title: CTCF WIZdel Rep 2

description: CTCF-WIZdel-ChIPseq.bw

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 2 minutes before quenching with 125 mM glycine. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before resuspension in Sonication Buffer 1. Human chromatin (from HEK293T cells) was spiked in (to final 5%) prior to sonication for the indicated experiments. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 8, PIP/W 210, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1,000 base pair size were generated.  Antibody was incubated with 100uL Protein G Dynabeads for 6 hours. Unbound antibody was removed via washing, as detailed above, before incubation of antibody bound beads with chromatin overnight. Beads were then washed with Sonication Buffer 1 and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. Zymo ChIP DNA Clean and Concentrate kit (D5205) was used to purify DNA following Proteinase digestion. Sequencing libraries were prepared using a Hyper Prep kit (Kapa Biosciences KK8502).

tag: genotype

value: WIZ deletion

value: mESC v6.5

value: anti-CTCF; Active Motif 61311


title: WT rep2 (Hi-C)

status: Public on Apr 14 2020

type: SRA

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive, CB 7100 3360 Genome Sciences Building

country: USA

institute: UNC Chapel Hill

description: collisions_WT.txt; inter_30_WT.hic; ; merged_loops_WT.bedpe; ; contact_domains_25kb_WT.bedpe

library_source: genomic

data_processing:
Initial data processing, including merging of replicates, alignment, filtering, and generation of Hi-C contact maps, was perfomed using the Juicer wrapper from the Lieberman-Aiden lab.
Contact domains were called from merged, Knight-Ruiz balanced contact maps at 25kb resolution using the Arrowhead algorithm with default parameters.
Loops were called from merged, Knight-Ruiz balanced contact maps at 5kb, 10kb, and 25kb resolution using the HiCCUPs algorithm with default parameters except: -p 8,4,2 -i 14,10,6
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C matrices are provided in .hic format. Loop and domain calls are provided in .bedpe format.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells v6.5

growth_protocol: V6.5 murine embryonic stem cells (mESCs) (male) were grown on irradiated murine embryonic fibroblasts under standard conditions, as previously described (Dowen et al, 2014)

extract_protocol:
Hi-C libraries were prepared using the Arima Hi-C kit (Arima Genomics) according to manufacturer's specifications, with one modification. Treatment with DNA ligase was performed for one hour instead of the recommended 15 minutes.
Dual-indexed Illumina sequencing libraries were prepared using Kapa Hyper Prep (Kapa Biosciences, cat.#KK8502) according to specifications provided by Arima Genomics, with one modification. Ligation of sequencing adapters was allowed to proceed for 1 hour instead of the recommended 15 minutes.

treatment_protocol: ESCs growing in exponential phase were placed in single cell suspension in 1x PBS with 1% formaldehyde. After 2 minutes, crosslinking was quenched with addition of glycine to 150mM

value: Wild Type

tag: cell line


title: Wiz-del rep1 (Hi-C)

description: collisions_Wiz-del.txt; inter_30_Wiz-del.hic; merged_loops_Wiz-del.bedpe; contact_domains_25kb_Wiz-del.bedpe


title: WIZ del Rep 3 (RNA-Seq)

library_source: transcriptomic

data_processing:
Alignment:  reads were aligned to the mm10 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Coverage File Generation: bigwig files were generated deeptools (v 3.0.1) genomecov with parameters -p 24 -bs 10 --normalizeUsing RPKM -ignore chrX
Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 24 -c SortedByCoordinate
Genome_build: mm10
Supplementary_files_format_and_content: For each replicate, a bigwig file is provided for viewing in UCSC genome browser.

molecule: polyA RNA

extract_protocol:
Cells were resuspended in 1ml Trizol (Invitrogen, 15596018). Chloroform (Sigma Aldrich, C2432) was added for phase separation. RNA was purified using the Zymo RNA Clean and Concentrator Kit (Zymo, R1013)
Libraries were prepared using a TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) with indexes AR001-AR009. Library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter A63881).


title: CTCF Rep 2

description: CTCF-ChIPseq.bw

data_processing:
Alignment:  reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v 2016-02-15) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.26) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Genome_build: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary_files_format_and_content: For each ChIPped factor, a BigWig coverage track of merged replicates is provided for viewing in UCSC genome browser.

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 2 minutes before quenching with 125 mM glycine. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before resuspension in Sonication Buffer 1. Human chromatin (from HEK293T cells) was spiked in (to final 5%) prior to sonication for the indicated experiments. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 8, PIP/W 210, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1,000 base pair size were generated.  Antibody was incubated with 100uL Protein G Dynabeads for 6 hours. Unbound antibody was removed via washing, as detailed above, before incubation of antibody bound beads with chromatin overnight. Beads were then washed with Sonication Buffer 1 and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. Zymo ChIP DNA Clean and Concentrate kit (D5205) was used to purify DNA following Proteinase digestion. Sequencing libraries were prepped using Hyper Prep kit (Kapa Biosciences KK8502).

tag: antibody


title: Flag ChIP CLC ID R2

city: New York

first: Nishana

last: Mayilaadumveettil

state: New York

address: 31st Street & East River DR, Receiving Department BLDG Smilow Floor 03, RM 307 (Jane Skok Laboratory)

department: Pathology

institute: NYU Langone health

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 2 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
raw counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: CLC  ID

growth_protocol: Mouse embryonic stem cells E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin (Sigma ES-006-B) coated dishes (Falcon, 353003) at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM (Thermo Fisher, 11965-118) supplemented with 15% fetal bovine serum (Thermo Fisher, SH30071.03), 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma, P4458), 1 X GlutaMax supplement (Thermo Fisher, 35050-061), 1 mM sodium pyruvate (Thermo Fisher, 11360-070), 1 X MEM non-essential amino-acids (Thermo Fisher, 11140-50), 50 μM b-mercaptoethanol (Sigma, 38171), 104 U/ml leukemia inhibitory factor (Millipore, ESG1107), 3 μM CHIR99021 (Sigma, SML1046) and 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162). The cells were passaged every alternate day by dissociation with TrypLE (Thermo Fisher, 12563011).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104) as per the manufacturer's protocol.
ChIP-seq libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA seq libraries were prepared using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.

treatment_protocol: For degradation of endogenous CTCF, 500 μM indole-3-acetic acid/IAA (Sigma, I5148) was added to the media. Expression of transgenes were achieved by the addition of doxycycline (Dox, 1 μg/ml) (Sigma, D9891) to the media. The cells were treated with IAA and/or Dox for 2 days for RNA seq and ChIP seq and 4 days for HiC.

tag: parental cell line

value: mouse ES cells E14Tg2a

tag: strain

value: 129/Ola, XY

tag: genotype/variation

value: CTCF-AID, Tir1, Flag-CLC-mRuby 2 transgene at Tigre

tag: kit

value: Nextera

tag: chip antibody

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)

tag: agent

value: IAA and Dox

tag: time point


title: WIZ Rep 1

description: WIZ-ChIPseq.bw

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 20 minutes then quenched with 125 mM glycine. Cells were lysed with Lysis Buffer 1 (50 mM Hepes-KOH pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) by incubating cells in the buffer for 10 minutes at 4C. Nuclei were next lysed with Lysis Buffer 2 (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, and 0.5 mM EGTA) by incubating nuclei in the buffer for 10 minutes at room temp. Finally, nuclear extracts were resuspended in Sonication Buffer 1 (20mM Tris-HCl pH 8, 150mM NaCl, 2mM EDTA, 0.1% SDS, and 1% Triton X-100). Cells were sonicated using a Branson probe sonicator with the following settings: 18% amplitude, 30 sec on, 60 sec off, 17 cycles, 8.5 minutes total. WIZ antibody (4ug, NBP1-80586) was incubated with Protein G Dynabeads (150ul, Thermo Fisher, 10004D) for 6 hours at 4C. Unbound antibody was removed by washing beads three times with PBS before sonicated chromatin was added to antibody conjugated beads and incubated overnight at 4C. Beads were washed with sonication buffer, wash buffer 1 (20mM Tris-HCl pH 8, 500mM NaCl, 2mM EDTA, 0.1% SDS, and 1% Triton X-100), wash buffer 2 (10mM Tris-HCl pH 8, 250mM LiCl, 1mM EDTA, and 1% NP-40), and wash buffer 3 (10mM Tris pH 8, 1mM EDTA, and 50mM NaCl). Chromatin was eluted from beads by adding elution buffer (50mM Tris pH 8, 10mM EDTA, and 1% SDS) and incubating at 65C for 1 hour, spinning down the mixture, then moving the supernatant to a new tube. Supernatant was left at 65C overnight to reverse crosslinks. RNA was degraded by adding TE and RNAse A to the tubes at 37C for 2 hours followed by protein degradation with CaCl2 and Proteinase K for 30 minutes at 55C. DNA was precipitated using phenol chloroform followed by NaCl, glycogen, and ethanol addition. Resulting DNA pellet was resuspended in 10 mM Tris HCl pH 8. ChIP-seq library was prepared using the ThruPLEX-FD Prep kit (Takara, R400428).

