title: p_287

tag: visit

tag: treatment arm

value: White


title: S113

status: Public on Feb 01 2022

type: RNA

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

country: USA

institute: The University of Texas Health Science Center at Houston

hyb_protocol: Fragmented Cy3-labeled cRNA was hybridized onto Agilent Human GE 44K V2 Microarray (Cat# G4845A, 4x44K) for 17 hrs at 65C with constant rotation (10 rpm).

scan_protocol: The slides were scanned using an Agilent microarray scanner.

data_processing: Data were examined for probes that were flagged by Agilent as non-uniform outliers.  Samples were excluded if >1% of probes for that sample were flagged.  Data were imported into BRB Array Tools (National Cancer Institute) as processed signal values, as recommended by Agilent.  Values were excluded if the mean signal was not significantly greater than background.  For genes with replicate probes, the average value of the replicates was used.  Values were then log2 transformed followed by quantile normalization.  Genes with >20% missing values across arrays were filtered out.

molecule: total RNA

organism: Homo sapiens

source_name: skin

label_protocol: Total RNA (100-200 ng) from each sample was reverse transcribed with Agilent spike RNA and amplification carried out using the one color Microarray-Based Gene Expression Analysis low RNA input quick amplification kit (Agilent).

growth_protocol: One 3-millimeter punch biopsy was obtained from the forearm skin.

extract_protocol: RNA was extracted using miRNeasy Mini kits (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Sample was immersed in RNAlater solution (Qiagen).

tag: condition

value: systemic sclerosis patient

tag: subject

tag: sample number within subject

tag: age

tag: gender

value: Female

tag: race

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere

value: Positive


title: p_288

type: SRA

library_source: transcriptomic

data_processing:
Globin related genes were removed prior to further analysis.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Transcript data were normalized with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: csv file format of DESeq2 normalized and log2 transformed counts.

source_name: whole blood sample, systemic sclerosis patient

extract_protocol:
PBC RNA was extracted according to the manufacturer’s protocol. RNA integrity was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).   mRNA was enriched from total RNA using oligo(dt) beads (NEBNext Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA.  The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing, and adapter ligation, size selection and PCR enrichment.
Libraries are pooled into Novaseq6000 machines according to molarity and expected data volume.

value: Baseline

value: mycophenolate mofetil

tag: age at baseline visit

value: Asian

tag: fvc at baseline visit

tag: diffuse


title: 40

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

description:
replicate 5
12:12-DARK-5

data_processing:
Kallisto (https://pachterlab.github.io/kallisto/) was used to align to the reference transcriptome (ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/cdna/) and estimate transcript abundance.
Supplementary_files_format_and_content: TPM

organism: Mus musculus

source_name: KrasG12D/+  murine lung tumor

growth_protocol: KrasLSL-G12D/+ (K) mice in pure C57BL/6J background were infected intratracheally with lentivirus containing Cre recombinase, lenti-Cre (PGK-Cre, gift from Tyler Jacks), at a viral titer of 5 x 10^5 plaque forming units (PFU) per mouse.

extract_protocol:
Total RNA from lung tumors and remaining lung tissues was isolated using Qiazol reagent using standard protocols (Qiagen cat # 799306). RNA purity was assessed by Agilent 2100 Bioanalyzer.
Total RNA samples were sent to BGI Group, Beijing, China, for library preparation and sequencing. Reads (single-end 50bp at a sequencing depth of 20 million reads per sample) were generated by BGISEQ-500

treatment_protocol: Mice were housed into standard light conditions (12:12LD) or chronic jetlag (CJL) 5 weeks post infection with lenti-Cre, for 20 weeks. Sacrifices during the light (ZT9) or dark phase (ZT21) were carried out under normal or red light, respectively, at 25 weeks post lentivirus infection. Mice were euthanized by carbon dioxide asphyxiation. Lung tumors and remaining lung tissues were snap-frozen into liquid nitrogen ad stored at -80∘C until RNA extraction.

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung tumor

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):12:12LD

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: S038

tag: condition

value: Control

tag: sample number within subject

value: Male


title: S114

tag: subject

tag: age

tag: gender


title: WT treated with PBS rep1

city: Ann Arbor

first: Swati

last: Bhattacharyya

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version2.1.0 with parameters -p --dta -x
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample.

extract_protocol:
Skin were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library  Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: 6-8 weeks female mice were randomized to start treatment with s.c. bleomycin, a fibrosis inducing agent (5 mg/kg/day), or PBS given for 10 days (5 days/week). Mice were then sacrificed at day 22

tag: strain

tag: tissue

value: skin

value: 9-11 week

tag: genotype

value: wild type

tag: treatment

value: subcutaneous injection with PBS for 10 days


title: S115

tag: race

value: White

tag: mrss at baseline sample

tag: diffuse at baseline sample

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii

tag: anti-centromere


title: 9_6_Null

city: Glasgow

first: Tom

last: Bird

address: Switchback Road

country: United Kingdom

institute: Beatson Insistute for Cancer Research

data_processing:
Reads were aligned with CellRanger v.4.0 to the ensemble GRCm38.99 reference genome with AAV8-TBG-Cre and AAV8-TBG-Null sequences.
Raw bc matrix files for each sample were processed in R bioconductor with the DropletUtils package to transform matrices into SingleCellExperiment objects and filter out empty droplets.
All SCE objects were merged into one and "bad quality" cells (<75 or >3000 genes expressed or >50% mitochondrial gene expression) were filtered out. Only genes expressed in at least 10 cells with 1 UMI count were kept for downstream analysis.
Counts were normalised and log-transformed using the normalisation by deconvolution method, PCA and UMAP were computed all using functions from the Scater package.
Clustering was performed using Seurat with eps = 0.5 using the control (Null) cells as a reference and projecting the Cre cells into the reference clustering as explained in the methods of the paper.
Genome_build: ensemble GRCm38.99 with AAV8-TBG-Cre and AAV8-TBG-Null sequences.
Supplementary_files_format_and_content: txt file containing a matrix with raw counts per gene and cells. Only cells that passed Quality Control thresholds are included in the matrix.
Supplementary_files_format_and_content: rds file containing a SingleCellExperiment object generated with R Bioconductor (version 4.0) with processed data of cells that passed Quality Control thresholds, including dimensionality reduction (PCA and UMAP) as well as clustering labelling of each cell type.

source_name: kidney

extract_protocol:
The left kidney was decapsulated, cut in several pieces and 0.15-0.20g of kidney tissue were put in a GentleMACs C tube with with dissociation buffer and were dissociated using the Multi-tissue dissociation kit 1 (Miltenyi, 130-110-201) (Composition of dissociation buffer: 2.35ml serum-free RPMI culture medium (Gibco), 100μl enzyme D, 50μl enzyme R and 12.5μl enzyme A). An initial round of dissociation in the GentleMACS dissociator (“heart_01_01” programme (15s)) was followed by 30 minute incubation in a waterbath (37 oC) which was followed by another round of dissociation (“heart_01_02” programme, 30s). When the second round of dissociation finished, 8ml of sterile PBS/10% FBS were added to the C tubes to stop the reaction. The samples were passed through a 40μm cell strainer into a 50ml falcon tube. The samples were washed with PBS, spun down and resuspended in 1ml red blood cell lysis buffer (8.29g NH4Cl, 1g KHCO3 and 37.2g Na2EDTA in PBS) for 30 seconds. This was followed by incubation with debris removal solution (Miltenyi) and eventually the cells were resuspended in 10ml cold PBS/10% FBS/2.5mM EDTA.
Cell viability and concentration were determined using the Trypan Blue assay. 20,000- 40,000 cells were loaded on a 10x Chromium chip (1 sample per lane). Cleanup, reverse transcription, cDNA amplification and library preparation were performed using the Chromium Single cell 3’ Reagent Kits (v3) as per the manufacturer’s instructions
Droplet-based scRNA-seq (Chromium 10x chip)

treatment_protocol: 6 mice with floxed Mdm2 exons 5 and 6 (Mdm2Ex5/6fl) were i.v. injected with 2x1011 genomic copies of AAV8-TBG-Cre (n=3 mice) (Addgene, 107787-AAV8) or AAV8-TBG-Null (n=3 mice) (Addgene, 105536-AAV8). 4 days post AAV injection the mice were culled and their kidneys were harvested.

value: kidney

value: mixed (129P2/OlaHsdWtsi;C57Bl/6J)

value: WT

tag: aav genotype

tag: sequencing batch


title: 9_5_Null


title: S311

tag: condition

value: systemic sclerosis patient

tag: sample number within subject

value: Female

value: Diffuse

value: Negative


title: 21

description:
replicate 4
12:12-DARK-4

tag: background strain

tag: tissue (lung tumor vs rest of lung)

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: 19

description:
replicate 3
12:12-DARK-1


title: 9_4_Cre

tag: tissue

tag: strain

tag: genotype

value: Cre


title: S012

tag: age

tag: gender

tag: race

value: Black


title: S092

value: Hispanic


title: p_286

tag: subject

tag: visit

value: Baseline

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit

tag: fvc at baseline visit

tag: diffuse


title: 9_3_Cre

tag: aav genotype

tag: sequencing batch


title: p_283

tag: condition

value: Asian


title: 9_2_Null


title: 3

description:
replicate 1
12:12-DARK-1

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung tumor

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):12:12LD


title: S052

value: Control

tag: sample number within subject

value: Male


title: p_282

value: cyclophosphamide

value: African American


title: 71

description:
replicate 6
CJL-LIGHT-6

value: 12ld vs chronic jetlag cjl):CJL

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: 9_1_Cre

tag: tissue

value: kidney

tag: strain

value: mixed (129P2/OlaHsdWtsi;C57Bl/6J)

tag: genotype

value: WT


title: p_281

value: systemic sclerosis patient

tag: subject

tag: race

value: White

tag: gender

value: Female


title: S276

tag: age


title: 70

description:
replicate 5
CJL-LIGHT-5


title: p_285

tag: visit

value: Month 12

tag: treatment arm

tag: age at baseline visit

tag: fvc at baseline visit


title: S014

tag: condition


title: p_280

value: Baseline

tag: diffuse


title: B6-pDC #3

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
RNAsik pipeline was used to process the data
It uses STAR to align the raw fastq files to the reference genome
Qualimap and samtools is used to collect QC metrics, multiqc is used to collate all QC metrics and evaluate each sample
FeatureCounts was run on the bam files to generate a counts matrix
The counts matrix was uploaded to Degust for analysis
Genome_build: ensembl mm10
Supplementary_files_format_and_content: counts - tab separated file

source_name: Spleen

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (QIAGEN) and residual genomic DNA removed using Rnase-free Dnase (QIAGEN).
Sample libraries were constructed using Illumina TruSeq Stranded mRNA kit. Libraries were quantitated using Qubit DNA HS kit (Thermofisher Scientific) and checked for adaptor contamination using Bioanalyzer 2100 (Agilent Technologies). Sample libraries were then sequenced by Micromon Genomics at Monash University on NextSeq500 using High-Output SBS chemistry (Illumina) at 1.8pM library concentration and 1x75b read length.

