title: EML1_GFP_ChIP

type: genomic

city: Columbus

first: Jelena

last: Brkljacic

address: 1060 Carmack Rd

institute: The Ohio State University

description: SAMPLE 1

hyb_protocol: Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing:
MAT was used to normalize data and call ChIP-chip peaks
The resulting BAR file was generated using MAT with parameters: Bandwidth=300, MaxGap=300

organism: Arabidopsis thaliana

source_name: EML1 ChIP DNA from p35S::EML1-GFP plants

label_protocol: The sample was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Three-week-old plants were grown under 16 h light on 1/2 MS plates

extract_protocol: Seedlings were immersed in buffer A (0.4 M Suc, 10 mm Tris-HCl, pH 8.0, 1 mM EDTA, 1 mM phenylmethylsulfonyl fluoride, and 1% formaldehyde) under vacuum for 20 min. Glycine was added to 0.1 M and incubation was continued for an additional 10 min. The plants were washed in distilled water and frozen in N2. Approximately 60 mg of tissue was ground for each immunoprecipitation. The tissue was resuspended in 0.1 mL Lysis buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 1 mM phenylmethylsulfonyl fluoride, 10 mM Na-butyrate) and plant proteinase inhibitor cocktail (Sigma). DNA was sheared by sonication to approximately 300- to 1,000-bp fragments with a main peak of 500 bp. Sonication was performed on ice with an amplitude of 10% using 5 × 15-s pulses (5 s between bursts). After preclearing with 40 μL of salmon sperm DNA/Protein A-agarose beads (Upstate) for 120 min at 4°C, immunoprecipitation was performed overnight at 4°C with 1 μL of anti-GFP antibody (ab290; Abcam). After incubation, beads were washed two times with lysis buffer, two times with LNDET buffer (0.25 M LiCl, 1% NP40, 1% Na-deoxycholate, 1 mM EDTA) and two times with Tris-EDTA buffer. The washed beads and input fraction were resuspended in elution buffer (1% SDS, 0.1 M NaHCO3) with 1 mg/mL proteinase K and incubated overnight at 65°C. After cross-link reversal of the immunoprecipitated and Input DNA (set aside from the sonication step), the DNA was purified using the PCR Purification kit (Qiagen), and amplified using the GenomePlex Whole Genome Amplification kit (Sigma).

tag: age

value: 3 weeks

value: seedling

tag: chip anitbody

value: anti-GFP antibody (ab290; Abcam)


title: EML1_GFP_input

status: Public on Apr 23 2021

country: USA

description: SAMPLE 2

label: biotin

molecule: genomic DNA

source_name: Sonicated genomic DNA from p35S::EML1-GFP plants

tag: genotype/variation

tag: tissue


title: MET-1

type: RNA

city: Beijing

first: Ping

last: Wang

address: Yong An Road No.95

country: China

institute: Beijing Friendship Hospital

hyb_protocol: standard Affymentrix protocol

scan_protocol: standard Affymentrix protocol

data_processing:
Affymetrix® Expression Console™ software (v.1.0)
Partek Genomics Suite 6.6
RMA normalization
Histogram analysis and PCA analysis
Differentially Expressed Genes Between Groups
raw CEL data for each gene and each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Hepatic progenitor cells

label_protocol: standard Affymentrix protocol

growth_protocol: Hepatic progenitor cells were cultured in 10%FBS DMEM/F12 with 1ng/ml EGF and 0.5ng/ml SCF.

extract_protocol:
Total RNA was isolated by TRIzol Reagent and RNA Neasy Mini Kit.
Target prepared by GeneChip WT PLUS Reagent kit.

treatment_protocol: Hepatic progenitor cells were treated with 1ng/ml TGF-b1 in 10%FBS DMEM/F12 for 16 days to induce epithelial-mesenchymal transition.  The 16-day TGF-b1-treated cells were cultured in 10%FBS DMEM/F12 with 1ng/ml EGF and 0.5ng/ml SCF for 7 days to induce mesenchymal-epithelial transition.

tag: cell type

value: In vitro cultured hepatic progenitor cells

tag: strain

value: SD Rat


title: Fruit fly whole animal(s) (Sample4079)

type: SRA

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (3D-DNA, Juicer)
Centromere position identification (repeat sequence mapping or structural analysis, 3D-DNA/JBAT)
Aggregate chromosome analysis (3D-DNA)
Variant calling (DRAGEN pipeline)
Chromosome-length variant phasing (3D-DNA)
Genome_build: In addition to those generate as part of the study, the following existing genome builds were used: GRCg6a (domestic chicken); Xla.v91 (African clawed frog); AaegL5.0 (Yellow fever mosquito), CpipJ3 (Southern domestic mosquito); Release_6_plus_ISO1_MT (fruit fly, with chromosome arms merged for ACA analysis resulting in Release_6_plus_ISO1_MT_merged); WBcel235 (C. elegans); sacCer3 (baker's yeast); arahy.Tifrunner.gnm2.J5K5 (ground nut); 161010_Chinese_Spring_v1.0_pseudomolecules (bread wheat).
Supplementary_files_format_and_content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary_files_format_and_content: hic: contact maps generated by aligning Hi-C data to corresponding chromosome-length reference sequences. In addition to standard contact maps generated for all genomic positions across chromosomes the uploaded files include ACA (aggregate chromosome analysis) maps and phasing contact maps representing interactions between positions on the genome that contain heterogyzous SNPs. For more details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: wig: tracks showing the alignment frequency of Hi-C reads from read pairs that contain centromere repeat-specifc sequences.
Supplementary_files_format_and_content: bedpe: Files describing the tentative position of centromeres in chromosome-length genome assemblies, identified either by mapping repeat sequences associated with the centromere or via analysis of the contact map for evidence of centromere-to-telomere folding axis. For details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: vcf.gz: Variants (specifically SNPs) identivied by the DRAGEN variant calling pipeline from aligning Hi-C data to chromosome-length references generated via Hi-C-guided assembly and phased using the 3D-DNA Hi-C-guided phasing module.

organism: Drosophila melanogaster

source_name: whole animal

extract_protocol:
Extraction protocol is described as part of the library construction protocol.
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: whole animal


title: CL5: Rat liver - normal

city: 成都

first: 熊

last: 肖

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院

library_source: transcriptomic

data_processing:
Using next-generation sequencing technology to perform RNA-seq analysis on an Illumina genome analyzer IIx.
The original reads containing more than 2-N bases were first discarded. Short reads of less than 16nt, the adapters and low-quality bases in the original sequencing reads were removed by the FASTX-Toolkit (Version 0.0.13).
Clean Reads was compared with the GRCH38 genome using TopHat2 allowing 4 mismatches.
Unique locational reads were used for gene reads count and FPKM (number of locational fragments per million segments per 1000 base transcript)
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Rat liver

extract_protocol:
TRIzol (Invitrogen, Carlsbad, California, USA) was used to extracted total RNA from rat liver tissues, and purified by the manufacturer's instructions.
Utilize NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, Ma, USA) to quantify total RNA and according Agilent 2100 system and RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) to determine RNA integrity. To achieve accurate lncRNA analysis, the Ribosomal RNA was removed using the Thermo Fisher Scientific Central Ribonucleic Acid Removal Kit. Using next-generation sequencing technology to perform RNA-seq analysis on an Illumina genome analyzer IIx.

value: liver

tag: disease state

value: normal


title: OVC EMT-2

tag: treatment

value: 1ng/ml TGF-beta1


title: Gfap sgScrmbl 3

status: Public on Apr 22 2021

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The reads are aligned to GrCM38 mouse genome using STAR (2.7.3)
The aligned reads were quantified using RSEM (v1.3)
Genome_build: GrCM38
Supplementary_files_format_and_content: Tab delimited gene expression table

molecule: polyA RNA

organism: Mus musculus

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were created according to the manufacturer's protocol for the NEB kit (#E6420)

