title: DMSO_rep2

description: Library name: S5

value: DMSO


title: MMV1545561_rep1

status: Public on Aug 19 2025

type: SRA

city: Edinburgh

first: Tianchi

last: Zhou

address: Crewe Rd S

country: United Kingdom

institute: University of Edinburgh

description: Library name: S4

library_source: transcriptomic

data_processing:
The sequencing quality was checked with FastQC (v0.11.9). Low-quality sequences and adapters were trimmed with Cutadapt (v3.5) . Alignment and feature calling was performed with HISAT2 (v2.2.1) , SAMtools (v1.12) and Rsubread (v2.0.1). Differential expression analysis was performed with DESeq2 (v1.36.0).
Assembly: Plasmoduim falciparum 3D7 65
Supplementary files format and content: csv normalised counts

molecule: polyA RNA

organism: Plasmodium falciparum 3D7

source_name: whole organism

extract_protocol:
Total RNA was extracted from the pellets with RNAzol (Sigma) according to the manufacture’s protocol, quality checked with nanodrop before being snap frozen.
The mRNA were enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module E7490 (New England Biolabs) for mRNA-Seq library construction.The cDNA library was prepared according to manufacturer’s instructions using the NEBNext® Ultra™ II Directional RNA Library Prep Kit E7760 and NEBNext® Multiplex Oligos E7710 (New England Biolabs). The libraries were purified with Beckman SPRIselect beads (Beckman Coulter). The library quality was checked using Agilent Bioanalyzer. A total of 12 qualified samples were sent for sequencing (Novogene, Illumina NovaSeq 6000 system).

tag: tissue

value: whole organism

tag: treatment

tag: batch


title: ATAC_4T1 cells, Vector, rep1

city: taipei

first: Tai-Lung

last: Cha

state: taipei

address: 11490 No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.

department: National Institute of Cancer Research

country: Taiwan

institute: National Defense Medical Center

description:
Library name: Smaple 43
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shCtrl

library_source: genomic

data_processing:
RNAseq:RNA-seq data were aligned to the UCSC reference genome using Bowtie2 (v2.4.5). The human genome (GRCh37/hg19) and mouse genome (GRCm38/mm10) assemblies from the UCSC Genome Browser were used as references. Aligned reads were processed with SAMtools (v1.3) to generate a read count table for each gene.
ATACsaq: Reads were mapped to the human genome (hg19) and mouse genome (mm10) using Bowtie2. PCR duplicates were removed using Picard Tools. For peak calling, biological replicates were merged and processed using MACS2. Peaks from all replicates were further merged using SAMtools. Variance-stabilizing transformation and principal component analysis (PCA) were performed using SeqMonk, based on the DESeq2 model. Visualization of ATAC-seq signals across specific genes was performed using the Integrative Genomics Viewer (IGV).
Assembly: hg19 and mm10
Supplementary files format and content: text files inculed raw counts for each sample
Supplementary files format and content: csv files include FPKM value for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: mammary gland

growth_protocol: Cell lines were cultured in media recommended by the American Type Culture Collection (ATCC) and maintained at 37°C in a humidified incubator with 5% CO₂. Bone marrow cells were isolated from mouse femurs and tibias by PBS flushing, followed by red blood cell lysis with Tris-ammonium chloride. Cells were filtered through a 70-μm strainer and cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS. For stimulation, cells were seeded at 0.5 × 10⁶ cells/ml with 20 ng/ml M-CSF. Fresh cytokine-containing medium was added on day 2, and cells were collected over a 5-day period.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN). RNA-seq libraries were prepared from pretreated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. For ATAC-seq, 1×10⁶ cells were collected, washed with PBS, and lysed in cold ATAC RSB lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1%Tween-20, and 0.01% digitonin). Nuclei were washed with ATAC RSB containing 0.1% Tween-20 and resuspended in transposition mix containing Tn5 transposase (Illumina). Transposition was carried out at 37°C for 30 min with shaking at 300 rpm. DNA was purified using the Qiagen MinElute PCR Purification Kit and libraries were amplified using NEBNext PCR master mix (NEB).
RNA-seq libraries were quantified using Qubit (Invitrogen), denatured to single-stranded DNA, loaded onto Illumina flow cells, amplified by in situ cluster generation, and sequenced for 150 cycles on an Illumina HiSeq 2500 platform following the manufacturer's instructions. ATAC-seq libraries were sequenced on an Illumina NextSeq 550 system using paired-end reads.

value: mammary gland

tag: cell line

tag: cell type

value: mouse mammary carcinoma cell

tag: genotype

value: wild-type

value: shRNA control vector


title: ATAC_4T1 cells, shMYADM#1, rep3

description:
Library name: Smaple 42
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shMY

value: MYADM knockdown

value: MYADM knockdown (shMYADM)


title: MMV085071_rep1

description: Library name: S3


title: ATAC_4T1 cells, shMYADM#1, rep2

description:
Library name: Smaple 41
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shMY


title: ATAC_4T1 cells, shMYADM#1, rep1

description:
Library name: Smaple 40
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shMY


title: CQ_rep1

description: Library name: S2

value: CQ


title: ATAC_4T1 cells, shContral, rep2

description:
Library name: Smaple 38
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shvec


title: ATAC_4T1 cells, shContral, rep3

description:
Library name: Smaple 39
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shvec


title: CScreen_LYN

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

country: USA

institute: NIH

description: Library name: CScreen_LYN

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file
Library strategy: CRISPR screen

organism: Homo sapiens

growth_protocol: SU-DHL-4 cells with doxycycline inducible Cas9 were described previously (Phelan et al. 2018). Cells were cultured in advanced RPMI-1640 media supplemented with 5% FBS (Gemini), 1% GlutaMAX, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). Peripheral blood mononuclear cells from healthy blood donors (NIH blood bank) were isolated over Ficoll and cryopreserved. Naïve CD19+ human B cells were isolated with EasySep Human Naïve B Cell Isolation Kit according to the manufacture’s instructions (Stemcell Technologies). Isolated B cells were grown in IMDM media supplemented with 10% FBS (Gemini), 50 µM of beta-mercaptoethanol, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). All cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
CRISPR screens:
SU-DHL-4 reporter cells were transduced with the Brunello library. For each screen, 6 replicates with 15 million cells (90 million in total) were transduced at a density of 5 million cells/ml in a 6 well plate. The amount of virus was adjusted according to the viral titer to obtain a multiplicity of infection (MOI) of 0.3. Cells were transduced by spinfection (1,460g for 90 min and 30°C) in the presence of 6 µg/ml polybrene. Infected cells were puromycin selected 24h post infection at a final concentration of 4 µg/ml. On day 3 post infection, the MOI was verified and cells were split in medium containing 200 ng/ml doxycycline. Cells were split every other day with fresh doxycycline containing medium. On day 10 post infection, for each of the six replicates 60 million cells were sorted using BD FACS Aria or Fusion cell sorters based on reporter fluorescence to capture the bottom and top 5% expressing cells. On average, for each screen 286 million cells were sorted yielding ~9 million low or high expressing cells (Table S1B). For the three mTORC1 inhibited CRISPR screens in BTG2, CD79B and OCAB reporter cell lines, 5 nM rapamycin was added on day 8 and cells were sorted on day 10 as for the other screens. Genomic DNA from sorted cells was extracted using DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq
Cells were either unperturbed, transduced with sgRNA, or treated with inhibitors as described above. Cells were split every other day and seeded at 200,000 cells/ml the day before harvest. Inhibitor treated cells were harvested on day 2 post-treatment and sgRNA transduced cells on day 10 post-infection. On the day of harvest, half a million cells were pelleted and lysed in 100 µl of the Ambion RNAqueous lysis solution. RNA was extracted and treated with DNase according to the RNAqueous-Micro Total RNA Isolation Kit protocol (Thermo Fisher Scientific). RNA-seq libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ChIP-seq
Cells for ChIP-seq analysis were either unperturbed or transduced with sgRNA for 10 days before harvesting. The day before harvest, cells were diluted to 200,000 cells/ml. Cultured cells were fixed at room temperature for 10 min with 1% formaldehyde (Sigma) and the reaction was quenched with 125 mM glycine (Sigma). Fixed cells were washed with PBS, snap-frozen, and stored at -80°C until further processing. For ChIP, 20 million cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and freshly added Complete Mini EDTA free proteinase inhibitor (Roche)). Chromatin was sheared by sonication on ice using a Branson Sonifier with an amplitude of 35% and 12 cycles of 20 sec sonication followed by 30 sec of pause. Supernatant was precleared with 20 µl Dynabeads Protein A (Thermo Fisher Scientific) for 1 hour at 4°C under rotation. Precleared chromatin was incubated with BRD4 (Abcam, ab128874) or FLI1 (Abcam, ab133485) antibody overnight at 4°C under rotation. The antibody-protein solution was then captured with 40 µl of Dynabeads Protein A for 1 hour at 4°C under rotation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K (Thermo Fisher Scientific). ChIP DNA was column purified with ChIP DNA Clean and Concentrator kit (Zymo research).
RNA-seq
Libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Single 50 cycles of sequencing data were acquired on HiSeq3000, NovaSeq6000, NovaSeqXplus (illumina).
ChIP-Seq
Libraries were prepared using the Ovation Ultralow Library System V2. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (illumina)
CRISPR screen
Libraries were prepared using staggered GeCKO readout primers following the recommended instructions (Shalem et al. 2014). Deep sequencing was performed on NextSeq550 and NovaSeq6000 (Illumina) using 75bp single-end reads.