tag: state

value: Steady State

value: Spleen

tag: cell type

value: DC

tag: cell subset

value: pDC


title: p_279


title: 68

description:
replicate 4
CJL-LIGHT-4

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung tumor

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: B6-CD8pos cDC1 #3

tag: strain

tag: tissue

value: CD8pos cDC1


title: 13

description:
replicate 2
12:12-DARK-2

value: 12ld vs chronic jetlag cjl):12:12LD


title: 10

description:
replicate 2
CJL-LIGHT-2


title: B6-pDC #2


title: S296

value: Control

tag: sample number within subject

tag: gender

tag: race


title: 2

description:
replicate 1
CJL-LIGHT-1

value: 12ld vs chronic jetlag cjl):CJL


title: B6-CD8neg cDC2 #3

value: CD8neg cDC2


title: S259

tag: age


title: S237

value: Hispanic


title: S230


title: B6-CD8neg cDC2 #2


title: 54

description:
replicate 6
12:12-LIGHT-6


title: S003

value: Male


title: p_278

value: systemic sclerosis patient

tag: subject

tag: visit

tag: treatment arm

value: mycophenolate mofetil

tag: age at baseline visit


title: 49

description:
replicate 3
CJL-LIGHT-3


title: 36

description:
replicate 4
12:12-LIGHT-4


title: p_222

tag: condition

value: White

value: Female

tag: fvc at baseline visit

tag: diffuse


title: p_225

value: Baseline

value: cyclophosphamide

value: African American


title: S102

value: Asian


title: B6-pDC #1

tag: state

value: Steady State

value: Spleen

tag: cell type

value: DC

tag: cell subset

value: pDC


title: S141

value: Control


title: p_221


title: S203

value: Black


title: B6-CD8neg cDC2 #1

value: CD8neg cDC2


title: p_277


title: p_224

value: Hispanic


title: 7

description:
replicate 1
12:12-LIGHT-1

tag: background strain

tag: tissue (lung tumor vs rest of lung)

value: lung tumor

tag: chronic jetlag conditions (standard light conditions 12

value: 12ld vs chronic jetlag cjl):12:12LD

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: EXP2 26_YFP_f480

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA), And R
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters.
Trimmed reads were mapped to the reference genome mus musculus mm10 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using mm10 assembly and Ensemble transcripts release 100.
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene counts normalized to RPKM

source_name: Microglia

extract_protocol:
Total RNA was extracted from FACS sorted cells by using SS2 lysis buffer as mentioned in the manuscript.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) , miRNA sequencing was performed as per the Hagemann et al 2018 protocol and sequencing was done in Illumina NextSeq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.

tag: sample type

value: YFP+F4/80high microglia after depletion and repopulation


title: B6-CD8pos cDC1 #2

tag: strain

tag: tissue

value: CD8pos cDC1


title: p_223

value: systemic sclerosis patient

tag: subject

tag: race

value: White

tag: gender

value: Female


title: 35

description:
replicate 3
12:12-LIGHT-3


title: p_217

tag: visit

value: Baseline

tag: treatment arm

value: cyclophosphamide

tag: age at baseline visit


title: S078

tag: condition

tag: sample number within subject

tag: age


title: p_218

value: mycophenolate mofetil

value: African American

tag: fvc at baseline visit

tag: diffuse


title: 33

description:
replicate 2
12:12-LIGHT-2

tag: background strain

tag: tissue (lung tumor vs rest of lung)


title: B6-CD8pos cDC1 #1

tag: state

value: Steady State

value: Spleen

tag: cell type

value: DC

tag: cell subset


title: EXP2 25_YFP_f480

tag: sample type


title: 52

description:
replicate 5
12:12-LIGHT-5

tag: chronic jetlag conditions (standard light conditions 12

tag: time of sample collection (zt9 light phase vs zt21 dark phase)


title: S204

value: Control

tag: gender

tag: race


title: S166


title: S242


title: EXP2 23_YFP_f480


title: GLC5_300_2

city: Zhengzhou

first: Xinyang

last: Li

address: Science Avenue

country: China

institute: Institute of Cotton Research, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Hiseq platform used for basecalling.
Clean Reads was compared with the reference genome using HISAT2 software to obtain the localization information of Reads on the reference genome.
featureCounts v1.5.0-p3 software was used to count the number of reads covered by each gene from the start to the end and used to calculate the FPKM of each gene.
Genome_build: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_hirsutum/UTX-TM1_v2.1/genes/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Gossypium hirsutum

source_name: Ovule

extract_protocol:
Ovules cultured on 50 mM, 150 mM and 300 mM Glc for 5 days are used to extract RNA.  Illumina NEBNext® UltraTM RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: ovule

tag: treatment

value: 300 mM Glc cultured for 5 days


title: EXP2 20_YFP_f480


title: GLC5_300_3


title: p_215

tag: condition

tag: subject

tag: visit

tag: treatment arm

tag: age at baseline visit


title: EXP2 28_YFP_f480


title: GLC5_300_1


title: S070

tag: sample number within subject

tag: age

value: Male

value: Black


title: EXP2 25_f480

value: YFP-F4/80high microglia after depletion and repopulation


title: GLC5_150_2

value: 150 mM Glc cultured for 5 days


title: GLC5_150_1


title: S084


title: GLC5_150_3


title: p_210

value: systemic sclerosis patient

value: Asian

tag: fvc at baseline visit

tag: diffuse


title: S159

value: Female


title: p_171

value: Baseline

value: White


title: S120


title: EXP2 28_f480

tag: sample type


title: EXP2 23_f480


title: S292


title: GLC5_50_3

value: 50 mM Glc cultured for 5 days


title: p_216

value: Month 12

value: cyclophosphamide


title: EXP2 26_f480


title: p_214

value: mycophenolate mofetil


title: EXP2 20_f480


title: GLC5_50_2


title: p_169

value: African American


title: p_209


title: EXP2 25_YFP

value: YFP+F4/80low microglia after depletion and repopulation


title: GLC5_50_1

value: ovule


title: p_170


title: p_205


title: p_168


title: EXP2 23_YFP


title: S053

value: Control


title: ChIPseq H3K4me3 in Zbtb11KO Zfp131KO ES cells (iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO) replicate 2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

library_source: genomic

data_processing:
Fastq files were aligned to the mouse genome (mm10) using Bowtie (v1.0.1) with options “-q–best–strata -m 1–chunkmbs 1024”.
MultiGPS (v.0.74) was used to call peaks after alignment on all transcription factors. A q-value cutoff of <0.01 was used to identify significant binding events. Histone modification and ATAC-seq peaks were called using the DomainFinder module in SeqCode (https://github.com/seqcode/seqcode-core/blob/master/src/org/seqcode/projects/seed/DomainFinder.java). Contiguous 50-bp genomic bins with significantly higher read enrichment compared with normalized input were identified (binomial test, p <0.05).
Differential binding and modification analyses were done using DESeq2 (v1.28.1) with an adjusted p-value cutoff of <0.05 and all default options. To create the count matrix for DESeq2, peaks were first called independently in the wildtype and knockout ChIP-seq datasets. Overlapping peak regions were merged between the wt and KO. Peak regions found exclusively in either file were also included. The final count matrix was created using Bedtools coverage with the “-counts” option separating each replicate into its own count column. Before running DESeq2 on the matrix, counts were normalized by the length of the corresponding region for histone modifications (domains have differing lengths).
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files (text format)

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on 0.1% gelatin (Milipore) coated dishes at 37 °C, 8% CO2 in ESC medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% mESC-grade fetal bovine serum (Corning), 1x N2 (Gibco), 1x B27 (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM ß-mercaptoethanol (Gibco)) supplemented with LIF (leukemia inhibitory factor, 1,000 U ml–1  (Millipore)) and 2-inhibitor cocktail (3 mM CHIR (BioVision) and 1 mM PD0325901 (Sigma)) unless stated otherwise.

extract_protocol:
Wildtype and mutant cells were collected after being grown for 3d in +2i or -2i conditions in the presence or absence of 3 ng/uL doxycycline. 1 mM DSG (ProteoChem) was used for crosslinking at RT for 15min. 1% Formaldehyde (vol/vol) was added for an additional 15min until quenched with glycine (Sigma). Cells were separated into aliquots of 25x106 and centrifuged to freeze pellets at -80°C. Thawed cells were lysed in 5mL of 50 mM HEPES-KOH pH 7.5 (Gibco), 140 mM NaCl (Thermo Fisher), 1 mM EDTA pH 8.0, 10% glycerol (vol/vol) (Thermo Fisher), 0.5% Igepal (vol/vol) (Sigma), 0.25% Triton X-100 (vol/vol) with 1×protease inhibitors (Roche) for 10min at 4°C. Cells were centrifuged for 5min at 1100 rpm and resuspended in 5mL of 10 mM Tris-HCl pH 8.0 (Boston BioProducts), 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 (Boston BioProducts) with 1×protease inhibitors, and incubated for an additional 10 min at 4°C on a rotating platform. Cells were centrifuged for 5min at 1100 rpm and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1×protease inhibitors). Sonication was performed in two Bioruptor tubes per sample with 0.45 g sonication beads. Bioruptor Pico (Diagenode) was used for 18 cycles of 30 sec on and 30 sec off to sonicate to an average size of approximately 200 bp. To immunoprecipitate, Dynabeads protein-G (Thermo Fisher) and antibodies (HA, H3K4me3, H3K27me3, H3K27ac, SIN3A, CHD4) were incubated with sonicated chromatin for 16h at 4°C on a rotating platform. After the immunoprecipitation, the sample was washed with sonication buffer, high salt sonication buffer (500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl (Sigma), 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). The sample was eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45min at 65°C. Crosslinks were reversed by incubating the sample for 16h at 65°C. RNA was removed by 0.2 mg/mL RNAse A (Sigma) in 200 μL of TE for 2h at 37°C. To remove protein, 0.2 mg/mL Proteinase K (Invitrogen) and CaCl2 (Sigma) were added and the sample incubated at 55°C for 30min. DNA was first purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then by performing salt-ethanol precipitation. DNA pellets were resuspended in 50 uL H2O.
Illumina DNA sequencing libraries were prepared with half of the ChIP sample and a 1:100 dilution of the input sample in H2O. Library preparation was performed with end repair, A-tailing and ligating multiplexed adapters (Illumina-compatible Bioo Scientific). Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. Libraries were then amplified by PCR with TruSeq primers (Sigma) and Phusion polymerase (New England Biolabs). Libraries with sizes ranging between 250-550bp were gel purified (Qiagen). KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing. Libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) at the Genomics Core Facility at NYU.

