title: Cyclophosphamide_4-cycles_pool2

description:
polyA-selected RNA, stranded library
G170_M14


title: Control TFR, rep1

status: Public on Mar 17 2022

type: SRA

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

country: USA

institute: UIC

library_source: transcriptomic

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: quant_counts.txt

molecule: total RNA

organism: Mus musculus

source_name: TFR cells sorted from control mice

growth_protocol: 23 weeks old female NZBWF1/j mice were used in this study.

extract_protocol:
Total RNA was purified from Tconv, Treg, TFH and TFR cells sorted from control and OX40L-JAG1 treated mice using Qiagen RNeasy kit with inclusion of on-column DNase treatment step.
CORALL prep kit (Lexogen) with RiboCop rRNA depletion kit (Lexogen)
Total RNA-seq

treatment_protocol: Mice were injected (i.p.) with recombinant mouse OX40L (2mg/kg body weight) and mouse JAG1 (2mg/kg body weight)  once a week for three consecutive weeks. Age and sex-matched control mice received PBS.

tag: strain

tag: Sex

value: female

tag: age

value: 23 weeks old

tag: treatment

value: control

tag: cell type

value: TFR cells


title: OX40L-JAG1 TFR, rep3

source_name: TFR cells sorted from OX40L-Jagged-1 treated mice

value: OX40L-Jagged-1 treated


title: AB51

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt]  single cell expression matrix include mRNA molecule count values for each Sample
[metadata_s.txt]  Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Foxa2-Venus mouse embryos

extract_protocol:
Embryos were dissociated with Accutase (Sigma) into singlet cells immediately after collection, the in vitro differentiated cells were dissociated by 0.1% trypsin.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

tag: developmental stage

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: Apoe_minus_minus_M_plus_5

city: New York

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 3h myelin treatment, cells were collected at 24h

data_processing:
Normalized libraries were sequenced as paired-end 150bp reads (15-20 million reads/sample) on the Illumina HiSeq 4000
Reads were screened and trimmed for adaptor contamination and paired-end sequencing reads were pseudoaligned to the Gencode m
Expression was quantified and normalized as transcripts per million (TPM) using Salmon (version 0.13.1)
Genome_build: mm10 transcriptome (version M20)
Supplementary_files_format_and_content: Differentially expressed protein-coding genes (DEGs) across comparisons of interest were identified by using the limma (version 3.40.6) package in the R programming environment (version 3.6.3)

source_name: Forebrain primary microglia

growth_protocol: Microglia cells were cultured in DMEM containing 10% fetal bovine serum (FBS, Gibco #16140), and 100µg/ml penicillin/streptomycin (Pen/Strep, Gibco #15140)

extract_protocol:
RNA was extracted using the RNeasy (Qiagen) kit following manufacturer's guidelines
Libraries were prepared from polyA-enriched mRNA using the universal low-input kit (SMARTer #634940), validated using Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystem, Wilmington, MA, USA).

treatment_protocol: Microglia were either left untreated or were challenged with myelin for 3 hours as in our phagocytosis experiment and were collected 21 hours later for RNA-sequencing

tag: strain model no.

value: Jackson Laboratory, 002052

value: Myelin treated


title: Cyclophosphamide_7-cycles_pool1

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
polyA-selected RNA, stranded library
G170_M16

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (ratio, fold-change, FPKM for treated sample (Intensity-1), FPKM for vehicle control (Intensity-2), adjusted p-value) for 4 pairwise comparisons: Cyclophosphamide_2-cycles vs Vehicle control, Cyclophosphamide_4-cycles vs Vehicle control, Cyclophosphamide_7-cycles vs Vehicle control, and Cyclophosphamide_4-cycles-then-regrowth vs Vehicle control, respectively numbered as Experiments # 700, 701, 702 and 703.

source_name: 4T1 tumor tissue_total RNA fraction

growth_protocol: 7-week-old female BALB/c mice (Taconic Farms, Germantown, NY) were were implanted with 4T1 tumor cells (approx. 100,000/mouse) resuspended in 0.1 ml PBS were inoculated into the fourth mammary fat pad. Tumor growth was monitored every 3 d using a vernier caliper, and tumor volumes were calculated: Volume = (π/6) x (L x W)3/2.

extract_protocol:
Tumors were excised, washed with PBS and flash-frozen in liquid nitrogen after placing ~1/3 piece of fresh tumor in 1 mL TRIzol for immediate downstream extraction of tumor RNA.
Polyadenylated mRNA was isolated from 1 μg of total tumor RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs) and used for lllumina RNA-seq library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (cat. #E7420L, New England Biolabs), NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (cat. #E7600, New England Biolabs), and AMPure® XP Beads (cat. #A63881, Beckman Coulter Inc., Indianapolis, IN) per the manufacturer’s instructions.

treatment_protocol: Mice were randomized into two groups, cyclophosphamide (treatment) and PBS vehicle (control), when average tumor volumes reached 100-150 mm3. Cyclophosphamide (cat. # C0768, Sigma-Aldrich, St. Louis, MO) dissolved in sterile PBS and passed through a 0.2 µm filter was then injected i.p. at 0 (vehicle control) or 130 mg/kg. CPA injections were repeated every 6 days for a total of 2, 4 or 7 treatment cycles, at which point the mice were euthanized and tumors were excised. Where indicated, treatment was halted after 4 treatment cycles, and the tumor were allowed to grow for a further 18 days, during which time substantial tumor regrowth was observed.

value: BALB/c

value: Female

value: 14-15 weeks

value: Cyclophosphamide_7-cycles at 130 mg/kg each cycle


title: P65

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description:
205243950080_R04C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

hyb_protocol: The samples were bisulfite converted using EZ DNA Methylation-Gold™ Kit (Zymo Research, CA, USA).

scan_protocol: The samples were hybridized in the Infinium Mouse Methylation BeadChip microarray following the manufacturer’s instructions.

data_processing:
The raw signal intensities for each array were assessed and analyzed with GenomeStudio Software 2011.1 (Illumina) using default normalization (control probes and background substraction). Raw signal intensity data were later QC’d and processed in R statistical environment (v4.0.3) . A number of quality control steps were applied to minimize errors and remove erratic probe signals, such removal of failed probes (probes with detection P value > 0.01), XY chromosome probes, genotyping probes and MFG probes.
GenomeStudio Software 2011.1 (Illumina) default normalization using control probes and background substraction.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: High molecular weight DNA

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was isolated with the DNAeasy blood & tissue kit (Qiagen GmbH, Hilden, Germany) and ReliaPrep™ FFPE gDNA Miniprep System (Promega, Wisconsin, USA) for fresh frozen and formalin-fixed paraffin-embedded samples respectively.

tag: tissue

value: Lung

tag: tissue type

value: Normal

tag: biological sex

tag: sample preservation

value: FFPE


title: Cyclophosphamide_4-cycles_pool1

description:
polyA-selected RNA, stranded library
G170_M13

value: 12-13 weeks

value: Cyclophosphamide_4-cycles at 130 mg/kg each cycle


title: AB48

value: Foxa2-Venus positive populations - notochord, gut, liver


title: AB47


title: AB54

value: Foxa2-Venus positive populations - primitive streak, node, definitive endoderm, visceral endoderm


title: Cyclophosphamide_2-cycles_pool2

description:
polyA-selected RNA, stranded library
G170_M11

value: 10-11 weeks

value: Cyclophosphamide_2-cycles at 130 mg/kg each cycle


title: OX40L-JAG1 TFR, rep2

value: female

value: 23 weeks old

value: OX40L-Jagged-1 treated

value: TFR cells


title: Control Treg, rep1

source_name: Treg cells sorted from control mice

value: control

value: Treg cells


title: P63

description:
205243950014_R06C02
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Skin

value: Male

value: C57BL/6J & FVB

value: FF


title: Control Treg, rep3


title: AB36

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: P62

description:
205243950014_R06C01
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Normal


title: Apoe_minus_minus_M_minus_3

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052

value: untreated


title: U5NSC_RNAseq_WT_2

city: Seattle

first: Heshani

middle: Nayanga

last: Thirimanne

state: WA

address: 1100 Fairview AV N, D2-213

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
Replicate 2
U5NSC_RNASeq_DGE.txt

data_processing:
STAR v2.7.1 with 2-pass mapping was used to align paired-end reads to hg19 and GENCODE gene annotation v31lift37.
FastQC 0.11.8 and RseQC 3.0.0 were used for QC.
FeatureCounts in Subread 1.6.5 was used to quantify gene-level expression.
Bioconductor package edgeR 3.26.8 was used determine differential gene expression.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text file with CPM and FPKM values for each sample and differentially expressed genes.

organism: Homo sapiens

source_name: RNA-Seq

extract_protocol:
Total RNA was isolated from three million cells per sample using the Quaigen RNAeasy Mini Kit (Cat# 74104) following the manufacturer's instructions.
Libraries for Hct116  were prepared using TruSeq RNA Samples Prep Kit v2 (Illumina Inc., San Diego CA, USA). Libraries for U5NSCs were prepared using TruSeq Stranded mRNA kit.

value: U5 neural stem cells

tag: genotype


title: Control Tconv, rep3

source_name: Tconv cells sorted from control mice

value: Tconv cells


title: AB52


title: OX40L-JAG1 TFH, rep3

source_name: TFH cells sorted from OX40L-Jagged-1 treated mice

value: TFH cells


title: Vehicle pool3

description:
polyA-selected RNA, stranded library
G170_M9

value: BALB/c

value: Female

value: 10-11 weeks

value: Vehicle


title: Control Treg, rep2

value: female

value: 23 weeks old

value: control


title: OX40L-JAG1 TFH, rep2

value: OX40L-Jagged-1 treated


title: U5NSC_RNAseq_WT_1

description:
Replicate 1
U5NSC_RNASeq_DGE.txt


title: Control TFR, rep2

value: TFR cells


title: P61

description:
205243950014_R05C02
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Skin

value: Male

value: C57BL/6J & FVB

value: FF


title: AB33

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: P67

description:
205243950009_R02C01
Normal sample from Liver tissue
Infinium Mouse Methylation BeadChip

value: Liver

value: Normal

value: FFPE


title: Apoe_minus_minus_M_minus_1

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052

value: untreated


title: Control Tconv, rep1

value: Tconv cells


title: OX40L-JAG1 TFH, rep1

value: TFH cells


title: P66

description:
205243950080_R06C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung

value: Female


title: OX40L-JAG1 Treg, rep3

source_name: Treg cells sorted from OX40L-Jagged-1 treated mice

value: female

value: 23 weeks old

value: Treg cells


title: AB32


title: AB35


title: AB49

source_name: ESC differentiation

value: in vitro ESC-derived primitive streak


title: P58

description:
205243950014_R04C01
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip


title: U5NSC_RNAseq_Del_1

description:
Replicate 1
U5NSC_RNASeq_DGE.txt

value: U5 neural stem cells


title: Apoe_minus_minus_M_plus_3

value: Myelin treated


title: P64

description:
205243950080_R04C01
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: FF


title: Apoe_minus_minus_M_minus_5

description: cells remained unchallenge for 24h


title: P56

description:
205243950008_R04C02
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Skin

value: Male

value: C57BL/6J & FVB


title: AB30

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: Apoe_minus_minus_M_minus_4