value: anti-WIZ; Novus NBP1-80586


title: WIZ del Rep 2 (RNA-Seq)


title: WIZ del Rep 1 (RNA-Seq)


title: WT Rep 3 (RNA-Seq)


title: WT Rep 2 (RNA-Seq)


title: Prostate_S1_32w

city: Campinas

first: Danilo

middle: Lopes

last: Ferrucci

state: SP

address: Rua Monteiro Lobato, 255

department: Genetic and Molecular Biology

country: Brazil

institute: Unicamp

data_processing:
The sequences were aligned with TopHat2 (http://ccb.jhu.edu/so ware/tophat/index.shtml) to Mus Musculus genome (GRCm38.p6)
The HTSeqCount and DESeq2 packages (http://www-huber.embl.de/users/ anders /HTSeq/doc/overview.html, as well as http://www.bioconductor.org/ packages/release/bioc/html/DESeq2. html) were used for the estimation of gene expression and statistical analysis
HTSeqCount performs the counting of aligned sequences to genome elements.
DESeq2 employs a negative-binomial distribution for data normalization, corrects for outliers and the contribution of low expression genes for the analysis of variance, and it uses diferential expression statistical Wald tests and corrects for multiple tests employing the Benjamini and Hochberg procedures
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: counts

molecule: total RNA

source_name: Prostate

extract_protocol:
Prostate total RNA was extracted using TrIzol reagent following the manufacturer’s instructions (Life Technologies). RNA integrity was checked in a 2100 Bionalyzer (Agilent), and all samples with RNA integrity number (RIN) above 8 were selected and used for the RNAseq procedure.
cDNA libraries were produced from 200ng of RNA purified from the ventral prostate samples using the TruSeq Stranded mRNA kit (Illumina), according to the manufacturer ́s instructions

tag: tissue

value: Prostate

tag: diet

value: Soybean oil (SO)

tag: time

value: 32 weeks of  treatment


title: Prostate_S5_32w


title: Flag ChIP CTCF D R2

description: Flag antibody ChIP seq in cells treated with Dox for 24 h. Replicate 2 of 2

source_name: CTCF D

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre

value: Dox


title: Flag ChIP CTCF ID R2

source_name: CTCF ID


title: Prostate_S3_32w


title: Prostate_S2_32w


title: Prostate_P2_32w

value: Por Fat (PF)


title: Prostate_S4_32w


title: Prostate_P5_32w


title: WT Rep 1 (RNA-Seq)


title: Prostate_P4_32w


title: G1sE135_R3_H3K27me3rep1

city: Chicago

first: John

last: Crispino

address: 300 Superior St

institute: Northwestern University

description: CUT&RUN-seq

data_processing:
Library strategy: CUT&RUN
RNA-seq: Sequencing data was analyzed using the protocol by Anders et al.(Anders et al., 2013). Briefly, raw reads were aligned by TopHat2(Kim et al., 2013) to the mouse reference genome (UCSC mm10). Aligned reads were counted by HTSeq(Anders et al., 2015). Data normalization and differential gene expression were done by DESeq2(Love et al., 2014). Clustering and PCA were performed in matlab. GSEA(Subramanian et al., 2005) was used to find groups of enriched genes between different groups of samples.
CUT&RUN-seq: Briefly, paired-end sequences were merged and we used trimgalore to remove adaptor sequence and applied bowtie2 to align reads to the reference genome (UCSC mm9). We used MACS1.4 to call the binding peaks.  P values of differentially enriched binding peaks between Gata1 and Gata1s were calculated using DESeq2.
ATAC-seq:Paired-end sequences were merged and aligned to the mouse reference genome (UCSC mm9). We used trimgalore to remove adaptor sequence and applied bowtie2 to align reads of the ATAC-seq samples to the reference genome (mm9). We used MACS1.4 to call the binding peaks.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: bigwig

source_name: Erythroblasts

extract_protocol:
DNA after CUT&RUN protocol was isolated using phenol-chloroform-isoamyl alcohol method.
To generate RNA sequencing libraries, RNA quality was determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of > 7 and quantified using Qubit. Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions. Briefly, polyadenylated mRNAs were captured from total RNA using oligo-dT selection. Next, samples were converted to cDNA by reverse transcription, and each sample was ligated to Illumina sequencing adapters containing unique barcode sequences. Barcoded samples were then amplified by PCR and the resulting cDNA libraries by quantified using qPCR. CUT&RUN-sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina complemented with NEBNext Multiplex Oligos for Illumina. The dA-tailing temperature was decreased to 50oC, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. Next, 2.1x AMPure XP beads (Beckman) were added for cleanup of adaptor-ligated DNA without size selection. After PCR amplification, the reaction was cleaned up with AMPure XP beads. Libraries were validated using the Agilent High Sensitivity DNA Kit on Bioanalyzer.

treatment_protocol: Fetal liver cells were suspended in sterile FACS buffer (PBS, 0.5% BSA, 2 mM EDTA) and stained with indicated surface markers for 30 minutes at 4oC, then sorted R1/2 (CD71hiTer119neg/med) and R3 (CD71hiTer119hi) populations of erythroblasts using a FACSAria IIu (BD).

tag: strain background

value: mutant

tag: cell type

value: Erythroblasts

tag: cell population

value: CD71hiTer119hi (R3) population

value: Millipore, 07-449


title: Prostate_P3_32w


title: G1sE135_R1/2_H3K27me3rep1

description: CUT&RUN-seq

value: CD71hiTer119neg/med (R1/2) population


title: Flag ChIP CTCF ID R1

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 1 of 2

value: mouse ES cells E14Tg2a

value: 129/Ola, XY


title: WTE135_R1/2_H3K27me3rep1

description: CUT&RUN-seq

value: wildtype


title: G1sE135_R1/2_GATA1srep1

description: CUT&RUN-seq

value: Abcam, ab11852


title: G1sE135_R3_GATA1srep1

description: CUT&RUN-seq


title: Prostate_L5_32w

value: Linseed oil (LO)


title: CUTRUN_IgGrep2

description: CUT&RUN-seq

value: Abcam, ab46540


title: Prostate_L3_32w

value: Prostate


title: WTE135_R1/2_GATA1rep1

description: CUT&RUN-seq


title: CUTRUN_IgGrep1

description: CUT&RUN-seq


title: Prostate_L4_32w


title: Prostate_L2_32w


title: Prostate_L1_32w


title: G1sE135_R3_H3K27me3rep2

data_processing:
library strategy: CUT&RUN-seq
RNA-seq: Sequencing data was analyzed using the protocol by Anders et al.(Anders et al., 2013). Briefly, raw reads were aligned by TopHat2(Kim et al., 2013) to the mouse reference genome (UCSC mm10). Aligned reads were counted by HTSeq(Anders et al., 2015). Data normalization and differential gene expression were done by DESeq2(Love et al., 2014). Clustering and PCA were performed in matlab. GSEA(Subramanian et al., 2005) was used to find groups of enriched genes between different groups of samples.
CUT&RUN-seq: Briefly, paired-end sequences were merged and we used trimgalore to remove adaptor sequence and applied bowtie2 to align reads to the reference genome (UCSC mm9). We used MACS1.4 to call the binding peaks.  P values of differentially enriched binding peaks between Gata1 and Gata1s were calculated using DESeq2.
ATAC-seq:Paired-end sequences were merged and aligned to the mouse reference genome (UCSC mm9). We used trimgalore to remove adaptor sequence and applied bowtie2 to align reads of the ATAC-seq samples to the reference genome (mm9). We used MACS1.4 to call the binding peaks.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
RNA was extracted followed by manufacturer’s instructions of TRIzol (Invitrogen).
DNA after ATAC protocol was isolated using QIAGEN MiniElute PCR purification kit.
DNA after CUT&RUN protocol was isolated using phenol-chloroform-isoamyl alcohol method.
To generate RNA sequencing libraries, RNA quality was determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of > 7 and quantified using Qubit. Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions. Briefly, polyadenylated mRNAs were captured from total RNA using oligo-dT selection. Next, samples were converted to cDNA by reverse transcription, and each sample was ligated to Illumina sequencing adapters containing unique barcode sequences. Barcoded samples were then amplified by PCR and the resulting cDNA libraries by quantified using qPCR. CUT&RUN-sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina complemented with NEBNext Multiplex Oligos for Illumina. The dA-tailing temperature was decreased to 50oC, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. Next, 2.1x AMPure XP beads (Beckman) were added for cleanup of adaptor-ligated DNA without size selection. After PCR amplification, the reaction was cleaned up with AMPure XP beads. Libraries were validated using the Agilent High Sensitivity DNA Kit on Bioanalyzer.
Cleavage Under Targets and Release Using Nuclease (CUT&RUN)


title: G1sE135_R1/2_H3K27me3rep4

value: CD71 and Ter119, CD71hiTer119neg/low population (R1/2)


title: Prostate_S5_12w

value: Soybean oil (SO)

value: 12 weeks of  treatment


title: Prostate_P1_32w

value: 32 weeks of  treatment


title: Prostate_S4_12w


title: G1sE135_R1/2_H3K27me3rep3


title: Prostate_S3_12w


title: Prostate_S2_12w


title: WTE135_R1/2_H3K27me3rep2

value: wild type


title: G1sE135_R1/2_H3K27me3rep2

value: mutant


title: Prostate_P5_12w

value: Por Fat (PF)


title: WTE135_R1/2_H3K27me3rep4

value: Erythroblasts


title: Prostate_S1_12w


title: WTE135_R3_H3K27me3rep2

value: CD71hiTer119hi (R3) population

value: Millipore, 07-449


title: Prostate_P3_12w


title: WTE135_R1/2_H3K27me3rep3


title: G1sE135_R3_GATA1srep5


title: Prostate_P4_12w


title: G1sE135_R3_GATA1srep4


title: Prostate_P1_12w


title: Prostate_L3_12w


title: G1sE135_R3_GATA1srep2


title: Prostate_L5_12w


title: G1sE135_R3_GATA1srep3


title: WTE135_R3_GATA1rep4


title: Prostate_L2_12w


title: WTE135_R3_GATA1rep2


title: Prostate_L4_12w


title: WTE135_R3_GATA1rep3


title: WTE135_R3_H3K27me3rep1


title: G1sE135_R1/2_GATA1srep2


title: Prostate_P2_12w


title: G1sE145_R3_RNArep2 [MS29_KO_R3_14.5d]

data_processing:
RNA-seq: Sequencing data was analyzed using the protocol by Anders et al.(Anders et al., 2013). Briefly, raw reads were aligned by TopHat2(Kim et al., 2013) to the mouse reference genome (UCSC mm10). Aligned reads were counted by HTSeq(Anders et al., 2015). Data normalization and differential gene expression were done by DESeq2(Love et al., 2014). Clustering and PCA were performed in matlab. GSEA(Subramanian et al., 2005) was used to find groups of enriched genes between different groups of samples.
CUT&RUN-seq: Briefly, paired-end sequences were merged and we used trimgalore to remove adaptor sequence and applied bowtie2 to align reads to the reference genome (UCSC mm9). We used MACS1.4 to call the binding peaks.  P values of differentially enriched binding peaks between Gata1 and Gata1s were calculated using DESeq2.
ATAC-seq:Paired-end sequences were merged and aligned to the mouse reference genome (UCSC mm9). We used trimgalore to remove adaptor sequence and applied bowtie2 to align reads of the ATAC-seq samples to the reference genome (mm9). We used MACS1.4 to call the binding peaks.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: bigwig


title: WTE135_R1/2_GATA1rep3


title: WTE135_R1/2_GATA1rep2


title: G1sE145_R1/2_RNArep3 [MS28_KO_R2_14.5d]


title: G1sE135_R3_ATACrep2


title: G1sE135_R3_ATACrep1


title: G1sE145_R1/2_RNArep2 [MS22_KO_R2_14.5d]


title: G1sE145_R1/2_RNArep1 [JC08_KO_R2_14.5d]


title: G1sE125_R3_RNArep2 [MS27_KO_R3_12.5d]


title: G1sE135_R1/2_ATACrep3


title: G1sE125_R3_RNArep1 [MS25_KO_R3_12.5d]