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: WT C57Bl/6

tag: Sex

value: Female


title: Itgam sgSema4d 1


title: CONT-3


title: CONT-1


title: Itgam sgScrmbl 3


title: Itgam sgSema4d 3


title: Mouse, RABID.transcriptome.EAE

data_processing:
R1: biological (all 61bp)
R2: technical -- part 1 of cell barcode (all 8bp)
R3: technical -- library barcode (all 8bp)
R4: technical -- part 2 of cell barcode (1-8bp) and UMI (9-14bp)
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were aligned to mouse (GRCm38) genome by bowtie.
The reads were quantified and expression of genes was calculated using the inDrop pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X format output including sparse matrix, barcode.tsv and gene.tsv

source_name: CNS

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, labeled with Miltenyi anti-Dead Cell and anti-myelin kits, then magnetically purified and washed. Cells were sorted by flow cytometry based on mCherry fluorescence. Post-sort, cells were washed then processed by inDrop
Libraries were created according to the InDrop v3 protocol derived from Klein et al. Cell 2015.
inDrop scRNA-Seq

value: Male

value: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA

value: Induction of EAE


title: Gfap sgPlxnb1 2


title: Mouse, RABID.transcriptome.naive

data_processing:
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were aligned to mouse (GRCm38) genome by bowtie.
The reads were quantified and expression of genes was calculated using the inDrop pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X format output including sparse matrix, barcode.tsv and gene.tsv


title: Mouse, RABID.BC.naive

data_processing:
R1: biological (all 61bp)
R2: technical -- part 1 of cell barcode (all 8bp)
R3: technical -- library barcode (all 8bp)
R4: technical -- part 2 of cell barcode (1-8bp) and UMI (9-14bp)
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatics (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were trimmed and filtered based on the Rabid barcode structure described in paper.
The filtered reads were clustered within 1 levenshtein distance using starcode v1.3.
The rabid reads were corrected based on the results from starcode clustering, and then the corrected reads were quantified.
Supplementary_files_format_and_content: Tab-delimited csv file consisting of UMI rabid barcode counts for cells

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, labeled with Miltenyi anti-Dead Cell and anti-myelin kits, then magnetically purified and washed. Cells were sorted by flow cytometry based on mCherry fluorescence. Post-sort, cells were washed then processed by inDrop
Libraries were created according to the InDrop v3 protocol derived from Klein et al. Cell 2015. Barcodes from inDrop-processed cDNA were amplified using a combination of inDrop and RABID-seq primers.
RABID-seq modified inDrop scRNA-Seq


title: Gfap sgPlxnb2 3


title: APTM3_4

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
Reads were aligned against the GRCm38 mouse genome using STAR v2.7.3
The alignment results were quantified using RSEM v1.3.1
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM output which includes gene level quantification and transcript level quantification

source_name: Colon tissue

growth_protocol: A piece of medial colon was isolated from each mouse and inmediately frozen in liquid nitrogen. RNA was extracted afterwards.

extract_protocol:
Trizol and RNAeasy Qiagen kit following manufacturers instructions
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

treatment_protocol: TNBS colitis was induced in C57BL/6J males. Mice were pre-sensitized on the skin one week before the colitis induction by rectal administration of TNBS. Control group was treated only with 50% Ethanol. From the day of pre sensitization mice were given the corresponding yeast strain by oral gavage: CB008 unmodified yeasts; BS029 apyrase secreting yeast; APTM3 mutant P2Y2 controlled apyrase secreting yeast.

value: M

value: 10 weeks

tag: sample type

value: TNBS induced, APTM3 treated


title: BS029_4

value: TNBS induced, BS029 treated


title: Itgam sgScrmbl 2


title: APTM3_1


title: BS029_2


title: Gfap sgScrmbl 2


title: Gfap sgScrmbl 1


title: Pool4

data_processing:
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were trimmed and filtered based on the Rabid barcode structure described in paper.
The filtered reads were clustered within 1 levenshtein distance using starcode v1.3.
Genome_build: The rabid reads were corrected based on the results from starcode clustering, and then the corrected reads were quantified.
Supplementary_files_format_and_content: 3 Column csv file consisting cell name, Rabid read in the cell and count of reads in  cell

source_name: CNS cells

tag: timepoint

value: EAE peak phase

value: central nervous system (CNS) cells

tag: cell sybtype


title: Pool3


title: APTM3_5


title: CB008_2

value: TNBS induced, CB008 treated


title: Health Control_4

value: Health Control_4


title: APTM3_2


title: BS029_3


title: Health Control_2

value: Health Control_2


title: Index6OtC3512+cells-mice

city: Lubbock

first: Beverly

middle: S

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

description:
rRNA depleted
Index6_OtC3512

data_processing:
Paired-end 106 nucleotide reads were subjected to species-specific mapping against the mouse (mm10) and human (hg38) reference genomes
sequencing depth was a minimum of 40 million reads
Comparison of expression (fpkm_tracking) and differential expression analysis was conducted withcufflinks.cuffdiff (2.2.1).
Exon quantification was performed to show the relative expression of all known HLTF/Hltf exons in control tumr and control microenvironment (mouse)
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files for RPKM vlaues for human and mouse for each sample

organism:
Homo sapiens
Mus musculus

source_name: primary CDX tumor

extract_protocol:
primary CDX tumor x 3 biological replicates for test and control mice = 6 total samples were flashfrozen and sent to Otogenetics for RNAseq
Random-primed cDNA (rRNA depleted) using standard Illumina Protocols

value: human tumor and mouse microenvironment cells

tag: host mouse background strain

tag: human cell line

value: HCT116 cells HLTF+/+

tag: mouse genotype

value: test Hltf -/- mouse


title: Health Control_1

value: Health Control_1


title: BS029_1


title: CB008_3


title: CB008_1


title: APTM3_3


title: N6 Assay sequencing sample

city: Chicago

first: Xiaowei

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

description: Mini-seq read counts combined from two sequencing runs

data_processing:
The adaptor sequence were removed from raw sequence reads. Then all the remaining sequence were clustered to show the most abundant sequence.
Supplementary_files_format_and_content: Tab-delimited text file containing raw read count values for individual samples if the raw read count values is equal or greater than 10.

molecule: other

organism: synthetic construct

source_name: N6 Assay LAMP reaction

extract_protocol:
MagMAX Viral/Pathogen Nucleic Acid Isolation Kit to isolate saliva RNA
DNA sequencing libraries were prepared by PCR amplification of LAMP or RT-LAMP products with modified universal primers for Illumina sequencing

treatment_protocol: LAMP or RT-LAMP reactin products were amprified by PCR

value: Plasmid containing SARS-CoV-2 N gene


title: DNase-seq from HK-2 (ENCLB174TDO)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR634YVQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR634YVQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB174TDO

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens HK-2 cell line

tag: line

value: cell line

tag: biosample encode accession

value: male

tag: dev stage

value: unknown

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: ATCC

tag: link

value: ENCBS188NWH at ENCODE; https://www.encodeproject.org/ENCBS188NWH/

value: Derived from ENCODE donor ENCDO592BBN; https://www.encodeproject.org/ENCDO592BBN/


title: DNase-seq from HK-2 (ENCLB722RNZ)

description:
https://www.encodeproject.org/experiments/ENCSR634YVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR634YVQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB722RNZ

tag: age


title: bcpairing_tile_3

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

data_processing:
Reverse reads containing the plasmid barcode were searched for exact match to a known barcode from the plasmid library with custom scripts.
Forward reads containing the spliced sequence were mapped to a variant-specific reference consisting of the POU1F1 exon trap reference sequence with the respective mutation introduced in silico, using GMAP (arguments “ -t 8 -f samse --microexon-spliceprob=1.0 --allow-close-indels=2”)
From the spliced reads, an isoform catalog was tallied requiring each isoform to be represented by at least three distinct barcodes and nine reads.  Spliced reads associated with each barcode were tallied to produce per-barcode isoform usage counts, and percent spliced in (PSI) fractions.  Barcodes corresponding to the same POU1F1 variant were then aggregated (weighted by the number of reads obtained) to generate for each variant a mean PSI score for all known isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: Per-barcode file contains one row per splice reporter barcode; columns indicate for each replicate, count of reads mapping to each isoform (ALPHA,BETA,SKIP,OTHER) and resulting PSI values.  Per-variant file contains one row per tested variant, with annotations (e.g., genomic position, coding consequence),  columns indicating overall splice disruptiveness (sdv) and per-isoform calls (sdv_ISOFORM). For each replicate, the number of barcodes detected (_n_bc), number of valid reads (_sum_reads_passfilt), weighted means for each isoform (_wmean_ISOFORM), fold change for each isoform over background (_fc_ISOFORM) and corresponding z-scores (_zwmean_ISO) are indicated.   Barcode-variant pairing file contains a barcode plus comma-separated list of mutation(s) present on the associated haplotype, each encoded as seqname:position:ref:alt.

source_name: Mutant POU1F1 exon2 minigene plasmid library

growth_protocol: COS-7 cells were plated at 5e6 cells/60mm plate, and maintained in DMEM with 10% FBS and pen-strep.

extract_protocol:
Total RNA was purified with the RNeasy kit at 24 hrs post-transfection
5 ug of total RNA was used to prepare first-strand cDNA using the SuperScript III First-Strand Synthesis kit (Invitrogen) with oligo dT primers.  Spliced transcript was amplified using nested PCR, initially for 6 cycles using the SD6F/SA2R primers, followed by 20 cycles using primers SD2F/jklab0046. Paired-end Illumina sequencing libraries were generated by tailing PCR (6 cycles) with a forward primer within the constant upstream exon and a reverse primer immediately downstream of the N20 barcode. Unique dual i5/i7 indices were added by a second round of tailing PCR (6 cycles), and the resulting products were purified by SPRI bead cleanup.

