title: Pooled input for CDKI-73 48h samples

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

data_processing:
Raw data were analyzed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters. Duplicate and non-uniquely mapping (MAPQ cutoff 20) reads were removed using SAMtools.
Diffbind (version 3.10.1, running in R version 4.3.0) was used to identify sites with differential H3K27ac intensity in response to CDKI-73 treatment.
Overlaps between our data and other ChIP-seq datasets and peak sets were determined using Cistrome DB Toolkit or BEDTools.
Deeptools was used to convert BAM files to bigwigs and for visualizing ChIP-seq data.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: LNCaP

growth_protocol: LNCaP cells were grown in baseline conditions (RPMI-1640 supplemented with 10% FBS).

extract_protocol:
After 48 hours, cells were fixed with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 2 ug H3K27ac antibody (Abcam ab4729). DNA was purified using phenol:chloroform extraction and isopropanol precipitation.
Libraries were prepared from 5 ng of ChIP DNA using a Qiaseq UltraLow Input Library Kit (Qiagen)according to the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or 150 nM CDKI-73 for 48h.

tag: cell line

value: LNCaP

value: 250nM CDKI-73


title: Pooled input for DMSO 48h samples

status: Public on Feb 25 2024

type: SRA

country: Australia

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: treatment

value: DMSO (vehicle control)


title: DMSO, CDKI-73, 48h, rep2


title: DMSO, CDKI-73, 48h, rep1


title: 2754-0h

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

library_source: transcriptomic

data_processing:
Fastq files generation and demultiplexing were performed using bcl2fastq v2.20.0. ; residual adapter sequences, ambiguous bases, low quality reads and reads with a length below 25 were removed by AdapterRemoval (version 2.2.3 )
alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized either using normTransform function (pseudocount=1, log2-transformation) or variancestabilising transformation of the DESeq2 package (v1.6.3)
Genome_build: GRCm38 Ensembl version (mm10)
Supplementary_files_format_and_content: raw_counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: norma_data - tab-deliminated file with normalized data of protein-coding genes
Supplementary_files_format_and_content: vst_data - tab-deliminated file with variancestabilising transformed data of protein-coding genes
Supplementary_files_format_and_content: fpkm - tab-deliminated file with fpkm values of protein-coding genes

molecule: total RNA

organism: Mus musculus

source_name: CD8+ T lymphocytes

growth_protocol: Naive CD8+ T cells were isolated by magnetically depletion of non-target cells from single cell suspensions of spleen and lymph nodes of indicated mice.

extract_protocol:
Cells were harvested after culture and RNA was isolated using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. Samples concentration was measured with Qubit Fluorometer (ThermoFischer). RNA integrity was assessed using Agilent 2100 BioAnalyser. RIN values were between 7.7 and 9.4.
mRNA-Seq libraries were prepared from 100ng of input total RNA samples using TruSeq stranded mRNA kit (Illumina). Barcoded and pooled libraries were sequenced on 5,5 lanes of Illumina HiSeq 4000 platform (HCS version 3.3.76, RTA version 2.7.6) in a paired-end 2x75 nt sequencing mode.

treatment_protocol: Isolated naive CD8+ T cells were polyclonally stimulated with 2 µg/ ml plate bound αCD3 (145-2C11, eBioscience) and 1 µg/ ml soluble αCD28 (37.51, eBioscience) for 24 - 48 hours.

tag: line

value: Tcaim KI Cd4Cre

tag: genotype

value: wtcre

tag: activation status

value: naive

tag: mouse

tag: Sex

value: male

tag: experiment


title: OA4-1_Condition_NWB_Rep4

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

country: China

institute: Xi'an Jiaotong University

library_source: transcriptomic single cell

data_processing:
Unique molecular identifier (UMI) counts were obtained by aligning FASTQ files to the human reference genome (GRCh38 3.0.0) through Cell Ranger (version 4.0) software from the 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). Gene expression raw count matrices were used for downstream analyses. Specifically, for each scRNA-seq dataset, the quality control steps included low-quality cell removal and mitochondrial count filtering. We performed the doublets removal step using the DoubletFinder (version 2.0.3) when the captured cell was larger than 10,000, with pK (the principal component neighbourhood size used to calculate pANN) set to 0.09, nEXP (the total number of doublet predictions produced) set to 0.075, and other parameters as the default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes annotation information for each Sample

molecule: polyA RNA

source_name: Cartilage

extract_protocol:
Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000.

tag: tissue

value: Cartilage


title: 2753-48h

value: hocre

value: 48h polyclonally activated


title: mouse 3, unsort, scRNAseq

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

description:
10x Genomics
pfc_exn.Robj
pfc_exn_meta.csv

data_processing:
ScRNA-seq data were aligned with the modified mouse reference genome mm10-3.0.0 adding five projection barcodes as separate genes.ScRNA-seq data was demultiplexed using the default parameters of Cellranger software (10X Genomics, v3.0.2). Obtained filtered transcription count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Supplementary files format and content: Output files of cellranger: Filtered feature-barcode matrix.
Supplementary files format and content: pfc_exn.Robj: R object which contain all excitatory neurons.
Supplementary files format and content: pfc_exn_meta.csv: metadata file containing clustering and annotation results of pfc_exn.Robj.
Assembly: mm10-3.0.0

source_name: retrograde labeled vmPFC neurons

extract_protocol:
For mice without FAC-sorting, three mice that had been injected with virus were anaesthetized and then subjected to transcranial perfusion with ice-cold oxygenated self-made dissection buffer (in mM: 92 Choline chloride, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 Glucose, 5 Sodium ascorbate, 2 Thiourea, 3 Sodium pyruvate, 10 MgSO4.7H2O, 0.5 CaCl2.2H2O, 12 N-Acetyl-L-Cysteine). The brain was removed, 300 µm vibratome sections were collected, and the PrL and IL regions were microdissected under a stereo microscope with a cooled platform. Brain slices were incubated in dissection buffer with 10 µM AMPA receptor antagonist CNQX (Abcam, Cat #ab120017) and 50 µM NMDA receptor antagonist D-AP5 (Abcam, Cat #ab120003) at 33°C for 30 min. The pieces were dissociated first using the ice-cold oxygenated dissection buffer added papain (20 units/ml, Worthington, Cat #LS003126), 0.067 mM 2-mercaptoethanol (Sigma, Cat #M6250), 1.1 mM EDTA (Invitrogen, Cat #15575020), L-Cysteine hydrochloride monohydrate (Sigma, Cat #C7880) and Deoxyribonuclease I (Sigma, Cat #D4527), with 30-40 min enzymatic digestion at 37°C, followed by 30 min 1 mg/ml protease (Sigma, Cat #P5147) and 1 mg/ml dispase (Worthington, Cat #LS02106) enzymatic digestion at 25°C. Supernatant was removed and digestion was terminated using dissection buffer containing 2% fetal bovine serum (FBS, Bioind, Cat #04-002-1A). Single-cell suspension was generated by manual trituration using fire-polishing pasteur pipettes and filtered through a 35 µm DM-equilibrated cell strainer (Falcon, Cat #352052). Cells were then pelleted at 400 g for 5 min. The supernatant was carefully removed and resuspended in 1-2 ml dissection buffer containing 2% FBS. The suspension was then subjected to the debris removal step using the Debris Removal Solution (Miltenyi, Cat #130-109-398). Cell pellets were resuspended and 48,000 cells were loaded into 3 lanes to perform 10X Genomics sequencing. For mice with FAC-sorting, PrL and IL regions were microdissected and dissociated as mice without FAC-sorting, cells were sorted to enrich for EGFP-positive retro-AAV-labeled cells. About 4893 EGFP-positive cells were captured and loaded to perform 10X Genomics sequencing.
Chromium Single Cell 3' Reagent Kits (v3) were used for library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000 system.

tag: cell type

value: retrograde labeled vmPFC neurons

tag: strain

value: Male

tag: age

value: 8 weeks


title: OA2-2_Condition_WB_Rep2


title: LNCaP, CDKI-73, 48h, rep2


title: RPMI multiple myeloma cells without co-culture of J3 stromal cells rep2

city: Boston

first: Mehmet

middle: K.

last: Samur

state: MA

address: 440 Brookline Avenue

department: Department of Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Technical Replicate 2

data_processing:
Perform pre-alignment quality control (FastQC v0.11.9)
Trim reads for quality (Trim Galore v0.5.0)
Adapter removal (Cutadapt v1.18)
Align to GRCh38 reference genome (bowtie2 v22.4.1)
Perform post-alignment quality control (FastQC v0.11.9)
Assembly: Call peaks (MACS2 v2.2.7.1)
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Hematopoietic

growth_protocol: The human multiple myeloma cell lines MM.1S, RPMI-8226, INA-6, and the human stromal cell line HS5 were cultured in RPMI-1640 medium supplemented with complete medium (10% fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine) at 37°C and 5% CO2. Recombinant human IL-6 at a concentration of 1 ng/mL (R&D Systems, Minneapolis, United States) was added to INA-6 culture medium.

extract_protocol:
For each condition, 50,000 CD138+ multiple myeloma cells were aliquoted and prepared in duplicates as previously reported.46 Cells were lysed for 10 minutes at 4°C in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360). After lysis, the pellets were subject to a transposition reaction (at 37°C for 60 minutes) using the TD buffer and transposase enzyme (Illumina Nextera DNA preparation kit, FC-121–1030). The transposition mixture was purified using a MinElute PCR purification kit (Qiagen).
Library amplification was performed using custom Nextera primers and the number of total cycles determined by running a SYBR-dye based qPCR reaction. Amplified libraries were purified using a PCR purification kit (Qiagen) and sequenced.

treatment_protocol: For co-culture experiments, the multiple myeloma cell lines and HS5 were passaged and cultured separately for 24 hours in a 75 cm2 flask. After 24 hours of culture and once HS5 50% confluency was observed, the multiple myeloma cells were manually counted and 10 million multiple myeloma cells with 90% or greater viability (assessed using Tryptan Blue staining), were transposed into 20 ml of fresh RPMI-1640 medium and either added into a 75 cm2 flask containing HS5 cells or cultured alone in a new flask. After 72 hours of culture, total cells were collected from each condition using adherent culture protocol and Trypsin-EDTA to remove attached cells.

value: Hematopoietic

value: RPMI

value: Plasma Cell

value: 46XY, KRAS p.Gly12Ala, TP53 p.Glu285Lys, TRAF3 p.Lys191Leufs*60, EGFR p.Thr751Ile


title: 2630-48h

value: Tcaim KO Cd4Cre

value: female


title: CCBC-Hesx1+rESCs 2#

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
For the raw sequencing data, the Cell Ranger (v3.1.0; 10× Genomics) was used for reads alignment, deduplication and quantification of gene expression with default parameters. Raw reads were aligned to the two-species reference genome (Mus musculus, GRCm38.p6 and Rattus norvegicus, Rnor_6.0) and quality checked. The filtered feature-barcode matrices were constructed by the Cell Ranger (v3.1; 10× Genomics) and used for the downstream analysis.
As quality control, cells were included if they passed the following filters: 1) the number of counts was more than 25,000, 2) the number of unique detected genes was more than the half of the average unique detected genes across the cells within the same sample and 3) the percentage of counts from the mitochondrial genome was less than 10%.
Genome_build: GRCm38.p6 and Rnor_6.0
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5 or H5) files contains gene expression values  (counts).

source_name: Chimaera Forebrain Cells

extract_protocol:
Cell isolation for 10× single cell RNA-seq was conducted as described.
Sample loading and library construction were performed according to the manufacturer’s protocol, Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: forebrain


title: 2630-0h


title: mouse 2, unsort, scRNAseq


title: 2508-48h

value: Tcaim KI Cd4Cre


title: LNCaP, CDKI-73, 48h, rep1

value: LNCaP

value: 250nM CDKI-73


title: CCBC-Hesx1+rESCs 1#


title: RPMI multiple myeloma cells without co-culture of J3 stromal cells rep1

description: Technical Replicate 1


title: RPMI multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours rep2

description: Technical Replicate 2

value: Co-Culture with J3 bone marrow stromal cells


title: OA2-1_Condition_NWB_Rep2

value: Cartilage


title: OA3-1_Condition_NWB_Rep3


title: 2753-0h

value: hocre

value: naive

value: male


title: mouse 1, unsort, scRNAseq

value: retrograde labeled vmPFC neurons

value: Male


title: 2508-24h

value: wtcre

value: 24h polyclonally activated


title: C3_Condition_Control_Rep3


title: CCBC-Hesx1+rESCs 3#


title: OA1-1_Condition_NWB_Rep1


title: 2753-24h


title: C2_Condition_Control_Rep2


title: 2508-0h


title: OA1-2_Condition_WB_Rep1


title: MM1S multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours

value: Hematopoietic

value: Plasma Cell

value: 45XX, KRAS p.Gly12Ala, TRAF3 p.Val536_Asn545delValPheValAlaGlnThrValLeuGluAsninsAsp

value: Co-Culture with HS5 bone marrow stromal cells


title: WT mouse

source_name: Mouse Forebrain Cells

value: wild type

value: forebrain


title: 2507-24h

value: Tcaim KI Cd4Cre


title: MM1S multiple myeloma cells without co-culture of HS5 stromal cells


title: C1_Condition_Control_Rep1


title: RPMI multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours rep1

description: Technical Replicate 1

value: RPMI

value: 46XY, KRAS p.Gly12Ala, TP53 p.Glu285Lys, TRAF3 p.Lys191Leufs*60, EGFR p.Thr751Ile


title: INA6 multiple myeloma cells without co-culture of HS5 stromal cells

value: 46XY, NRAS p.Gly12Asp, TP53 p.Lys132Met , TP53 p.Gln331Ter


title: 2507-48h

value: hocre

value: 48h polyclonally activated


title: subcutaneous,17,317

city: Changsha

first: Haicheng

last: Wen

state: State...