title: G1sE135_R1/2_ATACrep2


title: WTE135_R3_ATACrep3


title: G1sE125_R1/2_RNArep3 [MS24_KO_R2_12.5d]


title: Prostate_L1_12w


title: WTE135_R3_ATACrep1


title: WTE135_R3_GATA1rep1


title: WTE135_R1/2_ATACrep3


title: WTE145_R3_RNArep1 [JC05_WT_R3_14.5d]


title: WTE145_R3_RNArep2 [MS21_WT_R3_14.5d]


title: G1sE145_R3_RNArep1 [MS23_KO_R3_14.5d]


title: WTE145_R1/2_RNArep2 [MS20_WT_R2_14.5d]


title: G1sE125_R1/2_RNArep1 [JC06_KO_R2_12.5d]


title: WTE135_R1/2_ATACrep2


title: WTE135_R1/2_ATACrep4


title: WTE145_R1/2_RNArep1 [JC02_WT_R2_14.5d]


title: WTE135_R1/2_ATACrep1


title: WTE125_R3_RNArep2 [JC04_WT_R3_12.5d]


title: WTE125_R3_RNArep3 [MS19_WT_R3_12.5d]


title: G1sE125_R1/2_RNArep4 [MS26_KO_R2_12.5d]


title: WTE125_R1/2_RNArep1 [JC01_WT_R2_12.5d]


title: WTE125_R3_RNArep1 [JC03_WT_R3_12.5d]


title: G1sE135_R1/2_ATACrep1


title: G1sE125_R1/2_RNArep2 [JC07_KO_R2_12.5d]


title: 231-miR200a-plus-ELK3 rep2

city: Seongnam-si

first: Joo Dong

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro

department: Biomedical Science

country: South Korea

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Homo sapiens

source_name: Triple negative breast cancer (TNBC)

growth_protocol: The human breast cancer cell line MDA-MB 231 were obtained from the American Type Culture Collection (ATCC, Manassas , VA, USA) and were cultured in Dulbecco’s modified Eagle’s medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco) and 5% penicillin-streptomycin (Gibco).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The human breast cancer cell line MDA-MB-231 were transfected with miR-200a (100 nM) and pcDNA3.1-Flag-ELK3 (30 ng) using Lipofectamine 3000

tag: treatment

value: 48hrs after miR-200a and pcDNA3.1 Hygro(+)-ELK3 Co-transfection


title: WTE125_R1/2_RNArep2 [MS18_WT_R2_12.5d]


title: WTE135_R3_ATACrep2


title: 231-miR200a-plus-ELK3 rep1


title: 231-miR200a rep2

value: 48hrs after miR-200a transfection


title: 231-miR200a rep1


title: 231-C rep 2

value: 48hrs after NC mimic transfection


title: 231-C rep 1


title: NAc_V4: VehicleOIH_V4_Nucleus_Accumbens

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
100 nt paired-end reads were assembled into transcript isoforms and mapped to the C57Bl/6J mouse genome (version GRCm38) using Kallisto v0.43 (Bray et al., 2016)
Genome_build: C57Bl/6J mouse genome (version GRCm38)
Supplementary_files_format_and_content: csv format, comma-delimited file including transcripts per million (TPM) values for each sample, one column per sample

source_name: Nucleus accumbens

extract_protocol:
Nucleus accumbens was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000   using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Nucleus accumbens

value: Vehicle

tag: age

value: 9-12 weeks old

tag: Sex

value: male


title: NAc_M5: OIH_M5_Nucleus_Accumbens

value: OIH


title: NAc_V3: VehicleOIH_V3_Nucleus_Accumbens


title: NAc_V5: VehicleOIH_V5_Nucleus_Accumbens


title: NAc_V2: VehicleOIH_V2_Nucleus_Accumbens


title: NAc_M4: OIH_M4_Nucleus_Accumbens


title: NAc_V1: VehicleOIH_V1_Nucleus_Accumbens


title: NAc_M3: OIH_M3_Nucleus_Accumbens


title: NAc_M2: OIH_M2_Nucleus_Accumbens


title: NAc_M1: OIH_M1_Nucleus_Accumbens


title: TG_V5: VehicleOIH_V5_Trigeminal_Ganglia

source_name: Trigeminal ganglia

extract_protocol:
Trigeminal ganglia was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000   using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Trigeminal ganglia


title: TG_V4: VehicleOIH_V4_Trigeminal_Ganglia


title: TG_M5: OIH_M5_Trigeminal_Ganglia


title: TG_M4: OIH_M4_Trigeminal_Ganglia


title: TG_V2: VehicleOIH_V2_Trigeminal_Ganglia


title: TG_V3: VehicleOIH_V3_Trigeminal_Ganglia


title: TG_V1: VehicleOIH_V1_Trigeminal_Ganglia


title: RNA 3 rep1

city: Toronto

first: Rashim Pal

last: Singh

address: 101, College Street

country: Canada

institute: Princess Margaret Cancer Centre, UHN

data_processing:
ATAC: Differentially accessible regions were calculated using the DiffBind and EdgeR packages in R. Regions with an absolute fold-change >= 1.5 and an FDR value <= 0.05 were defined as significantly differentially accessible regions.
RNA seq: After removing genes whose cpm (counts per million reads) were less than 0.5 to remove noise, edgeR was used to estimate differential expression by applying a generalized linear model between the control samples and the cells isolated after MB6 treatment and MB6 and PEN treatment. A score that ranks genes from top up regulated in the MB6 samples and MB6PEN samples to top down regulated when compared to control samples was calculated using the formula `-log10(pvalue) * sign(logFC)`.
Cap meth seq: Data is analyzed using the MethylKit R package. Differentially methylated sites were identified and ranked based on percentage of methylation difference >25% and q-value <0.01. Differentially methylated sites were mapped and associated to their nearby genes (5kb upstream, 1kb downstream of transcription start site) for annotation purpose. Gene Ontology (GO) and pathway analysis were performed using default parameters of Bioconductor package rGREAT
Genome_build: Human
Supplementary_files_format_and_content: bigwig for ATAC seq, tsv for RNA and cap meth seq

source_name: OCI-AML2 cells

growth_protocol: Cells were grown in IMDM+10% FCS and passaged every 3 days.

extract_protocol:
For cap meth seq DNA was extracted with Dneasy kit for qiagen (Cat 67506), For RNA seq RNA was isolated with RNeasy kit (Cat 74134). ATAC seq was performed as described previously (Corces, R., Trevino, A.E., Hamilton, E.G., Greenside, P.G., Sinnott-Armstrong, N.A., Vesuna, S., Satpathy, A.T., Rubin, A.J., Montine, K.S., Wu, B., et al. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962.)
For RNA seq: Prior to analysis, read adapters and low quality ends were removed using Trim Galore v. 0.4.0. Reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.    Gene read counts were normalized using the TMM method available from the edgeR_3.24.3 package.
For ATAC seq: ATAC samples were preprocessed according to the ENCODE ATAC-seq pipeline. Single-end reads were aligned to the hg19 genome using Bowtie2 with the --local parameter, reads with MAPQ scores < 30 were filtered out with Samtools, duplicates were removed using Sambamba, and TN5 tagAlign shifted files were created. MACS2 was used to call peaks with the following parameters: -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR –keep-dup all --call-summits. Peaks were later filtered at a q-value threshold of 0.0001 for further analyses.  Peak counts and sizes for each replicate were calculated using a custom Python script, and Jaccard indices for similarities between called peaks was calculated using BEDTools.
For cap meth seq: Following company’s protocol (TruSeq-Methyl Capture EPIC, cat # FC-151-1002, Illumina Inc., San Diego, CA) libraries were prepared using 500 ng of genomic DNA. DNA was sonicated using a Covaris LE220 sonicator (Covaris, Woburn, MA) to obtain products of 180–220 bp. DNA was end-repaired, A-tailed and ligated with methylated indexed-adapters to create pre-capture DNA libraries. All pre-capture libraries were hybridized to the EPIC oligos. Hybridized products were subjected to bisulfite conversion. The bisulfite-treated libraries were PCR-amplified. Libraries were sequenced 100 bp paired-end on Illumina NovaSeq-6000

treatment_protocol: Cells were treated with drugs for 48 hrs before processing

value: Acute Myeloid leukemia cell line

value: mitoblock-6 and penicillamine


title: RNA 3 rep2


title: RNA 2  rep2


title: RNA 3 rep3


title: RNA 2  rep3


title: RNA 1 rep3

value: untreated


title: RNA 2  rep1


title: TG_M3: OIH_M3_Trigeminal_Ganglia


title: TG_M2: OIH_M2_Trigeminal_Ganglia


title: 6_control [s_6_cut_GATCAG_2]

city: Jinan

first: Yujie

last: Jiang

address: No.324, Jingwu Road, Jinan, Shandong 250021, People’s Republic of China

country: China

institute: Shandong Provincial Hospital affiliated to Shandong University

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
Trimmed reads (with 5’, 3’-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences.
The alignment statistical analysis was applied to retain the valid sequences for subsequent tRF & tiRNA expression profiling and differential expression analysis.
The remaining reads are aligned to the transcriptome which includes mRNA/ rRNA /snRNA/piRNA /snoRNA /miRNA biotypes.
The expression profiling and differential expression of tRFs & tiRNAs & known miRNAs were calculated based on normalized TPM
Genome_build: GtRNAdb and miRBase 21
Supplementary_files_format_and_content: text files include TPM values for each Sample

source_name: control

extract_protocol:
RNA was harvested using Trizol reagent.
total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~135-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.

tag: subject status

value: healthy/normal

value: peripheral blood

tag: sample group

value: control


title: TG_M1: OIH_M1_Trigeminal_Ganglia

tag: strain


title: 4_test [s_4_cut_AGTTCC_5]

source_name: test

value: patients with CD5+ R/R DLBCL

value: test


title: 5_test [s_5_cut_TAGCTT_3]


title: B08: macrophage RNA seq

city: La Jolla

first: Shweta

last: Joshi

state: CA

address: 3855 Health Sciences Drive, MC 0815

department: Department of Pediatrics

institute: UCSD Moores Cancer Center

data_processing:
Bases called with bcl2fastq Conversion Software v2.20
FASTQ aligned to Ensembl GRCm38 with STAR v2.6.1a using parameters: --outFilterMultimapNmax 1  --outReadsUnmapped  Fastx  --outSAMtype  BAM  SortedByCoordinate  --twopassMode  Basic
Reads mapped to genes with featureCounts v1.6.2 using  GRCm38 GTF from Ensembl
Read counts normalized to RPKM with custom code from https://github.com/KwatME/sequencing_process/pull/2/commits/381299448a7281a7ae42c22f8359d7df0c738349
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited text files include RPKM values for each sample

source_name: macrophage

growth_protocol: Bone marrow derived macrophages were isolated from mice and were grown in MCSF conditions.