treatment_protocol:
primary human B cells:
Cells were activated with 100 ng/ml MEGACD40L (Enzo Life Sciences), 1 µg/ml CpG oligodeoxynucleotide ODN 2006 (Invivogen), 50 ng/ml human IL-2, 50 ng/ml human IL-10, and 10 ng/ml human IL-15 (all interleukins from PeproTech). Every other day the medium was fully removed and cells diluted in fresh activation medium.
Inhibitor treatments:
SU-DHL-4 or primary B cells were seeded at 0.2 million cells/ml and treated with DMSO or inhibitors. Inhibitors were purchased from MedChemExpress or Selleck Chemicals and dissolved in DMSO. Inhibitors were titrated and used at the following concentrations: rapamycin (5 nM), MK2206 (250 nM), AS1842856 (50 nM), LY2090314 (2 nM), CHIR99021 (1 µM). After two days of treatment, cells were analyzed by flow cytometry or harvested for RNA-seq.

value: B cell lymphoma

value: no


title: CScreen_IRF8

description: Library name: CScreen_IRF8


title: DMSO_rep1

description: Library name: S1


title: Liver, INT-767, Rep 4

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: library name: 12018

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.4.0 with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Liver

extract_protocol:
Liver tissue was harvested from the left lateral lobe and snap frozen in liquid nitrogen. Tissue sections (about 50 mg) were homogenized in lysis buffer containing protease inhibitors and used for RNA extraction using NucleoSpin Plus RNA columns (Macherey-Nagel). The quantity of the RNA was analyzed using a Nano Drop 2000 spectrophotometer (Thermo Scientific, United States)
RNA-seq libraries were prepared with NeoPrep (Illumina Inc., San Diego, CA, US) using Illumina TruSeq stranded mRNA Library kit for NeoPrep (Illumina) and sequenced on the NextSeq 500 (Illumina) with NSQ 500 hi-Output KT v2 (75 CYS; Illumina).

value: Liver


title: CScreen_IKZF1

description: Library name: CScreen_IKZF1


title: Liver, INT-767, Rep 3

description: library name: 12003


title: ChIP-seq ESC Irx3-anchor KO Ctcf

city: Hershey

first: Zhonghua

last: Gao

state: PA

address: 700 HMC Cres Rd

department: Biochemistry

institute: Pennsylvania State University

description: Library name: ChIP-seq Sample 12

data_processing:
For ChIP-seq samples, alignment was performed using BWA and mm10 (mouse) and hg38 (human) were used as reference genomes. Samtools was used to generate bam/sam files. Deeptools were used for bigwig file and visualization. MACS2 was used for peak calling using default parameters.
Assembly: mm10, hg38
Supplementary files format and content: For ChIP-seq, BigWig (.bw) files containing read density data of respective immunoprecipitated proteins at mapped genomic loci.

growth_protocol: ESCs and NPCs were cultured in basic stem cell media (DMEM, 15% FBS, 1 X non-essential amino acids, 0.1 mM β-mercaptoethanol, 0.5 X penicillin/streptomycin, 1X sodium pyruvate). For ESCs, 0.003 µg/mL LIF, 1 µM PD0325901 (PD), and 3 µM Chir99021 (CH) were added to the media. For NPCs, 5 µM retinoic acid was added starting from day 4 of differentiation until day 8. U2OS cells were cultured on standard attachment cell culture plates in DMEM, 10% FBS, 10% newborn calf serum (NCS), and 0.5X penicillin/streptomycin.

extract_protocol:
For ChIP-seq samples, cells were cross-linked with 1% formaldehyde for 8 minutes at room temperature. After washing, cells were sonicated with Diagenode Bioruptor in ChIP lysis buffer. Samples were cleaned up for immunoprecipitation using protein G agarose beads with antibodies of interest. Bound protein-DNA complexes were collected from beads and reverse crosslinked before being purified for DNA. Futher procedure details are described in the main associated article.
The ChIP-seq libraries were constructed using the sparQ DNA Library Prep kit.

treatment_protocol: NPCs were cultured in basic stem cell media with 5 µM retinoic acid (RA) starting from day 4 of differentiation until day 8. U2OS cells were transfected with either siControl or siRING1B for 2 days before collection.

value: Mouse embryonic stem cells

value: Irx3-anchor knock-out

value: ESC culture (+LIF, 2i)


title: CScreen_IGK

description: Library name: CScreen_IGK


title: ChIP-seq ESC Irx3-anchor KO Input

description: Library name: ChIP-seq Sample 11


title: Liver, Vehicle, Rep 7

description: library name: 12010

value: Vehicle


title: Liver, INT-767, Rep 1

description: library name: 11983


title: Liver, INT-767, Rep 2

description: library name: 11984


title: ChIP-seq ESC Pcgf2 KO Ctcf

description: Library name: ChIP-seq Sample 10

value: Pcgf2 knock-out


title: Liver, Vehicle, Rep 5

description: library name: 12007


title: CScreen_ID3

description: Library name: CScreen_ID3


title: CScreen_IGH

description: Library name: CScreen_IGH


title: ChIP-seq ESC Pcgf2 KO Input 2

description: Library name: ChIP-seq Sample 9


title: Liver, Vehicle, Rep 4

description: library name: 12005


title: Liver, Vehicle, Rep 2

description: library name: 11994


title: Liver, Vehicle, Rep 3

description: library name: 11999


title: CScreen_HDAC1

description: Library name: CScreen_HDAC1


title: ChIP-seq ESC WT Ctcf

description: Library name: ChIP-seq Sample 8

value: WT


title: CScreen_E2F2

description: Library name: CScreen_E2F2


title: Liver, Vehicle, Rep 1

description: library name: 11976


title: Liver, Vehicle, Rep 6

description: library name: 12009


title: ChIP-seq ESC WT Input 2

description: Library name: ChIP-seq Sample 7


title: D6-ANGPTL4-4

city: Athens

first: Chad

middle: Michael

last: Paton

state: Georgia

address: 100 Cedar St.

department: Nutritional Sciences

institute: University of Georgia

data_processing:
Single-read sequencing was performed on Illumina (Illumina, San Diego, CA) NexSeq 500 (PE75)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with following settings: adapters/TruSeq3-SE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:30.
Trimmed, filtered reads were then mapped against MM39 using the STAR aligner, ver. 2.7.1a.
HTSeq, ver. 0.9.1 (33) was used to extract raw count data from each BAM file and output files containing gene-to-count information for each sample were concatenated to generate a raw count matrix that was manually filtered to remove rows containing zero counts or rows whose summation of counts was less than 50.
Count matrix normalization, DESeq2
Assembly: mm39
Supplementary files format and content: Excel sheet including DESeq values for each sample

molecule: total RNA

source_name: C2C12 cells, ANGPTL4, Day6

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
100uM of bovine serum albumin-conjugated linoleic acid (18:2n6) or 10 ng/mL of recombinant mouse ANGPTL4 was added to the cellls during differentiation.
RNA was harvested and total RNA (RIN value >7.0) was submitted.
RNA-Seq libraries were synthesized using a QuantSeq 3’ mRNA-Seq library kit following manufacturer's protocols.

treatment_protocol: Skeletal muscle differentiation was induced by changing 10% FBS to 2% Horse serum.

value: C2C12 cells

value: Mouse myoblast

tag: time

value: Day 6


title: D6-ANGPTL4-3


title: D6-ANGPTL4-1


title: CScreen_CSK

description: Library name: CScreen_CSK


title: D6-ANGPTL4-2


title: CScreen_CD81

description: Library name: CScreen_CD81


title: GPSM1_LKO-2

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: Samples 6

data_processing:
The cleaned reads were aligned to the index file of the mm10 genome generated by HISAT2 version 2.0.5. Read counts for each gene were calculated by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone Marrow-Derived Macrophages

growth_protocol: BMDMs were cultured in DMEM containing 10% FBS , and 1% penicillin/streptomycin supplemented with murine M-CSF to induce differentiation.

extract_protocol:
Total RNA was extracted from BMDMs via TRIzol reagent (Thermo Fisher).
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina Vazyme, according to the manufacturer’s protocol, and paired-end reads were obtained on the NovaSeq 6000 platform.

treatment_protocol: BMDMs from GPSM1fl/fl and GPSM1LKO mice were treated with CCL2  for 1 h.

value: Bone Marrow-Derived Macrophages

value: CCL2 stimulation


title: GPSM1_LKO-3

description: Library name: Samples 7


title: CScreen_CD79B

description: Library name: CScreen_CD79B


title: GPSM1_LKO-1

description: Library name: Samples 5


title: D6-18-2-2

source_name: C2C12 cells, 18:2, Day6

value: 18:2 linoleic acid


title: D6-18-2-1


title: hrp1Δ-1

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

description: Library name: 206651

data_processing:
Data analysis was conducted using a custom Nextflow pipeline (https://github.com/Gregor-Mendel-Institute/PROalign) for QC, alignment, and read processing, generating strand-specific bigwig files for downstream analysis.
Assembly: ASM294v2
Supplementary files format and content: Provided are strand-specific bigWig files representing the read-depth normalized PRO-seq signal for each sample.
Library strategy: PRO-Seq

organism: Schizosaccharomyces pombe

growth_protocol: Cells were revived from frozen (-70 ºC) stocks on YES plates at 32 ºC. Cells were then grown to saturation in YES at 32 ºC, subcultured and grown to mid-log (OD600 ~ 0.5) before being harvested.

