title: wt_m1_aba_3

city: Bothell

first: Thelma

middle: F

last: Madzima

state: WA

address: 18115 Campus Way NE

department: Division of Biological Sciences

institute: University of Washington Bothell

data_processing:
Illumina base-calling
FASTQ adapters were trimmed by Cutadapt 1.8.1 and Quality Control was performed using FASTQC v0.11.2 . Reads were mapped to the B73 maize genome (AGP B73v4 version 40) by HISAT2 v2.04
Transcripts were assembled and quantified using Stringtie v1.3.4d. Gene count matrices were generated from this data using the prepDE.py python script available in the Stringtie website
Genome_build: AGPv B73
Supplementary_files_format_and_content: comma separated values files include gene counts for each Sample

organism: Zea mays

source_name: Seedling

growth_protocol: Maize plants were grown in greenhouse conditions (16 h light period, 25°C, 50% humidity) until V3 stage was reached.

extract_protocol:
Seedling shoots were flash frozen and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit from Illumina (NEB #E7770) was used with 1 µg of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Paired-end 150 bp (PE 150) RNA-sequencing.

treatment_protocol: Maize seedlings at the V3 stage were removed from the soil, roots were rinsed in water, dried and then submerged in a 1 L beaker with 250 mL of liquid Murashige and Skoog (MS) media (Sigma Aldrich, M6899) with 50 μM ABA (ABA; (Sigma Aldrich, (+/-) Abscisic Acid, A1049)) or without ABA (MS)  for 8 hours .

tag: develpmental stage

value: seedling shoots

value: ABA 50 microM

value: 8 h

value: Mop1 homozygous wildtype


title: wt_m1_aba_2

status: Public on Mar 22 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: treatment

tag: time point

tag: genotype


title: RRBS_APCLgr5-HT1

city: Montpellier

first: Philippe

last: Jay

address: 141 rue de la Cardonille

country: France

institute: CNRS-Inserm-University

library_source: genomic

data_processing:
Sequenced reads were trimmed using Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired).
Reads were aligned to the mouse mm10 genome using BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -n 1 -D C-CGG).
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 (parameters -z -u -g).
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8x sequencing depth.

molecule: genomic DNA

organism: Mus musculus

source_name: Lgr5+-GFP+ cells

extract_protocol:
Lgr5-GFP+ cells were FACS-sorted in RLT+ buffer for further gDNA/RNA extraction performed with Allprep mini Kit (Qiagen) at day 15.
RRBS libraries were prepared as previously described (Auclair G. et al, Genome Biol. 15, 545, 2014). Briefly, we digested 100 ng of genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14 cycles of PCR.

treatment_protocol: Mice injected once with tamoxifen followed by 5 consecutive days of tamoxifen-containing diet.

tag: strain

value: intestinal epithelium

tag: cell type

value: Lgr5+-GFP+ intestinal stem cells

value: ApcFlox/+ ; Lgr5-CreERT2-ires-eGFP


title: 3610_WT2_24h

city: Malaga

first: Jesus

last: Camara-Almiron

address: Calle Severo Ochoa, 34

country: Spain

institute: University of Malaga

description: Bacillus subtilis NCIB3610

data_processing:
Raw reads were pre-processed with SeqTrimNext, using the specific NGS technology configuration parameters.
Clean reads were aligned and annotated using the Bacillus subtilis subsp. subtilis str. 168 genome (NC_000964.3) as a reference with Bowtie2.
Uniquely localized reads were used to calculate the read number value for each gene by using Sam2counts.
Differentially expressed genes (DEGs) between WT and ΔtasA were analyzed using DEgenes Hunter that provides a combined P-value from edgeR and DEseq2 that allowed differentially expressed genes ranking.
Genome_build: ASM904v1
Supplementary_files_format_and_content: Tab-delimited text files include the raw counts per gene for each sample.
Supplementary_files_format_and_content: Excel files include Log2FC of the comparison of WT strain and TasA mutant strain, with combined p-values.

molecule: total RNA

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: B. subtilis 3610 WT

extract_protocol:
Single colonies of B. subtilis NCIB 3610 WT and tasA mutant were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on MSgg-agar plates. Cultures were grown for 24 and 48 h at 30°C. After 72 h of growth, colonies were recovered and stored at -80ºC. The collected cells were resuspended and homogenized by passing through a 25 5/8 G needle in BirnBoim A (20% sucrose, 10mM tris-HCl pH 8, 10mM EDTA and 50mM NaCl). Lysozyme (10 mg/ml) was added and incubated 30 min at 37ºC. After disruption, suspensions were centrifuged, and pellets were resuspended in Trizol reagent (Invitrogen). Total RNA extraction was performed as indicated by the manufacturer. Removal of DNA was carried out by in-column treatment with the rDNase included in the Nucleo-Spin RNA Plant (Macherey-Nagel) following instructions from the manufacturer. Integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NCIB 3610

value: WT

tag: medium

value: Biofilm-inducing solid medium (MSgg)


title: Input control in 10μM curaxin treated mouse ESC replicate 2

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description:
E14_10uM_Input_rep2
We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC.
Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

data_processing:
Basecalls performed using CASAVA.
Reads were aligned with bowtie 2.2.4 using default settings.
Genome coverage was calculated with genomeCoverageBed -bg -scale, with scaling factor 10^-6*total aligned reads.
Genome coverage file was converted to bigwig with bedGraphToBigWig (Kent tools).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: BigWig of normalized ChIP read density: reads per base per million.

source_name: E14 mouse ESC

growth_protocol: E14Tg2a (E14) male mouse ESC were maintained as previously described (Buecker et al., 2014) on 7.5μg/ml poly-l-ornithine (Sigma) and 5μg/ml laminine (Life Technologies) coated tissue culture dishes, in a serum-free N2B27-based DMEM/F12 medium supplemented with 5mg/ml BSA Albumax II, sodium pyruvate, L-glutamine, N2 Neuroplex, B27 without retinoic acid, non-essential amino acids, Beta-mercaptoethanol, penicillin/streptomycin, 0.8μM MEK inhibitor (PD0325901, Selleck Chemicals) and 3.3μM GSK3β inhibitor (CHIR99021, Selleck Chemicals).

extract_protocol:
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. After reverse-crosslinking, input and ChIP DNA were purified by phenol:chloroform extraction.
Sequencing libraries were prepared starting from ~30ng of input or ChIP DNA with NEBNext Multiplex Oligos for Illumina kit.

treatment_protocol: Cells were treated with DMSO or curaxin (CBL0137, Cayman Chemical) for 1 hour and immediately crosslinked in 1% formaldehyde for 10 minutes followed by quenching with 0.125M glycine for 5 minutes. Cells were lysed and sonicated with a bioruptor sonicator (Diagenode).

tag: cell line

value: Embryonic stem cells (ESC)

value: 10uM Curaxin

tag: chip antibody


title: tasA1_24h

description: Bacillus subtilis NCIB3610

source_name: B. subtilis tasA mutant

value: Single tasA mutant


title: wt_m1_aba_1


title: tasA2_72h

extract_protocol:
Single colonies of B. subtilis NCIB 3610 WT and tasA mutant were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on MSgg-agar plates. Cultures were grown for 72h at 30°C. After 72 h of growth, colonies were recovered and stored at -80ºC. The collected cells were resuspended and homogenized by passing through a 25 5/8 G needle in BirnBoim A (20% sucrose, 10mM tris-HCl pH 8, 10mM EDTA and 50mM NaCl). Lysozyme (10 mg/ml) was added and incubated 30 min at 37ºC. After disruption, suspensions were centrifuged, and pellets were resuspended in Trizol reagent (Invitrogen). Total RNA extraction was performed as indicated by the manufacturer. Removal of DNA was carried out by in-column treatment with the rDNAse included in the Nucleo-Spin RNA Plant (Macherey-Nagel) following instructions from the manufacturer. Integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RRBS_APCLgr5-HT3


title: 3610_WT1_24h

description: Bacillus subtilis NCIB3610


title: CC141_eCCA

type: RNA

city: Barcelona

first: Robert

last: Montal

address: Rosselló 153

institute: IDIBAPS

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with GenePattern (Broad Institute) using Expression file creator module and the RMA algorithm.

label: Biotin

organism: Homo sapiens

source_name: extrahepatic cholangiocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Samples collected after surgical resection and FFPE

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Not applicable. Archived tissue was obtained at our Insitution upon patient's consent

value: extrahepatic cholangiocarcinoma

tag: center

value: JH


title: RRBS_APCLgr5-WT3

value: Apc+/+ ; Lgr5-CreERT2-ires-eGFP


title: CC137_eCCA


title: CC133_eCCA


title: wt_m1_ms_1

value: MS


title: CC135_eCCA


title: wt_m1_ms_2

value: seedling shoots


title: tasA1_72h


title: CC139_eCCA


title: mut_m1_aba_3

value: ABA 50 microM

value: mop1-1 homozygous mutant


title: RRBS_APCLgr5-WT2


title: 3610_WT2_72h


title: RRBS_APCLgr5-WT1


title: 3610_WT1_72h


title: mut_m1_aba_2

value: 8 h


title: CC129_eCCA


title: RRBS_APCLgr5-WT4

value: intestinal epithelium


title: mut_m1_aba_1


title: UNC0642 recovery rep 4

city: Madison

first: Spencer

last: Haws

state: WI

address: 330 N. Orchard St.