extract_protocol:
Bulk mRNA was extracted using Qiagen RNAeasy kit
For RNA sequencing, RNA libraries were prepared and sequenced on Illumina HiSeq4000 using standard Illumina protocols

treatment_protocol: After 5 days of culture in MCSF, BMDMs were treated with JQ1 or SF2523 followed by stimualtion with LPS or IL4

value: macrophage

tag: exposure

tag: drug


title: B06: macrophage RNA seq

value: LPS


title: 3_control [s_3_cut_CTTGTA_1]


title: B07: macrophage RNA seq


title: B09: macrophage RNA seq


title: B05: macrophage RNA seq


title: B04: macrophage RNA seq


title: 1_test [s_1_cut_GGCTAC_6]


title: B03: macrophage RNA seq


title: 2_control [s_2_cut_AGTCAA_4]


title: RNA 1 rep2


title: Urinary exosomes, NCAME_children_212

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalized and statistically analyzed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts

source_name: Urine-derived exosomes

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 100 to 300 ng of exosomal RNA was used as input for library construction.

tag: developmental stage

value: child

tag: condition

value: NCAME

tag: sample type

value: Urine-derived exosomes


title: A09: macrophage RNA seq

tag: tissue


title: B01: macrophage RNA seq


title: Urinary exosomes, NCAME_children_262


title: B02: macrophage RNA seq


title: Urinary exosomes, NCAME_adult_245

value: adult


title: A11: macrophage RNA seq


title: Urinary exosomes, NCAME_children_208


title: Urinary exosomes, NCAME_children_269


title: Urinary exosomes, NCAME_adult_276


title: A12: macrophage RNA seq


title: Urinary exosomes, NCAME_children_254


title: RNA 1 rep1


title: Urinary exosomes, NCAME_adult_137


title: A10: macrophage RNA seq


title: A08: macrophage RNA seq


title: Urinary exosomes, NCAME_adult_385


title: Urinary exosomes, NCAME_adult_135


title: A05: macrophage RNA seq


title: A04: macrophage RNA seq


title: A06: macrophage RNA seq


title: Urinary exosomes, Control_children_157

value: Control


title: Urinary exosomes, Control_children_239


title: A03: macrophage RNA seq

value: NS


title: A02: macrophage RNA seq


title: Urinary exosomes, Control_children_240


title: Urinary exosomes, Control_adult_197


title: Urinary exosomes, Control_adult_290


title: Urinary exosomes, Control_adult_163


title: Unstim 3 [U3]

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

institute: University of Illinois at Champaign-Urbana

description:
U3_GAGATTCC-ATAGAGGC_L002
WT, not exercised, replicate 1

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Each sample's fastq file run through trimmomatic (v 0.36) to first remove any remaining standard Illumina adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-SE:2:15:10 LEADING:28 TRAILING:28 MINLEN:30)
Salmon (v 0.8.2) was used to quasi-map reads to Gencode's Release M17 transcript sequences with arguments --seqBias, --gcBias and --numBootstraps=30
tximport (v 1.8.0, R 3.5.1) was used to sum the transcript counts to the gene level using the lengthScaledTPM method
Genome_build: Gencode M17, based on GRCm38
Supplementary_files_format_and_content: The quant.sf files are tab-delimited text files containing transcript names, lengths, effective lengths, Transcript Per Million values and estimated count values. The gene-level counts are in the tab-delimited supplementary data file Boppart_GeneCounts_GEO.txt; these counts were analyzed directly using the edgeR-quasi method, and hence are the final normalized data.

source_name: unstimulated sham control (U)

growth_protocol: All mice were housed in the animal facility at the University of Illinois in a temperature-controlled specific pathogen-free animal room maintained on a 12:12 light-dark cycle. The animals were fed standard laboratory chow and water ad libitum. Protocols for animal use were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Illinois at Urbana-Champaign.

extract_protocol:
The sorted CD146+CD45-CD31- pericytes were frozen in QIAzol Lysis Reagent and later homogenized and processed using the Qiagen miRNeasy Mini Kit. Spectrophotometer was used to determine approximate concentration and quality control was performed using the 2100  Bioanalyzer (Agilent, Santa Clara, CA).
The RNAseq libraries were prepared with the SMARTer Stranded Total RNAseq kit v2 Pico input Mammalian from Clontech.

treatment_protocol: 14 week-old WT mice were randomly assigned to a unstimulated sham control (U) or an acute electrical stimulation (S) group.  Males (n=3/group) were equally represented in each of the two groups. Crural muscles (anterior, posterior, and lateral muscles responsible for foot movement) are stimulated to rotate from 19° of ankle dorsiflexion to 19° ankle plantarflexion (for eccentric contraction) and vice versa (for concentric contraction). The electrical stimulation is then applied for a total of 40 contractions (20 eccentric and 20 concentric) lasting approximately 10 minutes per animal. Mice were euthanized via carbon dioxide asphyxiation 3 hr post-exercise. The gastrocnemius-soleus complexes were rapidly dissected and processed for cell sorting of CD146+CD45-CD31- pericytes.

tag: genotype/variation

value: WT

value: 14 weeks

value: male

value: Not Exercised

value: skeletal muscle

value: gastrocnemius-soleus complexes

value: CD146+CD45-CD31- pericytes


title: A01: macrophage RNA seq


title: Urinary exosomes, Control_adult_145


title: Stim 2 [S2]

description:
S2_GAATTCGT-ATAGAGGC_L002
WT, exercised, replicate 1

source_name: acute electrical stimulation (S)

value: Exercised


title: Unstim 1 [U1]

description:
U1_TCCGGAGA-ATAGAGGC_L002
WT, not exercised, replicate 1


title: WT-H3K4me1

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

data_processing:
1. All the raw sequencing data were mapped to Mus musculus genome assembly NCBI build 37 (mm9) using bowtie 1.1.2. Only the uniquely aligned reads were kept.
2. Aligned reads were used to call peaks using SICER v1 using window size 200 bp and FDR 1e-8. 200bp was used as  a gap size for H3K4me3 and H3K27ac and 600bp was used for H3K27me3, H3K4me1, H2AK119Ub, H2BK120Ub. 600 bp was used for the fragment size. Reads with the same coordinate information were considered as duplicates and were discarded.
Genome_build: NCBI build 37, mm9
Supplementary_files_format_and_content: Processed data are the peaks in BED4 format (chrom+start+end+intensity).

source_name: pancreas

growth_protocol: F12/DMEM, without phenol red, supplemented with EGF

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies.
Libraries were prepared according to NEBNext® Ultra™ II DNA Library Prep Kit and sequenced on the Illumina HiSeq4000 platform.

value: Mixed C57BL6/Sv129

tag: chip antibody

value: Mono-Methyl-Histone H3 (Lys4) (D1A9), Cell Signaling Technology, Cat# 5326, RRID:AB_10694535

tag: genotype

value: Bap1 WT;KrasG12D

tag: input used for data normalization


title: Unstim 2 [U2]

description:
U2_CGCTCATT-ATAGAGGC_L002
WT, not exercised, replicate 1

tag: strain background

tag: cell type


title: Stim 3 [S3]

description:
S3_CTGAAGCT-ATAGAGGC_L002
WT, exercised, replicate 1

tag: age

tag: treatment


title: A07: macrophage RNA seq

value: macrophage


title: KO-H3K4me1

value: Bap1 KO;KrasG12D


title: WT-H3K4me3

value: Tri-Methyl Histone H3 (Lys4) (C42D8), Cell Signaling Technology, Cat# 9751, RRID:AB_2616028


title: Urinary exosomes, Control_children_343

value: child

value: Urine-derived exosomes


title: MTG PD Male [MTG20]

city: Jerusalem

first: Alon

last: Simchovitz

address: Silberman Building, Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Adaptor sequences were clipped from 75-bp long reads.
Further processing of the data was performed using the Galaxy platform. Alignment to the hg38 version of the human genome was performed using the HISAT2 algorithm, using default parameters
BAM files were then subjected to the Rmdup algorithm to remove duplicated reads originating from the final PCR stage of the library preperation method.
Processed BAM files were annotated using the htseq-count algorithm, using default parameters and the Gencode23 Human annotation.
Files with >500K annotated counts were then subjected to the edgeR algorithm for disease-related differential expression, while accounting for age, sex and RNA integrity number
Genome_build: Homo Sapiens, Hg38
Supplementary_files_format_and_content: tab-delimited text file of gene names and counts for each sample + comma-seperated values file for differential expression extracted from the edgeR algorithm

source_name: Medial Temporal Gyrus

extract_protocol:
miRNeasy RNA Extraction Kit
RNA-Tag Seq

tag: disease state

value: Parkinson's disease+Dementia

tag: Sex

value: Male

value: Medial Temporal Gyrus

tag: rna integerity number


title: MTG PD Male [MTG23]


title: MTG PD Male [MTG19]


title: MTG PD Male [MTG17]


title: MTG PD Male [MTG18]


title: MTG PD Male [MTG21]


title: MTG PD Male [MTG16]


title: WT-H3K27ac

tag: strain

value: Acetyl-Histone H3 (Lys27) (D5E4) XP, Cell Signaling Technology, Cat# 8173P, RRID:AB_10949887


title: MTG PD Male [MTG14]


title: KO-H3K27ac


title: MTG PD Female [MTG13]

value: Female


title: MTG PD Male [MTG22]


title: WT-H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11), Cell Signaling Technology, Cat# 9733, RRID:AB_2616029


title: Stim 1 [S1]

description:
S1_ATTCAGAA-ATAGAGGC_L002
WT, exercised, replicate 1

value: WT

value: 14 weeks

value: male

value: skeletal muscle

value: gastrocnemius-soleus complexes


title: WT-H2BK120ub

value: Mixed C57BL6/Sv129

value: Ubiquityl-Histone H2B (Lys120) (D11), Cell Signaling Technology, Cat# 5546, RRID:AB_10693452

value: Bap1 WT;KrasG12D


title: KO-H2BK120ub

value: Bap1 KO;KrasG12D


title: MTG PD Female [MTG11]


title: KO-H2AK119ub

value: Ubiquityl-Histone H2A (Lys119) (D27C4), Cell Signaling Technology, Cat# 8240, RRID:AB_10891618


title: MTG PD Female [MTG10]


title: MTG Cont Male [MTG8]

value: Non-Demented Control


title: MTG Cont Male [MTG9]


title: WT-H2AK119ub


title: Input 2

value: Beads-IgG control


title: MTG Cont Male [MTG7]

value: Male


title: Input 1


title: MTG Cont Male [MTG6]

value: Medial Temporal Gyrus


title: MTG Cont Female [MTG3]


title: I33268-L2: Healthy individual, no Globin-Block 8 resequenced

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

country: Germany

institute: Christian-Albrechts Universität zu Kiel

description:
I33268-L2
globinblock_rawcounts_resequenced.csv

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Reads were aligned with STAR (2.5.2b-2) on usegalaxy.eu
Alignments were sumarized on transcript level by htseq-count (0.9.1) yielding raw counts.
The summarized read tables were merged into one file using R and the data.table package.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: Comma separated values (csv) with gene names, sample name (name of the raw data), if the sample was treated with Globin-Block (condition), and raw htseq-count counts.