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052


title: Apoe_minus_minus_M_plus_1


title: OX40L-JAG1 Tconv, rep2

source_name: Tconv cells sorted from OX40L-Jagged-1 treated mice

value: OX40L-Jagged-1 treated


title: P55

description:
205243950008_R04C01
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Normal

value: FFPE


title: P60

description:
205243950014_R05C01
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip


title: AB28


title: Control Tconv, rep2

value: control

value: Tconv cells


title: AB26


title: P53

description:
204986320002_R06C01
Normal sample from Liver tissue
Infinium Mouse Methylation BeadChip

value: Liver


title: P59

description:
205243950014_R04C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung

value: Female


title: OX40L-JAG1 Treg, rep1

value: female

value: 23 weeks old

value: Treg cells


title: AB31


title: Apoe_minus_minus_M_plus_2

description: 3h myelin treatment, cells were collected at 24h

value: Myelin treated


title: AB29


title: Apoe_plus_minus_M_plus_1


title: AB24

value: Foxa2-Venus positive populations - primitive streak, visceral endoderm


title: P52

description:
204986320002_R02C01
Normal sample from Breast tissue
Infinium Mouse Methylation BeadChip

value: Breast

value: FF


title: OX40L-JAG1 Treg, rep2


title: P57

description:
205243950008_R06C02
Normal sample from Liver tissue
Infinium Mouse Methylation BeadChip

value: Male


title: Apoe_plus_minus_M_minus_5

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052

value: untreated


title: Tyrobp KO hippocampus Input rep1

city: Jining

first: Zhanyun

last: Lv

state: Shandong

address: Guhuai Road

country: China

institute: the Affiliated Hospital of Jining Medical University

description: TYROBP_IP VS TYROBP_input_peak.txt

data_processing:
Fastp software (https://github.com/OpenGene/fastp) and default parameters were used to remove adaptor contamination and low-quality reads (defined as bases with Q≤10 accounting for more than 20% of the total reads). Sequence quality of the input and immunoprecipitated samples was also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map the reads to the reference genome Mus musculus (Version: v96).
Mapped reads of immunoprecipitated and input libraries were provided for R package exomePeak analysis (https://bioconductor.org/packages/exomePeak), which identified m6A peaks with bed or bigwig format.
Output was visualized on IGV software (http://www.igv.org). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif identification, followed by localization of the motif with respect to the peak summit.
Peaks were annotated by intersection with gene architecture using the R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Supplementary_files_format_and_content: txt.

source_name: hippocampus

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (cat#15596018, Invitrogen, Carlsbad, CA, USA).
RNA integrity was assessed using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Samples were used only if RNA integrity number (RIN) was >7.0 and appeared high-quality on denaturing agarose gel electrophoresis. Poly (A) RNA was purified from 50 μg total RNA using Dynabeads Oligo (dT)25 (cat# 61005, Thermo Fisher Scientific), and fragmented into small pieces at 86 ℃ for 7 min using Magnesium RNA Fragmentation Module (cat# e6150, New England Biolabs, Ipswich, MA, USA). The cleaved RNA fragments were incubated at 4 ℃ for 2 h with an m6A-specific antibody (cat# 202003, Synaptic Systems, Göttingen, Niedersachsen, Germany) in 50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630.
Immunoprecipitated RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (cat# 1896649, Invitrogen). The cDNA was then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (cat# m0209, New England Biolabs), RNase H (cat# m0297, New England Biolabs) and dUTP (cat# R0133, Thermo Fisher Scientific). A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After treatment with a heat-labile UDG enzyme (cat# m0280, New England Biolabs), the ligated products were amplified by PCR under the following conditions: initial denaturation at 95 ℃ for 3 min; 8 cycles of denaturation at 98 ℃ for 15 sec, annealing at 60 ℃ for 15 sec, and extension at 72 ℃ for 30 sec; and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. We then performed the 2×150-bp paired-end sequencing (PE150) on an illumine Novaseq™ 6000 (LC-Bio Technology, Hangzhou, Zhejiang, China).

value: hippocampus

value: 6 months

tag: genotype/variation

value: Tyrobp KO


title: OX40L-JAG1 Tconv, rep1

value: OX40L-Jagged-1 treated

value: Tconv cells


title: AB23


title: P51

description:
204986320011_R02C02
Normal sample from Breast tissue
Infinium Mouse Methylation BeadChip

value: Normal


title: OX40L-JAG1 Tconv, rep3


title: P50

description:
204986320005_R02C02
Normal sample from Pancreas tissue
Infinium Mouse Methylation BeadChip

value: Pancreas


title: Apoe_minus_minus_M_plus_4


title: Apoe_plus_minus_M_plus_4


title: Apoe_plus_minus_M_minus_2

description: cells remained unchallenge for 24h


title: P48

description:
204986320004_R02C02
Normal sample from Pancreas tissue
Infinium Mouse Methylation BeadChip


title: AB20

value: in vitro ESC-derived definitive endoderm


title: Apoe_plus_minus_M_minus_1

description: cells remained unchallenge for 24h


title: P54

description:
204986320002_R02C02
Normal sample from Breast tissue
Infinium Mouse Methylation BeadChip

value: Female

value: FVB


title: AB19


title: Apoe_plus_minus_M_plus_3

value: Myelin treated


title: Tyrobp KO hippocampus Input rep3

description: TYROBP_IP VS TYROBP_input_peak.txt


title: AB25

value: Foxa2-Venus positive populations - primitive streak, visceral endoderm


title: Tyrobp KO hippocampus IP rep2

description: TYROBP_IP VS TYROBP_input_peak.txt


title: E4_M_plus_4

value: Taconic, 1549


title: AB27

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: Apoe_plus_minus_M_minus_4

description: cells remained unchallenge for 24h


title: WT hippocampus Input rep2

description: WT_IP VS WT_input_peak.txt

value: WT


title: Tyrobp KO hippocampus Input rep2

description: TYROBP_IP VS TYROBP_input_peak.txt


title: WT hippocampus Input rep3

description: WT_IP VS WT_input_peak.txt


title: AB22


title: P49

description:
204986320005_R02C01
Normal sample from Pancreas tissue
Infinium Mouse Methylation BeadChip

value: Male

value: FF


title: Apoe_plus_minus_M_minus_3

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052

value: untreated


title: E4_M_plus_3


title: WT hippocampus Input rep1

description: WT_IP VS WT_input_peak.txt

value: hippocampus

value: 6 months


title: Apoe_plus_minus_M_plus_2


title: Spleen2_replicate2

description:
204998560003_R01C02
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip

value: Spleen

value: FFPE


title: AB16

value: Foxa2-Venus positive populations - primitive streak, node, definitive endoderm, visceral endoderm


title: P47

description:
204986320004_R03C01
Normal sample from Breast tissue
Infinium Mouse Methylation BeadChip

value: Breast

value: Normal


title: E4_M_plus_2


title: AB21


title: WT hippocampus IP rep2

description: WT_IP VS WT_input_peak.txt


title: E4_M_plus_5


title: Tyrobp KO hippocampus IP rep1

description: TYROBP_IP VS TYROBP_input_peak.txt

value: Tyrobp KO


title: P46

description:
204986320004_R02C01
Normal sample from Pancreas tissue
Infinium Mouse Methylation BeadChip

value: Pancreas


title: P43

description:
204998560003_R01C01
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip

value: Thymus


title: P45

description:
204998560003_R05C02
Normal sample from Prostate tissue
Infinium Mouse Methylation BeadChip

value: Prostate


title: P42

description:
204986320010_R01C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung


title: Tyrobp KO hippocampus IP rep3

description: TYROBP_IP VS TYROBP_input_peak.txt


title: BC3_CHi-C

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Homo sapiens; KSHV

library_source: genomic

data_processing:
Basecalling and quality scoring were performed using Real-Time Analysis software (RTA2).
The HiC-Pro v2.11.1 pipeline was used to process the CHi-C data by performing read alignment, detection and filtering of valid interaction products, binning, and contact map normalization. Read alignment was performed with bowtie2 using a combined assembly of the human hg19 (GRCh37) and KSHV (NC_009333.1) reference genomes and by first mapping each read independently. The reads were filtered to remove duplicates and to keep only reads that mapped to the KSHV genome by using the Python module Pysam v0.14.1. Valid Hi-C interactions were detected based on several criteria, including the assignment of each read to a different restriction fragment and being located within a specified distance to a restriction site consistent with the size distribution of the sheared ligation products. Read pairs from invalid ligation products (e.g., self-circle ligation, dangling end, random breaks) and PCR duplicates were discarded. The valid reads were stored as matrices and binned with resolution of 500 bp (2 kb for density plots), the bins with more than 100 counts and at least 75% of cells with no-zero counts were used in the next steps. Iterative Correction and Eigenvector decomposition (ICE) normalization was used to treat the data with iteration of 100.
Genome_build: GRCh37 (hg19) + KSHV genome (GQ994935.1)
Supplementary_files_format_and_content: Processed data files are in hic format, which is an indexed binary format that is generated from Hi-C tag directories. This file format is designed to permit fast random access to contact matrix heatmaps in Juicebox.

organism:
Homo sapiens
Human gammaherpesvirus 8

growth_protocol: ORF57-Wt iSLK and ORF57-KO iSLK cells were cultured in complete DMEM supplemented with 10% FBS. BC3 and BC1 cells were grown in RPMI 1640 medium supplemented with 15% FBS. TREx-F3H3-K-Rta BCBL-1 (TREx-K-Rta BCBL-1, which have tetracycline/doxycycline (Dox)-inducible expression of N-terminal Flagx3- and HAx3-tagged K-Rta, were cultured in complete RPMI 1640 (supplemented with 15% FBS) containing blasticidin (10 μg/ml) and hygromycin B (200 μg/ml). TREx-F3H3-K-Rta BCBL-1, ORF57-Wt iSLK and ORF57-KO iSLK cells were treated with or without 1 µg/mL doxycycline for 28 h.