address: Hunan

institute: Central South University

description: BD Rhapsody

data_processing:
The UMI-based clean data was mapped to human genome (Ensemble version 91) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample
Cells contained over 300 expressed genes and mitochondria UMI rate below 40% passed the cell quality filtering and mitochondria genes were removed in the expression table
Seurat package was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data
Assembly: hg38
Supplementary files format and content: Comma--delimited text files include single cell expression matrix

source_name: Subcutaneous fat of back

extract_protocol:
The adipose tissue was placed in PBS buffer, and then the cells were dissociated and placed in BD Rhapsody platform for single-cell sequencing
The pooled cells were loaded on a BD Rhapsody™ Cartridge for capturing the single cells by pairing one cell with one barcoded beads. Then the cells were lysed to release mRNA, which were captured by barcoded oligo on bead, which has the cell label information and unique molecular identifiers information. Then the beads were retrieved from Cartridge into one tube and performed reverse transcription. The cDNA of captured mRNA was first synthesized on BD Rhapsody™ Cell Capture Beads as described in the instrument user guides. At the same time, the barcode information from BD Rhapsody Cell Capture Beads is also added to Sample Tags during reverse transcription.

value: Subcutaneous fat of back

tag: disease

value: spinal tuberculosis


title: 2507-0h

value: naive

value: male


title: INA6 multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours


title: subcutaneous,16,330

description: BD Rhapsody


title: subcutaneous,16,401

description: BD Rhapsody


title: leaves, sprayed with 200 mM IAA, 24 h, rep1 [R24h_1]

status: Public on Feb 24 2024

first: Yi-Qing

last: Wang

address: Beijing University of Agriculture Street

institute: Beijing University of Agriculture

description: the sample is the leaves of Rosa hybrida after sprayed with 200 mM IAA for 24 h

data_processing:
The rawdata data measured by small RNA will be evaluated firstly, mainly for spurious filtering and preliminary judgment of the data.
Sequence reads were 1)Remove low quality tags 2)Remove tags with 5' primer contaminants 3) Remove tags without 3'primer 4) Remove tags without insertion 5)Remove tags with polyA 6) Remove tags shorter than 18nt 7)Summarize the length distribution of the cleantags
We used the alignment software AASRA to align clean reads to the reference base and other small RNA databases, except for Rfam which was matched using cmsearch.
Assembly: the reference genome is Rosa multiflora
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rosa hybrid cultivar

source_name: leaves

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: leaves

value: leaf cells

value: spraying with 200 mM IAA


title: leaves, sprayed with 200 mM IAA, 18 h, rep1 [R18h_1]

description: the sample is the leaves of Rosa hybrida after sprayed with 200 mM IAA for 18 h


title: leaves, sprayed with 200 mM IAA, 24 h, rep2 [R24h_2]


title: leaves, sprayed with 200 mM IAA, 18 h, rep2 [R18h_2]


title: leaves, sprayed with 200 mM IAA, 6 h, rep2 [R6h_2]

description: the sample is the leaves of Rosa hybrida after sprayed with 200 mM IAA for 6 h


title: leaves, sprayed with 200 mM IAA, 12 h, rep2 [R12h_2]

description: the sample is the leaves of Rosa hybrida after sprayed with 200 mM IAA for 12 h


title: leaves, sprayed with 200 mM IAA, 12 h, rep1 [R12h_1]


title: leaves, sprayed with 200 mM IAA, 6 h, rep1 [R6h_1]


title: leaves, without spraying with 200 mM IAA, 0 h, rep2 [R0h_2]

description: control

value: without spraying


title: leaves, without spraying with 200 mM IAA, 0 h, rep1 [R0h_1]

description: control


title: Urine Epithelial Colony 7

city: Rockville

first: David

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

institute: NCATS/NIH

data_processing:
Fastq file pairs were aligned using STAR Aligner against GRCh38 Human Genome.
bam files from different lanes for the same samples were merged into one bam file using samtools
bam files were analyzed by HTSeq htseq-count to generate raw read count files.
DESeq2 was used to normalize raw read counts into a normalized read count data matrix.
Assembly: GRCh39, Ensembl Release 94

source_name: renal glomerular

growth_protocol: (REBM medium with REGM “bullet kit” supplements, Lonza Cat#: CC-3190, include 50 micrograms/mL Penicillin and Streptomycin

extract_protocol:
Total RNA samples were selected for polyA+ transcripts using the Qiagen Oligotex midi kit. Resulting samples were depleted of ribosomal sequences using two rounds of RiboZero Gold™, Illumina Inc.
mRNAs were fragmented by sonication, adaptors were ligated onto ends for paired-end multiplex sequencing, first and second strand DNA was synthesized.

value: renal glomerular

value: primary cells, clone P7

value: epithelial from urine


title: Urine Epithelial Colony 8

value: primary cells, clone P8


title: Urine Epithelial Colony 6

value: primary cells, clone P6


title: Urine Epithelial Colony 5

value: primary cells, clone P5


title: Urine Epithelial Colony 3

value: primary cells, clone P3


title: Quercetin_2 [miRNA-Seq]

city: Tai’an City

first: Yang

last: Jiang

state: Shandong Province

address: 61 Daizong Street

institute: Shandong Agricultural University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: tab-delimited text files include sequence and expression of all miRNAs

source_name: Human Umbilical Vein Endothelial Cells (HUVECs)

growth_protocol: The human umbilical vein endothelial cells were cultured in DMEM, supplemented with 10% of FBS, 0.6‰ of VEGF and 1% of a penicillin (100 U/mL)-streptomycin (100 μg/mL) mixture, in a humidified atmosphere with 5% CO2 and 95% room air at 37 ℃.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).

treatment_protocol: The HUVECs were seeded into 96-well plates and treated for 24 h with quercetin. Then, the cells were washed with PBS and incubated with 125μg/mL ox-LDL for another 24 h.

tag: protocol

value: ox-LDL injured pretreated with quercetin


title: Quercetin_3 [miRNA-Seq]

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: Quercetin_1 [miRNA-Seq]


title: Ox_ldl_3 [miRNA-Seq]

value: ox-LDL injured


title: Ox_ldl_2 [miRNA-Seq]


title: Control_3 [miRNA-Seq]

value: normal


title: Control_1 [miRNA-Seq]


title: Ox_ldl_1 [miRNA-Seq]


title: Control_2 [miRNA-Seq]


title: RNA_T8_STAT3VAV_IFNb_20h00min_VSVG036

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

description: RNA-seq sample of spleen CD8 T cell cells and treatment: IFNb for 20h00min

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using STAR (version 2.7.1)
Gene expression was quantified by counting uniquely aligned reads in exons using the function summarizeOverlaps from the GenomicAlignments package (version 1.6.3) in R (version 3.2.3)
Gene annotations were based on the Ensembl GENCODE Basic set (genome build GRCm38 release 93)
Assembly: mm10
Supplementary files format and content: csv file of read counts

source_name: Murine spleenic cells

growth_protocol: Ex vivo harvesting of cells was conducted following this protocol: We established and validated a robust isolation and staining protocol, which was used consistently across all experiments. Spleens were resected and immediately placed into tubes containing cold PBS (Gibco). Tissue was smashed with a 100µm strainer (SPL Life Sciences) using a syringe plunger and a 50ml tube. A new strainer was used for each spleen and rinsed with 10 to 20ml DMEM (Gibco) con-taining 10% FCS (Sigma) and 5ml penicillin streptomycin with 10,000 U/ml (Gibco). For the isolation of dendritic cells (DCs) spleens were injected with and placed in a digestion mixture (RPMI (Sigma), 2% FBS, 1mg/ml Collagenase D, 20µg/ml DNase I) and then incubated at 37°C for 30 minutes in a 24-well cell culture dish, before proceeding with the same mashing through a 100µm strainer. We pooled three littermates to obtain sufficient cell numbers. Samples were centrifuged at 500g for 5 min at 4 °C. Pellets were resuspended in 1ml Red Blood Cell Lysis Solution (Promega, Z3141) and incubated for 5min on ice. The lysis was stopped by adding 50ml 1x PBS. Samples were centrifuged at 500g for 5 min at 4 °C. Supernatant was discarded and pellets were resuspended in 1ml PBS supplemented with 2% BSA (Sigma). Samples were filtered through a 70µm strainer (SPL Life Sciences). The strainer was washed with 1ml PBS supplemented with 2% BSA. MHCII+ CD11c+ DCs were isolated from a DC MACS enriched population. Dendritic cells were enriched using the Miltenyi Pan Dendritic Cell Isola-tion Kit (mouse) according to the manufacturer’s instructions (Miltenyi Biotec, 130-100-875). Samples were centrifuged at 500g for 5 min at 4 °C and supernatant was discarded.   Cell pellets were resuspended in 100µl PBS (2% BSA) and anti-CD16/CD32 (clone 93, Biolegend) was added at a concentration of 1:500 for 15 min to prevent nonspecific binding. Single-cell suspensions were then stained with combinations of antibodies against TER-119 (APC-Cy7, clone TER-119), CD8 (APC, clone 53-6.7), F4/80 (FITC, clone BM8), CD19 (PerCPCy5.5, clone 6D5), CD3 (PE, clone 17A2), Ly-6C (PECy7, clone HK1.4), Ly-6G (PECy7, clone 1A8), NK1.1 (PECy7, clone PK136), CD45 (AF700, clone 30-F11, Biolegend) and Fixable Viability Dye eFluor 780 (APC-eFluor 780, eBio-science). In case of dendritic cell purification CD11c (PECy7, clone N418, eBioscience), MHCII (PE, MHC Class II (I-A/I-E) Monoclonal Antibody (M5/114.15.2), eBioscience) was used. Cells were stained for 30 min at 4 °C in the dark. 1ml PBS supplemented with 2% BSA was added and suspen-sions were centrifuged at 500g for 5 min at 4 °C. Pellets were resuspended in 300µl PBS supplemented with 2% BSA and filtered over 40µm strainer (SPL Life Sciences), filters were rinsed with 1ml PBS supplemented with 2% BSA. Cells were sorted with a BD FACS-Aria III Fusion instrument into PBS supplemented with 20% BSA.

extract_protocol:
RNA was isolated with the AllPrep RNA/DNA Micro Kit (Qiagen) following the manufacturer’s instructions and stored as recommended.
500pg of RNA was used as input. Reverse transcription and PCR were performed as described (Picelli et al., 2014). Library preparation was conducted on 1ng of cDNA using the Nextera XT DNA Sample Preparation Kit (Illumina) followed by SPRI (Beckman Coulter) size selection. Sequencing was performed by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50bp single-end configuration.

treatment_protocol: In vitro culture and treatment of ex vivo sort purified cells was done following this protocol: Aliquots of the sort-purified cell populations were stored for RNA/DNA isolation in RLT-buffer (Qi-agen) or directly processed using the ATAC-seq assay (as described below).  Splenic macrophages and CD8+ T cells were cultured in 48 well tissue culture treated plates for in vitro treatment with different stimuli. To that end, the cells were centrifuged at 500g for 5 min at 4 °C. 1*105 macrophages and 3*105 T cells were seeded per well in 300µl media. Macrophages were resuspended in DMEM (10% FCS, 5 ml penicillin streptomycin with 10,000 U/ml) and T cells in RPMI (10% FCS, 5 mL penicillin streptomycin with 10000 U/ml). The following conditions were applied: (i) 20 hours in culture untreated, (ii) 20 hours in culture with treatment, and (iii) 18.5 hours in culture followed by treatment for the last 1.5 hours. Treatments included murine recombinant IFN-β carrier-free (PBL as-say science, Cat. No. 12401-1) at a final concentration of 1,000 U/ml or recombinant murine IL-2 (PeproTech, Cat. No. 212-12) at a final concentration of 1,000 ng/ml or murine M-CSF (PeproTech, Cat. No. 315-02) at a final concentration of 100 ng/ml.  T cells were harvested by transferring them into a reaction tube, additional cold PBS (0.2% BSA) was added, centrifuged at 500g for 5 min at 4 °C and supernatant was removed. T cells were resuspended in 1ml PBS (0.2% BSA) and split equally between the two tubes. Macrophages were harvested by remov-ing the supernatant, gently rinsed the cells with cold PBS (0.2% BSA), followed by the addition of cold PBS (0.2% BSA). Macrophages were scraped and equally split between the two tubes. Tubes were then centrifuged at 500g for 5 min at 4 °C and either taken for RNA/DNA isolation or ATAC-seq (as de-scribed below). After centrifugation, the supernatant was carefully removed and the pellet was resus-pended in 350μl RLT buffer (Qiagen) with 3.5µl ß-mercaptoethanol (Sigma). After vortexing the sam-ple for one minute, it was stored at -80°C until further processing. RNA and DNA were isolated with the AllPrep RNA/DNA Micro Kit (Qiagen) following the manufacturer’s instructions and stored as recommended.

