title: JAK00006 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_10


title: Input_repeat1

status: Public on Mar 01 2021

type: SRA

city: Bethesda

first: Jing

last: Huang

state: MD

country: USA

institute: National Cancer Institute

description:
Input DNA
Tfcp2l1_peaks_rep1.txt

library_source: genomic

data_processing:
Bascalling: RTA 1.8.70.0 and Sequencing Chemistry: Illumina TruSeq 2.0.
Alignment: Illumina Casava 1.8.2.
Processed files are peak files. Peak calling was performed using MACS (1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Peak files in Bed format.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: A base medium made from a 1:1 mix of DMEM/F12 (Life technologies, 11032-033) and Neurobasal medium (Life Technologies, 21103-049) including N2 supplement (Life Technologies, 17502-048, 1:100 dilution), B27 supplement (Life Technologies (Life Technologies, 17504-044, 1:50 dilution), 0.1 mM 2-mercaptoethanol, 1,000 units/mL of LIF, 3 µM of CHIR99021 (Cayman Chemical) and 1 µM of PD0325901 (Cayman Chemical).

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit.

treatment_protocol: No treatment.

tag: genotype

value: wild type

tag: cell type

value: embryonic stem cells

tag: growth condition

value: in vitro cell culture in 2i

tag: chip antibody

tag: repeat


title: Tfcp2l1_ChIPseq_repeat1

description:
ChIP DNA
Tfcp2l1_peaks_rep1.txt


title: JAK00005 Placebo Day 84

first: Stephen

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_09

library_source: transcriptomic

data_processing:
Demultiplex to FastQ using bcl2fastq version 2.17.1
Map to hg19 using Tophat 2.1.1
Calculate RPKM using Partek 7.18.0723
ANOVA comparison using Partek 7.18.0723
Paired T-test using Partek 7.18.0723
Genome_build: hg19
Supplementary_files_format_and_content: Excel RPKM, ANOVA and Paired T-test results

molecule: total RNA

organism: Homo sapiens

source_name: whole blood (paxgene tube)

extract_protocol:
PAXgene Blood RNA Kit (Qiagen)
TruSeq Stranded mRNA NeoPrep Kit (Illumina)

tag: treatment

value: Placebo

tag: stat4 risk allele

value: Positive

tag: Sex

value: FEMALE


title: Control_Sample_4

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Genome_build: human reference genome (GRCh37)

source_name: human trophoblast stem cells

extract_protocol:
Human TS cells were transduced with shControl or shASCL2 lentiviral supernatant and incubated for 24 h. Media was changed 24 h post-transduction and selected with puromycin dihydrochloride (5mg/mL, cat. no. A11138-03, Thermo-Fisher) for two days. Cells recovered for 1-3 days in complete human TS medium prior to splitting for EVT differentiation. RNA was isolated on the eighth day of differentiation.
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: extravillous trophoblast

tag: shRNA

value: Control shRNA


title: BR.h9

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw data obtained from the Illumina NextSeq 500 was trimmed and aligned as described in Yuan et al, Genome Medicine, 2018. For each read with a unique, strand specific alignment to exonic sequence, we constructed an address comprised of the sample barcode, unique molecular identifier (UMI) barcode, and gene identifier. The resulting address file only contained the addresses from reads with corresponding single index. We generated a digital gene expression matrix and filter sample barcodes as described previously (Yuan et al. 2018). Briefly, reads with the same sample barcode, UMI and aligned gene were collapsed and sequencing errors in the sample barcode and UMI were corrected to generate a  matrix of molecular counts for each cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file that contains the gene expression counts of each sample.

molecule: polyA RNA

organism: blank sample

source_name: blank

growth_protocol: PBMCs from donors' blood were isoalted by Ficoll gradient (GE Healthcare). pDCs and pan-DCs wre enriched from PBMCs by negative selection using EasySep Human Plasmacytoid DC Enrichment Kit and EasySep Human pan-DC Pre-Enrichment Kit (STEM CELL Technologies) with ~80-90% purity and cultured in RPMI-1640 complete medium with 2 mM L-gluatamine, 1 mM sodium pyruvate, 1x MEM non-essential amino acids, 100 U/mL penicillin-streptomycin, and 10% fetal bovine serum. MRC5 human lung fibroblasts were cultured under the same conditions. All cells were incubated at 37C with 5% carbon dioxide.

extract_protocol:
pDCs were detached from plates by gentle pipetting and stained for viability with the Zombie Aqua Fixable Vaiability Kit in PBS for 20 mins at 4C. Cells were washed in 4C medium and FAC-sorted to remove MRC5 cells based on forward and side-scatter using an SH800Z sorter (SONY Biotechnology). Total RNA from sorted live pDCs was isolated using an RNeasy Mini Kit (QIAGEN).
Pooled RNA-seq was performed using the low-input RNA-seq protocol reported in Snyder et al, Science Immunology, 2019. All of the steps prior below that  come before the barcoded cDNA libraries are pooled were performed using a BioMek  4000 automated liquid handling robot (Beckman). Briefly, we added deoxyribonucleotides  (dNTPs) (ThermoFisher) to a final concentration of 2 mM and reverse transcriptase primer  to 2 uM followed by primer annealing at 72C for 3 mins. We then added 7.5 uL of reverse  transcription mixture to each well comprised of 2M betaine (Affymetrix), 2x ProtoScript  Buffer (NEB), 12 mM MgCl2 (ThermoFisher), 10 mM dithiothreitol (ThermoFisher), 5.3 U  of Protoscript II reverse transcriptase (NEB), 0.53 U of SUPERaseIN (ThermoFisher), and  2 uM template-switching oligo. The reverse transcription reaction was incubated at 42C  for 90 mins followed by 10 cycles of 50C for 2 mins, 42C for 2 mins, and 70C for 10 mins.  Next, 2 uL of exonuclease I (ThermoFisher) was added to each well (1.875 U of  exonuclease I in water) and the resulting mixture was incubated at 37C for 30 mins, 85C  for 15 mins, and 75C for 30s.

treatment_protocol: Cells were stimulated or co-cultured with 2.5 uM CpG, IL-3, 10 MOI CMV, MRC5 cells, or CMV-infected MRC5 cells for 2, 4, 8, 16, or 32 hours.

tag: donor number

value: blank

tag: time


title: JAK00005 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_08


title: Knockdown_Sample_1

value: ASCL2 shRNA


title: Control_Sample_3


title: BR.h7


title: JAK00005 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_07


title: Input_repeat2

description:
Input DNA
Tfcp2l1_peaks_rep2.txt


title: BR.h8


title: BR.h6


title: Control_Sample_2


title: JAK00002 Tofacitinib Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_06

value: Tofacitinib

value: Negative


title: tma20∆ [DY154Ffx]

first: Nicholas

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: Biological replicate of DY186Ffx. Wig files composed of combination of two biological replicates (DY154Ffx and DY186Ffx).

data_processing:
Multiple sequencing lanes were pooled together to create a single fastq file.
Base calling and demultiplexing was performed at the NIDDK DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD for samples run on theHiseq2500. Demultiplexing was performed using CutAdapt for samples run on the HiSeq3000.
Reads were aligned to a library of RNA genes and those not matching were retained.
Samples sequenced on the HiSeq3000 had PCR duplicates removed according to McGlincy and Ingolia, 2017.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Trimming of consecutive 3'As was not performed for 40S samples.
Replicates for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome). 26-45 nt 5' end aligned for 40S profiling and 25-34 nt 5' end aligned for 80S profiling.

organism: Saccharomyces cerevisiae

source_name: tma20∆_whole cells

growth_protocol: Cells were grown to an OD of ~1.5 for 40S profiling or ~0.6 for 80S profiling and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose gradients to isolate either the 40S peak (40S profiling) or the monosome peak (80S profiling). RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription (rRNA was subtracted using Ribo-Zero after ligation for 40S profiling). cDNAs were then circularized and PCR amplified. (Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos for 80S profiling).
40S ribosome profiling; 80S ribosome profiling

treatment_protocol: Cells were cross-linked with formaldehyde for 1h, spun down, resuspended in lysis buffer, and beaded into liquid nitrogen for 40S profiling. Cells were rapidly vacuum filtered and flash frozen for 80S profiling. Samples were lysed in a freezer mill with lysis buffer.

tag: strain

tag: molecule subtype

value: 40S Ribosome-protected RNA 15-80 nt


title: JAK00006 Placebo Day 56 error

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_11

value: MALE


title: BR.h5


title: Control_Sample_1


title: TFEB 4 [141401_GGTAGCGT-TCTTTCCC_S50]

city: ANN ARBOR

first: Jinjian

last: Sun

state: Michigan

address: 2415 LANCASHIRE DR APT 2B

institute: university of michigan

data_processing:
Small RNA-Seq data were analyzed using OASIS 2.0(https://oasis.ims.bio/index.php)1 with the default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft excel worksheet containing read count

growth_protocol: Human Coronary Artery Endothelial Cells (HCAECs) were purchased from Lonza (Cat# CC-2585) and cultured on the collagen type I (354236, Corning)-coated dishes in the EGMTM -2 MV Microvascular Endothelial Cell Growth Medium (Cat# CC-3202, Lonza). Cells were cultured at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Cat# 217004, Qiagen)
The small RNA library preparation and deep sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, RNA quality was assessed by TapeStation RNA ScreenTape (Cat # 5067-5576, Agilent), and RNA abundance was quantified by Qubit RNA BR Assay Kit (Cat #Q10210, Thermo Fisher). Indexed small RNA libraries were prepared with NEB Small RNA kit with Size Selection Using Pippin Prep per protocol (NEB #E7300S) and sequenced on a NovaSeq 6000 platform (Illumina).

treatment_protocol: At 80% confluence, HCAECs were infected with adenovirus encoding LacZ (Ad-LacZ, 10 MOI) or adenovirus encoding TFEB (Ad-TFEB, 10 MOI) for 48 hours.

value: primay coronary artery endothelial cells (HCAECs)

tag: passage


title: JAK00002 Tofacitinib Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_04


title: JAK00002 Tofacitinib Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_05


title: BR.h4


title: BR.h3


title: JAK00001 Placebo Day 84

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_03


title: HT29M Input

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

data_processing:
ChIP-Seq reads were mapped to the human reference genome assembly hg38(GRCh38) using STAR and reads which assigned to multiple locations were discarded. P65-binding sites were identified by HOMER applying a false dis-covery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Peaks present in at least 2 out of 3 replicates were considered for downstream analysis. De novo motif analysis of identified binding sites was performormed using HOMER.
Genome_build: hg38(GRCh38)
Supplementary_files_format_and_content: bed

source_name: colon

growth_protocol: Cells were cultured in Dulbecco's modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (P/S) and 1% blasticidine (Sigma Aldrich).