treatment_protocol: Wildtype, iZbtb10-HA Zbtb10KO, iZbtb11-HA Zbtb11KO, iZfp131-HA Zfp131KO cells, and iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO cells were grown in the absence of doxycycline in +2i+LIF or -2i +LIF media for 3 days.

value: Ainv15(iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO)

tag: chip target

tag: chip antibody

value: anti-H3K4me3 (ActiveMotif 39159)

value: 3d without doxycycline in -2i+LIF

tag: cell type

value: Embryonic stem cells


title: EXP2 28_YFP


title: S341

tag: gender

tag: race


title: S191

value: Black


title: S285


title: ChIPseq H3K4me3 in Zbtb11KO Zfp131KO ES cells (iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO) replicate 1

tag: strain


title: p_166

value: systemic sclerosis patient


title: EXP2 26_YFP


title: ChIPseq NELF in Zbtb11KO Zfp131KO ES cells (iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO) replicate 2

value: NELF

value: anti-NELF (Sigma HPA007187)

tag: treatment


title: EXP2 20_YFP


title: S185

tag: condition

value: Female

value: White


title: S029

value: Male


title: EXP2 25_S14

value: YFP-F4/80low microglia after depletion and repopulation


title: S154


title: p_167

tag: subject

value: Baseline

value: cyclophosphamide


title: ChIPseq NELF in Zbtb11KO Zfp131KO ES cells (iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO) replicate 1


title: RNAseq in Zbtb11KOZfp131KO ES grown in -2i+LIF replicate 1

data_processing:
RNA-seq fastq files were aligned to the mouse genome (version mm10) using Hisat2 (version 2.1.0)(D. Kim, Langmead, and Salzberg 2015)
FeatureCounts R package was used to assign reads to genomic features (Liao, Smyth, and Shi 2014).
The DESeq2 package was used for differential gene expression analysis and for data visualization (volcano plots, heatmaps, PCA plots)(Love, Huber, and Anders 2014). A q-value cutoff of < 0.01 was used for significantly misregulated genes.
PANTHER (version 14) (http://geneontology.org) was used to perform Gene Ontology term enrichment analysis (Mi et al. 2019).
Genome_build: mm10
Supplementary_files_format_and_content: TXT: tab-delimited text files containing output of featurecounts or DEseq2 for Refseq genes.

extract_protocol:
RNA-seq: 500K cells were collected and RNA was extracted by resuspending in Trizol reagent (Invitrogen, 15596026) followed by purification using Qiagen RNeasy mini kit (Qiagen, 74106).
TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594) was used to prepare RNA-seq libraries. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify library sizes. A KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing.

treatment_protocol: Wildtype, iZbtb10-HA Zbtb10KO, iZbtb11-HA Zbtb11KO and iZfp131-HA Zfp131KO cells were grown in the absence of doxycycline in +2i+LIF or -2i +LIF media for 3 days.

value: No treatment


title: p_165

tag: visit

value: mycophenolate mofetil


title: RNAseq in Zbtb11KOZfp131KO ES grown in -2i+LIF replicate 3


title: EXP2 23_S13


title: S023

value: Control


title: p_163

tag: treatment arm


title: S307


title: S322


title: S233

value: Hispanic


title: S037


title: EXP2 26_S15


title: p_160

tag: age at baseline visit

value: Native American


title: p_161


title: p_162


title: RNAseq in Zbtb11KOZfp131KO ES grown in +2i+LIF replicate 2

value: Ainv15(iZbtb11-HA iZfp131-V5 Zbtb11KO Zfp131KO)


title: RNAseq in Zbtb11KOZfp131KO ES grown in +2i+LIF replicate 1

value: Embryonic stem cells


title: RNAseq in Zbtb11KOZfp131KO ES grown in +2i+LIF replicate 3


title: RNAseq in Zbtb11KOZfp131KO ES grown in -2i+LIF replicate 2


title: EXP2 20_S12


title: RNAseq in Zfp131KO ES grown in -2i+LIF replicate 3

value: Ainv15(iZfp131-HA Zfp131KO)


title: EXP1 5P

value: Ctrl without microglia depletion and repopulation


title: p_158

value: systemic sclerosis patient

value: Month 12


title: S060

tag: sample number within subject


title: S260

tag: age

value: Female

value: Black


title: S176


title: EXP2 28_S16


title: RNAseq in Zbtb11KO ES grown in -2i+LIF replicate 3

value: Ainv15(iZbtb11-HA Zbtb11KO)


title: EXP1 4P


title: p_157

tag: fvc at baseline visit


title: p_156

value: African American

tag: diffuse


title: EXP1 3P

tag: sample type


title: p_159

value: Baseline


title: EXP1 2P


title: p_154

value: cyclophosphamide

value: White


title: RNAseq in Zfp131KO ES grown in +2i+LIF replicate 3

value: No treatment


title: RNAseq in Zbtb11KO ES grown in +2i+LIF replicate 3


title: EXP1 1P


title: p_155

value: mycophenolate mofetil


title: S103

value: Control


title: S116


title: RNAseq in Zbtb10KO ES grown in -2i+LIF replicate 3

value: Ainv15(iZbtb10-HA Zbtb10KO)


title: p_153


title: EXP1 6N


title: EXP1 6P


title: RNAseq in Zbtb10KO ES grown in +2i+LIF replicate 3


title: Dam in spermatocytes, rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

institute: Stockholm University

data_processing:
Library strategy: DamID-seq
Two biological replicates of Dam-only or Dam-Lam DamID-seq reads were adapter clipped, mapped to the dm3 genomic assembly by bowtie2 (Langmead 2012) and counted by ‘HTSeq-count’ software (Anders et al, 2015) on the 500-bp genomic bins. The resulted counts of Dam-Lam samples were converted to RPM, normalized to the Dam-only samples counts and log2-transformed. The domain calling was performed with the 2-state HMM algorithm as described earlier (Pindyurin et. al, 2018) without taking the heterochromatin portion of dm3 genome build into account.
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files for Dam and Dam-Lam profiles of individual replicates in spermatogonia (SG) and spermatocytes (SCL) represent read counts  per 300-nt bins generated using HTSeq-count software and R via Rstudio.

organism: Drosophila melanogaster

source_name: Spermatocytes from 3rd instar larvae testes

growth_protocol: Flies were grown according to standard protocols.

extract_protocol: after in vivo Dam-methylation, genomic DNAs from either ~200 bam∆86 or 3rd instar larvae testes  were manually dissected using dissection needles in PBS at 4°C. Isolation of genomic DNA was performed by DNeasy Blood and Tissue kit (Qiagen), following the protocol for cultured cells. DNA was concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g and its concentration was measured using a NanoDrop spectrophotometer. For the selective amplification of methylated GATC-GATC fragments, genomic DNA was first digested by DpnI, followed by ligation of adaptors, DpnII digestion and PCR-amplification as described previously (Vogel et al. 2007) with a minor modification: ~0.5 µg instead of 2.5 µg of genomic DNA was used as an input.We applied 16 cycles of PCR (1 min at 94°C, 1 min at 65°C, 2 min at 68°C) for Dam-only and Dam-Lam DNA samples. Adaptors were removed by DpnII digestion for 2 h at 37°C. The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (Qiagen), concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g, and quantified on a NanoDrop spectrophotometer. 0.5 µg of Dam-only and Dam-Lam DNA samples (each in two biological replicates) were subjected to next generation sequencing (NGS) on Illumina HiSeq 2000 resulting in 41-52 million 100 nt single-end reads per sample.

tag: tissue

value: Testes

tag: developmental stage

value: third instar larvae

tag: biological replicate


title: EXP1 3N


title: p_152

tag: gender


title: Dam in spermatocytes, rep 1


title: p_151

tag: race


title: S028

value: Male

value: Hispanic


title: S217


title: Dam-Lam in spermatocytes, rep 2

tag: strain


title: EXP1 4N

value: Ctrl without microglia depletion and repopulation


title: p_150

value: systemic sclerosis patient


title: p_148


title: spinal cord WT rep6

city: nantong

first: songlin

last: zhou

state: jiangsu

address: 19 qixiu road

institute: Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education

description: Sample B1

data_processing:
library strategy: Spatial transcriptomics sequencing
The raw data was processed with the spaceranger pipeline (version 1.2.0, 10X Genomics)using default parameters and mapped to the mm10 genome assembly
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files of each sample with raw gene UMI counts for every gene and every spot under the tissues

source_name: scar

extract_protocol:
Frozen samples were embedded in OCT (TissueTek Sakura) and stored at −80 °C until cryosectioning.For cryo-  sectioning, samples were equilibrated to −22 °C and were cryosectioned at 10 μm thickness using Leica CM3050 S  Cryostat .    Sections were placed on chilled Visium Tissue Optimization Slides (3000394, 10X Genomics) and Visium Spatial Gene Expression Slides (2000233, 10X Genomics), and adhered by warming the back of the slide.     Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics) or Visium Spatial Tissue Optimization User Guide (CG000238 Rev C, 10X Genomics).     For gene expression samples, tissue was permeabilized for 24 minutes, which was selected as the optimal time based on tissue optimization time course experiments.     Brightfield histology images were taken using a 10X objective on a  Slide Scanner（Leica SCN400）.     Raw images were stitched together using Image J and exported as .tiff files with low and high resolution settings.     For tissue optimization experiments, fluorescent images were taken with a TRITC filter (ex/em brand) using a 10X objective and 200 ms exposure time.
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics).    Libraries were loaded at 300 pM and sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq S4 Reagent Kit (200 cycles, 20027466, Illumina. Sequencing was performed using the following read protocol: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.

