title: adult mouse testis H3K27Ac ChIP-Seq

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Library name: H3K27Ac ChIP adult

data_processing:
Datasets were mapped to the Mus musculus GRCm38/mm10 genome assembly containing chromosomes 1-19, X, Y and M and the refSeq annotations (UCSC) in refflat gtf format.
RNA-seq reads were mapped with TopHat2 (version 2.1.0) using bowtie (version 1.1.2), providing refSeq annotations and the options ‘–no-coverage-search –no-mixed –no-discordant -g1 –library-type fr-secondstrand’. FPKM’s were calculated using Cuffdiff, part of Cufflinks (version 2.2.1), with the options ‘-u –no-effective-length-correction -b’.  ChIP-seq data was mapped using bowtie (version 1.1.2) with the options ‘-m 1 -S -y’. We then used MACS to determine the average fragment length of the sequenced samples and a custom perl script to elongate the mapped reads to this length. Duplicates were then removed and .wig files were generated using BEDtools (version 2.23.0).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig tag density files for ChIP-Seq
Supplementary files format and content: tab-delimited tex file containing normalized counts (FPKM) for RNA-Seq

source_name: testis

extract_protocol:
For RNA-isolation, a testis piece, freshly isolated or stored at -80°C was homogenized using a tissueLyser (Qiagen cat. 85220) in a 2 ml Eppendorf tube, 1 min, frequency 30.0. Total RNA prepared with Trizol (Invitrogen, Thermo Scientific, see below) was DNAse digested and further purified using the RNeasy Micro kit (Qiagen). Any residual genomic DNA was digested on column according to manufacturer’s instructions, with the addition of an extra 1µl of RNase-free DNase I (Roche). The RNA was eluted using RNase-free water, quantified using the Qubit RNA HS Assay and the integrity was verified using Bioanalyzer RNA Pico chips (Agilent).  For ChIP-Seq, we isolated single cells from mouse testes. Crosslinking of approximately 1x10^6 cells was performed in PBS. Cells were washed twice with cold PBS containing 0.05% Triton X-100, pelleted, snap frozen and stored at -80°C until sonication. Cells were processed using the iDeal ChIP-Seq kit (Diagenode) according to manufacturer’s instructions. Sonification was performed on a Bioruptor Pico (Diagenode) using 3 runs of 10 cycles (30 s on, 30 s off) in a 4°C water bath. Sheared chromatin was purified and the size distribution was verified using a DNA HS Bioanalyzer chip (Agilent). Approximately 200,000 cells were used for ChIP with the anti-H3K27ac (ab4729, Abcam) antibody.
Approximately 150-200 ng of total RNA was used for the generation of strand-specific RNA-seq libraries using the ScriptSeq v2 (Epicentre) low input libarary preparation kit according to manufacturer’s instructions. The RNA-seq libraries were quantified using the Qubit high sensitivity DNA assay (Life Technologies) and the size distribution was verified using the DNA HS Bioanalyzer chips (Agilent). Libraries were paired-end sequenced on a HiSeq 2000 (Illumina) with 2x50 bp read length.  Approximately 1-5 ng of ChIP DNA was used to generate libraries using the TrueSeq ChIP-Seq kit (Ilumina) with minor modifications. After adapter ligation, a 0.95x volume of AMPure XP beads (Beckman Coulter) was used for a single round of purification. After the addition of 1 µl primer mix (25 mM each, Primer 1: 5’-AATGATACGGCGACCACCGAG-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGAG-3’) and 15 µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 s at 98°C, 5 cycles of [15 seconds at 98°C, 30 s at 63°C and 30 s at 72°C] and a final 1 min incubation at 72°C. The PCR products were purified using a 0.95x volume of AMPure XP beads. The libraries were amplified for further 13 cycles, purified using a 0.95x volume of AMPure XP beads, quantified using the Qubit DNA HS assay and the size was validated using DNA HS Bioanalyzer chips (Agilent). Libraries were sequenced on a NextSeq500 (Illumina) with 1x75 bp read length.

value: testis

value: anti-H3K27Ac (Abcam, #ab4729)

tag: age

value: adult


title: Input

status: Public on Nov 06 2025

type: SRA

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: AL1_S17_R1_001.fastq.gz

library_source: genomic

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.17.1.14)
adaptor sequences were removed using Trim Galore (-q 30) (v0.4.4)
reads aligned to the mouse genome (mm10) using Bowtie2 (v2.3.3) using default parameters
Samtools (v1.9) was used for processing SAM and BAM files.
Picard (v2.6.0) was used to remove duplicate reads
Peaks were called using Macs2 callpeak (v2.2.7.1) with default settings
bedtools intersect (v 2.31.1) used to exclude peaks that overlap with blacklisted regions (ENCODE).
Motif analysis was performed using Homer (v4.11)
Bigwig files were generated with deeptools (v 3.5.0) bamCoverage (-bl $blacklist --effectiveGenomeSize 2652783500 --binSize 10 --smoothLength 50 --normalizeUsing CPM --extendReads 200)
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: 1.5x107 HoxB8 EV and DNMT3AR882H cells were seeded at 5x105 per ml in POG complete media.

extract_protocol:
Samples were fixed with formaldehyde solution (1% w/v) for 15mins with gentle rocking and quenched by adding 2.5M glycine for 5mins.  2x107 cells were washed twice in ice cold PBS and resuspended in 1ml of ChIP Lysis buffer (1% SDS (w/v), 10mM EDTA, 50mM Tris-HCl pH 8.0, cOmplete mini EDTA-free protease inhibitor cocktail (Sigma-Aldrich)). Each sample was sonicated using a Covaris S220 Focused Ultrasonicator for 40 cycles (30s on (5% duty cycle; intensity - 5200 cycles per burst), 20s off). 9ml of modified RIPA buffer (1% (v/v) TritonX100, 0.1% (v/v) deoxycholate, 90mM NaCl, 10mM Tris-HCl pH8, cOmplete mini EDTA-free protease inhibitor cocktail (Sigma-Aldrich)) was added to each sample. 5% from each sample was collected and pooled for an input sample. 2.5µg of Bach1 antibody (R&D systems #AF5777) was added to each sample with gentle rocking overnight at 4°C. Protein G Dynabeads (Theromo Fisher) were washed twice in modified RIPA buffer and added to each sample for 2hrs with gentle mixing at 4°C. Dynabeads were washed 3 times in wash buffer (0.1% (w/v) SDS, 1% (v/v) TritonX100 v/v, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8) for 5 min.  Reverse crosslinking buffer: (1% (w/v) SDS, 100mM NaHCO3, 200mM NaCl, 300µg/ml Proteinase K) was added to each sample and incubated at 65°C for overnight. DNA was extracted with ChIP DNA Clean & Concentrator kit (Zymo Research).
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina kit (New England Biolabs) according to the manufacturer's protocol. Cleanup of adaptor ligated DNA was performed using AMPure XP beads. Purified DNA was amplified using PCR enrichment with 12 and 16 cycles for input and ChIP samples respectively. Libraries were sequenced on an Illumina Nextseq500 with 75bp single end reads to a depth of 21-35 million reads.

treatment_protocol: DNMT3AR882H cells were treated with DMSO (0.16% v/v) or hemin (40μM) for 24hrs.

tag: cell line


title: Pt04 [0521_12145_H133A_DMG47]

type: RNA

city: Atlanta

first: Luke

last: Brewster

state: GA

address: 101 Woodruff Circle

department: Surgery

country: USA

institute: Emory University

hyb_protocol: Complementary DNA probes were generated without amplification and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Partek Genomic Suite using Affymetrix default analysis settings and RMA was used as normalization
Using Partek Genomic Suite, the expression profile of Stenosis IV and Stenosis V grade were compared to Stenosis I grade and Processed Data files were exported.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: posterior tibial artery from Patient Pt04 with stenosis score 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). RNA quality was assessed by electropherogram using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

growth_protocol: Human PAD arteries were obtained from patients undergoing amputation.

extract_protocol: About 150 mg tissues were collected for RNA extraction using the standard TRIzol protocol

treatment_protocol: Two-millimeter cross sections were processed for histology at representative points along each artery. Histologic sections were graded for the degree of stenosis as follows: zero – none, one - 1-25%, two – 26-50%, three – 51-75%, four – 76-95%, five – 96-100%

tag: tissue

value: pheripheral artery

tag: patient age

tag: stenosis score


title: PRO-seq_Rep2_HS30min

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A, 17165 Solna, Sweden

department: Department of Gene Technology

country: Sweden

institute: Science for Life Laboratory, KTH Royal Institute of Technology

library_source: other

data_processing:
In-line adapters were removed using Fastp tool (Chen et al., 2018, Bioinformatics, 34, i884-i890) and the read 1 reverse complemented with Fastx toolkit (https://github.com/agordon/fastx_toolkit).
Reads were mapped to canFam6 genome using Bowtie2 (Langmead et al., 2009, Genome Biol. 10, R25) with parameters --end-to-end --ff.
Mapped reads were processed to bigWig files.
Nascent transcription was quantified at promoter-proximal regions, gene bodies and enhancers as described in Rabenius et al. (2022), STAR protocols 3, 101036.
DESeq2 (Love et al., 2014, Genome Biol. 15, 550) was used to determine statistically significant changes in gene and enhancers transcription.
Assembly: canFam6
Supplementary files format and content: bigWig files are provided for visualization of PRO-seq data for each sample. Two separate bigWig files are provided for plus (pl) and minus (mn) strand. bigWig files were normalized to read counts in the ends of long genes as described in Vihervaara et al., (2017), Nat. Commun. 8(1):255.
Library strategy: PRO-seq

molecule: other

organism: Canis lupus familiaris

growth_protocol: DH82 cells were grown in EMEM medium supplemented with 10% FBS, 100 U/ml penicillin/streptomycin, non-essential aminoacids including L-glutamine, and maintained at 37°C in a humidified 5 % CO2 atmosphere.

extract_protocol:
Chromatin was used as starting material, after which Precision Run-On sequencing (PRO-seq) was performed as previously described in Mahat et al. (2016), Nat. Protocol 11, 1455–1476, using sample-specific in-line barcodes described in Vihervaara et al. (2023), Nat. Commun 14, 7039.
Libraries were constructed using TruSeq small-RNA adaptors as described in VIhervaara et al. (2023), Nat. Commun 14, 7039.

treatment_protocol: Cells were either non-treated (cultured in optimal growth conditions) or exposed to heat shock at 42°C for 30 min by submerging cell culture plates into a pre-warmed waterbath.

tag: cell type

value: Macrophage-like cell line

tag: genotype

value: WT

tag: treatment

value: Heat shock (42, 30 min)


title: PRO-seq_Rep2_C

value: Control


title: Pt010 [0521_12144_H133A_DMG55]

source_name: peroneal artery from Patient Pt010 with stenosis score 1


title: S37F_1_H2

city: Leiden

first: Karamjit

middle: Singh

last: Dolt

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: Sample-13

library_source: transcriptomic

data_processing:
A Galaxy workflow consisting of the following tools were used to perform (reads to count) transcriptome analysis.
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2
Assembly: mm10 full
Supplementary files format and content: FeatureCount output file in text file format containing raw counts.

source_name: Embryonic

growth_protocol: E14 cells were cultured in ES medium with serum at 5%CO2 and humidified incubator at 37 degree celcius

extract_protocol:
Total RNA isolation was performed using the RNAeasy mini kit (Qiagen) according to the manufacturer’s instructions.
the generation of cDNA and the RNA-seq library, we used the method that was described as mcSCRB-seq (PMID 30050112).

treatment_protocol: Respective Chiron treatment was performed for 48 hours

value: Embryonic

value: Embryonic Stem Cells

tag: duration

value: 48 Hours


title: Pt04 [0521_12078_H133A_DMG46]

source_name: anterior tibial artery from Patient Pt04 with stenosis score 4


title: Pt09 [0521_12142_H133A_DMG53]

source_name: anterior tibial artery from Patient Pt09 with stenosis score 4


title: Pt05 [0521_12146_H133A_DMG48]

source_name: anterior tibial artery from Patient Pt05 with stenosis score 0


title: Pt05 [0521_12079_H133A_DMG49]

source_name: peroneal artery from Patient Pt05 with stenosis score 1


title: S37C_1_G12

description: Library name: Sample-12


title: d24 mouse testis H3K27Ac ChIP-Seq

description: Library name: H3K27Ac ChIP d24

tag: chip antibody


title: Pt020 [0521_12143_H133A_DMG54@N2]

source_name: peroneal artery from Patient Pt020 with stenosis score 1


title: S45C_1_D3

description: Library name: Sample-16


title: HIV+ subject 7 post-therapy

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression from ARVMs treated with serum from HIV+ subject 7, post-therapy.