extract_protocol:
Chimeric DNA ligation products were prepared for KSHV Capture Hi-C (CHi-C) using kitted reagents from Arima Genomics (San Diego, CA) based on methods described for in situ Hi-C and CHi-C. Briefly, cells were crosslinked with 2% formaldehyde, lysed, and the genomic DNA digested with a cocktail of 4-cutter restriction endonucleases by incubation for 30 minutes at 37°C. The 5’-overhangs were then filled in and labeled with biotinylated dATP (biotin-14-dATP) by incorporation with Klenow fragment of DNA polymerase I (incubation for 45 minutes at 25°C). Ligation of the spatially proximal blunt-ended fragments was then performed with T4 DNA ligase (incubation for 15 minutes at 25°C). The formaldehyde crosslinks were reversed and the proximally-ligated, chimeric DNA products were purified with Agencourt AMPure XP paramagnetic beads (Beckman Coulter).
Hi-C and KSHV Capture Hi-C (CHi-C) libraries were prepared from the chimeric DNA ligation products using kitted reagents from Arima Genomics (San Diego, CA). The DNA was fragmented to an average size of 400 bp with a Covaris E220 Focused-ultrasonicator (Covaris, Inc.) and size-selected to have a fragment size distribution of 200-600 bp with AMPure XP beads. The biotin-labeled ligation products were then selectively enriched by affinity capture with streptavidin magnetic beads (Arima Enrichment Beads). Subsequently, sequencing libraries were prepared with the Kapa HyperPrep Kit with Library Amplification Module (Roche) using a modified protocol for on-bead end repair, dA-tailing, and ligation of Illumina TruSeq sequencing adaptors. The KSHV CHi-C library was then prepared from the above Hi-C libraries. Briefly, target enrichment for KSHV genomic content was performed by solution hybridization with a custom-designed KSHV genomic capture probe library (xGen Lockdown Probes; IDT) and subsequent capture of the hybridized targets with streptavidin beads (DynaBeads MyOne Streptavidin C1; Thermo Fisher Scientific) according to the manufacturer’s standard protocol (IDT). The KSHV genome-enriched CHi-C library DNA was eluted and PCR enrichment (12 cycles) performed with high-fidelity KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems).

value: human primary effusion lymphoma

tag: cell line

value: KSHV-positive human B cell lymphoma cells

tag: viral infection

value: KSHV

tag: virus status

value: latent


title: WT hippocampus IP rep3

description: WT_IP VS WT_input_peak.txt

value: WT


title: AB18

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: AB13


title: AB17


title: E4_M_minus_4

description: cells remained unchallenge for 24h

value: Taconic, 1549

value: untreated


title: BC1_CHi-C

description: Homo sapiens; KSHV

value: KSHV+EBV


title: P40

description:
204986320008_R01C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Male

value: FFPE


title: WT hippocampus IP rep1

description: WT_IP VS WT_input_peak.txt

value: hippocampus

value: 6 months


title: AB15

value: Foxa2-Venus positive populations - primitive streak, node, definitive endoderm, visceral endoderm


title: E4_M_plus_1

value: Myelin treated


title: E4_M_minus_2

description: cells remained unchallenge for 24h


title: P39

description:
204986320008_R06C01
Normal sample from Prostate tissue
Infinium Mouse Methylation BeadChip

value: Prostate

value: Normal

value: FF


title: AB10


title: BCBL-1_TREx-K-Rta_lytic_CHi-C_Rep1

description: Homo sapiens; KSHV

source_name: TREx-F3H3-K-Rta BCBL-1

value: human primary effusion lymphoma

value: TREx-F3H3-K-Rta BCBL-1

value: KSHV-positive human B cell lymphoma cells

value: lytic


title: AB12

value: in vitro ESC-derived definitive endoderm


title: Apoe_minus_minus_M_minus_2

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 002052


title: E4_M_minus_3

description: cells remained unchallenge for 24h

value: Taconic, 1549

value: untreated


title: AB14


title: BCBL-1_TREx-K-Rta_latent_CHi-C_Rep3

description: Homo sapiens; KSHV

value: KSHV

value: latent


title: P37

description:
204998560006_R06C02
Normal sample from Prostate tissue
Infinium Mouse Methylation BeadChip

value: Male


title: AB8


title: BCBL-1_TREx-K-Rta_lytic_CHi-C_Rep3

description: Homo sapiens; KSHV


title: P41

description:
204986320010_R01C01
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip

value: Thymus

value: FFPE


title: AB11


title: BCBL-1_TREx-K-Rta_latent_CHi-C_Rep2

description: Homo sapiens; KSHV


title: Spleen1_replicate2

description:
204986320008_R01C01
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip

value: Spleen


title: BCBL-1_TREx-K-Rta_lytic_CHi-C_Rep2

description: Homo sapiens; KSHV


title: E3_M_plus_3

description: 3h myelin treatment, cells were collected at 24h

value: Taconic, 1548

value: Myelin treated


title: P35

description:
204998560006_R06C01
Normal sample from Prostate tissue
Infinium Mouse Methylation BeadChip

value: Prostate

value: Normal

value: FF


title: E3_M_plus_4


title: P36

description:
204998560006_R01C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung


title: E4_M_minus_1

description: cells remained unchallenge for 24h


title: P34

description:
204998560006_R01C01
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip


title: E4_M_minus_5

description: cells remained unchallenge for 24h


title: iSLK_ORF57-KO_latent_CHi-C

description: Homo sapiens; KSHV

source_name: ORF57-KO iSLK

value: human epithelial cells

value: iSLK epithelial cells

value: Stable doxycycline-inducible K-Rta expression and infected with ORF57-KO KSHV BAC16


title: BCBL-1_TREx-K-Rta_latent_CHi-C_Rep1

description: Homo sapiens; KSHV

value: human primary effusion lymphoma

value: TREx-F3H3-K-Rta BCBL-1

value: KSHV-positive human B cell lymphoma cells


title: AB6

value: Foxa2-Venus positive populations - primitive streak, node, definitive endoderm, visceral endoderm


title: iSLK_ORF57-KO_lytic_CHi-C

description: Homo sapiens; KSHV

value: KSHV

value: lytic


title: E3_M_plus_2


title: iSLK_ORF57-Wt_lytic_CHi-C

description: Homo sapiens; KSHV

source_name: ORF57-Wt iSLK

value: Stable doxycycline-inducible K-Rta expression and infected with wild-type KSHV BAC16


title: AB4


title: E3_M_plus_1


title: P33

description:
204986320001_R06C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Male

value: FFPE


title: AB9


title: iSLK_ORF57-Wt_latent_CHi-C

description: Homo sapiens; KSHV

value: latent


title: P32

description:
204986320001_R05C02
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Skin


title: E3_M_minus_4

description: cells remained unchallenge for 24h

value: Taconic, 1548

value: untreated


title: AB5


title: AB3


title: WT_M_plus_1

value: Jackson Laboratory, 000664

value: Myelin treated


title: E3_M_minus_3

description: cells remained unchallenge for 24h


title: P30

description:
204986320001_R05C01
Normal sample from BM tissue
Infinium Mouse Methylation BeadChip

value: BM

value: Normal

value: FF


title: E3_M_minus_2

description: cells remained unchallenge for 24h


title: AB2

value: in vitro ESC-derived definitive endoderm


title: AB7


title: E3_M_minus_1

description: cells remained unchallenge for 24h


title: AB1


title: Spleen2_replicate1

description:
204986320001_R03C01
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip

value: Spleen


title: LANA_BcBL-1_1_CUT&RUN

data_processing:
Base calling and quality scoring were performed with Real-Time Analysis (RTA2) software.
CUT&RUN reads were aligned to the GRCh38 (hg38) human reference genome and KSHV reference genome (Human herpesvirus 8 strain: GQ994935.1) with Bowtie2.
MACS2 was used for detecting peaks following the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
Genome_build: GRCh38 (hg38) + KSHV genome (Accession: GQ994935.1)
Supplementary_files_format_and_content: Processed data are in bigWig format.

growth_protocol: ORF57-Wt iSLK and ORF57-KO iSLK cells were cultured in complete DMEM supplemented with 10% FBS. Cells were treated with or without 1 µg/mL doxycycline for 28 h. BCBL-1, BC-1, and BC-3 cells were grown in RPMI 1640 medium supplemented with 15% FBS.

extract_protocol:
Cells were washed with PBS and wash buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine (Sigma, S2626) and proteinase inhibitor (Roche). After removing wash buffer, cells were captured on magnetic ConA beads (Polysciences), in presence of CaCl2. Beads/cells complexes were washed with digiton wash buffer (0.02% digitonin, 20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1x proteinase inhibitor) three times, and incubated with specific antibodies in 250 mL volume. After incubation, unbound antibody was washed by digitonin wash buffer 3 times. Beads were then incubated with the recombinant pAG-MNase, in 250 μl digitonin wash buffer (1.0 mg/mL final concentration) for an hour at 4°C with rotation. Unbound pAG-MNase was removed by washing with digitonin wash buffer 3 times. Pre-chilled 2 mM CaCl2 containing digitonin wash buffer (200 mL) was added to beads and incubate on ice for 30 min. The pAG-MNase digestion was halted by the addition of 200 μl 2× STOP solution (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNase A, 50 mg/ml Glycogens). The beads were incubated/shaked at 37°C for 10 min in tube shaker at 500 rpm to release digested DNA fragments from the insoluble nuclear chromatin. The supernatant was collected after centrifuge (16,000 x g for 5 min at 4°C) and place on magnetic stand. DNA was extracted using NucleoSpin kit (Takara).
Sequencing libraries were prepared from 3 ng of CUT&RUN DNA with the Kapa HyperPrep Kit (Roche) according to the manufacturer’s standard protocol. Libraries were multiplex sequenced (2 x 150bp, paired-end) on an Illumina HiSeq 4000 sequencing system.
Other: CUT&RUN

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells

tag: cut&run antibody

value: LANA (Sigma, clone LN53)


title: P28

description:
204986320001_R02C01
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung

tag: strain


title: P31

description:
204986320001_R02C02
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip

value: Thymus

value: Male


title: WT_M_plus_5


title: Astrocyte 2-2_KO_scRNA-seq

city: shanghai

first: Yana

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, China

department: Computational Biology

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adapter sequence and timmed reads shorter than 30 bp were discarded using TrimGalore 0.4.4_dev. Then mapped to hg19 reference genome using STAR 2.5.3a_modified with parameters  --AlignEndsType EndToEnd --out FileterMismatchNoverReadLmax 0.04 --outSAMattrIHstart 0 --outSAMmultNmax 1 --outFilterMultimapNmax 1.
Uniquely mapped reads were demultiplexed by Cutadapt 1.17 and reads assigned into individual cells were deduplicated by UMI-tools 0.5.4.
UMIs of genes in cells were counted using featureCounts 1.6.2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for every gene and every cell.