value: spinal cord

tag: time point

value: day 7


title: spinal cord WT rep7

description: Sample C1

value: day 14


title: S269

tag: condition

value: Female


title: spinal cord WT rep8

description: Sample D1

value: day 28


title: S331


title: Dam-Lam in spermatocytes, rep 1


title: EXP1 5N


title: Dam in spermatogonia, rep 1

data_processing:
Library strategy: DamID-seq
Two biological replicates of Dam-only or Dam-Lam DamID-seq reads were adapter clipped, mapped to the dm3 genomic assembly by bowtie2 (Langmead 2012) and counted by ‘HTSeq-count’ software (Anders et al, 2015) on the 500-bp genomic bins. The resulted counts of Dam-Lam samples were converted to RPM, normalized to the Dam-only samples counts and log2-transformed. The domain calling was performed with the 2-state HMM algorithm as described earlier (Pindyurin et. al, 2018) without taking the heterochromatin portion of dm3 genome build into account.
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files for Dam and Dam-Lam profiles of individual replicates in spermatogonia (SG) and spermatocytes (SCL) represent read counts  per 300-nt bins generated using HTSeq-count software and R via Rstudio

source_name: Spermatogonia from bam∆86 testes

value: adult


title: Dam in spermatogonia, rep 2


title: p_147

tag: subject

value: Baseline

value: White


title: spinal cord WT rep4

description: Sample D


title: EXP1 1N


title: spinal cord WT rep5

description: Sample A1

value: day 3


title: p_145

tag: visit

value: mycophenolate mofetil


title: p_146

tag: treatment arm

value: cyclophosphamide


title: Dam-Lam in spermatogonia, rep 2

value: Testes


title: p_144

tag: age at baseline visit


title: Dam-Lam in spermatogonia, rep 1


title: spinal cord WT rep2

description: Sample B


title: spinal cord WT rep3

description: Sample C


title: cDNA fraction from wild-type and double knock-out nuclei

city: San Francisco

first: Kai-Chun

last: Chang

state: CA

department: Bioengineering

institute: University of California, San Francisco

description:
nuclear RNA
The file contains reads from both wild-type and double knock-out mice nuclei. The samples are later demultiplexed based on nanowell indexes

data_processing:
Basecalls on Nextseq were performed with Illumina RTA version 2.4.11. Basecalls on Miseq were performed with Illumina RTA version 1.18.54
Read alignment and transcript counting was performed with Drop-Seq v2.4.0 bioinformatic pipeline and STAR-2.7.6a.
Nanowell indexes were extracted with CITE-seq-Count v1.4.2 bioinformaticpackage
Gene counts were processed with Seurat v4.0
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Filtered mRNA count matrix contains gene-by-barcode counts in TSV format; rows are gene symbols, and columns are barcodes. Nanowell index count matrix contains index-by-barcode counts in TSV format; rows are nanowell indexes in MEX format, and columns are barcodes in TSV format

source_name: hippocampus

extract_protocol:
After microdissection of hippocampal tissues from wild-type and double knock-out mice, nuclei extraction was performed with EZ PREP buffer and then resuspended in DPBS with 0.01% BSA and 0.1% RNase inhibitor (Habib et al, Nature Methods, 2017) . Extracted nuclei were then stained with 10 μM DRAQ5 (Life Technologies) and passed through 40um strainers. Nuclei were diluted to 300,000 per ml for droplet encapsulation. The nuceli drops were reinjected into printed droplet microfluidics (PDM; Zhang et al. Genome Biology, 2020) for DRAQ5 recording and sorting. Nuclei from both wild-type and double knock-out mice were printed onto the same 64x64 nanowell array deposited with drop-seq beads and nanowell indexes. The drop-seq beads were resuspended from the nanowell and subjected to standard drop-seq and CITE-seq protocol
Amplification of cDNA and nanowell indexes and library preparation was carried out following Drop-seq and CITE-seq protocols without modifications. Librarys were prepared using illumina Nextera XT kit.
Drop-seq, single-cell RNAseq

tag: genotype

value: wildtype and double knockout of  Ezh2 and Suv4-20h

value: brain


title: spinal cord WT rep1

description: Sample A


title: p_142


title: p_143


title: p_141


title: 3day_Vehicle_KLB_BLA

city: Iowa City

first: Kyle

middle: Harrington

last: Flippo

state: IA

address: 169 Newton Road, 3320 PBDB

department: Neuroscience and Pharmacology

institute: University of Iowa

data_processing:
Analysis of the sequencing data was performed using the BD Rhapsody WTA analysis pipeline on the SevenBridges server. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file and a transcriptome annotation file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.
Filter by read quality
Annotate R1 reads
Annotate R2 reads
Annotate molecules
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files contain a matrix with UMIs for each cell

molecule: polyA RNA

source_name: basolateral amygdala

extract_protocol:
The method used here for generating single cell suspensions was modified from a previously published protocol (Wu et al., 2017). Individual mice were quickly decapitated, the brain was immediately extracted and placed in fresh ice-cold artificial cerebrospinal fluid (aCSF) containing 124 mM NaCl, 2.5 mM KCl, 1.2 mM NaH2PO4, 24 mM NaHCO3, 5 mM HEPES, 13 mM glucose, 2 mM MgSO4, and 2 mM CaCl2, bubbled with a carbogen gas (95% O2 and 5% CO2) and with a pH of 7.3 - 7.4. Brains were then sectioned on a vibratome and sections containing the BLA were placed in ice cold aCSF w/ actinomycin D (93 mM N-methyl-D-glucamine, 2.5 mM KCl, 1.2 mM NaH2FACs sorting for tdTomato positive cells was performed as previously described (Jensen-Cody et al., 2020). Hoechst cell viability dye (Hoechst 33258) was added to the cell suspension at a final dilution of 4ug/ml just prior to sorting to allow for selection of living cells during FACs sorting. Cells were then FACs sorted for tdTomato fluorescence and viability via Hoechst staining. Sorting was performed on a BD FACS Aria II using a 130 mM nozzle, a sheath pressure of 10 p.s.i., and in the single cell sorting mode at the University of Iowa Flow Cytometry Facility.PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 0.5 mM CaCl2, 5 mM sodium ascorbate, 2 mM thiourea, and 3 mM sodium pyruvate, 45 µM actinomycin D, pH of 7.3-7.4, bubbled with carbogen gas (95% O2 and 5% CO2) on ice for at least 15 minutes prior to dissection). The BLA was then dissected from each section, and BLA tissue derived from three mice were pooled for each experimental condition. The tissue was then minced and placed in 2mg/ml Pronase in aCSF w/ actinomycin D and incubated at 37°C for 30 minutes. Following digestion, the Pronase solution was exchanged with ice-cold, carbogen-bubbled ACSF containing 1% fetal bovine serum and .01% BSA. The tissue was then titrurated using fire polished Pasteur pipets and strained through a 70 µM cell strainer.
FACS isolated cells were then loaded on the BD Rhapsody where capture of the single cells was performed per manufacturer instructions. Following lysis of the cells and capture of mRNA on oligonucleotide barcoded beads the cDNA synthesis was performed and cDNA libraries with Illumina sequencing adapters were generated per manufacturer instructions using the BD Rhapsody whole transcriptome analysis amplification kit. cDNA libraries were then sequenced on Illumina HiSeq 4000 sequencers at the University of Iowa Genomics Core. Sequencing data was then quality filtered and annotated using the BD Rhapsody analysis pipeline while also correcting for artifacts which arise during library construction. Filtered and annotated data from vehicle and FGF21 treated mice were then normalized in the R package Seurat using SCTransform and integrated using Seurat scRNA-seq integration (Stuart et al., 2019). Imputation was performed using the Seurat Wrapper ALRA on the integrated data set before final clustering (clustering resolution was set at 0.5 based on the number of cells sequenced)(Table S2) and gene expression analysis to account for dropout associated with 3’-barcoding-based approaches (Ziegenhain et al., 2017). “Cell type” classification of the clusters was determined based on expression of previously identified marker genes for neuronal and non-neuronal cell types.

tag: development stage

tag: treatment

value: vehicle


title: 3day_FGF21_KLB_BLA

value: FGF21 (1mg/kg)


title: p_140

value: systemic sclerosis patient

tag: fvc at baseline visit

tag: diffuse


title: Female Smarcc1.6

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

institute: The Waler and Eliza Hall Institute of Medical Research

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10  using bowtie2
Peak calling was performed using the macs2 peak calling function within Seqmonk. All other analysis was performed using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: List of macs2 called peak regions, with associated quantification (reads per million).

source_name: mESC

growth_protocol: mESC lines were established as described in the associated manuscript, before being differentiated by weaning out of 2i media.

extract_protocol:
ChIP was performed using the ChIP-IT High Sensitivity kit from Active Motif.
Libraries were prepared using an Illumina TruSeq library preparation kit

treatment_protocol: Samples were challenged with a hairpin against Smarcc1 or a nontargeting control, then fixed with formaldehyde at day 4 of differentiation.

tag: Sex

tag: antibody


title: Male Nons

value: Male

value: nontargeting control


title: Male Smarcc1.6


title: Input


title: Female Nons


title: p_139

value: Hispanic


title: EXP1 2N

tag: sample type

value: Ctrl without microglia depletion and repopulation


title: Microglia, AD

city: Rochester

first: O'Banion

last: Kerry

state: United States of America

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
DEMULTIPLEXING - cellranger 3.1 mkfastq --use-bases-mask y*,I8,y* --nopreflight
COUNTING - cellranger-3.1.0 count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=refdata-cellranger-mm10-3.0.0/ --project=${PROJECT} --indices=SI-GA-${INDEX} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
Genome_build: Reference Genome: mm10-3.0.0
Supplementary_files_format_and_content: A tar file containing gene-barcode matrix output: barcodes.tsv.gz (cell barcodes), genes.tsv.gz (annotated genes) and matrix.mtx.gz (UMI counts)

source_name: hippocampal microglia

extract_protocol:
Microglia (CD45int CD11b+) from the 3-5 pooled hippocampi were sorted with FACSAria II (BD). Cellular suspensions were then loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs).
Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations. GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, ThermoFisher Scientific). The entire purified post GEM-RT product was amplified by PCR. Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.