data_processing:
STAR (version 2.7.9a) was used to align sequence reads to human genome build hg38.
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 109 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.32.0).
Assembly: rn7
counts.txt: 30523 x 18 matrix of counts produced by Subread featureCounts
varianceStabilizingTransformation.txt: 30523 x 18 matrix of variance-stabilizing-transformed (VST) expression values

molecule: polyA RNA

organism: Rattus norvegicus

source_name: adult rat ventricular myocytes (ARVMs)

growth_protocol: Dulbecco's Modified Eagle Medium (DMEM) was supplemented with 2mg/mL bovine serium albumin, 2mmol/L L-carnitine, 5 mmol/L creatine, 5 mmol/L taurine, 100 IU/mL penicillin and 10 g/mL streptomycin.

extract_protocol:
RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
Libraries were prepared from 100 ng total RNA enriched for mRNA using Illumina’s Stranded mRNA Library Preparation kit.

treatment_protocol: Cells were incubated in supplemented DMEM with addition of 10% human serum from HIV patients before and after receiving ART and non-HIV-infected control subjects for 24 hours.

value: adult rat ventricular myocytes (ARVMs)

tag: batch

value: batch 2

tag: subject

value: HIV+ subject 7

tag: group

value: post-therapy


title: P0010  [0521_12080_H133A_DMG26]

source_name: posterior tibial artery from Patient P0010  with stenosis score 4


title: d16 mouse testis H3K27Ac ChIP-Seq

description: Library name: H3K27Ac ChIP d16


title: S37A_1_A10

description: Library name: Sample-11


title: HIV+ subject 6 post-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 6, post-therapy.

value: HIV+ subject 6


title: d12 mouse testis H3K27Ac ChIP-Seq

description: Library name: H3K27Ac ChIP d12


title: HIV+ subject 2 post-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 2, post-therapy.

value: HIV+ subject 2


title: 10uM_Chiron_E14_2

description: Library name: Sample-10


title: Pt02 [0521_12074_H133A_DMG42]

source_name: posterior tibial artery from Patient Pt02 with stenosis score 1


title: Tumor Sample 30

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: TC902

data_processing:
Illumina sequence reads were mapped to CanFam3.1 genome using STAR aligner with default settings
The --quantMode GeneCounts paramater was used extracting raw gene count data
Assembly: CanFam3.1
Supplementary files format and content: comma-separated csv file include raw count values for each tumor samples: Canine_Thyroid_Carcinoma_Raw_CountData.csv

source_name: Thyroid gland

extract_protocol:
TRIzol (Invitrogen), was used to  extract total RNA from 30 primary tumors. The RNA samples were cleaned using RNeasy cleanup (Qiagen), respectively. RNA was quantified on a NanoDrop Microvolume  Spectrophotometer and quality was assessed by Bioanalyzer (Agilent).
The total RNA was extracted from 30 samples were 300 ng were processed using Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, CA, USA, Catalogue # R3000) to generate RNAseq libraries.

value: Thyroid gland

value: tumor tissue


title: P0013  [0521_12073_H133A_DMG35]

source_name: peroneal artery from Patient P0013  with stenosis score 4


title: HIV+ subject 7 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 7, pre-therapy.

value: pre-therapy


title: 10uM_Chiron_E14_1

description: Library name: Sample-09


title: P0015  [0521_11506_H133A_DMG41]

source_name: peroneal artery from Patient P0015  with stenosis score 4

value: pheripheral artery


title: Tumor Sample 29

description: Library name: TC815


title: P0012  [0521_12072_H133A_DMG31]

source_name: posterior tibial artery from Patient P0012  with stenosis score 4


title: HIV+ subject 6 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 6, pre-therapy.


title: Tumor Sample 28

description: Library name: TC812


title: 7_5uM_Chiron_E14_2

description: Library name: Sample-08


title: 7_5uM_Chiron_E14_1

description: Library name: Sample-07


title: HIV+ subject 2 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 2, pre-therapy.


title: Tumor Sample 26

description: Library name: TC640


title: Tumor Sample 27

description: Library name: TC67


title: Healthy control 6

description: Gene expression from ARVMs treated with serum from healthy control 6.

value: healthy control 6

value: control


title: Tumor Sample 25

description: Library name: TC627


title: 5uM_Chiron_E14_2

description: Library name: Sample-06

value: WT


title: 2.5uM_Chiron_E14_2

description: Library name: Sample-04


title: Tumor Sample 24

description: Library name: TC538


title: 5uM_Chiron_E14_1

description: Library name: Sample-05


title: P0015  [0521_11504_H133A_DMG39]

source_name: anterior tibial artery from Patient P0015  with stenosis score 4


title: Healthy control 5

description: Gene expression from ARVMs treated with serum from healthy control 5.

value: healthy control 5


title: HIV+ subject 4 post-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 4, post-therapy.

value: batch 1

value: HIV+ subject 4


title: Tumor Sample 23

description: Library name: TC2402


title: 2.5uM_Chiron_E14_1

description: Library name: Sample-03

value: Embryonic

value: Embryonic Stem Cells

value: 48 Hours


title: P0013  [0521_11500_H133A_DMG33]

source_name: anterior tibial artery from Patient P0013  with stenosis score 4


title: P0004  [0521_11408_H133A_DMG9]

source_name: popliteal  artery from Patient P0004  with stenosis score 4


title: P0010  [0521_11495_H133A_DMG24]

source_name: peroneal artery from Patient P0010  with stenosis score 4


title: P0005  [0521_11493_H133A_DMG12]

source_name: anterior tibial artery from Patient P0005  with stenosis score 5


title: HIV+ subject 3 post-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 3, post-therapy.

value: adult rat ventricular myocytes (ARVMs)

value: HIV+ subject 3


title: Tumor Sample 22

description: Library name: TC22


title: 0uM_Chiron_E14_2

description: Library name: Sample-02

source_name: Embryonic


title: HIV+ subject 1 post-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 1, post-therapy.

value: HIV+ subject 1

value: post-therapy


title: Healthy control 7

description: Gene expression from ARVMs treated with serum from healthy control 7.

value: batch 2

value: healthy control 7


title: P0003  [0521_11406_H133A_DMG7]

source_name: anterior tibial artery from Patient P0003  with stenosis score 5


title: Tumor Sample 21

description: Library name: TC2289

value: Thyroid gland

value: tumor tissue


title: Tumor Sample 20

description: Library name: TC2288


title: 0uM_Chiron_E14_1

description: Library name: Sample-01


title: HIV+ subject 3 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 3, pre-therapy.

value: pre-therapy


title: CD45+ cells from the brain tissue

city: nanjing

first: ying

last: gong

address: The Jiangning Campus of Nanjing Medical University is located at No. 101 Longmian Avenue, Jiangning District, Nanjing, China.

country: China

institute: nanjing medical university

description: Library name: A_161266_R1

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.12.0 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR (v2.6.1a). Uniquely mapped reads were then assigned to genes with FeatureCounts (v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: brain tissue

extract_protocol:
Six- to eight-week-old wild-type mice were injected via the tail vein with Cryptococcus neoformans (H99Tdtomato, expressing the fluorescent protein Tdtomato) to simulate fungal bloodstream infection. Six hours post-infection, the mice were euthanized, and cardiac perfusion with saline was performed to thoroughly remove free cells from the vasculature. Brain tissue was then harvested and prepared into a single-cell suspension. Flow cytometry was used to sort CD45+ leukocytes for subsequent single-cell sequencing.
Inject the cell suspension into the SCOPE-chip™ microfluidic chip. Based on the principle of “Poisson distribution”, single cells randomly settle into pre-fabricated microwells within the chip under the influence of gravity, ensuring that each microwell captures only one cell. Millions of barcoding beads carrying unique cell barcodes and molecular tags (UMIs) are added to the microwells. Through optimized design, it is ensured that each microwell contains only one bead coexisting with a single cell. Cell lysis is performed within the chip, releasing mRNA that binds to oligo(dT) sequences on the beads through its poly(A) tail, achieving mRNA capture. Simultaneously, each cell and its mRNA molecules are labeled with unique cell barcodes and UMIs. The beads containing the captured mRNA are collected, and the mRNA is reverse transcribed into cDNA, followed by amplification of the cDNA. The amplified cDNA is then fragmented, and adapter sequences are added to construct a sequencing library compatible with the Illumina sequencing platform. The constructed sequencing library is loaded onto the Illumina sequencing platform for high-throughput sequencing, ultimately obtaining gene expression data at the single-cell level.

value: brain tissue

value: CD45+ cells

value: infected with the H99Tdtomato strain


title: HIV+ subject 4 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 4, pre-therapy.

value: batch 1


title: Tumor Sample 19

description: Library name: TC2110


title: HIV+ subject 1 pre-therapy

description: Gene expression from ARVMs treated with serum from HIV+ subject 1, pre-therapy.


title: P0010  [0521_11403_H133A_DMG23]

source_name: anterior tibial artery from Patient P0010  with stenosis score 4

value: pheripheral artery


title: Tumor Sample 18

description: Library name: TC2089


title: P0014  [0521_11502_H133A_DMG36]

source_name: anterior tibial artery from Patient P0014  with stenosis score 4


title: Bleo2

city: Saint Louis

first: Jeffrey

last: Koenitzer

state: MO

address: 660 Euclid Ave.

institute: Washington University in St. Louis

data_processing:
Demultiplexing, barcode processing, and gene counting were performed using CellRanger software (v7.0.0) including intronic reads
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: lung

extract_protocol:
Mice (n=3) were treated with intranasal bleomycin and lungs harvested at 14 days post-injury. Lungs were minced and digested in a solution containing 1 mg/ml collagenase A, 0.08 mg/mL DnaseI, 5% FBS, and 10 mM HEPES in PBS. Digests were passed through a 70 micron strainer followed by 10X Chromium encapsulation using v3'3.1 kits.
Libraries were constructed according to manufacturer's protocol (10X Genomics, 3'v3.1). Cells were loaded in master mix with partitioning oil and beads to a chip and GEMs formed using a 10X Chromium device. Reverse transcription was performed to create barcoded cDNA from poly-A RNAs in each GEM. Pooled cDNA was cleaned with Silane Dynabeads, amplified, and size-selected using SPRIselect. Illumina R2 primer sequence was added along with paired-end constructs with P5/P7 sequences and a sample index for sequencing.

value: lung

value: lung cells


title: Bleo3


title: P0003  [0521_11405_H133A_DMG6]

source_name: posterior tibial artery from Patient P0003  with stenosis score 5


title: Tumor Sample 17

description: Library name: TC2011


title: P0009  [0521_11402_H133A_DMG22]

source_name: peroneal artery from Patient P0009  with stenosis score 4


title: Bleo1


title: P0008  [0521_11400_H133A_DMG19]

source_name: peroneal artery from Patient P0008  with stenosis score 5


title: Healthy control 3

description: Gene expression from ARVMs treated with serum from healthy control 3.

