μM Idelalisib for 2 h, followed by an additional 6 h incubation with Streptococcus pneumoniae (Pathogen to cell ratio: 30) in the presence of Idelalisib.

value: lung

tag: drug

tag: concentration

tag: infection

value: Streptococcus pneumoniae


title: Kidney_Saline Control_rep3

description: Gene expression in control rat kidney


title: M2_15AcDON3

description:
Library name: sample3
M2_15AcDON3

tag: treatment


title: Veh_Spn_4


title: KCCPA5608, 8 weeks

description:
Library name: KCCPA5608
early_ages_FPKM.csv

extract_protocol:
Total RNA was isolated from pancreatic tissue (proximal to duodenum) using a combination of QIAzol lysis reagent (Qiagen, ID.79306) and chloroform-based (Serva, 39553.01) phase separation, followed by purification with the RNeasy Mini Kit (Qiagen, ID.74106), according to the manufacturer’s protocol. Approximately 2–3 mm³ of snap-frozen tissue was transferred into 200 µL of ice-cold QIAzol containing 1% β-mercaptoethanol (final concentration; Sigma Aldrich, M6250). Samples were immediately frozen in liquid nitrogen and stored at –80°C until further processing. For homogenization, a sterile, RNase-free stainless steel bead was added, and 1.3 mL of additional ice-cold QIAzol was added while maintaining the samples on dry ice to prevent thawing. Tissue homogenization was performed using a pre-cooled Qiagen TissueLyser II at 30 Hz for 20 minutes at 4°C. Lysates were centrifuged at 13,000 × g for 5 minutes at 4°C, and the supernatant was carefully transferred to a fresh tube, avoiding residual tissue fragments. Phase separation was performed by adding 300 µL of ice-cold chloroform, followed by vigorous vortexing for 10 seconds. After centrifugation at 13,000 × g for 5 minutes at 4°C, the upper aqueous phase (∼600 µL) was carefully collected, avoiding contamination from the interphase, and mixed with an equal volume of isopropanol (Fisher Scientific, BP2618-500). RNA purification was completed using the RNeasy Mini Kit, including on-column DNase I digestion (Macherey-Nagel, 740963) to eliminate residual genomic DNA.
Library construction was performed by Novogene (Cambridge, UK).

value: 8 weeks


title: KCCPA5678, 8 weeks

description:
Library name: KCCPA5678
early_ages_FPKM.csv


title: Cheetah liver female 7.6y

description: Cheetah liver DNA, female 7.6y


title: Kidney_Colistin_rep1


title: M2_15AcDON2

description:
Library name: sample2
M2_15AcDON2


title: KCCPA5698, 8 weeks

description:
Library name: KCCPA5698
early_ages_FPKM.csv


title: M2_15AcDON1

description:
Library name: sample1
M2_15AcDON1


title: Kidney_Saline Control_rep2

description: Gene expression in control rat kidney


title: Cheetah liver male 0.0y 2

description: Cheetah liver DNA, male 0.0y


title: Veh_Spn_2


title: Kidney_Saline Control_rep1

description: Gene expression in control rat kidney


title: Cheetah liver female 6.9y

description: Cheetah liver DNA, female 6.9y


title: KCCPA5948, 8 weeks

description:
Library name: KCCPA5948
early_ages_FPKM.csv


title: Veh_Spn_1


title: V3

city: Chapel Hill

first: Ran

last: Zhang

address: Its Manning, 211 Manning Dr

institute: UNC Chapel Hill

description:
Library name: V3
V3

data_processing:
RNAseq reads were mapped to the mouse genome Ensembl 75 using STAR (version 2.3.0e, default parameters) gene level counts were quantified using htseq-count (version 0.9.1) Genes were subjected to an expression detection threshold of 1 count per million reads per gene in more than 3 samples.
Assembly: Ensembl 75
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: ventral-striatum

extract_protocol:
total RNA
see bacTRAP protocol in Roussarie et al., Neuron, 2020 5 ng of immunoprecipitated RNA was reverse transcribed and amplified using the Ovation RNAseq v2 kit. cDNA were then ultrasonicated and used to generate sequencing library using the Truseq RNA sample prep kit