treatment_protocol: Male 3xTg mice (>24 month-old) were given PLX chow for 2 weeks and microglia were allowed to repopulate for approximately 4-weeks under control chow treatment.

tag: cell type

value: hippocampal microglia

tag: disease state

value: mouse model of Alzheimer's Disease

value: M


title: Microglia, NTg

value: non-transgenic

value: control


title: c_90169

source_name: whole blood sample, healthy control

value: Control

tag: race

value: African American

tag: gender


title: Microglia, AD_PLX


title: PC_IgG_dKO3 [CUT&Tag]

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
library strategy: CUT&Tag
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rppm) using R/Bioconductor

source_name: splenic plasma cells

extract_protocol:
100,000 Cells were FACS sorted into FACS buffer and resuspended in chilled nuclear extraction (NE) buffer (20mM HEPES-KOH at pH7.9, 10mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 20% glycerol) to exact nuclei, which are then bound to Conconavalin A (conA) coated magnetic beads.
Following incubations with primary and secondary antibodies, the nuclei-Con A complex was incubated with pA-Tn5 in tagmentaion buffer (20mM HEPES at pH7.5, 300mM NaCl, 0.5mM spermidine, 10mM MgCl2), DNA released and purified, and PCR amplified into a final CUT&Tag library

treatment_protocol: PC from CreCtrl and dKO were FACS sort three days after stimulation with LPS in vivo

tag: sorting markers

value: CD11b-F4/80-,Thy1.2-CD138+ plasma cells

tag: strain

value: female

tag: stimulation

value: 50ug LPS

value: Utxfl/fl Jmjd3fl/fl CD19cre+

value: plasma cells

tag: chip enrichment

value: IgG


title: PC_IgG_dKO4 [CUT&Tag]


title: PC_IgG_Ctrl4 [CUT&Tag]

value: Utx+/+ Jmjd3+/+ CD19cre+


title: c_90167

data_processing:
Globin related genes were removed prior to further analysis.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Transcript data were normalized with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: csv file format of DESeq2 normalized and log2 transformed counts.

tag: condition

tag: age at baseline visit

value: Female


title: Gluten free ID S8

city: Frederiksberg C

first: Camilla

middle: Hartmann Friis

last: Hansen

address: Ridebanevej 9, 2nd floor

department: Faculty of Health Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina CASAVA software used for basecalling.
Adaptors trimmed with Fastp, filtered for low quality sequence and mapped to Mus Musculus(GRCm38/mm10) genome with HISAT2 v 2.0.5
Gene count file made using FeatureCounts v 1.5.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole spleen tissue

extract_protocol:
Rneasy lipid kit with Dnase treatment
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq ( Illumina Novaseq 6000 platform)

tag: tissue

value: Spleen

value: Gluten Free


title: Gluten free ID S6

tag: treatment


title: Gluten free ID S5


title: PC_IgG_Ctrl3 [CUT&Tag]

tag: genotype


title: Ulcerative colitis-associated colorectal carcinoma [UC16CA]

type: genomic

city: Bethesda

first: Daniela

last: Hirsch

address: 50 South Drive

department: National Cancer Institute

institute: National Institutes of Health

description: aCGH

hyb_protocol: Combined samples were hybridized at 65 °C and 20 rpm for 48 hours to the CGH microarrays.

scan_protocol: Scanned with microarray scanner G2565BA (Agilent)

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Linear normalization was used following the CGH protocol of Agilent Feature extraction software (CGH_107_Sep09 protocol).

source_name: Tumor

label_protocol: FFPE tumor DNA was labeled with the Genomic DNA ULS Labeling Kit (Agilent). Tumor DNA was labeled with Cy-3, genomic reference DNA (Promega) with Cy-5.

growth_protocol: N/A Formalin-fixed paraffin-embedded tumor tissue was used.

extract_protocol: DNA was isolated from punch biopsies (0.6 mm in diameter) or 20 um sections from the FFPE blocks after determining the tumor areas on H&E sections, avoiding foci of inflammation as well as foci of high mucin and low cellular content. The biopsies were deparaffinized in 300 µl of mineral oil (cat # 69794, Sigma-Aldrich, St. Louis, MO, USA) in a thermomixer at 800 rpm at 65 °C overnight before 100 µl of ATL lysis buffer (Qiagen, Hilden, Germany) and 20 µl Proteinase K was added followed by agitation at 450 rpm at 56°C. After 8 hours, another 20 µl of Proteinase K was added followed by incubation overnight. When digestion of the tissue pieces was complete, 120 µl of the lysate, i.e., aequous phase, was transferred to a fresh 1.5 ml tube, treated with 2.0 µl RNAse A (100 mg/ml; Qiagen) for five minutes at room temperature and mixed with 600 µl PM buffer (Qiagen) and 10 µl of 3M sodium acetate (pH 5.2; cat # R1181, Thermo Fisher Scientific, Waltham, MA, USA). Subsequent spin column purification was done using the QIAquick PCR Purification kit (Qiagen) according to the manufacturer’s protocol with minor modifications.

value: male

tag: tumor type

value: Colorectal adenocarcinoma

source_name: Genomic reference DNA


title: Ulcerative colitis-associated colorectal carcinoma [UC18CA]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC17CA]

description: aCGH


title: Gluten free ID S3


title: c_90152

city: Houston

first: Shervin

last: Assassi

institute: The University of Texas Health Science Center at Houston

extract_protocol:
PBC RNA was extracted according to the manufacturer’s protocol. RNA integrity was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).   mRNA was enriched from total RNA using oligo(dt) beads (NEBNext Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA.  The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing, and adapter ligation, size selection and PCR enrichment.
Libraries are pooled into Novaseq6000 machines according to molarity and expected data volume.


title: c_90138

value: White


title: c_90145


title: Ulcerative colitis-associated colorectal carcinoma [UC15CA]

description: aCGH


title: PC_H3K27me3_dKO4 [CUT&Tag]

tag: Sex


title: PC_H3K27me3_dKO3 [CUT&Tag]


title: Ulcerative colitis-associated colorectal carcinoma [UC12CA2]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC13CA]

description: aCGH


title: Gluten free ID S1


title: Control ID S2


title: Control ID S6


title: Control ID S1


title: Ulcerative colitis-associated colorectal carcinoma [UC14CA]

description: aCGH


title: c_90134

value: Native American

value: Male


title: PC_H3K27me3_dKO1 [CUT&Tag]


title: c_90096

value: Control


title: PC_H3K27me3_dKO2 [CUT&Tag]


title: PC_H3K27me3_Ctrl3 [CUT&Tag]


title: PC_H3K27me3_Ctrl4 [CUT&Tag]


title: Control ID 5


title: PC_H3K27me3_Ctrl2 [CUT&Tag]


title: c_70247


title: c_70146


title: Gluten free ID 10


title: PC_H3K27me3_Ctrl1 [CUT&Tag]


title: c_90116

value: African American


title: Gluten free ID 9


title: Ulcerative colitis-associated colorectal carcinoma [UC11CA]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC10CA1]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC12CA1]

description: aCGH


title: c_70116


title: dKO_4 [ChIP-seq]

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
For each sample peaks of accessibility were identified and annotated using MACS2 with the following parameters "--nomodel --nolambda --broad"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak per million (rppm) using R/Bioconductor

source_name: LPS in vivo

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, 10^7 B cells or 1^6 Plasmablasts were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp. Chromatin was immunoprecipitated with 1 ug anti-H3K27me3 antibody over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.
ChIP-seq libraries were constructed from total IP DNA using the KAPA HyperPrep Kit.

value: splenic plasma cells


title: Ulcerative colitis-associated colorectal carcinoma in situ [UC09CAis]

description: aCGH

value: Colorectal adenocarcinoma in situ


title: Ulcerative colitis-associated colorectal carcinoma [UC10CA2]

description: aCGH

value: female


title: Gluten free ID 8


title: c_70093


title: dKO_3 [ChIP-seq]

value: 50ug LPS

value: Utxfl/fl Jmjd3fl/fl CD19cre+


title: dKO_2 [ChIP-seq]


title: c_70127


title: dKO_1 [ChIP-seq]


title: Gluten free ID 7


title: c_70080


title: c_70074


title: CreCtrl_3 [ChIP-seq]


title: Control ID 7


title: Ulcerative colitis-associated colorectal carcinoma [UC08CA2]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC07CA]

description: aCGH


title: Control ID 8


title: Ulcerative colitis-associated colorectal carcinoma [UC06CA]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC08CA1]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC05CA3]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC05CA2]

description: aCGH


title: Control ID 6


title: c_70059


title: CreCtrl_2 [ChIP-seq]


title: CreCtrl_1 [ChIP-seq]


title: Control ID 4


title: c_70047


title: c_70042


title: Control ID 3


title: Ulcerative colitis-associated colorectal carcinoma [UC03CA]

description: aCGH


title: c_70056


title: Control ID 2


title: FOB_PC_dKO_3 [RNA-seq]

description: processed data file: GEO.WT.dKO.FoB.MZ.geneRpkm.detected.RPM.3.exon.csv

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.

source_name: ex vivo cultured FOB cells

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: strain background

value: 20ug/ml LPS, 20ng/ml  IL-2, 5ng/ml IL-5 ex vivo

value: plasma cells (PC)


title: FOB_PC_dKO_1 [RNA-seq]


title: Ulcerative colitis-associated colorectal carcinoma [UC05CA1]

description: aCGH


title: Ulcerative colitis-associated colorectal carcinoma [UC04CA]

description: aCGH


title: c_70007

value: Asian


title: PC_dKO_4 [ATAC-seq]

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
For each sample peaks of accessibility were identified and annotated using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing reads per peak per million (rppm) normalized read counts for all peaks with at least 1 read per million in all samples of at least 1 group.