extract_protocol:
Cells were permeabilized in ice-cold yeast permeabilization buffer, and subjected to a run-on reaction with biotin-labeled nucleotides at 30 ºC. RNA was extracted using the Norgen RNA Extraction Kit, treated with NaOH, and cleaned via ethanol precipitation. Final RNA was resuspended in DEPC-treated water for downstream analysis.
RNA was processed using streptavidin bead-based purification and ligation of 3’ and 5’ adapters. Reverse transcription was performed with Maxima H Minus RT, followed by PCR amplification to the logarithmic phase. Libraries were sequenced at the Vienna BioCenter Core Facilities.

treatment_protocol: No treatment was used.

value: h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX


title: CScreen_CD79A

description: Library name: CScreen_CD79A


title: D6-Veh-4

source_name: C2C12 cells, control, Day6


title: GPSM1_FLOX-4

description: Library name: Samples 4


title: D6-Veh-3


title: snf22Δ-expA-b2-1

description:
Library name: 206646
Experiment A, batch 2

data_processing:
Alignments, quality control, and initial processing of the raw fastq files or bam files from the sequencing run were performed using a custom pipeline.
Raw count files for each gene were subsequently generated using Kallisto.
Assembly: ASM294v2
Supplementary files format and content: Raw count tsv files for each sample are provided.

extract_protocol:
Total RNA was extracted from yeast cells using a standard hot acid phenol protocol, followed by phenol-chloroform-isopropanol (PCI) extraction and DNase digestion
RNA-seq libraries were prepared with polyA-tail enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, followed by using the NEBNext Ultra II library preparation kit for Illumina complemented with custom synthesized barcoded sequencing adapters provided by the Vienna BioCenter Core Facilities Next Generation Sequencing Facility. PCR was performed as a 50 µl reaction using the Q5 polymerase (NEB). Samples were PCR-amplified to the beginning of the logarithmic phase, as determined using a small-scale qPCR reaction run in parallel (typically around 8-10 cycles). Following quality control by Agilent Fragment Analyzer and quantification by RT-qPCR using a Kapa Library Quantification Kit, libraries were sequenced at the Vienna BioCenter Core Facilities Next Generation Sequencing Core Facility on an Illumina sequencer.

value: h+ ade6-M216 ura4-D18 leu1-32 snf22del::hygMX


title: D6-Veh-1


title: CScreen_BTK

description: Library name: CScreen_BTK

value: B cell lymphoma


title: CScreen_CD27

description: Library name: CScreen_CD27

value: no


title: CScreen_BTG2

description: Library name: CScreen_BTG2


title: GPSM1_FLOX-2

description: Library name: Samples 2


title: D2-ANGPTL4-2

source_name: C2C12 cells, ANGPTL4, Day2

value: Day 2


title: D6-Veh-2


title: GPSM1_FLOX-3

description: Library name: Samples 3


title: D6-18-2-3


title: GPSM1_FLOX-1

description: Library name: Samples 1


title: CScreen_BLNK

description: Library name: CScreen_BLNK


title: D2-ANGPTL4-3


title: D2-ANGPTL4-1


title: CScreen_BLK-IGK_2

description:
Library name: CScreen_BLK-IGK_2
processed file: BLK_count.txt
processed file: IGK_count.txt

value: mOrange_BLK, mOrange-IGK


title: D2-18-2-2

source_name: C2C12 cells, 18:2, Day2


title: D2-18-2-3


title: D2-18-2-1


title: D2-Veh-2

source_name: C2C12 cells, control, Day2


title: CScreen_BCL-XL

description: Library name: CScreen_BCL-XL


title: D2-Veh-1


title: Artificially reared hypothalamus RNA, PND13, replicate 1

city: Ota-ku

first: Sachine

last: Yoshida

address: 5-21-16 Omori-Nishi

department: Faculty of Medicine

country: Japan

institute: Toho University

description: Library name: AR_PND13_06

data_processing:
Base calling and demultiplexing were performed using NovaSeq Control Software, Real Time Analysis (RTA), and bcl2fastq2 (Illumina). Reads were processed and aligned to the mouse reference genome using the DRAGEN Bio-IT Platform (Illumina).
Assembly: GRCm39 (GENCODE vM28)
Supplementary files format and content: Processed data files are provided in tab-delimited text (.tsv) or comma-separated values (.csv) format. Each file contains a gene-by-sample read count matrix, where rows correspond to Ensembl gene IDs and columns to individual samples; values represent raw read counts prior to normalization.

source_name: brain

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Takara Bio, Shiga, Japan) from four MR and three AR pups, each derived from three different litters.
RNA libraries for RNA-seq were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio) and the Nextera XT DNA Library Prep Kit (Illumina) with IDT for Illumina DNA/RNA UD Indexes, following the manufacturers’ protocols.

value: brain

value: artificial rearing(AR)


title: CScreen_BCL2

description: Library name: CScreen_BCL2


title: D2-18-2-4


title: Artificially reared hypothalamus RNA, PND13, replicate 3

description: Library name: AR_PND13_09


title: CScreen_BCL11A

description: Library name: CScreen_BCL11A


title: Heart specific NG neuron sample 1

city: Istanbul

first: Tuba

last: Akgül Çağlar

address: Kavacik Neighborhood, Ekinciler Street No:19

department: SABITA

country: Turkey

institute: Istanbul Medipol University

data_processing:
Transcript level abundances were calculated with Salmon v.0.8.2 , using default parameters. Transcript level count matrix was converted to gene-level count matrix by Tximport package.
DESeq2 package was used for differential expression analysis with alpha (p value) set as 0.05.
FPKM matrix is generated by fpkm () function within DESeq2, using avgTxLength as option for normalisation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file which includes FPKM values for each sample

source_name: Heart specific NG neuron

extract_protocol:
RNA was extracted from the samples using the RNeasy micro kit (Qiagen).
RNA libraries were prepared for sequencing using the protocol provided within Truseq Total RNA Sample Preparation Kit v2 (Illumina)

value: Heart specific NG neuron

value: WT female Balb-C

tag: age

value: 8-12 weeks


title: Control NG neuron sample 2

source_name: Control NG neuron

value: Control NG neuron


title: Artificially reared hypothalamus RNA, PND13, replicate 2

description: Library name: AR_PND13_08


title: Control NG neuron sample 1


title: CScreen_BLK

description: Library name: CScreen_BLK


title: Heart specific DRG neuron sample 3

source_name: Heart specific DRG neuron

value: Heart specific DRG neuron


title: D2-Veh-3

value: C2C12 cells

value: Mouse myoblast

value: WT

value: Vehicle


title: Maternally reared hypothalamus RNA, PND13, replicate 1

description: Library name: MR_PND13_01

value: maternal rearing(MR)


title: Maternally reared hypothalamus RNA, PND13, replicate 4

description: Library name: MR_PND13_05


title: fft1Δ-expA-b2-1

description:
Library name: 206637
Experiment A, batch 2

value: h+ ade6-M216 ura4-D18 leu1-32 fft1del::hygMX


title: Heart specific NG neuron sample 2


title: ColombiaWT_3

city: Taian

first: Yan

last: kang

state: Shandong

address: No.61, Daizong Street

department: College of Life Sciences

institute: Shandong Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
RNA was harvested using TRIzol® Reagent (Ambion). 1 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: seedlings

value: wild type

value: 100 μM cadmium 6h


title: Maternally reared hypothalamus RNA, PND13, replicate 3

description: Library name: MR_PND13_04


title: Maternally reared hypothalamus RNA, PND13, replicate 2

description: Library name: MR_PND13_03


title: D2-Veh-4

value: Day 2


title: CScreen_BACH2

description: Library name: CScreen_BACH2

value: B cell lymphoma

value: no


title: WT1

city: shanghai

first: Rufeng

last: Dai

address: 399 Wanyuan Road，Minhang District

institute: Children’s Hospital of Fudan University

description:
Library name: sample 7
WT group, replicate biosample 1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: Whole embryo tissue

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Whole embryo tissue

tag: Sex

value: male


title: Heart specific DRG neuron sample 2

value: WT female Balb-C

value: 8-12 weeks


title: CScreen_AKT2

description: Library name: CScreen_AKT2


title: Colombia1C9_2


title: WT3

description:
Library name: sample 9
WT group, replicate biosample 3


title: Heart specific DRG neuron sample 1

value: Heart specific DRG neuron


title: Control DRG neuron sample 2

source_name: Control DRG neuron

value: Control DRG neuron


title: Undamaged, CRY2, ChIP

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

country: Spain

institute: University of Sevilla

description: Library name: U2OS_AsiSI_ER_Undamaged_CRY2

data_processing:
Raw sequencing files (fastq) quality was assessed using FastQC 0.12.0
Aligment to the reference human genome (version hg19) using bwa 0.7.17
Mapped sequences were sorted and indexed using samtools 1.19.2
Coverage of mapped reads in bigwig format was obtained using deepTools 3.5.3 bamCoverage
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Bone

growth_protocol: Low-glucose Dulbecco’s Modified Eagle Medium (DMEM) + 10% charcoal-stripped FBS