value: ventral-striatum

value: astrocyte

value: WT

tag: batch


title: KCCPA5958, 8 weeks

description:
Library name: KCCPA5958
early_ages_FPKM.csv


title: V2

description:
Library name: V2
V2


title: Veh_5

value: DMSO


title: Cheetah liver female 9.7y

description: Cheetah liver DNA, female 9.7y

value: liver


title: KCCPA60210, 10 weeks

description:
Library name: KCCPA60210
early_ages_FPKM.csv

value: 10 weeks


title: Veh_Spn_3


title: Cheetah liver male 7.3y

description: Cheetah liver DNA, male 7.3y


title: Veh_4


title: Veh_3


title: KCCPA812, 2 weeks

description:
Library name: KCCPA812
early_ages_FPKM.csv

value: 2 weeks


title: Cheetah liver male 0.0y 1

description: Cheetah liver DNA, male 0.0y


title: P3

description:
Library name: P3
P3

source_name: prefrontal-cortex

value: prefrontal-cortex


title: KCCPA822, 2 weeks

description:
Library name: KCCPA822
early_ages_FPKM.csv


title: Cheetah liver female 0.0y 4

description: Cheetah liver DNA, female 0.0y


title: Veh_2


title: Veh_1


title: P2

description:
Library name: P2
P2


title: P1

description:
Library name: P1
P1


title: KCL4, 4 weeks

description:
Library name: KCL4
early_ages_FPKM.csv

value: KC

value: 4 weeks


title: 10_uM_IDELA_Spn_5

value: Idelalisib


title: H3

description:
Library name: H3
H3

source_name: hippocampus

value: hippocampus


title: KCRR4, 4 weeks

description:
Library name: KCRR4
early_ages_FPKM.csv

value: pancreas


title: 10_uM_IDELA_Spn_4


title: V1

description:
Library name: V1
V1


title: KC_65_8, 8 weeks

description:
Library name: KC_65_8
early_ages_FPKM.csv


title: H2

description:
Library name: H2
H2


title: H1

description:
Library name: H1
H1


title: MTP.CPI rep2

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description: 10x Genomics

data_processing:
Cellranger count (v3.1.0) was run
Data was analysed using the Seurat (v4.3.0) package in a R (v4.2.1) environment.
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated files
Supplementary files format and content: Matrix files

source_name: Tumor

growth_protocol: B16F10 tumor cells were subcutaneously administered.

extract_protocol:
Viable CD45+ cells were isolated from B16F10 tumors using flow sorting.
Libraries were constructed according to manufactures instruction (Single Cell 3' v3 protocol, 10x Genomics).

treatment_protocol: After a B16F10 tumor was formed, mice were treated with PBS, MTP, CPI, or MTP+CPI.