treatment_protocol: Cells were transfected with plasmid libraries using ViaFect reagent (3:1 ratio to plasmid DNA).

tag: replicate


title: bcpairing_tile_2


title: bcpairing_tile_1


title: bcpairing_tile_4


title: Health Control_3

tag: strain

value: M

value: 10 weeks

value: Health Control_3


title: MDA-MB-231 control - rep3

city: Seoul

first: Yebin

last: Im

address: 504-302, 1, Gwanak-ro, Gwanak-gu,

department: Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
For the read sequences resulting from the RNA sequencing, the adapter sequences (TruSeq universal and indexed adapters) were removed using the Cutadapt software (ver. 2.8).
The resulting reads were then aligned to the human reference genome (GRCh38) using TopHat aligner (ver. 2.1.1) with the default options.
After the alignment, the mapped reads were counted for gene features (GTF file of GRCh38) using HTSeq (ver. 0.11.3).
The estimated fragments per kilobase of transcript per million fragments (FPKM) were manually mapped by using gene length data and total mapped reads of protein coding gene given by ensemble(GRCh38.p13).
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM xlsx file

source_name: TNBC cell MDA-MB-231

growth_protocol: BT20 and MDA-MB-468 cell lines were obtained from the Korea Cell Line Bank (KCLB; Seoul, Korea). MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC; Manassas, VA). BT20 cells were cultured in RPMI (Gibco, Carlsbad, CA) containing 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA) and 1% penicillin/streptomycin (PS; Gibco). MDA-MB-468 and MDA-MB-231 cells were cultured in DMEM (Gibco) containing 10% FBS and 1% PS. Cells were maintained at 37°C in a humidified atmosphere of 95% air and 5% CO2 and periodically screened for mycoplasma contamination.

extract_protocol:
Total RNA was isolated from all cell lines (n = 3 per cell type) before and 48 hours after treatment of 20mM-NAM, using TRIzol® RNA Isolation Reagent (Invitrogen), and purified according to the manufacturer’s instructions. The RNA concentration was determined using a NanoDrop ND-1000 spectrometer (Thermo Fisher, Waltham, MA), and the RNA integrity number (RIN) for each RNA sample was analyzed using a 2100 Bioanalyzer and the Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA).
The isolated total RNA was processed for preparing RNA sequencing library using TruSeq stranded total RNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Cell lines were treated with 20mM-NAM for 48 hours which was purchased from Sigma-Aldrich (St. Louis, MO).

tag: treatment

value: untreated

tag: cell line

tag: cell type

value: Human breast TNBC


title: MDA-MB-231 NAM treated - rep1

value: 20mM nicotinamide treated, 48hrs


title: MDA-MB-231 NAM treated - rep2


title: MDA-MB-231 NAM treated - rep3


title: MDA-MB-231 control - rep1


title: MDA-MB-231 control - rep2


title: MDA-MB-468 NAM treated - rep3

source_name: TNBC cell MDA-MB-468


title: MDA-MB-468 NAM treated - rep2


title: MDA-MB-468 control - rep3


title: MDA-MB-468 NAM treated - rep1


title: MDA-MB-468 control - rep1


title: MDA-MB-468 control - rep2


title: BT20 NAM treated - rep3

source_name: TNBC cell BT-20


title: BT20 NAM treated - rep2


title: Subject RL14, leprosy progressor first timepoint

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
FastQC was used for checking raw read QC.
Adapter clipping was performed using Cutadapt (v2.4) with default settings.
RNA-Seq reads’ alignment was performed using HISAT2 (v2.1.0) on GRCh38 reference genome analysis set.
The gene read quantification was performed using HTSeq-count (v0.9.1) with setting “–stranded reverse”. The gene annotation used for quantification was Ensembl version 94.
Genome_build: GRCh38, Ensembl gene annotation 94
Supplementary_files_format_and_content: CSV format, gene raw read and CPM counts

source_name: whole blood

extract_protocol:
Whole blood was collected in PAXgene tubes and frozen. RNA was extracted automatically using a QIAcube with the PAXgene Blood miRNA Kit. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) including poly(A) enrichment. Additionally, globin reduction was performed using GLOBINclear kit (Cat#AM1980). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA cDNA was synthesized. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. Libraries were sequenced on the Illumina NovaSeq6000 System with a 150bp paired-end protocol.

tag: tissue

value: whole blood

tag: subject

tag: disease state

value: leprosy progressor

tag: time point

value: First

tag: ridley-jopling classification

value: I


title: Index13OtC3221+cells+mice

description:
rRNA depleted
Index13_OtC3221

value: human tumor and mouse microenvironment cells

tag: host mouse background strain

tag: human cell line

value: HCT116 cells HLTF+/+

tag: mouse genotype

value: control Hltf +/+ mouse


title: BT20 control - rep2


title: BT20 NAM treated - rep1


title: BT20 control - rep3


title: BT20 control - rep1


title: Balb/c_Tumor(A20)_20% HPbCD_._4hr_repl.1

city: Cambridge

first: Eric

middle: Scott

last: Lightcap

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

description: Balb/c_Tumor(A20)_20% HPbCD_._4hr

data_processing:
Raw fastq files were processed using the RNA-seq pipeline within Array Studio. Briefly, reads with bad qualities, or from IlluminaAdapters, Ercc, rRNA and tRNA were first filtered from raw data, the cleaned reads were then aligned to the genome through OmicSoft Aligner (OSA). The reads mapped to the exonic region were counted for each gene and then normalized into FPKM for the downstream analysis.
Genome_build: mouse NCBI genome build 38
Supplementary_files_format_and_content: The reads count and FPKM value of each gene in each sample are uploaded as the processed data files

growth_protocol: Mouse B16-F10 melanoma cells were grown in DMEM medium containing 10% FBS. Mouse A20 B-lymphoma cells were grown in RPMI-1640 medium containing 10%FBS and 0.05 mM 2-mercaptoethanol. When preparation of tumor cell inoculation, the cells were harvested and washed in DMEM or RPMI medium. Then 0.1 million of B16-F10 cells in 0.1ml DMEM medium or 1 million of A20 cells in 0.1 ml RPMI medium were inoculated subcutaneously into C57BL/6 or BALB/c mice in flank respectively.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tumor volumes were around 500 mm^3, C57BL/6 bearing B16-F10 tumors and BALB/c mice bearing A20 tumors were given one dose of TAK-981 at 2.5 mg/kg, 5 mg/kg, 7.5 mg/kg, or 15 mg/kg intravenously, each dose level had 4-hour and 8-hour time points, and each time point had three mice per group. By 4 hours and 8 hours post TAK-981 treatment, samples of whole of blood, tumor, and spleen were harvested for further analysis.

value: Balb/c

value: 20% HPbCD

tag: dosage


title: SingleGamma

city: Memphis

first: Mitchell

middle: J.

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: HiC

data_processing:
HiC-Pro (v2.11.1) was used with default parameters; For global read mapping: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder; For local read mapping: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder ; Cutoffs for minimal and maximal values are not defined for FRAG_SIZE, INSERT_SIZE, and CIS_DIST; For read pair filtering: RM_SINGLETON = 1, RM_MULTI = 1, RM_DUP = 1.
Then all HiC data were downsampled to 200 million valid read pairs based on .allValidPairs files. HiC-Pro was used for iced matrix generation with default parameters of BIN_SIZE = 10000, MAX_ITER = 100, FILTER_LOW_COUNT_PERC = 0.02, FILTER_HIGH_COUNT_PERC = 0, EPS = 0.1.
HicFindTADs from HiCExplorer (v3.5.1) was used for topologically associating domain (TAD) calling with default parameters after converting HiC-Pro iced matrix to H5 format (hicConvertFormat).
Genome_build: hg19
Supplementary_files_format_and_content: bw file

source_name: SingleGamma

growth_protocol: HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin.

extract_protocol:
5e6 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched for 5 minutes at room temperature with a final concentration of 200 mM glycine. Fixed cells were lysed in 1mL cell lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 30 minutes on ice. The cell suspension was pelleted at 2500 x g for 5 minutes at 4oC and washed once with lysis buffer. The cell pellet was resuspended in 0.5% SDS and incubated at 62oC for 10 minutes. 10% Triton X-100 was used to quench the SDS and incubated at 37oC for 15 minutes. 100U of MboI was used to digest the chromatin overnigt at 37oC with shaking. Following heat inactivation of MboI, restriction fragment overhangs where marked with biotin. Ligation of marked ends was performed using T4 ligase at room temperature for 4 hours. Ligated DNA was sheared using a Covaris M220 with the power settings of peak incident power of 50, duty cycle 200, 200 cycles/burst, for 90 seconds. Sheared DNA was purified using AMPure XP beads (Beckman Coulter, A63881). Biotin-labelled DNA was isolated using Dynabeads MyOne Streptavidin C1 beads
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing


title: 113G_S3

data_processing:
Adapter sequences were trimmed by skewer. BWA mem mapping to hg19
Duplicated reads were removed using samtools
normalized signal (bw file) was generated using s3norm_pipeline.py -r mean
Genome_build: hg19
Supplementary_files_format_and_content: bw

extract_protocol:
60,000 HUDEP-2 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above. Cells were resuspended using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina cat# 20034197) and incubated for 30 min at 37 °C. . Following purification, library fragments were amplified using NEBnext PCR master mix and custom Nextera PCR primers 1 and 2. Library amplification was determined using qPCR for a total of 13-15 cycles and then purified using a QIAGEN PCR purification kit.
Library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.  Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads.