extract_protocol:
Cells were crosslinked with DSG (20593, lot TF263080, Thermo Scientific) for 45 min and then incubated with formaldehyde (1%) for 10 minutes. Nuclear chormatin fractions were separted and immunoprecipitated with P65 anitboides.
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

treatment_protocol: All Cells were treated with TNFα (30ng/ml, 11088939001, Roche, lot no: 25885600) for 30 minutes before ChIP experiment.

value: cat no:33-9900, lot no:QJ216251, mouse monoclonal, Invitrogen

tag: cell line

tag: transfection

value: stably transfected with empty vector


title: TFEB 3 [141400_GAGTGGGT-TCTTTCCC_S49]

value: adenovirus encoding TFEB (Ad-TFEB, 10 MOI)


title: BR.h2


title: JAK00001 Placebo Day 56

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_02


title: TFEB 2 [141399_CGTACGGT-TCTTTCCC_S48]


title: Knock-in 3

type: RNA

city: Frederick

first: Feng

last: Zhu

address: 1050 Boyles Street

institute: National Cancer Institute, NIH

hyb_protocol: Standard protocol.

scan_protocol: Standard protocol.

label: biotin

label_protocol: Standard protocol.

growth_protocol: All mice were housed under ACUC guideline.

extract_protocol: TRIzol reagent was used for total RNA extraction.

tag: strain/background

tag: genotype/variation

value: KA

tag: tissue

value: Skin


title: TFEB 1 [141398_GTTTCGGT-TCTTTCCC_S47]

tag: cell type


title: BR.h1


title: Knock-in 1


title: JAK00001 Placebo Day 1

description:
180821_lupus_RNA-seq_results.gene.rpkm.xlsx
Sample_01

value: Placebo


title: Knock-in 2


title: LacZ 4 [141397_GTGGCCGT-TCTTTCCC_S46]

value: adenovirus encoding LacZ (Ad-LacZ, 10 MOI)


title: BR.g12


title: HT29M P65 ChIP-Seq rep 3

tag: chip antibody


title: HT29M P65 ChIP-Seq rep 2


title: HT29M P65 ChIP-Seq rep 1


title: WT 2

value: WT


title: WT 1


title: LacZ 3 [141396_GTGAAAGT-TCTTTCCC_S45]


title: BR.g11


title: WT 3


title: Patient BS418 timepoint N2

city: Basel

first: Heinz

last: Läubli

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the UCSC hg19 version of the human genome using
the spliced read aligner STAR (2.5.1). The R/Bioconductor package
QuasR (version 1.10.1, R version 2.3.4) was used to assess read and
alignment quality. Gene expression was quantified by the qCount
function of QuasR using an exon-union model of hg19 RefSeq genes (downloaded from UCSC 2015-02-09).
Genome_build: hg19
Supplementary_files_format_and_content: gene_counts.csv; text file with comma separated values; columns correspond to: 1. ENTREZ ID, 2. gene name, 3. symbol, 4. gene length (exon-union model), 5.-24. raw counts for each sample

extract_protocol:
PBMCs were isolated from freshly drawn whole blood by histopaque density centrifugation and frozen to liquid nitrogen until further use. Afterwards cells were thawed and stained with fluorescently labeled antibodies for markers of CD8+ T cells (CD45 CD3 CD8) and CD8+ T cells sorted directly into RNA lysis buffer. RNA was isolated using the SMARTer Universal Low Input RNA Kit (TaKaRa/Clontech).
Illumina TruSeq Nano

tag: subject id

value: Patient BS418

tag: subject status

value: non-small cell lung cancer (NSCLC) patient

tag: age

value: M

tag: kir3ds1/l1 genotype

value: L/L

tag: response

value: nonresponder; progressive disease (PD)

tag: timepoint

value: Peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: CD8+ T cell


title: Patient BS418 timepoint N1

tag: Sex


title: LacZ 2 [141395_GTCCGCGT-TCTTTCCC_S44]

tag: treatment


title: BR.g10

tag: donor number

value: blank

tag: time


title: Patient BS409 timepoint N2

value: Patient BS409

value: F

value: S/L


title: HT29ERB Input

value: cat no:33-9900, lot no:QJ216251, mouse monoclonal, Invitrogen

tag: cell line

tag: transfection

value: stably transfected with ERBeta


title: HT29ERB P65 ChIP-Seq rep 3


title: Patient BS409 timepoint N1


title: BR.f12


title: Patient BS395 timepoint N2

value: Patient BS395

value: responder; partial response (PR)


title: BR.f11


title: Osteoblast

city: New Orleans

first: Hong-Wen

last: Deng

state: Louisiana

address: 1324 Tulane Ave

institute: Tulane

data_processing:
Raw FASTQ files were mapped to the Reference genome (GRCh38/hg38) using Cell Ranger 3.0
The references were rebuilt according to instructions from 10x Genomics, which performs alignment, filtering, barcode counting and UMI counting. Following alignment, digital gene expression (DGE) matrices were generated for each sample and for all samples. Merged 10x Genomics DGE files were generated using the aggregation function of the Cell Ranger pipeline.
All the cells in different batches were merged and normalized by equalizing the read depth among libraries. Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Gene by cell expression matrix (raw counts)

source_name: Bone

extract_protocol:
Osteoblasts were extracted from the human femur head based on widely used dissociation protocols with a few minor adjustments. Bone tissue was stored on ice and quickly transferred into the lab, where the samples were chopped into small fragments and washed twice with phosphate-buffered saline (PBS). These fragments were then incubated with a highly purified, endotoxin-free type II collagenase (1 mg/ml, Cat: A004174-0001, Sangon Biotech) at 37.0°C for 30 mins and 60 mins in the first and second digestion respectively. After the incubation, the solution was filtered in a 70 μm filter and incubated with RBC lysis buffer for 5 mins. The collected cells were washed twice with PBS for fluorescence-activated cell sorting (FACS). Before FACS, collected cells were incubated with human CD31/34/45-PE (Cat:303106, Cat:343606, Cat:304008, BioLegend), human ALPL-APC (Cat: FAB1448A, R&D), and 7-AAD (488 nm) antibody (R&D). FACS was performed on a BD FACS Aria II sorter where dead cells and debris were excluded by forward versus side scatter (FSC/SSC), and live cells were further enriched by negative selection of 7-AAD. ALP+/CD45/34/31- cells were collected as osteoblasts. Gating schemes were established with fluorescence-minus-one (FMO) controls and 7-AAD was used as a measure for cell viability.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 following the manufacturer’s guide. Sequencing was performed on an Illumina Novaseq6000 with a sequencing depth of at least 100,000 reads per cell for a 150bp paired end (PE150) run.

tag: gender

value: Male

tag: disease

value: Osteopenia

value: Bone


title: LacZ 1 [141394_GTAGAGGT-TCTTTCCC_S43]

tag: cell type

value: primay coronary artery endothelial cells (HCAECs)

tag: passage

value: adenovirus encoding LacZ (Ad-LacZ, 10 MOI)


title: HT29ERB P65 ChIP-Seq rep 1

tag: chip antibody


title: HT29ERB P65 ChIP-Seq rep 2


title: BR.f10


title: Patient BS395 timepoint N1

tag: subject id

tag: subject status

value: non-small cell lung cancer (NSCLC) patient

value: M

value: L/L


title: Sample-16-HT-29-IL17

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.

source_name: IEC

extract_protocol:
RNA extracted with RNeasy Mini kit plus (QIAGEN).
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-NovaSeq(depth was above 150 million reads).
RNA-Seq (rRNA-depleted stranded (HMR))

value: Intestinal Epithelial Cells (IEC)

tag: stimulation

tag: randomization code

value: HT-29 (IEC)

tag: barcode


title: Sample-15-HT-29-TNFIL17


title: BR.d12

value: blank


title: Patient BS394 timepoint N2

value: Patient BS394

tag: age

tag: kir3ds1/l1 genotype

tag: response

tag: timepoint

value: Peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: CD8+ T cell


title: SW480M P65 ChIP-Seq rep 3

value: cat no:33-9900, lot no:QJ216251, mouse monoclonal, Invitrogen

tag: cell line

value: stably transfected with empty vector


title: Sample-14-HT-29-TNF

value: TNF


title: BR.d11

tag: donor number

tag: treatment

tag: time


title: Patient BS394 timepoint N1

tag: Sex

value: responder; partial response (PR)

tag: cell type


title: SW480M Input

tag: chip antibody

tag: transfection


title: Sample-13-HT-29-Medium

value: Medium


title: SW480M P65 ChIP-Seq rep 2


title: SW480M P65 ChIP-Seq rep 1


title: BR.b12


title: SW480ERB Input

value: stably transfected with ERBeta


title: Patient BS391 timepoint N2

tag: subject id

value: Patient BS391

tag: subject status

value: S/L

value: nonresponder; progressive disease (PD)


title: Patient BS391 timepoint N1

value: non-small cell lung cancer (NSCLC) patient

value: M


title: BR.d10


title: Sample-11-AS1303-TNFIL17

value: Intestinal Epithelial Cells (IEC)

tag: stimulation

tag: randomization code


title: BR.b11


title: Sample-10-AS1303-TNF

tag: barcode


title: Patient BS385 timepoint N1

value: Patient BS385

tag: age

value: F

tag: kir3ds1/l1 genotype

value: L/L


title: Sample-12-AS1303-IL17


title: SW480ERB P65 ChIP-Seq rep 3


title: Patient BS385 timepoint N2

tag: response

tag: timepoint

value: Peripheral blood mononuclear cells (PBMCs)


title: SW480ERB P65 ChIP-Seq rep 2

tag: cell line


title: BR.a11

tag: donor number

value: blank


title: BR.a12

tag: treatment


title: SW480ERB P65 ChIP-Seq rep 1

value: cat no:33-9900, lot no:QJ216251, mouse monoclonal, Invitrogen


title: Sample-9-AS1303-Medium


title: Sample-7-ST051-TNFIL17


title: Patient BS381 timepoint N1

value: Patient BS381

tag: cell subtype

value: CD8+ T cell


title: ywF2_input

city: Shanghai

first: Dong

last: Yan

address: 2005 Songhu Road

department: School of life sciences

country: China

institute: Fudan University

data_processing:
fastp software was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameters.
We used HISAT2 to map reads to the genome of Drosophila_melanogaster (Version: v96) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker.
StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM.
Genome_build: Genome of Drosophila_melanogaster (Version: v96)
Supplementary_files_format_and_content: bigWig flies for visualization
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Flies were grown on standard cornmeal food at 25°C.