value: Tumor

value: Viable CD45+ cells

value: MTP and CPI

tag: replicate


title: 10_uM_IDELA_Spn_3

value: lung

value: Streptococcus pneumoniae


title: Cheetah liver male 15.7y

description: Cheetah liver DNA, male 15.7y


title: Cheetah liver female 15.4y

description: Cheetah liver DNA, female 15.4y


title: KCCPA9994, 4 weeks

description:
Library name: KCCPA9994
early_ages_FPKM.csv


title: 10_uM_IDELA_Spn_2


title: C3

description:
Library name: C3
C3

source_name: dorsal-striatum

value: dorsal-striatum

tag: cell type

value: astrocyte


title: CPI rep2

description: 10x Genomics

tag: cell line

value: WT

value: CPI


title: C2

description:
Library name: C2
C2


title: C1

description:
Library name: C1
C1


title: 10_uM_IDELA_Spn_1


title: Cheetah liver female 0.0y 2

description: Cheetah liver DNA, female 0.0y

value: liver


title: Cheetah liver female 0.6y

description: Cheetah liver DNA, female 0.6y


title: Cheetah liver female 0.0y 3

description: Cheetah liver DNA, female 0.0y


title: PBS rep2

description: 10x Genomics

value: PBS


title: 10_uM_IDELA_4


title: Cheetah liver female 12.0y

description: Cheetah liver DNA, female 12.0y


title: Cheetah liver female 9.1y

description: Cheetah liver DNA, female 9.1y


title: A3

description:
Library name: A3
A3

source_name: amygdala

value: amygdala


title: Cheetah liver male 0.1y 1

description: Cheetah liver DNA, male 0.1y


title: Cheetah liver female 14.7y

description: Cheetah liver DNA, female 14.7y


title: A2

description:
Library name: A2
A2


title: MTP.CPI rep1

description: 10x Genomics


title: Cheetah liver female 0.0y 1

description: Cheetah liver DNA, female 0.0y


title: 10_uM_IDELA_3


title: 10_uM_IDELA_2


title: A1

description:
Library name: A1
A1


title: Cheetah liver female 0.1y

description: Cheetah liver DNA, female 0.1y


title: Cheetah liver female 16.7y

description: Cheetah liver DNA, female 16.7y


title: CPI rep1

description: 10x Genomics


title: CV3

description:
Library name: CV3
CV3

value: ventral-striatum


title: Cheetah liver male 15.2y

description: Cheetah liver DNA, male 15.2y


title: MTP rep2

description: 10x Genomics

value: MTP


title: 10_uM_IDELA_5

value: Idelalisib


title: 10_uM_IDELA_1


title: MTP rep1

description: 10x Genomics


title: PBS rep1

description: 10x Genomics


title: 1_0_uM_IDELA_Spn_5


title: CP3

description:
Library name: CP3
CP3

value: prefrontal-cortex


title: 1_0_uM_IDELA_Spn_4


title: Cheetah liver male 15.4y

description: Cheetah liver DNA, male 15.4y


title: MTP and CPI rep2

description: 10x Genomics

data_processing:
Cellranger atac (v2.1.0) was run
Data was analysed using the packages Seurat (v4.3.0) and Signac (v1.9.0) in a R (v4.2.1) environment.
Assembly: mm10
Supplementary files format and content: Tab-separated fragment files
Supplementary files format and content: Matrix files
Supplementary files format and content: Peak bed files
Supplementary files format and content: Metadata files
Supplementary files format and content: Tab-separated fragment index files

source_name: Bone Marrow

growth_protocol: B16F10 tumor cells were subcutaneously administered. Control mice without tumor cell injection were taken along.

extract_protocol:
Bone marrow was isolated from femurs. scATACseq was performed using 10x Genomics scMULTIome.
Libraries were constructed according to manufactures instruction (scMULTIome, 10x Genomics). Chemistry: ARC-v1
scMULTIome

treatment_protocol: After a B16F10 tumor was formed, mice were treated with MTP+CPI.

value: Bone Marrow

value: Bone marrow cells


title: CH3

description:
Library name: CH3
CH3

value: hippocampus


title: Cheetah liver male 14.3y

description: Cheetah liver DNA, male 14.3y


title: CD3

description:
Library name: CD3
CD3


title: MTP and CPI rep1

description: 10x Genomics

value: MTP and CPI


title: 1_0_uM_IDELA_Spn_3

value: lung


title: tumor

description: 10x Genomics


title: Cheetah liver female 8.8y

description: Cheetah liver DNA, female 8.8y


title: 1_0_uM_IDELA_Spn_2

value: Streptococcus pneumoniae


title: Zbtb32-Igg

first: Birui

last: Pan

address: Shuang qing road, haidian district

institute: Tsinghua university

description: Library name: Zbtb32-Igg

data_processing:
All sequencing reads were mapped to the mouse genome mm10 by bowtie2 PCR duplicates were removed using picard MarkDuplicates The uniquely mapped reads were used to call peak with MACS2 using a q value cutoff 0.05 ChIPseeker was used for peak annotation
Assembly: mm10
Supplementary files format and content: bigwig

source_name: spleens and lymph nodes

extract_protocol:
ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications
ChIP samples were prepared according to the Active Motif protocol. In brief, CD8+ T cells were activated with anti-CD3/CD28 for 48 h, after 24h of infection with Zbtb32-HA-GFP or Zbtb32-HA-GFP and Bcl6-RFP. Infected CD8+ T cells were purified and cultured in the presence of IL-2 (10U/mL) for another 48h. ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications. A total of 1 x 107 cells were lysed and digested with shearing enzyme followed by sonication. Antibody against HA tag (3724, clone C29F4; Cell Signaling Technology) was added to supernatant followed by Dynabeads Protein A (LifeTechnologies) pulling down target fragment.

