title: post HBV infection liver cirrhosis sample 6F

description: treatment group


title: post HBV infection liver cirrhosis sample 1

status: Public on Dec 01 2019

type: RNA

city: guangzhou

first: leijia

last: Li

address: Tianhe road

country: China

institute: The third affiliated hospital of sun yat-sen university

description: treatment group

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Fresh whole blood from healthy volunteers and patients with post hepatitis B infection liver cirrhosis was collected and stored in BD PAXgeneTM whole blood RNA tubes and mixed upside down，- 20 ℃ to -80 ℃ cryopreserved

tag: tissue

value: whole blood

tag: Sex

value: female

tag: group

value: post HBV infection

tag: age


title: healthy group sample4

description: control group

value: male

value: healthy


title: healthy group sample3F

description: control group


title: post HBV infection liver cirrhosis sample 2

description: treatment group


title: healthy group sample1F

description: control group


title: post HBV infection liver cirrhosis sample 3

description: treatment group


title: healthy group sample2F

description: control group


title: L488-ChIP-Diamide-30min-Pol2

type: SRA

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

library_source: genomic

data_processing:
base calling: Casava1.8
read alignment, dSMF data: Bismark_v0.19.0
read alignment, ChIP-seq and ATAC-seq data: Bowtie 1.0.1
read alignment, RNA-seq data: TopHat 2.0.8
bedgraph track generation: custom-written python scripts
Genome_build: sacCer3, dm6, hg19
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for dSMF samples, where the bedGraph shows the methylation percentage

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes (Rpb1-CTD and Rbp1-CTD-S2P ChIP) or 30 minutes (Hsf1-V5 ChIP) and quenched with 0.125 M glycine for 5 minutes. A total of ~50 ODs of cells were used per Rpb1-CTD or Rpb1-CTD-S2P ChIP and ~300 ODs per Hsf1-V5 ChIP. Fixed cell were washed 2X in cold 1X PBS, pelleted and stored at -80C. Pellets were lysed in 300 uL FA lysis buffer (50 mM HEPES--KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF, Roche protease inhibitor) with ~1 mL ceramic beads on a Fastprep-24 (MP Biomedicals). The entire lysate was then collected and adjusted to 1 mL with FA lysis buffer before sonication with a 1/8' microtip on a Q500 sonicator (Qsonica) for 14 minutes (10 seconds on, 20 seconds off). The sample tube was held in a -20C 80% ethanol bath throughout sonication to prevent sample heating. After sonication, cell debris was pelleted and the supernatant was retained for ChIP. For each ChIP reaction, 30 uL Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA), prebound with 5-10 uL antibody (8wG16 Rpb1-CTD, Abcam cat # ab817); 3E10 Rpb1-CTD-S2P, Milipore cat \# 04-1571-1) or SV5-Pk1 (anti-V5, BioRad cat # MCA1360G)) and washed 1X with PBS before incubation with supernatant (4C, overnight). Dynabeads were then washed (5 minutes per wash) 3X in FA lysis buffer, 3X in high-salt FA lysis buffer (50 mM Hepes–KOH pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF), 1X in ChIP wash buffer (10 mM Tris–HCl pH 7.5, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF) and 1X in TE wash buffer (10 mM Tris–HCl pH 7.5, 1 mM EDTA, 50 mM NaCl). DNA was eluted from the beads in ChIP elution buffer (50 mM Tris–HCl pH 7.5; 10 mM EDTA; 1% SDS) at 65C for 20 min. Eluted DNA was incubated at 65C overnight to reverse crosslinks, before treatment with RNAse A (37C, 1 hour) and then Proteinase K (65C, 2 hours). DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep kit  (NEB Cat # E7645) and sequenced on a Illumina NextSeq instrument as 2x36mers or as 2x75mers.

tag: strain background

tag: genotype/variation

value: wild type

tag: treatment

value: Diamide 30min

tag: chip antibody

value: 8wG16 Rpb1-CTD, Abcam cat# ab817


title: RNA-seq-Diamide_0min

library_source: transcriptomic

molecule: polyA RNA

extract_protocol:
Cells (1 mL) were pelleted and flash frozen in liquid nitrogen. Pellets were resuspended in 300 uL TRIzol and lysed with ~1 mL ceramic beads on a Fastprep-24 (MP Biomedicals). Cell debris were pelleted and RNA was extracted from the supernatant using the Direct-Zol RNA Microprep Kit (Zymo Research).
RNA-seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (NEB Cat # E7420)

value: Diamide 0min


title: L465-ATAC-Diamide-0_min-rep2

extract_protocol:
ATAC-seq was carried out on the same nuclei isolated for SMAC-seq (before resuspension in M.CviPI Reaction Buffer), by resuspending nuclei with 25 uL 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL transposase (custom produced) and 22.5 uL nuclease-free H2O, and incubating at 37C for 30 min in a Thermomixer at 1000 RPM. Transposed DNA was isolated using the DNA Clean & Concentrator Kit (Zymo, cat # D4014) and PCR amplified. Libraries were then sequenced on a Illumina NextSeq instrument as 2x36mers or as 2x75mers.
ATAC-seq was carried out on the same nuclei isolated for SMAC-seq (before resuspension in M.CviPI Reaction Buffer), by resuspending nuclei with 25 uL 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL transposase (custom produced) and 22.5 uL nuclease-free H2O, and incubating at 37C for 30 min in a Thermomixer at 1000 RPM. Transposed DNA was isolated using the DNA Clean & Concentrator Kit (Zymo, cat # D4014) and PCR amplified. Libraries were then sequenced on a Illumina NextSeq instrument as 2x36mers or as 2x75mers.


title: L482-ChIP-Diamide-0min-Input

value: none (ChIP Input)


title: L483-ChIP-Diamide-0min-Pol2


title: L487-ChIP-Diamide-30min-Input


title: L486-ChIP-Diamide-0min-V5_HSF1

value: HSF1 V5-tagged

value: anti-V5 BioRad cat# MCA1360G


title: L471-ATAC-Diamide-45_min-rep2

value: Diamide 45min


title: L472-ATAC-Diamide-60_min-rep1

value: Diamide 60min


title: L469-ATAC-Diamide-30_min-rep2


title: L470-ATAC-Diamide-45_min-rep1


title: L464-ATAC-Diamide-0_min-rep1


title: L485-ChIP-Diamide-0min-V5_Input


title: L473-ATAC-Diamide-60_min-rep2


title: L467-ATAC-Diamide-15_min-rep2

value: Diamide 15min


title: MK5719Glc_GCG

city: Uji city

first: Fumiya

last: Matsuoka

state: Kyoto prefecture

address: Gokasyo

department: Agriculture

country: Japan

institute: Kyoto University

data_processing:
Illumina RTA (Real Time Analysis) software was used for basecalling.
Sequenced reads were mapped to mm9 whole genome using BWA without changing any parameters.
Unmapped reads are then mapped to mm9 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: whole cell

growth_protocol:
All the strains were precultured on YPGA solid medium and cultured in 10 mL liquid medium with shaking at 145 strokes per minutes, 30°C.
Concentrations of carbon source in each liquid media were 1% (w/v).
Components expect for carbon source were based on HC-LN medium (Matsuoka et al. Sci. Rep. 2017, 7, 4206).

extract_protocol:
RNAs were extracted by acid phenol-chloroform extraction method.
Total RNAs were used for synthesis of the cDNA using a Library Preparation kit (DNAFORM, Japan). 5'caps of RNAs are biotinylated after reverse transcription.RNA-cDNA hybirds are captured by streptavidin-conjugated magnetic beads.The cDNAs were released from RNAs and ligated with a barcode sequence linkers. CAGE sequencing were performed using the Illumina NextSeq500.

tag: strain

tag: carbon source in media

value: Glucose

tag: growth protocol

value: Cells were innoculated into glucose media (initial OD600=0.05) and cultured overnight (final OD600=0.95).


title: MK5719DEH_TAC

value: DEH

value: Cells were innoculated into DEH media (initial OD600=0.05) and cultured for 2 days (final OD600=0.55).


title: MK5622Glc_ACC

value: Cells were innoculated into glucose media (initial OD600=0.05) and cultured overnight (final OD600=0.91).


title: L484-ChIP-Diamide-0min-Pol2pS2


title: L466-ATAC-Diamide-15_min-rep1


title: MK5622DEH_AGT

value: Cells were innoculated into DEH media (initial OD600=0.2) and cultured for 3 days (final OD600=0.63).


title: PCOS 4

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

description: PCOS hormone treatment

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: endometrial organoids

growth_protocol: Endometrial epithelial and stromal cells were isolated from endometrial biopsies from premenopausal women undergoing routine hysterectomy for benign uterine conditions. Both epithelial and stromal cells were seeded in 1.5% agarose 3D Petri Dishes®at 3:1 ratio by volume. Cells were let form organoids in complete MammoCult human medium for 7 days before hormone treatments.

extract_protocol:
All endometrial organoids were harvested from 3D Petri Dishes® by pipetting. Total RNA was extracted from organoids using Tri Reagent (Sigma Aldrich, 93289) and  Direct-zol™ RNA MicroPrep (Zymo Research, R2060) with an additional step of DNase I treatment to remove any contaminating DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A stepwise estradiol treatment was used to treat endometrial organoids within agarose 3D Petri Dishes® to mimic the 14 days of follicular phase of human menstrual cycle with the addition of testosterone. The normal hormone treatment was 0.1 nM E2 + 0.8 nM testosterone (day 0–7), 1 nM E2 + 0.8 nM testosterone (day 7–13) and 1 nM E2 + 1.25 nM testosterone (day 13–14). The PCOS hormone treatment was 0.1 nM E2 + 3 nM testosterone (day 0–7) and 1 nM E2 + 3 nM testosterone (day 7–14). Media was changed every second day.