institute: University of Wisconsin-Madison

data_processing:
Sequenced reads were trimmed for adaptor sequence then mapped to hg18 transcriptome using RSEM v1.2.4  with argumemts  -bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 -p 15
Genome_build: hg18
Supplementary_files_format_and_content: rsem.genes.results.txt output files containing gene_id, transcript_id, effective_length, expected_count, TPM, and FPKM data.

source_name: HCT116 cells

growth_protocol: HCT116 cells grown in RPMI-1640 (Gibco) +10% FBS (Gibco).

extract_protocol:
Total RNA was extracted with Trizol.
Library construction was performed by Novogene.

treatment_protocol: Cells were washed 2x with PBS pH 7.4 and cultured in methionine free RPMI-1640 (Gibco) + 10% FBS (Gibco) for 24 hours +/- UNC0642, washed 2x with PBS, and cultured for another 24 hours in methionine replete RPMI-1640 (Gibco) + 10% FBS (Gibco) without inhibitior.

value: HCT116 cells

value: colorectal carcinoma

value: 24 hours of metabolic recovery from methionine restriction + UNC0642


title: mut_m1_ms_3


title: UNC0642 recovery rep 3


title: UNC0642 recovery rep 1


title: UNC0642 recovery rep 2


title: DMSO recovery rep 4

value: 24 hours of metabolic recovery from methionine restriction + DMSO


title: mut_m1_ms_1


title: DMSO recovery rep 3


title: DMSO recovery rep 2


title: CC131_eCCA


title: SK-Mel5 shP300 1

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from SK-Mel5 cells treated with shp300.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

label: biotin

source_name: SK-Mel5 melanoma cell line

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Melanoma cells were maintained in Dulbecco’s modified Eagle medium. The medium was supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (pen-strep), and 1% L-glutamine. The media, pen-strep, and L-glutamine, FBS were purchased from Invitrogen. All cell lines were grown at 37°C in an atmosphere containing 5% CO2.

extract_protocol: RNA from melanoma cells transduced with either shp300 or scrambled lentiviruses was purified using the Qiagen RNAeasy Plus Kit.

treatment_protocol: 250,000 human melanoma cells were transduced with each harvested lentivirus (500μL) in the presence of 8 μg/mL of polybrene. Subsequently, melanoma cells transduced with pLKO1-based shRNAs were selected in 1.5 μg/mL of puromycin after 48 hour following transduction in their respective culture medium.

value: SK-Mel5 melanoma cell line

tag: shRNA


title: SK-Mel5 shP300 2


title: WM983B scrambled 2

description: Gene expression data from WM983B cells treated with scrambled control shRNA.

source_name: WM983B melanoma cell line

value: WM983B melanoma cell line

value: scrambled control shRNA


title: mut_m1_ms_2


title: seqcap_B73_ABA

data_processing:
Illumina base-calling
FASTQ adapters were trimmed by Cutadapt 1.8.1 and Quality Control was performed using FASTQC v0.11.2 . Reads were mapped to the B73 maize genome (AGP B73v4 version 40) by HISAT2 v2.04
Transcripts were assembled and quantified using Stringtie v1.3.4d. Gene count matrices were generated from this data using the prepDE.py python script available in the Stringtie website
For methylation data, adapters were trimmed using Trim Galore!. Reads were mapped to maize B73 reference genome AGPv4 using BSMAP-2.90(Xi and Li 2009), allowing 5 mismatches or less in a read  and  quality  threshold  20  in  trimming  3'  end  of  reads  (-v  5 -q  20).  Only  uniquely mapped reads were kept for subsequent analysis. PCR duplicates were removed using picard-tools-1.102 ‘MarkDuplicates’,  and bamtoolswas  used  to  remove  any  improperly paired  reads.  Overlapping  reads  were  then  clipped  using  ‘bam  clipOverlap’  command from bamUtils.
Genome_build: AGPv4 B73
Supplementary_files_format_and_content: comma separated values files include gene counts and methylation ratios for each Sample

growth_protocol: Maize plants were grown in greenhouse conditions (16 h light period, 25°C, 50% humidity) for 10 days or until V3 stage was reached.

extract_protocol:
Seedling shoots were flash frozen. RNA was harvested using Trizol reagent, NEBNext Ultra RNA Library Prep Kit from Illumina (NEB #E7770) was used with 1 µg of RNA for the construction of sequencing libraries. Genomic DNA was extracted using standard CTAB protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. SeqCap libraries were constructed as described previously (Li et al. 2015a). Briefly, DNA was isolated using the standard CTAB method. Five hundred to 1,000 nanograms of genomic DNA was used for sequence capture library construction. DNA was sheared to fragments between 180 and 250 bp. The fragments were subject to end repair, dA tailing, ligating to index adapters, and Dual-SPRI Size Selection, followed by bisulfite conversion. The bisulfite converted libraries were then subject to Pre-Capture LM-PCR amplification, purification and quantified using a PicoGreen™ dsDNA Assay Kit. Then the amplified sample library was hybridized to probes designed to target the set of genomic regions selected for analysis. After hybridization, the captured DNA library was bounded to capture beads and the bead-bound DNA was washed. Post-Capture LM-PCR amplification was performed, and following PCR cleanup the libraries were quantitated using PicoGreen. Libraries were pooled together in several batches and the pools sequenced over multiple lanes at the University of Minnesota Genomics Center on a HiSeq2500, in High-output 2x125 bp paired end (PE) mode.
Paired-end 150 bp (PE 150) for RNA-seq and 125 bp (PE 125) for Bisulfite-seq.

treatment_protocol: 10-day old maize seedlings or seedlings at the V3 stage were removed from the soil, roots were rinsed in water, dried and then submerged in a 1 L beaker with 250 mL of liquid Murashige and Skoog (MS) media (Sigma Aldrich, M6899) with 50 μM ABA (ABA; (Sigma Aldrich, (+/-) Abscisic Acid, A1049)) or without ABA (MS)  for 7 or 8 hours .

tag: develpmental stage and tissue

value: 10-day old seedling shoots

value: Treated with ABA 50 µM for 7 h

value: Mop1 homozygous wildtype


title: SK-Mel5 scrambled 2

description: Gene expression data from SK-Mel5 cells treated with scrambled control shRNA.


title: iL4

description: Gene expression data from iPSCs with low mitochondrial membrane potential.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: Induced pluripotent stem cells

growth_protocol: Female mouse embryonic stem cells (mESCs) and mouse induced pluripotent stem cells (iPSCs) were cultured in serum-free, feeder-free media conditions in 2iLIF media on gelatin coated tissue culture treated plastic in humidified 37ºC, 5% CO2 incubators and passaged by dissociating with Accutase cell dissociation reagent.

extract_protocol: RNA was extracted from sorted cells by ReliaPrep RNA Miniprep Kit (Promega) following the manufacturer's recommendations.

treatment_protocol: Undifferentiated mESCs and iPSCs were stained with mitochondrial membrane potential dye tetramethylrhodamine methyl ester (TMRM) and sorted by fluorescence activated cell sorting into populations of low- or high-membrane potential.

tag: strain/background

value: iPSC

tag: gender

value: Female

tag: mitochondrial membrane potential

value: Low


title: iH3

description: Gene expression data from iPSCs with high mitochondrial membrane potential.

value: High


title: DMSO recovery rep 1


title: iH4


title: WM983B shP300 2

description: Gene expression data from WM983B cells treated with shp300.


title: iL3


title: iH2


title: WM983B shp300 1


title: NFKBIA_IEC_KO_biol_rep_4

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Center

hyb_protocol: 73 µl hybridization cocktail was added to 2.5 µg fragmented and labled ss-cDNA and 80 µl of this cocktail was applied to the Mouse Clariom S arrays (Affymetrix) and hybridized for 16 hours at 45°C in a Genechip Hybridization Oven 640 (Affymetrix). After hybridization the arrays were washed and stained with a Genechip Fluidics Station 450 (Affymetrix) using the genechip hybridization wash and stain kit according to protocol FS450_0007.