value: spleens and lymph nodes

value: CD8+ T cell

value: Zbtb32-HA-GFP transfected

tag: antibody

value: Igg ChIP antibody


title: CA3

description:
Library name: CA3
CA3

value: astrocyte

value: WT


title: 1_0_uM_IDELA_Spn_1


title: Cheetah liver female 13.7y

description: Cheetah liver DNA, female 13.7y

source_name: liver

value: liver


title: Zbtb32-HA

description: Library name: Zbtb32-HA

value: HA ChIP antibody


title: CP2

description:
Library name: CP2
CP2


title: Zbtb32-HA-Bcl6-OE

description: Library name: Zbtb32-HA-Bcl6-OE

value: Zbtb32-HA-GFP and Bcl6-RFP transfected


title: 1_0_uM_IDELA_5

value: Idelalisib


title: 1_0_uM_IDELA_4


title: Cheetah liver female 2.8y

description: Cheetah liver DNA, female 2.8y


title: Input

description: Library name: Input


title: CH2

description:
Library name: CH2
CH2


title: SUM159_shPLPP1_replicate2

description: Cell preparation protocol: SUM159 cells were infected with lentiviral vectors of either LKO1 vectorred shRNAs targeting PLPP1 or non-targeting control. Cells were treated and selected with puromycin and the expression of PLPP1 was determined by qRT-PCR and Western blot to confirm the designed reduction.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (v11.0.1.1).

data_processing: Agilent Feature Extraction Software (v11.0.1.1) was used for background subtraction and linear Lowess normalization.

source_name: SUM159 cells engineered with pLKO1 driven shRNA#1 targeting PLPP1, replicate 2

value: Breast cancer

tag: exogenous manipulation

source_name: Universal human Reference RNA

value: Mix of 10 human cell lines


title: 1_0_uM_IDELA_3

tag: tissue


title: Zbtb32

description: Library name: Zbtb32


title: CD2

description:
Library name: CD2
CD2

value: dorsal-striatum


title: 1_0_uM_IDELA_2


title: RNA-Seq, Terminal-WT-2

description: Library name: Terminal-WT-2

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
The clean reads were aligned to Mus musculus genome (mm10) by bowtie2 with default parameter, and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by DESeq2 with a cut-off threshold of 1.5-fold change and FDR adjusted p-value 0.05.
Assembly: mm10
Supplementary files format and content: Excel or CSV file includes normalized counts for each Sample

extract_protocol:
Total RNA from CD8+ T cells was extracted by TRIzol (Invitrogen) according to manufacturer’s
Total RNA was sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.

value: Tumor

value: CD8+ Tim-3+ Ttex


title: 1_0_uM_IDELA_1

value: lung


title: SUM159_shCtrl_replicate2

source_name: SUM159 cells engineered with pLKO1 driven non-targeting shRNA (shc002), replicate 2


title: CV1

description:
Library name: CV1
CV1

value: ventral-striatum


title: SUM159_shPLPP1_replicate1

source_name: SUM159 cells engineered with pLKO1 driven shRNA#1 targeting PLPP1, replicate 1


title: CV2

description:
Library name: CV2
CV2


title: no tumor

description: 10x Genomics

value: Bone Marrow

value: Bone marrow cells


title: RNA-Seq, Terminal-WT-1

description: Library name: Terminal-WT-1


title: RNA-Seq, Terminal-KO-2

description: Library name: Terminal-KO-2

value: Zbtb32 knockout


title: 0_1uM_IDELA_Spn_5

value: Streptococcus pneumoniae


title: SUM159_shCtrl_replicate1

source_name: SUM159 cells engineered with pLKO1 driven non-targeting shRNA (shc002), replicate 1