tag: organ

value: spleen

value: CD8 T cell

value: IFN-beta (20h)

value: 8-12 weeks

tag: research group

value: VS

tag: batch


title: RNA_T8_STAT3VAV_IFNb_01h30min_VSVG036

description: RNA-seq sample of spleen CD8 T cell cells and treatment: IFNb for 01h30min

value: IFN-beta (1.5h)


title: RNA_T8_STAT3VAV_UT_UT_VSVG036

description: RNA-seq sample of spleen CD8 T cell cells and treatment: UT for UT

value: None (20h)


title: RNA_M_STAT3VAV_IFNb_20h00min_VSVG036

description: RNA-seq sample of spleen Macrophage cells and treatment: IFNb for 20h00min

value: Macrophage


title: RNA_T8_WT_IFNb_20h00min_VSVG036

value: Wildtype


title: RNA_T8_WT_UT_UT_VSVG036


title: RNA_T8_WT_IFNb_01h30min_VSVG036


title: RNA_M_WT_UT_UT_VSVG036

description: RNA-seq sample of spleen Macrophage cells and treatment: UT for UT


title: RNA_M_STAT3VAV_UT_UT_VSVG036


title: RNA_M_STAT3VAV_IFNb_01h30min_VSVG036

description: RNA-seq sample of spleen Macrophage cells and treatment: IFNb for 01h30min


title: Urine Epithelial Colony 4

value: renal glomerular

tag: cell line

value: primary cells, clone P4

value: epithelial from urine


title: RNA_M_WT_IFNb_20h00min_VSVG036

tag: treatment


title: RNA_M_WT_IFNb_01h30min_VSVG036


title: Urine Epithelial Colony 2

value: primary cells, clone P2


title: RNA_T8_WT_IFNb_20h00min_VSVG029


title: RNA_T8_WT_IFNb_01h30min_VSVG029


title: RNA_T8_STAT3VAV_UT_UT_VSVG029


title: RNA_T8_WT_UT_UT_VSVG029


title: Urine Epithelial Colony 1

value: primary cells, clone P1


title: RNA_T8_STAT3VAV_IFNb_20h00min_VSVG029


title: RNA_T8_WT_IFNb_20h00min_VSMF248


title: RNA_T8_WT_IFNb_01h30min_VSMF248


title: RNA_M_WT_UT_UT_VSMF248


title: RNA_M_WT_IFNb_20h00min_VSMF248


title: RNA_M_WT_IFNb_01h30min_VSMF248


title: RNA_T8_STAT3VAV_UT_UT_VSMF248


title: RNA_T8_STAT3VAV_IFNb_01h30min_VSMF248


title: RNA_M_STAT3VAV_UT_UT_VSMF248


title: RNA_M_STAT3VAV_IFNb_01h30min_VSMF248


title: RNA_T8_STAT3VAV_UT_UT_VSMF246


title: RNA_T8_STAT3VAV_IFNb_20h00min_VSMF246


title: RNA_T8_STAT3VAV_IFNb_01h30min_VSVG029


title: RNA_M_WT_IFNb_20h00min_TDAL013

value: TD


title: RNA_T8_WT_IFNb_20h00min_TDAL013


title: RNA_M_WT_IFNb_01h30min_TDAL013


title: RNA_T8_STAT3VAV_IFNb_20h00min_VSMF248


title: RNA_T8_WT_IFNb_20h00min_VSMF246


title: RNA_T8_WT_IFNb_01h30min_TDAL013


title: RNA_M_STAT3VAV_IFNb_20h00min_VSMF248


title: RNA_T8_STAT2KO_IFNb_20h00min_TDAL013


title: RNA_M_STAT3VAV_UT_UT_VSMF246


title: RNA_T8_WT_UT_UT_VSMF248


title: RNA_M_STAT2KO_IFNb_20h00min_TDAL013


title: RNA_M_STAT2KO_UT_UT_TDAL013


title: RNA_M_STAT3VAV_IFNb_20h00min_VSVG029


title: RNA_T8_WT_UT_UT_VSMF246


title: RNA_T8_WT_UT_UT_TDAL013


title: RNA_M_STAT2KO_IFNb_01h30min_TDAL013


title: RNA_T8_IRF9KO_UT_UT_TDAL013


title: RNA_T8_IRF9KO_IFNb_20h00min_TDAL013


title: RNA_T8_IRF9KO_IFNb_01h30min_TDAL013


title: RNA_M_IRF9KO_IFNb_20h00min_TDAL013


title: RNA_M_IRF9KO_UT_UT_TDAL013


title: RNA_M_IRF9KO_IFNb_01h30min_TDAL013


title: RNA_T8_STAT2KO_UT_UT_TDAL011


title: RNA_T8_STAT2KO_IFNb_20h00min_TDAL010


title: RNA_T8_STAT2KO_UT_UT_TDAL013


title: RNA_M_STAT2KO_IFNb_01h30min_TDAL010


title: RNA_M_WT_UT_UT_TDAL013


title: RNA_T8_STAT2KO_IFNb_01h30min_TDAL013


title: RNA_T8_IRF9KO_UT_UT_TDAL009


title: RNA_T8_IRF9KO_IFNb_01h30min_TDAL009


title: RNA_T8_IRF9KO_IFNb_20h00min_TDAL009


title: RNA_M_WT_UT_UT_RMVG028

value: RM


title: RNA_T8_WT_IFNb_01h30min_RMVG028


title: RNA_M_IRF9KO_IFNb_20h00min_TDAL008


title: RNA_T8_WT_IFNb_20h00min_RMVG028


title: RNA_T8_IRF9KO_IFNb_20h00min_TDAL008


title: RNA_M_WT_IFNb_20h00min_RMVG028


title: RNA_T8_WT_UT_UT_RMVG028


title: RNA_M_WT_IFNb_01h30min_RMVG028


title: RNA_T8_STAT5VAV_IFNb_20h00min_RMVG028


title: RNA_T8_STAT5VAV_IFNb_01h30min_RMVG028


title: RNA_M_STAT5VAV_IFNb_01h30min_RMVG028


title: RNA_M_STAT5VAV_IFNb_20h00min_RMVG028


title: RNA_T8_STAT5VAV_UT_UT_RMVG028


title: RNA_NK_WT_IFNb_20h00min_MMAK018

description: RNA-seq sample of spleen NK cell cells and treatment: IFNb for 20h00min

value: NK cell

value: MM


title: RNA_NK_WT_UT_UT_MMAK018

description: RNA-seq sample of spleen NK cell cells and treatment: UT for UT

value: spleen


title: RNA_M_STAT2KO_IFNb_20h00min_TDAL011

value: IFN-beta (20h)


title: RNA_M_IRF9KO_UT_UT_TDAL008

value: 8-12 weeks


title: RNA_NK_WT_IFNb_01h30min_MMAK018

description: RNA-seq sample of spleen NK cell cells and treatment: IFNb for 01h30min


title: RNA_T8_IRF9KO_UT_UT_TDAL008

value: CD8 T cell


title: RNA_NK_TYK2KE_UT_UT_MMAK018


title: RNA_M_IRF9KO_IFNb_01h30min_TDAL008

value: IFN-beta (1.5h)


title: RNA_NK_TYK2KE_IFNb_20h00min_MMAK018


title: RNA_NK_TYK2CMV_UT_UT_MMAK018

value: None (20h)


title: RNA_NK_TYK2CMV_IFNb_20h00min_MMAK018


title: RNA_NK_WT_UT_UT_MMAK017


title: RNA_NK_WT_IFNb_20h00min_MMAK017


title: RNA_NK_TYK2KE_IFNb_01h30min_MMAK018


title: RNA_NK_WT_IFNb_01h30min_MMAK017


title: RNA_NK_TYK2CMV_IFNb_01h30min_MMAK018


title: RNA_NK_TYK2CMV_IFNb_20h00min_MMAK017


title: RNA_NK_TYK2CMV_IFNb_01h30min_MMAK017


title: RNA_NK_TYK2KE_UT_UT_MMAK017


title: RNA_NK_WT_UT_UT_MMAK016


title: RNA_NK_WT_IFNb_20h00min_MMAK016


title: RNA_NK_TYK2KE_IFNb_20h00min_MMAK017


title: RNA_M_STAT5VAV_UT_UT_RMVG028

value: Macrophage


title: RNA_NK_WT_IFNb_01h30min_MMAK016

value: Wildtype


title: RNA_NK_TYK2KE_IFNb_20h00min_MMAK016


title: RNA_NK_TYK2KE_IFNb_01h30min_MMAK016


title: RNA_NK_TYK2KE_UT_UT_MMAK016


title: RNA_NK_TYK2CMV_UT_UT_MMAK016


title: RNA_NK_TYK2CMV_IFNb_20h00min_MMAK016


title: RNA_NK_TYK2CMV_IFNb_01h30min_MMAK016


title: RNA_T8_WT_UT_UT_MMAK015


title: RNA_T8_WT_IFNb_01h30min_MMAK015


title: RNA_T8_WT_IFNb_20h30min_MMAK015

description: RNA-seq sample of spleen CD8 T cell cells and treatment: IFNb for 20h30min


title: RNA_M_WT_IFNb_01h30min_MMAK015


title: RNA_M_WT_UT_UT_MMAK015


title: RNA_T8_TYK2KE_IFNb_20h30min_MMAK015


title: RNA_M_WT_IFNb_20h30min_MMAK015

description: RNA-seq sample of spleen Macrophage cells and treatment: IFNb for 20h30min