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at 37°C. Crosslinking reaction was quenched with 125mM glycine for 5 minutes and cells were washed 3 times with PBS. Cell pellets were resuspended in 2.5 mL lysis buffer A (5 mM Pipes pH 8.0, 85 mM KCl, 0.5% NP40, 1mM PMSF) supplemented with protease inhibitors and incubated for 10 minutes on ice.
Libraries were amplified for N-1 cycles (being N the optimum Cq determined by qPCR reaction) using NEBNext High-Fidelity Polymerase (New England Biolabs, M0541). Libraries were purified with Sera-Mag Select Beads (GE Healthcare, 29343052)

treatment_protocol: 300 nM 4-OHT for 4h

value: Bone

value: AsiSI-ER U2OS

value: Bone epithelium

value: 300 nM 4-OHT for 4h


title: ColombiaYK2_3


title: Damaged, CtIP, ChIP

description: Library name: U2OS_AsiSI_ER_Damaged_CtIP


title: Control DRG neuron sample 1


title: WT2

description:
Library name: sample 8
WT group, replicate biosample 2


title: ColombiaYK2_2


title: Undamaged, CtIP, ChIP

description: Library name: U2OS_AsiSI_ER_Undamaged_CtIP


title: ChIPseq_WT_Brd4_rep2

description: Library name: ChIPseq_WT_Brd4_rep2

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file

value: WT

tag: chip antibody

value: Abcam, ab128874


title: Undamaged, CRY1, ChIP

description: Library name: U2OS_AsiSI_ER_Undamaged_CRY1


title: CScreen_MSH2

description: Library name: CScreen_MSH2


title: HE3

description:
Library name: sample 3
HE group, replicate biosample 3


title: ColombiaWT_2

value: seedlings

value: wild type


title: Cx43KO2-HSC (48h) rep2

city: BOSTON

first: Jose

last: Cancelas

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: Cx43KO-2T-18684

data_processing:
Reads were aligned with TopHat software, using  mm10 as the reference genome and Reads Per Kilobase of transcript per Million mapped reads (RPKM) as output.
To identify differentially expressed genes using default parameters moderated t-test, raw p-value cut-off of 0.05, and an expression cut-off of 1.5-fold using AltAnlayze v2.1.0 (developed at Cincinnati Children's Hospital Medical Center). The Gene ontology pathway analyses and heatmaps were generated using Altanalyze v2.1.0 software.
Assembly: mm10
Supplementary files format and content: excel files (expression values and group comparison statistics)

source_name: Bone Marrow

growth_protocol: WT and Connexin 43 knockout bone marrow HSC (Lin- /cKit+/Sca1+/CD48-/CD150+) were cultured in IMDM medium supplemented with 10% FBS, 100 IU/mL penicillin, 0.1 mg/ml streptomycin and 2mM L-glutamine, recombinant murine stem cell factor (rm-SCF, 50 ng/mL, Peprotech Inc) and recombinant mouse thrombopoietin (rm-TPO, 25 ng/mL, Peprotech Inc). The cells were analyzed after cell division (48 hours in culture).

extract_protocol:
Total RNA was extracted from WT and Connexin 43 knockout quiescent (0h) and dividing (48h) HSC (Lin- /cKit+/Sca1+/CD48-/CD150+) using RNeasy Mini Kit (QIAGEN) according to manufacturer's protocols. RNA quality and concentration were measured by Bioanalyzer 2100 using the RNA 6000 Nano Assay (Agilent Technologies).
RNA-seq libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocol. The concentration of the pool was optimized to acquire at least 25-30 million reads per sample using Paired-End Reads with a read length of 75 bps.

value: Bone Marrow

value: LT-HSC

value: Connexin 43 Knockout

value: Dividing (48 h culture)


title: Colombia1C9_3

value: 100 μM cadmium 6h


title: Damaged, CRY2, ChIP

description: Library name: U2OS_AsiSI_ER_Damaged_CRY2


title: HO3

description:
Library name: sample 6
HO group, replicate biosample 3

value: Whole embryo tissue

value: male


title: ColombiaWT_1


title: WT2-HSC (48h) rep2

description: Library name: WT-2T-18682


title: Cx43KO2-HSC (0h) rep2

description: Library name: Cx43KO-2-18688

value: Quiescent (0 h)


title: Colombia1C9_1


title: Damaged, CRY1, ChIP

description: Library name: U2OS_AsiSI_ER_Damaged_CRY1


title: HO2

description:
Library name: sample 5
HO group, replicate biosample 2


title: WT2-HSC (0h) rep2

description: Library name: WT-2-18686


title: MC3T3-E1 cells, CaSRmut plasmid,48h, Biological repetition group 3

city: chengdu

first: Han

last: Fang

state: yunnan

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

institute: 四川大学

description:
Library name: Mutation_3
CaSRmut plasmid,48h, Biological repetition group 3

data_processing:
CLC Genemies Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameters-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost:2 insertion cost:3 deletion cost: 3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MC3T3-E1 cells

growth_protocol: The MC3T3-E1 cells were plated at a cell density between 500,000 and 800,000 cells/well in a 6-well plate and cultured with Dulbecco’s modified Eagle’s medium + GlutaMAX (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug 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 manufacture's protocols.

treatment_protocol: Plated in 6-well plate for 24 h, then the CaSRmut plasmid and CaSRwt  plasmid were transfected into the cells with Lipofectamine 3000 (Thermo Fisher Scientific). After 48 h, cells were harvested,

value: MC3T3-E1 cells

value: embryonic mouse calvarial cell line

value: Casr with mutation p.N594S(AAT to AGT))

value: CaSRmut plasmid


title: HO1

description:
Library name: sample 4
HO group, replicate biosample 1


title: Sum159 ITGB4 low clone 1 biol rep 3

city: Cambridge

first: Jingwei

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description:
Library name: Sample5
Sum159low-1_3

data_processing:
The Illumina 50bp long paired-end reads were mapped with STAR(version 2.7.1a), using index files created with the gene annotation from Ensemble human hg38 version 93 with the ‘--sjdbOverhang 49 --alignIntronMax 104052’ options, and reads corresponding to the second read strand aligned with RNA were assigned to features.
Assembly: hg38
Supplementary files format and content: tab delimited text with raw counts for each sample

growth_protocol: The cancer cells harvested from lungs of mice were cultured in Ham's F-12 medium supplemented with 5% inactivated fetal bovine serum (FBS), 5 μg/mL insulin, 1 μg/mL hydrocortisone, and 1% penicillin/streptomycin at 37℃ in a 5% CO2 incubator.

extract_protocol:
RNA was extracted and purified with RNeasy Micro Kit (Qiagen).
Libraries were prepared for RNA-Seq using Watchmaker mRNA Library Prep Kit, according to manufacturer’s directions. The Watchmaker mRNA Library Prep Kit first enriches for mature, polyadenylated mRNAs using oligo dT beads. The enriched mRNA is then fragmented, and undergoes 1st and 2nd strand cDNA synthesis, incorporating dUTP to maintain strand information. The double stranded cDNA is then A-tailed, ligated to universal adapters, and amplified using indexed primers to allow sample multiplexing.

treatment_protocol: Mice transplanted with Sum159low-1 cells were treated with bleomycin through trachea. At the end point of the experiment, lungs were harvested and dissociated into cell suspension.

value: ITGB4 low


title: ColombiaYK2_1


title: Sum159 ITGB4 low clone 1 biol rep 2

description:
Library name: Sample4
Sum159low-1_2


title: 3xTG brain, 11months, rep3

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

description: Library name: 3xTG-sham-ND3

data_processing:
FASTQ files were mapped to the mouse mm10 genome using the STAR Aligner. Data analysis was performed using the statistical computing environment R, along with the Bioconductor suite of packages and RStudio. Raw data underwent background subtraction, variance stabilization, and normalization via robust spline normalization.
Assembly: Mus musculus (UCSC version mm10, based on GRCm38.p6)
Supplementary files format and content: tab-delimited text file includes gene Log2TPM values for each Sample

source_name: Brain

extract_protocol:
RNAs were isolated using TRIzol  per the manufacturer’s instructions. RNA was quantified using Nanodrop and stored at −80°C until shipped to RNA Sequencing
Total RNA libraries were prepared with the Pico Input SMARTer Stranded Total RNA-seq Kit (Takara). Briefly, 10 ng of RNA from each sample was reverse transcribed using random priming and reverse transcriptase. Full-length cDNA was obtained with SMART (Switching Mechanism At 5′end of RNA Template) technology, which preserves the strand orientation of the RNAs. Ribosomal cDNAs were hybridized to mammalian-specific R-Probes and cleaved by ZapR. Libraries containing Illumina adapters with TruSeq HT indexes were then pooled and loaded onto the Hiseq 2500 platform. Single end reads at 75 base pair with 30 million reads per sample were generated for subsequent bioinformatic analysis.