extract_protocol:
Total RNA was isolated from adult flies about 1-2 days old using TRIzol. Poly(A) RNA was purified and fragmented, then incubated with Dynabeads coupled with m6A-specific antibody (202003, Synaptic Systems).
The IP RNA fragments and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method.

tag: strain

value: yw

tag: tissue

value: whole fly

tag: developmental stage

value: adult

tag: Sex

value: female


title: Patient BS379 timepoint N4

tag: subject id

value: Patient BS379

value: S/L

tag: cell type


title: ywF1_input


title: BR.a10

tag: time


title: Sample-6-ST051-TNF

tag: stimulation

value: TNF

tag: randomization code


title: Z69 glycerol rep 2

city: Montevideo

first: Ana Karen

middle: Karen

last: Malan

state: Montevideo

address: Avenida Italia 3318

department: Bioquímica y Genómica Microbianas

country: Uruguay

institute: Instituto de Investigaciones Biológicas Clemente Estable

data_processing:
Data obtained were analysed using CLC Genomics Workbench 7.5.5. First, reads were trimmed and those with high quality were mapped against H. seropedicae SmR1 genome (NC_014323). The number of mapped - unique gene reads in coding regions in each condition was analysed using the R/Bioconductor package DESeq2 (Love et al. 2014) to calculate fold-changes and to perform statistical analysis. Genes with p-adj < 0.01 were considered as differential expressed. RPKM were calculated with CLC Genomics Workbench7.5.5.
Genome_build: Data obtained were mapped against H. seropedicae SmR1 genome (NC_014323) using CLC Workbench 7.5.5
Supplementary_files_format_and_content: RPKM and mapped reads in excel sheet
Supplementary_files_format_and_content: Log2FoldChange and pvalues in excel sheet separated by coma

organism: Herbaspirillum seropedicae

source_name: cell culture

extract_protocol:
For RNA extraction, 5 ml of RNAlater stabilization solution (ThermoFisher Scientific) was added to an aliquot of 5 ml of culture, mixed and frozen. Cells were then collected by centrifugation and total RNA was purified using TRIzol reagent (Invitrogen, USA) followed by chloroform extraction according to manufacturer’s instructions. Total RNA was treated with DNaseI (ThermoFisher Scientific) and depleted using the MICROBExpress™ Bacterial mRNA Enrichment Kit (ThermoFisher Scientific).
The resulting mRNA was used to perform library construction with the Ion total RNA-seq v2 for Whole Transcriptome Library Kit (ThermoFisher Scientific). Sequencing was done using the Next Generation sequencing platform Ion Proton™ System®- Life Technologies. The Ion PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (ThermoFisher Scientific) were used following manufacture instructions.

tag: genotype

value: wild type

tag: carbon source

value: glycerol


title: Z69 glycerol rep 1


title: Sample-5-ST051-Medium

value: Intestinal Epithelial Cells (IEC)

value: Medium

tag: barcode


title: ywF2_IP


title: Patient BS375 timepoint N2

value: Patient BS375

tag: subject status

value: non-small cell lung cancer (NSCLC) patient

tag: age

value: M

tag: kir3ds1/l1 genotype

tag: response

value: nonresponder; progressive disease (PD)

tag: timepoint


title: BR.b10

tag: donor number

tag: treatment

value: blank


title: Patient BS379 timepoint N1

value: F

value: Peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: CD8+ T cell


title: Sample-4-ALET-UNT-4ST-IL17


title: xylB mutant xylose rep 2

tag: strain

value: xylB knock-out mutant

value: xylose


title: Patient BS375 timepoint N1

tag: subject id

tag: Sex


title: Sample-3-ALET-UNT-4ST-TNFIL17

tag: cell type


title: Patient BS381 timepoint N2

value: Patient BS381

value: L/L

value: responder; partial response (PR)


title: ywF1_IP

value: yw

tag: tissue

value: whole fly

tag: developmental stage

value: adult

value: female


title: xylB mutant xylose rep 1

tag: genotype


title: Sample-2-ALET-UNT-4ST-TNF

value: Intestinal Epithelial Cells (IEC)

tag: stimulation

value: TNF

tag: randomization code


title: Patient BS373 timepoint N1

value: Patient BS373

tag: subject status

value: non-small cell lung cancer (NSCLC) patient


title: Z69 xylose rep 1

value: wild type

tag: carbon source


title: Z69 xylose rep 2


title: Patient BS373 timepoint N2

tag: age

value: F

tag: kir3ds1/l1 genotype


title: Hakai4M2_input

extract_protocol:
Total RNA was isolated from male adult flies about 1-2 days old using TRIzol. Poly(A) RNA was purified and fragmented, then incubated with Dynabeads coupled with m6A-specific antibody (202003, Synaptic Systems).
The IP RNA fragments and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method.

value: male


title: Hakai4M1_input


title: Mettl14M1_input


title: Sample 12

city: Guangzhou

first: Yingfeng

last: Zheng

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Centre

institute: Sun Yat-sen University

description: single-cell RNA

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software (v3.0.2).
Genome_build: GRCh38/macFas5/mm10.
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing cellular barcodes in MEX format

source_name: central corneal epithelial cells

extract_protocol:
Human, monkey and mouse single cell suspensions in 0.4% BSA-PBS were processed for single-cell sequencing using the Chromium Single Cell 3’ Reagent Version 1 Kit and Chromium Controller (10xGenomics, CA, USA).
In each experiment, 20,000 cells per reaction were loaded for Gel Bead-in-Emulsion (GEM) generation in the GemCode instrument, followed by cell lysis, barcoded reverse transcription of RNA, cDNA amplification, shearing, adaptor and sample index attachment.
scRNA-Seq

treatment_protocol: The injury experiment was performed under in vivo condition for mouse and monkey eyes, and under ex vivo condition for human donor eyes. To mimic central corneal injury, an excimer laser (Allegretto Wave Eye-Q) was used to make a wounding by removing a small portion of the central epithelium and anterior stroma. The full thickness of the limbal epithelium and a layer of stroma beneath were excised to exclude the potential influence of limbal cells. Normal central corneas from contralateral eyes from the same donors without laser injury and limbal excision were used as uninjured controls.

value: central corneal epithelium

value: 24 hours after surgical injury


title: Mettl14M2_input


title: OV015

city: Ness Ziona

first: Ofir

last: Israeli

address: R lerrer

country: Israel

institute: IIBR

description:
Supp1_Differential expression impaired vs naïve.xls
Supp2_Differential expression non-impaired vs naïve.xls
Supp4_comparison analysis heatmap canonical pathways.jpg

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.17) for converting BCL to fastq format
Tophat (version 2.1.0) for mapping, with  with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10)
Cufflinks  (version 2.0.2) with default settings for the relative abundance (aka expression level) of genes and splice isoforms
Deseq for testing differentially expressed genes under various conditions
Ingenuity Pathway Analysis (IPA) , Qiagen, for canonical pathway analysis and heatmap generation
Genome_build: Rabbit: OryCun2.0 (GCA_000003625.1)
Supplementary_files_format_and_content: excel files including expression values , fold change and p-value for each gene in the comparison analysis; jpeg file including a heatmap comparing  canonical pathways between the different sample comparisons, generated by Qiagen Ingenuity Pathway Analysis (IPA)

organism: Oryctolagus cuniculus

source_name: Cornea

extract_protocol:
Corneas were removed, incubated  in RNA later over night and RNA was harvested using Tri-reagent (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq RNA Sample Prep Kit

treatment_protocol: Rabbit eyes were exposed to SM vapor. At 4w, corneal tissues from clinically impaired, clinically non-impaired and naïve eyes were processed for RNA-seq.

value: New Zealand White

tag: exsposure

value: 4 weeks Naïve

tag: clinical status

value: Naïve


title: OV013


title: Sample 11

description: single-cell RNA

tag: treatment


title: hDNMT3A_brain_rep3

first: Xiaoguo

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

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 Rattus_norvegicus.Rnor_6.0.89.chr using bowtie v1.0.1 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The expression level of each transcript was calculated using the fragments per kilobase of exon per million mapped reads (FPKM) method. Differentially expressed genes between two samples were identified based on a cutoff P value for per-gene variance less than 0.05 with conservative Bonferroni correction
Genome_build: Rattus_norvegicus.Rnor_6.0.89.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: Sprague Dawley

value: 15 weeks

tag: genotype/variation

tag: development stage


title: Sample 10

description: single-cell RNA

value: Normal


title: Ime4M1_input

tag: strain

value: whole fly

value: adult


title: hDNMT3A_brain_rep2

tag: Sex


title: ywM2_input

value: yw


title: Sample 9

description: single-cell RNA


title: ywM1_input


title: OV010

description:
Supp2_Differential expression non-impaired vs naïve.xls
Supp3_Differential expression impaired vs non-impaired.xls
Supp4_comparison analysis heatmap canonical pathways.jpg

value: 4 weeks post exposure to sulfur mustard vapor

value: Clinically non-impaired


title: OV011

value: 4 weeks Naive


title: WT_brain_rep3

value: wild-type


title: 8_ChIP: ME3

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

data_processing:
Adapter sequence from raw sequencing reads were removed using TrimGalore (v0.4.4）
Sequenced reads from H3K27ac and H3K4me1 immunoprecipitated and matched input controls from human appendix were mapped to the human reference genome (GRCh37/hg19) with BWA (v0.7.15)
 A combination of Picard and Samtools (v1.9) was used to mark and remove PCR duplicates, respectively. Deeptools (v2.3.1) was used for quality controls and narrow peaks were called using MACS2167 for each sample
 Consensus peaks were called using MACS2 combined peak calls, removing blacklist regions and IDR, following ENCODE ChIP-seq guidelines, yielding 26,381 H3K27ac peaks and 37,727 H3K4me1 peaks
Genome_build: hg19
Supplementary_files_format_and_content: Each peaks file contains: chr, start, end, length, abs_summit, pileup, -LOG10(pvalue), fold_enrichment, -LOG10(qvalue), name