source_name: Astrocytes differentiated from WFS1-/- HuES8-NPCs

growth_protocol: The wild-type (WT) HuES8 were plated on Matrigel-coated plates and maintained in mTeSR1 medium for 5 to 7 days, after that medium was changed to N2 medium (DMEM/F12 supplemented with 0.5x N2-Supplement) with 1μM dorsomorphin and 1μM SB431542 for 2 days. hESCs colonies were lifted off and cultured in suspension as embryoid bodies for 1 week within N2 medium on the orbital shaker (95 r.p.m.). Embryoid bodies then were mechanically dissociated using a p1000 pipette, and plated on 10 μg/mL poly-L-ornithine (Sigma) and laminin (Gibco™)-coated dishes, and cultured in N/B meidum (DMEM/F12 supplemented with 0.5x N2-Supplement, 0.5x B27-Supplement) with 20 ng/mL basic fibroblast growth factor (bFGF) (Stemcell Technologies). Formed neural rosettes were manually isolated, dissociated with accutase (Stemcell Technologies) and plated on dishes coated with poly-L-ornithine/laminin. NPCs were cultured in N/B medium with 20 ng/mL bFGF and fed every other day. To differentiate NPCs into neurons, bFGF was withdrawn from medium and added 5 μM RI for 24 hours. After that N/B medium was changed every other day. NPCs were lifted off and gently dissociated by pipetting, and cultured in suspension to form neurospheres within N/B medium for 1 week on the shaker (95 r.p.m.). Next, astrocyte growth medium (AGM) (Lonza) was added to the neurospheres for 2 weeks and cells were maintained on the shaker (95 r.p.m.) to induce astrocytes differentiation, and medium was changed every other day. Spheres were plated on poly-L-ornithine/laminin-coated dishes, and astrocytes were migrated from spheres and maintained in AGM. Astrocytes were dissociated using Papain and DNase I (Worthington) until analysis was performed.

extract_protocol:
Neurons expressing Syn1::GFP were digested using Neurosphere dissociation kit (MACS) according to the manufacturer’s instructions and astrocytes expressing GFAP::tdTomato were digested using Papain and DNase I (Worthington) for 30 min at 37℃. Syn1-GFP+ or GFAP-tdTomato+ single cells were sorted using Moflo Astrios (Beckman Coulter) and collected in RNase-free 96-well-plate.
An optimized Smart-seq2 protocol was used to construct single-cell RNA-seq libraries while sample pooling and molecular counting were using oligo-d (T) primers comprising 16-bp cell barcode sequence and 9-bp molecular barcode sequence. For compatible with Illumina sequence platform, part of the ISPCR sequence was replaced by read2 sequence in the oligo-d(T) primer. Sorted neuron and astrocytes were denatured in lysis buffer on 72°C for 3min, and put on ice for annealing immediately, then reverse transcribed with template switching oligos and pre-amplified with both ISPCR and read2 primers. cDNA libraries from different cells with different barcodes were pooled together and purified with 0.8x AMPure XP beads. Purified cDNA was fragmented with homemade Tn5 enzyme, and final amplification using Tn5PCR-7 primers and Tn5PCR-5 primers (Nextera). Amplificated cDNA libraries were purified twice with AMPure XP beads.

treatment_protocol: Except for the WFS1-/- HuES8, everything else is the same with the protocol of the WT group.

value: Astrocytes

tag: batch

tag: cell number


title: LANA_BC3_2_CUT&RUN

source_name: BC3 cell line


title: P27

description:
204998560001_R03C02
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip


title: LANA_BC3_1_CUT&RUN


title: LANA_BC1_1_CUT&RUN

source_name: BC1 cell line


title: LANA_BcBL-1_2_CUT&RUN


title: WT_M_plus_3

source_name: Forebrain primary microglia

tag: treatment


title: P25

description:
204998560001_R03C01
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip


title: Astrocyte 1-1_WT_scRNA-seq

source_name: Astrocytes differentiated from WT HuES8-NPCs

tag: cell type

value: WT


title: Astrocyte 2-1_KO_scRNA-seq


title: LANA_BC1_2_CUT&RUN


title: P26

description:
204998560001_R02C02
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip

source_name: High molecular weight DNA


title: P24

description:
204998560001_R02C01
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip


title: Astrocyte 1-2_WT_scRNA-seq


title: WT_M_plus_4


title: WT_M_minus_5

description: cells remained unchallenge for 24h


title: Neuron 4-2_KO _scRNA-seq

source_name: Neurons differentiated from WFS1-/- HuES8-NPCs

value: Neurons


title: P23

description:
204998560004_R06C02
Normal sample from Colon tissue
Infinium Mouse Methylation BeadChip

value: Colon


title: H3K4me3_BC1_2_CUT&RUN

value: H3K4me3 (CST, C42D8)


title: Neuron 3-2_WT _scRNA-seq

source_name: Neurons differentiated from WT HuES8-NPCs


title: Neuron 4-1_KO _scRNA-seq


title: H3K4me3_BC1_1_CUT&RUN


title: H3K27me3_BC3_2_CUT&RUN


title: P22

description:
204998560004_R03C02
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip


title: H3K27me3_BC3_1_CUT&RUN


title: Neuron 3-1_WT _scRNA-seq


title: P21

description:
204998560004_R02C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip


title: WT_M_minus_2

description: cells remained unchallenge for 24h

value: Jackson Laboratory, 000664

value: untreated


title: CHD4_BcBL-1_2_CUT&RUN

value: CHD4 (CST, D4B7)


title: WT_M_minus_4

description: cells remained unchallenge for 24h


title: P19

description:
204998560004_R03C01
Normal sample from Thymus tissue
Infinium Mouse Methylation BeadChip

value: Normal

value: FF


title: P20

description:
204998560004_R06C01
Normal sample from Skin tissue
Infinium Mouse Methylation BeadChip

value: Skin


title: P18

description:
204998560004_R01C01
Normal sample from Brain tissue
Infinium Mouse Methylation BeadChip

value: Brain

value: Female


title: WT_M_minus_1

description: cells remained unchallenge for 24h


title: CHD4_BcBL-1_1_CUT&RUN

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells


title: WT_M_plus_2

description: 3h myelin treatment, cells were collected at 24h

value: Myelin treated


title: WT_M_minus_3

description: cells remained unchallenge for 24h


title: Neuron 2-2_KO _scRNA-seq


title: P16

description:
204998560005_R03C02
Normal sample from Lung tissue
Infinium Mouse Methylation BeadChip

value: Lung

value: Male


title: Neuron 1-2_WT _scRNA-seq

value: WT


title: 50-week-old SAMP1-11

type: RNA

city: Saitama City

first: Katsunori

last: Yanai

address: 1-847, Amanuma-cho, Omiya-ku

country: Japan

institute: Jichi Medical University, Saitama Medical Center

hyb_protocol: The hybridization mixture was denatured at 100°C for 5 minutes in a reaction volume of 45 ul containing 2x Agilent GE hybridization buffer HI-RPM and 10x Agilent blocking agent following the manufacturers instructions and immediately transferred to ice water bath. Each sample was hybridized to SurePrint G3 Mouse miRNA microarray 8 x 60K  Rel.21.0 (Agilent, G4872A#70155) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using miRNA setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol miRNA_1200_Jun14 and Grid 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities. The 90th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.1. Data were baseline shifted to the mean of 10-week-old SAMR1 samples.

source_name: 50-week-old, SAMP1

label_protocol: RNA labeling was performed using miRNA Complete Labeling Reagent and Hyb Kit (Agilent, 5190-0456) following the Agilent protocols v.2.4. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. After adding DMSO, the reaction mixture was incubated at 100°C for 7 minutes and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hours.The labeled RNA were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: After crushing 10 mg of the removed cortical tissue piece of kidney tissue in a silicon homogenizer, transfer to a filter column crusher (QIA Shredder; Qiagen, Valencia, CA, USA) and centrifuge at 25 ° C, 14,000 × g, 3 minutes. The filtrate was transferred to a new tube and 140 µL of chloroform was added. After that, the protein and nucleic acid were separated by centrifugation at 12,000 × g at 4 ° C for 15 minutes. The supernatant was transferred to a new tube and 1.5 times the amount of 100% ethanol was added. Subsequently, DNA and RNA were separated using the miRNeasy Mini Kit (Qiagen), and total RNA was extracted.

tag: mouse line

value: senescence-accelerated prone (SAMP1)

value: kidney

tag: gender

value: male

tag: age


title: 50-week-old SAMP1-4

tag: tissue


title: CHD4_BC1_2_CUT&RUN


title: P17

description:
204998560005_R06C02
Normal sample from BM tissue
Infinium Mouse Methylation BeadChip

value: BM

tag: tissue type

tag: biological sex


title: CHD4_BC3_1_CUT&RUN


title: CHD4_BC3_2_CUT&RUN


title: Neuron 2-1_KO _scRNA-seq

value: Neurons

tag: genotype


title: KO IFNa+ RUX, TGFB, DOX2

city: Hannover

first: Frank

last: Pessler

state: Niedersachsen

address: Feodor Lynen Str. 7

country: Germany

institute: Twincore

hyb_protocol: Hybridization was done for 16 hrs at conditions recommended by the manufacturer. Clariom™ S  chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000. Image analysis was done by Affymetrix® GeneChip® Command Console® Software (AGCC) and  Affymetrix® Expression Console™ Software

data_processing: Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions.

label: biotin

source_name: HaCaT cells

label_protocol: Standard Affymetrix protocol

growth_protocol: HaCaT cells were cultured in 6-well plates.

extract_protocol:
mRNA was extracted and purified from HaCaT cells using MN NucleoSpin RNA kit.
Complementary RNA (cRNA) amplification and coversion to biotinylated double-stranded cDNA (ds-cDNA) was done by Clariom™ S Pico Assay, human Affymetrix protocol from10 ng total RNA (GeneChip® Pico UserGuide 703308 Rev. 4 Affymetrix).

treatment_protocol: HaCaT cells  were stimulated with interferon-a for 8 hours and treated with combination treatment of RUX, TGFB and DOXY for 16 hours.