source_name: Whole Blood

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in samples with “yes” in the column “Globin Block applied”. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

tag: globin-block applied

value: no

tag: identifier

value: Whole Blood


title: MTG Cont Female [MTG5]

value: Female


title: KO-H3K4me3

value: Tri-Methyl Histone H3 (Lys4) (C42D8), Cell Signaling Technology, Cat# 9751, RRID:AB_2616028


title: I33269-L2: Healthy individual, no Globin-Block 10 resequenced

description:
I33269-L2
globinblock_rawcounts_resequenced.csv


title: MTG Cont Female [MTG4]


title: MTG PD Male [MTG15]

value: Parkinson's disease+Dementia


title: MTG PD Female [MTG12]


title: I33265-L2: Healthy individual, no Globin-Block 5 resequenced

description:
I33265-L2
globinblock_rawcounts_resequenced.csv


title: AM PD Female [AM23]

source_name: Amygdala

value: Amygdala


title: MTG Cont Female [MTG1]


title: MTG Cont Female [MTG2]


title: AM PD Male [AM22]


title: I33264-L2: Healthy individual, no Globin-Block 4 resequenced

description:
I33264-L2
globinblock_rawcounts_resequenced.csv


title: I33266-L2: Healthy individual, no Globin-Block 6 resequenced

description:
I33266-L2
globinblock_rawcounts_resequenced.csv


title: KO-H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11), Cell Signaling Technology, Cat# 9733, RRID:AB_2616029


title: I33263-L2: Healthy individual, no Globin-Block 3 resequenced

description:
I33263-L2
globinblock_rawcounts_resequenced.csv


title: AM PD Male [AM21]


title: I33269-L1: Healthy individual, with Globin-Block 10 resequenced

description:
I33269-L1
globinblock_rawcounts_resequenced.csv

value: yes


title: AM PD Male [AM20]


title: AM PD Male [AM19]


title: I33268-L1: Healthy individual, with Globin-Block 8 resequenced

description:
I33268-L1
globinblock_rawcounts_resequenced.csv


title: I33266-L1: Healthy individual, with Globin-Block 6 resequenced

description:
I33266-L1
globinblock_rawcounts_resequenced.csv


title: I33262-L2: Healthy individual, no Globin-Block 2 resequenced

description:
I33262-L2
globinblock_rawcounts_resequenced.csv


title: AM PD Male [AM18]


title: I33267-L2: Healthy individual, no Globin-Block 7 resequenced

description:
I33267-L2
globinblock_rawcounts_resequenced.csv


title: AM PD Female [AM17]


title: AM PD Male [AM16]


title: I33262-L1: Healthy individual, with Globin-Block 2 resequenced

description:
I33262-L1
globinblock_rawcounts_resequenced.csv


title: I33263-L1: Healthy individual, with Globin-Block 3 resequenced

description:
I33263-L1
globinblock_rawcounts_resequenced.csv


title: AM PD Male [AM15]


title: I33264-L1: Healthy individual, with Globin-Block 4 resequenced

description:
I33264-L1
globinblock_rawcounts_resequenced.csv


title: AM PD Male [AM14]


title: AM PD Male [AM13]


title: AM PD Male [AM12]


title: AM PD Male [AM11]


title: AM PD Male [AM10]


title: AM PD Male [AM9]


title: AM Cont Male [AM7]


title: AM Cont Male [AM5]


title: AM Cont Female [AM6]


title: AM Cont Female [AM4]


title: I33267-L1: Healthy individual, with Globin-Block 7 resequenced

description:
I33267-L1
globinblock_rawcounts_resequenced.csv


title: AM Cont Female [AM3]


title: AM Cont Male [AM1]


title: I33265-L1: Healthy individual, with Globin-Block 5 resequenced

description:
I33265-L1
globinblock_rawcounts_resequenced.csv


title: AM Cont Male [AM2]


title: 114_Exp-A: TBP3X-T114A sh BTAF1 A

city: Baltimore

first: Gerald

middle: W

last: Hart

state: MD

address: 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins School of Medicine

data_processing:
Single-end 75nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Homo sapiens sequence GRCh38.p12 Apr-'18, with CLCGenomicsServer 10.0.1 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 9.1.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: NCBI GRCh38.p12
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.  Contains nulls for FPKM = 0

source_name: HeLa cell

growth_protocol: DMEM 10% FCS, 2mM L glutamine, 1mM sodium pyruvate, 25mM glucose,  2ug/ml puromycin at 37°C and under 5% CO2

extract_protocol:
RNAs were extracted using RNeasy plus kit (QIAGEN)following manufacturer’s instructions.
RNA-Seq libraries were constructed using TruSeq stranded Total mRNA library kit (Illumina, Inc.).

treatment_protocol: Endogenous TBP gene was edited using CRISPR/Cas9 technology in HeLa cells. The 3X-FLAG was inserted in phase at the N-terminal of the protein and the T114 O-GlcNAcylation site was replaced by an alanine. Transduction of lentivirus encoding shRNA targeting BTAF1 transcripts or shRNA control were performed following manufacturer’s instruction and stably shRNA expressing cell were selected 48h later with DMEM 2ug/ml puromycin.

tag: cell line

value: HeLa

value: tagged T114A O-GlcNAc TBP mutant + shBTAF1

tag: transduction

tag: genotype ii

value: O-GlcNAc TBP mutant


title: 114_Exp-C: TBP3X-T114A sh BTAF1 C


title: 114_Cont-C: TBP3X-T114A sh control C

value: tagged T114A O-GlcNAc TBP mutant + sh control

value: control


title: 114_Exp-B: TBP3X-T114A sh BTAF1 B


title: 3x_Exp-B: TBP3X-WT sh BTAF1  B

value: tagged TBP wild type + shBTAF1

value: wild type


title: 3x_Exp-A: TBP3X-WT sh BTAF1 A


title: 114_Cont-B: TBP3X-T114A sh control B


title: 3x_Exp-C: TBP3X-WT  sh BTAF1 C


title: 114_Cont-A: TBP3X-T114A sh control A


title: 3x_Cont-A: TBP3X-WT sh control A

value: tagged TBP wild type + sh control


title: 3x_Cont-C: TBP3X-WT  sh control C


title: 3x_Cont-B: TBP3X-WT  sh control B


title: SN PD Male [SN28]

description: Ribosomal-depleted RNA

data_processing:
Adaptor sequences were clipped from 75-bp long reads.
Further processing of the data was performed using the Galaxy platform. Alignment to the hg38 version of the human genome was performed using the HISAT2 algorithm, using default parameters
BAM files were then subjected to the Rmdup algorithm to remove duplicated reads originating from the final PCR stage of the library preperation method.
Processed BAM files were annotated using the htseq-count algorithm, using default parameters and the Gencode23 Human annotation.
Files with >500K annotated counts were then subjected to the edgeR algorithm for disease-related differential expression, while accounting for age, sex and RNA integrity number
Genome_build: Homo Sapiens, hg38
Supplementary_files_format_and_content: tab-delimited text file of gene names and counts for each sample + comma-seperated values file for differential expression extracted from the edgeR algorithm

source_name: SN PD Male

tag: subject status

value: PD+Dementia

tag: gender

value: Male

tag: tissue

value: Substantia nigra


title: SN Cont Male [SN27]

description: Ribosomal-depleted RNA

source_name: SN Cont Male

value: Non-Demented Control


title: SN PD Male [SN26]

description: Ribosomal-depleted RNA


title: SN Cont Male [SN24]

description: Ribosomal-depleted RNA


title: SN PD Male [SN23]

description: Ribosomal-depleted RNA


title: SN Cont Female [SN29]

description: Ribosomal-depleted RNA

source_name: SN Cont Female

value: Female


title: SN Cont Female [SN25]

description: Ribosomal-depleted RNA


title: SN PD Female [SN21]

description: Ribosomal-depleted RNA

source_name: SN PD Female


title: SN PD Male [SN20]

description: Ribosomal-depleted RNA


title: SN PD Male [SN19]

description: Ribosomal-depleted RNA


title: SN Cont Female [SN17]

description: Ribosomal-depleted RNA


title: SN PD Male [SN22]

description: Ribosomal-depleted RNA


title: SN PD Female [SN18]

description: Ribosomal-depleted RNA


title: SN PD Male [SN16]

description: Ribosomal-depleted RNA


title: SN Cont Female [SN13]

description: Ribosomal-depleted RNA


title: SN PD Male [SN15]

description: Ribosomal-depleted RNA


title: SN PD Male [SN12]

description: Ribosomal-depleted RNA


title: SN PD Male [SN9]

description: Ribosomal-depleted RNA


title: SN PD Male [SN11]

description: Ribosomal-depleted RNA


title: SN Cont Male [SN14]

description: Ribosomal-depleted RNA


title: SN PD Female [SN8]

description: Ribosomal-depleted RNA


title: SN PD male [SN10]

description: Ribosomal-depleted RNA

source_name: SN PD male


title: T-2

city: Harbin

first: yandong

last: zhang

address: 92 xidazhi street

institute: Harbin Institute of Technology

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official database information, then to calculate FPKM the gene or transcript level separately and to find the difference using Ballgown software.
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome HG19, by Hisat2 software（v2.0.4）
Genome_build: HG19
Supplementary_files_format_and_content: Xlsx include FPKM values for all sample

source_name: gastric cells_treatment

growth_protocol: MGC-803 cells were were maintained in high glucose DMEM supplemented with 10% fetal bovine serum in a humidiﬁed atmosphere with 5% CO2 at 37 oC.

extract_protocol:
The whole RNA of MGC-803 cell lines was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for sequencing library construction.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.

treatment_protocol: Cells were treated without or with 50 µg/mL of essential oil from Pinus Koraiensis pinecones for 24 h.