source_name: Appendix

extract_protocol:
Appendix tissue was first cryoground into a fine powder using liquid nitrogen and a mortar and pestle. Frozen appendix tissue powder (~50 mg) for each sample was quickly suspended into 5 mL of ice-cold PBS and 0.5 mL of fresh crosslinker buffer (0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM Hepes pH 8.0, and 11% formaldehyde), and the sample was nutated for 7 min at room temperature. Crosslinking was quenched by adding 0.275 mL of 2.5 M Tris-HCl pH 8.0 and rotation for 5 min at room temperature. Samples were then centrifuged for 15 min at 2,000 x g and the pellet was washed with 5 mL of ice-cold PBS. Samples were then centrifuged again for 10 min at 2000 x g and the pellet was stored at -80°C until further processing. Each cross-linked tissue sample was then lysed by adding 100 μl of lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 20 mM EDTA, Complete protease inhibitor cocktail (Roche), and 1 mM PMSF), passing the solution through a 26g needle 10 times, followed by incubation on ice for 10 min. Samples were then placed into 1 mL of ice-cold TE buffer (1 mM EDTA, 10 mM Tris-HCl pH 8.0) and sonicated for 20 min using the E220 ultrasonicator (Covaris), which obtained a 200-500 bp sheared DNA length. To perform the ChIP, 200 µl of sheared DNA was exposed to 5 µg of anti-histone H3 acetyl K27 antibody (Abcam #4729), anti-histone H3 mono methyl K4 antibody (Abcam #8895), or control IgG (Cell Signaling). Sample tubes were then incubated overnight at 4°C with gentle nutation. Samples were then incubated with Dynabead Protein G beads (Thermo Fisher Scientific) for 10 min at room temperature. DNA-protein complexes on beads were washed 5 times with ice-cold modified RIPA (5 mM Hepes pH 8.0, 1% NP-40, 0.7% Sodium Deoxycholate, 0.5 M LiCl, Complete protease inhibitor cocktail, 1 mM EDTA) and then once with 150 µl of TE buffer. To elute DNA and reverse crosslinks, beads were incubated in 120 µl elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) at 65°C overnight. For input DNA, 20 µl of sheared chromatin was added to 130 µl elution buffer and now processed in parallel with the ChIP samples. Following overnight incubation, 250 µl of TE was added to each sample with 0.2 mg/mL RNase A (Thermo Fisher Scientific) and incubated at 37°C for 1 h. Then 0.4 mg/mL proteinase K (Thermo Fisher Scientific) was added to each sample and incubated at 55°C for 1 h. DNA was then purified with phenol-chloroform extraction (Thermo Fisher Scientific) and suspended in 10 mM Tris-HCl pH 8.0. Target fold enrichment relative to IgG control (205.0 for H3K27ac, 44.5 for H3K4me1) was confirmed by qPCR on an ABI StepOne Plus system
Libraries for appendix ChIP (H3K27ac, H3K4me1) and input samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available immunoprecipitated material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina TruSeq UD Indexed Adapters (Illumina Inc.). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), and QuantiFluor dsDNA System (Promega Corp.). Sequencing (single-end 100 bp) was performed on an Illumina NovaSeq6000 sequencer producing ~99.6 million reads per sample. Base calling was done by Illumina RTA3, and output was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq2 v2.19.

value: Appendix

tag: chip antibody


title: WT_brain_rep2

tag: tissue

value: male


title: OV009


title: Hakai4M1_IP

tag: developmental stage


title: Hakai4M2_IP


title: OV008


title: WT_brain_rep1


title: 8_ChIP: ME1


title: 8_ChIP: ME2


title: OV007


title: Mettl14M1_IP


title: 8_ChIP: AC3


title: Ime4M2_input


title: hDNMT3A_testis_rep3

source_name: testis

value: testis


title: OV012

value: New Zealand White


title: 8_ChIP: AC2


title: hDNMT3A_brain_rep1


title: NHEK Control vs TCE treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: TCE+

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Normal human epidermal keratinocytes were cultured in HuMedia-KG2 medium.

extract_protocol: Total RNA was extracted from NHEK by Torizol reagent kit and then purified by Qiagen RNeasy Mini Kit.

treatment_protocol: After incubation with or without 2mM TCE for 36 hours, cells were harvested, and total RNA was extracted immediately.

tag: cell type

value: Keratinocytes (NHEKs)

source_name: TCE-


title: hDNMT3A_testis_rep1


title: OV004

description:
Supp1_Differential expression impaired vs naïve.xls
Supp3_Differential expression impaired vs non-impaired.xls
Supp4_comparison analysis heatmap canonical pathways.jpg

value: Clinically impaired


title: OV005


title: 8_ChIP: input3

value: INPUT


title: OV003


title: Ime4M1_IP


title: ywM2_IP


title: Mettl14M2_IP


title: 8_ChIP: input1


title: ywM1_IP


title: 8_ChIP: input2


title: WT_testis_rep1

value: Sprague Dawley


title: hDNMT3A_testis_rep2

value: 15 weeks


title: OV001


title: OV002


title: OV006


title: WT_testis_rep2


title: 8_ChIP: AC1


title: Cy5-TMX_1_Cy3-OIL_1

status: Public on Feb 28 2021

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse 8 x 60K v2 Microarray (G4851B) 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: Agilent SurePrint G3 Mouse 8 x 60K v2 Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2505C, Agilent Technologies).Images were quantified using Agilent Feature Extraction (version 12.0.3.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction (version 12.0.3.1).

source_name: Lung tumor, tamoxifen treatment, 4 weeks

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Mouse 8 x 60K v2 Microarray kit (Agilent Technologies) with 60k distinct probes.

growth_protocol: Mice were housed in groups of four or five in standard cages in a temperature and humidity controlled room, with a 12-h light/dark cycle (lights on at 08:00), and had access to standard lab chow and water ad libitum.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA). Double-stranded cDNA was synthesized from 50 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: Ror1f/f; CAG-CreER; SPC-hEGFRdel746-750 mice were treated with tamoxifen or corn oil between 16 weeks to 20 weeks. Lung tumor was collected at 20 weeks of age. After that, we isolated RNA.

tag: agent

value: Tamoxifen

value: Lung tumor

source_name: Lung tumor, Oil treatment, 4 weeks

value: Corn oil


title: WT_testis_rep3

value: adult


title: Cy5-OIL_2_Cy3-TMX_2


title: Cy5-TMX_2_Cy3-OIL_2


title: Cy5-OIL_1_Cy3-TMX_1


title: Ime4M2_IP

value: whole fly


title: Liver_ERaLiverKOmale_untreated_Replicate1 [D5]

city: Madison

first: Andrea

last: Bilger

state: WI

address: 1111 Highland Avenue

department: McArdle Laboratory for Cancer Research

institute: UW-Madison

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg Celsius Surehyb chamber.

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit.

data_processing: Agilent Feature Extraction versions 9.1 and 9..5 for background subtraction - localbackground and normalization Linear LOWESS, Goodspots were designated as those features with both channels r and g where controltype=0, issaturated=0,isfeatnonunifol=0,isfeatpopnol=0,iswellabovebg=1 in 80% of arrays

source_name: Liver from one intact male at 11 weeks

label_protocol: Total RNA was amplified and labeled according to manufacturer's instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS.

growth_protocol: Mouse Diet 9F5020.

extract_protocol: Homogenized with Polytron for 1 minute at 24 krpm, then processed with an Qiagen RNeasy kit.

treatment_protocol: Sacrificed and dissected at given time and placed in RNAlater.

value: Liver

tag: genotype

value: Male

source_name: RNA from untreated livers: 1/2 intact female (18 mice) and 1/2 intact male (15 mice), 9-10 weeks

value: Pooled male and female


title: Liver_ERaWTmale_untreated_Replicate3 [E4]


title: Cy5-OIL_3_Cy3-TMX_3


title: Cy5-TMX_3_Cy3-OIL_3


title: Liver_ERaWTmale_untreated_Replicate2 [D2]


title: Liver_ERaLiverKOfemale_untreated_Replicate3 [B9]

source_name: Liver from one intact female at 11 weeks

value: Female


title: Liver_ERaWTmale_untreated_Replicate1 [F1]

source_name: Liver from one intact male at 10 weeks


title: Liver_ERaLiverKOfemale_untreated_Replicate2 [B7]


title: Liver_ERaLiverKOmale_untreated_Replicate2 [B5]


title: Liver_ERaLiverKOmale_untreated_Replicate3 [B6]


title: Liver_ERaWTfemale_untreated_Replicate3 [A10]


title: Liver_ERaWTfemale_untreated_Replicate1 [F10]

source_name: Liver from one intact female at 10 weeks


title: Liver_ERaWTfemale_untreated_Replicate2 [A7]


title: Liver_ERaLiverKOfemale_untreated_Replicate1 [A8]


title: Liver_Ovx_0.1mgEstradiolPellet_Replicate1

description: Ovx E2-Rep1

source_name: Liver from 6 females, ovex at 6 wks, pellet at 7 weeks, collected at 9 weeks

value: Ovex; 0.1 mg estrogen pellet


title: Liver_ERaKOmale_untreated_Replicate1

description: ERalpha KO Male-Rep1

source_name: Untreated liver from 6 intact males, 9-10 weeks


title: Liver_ShamOperation_PlaceboPellet_Replicate1

description: Sham Placebo-Rep1

source_name: Liver from 7 females, sham ovex at 6 wks, pellet at 7 wks, collected at 9 weeks

value: Sham ovex; placebo pellet


title: Liver_Ovx_0.1mgEstradiolPellet_Replicate2

description: Ovx E2-Rep2


title: Liver_ERaWTmale_untreated_Replicate1

description: ERalpha WT Male-Rep1


title: Liver_ERbKOfemale_untreated_ShamOperation_PlaceboPellet_Replicate2

description: ERbetaKOFemale Sham Placebo-Rep2

source_name: Liver from 6 females, sham ovex at 6-7 wks, pellet at 7-8 wks, collected at 9-10 weeks


title: Liver_ERbHetfemale_untreated

description: ERbetaHetFemale

source_name: Liver from 6 intact females, 9-10 weeks


title: Liver_ShamOperation_PlaceboPellet_Replicate2

description: Sham Placebo-Rep2


title: Liver_ERbWTmale_untreated_Replicate1

description: ERbeta WT Male-Rep1


title: Liver_ERaKOmale_untreated_Replicate2

description: ERalpha KO Male-Rep2


title: Liver_ERaHetfemale_untreated

description: ERalphaHetFemale


title: Liver_ERbKOfemale_untreated_ShamOperation_PlaceboPellet_Replicate1

description: ERbetaKOFemale Sham Placebo-Rep1


title: Liver_Ovx__Replicate1

description: Ovx

source_name: Liver from 6 females, ovex at 6 wks, collected at 10 weeks

value: Ovex


title: Liver_ERbWTmale_untreated_Replicate2

description: ERbeta WT Male-Rep2


title: Liver_Ovx_PlaceboPellet_Replicate2

description: Ovx Placebo

value: Ovex; placebo pellet


title: Liver_male_untreated_Replicate1

source_name: Untreated liver from 15 intact males, 9-10 weeks


title: Liver_ERbWTfemale_untreated_Replicate1

source_name: Untreated liver from 6 intact females, 9-10 weeks


title: Liver_ERaWTfemale_untreated_Replicate2


title: Liver_ERaWTmale_untreated_Replicate2

description: ERalpha WT Male-Rep2


title: Liver_ERbKOfemale_untreated_Replicate1

source_name: Untreated liver from 8 intact females, 9-10 weeks


title: Liver_male_untreated_Replicate2


title: Liver_ERaWTfemale_untreated_Replicate1


title: HCC1395 GapmeR 2 N3

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

institute: Dalhousie University

hyb_protocol: 16h at 45oC, Affymetrix Human Gene 2.0 ST microarray platform

scan_protocol: Affymetrix genechip scanner 3000 (Scanner#4)

data_processing: RMA expression value derived from Expression Console software

source_name: HCC1395 cells

label_protocol: Affymetrix WT Plus kit and biotin allonamide triphosphate

growth_protocol: The cell lines were obtained from the American Type Culture Collection (ATCC) and were cultured as per ATCC guidelines

extract_protocol: cells were collected in TRIzol and total RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) and incorporating a DNAse treatment step following the manufacturer’s instructions.