title: CP1

description:
Library name: CP1
CP1

value: prefrontal-cortex

value: astrocyte


title: CH1

description:
Library name: CH1
CH1

value: hippocampus

value: WT


title: 0_1uM_IDELA_Spn_4


title: 0_1uM_IDELA_Spn_3


title: RNA-Seq, Terminal-KO-1

description: Library name: Terminal-KO-1


title: CA2

description:
Library name: CA2
CA2

value: amygdala


title: CD1

description:
Library name: CD1
CD1


title: 0_1uM_IDELA_Spn_2

value: Idelalisib


title: RNA-Seq, WT-2

description: Library name: WT-2

value: CD8+ T cell


title: RNA-Seq, WT-1

description: Library name: WT-1


title: 0_1uM_IDELA_Spn_1


title: CA1

description:
Library name: CA1
CA1


title: s_fescd_control_2

city: Los Angeles

first: Kitai

last: Kim

state: California

address: 650 Charles E Young Drive South

institute: UCLA

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: mm10
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: ESC

extract_protocol: 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

value: ESC

value: Embryonic Stem Cells


title: RNA-Seq, Zbtb32-KO-2

description: Library name: Zbtb32-KO-2

value: Tumor


title: 0_1uM_IDELA_4


title: s_fescd_shEXOSC2_clone_6


title: RNA-Seq, Zbtb32-KO-1

description: Library name: Zbtb32-KO-1


title: 0_1uM_IDELA_5


title: s_fescd_shEXOSC2_clone_7


title: WT-2

description: Library name: WT-2

data_processing:
Raw ATAC-seq reads were trimmed and ﬁltered for quality control using Trim Galore v0.4.4 with parameters ‘-q 10 –length 30 –strin- gency 5 0 . Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2 v2.2.9 with –x2000. Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were ﬁltered by Samtools. PCR duplicates were removed with picard MarkDuplicates. Only concordantly mapped reads were used for further analyzing. Peaks were determined by MACS2 with parameters ‘–nomodel–keep-dup all -q 0.01-shift 100-extsize 200 -call-summits -g mm’. Peaks with differential accessibility were determined using DiffBind with at least 2 folds of change and FDR adjusted p value of 0.01. ATAC-seq peak were annotated to the nearest gene using R package ChIPseeker. BedTools was used to ﬁnd common intersection between identiﬁed peaks (1 bp minimum overlap) and merged together. HOMER was used to ﬁnd TF motifs.
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Naive Zbtb32-/- and WT OT-I cells were co-transferred into B6 recipient mice one day prior to sub-cutaneous implantation of B16-OVA tumor cells. 30 days later, Zbtb32-/- and WT OT-I cells amongst tumor infiltrating lymphocytes (TILs) were flow sorted for ATAC-seq.

extract_protocol:
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 and TruePrep Index Kit V2 for Illumina.
Total RNA was sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.


title: s_fescd_control_3


title: 0_1uM_IDELA_3


title: WT-1

description: Library name: WT-1


title: LM2 cells transfected with USP20 siRNA#2, replicate 2

description: See Agilent Cat#740000 for product details

treatment_protocol: MDA-MB-231 lung metastasis subline LM2 cells were used for the experiment. 48 hours after LM2 cells were transfected with control non-targeting siRNA, USP20 siRNA#1, USP20 siRNA#2, and SLUG siRNA, cells were lysed for RNA preparation.

tag: subline

tag: sirna

tag: cell lines

value: Mix of 10 human cell lines


title: 0_1uM_IDELA_2

value: lung


title: LM2 cells transfected with USP20 siRNA#2, replicate 1


title: s_fescd_shEXOSC2_clone_5


title: TNBC4T1-cmLumi-ADC16mg-Tumor in Lung, sample 2

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

description: Library name: T32

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Assembly: mm39
Supplementary files format and content: The processed data file was saved in text format, which contains gene ENSEMBL ID, sample names, gene symbol, gene location, gene length, gene biotype and gene description.