extract_protocol: 10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: CD11b-F4/80-Thy1.2-CD138+ plasma cells

value: PC; plasma cells


title: MZB_PC_dKO_3 [RNA-seq]

source_name: ex vivo cultured MZB cells


title: MZB_PC_dKO_2 [RNA-seq]


title: c_50385

value: Female


title: MZB_PC_dKO_1 [RNA-seq]


title: PC_dKO_3 [ATAC-seq]


title: Ulcerative colitis-associated colorectal carcinoma in situ [UC02CAis]

description: aCGH


title: LT-HSC from 2 Gy-irradiated CD169DTR/+ mouse_rep1

city: Fontenay-aux-roses

first: Stephanie

middle: G.

last: MORENO

address: 18 route du Panorama

department: DRF / iRCM

country: France

institute: CEA

hyb_protocol: Following fragmentation, 5.5 µg of Labeled ss-cDNA were hybridized with rotation at 60 rpm  for 16 h at 45°C on GeneChip Clariom S array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with TAC 4.0.1.36 software, normalized with SST-RMA algorithm (ThermoFisher) and corrected by global scaling.

label: Biotin

source_name: Long-term hematopoietic stem cells from CD169DTR/+ mouse 5 days post 2Gy-TBI

label_protocol: Biotinylated cDNA were prepared according to the GeneChip whole Transcript (WT) Pico Reagent Kit protolcol (Affymetrix).

growth_protocol: Long-term hematopoietic stem cells (LT-HSC) from non-irradiated or from 2 Gy-irradiated mice were isolated 5 days after TBI, based on a Lin- cKit+ Sca+ Flk2- CD48- CD150+ phenotype.

extract_protocol: Total RNA was extracted according to the protocol of RNeasy Plus Micro Kit (QIAGEN) and The RNA integrity (RNA Integrity Score≥7.0) was checked on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: To deplete CD169+ macrophages, diphtheria toxin was injected to CD169DTR/+ mice (and WT mice as a control). 72h later, mice were sham- or 2 Gy-total body irradiated and LT-HSC were isolated 5 days after irradiation.

value: Bone marrow

value: CD169DTR/+ (CD169+ macrophage-depleted)

value: 2Gy-irradiated 5 days post-TBI


title: c_50374

value: White

value: Male


title: Control ID 1

value: Spleen

value: Control


title: Ulcerative colitis-associated colorectal carcinoma [UC01CA]

description: aCGH

value: male

value: Colorectal adenocarcinoma


title: PC_dKO_2 [ATAC-seq]

value: female

value: 50ug LPS


title: FOB_dKO_1 [RNA-seq]

source_name: splenic mouse FOB cellls

value: CD11b-,F4/80-,Thy1.2-B220+CD93-CD21mid/lowCD23+ follicular B cells

value: Utxfl/fl Jmjd3fl/fl CD19cre+

value: no stimulation

value: follicular B cells (FOB)


title: PC_dKO_1 [ATAC-seq]

value: CD11b-F4/80-Thy1.2-CD138+ plasma cells

value: PC; plasma cells


title: LT-HSC from non-irradiated CD169DTR/+ mouse_rep2

source_name: Long-term hematopoietic stem cells from CD169DTR/+ mouse

value: Bone marrow

value: non-irradiated


title: LT-HSC from 2 Gy-irradiated CD169DTR/+ mouse_rep2

value: CD169DTR/+ (CD169+ macrophage-depleted)

value: 2Gy-irradiated 5 days post-TBI


title: c_180058

value: African American

value: Male


title: LT-HSC from non-irradiated CD169DTR/+ mouse_rep1


title: PC_Cre_Ctrl_3 [ATAC-seq]

value: Utx+/+ Jmjd3+/+ CD19cre+


title: PC_Cre_Ctrl_2 [ATAC-seq]


title: MZB_dKO_3 [RNA-seq]

source_name: splenic mouse MZB cellls

value: marginal zone B cells (MZB)


title: PC_Cre_Ctrl_1 [ATAC-seq]


title: FOB_dKO_3 [RNA-seq]


title: LT-HSC from 2 Gy-irradiated WT mouse_rep2

source_name: Long-term hematopoietic stem cells from WT mouse 5 days post 2Gy-TBI

value: Wild-type


title: MZB_dKO_1 [RNA-seq]

value: female


title: c_170123

value: Control

value: White

value: Female


title: LT-HSC from 2 Gy-irradiated WT mouse_rep1


title: c_180067


title: LT-HSC from non-irradiated WT mouse_rep2

source_name: Long-term hematopoietic stem cells from WT mouse


title: FB_dKO_3 [ATAC-seq]

value: CD93-CD21mid/lowCD23+  follicular B cells

value: no stimulation

value: Utxfl/fl Jmjd3fl/fl CD19cre+

value: FOB; follicular B cells


title: FOB_PC_CreCtrl_3 [RNA-seq]

value: 20ug/ml LPS, 20ng/ml  IL-2, 5ng/ml IL-5 ex vivo

value: plasma cells (PC)


title: LT-HSC from non-irradiated WT mouse_rep1

value: Bone marrow

value: non-irradiated


title: c_160143

value: Asian


title: FB_dKO_2 [ATAC-seq]

value: CD11b-F4/80-Thy1.2-B220+CD93-CD21mid/lowCD23+  follicular B cells


title: c_180047

value: African American

value: Male


title: RBE-elemene-48h_rep1

city: shanghai

first: yating

last: pan

address: 725 Wanping South Road, Xuhui District, Shanghai

institute: Longhua Hospital

description: gene expression after 48h in elemene

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k 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 (version10.7.1.1, Agilent Technologies) was used to process the original image and extract the original data. Then Genespring software (version13.1, Agilent Technologies) was used for quantile standardization and subsequent processing. The standardized data is filtered and at least one set of probes labeled 100% Detected is left for subsequent analysis in each set of samples used for comparison. Differential gene screening was carried out by multiple change value, and the screening criterion was up-regulation or down-regulation multiple change value >= 2.0.

source_name: RBE, 48hr, elemene, replicate 3

label_protocol: Total RNA was reversely transcribed into double-stranded cDNA, and then cRNA labeled by Cyanine-3-CTP(Cy3) was synthesized. The labeled cRNA was hybridized with the chip, and the original image was scanned by Agilent Scanner G2505C(Agilent Technologies) after elution.

growth_protocol: RBE cell was incubated in RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was quantified by NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was detected by Agilent Bioanalyzer 2100 (Agilent Technologies). After passing RNA quality inspection, sample labeling, hybridization and elution of the chip shall follow the standard chip process. First, total RNA was reversely transcribed into double-stranded cDNA, and then cRNA labeled by Cyanine-3-CTP(Cy3) was synthesized. The labeled cRNA was hybridized with the chip, and the original image was scanned by Agilent Scanner G2505C(Agilent Technologies) after elution.

treatment_protocol: RBE cells were treated with elemene and cultured in RPMI 1640 medium containing 10% heat-inactivated fetal bovine serum in a humidified incubator at 37℃ with 5% CO2 for 0,24 or 48 h.

value: cholangiocarcinoma


title: c_160020

address: 6431 Fannin


city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of Untreated FRT cells, biological replicate 4

data_processing:
Sequence reads were trimmed using BBduk software (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) to remove adapter sequences and low-quality end bases and then aligned on rn6 reference sequence using STAR.The expression levels of genes were determined with htseq-count (PMCID: PMC4287950) using the Gencode/Ensembl gene model.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

source_name: Fischer rat thyroid

growth_protocol: FRT cells were grown in Coon's modification of Ham's F12 supplemented with 10% Fetal Bovine Serum plus sodium bicarbonate (2.68 g/l), and L-glutamine (2 mM)

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Mini Kit Cat No./ID: 74106 (250), Quiagen). RNA extract was precisely quantified and mixed at 50ng/5 µL
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaseqNovaSeq 6000 Sequencing System (Illumina) with a read length of 100bp

treatment_protocol: No treatment was applied.

tag: cell line

value: FRT

value: Rat cell line


title: FB_dKO_1 [ATAC-seq]

value: female

tag: cell type


title: MZB_dKO_2 [RNA-seq]

value: marginal zone B cells (MZB)


title: c_70031

value: Control

value: White

value: Female


description: Transcriptome profile of Untreated FRT cells, biological replicate 3


title: RBE-ctrl-0h_rep1

description: gene expression after 0h in elemene

source_name: RBE, 0hr, ctrl, replicate 3


title: MZB_PC_CreCtrl_3 [RNA-seq]

value: Utx+/+ Jmjd3+/+ CD19cre+


description: Transcriptome profile of Untreated FRT cells, biological replicate 2


title: RBE-elemene-24h_rep1

description: gene expression after 24h in elemene

source_name: RBE, 24hr, elemene, replicate 3


title: MzB_dKO_3 [ATAC-seq]

value: CD11b-F4/80-Thy1.2-B220+CD93-CD21+CD23- marginal zone cells

value: no stimulation

value: Utxfl/fl Jmjd3fl/fl CD19cre+

value: MZB; marginal zone B cells


title: FOB_PC_CreCtrl_1 [RNA-seq]

value: 20ug/ml LPS, 20ng/ml  IL-2, 5ng/ml IL-5 ex vivo

value: plasma cells (PC)


title: c_160003

source_name: whole blood sample, healthy control


title: FB_Cre_Ctrl_3 [ATAC-seq]

value: CD11b-F4/80-Thy1.2-B220+CD93-CD21mid/lowCD23+  follicular B cells

value: FOB; follicular B cells


title: c_150181


title: NAFLD liver sample 1 scRNA-seq

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Demultiplexing, alignment to the GRCh38 reference, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample

source_name: NAFLD liver explant

extract_protocol:
Enzymatic digestion (pronase, collagenase, DNAse), followed by FACS sorting
10x Genomics single cell 3' gene expression v3

tag: source

value: NAFLD liver explant

value: NAFLD


title: c_150089

tag: race


title: FB_Cre_Ctrl_1 [ATAC-seq]


title: c_150162

tag: gender

value: Male


title: c_130158


title: c_160024


description: Transcriptome profile of Untreated FRT cells, biological replicate 1

value: FRT

value: Rat cell line


title: MZB_CreCtrl_2 [RNA-seq]

tag: sorting markers

value: female

value: marginal zone B cells (MZB)


title: c_150108

value: Control

value: White

value: Female


title: FOB_CreCtrl_3 [RNA-seq]