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000 7G.

data_processing: Affymetrix CEL files were normalized using RMA. Data analysis was performed with the Transcriptome Analysis Console 4.0 (ThermoFisher Scientific).

label_protocol: 250 ng RNA was amplified, fragmented and biotin-labelled using the GeneChipTM WT PLUS Reagent kit (ThermoFisher Scientific) according to the manufacturer’s instructions.

growth_protocol: All mouse protocols in this study followed the regulatory standards of the governmental review board (Landesamt Berlin, LaGeSo, Reg. G007/08, G 0082/13, G0358/13 and X9013/11). Mice were fed standard pellets and health was monitored according to LaGeSo regulations. Mice were sacrificed according to humane protocol and the small intestine was removed and washed with ice cold PBS and then snap frozen in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The mice were not treated

tag: genotype/variation

value: depletion of IκBα

value: female

tag: age

value: 9 weeks

value: small intestine

tag: rin


title: SK-Mel5 scrambled 1


title: 0hr rep 4

value: HCT116 cells

value: colorectal carcinoma

tag: treatment

value: 0 hours


title: iL2


title: seqcap_B73_ms

value: Treated with MS for 7 h


title: EH3

description: Gene expression data from ESCs with high mitochondrial membrane potential.

source_name: Embryonic stem cells

value: ESC


title: NFKBIA_IEC_WT_biol_rep_4

value: WT

value: male

tag: tissue


title: NFKBIA_IEC_WT_biol_rep_3

value: 8 weeks


title: WM983B scrambled 1

value: WM983B melanoma cell line

value: scrambled control shRNA


title: seqcap_wt_ms

value: 10-day old seedling shoots

tag: genotype

value: Mop1 homozygous wildtype


title: EH2

value: Female

value: High


title: NFKBIA_IEC_KO_biol_rep_3

value: depletion of IκBα


title: EH4


title: NFKBIA_IEC_WT_biol_rep_2

value: female

value: 11 weeks


title: EL4

description: Gene expression data from ESCs with low mitochondrial membrane potential.

value: Low


title: 0hr rep 2

value: HCT116 cells

value: colorectal carcinoma


title: seqcap_mut_aba

value: Treated with ABA 50 µM for 7 h

value: mop1-1 homozygous mutant


title: 0hr rep 3

value: 0 hours


title: seqcap_wt_aba


title: 0hr rep 1


title: seqcap_mut_ms

value: Treated with MS for 7 h


title: DNA_vector v4

status: Public on Mar 21 2020

city: London

first: James

middle: C

last: Lee

address: The Francis Crick Institute, 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
v4_GATCAG

data_processing:
Quality control was performed using FastQC (v0.11.8)
Barcode counts were generated using a Python script - to be counted a sequenced barcode had to be a perfect match for an oligonucleotide library barcode and be followed by at least 10 bases of the expected constant sequence (XbaI restriction site and GFP).
To be deemed a successful transfection, at least 70% of the oligonucleotide library had to be represented in the resulting count file (i.e. count >1).
Raw count data was then normalized to correct for sequencing depth (counts per million mapped reads, cpm - using cpm function in edgeR package in R version 3.5.1) and then filtered to remove barcodes with a median cpm < 0.5 in either the mRNA or DNA samples (equivalent to a barcode count between 20-25).
Barcode counts for identical constructs were then collapsed (summed) and quantile normalized (normalize.quantiles function in preprocessCore package in R version 3.5.1)
Genome_build: hg19
Supplementary_files_format_and_content: barcode_counts.txt is a tab-delimited text file containing the raw barcode count data for every sample; normalised_collapsed_constructs.txt is a tab delimited text file containing the normalized, filtered, quantile-normalized and collapsed count data for every unique genomic construct tested in the MPRA

molecule: other

organism: synthetic construct

extract_protocol:
Lysates were DNA depleted using a gDNA eliminator column (Qiagen) and RNA was extracted using a RNeasy Plus micro kit according to the manufacturer’s instructions (Qiagen).
For library preparation, 1μg RNA was treated with TURBO DNAse (ThermoFisher) and reverse transcribed (SuperScript IV VILO, ThermoFisher) according to the manufacturer’s instructions. DNA removal was confirmed by qPCR for GFP and compared to a no-RT control (all performed in triplicate). Sequencing libraries were prepared by PCR amplification (30 cycles, annealing temperature 55C) using PfuUltra II Fusion DNA polymerase (Agilent) and custom primers that were designed to anneal to a 3’ site within the EGFP gene (F) and the 3’ universal primer site within the oligonucleotide sequences (R). These primers contained sequencing indices to enable multiplexing. Amplified libraries were cleaned using sequential SPRI bead clean-up (0.6X, 1.6X, 1.0X; Agencourt AMPure XP, Beckman Coulter). 4 sequencing libraries were made from the MPRA vector using 50ng input and 18 cycles of PCR (other conditions were the same as for the RNA libraries).

tag: sample type


title: DNA_vector v2

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
v2_GCCAAT


title: DNA_vector v3

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
v3_ACTTGA


title: DNA_vector v1

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
v1_TTAGGC


title: MH001

city: New York

first: Muredach

last: Reilly

address: 630 West 168th Street

department: Department of Medicine

institute: Columbia University Medical Center

data_processing:
Gene-barcode matrices were determined using 10X Genomics Cellranger v2.0.
eliminated cells with percentage of mitochondrial UMI counts >25% or gene counts <200 or total UMI counts <1000
Genome_build: GRCh38

source_name: Blood

extract_protocol:
Monocyte preparation uses a modification of published protocols. Briefly, ~20 ml blood drawn in sodium heparin was processed immediately in the lab in the Clinical Research Center at Columbia University. PBMCs were isolated by gradient Ficoll paque centrifugation, which maintains cell viability and prevents ex vivo activation during cell recovery. Cells were stained with antibodies against human HLADR, CD14 and CD16 and monocyte subsets defined as HLADR+CD14++CD16-(classical), HLADR+CD14++CD16+ (intermediate), HLADR+CD14dim/CD16++ (nonclassical, patrolling monocyte). DAPI staining was used to exclude dead cells. Monocytes were sorted by a BD Influx Sorter into tubes for real-time 10x Genomics analysis.
Samples were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s instructions.12 cycles for cDNA amplification and 12 cycles for sample index PCR were used.

value: PBMC

tag: status

value: Healthy

tag: cell type

value: Monocytes


title: MCF10A replicate 1

first: Manuela

last: Benary

address: Chariteplatz 1

institute: Charité

data_processing:
Read mapping and counting was done using cellranger version 3.0.2 using a dual genome reference consisting of the human genome GRCh38 as supplied by cell ranger, and an artificial genome containing the BD sequence tags
Demultiplexing was done using a custom script that reads  the  BAM file and  counts sequences that map to the artificial BD  sequence tags genome, and removes duplicate UMIs per cell. Subsequently, cells were  assigned to samples (or duplets) using the HTODemux() function of Seurat after normalisation (as described in the Seurat manual).
Transcriptome Initial analysis of the single cell RNA sequencing samples was done using Seurat. In brief, low quality cells were removed based on mitochondrial contamination and number of unique genes. Cell cycle status was defined using a list of cell cycle markers, from Tirosh et al, 2016  as provided by Seurat.
Demultiplexing was done using a custom script that reads  the  BAM file and  counts sequences that map to the artificial BD  sequence tags genome, and removes duplicate UMIs per cell. Subsequently, cells were  assigned to samples (or duplets) using the HTODemux() function of Seurat after normalisation (as described in the Seurat manual).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Epithelial breast

growth_protocol: 6-cm plates were used with 4.3× 105 cells per plate and treated

extract_protocol:
Each sample was resuspended in 50 µl BD Stain Buffer (FBS) and labelled with a specific Sample Tag (10 µl) for 20 min at room temperature. After adding 100 µl BD Stain Buffer, cells were mixed, centrifuged and washed with 500 µl BD Stain Buffer. Using 500 µl RNAse free PBS, all cells were pooled in a single tube and counted to ensure a sufficient cell number. After centrifugation and resuspension in RNAse free PBS, pre-chilled methanol was added dropwise to the sample while mildly vortexing. Cells were kept on ice for 15 min, mixed, divided into 1 ml aliquots and stored at -80°C.
BD Single-Cell Multiplexing Kit - Human”-protocol (Reagent Kit v2, Doc ID: 179682 Rev. 1.0)

tag: cell line

value: human breast epithelial cell line

value: stimulated with EGF and inhibited MEK and PI3K activity 15 h later


title: MCF10A replicate 2


title: RP002


title: embryos supplemented with fresh oEVs replicate 1

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

data_processing:
Trim Galore! Galaxy version 0.4.3.1, adapter trimming, trim low quality bases (phred quality score threshold 30), remove 5 bp from 5' end, discard reads that became shorter than 50 bp
HISAT2 2.1.0+galaxy4, mapping to bovine genome assembly bosTau9_ARS-UCD1.2, strand information Forward (F)
NUDUP nudup.py 2.3.2, removal of PCR duplicates
featureCounts v1.6.3 +galaxy2, generation of read count table for all annotated bovine genes based on the NCBI GFF3 annotation file
Counts per million (CPM) per sample filtering tool (Chen et al. 2014), remove sequences with negligible read counts, CPM cutoff: 4.72 (corresponding to an average of 20 reads per library) for at least 5 out of 15 libraries
Genome_build: bosTau9_ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files, 'Read count table Embryo exo 2019_unfiltered.txt' contains mapped read counts, 'Read count table Embryo exo 2019_filtered.txt' contains mapped read counts of the genes that passed the CPM filter

organism: Bos taurus

source_name: bovine embryo IVF day 7

growth_protocol: In vitro produced bovine embryos were cultured in the presence or absence of oviductal EVs for 7 days as previously described (PMID 28630101)