treatment_protocol: cultured cells treated for 48hours with GapmeRs

tag: cell line

value: HCC1395 cells

value: GapmeR 2


title: Liver_ERbKOfemale_untreated_Replicate2


title: Liver_ERaKOfemale_untreated_Replicate1


title: Liver_ERaKOfemale_untreated_Replicate2


title: Liver_female_untreated_Replicate1

source_name: Untreated liver from 18 intact females, 9-10 weeks


title: HCC1395 negative control GapmeR N2

value: negative control GapmeR


title: HCC1395 GapmeR 2 N1


title: HCC1395 GapmeR 1 N3

value: GapmeR 1


title: HCC1395 GapmeR 2 N2


title: Liver_ERbWTfemale_untreated_Replicate2


title: HCC1806 GapmeR 2 N3

source_name: HCC1806 cells

value: HCC1806 cells


title: HCC1395 negative control GapmeR N1


title: Liver_female_untreated_Replicate2


title: HCC1395 GapmeR 1 N2


title: HCC1395 negative control GapmeR N3


title: HCC1806 GapmeR 2 N1


title: HCC1806 GapmeR 2 N2


title: HCC1806 GapmeR 1 N1


title: HCC1806 GapmeR 1 N3


title: HCC1395 GapmeR 1 N1


title: C57BL/6J pancreas

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

description: scRNA-Seq

data_processing:
For scRNA-Seq: data was generated on the 10X platform (10X Genomics, Pleasanton, CA) according to Single Cell 3’ protocol (v2 Chemistry) recommended by the manufacturer .The Cell Ranger software pipeline (version 2.1.1) was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and produce a  matrix of gene counts versus cells. The R package Seurat (version 3.1.1) was used to process the unique molecular identifier (UMI) count matrix, and to perform data normalization (gene expression measurements for each cell were normalized by total expression, and log-transformed), dimensionality reduction, clustering, and differential expression analysis. DE analysis was performed with the R packages DESeq2 (v.1.16.0) and MAST. Gene-set enrichment analysis was performed on the identified differentially expressed genes with the GSEA software in the pre-ranked mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: C57BL6J_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: C57BL6J_gene.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: C57BL6J_cell.tsv: cell names (colname names of the sparse count matrix)
For RNA-Seq: Quality of raw FASTQ sequences was assessed using FASTQC. To process RNA-Seq libraries,  adaptor sequences were trimmed using Cutadapt version 1.14 (requiring a length greater than 10 nt after trimming) and quality-filtered by requiring all bases to have a minimum score of 20 (-m 20 -q 20). Only reads that passed the quality or length threshold on both strands were considered for mapping. Reads were aligned to the human genome GRCh38 (hg38) with the STAR Aligner (version 020201). Ensembl reference annotation version 89 was used to define gene models for mapping quantification. Uniquely mapped reads for each gene model were produced using STAR parameter “--quantMode GeneCounts”. Differential expression analysis was performed in R using DESeq2 (v.1.16.0) with the default parameters, including the Cook’s distance treatment to remove outliers.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts_all_genes.tsv: tab-delimited file containing the raw reads count matrix

source_name: mouse pancreas cells

growth_protocol: For RNA-Seq: 10% FBS, 1X P/S, DMEM

extract_protocol:
Qiagen RNeasy kit
For RNA-Seq: Eukaryotic stranded library
DBA-lectin based generation of single cell suspension of pancreatic duct cells
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2

treatment_protocol: Viral transduction of gRNA followed by stable selection with puromycin

value: pancreas

value: 9 weeks


title: HSE-K27AC-TNF-1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg38) using bowtie2 with default parameters
Peaks were called using MACS2
Genome_build: hg38
Supplementary_files_format_and_content: Peak files from MACS2; TDF Files

source_name: liver

growth_protocol: Human liver sinusoidual endothelial cells were purchased from Sciencell #5000 and maintained in endothelial medium

extract_protocol:
Chromatin input was prepeared by the combination of MNase treatment and sonication, and the chromatin associated with histone modification and transcription factor was isolated using indicated antibody.
Illumina NGS library preparation and paired-end index kits

treatment_protocol: LSEC cells were serum starved for 2 hours, treated with human TNFa or control for 90 mins and cells were harvested

value: Human primary LSEC


title: ChIP_mESC_KANSL3-KI_2hr_aH4K5ac#1

city: London

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.4.5), with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to human assembly hg38 or mouse assembly mm10 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in Picard Tools (v2.16.0).
For KANSL3 and KAT8 ChIP-seq analysis, to ascertain enriched regions, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 with KANSL3 KD cells as background controls or input, respectively.
The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized read density profiles, using a read extension of 200 bp for ChIP samples
Genome_build: GRCh38/hg38 or GRCm38/mm10
Supplementary_files_format_and_content: BigWig files and, where indicated, normalization factor tables and called peaks tables

source_name: Preimplantation epiblast

growth_protocol: HEK293, HeLa and U2OS cells were cultured in DMEM, high glucose, GlutaMAX supplement, sodium pyruvate medium (Thermo Fisher SCIENTIFIC) containing 10% heat-inactivated FBS (HyClone) and 1x Penicillin/Streptomycin (Thermo Fisher SCIENTIFIC). THP-1, K562, MOLM13 cells were cultured in RPMI 1640, GlutaMAX supplement, sodium pyruvate medium (Thermo Fisher SCIENTIFIC) containing 10% heat-inactivated FBS (HyClone) and 1x Penicillin/Streptomycin (Thermo Fisher SCIENTIFIC). Mouse MLL-AF9 secondary leukemia cells were generated in the Helin lab and were cultured in RPMI 1640, GlutaMAX supplement, sodium puryvate medium (Thermo Fisher SCIENTIFIC) containing 20% heat-inactivated FBS (HyClone), 1x Penicillin/Streptomycin (Thermo Fisher SCIENTIFIC) and 20% of culture media supernatant from the IL-3-secreting cell line (homemade). E14 mouse embryonic stem cells were cultured in the serum/LIF medium containing Glasgow Minimum Essential Media (Sigma), 10% heat-inactivated FBS (HyClone), 1x Penicillin/Streptomycin (Thermo Fisher SCIENTIFIC), 2 mM GlutaMAX (Thermo Fisher SCIENTIFIC), 100 µM β-Mercaptoethanol (Thermo Fisher SCIENTIFIC), 1 mM sodium pyruvate (Thermo Fisher SCIENTIFIC), 0.1 mM MEM Non-Essential Amino Acids Solution (Thermo Fisher SCIENTIFIC) and Leukemia Inhibitory Factor (homemade).

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min, after which the reaction was quenched by the addition of glycine to the final concentration of 0.125 M. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer at 1 ml per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM TrisHCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps. Chromatin concentrations were estimated using Bradford (Bio-Rad) or BCA assays (Thermo Fisher SCIENTIFIC) according to manufacturer’s protocols. The immunoprecipitation reactions were set up in 1 ml of the immunoprecipitation buffer as indicated below and incubated overnight at 4C. The next day, BSA-blocked Fast-flow Protein G Sepharose beads (GE Healthcare) or Protein G Dynabeads (Thermo Fisher SCIENTIFIC) were added to the reactions and incubated for 3 hours at 4C. The beads were then washed three times with low-salt washing buffer (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM TrisHCl pH8.0) and two times with high-salt washing buffer (500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM TrisHCl pH8.0). The samples were then reverse-crosslinked overnight in the elution buffer (1% SDS, 0.1 M NaHCO3) and purified using QIAQuick PCR purification kit (QIAGEN).
NEBNext® Ultra™ II for DNA Library Prep

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for sequencing 3 days post-transduction

tag: antibody

value: embryonic

value: mouse embryo

tag: culture type

value: adherent


title: ChIP_mMLL-AF9_aH4K16ac

source_name: Acute myeloid leukemia cell line

value: myeloid

value: spleen

value: suspension


title: ChIP_mESC_KANSL3-KI_0hr_aH4K5ac#1


title: ChIP_mESC_KANSL3-KI_2hr_aH4K8ac


title: HSE-K27AC-Ctrl-2_input


title: ChIP_mESCs_aH4K16ac


title: HSE-NF-kB-Ctrl-2

description: Control


title: ChIP_mESC_KANSL3-KI_0hr_aH4K8ac


title: HSE-K27AC-TNF-2


title: HSE-K27AC-TNF-2_input


title: HSE-K27AC-TNF-1_input


title: HCC1806 negative control GapmeR N2


title: HCC1806 GapmeR 1 N2


title: MM1.S_IRF3 ChIP_rep2

first: Kanagaraju

last: Ponnusamy

address: 4th Floor common wealth building, Du Cane Road

department: Hematology

institute: Imperial College London

data_processing:
IRF3 ChIP sequencing reads were aligned with BWA MEM (v0.7.15) to GRCh38 genome (Gencode v28) with standard settings.
QC and duplicate marking were performed with Picard (v2.6.0) and samtools (v1.2).
Tracks were generated with Deeptools (v3.3.1),7 and peaks were called with MACS2 (v2.1.1).
Genome_build: GRCh38 genome (Gencode v28)
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: bigWig

source_name: Myeloma cell line

growth_protocol: cells were cultured in RPMI 1640 medium with 10% FBS

extract_protocol:
MM1.S cells were fixed with 1% formaldehyde and nuclear extracts were collected. IRF3 was immunoprecipitated after shearing the chromatin below 500bp and pre-clear with protein G beads. IRF3 bound DNA was collected after reverse cross-linking.
Libraries were prepared using NEBNext kit for Illumina (New England Biolabs) according to manufacturer's protocol


title: HSE-K27AC-Ctrl-2


title: HCC1806 negative control GapmeR N1


title: HSE-K27AC-Ctrl-1


title: HSE-NF-kB-TNF-2

description: NFKB TNF


title: HCC1806 negative control GapmeR N3


title: MM1.S_Input_rep2


title: MM1.S_IRF3 ChIP_rep1


title: MM1.S_Input_rep1


title: M2-rep5

first: Fei

last: Gao

address: 200 2st NW

description: lncRNA expression

hyb_protocol: The labeled/amplified RNA and labeled cRNA was purified and hybridizated using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: Microarray slides were washed and scanned on an Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Data were extracted using Agilent Feature Extraction Software.