tag: library

value: ATAC-seq


title: WT_S6


title: Acvr2aPRcre_3

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.2).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse uterine tissues

growth_protocol: For fertility analyses, 6-week-old female mice were mated to WT males of proven fertility for 6 months and the total number of pups was quantified. Smad1flox/flox and Smad5flox/flox mice were previously generated and described. To generate Smad1/5 cKO females, female mice carrying homozygous Smad1flox/flox; Smad5flox/flox alleles were crossed to males carrying the double Smad1flox/flox; Smad5flox/flox alleles and the progesterone receptor-cre (PRcre/+). A similar breeding scheme was used to generate Acvr2aflox/flox-PRcre/+ and Acvr2bflox/flox-PRcre/+ mice using Acvr2aflox/flox and Acvr2bflox/flox mice that were generated in collaboration with Dr. Se-Jin Lee. The mice were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. Animal handling and experimental studies were performed following the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine.

extract_protocol:
Uterine tissues were collected from control, Smad1/5 cKO, and Acvr2a cKO mice at 3.5dpc of pseudopregnancy and immediately snap frozen on dry ice or fixed in formalin. Mice were determined to be 3.5dpc pseudopregnant according to the levels of serum progesterone. RNA was extracted from the tissues, processed in Trizol and isolated with the Direct-zol RNA extraction kit (Zymo).
Quality control of the samples was determined by assessing the RNA Integrity Number (RIN) and then used for library preparation and sequencing. Sequencing (>20M reads per sample) was performed by Novogene Corporation (Santa Cruz, CA), on the Illumina Platform (PE150).

value: uterine

tag: genotype/variation


title: 117A_S2


title: GATA1_13nt_input_revision

description: ChIP-seq

data_processing:
BWA mem mapping to hg19
Duplicated reads were removed using samtools
normalized signal (bw file) was generated using s3norm_pipeline.py -r mean
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

extract_protocol:
2e7 HUDEP-2 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched for 5 minutes at room temperature with a final concentration of 125 mM glycine. Fixed cells were lysed in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysed in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C using a Branson 250 micro-tip sonicator with the power settings of 100% duty cycle, 10 second pulses for 2 minutes, with 90 seconds on ice between pulses. The sonicated chromatin was pre-cleared overnight at 4°C using protein A/G agarose beads. Pre-cleared chromatin was incubated with antibody. Following elution, DNA-protein complexes were treated with RNase for 30 minutes at 37°C followed by proteinase K treatment for 30 minutes at 45°C and overnight at 60°C with shaking. DNA was purified using a Qiagen MinElute kit.
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing

tag: antibody

value: input


title: GATA1_186T_113G_revision

description: ChIP-seq


title: GATA1_110C_revision

description: ChIP-seq


title: 114A_S8


title: 110G_S4


title: 110T_S5


title: GATA1_113G_revision

description: ChIP-seq


title: 110C_S7


title: GATA1_13nt_revision

description: ChIP-seq


title: NFYB_186T_13nt

description: ChIP-seq

growth_protocol: HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemCell SFEM with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin.

extract_protocol: Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing

value: NFYB


title: H2_HiC

description: HiC


title: GATA1_186T_110C_revision

description: ChIP-seq


title: GATA1_186T_13nt_revision

description: ChIP-seq


title: NFYB_13nt_dp

description: ChIP-seq


title: NFYB_13nt_input

description: ChIP-seq


title: NFYB_13nt_rep2

description: ChIP-seq


title: GATA1_186T_13nt_dp

description: ChIP-seq


title: 13nt_S1


title: GATA1_13nt_dp

description: ChIP-seq


title: NFYB_110C

description: ChIP-seq


title: GATA1_13nt_rep3

description: ChIP-seq


title: GATA1_13nt_input_rep2

description: ChIP-seq


title: NFYB_113G

description: ChIP-seq


title: NFYB_186T_13nt_dp

description: ChIP-seq


title: Itgam sgScrmbl 1

data_processing:
The reads are aligned to GrCM38 mouse genome using STAR (2.7.3)
The aligned reads were quantified using RSEM (v1.3)
Genome_build: GrCM38
Supplementary_files_format_and_content: Tab delimited gene expression table

value: WT C57Bl/6

tag: Sex

value: Female


title: NFYB_WT_input

description: ChIP-seq


title: GATA1_186T_13nt_rep2

description: ChIP-seq


title: GATA1_186T_113G

description: ChIP-seq


title: GATA1_WT

description: ChIP-seq


title: GATA1_WT_input

description: ChIP-seq


title: GATA1_13nt_rep1

description: ChIP-seq


title: GATA1_186T_13nt_rep1

description: ChIP-seq


title: GATA1_186T_110C

description: ChIP-seq


title: NFYB_WT

description: ChIP-seq


title: GATA1_113G_2

description: ChIP-seq


title: GATA1_13nt_input_rep1

description: ChIP-seq


title: GATA1_13nt_rep2

description: ChIP-seq


title: GATA1_110C_rep1

description: ChIP-seq


title: RRBS FoxA1L/L;FoxA2L;L;FoxA3-/- 7 days after GFP induction (control for FoxA triple null) - Sample 2

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Single-end RRBS runs were trimmed with trim galore (v.0.3.3), then we employed diversity trimming and filtering with NuGENs diversity trimming script trimRRBSdiversityAdaptCustomers.py. Read alignment (genome build mm9) and extraction of methylation levels were carried out by BSMAP v.2.74 (Xi and Li, 2009) using the following commands: bsmap -a sample_R1_val_1.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file. Percent methylation was calculated for 100 bp tiles with a minimum coverage of 10 CpGs. In order to examine methylation levels at hypermethylated sites in developmental FoxA double null of hepatocytes isolated from newborns, Tet2/3 ko, partial hepatectomy samples and FoxA triple null, we determined methylation levels of 100 bp tiles overlapping with these hypermethylated sites and took only tiles in which score was achieved among compared samples. We also rescored WGBS samples with the same parameters in order to get a comparable value. Heatmaps and dendrograms were generated with R library heatmap.2 and density plot were generated with stata – software for statistics and data science.
Genome_build: mm9
Genome_build: mm9

extract_protocol:
DNA was isolated from hepatocytes by DNeasy (Qiagen).
RRBS was performed using Ovation RRBS Methyl-Seq according to the manufacturer’s instruction. We used 100 ng hepatocyte DNA. Libraries were then amplified, purified, pooled, and sequenced on the Illumina HiSeq 4000 with 100 bp single-end sequencing with a minimum of 25 million reads per sample.

tag: age

value: 9 weeks old

value: Liver


title: RRBS FoxA triple null 7 days after Cre induction - sample 3


title: GATA1_110C_rep2

description: ChIP-seq


title: RRBS FoxA1L/L;FoxA2L;L;FoxA3-/- 7 days after GFP induction (control for FoxA triple null) - Sample 3


title: RRBS on control livers injected with AAV GFP followed by partial hepatectomy - Sample 1

value: 12 weeks old


title: NFYB_13nt_rep1

description: ChIP-seq


title: RRBS on control livers injected with AAV GFP followed by partial hepatectomy - Sample 2


title: GATA1_113G_rep1

description: ChIP-seq


title: RRBS FoxA double null in adulthood followed by partial hepatectomy - Sample 3


title: RRBS FoxA1L/L;FoxA2L;L;FoxA3-/- 7 days after GFP induction (control for FoxA triple null) - Sample 1


title: RRBS FoxA triple null 7 days after Cre induction - sample 2


title: RRBS FoxA triple null 7 days after Cre induction - sample 1


title: RRBS FoxA double null in adulthood followed by partial hepatectomy - Sample 2


title: ChIP Input on FoxA adukt double null - sample 2

data_processing:
Single-end sequencing reads were trimmed with Cutadapt and aligned to mouse genome (genome build mm9) using Bowtie2 version 2.3.4.1. PCR duplicates were removed using picard.jar tool and the command MarkDuplicates with the following flags:”REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. In order to compare differential binding between controls and FoxA double nulls in hyper- or isomethylated sites, we used DiffBind version 2.10.0 (Ross-Innes et al., 2012). Peaks were defined as ±250 base pairs from peak center. Bam files were converted to Bedgraph files after normalizing to 1 million reads per library using BEDtools (“genomecov”) and then converted to bigwig format using UCSC toolkit (“bedGraphToBigWig”). For control and FoxA triple null groups, an average bigwig file was also generated from the replicates (“bigWigMerge“).
Genome_build: mm9
Genome_build: mm9