extract_protocol:
Total RNA from these 21 embryo pool samples was isolated using the RNeasy Micro kit (QIAGEN) according to the manufacturer's instructions. RNA quality and concentration were analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA.), NanoDrop (ThermoFisher) and Quantus Quantiflour® RNA system (Promega).
Samples with best RNA quality and concentration were selected for generation of RNA-Seq libraries (15 libraries, 5 replicates/embryo treatment). For library preparation, the Ovation SOLO RNA-Seq System Kit from NUGEN Technologies was used. Library preparation followed the manufacturer's instructions. In brief, aliquots of 1 ng of total RNA were prepared for each embryo sample as starting material for RNA-Seq library preparation. First, samples were subjected to DNase treatment and primer annealing, followed by cDNA processing and second strand synthesis. After end repair, adapters were ligated and the first step of library amplification was performed using a number of PCR cycles based on the results of the library amplification optimization step by qPCR. To remove fragments derived from ribosomal RNAs, NuGEN’s insert-dependent adaptor cleavage (InDA-C) technology was performed in the next step. At the same time, strand selection is performed. After this step, the second library amplification and purification were performed for each sample using a universal primer and a set of barcode primers for sample multiplexing. Once RNA-seq libraries were prepared, quantitative and qualitative analyses were performed for each of the libraries using Agilent Bioanalyzer 2100 DNA High Sensitivity assays and Quantus Quantiflour® ONE dsDNA system (Promega).
low-input total RNA-Seq

treatment_protocol: Pools of 8-14 embryos were cultured under 3 different treatments during in vitro embryo culture (IVC): 1) embryo samples supplemented with fresh oEVs (7 replicates, a total of 74 embryos in 7 embryo pools); 2) embryo samples supplemented with frozen oEVs (8 replicates, a total of 81 embryos in 8 embryo pools); and 3) embryo samples without supplementation (control) (6 replicates, a total of 68 embryos in 6 embryo pools).

tag: embryo stage

value: blastocyst day 7

value: supplementation with freshly isolated postovulatory oviductal EVs


title: embryos supplemented with fresh oEVs replicate 5


title: embryos supplemented with fresh oEVs replicate 3


title: embryos supplemented with fresh oEVs replicate 2


title: control embryos replicate 2

value: no supplementation control


title: NFKBIA_IEC_KO_biol_rep_2

value: depletion of IκBα

value: female

value: small intestine


title: embryos supplemented with frozen oEVs replicate 3

value: supplementation with frozen-thawed postovulatory oviductal EVs


title: control embryos replicate 1


title: embryos supplemented with frozen oEVs replicate 5


title: embryos supplemented with frozen oEVs replicate 1


title: EL2

value: ESC

value: Female

value: Low


title: control embryos replicate 3


title: embryos supplemented with fresh oEVs replicate 4


title: control embryos replicate 4


title: embryos supplemented with frozen oEVs replicate 2


title: d4WT RNA-seq

first: Pietro

last: Fratta

address: Queen Square House

institute: University College London

data_processing:
Alignment with STAR (v2.4.2) to mouse mm10 genome
Assigning reads to genes with subread (v1.6.4) FeatureCounts. Command used: featureCounts -p -t exon -g gene_id -a gencode.vM22.annotation.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab separated table containing read counts for each sample for each gene.

source_name: Embryonic (E17.5) spinal cord

growth_protocol: Spinal cords were collected from E17.5 mouse embryos.

extract_protocol:
Tissues were snap frozen, genotyped and total RNA was extracted from the appropriate samples using Qiazol followed by the mini RNAeasy kit (Qiagen). RNA samples used for sequencing all had RIN values of 9.9 or 10.
cDNA libraries were made at the Oxford Genomics facility using a TruSeq stranded total RNA RiboZero protocol (Illumina). Libraries were sequenced on an Illumina HiSeq to generate paired end 150bp reads.

tag: strain

tag: embryonic day

tag: developmental stage

value: embryo

value: spinal cord

value: FUS delta 14 wildtype


title: d4HET RNA-seq

value: FUS delta14 heterozygous


title: d4HOM RNA-seq

value: FUS delta14 homozygous


title: NFKBIA_IEC_WT_biol_rep_1

value: WT

value: male

value: 8 weeks


title: NFKBIA_IEC_KO_biol_rep_1


title: EL3

tag: strain/background


title: d3HOM RNA-seq


title: d3WT RNA-seq


title: d3HET RNA-seq


title: control embryos replicate 5

value: blastocyst day 7


title: d2WT RNA-seq


title: embryos supplemented with frozen oEVs replicate 4


title: d2HOM RNA-seq


title: d2HET RNA-seq


title: scRNAseq_APOE2

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

institute: Charité University Medicine

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger pipeline with default settings (v3.0.1) and aligning to the mm10 genome build.
Data from the two samples were integrated using Seurat v3.0.2.
Further processing was done with Seurate v3.0.2 (cell and gene filtering, clustering, differential gene expression analysis).
Genome_build: mm10
Supplementary_files_format_and_content: Output of the Cell Ranger pipeline representing tsv and mtx files containing count matrices.

source_name: CD45+ leukocytes extracted from YUMM1.7 melanomas hosted by APOE2 mice

growth_protocol: Human APOE knock-in mice (n = 6 per group) were subcutaneously injected with 1 × 10^5 YUMM1.7 cells on the flank (mixed 1:1 with growth factor reduced Matrigel).

extract_protocol:
Tumors were resected on day 19 after injection and tumor-infiltrating leukocytes were isolated with mechanic and enzymatic dissocation and gradient density centrifugation. 10,000 CD45+/DAPI- leukocytes from each mouse were independently sorted on a BD FACSAria II cell sorter and samples from the same genotype were pooled for library preparation (i.e., total of 60,000 cells per genotype).
Five-thousand cells per genotype were targeted for single-cell RNA-sequencing on a Chromium Single Cell System (10x Genomics). Samples were processed as per the manufacturer’s instructions (Chromium single cell 3’ reagents, v3 chemistry) and libraries were sequenced on an Illumina NextSeq sequencer.

value: human APOE2 knock-in

value: CD45+ melanoma-infiltrating leukocytes


title: P010_plus_1 Sample 96

city: Leiden

first: Agnieszka

last: Wegrzyn

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description:
P010_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

data_processing:
The trimmed fastQ files were aligned to build human_g1k_v37 Ensemble [51] release 75 reference genome using hisat/0.1.5-beta-goolf-1.7.20 [52] with default settings.
Before gene quantification SAMtools/1.2-goolf-1.7.20 [53] was used to sort the aligned reads.
The gene-level quantification was performed by HTSeq-count: HTSeq/0.6.1p1 [54] using --mode=union, with Ensembl release 75 [51] was used as a gene annotation database.
Quality control (QC) metrics are calculated for the raw sequencing data. This is done using the tool FastQC (FastQC/0.11.3-Java-1.7.0_80) [55]. QC metrics are calculated for the aligned reads using Picard-tools (picard/1.130-Java-1.7.0_80) [56] CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize- Metrics and SAMtools/1.2-goolf-1.7.20 flagstat.
Genome_build: Ensembl release 75
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene per sample

source_name: Fibroblasts

growth_protocol: Fibroblasts were cultured in 75-cm2 flasks. Cells were cultured in Ham’s F-10 medium with L-glutamine, supplemented with 10% foetal calf serum (Invitrogen, Carlsbad, CA, USA), 25 mM Hepes, 100 U/mL penicillin and 100 μg/mL streptomycin and 250 μg/mL amphotericin in a humidified atmosphere of 5% CO2 at 37C. Cells were seeded on the same day and incubated for 96h.

extract_protocol:
Cells were harvested by trypsinisation (0.5% trypsin-EDTA, Invitrogen) and washed once with phosphate-buffered saline and twice with 0.9% NaCl, followed by centrifugation at  4C (16100 × g for 5 min) to obtain cell pellets. Total RNA was isolated from the cell pellets from the T75 cultures using TRIzolTM Reagent (ThermoFisher Scientific) using supplier protocol for RNA extraction. RNA pellets were dissolved in 50uL of RNase free water, and RNA concentrations were measured using NanoDropTM 2000 Spectrophotometer (ThermoFisher Scientific).
Sequence libraries were generated using the Nextflex Rapid Illumina Directional RNA-Seq Library Prep Kit (Bioo Scientific) using the Sciclone NGS Liquid Handler (Perkin Elmer).

treatment_protocol: Cells were incubated with phytol, dissolved in ethanol, or ethanol as the vehicle.