source_name: adult rat ventricular myocytes (ARVMs)

value: healthy control 3

value: control


title: Motor cortex, Pgbd5-/-, ATAC, rep 3

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

country: Canada

institute: Lady Davis Institute for Medical Research

description: ATAC part of a 10X Genomics scMultiome sample

data_processing:
Cell Ranger ARC v2.0.0 (10X Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for scMultiome samples. Alignment was performed using the mm10 reference genome build coupled with the Ensembl 98 gene annotation. Reads that mapped to the intronic regions were excluded for the RNA modality.
Quality control (QC) and data processing steps were performed using Signac v1.3.0 and Seurat v4.3.0. QC metrics for RNA and ATAC modalities were calculated independently but were jointly used to filter cells. In the RNA modality, cells were filtered on the number of genes, unique molecular identifiers (UMIs), and mitochondrial content. In the ATAC modality, cells were filtered on the number of peaks detected, transcription start site enrichment, and nucleosome signal.
Normalization and dimensionality reduction: For the RNA modality, libraries were scaled to 10,000 UMIs per-cell and log normalized. UMI counts and mitochondrial content were regressed out from normalized gene counts and the residuals z-scored gene-wise. Dimensionality reduction was performed using principal-component analysis (PCA) on the top 2,000 most variable features. For the ATAC modality, peaks were called using MACS2 (v2.2.7.1) using the CallPeaks function from Signac library with default parameters. ATAC reads were quantified in each peak per cell and a resulting count matrix was generated. Dimensionality reduction was performed using latent semantic indexing (LSI). A weighted nearest neighbor graph was constructed between all cells using the first 30 principal components from the RNA data and the top 6 dimensions of the LSI reduction from the ATAC data with the following default parameters: 20 multimodal neighbors, 200 approximate neighbors and L2 normalization enabled. This weighted nearest neighbor graph was used as input for projection into two dimensions using uniform manifold approximation and projection (UMAP) and for clustering using a shared nearest-neighbor (SNN) algorithm based on the Louvain algorithm on a k-nearest neighbor graph with k = 20 and resolution 0.2.
Doublet detection: For each sample, doublets were identified using scDblFinder v1.8.0 with the recommended cluster-based approach and with the RNA modality counts.
Cell type annotation in single nuclei RNA data: Annotation of cell types was performed using a consensus approach between seven different reference-based annotation tools, using two references separately. Six machine learning-based prediction tools (ACTINN, scAnnotate, SciBet, SingleR, scClassify, and Support Vector Machines) and one model based on maximum Spearman correlation were trained on a developmental murine atlas of the forebrain (Jessa et al., Nat. Genet. 2022) or a postnatal murine atlas of the isocortex with high neuronal diversity (Yao et al., Cell 2021). A consensus label annotation was assigned to each cell using a majority vote approach between tools (with at least two tools agreeing). Predictions based on the developmental atlas (Jessa et al.) were used to assign broad cell types, while predictions based on Yao et al. were used to annotate neuronal types. For visualizing multiple samples, samples were first merged by genotype, generating a joint sample object for Pgbd5wt/wt and Pgbd5-/- separately. Clusters in the genotype joint objects consisting of a mixture of conflicting cell lineage annotations were manually inspected by assessing their gene signatures. Some of these clusters were then reannotated as “Striatal Neurons” or “Other Neurons” by assessing the expression of the cluster gene signatures in a whole adult mouse brain atlas.
Assembly: mm10
Supplementary files format and content: *.Rds: R Seurat object containing RNA data (assay RNA), ATAC data (assay ATAC) and metadata for each cell, including cell type annotation (Level1_CellClass_Prediction and Level2_CellClass_Prediction)

source_name: Motor cortex

growth_protocol: Cells were harvested from 21 days old mice of Pgbd5wt/wt and Pgbd5-/- genotypes

extract_protocol:
Brains from 21 days old Pgbd5wt/wt (n=3) and Pgbd5-/- (n=3) littermates were extracted. Motor cortices were dissected, flash frozen and stored at –80 C. Nucleus extraction was performed according to the protocol from Masilionis et al (62) using the Singlulator100 (S2 Genomics). Extracted nuclei were stained with 7-aminoactinomycin D (Invitrogen) and FAC-sorted for further nuclei purification.
Ten thousand nuclei were targeted for library construction using ChromiumNextGEM Multiome ATAC + Gene Expression kit (10xGenomics)
Other: Single cell multiome ATAC + Gene Expression

treatment_protocol: No treatment was used

value: Motor cortex

value: Pgbd5 -/-

tag: Sex

value: Female


title: Tumor Sample 16

description: Library name: TC1994

source_name: Thyroid gland


title: Tumor Sample 15

description: Library name: TC1979


title: Motor cortex, Pgbd5-/-, ATAC, rep 2

value: Male


title: P0007  [0521_11398_H133A_DMG17]

source_name: posterior tibial artery from Patient P0007  with stenosis score 4


title: SCAF3943_MAF1433_B7H3

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

description: 10X Genemics

data_processing:
Base calling was performed using RTA v3.4.4 before demultiplexing using CellRanger v7.2.0 (10X Genomics, Bcl2fastq 2.20.0). The resulting FASTQ files were aligned to a custom human GRCh38 and mouse mm10 reference sequence with the binding domain sequences of CAR T, using CellRanger v7.2.0 (STAR v2.7.2a). Both raw and filtered gene-barcode matrices were created with CellRanger and further analyzed in Seurat (v5.1.0, R package). Ambient RNA was removed with SoupX, and doublets with scrublet. Low-quality cells with < 300 genes, > 7500 genes, > 70% of reads mapped to mitochondrial genes, < 500 unique molecular identifiers (UMI), or > 50,000 UMI were removed. The data was integrated across different samples with the reciprocal principal component analysis (RPCA) in Seurat. To normalize the data, we used the ‘NormalizeData’ function with the following parameters: normalization.method = "LogNormalize" and scale.factor = 10,000. The ‘FindVariableFeatures’ function with ‘vst’ method was applied to identify 3,000 highly variable genes. The ‘ScaleData’ function with default parameters was used to scale and center gene expression matrices. To create PCA plots, we ran the ‘RunPCA’ function. The shared nearest neighbor (SNN) graph was created with the ‘FindNeighbors’ function. We determined the clusters by applying the Louvain algorithm via the ‘FindClusters’ function, with a resolution set to 0.8. Manual cluster annotation was done by examining the top-ranked differentially expressed genes using the ‘FindAllMarkers’ function. CAR T cells were identified when the cells had more than 0 reads aligned to the corresponding binding domain sequence. Differential gene expression was calculated among all clusters. Data was visualized through uniform manifold approximation and projection (UMAP).
Assembly: GRCh38, mm10
Supplementary files format and content: matrix.h5

organism: Homo sapiens/Mus musculus xenograft

source_name: cerebella

extract_protocol:
Mice injected with the PDX MAF1433 in the cerebellum were treated with mock, GD2-CAR, GPC2-CAR, or B7-H3 CAR T-cells, or PBS. On day 10 post CAR injection, the cerebella were extracted and dissociated. Cells were submitted for scRNA-seq.
Library was constructed as per the manufacturer's instructions (10x Genomics, 5' protocol, v2).

value: cerebella

tag: pdx

value: Medulloblastoma

value: B7-H3-CAR T


title: Tumor Sample 14

description: Library name: TC1953

value: Thyroid gland

value: tumor tissue


title: SCAF3942_MAF1433_GPC2

description: 10X Genemics

value: GPC2-CAR T


title: P0007  [0521_11397_H133A_DMG16]

source_name: anterior tibial artery from Patient P0007  with stenosis score 4


title: Tumor Sample 13

description: Library name: TC1936


title: Motor cortex, Pgbd5-/-, ATAC, rep 1


title: Motor cortex, Pgbd5wt/wt, ATAC, rep 2

value: Pgbd5 +/+


title: Tumor Sample 12

description: Library name: TC1869


title: SCAF3941_MAF1433_GD2

description: 10X Genemics

value: GD2-CAR T


title: P0008  [0521_11399_H133A_DMG18]

source_name: anterior tibial artery from Patient P0008  with stenosis score 4

value: pheripheral artery


title: SCAF3940_MAF1433_Mock

description: 10X Genemics

value: not transduced (mock) T cell


title: P0005  [0521_11394_H133A_DMG11]

source_name: posterior tibial artery from Patient P0005  with stenosis score 5


title: Tumor Sample 11

description: Library name: TC1744


title: P0004  [0521_11393_H133A_DMG10]

source_name: proximal anterior tibial artery from Patient P0004  with stenosis score 4


title: SCAF3939_MAF1433_PBS

description: 10X Genemics

value: PBS


title: Motor cortex, Pgbd5-/-, RNA, rep 3

description: RNA part of a 10X Genomics scMultiome sample


title: Healthy control 4

description: Gene expression from ARVMs treated with serum from healthy control 4.

value: adult rat ventricular myocytes (ARVMs)

value: batch 1

value: healthy control 4


title: Tumor Sample 10

description: Library name: TC1601


title: P0002 [0521_11262_H133A_DMG5]

source_name: peroneal artery from Patient P0002 with stenosis score


title: Healthy control 1

description: Gene expression from ARVMs treated with serum from healthy control 1.

value: healthy control 1

value: control


title: Lung

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: Lung

data_processing:
The raw data was quality control using fastqc and then trimmed of the Nextera adaptor. Following trimming , the Drop-seq-Tools pipeline was used to filter the data with a Phred quality score threshold of 30 for sample barcode and UMI identify and poly(A) trimming. The filtered data was mapped to the mouse genome(mm10) using STAR 2.5.1a,and the reads counted using Drop-seq-Tools.
Assembly: mm10
Supplementary files format and content: csv

source_name: Lung

extract_protocol:
The RNA was isolated by Trizol from the Lung
The isolated RNA was eluted with the 20 μL reverse transcription mix consisting of 100 unit Hiscript III Reverse Transcriptase (Vazyme, R303), 40 unit RNase Inhibitor (Vazyme, R301),1 μL 25 mM dNTP mix, 1 μL 100 mM DTT, 1 μL 1 val Betaine (Sigma, B0300-1VL), 0.5 μL 5% Digitonin, 0.5 μL TSO-LNA and 0.5 μL 5 μM Probe. The reaction was incubated at 42℃ for 90 min. Following cDNA synthesis, the sample were pooled, cleaned and concentrated with cleanup beads at a 1:0.8 of DNA to beads ration and eluted in 30 μL of ddH2O. Second-strand synthesis and pre-amplification were performed in a 50 μL reaction, consisting of 2x KAPA HiFi Ready mix and 0.5 μM TSO-PCR primer, with the following PCR setup initial denaturation at 98 °C for 3 min, (denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, elongation at 72 °C for 6 min) repeated for 8 cycle, and a final elongation at 72 °C for 10 min. The DNA was cleanup using DNA cleanup beads at a ratio of 1:0.8 of DNA to beads and eluted with 30 μL of ddH2O. The library were prepared with the TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer. Probe was designed by TSO, sample barcode(7-mer),UMI(8-mer) and Oligo(dT).

value: Lung

value: tissue


title: P0032  [0092_39825_H133A_13845_DMG114]

source_name: peroneal artery from Patient P0032  with stenosis score 4


title: P0029  [0092_39822_H133A_13842_DMG103]

source_name: anterior tibial artery from Patient P0029  with stenosis score 5


title: Motor cortex, Pgbd5-/-, RNA, rep 2

value: Motor cortex

value: Pgbd5 -/-

value: Male


title: P0033 [0092_39826_H133A_13846_DMG115]

source_name: anterior tibial artery from Patient P0033 with stenosis score 4


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, LRFR 25h, R3

city: Lausanne

first: Christian

last: Fankhauser

state: Vaud

address: Batiment Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Library name: sav3_atac_LRFR25_R3

data_processing:
Reads were mapped to the A. thaliana reference genome (TAIR10) using STAR (Dobin et al., 2013).
Duplicates were removed with MarkDuplicates and sorted with SortSam from Picard.
Blacklisted regions as defined in (Yin et al., 2021) were removed with BEDTools intersect (Quinlan, 2014).
To identify ATAC-seq peaks we employed MACS3 (Zhang et al., 2008) without shifting the reads introduced by Tn5. Consensus peaks were generated based on an overlap of at least 50% of length in all replicates. Only peaks detected in all replicates were considered and chloroplast and mitochondrial peaks were removed.
Bedgraph files created from BAM files with bamCoverage from deepTools (Ramirez et al., 2016) were scaled using –scaleFactor and converted to BigWig format with bedGraphToBigWig.
Assembly: TAIR10.45
Supplementary files format and content: scaled bigWig files at 10bp resolution
Supplementary files format and content: tab-delimited text file with raw counts for each peak obtained with MACS3

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown on 1/2 MS media without vitamins in HRFR until LRFR treatment

extract_protocol:
Nuclei were isolated using the INTACT method (You et al., 2017). Briefly, nuclei were conjugated to Dynabeads™ M-280 Streptavidin and captured on the magnetic rack. Supernatant was removed and beads were washed twice with NPB, then left resuspended in NPB on ice. The purified nuclei (25000 – 50000 nuclei) were incubated with Tagment DNA TDE1 Enzyme and Buffer mix at 37°C for 30 min. DNA was purified with Wizard SV Gel and PCR clean-up system.
Library was amplified using 2X KAPA HiFi HotStart and Nextera Primer Mix (i7+i5). Amplified libraries were purified with ProNEx Size selective Purification System and only libraries with fragments between 100 bp and 600 bp, peaking at 300 bp were considered.