title: RNA_T8_TYK2KE_IFNb_01h30min_MMAK015


title: RNA_M_TYK2KE_IFNb_20h30min_MMAK015


title: RNA_NK_TYK2CMV_UT_UT_MMAK017


title: RNA_T8_TYK2CMV_IFNb_20h30min_MMAK015


title: RNA_M_TYK2KE_UT_UT_MMAK015


title: RNA_M_TYK2KE_IFNb_01h30min_MMAK015


title: RNA_T8_TYK2CMV_UT_UT_MMAK015


title: RNA_M_TYK2CMV_UT_UT_MMAK015


title: RNA_T8_TYK2CMV_IFNb_01h30min_MMAK015


title: RNA_M_TYK2CMV_IFNb_01h30min_MMAK015


title: RNA_T8_WT_UT_UT_MMAK014


title: RNA_T8_WT_IFNb_20h30min_MMAK014


title: RNA_M_WT_UT_UT_MMAK014


title: RNA_T8_WT_IFNb_01h30min_MMAK014


title: RNA_T8_TYK2KE_UT_UT_MMAK015


title: RNA_NK_TYK2KE_IFNb_01h30min_MMAK017


title: RNA_M_WT_IFNb_01h30min_MMAK014


title: RNA_T8_TYK2KE_IFNb_20h30min_MMAK014


title: RNA_T8_TYK2KE_IFNb_01h30min_MMAK014


title: RNA_M_TYK2KE_UT_UT_MMAK014


title: RNA_M_TYK2KE_IFNb_20h30min_MMAK014


title: RNA_M_TYK2KE_IFNb_01h30min_MMAK014


title: RNA_T8_TYK2CMV_IFNb_20h30min_MMAK014


title: RNA_M_TYK2CMV_UT_UT_MMAK014


title: RNA_T8_TYK2CMV_IFNb_01h30min_MMAK014


title: RNA_M_TYK2CMV_IFNb_01h30min_MMAK014


title: RNA_T8_WT_IFNb_20h30min_MMAK013


title: RNA_T8_WT_UT_UT_MMAK013


title: RNA_T8_WT_IFNb_01h30min_MMAK013


title: RNA_M_WT_IFNb_01h30min_MMAK013


title: RNA_M_WT_IFNb_20h30min_MMAK014


title: RNA_T8_TYK2KE_IFNb_01h30min_MMAK013


title: RNA_T8_TYK2KE_UT_UT_MMAK013


title: RNA_M_WT_IFNb_20h30min_MMAK013


title: RNA_M_TYK2KE_UT_UT_MMAK013


title: RNA_T8_TYK2KE_IFNb_20h30min_MMAK013


title: RNA_T8_TYK2CMV_UT_UT_MMAK013


title: RNA_M_TYK2KE_IFNb_20h30min_MMAK013


title: RNA_M_TYK2KE_IFNb_01h30min_MMAK013


title: RNA_M_TYK2CMV_IFNb_20h30min_MMAK013


title: RNA_M_TYK2CMV_UT_UT_MMAK013


title: RNA_T8_WT_IFNb_20h00min_BSMJ023

value: BS


title: RNA_T8_TYK2KE_UT_UT_MMAK014


title: RNA_T8_WT_UT_UT_BSMJ023


title: RNA_T8_WT_IFNb_01h30min_BSMJ023


title: RNA_M_TYK2CMV_IFNb_01h30min_MMAK013


title: RNA_T8_TYK2CMV_UT_UT_MMAK014


title: RNA_M_TYK2CMV_IFNb_20h30min_MMAK014


title: RNA_T8_STAT4KO_UT_UT_BSMJ023


title: RNA_M_WT_IFNb_01h30min_BSMJ023


title: RNA_M_STAT4KO_UT_UT_BSMJ023


title: RNA_T8_STAT4KO_IFNb_01h30min_BSMJ023


title: RNA_T8_WT_UT_UT_BSMJ022


title: RNA_M_STAT4KO_IFNb_20h00min_BSMJ023


title: RNA_M_STAT4KO_IFNb_01h30min_BSMJ023


title: RNA_T8_STAT4KO_IFNb_20h00min_BSMJ023


title: RNA_T8_WT_IFNb_01h30min_BSMJ022


title: RNA_T8_WT_IFNb_20h00min_BSMJ022


title: RNA_M_WT_IFNb_01h30min_BSMJ022


title: RNA_T8_STAT4KO_UT_UT_BSMJ022


title: RNA_T8_STAT4KO_IFNb_01h30min_BSMJ022


title: RNA_M_WT_IFNb_20h00min_BSMJ022


title: RNA_M_STAT4KO_UT_UT_BSMJ022


title: RNA_T8_STAT4KO_IFNb_20h00min_BSMJ022


title: RNA_M_WT_UT_UT_BSMJ023


title: RNA_M_STAT4KO_IFNb_20h00min_BSMJ022


title: RNA_T8_WT_UT_UT_BSMJ021


title: RNA_T8_WT_IFNb_01h30min_BSMJ021


title: RNA_M_WT_IFNb_20h00min_BSMJ023


title: RNA_M_WT_UT_UT_MMAK013


title: RNA_M_WT_IFNb_20h00min_BSMJ021


title: RNA_T8_STAT4KO_IFNb_20h00min_BSMJ021


title: RNA_M_WT_IFNb_01h30min_BSMJ021


title: RNA_T8_STAT4KO_UT_UT_BSMJ021


title: RNA_M_STAT4KO_IFNb_01h30min_BSMJ021


title: RNA_M_WT_UT_UT_BSMJ022


title: RNA_T8_WT_IFNb_01h30min_BSMJ017


title: RNA_T8_STAT4KO_IFNb_01h30min_BSMJ021


title: RNA_M_STAT4KO_UT_UT_BSMJ021


title: RNA_T8_WT_UT_UT_BSMJ017


title: RNA_M_WT_UT_UT_BSMJ017


title: RNA_T8_WT_IFNb_20h00min_BSMJ017


title: RNA_M_WT_IFNb_01h30min_BSMJ017


title: RNA_M_STAT4KO_IFNb_01h30min_BSMJ022


title: RNA_T8_STAT1KO_IFNb_20h00min_BSMJ017


title: RNA_T8_STAT1KO_IFNb_01h30min_BSMJ017


title: RNA_M_STAT1KO_UT_UT_BSMJ017


title: RNA_T8_WT_IFNb_20h00min_BSMJ021


title: RNA_T8_STAT1KO_UT_UT_BSMJ017


title: RNA_M_WT_IFNb_20h00min_BSMJ017


title: RNA_M_STAT1KO_IFNb_01h30min_BSMJ017


title: RNA_T8_STAT1BB_IFNb_20h00min_BSMJ017


title: RNA_M_WT_UT_UT_BSMJ021


title: RNA_T8_STAT1BB_UT_UT_BSMJ017


title: RNA_T8_STAT1BB_IFNb_01h30min_BSMJ017


title: RNA_M_STAT1BB_IFNb_20h00min_BSMJ017


title: RNA_M_STAT1BB_UT_UT_BSMJ017


title: RNA_M_STAT1BB_IFNb_01h30min_BSMJ017


title: RNA_T8_WT_UT_UT_BSMJ016


title: RNA_T8_WT_IFNb_20h00min_BSMJ016


title: RNA_M_STAT4KO_IFNb_20h00min_BSMJ021


title: RNA_T8_WT_IFNb_01h30min_BSMJ016


title: RNA_M_WT_UT_UT_BSMJ016


title: RNA_M_WT_IFNb_20h00min_BSMJ016


title: RNA_M_WT_IFNb_01h30min_BSMJ016


title: RNA_T8_STAT1BB_IFNb_20h00min_BSMJ016


title: RNA_M_STAT1BB_IFNb_20h00min_BSMJ016


title: RNA_T8_STAT1BB_IFNb_01h30min_BSMJ016


title: RNA_M_STAT1BB_IFNb_01h30min_BSMJ016


title: RNA_M_STAT1KO_IFNb_20h00min_BSMJ017


title: RNA_T8_STAT1AA_UT_UT_BSMJ016


title: RNA_T8_STAT1BB_UT_UT_BSMJ016


title: RNA_T8_STAT1AA_IFNb_20h00min_BSMJ016


title: RNA_M_STAT1AA_UT_UT_BSMJ016


title: RNA_T8_STAT1AA_IFNb_01h30min_BSMJ016


title: RNA_M_STAT1AA_IFNb_20h00min_BSMJ016


title: RNA_T8_WT_IFNb_20h00min_BSMJ015


title: RNA_T8_WT_IFNb_01h30min_BSMJ015


title: RNA_M_WT_UT_UT_BSMJ015


title: RNA_M_WT_IFNb_20h00min_BSMJ015


title: RNA_T8_STAT1AA_UT_UT_BSMJ015


title: RNA_T8_STAT1AA_IFNb_01h30min_BSMJ015


title: RNA_M_WT_IFNb_01h30min_BSMJ015


title: RNA_T8_WT_UT_UT_BSMJ015


title: RNA_T8_STAT1AA_IFNb_20h00min_BSMJ015


title: RNA_M_STAT1AA_IFNb_20h00min_BSMJ015


title: RNA_M_STAT1AA_IFNb_01h30min_BSMJ015


title: RNA_M_STAT1AA_UT_UT_BSMJ015


title: RNA_T8_WT_IFNb_20h00min_BSMJ014


title: RNA_T8_WT_UT_UT_BSMJ014


title: RNA_T8_WT_IFNb_01h30min_BSMJ014


title: RNA_M_WT_IFNb_20h00min_BSMJ014


title: RNA_T8_STAT1KO_UT_UT_BSMJ014


title: RNA_M_STAT1KO_UT_UT_BSMJ014


title: RNA_M_STAT1KO_IFNb_20h00min_BSMJ014


title: RNA_T8_STAT1AA_UT_UT_BSMJ014


title: RNA_T8_STAT1KO_IFNb_20h00min_BSMJ014


title: RNA_M_STAT1AA_IFNb_20h00min_BSMJ014


title: RNA_M_STAT1KO_IFNb_01h30min_BSMJ014


title: RNA_T8_STAT1KO_IFNb_01h30min_BSMJ014


title: RNA_M_WT_UT_UT_BSMJ013


title: RNA_T8_WT_UT_UT_BSMJ013


title: RNA_M_WT_IFNb_20h00min_BSMJ013


title: RNA_T8_STAT1KO_IFNb_20h00min_BSMJ013


title: RNA_M_STAT1KO_UT_UT_BSMJ013


title: RNA_M_STAT1AA_IFNb_01h30min_BSMJ014


title: RNA_T8_STAT1AA_IFNb_20h00min_BSMJ014


title: RNA_T8_STAT1KO_UT_UT_BSMJ013


title: RNA_M_WT_UT_UT_BSMJ014


title: RNA_M_WT_IFNb_01h30min_BSMJ014


title: RNA_T8_STAT1BB_UT_UT_BSMJ013


title: RNA_M_WT_IFNb_01h30min_BSMJ013


title: RNA_T8_STAT1BB_IFNb_01h30min_BSMJ013


title: RNA_T8_WT_IFNb_20h00min_BSMJ013


title: RNA_M_STAT1KO_IFNb_20h00min_BSMJ013


title: RNA_T8_STAT1KO_IFNb_01h30min_BSMJ013


title: RNA_T8_STAT1AA_IFNb_01h30min_BSMJ014


title: RNA_M_STAT1KO_IFNb_01h30min_BSMJ013


title: RNA_T8_WT_IFNb_01h30min_BSMJ013


title: RNA_M_STAT1BB_UT_UT_BSMJ013


title: RNA_M_STAT1AA_UT_UT_BSMJ014


title: RNA_M_STAT1BB_IFNb_01h30min_BSMJ013


title: RNA_M_STAT1BB_IFNb_20h00min_BSMJ013


title: RNA_T8_STAT6KO_H_H_SKAF003

description: RNA-seq sample of spleen CD8 T cell cells and treatment: H for H

value: Homeostatic

value: SK


title: RNA_NK_STAT6KO_H_H_SKAF003

description: RNA-seq sample of spleen NK cell cells and treatment: H for H


title: RNA_M_STAT6KO_H_H_SKAF003

description: RNA-seq sample of spleen Macrophage cells and treatment: H for H


title: RNA_T8_WT_H_H_SKAF003


title: RNA_NK_WT_H_H_SKAF003


title: RNA_T8_STAT1BB_IFNb_20h00min_BSMJ013


title: RNA_M_WT_H_H_SKAF003


title: RNA_B_STAT6KO_H_H_SKAF002

description: RNA-seq sample of spleen B cell cells and treatment: H for H

value: B cell


title: RNA_NK_STAT6KO_H_H_SKAF002


title: RNA_T8_STAT6KO_H_H_SKAF002


title: RNA_M_STAT6KO_H_H_SKAF002


title: RNA_M_WT_H_H_SKAF002


title: RNA_B_STAT6KO_H_H_SKAF001


title: RNA_NK_STAT6KO_H_H_SKAF001


title: RNA_T8_WT_H_H_VSMF230

value: VS


title: RNA_T8_STAT6KO_H_H_SKAF001


title: RNA_T8_WT_H_H_SKAF002


title: RNA_NK_WT_H_H_VSMF230


title: RNA_M_STAT6KO_H_H_SKAF001


title: RNA_NK_WT_H_H_SKAF002


title: RNA_M_WT_H_H_VSMF230


title: RNA_NK_STAT3VAV_H_H_VSMF230


title: RNA_T8_STAT3VAV_H_H_VSMF230


title: RNA_T8_WT_H_H_SKAF001


title: RNA_B_WT_H_H_VSMF230


title: RNA_M_WT_H_H_SKAF001


title: RNA_M_STAT3VAV_H_H_VSMF230


title: RNA_B_STAT3VAV_H_H_VSMF230


title: RNA_NK_STAT3VAV_H_H_VSMF216


title: RNA_NK_WT_H_H_SKAF001


title: RNA_T8_WT_H_H_VSMF216


title: RNA_M_STAT3VAV_H_H_VSMF216


title: RNA_M_WT_H_H_VSMF216


title: RNA_T8_IRF9KO_H_H_TDAL007

value: TD


title: RNA_NK_WT_H_H_VSMF216


title: RNA_B_WT_H_H_VSMF216


title: RNA_M_IRF9KO_H_H_TDAL007


title: RNA_T8_IRF9KO_H_H_TDAL006


title: RNA_T8_IRF9KO_H_H_TDAL005


title: RNA_M_IRF9KO_H_H_TDAL005


title: RNA_T8_STAT1VAV_H_H_TDAL001


title: RNA_T8_STAT2KO_H_H_TDAL004


title: RNA_T8_STAT2KO_H_H_TDAL002


title: RNA_M_STAT2KO_H_H_TDAL004


title: RNA_T8_WT_H_H_TDAL002


title: RNA_M_STAT2KO_H_H_TDAL003


title: RNA_M_STAT1VAV_H_H_TDAL001


title: RNA_M_STAT2KO_H_H_TDAL002


title: RNA_M_WT_H_H_TDAL002


title: RNA_M_WT_H_H_TDAL001


title: RNA_T8_STAT2KO_H_H_TDAL003


title: RNA_B_STAT3VAV_H_H_VSMF216


title: RNA_B_WT_H_H_RMMF226

value: RM


title: RNA_T8_WT_H_H_TDAL001


title: RNA_T8_WT_H_H_RMMF226


title: RNA_NK_STAT5BN642H_H_H_RMMF226

value: NK cell


title: RNA_T8_STAT5BN642H_H_H_RMMF226


title: RNA_B_STAT5BN642H_H_H_RMMF226


title: RNA_NK_WT_H_H_RMMF226


title: RNA_T8_STAT5VAV_H_H_RMMF211


title: RNA_M_IRF9KO_H_H_TDAL006


title: RNA_T8_WT_H_H_RMMF211


title: RNA_M_WT_H_H_RMMF211


title: RNA_B_STAT5VAV_H_H_RMMF211


title: RNA_M_STAT5VAV_H_H_RMMF211


title: RNA_B_WT_H_H_RMMF211


title: RNA_T8_WT_H_H_RMMF209


title: RNA_M_WT_H_H_TDAL005


title: RNA_NK_WT_H_H_RMMF209


title: RNA_B_WT_H_H_RMMF209


title: RNA_NK_STAT5BN642H_H_H_RMMF209


title: RNA_NK_WT_H_H_RMMF208


title: RNA_DC_WT_H_H_MMSH001

description: RNA-seq sample of spleen Dendritic cell cells and treatment: H for H