value: skin

value: PHYH-/-

tag: allel 1 mutation

tag: Sex

value: F

tag: perturbation

value: 25uM phytol


title: RP009

value: PBMC

value: Healthy

value: Monocytes


title: scRNAseq_APOE4

source_name: CD45+ leukocytes extracted from YUMM1.7 melanomas hosted by APOE4 mice

value: human APOE4 knock-in


title: d1WT RNA-seq

value: embryo

value: spinal cord

tag: genotype/variation

value: FUS delta 14 wildtype


title: P002_plus_1 Sample 91

description:
P002_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: M


title: P005_plus_1 Sample 93

description:
P005_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P007_plus_1 Sample 95

description:
P007_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P003_plus_1 Sample 92

description:
P003_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: d1HOM RNA-seq

value: FUS delta14 homozygous


title: d1HET RNA-seq

value: FUS delta14 heterozygous


title: C130_plus_1 Sample 90

description:
C130_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: healthy


title: k4HET RNA-seq

value: FUS knockout heterozygous


title: k4KO RNA-seq

value: FUS knockout homozygous


title: k4WT RNA-seq

value: FUS knockout wildtype


title: C126_plus_1 Sample 89

description:
C126_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: C109_plus_1 Sample 87

description:
C109_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: F


title: k3WT RNA-seq


title: k2WT RNA-seq


title: k3HET RNA-seq


title: k3KO RNA-seq


title: C105_plus_1 Sample 86

description:
C105_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: 25uM phytol


title: C114_plus_1 Sample 88

description:
C114_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C102_plus_1 Sample 85

description:
C102_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: k2HET RNA-seq


title: P010_minus_1 Sample 84

description:
P010_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-


title: P006_plus_1 Sample 94

description:
P006_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: k1WT RNA-seq


title: P007_minus_1 Sample 83

description:
P007_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P002_minus_1 Sample 79

description:
P002_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: k1KO RNA-seq


title: P003_minus_1 Sample 80

description:
P003_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P006_minus_1 Sample 82

description:
P006_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C126_minus_1 Sample 77

description:
C126_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C130_minus_1 Sample 78

description:
C130_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: k2KO RNA-seq


title: P005_minus_1 Sample 81

description:
P005_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t45 tac 6

city: East Lansing

first: Courtney

last: Hollender

state: MI

address: 1066 Bogue St

department: Dept. of Horticulture

institute: Michigan State University

description: RNA from ~ 1cm shoot tip from primary inflorescence shoot with open flowers removed as well as floral buds showing petal

data_processing:
barcodes removed by sequencing facility
Raw sequencing data was uploaded to CLC Genomics Workbench Version 9.5.3 (Qiagen, Redwood City, CA) and trimmed based on a QC limit of 0.05, an ambiguity max of 2 nucleotides, and a minimum length of 40 nucleotides.
Using the CLC RNAseq analysis tool trimmed reads were aligned to the arabidopsis genome (TAIR10) with the following parameters: 2 maximum mismatches, a minimum length fraction of 0.9, a minimum similarity fraction of 0.8, a nonspecific match limit of 10, a minimum exon coverage fraction of 0.2, and 10 minimum reads. Expression values were reported as RPKM.
Next, the RNAseq Experiment function was used to perform differential expression analysis. Five separate experimental comparisons were performed. A multiple comparison of all three types of t0 plants (Col, tac1, and lazy1) with three biological replicates for each. A multiple comparison of the t45 samples for all three plants, which included 4 biological replicates of Col and lazy1 and 5 biological replicates for tac1. Individual analyses, comparing t0 to t45 samples of the same genome were also performed. All five experimental analyses were normalized by quantiles and then a proportion-based statistical analysis with Baggerley’s test as performed. Bonferroni corrected p-values and FDR-corrected p-values were also determined.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Excel document with multiple tabs containing gene mapping information, fold change,  statistics, and differentially expressed genes for all RNAseq samples and transcriptome comparisons.

organism: Arabidopsis thaliana

source_name: Arabidopsis primary shoot tip

growth_protocol: All plants were grown in either 2--inch pots with one plant per pot and 16-hour light (~100 µmol m-2 s-1) in growth chambers set to ~22°C.

extract_protocol:
Total RNA was extracted from apical tissues using the Qiagen Plant Mini RNeasy kit (Germantown, MD) including a DNAse treatment with Invitrogen Turbo DNA-free (Carlsbad, CA).
TruSeq 50 bp unpaired barcoded libraries

treatment_protocol: Arabidopsis plants containing only a single inflorescence shoot, with a height of ~15-18 cm, and no more than 3 lateral shoots (each no larger than ~1 cm) were used for expression profiling. Prior to collection, plants were left for at least 12 hours in a dark chamber with wooden stakes to support primary shoots to ensure they would be vertical at the time of collection. Primary shoot tips from upright (t0) plants and plants after 45 minutes of gravistimulation in the dark by a 90° reorientation (t45 plants) were collected on the same day. The t0 collections were at ~10 AM and t45 collections were at ~10:45 AM (having been reoriented at ~10 AM). From all plants, the upper most ~1 cm of primary shoot apical tissue (minus any leaves, flowers, or opening buds) was harvested and immediately frozen in liquid nitrogen

value: tac1 mutant

tag: ecotype

value: Columbia

tag: condition

value: 45 minutes after 90 degree gravistimulation


title: t45 tac 5


title: t45 tac 13


title: C109_minus_1 Sample 75

description:
C109_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

tag: tissue


title: t45 lazy 4

tag: genotype

value: lazy1 mutant


title: t45 tac 14


title: t45 col 6

value: wild type


title: t45 lazy 13


title: C102_minus_1 Sample 73

description:
C102_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t45 lazy 5


title: t45 col 5


title: P007_plus_3 Sample 71

description:
P007_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P006_plus_3 Sample 70

description:
P006_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t45 col 1B


title: k1HET RNA-seq

value: embryo

value: spinal cord


title: P005_plus_3 Sample 69

description:
P005_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: M


title: t45 lazy 6


title: t0 tac 3B

value: normal (not gravistimulated)


title: P003_plus_3 Sample 68

description:
P003_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t0 tac C


title: t45 col 13


title: C130_plus_3 Sample 66

description:
C130_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: healthy


title: t0 tac B


title: C105_minus_1 Sample 74

description:
C105_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P010_plus_3 Sample 72

description:
P010_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t0 lazy 6B


title: C109_plus_3 Sample 63

description:
C109_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C114_plus_3 Sample 64

description:
C114_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C126_plus_3 Sample 65

description:
C126_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C105_plus_3 Sample 62

description:
C105_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P010_minus_3 Sample 60

description:
P010_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C102_plus_3 Sample 61

description:
C102_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t0 lazy A


title: t0 Col A


title: P007_minus_3 Sample 59

description:
P007_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t0 Col C

description: RNA from ~ 1cm shoot tip from primary inflorescence shoot with open flowers removed as well as floral buds showing petal


title: t0 Col B


title: KW07_Vehicle

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Reads aligning to human ribosoma RNA transcripts were removed with BBSplit
Remaining reads were pseudoaligned against human transcriptome using Salmon v1.1.0
Quantified transcripts were combined into gene level counts with tximport_1.12.3
Differential expression analysis was performed with DESeq2_1.24.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quant files containing transcript level counts for each sample

source_name: iPSC

growth_protocol: iPSC derived OPCs were sorted on PDGFRa+ and then replated, allowed to proliferate prior to being treated

extract_protocol:
Media was aspirated, cells were washed, then cells were lysed and RNA purified using QIAGEN RNeasy Protocol with gDNA removal column
libraries were generated with Illumina TruSeq Stranded Total RNA LT Sample Prep

treatment_protocol: Cells were treated overnight with either vehicle or human IFNg (10ng/ml)

tag: participant

value: MS

value: iPSC derived OPCs

tag: treatment

value: Vehicle

tag: batch


title: P005_minus_3 Sample 57

description:
P005_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: P003_minus_3 Sample 56

description:
P003_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_RiskAlleleHom3_rep2

description:
InputDNA_RiskAlleleHom3.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed

data_processing:
Sequencing reads were trimmed to remove low quality base calls and residual adaptors at the 3’ end using TrimGalore! (v0.6.1, Phred score 24) and filtered to remove reads shorter than 36bp.
Trimmed reads were then aligned to the reference human genome (hg19) using Burrows-Wheeler Aligner (v0.7.12) with default parameters.
Aligned reads were converted to BAM files, sorted, and technical duplicates merged before indexing – all using SAMtools (v1.4)
PCR duplicates were identified using Picard tools (v2.18.1) and removed together with unmapped reads using SAMtools (v1.4). The resulting BAM files were re-sorted and indexed after filtering.
For visualisation in Integrated Genome Viewer, bigWig files were generated using bamCoverage (deepTools2, v3.1.3) with the following parameters: --binSize 5 --normalizeUsing CPM --effectiveGenomeSize 2685511504 --extendReads 200.)
Biological replicates and inputs for each genotype were then merged using SAMtools (v1.4) and peaks were identified in H3K27ac and input libraries using MACS2 (v2.1.2) after downsampling the input files to have the same number of reads as the H3K27ac samples. The following parameters were used: -g hs -f AUTO --qvalue 0.01 -B --nomodel --extsize=200.
MACS peaks of H3K27 acetylation were used as constituent enhancers for super-enhancer identification using Rank Ordering of Super-Enhancers (ROSE, https://bitbucket.org/young_computation/rose). A stitching distance of 12,500bp and a promoter exclusion zone ± 2,000bp were used.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated for individual samples using bamCoverage (deepTools2 v3.1.3) with the following parameters: --binSize 5 --normalizeUsing CPM --effectiveGenomeSize 2685511504 --extendReads 200. Rank Ordering of Super-Enhancer bed files were generated using ROSE for merged minor allele homozygotes and merged major allele homozygotes using a stitching distance of 12,500bp and a promoter exclusion zone ± 2,000bp.