treatment_protocol: Exposure to 1h or 25h of LRFR

value: seedling

value: sav3-2; pUBQ10::BirA; pUBQ10::NTF

value: LRFR 25h


title: Motor cortex, Pgbd5wt/wt, ATAC, rep 3

value: Pgbd5 +/+

value: Female


title: Motor cortex, Pgbd5-/-, RNA, rep 1


title: Tumor Sample 8

description: Library name: TC1473

value: Thyroid gland

value: tumor tissue


title: Motor cortex, Pgbd5wt/wt, ATAC, rep 1


title: Arabidopsis seedlings, ATAC, sav3-2, Col-0, 7-day-old, LRFR 1h, R3

description: Library name: sav3_atac_LRFR1_R3

value: LRFR 1h


title: Motor cortex, Pgbd5wt/wt, RNA, rep 3


title: P0027 [0092_39821_H133A_13841_DMG98]

source_name: posterior tibial artery from Patient P0027 with stenosis score 1

value: pheripheral artery


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, HRFR, R3

description: Library name: sav3_atac_HRFR_R3

value: HRFR


title: Motor cortex, Pgbd5wt/wt, RNA, rep 2


title: Tumor Sample 7

description: Library name: TC1241


title: P0037  [0092_39820_H133A_13840_DMG129]

source_name: superficial femoral artery from Patient P0037  with stenosis score 1


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 25h, R3

description: Library name: Col-0_atac_LRFR25_R3

value: Col-0; pUBQ10::BirA; pUBQ10::NTF


title: Tumor Sample 6

description: Library name: TC1218


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 1h, R3

description: Library name: Col-0_atac_LRFR1_R3


title: P0022  [0092_39815_H133A_13835_DMG86]

source_name: posterior tibial artery from Patient P0022  with stenosis score 1


title: P0026  [0092_39817_H133A_13837_DMG96]

source_name: peroneal artery from Patient P0026  with stenosis score 1


title: FxrKI3_scRNAseq

city: Shanghai

first: Chenyang

last: Fu

address: 197 Ruijin Road II

department: Department of Endocrine and Metabolic Diseases

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)  and Seurat v4.0.3 was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islet tissue

growth_protocol: Primary mouse islets were maintained in Hanks' balanced  salt solution supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were isolated per 10x Genomics manufacture instructions.
Cellular suspensions were loaded on the Chromiu Controller (10x Genomics, Pleasanton) to generate Gel Bead-In-Emulsions (GEMs). Barcoded sequencing libraries were conducted following the instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics).

treatment_protocol: We generated a knock-in mouse that could overexpress Fxr specifically in β cells (βFxrKI) by crossing with Ins2-Cre mice. A cassette of Fxr (Nr1h4) cDNA sequence with a 3xflag in N terminal followed a sequence containing the CAG promoter and loxp-PGK-Neo-polyA-loxp and was knocked in the first intron of the Rosa26 site.

value: islet cells

value: pancreatic islet tissue

tag: strain

value: postnatal 3 weeks


title: Tumor Sample 4

description: Library name: TC1164

source_name: Thyroid gland


title: Tumor Sample 9

description: Library name: TC1593


title: P0022  [0092_39814_H133A_13834_DMG83]

source_name: peroneal artery from Patient P0022  with stenosis score 1


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, HRFR, R3

description: Library name: Col-0_atac_HRFR_R3


title: Tumor Sample 3

description: Library name: TC1123


title: FxrKI1_scRNAseq

description: 10x Genomics

value: postnatal 1 week


title: Tumor Sample 2

description: Library name: TC1088


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, LRFR 25h, R2

description: Library name: sav3_atac_LRFR25_R2


title: P0020  [0092_39812_H133A_13832_DMG77]

source_name: peroneal artery from Patient P0020  with stenosis score 1


title: Control3_scRNAseq

description: 10x Genomics


title: adult mouse testis RNA-Seq

description: Library name: RNA adult

source_name: testis

value: testis

value: adult


title: Tumor Sample 1

description: Library name: TC1020


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, HRFR, R2

description: Library name: sav3_atac_HRFR_R2

value: seedling


title: Control2_scRNAseq

description: 10x Genomics

value: postnatal 2 weeks


title: Motor cortex, Pgbd5wt/wt, RNA, rep 1

source_name: Motor cortex

value: Motor cortex

value: Male


title: P0018  [0092_39809_H133A_13829_DMG63]

source_name: anterior tibial artery from Patient P0018  with stenosis score 4


title: d24 mouse testis RNA-Seq

description: Library name: RNA d24


title: RNA-seq_Rep3_HS60min

data_processing:
Reads were mapped to canFam6 genome using HISAT2 (Kim et al., 2019, Nat. Biotech. 37, 907-915) with parameters --rna-strandness FR --no-mixed --no-discordant.
Mapped reads were processed to bigWig files.
Reads mapping to exons were counted using featureCounts tool (Liao et al., 2014. Bioinformatics, 30(7):923-30).
DESeq2 (Love et al., 2014, Genome Biol. 15, 550) was used to determine statistically significant changes in mature mRNA expression.
Assembly: canFam6
Supplementary files format and content: bigWig files are provided for visualization of RNA-seq data for each sample. Two separate bigWig files are provided for plus (pl) and minus (mn) strand. bigWig files were normalized to total read counts.

extract_protocol:
Total RNA was extracted with Trizol, and mRNA isolated using polyA selection according to Illumina's strand-specific mRNA-seq kit.
Libraries were generated using Illumina Stranded mRNA Prep kit (Illumina) and the commercial (IDT) dual-index primers.

treatment_protocol: Cells were either non-treated (cultured in optimal growth conditions) or exposed to heat shock at 42°C for 30 min or 60 min by submerging cell culture plates into a pre-warmed waterbath.

value: Macrophage-like cell line

value: WT

value: Heat shock (42C, 60 min)


title: Tumor Sample 5

description: Library name: TC1213

value: Thyroid gland

value: tumor tissue


title: P0020  [0092_39811_H133A_13831_DMG75]

source_name: anterior tibial artery from Patient P0020  with stenosis score 5

value: pheripheral artery


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 25h, R2

description: Library name: Col-0_atac_LRFR25_R2

value: Col-0; pUBQ10::BirA; pUBQ10::NTF

value: LRFR 25h


title: d16 mouse testis RNA-Seq

description: Library name: RNA d16


title: Control1_scRNAseq

description: 10x Genomics

value: islet cells

value: pancreatic islet tissue


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 1h, R2

description: Library name: Col-0_atac_LRFR1_R2

value: LRFR 1h


title: FxrKI2_scRNAseq

description: 10x Genomics


title: FxrKI3_scATACseq

description: 10x Genomics

library_source: genomic single cell

data_processing:
Single cell ATAC-seq processed data was generated using cellranger ATAC v1.1.0 software. Seurat v4.0.3 and Signac v1.2.1 was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells were isolated per 10x Genomics manufacture instructions. Nuclei isolation was performed according to the protocol of 10× Genomics.
The library was constructed according to the Chromiun signal Cell ATAC Reagent Kits protocol (10× Genomics).

value: postnatal 3 weeks


title: d12 mouse testis RNA-Seq

description: Library name: RNA d12

value: testis


title: RNA-seq_Rep3_C

value: Control


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, HRFR, R2

description: Library name: Col-0_atac_HRFR_R2

value: seedling

value: HRFR


title: PBS_72h_W48h_Rep2

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: ATAC_Sample_8

data_processing:
Adapters and low-quality sequences were removed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using Bowtie2 (v2.4.4) with parameters optimized for ATAC-seq. PCR duplicates, mitochondrial reads, and reads mapping to ENCODE blacklist regions were removed. Peaks were called using MACS3 (v3.0.0a7) with the --nomodel --shift -100 --extsize 200 options. BigWig files for visualization were generated using deepTools (v3.5.1).
Assembly: hg38
Supplementary files format and content: BigWig File

source_name: endothelium

growth_protocol: Primary human umbilical vein endothelial cells (HUVECs) were cultured in EGM-2 medium at 37°C in a humidified incubator with 5% CO₂. Cells were used at passage 4–6 and seeded in 12-well plates at a density of 3.2 × 10⁵ cells/well.

extract_protocol:
Nuclei were isolated from HUVECs and subjected to tagmentation using the Omni-ATAC protocol. Transposed DNA was purified using a MinElute PCR Purification Kit (Qiagen) prior to library amplification.
ATAC-seq libraries were prepared using the Nextera DNA Library Preparation Kit (Illumina) according to the Omni-ATAC protocol. Libraries were PCR-amplified, purified with AMPure XP beads (Beckman Coulter), quantified by Qubit and qPCR, and sequenced on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.

treatment_protocol: Cells were treated with recombinant human IL-6 (50 ng/mL) or PBS for 72 hours (first hit), followed by a 48-hour washout phase in fresh media. Subsequently, cells were re-stimulated with LPS (1 μg/mL) or PBS for 6 hours (second hit). Samples were collected after each phase to capture acute and memory responses.

value: endothelium

value: HUVEC

value: endothelial cells


title: RNA-seq_Rep2_HS60min

value: Macrophage-like cell line

value: WT

value: Heat shock (42C, 60 min)


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, LRFR 1h, R2

description: Library name: sav3_atac_LRFR1_R2

value: sav3-2; pUBQ10::BirA; pUBQ10::NTF


title: FxrKI1_scATACseq

description: 10x Genomics

value: postnatal 1 week


title: RNA-seq_Rep2_HS30min

value: Heat shock (42C, 30 min)


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, LRFR 1h, R1

description: Library name: sav3_atac_LRFR1_R1


title: RNA-seq_Rep2_C


title: RNA-seq_Rep3_HS30min


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, HRFR, R1

description: Library name: sav3_atac_HRFR_R1


title: Control2_scATACseq

description: 10x Genomics

value: islet cells

value: postnatal 2 weeks


title: RNA-seq_Rep1_HS60min


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 25h, R1

description: Library name: Col-0_atac_LRFR25_R1

value: Col-0; pUBQ10::BirA; pUBQ10::NTF

value: LRFR 25h


title: IL6_72h_W48h_Rep2

description: Library name: ATAC_Sample_6


title: P0017  [0092_39808_H133A_13828_DMG62]

source_name: peroneal artery from Patient P0017  with stenosis score 4

value: pheripheral artery


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, LRFR 1h, R1

description: Library name: Col-0_atac_LRFR1_R1

value: LRFR 1h


title: IL6_72h_W48h_Rep1

description: Library name: ATAC_Sample_5


title: Control1_scATACseq

description: 10x Genomics

value: pancreatic islet tissue


title: FxrKI2_scATACseq

description: 10x Genomics


title: Arabidopsis seedlings, ATAC, Col-0, 7-day-old, HRFR, R1

description: Library name: Col-0_atac_HRFR_R1

value: seedling

value: HRFR


title: MTHFD1-K56R cells cultured in dialysed IMDM supplemented with 50µM adenosine, replicate 2

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Library name: ADE2

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling was performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Sequencing data was analyzed using PinAPL-Py online tool (https://pinapl-py.ucsd.edu; Sci Rep. 2017 Nov 20;7(1):15854). PinAPL-PY matches obtained sgRNA reads to sgRNA sequences the Brunello reference library, which was desgined based on hg38. The sgRNA reference library list was selected at the PinAPL-PY, but can be optionally found at the respective Addgene (#73179) website.
Assembly: hg38
Supplementary files format and content: count files
Library strategy: CRISPR Screen

extract_protocol:
After the end of the genome-wide KO screen, remaining cells were collected and gDNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen).
The library was amplified using Takara Ex Taq DNA polymerase, yielding the sgRNA sequence. P5 and P7 index primers in unique combination were used for amplification (primers adapted from Mol Cell 75, 849-858 e848 (2019)). PCRs were run with cycle numbers below saturation, as judged by initial control PCRs. Gel bands of expected size were gel extracted and gel purified. Quantity was determined using Qubit and equal amounts were pooled and sent for sequencing.