source_name: macrophage M2

label_protocol: RNA was labeled using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442).

growth_protocol: THP-1 monocytes were activated into macrophages by exposing to 100  ng/mL phorbol-12-myristate-13-acetate (PMA) in the culture medium for 2 days followed by an additional 72 hours in PMA-free medium.

extract_protocol: Total RNAs from six independent groups of M0 macrophages or M2 macrophages were isolated using Trizol reagent (Invitrogen life technologies, CA, USA).

treatment_protocol: To generate M2-polarized THP-1 macrophages, dTHP-1 cells were cultured with 20 ng/ml IL-4 and IL-13 for 24 hours.

value: Human monocytic THP-1 cells


title: M2-rep2

description: lncRNA expression


title: AZD

city: Charlottesville

first: Erin

last: Moran

state: VA

address: 1340 Jefferson Park Avenue, Pinn 6014

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: DRIP-seq

data_processing:
Raw sequence files were filtered for quality using Prinseq and downsampled to 6.5M reads each
Spike-in quantification was performed by aligning reads to the SacCer3 genome using BWA-MEM (HEK293T samples were also aligned to determine a background level of alignment)
Reads were aligned using BWA-MEM paired end options to hg38 genome
Model build using MACS2 estimated ~290 as a shift between paired end sequences. Peaks were called using paired end settings using a -d value of 290.
Repetitive elements from DLD1 cells were determined de novo using the RepeatExplorer package and a subset of the reads from both input files (~1M reads from each)
Count tables of DRIP enrichments within repetitive elements was determined using ChIP-seq mapper (Neumann et al., 2012), a BLASTN style mapper to determine reads within repetitive contigs.
Count tables were then normalized based on Spike-in quantification scale factors, found in table 4 of the Materials and methods section of Moran et al
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files
Supplementary_files_format_and_content: NarrowPeak bed files were created from individual alignment files using MACS2 callpeaks -pe
Supplementary_files_format_and_content: Inputs, treatment files across duplicates were compiled after alignment using BWA-MEM using Samtools. Compiled files were used to call peaks using MACS2 callpeak.

growth_protocol: DLD1 cells grown in RPMI-1640 with 10% FBS

extract_protocol:
Nucleic acids were extracted from sonicated chromatin, and RNA-DNA hybrids were precipitated with the S9.6 hybridoma.
Libraries were prepared using Takara SMARTer ThruPLEX DNA seq using Illumina compatible DNA HT dual Index kit N1-N12. Sonicated yeast DNA was spiked in at a 10% rate prior to library preparation.

tag: precipitating antibody

value: S9.6 hybridoma

value: Colcemid, AZD1152 500 nM

tag: rnaseh1 treatment


title: M2-rep4

description: lncRNA expression


title: ZM

description: DRIP-seq

value: Colcemid, ZM447439 2 uM


title: dPPRrbcL rep2

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

country: France

institute: IBMP-CNRS

data_processing:
Raw data were imported into CLC Genomics Workbench. Paired trimmed reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench 6.5.1 (Qiagen) utilizing the following parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.5, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes.
Reads of the two replicates aligned in CLC Genomics Workbench were extracted as coverage (reads per nucleotide, csv files). Graphs were created with excel using the extracted coverage values.
Genome_build: NC_000932.1, Arabidopsis thaliana chloroplast genome

organism: Arabidopsis thaliana

source_name: chloroplast; stroma extract

growth_protocol: Plants were grown under controlled conditions (12-h-light (21°C)/12-h-dark (18°C) at a PFD of 160-175 µmol photons m-2 sec-1)

extract_protocol:
Isolation of chloroplasts and stroma extracts as well as immunprecipitation protocol see: Jiang,J., Chai,X., Manavski,N., Williams-Carrier,R., He,B., Brachmann,A., Ji,D., Ouyang,M., Liu,Y., Barkan,A., et al. (2019) An RNA Chaperone-Like Protein Plays Critical Roles in Chloroplast mRNA Stability and Translation in Arabidopsis and Maize. Plant Cell, 31, 1308–1327.
Recovered RNA was further purified with Monarch® RNA Cleanup Kit (NEB) and 50 ng of each RNA were used for libraries generation with the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer's instructions.

tag: age

value: 2 weeks

value: transgenic dPPRrbcL


title: M2-rep1

description: lncRNA expression


title: DMSO2

description: DRIP-seq

tag: treatment

value: Colcemid, DMSO


title: WT rep1

tag: genotype/variation

value: WT (Col-0)


title: WT rep2


title: Input2

description: DRIP-seq


title: DMSO1

description: DRIP-seq


title: Input1

description: DRIP-seq


title: dPPRrbcL rep1


title: ChIP_THP1_KAT8-KD_aKAT8

value: monocyte

value: peripheral blood


title: M0-rep4

description: lncRNA expression

source_name: macrophage M0


title: M0-rep5

description: lncRNA expression


title: M0-rep2

description: lncRNA expression


title: M0-rep3

description: lncRNA expression


title: ChIP_THP1_WT_aKAT8

value: WT


title: M2-rep3

description: lncRNA expression


title: DMSO2-RNH1

description: DRIP-seq


title: M0-rep6

description: lncRNA expression


title: M2-rep6

description: lncRNA expression


title: DMSO1-RNH1

description: DRIP-seq


title: ChIP_THP1_shMSL1_KO_aH4K16ac


title: Gastric IM 2006-008 AntB

city: East Melbourne

first: Rita

middle: Ann

last: Busuttil

state: VIC

address: St Andrews Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files were produced using the Affymetrix ® GeneChip ® Command console ® Software (AGCC).

source_name: Gastric intestinal metaplasia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Gastric Intestinal metaplasia tissue

extract_protocol: Total RNA was extracted from gastric tissue using mirVana RNA isolation kit according to the instructions of the manufacturer.

treatment_protocol: Gastric tissue was macrodisected to enrich for regions of intestinal metaplasia

tag: gender

value: M

value: gastric intestinal metaplasia


title: ChIP_THP1_sgKAT8_aH4K8ac


title: ChIP_THP1_sgKANSL3_aH4K8ac


title: ChIP_THP1_sgNegCtrl_KO_aH4K16ac

value: sgNegCtrl


title: ChIP_THP1_sgNegCtrl_aH4K8ac


title: ChIP_THP1_sgKANSL2_aH4K8ac


title: Gastric IM 2007-0015 Antrum


title: ChIP_THP1_sgKAT8_aH4K5ac#2


title: ChIP_THP1_sgKANSL2_aH4K5ac#2


title: ChIP_THP1_sgNegCtrl_aH4K5ac#2


title: ChIP_THP1_sgKAT8_aH4K5ac#1


title: ChIP_THP1_sgKANSL3_aH4K5ac#2


title: Gastric IM2006-0011 AntB


title: Gastric IM 10-043-01 B3

value: F


title: ChIP_THP1_sgKANSL3_aH4K5ac#1


title: Gastric IM 09-0025-01_B1


title: Gastric IM 09-033-03B3


title: Gastric IM 09-0032-01_B3


title: ChIP_THP1_sgNegCtrl_aH4K5ac#1


title: ChIP_THP1_sgKANSL2_aH4K5ac#1


title: Gastric IM 09-0003-01_B4


title: Gastric IM 09-0020-02_B1


title: ChIP_THP1_sgKAT8_input


title: Gastric IM 09-0024-02_B5


title: wt_Fkh1_b

type: genomic

first: Catherine

middle: Anne

last: Fox

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

description:
yeast, formaldehyde fixation, sonciated
wt_Fkh1_ChIP_IP_b
wt_Fkh1_ChIP_input_b

hyb_protocol: Hybridization performed by NimbleGen.

scan_protocol: Scanning performed by NimbleGen.

data_processing: The log2 ratios of IP over input were obtained from the values extracted from the S. cerevisiae tiling microarray for each feature. These log2 ratios for each experiment were plotted as a histogram and then background subtracted so that the peak of each histogram was centered over 0. The most repetitive probes (1.1%) were removed from the dataset.

source_name: Sonication + antibody (ChIP)

label_protocol: Labeling performed by NimbleGen.

growth_protocol: Cultures were grown to OD600 of0.5 to 0.9 and ChIPs were performed as described previously (Shor et al, 2009) using a polyclonal antibody against Fkh1.

extract_protocol: IP and total DNA were amplified using ligation-mediated PCR and mailed to Nimblegen for hybridization to high density tiled arrays (2006-10-12_Ansari_tiling_51mer).

treatment_protocol: Average chromatin shearing size was around 0.5 Kb. IP and total DNAs were purified using QIAquick PCR

tag: strain

value: wild type

source_name: Sonication - antibody (Input)


title: null_Fkh1

description:
yeast, formaldehyde fixation, sonciated
null_Fkh1_Chip_IP_a
null_Fkh1_ChIP_input_a


title: ChIP_THP1_sgKANSL3_input

value: suspension


title: Gastric IM 08-0017 AntA


title: Gastric IM 08-020_AntB


title: wt_Fkh1_a

description:
yeast, formaldehyde fixation, sonciated
wt_Fkh1_ChIP_iP_a
wt_Fkh1_ChIP_input_a


title: Gastric IM 10-0038-01_B1


title: Gastric IM 08-0021 Body2


title: M0-rep1

description: lncRNA expression

value: Human monocytic THP-1 cells


title: ChIP_THP1_sgKANSL2_input


title: KPL4 cells, ERβ Knockout, biological rep 3

city: Philadelphia

first: Christoforos

last: Thomas

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Gene expression data from ERβ Knockout Inflammatory breast cancer cells

hyb_protocol: 5.5 μg of fragmented biotinilated cDNA was hybridized for 16 hr at 45C to Clariom D Human Arrays. GeneChips were washed and stained with streptavidin-phycoerythrin

scan_protocol: GeneChips were scanned using the A GeneChip 3000 7G.