value: human gastric cancer cell line


title: SN Cont Male [SN6]

description: Ribosomal-depleted RNA


title: T-3

value: 50 µg/mL of essential oil from Pinus Koraiensis pinecones for 24 h


title: SN PD Male [SN7]

description: Ribosomal-depleted RNA


title: T-1


title: C-3

source_name: gastric cells_control

value: none (control)


title: SN Cont Male [SN4]

description: Ribosomal-depleted RNA


title: SN PD Female [SN3]

description: Ribosomal-depleted RNA


title: SN Cont Female [SN5]

description: Ribosomal-depleted RNA


title: C-1


title: SN Cont Female [SN2]

description: Ribosomal-depleted RNA


title: C-2


title: SN Cont Male [SN1]

description: Ribosomal-depleted RNA


title: TBP_3XT114A_C

data_processing:
Single-end 75nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to homo sapiens sequence GRCh38.p11 with CLCGenomicsServer 8.5.3 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 8.5.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v6.6
Genome_build: Human NCBI build GRCh38.p11 (RefSeq)
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.

source_name: TBP3X-T114A C

growth_protocol: DMEM 10% FCS, 2mM L glutamine, 1mM sodium pyruvate, 25mM glucose at 37°C and under 5% CO2

extract_protocol:
RNAs were extracted using RNeasy plus kit (QIAGEN).
Single-end 75nt Illumina sequencing libraries were constructed according to the manufacturer’s TruSeq RNA library prep standard protocol and sequenced on the Illumina NextSeq 500 sequencer.

tag: genotype

value: tagged T114A O-GlcNAc TBP mutant

value: HeLa cell


title: TBP_3XT114A_B

source_name: TBP3X-T114A B


title: TBP_3XT114A_A

source_name: TBP3X-T114A A


title: AM Cont Female [AM8]

value: Amygdala


title: HPDE_BAP1

data_processing:
1. All the raw sequencing data were mapped to Human genome assembly GRCh37/hg19 using bowtie 1.1.2. Only the uniquely aligned reads were kept.
2. Aligned reads were used to call peaks using SICER v1 using window size 200 bp and FDR 1e-5 for BAP1 and 1e-8 for H2AK119Ub.  600bp were used as the gap size. 600 bp was used for the fragment size.Reads with the same coordinate information were considered as duplicates and were discarded.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data are the peaks in BED4 format (chrom+start+end+intensity).

growth_protocol: DMEM + 10% serum

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies.
Libraries were prepared according to NEBNext® Ultra™ II  DNA Library Prep Kit for Illumina and libraries were sequenced on the HiSeq4000 platform.

treatment_protocol: 10Gy of IR

value: HPDE

value: human pancreatic duct epithelial (HPDE) cells

tag: chip antibody

value: BAP1 (D1W9B) (ChIP), Cell Signaling Technology, Cat# 78105

tag: input used for data normalization


title: HPDE_H2AK119Ub

tag: cell type

value: Ubiquityl-Histone H2A (Lys119) (D27C4), Cell Signaling Technology, Cat# 8240, RRID:AB_10891618


title: HPDE_BAP1_IR

tag: treatment

value: 10Gy of ionizing irradiation


title: PANC1_H2AK119Ub_IR

value: human pancreatic cancer cell line


title: TBP_3XWT_C

source_name: TBP3X-WT  C

value: tagged TBP wild type


title: TBP_3XWT_A

source_name: TBP3X-WT  A


title: TBP_WT_C

source_name: TBPWT C

value: parental cell line


title: PANC1_BAP1

source_name: pancreas


title: PANC1_BAP1_IR


title: Input#2

value: Input#2 (Control)

value: Beads-IgG control


title: TBP_WT_B

source_name: TBPWT B


title: Input#1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies.
Libraries were prepared according to NEBNext® Ultra™ II  DNA Library Prep Kit and sequenced on the Illumina HiSeq4000 platform.

value: Input#1 (Control)


title: TBP_WT_A

source_name: TBPWT A


title: HPDE_H2AK119Ub_IR


title: TAT-11-663R-miRNA_S23

city: Los Angeles

first: Sanda

last: Win

address: 2011 Zonal Ave

department: Medicine

institute: Univeristy of Southern California

description: RNA/miRNA

data_processing:
miRNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed for QIAseq miRNA NGS 3’ (AACTGTAGGCACCATCAAT) and 5' adapters (GTTCAGAGTTCTACAGTCCGACGATC) then for low quanlity bases (Quality Score trimming, min quality level 20, trim from both ends, min read length 15)
Trimmed reads were aligned to mm10 using Bowtie (seed mismatch limit 1, seed length 10)
Aligned reads were quantified to mirBase mature miRNAs v21 using Partek E/M
Raw read counts were filtered (exclude a feature where its maximum reads <= 5 in all samples) and normalized (offset by 1 and then upper-quartile normalization)
Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw read counts

source_name: Liver

growth_protocol: Normal body weight and growth

extract_protocol:
Liver was cut into pieces in RNAlater RNA stabilizing buffer (Qiagen) and frozen in same buffer in liquid nitrogen and stored in -80C.
Qiagen miRNA library construction kit

tag: age

value: 12 week adult

tag: health status

value: Normal

value: Female

value: liver


title: TAT-10-661R-miRNA_S22

description: RNA/miRNA

tag: Sex


title: TAT-08-658R-miRNA_S20

description: RNA/miRNA

tag: strain

value: Male


title: TAT-09-659R-miRNA_S21

description: RNA/miRNA


title: PANC1_H2AK119Ub


title: TAT-07-657R-miRNA_S19

description: RNA/miRNA


title: TBP_3XWT_B

source_name: TBP3X-WT  B

value: HeLa cell


title: TAT-12-664R-miRNA_S24

description: RNA/miRNA


title: SP25_3

city: New Haven

first: Douglas

middle: E.

last: Brash

state: CT

address: 333 Cedar St. / HRT213

department: Therapeutic Radiology

institute: Yale School of Medicine

data_processing:
The sequencing reads were processed using a homebrew script to detect and clip the linkers. A new fastq file was created such that all the reads that had the linker were designated as Read1, and hence always defined the lesion end of the fragment, and the R2 was always the distal end.  We used first 7 bases of the read to look for the presence of the linker.
The clipped sequences were then aligned with the reference human genome (UCSC hg19) using bwa mem.
The resulting alignment file was further filtered such that all the read-pairs that started and ended at exactly same place were considered to be PCR duplicates, and removed.  All the reads where only the lesion end aligned at the same position were considered "recurrent", and saved separtely.
The filtered files were then processed with R
Genome_build: hg19
Supplementary_files_format_and_content: The files are tab separated text files, with the following columns, loc, strand, total count, sample-names.  Under each sample name the number denotes number of time that location was seen in that sample.

source_name: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC569

extract_protocol:
Phenol:chloroform extraction of genomic DNA from cells,followed by blocking of spontaneous DNA damage, nicking of DNA at cyclobutane dimer sites, second strand synthesis, linker ligation, sonication, and purification as described earlier.
Bioanalyzer, size selection, end repair, ligate barcoded Illumina adapters, and PCR several cycles

value: melano sgl #3

value: 2000 nbUVB

tag: linker

tag: pre-incision

value: yes

tag: molecule subtype

value: genomic + mito DNA


title: SP15_3

source_name: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC484

value: melano sgl


title: Daoy_DMEM_passage3_3

type: RNA

city: Milwaukee

first: Ramani

last: Ramchandran

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Gene expression after 3 passages cultured in DMEM

hyb_protocol: The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000. 1 ug of each labeled cRNA was fragmented by adding 11 uL 10X Blocking Agent and 2.2 uL of 25X Fragmentation Buffer, then heated at 60C for 30 min, and finally 55 uL 2X GE Hybridization buffer was added to dilute the labeled cRNA. 100 uL of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: Daoy (HTB-186)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Daoy cells were grown in ACM or DMEM (Gibco) supplemented with 10% fetal bovine serum and 1X antibiotic antimycotic (Gibco). Passaged cells were detached with 0.25% Trypsin EDTA (Gibco) and reseeded in full media (control or experimental) at 1:3 density. Astrocytes were cultured with DMEM (Gibco) supplemented with 10% fetal bovine serum.

extract_protocol: The RNAs were extracted by standard TRIzol method.

treatment_protocol: Experimental condition was Daoy cells cultured normally (see growth protocol) in ACM.

tag: cell line

value: Daoy (HTB-186)

tag: passage

value: 3 passages

tag: agent

value: DMEM


title: Daoy_DMEM_passage3_1


title: Daoy_ACM_passage3_2

description: Gene expression after 3 passages cultured in ACM

value: ACM


title: SP21_3

source_name: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC572

value: melano sgl #2


title: Daoy_ACM_passage1_1

description: Gene expression after 1 passage cultured in ACM

value: 1 passage


title: SP35_2

description:
processed data file: da7_x.txt
SP35-AH5NFCBCX2

source_name: Primary fibroblast, foreskin

value: Primary fibroblast, foreskin

value: fibro

value: 20 UVC +    7 d repair


title: Daoy_DMEM_passage1_1

description: Gene expression after 1 passage cultured in DMEM


title: Daoy_ACM_passage3_1


title: Daoy_DMEM_passage3_2


title: Daoy_ACM_passage1_3


title: SP27_2

description:
processed data file: da3_x.txt
SP27-BH5GK2BCX2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC569

value: melano     sgl #3

value: 2000 nbUVB +    3 d repair


title: Daoy_ACM_passage1_2


title: Daoy_DMEM_passage1_2


title: SP26_2

description:
processed data file: da1_x.txt
SP26-AH5NFCBCX2

value: 2000 nbUVB +    1 d repair


title: Daoy_ACM_passage3_3


title: SP24_2


title: Sample_40mHKST_20U_r2

city: TALLAHASSEE

first: LAUREN

middle: A

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

description: Normal

data_processing:
Basecalls performed with CAVASA version v1.8.4
Sequencing data aligned to the HG19 genome using bowtie2 version 2.2.2, --wrapper basic -0 --end-to-end -p 23 --no-mixed --no-discordant -I 0 -X 500 -q -x -S
Using samtools via the R package gyro (https://github.com/dvera/gyro), raw files converted from sam to bam files, minQual=20
Bed files were generated using bedtools via the R package travis (https://github.com/dvera/travis) and mat10 files were created using the package genmat (https://github.com/dvera/genmat). Nucleosome distributions were calculated by fragments per million for each bp in the 2kb surrounding each TSS (bedtoolsCoverage). Midpoints for nucleosome distributions were determined through the calculation of center fragments in 60 bp windows at a 10 bp step in the 2kb surrounding each TSS.
Genome_build: hg19
Supplementary_files_format_and_content: mat10 files

source_name: B-Lymphocyte

growth_protocol: GM12878 cells were grown in RPM1 1640 media, supplemented with 15% Fetal Bovine Serum and 1X PSG.