value: Dendritic cell

value: MM


title: RNA_B_WT_H_H_RMMF208

value: spleen


title: RNA_T8_STAT5BN642H_H_H_RMMF209

value: 8-12 weeks


title: RNA_DC_WT_H_H_MMSH002


title: RNA_DC_TYK2KO_H_H_MMSH001


title: RNA_T8_STAT5BN642H_H_H_RMMF208

value: CD8 T cell


title: RNA_T8_WT_H_H_RMMF208


title: RNA_DC_TYK2CMV_H_H_MMSH002


title: RNA_B_STAT5BN642H_H_H_RMMF208


title: RNA_NK_STAT5BN642H_H_H_RMMF208


title: RNA_DC_TYK2KE_H_H_MMSH001


title: RNA_DC_WT_H_H_MMSH010


title: RNA_DC_TYK2KE_H_H_MMSH011


title: RNA_DC_WT_H_H_MMSH011


title: RNA_DC_TYK2KE_H_H_MMSH010


title: RNA_DC_TYK2CMV_H_H_MMSH010


title: RNA_DC_TYK2CMV_H_H_MMSH011


title: RNA_M_WT_H_H_MMAK012


title: RNA_T8_WT_H_H_MMAK012


title: RNA_M_TYK2KE_H_H_MMAK012


title: RNA_T8_TYK2CMV_H_H_MMAK012


title: RNA_T8_TYK2KE_H_H_MMAK012


title: RNA_M_TYK2CMV_H_H_MMAK012


title: RNA_M_TYK2KE_H_H_MMAK011


title: RNA_DC_TYK2KO_H_H_MMSH002


title: RNA_M_TYK2CMV_H_H_MMAK011


title: RNA_DC_TYK2KE_H_H_MMSH002


title: RNA_M_WT_H_H_MMAK010


title: RNA_T8_WT_H_H_MMAK010


title: RNA_M_TYK2CMV_H_H_MMAK010


title: RNA_T8_TYK2KE_H_H_MMAK010


title: RNA_M_TYK2KE_H_H_MMAK010


title: RNA_T8_TYK2KE_H_H_MMAK009


title: RNA_M_WT_H_H_MMAK009


title: RNA_T8_WT_H_H_MMAK008


title: RNA_T8_TYK2CMV_H_H_MMAK010


title: RNA_M_WT_H_H_MMAK011


title: RNA_M_TYK2CMV_H_H_MMAK009


title: RNA_M_TYK2CMV_H_H_MMAK008


title: RNA_T8_TYK2CMV_H_H_MMAK008


title: RNA_NK_TYK2CMV_H_H_MMAK007


title: RNA_NK_WT_H_H_MMAK007


title: RNA_NK_TYK2KE_H_H_MMAK007


title: RNA_M_TYK2KE_H_H_MMAK008


title: RNA_NK_WT_H_H_MMAK006


title: RNA_NK_WT_H_H_MMAK005


title: RNA_NK_TYK2CMV_H_H_MMAK005


title: RNA_NK_TYK2KE_H_H_MMAK006


title: RNA_NK_TYK2CMV_H_H_MMAK006


title: RNA_NK_TYK2KE_H_H_MMAK005


title: RNA_T8_TYK2CMV_H_H_MMAK009


title: RNA_M_TYK2KE_H_H_MMAK009


title: RNA_T8_TYK2KE_H_H_MMAK004


title: RNA_T8_TYK2KE_H_H_MMAK002


title: RNA_T8_WT_H_H_MMAK003


title: RNA_T8_TYK2CMV_H_H_MMAK002


title: RNA_T8_TYK2KE_H_H_MMAK003


title: RNA_M_WT_H_H_MMAK008


title: RNA_T8_STAT5BN642H_H_H_RMMF196


title: RNA_T8_TYK2KE_H_H_MMAK008


title: RNA_NK_WT_H_H_RMMF196


title: RNA_NK_STAT5BN642H_H_H_RMMF196


title: RNA_DC_TYK2CMV_H_H_MMSH001


title: RNA_T8_WT_H_H_VSMF192


title: RNA_NK_WT_H_H_VSMF192


title: RNA_NK_STAT3VAV_H_H_VSMF192


title: RNA_B_WT_H_H_RMMF196


title: RNA_T8_WT_H_H_RMMF189


title: RNA_B_STAT5BN642H_H_H_RMMF196


title: RNA_B_STAT3VAV_H_H_VSMF192


title: RNA_NK_WT_H_H_RMMF189


title: RNA_T8_STAT5VAV_H_H_RMMF189


title: RNA_B_WT_H_H_RMMF189


title: RNA_T8_TYK2CMV_H_H_MMAK004


title: RNA_M_STAT3VAV_H_H_VSMF192


title: RNA_T8_TYK2CMV_H_H_MMAK003


title: RNA_T8_STAT3VAV_H_H_VSMF192


title: RNA_T8_WT_H_H_RMMF196


title: RNA_B_STAT5VAV_H_H_RMMF189


title: RNA_M_STAT5VAV_H_H_RMMF189


title: RNA_B_STAT5VAV_H_H_RMMF186


title: RNA_T8_STAT3VAV_H_H_VSMF178


title: RNA_T8_STAT5VAV_H_H_RMMF174


title: RNA_M_STAT5VAV_H_H_RMMF174


title: RNA_T8_WT_H_H_RMMF173


title: RNA_T8_STAT5BN642H_H_H_RMMF173


title: RNA_T8_WT_H_H_CBMF168

value: CB


title: RNA_T8_WT_H_H_CBMF1681


title: RNA_B_WT_H_H_VSMF192


title: RNA_M_WT_H_H_BSMJ020


title: RNA_T8_WT_H_H_BSMJ020


title: RNA_T8_WT_H_H_BSMJ019


title: RNA_T8_STAT4KO_H_H_BSMJ020


title: RNA_M_STAT4KO_H_H_BSMJ020


title: RNA_M_WT_H_H_BSMJ019


title: RNA_T8_STAT4KO_H_H_BSMJ019


title: RNA_M_STAT4KO_H_H_BSMJ019


title: RNA_T8_WT_H_H_BSMJ018


title: RNA_T8_STAT4KO_H_H_BSMJ018


title: RNA_T8_WT_H_H_BSMJ005


title: RNA_M_WT_H_H_BSMJ018


title: RNA_T8_WT_H_H_BSMJ003


title: RNA_M_STAT4KO_H_H_BSMJ018


title: RNA_M_WT_H_H_BSMJ003


title: RNA_M_WT_H_H_BSMJ005


title: RNA_T8_WT_H_H_BSMJ004


title: RNA_M_WT_H_H_BSMJ004


title: RNA_M_STAT1BB_H_H_BSMJ004


title: RNA_T8_STAT1BB_H_H_BSMJ004


title: RNA_T8_STAT1BB_H_H_BSMJ003


title: RNA_T8_STAT1AA_H_H_BSMJ005


title: RNA_M_STAT1AA_H_H_BSMJ005


title: RNA_M_STAT1BB_H_H_BSMJ003


title: RNA_M_STAT1AA_H_H_BSMJ004


title: RNA_M_STAT1AA_H_H_BSMJ003


title: RNA_T8_STAT1KO_H_H_BSMJ005


title: RNA_M_STAT1KO_H_H_BSMJ005


title: RNA_M_WT_H_H_BSMJ002


title: RNA_T8_STAT1BB_H_H_BSMJ002


title: RNA_T8_STAT1AA_H_H_BSMJ001


title: RNA_T8_STAT1KO_H_H_BSMJ002


title: RNA_M_STAT1BB_H_H_BSMJ002


title: RNA_M_STAT1KO_H_H_BSMJ002


title: ATAC_T8_WT_IFNb_01h30min_VSVG038

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen CD8 T cell cells and treatment: IFNb for 01h30min

data_processing:
Raw reads were trimmed with trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using bowtie2 (version 2.2.4)
Primary alignments with mapping quality greater than 30 were retained.
ATAC-seq peaks were called using MACS (version 2.7.6 (Zhang et al., 2008)) on each individual sample.
Peaks were aggregated into a list of consensus peaks using the function reduce of the package GenomicRanges (version 1.38.0) in R (version 3.6.1).
Consensus peaks that overlapped with blacklisted genomic regions (downloaded from https://github.com/Boyle-Lab/Blacklist/tree/master/lists) were discarded.
Quantitative measurements were obtained by counting reads within consensus peaks using the function summarizeOverlaps from the GenomicAlignments (version 1.22.1) package in R (version 3.6.1).
Assembly: mm10
Supplementary files format and content: csv file of read counts

extract_protocol:
Chromatin accessibility mapping by ATAC-seq was performed as previously described (Buenrostro et al., 2013; Corces et al., 2016), with minor adaptations. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5µl 2xTD buffer, 2µl TDE1 (Illumina), 10.25µl nuclease-free water, and 0.125µL 10% NP-40 (Sigma) for macrophages and dendritic cells or 0.25µl 1% digitonin (Promega) for all other cell types) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11µl, 1µl of the eluted DNA was used in a quantitative PCR reaction to estimate the optimum number of amplification cycles.
The remaining 10μl of each library were amplified for the number of cycles corresponding to the Cq value from the qPCR (i.e., the cycle number at which fluorescence has increased above background levels, rounded down). Library amplification was followed by SPRI beads (Beckman Coulter) size selection to exclude fragments larger than 1,200bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro et al., 2013). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50bp single-end configuration.

value: IFN-beta (1.5h)


title: ATAC_T8_STAT3VAV_UT_UT_VSVG038

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen CD8 T cell cells and treatment: UT for UT

value: None (20h)


title: ATAC_T8_WT_UT_UT_VSVG038

value: Wildtype


title: ATAC_T8_STAT3VAV_UT_UT_VSVG036


title: ATAC_T8_STAT3VAV_IFNb_20h00min_VSVG038

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen CD8 T cell cells and treatment: IFNb for 20h00min

value: IFN-beta (20h)


title: RNA_T8_STAT1AA_H_H_BSMJ004

value: Homeostatic

value: BS


title: ATAC_T8_STAT3VAV_IFNb_01h30min_VSVG038


title: ATAC_M_WT_IFNb_01h30min_VSVG038

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Macrophage cells and treatment: IFNb for 01h30min

value: Macrophage


title: ATAC_M_WT_UT_UT_VSVG038

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Macrophage cells and treatment: UT for UT

value: VS


title: RNA_T8_STAT1AA_H_H_BSMJ003


title: ATAC_T8_WT_IFNb_20h00min_VSVG038


title: ATAC_M_STAT3VAV_UT_UT_VSVG036


title: ATAC_M_STAT3VAV_UT_UT_VSVG038


title: ATAC_M_WT_UT_UT_VSVG036


title: ATAC_T8_WT_IFNb_20h00min_VSVG036


title: ATAC_T8_STAT3VAV_IFNb_01h30min_VSVG036


title: ATAC_M_STAT3VAV_IFNb_20h00min_VSVG036

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Macrophage cells and treatment: IFNb for 20h00min


title: ATAC_T8_STAT3VAV_IFNb_20h00min_VSVG036


title: ATAC_T8_WT_UT_UT_VSVG036


title: ATAC_M_WT_IFNb_20h00min_VSVG036


title: ATAC_M_WT_IFNb_01h30min_VSVG036


title: RNA_T8_WT_H_H_BSMJ002


title: ATAC_T8_WT_IFNb_20h00min_VSVG029


title: ATAC_M_WT_IFNb_01h30min_VSVG029


title: ATAC_T8_WT_IFNb_01h30min_VSVG029


title: ATAC_M_WT_UT_UT_VSVG029


title: ATAC_M_STAT3VAV_IFNb_01h30min_VSVG038


title: ATAC_M_STAT3VAV_IFNb_01h30min_VSVG036


title: ATAC_T8_WT_IFNb_01h30min_VSVG036


title: ATAC_T8_STAT3VAV_IFNb_20h00min_VSVG029


title: ATAC_M_STAT3VAV_UT_UT_VSVG029


title: ATAC_M_STAT3VAV_IFNb_20h00min_VSVG029


title: ATAC_M_STAT3VAV_IFNb_01h30min_VSVG029


title: ATAC_T8_WT_IFNb_20h00min_TDAL014

value: TD


title: ATAC_M_WT_UT_UT_TDAL014


title: ATAC_M_STAT2KO_IFNb_20h00min_TDAL014


title: ATAC_M_STAT2KO_UT_UT_TDAL014


title: ATAC_M_STAT2KO_IFNb_01h30min_TDAL014


title: ATAC_M_WT_IFNb_01h30min_TDAL014


title: ATAC_T8_IRF9KO_IFNb_01h30min_TDAL014


title: ATAC_T8_WT_IFNb_01h30min_TDAL014


title: ATAC_M_IRF9KO_IFNb_01h30min_TDAL014


title: ATAC_M_WT_IFNb_20h00min_TDAL014


title: ATAC_T8_IRF9KO_IFNb_20h00min_TDAL014


title: ATAC_M_IRF9KO_IFNb_20h00min_TDAL014


title: ATAC_T8_WT_UT_UT_VSVG029


title: ATAC_T8_STAT2KO_IFNb_20h00min_TDAL014


title: ATAC_T8_IRF9KO_UT_UT_TDAL014


title: ATAC_T8_WT_UT_UT_TDAL013


title: ATAC_M_IRF9KO_UT_UT_TDAL014


title: ATAC_T8_WT_IFNb_20h00min_TDAL013


title: ATAC_M_WT_IFNb_20h00min_TDAL013


title: ATAC_T8_STAT2KO_IFNb_20h00min_TDAL013


title: ATAC_T8_STAT2KO_IFNb_01h30min_TDAL013


title: ATAC_M_STAT2KO_UT_UT_TDAL013


title: ATAC_T8_STAT3VAV_UT_UT_VSVG029


title: ATAC_T8_STAT3VAV_IFNb_01h30min_VSVG029


title: ATAC_T8_WT_UT_UT_TDAL014


title: ATAC_T8_IRF9KO_UT_UT_TDAL013


title: ATAC_M_IRF9KO_IFNb_20h00min_TDAL013


title: ATAC_M_IRF9KO_UT_UT_TDAL013


title: ATAC_T8_WT_IFNb_20h00min_TDAL011


title: ATAC_M_WT_UT_UT_TDAL011


title: ATAC_T8_IRF9KO_IFNb_01h30min_TDAL013


title: ATAC_T8_STAT2KO_UT_UT_TDAL011


title: ATAC_T8_STAT2KO_IFNb_20h00min_TDAL011


title: ATAC_M_STAT2KO_IFNb_20h00min_TDAL011


title: ATAC_T8_WT_UT_UT_TDAL010


title: ATAC_M_WT_IFNb_20h00min_TDAL011


title: ATAC_M_STAT2KO_IFNb_01h30min_TDAL011


title: ATAC_T8_STAT2KO_IFNb_01h30min_TDAL011


title: ATAC_T8_WT_IFNb_01h30min_TDAL011


title: ATAC_M_STAT2KO_UT_UT_TDAL011


title: ATAC_T8_WT_UT_UT_TDAL011


title: ATAC_T8_WT_IFNb_01h30min_TDAL010


title: ATAC_M_WT_UT_UT_TDAL010


title: ATAC_M_WT_IFNb_20h00min_TDAL010


title: ATAC_M_WT_IFNb_01h30min_TDAL011


title: ATAC_M_WT_IFNb_01h30min_TDAL010


title: ATAC_T8_STAT2KO_UT_UT_TDAL010


title: ATAC_T8_STAT2KO_IFNb_20h00min_TDAL010


title: ATAC_T8_STAT2KO_IFNb_01h30min_TDAL010


title: ATAC_M_STAT2KO_IFNb_20h00min_TDAL010


title: ATAC_M_STAT2KO_UT_UT_TDAL010


title: ATAC_M_STAT2KO_IFNb_01h30min_TDAL010


title: ATAC_T8_IRF9KO_IFNb_20h00min_TDAL013


title: ATAC_T8_WT_UT_UT_TDAL009


title: ATAC_T8_WT_IFNb_01h30min_TDAL009


title: ATAC_T8_WT_IFNb_20h00min_TDAL009


title: ATAC_M_WT_UT_UT_TDAL009


title: ATAC_M_WT_IFNb_20h00min_TDAL009


title: ATAC_T8_IRF9KO_UT_UT_TDAL009


title: ATAC_T8_IRF9KO_IFNb_01h30min_TDAL009


title: ATAC_T8_IRF9KO_IFNb_20h00min_TDAL009


title: ATAC_M_IRF9KO_IFNb_01h30min_TDAL009


title: ATAC_T8_WT_IFNb_20h00min_TDAL010


title: ATAC_M_IRF9KO_UT_UT_TDAL009


title: ATAC_M_WT_IFNb_01h30min_TDAL009


title: ATAC_M_WT_IFNb_20h00min_TDAL008


title: ATAC_T8_WT_UT_UT_TDAL008


title: ATAC_M_IRF9KO_IFNb_20h00min_TDAL009


title: ATAC_T8_WT_IFNb_01h30min_TDAL008


title: ATAC_T8_WT_IFNb_20h00min_TDAL008


title: ATAC_M_IRF9KO_IFNb_20h00min_TDAL008


title: ATAC_M_WT_IFNb_01h30min_TDAL008


title: ATAC_T8_IRF9KO_IFNb_01h30min_TDAL008


title: ATAC_M_IRF9KO_IFNb_01h30min_TDAL008


title: ATAC_T8_IRF9KO_UT_UT_TDAL008


title: ATAC_T8_WT_UT_UT_SKAF006

value: SK


title: ATAC_T8_IRF9KO_IFNb_20h00min_TDAL008


title: ATAC_T8_WT_IFNb_20h00min_SKAF006


title: ATAC_M_WT_UT_UT_SKAF006


title: ATAC_T8_STAT6KO_IFNb_20h00min_SKAF006


title: ATAC_T8_STAT6KO_UT_UT_SKAF006


title: ATAC_M_STAT6KO_UT_UT_SKAF006


title: ATAC_M_STAT6KO_IFNb_20h00min_SKAF006


title: ATAC_T8_STAT5VAV_UT_UT_RMVG039

value: RM


title: ATAC_T8_STAT5VAV_IFNb_20h00min_RMVG039


title: ATAC_M_STAT5VAV_IFNb_20h00min_RMVG039


title: ATAC_M_WT_UT_UT_TDAL008


title: ATAC_T8_WT_IFNb_20h00min_RMVG039


title: ATAC_M_IRF9KO_UT_UT_TDAL008


title: ATAC_T8_WT_UT_UT_RMVG039


title: ATAC_M_WT_IFNb_20h00min_SKAF006


title: ATAC_T8_WT_IFNb_01h30min_RMVG039


title: ATAC_M_WT_UT_UT_RMVG039


title: ATAC_M_WT_IFNb_20h00min_RMVG039


title: ATAC_T8_STAT5VAV_IFNb_20h00min_RMVG037


title: ATAC_M_WT_IFNb_01h30min_RMVG039


title: ATAC_M_STAT5VAV_UT_UT_RMVG037


title: ATAC_T8_WT_UT_UT_RMVG037


title: ATAC_M_STAT5VAV_IFNb_01h30min_RMVG037


title: ATAC_T8_WT_IFNb_20h00min_RMVG037


title: ATAC_T8_WT_IFNb_01h30min_RMVG037


title: ATAC_T8_STAT5VAV_UT_UT_RMVG037


title: ATAC_M_STAT5VAV_IFNb_20h00min_RMVG037


title: ATAC_M_WT_UT_UT_RMVG037


title: ATAC_T8_WT_UT_UT_RMVG028


title: ATAC_T8_WT_IFNb_01h30min_RMVG028


title: ATAC_M_WT_UT_UT_RMVG028


title: ATAC_T8_WT_IFNb_20h00min_RMVG028


title: ATAC_M_WT_IFNb_20h00min_RMVG037


title: ATAC_M_WT_IFNb_20h00min_RMVG028


title: ATAC_M_WT_IFNb_01h30min_RMVG028


title: ATAC_T8_STAT5VAV_UT_UT_RMVG028


title: ATAC_M_STAT5VAV_UT_UT_RMVG039


title: ATAC_T8_STAT5VAV_IFNb_20h00min_RMVG028


title: ATAC_T8_STAT5VAV_IFNb_01h30min_RMVG028


title: ATAC_M_STAT5VAV_IFNb_20h00min_RMVG028


title: ATAC_M_STAT5VAV_UT_UT_RMVG028


title: ATAC_M_WT_IFNb_20h30min_MMAK015

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Macrophage cells and treatment: IFNb for 20h30min