data_processing: cel files were normalized with RMA in Transcriptome Analysis Console (TAC) Software using default settings

source_name: Inflammatory breast cancer cells, ERβ Knockout

label_protocol: cDNA was prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, Affymetrix)

growth_protocol: KPL4 cells were maintained in HAM’s-F12 media supplemented with 7% fetal bovine serum, 10 mM HEPES, 5 μg/mL insulin, 1μg/mL hydrocortisone at 37°C in 5% CO2

extract_protocol: Total RNA was isolated using Qiagen RNeasy Mini kit according to the manufacturer's instructions

value: ER-beta Knockout


title: ChIP_THP1_sgNegCtrl_input


title: KPL4 cells, ERβ Knockout, biological rep 2


title: KPL4 cells, control, biological rep 3

description: Gene expression data from control KPL4 Inflammatory breast cancer cells

source_name: Inflammatory breast cancer cells, control

value: Control


title: KPL4 cells, ERβ Knockout, biological rep 1


title: KPL4 cells, control, biological rep 2


title: KPL4 cells, control, biological rep 1


title: ChIP_THP1_sgKAT8_aH4K16ac


title: ChIP_THP1_sgNegCtrl_aH4K16ac


title: ChIP_HEK293_WT_aH4K16ac

source_name: Embryonic kidney cell line

value: epithelial

value: embryonic kidney

value: adherent


title: ChIP_THP1_sgKANSL2_aH4K16ac


title: s1: siRNA_ctrl_rep1

description: mRNA expression

hyb_protocol: The labeled/amplified RNA and labeled cRNA was purified and hybridizated using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Microarray slides were washed and scanned on an Agilent Microarray Scanner (Agilent p/n G2565CA).

data_processing: Data were extracted using Agilent Feature Extraction Software 10.7.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: THP-1 monocytes were activated into macrophages by exposing to 100  ng/mL phorbol-12-myristate-13-acetate (PMA) in the culture medium for 2 days followed by an additional 72 hours in PMA-free medium.To generate M2-polarized THP-1 macrophages, dTHP-1 cells were cultured with 20 ng/ml IL-4 and IL-13 for 24 hours.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Macrophage M2 cells were treated with lnc-M2_siRNA and the siRNA control.


title: s4: lnc-M2_siRNA_rep2

description: mRNA expression


title: ChIP_U2OS_WT_aH4K16ac

source_name: Osteosarcoma cell line

value: bone


title: s2: lnc-M2_siRNA_rep1

description: mRNA expression


title: ChIP_MOLM13_WT_aH4K16ac


title: ChIP_HeLa_WT_aH4K16ac

source_name: Adenocarcinoma cell line

value: cervix


title: ChIP_THP1_sgKANSL3_aH4K16ac

value: monocyte


title: ChIP_K562_WT_aH4K16ac

source_name: Chronic myelogenous leukemia cell line

value: lymphoblast

value: bone marrow


title: ChIP_THP1_WT_input

value: WT

value: peripheral blood


title: ChIP_THP1_WT_aH3K4me3


title: ChIP_THP1_KANSL3-KD_aKANSL3


title: ChIP_THP1_WT_aKANSL3


title: H2_lung_3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: the lung at 24 hours after CLP with H4 treated

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 or HiSeq 3000 platforms in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Nine-week-old C57BL/6 male mice underwent cecal ligation and puncture procedure (CLP) or sham procedure. Subsequently, the CLP model received an immediate +/- continuous inhalation of 7% H2. The H2 gas-treated groups were housed in the same cage, and they were put in a designated box that was able to maintain the concentration of H2 through constant H2 supply by a gas generator. Mice were observed for a week to assess their survival rates. Serum inflammatory cytokines were evaluated with ELISA at 24 h after the CLP procedure. The liver, the intestine, and the lungs in the CLP model received +/- H2 therapy for 24 h were assessed by RNA-seq.

tag: line

value: lung


title: H2_lung_2

description: the lung at 24 hours after CLP with H3 treated


title: IR1

city: Dalian

first: Yan

last: Hu

state: Liaoning

address: 467 Zhongshan Road

institute: Department of Pharmacy, Second Affiliated Hospital of Dalian Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze array images. When Data was extracted, Quantile normalization and subsequent data processing were conducted to use the R software limma package.

label_protocol: Labeling were operated following the Agilent One-Color Microarray-Based Gene Expression Analysis construction.

growth_protocol: Each mice was fostered in a temperature-constant room and nourished by a standard chow pellet diet.

extract_protocol: Tissue RNA was extracted from each hepatic sample using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.

value: male

value: ischemia 1h and reperfusion 6h


title: IPC1

value: 10 minutes of ischemia and 10 minutes of reperfusion was induced before 1h ischemia and 6h reperfusion


title: OS20

city: Kongens Lyngby

first: Julia

last: Villarroel

address: Kulsviervænget 41

country: Denmark

institute: University of Copenhagen

data_processing:
1) Paired reads' quality was checked via fastQC
2) Paired reads were quality-trimmed with Trim Galore using default options
3) RNAseq raw reads were aligned to the human genome (GRCh38.p13) using STAR v2.7.2b.
4) Gene read coverages were computed with featureCounts v1.6.2 using GENCODE annotation release version 35
5) Differential expression analysis was performed using edgeR v3.30.3 with "y ~ 0 + group" design, where group combined information on disease and insuline R/S. Low count reads were filtered filterByExpr
Genome_build: GRCh38.p13, version 35
Supplementary_files_format_and_content: Text file in comma separated format with gene coverages in units of read counts

source_name: Omental Adipose Tissue

extract_protocol: none provided by the submitter

tag: disease

value: Obese

tag: insulin

value: Sensitive

tag: Sex

value: Male


title: Sham3

source_name: liver

value: sham


title: H2_lung_1

description: the lung at 24 hours after CLP with H2 treated

tag: tissue


title: IR3


title: IR2


title: IPC3


title: IPC2


title: OR19

value: Resistant


title: s3: siRNA_ctrl_rep2

description: mRNA expression

tag: cell type

value: Human monocytic THP-1 cells


title: LS18

value: Lean


title: Control_  intestine_3

description: the intestine at 24 hours after CLP

value: intestine


title: Control_  intestine_1

description: the intestine at 24 hours after CLP


title: LS17


title: Sham1


title: Control_  intestine_2

description: the intestine at 24 hours after CLP


title: Sham2


title: nc.F5.T rep2

city: Wuhan

first: Ying

last: Huang

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University

data_processing:
Reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Gallus_gallus-5.0 of ensembl using HISAT2 v2.1.0
Genes expression level were quantified by a software package: stringtie v1.3.4d
Differentially expressed genes were calculated by Deseq2 v1.26.0
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited gtf files include "cov", "FPKM", "TPM" values for each Sample, which generated by stringtie

organism: Gallus gallus

source_name: ovary

extract_protocol:
Granulosa cells and theca cells were isolated from fresh follicular tissue of hens and were sent to Novogene Co., Ltd. (Beijing, China) for RNA extraction, library construction, and sequencing.
The sequencing library was generated under the instruction manual with NEB Next UltraTM RNA Library Prep Kit for Illumina (NEB, USA). Obtained cDNA libraries were sequenced on an Illumina Nova platform and generated paired-end reads.

treatment_protocol: All experimental hens (35-40 weeks of age) were obtained from Wuhan  458 Xintianmu Agricultural Science and Technology Development Co. Ltd. (Hubei, China). For the androgen receptor-related drug experiment, chickens were randomly divided into 7 groups (10 hens/group). The androgen receptor antagonist-treated groups (3 groups) were fed 5 mg, 10 mg, and 15 mg of bicalutamide (AbMole, M1960) respectively, and the androgen agonist-treated groups (3 groups) were fed 1 mg, 10 mg, and 100 mg of mestanolone (AbMole, M3748) respectively, and the blank group (1 group) was fed with water as control. All drugs were fed for 4 days, and follicles were collected after 1 day of drug withdrawal. All hens were freely fed and watered.

tag: breed

value: White Leghorns

value: follicle

value: theca

tag: development stage

value: nc


title: nc.F5.T rep3


title: nc.F5.T rep1


title: nc.F5.G rep3

value: granulosa


title: OR12


title: H2_liver_2

description: the liver at 24 hours after CLP with H3 treated

value: liver


title: OS11


title: H2_liver_1

description: the liver at 24 hours after CLP with H2 treated


title: nc.F5.G rep2


title: nc.F1.T rep3


title: Control_liver_3

description: the liver at 24 hours after CLP


title: OR10


title: OS9


title: Control_liver_2

description: the liver at 24 hours after CLP


title: HSE-K27AC-Ctrl-1_input

value: Human primary LSEC


title: nc.F1.T rep2


title: nc.F1.T rep1


title: LS8


title: OS7


title: Control_liver_1

description: the liver at 24 hours after CLP


title: JJ_TG_141055

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

hyb_protocol: Hybridization  was performed on Affymetrix GeneChip HTA 2.0 Array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Transcription Analysis Console using the SST-RMA method for normalization.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

source_name: JJN3 cell line

label_protocol: As per manufacturer's instructions (Affymetrix)

growth_protocol: All cell lines were cultured in RPMI 1640 medium supplemented with 10% (JJN3) or 20% KMS12M) fetal bovine serum and antibiotics (Gibco). Cells were routinely checked for the presence of mycoplasma with MycoAlert  kit  (Lonza  GmBH)  and  only  mycoplasma-free  cells were used in the experiments.

extract_protocol: RNA was extracted using the RNeasy Plus Mini kit (Qiagen). The RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: KMS12-BM and JJN3 cells untreated or treated with amiloride or TG003 (0.1 mM, 0.4mM and 0.4 mM, respectively) for 24 h was isolated and prepared for RNA-seq

tag: cell line

value: plasma cell leukemia


title: JJ_TG_141049


title: JJ_TG_141061


title: nc.F1.G rep2


title: BM_TG_141064

source_name: KMS12-BM cell line

value: multiple myeloma


title: nc.F1.G rep3


title: nc.F5.G rep1


title: BM_TG_141058


title: OR5

value: Obese


title: OR6


title: nc.6mm.T rep3

value: syf 6mm


title: OS4

value: Sensitive

value: Male


title: LS3


title: nc.F1.G rep1


title: nc.6mm.T rep2


title: BM_TG_141052


title: JJ_AMIL_141050

value: Amiloride 0.4 mM 24h


title: JJ_AMIL_141062


title: nc.6mm.T rep1


title: JJ_AMIL_141056


title: OS1


title: JJ_DM_141054

value: Untreated (DMSO)


title: JJ_DM_141060


title: mes100.F5.T rep2


title: mes100.F5.T rep3


title: nc.6mm.G rep1


title: H2_liver_3

description: the liver at 24 hours after CLP with H4 treated


title: nc.6mm.G rep2


title: JJ_DM_141048


title: mes100.F5.G rep3


title: mes100.F5.G rep2


title: BM_AMIL_141059

value: Amiloride 0.1 mM 24h


title: BM_AMIL_141065


title: mes100.F5.G rep1


title: mes100.F1.T rep3


title: mes100.F1.T rep1


title: mes100.F1.T rep2


title: mes100.F1.G rep3


title: mes100.F1.G rep2


title: nc.6mm.G rep3


title: Pcdhb_Rad21Cleaved_rep3

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: Pcdhb_Rad21Cleaved_rep1-4.nearcis.norm.txt.mean.scales.txt.gz