source_name: Stimulated CD4 T cells

extract_protocol:
Cells were harvested, counted and resuspended in fresh cell culture media (10^6 cells/ml). For cross-linking, 37% Formaldehyde was added to a final concentration of 1%, and cells were placed on a rocker for 10 minutes (room temperature). Cross-linking was quenched by adding Glycine (final concentration 0.125M) and shaking for 5 min (room temperature). Cells were washed twice in ice cold PBS and cell pellets were lysed for 10 min at a density of 10^7 cells/ml in lysis buffer supplemented with Protease inhibitor (Complete Mini EDTA-free Protease Inhibitor cocktail tablets; Roche). Lysis buffer: 50mM HEPES pH 7.9, 140mM NaCl, 1mM EDTA pH 8.0, 10% v/v Glycerol, 0.5% v/v IGEPAL CA-630, 0.25% v/v Triton X-100. Lysates were washed twice with wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0) and nuclei were prepared by washing twice with shearing buffer (0.1% w/v SDS, 1mM EDTA, 10mM Tris-HCl pH 8.0). Nuclei were resuspended in 200µl shearing buffer per 10^7 cells and sonicated for 9 cycles (30s ON/30s OFF) using a Bioruptor Pico. Triton X-100 and NaCl were added to the sheared chromatin to a final concentration of 1% and 100mM, respectively. 10µg of sheared chromatin were cleared by centrifugation (21,000G, 10min, 4C) and immunoprecipitation of histone-DNA complexes was performed overnight at 4ºC with rotation using an anti-H3K27ac antibody and the SimpleChIP Plus Sonication ChIP kit (Cell Signaling Technology).
50ng of immunoprecipitated DNA or input DNA were used to prepare sequencing libraries using the iDeal Library Preparation kit (Diagenode), according to manufacturer instructions. 10 PCR cycles were used for the amplification step and size selection was not performed. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 (Agilent) and the libraries were sequenced in pools of 8, with each pool being sequenced in 2 lanes of an Illumina HiSeq2500 high output flow-cell (50bp, single-end reads)

treatment_protocol: CD4 T cells were stimulated for 4 days using anti-Biotin MACSiBead Particles loaded with CD2, CD3, and CD28 antibodies (Miltenyi Biotec) and 10ng/ml recombinant IL-2 in complete RPMI (RPMI-1640 containing 10% Fetal Bovine Serum, 2mM glutamine, 10mM HEPES, 1% sodium pyruvate, 50μM 2-Mercaptoethanol, and Penicillin-Streptomycin 100u/ml )

tag: rs6927172 genotype

value: Minor (risk) allele homozygote

tag: sample

tag: antibody


title: P002_minus_3 Sample 55

description:
P002_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_RiskAlleleHom3_rep1


title: C130_minus_3 Sample 54

description:
C130_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: KW01_IFNg

tag: cell type

value: IFNg


title: C114_minus_3 Sample 52

description:
C114_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: F


title: InputDNA_RiskAlleleHom2_rep2

description:
InputDNA_RiskAlleleHom2.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: C126_minus_3 Sample 53

description:
C126_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_RiskAlleleHom1_rep2

description:
InputDNA_RiskAlleleHom1.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: InputDNA_RiskAlleleHom2_rep1


title: C109_minus_3 Sample 51

description:
C109_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C105_minus_3 Sample 50

description:
C105_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C102_minus_3 Sample 49

description:
C102_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P006_minus_3 Sample 58

description:
P006_minus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-


title: KW07_IFNg


title: KW01_Vehicle


title: InputDNA_MajorAlleleHom3_rep1

description:
InputDNA_MajorAlleleHom3.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed

value: Major allele homozygote


title: InputDNA_MajorAlleleHom2_rep2

description:
InputDNA_MajorAlleleHom2.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed


title: InputDNA_MajorAlleleHom2_rep1


title: P010_plus_2 Sample 48

description:
P010_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: 25uM phytol


title: P006_plus_2 Sample 46

description:
P006_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_MajorAlleleHom1_rep2

description:
InputDNA_MajorAlleleHom1.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed


title: P005_plus_2 Sample 45

description:
P005_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_MajorAlleleHom1_rep1


title: C114_minus_1 Sample 76

description:
C114_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P003_plus_2 Sample 44

description:
P003_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: t0 lazy B

description: RNA from ~ 1cm shoot tip from primary inflorescence shoot with open flowers removed as well as floral buds showing petal

value: lazy1 mutant

value: Columbia


title: P007_plus_2 Sample 47

description:
P007_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: P002_plus_2 Sample 43

description:
P002_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_MajorAlleleHom3_rep2


title: H3K27ac_ChIP_RiskAlleleHom3_rep1

description:
H3K27ac_ChIP_RiskAlleleHom3.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed

value: anti-H3K27ac (abcam; ab4729)


title: C130_plus_2 Sample 42

description:
C130_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: InputDNA_RiskAlleleHom1_rep1

description:
InputDNA_RiskAlleleHom1.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: H3K27ac_ChIP_RiskAlleleHom3_rep2


title: H3K27ac_ChIP_RiskAlleleHom2_rep2

description:
H3K27ac_ChIP_RiskAlleleHom2.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: C126_plus_2 Sample 41

description:
C126_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C109_plus_2 Sample 39

description:
C109_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: H3K27ac_ChIP_RiskAlleleHom1_rep2

description:
H3K27ac_ChIP_RiskAlleleHom1.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: C105_plus_2 Sample 38

description:
C105_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: H3K27ac_ChIP_RiskAlleleHom1_rep1


title: C102_plus_2 Sample 37

description:
C102_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: H3K27ac_ChIP_MajorAlleleHom3_rep2

description:
H3K27ac_ChIP_MajorAlleleHom3.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed


title: H3K27ac_ChIP_MajorAlleleHom3_rep1


title: P010_minus_2 Sample 36

description:
P010_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: H3K27ac_ChIP_MajorAlleleHom2_rep2

description:
H3K27ac_ChIP_MajorAlleleHom2.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed


title: H3K27ac_ChIP_MajorAlleleHom2_rep1


title: P002_plus_3 Sample 67

description:
P002_plus_3
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C114_plus_2 Sample 40

description:
C114_plus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: H3K27ac_ChIP_MajorAlleleHom1_rep2

description:
H3K27ac_ChIP_MajorAlleleHom1.bw
H3K27ac_hg19_major_fromMergedBAM_Enhancers_withSuper.bed


title: P002_minus_2 Sample 31

description:
P002_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: Jurkats J4S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J4S_CTTGTA

source_name: Jurkats

tag: cell line

value: Jurkats

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep4


title: H3K27ac_ChIP_MajorAlleleHom1_rep1


title: Jurkats J3S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J3S_GATCAG

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep3


title: C126_minus_2 Sample 29

description:
C126_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: healthy

value: M


title: Jurkats J1S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J1S_GCCAAT

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep1


title: Jurkats J2S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J2S_ACTTGA

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep2


title: H3K27ac_ChIP_RiskAlleleHom2_rep1

description:
H3K27ac_ChIP_RiskAlleleHom2.bw
H3K27ac_hg19_minor_fromMergedBAM_Enhancers_withSuper.bed


title: C109_minus_2 Sample 27

description:
C109_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: C102_minus_2 Sample 25

description:
C102_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: Jurkats J4U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J4U_TTAGGC

value: Unstimulated (resting) - rep4


title: Jurkats J3U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J3U_ATCACG

value: Unstimulated (resting) - rep3


title: C105_minus_2 Sample 26

description:
C105_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 12S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
12S_CTTGTA

tag: individual

value: healthy individual 12

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep12


title: P007_minus_2 Sample 35

description:
P007_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-

tag: allel 1 mutation

value: F


title: P006_plus_1 Sample 22

description:
P006_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

tag: Sex

value: 25uM phytol


title: CD4_Tcells 10S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
10S_GCCAAT

value: healthy individual 10

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep10


title: Jurkats J2U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J2U_CTTGTA

value: Jurkats

value: Unstimulated (resting) - rep2


title: P010_plus_1 Sample 24

description:
P010_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

tag: perturbation


title: Jurkats J1U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
J1U_GATCAG

value: Unstimulated (resting) - rep1


title: P007_plus_1 Sample 23

description:
P007_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C130_minus_2 Sample 30

description:
C130_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: healthy


title: P003_plus_1 Sample 20

description:
P003_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: M


title: CD4_Tcells 11S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
11S_GCCAAT

value: healthy individual 11

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep11


title: P003_minus_2 Sample 32

description:
P003_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: P002_plus_1 Sample 19

description:
P002_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 8S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
8S_TTAGGC

value: healthy individual 8

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep8


title: C130_plus_1 Sample 18

description:
C130_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 7S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
7S_CTTGTA