treatment_protocol: The Human CRISPR Knockout Pooled Library (Brunello) was obtained from Addgene (#73179) and lentiviral packed according to standard procedures. HAP1 MTHFD1-K56R cells were transduced aiming for an MOI of approx. 1 and >500x sgRNA. After puromycin selection, cells were cultured in dialysed medium or dialysed medium supplemented with 50µM adenosine for 14 days (cells were expanded to maintain coverage). Cells were collected and subjected to downstream processing.

value: dialysed medium with 50µM adenosine


title: RNA-seq_Rep1_HS30min


title: MTHFD1-K56R cells cultured in dialysed IMDM supplemented with 50µM adenosine, replicate 1

description: Library name: ADE1


title: RNA-seq_Rep1_C

value: Control


title: PRO-seq_Rep1_HS30min

value: Macrophage-like cell line


title: PBS_72h_Rep1

description: Library name: ATAC_Sample_3

value: endothelium

value: HUVEC

value: endothelial cells


title: Arabidopsis seedlings, ATAC, sav3-2, 7-day-old, LRFR 25h, R1

description: Library name: sav3_atac_LRFR25_R1

value: sav3-2; pUBQ10::BirA; pUBQ10::NTF


title: MTHFD1-K56R cells cultured in dialysed IMDM, replicate 2

description: Library name: CTRL2

value: dialysed medium


title: PRO-seq_Rep1_C

value: WT


title: IL6_72h_Rep2

description: Library name: ATAC_Sample_2


title: WT and GeneX-/-; 0,4,14 days post Cryptococcus infection - CPB

city: Durham

first: Mari

middle: L.

last: Shinohara

state: NC

address: 207 Research Dr.

department: Integrative Immunobiology

institute: Duke University School of Medicine

description:
Library name: CPB
10x Genomics

data_processing:
The demultiplexing barcoded processing, gene counting and aggregation were made using Cell Ranger version 4.0.10 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
CMO#301:GeneX-/-,0d; CMO#302:GeneX-/-,4d; CMO#303:GeneX-/-,14d; CMO#304:WT,0d; CMO#305:WT,4d; CMO#306:WT,14d
Assembly: Mouse reference, mm10 (GENCODE vM23/Ensembl 98) (https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps#mouse-ref-2020-a)
Supplementary files format and content: Cell barcodes, expression matrix, and features outputs files

source_name: Brain

growth_protocol: A single colony of Cryptococcus 52D was grown in 4mL of YPD broth overnight in an incubator at 30C with 225 RPM rotation speed. Cryptococcus yeast washed, counted and resuspended in 1X phosphate buffered saline (PBS) at a concentration of 10^6 yeast cells/100uL of 1X PBS.

extract_protocol:
To prepare brain single cell suspensions, tissues within the skull were harvested from mice. Isolated tissues (brain parenchyma including a trace amount of border tissues) were minced and digested in 1X PBS containing 5% heat-inactivated fetal bovine serum, 1mM HEPES, Collagenase D Type IV, and DNase I for 30 minutes at 37°C with constant shaking. Following digestion, tissue was passed through an 25G needle and filtered through a cell strainer. Samples were then resuspended in 38% Percoll and centrifuged at 532 x g for 30 minutes without brake. Following centrifugation, lipid and debris layer was aspirated from the top of the tube and pelleted brain cells were treated with red blood cell lysis. Cells were resuspended in 1X PBS containing 5% heat-inactivated fetal bovine serum, 1mM HEPES.
Library was performed according to the manufacturer's instructions using the  Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics)

treatment_protocol: Mice were retro-orbitally infected with 10^6 yeasts/mouse of Cryptococcus neoformans (deneoformans) strain 52D in 100uL of 1X PBS; brains were collected at 0, 4, and 14 days post infection

value: Brain

value: female

value: 9-10 weeks old

value: Whole brain cells (parenchyma and border-associated tissue of the brain)

value: Wildtype and GeneX-/-

value: Cryptococcus 52D infection; 0, 4, 14 days post infection

tag: library type

value: CellPlexBarcodes


title: PBS_72h_W48h_Rep1

description: Library name: ATAC_Sample_7


title: WT and GeneX-/-; 0,4,14 days post Cryptococcus infection - RNA

description:
Library name: RNA
10x Genomics

tag: age

value: Gene Expression


title: IL6_72h_Rep1

description: Library name: ATAC_Sample_1

tag: cell line


title: Control3_scATACseq

description: 10x Genomics

value: islet cells

tag: tissue

value: pancreatic islet tissue

value: postnatal 3 weeks


title: PBS_72h_Rep2

description: Library name: ATAC_Sample_4

value: endothelium


title: MTHFD1-K56R cells cultured in dialysed IMDM, replicate 1

description: Library name: CTRL1


title: TE5.LK.GEX

status: Public on Nov 05 2025

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: gene expression

data_processing:
DNA barcoding data were analyzed using the RPBPBR pileline (https://github.com/hoefer-lab/RPBPBR)
RNA barcoding data were analyzed using the single-cell veresion (https://github.com/WXlab-NJMU/scPolylox)
CITE-seq data were analyzed using the CellRanger software (version 7.1.0)
Assembly: mm10
Supplementary files format and content: tsv, Polylox barcode count table
Supplementary files format and content: h5, single-cell gene expression matrix
Supplementary files format and content: tsv, ADT count table
Library strategy: CITE-seq

source_name: Bone marrow

extract_protocol:
In bulk analysis, genomic DNA was prepared from sorted cells (30,000 cells) by proteinase K treatment and heat inactivation; Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit protocol.
cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit protocol. The PolyloxExpress cassette was amplified by PCR with the Polylox-specific primers.

value: Tie2MCM x RosaPolyloxExpress

value: Bone marrow

value: LK

tag: induction time_point

tag: analysis time_point

value: 17 week


title: TE5.LSK.ADT

description: antibody-derived tags

molecule: protein

tag: cell type

value: LSK


title: TE5.LK.ADT

description: antibody-derived tags


title: RA8.MPP.ADT

description: antibody-derived tags

value: MPP

value: 27 week


title: RA8.MPP.GEX

description: gene expression


title: TE5.LSK.GEX

description: gene expression


title: FLAG 24hr 4

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

description:
FLAG.consensus_peaks.featureCounts.txt
FLAG.consensus_peaks.annotatePeaks.txt
FLAG.consensus_peaks.bed
FLAG.consensus_peaks.boolean.annotatePeaks.txt

data_processing:
Basecalls were performed using bclconvert (v3.10.5). Fastq files were processed using the nf-core/chipseq workflow (version 2.0.0)
Raw sequencing reads were preprocessed using FastQC and Trim Galore! to remove low-quality reads and adapters.
Alignment to GRCh38 with BWA
Picard’s MarkDuplicates, SAMtools and BAMTools were used post-alignment for filtering and removing unmapped, multi-mapped, PCR duplicate and mismatched reads
BEDTools and bedGraphToBigWig were used to create normalized bigwig files. high-quality alignment results were used to call narrow peaks by MACS2 against an IgG control with a P-value < 0.01. Consensus peaks set across all FLAG antibody samples are created using BEDTools.
Assembly: GRCh38
Supplementary files format and content: bigwigs for individual replicate,  and bed formats for consensus peaks and featurecounts

source_name: Skin

growth_protocol: Fibroblasts plated in DMEM supplemented with 10% FBS.

extract_protocol:
ChIP Seq according to methods of Tian et al.
RNA libraries for RNA-seq were prepared using Nextera XT DNA library Preparation Kit (Illumina) following the manufacturer's protocols.
Libraries were sequenced on the Illumina NextSeq 2000 P3 upto 200 cycles per manufacturer’s instructions.

treatment_protocol: Fibroblasts were stimulated with 10ng/ml recombinant human TGFb+IL1b.

value: Skin

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, GLIS3-FLAG

value: Fibroblast

tag: timepoint

tag: antibody

value: FLAG


title: FLAG 24hr 1


title: RA9.MPP.GEX

description: gene expression


title: FLAG 0hr 5


title: FLAG 24hr 2


title: IgG 0hr 4

description:
IgG.bigWig
FLAG.consensus_peaks.featureCounts.txt
FLAG.consensus_peaks.annotatePeaks.txt
FLAG.consensus_peaks.bed
FLAG.consensus_peaks.boolean.annotatePeaks.txt

value: IgG


title: FLAG 0hr 1


title: FLAG 0hr 3


title: FLAG 0hr 2


title: IgG 0hr 3


title: IgG 0hr 2


title: FLAG 24hr 3


title: LO, MB15A5, 72hr, rep4

city: Pasadena

first: Vera

last: Beilinson

state: CA

address: 1200 E. California Blvd

department: Biology and Bioengineering

institute: Caltech

description: Library name: c221_MB15A5_72hr_S4

data_processing:
Sequencing reads were quality-trimmed using fastp (v0.24.0) with default parameters.
Reads were quantified using featureCounts (v2.0.1).
Assembly: Genome V2. Genome annotations where based on V2.2 but updated using these samples.
Supplementary files format and content: .txt file, unnormalized counts

organism: Euprymna scolopes

source_name: light organ

extract_protocol:
Total light-organ RNA was isolated using an RNeasy Mini Kit (Qiagen, Germantown, MD, #74106) and Qiagen QIAshredder according to the manufacturer’s instructions. Samples were treated with TURBO DNase (Thermo Fisher Scientific, #AM1907) to remove DNA contamination.
mRNA was isolated from total RNA using NEBNect Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), and RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Ilumina (NEB, #E7770) following the manufacturer’s protocols

treatment_protocol: Juvenile hatchlings where exposed to bacteria for 3hr at 50,000 CFUI/mL.. Colonized squid (determined by luminesce) where kept till 72hrs. At 72hrs squid where placed in RNALater.

value: light organ

tag: treatment


title: LO, SR5, 72hr, rep4

description: Library name: c221_SR5_72hr_S5


title: LO, MJ11, 72hr, rep4

description: Library name: c221_MJ11_72hr_S2


title: LO, MB11B1, 72hr, rep4

description: Library name: c221_MB11B1_72hr_S3


title: LO, MJ11, 72hr, rep3

description: Library name: c217_MJ11_72hr_S7


title: LO, SR5, 72hr, rep3

description: Library name: c217_SR5_72hr_S10


title: LO, MB11B1, 72hr, rep3

description: Library name: c217_MB11B1_72hr_S8


title: LO, MB15A5, 72hr, rep3

description: Library name: c217_MB15A5_72hr_S9


title: RA9.MPP.ADT

description: antibody-derived tags


title: LO, ES114, 72hr, rep3

description: Library name: c217_ES114_72hr_S6


title: LO, SR5, 72hr, rep2

description: Library name: c211_SR5_72hr_S1


title: LO, MJ11, 72hr, rep2

description: Library name: c211_MJ11_72hr_S12


title: LO, MB11B1, 72hr, rep2

description: Library name: c211_MB11B1_72hr_S13


title: LO, ES114, 72hr, rep2

description: Library name: c211_ES114_72hr_S11


title: FLAG 0hr 4


title: LO, SR5, 72hr, rep1

description: Library name: c198_SR5_72hr_S4


title: IgG 0hr 1


title: LO, MB15A5, 72hr, rep1

description: Library name: c198_MB15A5_72hr_S6


title: LO, MJ11, 72hr, rep1

description: Library name: c198_MJ11_72hr_S3


title: LO, ES114, 72hr, rep4

description: Library name: c221_ES114_72hr_S1


title: LO, ES114, 72hr, rep1

description: Library name: c198_ES114_72hr_S2


title: TA8.proB_2

description:
Library name: TA8.proB_2
TA8.barcode.count.tsv

data_processing:
DNA barcoding data were analyzed using the RPBPBR pileline (https://github.com/hoefer-lab/RPBPBR).
Assembly: mm10
Supplementary files format and content: tsv, Polylox barcode count table

extract_protocol:
Genomic DNA was prepared from sorted cells (30,000 cells) by proteinase K treatment and heat inactivation.
DNA molecules were amplified using oligonucleotides #2426 and #2702, and PCR products were cleaned up using 0.7X AmpureXP beads for SMRT sequencing.