data_processing:
Basecalls performed using CASAVA-2.17
Sequenced data was analysed using the 4Cseqpipe software suite (Van De Werken, Harmen JG, et al. "Robust 4C-seq data analysis to screen for regulatory DNA interactions." Nature methods 9.10 (2012): 969) with the setting of "-stat_type mean -trend_resolution 40000"
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized contact intensity

source_name: Primary neuron

extract_protocol:
Neuronal cells were cross-linked in PBS buffer with 1% formaldehyde for 10 min at RT and nuclei were isolated in the lysis buffer containing 10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% NP-40 and 1×protease inhibitors.
After digestion using HindIII, digested products were ligated by T4 DNA ligase. 3C templates were purified and then digested again using a second enzyme, NlaIII. Final 4C sequencing libraries were purified using a Roche High-Pure PCR Product Purification Kit, and then sequenced using an Illumina HiSeq 2500 platform.
4C-seq

tag: genotype

value: RAD21-TEV cleaved


title: Pcdhb_Rad21Cleaved_rep1


title: mes100.F5.T rep1

value: White Leghorns


title: Pcdhb_Rad21Cleaved_rep2


title: Pcdhb_Ctr_rep4

description: Pcdhb_Ctr_rep1-4.nearcis.norm.txt.mean.scales.txt.gz

value: Control


title: mes100.F1.G rep1

value: follicle


title: BM_DM_141063


title: Pcdhb_Rad21Cleaved_rep4


title: BM_AMIL_141053


title: BM_DM_141057


title: BM_DM_141051


title: Pcdhb_Ctr_rep3


title: mes100.6mm.T rep3

value: theca


title: Pcdhb_Ctr_rep1


title: mes100.6mm.T rep1


title: mes100.6mm.T rep2


title: Pcdhb_Ctr_rep2


title: mes100.6mm.G rep2

value: granulosa


title: mes100.6mm.G rep1


title: bic15.F5.T rep3


title: bic15.F5.G rep1


title: bic15.F5.G rep2


title: bic15.F5.G rep3


title: mes100.6mm.G rep3


title: bic15.F5.T rep2


title: bic15.F1.T rep2


title: bic15.F1.T rep3


title: bic15.F1.T rep1


title: bic15.F1.G rep3


title: bic15.6mm.T rep1


title: bic15.F1.G rep2


title: bic15.F1.G rep1


title: bic15.6mm.T rep2


title: Control_  lung_3

description: the lung at 24 hours after CLP

value: lung


title: bic15.6mm.G rep3


title: Control_  lung_2

description: the lung at 24 hours after CLP


title: LS13

value: Lean


title: Control_  lung_1

description: the lung at 24 hours after CLP


title: bic15.F5.T rep1


title: bic15.6mm.G rep1


title: poGC_H3K27ac

data_processing:
Reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Gallus_gallus-5.0 of ensembl using Bowtie2 v2.3.4.1
MACS2 (v2.1.1.20160309) was used for peak calling with parameters -B -p 1e-9, where chicken genome size is set to 1.2e9
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: bedGraph files were generated using MACS2

growth_protocol: The primary granulosa cells were pre-cultured with Medium 199 (Gibco, USA) and 5% FBS (Gibco, USA) overnight (8h).

extract_protocol: The chromatin was obtained by cell lysis (50 mM HEPES, pH 7.5; 150 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; and proteinase inhibitors) and was followed by sonication (Sonics VCX130, USA) on ice for 6 min. DNA (1 μg) was used for the preparation of the Chromatin Immunoprecipitation Sequencing (ChIP-Seq) library by NEBNext UltraII DNA Library Prep Kit for Illumina (NEB, USA, E7645 and E7335), according to the manufacturer’s instructions. The ChIP DNA library was sent to Novogene Co., Ltd. (Beijing, China) for paired-end 150 bp sequencing on the Illumina Nova platform.

value: Hy-Line Brown

value: pre-ovulation

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: H2_intestine_2

description: the intestine at 24 hours after CLP with H3 treated

value: intestine


title: H2_intestine_3

description: the intestine at 24 hours after CLP with H4 treated


title: CdLS Patient764P [ATAC-seq]

description: ATAC-seq of CdLS cortical neuronal nuceli

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Raw reads were trimmed with Trim Galore! (trim_galore_v0.4.4) with arguments "--trim-n --paired".
The trimmed reads were then aligned to hg38 using bowtie2 (bowtie2/2.2.9), with arguments "-p8 -t –very-sensitive -X 2000".
Samtools (1.2) was applied for sorting the reads and picardtools MarkDuplicates (1.90) was used for marking duplicated reads. R bioconductor package ATACseqQC (Ou et al., 2018) was applied for removing duplicated reads, reads without properly mapped mates, and reads mapped to chrMT.
alignmentSieve function from deeptools (Ramírez et al., 2014) was applied for shifting ATACseq reads (Buenrostro et al., 2013) and keeping nucleosome-free reads (fragment length <=100 bps) with arguments "--ATACshift --minFragmentLength 0 --maxFragmentLength 100". Reads overlapped with the black list hg38 v2 (Amemiya et al., 2019; ENCODE Project Consortium, 2012) were removed and bigwig files were created using bamCoverage function from deeptools with arguments "--blackListFileName hg38-blacklist.v2.bed --effectiveGenomeSize 2913022398 --normalizeUsing CPM".
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files

source_name: cortical non-neuronal nuclei

extract_protocol:
ATAC-seq was performed on 5 x 105 nuclei isolated from control and CdLS patients per samples, following the omni-ATAC protocol (Corces et al., 2017). Omni-ATAC is an improvement of the original ATAC protocol, with the inclusion of several additional detergents, NP-40, Tween-20 and digitonin in the nuclei digestion. After 30 minutes of incubation, samples were purified using the Zymo ChIP DNA Clean and Concentrator (Zymo Research) and libraries prepared as previously described (Buenrostro et al., 2013).
Collected DNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (ribozero ribosomal RNA depletion), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library..

treatment_protocol: Isolation of nuclei was performed as previously described (Krishnaswami et al., 2016) with minor modifications. Briefly, 50-250mg of pre-frontal cortical grey matter was homogenised in homogenisation buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 1μM DTT, 1X Proteinase Inhibitor w/o EDTA (Roche), 0.4U μl-1 RNaseIn (ThermoFisher) 0.2U μl-1 Superasin (ThermoFisher), 1μM DAPI) and centrifuged through an iodixanol gradient (Sigma). Pelleted nuclei were washed and then stained with NeuN antibody (Abcam, ab190195) in staining buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher), NeuN antibody (1:200)) for one hour at 4oC. For negative controls antibody was excluded. Nuclei were then sorted on BD Fusion, and collected in wash buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher)).

tag: disorder

value: CdLS

value: Female


title: phGC_H3K27ac

value: pre-hierarchical

tag: age


title: H2_intestine_1

description: the intestine at 24 hours after CLP with H2 treated


title: CdLS Patient380P [ATAC-seq]

value: Male


title: bic15.6mm.T rep3

value: syf 6mm

tag: treatment


title: healthy control Patient2308 [ATAC-seq]

description: ATAC-seq of healthy control cortical neuronal nuceli

value: healthy control


title: healthy control Patient4715 [ATAC-seq]


title: CdLS Patient2082 [ATAC-seq]


title: healthy control Patient1739 [ATAC-seq]


title: healthy control Patient4788 [ATAC-seq]


title: bic15.6mm.G rep2

value: White Leghorns


title: CdLS Patient744P [ATAC-seq]


title: healthy control Patient3011 [ATAC-seq]


title: Mock

city: New Haven

first: Craig

middle: B

last: Wilen

state: CT

address: 333 Cedar Street

department: Laboratory Medicine

institute: Yale School of Medicine

data_processing:
See manuscript (Ravindra et al. PLoS Biol, 2021) for full details. Reads with a cell barcode were retained and reads with UMIs were aligned to a combined human, viral reference (GenBank MT020880.1) to create a gene counts matrix using cellranger v3.1.0.
Gene counts matrix was filtered, normalized, and square root transformed for downstream analysis, using the standard scRNA-seq pre-processing recipe in SCANPY v1.4.6 (see manuscript, Ravindra et al. PLoS Biol, 2021) for full details. Imputed data, embedding coordinates, and metadata are stored in the standard AnnData object slots.

source_name: Human bronchial epithelial cells

growth_protocol: Human bronchial epithelial cells were maintained in PneumaCult-ALI Medium.

extract_protocol:
All preparation of samples were done using the Chromium Next GEM 3' protocol by 10X Genomics.
All library preparation were done using the Chromium Next GEM 3' protocol by 10X Genomics.

treatment_protocol: Differentiated human bronchial epithelial cells were infected with SARS-CoV-2 on the apical side of the transwell.

value: Primary cell line

tag: sample type

value: Control sample


title: 1dpi

value: Co-cultured with SARS-CoV-2 for 1 day


title: HCC1395 GapmeR 1 N3

first: Paola

last: Marcato

address: 11F11, 5850 College Street

institute: Dalhousie University

description: cultured cells

hyb_protocol: 16h at 48oC, Affymetrix miRNA 4.0

scan_protocol: Affymetrix GeneChip Scanner 3000(Scanner#4)

data_processing: RMA expression value derived from Expression Console software

label: FlashTag Biotin HSR RNA Labeling Kit

source_name: HCC1395 cells

label_protocol: FlashTag Biotin HSR RNA Labeling Kit

extract_protocol: cells were collected and RNA purified using the mirVana™ miRNA Isolation Kit following the manufacturer’s instructions.

value: PART1 GapmeR 1


title: HCC1395 negative control GapmeR N3

description: cultured cells

value: negative control GapmeR


title: Histone ChIP-seq from spleen (ENCLB375JPN)

status: Public on Feb 27 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR756THI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on spleen male adult (26 years)
experiment encode accession: ENCSR756THI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR200QAA
encode release date: 2020-09-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375JPN
fragmentation methods: sonication (generic)
size range: 200-600

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

source_name: Homo sapiens male adult (26 years) spleen tissue, preserved by flash-freezing

tag: antibody

value: spleen

value: tissue

tag: biosample encode accession

value: male

tag: health state

value: DM:no; HTN:no; CAD:no

tag: dev stage

value: adult

value: 26 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS498SQU at ENCODE; https://www.encodeproject.org/ENCBS498SQU/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/