extract_protocol:
Nuclei were isolated in nucleus isolation buffer containing: 10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2, and 1% Nonidet P-40. The nuclei were then pelleted by centrifugation at 1000g for 5 min at 4°C.
Using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), DNA sequencing libraries were prepared for the mononucleosomal-sized and sub-nucleosomal-sized fragments for each sample. DNA was end-prepped using NEB Prep enzyme mix, end-repair reaction buffer (10X), and 30 ng of DNA for each samples, then held at 30 degrees Celsius for 30 minutes and then at 65 degrees Celsius for 30 minutes. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted ligated products. The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina. Then PCR was done for 8 cycles (not including the initial denaturation and final extension). The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted products. The libraries were quality-checked using Agilent 2100 Bioanalyzer High-Sensitivity. Across the libraries, the samples ranged between 200-400bp and there were no adapter or primer dimers.

treatment_protocol: For HKST treatment, GM12878 cells were stimulated with 1.0X10e9 heat-killed Salmonella typhimurium for 20 minutes, 40 minutes and 60 minutes and subsequently harvested.

value: B-lymphoblastoid cell line

value: 40 minute incubation with HKST rep 2

tag: mnase digest

value: Light


title: Sample_20mHKST_200U_r2

description: Normal

value: 20 minute incubation with HKST rep 2

value: Heavy


title: Sample_Cont_20U_r2

description: Normal

value: Untreated cells rep 2


title: Sample_Cont_200U_r2

description: Normal


title: Sample_20mHKST_20U_r2

description: Normal


title: Sample_60mHKST_20U_r2

description: Normal

value: 60 minute incubation with HKST rep 2


title: Sample_60mHKST_200U_r2

description: Normal


title: Sample_40mHKST_200U_r2

description: Normal


title: SP33_2

description:
processed data file: pos_x.txt
SP33_NOBCX-BCC8UGANXX

value: 20 UVC

value: yes

value: genomic + mito DNA


title: Daoy_DMEM_passage1_3

value: Daoy (HTB-186)

value: 1 passage

value: DMEM


title: SP23_2

description:
processed data file: da3_x.txt
SP23-AH5NFCBCX2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC572

value: melano     sgl #2


title: SP22_2

description:
processed data file: da1_x.txt
SP22-AH5NFCBCX2


title: SP20_2


title: SP21_2

value: 2000 nbUVB


title: SP15_2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC484

value: melano     sgl


title: SP16_2

description:
processed data file: da3_x.txt
SP16-AH5NFCBCX2

value: 2000 nbUVB +    3 d repair


title: SP32_1

description:
processed data file: neg_x.txt
SP32-BCB64FANXX

value: Primary fibroblast, foreskin

value: fibro

value: 0 UVC


title: SP26_1

description:
processed data file: da1_x.txt
SP26-ACBCV2ANXX
SP26-BH5GK2BCX2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC569

value: melano     sgl #3

value: 2000 nbUVB +    1 d repair


title: SP22_1

description:
processed data file: da1_x.txt
SP22-ACBCV2ANXX

value: 2000  nbUVB +    1 d repair

value: yes


title: SP35_1

description:
processed data file: da7_x.txt
SP35-BCB64FANXX

value: 20 UVC +    7 d repair

value: genomic + mito DNA


title: SP27_1

description:
processed data file: da3_x.txt
SP27-ACBCV2ANXX


title: SP34_1

description:
processed data file: ho4_x.txt
SP34-BCB64FANXX

value: 20 UVC +    4 hr repair


title: SP21_1

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC572

value: 2000  nbUVB


title: SP23_1

description:
processed data file: da3_x.txt
SP23-ACBCV2ANXX
SP23-BH5GK2BCX2

value: melano     sgl #2

value: 2000  nbUVB +    3 d repair


title: SP33_1

description:
processed data file: pos_x.txt
SP33-BCB64FANXX

value: 20 UVC


title: SP24_1


title: SP20_1


title: SP15_1

description:
SP15-ACBCV2ANXX
SP15-BH5GK2BCX2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC484

value: melano     sgl

value: 2000 nbUVB


title: SP12L17

description:
processed data file: neg_x.txt
SP12L17-ACBCV2ANXX

value: Primary fibroblast, foreskin

value: fibro

value: no


title: Erg fl/fl control rep 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 100 kB bin pairs using the R package diffHic v1.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 100 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: Bone marrow derived B220+ B-cell progenitors

extract_protocol:
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).
DNA was sequenced on an Illumina NextSeq 500 to produce 80bp paired-end reads using standard Illumina protocols.

treatment_protocol: Lineage negative bone marrow was cultured for 8 days on OP9 stromal cells with SCF, IL7 and FL cytokines, and purified using B220 positive selection.

tag: background strain

value: Rag1Cre+/+;Erg fl/fl (control)

tag: gender

value: male

value: B-cell progenitor


title: SP08

source_name: Primary melanocytes, foreskin, 3 donors, light + medium dark + very dark

value: melano  v dk + m dk + v light


title: SP13L17

value: 40 UVC

value: genomic + mito DNA


title: SP07

value: Primary melanocytes, foreskin, 3 donors, light + medium dark + very dark


title: SP16_1

description:
processed data file: da3_x.txt
SP16-ACBCV2ANXX
SP16-BH5GK2BCX2

value: 2000  nbUVB +     3 d repair

value: yes


title: SP09

value: 2000 nbUVB +    7 hr repair


title: SP14_1


title: SP06

source_name: 293T tumor cells

value: 293T tumor cells

value: 200 UVC


title: SP14_2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC484

value: melano     sgl


title: CreT control rep 2

tag: genotype

value: Rag1CreT/+ (control)

value: female


title: Erg fl/fl control rep 1


title: CreT control rep 1


title: SP25_1

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC569

value: melano     sgl #3

value: 2000 nbUVB


title: SP05

value: 40 J/m2 254 nm UVC

value: no


title: SP04


title: Erg KO rep 1

value: Rag1CreT/+;Erg fl/fl (Erg KO)

value: B-cell progenitor


title: tongue_KO_4

city: Bethesda

first: Roman

last: Szabo

state: Maryland

address: 30 Convent Drive, Rm.3A308

institute: National Institute of Dental and Craniofacial Research

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: tongue

extract_protocol:
Skin and tongue were collected from newborn mice. Tissues were frozen on dry ice and stored at -80 °C before further processing. Epidermis was manually separated from dermis after incubation for 5 min at 60 °C in 5 mM EDTA. Tissues were homogenized in Trizol reagent, and RNA was extracted according to the manufacturer’s protocol.
Double-stranded cDNA was prepared using the SMARTer V4 Ultra Low Input Kit (Clontech, Mountain View, CA).  Libraries were prepared using a TruSeq v2 kit (Illumina, San Diego, CA), individually barcoded, pooled to a 2 nM final concentration, and sequenced on a NextSeq500 sequencer (Illumina) using 37 x 37 paired-end mode.


title: 200673: Healthy individual, with Globin-Block 91

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Reads were aligned with STAR (2.5.2b-2) on usegalaxy.eu
Alignments were sumarized on transcript level by htseq-count (0.9.1) yielding raw counts and with StringTie (1.3.4d) yielding TPM. TPM values were not computed from the raw counts. The intention was to check if the findings hold irrespective of the read summarizer.
The summarized read tables were merged into one file using R and the data.table package.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: Tab separated values (tsv) with EnsemblID transcripts, sample name (name of the raw data), if the sample was treated with Globin-Block (condition), and the ensembl gene ID and the gene name.

source_name: Whole Blood

tag: globin-block applied

tag: identifier

tag: tissue

value: Whole Blood


title: 200672: Healthy individual, with Globin-Block 90


title: tongue_KO_3

tag: age


title: 200671: Healthy individual, with Globin-Block 89


title: 200670: Healthy individual, with Globin-Block 88


title: tongue_KO_2


title: tongue_KO_1


title: tongue_WT_1

value: wildtype


title: 200666: Healthy individual, with Globin-Block 84

value: yes


title: tongue_WT_2


title: 200668: Healthy individual, with Globin-Block 86


title: 200664: Healthy individual, with Globin-Block 83


title: 200663: Healthy individual, with Globin-Block 82


title: epidermis_KO_3

source_name: epidermis


title: 200662: Healthy individual, with Globin-Block 81


title: epidermis_KO_2


title: Erg KO rep 2

value: male

tag: cell type


title: 200659: Healthy individual, with Globin-Block 79


title: 200660: Healthy individual, with Globin-Block 80


title: epidermis_KO_1


title: 200658: Healthy individual, with Globin-Block 78


title: 200669: Healthy individual, with Globin-Block 87


title: epidermis_WT_3


title: epidermis_WT_2


title: epidermis_WT_1


title: tongue_WT_3


title: tongue_WT_4


title: 200655: Healthy individual, with Globin-Block 76


title: 200654: Healthy individual, with Globin-Block 75


title: 200667: Healthy individual, with Globin-Block 85


title: Rag1CreT/+;ErgΔ/Δ pre-proB cell replicate 2

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

data_processing:
Base-calling was performed using Illumina Casava v1.8.2
Adapters were trimmed using Trimgalore
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using STAR
Genewise counts were obtained using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: gzip compressed tab-delimited txt of raw counts

source_name: pre-proB cells

extract_protocol:
Total RNA was extracted using RNAeasy Kit from Qiagen from sorted primary B-cell progenitor populations
Illumina - Library Prep mRNA. HiSeq HT chemistry Paired Read (50/100)


title: Rag1CreT/+;ErgΔ/Δ pre-proB cell replicate 1


title: 200653: Healthy individual, with Globin-Block 74


title: Ergfl/fl preB cell replicate 2

source_name: preB cells

value: Ergfl/fl


title: epidermis_KO_4


title: Ergfl/fl preB cell replicate 1


title: Ergfl/fl proB cell replicate 2

source_name: proB cells


title: 200651: Healthy individual, with Globin-Block 72


title: 200652: Healthy individual, with Globin-Block 73


title: 200649: Healthy individual, with Globin-Block 70


title: 200650: Healthy individual, with Globin-Block 71


title: 200648: Healthy individual, with Globin-Block 69


title: Ergfl/fl proB cell replicate 1


title: Ergfl/fl pre-proB cell replicate 2


title: Ergfl/fl pre-proB cell replicate 1


title: 200647: Healthy individual, with Globin-Block 68


title: 200646: Healthy individual, with Globin-Block 67


title: 200656: Healthy individual, with Globin-Block 77


title: C17 ChIP in OP9 culture B-progenitor cells

description: genomic DNA bound to antibody

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Adapter sequence was trimmed using Trimmomatic
Reads were aligned to the mouse genome (GRCm38.73) using BWA
Peaks were called using MACS2 with settings --nomodel
Genome_build: mm10
Supplementary_files_format_and_content: bed files from MACS2 for each sample

growth_protocol: Lineage negative bone marrow cells were cultured in IL7, SCF and FL for 7 days on OP9 stromal cells