tag: source tissue

value: endometrium

tag: patient age


title: PCOS 3

description: PCOS hormone treatment


title: PCOS 2

description: PCOS hormone treatment


title: CONTROL 3

description: normal hormone treatment


title: CONTROL 2

description: normal hormone treatment


title: CONTROL 4

description: normal hormone treatment


title: PCOS 1

description: PCOS hormone treatment


title: CONTROL 1

description: normal hormone treatment


title: L198-PBAT-dSMF

description: PBAT (post-bisulfite adaptor tagging)/dSMF (dual-enzyme Single Molecule Footprinting)

extract_protocol:
Yeast cells in log phase (OD660 <1.0) were first centrifuged at 13,000 rpm for 1 minute, then washed with 100 uL Sorbitol Buffer(1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), and centrifuged again at 13,000 rpm for 1 minute. Cells were then spheroplasted by resuspending in 200 uL Sorbitol Buffer with DTT added at a final concentration of 10 mM and 0.5 mg/mL 100T Zymolase, followed by incubating for 5 minutes at 30C at 300 rpm in a Thermomixer. The pellet was centrifuged for 2 minutes at 5,000 rpm, washed in 100 uL Sorbitol Buffer, and centrifuged again at 5,000 rpm for 2 minutes. Cells were then resuspended in 100 uL ice-cold Nuclei Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 0.5% NP-40) and incubated on ice for 10 minutes. Nuclei were then centrifuged at 5000 rpm for 5 min at 4C, resuspended in 100 uL cold Nuclei Wash Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA), and centrifuged again at 5,000 rpm for 5 min at 4C. Finally, nuclei were resuspended in 100 uL M.CviPI Reaction Buffer (50 mM Tris-HCl pH 8.5, 50 mM NaCl, 10 mM DTT). Nuclei were then first treated with M.CviPI + EcoGII by adding 200 U of M.CviPI (NEB) and 200 units of EcoGII (NEB), SAM at 0.6 mM and sucrose at 300 mM, and incubating at 30C for 7.5 min. After this incubation, 128 pmol SAM and another 100 U of enzymes were added, and a further incubation at 30C for 7.5 min was carried out. Immediately after, M.SssI treatment followed, by adding 60 U of M.SssI (NEB), 128 pmol SAM, MgCl2 at 10 mM and incubation at 30C for 7.5 min.
HMW DNA (~500 ng) was bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo, Cat # D5030) by mixing 20 uL of purified DNA (~500 ng) with 130 uL DNA Methylation Lightning Conversion reagent and incubating at 98C for 8 minutes and then at 64C for 60 minutes. Bisulfite converted DNA was then cleaned up using the EZ DNA Methylation-Lightning Kit following manufacturer's instructions.  First strand synthesis was carried out by mixing 20 uL bisulfite converted DNA, 19.75 uL H2O, 5 uL 10X Blue Buffer (ThermoFisher), 1.25 uL 10 mM dNTP (NEB), and 4 uL custom-designed biotinylated adapter. Samples were then incubated at 94C for 5 minutes, and at 4C for 5 minutes, after which 1.5 uL Klenow (3’ -> 5’ exo minus; MCLab) were added, and the reaction was incubated at 4C for 15 minutes, at 37C for 90 minutes, and at 70C for 5 minutes. First-strand reaction cleanup was carried out using 50 uL AMPure XP beads (Beckman Coulter); DNA was eluted 50 uL EB buffer.  Biotinylated DNA was captured on streptavidin beads. A total of 20 uL streptavidin Dybaneads M-280 (ThermoFisher) per sample were added to a PCR tube, separated on a magnet and then resuspended in 50 uL 2X BW(Li) buffer (6.3 g LiCl, 0.5 mL Tris-HCL pH 8.0, and 0.1 mL 500 mM EDTA for 50 mL total volume), to which the 50 uL of eluted first-strand reaction DNA was added. Beads were then incubated at room temperature for 30 minutes, washed with 180 uL 2X BW(Li) buffer, twice with 0.1 N NaOH (by resuspending well and incubating at room temperature for 2 minutes), washed again with 180 uL 2X BW(Li) buffer, then with 180 uL 10 mM Tris-HCL pH 7.5.  Second-strand synthesis was carried out by resuspending streptavidin beads in the following reaction mix: 5 uL 10 X Blue Buffer, 1.25 uL 10 mM dNTPs, 39.75 uL H2O, 4 uL custom-designed second-strand adapter. Samples were then incubated at $94C for 5 minutes, and at 4C for 5 minutes, after which 1.5 uL Klenow (3’ -> 5’ exo minus) were added, followed by further incubation at 4C for 15 minutes, at 37C for 30 minutes, and at 70C for 5 minutes. Beads were separated on magnet and the chase reaction was carried out by resuspending in a mix of 5 uL 10X Thermo Pol Buffer, 1.25 uL 10 mM dNTPs, 43.5  uL H2O, and 1  uL Bst DNA Polymerase Large Fragment (NEB). Samples were incubated at 65C for 30 minutes, then again separated on magnet.

value: wild type


title: siTIP60_rep2

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Basecalling
RNA-Seq paired reads were aligned to the human reference genome (UCSC Hg19) and transcript models (gencode release 19) using ‘STAR Aligner’ (v2.5.1b) with default parameters.
Aligned RNA-Seq reads were counted onto genes (gencode release 19) using ‘FeatureCounts’ from ‘Rsubread’ (v1.24) with the parameter strandSpecific set to 1, the rest of the parameters was set to default
The gene counts were subsequently normalized and transformed using the Variance Stabilizing Transformation from ‘DESeq2’ (v1.14.1).
Genome_build: hg19
Supplementary_files_format_and_content: CSV (matrix of normalized counts)

source_name: MCF10A cells (ATCC CRL-10317TM)

growth_protocol: MCF10A cells (ATCC CRL-10317TM) were cultured in Dulbecco’s modified eagle’s media (DMEM)/F12 (1:1) media (Gibco, Cat. No. 11330-032) with 5% horse serum (Gibco, Cat.No. 16050-122), 1% penicillin streptomycin (Gibco Cat. No. 15140-122), 20 ng/ml epithelial growth factor (Peprotech, Cat. No.AF-100-15), 0.5 mg/ml hydrocortisone (Sigma-Aldrich, Cat. No. H-0888), 100 ng/ml cholera toxin (Sigma-Aldrich, Cat. No. C-8052) and 10 μg/ml insulin (Sigma-Aldrich, Cat. No. I-1882).Cell cultures were incubated at 37ºC with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNAs targeting Control or TIP60 were transfected  using Lipofectamine RNAiMax reagent from Invitrogen/Life Technologies (Cat. No. 56532). The siRNA mixture used contained 15 l LipofectamineRNAiMax, 2 ml optimum media (Gibco, Cat. No. 31985-070) and 20 nM siRNA. The transfection mixture was incubated for 20 min at room temperature and then 8×10^5 cells were seeded in a 10-cm plate together with the siRNA mixture. After 6 h, the transfection mixture was replaced by growth media. Cells were harvested 72 h after siRNA transfection.

tag: cell line


title: siControl_rep2

value: siControl


title: MK5719New_MK5719New

value: Mannitol

value: Cells were innoculated into mannitol media (initial OD600=0.02) and cultured for 1 day (final OD600=0.79).


title: input_siTIP60_ChIPSeq

data_processing:
Basecalling
ChIP-seq reads were aligned to the hg19 genome assembly using ‘STAR Aligner’ (v2.5.1b) with EndToEnd as the alignEndsType option and 1 as the alignIntronMax threshold. All other parameters were set to the default.
Read duplicates were removed from the bam files using the  ‘MarkDuplicates’ module from ‘Picard’ (v1.140).
BigWig files were created  generated from the bam files without duplicates duplicated reads using the  ‘bamCoverage’ module from ‘Deeptools’ (v2.2.2-1)
Genome_build: hg19
Supplementary_files_format_and_content: bw

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: siRNAs targeting different genes were transfected  using Lipofectamine RNAiMax reagent from Invitrogen/Life Technologies (Cat. No. 56532). The siRNA mixture used contained 15 l LipofectamineRNAiMax, 2 ml optimum media (Gibco, Cat. No. 31985-070) and 20 nM siRNA. The transfection mixture was incubated for 20 min at room temperature and then 4×106 cells were seeded in a 15-cm plate together with the siRNA mixture. After 6 h, the transfection mixture was replaced by growth media. Cells were harvested 72 h after siRNA transfection.

value: none (input)


title: siTIP60_rep1


title: acH2AZ_siTIP60_ChIPSeq

value: H2A.Z Acetyl K4+K7+K11 (Abcam catalog No:ab18262)


title: H2AZ_siControl_ChIPSeq

value: H2A.Z (Abcam catalog No:ab4174)


title: input_siControl_ChIPSeq


title: H2AZ_siTIP60_ChIPSeq


title: acH2AZ_siControl_ChIPSeq


title: DMSO treatment

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and filtered low-quality sequence  using trimmomatic.
Bowtie was used to align the RNA-Seq paired reads to hg19 allowing only unique mapped reads (-m1) and output the multimapping reads to a fastq file with the --max option.
Genome_build: hg19
Supplementary_files_format_and_content: Bam files and fastq files to be used as an input for RepEnrich

source_name: Colorectal Carcinoma (HCT116)

extract_protocol:
Cells were harvested and total RNA was isolated using TRIZOL reagent (Life Technologies, Cat. No. 15596-026) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A commercially available siRNA targeting TIP60 (siTIP60B) was purchased (Sigma Aldrich, SASI_Hs01_00073301) and used in experiments to reduce the possibility of off-target effects. Briefly, 1 million cells were seeded in a 10-cm plate and were used for transfection along with 15 μl Lipofectamine RNAiMax (Invitrogen, Cat. No. 56532) following the manufacturer’s protocol. Six-hour post transfection, the transfection mixture was replaced with growth medium and the cells were harvested 72 h after transfection for further analysis.

value: Colon

tag: passage

tag: retrovirus

value: MSCV plasmid

value: DMSO


title: JQ1 treatment


title: siC and DMSO treatment

value: siControl tranfection and DMSO


title: siControl rep1

value: siControl tranfection


title: siControl rep2


title: siTIP60 rep1

value: siTIP60 tranfection


title: NHT160154-9_YYX2-12

city: Hangzhou

first: Ling

last: Yang

address: 34th, Yanguan alley

institute: Hangzhou cancer institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p2 whole genome using HISAT v2.0.5 with parameters -p 16 --dta
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mihaela Pertea et al., Nature Protocol, 2016.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.

source_name: Colon

extract_protocol:
The poly(A) RNAs were amplified using a Smart-seq2 protocol from Simone Picelli etal., Nature Method, 2013 and Nature Protocol, 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: kit

value: FACS-based DCR kit

tag: single-cell rna kit


title: NHT160154-2_YYX2-11

tag: tissue


title: NHT160154-9_YYX2-10


title: NHT160154-9_YYX2-8


title: NHT160154-2_YYX2-7


title: NHT160154-9_YYX1-7

value: Beads-based DCR kit


title: NHT160154-9_YYX1-8


title: NHT160154-9_YYX1-12


title: NHT160154-9_YYX1-2


title: NHT160154-9_YYX1-9


title: Male 2-4hr H4K16ac IP

city: Providence

first: Erica

last: Larschan

address: 185 Meeting St.

institute: Brown University

data_processing:
We mapped sequencing reads to release 6 of the Drosophila melanogaster genome (dm6) using Bowtie2 with default parameters. We identified reads with a MAPQ < 30 and removed PCR duplicate reads using Picard MarkDuplicates (version 2.9.2) using SAMtools (version 1.9). We used MACS2 (version 2.1.1) to identify peaks with the following parameters: --nomodel -B –SPMR –keep-dup all -g dm. We used input for peak calling in all samples with the exception of male 2-4 hour time point. We used a narrow peak calling with a q cutoff of 0.01 for CLAMP ChIPs and broad peak calling with a q cutoff of 0.05 for MSL3 and H4K16ac ChIPs; we also used --extsize of 147 for H4K16ac ChIPs.
Genome_build: dm6