value: CD11b-,F4/80-,Thy1.2-B220+CD93-CD21mid/lowCD23+ follicular B cells

value: Utx+/+ Jmjd3+/+ CD19cre+

value: no stimulation

value: follicular B cells (FOB)


title: MzB_dKO_2 [ATAC-seq]

value: CD11b-F4/80-Thy1.2-B220+CD93-CD21+CD23- marginal zone cells

tag: strain

value: Utxfl/fl Jmjd3fl/fl CD19cre+

value: MZB; marginal zone B cells


title: MzB_dKO_1 [ATAC-seq]

tag: stimulation


title: K562_LINE_B

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

description: processed QC metrics is Sup.Table1

data_processing:
Pepatac
Custom peak merging script found here: https://github.com/corceslab/ATAC_IterativeOverlapPeakMerging
TSS enrichment was calculated using PEPATAC and used to determine library quality.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from bam files using a custom script

growth_protocol: cells were grown in RPMI media with 10% FBS and 1/ P/S according to guidelines from ATCC

extract_protocol:
Cells were lyzed in ATAC-seq lysis buffer and processed as detailed in the corresponding protocol paper and described in Corces 2017.
Libraries were constructed as detailed in the corresponding protocol paper

value: lymphoblast


title: FOB_CreCtrl_2 [RNA-seq]


title: MZB_PC_CreCtrl_2 [RNA-seq]

value: 20ug/ml LPS, 20ng/ml  IL-2, 5ng/ml IL-5 ex vivo

value: plasma cells (PC)


title: MZB_CreCtrl_3 [RNA-seq]


title: GM12878_LINE_B

description: processed QC metrics is Sup.Table1

value: b-lymphocyte


title: MzB_Cre_Ctrl_3 [ATAC-seq]


title: c_130085


title: c_130062

value: African American


title: MzB_Cre_Ctrl_1 [ATAC-seq]

value: female


title: MZB_CreCtrl_1 [RNA-seq]

value: marginal zone B cells (MZB)


title: Wt_HFD_16w_animal4

city: Newcastle upon Tyne

first: Olivier

last: Govaere

address: Framlington Place

institute: Newcastle University

data_processing:
RNA-seq reads were cleaned with fastq-mcf (ea-utils) and mapped to the genome (mm10) using STAR.
Read counts per gene were obtained using htseq-count and DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text file format containing normalized reads for each sample.

source_name: liver

extract_protocol:
Snap frozen tissue samples were lysed using Trizol (Sigma-Aldrich) and mRNA was extracted with the Allprep DNA/RNA Micro kit (Qiagen).
TruSeq RNA Library Prep Kit v2

tag: disease state

value: NAFLD

value: HFD for 16 weeks

value: liver


title: GR_8

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

description:
GR_8
Cerebral Cortex
Cortical Astroglial RNA

data_processing:
Library strategy: TRAP-Seq
Illumina Casava software used for basecalling.
Sequencing reads were mapped to the mouse genome (GRCm38.p5) and the Ensembl (release-84) transcriptome annotation, using HISAT2 (Pertea et al., 2016). The resulting SAM files were converted to BAM formant using SAMtools (Li et al., 2009). The gene expression levels as counts were estimated using featureCounts (Liao et al., 2014) with the following options: -t exon; -g gene_id; -F “GTF”; -B; -s 0; -p; -a. Counts from technical replicates were added.
Raw read counts were then filtered requiring more than 1 CPM (counts per million) in at least 25% of the samples and 16208 survived the filter and were considered for further analysis.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: data_Counts.tsv: Matrix table with raw counts for every gene and every sample.

source_name: P7 Female 6

growth_protocol: Mice raised in conventional housing (ad lib food and water) with enrichment (house and chew block) and group housed with littermates until tissue collection.

extract_protocol:
Whole cortex of Aldh1l1-L10-GFP+ mice were used; mice underwent rapid decapitation and cortex was dissected and fixed in cyclohexamide to fix the polysomes (mRNA with ribosomal subunits). Cortical tissues were homogenized and then incubated with biotinylated magnetic beads coated with protein L + anti-GFP to immunoprecipitate astroglial-specific polysomes. Polysomes were lysed and mRNA was extracted (see previous work for detailed methods: Simard et al., (2018) Neuropsychopharmacol.)
RNA samples were sent to the Yale K.E.C.K facility for sample QC as per Simard et al. 2018: RNA quality was determined using a nanodrop and RNA integrity was determined by running an Agilent Bioanalyzer gel (RINs >8). mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C. Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries. The cDNA library was then end-repaired and A-tailed, adapters were ligated and second-strand digestion was performed by Uricil-DNA-Glycosylase. Indexed libraries that met appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit: Kapa Library Quant Kit (Illumina) (KAPA Biosystems # KK4854-07960298001) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Only samples with a yield of ≥0.5 ng/ul were used for sequencing.

tag: age

value: postnatal day 7

tag: background strain

value: Astroglial Cells


title: PC_dKO_4 [RNA-seq]

description: processed data file: RNA.geneRpkm.detected.RPM.3.exon

source_name: splenic plasma cells

value: 50ug LPS in vivo


title: PC_dKO_3 [RNA-seq]


title: GR_6

description:
GR_6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female S2


title: c_130043

tag: condition

value: Control

tag: age at baseline visit

value: Asian

value: Female


title: c_130057

value: White


title: Wt_HFD_16w_animal3

tag: genotype

tag: treatment

tag: tissue


title: Wt_HFD_16w_animal2


title: c_110162

value: Male


title: GR_5

description:
GR_5
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female S1

tag: Sex


title: c_100155


title: PC_Cre_Ctrl_3 [RNA-seq]

tag: strain background

value: Utx+/+ Jmjd3+/+ CD19cre+


title: c_110045


title: Msr1-/-_HFD_16w_animal5


title: PC_dKO_1 [RNA-seq]

value: Utxfl/fl Jmjd3fl/fl CD19cre+

tag: cell type

value: plasma cells (PC)


title: GR_2

description:
GR_2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male 2

value: male


title: PC_Cre_Ctrl_2 [RNA-seq]

value: female


title: MZB_PC_CreCtrl_1 [RNA-seq]

source_name: ex vivo cultured MZB cells

value: 20ug/ml LPS, 20ng/ml  IL-2, 5ng/ml IL-5 ex vivo


title: GR_4

description:
GR_4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male S1


title: GR_3

description:
GR_3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male 6


title: GR_7

description:
GR_7
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male S2


title: Msr1-/-_HFD_16w_animal3

value: NAFLD


title: PC_Cre_Ctrl_1 [RNA-seq]


title: Msr1-/-_HFD_16w_animal4

value: HFD for 16 weeks


title: GR_1

description:
GR_1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 10


title: FOB_CreCtrl_1 [RNA-seq]

source_name: splenic mouse FOB cellls

value: CD11b-,F4/80-,Thy1.2-B220+CD93-CD21mid/lowCD23+ follicular B cells

value: no stimulation

value: follicular B cells (FOB)


title: F1-6

description:
72F1-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Female 6

value: postnatal day 1

value: Astroglial Cells


title: PC_dKO_2 [RNA-seq]

value: 50ug LPS in vivo


title: Msr1-/-_HFD_16w_animal2

value: liver


title: Msr1-/-_HFD_16w_animal1


title: F4-6

description:
71F4-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Female 6

value: postnatal day 4


title: Wt_HFD_16w_animal1


title: MLE12_p213-Ad

city: Beijing

first: Chang

last: Liu

address: 1 Xian Nong Tan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Gene expression data from p21-overexpressed adenovirus treated MLE-12 cells

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome
The mapped reads of each sample were assembled using StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: MLE-12 cells

growth_protocol: MLE-12 cells were cultured in DMEM/F12 medium with 10% FBS at 37℃ in 5% CO2 incubator.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by 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. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: The cells were infected with control and p21-overexpressed adenovirus. Then the stably transfected samples were collected in trizol for RNA extraction.

value: mouse lung epithelial cells

tag: cell line

value: infected with p21-overexpressed adenovirus


title: COV_2

city: Modena

first: Andrea

last: Cossarizza

state: Modena

address: Via Campi 287

institute: University of Modena and Reggio Emilia

data_processing:
Fastq alignment to the human genome and features quantification were performed using Rsubread v2.4.3.
The gene read count matrices were used for downstream analysis with edgeR v3.32.1.
Genome_build: GRCh38 release 37
Supplementary_files_format_and_content: Matrix table with genes read count for every sample

source_name: FACS sorted central memory CD4 T cells (TCM)

extract_protocol:
Total RNA was extracted from sorted CD4+ TCM cells by using Quick-RNA™ Miniprep Kit (Zymo Research, Irvine, CA, USA) and eluted in 30 μL of DNase/RNase-Free water. Therefore, RNA was quantified using RNA 6000 Nano Reagent (Agilent Technologies, Santa Clara, CA) on a 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard kit Illumina Stranded mRNA Prep

tag: group

value: central memory CD4 T cells (TCM)

value: elderly


title: COV_3


title: c_100114

source_name: whole blood sample, healthy control

value: Control

tag: race

value: White

tag: gender

value: Female


title: MLE12_p212-Ad


title: COV_1


title: F14-6

description:
69F14-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Female 6

value: postnatal day 14

value: female


title: MLE12_p211-Ad


title: Smarca4-6-Day6-rep3_S18

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using hisat2 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

source_name: mESC

growth_protocol: Xmas mESC lines were established as described in the associated manuscript.  Cells were expanded in 2i, then induced to differentiate by weaning into DME HiHi media.