value: proB

value: Adult

value: 1 month


title: TA8.proB_1

description:
Library name: TA8.proB_1
TA8.barcode.count.tsv


title: TA8.STHSC

description:
Library name: TA8.STHSC
TA8.barcode.count.tsv

value: STHSC


title: TA8.preT

description:
Library name: TA8.preT
TA8.barcode.count.tsv

source_name: Thymus

value: Tie2MCM x RosaPolyloxExpress

value: Thymus

value: preT


title: TA8.MPP

description:
Library name: TA8.MPP
TA8.barcode.count.tsv

value: Bone marrow


title: TA8.MkMkP_1

description:
Library name: TA8.MkMkP_1
TA8.barcode.count.tsv

value: Mk&MkP


title: TA8.MkMkP_2

description:
Library name: TA8.MkMkP_2
TA8.barcode.count.tsv


title: TA8.LTHSC

description:
Library name: TA8.LTHSC
TA8.barcode.count.tsv

value: LTHSC


title: TA8.MEP_2

description:
Library name: TA8.MEP_2
TA8.barcode.count.tsv

value: MEP


title: TA8.GMP_1

description:
Library name: TA8.GMP_1
TA8.barcode.count.tsv

value: GMP


title: TA8.CMP_2

description:
Library name: TA8.CMP_2
TA8.barcode.count.tsv

value: CMP


title: TA8.MEP_1

description:
Library name: TA8.MEP_1
TA8.barcode.count.tsv


title: TA8.GMP_2

description:
Library name: TA8.GMP_2
TA8.barcode.count.tsv


title: TA8.CMP_1

description:
Library name: TA8.CMP_1
TA8.barcode.count.tsv


title: TA7.STHSC

description:
Library name: TA7.STHSC
TA7.barcode.count.tsv


title: LO, MB15A5, 72hr, rep2

description: Library name: c211_MB15A5_72hr_S14


title: TA7.proB_1

description:
Library name: TA7.proB_1
TA7.barcode.count.tsv


title: TA7.proB_2

description:
Library name: TA7.proB_2
TA7.barcode.count.tsv


title: TA7.preT

description:
Library name: TA7.preT
TA7.barcode.count.tsv


title: TA7.MPP

description:
Library name: TA7.MPP
TA7.barcode.count.tsv

value: MPP


title: TA7.MkMkP_2

description:
Library name: TA7.MkMkP_2
TA7.barcode.count.tsv


title: TA7.MkMkP_1

description:
Library name: TA7.MkMkP_1
TA7.barcode.count.tsv


title: TA7.MEP_2

description:
Library name: TA7.MEP_2
TA7.barcode.count.tsv


title: TA7.MEP_1

description:
Library name: TA7.MEP_1
TA7.barcode.count.tsv


title: TA7.LTHSC

description:
Library name: TA7.LTHSC
TA7.barcode.count.tsv


title: LO, MB11B1, 72hr, rep1

description: Library name: c198_MB11B1_72hr_S5


title: TA7.GMP_1

description:
Library name: TA7.GMP_1
TA7.barcode.count.tsv


title: TA7.CMP_1

description:
Library name: TA7.CMP_1
TA7.barcode.count.tsv


title: TA7.CMP_2

description:
Library name: TA7.CMP_2
TA7.barcode.count.tsv


title: RCP4.T_6

description:
Library name: RCP4.T_6
RCP4.barcode.count.tsv

source_name: Spleen

value: Spleen

value: T

value: 12 month


title: TA7.GMP_2

description:
Library name: TA7.GMP_2
TA7.barcode.count.tsv


title: RCP4.T_4

description:
Library name: RCP4.T_4
RCP4.barcode.count.tsv


title: RCP4.T_5

description:
Library name: RCP4.T_5
RCP4.barcode.count.tsv


title: RCP4.T_3

description:
Library name: RCP4.T_3
RCP4.barcode.count.tsv


title: RCP4.T_2

description:
Library name: RCP4.T_2
RCP4.barcode.count.tsv


title: RCP4.ProB_2

description:
Library name: RCP4.ProB_2
RCP4.barcode.count.tsv

value: ProB


title: RCP4.ST_MPP

description:
Library name: RCP4.ST_MPP
RCP4.barcode.count.tsv

value: STHSC&MPP

value: Adult


title: RCP4.MyP_2

description:
Library name: RCP4.MyP_2
RCP4.barcode.count.tsv

value: MyP


title: RCP4.MyP_4

description:
Library name: RCP4.MyP_4
RCP4.barcode.count.tsv


title: RCP4.MyP_3

description:
Library name: RCP4.MyP_3
RCP4.barcode.count.tsv


title: RCP4.MyP_5

description:
Library name: RCP4.MyP_5
RCP4.barcode.count.tsv


title: RCP4.MyP_6

description:
Library name: RCP4.MyP_6
RCP4.barcode.count.tsv


title: RCP4.MyP_1

description:
Library name: RCP4.MyP_1
RCP4.barcode.count.tsv


title: RCP4.Mk

description:
Library name: RCP4.Mk
RCP4.barcode.count.tsv

value: Mk


title: RCP3.T_4

description:
Library name: RCP3.T_4
RCP3.barcode.count.tsv


title: RCP3.T_3

description:
Library name: RCP3.T_3
RCP3.barcode.count.tsv


title: RCP3.ST_MPP

description:
Library name: RCP3.ST_MPP
RCP3.barcode.count.tsv


title: RCP3.T_6

description:
Library name: RCP3.T_6
RCP3.barcode.count.tsv


title: RCP3.T_2

description:
Library name: RCP3.T_2
RCP3.barcode.count.tsv


title: RCP3.proB

description:
Library name: RCP3.proB
RCP3.barcode.count.tsv

value: proB


title: RCP3.MyP_6

description:
Library name: RCP3.MyP_6
RCP3.barcode.count.tsv


title: RCP3.T_5

description:
Library name: RCP3.T_5
RCP3.barcode.count.tsv


title: RCP3.MyP_5

description:
Library name: RCP3.MyP_5
RCP3.barcode.count.tsv


title: RCP4.T_1

description:
Library name: RCP4.T_1
RCP4.barcode.count.tsv


title: RCP3.MyP_4

description:
Library name: RCP3.MyP_4
RCP3.barcode.count.tsv


title: RCP3.MyP_3

description:
Library name: RCP3.MyP_3
RCP3.barcode.count.tsv


title: RCP3.MyP_1

description:
Library name: RCP3.MyP_1
RCP3.barcode.count.tsv


title: RCP3.MyP_2

description:
Library name: RCP3.MyP_2
RCP3.barcode.count.tsv


title: RCP3.T_1

description:
Library name: RCP3.T_1
RCP3.barcode.count.tsv


title: RA11.T_2

description:
Library name: RA11.T_2
RA11.barcode.count.tsv

value: 24 month


title: RCP4.proB_1

description:
Library name: RCP4.proB_1
RCP4.barcode.count.tsv

value: Bone marrow


title: RCP3.LTHSC

description:
Library name: RCP3.LTHSC
RCP3.barcode.count.tsv


title: RA11.proB

description:
Library name: RA11.proB
RA11.barcode.count.tsv


title: RA11.T_1

description:
Library name: RA11.T_1
RA11.barcode.count.tsv


title: RA11.MPP4_CD138p

description:
Library name: RA11.MPP4_CD138p
RA11.barcode.count.tsv


title: RA11.LK_2

description:
Library name: RA11.LK_2
RA11.barcode.count.tsv

value: LK


title: RA11.MPP4_CD138n

description:
Library name: RA11.MPP4_CD138n
RA11.barcode.count.tsv


title: RA11.LK_1

description:
Library name: RA11.LK_1
RA11.barcode.count.tsv


title: RA11.LTHSC

description:
Library name: RA11.LTHSC
RA11.barcode.count.tsv

value: LTHSC


title: RCP4.LTHSC

description:
Library name: RCP4.LTHSC
RCP4.barcode.count.tsv


title: RA11.Gr_1

description:
Library name: RA11.Gr_1
RA11.barcode.count.tsv

value: Gr


title: RA11.Gr_2

description:
Library name: RA11.Gr_2
RA11.barcode.count.tsv


title: RA11.EryP_2

description:
Library name: RA11.EryP_2
RA11.barcode.count.tsv

value: EryP


title: RA11.EryP_1

description:
Library name: RA11.EryP_1
RA11.barcode.count.tsv


title: RA11.DP_3

description:
Library name: RA11.DP_3
RA11.barcode.count.tsv

value: Thymus

value: DP


title: RA11.DP_2

description:
Library name: RA11.DP_2
RA11.barcode.count.tsv


title: RA11.DP_1

description:
Library name: RA11.DP_1
RA11.barcode.count.tsv


title: RA11.T_3

description:
Library name: RA11.T_3
RA11.barcode.count.tsv

value: Spleen


title: RCP3.Mk

description:
Library name: RCP3.Mk
RCP3.barcode.count.tsv


title: RA11.B_1

description:
Library name: RA11.B_1
RA11.barcode.count.tsv

value: B


title: RA10.T_3

description:
Library name: RA10.T_3
RA10.barcode.count.tsv

value: T


title: RA10.T_2

description:
Library name: RA10.T_2
RA10.barcode.count.tsv


title: RA11.B_2

description:
Library name: RA11.B_2
RA11.barcode.count.tsv


title: RA10.T_1

description:
Library name: RA10.T_1
RA10.barcode.count.tsv


title: RA10.proB

description:
Library name: RA10.proB
RA10.barcode.count.tsv


title: RA10.MPP4_CD138p

description:
Library name: RA10.MPP4_CD138p
RA10.barcode.count.tsv

value: CD138+ MPP4


title: RA10.MPP4_CD138n

description:
Library name: RA10.MPP4_CD138n
RA10.barcode.count.tsv

value: CD138- MPP4


title: RA10.LTHSC

description:
Library name: RA10.LTHSC
RA10.barcode.count.tsv


title: RA10.LK_2

description:
Library name: RA10.LK_2
RA10.barcode.count.tsv


title: RA10.LK_1

description:
Library name: RA10.LK_1
RA10.barcode.count.tsv


title: RA10.Gr_2

description:
Library name: RA10.Gr_2
RA10.barcode.count.tsv


title: RA10.Gr_1

description:
Library name: RA10.Gr_1
RA10.barcode.count.tsv


title: RA10.EryP_1

description:
Library name: RA10.EryP_1
RA10.barcode.count.tsv


title: RA10.B_2

description:
Library name: RA10.B_2
RA10.barcode.count.tsv


title: RA10.EryP_2

description:
Library name: RA10.EryP_2
RA10.barcode.count.tsv


title: RA10.B_1

description:
Library name: RA10.B_1
RA10.barcode.count.tsv


title: RA11.B_3

description:
Library name: RA11.B_3
RA11.barcode.count.tsv


title: RA10.DP_2

description:
Library name: RA10.DP_2
RA10.barcode.count.tsv


title: RA9.B_2

data_processing:
DNA barcoding data were analyzed using the RPBPBR pileline (https://github.com/hoefer-lab/RPBPBR)
RNA barcoding data were analyzed using the single-cell veresion (https://github.com/WXlab-NJMU/scPolylox)
CITE-seq data were analyzed using the CellRanger software (version 7.1.0)
Assembly: mm10
Supplementary files format and content: tsv, Polylox barcode count table
Supplementary files format and content: h5, single-cell gene expression matrix
Supplementary files format and content: tsv, ADT count table
Library strategy: Amplicon-seq