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Meiotic drive fly stocks (both gifts from Cynthia Staber), +; SD72/CyO and 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO (Bloomington BSC64332) are published in (Rieder et al., 2017). To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males. To obtain male embryos, we mated +; SD72/CyO males to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO females to obtain 19-3, yw, Rsp[s]-B[s]/Y; SPSD/SD72 males. We mated males of both genotypes to yw; attP2{PCNA-EGFP} virgin females (Blythe and Wieschaus, 2016). We grew flies on standard sucrose/cornmeal media at 24 degrees C. We collected embryos on grape juice plates with yeast paste. Embyros were aged at 24 degrees C.

extract_protocol: We performed 0- to 4-h timed lays and collected and fixed embryos according to Blythe and Wieschaus (2015). We then hand-sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample.

tag: antibody

tag: nuclear cycle

tag: Sex

value: Male

value: embryo


title: siC and JQ1 treatment

value: siControl tranfection and JQ1


title: siTIP60 rep2


title: Male 2-4hr Input


title: Male 2-4hr MSL3 IP


title: Male 2-4hr IgG IP

value: IgG


title: Male 2-4hr CLAMP IP

value: CLAMP


title: Female 2-4hr Input

value: none (input)

value: Female


title: Female 2-4hr IgG IP


title: Male NC14 MSL3 IP Replicate 2


title: Female 2-4hr H4K16ac IP


title: Female 2-4hr CLAMP IP


title: Male NC14 H4K16ac IP


title: Male NC14 CLAMP IP Replicate 2


title: Male NC14 CLAMP IP Replicate 1


title: Male NC14 MSL3 IP Replicate 1


title: Male NC14 IgG IP Replicate 2


title: Male NC14 Input Replicate 2


title: Male NC14 IgG IP Replicate 1


title: Male NC14 Input Replicate 1


title: Female NC14 H4K16ac IP


title: Female NC14 IgG IP Replicate 2


title: Female NC14 IgG IP Replicate 1


title: Female NC14 CLAMP IP Replicate 2


title: Female NC14 CLAMP IP Replicate 1


title: Female NC14 Input Replicate 2


title: Male NC13 MSL3 IP Replicate 1


title: Male NC13 MSL3 IP Replicate 2


title: Male NC13 CLAMP IP Replicate 2


title: Female NC14 Input Replicate 1


title: Male NC13 H4K16ac IP


title: Male NC13 Input Replicate 2


title: Male NC13 IgG IP Replicate 1


title: Male NC13 CLAMP IP Replicate 1


title: Male NC13 Input Replicate 1


title: Female NC13 H4K16ac IP


title: Female NC13 IgG IP Replicate 2


title: Female NC13 Input Replicate 2


title: Female NC13 Input Replicate 1


title: Female NC13 IgG IP Replicate 1


title: Male NC12 MSL3 IP Replicate 1


title: Male NC12 CLAMP IP Replicate 2


title: Female NC13 CLAMP IP Replicate 1


title: Female NC13 CLAMP IP Replicate 2


title: Male NC12 H4K16ac IP


title: Male NC12 CLAMP IP Replicate 1


title: Male NC12 IgG IP Replicate 2


title: Male NC12 IgG IP Replicate 1


title: Male NC12 Input Replicate 2


title: Male NC13 IgG IP Replicate 2


title: Female NC12 H4K16ac IP


title: Female NC12 CLAMP IP Replicate 2


title: Female NC12 CLAMP IP Replicate 1


title: Female NC12 IgG IP Replicate 2


title: Female NC12 Input Replicate 2


title: Male NC11 H4K16ac IP


title: Female NC12 IgG IP Replicate 1


title: Male NC12 MSL3 IP Replicate 2


title: Male NC11 MSL3 IP


title: Male NC11 CLAMP IP


title: Male NC11 IgG IP


title: Female NC11 Input


title: Male NC11 Input


title: Hi-C: clamp RNAi rep2

description:
WJPool1_4_TGACCA_L007
CLAMP_replicate_2_S4

data_processing:
Library strategy: Hi-C
Each read pair (MAPQ ≥ 15) was mapped and proccessed for visualization using the HiC-Pro pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: hic files contain matrices that can be visualized using juicebox

source_name: Hi-C: clamp RNAi

growth_protocol: S2 cells were maintained at 25C in Gibco Schneider's media supplemnted with 10% heat-inactivated FBS and 1.4X antibiotic-antimycotic

extract_protocol:
Hi-C was carried out as describe by Rao et al (2014) with few modifications
Hi-C

treatment_protocol: RNAi treatment for 6 days at 25C

tag: cell line background

tag: genotype/variation

value: clamp RNAi

tag: primary restriction enzyme

value: HindIII


title: Female NC11 IgG IP


title: Female NC11 CLAMP IP


title: Female NC11 H4K16ac IP


title: Hi-C: clamp RNAi rep1

description:
WJPool1_2_CGATGT_L007
CLAMP_replicate_1_S2


title: Hi-C: gfp RNAi rep2

description:
WJPool1_3_CTTGTA_L007
GFP_replicate_2_S3

source_name: Hi-C: gfp RNAi

value: gfp RNAi


title: Hi-C: gfp RNAi rep1

description:
WJPool1_1_GCCAAT_L007
GFP_replicate_1_S1


title: 4C-seq: msl2 RNAi  CES viewpoint4 rep1

data_processing:
Library strategy: 4C-seq
Sequencing reads corresponding to the reading primer were aligned to a reduced genome derived from dm6 unique sequences adjacent to restriction enzyme sites using Bowtie2 with the following parameters: -N 0 -5 24 -3 101 --very-sensitive.
Aligned reads were then processed as described in Raviram et al (2016) for use with the 4C-Ker pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bedGraph files contain normalized read counts (cis)

source_name: 4C-seq: msl2 RNAi  CES viewpoint4

extract_protocol:
4C-seq was carried out as described by Helm et al (2014) with few modifications.
4C-seq

value: msl2 RNAi

value: NlaIII

tag: secondary restriction enzyme


title: 4C-seq: clamp RNAi  CES viewpoint4 rep2

source_name: 4C-seq: clamp RNAi  CES viewpoint4


title: 4C-seq: msl2 RNAi  CES viewpoint4 rep2


title: Male NC12 Input Replicate 1


title: 4C-seq: trl RNAi  CES viewpoint4 rep2

source_name: 4C-seq: trl RNAi  CES viewpoint4

value: trl RNAi


title: 4C-seq: gfp RNAi  CES viewpoint4 rep2

source_name: 4C-seq: gfp RNAi  CES viewpoint4


title: 4C-seq: trl RNAi  CES viewpoint4 rep1


title: 4C-seq: gfp RNAi  CES viewpoint4 rep1


title: Female NC12 Input Replicate 1


title: 4C-seq: clamp RNAi  CES viewpoint3 rep1

source_name: 4C-seq: clamp RNAi  CES viewpoint3

value: DpnII


title: 4C-seq: clamp RNAi  CES viewpoint3 rep2


title: 4C-seq: trl RNAi  CES viewpoint3 rep1

source_name: 4C-seq: trl RNAi  CES viewpoint3


title: 4C-seq: msl2 RNAi  CES viewpoint3 rep1

source_name: 4C-seq: msl2 RNAi  CES viewpoint3


title: 4C-seq: trl RNAi  CES viewpoint3 rep2


title: 4C-seq: msl2 RNAi  CES viewpoint3 rep2


title: 4C-seq: gfp RNAi  CES viewpoint3 rep2

source_name: 4C-seq: gfp RNAi  CES viewpoint3


title: 4C-seq: gfp RNAi  CES viewpoint3 rep1


title: 4C-seq: clamp RNAi  CES viewpoint2 rep1

source_name: 4C-seq: clamp RNAi  CES viewpoint2


title: 4C-seq: clamp RNAi  CES viewpoint4 rep1


title: 4C-seq: msl2 RNAi  CES viewpoint2 rep2

source_name: 4C-seq: msl2 RNAi  CES viewpoint2


title: 4C-seq: msl2 RNAi  CES viewpoint2 rep1


title: 4C-seq: trl RNAi  CES viewpoint2 rep1

source_name: 4C-seq: trl RNAi  CES viewpoint2


title: 4C-seq: clamp RNAi  CES viewpoint1 rep2

source_name: 4C-seq: clamp RNAi  CES viewpoint1


title: 4C-seq: gfp RNAi  CES viewpoint2 rep2

source_name: 4C-seq: gfp RNAi  CES viewpoint2


title: 4C-seq: clamp RNAi  CES viewpoint1 rep1


title: 4C-seq: msl2 RNAi  CES viewpoint1 rep2

source_name: 4C-seq: msl2 RNAi  CES viewpoint1


title: 4C-seq: gfp RNAi  CES viewpoint2 rep1


title: L468-ATAC-Diamide-30_min-rep1

tag: strain background

value: wild type

tag: treatment

value: Diamide 30min


title: 4C-seq: gfp RNAi  CES viewpoint1 rep2

source_name: 4C-seq: gfp RNAi  CES viewpoint1


title: 4C-seq: trl RNAi  CES viewpoint1 rep2

source_name: 4C-seq: trl RNAi  CES viewpoint1


title: 4C-seq: msl2 RNAi  CES viewpoint1 rep1


title: 4C-seq: gfp RNAi  CES viewpoint1 rep1


title: Slee139_mRNAseqFP_meg34_2: meg-3meg-4 mRNAseq-2

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

description: corresponding mRNAseq

data_processing:
Base calling and demultiplexing was performed at Johns Hopkins University  Gentic Resources Core Facility .
Read alignment was done using STAR with the following command: ‘--outFilterMismatchNoverLmax 0.3’. Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’
Aligned reads were than counted and analyzed using HTseq-count(Anders et al. 2015), DEseq2(Love et al. 2014) and custom R code (RStudio 1.2)
For differential translation analysis, Htseq-count output results were used for RiboRex, a R package.
Genome_build: ce10
Supplementary_files_format_and_content: 1. RiboRex output is in .xlsx formate and contain log2 Fold change of Translation efficiency between wild type and meg-3meg-4 mutant.
Supplementary_files_format_and_content: 2, processed count table contains mRNAseq and ribosome profiling results.

organism: Caenorhabditis elegans

source_name: Embryo

growth_protocol: To synchronize worm growth, embryos were initially collected from adult worms and cultured for overnight in M9 solution. Synchronized L1 were collected and plated on NA22 bacteria containing plate to reach adulthood at 20C. Early stage embryos were then collected from young adults.