tag: condition

value: RUX (0.5 µM), TGFB (10 nM), DOXY (50 µM)

value: HaCaT

value: ISG15 KO


title: BCBL-1_RNA Pol II_CUT&RUN

value: RNA Pol II (Millipore, clone CTD4H8)


title: KO IFNa+ RUX, TGFB, DOX3

tag: cell line


title: 50-week-old SAMP1-2


title: KO IFNa3

value: IFNa


title: P19_AZA

description:
204986320002_R03C02
Cell line sample from Embryonal tissue
Infinium Mouse Methylation BeadChip

value: Embryonal

value: Cell line


title: Neuron 1-1_WT _scRNA-seq


title: KO IFNa1


title: P15

description:
204998560005_R01C02
Normal sample from Brain tissue
Infinium Mouse Methylation BeadChip

value: Brain

value: Normal

tag: sample preservation

value: FF


title: P14

description:
204998560005_R06C01
Normal sample from Colon tissue
Infinium Mouse Methylation BeadChip

value: Colon

value: Male


title: CHD4_BC1_1_CUT&RUN

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells

value: CHD4 (CST, D4B7)


title: C2C12_AZA

description:
204986320011_R03C02
Cell line sample from Myoblasts tissue
Infinium Mouse Methylation BeadChip

value: Myoblasts


title: Spleen1_replicate1

description:
204998560005_R03C01
Normal sample from Spleen tissue
Infinium Mouse Methylation BeadChip

value: Spleen


title: iSLK_ORF57-KO_latent_H3K27ac_CUT&RUN

value: human epithelial cells

value: Stable doxycycline-inducible K-Rta expression and infected with ORF57-KO KSHV BAC16

value: H3K27ac(CST, D5E4)


title: KO con2

value: Control

value: HaCaT

value: ISG15 KO


title: BCBL-1_CHD4_CUT&RUN


title: P12

description:
204998560005_R01C01
Normal sample from Brain tissue
Infinium Mouse Methylation BeadChip


title: KO con3


title: 50-week-old SAMR1-12

source_name: 50-week-old, SAMR1

value: kidney

value: male


title: C2C12_replicate2

description:
204986320004_R04C02
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip

value: Hematopoietic precursor

value: Cell line


title: 10-week-old SAMP1-6

source_name: 10-week-old, SAMP1

value: senescence-accelerated prone (SAMP1)


title: 50-week-old SAMP1-1


title: WT IFNa+ RUX, TGFB, DOX2

value: RUX (0.5 µM), TGFB (10 nM), DOXY (50 µM)

value: WT


title: 50-week-old SAMR1-9


title: KO IFNa+ RUX, TGFB, DOX1


title: 10-week-old SAMP1-5


title: HAFTL_AZA

description:
204986320005_R03C01
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip


title: KO IFNa2

value: IFNa


title: HAFTL_No_AZA

description:
204986320004_R03C02
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip


title: 50-week-old SAMR1-6


title: 50-week-old SAMR1-2


title: WT IFNa3


title: BCBL-1_LANA_CUT&RUN

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells

value: LANA (Sigma, clone LN53)


title: BCBL-1_H3K27ac_CUT&RUN


title: iSLK_ORF57-KO_latent_CHD4_CUT&RUN

value: human epithelial cells

value: CHD4 (CST, D4B7)


title: iSLK_ORF57-KO_latent_LANA_CUT&RUN

value: Stable doxycycline-inducible K-Rta expression and infected with ORF57-KO KSHV BAC16


title: HAFTL_replicate2

description:
204986320004_R04C01
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip


title: 10-week-old SAMP1-3


title: 10-week-old SAMP1-4


title: DNMT1_KO

description:
204998560004_R02C01
Cell line sample from Embryonic fibroblasts tissue
Infinium Mouse Methylation BeadChip

value: Embryonic fibroblasts


title: iSLK_ORF57-Wt_latent_CHD4_CUT&RUN

value: Stable doxycycline-inducible K-Rta expression and infected with wild-type KSHV BAC16


title: iSLK_ORF57-KO_latent_RNA Pol II_CUT&RUN

value: RNA Pol II (Millipore, clone CTD4H8)


title: 10-week-old SAMR1-5

source_name: 10-week-old, SAMR1

value: kidney


title: iSLK_ORF57-Wt_lytic_RNA Pol II_CUT&RUN


title: C2C12_replicate1

description:
204986320001_R01C02
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip


title: HAFTL_replicate1

description:
204998560005_R02C01
Cell line sample from Hematopoietic precursor tissue
Infinium Mouse Methylation BeadChip


title: WT IFNa+ RUX, TGFB, DOX3

value: HaCaT


title: 10-week-old SAMR1-1

value: male


title: iSLK_ORF57-KO_lytic_RNA Pol II_CUT&RUN


title: P19_No_AZA

description:
204986320002_R03C01
Cell line sample from Embryonal tissue
Infinium Mouse Methylation BeadChip

value: Embryonal

value: Cell line


title: KO con1

value: Control

value: ISG15 KO


title: Wild-type Mouse Blastocyst 8

status: Public on Mar 16 2022

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

data_processing:
Reads were mapped via STAR (2.5.2a) (Dobin and Gingeras, 2015; Dobin et al., 2013) after trimming for adapter sequences.
Samtools (Li et al., 2009) was used to process sam files, as well as to sort and remove PCR duplicates of bam files.
Counts for each gene were quantified using the Subread package FeatureCounts using the gene level quantification in paired-end mode (release 1.5.2) (Liao et al., 2014), and annotated using the Ensembl GRCm38 genome. Reads were filtered such that genes without at least one sample with at least 10 raw reads were removed from the analysis. Count data was normalized to TPM using the Bioconductor package edgeR (McCarthy et al., 2012; Robinson et al., 2010). Differential expression was calculated using DESeq2 (Love et al., 2014) based on a model using the negative binomial distribution. Genes with an adjusted P value less than 0.05 were considered differentially expressed unless otherwise noted.
Reads were filtered such that genes without at least one sample with at least 10 raw reads were removed from the analysis. Count data was normalized to TPM using the Bioconductor package edgeR (McCarthy et al., 2012; Robinson et al., 2010).
Differential expression was calculated using DESeq2 (Love et al., 2014) based on a model using the negative binomial distribution. Genes with an adjusted P value less than 0.05 were considered differentially expressed unless otherwise noted.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every sample

source_name: mouse blastocyst

growth_protocol: Female mice of age 4-8 weeks were stimulated with intraperitoneal injection of 5 IU equine Chorionic Gonadotropin (eCG; Lee BioSolutions, 493-10) followed by intraperitoneal injection of 5 IU human Chorionic Gonadotropin (hCG; Sigma, C1063) 46-48 hours later. Immediately after hCG injection, female mice were placed in the same cage as a stud male of known fertility for mating. The contents of the ampulla were collected only from females with a visible plug 18 hrs after hCG injection. Ampulla contents were evaluated for the presence of zygotes by microscopy following a brief digestion in 0.1mg/mL hyaluronidase (Sigma, H4272) dissolved in M2 media (Sigma, M7176). Zygotes were washed 4 times in M2 before being transferred to M16 (Sigma, M7292) for culture. Embryos were cultured in 20uL drops of M16, overlaid with mineral oil, 20 embryos per drop. For blastocyst experiments, zygotes were cultured at 37C, and were isolated 90-94 hours post-hCG, 100-104 hours post-hCG, and 110-114 hours post-hCG, for early-, mid-, and late- blastocyst stages, respectively.

extract_protocol:
In total, 19 early (E3.25) stage blastocysts (8 Upf2-/-, 11 Upf2+/+) were subjected to mRNA sequencing. As a means of normalization, ERCC Spike-In RNAs (Life Technologies, Cat.no. 4456740) were added to the samples. The ERCC stock provided by the manufacturer was diluted 1:25,000 and 0.25 µl of the dilution was added to each embryo sample before cell lysis and RNA-seq library preparation, and ERCC reads were analyzed downstream in parallel with reads from the embryo transcriptome. RNA isolation and cDNA synthesis were carried out using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Clontech, Cat.no. 634888). Genotyping of cDNA was performed using custom primers. In brief, since loxP sites surround exons 2 and 3 of the Upf2 gene, the wild-type locus was detected using forward and reverse primers in exons 1 and 2, respectively; the knock-out locus was detected using forward and reverse primers in exons 1 and 4, respectively.
Libraries were generated from the resulting cDNA (0.2ng/ul per sample) of wild-type and Upf2-null embryos using the Nextera XT DNA library preparation kit (Illumina, Cat.no. FC-131-1024) as previously described (Mora-Castilla et al., 2016). Indexed sequence libraries were pooled for multiplexing, normalized by MiSeq read number, and paired-end sequencing was performed on a HiSeq 4000.

value: mouse blastocyst

tag: developmental stage

value: mouse embryo


title: Wild-type Mouse Blastocyst 7


title: Wild-type Mouse Blastocyst 5


title: WT con1

value: WT


title: iSLK_ORF57-Wt_latent_LANA_CUT&RUN

tag: cut&run antibody

value: LANA (Sigma, clone LN53)


title: iSLK_ORF57-Wt_latent_RNA Pol II_CUT&RUN

value: human epithelial cells


title: DNMT1_WT

description:
204998560005_R02C02
Cell line sample from Embryonic fibroblasts tissue
Infinium Mouse Methylation BeadChip


title: WT IFNa2

value: IFNa


title: Wild-type Mouse Blastocyst 2


title: Wild-type Mouse Blastocyst 6


title: 10-week-old SAMR1-7


title: WT IFNa+ RUX, TGFB, DOX1

value: RUX (0.5 µM), TGFB (10 nM), DOXY (50 µM)


title: WT IFNa1


title: WT con2


title: Wild-type Mouse Blastocyst 11


title: iSLK_ORF57-Wt_latent_H3K27ac_CUT&RUN

value: H3K27ac(CST, D5E4)


title: Wild-type Mouse Blastocyst 10


title: Knock-out Mouse Blastocyst 6


title: Knock-out Mouse Blastocyst 2


title: Wild-type Mouse Blastocyst 4


title: Wild-type Mouse Blastocyst 3


title: Knock-out Mouse Blastocyst 4


title: Knock-out Mouse Blastocyst 8


title: Wild-type Mouse Blastocyst 1


title: Knock-out Mouse Blastocyst 7


title: WT con3


title: Knock-out Mouse Blastocyst 1


title: scar_3

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

description: Single-cell RNAseq data

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome and counted using Cell Ranger (version 3.0.2; except 5.0.1 [skin_7]; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample

source_name: normal scar

extract_protocol:
6mm tissue-biopsies were dissociated using MACS Miltenyi Whole Skin Dissociation Kit (Miltenyi)
libraries were prepared using Chromium Next GEM Single Cell 3´GEM, Library & Gel Bead Kit v3.1, Chromium Nexxt GEM Chip G Single Cell Kit and Single Index Kit T Set A (all 19x Genomics, Pleasanton, CA, USA)

tag: site

value: abdomen

tag: Sex

tag: race

value: caucasian


title: 10-week-old SAMR1-4

value: kidney


title: Knock-out Mouse Blastocyst 5


title: Wild-type Mouse Blastocyst 9


title: scar_2

description: Single-cell RNAseq data

value: female


title: keloid_3L

description: Single-cell RNAseq data

source_name: keloid

value: earlobe - left

value: male


title: 32_Skin_CompoundHetero_rep2

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Fastq files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.6a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Processed data files are zipped STAR output directory (Solo.out).