value: healthy individual 7

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep7


title: P006_minus_2 Sample 34

description:
P006_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-


title: P005_plus_1 Sample 21

description:
P005_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C114_minus_2 Sample 28

description:
C114_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: F


title: CD4_Tcells 5S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
5S_GCCAAT

value: healthy individual 5

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep5


title: C126_plus_1 Sample 17

description:
C126_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: 25uM phytol


title: C114_plus_1 Sample 16

description:
C114_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 4S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
4S_TTAGGC

value: healthy individual 4

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep4


title: C105_plus_1 Sample 14

description:
C105_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 2S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
2S_GCCAAT

value: healthy individual 2

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep2


title: CD4_Tcells 3S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
3S_ATCACG

value: healthy individual 3

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep3


title: CD4_Tcells 11U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
11U_GGCTAC

value: healthy individual 11

value: Unstimulated (resting) - rep11


title: CD4_Tcells 12U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
12U_ACTTGA

value: healthy individual 12

value: Unstimulated (resting) - rep12


title: P010_minus_1 Sample 12

description:
P010_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: CD4_Tcells 6S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
6S_CTTGTA

value: healthy individual 6

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep6


title: CD4_Tcells 1S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
1S_ATCACG

value: healthy individual 1

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep1


title: P006_minus_1 Sample 10

description:
P006_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-

value: F


title: P005_minus_1 Sample 9

description:
P005_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: M


title: P007_minus_1 Sample 11

description:
P007_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 10U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
10U_TTAGGC

value: healthy individual 10

value: Unstimulated (resting) - rep10


title: CD4_Tcells 9U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
9U_ATCACG

value: healthy individual 9

value: Unstimulated (resting) - rep9


title: P003_minus_1 Sample 8

description:
P003_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 8U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
8U_ATCACG

value: healthy individual 8

value: Unstimulated (resting) - rep8


title: CD4_Tcells 6U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
6U_GATCAG

value: Unstimulated (resting) - rep6


title: C130_minus_1 Sample 6

description:
C130_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: healthy


title: P002_minus_1 Sample 7

description:
P002_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C126_minus_1 Sample 5

description:
C126_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C109_plus_1 Sample 15

description:
C109_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: 25uM phytol


title: C102_plus_1 Sample 13

description:
C102_plus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: skin


title: C114_minus_1 Sample 4

description:
C114_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 9S

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
9S_TTAGGC

value: Stimulated (activated) - 4 days anti-CD2/CD3/CD28, IL-2 - rep9


title: CD4_Tcells 4U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
4U_CTTGTA

value: healthy individual 4

value: Unstimulated (resting) - rep4


title: CD4_Tcells 7U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
7U_ATCACG

value: healthy individual 7

value: Unstimulated (resting) - rep7


title: C105_minus_1 Sample 2

description:
C105_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: C102_minus_1 Sample 1

description:
C102_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.


title: CD4_Tcells 2U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
2U_GATCAG

value: healthy individual 2

value: Unstimulated (resting) - rep2


title: CD4_Tcells 5U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
5U_TTAGGC

value: healthy individual 5

value: Unstimulated (resting) - rep5


title: P005_minus_2 Sample 33

description:
P005_minus_2
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: PHYH-/-

value: M


title: C109_minus_1 Sample 3

description:
C109_minus_1
Cells were incubated for 96 hours with phytol (dissolved in ethanol) or ethanol as the vehicle.

value: F


title: YTH2_KD_4

city: Fort Collins

first: Carol

middle: J

last: Wilusz

state: Colorado

address: 1682 Campus Delivery

department: Microbiology, Immunology and Patholgy

institute: Colorado State University

data_processing:
Quality of sequence reads was assessed via FastQC v0.11.5.  Reads were trimmed of adaptor sequences and filtered for low-complexity or low-quality reads via Trimmomatic v0.32.  rRNA reads were filtered out using Bowtie2 v2.3.4.3 (Langmead and Salzberg, 2012) and a reference fasta file of mature 5S, 18S and 28S rRNA named mature_rRNA.fasta.  Filtered reads were mapped to the hg19 genome using TopHat2 v2.0.12 (Kim et al., 2013) under default parameters.  The output .bam alignment files were converted to .bam.tdf format using igv-tools and read distributions were viewed on IGV v2.3.91.  RNA-seq alignment files in .sam format were utilized to calculate read counts associated with each transcript using HTSeq v0.11.1 (Anders et al., 2015), Samtools v1.9 (Li et al., 2009) and the hg19 genome feature file obtained from GENCODE (hg19, Ensembl 74).  The HTseq function htseq-count was used with the following options: --stranded=no --minaqual=20.  Raw counts generated by this analysis can be found in the document 091417_raw_counts.txt.
Principle component analysis of the raw RNA-seq count data indicated there was unwanted variation in the sequencing data.  To remove the unwanted variation, raw RNA-seq count data was filtered for detectable genes (> 5 counts across all samples) and normalized via the RUVSeq package v1.16 (Risso et al., 2014) using the RUVr option in accordance with the published protocol.  Normalized count data was analyzed using DESeq2 v1.22.1 (Love et al., 2014) under default parameters.  Results of the DESeq2 analysis can be found in the document 091417_DESeq_results.xlsx.
Genome_build: hg19
Supplementary_files_format_and_content: .tdf files: IGV-ready alignment files for individual samples.  Control_YTH2KD_HTseq_raw_counts.txt file: Tab-delimited text file of raw read counts generated by HTseq.   ControlvsYTHDF2KD_DESeqResults.xlsx: Excel file of DESeq2 results.  hg19_gene_annotations.gtf.gz:  Gene annotation file used for calculating raw read counts with HTSeq.  mature_rRNA.fasta.gz: Fasta file containing the mature rRNA sequences used for rRNA filtering.

source_name: induced pluripotent stem cell

growth_protocol: iPSCs (System Biosciences, #SC101A-iPSC, Lot #110415-01) were cultured on Matrigel (Corning #354277) in mTesR1 media (STEMCELL Technologies, #85850) at 37°C in 5% CO2.  Plates were coated with MatriGel in accordance with manufacturer protocols, MatriGel was diluted in DMEM/F12 (+ L-glutamine, + 15 mM HEPES, - phenol red; Gibco, #11039-021).

extract_protocol:
Total RNA extractions were performed in accordance with recommend protocols (Invitrogen, #15596026).
Libraries were constructed from 500 ng of total RNA using the SMARTer™ PCR cDNA Synthesis Kit (Clonetech, #634926) and Advantage 2 PCR kit (Clontech, #639207) followed by Tn5-mediated tagmentation (see Methods and Materials for in-depth protocol).

treatment_protocol: Cells were grown for 5 days before being transfected with an siRNA targeting YTHDF2 or a negative scrambled control using Stemfect RNA Transfection kit (Stemgent, #00-0069).  Transfection was repeated 24 hours later.  Immediately prior to collection after another 24 hours, cells were subjected to four hours of 4-thiouridine metabolic labeling at a concentration of 400 mM.  Cells were harvested in TRIzol Reagent (Invitrogen, #15596026) and stored at -80°C.

value: Fibroblast-derived stem cell

tag: passage

value: YTHDF2 KD


title: YTH2_KD_3


title: CD4_Tcells 3U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
3U_ATCACG

value: healthy individual 3

value: Unstimulated (resting) - rep3


title: TC-71-R sample 2

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
base calling with Illumina software (Firecrest/Bustard)
read trimming, adapter removal with trimmomatic
alignment with STAR 2.4
quantification with htseq-count
normalization, analysis with edgeR
Genome_build: GRCh38, GENCODEv27
Supplementary_files_format_and_content: TSV of HGNC symbol, transcripts per million (HGNC \t TPM)

source_name: Ewing sarcoma cell line

growth_protocol: RPMI + 10% FBS + 10mM HEPES

extract_protocol:
RNEasy Mini RNA extraction kit
TruSeq RNA Library preparation kit
Paired-end, 100bp reads

treatment_protocol: Treatment with DMSO or YK-4-279 at doses of 650uM (A4573) or 400uM (TC-71)


title: E8593-1: CNE-2Z cells transfected with control vector

city: Zibo

first: xin

middle: xin

last: xiang

state: China

address: No. 54 Gongqingtuan West Road, Zibo, 255036, China.