value: Brain

tag: strain

value: 11 months


title: 3xTG brain, 11months, rep1

description: Library name: 3xTG-sham-ND1


title: WT1-HSC (48h) rep1

description: Library name: WT-1T-18681

value: WT


title: CScreen_TCF3

description: Library name: CScreen_TCF3

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file
Library strategy: CRISPR screen

value: B cell lymphoma

value: no


title: MC3T3-E1 cells, CaSRmut plasmid,48h, Biological repetition group 1

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

description:
Library name: Mutation_1
CaSRmut plasmid,48h, Biological repetition group 1

value: Casr with mutation p.N592S(AAT to AGT))


title: Cx43KO1-HSC (48h) rep1

description: Library name: Cx43KO-1T-18683

value: Bone Marrow

value: LT-HSC

value: Connexin 43 Knockout


title: HE2

description:
Library name: sample 2
HE group, replicate biosample 2

value: Whole embryo tissue


title: Sum159 ITGB4 low clone 1 bleomycin treated biol rep 3

description:
Library name: Sample8
Sum159low-1_Bleo-LM_3

value: bleomycin treated


title: Sum159 ITGB4 low clone 1 bleomycin treated biol rep 2

description:
Library name: Sample7
Sum159low-1_Bleo-LM_2


title: Sum159 ITGB4 high cells biol rep 2

description:
Library name: Sample2
Sum159high_2

value: ITGB4 high


title: Cx43KO1-HSC (0h) rep1

description: Library name: Cx43KO-1-18687

value: Quiescent (0 h)


title: Sum159 ITGB4 low clone 1 bleomycin treated biol rep 1

description:
Library name: Sample6
Sum159low-1_Bleo-LM_1


title: Sum159 ITGB4 high cells biol rep 1

description:
Library name: Sample1
Sum159high_1


title: WT_C_3

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

description: Library name: WT_C_3

data_processing:
Pair-end FASTQ files were mapped to the Mus_musculus.GRCm38.101 reference genomes, via using the HISAT2 package. Then, the FPKM values were calculated with StringTie and Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html). Differential gene expression was analyzed using DESeq2, with genes having a P value ≤ 0.05 and absolute fold change ≥ 2 recognized as differentially expressed genes (DEGs). Heatmaps were generated, and Gene Ontology (GO) and KEGG pathway analyses were performed on DEGs using the OmicStudio tools at https://www.omicstudio.cn/tool. Gene set enrichment analysis (GSEA) was conducted using GSEA (v4.1.0) and MSigDB to identify gene sets involved in specific pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: csv. file including FRKM values for each sample

source_name: hepatocyte

extract_protocol:
High-throughput mRNA sequencing was performed by the LC-Bio Technology co.ltd., (HangZhou, China). The quality of total RNAs was assessed by BioAnalyzer 2100 (Agilent Technologies).
RNA libraries were constructed with TruSeq Stranded Total RNA Library Prep kit (Illumina). Libraries were quality-controlled for size distribution and quantified with Qubit Fluorometer (Thermo Fisher Scientific). The libraries were sequenced on an Illumina HiSeq sequencer for 150-bp paired-end reads according to the manufacturer’s instructions.

value: hepatocyte

value: DMSO


title: WT_T_1

description: Library name: WT_T_1

value: Ceefourin-1 treatment


title: WT_C_2

description: Library name: WT_C_2


title: ATAC_4T1 cells, shContral, rep1

first: Tai-Lung

institute: National Defense Medical Center

description:
Library name: Smaple 37
Column name in ATAC_4T1shMY_pvalue.csv :m4T1_shvec

data_processing:
RNAseq:RNA-seq data were aligned to the UCSC reference genome using Bowtie2 (v2.4.5). The human genome (GRCh37/hg19) and mouse genome (GRCm38/mm10) assemblies from the UCSC Genome Browser were used as references. Aligned reads were processed with SAMtools (v1.3) to generate a read count table for each gene.
ATACsaq: Reads were mapped to the human genome (hg19) and mouse genome (mm10) using Bowtie2. PCR duplicates were removed using Picard Tools. For peak calling, biological replicates were merged and processed using MACS2. Peaks from all replicates were further merged using SAMtools. Variance-stabilizing transformation and principal component analysis (PCA) were performed using SeqMonk, based on the DESeq2 model. Visualization of ATAC-seq signals across specific genes was performed using the Integrative Genomics Viewer (IGV).
Assembly: hg19 and mm10
Supplementary files format and content: text files inculed raw counts for each sample
Supplementary files format and content: csv files include FPKM value for each sample

source_name: mammary gland

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN). RNA-seq libraries were prepared from pretreated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. For ATAC-seq, 1×10⁶ cells were collected, washed with PBS, and lysed in cold ATAC RSB lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1%Tween-20, and 0.01% digitonin). Nuclei were washed with ATAC RSB containing 0.1% Tween-20 and resuspended in transposition mix containing Tn5 transposase (Illumina). Transposition was carried out at 37°C for 30 min with shaking at 300 rpm. DNA was purified using the Qiagen MinElute PCR Purification Kit and libraries were amplified using NEBNext PCR master mix (NEB).
RNA-seq libraries were quantified using Qubit (Invitrogen), denatured to single-stranded DNA, loaded onto Illumina flow cells, amplified by in situ cluster generation, and sequenced for 150 cycles on an Illumina HiSeq 2500 platform following the manufacturer's instructions. ATAC-seq libraries were sequenced on an Illumina NextSeq 550 system using paired-end reads.

value: mammary gland

value: mouse mammary carcinoma cell

value: wild-type

value: shRNA control vector


title: 3xTG brain, 11months, rep2

description: Library name: 3xTG-sham-ND2

value: Brain

value: 11 months


title: MC3T3-E1 cells, CaSRmut plasmid,48h, Biological repetition group 2

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

description:
Library name: Mutation_2
CaSRmut plasmid,48h, Biological repetition group 2

value: MC3T3-E1 cells

value: embryonic mouse calvarial cell line

value: Casr with mutation p.N593S(AAT to AGT))

value: CaSRmut plasmid


title: HE1

description:
Library name: sample 1
HE group, replicate biosample 1

value: Whole embryo tissue

value: male


title: WT_C_1

description: Library name: WT_C_1

value: WT


title: Sum159 ITGB4 low clone 1 biol rep 1

description:
Library name: Sample3
Sum159low-1_1

value: ITGB4 low


title: MC3T3-E1 cells, CaSRwt plasmid, 48h, Biological repetition group 3

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

description:
Library name: CaSR_3
CaSRwt plasmid, 48h, Biological repetition group 3

value: Calcium-sensing receptor (Casr) wildtype

value: CaSRwt plasmid


title: WT brain, 11months, rep2

description: Library name: WT-sham-ND2


title: PDAC CAFs, LPS stimulated, replicate 2

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

description: Samples were actually sequenced with the Singular Genomics G4 sequencer (https://singulargenomics.com/g4/)

data_processing:
Bulk RNA-seq library quality control, processing, and alignment were performed using nf-core/rnaseq, with Ensemble’s GRCh38 assembly as the reference genome and salmon for transcript quantification. The quant.sf and tx2gene.tsv files were processed with R package tximport for downstream analysis with DESeq2.
Assembly: Ensemble’s GRCh38 assembly
Supplementary files format and content: Output directory from Salmon quantification, containing quant.sf file (transcript-level quantification) and quant.genes.sf file (gene-level quantification) and other metadata for every sample. Tx2gene.tsv contains gene to transcripts ids mappings.

source_name: Fibroblast

growth_protocol: PDAC CAFs were isolated from surgical specimens using the Human Tumor Dissociation Kit (Miltenyi Biotec) under an institutional review board approved protocol with patient informed consent. Tumors were minced into 2-4 mm pieces in a petri dish containing a small volume of DMEM/F-12 to maintain specimen moisture. The minced tissue was then added to a gentleMACS C tube containing weight-based enzyme mixture as per manufacturer’s protocol (Miltenyi Biotec). Following dissociation, cells were filtered through a 100 µm and then a 40 µm filter, spun down at 300 RCF for 5 minutes in a 4°C centrifuge, and resuspended in 1 ml of growth medium with 20% FBS. Cells were plated in a gelatin (Sigma-Aldrich) coated flask at a concentration of 2000 cells/cm2. After 24 hours, the media was changed to growth medium with 10% FBS, with additional media changes every 2-3 days as needed. After 2-3 passages, cells were frozen in Bambanker (NIPPON Genetics) at roughly 1 million cells per vial. Prior to further experimentation, cells were thawed and maintained in sterile conditions in growth medium.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini kit (QIAGEN) per the manufacturer’s protocol.
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit with rRNA Depletion Kit v2 (New England Biolabs). Library conversion was done with Singular Genomics Library Compatibility Kit (Singular Genomics). Libraries were sequenced on the Singular Genomics G4 sequencer on F3 flow cells, with one lane per library, at 75 bp pair-end for 100 cycles.

treatment_protocol: Passage 4-7 fibroblasts were plated in a 12-well plate (105 cells per well, three replicates per condition), allowed to adhere overnight, and then treated with fresh media (control), or fresh media containing LPS (InvivoGen) at 100 ng/ml. After 24 hours, the cells were harvested.