source_name: skin

extract_protocol:
After euthanasia, back skins were removed from palm and dissociated into single cells by the Liberase enzyme.
RNA-seq library was constructed using a modified smart-seq2 protocol. Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI, USA). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

tag: strain

value: Col7a1 E2857X mut X Col7a1 5818delC mut

value: Live skin cells

value: post natal day 14


title: keloid_2

description: Single-cell RNAseq data

value: earlobe

value: african


title: keloid_3R

description: Single-cell RNAseq data

value: earlobe - right


title: 29_Skin_CompoundHetero_rep2

tag: cell type


title: keloid_1

description: Single-cell RNAseq data

value: sternum


title: 30_Skin_CompoundHetero_rep2


title: skin_7

description: Single-cell RNAseq data

source_name: healthy skin


title: 27_Skin_CompoundHetero_rep2


title: 28_Skin_CompoundHetero_rep2


title: input_HCC1954_1

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
ChIP-seq reads were trimmed using trim_galore (version 0.6.4 options -q 20 --stringency 2), mapped using bowtie2 (version 2.3.0) and reads with mapping quality >= 10 were selected using samtools (version 1.9).
Genome_build: hg38

source_name: HCC1954 cells

growth_protocol: HCC1954 cells (ATCC CRL-2328) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin streptomycin.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 8 minutes and quenched by 125mM glycine for 5 minutes at room temperature with gentle shaking. Cells were quickly rinsed in cold PBS twice then scraped in 5mL cold PBS on ice and collected in a 15mL conical tube. Cells were centrifuged at 4°C at 1250xg for 3 minutes. Cell pellets were rinsed with 5mL cold PBS, centrifuged at 4°C at 1250xg for 3 minutes and snap-frozen in liquid nitrogen. Cell pellets were thawed on ice and resuspended in 1mL lysis buffer 1 (50mM HEPES-KOH pH 7.5 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with protease inhibitors and incubated at 4°C on a rocker for 10 minutes. Lysates were centrifuged at 1000 rpm at 4°C for 5 minutes. Pellets were resuspended with 1mL lysis buffer 2 (10mM Tris pH 8.0 1mM EDTA 0.5mM EGTA 200mM NaCl) supplemented with protease inhibitors and incubated at 4°C on a rocker for 10 minutes. Lysates were centrifuged at 1000 rpm at 4°C for 5 minutes. Pellets were resuspended in 1mL shearing buffer (0.1% SDS, 1mM EDTA, 10mM Tris HCl pH 8.0) supplemented with protease inhibitors, then centrifuged at 1000 rpm at 4°C for 5 minutes. Pellets were resuspended in 500µL shearing buffer, transferred in a 1mL covaris milliTUBE and sonicated with a Covaris E220 sonicator for 8 minutes with 5% duty, 140 peak incident power and 200 cycles per burst. The sonicated lysates were centrifuged at 16000xg for 15 min at 4°C to pellet cellular debris. Sonicated chromatin in the supernatant was transferred to a new 1.5 ml LoBind Eppendorf tube. Immunoprecipitation and elution were performed using the ChIP- IT High Sensitivity kit (Active Motif #53040) according to the manufacturer’s instructions.
ChIP-seq libraries (GenomEast platform) were prepared from 3 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + (0-2) cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: HCC1954 cells

value: WT


title: GATA3_HCC1954_2

tag: antibody

value: GATA3 (Abcam, ab199428)


title: Knock-out Mouse Blastocyst 3

value: mouse blastocyst

value: mouse embryo


title: 26_Skin_CompoundHetero_rep2


title: FOXA1_HCC1954_2

value: FOXA1 (GeneTex, GTX100308)


title: 23_Skin_CompoundHetero_rep1


title: FOXA1_HCC1954_1


title: 25_Skin_CompoundHetero_rep2


title: 24_Skin_CompoundHetero_rep1


title: 20_Skin_CompoundHetero_rep1


title: 21_Skin_CompoundHetero_rep1


title: scar_1

description: Single-cell RNAseq data

value: abdomen

value: caucasian


title: drh3_l1pgcs_rep11

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

address: 329 sinsheimer labs

institute: University of California at Santa Cruz

description: Single set of sister Primordial Germ Cells (2 cells) dissected from an L1 larva (fed for 30-60 minutes immediately after hatching).

data_processing:
Libraries were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.
Illumina reads were mapped to the ce10 genome and  92 ERCC spike-in sequences  (Life Technologies, #4456740) using HISAT2 (v2.2.1) and parameters: --no-unal, --no-discordant, --no-mixed.  Known exons and splice sites were extracted from an Ensembl ce10 (WS220) GTF annotation file and given to HISAT2 for read mapping. Reads were de-duplicated using Samtools (v1.10) and then counted over exons and at the gene level (same ce10 annotation) using featureCounts from the Subread package (Liao et al., 2014).
Low quality transcript profiles from PGCs and EGCs were filtered from the dataset using scuttle in R (v1.2.0) (McCarthy et al., 2017). All PGCs and EGCs were used to calculate Median Absolute Deviations (MADs) for library size, number of detected features (genes), and % of library that aligned to ERCC spike-in transcripts. Samples were considered outliers and filtered from the dataset if they had a library size >3 MADs lower than the median, or a number of detected features >3 MADs lower than the median, or a % of library that aligned to ERCC spike-in transcripts >3 MADs greater than the median.
Scaling factors to normalize raw read counts were calculated using scran in R (v1.20.1) (Lun et al., 2016) for PGCs and EGCs and using DESeq2 (v1.32.0) (Love et al., 2014) for gonads. A matrix of normalized counts for samples of PGCs and EGCs is included in this submission: pgc_egcs_countsNormalized.txt
Differentially expressed genes were identified using DESeq2 (v1.32.0) (Love et al., 2014) as those with a Benjamini Hochberg-adjusted p-value < 0.05.
Assembly: ce10
Supplementary files format and content: allsamples_rawcounts_matrix.txt is a matrix containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file that also includes entries for 92 ERCC spike-in transcripts. Counts were generated using featureCounts from the subread package (Liao et al. 2014). pgcs_egcs_countsNormalized_matrix.txt contains normalized counts for all samples of PGCs and EGCs. adgerm_batch01_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch01".  adgerm_batch02_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch02".

organism: Caenorhabditis elegans

source_name: Primordial Germ Cells

growth_protocol: Animals were reared at 20˚C using standard protocols.

extract_protocol:
Single sets of 2 Primordial Germ Cells (PGCs) or 2 Early Germ Cells (EGCs) were dissected from L1 larvae or L2 larvae, respectively. PGCs and EGCs were used directly as starting material for library preparation. 20-60 gonads were dissected from 1st day adult hermaphrodites and then cut at the gonad bend. Only the distal halves were kept to exclude oocytes and several somatic gonad cells from our analysis. Gonads were vortexed in Trizol and stored at -80˚C. RNAs were then extract from those gonads using 1-bromo-3-chloropropane (Sigma #B9673), precipitated using isopropanol, pelleted by a 13,000 rcf spin for 15 minutes at 4˚C, and washed using ethanol.
Libraries were constructed according to manufacturer's recommendation. PGCs/EGCs: RNAs were converted into double-stranded cDNAs using a modified smart-seq2 protocol (Picelli et al., 2014). Illumina sequencing libraries were then prepared from those cDNAs using Illumina's Nextera XT kit. Gonads: mRNAs were isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then used to prepare Illumina sequencing libraries using the NEBNext Ultra RNA Library Prep Kit (#E7530).

tag: source strain

tag: stage and sex

value: L1 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: 19_Skin_CompoundHetero_rep1

value: Col7a1 E2857X mut X Col7a1 5818delC mut

tag: age


title: 17_Skin_CompoundHetero_rep1

tag: genotype

value: Live skin cells


title: 18_Skin_CompoundHetero_rep1

value: post natal day 14


title: 31_Skin_CompoundHetero_rep2


title: drh3_l1pgcs_rep09


title: drh3_l1pgcs_rep10


title: 16_Skin_WT_rep2

value: wild type


title: 15_Skin_WT_rep2


title: drh3_l1pgcs_rep07


title: 14_Skin_WT_rep2


title: drh3_l1pgcs_rep06


title: drh3_l1pgcs_rep04


title: 10_Skin_WT_rep2


title: 22_Skin_CompoundHetero_rep1


title: 11_Skin_WT_rep2


title: 13_Skin_WT_rep2


title: drh3_l1pgcs_rep05

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations higher than the median of all PGCs and EGCs and the number of detected features (genes) was >3 median absolute deviations lower than the median of all PGCs and EGCs.


title: 07_Skin_WT_rep1


title: drh3_l1pgcs_rep01

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations greater than the median of all PGCs and EGCs.


title: drh3_l1pgcs_rep03


title: 12_Skin_WT_rep2


title: mrg1_l1pgcs_rep09

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mrg-1(qa6200) M-Z- III


title: GATA3_HCC1954_1

value: HCC1954 cells


title: 06_Skin_WT_rep1


title: mrg1_l1pgcs_rep11


title: mrg1_l1pgcs_rep06


title: drh3_l1pgcs_rep08


title: mrg1_l1pgcs_rep10


title: 09_Skin_WT_rep2


title: 02_Skin_WT_rep1


title: mrg1_l1pgcs_rep08


title: 04_Skin_WT_rep1


title: 08_Skin_WT_rep1


title: drh3_l1pgcs_rep02

value: yes:the library size was >3 median absolute deviations lower than the median of all PGCs and EGCs.


title: mrg1_l1pgcs_rep07


title: 03_Skin_WT_rep1


title: mrg1_l1pgcs_rep05

value: yes:we found reads containing wild-type sequence that aligned to the mrg-1 locus. Thus, these PGCs did not come from mrg-1 M-Z- L1 larva. Furthmore, PCA analysis found that this sample clustered with samples of PGCs dissected from wild-type larvae.


title: mrg1_l1pgcs_rep03


title: mrg1_l1pgcs_rep01


title: 717/P/14_R3

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

institute: Max Perutz Labs

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to C. auris genome (B8441) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT).  Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B8441 (settings: -f bam  -t gene -i ID).
Assembly: Differential gene expression analysis was done using the glm approach in edgeR (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: Cells were grown to the logarithmic growh phase in YPD at 30 °C.

extract_protocol:
Total RNA was purified using GeneJET RNA purification kit (Thermo Scientific).
5μg DNase-treated total RNA was subjected to mRNA was enrichment using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: clinical isolate:717/P/14


title: mrg1_l1pgcs_rep04


title: 717/P/14_R2


title: mes3_l1pgcs_rep11

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I


title: mes3_l1pgcs_rep10


title: mes3_l1pgcs_rep09


title: 05_Skin_WT_rep1


title: 01_Skin_WT_rep1


title: 717/P/14_R1


title: mrg1_l1pgcs_rep02


title: 513/P/14_R3

value: clinical isolate:513/P/14


title: mes3_l1pgcs_rep06


title: mes3_l1pgcs_rep08


title: 471a/P/14-R_R2

value: clinical isolate:471a/P/14-R


title: 462/P/14_R3

value: clinical isolate:462/P/14


title: 513/P/14_R2


title: 471a/P/14-R_R1


title: mes3_l1pgcs_rep04

value: L1 hermaphrodite larva


title: 513/P/14_R1


title: mes3_l1pgcs_rep03

value: no


title: 471a/P/14-R_R3


title: mes3_l1pgcs_rep07

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations greater than the median of all PGCs and EGCs and the number of detected features (genes) was >3 median absolute deviations lower than the median of all PGCs and EGCs.


title: mes3_l1pgcs_rep05


title: 1184/P/13-R_R2

value: clinical isolate:1184/P/13-R


title: 462/P/14_R2


title: 1184/P/13-R_R3


title: 462/P/14_R1


title: mes4_l2germ_rep03

description: Set of 2 Early Germ Cells dissected from an L2 larva (fed for ~20 hours immediately after hatching).