extract_protocol:
Isolated embyros were freezed in liquied nitrogen with lysis buffer containing cycloheximide to stall ribosome. Freezed embryos were lyzed by freezer mill. Samples were cleared by centrifugation. Cleared lysates were then subject to ribosome profiling and RNAseq experiments
For mRNAseq,  500ng of total RNA were subjected to Ribozero kit (illumina, MRZE706) to remove rRNA. Libraries were constructed using Truseq Library Prep Kit V2. For Ribosome profiling, library preparation protocol is descrbied in Wu et al., 2019 Mol. Cell.

treatment_protocol: All worms were grown on NA22 bacteria plates.

value: mixed early embryo

tag: molecule subtype

value: Ribo-Zero treated total RNA


title: Slee125_mRNAseqFP_meg34_1: meg-3meg-4 mRNAseq-1

description: corresponding mRNAseq


title: Slee142_mRNAseqFP_N2_3: wild type mRNAseq-3

description: corresponding mRNAseq


title: Slee141_mRNAseqFP_meg34_3: meg-3meg-4 mRNAseq-3

description: corresponding mRNAseq


title: 4C-seq: clamp RNAi  CES viewpoint2 rep2


title: Slee138_mRNAseqFP_N2_2: wild type mRNAseq-2

description: corresponding mRNAseq


title: Slee132_N2: wild type Riboseq-2

description: Ribosome foot

data_processing:
Library strategy: ribosome profiling
Base calling and demultiplexing was performed at Johns Hopkins University  Gentic Resources Core Facility .
Read alignment was done using STAR with the following command: ‘--outFilterMismatchNoverLmax 0.3’. Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’
Aligned reads were than counted and analyzed using HTseq-count(Anders et al. 2015), DEseq2(Love et al. 2014) and custom R code (RStudio 1.2)
For differential translation analysis, Htseq-count output results were used for RiboRex, a R package.
Genome_build: ce10
Supplementary_files_format_and_content: 1. RiboRex output is in .xlsx formate and contain log2 Fold change of Translation efficiency between wild type and meg-3meg-4 mutant.
Supplementary_files_format_and_content: 2, processed count table contains mRNAseq and ribosome profiling results.

value: RNaseI treated Ribo-Zero treated ribosome bound RNA fragments


title: Slee123_meg34: meg-3meg-4 Riboseq-1

description: Ribosome foot


title: Slee135_meg34: meg-3meg-4 Riboseq-3

description: Ribosome foot


title: Slee133_meg34: meg-3meg-4 Riboseq-2

description: Ribosome foot


title: Slee136_N2: wild type Riboseq-3

description: Ribosome foot


title: 4C-seq: trl RNAi  CES viewpoint2 rep2


title: Slee111_N2: wild type Riboseq-1

description: Ribosome foot


title: Tu_m34-3_2_GTGAAA: meg-3meg-4 ( biological replicate)

data_processing:
Base calling and demultiplexing was performed at Johns Hopkins University  Gentic Resources Core Facility .
Differential expression analysis was done using Tophat (V.2.0.8) and Cufflink (V 2.0.2). The command lines for Tuxedo suit are listed as below:
$ tophat2 -p 12 -g 1 --output-dir <output> --segment-length 20 --min-intron-length 10 --max-intron-length 25000 -G <gene.gtf> --transcriptome-index <Name.fastq>
$ cuffdiff -p 12 -o <output> --compatible-hits-norm --upper-quartile-norm -b <genome.fa> <genes.gtf>  <tophat output1> <tophat output2>
Genome_build: ce10
Supplementary_files_format_and_content: Output file for pair-wise differential expression analysis is Cuffdiff_wholeEmb_3WTvs3meg-34.diff

extract_protocol:
Total RNAs were extracted using Trizol reagent and RNA purifiaction was done using RNA clean and concentrator-5 (Zymo researh).
TruSeq libraries: 500ng of total RNA were subjected to Ribozero kit (illumina, MRZE706) to remove rRNA. Libraries were constructed using Truseq Library Prep Kit V2.


title: Tu_WT2_2_CTTGTA: Wild type ( biological replicate)


title: Tu_WT1_1_ACAGTG: Wild type


title: TuGFP1_NNNGGCANN: GFP iCLIP

description: RNAs were extracted from protein-RNA complexes

data_processing:
iCLIP sequencing reads were trimmed to remove 3’ adaptor and 5’ randomized barcodes using -fastx_clipper and custom python codes base on Ule lab GitHub depository (https://github.com/jernejule/non-coinciding_cDNA_starts)
Trimmed reads were aligned to C. elegans ws235 reference genome using HISAT2(2.1.0), and PCR duplicated reads were removed
Reads aligning to genetic features were then counted using HTseq-count
Genome_build: ws235
Supplementary_files_format_and_content: csv formate. Compiled read counts from 6 iCLIP experiments.

extract_protocol:
Crosslinked embryos were collected and resuspended in Immunoprecipitation buffer (IP buffer) with freshly made protease inhibitors as described in this section [300 mM KCl, 50 mM HEPES pH7.4, 1 mM EGTA, 1 mM MgCl2, 10% glycerol, 0.1% NP-40]. Samples were lysed in a Spex 6870 freezer mill followed by centrifugation at 4ºC 21,000xg for 30 minutes to remove embryo debris. Cleared lysates were subjected to immunoprecipitation using anti-GFP antibody (Roche 11814460001) conjugated to protein G magnetic beads (Thermofisher) in the presence of 200unit of RNaseOut per milliliter of lysates.
Immunoprecipitated protein-RNA complexes were treated by RQ1 DNase treatment at 37º C for 10 minutes. To perform partial RNA digestion, RQ1 DNase treated bound fractions were washed and finally resuspend in 500 µL MNase reaction buffer. The MNase reaction was immediately transferred to a thermomixer for 2 minutes at 37ºC. The MNase reaction was stopped with ice-cold 1x PNK buffer with 5 mM EGTA followed by several washes. Treated sample were then subjected to L3 Adapter ligation, 5’ end labeling, SDS-PAGE and nitrocellulose transfer. After transfer, RNAs were isolated from the nitrocellulose membrane and the following reverse transcription, cDNA circularization and PCR amplification were performed as described in Huppertz et al. 2014.

treatment_protocol: All worms were grown on NA22 bacteria plates. After Embryos were harvested, Embryos were subjected to UV254nm for 3 times of 400 mJ/cm2 exposure.

value: UV crosslinked protein-RNA


title: TuGFP2_NNNAATANN: GFP iCLIP(replicate)


title: Tu_m34-2_1_GTGAAA: meg-3meg-4 ( biological replicate)


title: 4C-seq: trl RNAi  CES viewpoint1 rep1


title: Slee102_M3_NNNTTGTNN: MEG-3::GFP iCLIP


title: Slee110_M3_NNNCGGANN: MEG-3::GFP iCLIP(replicate)


title: Slee113_mRNAseqFP_N2_1: wild type mRNAseq-1

description: corresponding mRNAseq


title: Tu_WT3_2_GCCAAT: Wild type ( biological replicate)


title: Tu_m34-1_1_CTTGTA: meg-3meg-4


title: Slee109_PGL1_NNNGGCANN: PGL-1::GFP iCLIP(replicate)


title: Slee106_PGL1_NNNTGGCNN: PGL-1::GFP iCLIP


title: Adult_naive CD4+ T cells_H3K4me3_rep1_input

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

data_processing:
Adapter sequences were trimmed using Trimmomatic v0.39
ChIP-seq reads were aligned to the hg19 genome using HISAT2 v2.1.0 using default parameters
Peak calling was performed by comparing the ChIP samples to input samples with MACS2 v2.1.1.20160309 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files were generated as bedgraph files with MACS2 v2.1.1.20160309 and were then converted to bigwig files using bedGraphToBigWig

source_name: Adult_H3K4me3_peripheral blood

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA was end-repaired using a combination of T4 polynucleotide kinase and T4 DNA polymerase. The blunt phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a single 3' A to blunt DNA for ligation of Illumina adapters with a single 3' T overhang. After adapter ligation DNA was PCR amplified with Illumina adapters for 19 cycles and library fragments of ~250 bp (insert plus adapter and PCR primer) were selected by bead purification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 2500 following the manufacturer's instructions.

tag: age

value: 35 years

value: female

value: peripheral blood

tag: cell type

value: naive CD4+ T cells

tag: isolation

value: Miltenyi Biotec naive CD4+ T cell magnetic bead isolation


title: Adult_naive CD4+ T cells_H3K4me3_rep3_input

value: 44 years

value: male


title: Adult_naive CD4+ T cells_H3K4me3_rep1

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: Adult_naive CD4+ T cells_H3K4me3_rep2_input

value: 37 years


title: Adult_naive CD4+ T cells_H3K4me3_rep2


title: S Lycopersicum, Fny-CMV

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum lycopersicum

source_name: shoot apex

growth_protocol: the plants were grown in Conviron Chambers set at 28 and 22°C ( day and ngiht, respectively) with 16 hours of light

extract_protocol:
total RNA was extracted using Tri-reagent and 1.5 ug of total RNA was used for small RNA library construction using Illumina sRNA construction kit version 1.5
Illumina compatible method using standard Illumina adapters

treatment_protocol: the seedlings at 2-3 leaf stage were inoculated with viral RNA. The apical part of the plants were harvested at 9-10dpi.

tag: infection status

value: infected with Cucumber mosaic virus

value: shoot apex


title: small intestine from YMT mice, bio rep4

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

institute: DUKE-NUS Graduate Medical School

description: Gene expression data from small intestine of 12 week old mice, inoculated with microbiome from young (4wk) mice

hyb_protocol: Samples were hybridized on the GeneChip Mouse Gene 2.0 ST Array (Affymetrix Inc., Santa Clara, CA) for 16 hours at 45oC. GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were analyzed with Affymetrix Expression Console using Robust Mean Average (RMA) as the normalization method. Small intestine and liver samples were analyzed separately.

label: biotin

organism: Mus musculus

source_name: mouse small intestine

label_protocol: Fragmented, labelled single-stranded cDNA was prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® WT PLUS Reagent Kit User Manual, Affymetrix).

growth_protocol: Intestinal and hepatic metabolism in OMT vs YMT mice.

extract_protocol: Total RNA was extracted using Rneasy mini-kit (Qiagen) using manufacturer's protocol.