source_name: ChIP Input on FoxA adukt double null

extract_protocol:
130 mg of frozen liver was minced in 2 mL of cold 1X DPBS (Thermo Fisher 14080055). The volumes of liver slices were brought up to 10 mL of 1X DPBS and 1% formaldehyde and incubated at room temperature for 8 minutes with rotation. Reaction was brought to 0.125 M glycine for quenching and incubated for 5 minutes at room temperature with rotation. Samples were centrifuged at 2,500 RCF for 2 minutes at 4°C, the supernatants discarded, and pellets washed with 1X DPBS. The pellet was resuspended in 1 mL of cold ChIP cell lysis buffer (10 mM Tris- HCl pH 8.0, 10 mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630, 1X cOmplete protease inhibitor cocktail) and transferred on ice to a 10 mL tissue grinder. The samples were homogenized 20 times with a smooth Teflon pestle and incubated at 4°C for 5 minutes. Following incubation the samples were centrifuged for 5 minutes at 17,000 RCF at 4°C, to pellet the nuclei. After the supernatant was discarded, and nuclei were resuspended in 1 mL of cold ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 5 mM EDTA, 1% SDS, 1X cOmplete protease inhibitor cocktail). Then, we performed two rounds of sonication using the Standard Biruptor (Diagenode UCD-200) with the following parameters: Intensity = High (H), Multitimer = OFF: 30 sec, ON: 30 sec, Total timer = 7.5 minutes with maintaining 4°C. Following sonication, samples were centrifuged at 17,000 RCF for 10 minutes at 4°C and supernatant was recovered. We isolated DNA from the sonicated chromatin to determine the amount of material required for precipitation. The DNA concentration was quantified using a NanoDrop-1000 (Thermo Fisher) and run on a BioAnalyzer High Sensitivity ChIP to estimate the length distribution. Then, 10 μg of sonicated chromatin was added to 1 mL of ChIP dilution buffer (16. mM Tris-HCl pH 8.0, 167 mM NaCl, 0.01% SDS, 1.1% Triton-X 100, 1X cOmplete protease inhibitor cocktail). 3 μg of the following antibodies, H3K27ac (Active Motif 39133) and HNF4a (Abcam ab181604), were added to the samples and the samples were incubated at 4°C overnight with rotation. 40 μL of recombinant protein G agarose beads (Thermo Fisher) were washed three times with 1 mL of ChIP dilution buffer. Next, the beads were resuspended in 75 μL of ChIP Dilution Buffer and 5 μL of BSA (New England BioLabs) and incubated at 4°C overnight with   rotation for blocking. Then chromatin samples were added to the blocked beads and incubated at 4°C for 1 hour with rotation. Samples were centrifuged at 100 RCF for 30 seconds and the supernatant was discarded. The beads were then washed sequentially with each of the following buffers by resuspending the beads in 1 mL of buffer, incubating beads at room temperature for 5 minutes with rotation, pelleting beads, and discarding supernatant: TSE I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), TSE II ( 20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), ChIP Buffer III (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% IGEPAL CA-630, 1% Sodium Deoxycholate), TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After the washes, the beads were resuspended in 100 μL of elution buffer (0.1 M NaHCO3, 1% SDS) and incubated at room temperature for 15 minutes with rotation. 4 μL of 5M NaCl was added to the supernatant and then samples were incubated at 65°C overnight. Next, DNA was isolated from the samples using Minielute (Quiagen). Enrichment of IP samples was measured through qPCR using the following program: 95°C for 3 minutes, for 40 cycles, 95°C for 5 seconds, 60°C for 20 seconds.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were sequenced on the Illumina Hiseq 4000 with 50 bp single-end sequencing with a minimum of 20 million reads per sample.

value: 8 weeks old


title: RRBS FoxA double null in adulthood followed by partial hepatectomy - Sample 1


title: ChIP Input on FoxA adukt double null - sample 3


title: ChIP Input on FoxA1L/L;FoxA2L/L - sample 3

source_name: ChIP Input on FoxA1L/L;FoxA2L/L


title: ChIP Input on FoxA adukt double null - sample 1


title: ChIP HNF4a on FoxA1L/L;FoxA2L/L - sample 3

source_name: ChIP HNF4a on FoxA1L/L;FoxA2L/L


title: ChIP HNF4a on FoxA adukt double null - sample 1

source_name: ChIP HNF4a on FoxA adukt double null


title: ChIP Input on FoxA1L/L;FoxA2L/L - sample 2


title: ChIP HNF4a on FoxA Dev double null - sample 1

source_name: ChIP HNF4a on FoxA Dev double null


title: ChIP Input on FoxA Dev double null - sample 3

source_name: ChIP Input on FoxA Dev double null


title: ChIP Input on FoxA Dev double null - sample 2


title: ChIP Input on FoxA Dev double null - sample 1


title: ChIP HNF4a on FoxA adukt double null - sample 2


title: ChIP HNF4a on FoxA1L/L;FoxA2L/L - sample 2


title: ChIP HNF4a on FoxA1L/L;FoxA2L/L - sample 1


title: Nrf2 KO Untreated d0 after PHx_2

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

data_processing:
Base-calling and de-multiplexing of indexed reads was performed by CASAVA v1.8.2 (Illumina, UK). The raw fastq files were trimmed to remove Illumina adapter sequences using Cutadapt version 1.2.1 (Martin, 2011). The option “-O 3” was set, so the 3' end of any reads which matched the adapter sequence over at least 3 bp was trimmed off. The reads were further trimmed to remove low quality bases, using Sickle version 1.200 with a minimum window quality score of 20. After trimming, reads shorter than 10 bp were removed.
Alignment to the reference genome GRCm38.p5 was carried out using TopHat2 version 2.1.0. Reads aligning to the reference genome sequences were counted using HTSeq-count version 0.6.1p1.
Normalised gene expression values (fragments per kilobase million; FPKM) were then computed from counts and annotated gene features. The “median ratio method” in DESeq2 package was applied, with default parameters.
Differential gene expression analysis was applied to the read count data with a false discovery rate threshold of < 5 %.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalised gene expression (FPKM) for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was isolated from snap frozen liver tissue using an RNeasy Mini kit (Qiagen, UK). Ribosomal RNA was removed from 1 µg of total RNA using a Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, UK).
RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, UK) and purified using AMPure XP beads (Beckman Coulter, UK). RNA-Seq was carried out on three lanes of an Illumina HiSeq 4000 at 2x150 bp paired-end sequencing with v1 chemistry.

treatment_protocol: Mice were administered 3 mg/kg CDDO-Me (Cayman Chemical, USA) or 1 μL/g dimethyl sulfoxide (DMSO) by intra-peritoneal injection 24 h and 1 h prior to two-thirds PHx (days -1 and 0, respectively), or left untreated. CDDO-Me was solubilised in 100 % DMSO. Mice were subjected to partial hepatectomy (PHx) on day 0.

tag: strain

value: liver

tag: genotype

tag: treatment

value: Untreated

tag: days after phx


title: Nrf2 KO CDDO-Me d0 after PHx_3

tag: tissue

value: CDDO-Me


title: Nrf2 WT CDDO-Me d0 after PHx_4

value: wild type


title: ChIP HNF4a on FoxA Dev double null - sample 3


title: ChIP HNF4a on FoxA Dev double null - sample 2


title: Nrf2 WT CDDO-Me d0 after PHx_3


title: ChIP Input on FoxA1L/L;FoxA2L/L - sample 1


title: Nrf2 KO CDDO-Me d0 after PHx_4


title: Nrf2 KO CDDO-Me d0 after PHx_1


title: Nrf2 KO Untreated d0 after PHx_4


title: Nrf2 KO Untreated d0 after PHx_3


title: Nrf2 KO Untreated d0 after PHx_1


title: Nrf2 WT CDDO-Me d0 after PHx_2


title: Nrf2 KO CDDO-Me d0 after PHx_2


title: Nrf2 WT DMSO d0 after PHx_4

value: DMSO


title: Nrf2 WT DMSO d0 after PHx_3


title: Nrf2 WT CDDO-Me d0 after PHx_1


title: Nrf2 WT DMSO d0 after PHx_2


title: Nrf2 WT DMSO d0 after PHx_1


title: IgG control in terminally dysfunctional CD8 T cells at d35 from LCMV clone 13 infected B6 mice, rep1