source_name: Early Germ Cells

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

value: L2 hermaphrodite larva


title: mes3_l1pgcs_rep02


title: dscATAC-seq_P93

city: Koto-ku

first: Reo

last: Maruyama

state: Tokyo

department: Cancer Institute

institute: Japanese Foundation For Cancer Research

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Fragment files were generated using Bio-Rad ATAC-Seq Analysis Toolkit Tutorial with the default setting.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include chromosomal locations for each fragment with cell barcode ID.

source_name: Breast Cancer

extract_protocol:
Breast cancer specimens were obtained by core needle biopsy of surgically removed tumors. Specimens were dissociated into single cells using a MACS Tumor Dissociation Kit and a gentle MACS dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Single cells were cryopreserved using the Banbanker.
Libraries were prepared with the SureCell ATAC-seq Library Preparation kit (BioRad) for ddSEQ.

tag: disease status

value: Breast Cancer

tag: tissue

value: Breast Cancer Tissue

tag: subtype

tag: gender

value: Female


title: mes4_l1pgcs_rep11


title: dscATAC-seq_P64

value: Luminal


title: dscATAC-seq_P50


title: mes4_l1pgcs_rep10


title: mes4_l1pgcs_rep08


title: 1184/P/13-R_R1


title: dscATAC-seq_P40


title: dscATAC-seq_P51


title: dscATAC-seq_P52


title: dscATAC-seq_P49


title: mes4_l1pgcs_rep06


title: mes4_l1pgcs_rep02


title: dscATAC-seq_P34


title: mes4_l1pgcs_rep03


title: dscATAC-seq_P41

value: TNBC


title: mes4_l1pgcs_rep04


title: dscATAC-seq_P38


title: mes4_l1pgcs_rep07


title: dscATAC-seq_P54


title: dscATAC-seq_P20N

value: Lymph Node Metastasis


title: dscATAC-seq_P39


title: mes3_l1pgcs_rep01


title: mes4_l2germ_rep02


title: wt_l1pgcs_rep09

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I


title: ATAC-seq_H1hESC_dox_biologicalRep2

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

institute: RIKEN, Yokohama

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq program. STAR was used to index the human reference genome (hg19), obtained from UCSC, and align the resulting fastq files. The resulting bam files with the mapped reads were then converted to tag directories with subsequent peaks calling using the HOMER suit of programs. HOMER was also employed for counting the reads in the identified peak regions. The raw tag counts from the peaks were then imported to R/Bioconductor and differential peak analysis was performed using the edgeR package and its general linear models pipeline. Peaks with an FDR adjusted P-value < 0.05 were termed as control or DUX4-activated.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq peak bed files.

source_name: Embryo

growth_protocol: hESC lines H1 (WA01) and H9 (WA09) were maintained on Geltrex, hESC-qualified, reduced growth factor basement membrane matrix-coated tissue culture dishes in Essential 8 culture medium and passaged every three to five days by 3-5-min incubation with 0.5 mM EDTA (all from Thermo Fisher Scientific).

extract_protocol: The ATAC-sequencing libraries were prepared as in Buenrostro et al 2015 Curr. Protoc. Mol. Biol. 5×104 EmGFP (-) and EmGFP (+) TetOn-hESCs (H1 clone 2, H1 clone 8, H9 clone 3 and H9 clone 4) were centrifuged at 500×g for 5 min. The pellets were washed in cold 1× PBS by centrifugation at 500×g for 5min. Each cell pellet was lysed in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and centrifuged at 500×g at 4°C for 10 min. The pellet was then resuspended in the transposase reaction mix (2.5 μl of transposase in TD buffer (Nextera DNA library preparation kit, Illumina) and incubated at 37°C for 30 min. The reactions were purified through columns and eluted in 20 μl. After addition of the barcode oligos the DNA samples were amplified for 12 cycles (98°C for 10 s, 63°C for 30 s and 72°C for 60 s) in Phusion PCR master mix (Thermo Fisher Scientific). The PCR products were purified through the columns and eluted in 20 μl.

treatment_protocol: hESCs were incubated with StemPro Accutase (Thermo Fisher Scientific) until the edges of the colonies started to curl up. The Accutase was aspirated and the cells were gently detached in cold 5% FBS (Thermo Fisher Scientific) 1×PBS (Corning) and counted. One million cells were centrifuged at 107×g for 5 min and the pellet was transferred into 120 μl of R-buffer containing 1 μg of pB-tight-DUX4-ires-EmGFP-pA-PGK-Puro, 0.5 μg of pBASE and 0.5 μg of rtTA-M2-IN plasmids. 100 μl of the cell-plasmid suspension was electroporated with two pulses of 1100V, 20 ms pulse width, using Neon Transfection system (Thermo Fischer Scientific). The electroporated cells were plated on Geltrex-coated dishes in Essential 8 medium with 10 μM ROCK inhibitor Y27632 (Selleckhem). The following day, the medium was exchanged with fresh Essential 8 medium without ROCK inhibitor. The cells were selected with Puromycin at 0.3 μg/ml.  The TetOn-DUX4 hESC clones were picked manually on Geltrex-coated 96-well plates, expanded and selected again with Puromycin. Appearance of the EmGFP reporter protein was tested using Doxycycline at concentrations ranging from 0.2 μg/ml to 1.0 μg/ml and detected using an EVOS FL Cell imaging system (Thermo Fisher Scientific). For the experiments presented in this paper, the DUX4 TetOn hESCs have been treated with 1μg/ml of Doxycycline for 4 hours.

tag: cell line

value: H1 hESC

tag: treatment

value: Doxycycline treated

tag: rna population


title: mes4_l1pgcs_rep01


title: wt_l2germ_rep01


title: ATAC-seq_H9hESC_dox_biologicalRep2

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq program. STAR was used to index the human reference genome (hg19), obtained from UCSC, and align the resulting fastq files. The resulting bam files with the mapped reads were then converted to tag directories with subsequent peaks calling using the HOMER suit of programs. HOMER was also employed for counting the reads in the identified peak regions. The raw tag counts from the peaks were then imported to R/Bioconductor and differential peak analysis was performed using the edgeR package and its general linear models pipeline. Peaks with an FDR adjusted P-value < 0.05 were termed as control or DUX4-activated.
Supplementary_files_format_and_content: ATAC-seq peak bed files.

value: H9 hESC


title: wt_l1pgcs_rep11

value: L1 hermaphrodite larva


title: dscATAC-seq_P44


title: wt_l1pgcs_rep10

value: yes:the library size was >3 median absolute deviations lower than the median of all PGCs and EGCs and the number of detected features (genes) was >3 median absolute deviations lower than the median of all PGCs and EGCs.


title: wt_l1pgcs_rep08

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations higher from the median of all PGCs and EGCs.


title: wt_l1pgcs_rep07

value: no


title: ATAC-seq_H1hESC_dox_biologicalRep1


title: ATAC-seq_H9hESC_control_biologicalRep1

value: Control


title: ATAC-seq_H9hESC_dox_biologicalRep1


title: wt_l1pgcs_rep06


title: ATAC-seq_H1hESC_control_biologicalRep2


title: wt_l1pgcs_rep01


title: ATAC-seq_H1hESC_control_biologicalRep1


title: dscATAC-seq_P33


title: dscATAC-seq_P35


title: wt_l2germ_rep02

value: L2 hermaphrodite larva

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations higher than the median of all PGCs and EGCs and the number of detected features (genes) was >3 median absolute deviations lower than the meidan of all PGCs and EGCs.


title: wt_l1pgcs_rep02


title: wt_l1pgcs_rep03


title: ATAC-seq_H9hESC_control_biologicalRep2


title: wt_l1pgcs_rep04


title: Set_2_20d_Control_brain_3

city: Philadelphia

first: Ananth

last: Srinivasan

address: 433 S University Avenue

institute: University of Pennsylvania

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to Drosophila melanogaster genome r6.36 using HISAT2 default parameters
HTSeq-counts was used to generate gene counts (-f bam -r name -s reverse --additional-attr=transcript_symbol)
DESeq2 was used to perform a differential gene analysis
Genome_build: Drosophila melanogaster genome r6.36
Supplementary_files_format_and_content: Matrix table with counts and gene names for every sample and replicate (both RNA-seq sets)

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Flies were grown in vials with standard molasses food at 25ºC

extract_protocol:
Following brain dissections, RNA from tissue was extracted using standard trizol extraction method followed by purification with RNA Clean & Concentrator Kit R10114
RNA libraries were prepared using TruSeq w/PolyA selection

value: brain

value: 5905 (Control)


title: Set_2_50d_Control_brain_1


title: liver_het_rat6

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Genome_build: rn6
Expression levels of individual transcripts were estimated by kallisto (v0.46.0) using Ensembl transcriptome (release 97) as a reference.
Supplementary_files_format_and_content: Abundance files contain transcript expression levels as reported by kallisto.

organism: Rattus norvegicus

source_name: Liver, heterozygous Tti2 knockout

extract_protocol:
RNA was isolated from the frozen samples of the hippocampus, liver, soleus muscle and peritoneal adipose tissue using RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. Tissues were homogenised in QIAzol with TissueRuptor (Qiagen). Genomic DNA was removed by on-column DNase digestion.
Sequencing libraries were prepared using NEBNext¨ Ultraª II Directional RNA Library Prep Kit for Illumina¨ from 300 ng of total RNA, with mRNA enrichment by poly-dT pull down using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer's instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 1:0.9. Dual indexing was done during the following PCR enrichment (12 cycles, 65 ¡C) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent). For Illumina flowcell production, samples were equimolarly pooled and sequenced 75bp single-end on multiple Illumina NextSeq 500 flowcells, aiming for approximately 30 million sequencing reads per sample.