treatment_protocol: 5-6 weeks old mice were inoculated with microbiome from either 2 years old (OMT) or 4 weeks young (YMT) mice and then followed for 8 weeks. After 8 weeks the small intestine and liver samples were processed for microarray analysis

value: small intestine

tag: genotype

value: 13 weeks old mice


title: small intestine from OMT mice, bio rep2

description: Gene expression data from small intestine of 12 week old mice, inoculated with microbiome from old (2yr) mice

tag: tissue


title: small intestine from YMT mice, bio rep2


title: small intestine from YMT mice, bio rep3


title: small intestine from OMT mice, bio rep3


title: TermC_naive CD4+ T cells_H3K4me3_rep3_input

description:
87992_CTTGTA_S24_L004
sample comprised of 3 combined patient samples (41 week female, 41.14 week male, 40.57 week female)

source_name: TermC_H3K4me3_umbilical cord blood

value: over 37 weeks gestation preterm chorioamnionitis-exposed neonate

value: umbilical cord blood


title: liver from OMT mice, bio rep2

description: Gene expression data from liver of 12 week old mice, inoculated with microbiome from old (2yr) mice

source_name: mouse liver

value: liver


title: small intestine from OMT mice, bio rep4


title: liver from YMT mice, bio rep4

description: Gene expression data from liver of 12 week old mice, inoculated with microbiome from young (4wk) mice


title: liver from YMT mice, bio rep1


title: liver from OMT mice, bio rep5


title: liver from OMT mice, bio rep1


title: liver from YMT mice, bio rep2


title: small intestine from YMT mice, bio rep1


title: small intestine from OMT mice, bio rep1


title: small intestine from OMT mice, bio rep5


title: liver from YMT mice, bio rep3


title: liver from OMT mice, bio rep3


title: liver from OMT mice, bio rep4


title: TermC_naive CD4+ T cells_H3K4me3_rep3

description:
87989_ACAGTG_S21_L004
sample comprised of 3 combined patient samples (41 week female, 41.14 week male, 40.57 week female)


title: S Lycopersicum, FnyCMV-D

value: infected with Cucumber mosaic virus and D satellite RNA


title: Adult_naive CD4+ T cells_H3K4me3_rep3


title: S Lycopersicum, FnyCMV-Dm

value: infected with Cucumber mosaic virus and Dm satellite RNA


title: TermC_naive CD4+ T cells_H3K4me3_rep2_input

description:
87991_CAGATC_S23_L004
sample comprised of 3 combined patient samples (40.4 week female, 38.14 week male, 38.14 week male)


title: S Lycopersicum, healthy

value: not infected (healthy)


title: TermC_naive CD4+ T cells_H3K4me3_rep1_input

description:
87990_GCCAAT_S22_L004
sample comprised of 3 combined patient samples (40.6 week female, 41.14 week male, 41.14 week female)


title: TermC_naive CD4+ T cells_H3K4me3_rep1

description:
87987_CGATGT_S19_L004
sample comprised of 3 combined patient samples (40.6 week female, 41.14 week male, 41.14 week female)


title: TermC_naive CD4+ T cells_H3K4me3_rep2

description:
87988_TGACCA_S20_L004
sample comprised of 3 combined patient samples (40.4 week female, 38.14 week male, 38.14 week male)


title: Term_naive CD4+ T cells_H3K4me3_rep3_input

description:
87974_CTTGTA_S6_L003
sample comprised of 3 combined patient samples (37.43 week male, 39 week female, 39 week female)

source_name: Term_H3K4me3_umbilical cord blood

value: over 37 weeks gestation term healthy neonate


title: rdr2-2 Anther 2

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
Bn_rdr2_2
Small RNA
Anthers from a Brassica rapa rdr2 mutant, rep 2

data_processing:
Adapter sequences were removed using Trimmomatic and chopped to 18-34 nt in length for all the tags.
Supplementary_files_format_and_content: tag count format

organism: Brassica rapa

source_name: Anther

extract_protocol: Total RNA was isolated from anthers of the wild type and rdr2-2 mutant using TRIzol reagent (Invitrogen). Size selected RNA ~30 ng for each sample was used to construct the small RNA libraries using TruSeq small RNA kit from Illumina  following manufacture's protocol. Libraries were sequenced on an HiSeq2500 following the manufacturer's protocols at the University of Delaware DNA Sequencing & Genotyping Center.

value: Anther

value: rdr2 mutant


title: WT Anther 3

description:
Bn_wt_3
Small RNA
Anthers from Brassica rapa wild type, rep 3

value: R-o-18 (wild type)


title: Term_naive CD4+ T cells_H3K4me3_rep3

description:
87971_ACAGTG_S3_L003
sample comprised of 3 combined patient samples (37.43 week male, 39 week female, 39 week female)

value: naive CD4+ T cells

value: Miltenyi Biotec naive CD4+ T cell magnetic bead isolation


title: WT Anther 2

description:
Bn_wt_2
Small RNA
Anthers from Brassica rapa wild type, rep 2


title: rdr2-2 Anther 1

description:
Bn_rdr2_1
Small RNA
Anthers from a Brassica rapa rdr2 mutant, rep 1


title: Term_naive CD4+ T cells_H3K4me3_rep2

description:
87970_TGACCA_S2_L003
sample comprised of 3 combined patient samples (40.5 week male, 39.1 week female, 39.43 week female)

value: H3K4me3 (Abcam, ab8580)


title: Term_naive CD4+ T cells_H3K4me3_rep1_input

description:
87972_GCCAAT_S4_L003
sample comprised of 3 combined patient samples (37.3 week female, 39.3 week male, 41.86 week female)


title: prox 4

city: Eugene

first: Gabriel

last: Yette

state: Oregon

address: 1229 University of Oregon 1318 Franklin Blvd

department: Biology- Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling by Illumina Real-Time Analysis 2 (RTA2).
Sequence reads were mapped to GRCz11/danRer11 using TopHat2
Mapped reads were counted using HTSeq
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: Tab-delimited text files of HTSeq counts for each sample are provided

organism: Danio rerio

source_name: 96 hpa proximal regenerate

extract_protocol:
Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction.
Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA-Seq kit and protocol.

tag: transgene

value: regenerating caudal fin

tag: time

value: 96 hours post amputation


title: prox 3


title: O30C_naive CD4+ T cells_H3K4me3_rep2

description:
87982_TGACCA_S14_L005
sample comprised of 3 combined patient samples (34.43 week male, 34.14 week female, 30.14 week male)

source_name: O30C_H3K4me3_umbilical cord blood

value: 30-36 weeks gestation preterm chorioamnionitis-exposed neonate


title: Term_naive CD4+ T cells_H3K4me3_rep2_input

description:
87973_CAGATC_S5_L003
sample comprised of 3 combined patient samples (40.5 week male, 39.1 week female, 39.43 week female)


title: dist 2

source_name: 96 hpa distal regenerate


title: Term_naive CD4+ T cells_H3K4me3_rep1

description:
87969_CGATGT_S1_L003
sample comprised of 3 combined patient samples (37.3 week female, 39.3 week male, 41.86 week female)


title: DU145_AREG_03

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
Cancer cells cultured with AREG+ stromal cell media
AREG_3_S85_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using a protocol from Tajnik et al. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Research. 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: counts and FPKM

source_name: DU145 AREG

growth_protocol: Prostate cancer cells were routinely cultured and passaged (typically 0.5–1 × 106 cells in a T25 flask) in DMEM supplemented with 10% FBS.

extract_protocol:
At the end of cell coculture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Upon 80% confluency, cells were treated with conditioned media collected from control PSC27 cells or AREG-overexpressing PSC27 cells for consecutive 3 days.

tag: cell line

value: prostate cancer cells

tag: cell line source

value: Derived from the metastatic site, brain of a prostate cancer patient

tag: source type

value: Grade Iv, Adenocarcinoma

tag: culture condition

value: AREG+ stromal cell media


title: O30C_naive CD4+ T cells_H3K4me3_rep3

description:
input sample for O303C did not pass qc, so Input sample for O302C used instead
87983_ACAGTG_S15_L005
sample comprised of 3 combined patient samples (34.14 week female, 34 week male, 34.57 week female)

value: umbilical cord blood


title: O30C_naive CD4+ T cells_H3K4me3_rep1_input

description:
87984_GCCAAT_S16_L005
sample comprised of 3 combined patient samples (34.43 week male, 34 week male, 34.71 week female)


title: WT Anther 1

description:
Bn_wt_1
Small RNA
Anthers from Brassica rapa wild type, rep 1

tag: genotype/variation


title: O30C_naive CD4+ T cells_H3K4me3_rep1

description:
87981_CGATGT_S13_L005
sample comprised of 3 combined patient samples (34.43 week male, 34 week male, 34.71 week female)


title: O30C_naive CD4+ T cells_H3K4me3_rep2_input

description:
87985_CAGATC_S17_L005
sample comprised of 3 combined patient samples (34.43 week male, 34.14 week female, 30.14 week male)


title: DU145_AREG_02

description:
Cancer cells cultured with AREG+ stromal cell media
AREG_2_S84_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt


title: DU145_AREG_01

description:
Cancer cells cultured with AREG+ stromal cell media
AREG_1_S83_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt


title: O30_naive CD4+ T cells_H3K4me3_rep3_input

description:
87968_CTTGTA_S18_L003
sample comprised of 3 combined patient samples (31.71 week male, 33.43 week female, 34 week female)

source_name: O30_H3K4me3_umbilical cord blood

value: 30-36 weeks gestation preterm healthy neonate


title: DU145_control_03

description:
Cancer cells cultured with control media
control_3_S82_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt

source_name: DU145 control

value: control media


title: O30_naive CD4+ T cells_H3K4me3_rep3

description:
87965_ACAGTG_S15_L003
sample comprised of 3 combined patient samples (31.71 week male, 33.43 week female, 34 week female)


title: O30_naive CD4+ T cells_H3K4me3_rep2_input

description:
87967_CAGATC_S17_L003
sample comprised of 3 combined patient samples (32.43 week male, 33.43 week male, 34.29 week female)


title: DU145_control_02

description:
Cancer cells cultured with control media
control_2_S81_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt


title: dist 3


title: DU145_control_01

description:
Cancer cells cultured with control media
control_1_S80_L004
processed data file: Prostate_cellines (DU145)_AREGVsCTRL.FPKM.txt


title: O30_naive CD4+ T cells_H3K4me3_rep2

description:
87964_TGACCA_S14_L003
sample comprised of 3 combined patient samples (32.43 week male, 33.43 week male, 34.29 week female)


title: prox 2


title: dist 4


title: PC3_AREG_03

description:
Cancer cells cultured with AREG+ stromal cell media
AREG-3_H73NNDMXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt

source_name: PC3 AREG

value: Derived from the metastatic site, bone of a prostate cancer patient

value: Carcinoma


title: PC3_AREG_02

description:
Cancer cells cultured with AREG+ stromal cell media
AREG-2_H73NNDMXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt


title: O30_naive CD4+ T cells_H3K4me3_rep1_input

description:
87966_GCCAAT_S16_L003
sample comprised of 3 combined patient samples (30.71 week male, 31.43 week female, 31.43 week female)