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
CUTRUN_IgG_r1
tcf1-targets.txt.gz

data_processing:
Library strategy: CUT&RUN
scATAC-seq:
The data was preprocessed with cellranger-atac from 10X. Then using the BAM files with read alignments for the two samples produced by cellranger-atac, peaks were detected using MACS2. An extended list of peaks was formed by combining the previously constructed bulk ATAC-seq peaks with the non-overlapping newly identified peaks. The cellranger-atac tool was then rerun with this extended peak list as input to obtain a count matrix for each of the two samples.
scRNA-seq:
We analyzed scRNA-seq data from the six samples labeled “acute_d00”, “acute_d07”, “acute_d60”, “chronic_d07”, “chronic_d35”, “chronic_d35_b6”. Reads were aligned to the combined B6 and Spret genome using hisat2 v2.1.0. For this, files Mus_musculus.GRCm38.dna.toplevel.fa.gz and Mus_spretus_spreteij.SPRET_EiJ_v1.dna.toplevel.fa.gz with genomic sequences of B6 and Spret mice, respectively, were obtained from NCBI FTP server, and hisat2 index for the chromosomes from both files was constructed. Using the BAM files of scRNA-seq read alignment, UMI counts for each gene in B6 and Spret genomes were obtained using a custom script, by overlapping read alignments with exonic annotations of genes in either B6 or Spret and counting UMI corrected using the method from seqc. For this, files Mus_musculus.GRCm38.91.gtf.gz and Mus_spretus_spreteij.SPRET_EiJ_v1.86.gtf.gz with gene annotations for B6 and Spret genomes, respectively, were obtained from NCBI FTP server.
CUT&RUN:
CUT&RUN reads from B6 mouse samples were aligned to the genome using bowtie2 v2.3.4.3. Similar to RNA-seq, paired-end CUT&RUN reads from F1 B6/Spret mouse samples were mapped to the diploid genome using STAR with the splicing alignment feature switched off. The command line was as follow: $STAR --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMatchNmin 40 --outBAMcompression 6 --outFilterMatchNminOverLread 0.4 --seedSearchStartLmax 20 --alignIntronMax 1 --alignEndsType Local. We only used the read pairs if their fragment length is between 50 to 500 bp.
For analysis, we used two control IgG samples and biological replicates for TCF1 CUT&RUN, including two from B6 mice and two samples from F1 B6/Spret mice. CUT&RUN and control reads were counted in 150bp windows around ATAC-seq peak summits. To estimate library sizes, control regions were obtained by shifting ATAC-seq peak summit regions by 2Kb in either direction, extending the shifted segments by 500bp preserving their center, and excluding those that overlapped with ATAC-seq peak summit regions, and then calculating control and CUT&RUN read counts in these control regions and using DESeq2 v1.22.2, as described previously. Differential CUT&RUN count analysis was then run using DESeq2, identifying 3325 TCF1 binding sites in the progenitor dysfunctional cells defined as ATAC-seq peak summit regions with significantly higher TCF1 CUT&RUN read counts than IgG control (adjusted p-value < 0.1).
Genome_build: B6 (mm10) or F1 B6/Spret
Supplementary_files_format_and_content: scATAC_matrix.mtx, scATAC_peaks.bed, scATAC_barcodes.tsv: scATAC-seq count matrix with the corresponding peaks and barcodes, as produced by cellranger-atac, suffix -1 is for cells from Armstrong infection, suffix -2 is for cells from clone 13 infection
cd8t_scRNA_counts.txt: scRNA-seq count matrix (Note:  This scRNA-seq data is in F1 cross, so required custom scripts to process the data and produce count matrix. (The code will be released along with the publication.) Early in the preprocessing, sequence barcodes are substituted to integer IDs for cells. A combination of sample and integer ID forms a unique cell ID and is stored as cell ID in the count matrix.)
tcf1-targets.txt: the table with TCF1 peaks in progenitor dysfunctional cells obtained using differential count analysis in CUT&RUN vs. IgG control samples using DESeq2 (columns 1-3: genomic coordiantes, column 4: unique ID, columns 5-6: gene annotations, columns 7-10: DESeq2 results, column 11: presence of TCF1 motif)

source_name: CD8 T cells

growth_protocol: Mice were housed at the Memorial Sloan Kettering Cancer Center animal facility under specific pathogen free (SPF) conditions on a 12-hour light/dark cycle under ambient conditions with free access to food and water. All studies were performed under protocol 08-10-023 and approved by the MSKCC Institutional Animal Care and Use Committee. Mice used in this study had no previous history of experimentation or exposure to drugs. Male Spret/EiJ mice were purchased from Jackson laboratory and bred to female CD45.1 mice on a C57BL/6 genetic background. Adult (at least 8 weeks old) male and female F1 offspring were used for experiments as indicated.

extract_protocol:
scRNA-seq:
Acute infection: Splenocytes were stained with a cocktail of fluorescent antibodies, NP396 tetramer, and viability dye to mark dead cells, and sorted using flow cytometry. Naïve CD8 T cells were isolated from pooled spleens of 2 uninfected mice as CD44-CD62L+ CD8 T cells. Activated and memory effector cells were isolated as NP396+ CD8 T cells from pooled splenocytes of 2 or 3 mice on day 7 or day 40 post-infection, respectively and used as input for scRNA-seq analysis.
Chronic infection: Mice were depleted of CD4 T cells by injection of 200ug aCD4 antibody (BioXCell cat: BE0003-1) one day prior to and one day post-infection. Cells were isolated as live CD62L- CD8 T cells from spleens of 3 pooled mice per group and used as input for scRNA-seq analysis.
scRNA-seq after adoptive transfer of progenitor dysfunctional cells:
On day 7 post-infection donor cells were re-isolated based on expression of congenic markers and prepared for scRNA-seq.
scATAC-seq:
On day 7 post-infection, total CD8 T cells from pooled spleens were double sorted by flow cytometry and prepared for single cell ATAC-seq analysis.
CUT&RUN:
Terminal and progenitor dysfunctional cells were isolated from the spleens of 4 male B6/Spret F1 mice or B6 mice on day 35 post-infection, based on expression of cell surface markers.
scATAC-seq:
scATAC-seq was performed using Chromium instrument (10x Genomics) and Single Cell ATAC Reagent Kits (Chemistry v1). The suspension of cells was processed following the User Guide (CG000168 Rev A). Briefly, cells were lysed in bulk, washed and resulting nuclei suspension treated with ATAC reagents provided in the kit. Approximately, 8000 nuclei per sample were loaded onto microfluidics Chip E and encapsulated with DNA barcodes and reaction mix. Following emulsion-PCR the resulting material was purified and subjected to 12-cycles of indexing PCR. The indexed scATAC-Seq libraries were double-size selected using SPRI beads and sequenced on an Illumina NovaSeq 6000 instrument (Read 1 – 50 cycles, i7 index – 8 cycles, i5 index  – 16 cycles, and Read 2  – 50 cycles) at 125M reads per sample.
scRNA-seq:
Single-cell suspensions were loaded on 10x Genomics Chromium instrument and encapsulated in microfluidic droplets with barcoded DNA hydrogel beads and RT reagents from Chromium Single Cell 3’ Reagent kit (v3). The cDNA synthesis/barcoding was performed following manufacturer’s instructions: 53°C for 45 min followed by heat inactivation at 85°C for 5 min. The barcoded-cDNA was purified and PCR-amplified and prepared for sequencing according to the Single Cell 3′Reagent kit 3 User Guide (CG000183; Rev B). The DNA sequencing was performed on the Illumina NovaSeq 6000 instrument (R1 read – 26 cycles, R2 read – 70 cycles or higher, and index read – 8 cycles), aiming for ∼200 million reads per ~5,000 single cells.
CUT&RUN:
CUT&RUN libraries were prepared as described (83) with the modifications described below. Because Concanavalin-A (ConA) is a well-known T cell mitogen, we avoided the use of ConA-coated beads for cell isolation and handling. 70k cells per replicate were collected in a V-bottom 96 well plate by centrifugation and washed in antibody buffer (buffer 1 (1x permeabilization buffer from eBioscience Foxp3/Transcription Factor Staining Buffer Set diluted in nuclease free water, 1X EDTA-free protease inhibitors, 0.5mM spermidine) containing 2mM EDTA). Cells were incubated with TCF1 antibody for 1h on ice. After 2 washes in buffer 1, cells were incubated with pA/G-MNase at 1:4000 dilution in buffer 1 for 1h at 4 degrees. Cells were washed twice in buffer 2 (0.05% (w/v) saponin, 1X EDTA-free protease inhibitors, 0.5mM spermidine in PBS) and resuspended in calcium buffer (buffer 2 containing 2mM CaCl2) to activate MNase. Following a 30 minute incubation on ice, 2x stop solution (20mM EDTA, 4mM EGTA in buffer 2) was added and cells were incubated for 10 minutes in a 37 degree incubator to release cleaved chromatin fragments. Supernatants were collected by centrifugation and DNA was extracted using a Qiagen MinElute kit.
CUT&RUN libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems KK8504) and Kapa UDI Adapter Kit (Kapa Biosystems KK8727) according to manufacturers protocol with the modifications described below. A-tailing temperature was reduced to 50 degrees to avoid melting of short DNA fragments and reaction time was increased to 1h to compensate for reduced enzyme activity as described by Liu et al. 2018. Following the adapter ligation step, 3 consecutive rounds of Ampure purification were performed using a 1.4x bead to sample ratio to remove excess unligated adapters while retaining short adapter-ligated fragments. Libraries were amplified for an average of 15 cycles using a 10 second 60 °C annealing/extension step to enrich for shorter library fragments. Following amplification, libraries were purified using 3 consecutive rounds of Ampure purification with a 1.2x bead to sample ratio to remove amplified primer dimers while retaining short library fragments. A 0.5x Ampure purification step was included to remove large fragments prior to sequencing.
scATAC-seq, scRNA-seq, CUT&RUN