extract_protocol:
Total RNA was extracted from the harvested tumour cells using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). Bulk RNA sequencing with cDNA library construction were performed at Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.
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 dTTP for non strand specific library or dUTP for strand specific library.

value: Triple-negative breast cancer

value: cmLumi-Olap & CD276-DM1 16mg/kg


title: TNBC4T1-Saline-Tumor in Lung, sample 2, T26

description: Library name: T26

value: PBS control


title: TNBC4T1-cmLumi-ADC16mg-Tumor in Lung, sample 1

description: Library name: T31


title: Zbtb32-KO-2

description: Library name: Zbtb32-KO-2

value: Zbtb32 knockout


title: 0_1uM_IDELA_1


title: LM2 cells transfected with USP20 siRNA#1, replicate 2


title: LM2 cells transfected with USP20 siRNA#1, replicate 1


title: LM2 cells transfected with control non-targeting siRNA, replicate 1

value: CTRL


title: Zbtb32-KO-1

description: Library name: Zbtb32-KO-1


title: TNBC4T1-Saline-Tumor in Lung, sample 1, T25

description: Library name: T25


title: LM2 cells transfected with SLUG siRNA, replicate 2

value: SLUG


title: LM2 cells transfected with SLUG siRNA, replicate 1


title: Cultured spermatogonia, AGX51 treated, biol rep 2

status: Public on Dec 19 2025

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
The analysis was performed using the nf-core/rnaseq 3.3 pipeline, aligned with STAR + Salmon,using the Mus musculus GRCm38 (ver. GRCm38.90) reference genome, –with_umi.
Reads were quantified with featureCounts producing the raw gene count matrix.
Used Degust  to analysis table of counts, output form RNAsik. Degust is a webapp that uses either edgeR or limma-voom for differential gene analysis http://degust.erc.monash.edu
In the data provided there are fastq files for each library for R1 corresponding to the cDNA in sense orientation. The header of each read should also contain the 10 base UMI. There are also fastq files containing the index and UMI read if required (I1). These are named using the convention SampleName_SampleNumber_ReadNumber.
Assembly: Mus musculus GRCm38 (ver. GRCm38.90)
Supplementary files format and content: Excel spreadsheet includes raw counts for each sample, normalized counts for each sample (CPM)

source_name: Adult testis

growth_protocol: Undifferentiated spermatogonia were enriched from testis cell suspensions using biotinylated anti-CD9 antibody clone MZ3 (BioLegend) and EasySep Biotin Positive Selection kits (Stem Cell Technologies) and placed in culture.  Spermatogonial cultures were generated and maintained on mitotically-inactivated mouse embryonic fibroblasts (MEF) in StemPro-34 media (Thermo) with supplements as described (La, et al. 2018. Nat Commun 19;9(1):2819. doi: 10.1038/s41467-018-04827-z)

extract_protocol:
Cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Miniprep kit (Zymo Research).
Novel RNA-Seq pipeline. Index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by tagmentation by Nextera transposase and PCR. Sequencing was performed on NextSeq2000 (Illumina) following Illumina protocol 1000000109376 v3.

treatment_protocol: Feeders were depleted from harvested spermatogonia on tissue culture plates for 1-2 hours and non-adherent spermatogonia collected and plated onto 12-well plates coated with Geltrex (Thermo) and allowed to adhere and expand for 4 days and then re-fed with fresh medium containing vehicle (DMSO) or AGX51 at 80mM. Cells were harvested after 20 hours of treatment.

value: Adult testis

value: Cultured primary undifferentiated spermatogonia

value: Wildtype

tag: strain

value: CBA/J


title: Cultured spermatogonia, AGX51 treated, biol rep 1

tag: genotype


title: Cultured spermatogonia, vehicle control, biol rep 1

value: Vehicle (DMSO)


title: Cultured spermatogonia, vehicle control, biol rep 2


title: Cultured spermatogonia, vehicle control, biol rep 3


title: Cultured spermatogonia, AGX51 treated, biol rep 4