title: ATAC_M_STAT5VAV_IFNb_01h30min_RMVG028


title: ATAC_T8_WT_IFNb_20h30min_MMAK015

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen CD8 T cell cells and treatment: IFNb for 20h30min


title: ATAC_T8_TYK2KE_UT_UT_MMAK015


title: ATAC_T8_WT_UT_UT_MMAK015


title: ATAC_T8_TYK2KE_IFNb_20h30min_MMAK015


title: ATAC_T8_TYK2KE_IFNb_01h30min_MMAK015


title: ATAC_M_TYK2KE_IFNb_01h30min_MMAK015


title: ATAC_M_TYK2CMV_UT_UT_MMAK015


title: ATAC_M_TYK2CMV_IFNb_20h30min_MMAK015


title: ATAC_M_TYK2CMV_IFNb_01h30min_MMAK015


title: ATAC_M_TYK2KE_UT_UT_MMAK015


title: ATAC_T8_WT_UT_UT_MMAK014


title: ATAC_T8_TYK2CMV_IFNb_20h30min_MMAK015


title: ATAC_T8_WT_IFNb_20h30min_MMAK014


title: ATAC_T8_WT_IFNb_01h30min_MMAK014


title: ATAC_M_WT_IFNb_20h30min_MMAK014


title: ATAC_M_WT_IFNb_01h30min_MMAK014


title: ATAC_M_WT_UT_UT_MMAK014


title: ATAC_T8_TYK2KE_UT_UT_MMAK014


title: ATAC_T8_TYK2KE_IFNb_20h30min_MMAK014


title: ATAC_T8_TYK2KE_IFNb_01h30min_MMAK014


title: ATAC_M_TYK2KE_UT_UT_MMAK014


title: ATAC_M_TYK2KE_IFNb_20h30min_MMAK014


title: ATAC_T8_TYK2CMV_UT_UT_MMAK014


title: ATAC_T8_TYK2CMV_UT_UT_MMAK015


title: ATAC_M_TYK2CMV_IFNb_20h30min_MMAK014


title: ATAC_T8_TYK2CMV_IFNb_01h30min_MMAK015


title: ATAC_M_TYK2CMV_IFNb_01h30min_MMAK014


title: ATAC_T8_TYK2CMV_IFNb_01h30min_MMAK014


title: ATAC_M_TYK2CMV_UT_UT_MMAK014


title: ATAC_T8_TYK2CMV_IFNb_20h30min_MMAK014


title: ATAC_T8_WT_IFNb_20h30min_MMAK013


title: ATAC_T8_WT_UT_UT_MMAK013


title: ATAC_M_WT_IFNb_20h30min_MMAK013


title: ATAC_T8_TYK2KE_IFNb_01h30min_MMAK013


title: ATAC_M_WT_IFNb_01h30min_MMAK013


title: ATAC_T8_TYK2KE_UT_UT_MMAK013


title: ATAC_M_TYK2KE_IFNb_01h30min_MMAK013


title: ATAC_T8_TYK2KE_IFNb_20h30min_MMAK013


title: ATAC_M_TYK2KE_IFNb_20h30min_MMAK013


title: ATAC_M_TYK2KE_UT_UT_MMAK013


title: ATAC_M_TYK2CMV_UT_UT_MMAK013


title: ATAC_T8_WT_IFNb_01h30min_MMAK013


title: ATAC_T8_TYK2CMV_UT_UT_MMAK013


title: ATAC_T8_WT_IFNb_UT_RMMF167


title: ATAC_M_TYK2CMV_IFNb_01h30min_MMAK013


title: ATAC_M_TYK2KE_IFNb_01h30min_MMAK014


title: ATAC_M_TYK2CMV_IFNb_20h30min_MMAK013


title: ATAC_T8_TYK2CMV_IFNb_20h30min_MMAK013


title: ATAC_T8_TYK2CMV_IFNb_01h30min_MMAK013


title: ATAC_T8_WT_IFNb_20h00min_RMMF167


title: ATAC_M_WT_IFNb_20h00min_RMMF167


title: ATAC_M_WT_IFNb_UT_RMMF167


title: ATAC_T8_STAT5VAV_IFNb_UT_RMMF167


title: ATAC_T8_STAT5VAV_IFNb_20h00min_RMMF167


title: ATAC_T8_WT_IFNb_UT_VSMF166


title: ATAC_M_STAT5VAV_IFNb_20h00min_RMMF167


title: ATAC_M_STAT5VAV_IFNb_UT_RMMF167


title: ATAC_T8_STAT3VAV_IFNb_UT_VSMF166


title: ATAC_T8_STAT3VAV_IFNb_20h00min_VSMF166


title: ATAC_M_WT_IFNb_20h00min_VSMF166


title: ATAC_M_STAT3VAV_IFNb_UT_VSMF166


title: ATAC_T8_WT_IFNb_20h00min_VSMF166


title: ATAC_M_STAT3VAV_IFNb_20h00min_VSMF166


title: ATAC_M_WT_IFNb_UT_VSMF166


title: ATAC_T8_WT_IFNb_20h00min_BSMJ023


title: ATAC_M_WT_IFNb_01h30min_BSMJ022


title: ATAC_T8_WT_IFNb_01h30min_BSMJ017


title: ATAC_M_WT_UT_UT_BSMJ017


title: ATAC_T8_STAT1KO_IFNb_01h30min_BSMJ017


title: ATAC_T8_STAT4KO_IFNb_20h00min_BSMJ021


title: ATAC_M_STAT1KO_IFNb_01h30min_BSMJ017


title: ATAC_T8_STAT1BB_UT_UT_BSMJ017


title: ATAC_M_STAT1BB_IFNb_20h00min_BSMJ017


title: ATAC_M_STAT1BB_UT_UT_BSMJ017


title: ATAC_M_STAT1BB_IFNb_01h30min_BSMJ017


title: ATAC_T8_WT_IFNb_01h30min_BSMJ016


title: ATAC_M_WT_IFNb_20h00min_BSMJ016


title: ATAC_T8_STAT1BB_UT_UT_BSMJ016


title: ATAC_T8_STAT1BB_IFNb_20h00min_BSMJ016


title: ATAC_M_STAT1BB_UT_UT_BSMJ016


title: ATAC_M_STAT1BB_IFNb_20h00min_BSMJ016


title: ATAC_M_STAT1AA_UT_UT_BSMJ016


title: ATAC_M_STAT1BB_IFNb_01h30min_BSMJ016


title: ATAC_T8_STAT1AA_UT_UT_BSMJ016


title: ATAC_M_STAT1AA_IFNb_01h30min_BSMJ016


title: ATAC_T8_STAT1AA_IFNb_20h00min_BSMJ016


title: ATAC_T8_WT_IFNb_20h00min_BSMJ021


title: ATAC_T8_WT_IFNb_01h30min_BSMJ021


title: ATAC_M_WT_IFNb_01h30min_BSMJ017


title: ATAC_T8_WT_UT_UT_BSMJ015


title: ATAC_M_WT_IFNb_01h30min_BSMJ015


title: ATAC_T8_STAT1AA_UT_UT_BSMJ015


title: ATAC_T8_WT_UT_UT_BSMJ016


title: ATAC_M_STAT1AA_UT_UT_BSMJ015


title: ATAC_M_STAT1KO_UT_UT_BSMJ017


title: ATAC_T8_STAT1AA_IFNb_01h30min_BSMJ015


title: ATAC_M_STAT1AA_IFNb_20h00min_BSMJ015


title: ATAC_M_STAT1AA_IFNb_01h30min_BSMJ015


title: ATAC_M_WT_IFNb_20h00min_BSMJ014


title: ATAC_T8_WT_IFNb_20h00min_BSMJ014


title: ATAC_M_WT_UT_UT_BSMJ014


title: ATAC_T8_STAT1BB_IFNb_01h30min_BSMJ016


title: ATAC_T8_WT_UT_UT_BSMJ014


title: ATAC_M_WT_IFNb_01h30min_BSMJ014


title: ATAC_T8_STAT1KO_UT_UT_BSMJ014


title: ATAC_T8_STAT1AA_IFNb_01h30min_BSMJ016


title: ATAC_M_STAT1AA_IFNb_20h00min_BSMJ016


title: ATAC_T8_STAT1KO_IFNb_20h00min_BSMJ014


title: ATAC_M_STAT1KO_IFNb_20h00min_BSMJ014


title: ATAC_M_STAT1KO_IFNb_01h30min_BSMJ014


title: ATAC_T8_STAT1AA_UT_UT_BSMJ014


title: ATAC_T8_STAT1AA_IFNb_20h00min_BSMJ014


title: ATAC_T8_STAT1AA_IFNb_01h30min_BSMJ014


title: ATAC_T8_WT_IFNb_20h00min_BSMJ015


title: ATAC_M_STAT1AA_UT_UT_BSMJ014


title: ATAC_T8_STAT1AA_IFNb_20h00min_BSMJ015


title: ATAC_T8_WT_IFNb_20h00min_BSMJ013


title: ATAC_M_STAT1AA_IFNb_20h00min_BSMJ014


title: ATAC_T8_WT_IFNb_01h30min_BSMJ013


title: ATAC_T8_STAT1KO_UT_UT_BSMJ013


title: ATAC_T8_STAT1KO_IFNb_20h00min_BSMJ013


title: ATAC_M_STAT1KO_UT_UT_BSMJ013


title: ATAC_T8_STAT1KO_IFNb_01h30min_BSMJ013


title: ATAC_T8_STAT1BB_IFNb_20h00min_BSMJ013


title: ATAC_T8_STAT1BB_UT_UT_BSMJ013


title: ATAC_M_STAT1KO_IFNb_20h00min_BSMJ013


title: ATAC_M_STAT1BB_IFNb_20h00min_BSMJ013


title: ATAC_T8_STAT1BB_IFNb_01h30min_BSMJ013


title: ATAC_M_STAT1BB_UT_UT_BSMJ013


title: ATAC_T8_STAT1KO_IFNb_01h30min_BSMJ014


title: ATAC_M_STAT1BB_IFNb_01h30min_BSMJ013


title: ATAC_M_STAT1KO_UT_UT_BSMJ014


title: ATAC_T8_WT_H_H_VSMF230

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen CD8 T cell cells and treatment: H for H


title: ATAC_B_WT_H_H_VSMF230

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen B cell cells and treatment: H for H

value: B cell


title: ATAC_NK_STAT3VAV_H_H_VSMF230

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen NK cell cells and treatment: H for H

value: NK cell


title: ATAC_B_STAT3VAV_H_H_VSMF230

value: spleen


title: ATAC_T8_STAT3VAV_H_H_VSMF230

value: 8-12 weeks


title: ATAC_M_WT_H_H_VSMF230

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Macrophage cells and treatment: H for H


title: ATAC_M_STAT3VAV_H_H_VSMF230


title: ATAC_M_WT_H_H_TDAL012


title: ATAC_T8_STAT2KO_H_H_TDAL012

value: CD8 T cell


title: ATAC_T8_WT_H_H_TDAL007


title: ATAC_M_STAT1AA_IFNb_01h30min_BSMJ014


title: ATAC_M_STAT2KO_H_H_TDAL012


title: ATAC_T8_WT_H_H_TDAL012


title: ATAC_M_STAT1KO_IFNb_01h30min_BSMJ013


title: ATAC_T8_IRF9KO_H_H_TDAL007


title: ATAC_M_WT_H_H_TDAL007


title: ATAC_M_IRF9KO_H_H_TDAL007


title: ATAC_T8_WT_H_H_TDAL006


title: ATAC_M_IRF9KO_H_H_TDAL006


title: ATAC_M_IRF9KO_H_H_TDAL005


title: ATAC_T8_IRF9KO_H_H_TDAL006


title: ATAC_T8_IRF9KO_H_H_TDAL005


title: ATAC_M_WT_H_H_TDAL006


title: ATAC_T8_WT_H_H_TDAL004


title: ATAC_M_WT_H_H_TDAL004


title: ATAC_T8_STAT2KO_H_H_TDAL002


title: ATAC_T8_STAT2KO_H_H_TDAL004


title: ATAC_T8_WT_H_H_TDAL002


title: ATAC_T8_WT_H_H_SKAF008


title: ATAC_M_STAT2KO_H_H_TDAL004


title: ATAC_M_STAT2KO_H_H_TDAL002


title: ATAC_M_WT_H_H_SKAF008


title: ATAC_M_STAT6KO_H_H_SKAF008


title: ATAC_M_WT_H_H_SKAF007


title: ATAC_T8_STAT6KO_H_H_SKAF007


title: ATAC_T8_WT_H_H_SKAF007


title: ATAC_T8_STAT6KO_H_H_SKAF008


title: ATAC_M_STAT6KO_H_H_SKAF007


title: ATAC_M_STAT6KO_H_H_SKAF006


title: ATAC_T8_WT_H_H_SKAF006


title: ATAC_DC_WT_H_H_MMSH001

description:
open chromatin (ATAC-seq)
ATAC-seq sample of spleen Dendritic cell cells and treatment: H for H