value: 27 week


title: RA9.T_2


title: RA9.T_1


title: RA9.MPP_PCR2

description:
PCR replicates
RA9.barcode.count.tsv

value: MPP


title: RA10.B_3

description:
Library name: RA10.B_3
RA10.barcode.count.tsv


title: RA10.DP_1

description:
Library name: RA10.DP_1
RA10.barcode.count.tsv


title: RA9.B_3


title: RA9.MPP_PCR1

description:
PCR replicates
RA9.barcode.count.tsv


title: RA9.DP_1


title: RA9.Mono_1

value: Mono


title: RA9.MPP_PCR3

description:
PCR replicates
RA9.barcode.count.tsv


title: RA10.DP_3

description:
Library name: RA10.DP_3
RA10.barcode.count.tsv


title: RA9.Gr_2


title: RA9.B_1


title: RA9.CMP_GMP

value: CMP&GMP


title: RA9.Gr_1


title: RA9.MEP

value: MEP


title: RA9.Mono_2

value: Bone marrow


title: RA9.MkMkP

value: Mk&MkP


title: RA9.DP_2


title: RA9.Gr_3


title: RA8.MPP_PCR3

description:
PCR replicates
RA8.barcode.count.tsv


title: RA9.LTHSC

value: LTHSC


title: RA8.MPP_PCR2

description:
PCR replicates
RA8.barcode.count.tsv


title: RA9.DP_3


title: RA8.T_3


title: RA8.B_1


title: RA8.B_2


title: RA8.B_3


title: RA8.MPP_PCR1

description:
PCR replicates
RA8.barcode.count.tsv


title: RA8.T_2


title: RA8.T_1


title: RA8.DP_1


title: RA8.LTHSC


title: RA8.Gr_2

value: Gr


title: RA8.Mono_1


title: RA8.DP_3


title: RA8.MkMkP


title: RA8.Mono_2


title: RA8.Gr_3


title: RA7.B_2

value: 41 week


title: RA8.Gr_1


title: RA7.T_1


title: RA7.B_1


title: RA8.MEP


title: RA7.Gr_2


title: RA8.CMP_GMP


title: RA7.Gr_1


title: RA7.DP_2

value: Thymus


title: RA7.T_2


title: RA7.proB

value: proB


title: RA8.DP_2

value: DP


title: RA7.EryP_2

value: EryP


title: RA7.MyP_1

value: MyP


title: RA7.EryP_1


title: RA6.DP_2


title: RA7.MPP3


title: RA7.MPP4_CD138n


title: RA7.MyP_2


title: RA7.DP_1


title: RA7.MPP4_CD138p

value: CD138+ MPP4


title: RA7.LTHSC


title: RA6.T_2

value: Spleen

value: T


title: RA6.EryP_1


title: RA6.MyP_2


title: RA6.Gr_2


title: RA6.proB


title: RA6.MyP_1


title: RA6.DP_1


title: RA6.EryP_2


title: RA6.MPP3


title: RA6.B_1

value: B


title: RA6.MPP4_CD138n

value: CD138- MPP4


title: RA5.B_2


title: RA5.B_1


title: RA5.T_2


title: RA6.Gr_1


title: RA6.T_1


title: RA6.MPP4_CD138p


title: RA5.T_1


title: RA6.LTHSC


title: RA5.DP_2


title: RA5.DP_1


title: RA5.Gr_2


title: RA6.B_2


title: RA5.Gr_1


title: RA5.MyP_2


title: RA5.EryP_2


title: RA5.EryP_1


title: RA5.MPP3


title: RA5.MyP_1


title: RA4.Gr_2

value: 38 week


title: RA4.EryP_3


title: RA4.Gr_1


title: RA5.MPP4_CD138p


title: RA5.LTHSC


title: RA5.MPP4_CD138n


title: RA4.EryP_1


title: RA4.Mono_1

value: Mono


title: RA4.Mono_2

value: Bone marrow


title: RA4.EryP_2


title: RA4.B_3


title: RA5.proB


title: RA4.B_4


title: RA4.B_1


title: RA4.T_3


title: RA4.T_4


title: RA4.T_1


title: RA4.DP_2


title: RA4.T_2


title: RA4.DP_3


title: RA4.MyP_1


title: RA4.MyP_2


title: RA4.DP_1


title: RA4.MPP3


title: RA4.MPP4_CD138n


title: RA4.STHSC_2

value: STHSC


title: RA4.MPP4_CD138p


title: RA4.Gr_3


title: RA4.B_2


title: RA4.LTHSC

value: LTHSC


title: RA3.EryP_3


title: RA4.proB


title: RA3.Mono_1


title: RA3.EryP_1


title: RA3.T_2


title: RA3.EryP_2


title: RA3.T_1


title: RA3.B_2


title: RA3.T_3


title: RA3.B_3


title: RA3.B_4


title: RA3.T_4


title: RA3.B_1


title: RA3.DP_3


title: RA3.DP_2


title: RA3.DP_1


title: RA4.STHSC_1


title: RA3.proB


title: RA3.Mono_2


title: RA3.MyP_2


title: RA3.MPP4_1


title: RA3.Gr_1

value: Gr


title: RA3.Gr_3


title: RA3.MPP4_2


title: RA3.MPP3


title: RA3.Gr_2


title: RA3.STHSC_2


title: RA2.B_2

value: 24 week


title: RA3.STHSC_1


title: RA2.B_3


title: RA2.Mono_2


title: RA2.T_2


title: RA3.MyP_1


title: RA2.proB


title: RA2.B_1


title: RA2.Mono_1


title: RA2.Gr_1


title: RA2.DP_1

value: Thymus


title: RA2.T_1


title: RA2.Gr_2


title: RA2.EryP_3


title: RA2.DP_2


title: RA2.EryP_2


title: RA2.EryP_1


title: RA2.MEP

value: MEP


title: RA2.CMP_GMP_2

value: CMP&GMP


title: RA3.LTHSC


title: RA2.LTHSC


title: RA2.CMP_GMP_1


title: RA2.MkMkP

value: Mk&MkP


title: RA2.T_3


title: RA2.MPP4


title: RA2.DP_3

value: DP


title: RA2.MPP3


title: RA1.B_3


title: RA1.proB

value: proB


title: RA1.B_1

value: Spleen


title: RA1.B_2


title: RA1.DP_3


title: RA1.DP_2


title: RA1.Mono_2


title: RA1.Mono_1


title: RA1.Gr_2


title: RA1.T_3

value: T


title: RA1.T_2


title: RA2.Gr_3


title: RA1.EryP_3

value: EryP


title: RA1.MEP


title: RA1.CMP_GMP_2


title: RA1.Gr_3


title: RA1.T_1


title: RA1.DP_1


title: RE4.MPP_3

source_name: Fetal liver

value: Fetal liver

value: MPP


title: RA1.EryP_1


title: RA1.Gr_1


title: RE4.MPP_1


title: RA1.MkMkP


title: RA1.CMP_GMP_1


title: RA1.EryP_2


title: RA1.MPP4


title: RE3.MPP_2


title: RE3.DP_2


title: RA1.LTHSC


title: RE3.MPP_1


title: RE5.MPP_3


title: RE5.MPP_2


title: RE5.LTHSC


title: RE5.MPP_1


title: RE3.LTHSC


title: RE2.MyP_2

value: MyP


title: RE3.MyP_1


title: RE4.MPP_2


title: RE3.MPP_3


title: RE2.MyP_1


title: RE4.LTHSC


title: RE3.MyP_2


title: RE3.DP_1


title: RE2.MPP_3


title: RA1.MPP3

value: Bone marrow


title: RE2.LTHSC


title: RE2.DP_2


title: RE2.MPP_2


title: RE2.MPP_1


title: RE1.MyP_2


title: RE1.MPP_2


title: RE2.DP_1


title: RE1.MyP_1


title: RE1.MPP_3


title: RE1.DP_1


title: RE1.DP_2


title: TA6.T_4

value: Tie2MCM x RosaPolyloxExpress

value: Adult

value: 61 week


title: TA6.B_2

value: B


title: TA6.B_5


title: TA6.B_3


title: TA6.B_7


title: TA6.B_1


title: TA6.B_6


title: TA6.T_1


title: TA6.DP_3

value: Thymus


title: TA6.T_5


title: TA6.DP_2


title: TA6.T_2


title: TA6.DP_1


title: TA6.T_6


title: TA6.T_3


title: RE1.LTHSC

value: LTHSC


title: TA6.T_7


title: TA6.Gr_4

value: Gr


title: TA6.Mono_2

value: Mono


title: TA6.Mono_1


title: TA6.Gr_3


title: RE1.MPP_1


title: TA6.B_4


title: TA6.MEP_2

value: MEP


title: TA6.Gr_2


title: TA6.EryP_2


title: TA6.CMP_2

value: CMP


title: TA6.EryP_1


title: TA6.GMP_2

value: GMP


title: TA6.Gr_1


title: TA6.GMP_1


title: TA6.MEP_1


title: TA6.CMP_1


title: TA6.MkMkP_2

value: Mk&MkP


title: TA5.B_6

value: Spleen


title: TA5.B_4


title: TA6.MkMkP_1


title: TA5.B_5


title: TA5.B_2


title: TA5.T_4

value: T


title: TA6.LTHSC


title: TA5.B_1


title: TA5.B_7


title: TA5.Mono_2


title: TA5.DP_3

value: DP


title: TA5.T_6


title: TA6.ST_MPP

value: ST&MPP


title: TA5.DP_2


title: TA5.Gr_4

value: Bone marrow


title: TA5.T_2

value: Tie2MCM x RosaPolyloxExpress


title: TA5.Gr_1

value: Adult


title: TA5.T_1

value: 61 week


title: TA5.T_5


title: Tg_22002

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

data_processing:
Nextflow pipeline nf-core/rnaseq (V3.8) (ref) was used for the primary analysis of bulk RNA-seq data
Fastqc (v0.11.9) was used for quality control of the fastq data followed by adapter trimming using Trim Galore (v0.6.5)
Reads were alinged to the  mouse reference genome GRcm38.86 using STAR alinger (V2.7.10) and the subsequent read mapped to the genes were counted using featureCount module implemented in the subread R package (v1.6.4)
Further quality control was performed using dupRader and RSeQC  (V2.6.4).
Assembly: mm10
Supplementary files format and content: raw.read.counts_6months_upload.tsv

source_name: liver tissue

growth_protocol: Mouse liver tissue were immediately harvested and frozen in liquid nitrogen.

extract_protocol:
Animals were sacrificed and Livers were collected, snap frozed in liquid nitrogen.Total RNA isolation from snap-frozen liver tissue or cultured cells was performed with RNeasy Mini Kit (Qiagen, 74106). The on-column DNA digestion was carried out using an RNase-free DNase kit (Qiagen) or RNA samples were treated with TURBO DNase (ThermoFisher Scientific, AM1907) according to the manufacturer’s protocol to completely remove genomic DNA.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols ( TruSeq Stranded).

treatment_protocol: Murine liver samples without any additional treatment

tag: genotype

tag: disease state

value: hepatitis


title: TA5.Mono_1


title: TA5.EryP_2

value: EryP


title: TA5.T_3


title: TA5.Gr_5


title: TA5.Gr_3


title: TA5.EryP_1


title: TA5.MEP_1


title: TA5.GMP_2


title: TA5.DP_1

value: Thymus


title: TA5.GMP_1


title: TA5.B_3

value: B


title: TA5.CMP_2


title: TA5.CMP_1


title: TA5.Gr_2

value: Gr


title: WT_22009

value: wildtype

value: healthy liver


title: TA5.MEP_2

value: MEP


title: WT_22003


title: Tg_16156


title: WT_21297


title: Tg_16153


title: Tg_16155


title: Tg_16154


title: WT_21296


title: Tg_21298


title: WT_16151


title: TA4.B_2

value: 59 week


title: Tg_16152


title: Tg_15845

data_processing:
Nextflow pipeline nf-core/rnaseq (V3.8) (ref) was used for the primary analysis of bulk RNA-seq data
Fastqc (v0.11.9) was used for quality control of the fastq data followed by adapter trimming using Trim Galore (v0.6.5)
Reads were alinged to the  mouse reference genome GRcm38.86 using STAR alinger (V2.7.10) and the subsequent read mapped to the genes were counted using featureCount module implemented in the subread R package (v1.6.4)
Further quality control was performed using dupRader and RSeQC  (V2.6.4).
Assembly: mm10
Supplementary files format and content: raw.read.counts_3M.tsv


title: TA4.T_1

value: Spleen


title: TA5.MkMkP_1

value: Mk&MkP


title: TA5.MkMkP_2


title: TA5.ST_MPP


title: Tg_13010


title: TA5.LTHSC

value: LTHSC


title: Tg_15807


title: TA4.DP_2

value: DP


title: WT_21295


title: TA4.B_1


title: TA4.T_2

value: T


title: Tg_15116


title: TA4.DP_1

value: Tie2MCM x RosaPolyloxExpress


title: TA4.EryP_2

value: Bone marrow

value: Adult


title: Tg_15843

value: hepatitis


title: TA4.proB_1

value: proB


title: TA4.Mono_1

value: Mono


title: Tg_15014


title: Tg_15119


title: TA4.EryP_1

value: EryP


title: TA4.proB_2


title: WT_13011


title: TA4.Gr_1

value: Gr


title: WT_15729

value: wildtype


title: TA4.GMP_1

value: GMP


title: GEM07Tg

data_processing:
Raw base calls have been processed by CellRanger 2.1.1. to demultiplex reads and generate count matrices.
Assembly: mm10
Supplementary files format and content: Filtered and normalized counts per cell as generated by CellRanger. Each compressed file contains one text file with cell barcodes, gene per count and normalized counts.