country: China

institute: zibo central hospital

description: Gene expression data from HeLa cells transfected with control vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CNE-2Z cell line transfected with control vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CNE-2Z cells were cultured in RPMI 1640 for 24h, and then transfected with lentiviral vetors

treatment_protocol: CNE-2Z cells were transfected with TIPE1 or control vector

tag: genotype/variation

value: transfected with empty vector


title: YTH2_KD_2


title: E8593-2: CNE-2Z cells transfected with control vector


title: E8594-1: CNE-2Z cells transfected with TIPE1

description: Gene expression data from HeLa cells transfected with TIPE1

source_name: CNE-2Z cells transfected with TIPE1

value: transfected with TIPE1 lentiviral vector


title: E8594-2: CNE-2Z cells transfected with TIPE1


title: TC-71-R sample 1


title: E8593-3: CNE-2Z cells transfected with control vector


title: E8594-3: CNE-2Z cells transfected with TIPE1


title: YTH2_KD_1


title: CD4_Tcells 1U

description:
barcode_counts.txt
normalised_collapsed_constructs.txt
1U_ATCACG

value: healthy individual 1

value: Unstimulated (resting) - rep1


title: TC-71-R sample 3


title: TC-71 parental sample 3

value: DMSO


title: Control_KD_3

value: Control


title: TC-71 parental sample 2


title: A4573-R sample 2


title: A4573-R sample 3


title: Control_KD_1


title: MspI_reference_Kdm5b_KD

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: mm9
Supplementary_files_format_and_content: The hit count files were generated using in house pipeline (WASP - 3.1.4); The first line starts with "total" and displays total number of raw reads aligned to HpaII loci properly. For instance, "total 5249033" ; From the second line onward, each line represents one HpaII locus, showing the ID, chromosome, offset, HpaII count(F strand), HpaII count(R strand), HpaII count(both strands), respectively and space-delimited. For instance, "21 chr1 11961 9.8 17 26.8"
Supplementary_files_format_and_content: A bedgraph of the HpaII loci angle values was generated for each sample using custom script provided in the publication; Angle values represent degree of unmethylation at each HpaII site

source_name: WW6 cells

growth_protocol: mES cells were grown in a feeder cell-free environment on 0.1% gelatin covered dishes, in Dulbecco’s modified Eagle medium (DMEM, Mediatech) supplemented with 10% Fetal Bovine Serum (STEMCELL Technologies cat. no. 06952), 1X Nonessential amino acids (Gibco, cat.no. 11140-050), 1X Nucleoside mix (Sigma), 55 nM 2-Mercaptoethanol (Gibco) and 3,000 units of Leukemia inhibition factor (EMD Millipore ESG1106) per ml, at 37 °C in 5% CO2

extract_protocol:
mES cells were collected by washing and trypsinizing for three minutes, and FACS sorted by the GFP signal present in the transfected plasmid. Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight.  The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours.  The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  One micrograms of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 1 μg of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).

treatment_protocol: Cells were transiently transfected after 24 hours of seeding, using 6 µl of Lipofectamine LTX supplemented with 5 µl of Plus reagent per ml (Invitrogen), in serum-free media (OPTI-MEM, Invitrogen), with siRNA targeting Kdm5b, or GFP as control. After 4 hours of transfection, regular cultured media was added to transfected cells to assure optimal culture conditions.

value: embryonic stem cells

tag: strain

value: transfected cells with Kdm5b targeting construct


title: MspI_reference_Control

value: transfected cells with mock control construct


title: Control_KD_2


title: TC-71 parental sample 1


title: A4573 parental sample 3


title: Kdm5b_KD_B


title: Genomic DNA from peripheral blood monoculear cells 231

type: genomic

city: Jefferson

first: Stancy

last: Joseph

state: Ar

address: 3900 NCTR Road

department: Biochemical Toxicology

institute: FDA/NCTR

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R02C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R02C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R02C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R02C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R02C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R02C02_Red.idat

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader

data_processing: BeadStudio Software

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from normal human kidney tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: ethnicity

value: EA

tag: disease state

value: Lupus

tag: sledai score

tag: age


title: Genomic DNA from peripheral blood monoculear cells 211

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930011_R02C01_Grn.idat
location 1 (triplicate pair 1): 200556930011_R02C01_Red.idat
location 2 (triplicate pair 2): 200556930011_R02C02_Grn.idat
location 2 (triplicate pair 2): 200556930011_R02C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R02C01_Grn.idat
location 3 (triplicate pair 3): 200556930090_R02C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 214

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R03C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R03C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R03C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R03C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R03C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R03C02_Red.idat


title: Kdm5b_KD_C

tag: treatment


title: Genomic DNA from peripheral blood monoculear cells 223

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R04C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R04C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R04C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R04C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R04C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R04C02_Red.idat

value: AA

value: Non-lupus


title: Genomic DNA from peripheral blood monoculear cells 226

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R01C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R01C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R01C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R01C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R01C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R01C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 240

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R06C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R06C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R06C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R06C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R06C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R06C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 215

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930011_R05C01_Grn.idat
location 1 (triplicate pair 1): 200556930011_R05C01_Red.idat
location 2 (triplicate pair 2): 200556930011_R05C02_Grn.idat
location 2 (triplicate pair 2): 200556930011_R05C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R05C01_Grn.idat
location 3 (triplicate pair 3): 200556930090_R05C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 213

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930011_R04C01_Grn.idat
location 1 (triplicate pair 1): 200556930011_R04C01_Red.idat
location 2 (triplicate pair 2): 200556930011_R04C02_Grn.idat
location 2 (triplicate pair 2): 200556930011_R04C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R04C01_Grn.idat
location 3 (triplicate pair 3): 200556930090_R04C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 233

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R03C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R03C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R03C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R03C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R03C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R03C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 235

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R05C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R05C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R05C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R05C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R05C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 206

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R06C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R06C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R06C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R06C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R06C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R06C02_Red.idat


title: Kdm5b_KD_A


title: Genomic DNA from peripheral blood monoculear cells 212

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930011_R03C01_Grn.idat
location 1 (triplicate pair 1): 200556930011_R03C01_Red.idat
location 2 (triplicate pair 2): 200556930011_R03C02_Grn.idat
location 2 (triplicate pair 2): 200556930011_R03C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R03C01_Grn.idat
location 3 (triplicate pair 3): 200556930090_R03C01_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 192

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R01C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R01C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R01C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R01C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R01C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R01C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 242

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R05C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R05C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R05C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R05C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R05C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 190

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 3998419048_R02C01_Grn.idat
location 1 (triplicate pair 1): 3998419048_R02C01_Red.idat
location 2 (triplicate pair 2): 3998419048_R02C02_Grn.idat
location 2 (triplicate pair 2): 3998419048_R02C02_Red.idat
location 3 (triplicate pair 3): 3998419076_R02C02_Grn.idat
location 3 (triplicate pair 3): 3998419076_R02C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 196

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R03C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R03C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R03C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R03C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R03C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R03C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 237

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930010_R04C01_Grn.idat
location 1 (triplicate pair 1): 200556930010_R04C01_Red.idat
location 2 (triplicate pair 2): 200556930010_R04C02_Grn.idat
location 2 (triplicate pair 2): 200556930010_R04C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R04C02_Grn.idat
location 3 (triplicate pair 3): 200556930090_R04C02_Red.idat


title: Control_C


title: A4573 parental sample 1


title: A4573 parental sample 2


title: Donor 3_TGFbeta_36h

city: San Francisco

first: Mary Helen

last: Barcellos-Hoff

address: 2340 Sutter Street

department: Radiation Oncology

institute: UCSF

data_processing:
Base calling: HiSeq Control Software HCS
Sequenced reads were mapped to hg38 using TopHat v2.0.12 (Bowtie v2.2.3.0, Samtools v0.1.18.0) with parameters --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --no-closure-search --no-microexon-search --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3
Reads were counted using htseq-count script from HTSeq v0.5.4p3 with parameters -s no -a 10
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing raw counts of each sample

source_name: CD14+ IMC

extract_protocol:
Total mRNA (Qiagen)
Illumina TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes) (RS-122-2001)
Oligo-dT for Poly-A tail selection
HiSeq 2500, v4 chemistry

value: CD14+ human immature myeloid cells

value: Donor 3

value: Treated with TGF-beta

tag: time point

value: 36 hours


title: Donor 3_Untreated_36h

value: Un-treated


title: Genomic DNA from peripheral blood monoculear cells 182

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750149_R04C01_Grn.idat
location 1 (triplicate pair 1): 200490750149_R04C01_Red.idat
location 2 (triplicate pair 2): 200490750149_R04C02_Grn.idat
location 2 (triplicate pair 2): 200490750149_R04C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R04C01_Grn.idat
location 3 (triplicate pair 3): 200556930054_R04C01_Red.idat

source_name: Blood


title: Genomic DNA from peripheral blood monoculear cells 200

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200490750121_R05C01_Grn.idat
location 1 (triplicate pair 1): 200490750121_R05C01_Red.idat
location 2 (triplicate pair 2): 200490750121_R05C02_Grn.idat
location 2 (triplicate pair 2): 200490750121_R05C02_Red.idat
location 3 (triplicate pair 3): 200556930054_R05C02_Grn.idat
location 3 (triplicate pair 3): 200556930054_R05C02_Red.idat


title: Genomic DNA from peripheral blood monoculear cells 225

description:
Normal human blood
samples in triplicates
location 1 (triplicate pair 1): 200556930011_R06C01_Grn.idat
location 1 (triplicate pair 1): 200556930011_R06C01_Red.idat
location 2 (triplicate pair 2): 200556930011_R06C02_Grn.idat
location 2 (triplicate pair 2): 200556930011_R06C02_Red.idat
location 3 (triplicate pair 3): 200556930090_R06C01_Grn.idat
location 3 (triplicate pair 3): 200556930090_R06C01_Red.idat


title: A4573-R sample 1