value: Fibroblast


title: WT brain, 11months, rep1

description: Library name: WT-sham-ND1


title: WT_T_2

description: Library name: WT_T_2

value: hepatocyte

value: Ceefourin-1 treatment


title: WT_T_3

description: Library name: WT_T_3


title: Rosa26_3

description: Library name: Rosa26_3


title: PDAC CAFs, LPS stimulated, replicate 1


title: WT brain, 11months, rep3

description: Library name: WT-sham-ND3


title: MC3T3-E1 cells, CaSRwt plasmid, 48h, Biological repetition group 2

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

description:
Library name: CaSR_2
CaSRwt plasmid, 48h, Biological repetition group 2


title: Rosa26_2

description: Library name: Rosa26_2


title: MC3T3-E1 cells, CaSRwt plasmid, 48h, Biological repetition group 1

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

description:
Library name: CaSR_1
CaSRwt plasmid, 48h, Biological repetition group 1


title: Visium, Chronic Day 7 post injection of ECM-H,  biol rep 3

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

description: ChronicB

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v6.1.1 (normal v3.1 10X single cell kit), Cell Ranger software v7.1.0 (10X v3.1 HT kit), or Space Ranger v1.3.1
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: Rnor-6.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Cardiac

extract_protocol:
As mentioned before, harvested OCT-embedded cardiac tissue was cryosectioned onto the fiduciary regions on a 10X Visium slide at 10 µm thickness. Sections were then stained with hematoxylin and eosin, with images obtained on a Nikon Eclipse Ti2-E widefield microscope at 10X magnification. Visium was performed as per manufacturer’s kit instructions (Visium Spatial Gene Expression), with tissue permeabilization time of infarcted rat hearts optimized at 42 minutes. Both protocols utilized barcoding and library preparation, which was validated using an Agilent TapeStation prior to sequencing and quantified via Qubit HS DNA Kit. Paired-end sequencing was done on a NovaSeq6000 instrument. Low-level analysis was performed by mapping to a rat reference genome (Rnor6.0, including introns). The SpaceRanger 1.3 pipeline (10X Genomics) was used to remove redundant UMIs.
Nuclei from cardiac tissue was isolated as mentioned previously. In brief, flash frozen LV free wall samples were resuspended in nuclei lysis buffer (Millipore Sigma, Nuclei EZ prep, NUC101), 0.2 U/L RNase inhibitor (Enzymatic Y9240L) and finely chopped with scissors. Samples were homogenized with a 2 mL dounce grinder (KIMBLE) with the lysates filtered through a 100 µm, 50 µm, 20 µm strainers (CellTrics filters), respectively. The samples were centrifuged at 1000g for 5 min at 4C to pellet nuclei. The nuclear pellet was resuspended in a sucrose gradient buffer  and centrifuged at 1000g at 4ºC for 10 minutes. The pellet was then washed with a nuclei storage buffer containing 10 μg ml−1 4′,6-diamidino-2-phenylindole DAPI and centrifuged at 500 g and 4ºC for 5 minutes, with the pellet resuspending in 200 mL of 2% BSA in 1x PBS. Nuclei were then counted on a hemocytometer and volume adjusted to 1000 nuclei/µL for loading. snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics kits (Chromium Next GEM Single Cell 3’ GEM V3.1 and Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 pipeline from 10X Genomics.
snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics kits (Chromium Next GEM Single Cell 3’ GEM V3.1 and Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 6.1.0 pipeline and Cell Ranger 7.1.0 pipeline from 10X Genomics.

value: Cardiac

tag: disease state

value: IR surgery

value: intramyocardial injection of ECM hydrogel


title: Salmonella-Infected, CD4+ Tcells, cLP

first: Blanda

last: Di Luccia

state: CALIFORNIA

address: 299 Campus drive

department: Microbiology and Immunology

description:
Library name: 3
10X Genomics

data_processing:
Raw sequencing data was parsed through Cell Ranger (10x Genomics) to generate FASTQ files and facilitate further analysis.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separetd values files and matrix files

source_name: colonic lamina propria

extract_protocol:
The colon was harvested, cut longitudinally and washed with Hanks’ Balanced Salt Solution (HBSS, Gibco) for removing luminal content. Intestinal tissues were incubated twice with HBSS/HEPES supplemented with 5 mM DTT, 5mM EDTA and 5% v/v bovine calf serum (BCS) at 37°C for 15 min, and washed with HBSS/HEPES supplemented with 2% v/v BCS at 37°C for 5 min. Then, the colonic tissues were incubated in RPMI containing 0.167mg/mL liberase TL (Roche), 0.25mg/mL DNase I (Sigma), and 5% BCS on a shaker at 37°C for 30 min. Finally, they were dissociated with gentle MACS dissociator (Mylteni). Immune cells were enriched using a 40- 70% PERCOLL gradient (GE healthcare) and resuspended in FACS buffer (PBS 1X, 2mM EDTA and 2% v/v BCS. Single cell suspensions of the colonic lamina propria collected from 3 mice (age and gender matched littermates) were pooled together per each condition and then sorted on a BD FACSAria cell sorter.
Manufacturer’s instructions were followed without any significant modifications to capture the cells, generate NGS libraries and perform sequencing. Briefly, cells were captured on a 10x Chromium single cell instrument (10x Genomics) and subjected to single cell barcoded cDNA synthesis using NextGem V3.1 chemistry (10x Genomics). Purified cDNA was amplified and subjected to enzymatic fragmentation, end-repair, A-tailing, adapter ligation and sample indexing to generate sequencing ready libraries. Libraries were assessed by electrophoresis on a BioAnalyzer 2100 instrument (Agilent) and qPCR on a CFX96 (BioRad) instrument prior to sequencing.

value: colonic lamina propria

value: CD4+ T cells

value: infected with Salmonella Typhimurium SL1344

value: 8-10 weeks


title: KO_2_3

description: Library name: KO_2_3


title: Salmonella-Infected, Treg, cLP

description:
Library name: INF
10X Genomics

value: T regulatory cells


title: Uninfected, Treg, cLP

description:
Library name: UN
10X Genomics

value: uninfected


title: ChIL-seq sample for Foxa2 in iHepC

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

description: Library name: iHepC_Foxa2

data_processing:
Raw data are trimmed and removed PCR duplicates using fastp (v 0.23.4).
The sequence reads were aligned to a mouse reference genome (Ensemble mm10) using hisat2 (v2.0.5).
Peaks for Foxa2 are called by MACS2 (v2.2.9.1).
Assembly: mm10
Supplementary files format and content: Peak files (BED format)

source_name: Embryo

growth_protocol: MEFs are incubated in MEF medium [Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS), 2 mM l-glutamine (Nacalai Tesque), and penicillin/streptomycin (Nacalai Tesque)], and the reprogrammed cells derived from MEFs (iHepCs) are incubated in hepato-medium. This medium comprises a 1:1 mixture of DMEM and F-12 medium (Nacalai Tesque), supplemented with 10% FBS, 1 μg/ml insulin (Wako), 100 nM dexamethasone (Sigma–Aldrich), 10 mM nicotinamide (Sigma–Aldrich), 2 mM l-glutamine, 50 mM β-mercaptoethanol (Nacalai Tesque), penicillin/streptomycin, 20 ng/ml hepatocyte growth factor (PeproTech), and 20 ng/ml epidermal growth factor (Sigma–Aldrich).

extract_protocol:
ChIL-seq was performed following a modified protocol of the original ChIL-seq (PMID: 30532068). 10,000 cells were plated on typeⅠcollagen coated 96-well plates and let to attach for 16 h in culture. Cells were then fixed with 1% formaldehyde in PBS for 5 min and permeabilized with 1% Triton X-100 in PBS for 20 min.
Samples were incubated in 10% Blocking One-P (Nacalai Tesque) in PBS with anti-Foxa2 mAb (Cell Signaling Technology; #8186) for 6 h at room temperature, washed three times in PBS and then incubated at 4℃ overnight in 10% Blocking One-P in PBS containing 500 mM NaCl and the ChIL probe at 2 μg/ml. After washing in PBS, samples were incubated in 50 µl Tn5 solution [50 mM HEPES-KOH (pH 7.2), 0.1 M NaCl, 0.1 mM EDTA, 1 mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol] containing 0.5 µl Tn5 transposase (given by Dr. Yasuyuki Ohkawa) for 10 min at room temperature. Tn5-MEDS-B oligo (2 µM) was then added at 0.5 µl per well in 1× dialysis buffer [50 mM HEPES-KOH (pH 7.2), 0.1 M NaCl, 0.1 mM EDTA, 1 mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol] and incubated for 60 min at room temperature. Samples were then washed in 1× dialysis buffer and three times in PBS, incubated in 100 µl 1× TAPS-DMF buffer [10 mM TAPS-NaOH (pH 8.5), 5 mM MgCl2 and 10% N,N-dimethylformamide] for 1 h at 37℃, and washed at three times in PBS. To stop the Tn5 reaction, cells were incubated in 100 µl 0.2% SDS for 10 min at room temperature or embryos were incubated in 0.1% BSA/PBS containing 50 mM EDTA at 50℃ for 30 min. After washing at three times in PBS, samples were incubated in 50 µl reaction mixture [200 U T4 DNA ligase (New England Biolabs), and 1.5 U T4 DNA polymerase (New England Biolabs), in 1× T4 DNA ligase reaction buffer containing 0.1 mM dNTP] for 30 min at room temperature. After discarding the solution, 100 µl 0.2% SDS were added to remove DNA-bound enzymes, followed by incubation for 10 min at room temperature and three washes in PBS. In situ transcription was then carried out using T7 RNA polymerase (200 U per well; Ambion) for 20 h at 37 ℃. The samples were treated with DNase I (2.5 U per well; Thermo Fisher Scientific) for 30 min at 37℃ and RNA was extracted using a RNAClean XP beads (Beckman Coulter). Purified RNA was reverse-transcribed with SMARTScribe reverse transcriptase (Takara) following the manufacturer’s instructions and the resulting cDNA was amplified by SeqAmp DNA Polymerase (Takara) by 14 cycles. After amplification, small fragments (<150 bp) were removed and large size of fragments (>600 bp) were removed using AMPure XP beads (Beckman Coulter). The amplified DNA was purified using AMPure XP beads and the quality of the libraries was assessed using a Bioanalyzer 2100 (Agilent Technologies). Samples were paired-end sequenced at PE150 on an Illumina NovaSeq 6000 platform. As detailed described in previous report (PMID: 30532068).