title: U30C_naive CD4+ T cells_H3K4me3_rep3_input

description:
87980_CTTGTA_S12_L004
sample comprised of 3 combined patient samples (25.86 week female, 25.29 week female, 28.71 week female)

source_name: U30C_H3K4me3_umbilical cord blood

value: under 30 weeks gestation preterm chorioamnionitis-exposed neonate


title: O30_naive CD4+ T cells_H3K4me3_rep1

description:
87963_CGATGT_S13_L003
sample comprised of 3 combined patient samples (30.71 week male, 31.43 week female, 31.43 week female)


title: PC3_control_03

description:
Cancer cells cultured with control media
control-3_H2FTWDSXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt

source_name: PC3 control


title: PC3_control_02

description:
Cancer cells cultured with control media
control-2_H2FTWDSXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt


title: U30C_naive CD4+ T cells_H3K4me3_rep2_input

description:
87979_CAGATC_S11_L004
sample comprised of 3 combined patient samples (29.71 week male, 28.43 week male, 28.71 week female)


title: PC3_control_01

description:
Cancer cells cultured with control media
control-1_H2FTWDSXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt


title: PC3_AREG_01

description:
Cancer cells cultured with AREG+ stromal cell media
AREG-1_H2FTWDSXX_L1
processed data file: Prostate_cellines (PC3)_AREGVsCTRL.FPKM.txt


title: RPE, mm_21h_888L

city: Nijmegen

first: Elja

last: Louer

state: Select State

address: Geert Grootplein 26, M850 route 286

department: Physiology

country: Netherlands

institute: RadboudUMC

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR mapper two-pass mode and the gene-based read counts were quantified at the same time.
Genes with low read number (below 5) were removed
Cufflinks was employed to estimate gene-level abundance in FPKM (Fragments Per Kilobase per Million aligned reads value) values for ENSEMBL genes.
DESeq2 was used for DEG analysis. All time points were compared and. Only genes with a Benjamini-Hochberg-adjusted p-value < 0.05 and fold change > 1.5 were considered significantly deregulated.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample. Gene names and Ensembl codes are given.

extract_protocol:
10 to 13-week-old male mice were randomly distributed over 6 time points (ZT0, 2, 4, 9, 14, 19). Each time, one mouse was sacrificed using cervical dislocation and eyes were collected via enucleation (n=5 mice per time point). Anterior segments (cornea, iris and lens) were removed to expose the posterior eyecup. The retina was carefully peeled off, and the eyecup containing the RPE, sclera and choroid were stored in RNAlater solution.   For RNA isolation, the RPE was removed gently from the choroidal layer using fine forceps. The brown clumps of RPE cells were dissolved in RLT Buffer from RNeasy Micro Kit after which RNA was extracted using the RNeasy Micro Kit. Illumina Next Seq 500 sequencer was used for 1 x 75 bp single-read sequencing, sequencing an average of 20 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Retinal pigment epithelium (RPE)

value: 10-13 weeks

value: wild type

tag: time (zt)

tag: eye

value: left

tag: animal number


title: RPE, mm_16h_882R

tag: age

value: right


title: U30C_naive CD4+ T cells_H3K4me3_rep1

description:
87975_CGATGT_S7_L004
sample comprised of 3 combined patient samples (29.71 week male, 28 week female, 29 week male)

tag: cell type

value: naive CD4+ T cells

tag: isolation

value: Miltenyi Biotec naive CD4+ T cell magnetic bead isolation

value: H3K4me3 (Abcam, ab8580)


title: U30C_naive CD4+ T cells_H3K4me3_rep1_input

description:
87978_GCCAAT_S10_L004
sample comprised of 3 combined patient samples (29.71 week male, 28 week female, 29 week male)


title: RPE, mm_9h_871R


title: U30C_naive CD4+ T cells_H3K4me3_rep3

description:
87977_ACAGTG_S9_L004
sample comprised of 3 combined patient samples (25.86 week female, 25.29 week female, 28.71 week female)

tag: chip antibody


title: U30_naive CD4+ T cells_H3K4me3_rep3

description:
87959_ACAGTG_S9_L002
sample comprised of 3 combined patient samples (28.14 week male, 28.14 week female, 29.29 week male)

source_name: U30_H3K4me3_umbilical cord blood

value: under 30 weeks gestation preterm healthy neonate


title: RPE, mm_2h_889R

tag: genotype


title: U30C_naive CD4+ T cells_H3K4me3_rep2

description:
87976_TGACCA_S8_L004
sample comprised of 3 combined patient samples (29.71 week male, 28.43 week male, 28.71 week female)

tag: tissue


title: U30_naive CD4+ T cells_H3K4me3_rep3_input

description:
87962_CTTGTA_S12_L002
sample comprised of 3 combined patient samples (28.14 week male, 28.14 week female, 29.29 week male)


title: RPE, mm_21h_883L


title: U30_naive CD4+ T cells_H3K4me3_rep2

description:
87958_TGACCA_S8_L002
sample comprised of 3 combined patient samples (24.14 week female, 29.14 week female, 29.29 week male)


title: U30_naive CD4+ T cells_H3K4me3_rep1_input

description:
87960_GCCAAT_S10_L002
sample comprised of 3 combined patient samples (24.86 week female, 24 week male, 29.14 week male)


title: U30_naive CD4+ T cells_H3K4me3_rep2_input

description:
87961_CAGATC_S11_L002
sample comprised of 3 combined patient samples (24.14 week female, 29.14 week female, 29.29 week male)


title: RPE, mm_7h_861R


title: U30_naive CD4+ T cells_H3K4me3_rep1

description:
87957_CGATGT_S7_L002
sample comprised of 3 combined patient samples (24.86 week female, 24 week male, 29.14 week male)


title: RPE, mm_11h_862L


title: patient8_tumor_HOXB13Chip

city: AMSTERDAM

first: Yanyun

last: Zhu

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

description: The raw data cannot be stored with GEO due to patient privacy andwill be uploaded to the European Genome/Phenome Archive

data_processing:
The sequencing data were generated by the Illumina HiSeq 2500 Genome Analyzer (65-bp reads) and were aligned to the reference human genome (assembly hg19).
Reads with MAPQ below 20 were filtered. .
DFilter (bs = 50, ks = 30, refine) and MACS peak caller version 1.4 (P-value = 10−7) were used to identify peaks over input control and only peaks called by both peak callers were selected for the analysis
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: prostate tumor

growth_protocol: fresh frozen material

extract_protocol: Samples was processed as described elsewhere(Severson et al., 2018) using 5 μg of antibody and 50 μl of Protein A /G  magnetic beads (Invitrogen) per sample. Antibodies applied here were AR (Millipore, 06-  680); FOXA1 (Abcam, ab5089); HOXB13 (Santa Cruz, sc-66923). As control, mixed inputs  for normal and tumor were generated separately, using equimolar levels for all samples.

treatment_protocol: prostatectomy samples in which tumor-containing regions labled 'tumor'and tumor-free  benign areas from the same prostate labled 'healthy'.

tag: disease state

value: primary prostate cancer

value: HOXB13(Santa Cruz Cat# sc-66923)

value: prostate tumor


title: RPE, mm_7h_863L


title: RPE, mm_16h_844L


title: RPE, mm_21h_845R


title: patient6_tumor_HOXB13Chip


title: patient5_tumor_HOXB13Chip


title: RPE, mm_11h_842L


title: patient4_tumor_HOXB13Chip


title: RPE, mm_16h_843L


title: patient3_tumor_HOXB13Chip


title: RPE, mm_11h_841L


title: RPE, mm_7h_840L


title: RPE, mm_7h_839R


title: RPE, mm_2h_870R


title: RPE, mm_2h_837R


title: RPE, mm_9h_838R


title: patient2_tumor_HOXB13Chip


title: patient1_tumor_HOXB13Chip


title: patient7_tumor_FOXA1Chip

value: FOXA1(Abcam Cat# ab5089)


title: RPE, mm_9h_836R


title: RPE, mm_21h_832L


title: patient6_tumor_FOXA1Chip


title: patient4_tumor_FOXA1Chip


title: patient7_tumor_HOXB13Chip


title: RPE, mm_9h_830L


title: RPE, mm_11h_831L


title: patient2_tumor_FOXA1Chip


title: patient3_tumor_FOXA1Chip


title: RPE, mm_7h_825L


title: RPE, mm_16h_823R


title: RPE, mm_2h_822L


title: RPE, mm_16h_821R


title: patient6_tumor_ARChip

value: AR(Millipore Cat# 06-680)


title: patient5_tumor_ARChip


title: patient7_tumor_ARChip


title: patient8_tumor_FOXA1Chip


title: RPE, mm_9h_820R


title: RPE, mm_11h_819L


title: patient4_tumor_ARChip


title: patient3_tumor_ARChip


title: microglia isolated from early microglial repopulation mice (switched to ctrl diet for 2d after 14d of PLX5622) [D2]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

institute: Helen and Robert Appel Alzheimer’s Disease Research Institute

data_processing:
base calling was performed by Illumina NextSeq Control Software v1.4
BCL to Fastq was performed using the cellranger mkfastq function in Cellranger software (2.0.1, 10xGenomics)
sequencing reads were mapped to mouse genome mm10 using the cellranger count function in Cellranger software (2.0.1, 10xGenomics)
sequencing runs from each sample were aggregated using the cellranger aggr function in Cellranger software (2.0.1, 10xGenomics)
read depth normalization was performed using the "mapped" setting in cellranger aggr function. This step subsample reads from higher-depth GEM wells until they all have an equal number of reads that are confidently mapped to the transcriptome or assigned to the feature IDs per cell.
Genome_build: mm10
Supplementary_files_format_and_content: barcode table, gene table, count matrix

source_name: whole brain without cerebellum

growth_protocol: Mice were housed in a pathogen-free barrier facility operated on a 12 hr light on/off cycle with unrestricted access to water and food source.

extract_protocol:
Whole brain was then dissected, with the cerebellum removed, and homogenized in an enzymatic digestion buffer containing 0.2% Collagenase Type 3 (Worthington, LS004182) and 3 U/mL Dispase (Worthington, LS02104). The digestion was performed at 37 C for 45 min and was quenched by an inactivation buffer containing 2.5 mM EDTA (Thermofisher, 15575020) and 1% fetal bovine serum (Invitrogen, 10082147). The homogenates were kept at 4C for all downstream application onwards. The homogenates were then processed for myelin depletion using myelin removal beads (Miltenyi Biotec, 130-096-733) and passed through LD column (Miltenyi Biotec, 130-042-901). The myelin depleted faction was then used for FACS.
Single-cell expression libraries were prepared using the and the 10x genomics Chromium single cell 3′ bibrary & gel bead kit v2 reagents (10x Genomics, PN-120237). To minimize batch effects, all 4 samples were prepared simultaneously in a single assay. Briefly, suspension containing 2,000-10,000 single cells were loaded into the 10x single cell A chip and processed in the 10x Chromium controller. After reverse transcription, cDNAs were amplified by 12-14 PCR cycles. An aliquot of 35 ul cDNA product was then used for library construction, which included 14 cycles of sample index PCR to barcode samples. The quality of the cDNA library was checked by the Bioanalyzer (Agilent). KAPA qPCR was performed to measure the library quantities. A pool of all quanity-balanced libraries was then sequenced on the NextSeq 500 sequencer (Illumina) at an average sequencing depth of 45,002 reads/cell (post normalization).