value: liver

value: SHR/OlaIpcv


title: wt_l1pgcs_rep05


title: soleus muscle_het_rat5

source_name: Muscle, heterozygous Tti2 knockout

value: soleus muscle


title: Set_2_50d_Control_brain_2


title: soleus muscle_het_rat6


title: liver_het_rat5


title: Set_2_50d_Control_brain_3


title: peritoneal fat_het_rat5

source_name: Fat, heterozygous Tti2 knockout

value: peritoneal fat


title: Set_2_20d_Control_brain_2


title: liver_het_rat4


title: Set_2_3d_Control_brain_3


title: hippocampus_het_rat5

source_name: Hippocampus, heterozygous Tti2 knockout

value: hippocampus


title: mes4_l2germ_rep01

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V


title: Set_2_20d_Control_brain_1


title: Set_2_3d_Control_brain_2


title: soleus muscle_het_rat2


title: soleus muscle_het_rat3


title: peritoneal fat_het_rat3


title: soleus muscle_het_rat4


title: Set_1_20d_miR-34_brain_2


title: liver_het_rat2


title: Set_2_3d_Control_brain_1


title: Set_1_20d_miR-34_brain_3


title: hippocampus_het_rat3


title: Set_1_20d_miR-34_brain_1


title: peritoneal fat_het_rat2


title: liver_het_rat1


title: hippocampus_het_rat2


title: Set_1_20d_Control_brain_3


title: hippocampus_het_rat1


title: peritoneal fat_het_rat1


title: Set_1_20d_Control_brain_1


title: liver_wt_rat6

source_name: Liver, wild type

value: wild type


title: hippocampus_het_rat4


title: peritoneal fat_het_rat4


title: hippocampus_wt_rat6

source_name: Hippocampus, wild type


title: Set_1_20d_Control_brain_2


title: soleus muscle_wt_rat5

source_name: Muscle, wild type


title: Set_1_3d_miR-34_brain_3


title: Set_1_3d_miR-34_brain_2


title: liver_wt_rat5


title: hippocampus_wt_rat5


title: peritoneal fat_wt_rat5

source_name: Fat, wild type


title: mes4_l1pgcs_rep09


title: Set_1_3d_miR-34_brain_1


title: peritoneal fat_wt_rat4


title: liver_wt_rat4


title: soleus muscle_wt_rat4


title: Set_1_3d_Control_brain_3


title: soleus muscle_wt_rat3


title: peritoneal fat_wt_rat3


title: hippocampus_wt_rat3


title: Set_1_3d_Control_brain_2


title: soleus muscle_wt_rat2


title: Set_1_3d_Control_brain_1


title: liver_wt_rat2


title: soleus muscle_wt_rat6


title: hippocampus_wt_rat2


title: peritoneal fat_wt_rat2


title: liver_wt_rat1


title: Healthy_9

city: Zurich

first: Maria

middle: Desemparats

last: Saenz-de-Juano

address: Universitatstrasse 2

country: Switzerland

institute: ETH Zurich

description:
small RNA
C2_C3

data_processing:
Remove Adapter:  Tool “Clip” from Galaxy
Remove short reads (<25 nucleotides):  Tool “Clip” from Galaxy
Remove Low Quality reads:  Tool "FASTQ Quality Trimmer" from Galaxy
Remove PCR duplicates:  Tool “Collapse” from galaxy
Filtering:  "Count Per Million (CPM) Filter" from Galaxy
miRNA Aligment:  Aligment was performed using "blastn-short". Only alignments without any mismatch were included.
IsomiRs grouping:  IsomiRs  were grouped in their canonical form and their counts were sum, using the tool "Group on data" from Galaxy
Genome_build: miRBase database v22.1.
Supplementary_files_format_and_content: Normalization of read counts was done using TMM and GLM robust (estimateGLMRobustDisp) included in edgeR

organism: Bos taurus

source_name: Milk EV

extract_protocol:
miRNeasy MicroKit  (QIAGEN) following manufacturer's instructions
NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific)  following manufacturer's instructions

tag: type

value: Healthy

tag: animal

value: Cow 11

tag: sample type

value: Milk EV


title: cortex, YC151

city: Houston

first: Yi-Ting

last: Cheng

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression between different samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM normalized abundance measurements from astrocytes

source_name: cortex

extract_protocol:
Tissue was dissociated as previously described. (Lin et al., Nat Neurosci 2017)
Illumina sequencing libraries were constructed from 500pg - 1ng of total RNA using the Trio RNA-seq (Nugen)

value: cortex

tag: cell type

value: astrocyte

value: Gabbr1 cKO


title: cortex, YC148

value: Gabbr1 control


title: Low_SCC_9

description:
small RNA
C5_L1

value: Cow 14


title: peritoneal fat_wt_rat1

tag: strain


title: High_SCC_8

description:
small RNA
C5_H1


title: hippocampus_wt_rat1


title: RNA_Ctrl_4_ISC

city: Bethesda

first: Han-Yu

last: Shih

state: MD

address: 10 Center Drive Rm 5S261

institute: National Eye Institute

data_processing:
ATAC-seq:
Omni-ATAC-seq reads from biological replicates were mapped to the mouse genome (mm10 assembly) using Bowtie 1.3.0 with parameters -v 2 -m 1 --pairtries 200.
Peaks were called using Macs1 (version 1.4.3) with a p-value cutoff of 1E-5. Peak files were merged for each condition using homer’s mergePeaks command with parameter -d given. Peak files were converted to bed format using HOMER’s pos2bed.pl function and compared using bedtools (version 2.30.0). Only regions called in both replicates were used in downstream analysis. A master list of peaks was generated using HOMER’s mergePeaks function with -d given, and annotated using HOMER’s annotatePeaks.pl function, with reference genome mm10, -size given, and tag counts from tag directories created previously.
RNA-seq:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. Read counts were generated using HTSeq (version 0.11.4), with parameters -m union, --stranded=reverse, and the mm10 genes.gtf file from UCSC.
Differential gene expression analysis was performed using DESeq2 (version 1.30.1) in RStudio (version 1.4.1106) using R (version 4.0.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for ATAC-seq and RNA-seq

source_name: colon crypt cell

extract_protocol:
cell isolation protocol: For colon crypt cell isolation, take colon carefully and put into 10 cm dish containing cold PBS, associated fat tissue was removed carefully. Flush the lumen of the intestine with cold PBS, cut the colon longitudinally with scissors and place in a 50ml tube with 25ml cold PBS, invert 10~15 times and remove PBS (repeat until the supernatant no longer contains any visible debris), cut the colon into around 5mm pieces and place into cold 10ml 5mM EDTA-PBS. Vigorously triturate the fragments by pipetting up and down into a 10ml pipette 15 times, Let the fragments settle by gravity for 30 sec, aspirate the supernatant (Be careful to avoid the intestinal fragments). Replace with 10ml 5mM EDTA-PBS and place at 4°C on roller for 15 min and remove the EDTA-PBS from the tube by aspiration. Wash with PBS twice and add 3ml Basal media (RPMI 1640) containing 500U/ml Collagenase Type IV and pipette up and down 5 times using 5ml pipette. Place the tubes in 37°C water bath for 30-40min. Add 10ml cold PBS and then vigorously vortex with a 10ml pipette (x10 times), Collect this 10 ml supernatant fraction in a separate tube. Repeat the cold PBS/vortex 2 more times, and combined 2nd and 3rd round wash into 50ml tube to gather crypt cells.
Omni-ATAC protocol (Corces et al., 2017). Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. ImmediWe followed the Omni-ATAC protocol (Corces et al., 2017). Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500g for 10 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. ately after lysis, nuclei were spun at 500g for 10 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library.
ATAC-seq: PCR was performed to amplify the library. After the PCR reaction, libraries were purified with SPRI (Beckman) beads and deep sequencing was performed by Sequencing Facility in NCI.
For RNA-seq, the mRNA from fresh isolated 2-5 million colon crypt ISCs was isolated by using RNeasy Plus Micro Kit (Qiagen, cat:74034) and the concentration and QC was determined by Agilent technologies.
RNA-Seq samples were pooled and sequenced on NextSeq using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

value: Colon

tag: genotype/variation

tag: culture condition

value: ex vivo

value: intestinal epithelial cells.


title: RNA_Ctrl_2_ISC


title: Low_SCC_8

description:
small RNA
C4_L1

value: Cow 8


title: RNA_Ctrl_3_ISC


title: cortex, YC145


title: cortex, YC142


title: RNA_St6_4_ISC


title: High_SCC_7

description:
small RNA
C4_H3


title: High_SCC_9

description:
small RNA
C6_H2

value: Cow 15


title: olfactory bulb, YC99

source_name: olfactory bulb

value: olfactory bulb


title: olfactory bulb, YC98


title: High_SCC_6

description:
small RNA
C4_H2


title: cortex, YC154


title: olfactory bulb, YC97


title: High_SCC_5

description:
small RNA
C5_H5


title: ATAC_Ctrl_3_ISC


title: ATAC_Ctrl_2_ISC


title: RNA_St6_1_ISC


title: High_SCC_4

description:
small RNA
C5_H2


title: ATAC_St6_3_ISC


title: ATAC_Ctrl_1_ISC


title: olfactory bulb, YC84


title: olfactory bulb, YC81


title: Healthy_8

description:
small RNA
C3_C1

value: Cow 12


title: RNA_Ctrl_1_ISC


title: olfactory bulb, YC79


title: RNA_St6_3_ISC


title: SM_3A_3

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Reference mouse genome mm10 and gene model annotation files were directly downloaded from the genome website browser (NCBI/UCSC/Ensembl)
The STAR (Spliced Transcripts Alignment to a Reference) software was used to align paired-end clean reads to the reference genome, and to count number reads per gene while mapping.
FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: muscle

growth_protocol: Mice fed a standard normal diet.

extract_protocol:
Total RNA was extracted from frozen liver and skeletal muscle using a RNeasy Mini Kit (QIAGEN) and a RNeasy Fibrous Tissue Mini Kit (QIAGEN), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For liver RNA-sequencing of insulin stimulation, ERRα WT or KO mice on a C57BL/6N genetic background were randomly assigned to two groups and fasted for 12 h overnight followed by intraperitoneal injection of saline or 1 unit/kg insulin.

value: muscle

value: Err-alpha 3SA


title: Low_SCC_7

description:
small RNA
C4_L3


title: High_SCC_2

description:
small RNA
C6_H1


title: SM_3A_4


title: SM_WT_2

value: WT


title: SM_3A_2


title: SM_WT_4


title: olfactory bulb, YC73


title: ATAC_St6_1_ISC


title: Healthy_7

description:
small RNA
C1_C2

value: Healthy

value: Cow 9


title: SM_3A_1


title: olfactory bulb, YC71


title: Low_SCC_6

description:
small RNA
C5_L3

value: Milk EV


title: SM_WT_3


title: olfactory bulb, YC72

value: astrocyte


title: ATAC_St6_2_ISC


title: SM_WT_1


title: High_SCC_3

description:
small RNA
C6_H6


title: hippocampus, YC119v2

source_name: hippocampus

value: hippocampus


title: L_SA_2

source_name: Liver

value: Liver


title: hippocampus, YC118v2


title: hippocampus, YC120


title: L_WT_1


title: L_SA_3


title: KO_INS_2

value: Err-alpha KO

value: insulin


title: L_SA_1


title: L_WT_4


title: KO_INS_1


title: Healthy_6

description:
small RNA
C3_C2


title: hippocampus, YC102


title: hippocampus, YC100


title: High_SCC_1

description:
small RNA
C4_H1


title: L_WT_2


title: Low_SCC_4

description:
small RNA
C6_L1


title: Healthy_4

description:
small RNA
C3_C3


title: KO_C_1

value: control


title: hippocampus, YC105


title: L_SA_4


title: WT_INS_4


title: KO_C_4


title: hippocampus, YC75


title: Low_SCC_3

description:
small RNA
C6_L3


title: KO_INS_4


title: L_WT_3