treatment_protocol: Following the reported protocol (PMID: 21716291), iHepC was induced by using a retroviral vector to forcibly express Foxa2 and Hnf4a in MEFs.

value: Embryo


title: Visium, Chronic Day 7 post injection of ECM-H,  biol rep 2


title: PDAC CAFs, control, replicate 2


title: Visium, Chronic Day 7 post injection of ECM-H,  biol rep 1


title: KO_2_2

description: Library name: KO_2_2


title: PDAC CAFs, control, replicate 1


title: KO_2_1

description: Library name: KO_2_1


city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
Library name: I40H9_lung_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: TCR-seq

source_name: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

extract_protocol:
Single-cell suspensions of spleens and lymph nodes were prepared by mechanical disruption, followed by ACK-lysing buffer. For tissue preparations, siIEL were prepared by excision of Peyer’s patches and removal of luminal contents. Then the entire tissue section was cut longitudinally, then cut laterally into 1 cm pieces, which were then incubated at 37°C for 30 minutes in Hanks’ balanced salt solution with 2.4 mg ml−1 of Hepes, 2.1 mg ml−1 of sodium bicarbonate, 8% bovine growth serum and 0.154 mg ml−1 of DTE (EMD Millipore). After collecting the siIEL sample, RPMI with 1.2 mg ml−1 of Hepes, 292 µg ml−1 of L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% FBS and 100 U ml−1 of collagenase (Worthington) was added to the SI pieces at 37°C for 30 minutes for siLPL isolation. The SG and lung were cut into small pieces then incubated with shaking at 37°C for 30 minutes (SG) or 1 hour (lung) in the same RPMI-collagenase solution as listed previously for the siLPL. Prostate tissue was dissected from the bladder and seminal vesicles, cut into small pieces, the incubated shaking at 37°C for 30 minutes in the same RPMI-collagenase solution as listed previously. Bone marrow was isolated by harvesting the femurs and tibias and pushing out the bone marrow with a syringe. Lymphocytes from non-lymphoid tissues were further enriched using a 44%/67% Percoll density gradient. Cells were incubated with FC block and stained with Live/Dead, CD3, CD45.2 and CD45.1 on ice prior to sorting.
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: genetics

value: P14 and SMARTA > wt

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: lung

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: Visium, Chronic Day 7 post injection of saline,  biol rep 2

tag: tissue

value: Cardiac

tag: disease state

value: IR surgery

tag: treatment

value: Intramyocardial injection of saline


title: Rosa26_1

description: Library name: Rosa26_1

tag: cell line

value: hepatocyte

tag: genotype


title: HME1_WT_CUT&Tag_Rep2

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

description: Library name: HME1_WT_Rep2

data_processing:
CUT&Tag reads were aligned to the hg38 genome using nf-core/cutandrun pipeline v3.1 available at nf-core with parameter --normalisation_mode CPM
BigWig files were generated within the nf-core/chipseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization
Library strategy: CUT&Tag

growth_protocol: hTert-HME1 (ME16C, American Type Culture Collection (ATCC) CRL-4010) were grown in DMEM/F12 (Thermo Fisher, 11330057) with the addition of 2% Fetal Bovine Serum (FBS, Gibco 16000-044), 100 U/ml penicillin and 100 μg/mL streptomycin (Thermo Fisher 15140122), 20ng/ml EGF (Merck, E9644), 0.5μg/ml Hydrocortisone (Merck, H0888), 10ug/ml rh Insulin (Merck, I9278).

extract_protocol:
We performed two biological replicates of CUT&Tag on HME1 cells. Cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500 μL of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton-X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice followed by nuclei preparation. Nuclei were pelleted by centrifugation for 4 min 1300×g at 4 °C and resuspended in 500 μl of wash buffer and by placing the tubes on a magnet stand to clear and withdraw the liquid, then resuspended in 1.0 ml wash buffer and held on ice until beads are ready. For each tube, 10 μl of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were resuspended in the binding buffer and was kept on nutator for 10 minutes. After a pulse spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn, and we next added primary antibody (1ul per sample) resuspended in 800 μl of antibody buffer for targeting H4K16ac (Abcam, ab109463) or IgG (normal rabbit IgG, Santa Cruz Cat no sc-2027) and incubated overnight at 4 °C on a nutator. Next day, secondary antibodies (guinea pig α-rabbit antibody, Antibodies online cat. no. ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and squirt in 100 μl per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. We got rid of any unbound antibodies by 3X wash with 1 mL of dig-wash buffer. The complex was then incubated with 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters (prepared in the lab) in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA-free protease inhibitor) and placed on a nutator for 1 h followed by three washes with 1 ml of Dig-300 buffer to remove unbound pA-Tn5. Tagmentation was carried out by adding 300 μl Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) gently while mild vortexing and incubating for 1hr at 37 °C. Tagmentation was stopped by adding 10 µL 0.5 M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full-speed vortexing for ~2 s and incubated for 1 h at 55 °C to digest proteins. DNA was extracted by phenol: chloroform protocol using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (Cat number M0541S) with 72 °C gap filling step followed by 13 cycles of PCR with 10-s combined annealing and extension for enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads at Novogene sequencing service.

tag: chip antibody

value: H4K16ac Abcam, ab109463

tag: cell type

value: immortalized mammary epithelial cells

value: Ctrl KO


title: PDAC CAFs, LPS stimulated, replicate 3

value: Fibroblast


title: KO_1_3

description: Library name: KO_1_3


title: KO_1_2

description: Library name: KO_1_2


title: HME1_WT_CUT&Tag_Rep1

description: Library name: HME1_WT_Rep1


description:
Library name: I40H9_lung_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

tag: batch


description:
Library name: I40H9_lung_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: CITE-seq

tag: tissue

tag: infection agent

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: lung

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: Visium, Chronic Day 7 post injection of saline,  biol rep 1

value: Cardiac

tag: disease state

value: IR surgery

tag: treatment

value: Intramyocardial injection of saline


title: HME1_MSL3ko_CUT&Tag_Rep2

description: Library name: HME1_MSL3ko_Rep2

tag: chip antibody

value: H4K16ac Abcam, ab109463

tag: cell line

tag: cell type

value: immortalized mammary epithelial cells

tag: genotype

value: MSL3 KO


title: Salmonella-Infected + Treg-depleted, CD4+ Tcells, cLP

description:
Library name: 4
10X Genomics

value: colonic lamina propria

value: CD4+ T cells

value: infected with Salmonella Typhimurium SL1344 and treated with diphteria toxin (DT)

tag: age

value: 8-10 weeks


title: IgG_18

description: Library name: IgG_18

data_processing:
Pair-end FASTQ files were mapped to the Mus_musculus.GRCm38.101 reference genomes, via using the HISAT2 package. Then, the FPKM values were calculated with StringTie and Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html). Differential gene expression was analyzed using DESeq2, with genes having a P value ≤ 0.05 and absolute fold change ≥ 2 recognized as differentially expressed genes (DEGs). Heatmaps were generated, and Gene Ontology (GO) and KEGG pathway analyses were performed on DEGs using the OmicStudio tools at https://www.omicstudio.cn/tool. Gene set enrichment analysis (GSEA) was conducted using GSEA (v4.1.0) and MSigDB to identify gene sets involved in specific pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: Excel file including FRKM values for each sample

source_name: aorta

tag: tissue

value: aorta

value: WT

value: AngII/BAPN+IgG


title: KO_1_1

description: Library name: KO_1_1

value: hepatocyte


title: Visium, Subacute Day 7 post injection of ECM-H,  biol rep 1

value: intramyocardial injection of ECM hydrogel


description:
Library name: I40H8_smallintestineLP_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

tag: infection agent

value: LCMV armstrong

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, collagenase I

value: lamina propria of small intestine

value: P14, SMARTA

value: all T including P14 and SMARTA

value: IV- CD45+ CD3e+

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

tag: batch


title: HME1_MSL3ko_CUT&Tag_Rep1

description: Library name: HME1_MSL3ko_Rep1

tag: chip antibody

value: H4K16ac Abcam, ab109463

tag: cell line

tag: cell type

value: immortalized mammary epithelial cells

tag: genotype

value: MSL3 KO


description:
Library name: I40H8_smallintestineLP_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: tissue