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo Quick RNA kit
Libraries were prepared according to standard Illumina RNA-seq protocols

treatment_protocol: Cells were virally transduced with shRNA on day 2 of differentiation, then selected with puromycin on day3 and harvested on the indicated days.

value: FVB/CAST F1

value: mESC line

tag: genotype/variation

value: Smarcc knockdown


title: Nons-Day6-rep3_S16


title: CUN_3

value: young


title: c_100106


title: F35-6

description:
68F35-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Female 6

value: postnatal day 35

value: Astroglial Cells


title: Smarca4-4-Day6-rep3_S17


title: MLE12_con2-Ad

description: Gene expression data from control adenovirus treated MLE-12 cells

value: infected with control adenovirus


title: N-A-Hour0-rep3_S3

value: Nonsilencing control


title: MA-60

description:
67FA-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Male 60

value: adult

value: male


title: CUN_1

value: central memory CD4 T cells (TCM)


title: M14-6

description:
63M14-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Male 6


title: HOV_3

value: healthy donor

value: elderly


title: F1-4

description:
48F1-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Female 4

value: postnatal day 1


title: HOV_2


title: F7-6

description:
70F7-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 6

value: postnatal day 7


title: HOV_1


title: MLE12_con3-Ad

value: mouse lung epithelial cells


title: Male_Day4 Smarcc1.7

growth_protocol: Male C57/Bl6 mESC lines were established as described in the associated manuscript.  Cells were expanded in 2i, then induced to differentiate by weaning into DME HiHi media.

tag: strain

value: Male


title: HUN_3


title: Hypochlorite treatment after [AH]

city: Ames

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description:
RNA samples were collected after 15 minutes of exposure to 35 µM sodium hypochlorite (AH-aft/BH-aft/CH-aft)
AH-aft

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qulaity checked with fastqc, mapped to GCF_000005845.2_ASM584v2  using BWA
FeatureCounts from subread was used to estimate read counts for genes
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.39
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

organism: Escherichia coli

source_name: E. coli cultures

growth_protocol: E. coli cultures were grown in sterilized lake water supplemented with 100 mg/L yeast extract and 1 mM sodium phosphate buffer to a final pH of approximately 8.4 for 48 hours.

extract_protocol:
Cells were lysed using 5 mg/mL lysozyme in TE buffer. Following lysis, RNA was extracted using RNeasy Mini Kit (Qiagen Inc.) and following manufacturers recommended instructions. To ensure the elimination of contaminating DNA, RNA samples were also treated with DNAse 1 (Qiagen Inc.). Ribosomal RNA depletion was carried out to remove rRNA using Ribo-zero rRNA removal kit (Bacteria) from Illumina
RNA libraries of purified RNA were constructed with TruSeq Stranded mRNA library preparation kit following manufacturer’s instructions

treatment_protocol: Cultures were treated with either 35 µM hypochlorite, 400 µM ferrate, or water (control) for 15 minutes. Cultures were harvested through centrifugation, washed in 10 mM phosphate buffer and then suspended in RNAlater (Invitrogen). Samples were kept at 4°C for 48 hours before being centrifuged and stored at -20°C.

tag: replicate number


title: CUN_2

tag: age


title: M7-6

description:
64M7-6
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male 6

tag: background strain


title: Hypochlorite treatment after [BH]

description:
RNA samples were collected after 15 minutes of exposure to 35 µM sodium hypochlorite (AH-aft/BH-aft/CH-aft)
BH-aft


title: F4-4

description:
47F4-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Female 4

value: postnatal day 4

value: female


title: F7-4

description:
46F7-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 4


title: Ferrate treatment after [CF]

description:
RNA samples were collected after 15 minutes of exposure to 400 µM potassium ferrate (AF-aft/BF-aft/CF-aft)
CF-aft


title: Male_Day4 Smarca4.6

value: mESC line

value: Smarcc knockdown


title: Hypochlorite treatment after [CH]

description:
RNA samples were collected after 15 minutes of exposure to 35 µM sodium hypochlorite (AH-aft/BH-aft/CH-aft)
CH-aft


title: Male_Day5 Smarca4.4


title: HUN_2

value: young


title: Ferrate treatment after [AF]

description:
RNA samples were collected after 15 minutes of exposure to 400 µM potassium ferrate (AF-aft/BF-aft/CF-aft)
AF-aft


title: Male_Day4 Smarcc1.6


title: F14-4

description:
45F14-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Female 4

value: postnatal day 14

value: Astroglial Cells


title: HUN_1


title: MLE12_con1-Ad

value: infected with control adenovirus


title: Male_Day5 Nons1

value: Nonsilencing control


title: Ferrate treatment after [BF]

description:
RNA samples were collected after 15 minutes of exposure to 400 µM potassium ferrate (AF-aft/BF-aft/CF-aft)
BF-aft


title: Male_Day5 Nons2


title: Male_Day4 Smarca4.4


title: F35-4

description:
44F35-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Female 4

value: postnatal day 35


title: FA-4

description:
43FA-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Female 4

value: adult


title: Male_Day7 Smarcc1.7


title: HeLa MARCHF6 KO-3

city: Pohang

first: Cheol-Sang

last: Hwang

state: Gyeongbuk

address: 77, Cheongam-ro

department: Department of Life Sciences

country: South Korea

institute: POSTECH

data_processing:
The raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (GRCh38) using HISAT v2.1.0
Transcript assembly of known transcripts was processed by StringTie v2.1.3b
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.
Genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to RLE Normalization
False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm
Genome_build: Human NCBI GRCh38
Supplementary_files_format_and_content: txt file format and table with read counts, FPKM and TPM for every gene and every sample

source_name: HeLa MARCHF6 KO

growth_protocol: HeLa WT and KO cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. All cells were cultured in a 37℃ incubator with 5% CO2.

extract_protocol:
The wild-type (WT) and MARH6 KO HeLa cells were seeded into 10-cm culture plate at ~60% confluence in triplicate. The overnight cultured cells were then washed twice in ice-cold phosphate-buffered saline (PBS) and total RNAs were immediately extracted using RNeasy Mini Kit (QIAGEN, cat#?,  Germany) following the manufacturer’s instructions
The extracted RNA quality was validated by measuring RNA Integrity Number (RIN) ≥ 9.5 by Bioanalyzer (Agilent, USA), and subjected to library preparation using Illumina TruSeq Stranded total RNA Sample Prep kit (Illumina, USA) according to the manufacturer’s protocol.

tag: cell lines

value: HeLa cell lines


title: HeLa MARCHF6 KO-2


title: Water treatment (control) after [CW]

description:
RNA samples were collected after 15 minutes of exposure to water (AW-aft/BW-aft/CW-aft
CW-aft


title: Water treatment (control) after [BW]

description:
RNA samples were collected after 15 minutes of exposure to water (AW-aft/BW-aft/CW-aft
BW-aft


title: M1-4

description:
42M1-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Male 4

value: male


title: HeLa MARCHF6 KO-1


title: Male_Day7 Smarca4.6

last: Keniry

institute: The Waler and Eliza Hall Institute of Medical Research


title: Water treatment (control) after [AW]

description:
RNA samples were collected after 15 minutes of exposure to water (AW-aft/BW-aft/CW-aft
AW-aft


title: M4-4

description:
41M4-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Male 4


title: F7-40

description:
40M7-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 40


title: Hypochlorite treatment before [BH]

description:
RNA samples were collected before exposure to sodium hypochlorite hypochlorite (AH-bef/BH-bef/CH-bef)
BH-bef


title: M14-4

description:
39M14-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Male 4


title: Hypochlorite treatment before [CH]

description:
RNA samples were collected before exposure to sodium hypochlorite hypochlorite (AH-bef/BH-bef/CH-bef)
CH-bef


title: HeLa WT-2

source_name: HeLa wild-type


title: Male_Day7 Smarca4.4

source_name: mESC


title: Ferrate treatment before [CF]

description:
RNA samples were collected before exposure to potassium ferrate (AF-bef/BF-bef/CF-bef)
CF-bef


title: Hypochlorite treatment before [AH]

description:
RNA samples were collected before exposure to sodium hypochlorite hypochlorite (AH-bef/BH-bef/CH-bef)
AH-bef


title: MA-4

description:
37MA-4
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Male 4


title: HeLa WT-1


title: Male_Day4 Nons2


title: ChIP-MCF7_MTA3

first: Beibei

address: NO. 10 Xitoutiao Road

institute: Capital Medical University

data_processing:
Raw sequencing data was preprocessed using fastp v0.19.6
Alignment of the clean sequencing data was conducted using STAR v2.4.0 (RNA-seq) and Bowtie2 (ChIP-seq)
Abundance measurements of genes in RNA-seq was performed by using HTSeq-Count v0.12.4
Peak calling of ChIP-seq was conducted by using MACS2.
Differential gene expression analysis of RNA-seq was conducted using DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: xls: gene relative expression values from RNA-seq; bed: significant peaks from ChIP-seq

source_name: Cell line MCF-7

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS); MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS and without CO2.

extract_protocol:
For ChIP-seq assay,the chromatin DNA precipitated by antibodies against BRD4, LSD1, MTA3, or H3K4me1. Then the DNA was purified with the QIAquick PCR Purification Kit. For RNA-seq assay, total RNAs were extracted from MCF-7 and MDA-MB-231 cells that were untreated or treated with JQ1 for 4 weeks using Trizol reagent.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq assay, MCF-7 and MDA-MB-231 cells that were untreated or treated with JQ1 for 4 weeks.

tag: chip antibody


title: F1-3

description:
36F1-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Female 3

value: postnatal day 1

tag: genotype


title: F4-3

description:
35F4-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Female 3


title: Male_Day7 Smarcc1.6

first: Andrew


title: Male_Day7 Nons1


title: Input-MCF7


title: Male_Day6 Smarcc1.7


title: ChIP-MCF7_BRD4


title: Ferrate treatment before [BF]

description:
RNA samples were collected before exposure to potassium ferrate (AF-bef/BF-bef/CF-bef)
BF-bef

source_name: E. coli cultures


title: F7-3

description:
34F7-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 3

value: postnatal day 7


title: Male_Day6 Smarcc1.6


title: Ferrate treatment before [AF]

description:
RNA samples were collected before exposure to potassium ferrate (AF-bef/BF-bef/CF-bef)
AF-bef


title: F14-3

description:
33F14-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Female 3


title: ChIP-MCF7_LSD1


title: Male_Day6 Smarca4.6


title: Water treatment (control) before [CW]

description:
RNA samples were collected before exposure to water (AW-bef/BW-bef/CW-bef)
CW-bef


title: ChIP-MCF7_H3K4me1


title: HeLa WT-3


title: Male_Day7 Nons2


title: Male_Day6 Smarca4.4


title: FA-3

description:
31FA-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Female 3


title: F35-3

description:
32F35-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Female 3


title: Water treatment (control) before [BW]

description:
RNA samples were collected before exposure to water (AW-bef/BW-bef/CW-bef)
BW-bef


title: Male_Day6 Nons2