treatment_protocol:
scATAC-seq:
Four male C57BL/6J mice per group were infected with either LCMV Armstrong (2x10^5 p.f.u. via intraperitoneal injection) or LCMV Clone 13 (2x106 p.f.u. via retroorbital injection).
scRNA-seq:
For isolation of CD8 T cells responding to acute infection, B6/Spret F1 mice, where B6 stands for C57BL/6J and Spret stands for SPRET/EiJ, were infected with 2x10^5 p.f.u. of LCMV Armstrong via intraperitoneal injection or left uninfected.
For isolation of cells responding to chronic infection, B6/Spret F1 or B6 mice were infected with LCMV clone 13 by retroorbital injection of 4x10^6 p.f.u. of virus.
scRNA-seq after adoptive transfer of progenitor dysfunctional cells:
Four C57BL/6J mice were infected with LCMV Clone 13 (2x106 p.f.u. via retroorbital injection). On day 35 post-infection, splenocytes were pooled and stained using a cocktail of fluorescently labeled antibodies and Ghostdye Violet 510 (Tonbo cat: 13-0870-T100) to distinguish dead cells. Dysfunctional progenitor cells were isolated by flow cytometry-based sorting as PD1+, CD73+, CD39- CD8 T cells. This population was also CD9+ and CD38 low. 50,000 dysfunctional precursor cells/recipient were transferred into 4 CD45.1/CD45.2 mice via retroorbital injection. Recipients were infected with LCMV Armstrong (2x105 p.f.u. via intraperitoneal injection).
CUT&RUN:
B6/Spret F1 or B6 mice were infected with LCMV clone 13 by retroorbital injection of 4x10^6 p.f.u. of virus.

tag: cell type

value: PD1+, CD73-, CD39+ CD8 T cells

tag: infection


title: IgG control in terminally dysfunctional CD8 T cells at d35 from LCMV clone 13 infected B6 mice, rep2

description:
CUTRUN_IgG_r2
tcf1-targets.txt.gz


description:
scRNA_chronic_d35_b6
scRNA-seq in CD8 T cells at d35 from LCMV clone 13 infected B6 mice
cd8t_scRNA_counts.txt.gz

data_processing:
scATAC-seq:
The data was preprocessed with cellranger-atac from 10X. Then using the BAM files with read alignments for the two samples produced by cellranger-atac, peaks were detected using MACS2. An extended list of peaks was formed by combining the previously constructed bulk ATAC-seq peaks with the non-overlapping newly identified peaks. The cellranger-atac tool was then rerun with this extended peak list as input to obtain a count matrix for each of the two samples.
scRNA-seq:
We analyzed scRNA-seq data from the six samples labeled “acute_d00”, “acute_d07”, “acute_d60”, “chronic_d07”, “chronic_d35”, “chronic_d35_b6”. Reads were aligned to the combined B6 and Spret genome using hisat2 v2.1.0. For this, files Mus_musculus.GRCm38.dna.toplevel.fa.gz and Mus_spretus_spreteij.SPRET_EiJ_v1.dna.toplevel.fa.gz with genomic sequences of B6 and Spret mice, respectively, were obtained from NCBI FTP server, and hisat2 index for the chromosomes from both files was constructed. Using the BAM files of scRNA-seq read alignment, UMI counts for each gene in B6 and Spret genomes were obtained using a custom script, by overlapping read alignments with exonic annotations of genes in either B6 or Spret and counting UMI corrected using the method from seqc. For this, files Mus_musculus.GRCm38.91.gtf.gz and Mus_spretus_spreteij.SPRET_EiJ_v1.86.gtf.gz with gene annotations for B6 and Spret genomes, respectively, were obtained from NCBI FTP server.
CUT&RUN:
CUT&RUN reads from B6 mouse samples were aligned to the genome using bowtie2 v2.3.4.3. Similar to RNA-seq, paired-end CUT&RUN reads from F1 B6/Spret mouse samples were mapped to the diploid genome using STAR with the splicing alignment feature switched off. The command line was as follow: $STAR --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMatchNmin 40 --outBAMcompression 6 --outFilterMatchNminOverLread 0.4 --seedSearchStartLmax 20 --alignIntronMax 1 --alignEndsType Local. We only used the read pairs if their fragment length is between 50 to 500 bp.
For analysis, we used two control IgG samples and biological replicates for TCF1 CUT&RUN, including two from B6 mice and two samples from F1 B6/Spret mice. CUT&RUN and control reads were counted in 150bp windows around ATAC-seq peak summits. To estimate library sizes, control regions were obtained by shifting ATAC-seq peak summit regions by 2Kb in either direction, extending the shifted segments by 500bp preserving their center, and excluding those that overlapped with ATAC-seq peak summit regions, and then calculating control and CUT&RUN read counts in these control regions and using DESeq2 v1.22.2, as described previously. Differential CUT&RUN count analysis was then run using DESeq2, identifying 3325 TCF1 binding sites in the progenitor dysfunctional cells defined as ATAC-seq peak summit regions with significantly higher TCF1 CUT&RUN read counts than IgG control (adjusted p-value < 0.1).
Genome_build: B6 (mm10) or F1 B6/Spret
Supplementary_files_format_and_content: scATAC_matrix.mtx, scATAC_peaks.bed, scATAC_barcodes.tsv: scATAC-seq count matrix with the corresponding peaks and barcodes, as produced by cellranger-atac, suffix -1 is for cells from Armstrong infection, suffix -2 is for cells from clone 13 infection
cd8t_scRNA_counts.txt: scRNA-seq count matrix (Note:  This scRNA-seq data is in F1 cross, so required custom scripts to process the data and produce count matrix. (The code will be released along with the publication.) Early in the preprocessing, sequence barcodes are substituted to integer IDs for cells. A combination of sample and integer ID forms a unique cell ID and is stored as cell ID in the count matrix.)
tcf1-targets.txt: the table with TCF1 peaks in progenitor dysfunctional cells obtained using differential count analysis in CUT&RUN vs. IgG control samples using DESeq2 (columns 1-3: genomic coordiantes, column 4: unique ID, columns 5-6: gene annotations, columns 7-10: DESeq2 results, column 11: presence of TCF1 motif)

value: CD62L- CD8 T cells


description:
scRNA_chronic_d35
scRNA-seq in CD8 T cells at d35 from LCMV clone 13 infected F1 B6/Spret mice
cd8t_scRNA_counts.txt.gz

value: F1 B6/Spret


title: TCF1 CUT&RUN in progenitor dysfunctional CD8 T cells at d35 from LCMV clone 13 infected B6 mice, rep2

description:
CUTRUN_TCF1_b6_r2
tcf1-targets.txt.gz

value: PD1+, CD73+, CD39- CD8 T cells


description:
scRNA_acute_d40
scRNA-seq in CD8 T cells at d40 from LCMV Armstrong infected F1 B6/Spret mice
cd8t_scRNA_counts.txt.gz

value: NP396+ CD8 T cells


description:
scRNA_chronic_d07
scRNA-seq in CD8 T cells at d07 from LCMV clone 13 infected F1 B6/Spret mice
cd8t_scRNA_counts.txt.gz


title: scRNA-seq in CD8 T cells (obtained from LCMV clone 13 infected B6 mice) at d07 from LCMV Armstrong infected B6 mice

description:
scRNA_transfer_acute_d07
scRNA-seq in expanded transferred progenitor dysfunctional CD8 T cells (obtained at d35 from LCMV clone 13 infected B6 mice) at d07 from LCMV Armstrong infected B6 mice
cd8t_scRNA_counts.txt.gz

value: donor CD8 T cells


title: TCF1 CUT&RUN in progenitor dysfunctional CD8 T cells at d35 from LCMV clone 13 infected B6 mice, rep1