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: TRUE

tag: infection dose

tag: prep description

tag: organ

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: gating strategy

tag: sample comments

value: T cells


title: Visium, Subacute Day 7 post injection of saline,  biol rep 1 and 2

value: Cardiac

tag: disease state

value: IR surgery

tag: treatment

value: Intramyocardial injection of saline


title: Visium, Subacute Day 7 post injection of saline,  biol rep 3


description:
Library name: I40H7_smallintestineIEL_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: cite seq

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

tag: infection agent

value: LCMV armstrong

value: anti-CD45 IV injection before tissue harvest, DTE

value: epithelium of small intestine

tag: batch


title: IgG_20

description: Library name: IgG_20

tag: tissue

value: aorta

tag: genotype

value: WT

value: AngII/BAPN+IgG


title: Single nuclei, Chronic Day 7 post injection of ECM-H,  biol rep 2

value: intramyocardial injection of ECM hydrogel


description:
Library name: I40H8_smallintestineLP_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: TRUE

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, collagenase I

tag: organ

value: lamina propria of small intestine

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: IV- CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

tag: cell type


description:
Library name: I40H7_smallintestineIEL_LCMVarm_D60_allT_P14_SMARTA_mouse0142_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: cite seq

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: T cells


title: Ab_39

description: Library name: Ab_39

tag: tissue

value: aorta

tag: genotype

value: WT

tag: treatment

value: AngII/BAPN+Ab


description:
Library name: I40H7_smallintestineIEL_LCMVarm_D60_allT_P14_SMARTA_mouse0142_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

value: TRUE

tag: infection agent

value: LCMV armstrong

tag: infection dose

tag: prep description

value: anti-CD45 IV injection before tissue harvest, DTE

tag: organ

value: epithelium of small intestine

tag: organ uberon_id

tag: t specificity

tag: target cells

tag: batch


title: IgG_14

description: Library name: IgG_14

value: AngII/BAPN+IgG


title: Visium, Subacute Day 7 post injection of ECM-H,  biol rep 2

value: Cardiac

tag: disease state

value: IR surgery

value: intramyocardial injection of ECM hydrogel


title: HME_TNP2_spikein_Rep1

description: Library name: HME_TNP2_spikein_Rep1

data_processing:
RNAseq reads were aligned to the hg38 genome using nf-core/rnaseq pipeline version 3.13.2  with star_rsem aligner
BigWig files and count tables were generated within the nf-core/rnaseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig for genome browser visualization
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

extract_protocol:
RNA was extracted using a RNeasy Plus Micro Kit (Qiagen, 74034)
For total experiment, ribosomal RNA removal was performed with FastSelect -rRNA HMR Kit (Qiagen, 334386) and libraries were prepared using NEBNext UltraII Directional RNA Library Prep Kit (NEB, E7760). For spike-in experiment, RNA concentration was checked with the nanodrop. 1ug of RNA was taken from the lowest concentrated sample and same volume was taken for all the other samples. 2 μL (1:100) ERCC Spike-in (Thermo Fisher Scientific, 4456740) was added to each sample. Libraries were prepared using NEBNext UltraII Directional RNA Library Prep Kit (NEB, E7760) with polyA enrichment.

tag: cell line

tag: cell type

value: immortalized mammary epithelial cells

value: Ctrl KO

value: Stable KO cells


title: Single nuclei, Chronic Day 7 post injection of ECM-H,  biol rep 1

tag: tissue


title: Ab_7

description: Library name: Ab_7

tag: genotype


title: Single nuclei, Chronic Day 7 post injection of saline,  biol rep 2

tag: treatment

value: Intramyocardial injection of saline


title: Ab_5

description: Library name: Ab_5


description:
Library name: I40H6_LNmesenteric_LCMVarm_D60_allT_P14_SMARTA_mouse0142_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

tag: immgent igt_10xlane_id

tag: cite seq

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong day 60)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: mesenteric lymph node

value: P14, SMARTA

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: HME_MSL3_spikein_Rep1

description: Library name: HME_MSL3_spikein_Rep1

tag: cell line

tag: cell type

value: immortalized mammary epithelial cells

value: MSL3 KO


title: CScreen_MEF2B_2

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

description: Library name: CScreen_MEF2B_2

extract_protocol:
CRISPR screens:
SU-DHL-4 reporter cells were transduced with the Brunello library. For each screen, 6 replicates with 15 million cells (90 million in total) were transduced at a density of 5 million cells/ml in a 6 well plate. The amount of virus was adjusted according to the viral titer to obtain a multiplicity of infection (MOI) of 0.3. Cells were transduced by spinfection (1,460g for 90 min and 30°C) in the presence of 6 µg/ml polybrene. Infected cells were puromycin selected 24h post infection at a final concentration of 4 µg/ml. On day 3 post infection, the MOI was verified and cells were split in medium containing 200 ng/ml doxycycline. Cells were split every other day with fresh doxycycline containing medium. On day 10 post infection, for each of the six replicates 60 million cells were sorted using BD FACS Aria or Fusion cell sorters based on reporter fluorescence to capture the bottom and top 5% expressing cells. On average, for each screen 286 million cells were sorted yielding ~9 million low or high expressing cells (Table S1B). For the three mTORC1 inhibited CRISPR screens in BTG2, CD79B and OCAB reporter cell lines, 5 nM rapamycin was added on day 8 and cells were sorted on day 10 as for the other screens. Genomic DNA from sorted cells was extracted using DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq
Cells were either unperturbed, transduced with sgRNA, or treated with inhibitors as described above. Cells were split every other day and seeded at 200,000 cells/ml the day before harvest. Inhibitor treated cells were harvested on day 2 post-treatment and sgRNA transduced cells on day 10 post-infection. On the day of harvest, half a million cells were pelleted and lysed in 100 µl of the Ambion RNAqueous lysis solution. RNA was extracted and treated with DNase according to the RNAqueous-Micro Total RNA Isolation Kit protocol (Thermo Fisher Scientific). RNA-seq libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ChIP-seq
Cells for ChIP-seq analysis were either unperturbed or transduced with sgRNA for 10 days before harvesting. The day before harvest, cells were diluted to 200,000 cells/ml. Cultured cells were fixed at room temperature for 10 min with 1% formaldehyde (Sigma) and the reaction was quenched with 125 mM glycine (Sigma). Fixed cells were washed with PBS, snap-frozen, and stored at -80°C until further processing. For ChIP, 20 million cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and freshly added Complete Mini EDTA free proteinase inhibitor (Roche)). Chromatin was sheared by sonication on ice using a Branson Sonifier with an amplitude of 35% and 12 cycles of 20 sec sonication followed by 30 sec of pause. Supernatant was precleared with 20 µl Dynabeads Protein A (Thermo Fisher Scientific) for 1 hour at 4°C under rotation. Precleared chromatin was incubated with BRD4 (Abcam, ab128874) or FLI1 (Abcam, ab133485) antibody overnight at 4°C under rotation. The antibody-protein solution was then captured with 40 µl of Dynabeads Protein A for 1 hour at 4°C under rotation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K (Thermo Fisher Scientific). ChIP DNA was column purified with ChIP DNA Clean and Concentrator kit (Zymo research).
RNA-seq
Libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Single 50 cycles of sequencing data were acquired on HiSeq3000, NovaSeq6000, NovaSeqXplus (illumina).
ChIP-Seq
Libraries were prepared using the Ovation Ultralow Library System V2. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (illumina)
CRISPR screen
Libraries were prepared using staggered GeCKO readout primers following the recommended instructions (Shalem et al. 2014). Deep sequencing was performed on NextSeq550 and NovaSeq6000 (Illumina) using 75bp single-end reads.

value: B cell lymphoma

tag: genotype

value: no


title: Single nuclei, Chronic Day 7 post injection of saline,  biol rep 1

tag: tissue

value: Cardiac

tag: disease state

value: IR surgery

tag: treatment

value: Intramyocardial injection of saline


title: HME_MSL3_spikein_Rep2

description: Library name: HME_MSL3_spikein_Rep2

value: Stable KO cells


title: sg2_R_2

city: Shanghai

description: Library name: sg2_R_2

source_name: smooth muscle cell

value: smooth muscle cell

value: rhCTHRC1 treatment


title: Single nuclei, Subacute Day 7 post injection of ECM-H,  biol rep 2

value: intramyocardial injection of ECM hydrogel


title: sg2_R_3

description: Library name: sg2_R_3


title: HME_TNP2_1

description: Library name: HME_TNP2_1

value: Ctrl KO

value: Acute deletion of the indicated gene via crRNA transfection in Cas9 expressing cells


title: HME_TNP2_spikein_Rep2

description: Library name: HME_TNP2_spikein_Rep2


title: HME_TNP2_2

description: Library name: HME_TNP2_2