source_name: liver

growth_protocol: Mouse liver tissue were immediately digested and single cells harvested and stored.

extract_protocol:
Animals were sacrificed and livers perfused with 0.9% NaCl buffer. Livers were collected, minced, digested with Collagenase and DNase, and subsequently passed through a 100μm filter. Hepatic lymphocytes were then purified by a 2-step Percoll gradient.For live/dead cell discrimination, the ZombieDyeNIR dye was used according to the manufacturer's guidelines. In collaboration with the DKFZ FACS core facility, a FACS Aria II machine and a FACS Aria FUSION machine were employed for sorting CD45+ cells. Single-cell 3’ RNA (gene expression) libraries were generated according to the ‘Chromium Single Cell 3’ Reagents Kits User Guide (v3.1 Chemistry)’ (#CG000204, 10x Genomics).
Library construction was performed with Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) following the manufacturer’s protocol.

value: liver tissue

value: transgenic TGAlb-cre+


title: TA4.CMP_2

value: CMP

value: 59 week


title: TA4.Mono_2


title: GEM05Tg

value: transgenicTGAlb-cre+


title: WT_13013

value: healthy liver


title: WT_13012


title: TA4.Gr_2


title: TA4.Mk

value: Mk


title: TA4.MPP

value: Tie2MCM x RosaPolyloxExpress

value: MPP


title: TA4.GMP_2

value: Bone marrow

value: Adult


title: TA4.STHSC

value: STHSC


title: rn-52

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

data_processing:
Trimmomatic was used to remove adapter sequence and runs of low phread score bases
Sortmerna was used to remove rRNA contamination
STAR was used to align reads to the reference
htseq-count was used to get read counts for each gene.
Assembly: RNor6
Supplementary files format and content: Human readable, coma separated table of gene level read counts for each sample.

source_name: medial prefrontal cortex

growth_protocol: Animals were kept in standard environmental conditions of 22±1°C temperature and 60±10% relative humidity in a 12:12h reversed circadian light-cycle room, with lights off at 8.00 a.m. Animals were housed in groups of 2-5  in 1291H Eurostandard type III H cages (42.5x26.6x18.5 cm). Water and food (Sniff, Soest, Germany) were available ad libitum.

extract_protocol:
Whole-brain tissue was collected from resting-state Wistar rats (Charles-Rivers, n=27) during the early part of their active period. Animals were swiftly decapitated after being transferred directly from their home-cage, their brains were removed, then cooled and washed in ice-cold saline. A 0.5 mm coronal section between Bregma 2.0 and 1.5 mm was sliced in a cooled slice matrix. Bilateral medial prefrontal cortex samples were dissected on ice as defined by the forceps minor of corpus callosum and the medial wall of the hemisphere (i.e. including the infralimbic, prelimbic and anterior cingulate cortices). Samples were immediately placed in Eppendorf tubes on dry ice and stored on -80C temperature until RNA isolation. Whole transcriptome-analysis via RNASeq was performed on the homogenised mPFC tissue.
TRUseq (Illumina)

treatment_protocol: Animals underwent Elevated Plus-Maze test, Light-Dark test, Open Field test, acoustic startle, Fear conditioning

value: medial prefrontal cortex

value: Wistar rats

value: Learned helplessness


title: GEM06Tg

value: hepatitis


title: TA4.CMP_1


title: GEM04WT

value: healthy

value: wild type TGAlb-cre-


title: TA4.MEP

value: MEP


title: TA3.T_2

value: Spleen

value: T


title: rn-43


title: TA3.T_1

value: 59 week


title: GEM03WT

value: liver tissue


title: TA3.proB_2

value: proB


title: TA3.proB_1

value: Tie2MCM x RosaPolyloxExpress


title: TA4.MkP

value: MkP


title: WT_13014

value: wildtype

value: healthy liver


title: rn-35


title: GEM02WT


title: GEM01WT


title: TA4.LTHSC_2

value: Bone marrow

value: LTHSC

value: Adult


title: TA3.EryP_1

value: EryP


title: TA3.EryP_2


title: rn-53

value: medial prefrontal cortex

value: Wistar rats

value: Learned helplessness


title: TA4.LTHSC_1


title: rn-54


title: rn-26


title: TA3.Mono_1

value: Mono


title: TA3.B_2

value: Spleen

value: B


title: rn-51


title: rn-22


title: TA3.Gr_1

value: Gr

value: 59 week


title: GEM08Tg

value: liver tissue

value: hepatitis

value: transgenic TGAlb-cre+


title: TA3.MEP

value: Tie2MCM x RosaPolyloxExpress

value: MEP


title: rn-20


title: rn-19


title: TA3.B_1


title: rn-47


title: rn-39


title: rn-42


title: TA3.GMP_2

value: Bone marrow

value: GMP


title: rn-18


title: TA3.DP_2

value: Thymus

value: DP

value: Adult


title: TA3.GMP_1


title: rn-17

value: medial prefrontal cortex

value: Wistar rats


title: TA3.CMP_2

value: CMP


title: rn-34

value: Learned helplessness


title: TA3.DP_1


title: rn-13


title: rn-12


title: TA3.MkP

value: MkP


title: rn-9


title: rn-6


title: rn-31


title: rn-28


title: rn-3


title: TA3.Mono_2

value: Mono


title: rn-24


title: p14_T_48h

city: Piscataway

first: Lauren

last: Poole

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

description:
Library name: Sample 18
Column name in Raw_gene_counts_matrix.txt.gz: p14_T_48h

data_processing:
Sequence reads, Fastq were trimmed for adapter sequence/low quality FastQ files using cutadapt 4.9
Trimmed sequences were aligned to GRCh38/hg38 using Bowtie2 2.5.4
Aligned sequence files SAM were converted to BAM files by Samtools 1.21
Read count extraction utilized SummarizedOverlaps method and normalization was carried out with DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Subcultures of LX-2 cells were plated in 6-well tissue culture plates at a density of 180,000 cells per well for 48 h.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep according to the manufacturer’s protocol (Zymo Research Irvine, CA, R2052).
Novogene Eukaryotic mRNA library (poly A enrichment)

treatment_protocol: Cells were treated with a 1 h incubation in serum-free media followed by stimulation with thrombin (1 U/mL) or control (serum-free media) for 4, 24, or 48 h.

value: Hepatic stellate cell

value: Thrombin

tag: time


title: TA3.Gr_2

value: Gr

value: 59 week


title: p14_C_48h

description:
Library name: Sample 15
Column name in Raw_gene_counts_matrix.txt.gz: p14_C_48h

value: Control


title: TA2.EryP_2

value: Tie2MCM x RosaPolyloxExpress

value: EryP

value: 57 week


title: p13_C_48h

description:
Library name: Sample 14
Column name in Raw_gene_counts_matrix.txt.gz: p13_C_48h


title: rn-32


title: rn-15


title: TA3.Mk

value: Bone marrow

value: Mk


title: p14_T_24h

description:
Library name: Sample 12
Column name in Raw_gene_counts_matrix.txt.gz: p14_T_24h


title: TA3.MPP

value: MPP

value: Adult


title: rn-5

value: medial prefrontal cortex

value: Wistar rats


title: TA3.STHSC

value: STHSC


title: TA3.LTHSC_2

value: LTHSC


title: TA3.LTHSC_1


title: TA2.Gr_2


title: p12_T_24h

description:
Library name: Sample 10
Column name in Raw_gene_counts_matrix.txt.gz: p12_T_24h


title: p13_T_48h

description:
Library name: Sample 17
Column name in Raw_gene_counts_matrix.txt.gz: p13_T_48h


title: TA2.DP_2

value: Thymus

value: DP


title: TA2.B_3

value: Spleen

value: B


title: TA2.DP_1


title: TA2.B_2


title: TA2.Mono_2

value: Mono


title: TA3.CMP_1

value: CMP

value: 59 week


title: TA2.EryP_3

value: Tie2MCM x RosaPolyloxExpress

value: EryP


title: p13_C_24h

description:
Library name: Sample 8
Column name in Raw_gene_counts_matrix.txt.gz: p13_C_24h

value: Hepatic stellate cell

value: Control


title: p12_C_48h

description:
Library name: Sample 13
Column name in Raw_gene_counts_matrix.txt.gz: p12_C_48h


title: TA2.Gr_3

value: Bone marrow

value: Gr

value: 57 week


title: p12_C_24h

description:
Library name: Sample 7
Column name in Raw_gene_counts_matrix.txt.gz: p12_C_24h


title: TA2.Mono_1

value: Adult


title: p13_T_24h

description:
Library name: Sample 11
Column name in Raw_gene_counts_matrix.txt.gz: p13_T_24h

value: Thrombin


title: p12_T_4h

description:
Library name: Sample 4
Column name in Raw_gene_counts_matrix.txt.gz: p12_T_4h


title: p14_C_24h

description:
Library name: Sample 9
Column name in Raw_gene_counts_matrix.txt.gz: p14_C_24h


title: p12_T_48h

description:
Library name: Sample 16
Column name in Raw_gene_counts_matrix.txt.gz: p12_T_48h


title: p12_C_4h

description:
Library name: Sample 1
Column name in Raw_gene_counts_matrix.txt.gz: p12_C_4h


title: TA2.STHSC

value: STHSC


title: TA2.LTHSC

value: LTHSC


title: TA2.T_3

value: T


title: TA2.T_2

value: Spleen


title: NKO-NPM1 K257R_5

city: Chongqing

first: Xinyuan

last: Li

address: Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

description: Library name: Sample 11

data_processing:
Using the Illumina paired-end RNAseq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCh38
Supplementary files format and content: 1_genes_fpkm_expression text files include raw counts and FPKM values for each Sample

source_name: HK-2 cells

extract_protocol:
Total RNA was extracted using Trizol reagent (ThermoFisher, USA) following the manufacturer’s procedure.
mRNA was purified from total RNA (2 μg) using mRNA Caprure Beads2.0 (Yeasen, CHN) with two rounds of purification. RNA fragments were reverse-transcribed to synthesize first-strand cDNA by reverse transcriptase, which were next used to synthesise second-stranded DNAs with E.coli DNA polymerase I, RNase H and dUTP Solution (Yeasen, CHN).  An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and the ligated products were amplified with PCR Dual-index adapters were ligated to the fragments, followed by amplification with PCR. PCR amplification products were purified by Hieff NGS DNA Selection Beads (Yeasen, CHN) and subjuected to ssequencing on an Illumina Novaseq™ X Plus platform.

value: HK-2 cells

value: Human renal proximal tubular epithelial cell

value: NKO-NPM1 K257R


title: TA2.MkMkP

value: Mk&MkP


title: NKO-NPM1 K257R_4

description: Library name: Sample 10


title: p13_T_4h

description:
Library name: Sample 5
Column name in Raw_gene_counts_matrix.txt.gz: p13_T_4h


title: NKO-NPM1 K257R_3

description: Library name: Sample 9


title: NKO-NPM1 K257R_2

description: Library name: Sample 8


title: NKO-NPM1 K257R_1

description: Library name: Sample 7


title: TA2.Gr_1

value: Tie2MCM x RosaPolyloxExpress


title: TA2.CMP_MEP_2

value: CMP&MEP


title: TA2.CMP_MEP_1


title: p14_C_4h

description:
Library name: Sample 3
Column name in Raw_gene_counts_matrix.txt.gz: p14_C_4h

value: Hepatic stellate cell


title: NKO-NPM1 K257R_6

description: Library name: Sample 12


title: p13_C_4h

description:
Library name: Sample 2
Column name in Raw_gene_counts_matrix.txt.gz: p13_C_4h

value: Control


title: p14_T_4h

description:
Library name: Sample 6
Column name in Raw_gene_counts_matrix.txt.gz: p14_T_4h