value: Dendritic cell

value: MM


title: ATAC_DC_WT_H_H_MMSH002


title: ATAC_T8_STAT6KO_H_H_SKAF006


title: ATAC_DC_TYK2KO_H_H_MMSH002


title: ATAC_M_WT_H_H_SKAF006


title: ATAC_DC_TYK2CMV_H_H_MMSH001


title: ATAC_DC_TYK2CMV_H_H_MMSH002


title: ATAC_M_WT_H_H_MMAK012


title: ATAC_M_WT_H_H_TDAL002


title: ATAC_DC_TYK2CMV_H_H_MMSH009


title: ATAC_DC_WT_H_H_MMSH009


title: ATAC_M_TYK2KE_H_H_MMAK012


title: ATAC_M_TYK2CMV_H_H_MMAK012


title: ATAC_T8_TYK2CMV_H_H_MMAK012


title: ATAC_M_TYK2KE_H_H_MMAK011


title: ATAC_M_TYK2CMV_H_H_MMAK011


title: ATAC_M_WT_H_H_MMAK011


title: ATAC_M_WT_H_H_MMAK010


title: ATAC_T8_WT_H_H_MMAK010


title: ATAC_T8_TYK2KE_H_H_MMAK010


title: ATAC_T8_TYK2CMV_H_H_MMAK010


title: ATAC_M_TYK2KE_H_H_MMAK010


title: ATAC_M_TYK2CMV_H_H_MMAK010


title: ATAC_M_WT_H_H_MMAK009


title: ATAC_T8_WT_H_H_MMAK009


title: ATAC_M_TYK2KE_H_H_MMAK009


title: ATAC_T8_TYK2CMV_H_H_MMAK009


title: ATAC_DC_WT_H_H_MMSH008


title: ATAC_T8_TYK2KE_H_H_MMAK009


title: ATAC_DC_TYK2KE_H_H_MMSH008


title: ATAC_M_TYK2CMV_H_H_MMAK009


title: ATAC_NK_TYK2CMV_H_H_MMAK007


title: ATAC_T8_WT_H_H_MMAK012


title: ATAC_NK_TYK2CMV_H_H_MMAK006


title: ATAC_NK_TYK2KE_H_H_MMAK007


title: ATAC_T8_TYK2KE_H_H_MMAK012


title: ATAC_NK_TYK2KE_H_H_MMAK006


title: ATAC_NK_TYK2KE_H_H_MMAK005


title: ATAC_NK_TYK2CMV_H_H_MMAK005


title: ATAC_T8_WT_H_H_MMAK004


title: ATAC_M_WT_H_H_MMAK004


title: ATAC_M_TYK2KE_H_H_MMAK004


title: ATAC_T8_TYK2CMV_H_H_MMAK004


title: ATAC_T8_WT_H_H_MMAK003


title: ATAC_M_WT_H_H_MMAK003


title: ATAC_T8_TYK2CMV_H_H_MMAK003


title: ATAC_T8_TYK2KE_H_H_MMAK003


title: ATAC_M_WT_H_H_MMAK002


title: ATAC_T8_WT_H_H_MMAK002


title: ATAC_M_TYK2CMV_H_H_MMAK003


title: ATAC_NK_WT_H_H_MMAK007


title: ATAC_T8_TYK2CMV_H_H_MMAK002


title: ATAC_M_TYK2CMV_H_H_MMAK004


title: ATAC_M_TYK2KE_H_H_MMAK002


title: ATAC_T8_WT_H_H_VSMF178


title: ATAC_M_TYK2CMV_H_H_MMAK002


title: ATAC_NK_WT_H_H_MMAK005


title: ATAC_M_WT_H_H_VSMF178


title: ATAC_B_WT_H_H_RMMF174


title: ATAC_B_WT_H_H_VSMF178


title: ATAC_T8_STAT3VAV_H_H_VSMF178


title: ATAC_M_STAT3VAV_H_H_VSMF178


title: ATAC_M_WT_H_H_RMMF173


title: ATAC_NK_WT_H_H_MMAK006


title: ATAC_M_STAT5BN642H_H_H_RMMF173


title: ATAC_B_STAT3VAV_H_H_VSMF178


title: ATAC_NK_WT_H_H_RMMF226


title: ATAC_B_WT_H_H_RMMF226


title: ATAC_T8_WT_H_H_RMMF174


title: ATAC_NK_STAT5BN642H_H_H_RMMF226


title: ATAC_M_WT_H_H_RMMF174


title: ATAC_B_STAT5VAV_H_H_RMMF174


title: ATAC_NK_STAT3VAV_H_H_VSMF216


title: ATAC_M_STAT3VAV_H_H_VSMF216


title: ATAC_T8_WT_H_H_VSMF216


title: ATAC_T8_STAT3VAV_H_H_VSMF216


title: ATAC_T8_STAT5VAV_H_H_RMMF174


title: ATAC_T8_STAT5BN642H_H_H_RMMF173


title: ATAC_B_STAT5BN642H_H_H_RMMF226


title: ATAC_T8_STAT5VAV_H_H_RMMF211


title: ATAC_T8_WT_H_H_RMMF226


title: ATAC_B_STAT3VAV_H_H_VSMF216


title: ATAC_M_STAT5VAV_H_H_RMMF211


title: ATAC_B_STAT5VAV_H_H_RMMF211


title: ATAC_M_TYK2KE_H_H_MMAK003


title: ATAC_NK_WT_H_H_VSMF216


title: ATAC_M_WT_H_H_VSMF216


title: ATAC_B_WT_H_H_RMMF211


title: ATAC_T8_WT_H_H_RMMF209


title: ATAC_M_WT_H_H_RMMF209


title: ATAC_T8_STAT5BN642H_H_H_RMMF226


title: ATAC_T8_WT_H_H_RMMF211


title: ATAC_T8_STAT5BN642H_H_H_RMMF209


title: ATAC_NK_WT_H_H_RMMF209


title: ATAC_M_WT_H_H_RMMF211


title: ATAC_B_WT_H_H_RMMF209


title: ATAC_T8_WT_H_H_RMMF208


title: ATAC_NK_WT_H_H_RMMF208


title: ATAC_T8_STAT5BN642H_H_H_RMMF208


title: ATAC_B_WT_H_H_RMMF208


title: ATAC_M_WT_H_H_RMMF208


title: ATAC_B_STAT5BN642H_H_H_RMMF209


title: ATAC_NK_WT_H_H_RMMF196


title: ATAC_M_WT_H_H_RMMF196


title: ATAC_T8_WT_H_H_RMMF196


title: ATAC_M_STAT5BN642H_H_H_RMMF209


title: ATAC_B_WT_H_H_VSMF216


title: ATAC_NK_STAT5BN642H_H_H_RMMF196


title: ATAC_T8_STAT5BN642H_H_H_RMMF196


title: ATAC_B_WT_H_H_RMMF196


title: ATAC_B_STAT5BN642H_H_H_RMMF196


title: ATAC_M_STAT5BN642H_H_H_RMMF196


title: ATAC_B_STAT5BN642H_H_H_RMMF208


title: ATAC_T8_WT_H_H_VSMF192


title: ATAC_NK_STAT5BN642H_H_H_RMMF209


title: ATAC_T8_STAT3VAV_H_H_VSMF192


title: ATAC_M_STAT3VAV_H_H_VSMF192


title: ATAC_NK_STAT3VAV_H_H_VSMF192


title: ATAC_NK_WT_H_H_VSMF192


title: ATAC_T8_WT_H_H_RMMF189


title: ATAC_M_WT_H_H_VSMF192


title: ATAC_M_WT_H_H_RMMF189


title: ATAC_NK_STAT5BN642H_H_H_RMMF208


title: ATAC_T8_STAT5VAV_H_H_RMMF189


title: ATAC_B_STAT5VAV_H_H_RMMF189


title: ATAC_B_STAT3VAV_H_H_VSMF192


title: ATAC_T8_WT_H_H_RMMF186


title: ATAC_B_WT_H_H_RMMF189


title: ATAC_NK_WT_H_H_RMMF189


title: ATAC_M_WT_H_H_RMMF186


title: ATAC_M_STAT5VAV_H_H_RMMF189


title: ATAC_B_STAT5VAV_H_H_RMMF186


title: ATAC_B_WT_H_H_RMMF186


title: ATAC_M_WT_H_H_BSMJ019


title: ATAC_M_STAT4KO_H_H_BSMJ020


title: ATAC_T8_STAT4KO_H_H_BSMJ019


title: ATAC_T8_STAT5VAV_H_H_RMMF186


title: ATAC_T8_STAT4KO_H_H_BSMJ020


title: ATAC_M_WT_H_H_BSMJ020


title: ATAC_T8_WT_H_H_BSMJ020


title: ATAC_M_STAT5VAV_H_H_RMMF186


title: ATAC_M_STAT4KO_H_H_BSMJ019


title: ATAC_B_WT_H_H_VSMF192


title: ATAC_T8_WT_H_H_BSMJ019


title: ATAC_M_WT_H_H_BSMJ018


title: ATAC_T8_STAT4KO_H_H_BSMJ018


title: ATAC_T8_WT_H_H_BSMJ005


title: ATAC_T8_WT_H_H_BSMJ004


title: ATAC_T8_WT_H_H_BSMJ003


title: ATAC_M_WT_H_H_BSMJ005


title: ATAC_M_STAT4KO_H_H_BSMJ018


title: ATAC_M_WT_H_H_BSMJ004


title: ATAC_T8_STAT1BB_H_H_BSMJ003


title: ATAC_T8_STAT1BB_H_H_BSMJ004


title: ATAC_M_STAT1BB_H_H_BSMJ004


title: ATAC_M_WT_H_H_BSMJ003


title: siCARM1-1

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 38
Supplementary_files_format_and_content: abundance measurements

source_name: Human breast cancer cell line

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from the MDA-MB-231 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: siRNA was transfected into MDA-MB-231 cells using Lipofectamine RNAiMAX (Invitrogen).

tag: sirna


title: ATAC_M_STAT1BB_H_H_BSMJ003

tag: genotype


title: siControl-2

value: siControl


title: ATAC_M_STAT1AA_H_H_BSMJ005


title: ATAC_M_STAT1AA_H_H_BSMJ004


title: ATAC_T8_STAT1AA_H_H_BSMJ004


title: siControl-1


title: ATAC_T8_STAT1AA_H_H_BSMJ003


title: ATAC_T8_STAT1KO_H_H_BSMJ005


title: HiC, Zfp661 KO mESCs, replicate 2

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

description: Arima-HiC

data_processing:
Mouse genome (mm10) fragments were generated using the “digest_genome” tool in HiC-Pro utilities (Servant, Varoquaux et al. 2015) with restriction motifs “GATC” and “G^ANTC”. Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. HiC-Pro pipelines (v2.11.4) were then used with above genome fragments and the parameter “LIGATION_SITE = GATCGATC, GANTGATC, GANTANTC, GATCANTC” to generate valid interaction pairs and contact maps.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for valid interaction pairs (.allValidPairs.gz).

source_name: R1 mESCs

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min.
Cells with approximately 4 μg of DNA were used as input to generate proximally ligated DNA using the Arima-HiC kit (Arima, A510008) according to the manufacturer’s protocol (Arima, A160134 v01). Briefly, crosslinked cells were digested using the Arima restriction enzyme cocktail, the 5’ overhangs were filled in and labeled with a biotinylated nucleotide, and the spatially proximal ends were ligated. The proximally ligated DNAs were purified and sonicated using the Covaris ME220 (8 microTube-130 AFA fiber strip V2: duration 42s, peak power 70w, duty factor 20%, cycle per burst 1000#). Then, size selection was performed on the resulting DNA Fragments (for size ranging from 200 to 600 bp). 2 μg of the resulting DNA fragments were used as input, and fragments labelled with biotin were bound to beads to construct Hi-C libraries using the KAPA HyperPrep Kit (Roche, KK8502) following the protocol provided by Arima (A160139 v00). For Capture Hi-C, probes were designed to cover several regions bound by ZFP661 using the SureSelect DNA tool of Agilent SureDesign with the following settings: 2X tiling density, moderately stringent masking, and optimized performance for HS2/XT. The Capture Hi-C libraries were obtained by fast hybridization for 90 min with probes, followed by capture, washes and post-capture amplification using the SureSelect XT HS2 DNA Target Enrichment Kit (Agilent, G9987A) according to the protocol (Agilent, G9983-90000).

value: R1 mESCs

value: mouse embryonic stem cells

value: Zfp661 KO


title: Capture HiC, WT mESCs, replicate 1

description: Arima-HiC followed by capture

value: WT


title: Capture HiC, WT mESCs, replicate 2

description: Arima-HiC followed by capture


title: Capture HiC, Zfp661 KO mESCs, replicate 1

description: Arima-HiC followed by capture


title: Capture HiC, Zfp661 KO mESCs, replicate 2

description: Arima-HiC followed by capture


title: ATAC_M_STAT1AA_H_H_BSMJ003

value: Macrophage

value: Homeostatic

value: BS


title: HiC, Zfp661 KO mESCs, replicate 1

description: Arima-HiC


title: ATAC_M_STAT1KO_H_H_BSMJ005


title: HiC, WT mESCs, replicate 2

description: Arima-HiC


title: ATAC_T8_WT_H_H_BSMJ002

value: Wildtype


title: ATAC_T8_WT_H_H_BSMJ001


title: ATAC_M_WT_H_H_BSMJ001


title: Zfp661 KO, E16.5 forebrain (replicate 2), CTCF ChIP

description: ChIP-seq

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
MACS2 (v2.2.7.1) was used to call peaks with one duplicated tag kept, and the threshold q ≤ 0.01.
To generate ChIP signal (i.e., bigwig) files, deepTools (v3.5.1) was used with the parameters “--normalizeUsing CPM --binSize 10 –extendReads” (CPM represents counts per million) and with chrM and regions on ENCODE blacklist excluded. The ChIP signals were normalized by subtracting the ChIP input in each biological replicate (for ZFP661, subtracted by HA-ChIP in untagged controls).
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw), MACS2 peak files (.NarrowPeak).