description:
CUTRUN_TCF1_b6_r1
tcf1-targets.txt.gz


description:
scRNA_acute_d07
scRNA-seq in CD8 T cells at d07 from LCMV Armstrong infected F1 B6/Spret mice
cd8t_scRNA_counts.txt.gz


description:
scRNA_uninfected
scRNA-seq in CD8 T cells from uninfected F1 B6/Spret mice
cd8t_scRNA_counts.txt.gz

value: CD44-CD62L+ CD8 T cells


title: P60_2_P22

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCm38.p5 genome assembly using STAR 2.6.1c with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.4
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Sciatic nerve

tag: biological replicate

value: Schwann cells

value: postnatal day 60


title: P60_2_P19


title: P60_2_P17


description:
scATAC_acute_d07
scATAC-seq in CD8 T cells at d07 from LCMV Armstrong infected in B6 mice
scATAC_matrix.mtx.gz
scATAC_barcodes.tsv.gz
scATAC_peaks.bed.gz

value: CD8 T cells


title: P60_2_P24


title: TCF1 CUT&RUN in progenitor dysfunctional CD8 T cells at d35 from LCMV clone 13 infected F1 B6/Spret mice, rep2

description:
CUTRUN_TCF1_r2
tcf1-targets.txt.gz


title: P60_2_P23


title: P60_2_P20


title: P60_2_P21


description:
scATAC_chronic_d07
scATAC-seq in CD8 T cells at d07 from LCMV clone 13 infected in B6 mice
scATAC_matrix.mtx.gz
scATAC_barcodes.tsv.gz
scATAC_peaks.bed.gz


title: P60_2_P18


title: TCF1 CUT&RUN in progenitor dysfunctional CD8 T cells at d35 from LCMV clone 13 infected F1 B6/Spret mice, rep1

description:
CUTRUN_TCF1_r1
tcf1-targets.txt.gz


title: P60_2_P14


title: P60_2_P15


title: P60_2_P16


title: P60_2_P12


title: P60_2_P10


title: P60_2_P08


title: P60_2_P05


title: P60_2_P04


title: P60_2_P01


title: P60_2_P13


title: P60_2_P02


title: P60_2_P11


title: P60_2_P09


title: P60_2_O22


title: P60_2_P06


title: P60_2_O24


title: P60_2_O23


title: P60_2_O15


title: P60_2_O20


title: P60_2_O21


title: P60_2_O18


title: P60_2_O19


title: P60_2_O11


title: P60_2_O13


title: P60_2_O14


title: P60_2_O16


title: P60_2_P07


title: P60_2_O09


title: P60_2_O06


title: P60_2_O08


title: P60_2_O12


title: P60_2_O05


title: P60_2_O07


title: P60_2_O10


title: P60_2_O17


title: P60_2_P03


title: P60_2_O01


title: P60_2_O04


title: P60_2_N23


title: P60_2_O03


title: P60_2_O02


title: P60_2_N24


title: P60_2_N22


title: P60_2_N21


title: P60_2_N20


title: P60_2_N18


title: P60_2_N19


title: P60_2_N17


title: P60_2_N16


title: P60_2_N15


title: P60_2_N12


title: P60_2_N13


title: P60_2_N10


title: P60_2_N14


title: P60_2_N07


title: P60_2_N05


title: P60_2_N08


title: P60_2_N01


title: P60_2_M24


title: P60_2_N11


title: P60_2_M23


title: P60_2_N02


title: P60_2_N09


title: P60_2_M19


title: P60_2_M18


title: P60_2_M15


title: P60_2_M12


title: P60_2_N06


title: P60_2_M11


title: P60_2_M07


title: P60_2_M05


title: P60_2_M02


title: P60_2_N04


title: P60_2_L23


title: P60_2_L22


title: P60_2_L20


title: P60_2_M22


title: P60_2_M21


title: P60_2_M17


title: P60_2_L16


title: P60_2_M16


title: P60_2_M14


title: P60_2_L09


title: P60_2_L08


title: P60_2_M13


title: P60_2_M10


title: P60_2_L03


title: P60_2_M09


title: P60_2_M08


title: P60_2_N03


title: P60_2_M06


title: P60_2_M04


title: P60_2_M03


title: P60_2_M01


title: P60_2_L24


title: P60_2_L05


title: P60_2_L21


title: P60_2_L19


title: P60_2_L18


title: P60_2_M20


title: P60_2_L17


title: P60_2_K19


title: P60_2_K15


title: P60_2_K14


title: P60_2_K13


title: P60_2_L15


title: P60_2_L14


title: P60_2_L13


title: P60_2_K12


title: P60_2_L11


title: P60_2_L10


title: P60_2_K11


title: P60_2_L07


title: P60_2_L06


title: P60_2_L04


title: P60_2_K20


title: P60_2_K10


title: P60_2_K08


title: P60_2_K07


title: P60_2_L02


title: P60_2_L12


title: P60_2_L01


title: P60_2_K06


title: P60_2_K24


title: P60_2_K23


title: P60_2_K04


title: P60_2_K03


title: P60_2_K01


title: P60_2_K22


title: P60_2_K21


title: P60_2_J24


title: P60_2_J23


title: P60_2_J22


title: P60_2_J20


title: P60_2_J18


title: P60_2_J16


title: P60_2_J15


title: P60_2_J14


title: P60_2_J05


title: P60_2_J04


title: P60_2_J08


title: P60_2_K18


title: P60_2_J01


title: P60_2_J03


title: P60_2_K17


title: P60_2_K16


title: P60_2_I23


title: P60_2_I22


title: P60_2_I21


title: P60_2_I19


title: P60_2_I18


title: P60_2_I24


title: P60_2_I17


title: P60_2_I16


title: P60_2_I15


title: P60_2_I13


title: P60_2_I10


title: P60_2_I09


title: P60_2_I20


title: P60_2_I07


title: P60_2_I05


title: P60_2_K05


title: P60_2_I03


title: P60_2_I12


title: P60_2_I02


title: P60_2_K02


title: P60_2_I08


title: P60_2_H24


title: P60_2_H23


title: P60_2_H22


title: P60_2_H19


title: P60_2_H15


title: P60_2_H12


title: P60_2_H11


title: P60_2_H10


title: P60_2_H09


title: P60_2_H18


title: P60_2_K09


title: P60_2_J21


title: P60_2_J19


title: P60_2_H07


title: P60_2_J17


title: P60_2_H06


title: P60_2_H05


title: P60_2_H04


title: P60_2_H03


title: P60_2_J13


title: P60_2_J12


title: P60_2_J10


title: P60_2_J06


title: P60_2_J07


title: P60_2_J11


title: P60_2_J09


title: P60_2_G20


title: P60_2_J02


title: P60_2_G18


title: P60_2_I11


title: P60_2_I14


title: P60_2_I06


title: P60_2_I04


title: P60_2_G17


title: P60_2_I01


title: P60_2_G16


title: P60_2_H17


title: P60_2_H20


title: P60_2_H13


title: P60_2_H14


title: P60_2_G15


title: P60_2_G14


title: P60_2_H16


title: P60_2_G13


title: P60_2_H21


title: P60_2_H08


title: P60_2_G11


title: P60_2_H02


title: P60_2_G24


title: P60_2_H01


title: P60_2_G23


title: P60_2_G06


title: P60_2_G08


title: P60_2_G21


title: P60_2_G07


title: P60_2_G05


title: P60_2_G22


title: P60_2_G04


title: P60_2_G19


title: P60_2_G01


title: P60_2_F23


title: P60_2_G02


title: P60_2_G12


title: P60_2_F20


title: P60_2_F21


title: P60_2_F19


title: P60_2_F18


title: P60_2_G09


title: P60_2_G10


title: P60_2_F24


title: P60_2_F16


title: P60_2_G03


title: P60_2_F17


title: P60_2_F22


title: P60_2_F14


title: P60_2_F13


title: P60_2_F11


title: P60_2_F12


title: P60_2_F15


title: P60_2_F10


title: P60_2_F09


title: P60_2_F04


title: P60_2_F06


title: P60_2_F07


title: P60_2_F03


title: P60_2_F05


title: P60_2_F08


title: P60_2_E23


title: P60_2_E21


title: P60_2_F01


title: P60_2_E13


title: P60_2_E15


title: P60_2_E18


title: P60_2_E20


title: P60_2_E17


title: P60_2_E16


title: P60_2_F02


title: P60_2_E19


title: P60_2_E14


title: P60_2_E24


title: P60_2_E06


title: P60_2_E12


title: P60_2_E11


title: P60_2_D24


title: P60_2_E01


title: P60_2_D23


title: P60_2_E10


title: P60_2_D19


title: P60_2_D15


title: P60_2_E09


title: P60_2_D17


title: P60_2_E08


title: P60_2_D16


title: P60_2_E22


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title: N701_S502


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title: N701_S505


title: N701_S506


title: P14_2_P24

value: postnatal day 14


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title: N701_S513


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title: P14_2_C17


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