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin
KAPA Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: Positive selection for B220+ progenitor cells was performed to isolate B-cell progenitors

value: OP9 culture B-progenitor cells


title: 200644: Healthy individual, with Globin-Block 65


title: C17 ChIP in Rag1CreT/+;ErgΔ/Δ thymocyte

description: genomic DNA bound to antibody

value: Rag1CreT/+;Ergdelta/delta thymocyte


title: Erg Rescue preB

data_processing:
Base-calling was performed using Illumina Casava v1.8.2
Fastq files were aligned to the mm10 reference genome using Bowtie2 with default parameters.
Duplicate reads were removed using Picard.
ATACseq peaks were called using macs2 with the settings --nomodel --nolamda.
Normalized read counts were calculated by normalizing to the number of filtered mapped reads.
Genome_build: mm10

extract_protocol:
Nuclei were extracted using a cytoplasmic lysis buffer.
Extracted nuclei were tagmented using the Tn5 enzyme from the Nextera DNA library preparation Kit.


title: 200643: Healthy individual, with Globin-Block 64


title: 200642: Healthy individual, with Globin-Block 63


title: Erg Rescue pre-proB


title: Erg Rescue proB


title: 200641: Healthy individual, with Globin-Block 62


title: 200640: Healthy individual, with Globin-Block 61


title: 200639: Healthy individual, with Globin-Block 60


title: Erg KO pre-proB


title: WT proB


title: 200638: Healthy individual, with Globin-Block 59


title: WT preB


title: 200636: Healthy individual, with Globin-Block 58


title: mdx_1

city: Petah Tikva

first: Nurit

last: Yanay

address: Kaplan 14 St.

department: The Institute of Neurology

institute: Schneider Children's Medical Center of Israel

description: DMD mouse model

data_processing:
bcl2fastq, v2.15.0.4, was used to convert .bcl files to fastq files.
Raw reads were quality trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32. The scripts use a sliding window of 5 bases from the read's end and trim one base at a time until the average quality of the window passes the given threshold.
Adapter sequences were removed with Trim Galore!, version 0.3.7, keeping reads of length at least 15.
Reads were further filtered using the fastq_quality_filter program of the FASTX package, version 0.0.14, with parameters -q 20 -p 85.
Reads were mapped using TopHat, v2.0.13, with parameters -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 5, and providing an annotations file from Ensembl release 78 (-G parameter).
Quantification, normalization and differential expression were done with the Cufflinks package, v2.2.1. Cuffquant was run with parameters -b, -u and -M, masking for short non-coding genes. Cuffnorm was run with default parameters. Cuffdiff was run with -c 6 parameter. Significantly differentially expressed genes were defined as having at least 0.2 FPKM in at least one of the conditions and a q-value less than 0.05. Further filtering was done to include only known genes and exclude genes with infinite change.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_exp.xls, an Excel sheet with columns for general gene details, followed by columns of FPKM values for each sample, followed by groups of 10 columns for each of the 2 comparisons mdx/WT and dy2J/WT, with the output of cuffdiff. Missing values are marked with '?'.

source_name: Quadriceps muscle

extract_protocol:
Quadriceps muscle tissues were isolated from mice and immediately immersed in RNAlater RNA Stabilization Reagent (Qiagen, Valencia, CA), frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using the miRNeasy mini kit – cat: 217004 (QIAGEN Inc., Valencia, CA) according to manufacturer protocol. The resulting samples were then assessed with a spectrophotometer to estimate their total RNA concentration (NanoDrop 2000c, Thermo Fisher Scientific Waltham, MA, USA) and by the Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA) for quality control.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skeletal muscle

value: 8 weeks


title: mdx_2

description: DMD mouse model


title: mdx_3

description: DMD mouse model


title: dy2J_2

description: Lama2-CMD mouse model

value: C57BL/6J Lama2dy-2J


title: 200635: Healthy individual, with Globin-Block 57


title: 200633: Healthy individual, with Globin-Block 55


title: 200634: Healthy individual, with Globin-Block 56


title: dy2J_1

description: Lama2-CMD mouse model


title: 200631: Healthy individual, with Globin-Block 53


title: WT_3


title: 200630: Healthy individual, with Globin-Block 52


title: 200629: Healthy individual, with Globin-Block 51


title: WT_1


title: 200628: Healthy individual, with Globin-Block 50


title: 200626: Healthy individual, with Globin-Block 48


title: 200627: Healthy individual, with Globin-Block 49


title: 200624: Healthy individual, with Globin-Block 46


title: 200625: Healthy individual, with Globin-Block 47


title: WT_2


title: 200621: Healthy individual, with Globin-Block 43


title: WT pre-proB


title: 200622: Healthy individual, with Globin-Block 44


title: 200618: Healthy individual, with Globin-Block 40


title: 200617: Healthy individual, with Globin-Block 39


title: 200619: Healthy individual, with Globin-Block 41


title: 200620: Healthy individual, with Globin-Block 42


title: 200632: Healthy individual, with Globin-Block 54

description:
globinblock_rawcounts.csv
Outlier


title: 200615: Healthy individual, with Globin-Block 37

description:
globinblock_rawcounts.csv
Outlier


title: 200613: Healthy individual, with Globin-Block 35


title: 200616: Healthy individual, with Globin-Block 38


title: 200612: Healthy individual, with Globin-Block 34


title: 200614: Healthy individual, with Globin-Block 36

description:
globinblock_rawcounts.csv
Outlier


title: 200611: Healthy individual, with Globin-Block 33


title: 200623: Healthy individual, with Globin-Block 45


title: 200610: Healthy individual, with Globin-Block 32


title: 200607: Healthy individual, with Globin-Block 29


title: 200605: Healthy individual, with Globin-Block 27


title: 200606: Healthy individual, with Globin-Block 28


title: 180517_30: PROKR1 Knockout HEK293T cells before after stimulation

city: Gangwon-do

first: MOK

last: JONGSOO

state: Pyeongchang-gun

address: 25354 Pyeongchang-daero, Daehwa-myeon

department: Department of International Agricultural Technology

institute: Seoul National University

hyb_protocol: After fragmentation, 10 ug of cRNA is hybridized to GeneChip for 16 hours at 45C.

scan_protocol: GeneChips were scanned using the G2500A Hewlett-Packard GeneArray Scanner.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix as default.

label: biotin

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

growth_protocol: HEK293T cell line (ATCC, Manassas, VA) was maintained in DMEM (Gibco) with 10% Fetal Bovine Serum (FBS) (Gibco) under 5% CO2 condition at 37°C

extract_protocol: After washing and lysing the cells with Buffer RLT, the complete RNA was extracted using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) as instructed by the manufacturer, including the on-column DNA digestion stage (RNase-Free DNase Set; QIAGEN).

treatment_protocol: HEK293T cell line (ATCC, Manassas, VA) was treated in DMEM with 10% FBS (Gibco) and Pk2 (10 nM) or not after reaching 80%fluence.

value: Human embryonic kidney

tag: genotype/variation

value: PROKR1 Knockout HEK293T cells


title: 180517_26: PROKR1 Knockout HEK293T cells before Pk2 stimulation


title: 200645: Healthy individual, with Globin-Block 66

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in samples with “yes” in the column “Globin Block applied”. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.


title: 180517_28: PROKR1 overexpressed HEK293T cells after Pk2 stimulation

value: PROKR1 overexpressed HEK293T cells


title: 180517_27: Naive HEK293T cells before Pk2 stimulation

value: Naive HEK293T cells


title: 200604: Healthy individual, with Globin-Block 26


title: 180517_31: Naive HEK293T cells after Pk2 stimulation


title: 200602: Healthy individual, with Globin-Block 24


title: 200601: Healthy individual, with Globin-Block 23


title: 200603: Healthy individual, with Globin-Block 25


title: 200600: Healthy individual, with Globin-Block 22


title: 180517_29: Mock control HEK293T cells after Pk2 stimulation

value: Mock control HEK293T cells


title: 180517_24: PROKR1 overexpressed HEK293T cells before Pk2 stimulation


title: 200609: Healthy individual, with Globin-Block 31


title: SP25_2

value: Primary melanocytes, foreskin, 1 donor, medium dark, NBMELC569

value: melano     sgl #3

tag: treatment

value: 2000 nbUVB

value: genomic + mito DNA


title: R1131: Bone Marrow CD34+ cells - mast cell leukemia - rep5

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Total Mononuclear Cells were isolated from a bone marrow aspirate at the time of diagnosis using Ficoll. CD34+ cells were further purified by Fluorescence-activated cell sorting.

hyb_protocol: Affymetrix GeneChip®Human Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip WT Pico Reagent Kit User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1

label: Biotin

source_name: CD34+ cells isloated from the bone marrow of a patient with mast cell leukemia

label_protocol: 500pg of total RNA were amplified and labeled using the GeneChip WT Pico Reagent Kit (Catalog Number 902622,Affymetrix, Santa Clara, CA)

growth_protocol: mononuclear cells were isolated from bone marrow aspirates using Ficoll and frozen in FCS + 10% DMSO until sorting

extract_protocol: RNA was isolated using the Rneasy micro elute kit (Quiagen) according to the manufacturer's protocol

treatment_protocol: cells were incubated with fluorecence-labeled antibodies against CD45 and CD34 and sorted on a BD FACSAria I

tag: immune phenotype

tag: diagnosis

value: mast cell leukemia with associated myelodysplastic syndrome

value: Bone Marrow


title: R1130: Bone Marrow CD34+ cells - mast cell leukemia - rep4

value: male

value: mast cell leukemia with associated chronic erythroblastic leukemia


title: 200608: Healthy individual, with Globin-Block 30

value: yes

value: Whole Blood


title: R1132: Bone Marrow CD34+ cells - mast cell leukemia - rep6

value: aggressive systemic mastocytosis with associated chronic myelomonocytic leukemia


title: 180517_25: Mock control HEK293T cells before Pk2 stimulation


title: R320: Bone Marrow CD34+ cells - healthy - rep2

description: Cells were purchased from Lonza (Basel, Switzerland), cat # LON2M-101B

source_name: CD34+ cells isolated from healthy human bone marrow

value: Healthy