treatment_protocol: Mice were treated with PLX5622 containing diet as the only food source for 14 days.

tag: number of animal pooled

value: 5 months

tag: gender

value: female

value: whole brain without cerebellum


title: patient1_tumor_ARChip


title: patient5_tumor_FOXA1Chip


title: microglia isolated from PLX treated mice (PLX5622, 1200 mg/kg, 14 days) [D0]


title: patient2_tumor_ARChip


title: patient8_healthy_HOXB13Chip

source_name: prostate (healthy)

value: prostate (healthy)


title: patient1_tumor_FOXA1Chip


title: patient7_healthy_HOXB13Chip


title: ATAC-seq_Pgk_d2_rep2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: rafael_XXd2_idrValues_withpool_thrp05.bed

data_processing:
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
RNA sequencing reads were aligned on the mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
ATAC-seq paired-end reads were trimmed of the adaptor sequences and aligned to the NCBIm37 genome using STAR v2.4.2a.  Duplicate fragments were removed using PICARD tools v1.90, only unique mapped fragments between 38bp and 1500bp in length were retained.  ATAC-seq peaks were called on the 1bp transposase cut-sites using MACS2 (with shift size 100 and extension size 200). Only the peaks considered reproducible by IDR (version 2), with an IDR threshold of 0.05, were kept.
Genome_build: mm9 / NCBIm37

source_name: mouse ESC (Pgk12.1)

growth_protocol: Feeder-independent male mouse ESC (E14) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Feeder-independent female mouse ESC (Pgk12.1) were grown on gelatin-coated flasks in DMEM supplemented with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged when needed. Medium was changed daily. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates or flasks and scraped off. For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate. For ATAC-seq, cells were washed once with PBS and directly incubated in the transposition reaction.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using KAPA Hyper Prep Kit (KK8500, Kapa Biosystems); RNA-seq libraries were generated using the TruSeq Stranded Total RNA kit (Illumina); ATAC-seq libraries were generated based on a Nextseq-compatible protocol (Buenrostro et al 2013).

value: mouse ESC (Pgk12.1)

value: XX, 129/Ola-Hsd x (C3H/He-Pgk-1a/Ws x 129/Ola-Hsd)F1

tag: differentiation stage

value: day 2

tag: capture-c viewpoint


title: patient8_tumor_ARChip


title: RPE, mm_2h_818R

value: Retinal pigment epithelium (RPE)

value: 10-13 weeks

value: wild type

value: right


title: ATAC-seq_Pgk_d1_rep2

description: rafael_XXd1_idrValues_withpool_thrp05.bed

value: day 1


title: RPE, mm_21h_824L

value: left


title: patient6_healthy_HOXB13Chip

value: primary prostate cancer

value: HOXB13(Santa Cruz Cat# sc-66923)


title: ATAC-seq_Pgk_d2_rep1


title: patient5_healthy_HOXB13Chip


title: ATAC-seq_Pgk_d1_rep1


title: ATAC-seq_Pgk_d0_rep2

description: rafael_XXd0_idrValues_withpool_thrp05.bed

value: day 0 (undifferentiated)


title: patient4_healthy_HOXB13Chip


title: patient3_healthy_HOXB13Chip


title: ATAC-seq_Pgk_d0_rep1


title: patient2_healthy_HOXB13Chip


title: patient1_healthy_HOXB13Chip


title: patient8_healthy_FOXA1Chip

value: FOXA1(Abcam Cat# ab5089)


title: p38_LacZ_rep2

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.1.0) with the mouse GENCODE (version M17) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 2) were used for further analyses.
FPKM values were determined by Cuffdiff within Cufflinks version 2.2.1 package with the mouse GENCODE (version M17)
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

source_name: Germline stem cells

growth_protocol: Germline stem cells were derived from wild type DBA/2 mice, Mapk14f/f and Mapk7f/f conditional KO mice using culture medium based on Iscove’s modified MEM (Invitrogen, Carlsbad, CA), which was supplemented with 10 ng/ml human FGF2, 15 ng/ml recombinant rat GDNF (both from Peprotech, London, UK) and 1% fetal bovine serum (FBS), (Kanatsu-Shinohara et a.l, 2014)

extract_protocol:
RNA of Germline stem cells  was harvested using Trizol reagent.
RNA-seq libraries were generated from 200 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Mapk7 KO, Mapk14 KO : Germline stem cells  derived from Mapk14f/f or Mapk7f/f conditional KO mice were exposed to a Cre- or LacZ- expressing adenovirus(AxCANCre, AxCANLacZ) overnight. NOX1 KD, Bcl6b KD : Germline stem cells  derived from wild type DBA/2 mice were exposed to a control shRNA or Nox1 shRNA or Bcl6b shRNA  expressing lentivirus overnight.

value: testis

value: Mapk14 f/f


title: microglia isolated from naïve mice [Ctrl]

value: 5 months

value: female

value: whole brain without cerebellum


title: patient6_healthy_FOXA1Chip

value: prostate (healthy)


title: p38_LacZ_rep1


title: patient5_healthy_FOXA1Chip


title: patient4_healthy_FOXA1Chip


title: p38KOCre_rep1


title: Bcl6d_KD_rep2

value: Bcl6b -/-


title: Bcl6d_KD_rep1


title: Bcl6b_cont_rep2


title: patient3_healthy_FOXA1Chip


title: Bcl6b_cont_rep1


title: ERK5_LacZ_rep2

value: Mapk7 f/f


title: ERK5KOCre_rep1

value: Mapk7 -/-


title: patient6_healthy_ARChip

value: AR(Millipore Cat# 06-680)


title: patient8_healthy_ARChip


title: ERK5_LacZ_rep1


title: patient1_healthy_FOXA1Chip


title: patient7_healthy_ARChip


title: p38KOCre_rep2


title: ERK5KOCre_rep2


title: Nox1_KD_rep2


title: Nox1_cont_rep2

value: wild type


title: patient4_healthy_ARChip


title: patient3_healthy_ARChip


title: Nox1_KD_rep1


title: patient7_healthy_FOXA1Chip


title: Nox1_cont_rep1


title: patient2_healthy_ARChip


title: DNP-BSA (50 ng/ml) treated BMMC [Ag3]

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

data_processing:
The sequenced reads were mapped tomm9 build of the human genome using TopHat version 2.0.12 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: 10 ng/ml IL-3 and 10 ng/ml SCF for 4-6 weeks after bone marrow isolation

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

treatment_protocol: IgE (0.5 ug/ml) treatment for 18 h, Ag (50 ng/ml) treatment for 2h after IgE treatment

value: Bone marrow derived mast cells (BMMCs)

tag: passages

tag: treatment group

value: treated with DNP-BSA (50 ng/ml) for 2h

tag: molecule subtype

value: mRNA and lncRNA


title: patient1_healthy_ARChip

value: primary prostate cancer


title: DNP-BSA (50 ng/ml) treated BMMC [Ag2]

tag: strain

tag: genotype/variation


title: DNP-IgE (0.5 ug/ml) treated BMMC [IgE3]

value: sensitized overnight with DNP-IgE (0.5 ug/ml)


title: DNP-BSA (50 ng/ml) treated BMMC [Ag1]


title: WGBS_pG_cG50

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "ABT"

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was analyzed using FastQC tool. Adaptors and low quality bases were trimmed out using Cutadapt (settings: -u 7, -U 7,  -m 40,  -q 30, --trim-n). Reads were then aligned to the customized reference human genome GRCh38 (Release 86) available on the Ensembl FTP, using the Bismark aligner (v0.14.5, settings: --score_min L,0,-0.6 -X 1000 -I 0)
Methylation calls were performed using Bismark methylation extractor script. We used a R homemade script to calculate methylation percentages per each single CpG, by dividing the number of methylated Cs by the total coverage on that base. CpGs with a coverage of between 4x to 100x were retained for CpG methylation analysis.
Genome_build: hg38
Supplementary_files_format_and_content: BED files with the following columns: 1) chromosome, 2) start, 3) end, 4) CpGmethylation_level, 5) Subtelomere

growth_protocol: IPSCs were cultured on plates coated with Cultrex® Reduced Growth Factor Basement Membrane Matrix (343300501, Trevigen, MD, USA), and grown in either mTeSR-1 media (85850, StemCell Technologies, Vancouver, Canada) or PepRoGrow™ hESC Media (hESC-100, PepRoTech, NJ, USA). Cells were passaged every 4–6 days. Cell were dissociated from plates with 0.5 mM EDTA and following each passage, 2mM Thiazovivin (14245, Cayman CHEMICAL, MI, USA was added to the media.

extract_protocol:
Genomic DNA was extracted by using the Wizard Genomic DNA kit (Promega).
WGBS libraries were prepared and sequenced according to Illumina's instructions.

value: iPSCs

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: WGBS_pG_cG13


title: patient2_healthy_FOXA1Chip

value: FOXA1(Abcam Cat# ab5089)


title: WGBS_ICF1pG

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: DNP-IgE (0.5 ug/ml) treated BMMC [IgE1]


title: WGBS_cR35

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: WGBS_cR7


title: Untreated BMMC [UT3]

value: none (untreated control)


title: WGBS_Ctrl

value: healthy control (DNMT3B wt/wt)


title: patient5_healthy_ARChip

value: prostate (healthy)


title: Untreated BMMC [UT1]


title: WGBS_ICF1pR

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: Untreated BMMC [UT2]


title: ChIP-Seq of H3K4M3 in untreated BMMC rep 2

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet –solexa1.3-quals
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak files were generated by MACS 2.0.10

extract_protocol:
CHIP-seq libraries were prepared with NEB NEXT Ultra kit using 10 ng starting material
Single read - Illumina

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: Ci.10x

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: RIKEN

description:
10x.mat.count.qc.csv
10x.mat.cpm.qc.csv

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

source_name: Chemically induced fibroblasts

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

extract_protocol: Droplet-based single-cell RNAseq libraries were generated using the ChromiumTM Single Cell 3’ Reagent kits V1 (CG00026, 10x Genomics). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). Thereafter, cells were mixed with the Single Cell Master Mix and loaded together with Single Cell 3’ Gel beads and Partitioning Oil into a Single Cell 3’ Chip. RNA transcripts were uniquely barcoded and reverse-transcribed in droplets. cDNAs were pooled and amplified according to the manufacturer’s protocol. Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and the KAPA Library Quantification kit (KAPA BIOSYSTEMS). Libraries then were sequenced by Illumina Hiseq 2500 in rapid mode.