source_name: mouse embryonic brain

extract_protocol:
Embryonic forebrains were isolated and dissociated into a single-cell suspension using the Papain Dissociation System (Worthington LK003150) by incubating at 37°C for 45 min. The cell suspension was passed through cellTrics Cell Strainers (20 μm) to remove cell debris and clumps. Subsequently, the suspension underwent discontinuous density gradient centrifugation using the Papain Dissociation System at 70 g for 6 min to further remove any remaining debris and membrane fragments. Then, cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min.
ChIP assays were performed according to the ENCODE protocol with modifications. Eight E16.5 forebrains per ChIP were used for ZFP661-3HA (anti-HA: Abcam, ab9110) and CTCF (anti-CTCF: Millipore, 07-729). 5 μg of antibodies were used for each ChIP. ChIP DNA was purified, and 10 μl of ChIP DNA was used as input to construct the ChIP library using the ThruPLEX DNA-Seq Kit (Takara, R400676). The ChIP inputs from the same biological replicate were used to construct the corresponding ChIP input library.

value: mouse embryonic brain

tag: chip antibody

value: CTCF (Millipore, 07-729)


title: HiC, WT mESCs, replicate 1

description: Arima-HiC


title: ATAC_T8_STAT1AA_H_H_BSMJ005


title: ATAC_T8_STAT1BB_H_H_BSMJ002


title: WT, E16.5 forebrain (replicate 1), CTCF ChIP

description: ChIP-seq


title: ATAC_T8_STAT1AA_H_H_BSMJ001


title: siCARM1-2


title: ATAC_M_WT_H_H_BSMJ002


title: WT, E16.5 forebrain (replicate 2), CTCF ChIP

description: ChIP-seq


title: Zfp661 KO, E16.5 forebrain (replicate 2), ChIP input

description: ChIP-seq

value: Input control


title: ATAC_M_STAT1BB_H_H_BSMJ002

value: spleen


title: Zfp661 KO, E16.5 forebrain (replicate 1), ChIP input

description: ChIP-seq


title: ATAC_T8_STAT1KO_H_H_BSMJ002

value: 8-12 weeks


title: ATAC_M_STAT1KO_H_H_BSMJ002


title: ATAC_M_STAT1AA_H_H_BSMJ001


title: WT, E16.5 forebrain (replicate 1), ChIP input

description: ChIP-seq


title: WT, E16.5 forebrain (replicate 2), ChIP input

description: ChIP-seq


title: Endogenously tagged ZFP661-3HA mice, E16.5 forebrain (replicate 2), ChIP anti-HA

description: ChIP-seq

value: Endogenously tagged ZFP661-3HA

value: HA (Abcam, ab9110)


title: Zfp661 KO, E16.5 forebrain (replicate 1), CTCF ChIP

description: ChIP-seq


title: Endogenously tagged ZFP661-3HA mice, E16.5 forebrain (replicate 2), ChIP input

description: ChIP-seq


title: Endogenously tagged ZFP661-3HA mice, E16.5 forebrain (replicate 1), ChIP anti-HA

description: ChIP-seq


title: Untagged control, E16.5 forebrain (replicate 2), ChIP anti-HA

description: ChIP-seq


title: Untagged control, E16.5 forebrain (replicate 1), ChIP anti-HA

description: ChIP-seq


title: Kidney, Male_Norm_K_4

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: tab-delimited text file with FPKM

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney

value: Male

value: High NaCl and Normal K


title: Kidney, Male_Norm_K_2


title: Kidney, Male_Norm_K_3


title: Endogenously tagged ZFP661-3HA mice, E16.5 forebrain (replicate 1), ChIP input

description: ChIP-seq


title: Muscle, FRAIL1, rep6

city: Iowa City

first: Matthew

last: Miller

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
Galaxy online platform (www.usegalaxy.org).
Sequencing reads were trimmed to remove adaptor sequences using Trimmomatic and mapped to the M. musculus reference genome mm10 using RNA-star (v2.7.8a).
FeatureCounts (v2.0.1) was used to count the number of reads uniquely mapping to annotated genes.
Assembly: mm10
Supplementary files format and content: Comma-separated values file includes raw gene counts for each Sample

source_name: Tibialis anterior muscle

extract_protocol:
Freshly excised mouse TA muscles were immediately frozen in liquid N2 and stored at -80 °C. Muscle RNA was extracted using TRIzol solution (Thermofisher, catalog no. 15596018) and then homogenized with three 30 s cycles of Precellys Evolution (Bertin Technologies, catalog no. PE000062) homogenizer set at 8200 rpm.  RNA was then extracted following the manufacturer’s directions and purified using the RNeasy kit and RNase-free DNase Set (Qiagen) according to the manufacturer protocol.
RNA samples were subjected to poly(A)+ selection, cDNA synthesis and sequencing on Illumina NovaSeq by GENEWIZ (USA; www.GENEWIZ.com)

value: Tibialis anterior muscle

value: FRAIL1 transfection


title: Kidney, Male_Norm_K_5

value: WT


title: Kidney, Male_Norm_K_6


title: Kidney, Male_Norm_K_1


title: Kidney, Male_High_K_6

value: High NaCl and High K


title: Kidney, Male_High_K_5


title: Muscle, FRAIL1, rep4


title: Muscle, FRAIL1, rep5


title: Kidney, Male_High_K_3


title: Kidney, Male_High_K_2


title: Muscle, FRAIL1, rep1


title: Muscle, FRAIL1, rep3


title: Kidney, Male_High_K_1


title: Kidney, Male_Def_K_6

value: High NaCl and deficient in K


title: Muscle, Empty, rep5

value: Control transfection


title: Kidney, Male_Def_K_4


title: Muscle, FRAIL1, rep2


title: Muscle, Empty, rep6


title: Muscle, Empty, rep4


title: Kidney, Male_Def_K_5


title: Muscle, Empty, rep3


title: Muscle, Empty, rep1


title: Muscle, Empty, rep2


title: Kidney, Male_Def_K_2


title: Kidney, Male_Def_K_1


title: Kidney, Male_High_K_4


title: Kidney, Fem_Norm_K_4

value: Female


title: Kidney, Fem_Norm_K_6


title: Kidney, Fem_Norm_K_2


title: Kidney, Fem_Norm_K_5


title: Kidney, Fem_Norm_K_3


title: middle-aged, snRNAseq

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
FASTQ files were aligned against the mouse mm10 reference and converted to gene expression using Cell Ranger Software (version 7.0.1) with “--force-cells 10000”
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: brown adipose tissue

extract_protocol:
In preparation for snRNA-seq, harvested mouse interscapular brown adipose tissues were minced in nuclear preparation buffer (10mM HEPES, 1.5mM MgCl2, 10mM KCl, 250mM Sucrose, 0.1% NP-40, 0.6U/μl Rnase inhibitor), and then homogenized in a Dounce homogenizer. The homogenate was passed through a 100μM filter and centrifuged at 750xg for 5min. The pellet was resuspended in 2% BSA/PBS, filtered again and sorted using a MoFloXDP Cell Sorter using the gating strategy previously described 29.
cDNA synthesis were performed using the Single Cell 3' v3.1 Dual Index Gene Expression Reagent kit (10x Genomics) following the manufacturer’s instructions

value: brown adipose tissue

value: wild type

value: 12 months


title: Kidney, Fem_Norm_K_1


title: SIGNAL-seq ADT library of CRC PDO and CAF co-cultures sublibrary 78

city: London

first: James

last: Opzoomer

address: 72 Huntley Street

department: Department of Oncology

country: United Kingdom

institute: University College London

description: ADT library from PDO experiment generated using the SIGNAL-seq protocol, paired with index 78 RNA sublibrary.

library_source: other

data_processing:
Raw sequencing data were converted to fastq format using bcl2fastq (Illumina).
scRNA-seq reads were aligned and digital gene expression matrix generated with zUMIs-2.9.7e and  STAR-2.7.3a, (see https://github.com/TAPE-Lab/SIGNAL-seq) for more details on processing pipeline. implementation. Barcode maps are contained in the supplemental information.
ADT reads were assigned to individual cells using the Kallisto Kite workflow based on cell barcode, antibody barcode sequence, to generate UMI count data.
Assembly: GRCh38
Supplementary files format and content: ex0015_pdo_rna_adata.h5ad is an .h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq RNA data, X matrix represents scaled and UMI-depth corrected Log-normalised data. The Log-normalised data is contained in the .raw slot. Metadata .obs slot sample_id encodes culture condition, cell_type encodes cell type label. Sublibrary index is encoded in .obs slot sublib_index.
Supplementary files format and content: ex0015_pdo_adt_adata.h5ad is an h5ad-formatted file containing Scanpy AnnData object of processed SIGNAL-seq ADT data, X matrix represents CLR transformed data. Metadata .obs slot sample_id encodes culture condition, cell_type encodes cell type label.  Sublibrary index is encoded in .obs slot sublib_index.

molecule: other

source_name: Colorectal cancer

extract_protocol:
PDOs were extracted from matrigel with ice cold PBS. PDOs were then digested to a single-cell suspension with TrypLE Express Enzyme (Gibco #12604013) for 10 minutes at 37C on a heated orbital shaker at 300rpm. Cells were then re-suspended in 1 mL PBS + RNAse inhibitor cocktail (RI). Fixation and permeabilisation was then carried out with a modified SPLiT-seq protocol. Single-cell suspensions were fixed with on ice in 1% effective Formaldehyde for 10 minutes before the cells were permeabilized for a further 3 minutes with 0.2% effective Triton X-100. Fixation was then quenched with 50 mM of Tris-HCL (Invitrogen #15568025) before the cells were re-suspended in 300 μL of 0.5x PBS +RI +5% DMSO before freezing and storage at -80C until processing for SIGNAL-seq.
scRNA-seq RNA and ADT libraries were generated using a modified combinatorial barcoding (Rosenberg and Rocco et al., 2018) SIGNAL-seq protocol producing two sequencing libraries (RNA and ADT) for each sublibrary.
SIGNAL-seq

treatment_protocol: On Day 0 CRC PDOs were dissociated into single cells as described above, and expanded in 12-well plates in Growth Factor Reduced Matrigel with 1 mL per well of Advanced DMEM F/12, supplemented with 2 mML glutamine, 1 mM N-acetyl-l-cysteine, 10 mM HEPES, 1X HyClone Penicillin-Streptomycin Solution, 1X B-27 Supplement, 1X N-2 Supplement, 50 ng mL−1 EGF, 10 nM Gastrin I, 10 mM Nicotinamide, 500 nM A83-01 and 10 μM SB202190 at 5% CO2, 37◦C for 96 hours. On Day 1, CAFs were split into a new flask containing a low-serum media (DMEM supplemented with 2% FBS and 1X HyClone-Penicillin Streptomycin Solution). On Day 4, PDO culture media was changed to a reduced media; Advanced DMEM F/12 supplemented with 2 mM glutamine, 1 mM N-acetyl-L-cysteine, 10 mM HEPES, 1X B-27 Supplement, 1X N-2 Supplement, 10 mM Nicotinamide, 1X HyClone-Penicillin Streptomycin Solution and 25 ng mL−1 EGF). PDOs and CAFs were seeded on Day 5 in 96-well plates (Helena Biosciences #92696T) in 50 μL Growth Factor Reduced Matrigel with 300 μL of reduced media. PDOs were seeded at a density of approximately 1.5 x 103 organoids/well and CAFs at 3x 105 cells/well. PDOs and CAFs were either seeded in mono-culture alone, or in co-culture by mixing together in Matrigel on ice. Cultures were maintained for 72 hours at 5% CO2, 37◦C, with media changes every 24 hours. On Day 6 and 7, media was replaced with reduced media containing 15 nM SN-38 (Sigma #H0165) or DMSO (Merck #D2650), as a vehicle control. On Day 8, after 72-hours in culture and 48-hours of treatment, cultures were processed for SIGNAL-seq.

value: Colorectal cancer

value: CRC epithelial PDO and fibroblasts

tag: library type

value: ADT


title: SIGNAL-seq ADT library of CRC PDO and CAF co-cultures sublibrary 79

description: ADT library from PDO experiment generated using the SIGNAL-seq protocol, paired with index 79 RNA sublibrary.


title: SIGNAL-seq ADT library of CRC PDO and CAF co-cultures sublibrary 76

description: ADT library from PDO experiment generated using the SIGNAL-seq protocol, paired with index 76 RNA sublibrary.


title: Kidney, Fem_High_K_5

tag: Sex


title: Ucp1-Stx4KO, Rep4

data_processing:
Reads were aligned to mm10 reference genome using STAR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
We use Trizol and Qiagen RNeasy Mini Kit, following the manufacturer's protocol to ensure high-quality RNA isolation.
mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. NEB library method is used.


title: Kidney, Male_Def_K_3


title: Kidney, Fem_High_K_4


title: young, snRNAseq

value: 2 months


title: Kidney, Fem_Def_K_6

value: Kidney


title: Kidney, Fem_High_K_3


title: SIGNAL-seq RNA library of CRC PDO and CAF co-cultures sublibrary 79

description: RNA library from PDO experiment generated using the SIGNAL-seq protocol, index 79 was used to generate the sublibrary.

value: RNA


title: Kidney, Fem_Def_K_5


title: SIGNAL-seq RNA library of CRC PDO and CAF co-cultures sublibrary 77

description: RNA library from PDO experiment generated using the SIGNAL-seq protocol, index 77 was used to generate the sublibrary.


title: Ucp1-Stx4KO, Rep2


title: Kidney, Fem_Def_K_3