tag: cell type

value: Chemically induced fibroblasts

tag: time

value: 21 days after induction

tag: treatment

value: Chemical cocktail of small molecules

tag: batch


title: Tfi.10x

description:
10x.mat.count.qc.csv
10x.mat.cpm.qc.csv

source_name: Transcription factor induced fibroblasts

value: Ectopic expression of transcription factors


title: ChIP-Seq of H3K27ac in untreated BMMC rep 2

city: Singapore

value: Bone marrow derived mast cells (BMMCs)

tag: chip antibody

value: Abcam


title: TFi4.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

value: Transcription factor induced fibroblasts


title: ChIP-Seq of H3K4M1 in untreated BMMC rep 2


title: ChIP-Seq of H3K4M3 in untreated BMMC rep 1


title: TFi4.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M1 in untreated BMMC rep 1


title: TFi4.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M3 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2


title: ChIP-Seq of H3K27ac in untreated BMMC rep 1


title: TFi4.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M1 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2


title: ChIP-Seq of H3K27ac in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 2


title: TFi4.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DNP-IgE (0.5 ug/ml) treated BMMC [IgE2]

value: wild type

value: sensitized overnight with DNP-IgE (0.5 ug/ml)

value: mRNA and lncRNA


title: ChIP-Seq of H3K4M3 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1


title: ChIP-Seq of H3K4M1 in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1


title: TFi4.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M3 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2

value: treated with DNP-BSA (50 ng/ml) for 2h


title: ChIP-Seq of H3K27ac in BMMC sensitized overnight with DNP-IgE (0.5 ug/ml) rep 1


title: TFi4.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K27ac in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2


title: TFi4.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M3 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1


title: TFi4.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K27ac in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1


title: TFi4.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq input for H3K4me1, H3K4me3, H3K27Ac rep 1


title: ChIP-Seq input for H3K4me1, H3K4me3, H3K27Ac rep 2


title: TFi4.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 5.2_Term_Mock

city: Maastricht

first: Christof

last: Seiler

address: Bouillonstraat 8-10

department: Department of Data Science and Knowledge Engineering

institute: Maastricht University

description: Nicholas Bayless_US 5.2_(HTA-2_0)

hyb_protocol: Samples were hybridized to microarrays in a hybridization over, with rotation at 60 rpm for 16 hr at 45°C. Following hybridization, arrays were washed according to GeneChip WT Pico Reagent Kit instructions.

scan_protocol: Samples were scanned using a GeneChip Scanner 3000 7G, with GeneChip Command Console software.

data_processing:
Normalize raw expressions using the Robust Multichip Average (RMA) algorithm (R package oligo, version 1.40.2). Remove background probes and probes that cannot be mapped to known gene symbols (R package affycoretools, version 1.48.0)
The .csv files (linked as supplementary files on the Series record) report RMA-normalized signals.

source_name: Peripheral blood mononuclear cells

label_protocol: Extracts were labeled using the GeneChip Whole Transcript Pico Reagent Kit, according to kit instructions. Briefly, RNA was reverse transcribed, amplified, and terminally labeled with biotin.

growth_protocol: Human PMBC samples were thawed, washed twice with RPMI culture medium and maintained in RPMI for ~7 hours at 37C.

extract_protocol: After incubation, RNA was extracted from PBMC samples using the Qiagen RNeasy Mini kit, according to manufacturer's instructions. RNA quality was evaluated by Nanodrop and Bioanalyzer.

treatment_protocol: PMBC samples (10^5/well) were either left unstimulated (US samples), or stimulated with H1N1 influenza virus (MOI = 1) for 4 hours at 37C. See methods section for further details.

tag: condition

value: Term

value: Mock

tag: rin

tag: viability

tag: ptidno

value: peripheral blood mononuclear cells (PBMCs)


title: PBMCs, 4.2_Preterm_Mock

description: Nicholas Bayless_US 4.2_(HTA-2_0)

value: Preterm


title: PBMCs, 12.3_Term_H1N1

description: Nicholas Bayless_12.3 +_(HTA-2_0)


title: PBMCs, 3.1_Term_Mock

description: Nicholas Bayless_US 3.1_(HTA-2_0)


title: PBMCs, 21.3_Preterm_Mock

description: Nicholas Bayless_US 21.3_(HTA-2_0)


title: ChIP-Seq of H3K4M1 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 2


title: TFi4.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 21.2_Term_Mock

description: Nicholas Bayless_US 21.2_(HTA-2_0)


title: PBMCs, 21.2_Term_H1N1

description: Nicholas Bayless_H1N1 21.2_(HTA-2_0)


title: TFi4.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M1 in BMMC with DNP-BSA (50 ng/ml) for 2h rep 1


title: PBMCs, 21.3_Preterm_H1N1

description: Nicholas Bayless_H1N1 21.3_(HTA-2_0)


title: TFi4.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 21.1_Term_Mock

description: Nicholas Bayless_US 21.1_(HTA-2_0)


title: PBMCs, 21.1_Term_H1N1

description: Nicholas Bayless_H1N1 21.1_(HTA-2_0)


title: PBMCs, 20.3_Term_H1N1

description: Nicholas Bayless_H1N1 20.3_(HTA-2_0)


title: TFi4.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 20.2_Preterm_H1N1

description: Nicholas Bayless_H1N1 20.2_(HTA-2_0)


title: TFi4.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 20.3_Term_Mock

description: Nicholas Bayless_US 20.3_(HTA-2_0)


title: TFi4.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 20.2_Preterm_Mock

description: Nicholas Bayless_US 20.2_(HTA-2_0)


title: PBMCs, 20.1_Term_Mock

description: Nicholas Bayless_US 20.1_(HTA-2_0)


title: TFi4.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 19.3_Term_Mock

description: Nicholas Bayless_US 19.3_(HTA-2_0)


title: PBMCs, 20.1_Term_H1N1

description: Nicholas Bayless_H1N1 20.1_(HTA-2_0)


title: PBMCs, 19.2_Term_Mock

description: Nicholas Bayless_US 19.2_(HTA-2_0)


title: TFi4.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 19.2_Term_H1N1

description: Nicholas Bayless_H1N1 19.2_(HTA-2_0)


title: PBMCs, 19.1_Preterm_Mock

description: Nicholas Bayless_US 19.1_(HTA-2_0)


title: PBMCs, 19.1_Preterm_H1N1

description: Nicholas Bayless_H1N1 19.1_(HTA-2_0)


title: TFi4.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 18.3_Preterm_Mock

description: Nicholas Bayless_US 18.3_(HTA-2_0)


title: PBMCs, 18.1_Term_Mock

description: Nicholas Bayless_US 18.1_(HTA-2_0)


title: PBMCs, 18.3_Preterm_H1N1

description: Nicholas Bayless_H1N1 18.3_(HTA-2_0)


title: PBMCs, 18.1_Term_H1N1

description: Nicholas Bayless_H1N1 18.1_(HTA-2_0)


title: TFi4.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 17.3_Term_Mock

description: Nicholas Bayless_US 17.3_(HTA-2_0)


title: TFi4.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 19.3_Term_H1N1

description: Nicholas Bayless_H1N1 19.3_(HTA-2_0)


title: TFi4.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 17.1_Term_H1N1

description: Nicholas Bayless_H1N1 17.1_(HTA-2_0)


title: PBMCs, 17.1_Term_Mock

description: Nicholas Bayless_US 17.1_(HTA-2_0)


title: PBMCs, 16.3_Term_H1N1

description: Nicholas Bayless_H1N1 16.3_(HTA-2_0)


title: TFi4.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 16.3_Term_Mock

description: Nicholas Bayless_US 16.3_(HTA-2_0)


title: PBMCs, 16.2_Term_H1N1

description: Nicholas Bayless_H1N1 16.2_(HTA-2_0)


title: TFi4.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 16.2_Term_Mock

description: Nicholas Bayless_US 16.2_(HTA-2_0)


title: TFi4.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 16.1_Preterm_H1N1

description: Nicholas Bayless_H1N1 16.1_(HTA-2_0)


title: PBMCs, 17.3_Term_H1N1

description: Nicholas Bayless_H1N1 17.3_(HTA-2_0)


title: PBMCs, 14.3_Preterm_Mock

description: Nicholas Bayless_US 14.3_(HTA-2_0)


title: TFi4.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 17.2_Preterm_Mock

description: Nicholas Bayless_US 17.2_(HTA-2_0)


title: PBMCs, 16.1_Preterm_Mock

description: Nicholas Bayless_US 16.1_(HTA-2_0)


title: PBMCs, 17.2_Preterm_H1N1

description: Nicholas Bayless_H1N1 17.2_(HTA-2_0)


title: TFi4.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 14.3_Preterm_H1N1

description: Nicholas Bayless_H1N1 14.3_(HTA-2_0)


title: TFi4.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 14.2_Term_H1N1

description: Nicholas Bayless_H1N1 14.2_(HTA-2_0)


title: TFi4.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 14.2_Term_Mock

description: Nicholas Bayless_US 14.2_(HTA-2_0)


title: PBMCs, 14.1_Term_Mock

description: Nicholas Bayless_US 14.1_(HTA-2_0)


title: TFi4.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 13.3_Term_Mock

description: Nicholas Bayless_US 13.3_(HTA-2_0)


title: PBMCs, 14.1_Term_H1N1

description: Nicholas Bayless_H1N1 14.1_(HTA-2_0)


title: TFi4.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 13.3_Term_H1N1

description: Nicholas Bayless_H1N1 13.3_(HTA-2_0)


title: PBMCs, 13.2_Preterm_Mock

description: Nicholas Bayless_US 13.2_(HTA-2_0)


title: PBMCs, 13.2_Preterm_H1N1

description: Nicholas Bayless_H1N1 13.2_(HTA-2_0)


title: TFi4.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 13.1_Term_H1N1

description: Nicholas Bayless_H1N1 13.1_(HTA-2_0)


title: TFi4.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 12.2_Term_Mock

description: Nicholas Bayless_12.2 -_(HTA-2_0)


title: PBMCs, 12.2_Term_H1N1

description: Nicholas Bayless_12.2 +_(HTA-2_0)


title: PBMCs, 11.3_Term_H1N1

description: Nicholas Bayless_11.3 +_(HTA-2_0)


title: TFi4.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 12.1_Preterm_Mock

description: Nicholas Bayless_12.1 -_(HTA-2_0)


title: TFi4.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv