title: 4C_Seq_Forelimb_Rep1_N1

source_name: 4C-Seq from forelimb tissue, replicate 1, viewpoint 1, Nkx3-2


title: MDAMB231_BRD2_10uMGSK2801_48h

status: Public on Jul 09 2019

type: SRA

city: Boston

first: Bradley

middle: E

last: Bernstein

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

country: USA

institute: Dana Farber Cancer Institute

description: MDAMB231_BRD2_drug_treatment_peakclassification.xlsx

library_source: genomic

data_processing:
Reads were aligned to hg19 or to a single copy of the ribosomal DNA repeat (GenBank: U13369.1) using Bowtie v1.1.2 with parameters -v 2 -m 1.
Genome_build: hg19
Supplementary_files_format_and_content: The following processing steps were performed to generate peakclassification files:  Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm).  The read density of the input chromatin was subtracted from the ChIP read density for normalization.  Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions.  We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage.   Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153.  We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions.  Peak genic classification:  A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations.  If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak.   If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak.  If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak.  If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer.   All remaining peaks were designated as "other".

molecule: genomic DNA

organism: Homo sapiens

source_name: MDAMB231 breast carcinoma cell line

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification

tag: cell line

tag: treatment

tag: culture media

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone

tag: library preparation kit

value: KAPA Hyper Prep

tag: chip antibody

value: BRD2 Bethyl Laboratories A302-583A


title: 4C_Seq_Hindlimb_Rep1_N1

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

country: Germany

institute: Friedrich Miescher Laboratory

description: Cross-linked, proximity-ligated DNA from hindlimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 1

data_processing:
Library strategy: 4C-seq
Sequence data were processed cleaned up using cutadapt v1.10;
Sequence reads were mapped to the reference mm10 genome using bwa v0.7.10-r789 as paired end reads using the mem module.
Base quality recalibration, duplication marking and insertion/deletion realignment was performed using GATK v3.4-0-gf196186 modules BQSR, MarkDuplicates, IndelRealignment;
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247) and those with MAPQ scores below 30 were excluded from analysis.  Filtered alignments were binned into genome-wide BglII fragments, normalized to Reads Per Kilobase of transcript per Million mapped reads (RPKM), and plotted and visualized in R.
Genome_build: GRCm38, also known as mm10
Supplementary_files_format_and_content: bedgraph format with each interval corresponding to a BglII fragment

organism: Mus musculus

source_name: 4C-Seq from hindlimb tissue, replicate 1, viewpoint 1, Nkx3-2

extract_protocol:
Chromosome conformation capture (3C) template was prepared from pooled E14.5 liver, forelimb and hindlimb buds (n = 5–6 C57BL/6NJ embryos per replicate), with improvements to the primer extension and library amplification steps following Sexton et al., 2012 (doi: 10.1038/nprot.2012.071).  The template was amplified with Q5 High-Fidelity Polymerase (New England Biolabs GmbH, Frankfurt am Main, Germany) using a 4C adapter-specific primer and a pool of 6 Nkx3-2 enhancer viewpoint primers.
Amplified fragments were prepared for Illumina sequencing by ligation of TruSeq adapters, followed by PCR enrichment.

tag: strain

tag: developmental stage

tag: tissue

value: Hindlimb


title: MDAMB231_BRD2_100nMJQ1_48h


title: MDAMB231_BRD2_DMSO_48h

value: DMSO 48h


title: CES_WW Sample 518

city: Heidelberg

first: Karsten

last: Rippe

state: Germany

address: Im Neuenheimer Feld 267-BQ24

department: Division of Chromatin Networks

institute: DKFZ

description: bigWig

library_source: transcriptomic

data_processing:
Base calls performed with Illumina RTA 1.18.64.
Sequence reads were mapped to the human genome using STAR version 2.3.0 (Dobin et al, 2013) with the parameters: --genomeLoad LoadAndRemove --alignIntronMax 500000 --alignMatesGapMax 500000 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --outFilterMismatchNoverLmax 0.3 --sjdbOverhang 50 -- chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 -- chimJunctionOverhangMin 15.
The mapped reads were quantified using HTSeq-count from the HTSeq framework version 0.6.0 using the intersection_nonempty option in a stranded fashion according to the gencode17 annotation (Anders et al, 2015).
Genome_build: hs37d5
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage (deepTools). Coverage tracks were normalized to 1x.

molecule: total RNA

source_name: CD19+ B-cells from peripheral blood of CLL patient

extract_protocol:
Small and large RNA fractions were isolated with the miRNeasy Mini Kit (Qiagen), RNA was digested by DNase I (Promega) for 30 min at 37°C, depleted from rRNA with RiboZero Gold.
Directional cDNA synthesis and sequencing library preparation was conducted according to the NEBNext Ultra Directional RNA Library Prep Kit (NEB).

tag: disease

value: CLL

tag: donor

value: WW


title: CES_WW Sample 519

description: bigWig


title: Sh-cricMY1 rep2 (ribo)

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: sun yat sen university

data_processing:
Library strategy: Ribosome profiling
For Ribo-seq, adapters was removed  using cutadapt software, and only  25-34 bp read lengths was kept.
Preprocessed Ribo-seq reads was further aligned to rRNA and tRNA seqeuences using bowtie software, so as to filter rRNA and tRNA reads.
Remaining reads were aligned to human genome(hg38) downloaded from Ensembl website using hisat2 software,
Raw read counts was calculated by featureCounts software based on Ensembl human gene annotation(version 91), and were further normalized to RPKM.
Translation efficiency was calculated using RPKM values of Ribo-seq divided by FPKM values of RNA-seq, differential translation efficiency  was calculated through using DESeq2 package in R software.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: acute myeloid leukemia cells

extract_protocol:
QIAseq® FastSelectTM RNA Removal Kit
Precision small RNA library prep for Illumina® NGS systems

tag: cell type

value: acute myeloid leukemia cells


title: Sh-NC input rep2 (rna)

data_processing:
For Ribo-seq, adapters was removed  using cutadapt software, and only  25-34 bp read lengths was kept.
Preprocessed Ribo-seq reads was further aligned to rRNA and tRNA seqeuences using bowtie software, so as to filter rRNA and tRNA reads.
Remaining reads were aligned to human genome(hg38) downloaded from Ensembl website using hisat2 software,
Raw read counts was calculated by featureCounts software based on Ensembl human gene annotation(version 91), and were further normalized to RPKM.
Translation efficiency was calculated using RPKM values of Ribo-seq divided by FPKM values of RNA-seq, differential translation efficiency  was calculated through using DESeq2 package in R software.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …


title: Sh-NC input rep1 (rna)


title: Sh-NC rep1 (ribo)


title: Sh-cricMY1 rep1 (ribo)


title: Sh-cricMY1 input rep2 (rna)


title: Sh-NC rep2 (ribo)


title: CES_MA_2h_N Sample 517

description: bigWig

source_name: Non-malignant B cells of healthy donors

growth_protocol: Malignant and non-malignant B cells of each four individual CLL patients or healthy donors respectively were enriched for CD19-positive. 10,000 cells were seeded in serum-free medium and incubated for 30 min with DMSO as mock control or panobinostat.

value: Non-malignant

value: MA

value: 2h control for Panobinostat


title: CES_MA_2h_N Sample 516

description: bigWig


title: Sh-cricMY1 input rep1 (rna)


title: siPAK4 Hs578T Rep2

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
Costa.siPAK4.Hs578T.Rep2
Hs578T.siPAK4.Rep2
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt

data_processing:
Basecalls performed in phred64.
Sequenced reads were mapped to hg19 whole genome using Tophat with default settings.
FPKM matrix was derived using Cufflinks suite using default settings.
Differential expression quantified using DESeq2 (Bioconductor) following non-normalised read counting with HTSeq (intersection-nonempty).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Summary files describe the results of DESeq2 differential expression analysis for core comparisons as well as FPKM matrix for all replicates created using Cufflinks suite.
Supplementary_files_format_and_content: FPKM_Matrix.txt: Tab-delimited FPKM matrix.
Supplementary_files_format_and_content: DESeq2.BT549.siPAK4_vs_Control.csv: Comma-separated DESeq2 results.
Supplementary_files_format_and_content: DESeq2.Hs578T.siPAK4_vs_Control.csv: Comma-separated DESeq2 results.

extract_protocol:
Qiagen RNA extraction kit (74104, Qiagen).
PolyA, paired-end sequencing on Illumina HiSeq 2000 performed by SciLifeLab in Stockholm, Sweden.

treatment_protocol: Total RNA was isolated from Hs578T and BT-549 cells 72 hours after transient transfection with PAK4-targetting or control siRNAs.

value: breast cancer cell line

tag: sirna


title: siPAK4 Hs578T Rep3

description:
Costa.siPAK4.Hs578T.Rep3
Hs578T.siPAK4.Rep3
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: siPAK4 BT549 Rep3

description:
Costa.siPAK4.BT549.Rep3
BT549.siPAK4.Rep3
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: LNCaP LP FBS B

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LNCaP human prostate tumor cell line cultured in full growth media containing FBS

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.64.0 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg19 human genome using TopHat v2.0.9 and bowtie2 v2.1.0.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.6.3 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LNCaP human prostate tumor cell line

extract_protocol:
RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol.  On-column DNase digestion was performed.  RNA concentration, purity, and integrity was assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: LNCaP (ATCC CRL-1740)

value: prostate cancer

tag: cell culture media

value: cells were cultured in phenol-red free RPMI-1640 with 10% FBS for 24 hours


title: Liver5-RNAseq-wild

city: Barcelona

first: Dafni

last: Anastasiadi

address: Pg. Marítim de la Barceloneta 37-49

department: Renewable Marine Resources

country: Spain

institute: Institute of Marine Sciences-CSIC

description:
European sea bass
processed data file: Liver-RNAseq-Feature_Counts.txt

data_processing:
RRBS raw reads were quality trimmed by the Timmomatic v. 0.32 with the following parameters SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18.
RRBS: Trimmed reads were aligned to the reference genome dicLab v1.0c using BSMAP v. 2.90 in RRBS mode with the following parameters -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2.
RRBS: Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
RNA-seq reads were decontaminated by BBDuk (v. 37.61) using the following parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=30 minlen=23.
RNA-seq: Reads were aligned to the genome by HISAT2 (v. 2.1.0) using the core hisat2 function with default parameters.
RNA-seq: Reads were counted at the gene level by feature Counts of the Subread package.
Genome_build: dicLab v1.0c (June 2012); http://seabass.mpipz.mpg.de/
Supplementary_files_format_and_content: *.txt: Output of methratio.py was converted using awk to methylkit input. Tab-delimited files contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered.
Supplementary_files_format_and_content: *-RNAseq-Feature_Counts.txt: For each tissue, one plain text file is provided with the feature counts per gene per sample.

organism: Dicentrarchus labrax

source_name: Liver

growth_protocol: Wild fish: Tissues dissected on boat from wild fish caught in the sea by speargun. Farmed fish: Eggs fertilized in a commercial hatchery and raised at the Aquarium facilities of the Institute of Marine Sciences (CSIC) until 3 years old under natural conditions of temperature and photoperiod.

extract_protocol:
Trizol RNA extraction.
mRNA-Seq sample preparation kit (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina).

treatment_protocol: Wild fish samples stored in RNAlater immediately after dissection and farmed fish samples snap frozen in liquid nitrogen. All samples were then kept at -80ºC until DNA/RNA extraction.

value: Liver

tag: FISH origin

value: Wild (captured in NE Spain)

tag: age

value: Adults


title: Liver4-RNAseq-wild


title: Liver2-RNAseq-wild


title: Liver3-RNAseq-wild


title: siPAK4 BT549 Rep2

description:
Costa.siPAK4.BT549.Rep2
BT549.siPAK4.Rep2
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: LNCaP LP CSR100 B

value: cells were cultured in phenol-red free RPMI-1640 with 10% FBS

value: cells were cultured in phenol-red free RPMI-1640 with 5% charcoal-stripped serum plus 100nM R1881 for 24 hours


title: siPAK4 BT549 Rep1

description:
Costa.siPAK4.BT549.Rep1
BT549.siPAK4.Rep1
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: Liver1-RNAseq-wild


title: LNCaP LP CSR100 A


title: Brain5-RNAseq-wild

description:
European sea bass
processed data file: Brain-RNAseq-Feature_Counts.txt

source_name: Brain

value: Brain


title: LNCaP LP FBS A


title: siPAK4 Hs578T Rep1

description:
Costa.siPAK4.Hs578T.Rep1
Hs578T.siPAK4.Rep1
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: Brain3-RNAseq-wild


title: Brain2-RNAseq-wild


title: LNCaP LP CS A

value: cells were cultured in phenol-red free RPMI-1640 with 5% charcoal-stripped serum for 24 hours


title: Brain1-RNAseq-wild


title: MDAMB231_BRD2_100nMJQ1_48h_rDNA

value: 100nMJQ1 48h rDNA

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone

value: KAPA Hyper Prep

value: BRD2 Bethyl Laboratories A302-583A


title: siControl Hs578T Rep2

description:
Costa.siControl.Hs578T.Rep2
Hs578T.siControl.Rep2
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt

value: siControl


title: siControl BT549 Rep3

description:
Costa.siControl.BT549.Rep3
BT549.siControl.Rep3
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt

value: breast cancer cell line


title: siControl Hs578T Rep1

description:
Costa.siControl.Hs578T.Rep1
Hs578T.siControl.Rep1
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: siControl BT549 Rep2

description:
Costa.siControl.BT549.Rep2
BT549.siControl.Rep2
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: siControl Hs578T Rep3

description:
Costa.siControl.Hs578T.Rep3
Hs578T.siControl.Rep3
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.Hs578T.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: siControl BT549 Rep1

description:
Costa.siControl.BT549.Rep1
BT549.siControl.Rep1
RNA sequencing of breast cancer cell line.
processed data file: DESeq2.BT549.siPAK4_vs_Control.csv
processed data file: FPKM_Matrix.txt


title: Brain4-RNAseq-wild


title: LNCaP LP CS B

value: male


title: Liver5-RNAseq-farmed

value: Farmed (reared in aquarium facilities)

value: 3 years


title: Liver3-RNAseq-farmed


title: Liver4-RNAseq-farmed


title: Liver2-RNAseq-farmed


title: miRNA-E006AA-hT-ADT-2

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling.
For the smallRNA the after investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality and the counts of smallRNA were extracted using Etract and Count Module in CLC Genomics Workbench 10.0.1.
The extracted sequences were annotated against the miRBase database for Homo sapiens. The annotated smallRNAs and their counts were used for downstream analysis. Using Kal’s test, a comparison of smallRNA expression between the groups of samples was performed. The Kal’s test was used to generate p-values and Log2 fold changes. SmallRNA’s with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed for each comparison.
After sequencing, they were converted from bcl format to fastq, then trimmed for quality and adapter sequences, and finally mapped to the reference or annotated.
Expression values were calculated based on how many reads mapped to a given gene in the reference sequence.
Genome_build: miRBase database for Homo sapiens.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

growth_protocol: RC-77N cells were  grown in K-SFM media, RC-77T/E and E006AA-hT were cultured in DMEM supplemented with 10 % FBS.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Small RNA sequencing library is prepared by using Illumina TruSeq Small RNA library Prep Kit (Illumina, San Diego, CA). In brief, Illumina 3’ and 5’ adapter is added to RNA molecules with a 5’-phosphate and a 3’-hydroxyl group sequentially. A reverse transcription reaction were used to create single stranded cDNA. The cDNA was then PCR amplified using a common primer and a primer containing index sequence.
The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell will be loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples will be sequenced using a 1x50 Single End (SE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq will be converted into fastq files and de-multiplexed using Illumina bsl2fastq v. 2.17 program. One mis-match will be allowed for index sequence identification.

treatment_protocol: 20.0 μmol/L of Biculatamde were added for 24 h, DMSO (control) to dishes.  Media were changed after 48 h. Biculatamide treatment continued until the resistant clones were formed. Biculatamide resistant clones were treated with 20.0 μmol/L of Enzalutamide until the resistant Enzalutamide clones were formed.  Cells were reseeded once each week supplemented with the appropriate treatments. Cells from control plates were maintained until resistant clones were cryopreserved to maintain a constant culture time for control and experimental lines.

tag: cell line/backgound

value: African-American ADT Resistant prostate cell line

tag: tissue origin

value: prostate

tag: molecule subtype

value: miRNA


title: A5_B

first: Charlotte

last: Kuperwasser

address: 150 Harrison Ave

department: School of Medicine

institute: Tufts Univeristy

data_processing:
Demultiplexed reads were trimmed using FASTX followed by alignment to GRCm38.81 using Tophat (v2.0.13) and generation of reads per gene using htseq-count.
Pairwise comparisons were performed on genes that had a read count of >=33 in at least one replicate sample.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: tab-deliminted text file includes raw read count values for each sample

source_name: Mammary gland

extract_protocol:
Mammary glands were removed, minced, and stored in freezing media prior to single-cell dissociation. Single-cell dissociated mammary cells were pooled from 3 mice prior to sorting on EpCAM and CD49f expression via FACS. RNA was harvested using a combined protocol of Trizol extraction and column-based (Qiagen RNeasy Kit) isolation. NuGEN Ovation V2 system (#7102-32) was used to produce and amplify cDNA from 5 ng of total RNA input, followed by library construction using Illumina TruSeq Nano DNA Kit (#FC-121-4001) from 100 ng of cDNA input.
Standard protocols were used (a) to produce and amplify cDNA using NuGEN Ovation V2 System and (b) for library construction using Illumina system.

value: mammary gland

value: Basal

value: 12 mo

tag: genotype


title: A5_S

value: Stromal


title: A6_B


title: miRNA-E006AA-hT-ADT-1


title: Brain5-RNAseq-farmed

value: Brain


title: Brain4-RNAseq-farmed


title: miRNA-E006AA-hT-2

value: African-American ADT  Sensitive prostate cell line


title: A6_S


title: A6_LB

value: Luminal-Basal


title: A5_LB


title: Brain3-RNAseq-farmed


title: A6_L

value: Luminal


title: miRNA-E006AA-hT-1


title: Brain2-RNAseq-farmed


title: Liver1-RNAseq-farmed

value: Liver


title: WT (for Col1a1-Pth1r H223R) 9

first: Marc

last: Wein

state: MA

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9

source_name: cortical bone RNA

extract_protocol:
Femur were dissected, epiphyses cut off, and marrow was flushed with PBS until bone appeared white. Bone was flash frozen in TRIzol for RNA isolation. RNA was further purified using Qiagen Rneasy columns prior to library construction
Methods per BGI

tag: genotype/variation

value: WT (for Col1a1-Pth1r H223R)


title: WT (for Col1a1-Pth1r H223R) 11


title: WT (for Col1a1-Pth1r H223R) 10


title: A5_L


title: Brain1-RNAseq-farmed


title: WT (for Col1a1-Pth1r H223R) 8


title: miRNA-RC-77T/E-CD133-plus-1

value: African-American ADT Resistant Cancer stem cell population


title: Testis7-RNAseq-farmed

description:
European sea bass
processed data file: Testis-RNAseq-Feature_Counts.txt

source_name: Testis

value: Testis


title: miRNA-RC-77T/E-CD133-plus-2


title: WT (for Col1a1-Pth1r H223R) 5


title: WT (for Col1a1-Pth1r H223R) 4


title: Testis6-RNAseq-farmed

value: Farmed (reared in aquarium facilities)


title: miRNA-RC-77T/E-ADT-2


title: WT (for Col1a1-Pth1r H223R) 7


title: miRNA-RC-77T/E-2

value: African-American ADT Sensitive prostate cell line


title: miRNA-RC-77T/E-ADT-1

value: African-American ADT Resistant prostate cell line


title: F82_S

value: 3 mo


title: ATAC_Seq_Background_gDNA_Control

description: Genomic DNA after direct Tn5 transposition from forelimb tissue

data_processing:
mouse mm10 genome using bowtie2 v.2.1.0.
Peaks were called using MACS14 v.2.1 using the background genomic DNA as as pseudo input control
Genome_build: GRCm38, also known as mm10
Supplementary_files_format_and_content: bedgraph format

source_name: ATAC-Seq, genomic control

extract_protocol:
ATAC-seq was performed on dissected C57BL/6NJ E14.5 forelimb and hindlimb.  Nuclei preparation and tagmentation were performed as previously described in Buenrostro et al., 2013, doi: 10.1038/nmeth.2688., with the following modifications.  To minimize endogenous protease activity, cells were strictly limited to 5 + 5 minutes of collagenase A treatment at 37 ºC, with frequent pipetting to aid dissociation into single-cell suspensions.
Following wash steps and cell lysis, 50 000 nuclei were tagmented with expressed Tn5 transposase.  Each tagmented sample was then purified by MinElute columns (Qiagen) and amplified with Q5 High-Fidelity DNA Polymerase (New England Biolabs) using a uniquely barcoded i7-index primer (N701-N7XX) and the N501 i5-index primer.  PCR thermocycler programs were 72ºC for 4 min, 98ºC for 30 s, 6 cycles of 98ºC for 10 s, 65ºC for 30 s, 72ºC for 1 min, and final extension at 72ºC for 4 min.  PCR-enriched samples were taken through a double size selection with PEG-based SPRI beads (Beckman Coulter) first with 0.5X ratio of PEG/beads to remove DNA fragments longer than 600 bp, followed by 1.8X PEG/beads ratio in order to select for Fraction A as described in Milani et al., 2016, doi: 10.1038/srep25474.

value: Adult

value: Spleen


title: F84_S

value: mammary gland


title: WT (for Col1a1-Pth1r H223R) 6


title: F82_LB


title: miRNA-RC-77T/E-1

value: prostate

value: miRNA


title: Testis5-RNAseq-farmed

value: 3 years


title: WT (for Col1a1-Pth1r H223R) 3


title: F84_LB


title: Testis4-RNAseq-farmed


title: F84_L


title: WT (for Col1a1-Pth1r H223R) 2


title: miRNA-RC-77-N-2

value: African-American Normal prostate cell line


title: Testis3-RNAseq-farmed


title: WT (for Col1a1-Pth1r H223R) 1


title: miRNA-RC-77-N-1


title: Col1a1-Pth1r H223R 12

value: Col1a1-Pth1r H223R


title: F82_L

value: Luminal


title: A2_S

value: Stromal

value: 12 mo

value: wild type


title: E006AA-hT-ADT-2

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trim Sequences Module in CLC Genomics Workbench 10.0.1.
The trimmed reads were mapped separately to the long noncoding RNA and gene regions of the Homo sapiens GRCh38 reference genome available on ENSEMBL using the RNA-Seq Analysis Module in CLC Genomics Workbench 10.0.1. BAM files, Unique gene hit counts and Unique transcript hit counts for each mapping were generated as a result of this step.
After extraction of gene and transcript hit counts, the hit counts tables were used for downstream differential expression analysis. Using Kal’s test, a comparison of gene expression between the groups of samples was performed. The Kal’s test was used to generate p-values and Log2 fold changes. Genes and transcripts with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes and transcripts respectively for each comparison.
A gene ontology analysis was performed on the statistically significant set of genes by implementing the Hypergeometric tests in CLC Genomics Workbench 10.0.1. The goa human GO list was used to cluster the set of genes based on their biological process and determine their statistical significance
Genome_build: GRCh38 reference genome available on ENSEMBL

source_name: African American-Prostate

growth_protocol: RC-77-N, RC-77T/E and E006AA-hT were cultured in DMEM supplemented with 10 % FBS.

extract_protocol:
Total RNA were  extracted using Qiagen RNeasy Plus Mini Kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity were  checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). rRNA depletion was performed using Ribozero rRNA Removal Kit (Human/Mouse/Rat probe) (Illumina, San Diego, CA, USA). RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using a DNA Chip on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell were loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE).  Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq will be converted into fastq files and de-multiplexed using Illumina bsl2fastq v. 2.17 program. One mis-match will be allowed for index sequence identification.

tag: ethnicity

value: African American

tag: cell line

value: ADT resistant


title: Testis2-RNAseq-farmed

value: Testis

value: Farmed (reared in aquarium facilities)


title: Testis1-RNAseq-farmed


title: A1_S

tag: strain


title: A2_B

tag: tissue

value: Basal


title: E006AA-hT-ADT-1


title: Muscle4-RNAseq-farmed

description:
European sea bass
processed data file: Muscle-RNAseq-Feature_Counts.txt

source_name: Skeletal muscle

value: Skeletal muscle


title: E006AA-hT-2

value: ADT sensitive


title: Col1a1-Pth1r H223R 10


title: Trastuzumab-sensitive model (SK)

type: genomic

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

institute: IDIBELL

description:
SKBR3
Trastuzumab-sensitive HER2-positive breast cancer cell line.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: Minfi R package standard protocol.

label: Cy5 and Cy3

source_name: HER2-positive breast cancer

label_protocol: Standard Illumina labelling protocol.

growth_protocol: SKBr3 cells were routinely grown in McCoy’s supplemented with 10% FBS, 1% L-glutamine, 1% sodium pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol: Genomic DNA was extracted and purified using the QIAamp DNA Mini Kit. Total DNA was quantified using the NanoDrop 2000 spectrophotometer following the manufacturer’s specifications.

treatment_protocol: Trastuzumab-resistant SK cells (SKTR) were developed by exposing SK cells continuously to trastuzumab (Herceptin, Hoffmann-La Roche Pharma), starting with 1μM concentration for three months of exposure and increasing the concentration up to 2 μM for a 12 months period. Thus, cells resistant to trastuzumab were maintained in 2 μM trastuzumab, a concentration at which SK parental cells were not viable.

value: SK

value: Trastuzumab-sensitive breast cancer cells

value: Female


title: A1_B

value: mammary gland


title: Trastuzumab-resistant model (SKTR)

description:
SKTR
Trastuzumab-resistant HER2-positive breast cancer cell line.

value: SKTR

value: Trastuzumab-resistant breast cancer cells


title: A2_L

value: Luminal


title: RC-77T/E-CD133-plus-2

value: prostate


title: Muscle2-RNAseq-farmed

value: 3 years


title: Col1a1-Pth1r H223R 7

value: Col1a1-Pth1r H223R


title: Muscle1-RNAseq-farmed


title: F81_S

value: Stromal

value: 3 mo

value: wild type


title: E006AA-hT-1

value: African American


title: Col1a1-Pth1r H223R 6


title: RC-77T/E-ADT-2

value: ADT resistant


title: Eggs3-RRBS

description: European sea bass

source_name: Whole embryos

extract_protocol:
Phenol-Chloroform DNA extraction.
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030032).

value: Whole embryos

value: Farmed (reared in aquarium facilities)

value: Embryos


title: F79_S


title: Col1a1-Pth1r H223R 5


title: RC-77T/E-ADT-1


title: Eggs2-RRBS

description: European sea bass


title: RC-77T/E-CD133-plus-1


title: Col1a1-Pth1r H223R 4


title: Col1a1-Pth1r H223R 9


title: RC-77-T-2

value: ADT sensitive


title: Col1a1-Pth1r H223R 3


title: F79_B

value: Basal


title: F81_L

value: mammary gland


title: RC-77-T-1


title: HEK293T_NC-2

city: Baltimore

first: Christina

last: Castellani

state: MD

address: 733 N Broadway

department: McKusick-Nathans Department of Genetic Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: Cell lines were hybridized to the Illumina Infinium EPIC BeadChip at The University of Texas Health Science Center at Houston (UTHealth).

scan_protocol: Standard Illumina Protocol

data_processing: EPIC BeadChip analysis was performed using the minfi package(Fortin et al. 2017). Data was normalized using Functional Normalization(Fortin et al. 2014) and differential methylation was calculated using the dmpFinder function in minfi

source_name: No CRISPR

label_protocol: Standard Illumina Protocol

growth_protocol: HEK293T cells were grown in DMEM containing 10% FBS and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol: DNA extraction was performed on harvested HEK293T TFAM knockout cells using the AllPrep DNA/RNA Mini Kit (Qiagen #80204) following the manufacturer’s protocol. DNA was eluted in 100 µL ultrapure water.

treatment_protocol: The stable TFAM CRISPR-Cas9 knockout was generated in HEK293T cells using the Origene TFAM – Human Gene Knockout Kit via CRISPR (catalog number: KN215488) following the manufacturer’s protocol. The following sgRNA guide sequence was used to generate the stable TFAM knockout lines: GCGTTTCTCCGAAGCATGTG. Lipofection was conducted using Turbofectin 8.0 (catalog number: TF81001). Puromycin was used for selection at a concentration of 1.5 µg/mL. Fluorescence-activated cell sorting (FACS) was used for single cell sorting and clonal expansion.

value: control


title: Liver3-RRBS-wild

description: European sea bass

value: Liver

value: Wild (captured in NE Spain)

value: Adults


title: RC-77-N-2

value: prostate

value: normal


title: Liver2-RRBS-wild

description: European sea bass


title: Eggs1-RRBS

description: European sea bass


title: Col1a1-Pth1r H223R 1

value: Col1a1-Pth1r H223R


title: RC-77-N-1


title: F79_L

value: Luminal

value: 3 mo


title: TFAM_KO_Clone_6

source_name: TFAM CRISPR

value: TFAM Knockout


title: HEK293T_NC-3


title: WT (for Sik2/3 DKO) 8

value: WT (for Sik2/3 DKO)


title: Brain3-RRBS-wild

description: European sea bass

value: Brain


title: F81_B

value: wild type


title: WT (for Sik2/3 DKO) 7


title: TFAM_KO_Clone_11


title: Brain2-RRBS-wild

description: European sea bass


title: HEK293T_NC-1


title: TFAM_KO_Clone_5


title: HM20 Mock cells_Wnt3A treated 24h_rep1

type: RNA

city: Hsinchu

first: Jia-Lin

last: Lee

address: 101, Sec. 2, Kuang Fu Road

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (Dye channel: R ; Scan resolution : 10 um; Tiff: 16-bit; Red PMT gain: 100%; XDR: 100 10) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

source_name: Lung cancer cell line A549

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: HM20 Mock


title: WT (for Sik2/3 DKO) 6


title: Muscle3-RNAseq-farmed

value: Skeletal muscle

value: Farmed (reared in aquarium facilities)

value: 3 years


title: Brain1-RRBS-wild

description: European sea bass


title: Liver3-RRBS-farmed

description: European sea bass


title: WT (for Sik2/3 DKO) 4


title: Liver2-RRBS-farmed

description: European sea bass


title: HM20 SFRP4 cells_Wnt3A treated 24h_rep1

value: SFRP1-5-expressing stable clones


title: HM20 SFRP5 cells_Wnt3A treated 24h_rep1


title: HM20 SFRP3 cells_Wnt3A treated 24h_rep1


title: WT (for Sik2/3 DKO) 3


title: RNA-seq_3h1_rep3

city: Warsaw

first: Maciej

last: Lirski

address: Pawińskiego 5a

department: Department of Protein Biosynthesis

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: h1.1h1.2h1.3 K 3 BC006

data_processing:
Base calling and adapter trimming was performed automatically by Torrent Suite software.
Residual rRNA and ERCC reads were identified and filtered out using bbsplit and filterbyname scripts from BBTools suite (Brian Bushnell).
Reads were aligned to TAIR10 genome using TMAP 5.0.13. with soft clipping from both ends and returning all the mappings with the best score. Other settings were set according to Torrent Suite defaults. Unaligned reads were aligned with BBMap (Brian Bushnell)
Quantitation to ARAPORT11 transcripts was performed in Partek Flow (Partek Inc.) using Partek E/M algorithm.
Differential expression analysis was performed in Partek Flow (Partek Inc.) using  Partek GSA algorithm
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: tsv files with read count table and differential gene expression analysis results

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Medium (½ MS medium, 0.8% agar). Seedes were surfaced sterilized and placed on the plate using toothpick to ensure uniform distribution. They were stratified 2-4 days at 4°C and transferred into the plant growth incubator  with long-day photoperiod (16 h, 22 °C day/8 h, 18 °C night) and light flux around 120 µM*s-1*m-2.

extract_protocol:
RNA was isolated using modified TRIzol method (Chomczynski and Sacchi 1987). Ribosomal RNA was removed using RiboMinus Plant Kit (Thermo Fisher) and ERCC RNA Spike-In Mix 1 (Thermo Fisher) was added.
Libraries were prepaired with Ion Total RNA-Seq Kit v2 and Ion Xpress RNA-Seq Barcode 1-16 Kit according to user guide. Sequencing template was generated with Ion PI™ Template OT2 200 Kit v3 on Ion OneTouch™ 2 System. Sequencing was performed on Ion PI™ chip v2 and Ion Proton™ sequencer using Ion PI™ Sequencing 200 Kit v2 (all Ion Torrent kits and software are trademarks of Thermo Fisher).

value: seedlings

value: 3 week old

tag: ecotype


title: WT (for Sik2/3 DKO) 2


title: Brain3-RRBS-farmed

description: European sea bass


title: RNA-seq_3h1_rep2

description: h1.1h1.2h1.3 K 2 BC005


title: WT (for Sik2/3 DKO) 5


title: Col1a1-Pth1r H223R 2


title: Brain2-RRBS-farmed

description: European sea bass


title: Sik2/3 DKO 8

value: Sik2/3 DKO


title: Brain1-RRBS-farmed

description: European sea bass


title: RNA-seq_3h1_rep1

description: h1.1h1.2h1.3 K 1 BC004


title: RNA-seq_WT_rep3

description: WT K 3 BC003


title: Muscle5-RNAseq-farmed


title: HM20 SFRP1 cells_Wnt3A treated 24h_rep1


title: Col1a1-Pth1r H223R 11


title: RDM1-Flag ChIP-seq

city: Los Angeles

first: Steven E.

last: Jacobsen

address: 405 Hilgard Avenue

institute: UCLA

data_processing:
total reads were mapped using Bowtie (v1.0.0)
BAM files were sorted, duplicates removed and indexed using Samtools (0.1.19)
Pol V peaks were called comparing NRPE1 antibody ChIP againstpreimmune control ChIP described in(Liu et al, 2018. Nature plants, Series GSE100010,Samples GSM2667837 and GSM2667838, using MACS2 with q-value 0.05 (v 2.1.1)
Only summit of peaks with more than 2 folds of enrichment were used

source_name: Inflorescence

growth_protocol: plants were grown in on soil in a greenhouse until inflorescences were ready to be collected

extract_protocol:
Samples were grinded and fixed. Nuclei were extracted, chromatin sonicated and complexes isolated with FLAG antibody. Cromatin was reverse crosslinked and DNA purified.
Sequencing libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN), following the manufacturer’s instructions.cturer’s instructions

treatment_protocol: no treatment

tag: antibody

value: Flag


title: Testis3-RRBS-farmed

description: European sea bass

extract_protocol:
Phenol-Chloroform DNA extraction.
Custom RRBS library preparation with 100 ng of DNA, as in Klughammer et al., Cell 2015.

value: Testis


title: DRD1-Flag ChIP-seq


title: RNA-seq_WT_rep2

description: WT K 2 BC002


title: Sik2/3 DKO 6


title: Col0 ChIP-seq


title: Sik2/3 DKO 7


title: Liver1-RRBS-farmed

description: European sea bass

value: Liver


title: DMS3-Flag ChIP-seq


title: RNA-seq_WT_rep1

description: WT K 1 BC001


title: Testis1-RRBS-farmed

description: European sea bass


title: Mnase-seq_3h1_rep2

data_processing:
Base calling and adapter trimming was performed automatically by Torrent Suite Software.
Reads were aligned with TMAP 5.0.13. Soft clipping was turned off, end repair was allowed and all alignments for multi-mapping reads were reported. Other settings were set according to Torrent Suite defaults.
Multi mapping read positions were resolved using MMR (Kahles, Behr et al. 2016) with default settings.
Quantile normalized wiggle occupancy files were generated with DANPOS2 (Chen, Xi et al. 2013) with default settings. To avoid shifting of read positions (automatic procedure for single-end reads), program was fed with “fake 75 nt paired-end” bed files, generated from both ends of alignments of fully-sequenced reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: .wig files - quantile normalized wiggle occupancy profiles produced by DANPOS from pooled replicates

extract_protocol:
Nuclei were isolated from seedlings frozen in liquid nitrogen as described in (Chodavarapu, Feng et al. 2010) with following modifications: after resuspending in HBB, nuclei were applied to layer of HBB with 40% percoll (GE Healthcare), centrifuged at 1000g, 6 min, resuspended in HBB, applied to 40/75% percoll gradient, centrifuged at 400g, 40 min, collected and washed three times with HBC. The integrity of extracted nuclei was monitored using DAPI staining and fluorescence microscopy. The quantity of nuclei was measured by qPCR with primers targeting nuclear DNA. Digestion was performed by incubating nuclei suspended in DB buffer (16 mM Tris-HCl pH=7.6, 50 mM NaCl, 2.5 mM CaCl2, 0.01 mM PMSF, 1x Complete EDTA-free Protease Inhibitors (Roche)) with 1.5 μl of micrococcal nuclease (Thermo Fisher) and 2 μl of RNase A (Thermo Fisher) at 8°C for 90 min with gentle mixing. The reaction was stopped by adding equal volume of 2x Lysis buffer with EDTA (100 mM Tris-HCl pH=8, 200 mM NaCl, 50 mM EDTA, 1% SDS). The samples were lysed by incubation in 37°C for 60 min with shaking (1000 rpm). DNA was purified using phenol-chloroform extraction, precipitated with isopropanol and sodium acetate and resuspended in water. DNA was size selected by electrophoresis on 2% agarose gel with 1xTAE buffer with SYBR Gold (Invitrogen) stain. Mononucleosomal band was excised, frozen and squeezed by three cycles of spinning and rehydration on centrifuge column. DNA was purified and concentrated using Agencourt AMPure XP beads (Beckman Coulter).
Barcoded libraries were synthesized from 100 ng of mononucleosomal DNA using Ion Xpress™ Plus gDNA Fragment Library Preparation Kit and Ion Xpress™ Barcode Adapters.


title: 4_MED2_IP

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
MED2_ORF_RACS
MED2_IRG_RACS

data_processing:
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
RACS: Reads calling from the genetic and intergenic regions were respectively counted and extracted
Genome_build: T_thermophila_June2014_assembly.fasta
Supplementary_files_format_and_content: csv files containing reads were generated using RACS
Supplementary_files_format_and_content: MED1_ORF_RACS: contains the number of reads found in all annotated genic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED2_ORF_RACS: contains the number of reads found in all annotated genic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED1_IRG_RACS: contains the number of reads found in all (RACS-pipeline generated) intergenic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED2_IRG_RACS: contains the number of reads found in all (RACS-pipeline generated) intergenic regions of the Tetrahymena genome for the corresponding samples

organism: Tetrahymena thermophila

source_name: Cells grown in SPP liquid media

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
Lysates were clarified from sonicated nuclei and incubated with ANTI-FLAG® M2 Affinity Gel (Sigma) A2220
Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)

value: Med31-FZZ tagged cells

tag: developmental stage

value: Vegetative Growth

tag: process

tag: chip antibody


title: Sik2/3 DKO 4


title: 3_MED1_IP

description:
MED1_ORF_RACS
MED1_IRG_RACS

value: ANTI-FLAG® M2 Affinity Gel (Sigma) A2220


title: Testis2-RRBS-farmed

description: European sea bass


title: 2_MED2_INPUT

description:
MED2_ORF_RACS
MED2_IRG_RACS

value: Whole cell extraction


title: Mnase-seq_3h1_rep1


title: Sik2/3 DKO 3


title: Muscle3-RRBS-farmed

description: European sea bass


title: Sik2/3 DKO 2


title: Mnase-seq_WT_rep2


title: 1_MED1_INPUT

description:
MED1_ORF_RACS
MED1_IRG_RACS


title: Muscle1-RRBS-farmed

description: European sea bass


title: Sik2/3 DKO 1


title: Sik2/3 DKO 5


title: Mnase-seq_WT_rep1


title: L1_reference_3

status: Public on Jul 08 2019

city: Nashville

first: Sierra

middle: D

last: Palumbos

state: TN

address: 2201 West End Ave, Nashville

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Reads were mapped and analyzed using CLC Genomics Workbench Version 11. Mapping done with CLC Genomics Workbench reference genome for C. elegans
For statistical comparison a likelihood ratio test was used, adjusted for multiple testing using Benjamini-Hochberg
RIS enriched genes were determined using α = 5% for FACS/RNA-seq cutoff
A Principle Component Analysis was performed on all datasets to verify quality of RNA seq data and to determine variability between groups.
Genome_build: C. elegans reference genome
Supplementary_files_format_and_content: excel file includes CPM for RIS enriched genes

organism: Caenorhabditis elegans

source_name: Whole L1 worm reference

growth_protocol: L1 larva were synchronized by hypochlorite treatment of adult hermaphrodites were allowed to hatch overnight in M9

extract_protocol:
Dissociated larval cells were generated as described (Spencer et al., PLoS ONE, 2014) cDNA synthesis was prepared using Clonetech Smart-Seq V3 Ultra Low Input RNA Kit
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500

treatment_protocol: A flp-11 promoter (Turek et al., eLIFE, 2016) was used to limit RIS expression. RIS::mKate expression is limited to RIS neurons. mCherry-labeled AVK neurons were isolated by FACS and collected in Trizol

value: L1 synchronized animals

tag: cell type

value: all L1 cells

tag: cell isolation

value: All cells, frozen over LN2


title: L1_reference_1


title: L1_reference_2


title: RIS_L1_2

source_name: Isolated L1 RIS neurons

value: RIS neuron

value: FACS sorting to isolate AVK


title: CD56+CD16+CD57-NKG2A+ donor B repl 1

city: Stockholm

first: Jakob

last: Michaelsson

address: Alfred Nobels allé 8, ANA Futura, level 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
Read pairs were trimmed from Illumina adapters using cutadapt (version 1.14), and UrQt was used to trim all bases with a phred quality score below 20
Read pairs were aligned to the protein coding sequences of the human transcriptome (gencode.v26.pc_transcripts.fa) using Salmon (version 0.8.2) and gene annotation using gencode.v26.annotation.gtf
Genome_build: Homo sapiens, GRCh38
Supplementary_files_format_and_content: Comma-separated text file include raw counts for each sample

source_name: Human lung NK cells

extract_protocol:
Cells were sorted directly into lysis buffer (0.2% Triton X-100, 2.5uM oligo-dT (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), 2.5mM dNTP, RNAse Inhibitor (Takara), and ERCC RNA spike in controls (Ambion)) in a 96-well V-bottom PCR plate.
Standard SMART-Seq2 protocol with 22 cycles of cDNA amplification. Sample quality was determined using a bioanalyzer (Agilent, High Sensitivity DNA chip). 5ng of amplified cDNA was taken for tagmentation using a customized in-house protocol) and Nextera XT primers.

treatment_protocol: Fresh human lung tissue was digested using collagenase II and DNAse. Lymphocytes were isolated by Ficoll and were cryopresereved untill sorting of NK cell subsets by FACS.

tag: donor

value: B

tag: replicate


title: RIS_L1_1


title: CD56+CD16+CD57-NKG2A+ donor A repl 2

value: A


title: CD56+CD16+CD57-NKG2A+ donor B repl 2


title: CD56+CD16+CD57-NKG2A+ donor A repl 1


title: NKG2A+CD16-CD69-CD49a-CD103- donor B repl 2


title: RIS_L1_3


title: Muscle2-RRBS-farmed

description: European sea bass

value: Skeletal muscle

tag: FISH origin

value: Farmed (reared in aquarium facilities)

tag: age

value: 3 years


title: NKG2A+CD16-CD69+CD49a-CD103- donor B repl 2


title: NKG2A+CD16-CD69+CD49a-CD103- donor A repl 1


title: NKG2A+CD16-CD69+CD49a+CD1030+ donor B repl 1


title: NKG2A+CD16-CD69+CD49a+CD103+ donor B repl 2


title: NKG2A+CD16-CD69+CD49a-CD103- donor A repl 2


title: NKG2A+CD16-CD69-CD49a-CD103- donor A repl 1


title: HM20 SFRP2 cells_Wnt3A treated 24h_rep1

value: SFRP1-5-expressing stable clones


title: NKG2A+CD16-CD69+CD49a-CD103- donor B repl 1


title: NKG2A+CD16-CD69+CD49a+CD103+ donor A repl 2


title: NKG2A+CD16-CD69+CD49a+CD103- donor B repl 2


title: NKG2A+CD16-CD69+CD49a+CD103- donor A repl 1


title: NKG2A+CD16-CD69+CD49a+CD103- donor B repl 1


title: NKG2A+CD16-CD69+CD49a+CD103+ donor A repl 1


title: MB135.iDUXB.veh.2

first: Guo-Liang

last: Chew

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing:
Merge gene annotations from UCSC knownGene, Ensembl 71, MISO v2.0
RSEM v1.2.4 used to call Bowtie with option '-v 2' to align to merged annotation
Remaining reads mapped to genome with TopHat v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: TPMs

molecule: polyA RNA

growth_protocol: MB135iDUXB myoblasts were maintained in Ham’s F-10 Nutrient Mix (Gibco) supplemented with 20% HyClone Fetal Bovine Serum, 100 U/100 µg penicillin/streptomycin (Gibco), 10 ng/ml recombinant human basic fibroblast growth factor (Promega Corporation), 1 µM dexamethasone (Sigma-Aldrich), 2 µg/ml puromycin (Sigma-Aldrich)

extract_protocol:
RNA for RNA-seq was extracted with TRIzol (Thermo Fisher) according to manufacturer's protocols
RNA-seq libraries were prepared from TRIzol-isolated RNA using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina catalog no. RS-122-2001/2).

treatment_protocol: MB135iDUXB myoblasts were treated with equivalent volumes of water, or 1µg/ml of Doxycycline Hyclate (from a 1000x stock concentration of 1mg/ml in water) for 24h

value: myoblasts

tag: genotype

value: iDUXB

tag: lentiviral vector

tag: treatment

value: control


title: MB135.iDUXB.veh.1

tag: cell line


title: MB135.iDUXB.dox.2

value: dox


title: NKG2A+CD16-CD69-CD49a-CD103- donor A repl 2


title: MB135.iDUXB.dox.1


title: SAM24358426 MDST8_Liver 3

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing: Reads were aligned to the GRCh38 and GRCm38 genomes using GSNAP. Multimappers to both organisms were removed. Concordant and unique reads with <= 3 mismatches to the human genome and >3 mismatches to the mouse genome were called human-specific. Genes were quantified using human-specific reads via the HTSeqGenie Bioconductor package. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: Human CRC cell line (MDST8) implanted in liver of mice

extract_protocol: Total RNA from isolated tumor tissues was extracted using RNeasy Micro-Kit (Qiagen). 5 replicate samples were collected for each treatment condition. QC of total RNA was done to determine sample quantity and quality. The concentration of RNA was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies).

value: MDST8_Liver 3

tag: strain

value: Recipient animals:NSG mice (JAX00557)

value: Liver

tag: tissue diagnosis

value: Adenocarcinoma Metastatic


title: NKG2A+CD16-CD69-CD49a-CD103- donor B repl 1


title: SAM24358425 MDST8_Liver 2

value: MDST8_Liver 2

tag: tissue


title: SAM24358424 MDST8_Liver 1

value: MDST8_Liver 1


title: SAM24358423 MDST8_colon 5

source_name: Human CRC cell line (MDST8) implanted in colon of mice

value: MDST8_colon 5

value: Colon

value: Colorectal cancer


title: SAM24358421 MDST8_colon 3

value: MDST8_colon 3


title: SAM24358422 MDST8_colon 4

value: MDST8_colon 4


title: SAM24358420 MDST8_colon 2

value: MDST8_colon 2


title: SAM24358417 Ls180_Liver 4

source_name: Human CRC cell line (Ls180) implanted in liver of mice

value: Ls180_Liver 4


title: SAM24358418 Ls180_Liver 5

value: Ls180_Liver 5


title: SAM24358415 Ls180_Liver 2

value: Ls180_Liver 2


title: SAM24358416 Ls180_Liver 3

value: Ls180_Liver 3


title: SAM24358427 MDST8_Liver 4

value: MDST8_Liver 4


title: SAM24358428 MDST8_Liver 5

value: MDST8_Liver 5


title: WT_AngII

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
The reads were mapped to the mouse genome (m38, Ensembl version 89) and quantified using Cell Ranger 2.1.1 (10x Genomics).
We provided to Cell Ranger a custom built reference transcriptome generated by filtering the Ensembl transcriptome (Ensembl file: Mus_musculus.GRCm38.89.gtf) for the gene biotypes: protein coding, lincRNA and antisense. Cell Ranger was run with the expect number of cells parameter (expect-cells) set to 3000. Cell Ranger out filtered matrices (i.e. genes.tsv and barcodes.tsv) were then input into R and genes with zero counts in all cells were discarded.  Three cell quality control filtering steps were implemented. We removed: (a) cells with less than the 50th percentile of the distribution of the total cells library size, (b) cells with less than the 50th percentile of the distribution of total of number of detected genes, (c) cells with more than 50% of their total gene count coming from mitochondrial genes. This resulted in a final number of 508 cells. After applying these cell filtering steps, we carried out five gene quality control steps on the remaining cells: (a) we only kept “detectable” genes, defined as genes detected with more than one transcript in at least two cells, (b) we removed genes with low average expression in the data (i.e. genes with an average expression below 0.01, this cutoff was set based on the total distribution of average gene expression across all cells and all genes), (c) We removed genes encoded on the mitochondrial genome and the gene “Malat1” as it was an outlier in the gene expression distribution. After all the gene quality control steps, the resulting number of genes was 6,728.
Genome_build: Ensembl Gene annotation build 89 (m38)
Supplementary_files_format_and_content: Gene counts for all genes and cells that passed QC (raw_gene_counts.txt)
Supplementary_files_format_and_content: Raw gene counts from RSEM

source_name: Mouse heart left ventricle

extract_protocol:
Total RNA from tissue was isolated from the left ventricle of one WT mouse with 28 days of Angiotensin II infusion.
Single cell suspension was prepared from the adult left ventricle of one mice with Angiotensin II infusion for 28 days. After removal of dead cells with MACS dead cell removal kit (Miltenyi Biotec, #130-090-101), cells were lysed and subsequently RNA was reverse-transcribed and converted into cDNA libraries for RNA-seq analysis using a Chromium Controller and a Chromium Single Cell 3′ v2 Reagent kit (Genomics 10x) following the manufacturer’s protocol. The library was sequenced using the Illumina Hi-Seq3000 sequencing platform.

treatment_protocol: Alzet mini osmotic pump (Model No. 1004, Durect Corporation) was subcutaneuously implanted in eight-weeks old mice anaesthetized with 2% isoflurane. Miniosmotic pumps loaded with  Angiotensin II (Sigma Aldrich, #A9525) were implanted to deliver Ang II at 500ng/kg/min for a period of 4 weeks.

tag: stimulation

value: Angiotensin II 500ng/kg/min 28 days

tag: mutant/mutant ("ko") or control wild type ("wt") mice

value: WT


title: SAM24358412 Ls180_colon 4

source_name: Human CRC cell line (Ls180) implanted in colon of mice

value: Ls180_colon 4

value: Recipient animals:NSG mice (JAX00557)


title: SAM24358411 Ls180_colon 3

value: Ls180_colon 3


title: SAM24358414 Ls180_Liver 1

value: Ls180_Liver 1

value: Liver

value: Adenocarcinoma Metastatic


title: SAM24358410 Ls180_colon 2

value: Ls180_colon 2

value: Colon

value: Colorectal cancer


title: SAM24358413 Ls180_colon 5

value: Ls180_colon 5


title: SAM24358408 DLD1_Liver 5

source_name: Human CRC cell line (DLD1) implanted in liver of mice

value: DLD1_Liver 5


title: SAM24358407 DLD1_Liver 4

value: DLD1_Liver 4


title: WT-Ang_94-2

data_processing:
RNA-seq reads were assessed for quality, aligned to m38 (Ensembl Gene annotation build 89 using STAR 2.5.2b)
RNA-seq reads were quantified with RSEM 1.2.31
Genome_build: Ensembl Gene annotation build 89 (m38)
Supplementary_files_format_and_content: TPM values for all genes (TPM_genes.txt)
Supplementary_files_format_and_content: Gene counts for all genes from RSEM (raw_gene_counts.txt)

growth_protocol: WWP2 mut/wt mice were generated based on C57BL/6J in the laboratory of Dr. Weiping Yu at Agency for Science, Technology and Research (A*STAR), Singapore by CRISPR/Cas9 technology as previously reported [38, 39]. Briefly, mutant animals were generated by co-injection of Cas9 mRNA and individual gRNAs into one-cell mouse embryos. Founder animals carrying the indel mutations were identified first by PCR and T7 endonuclease I assay, and then by deep sequencing of the PCR products. Founders carrying the desired reading frame shift mutations were used to generate mutation-segregated heterozygous F1 animals by crossing with the wild type animals.  Homozygous mutant animals were generated by heterozygote crossing and used for experiments in comparison with the wild type littermates.

extract_protocol:
Total RNA from tissue was isolated from left ventricles of 9 Wwp2Mut/Mut and 9 WT mice with 28 days of Angiotensin II infusion.
mRNA libraries were constructed from poly(A)-selected RNA using the NEBNext Ultra Directional RNA library prep kit (Illumina, New England BioLabs)


title: SAM24358405 DLD1_Liver 2

value: DLD1_Liver 2


title: WT-Ang_67-1

description: NEBNext Ultra Directional RNA library prep kit (Illumina, New England BioLabs)


title: WT-Ang_45-1


title: WT-Ang_45-3


title: SAM24358419 MDST8_colon 1

value: MDST8_colon 1


title: WT-Ang_39-1


title: WT-Ang_84-2


title: IVF-derived ESC-11 (Rep.2)

city: Seoul

first: Chang-Kyu

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
The paired-end sequencing (2 × 100 bp) was performed using an Illumina HiSeq2500 (Illumina). Low-quality reads were filtered according to the following criteria: > 10% skipped bases (marked as ‘N’s), > 40% of bases with a quality score < 20, and reads with an average quality score of < 20.
Filtered reads were mapped to the reference genome using STAR v. 2.4.0b. Gene expression levels were measured with Cufflinks v. 2.1.1 using the gene annotation database.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: IVF-derived ESC-11

growth_protocol: The pig ESCs were cultured in ESC medium [KO-DMEM containing 15% (v/v) KSR, 0.1% (v/v) LC, 1× glutamax, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic (all from Gibco) supplemented with 20 ng/mL FGF2 (R&D Systems), 5 ng/mL ActA (R&D Systems), 1.5 µM CH (Cayman Chemical), and 2.5 µM IWR-1 (Sigma-Aldrich)]. Pig ESCs were subcultured every 5–7 days. At 24 h before subculturing, pig ESCs were cultured with ESC culture medium containing 10 µM Y-27632 (Santa Cruz Biotechnology, Dallas, TX, USA). Next, expanded colonies were dissociated into small clumps using TrypLE™ Express (Gibco). These clumps were transferred onto new feeder cells and cultured with ESC medium containing 10 µM Y-27632 (Santa Cruz Biotechnology) for 24 h. Next, attached clumps were cultured with ESC medium lacking Y-27632 for 4–6 days. Medium was changed every 24 h and pig ESCs were cultured under humidified conditions in an atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Before RNA extraction, SSEA1-positive undifferentiated pig ESCs were sorted using a MACS Cell Separation System (Miltenyi Biotec, Germany) to remove differentiated cells and feeder cells. Total RNA was extracted from pig fetal fibroblasts and sorted SSEA1-positive ESCs using TRIzol reagent (Invitrogen).
The quality of RNA samples was examined using the Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA, USA) (Table S5). The extracted RNA samples were used for construction of cDNA libraries. The cDNA library preparation and RNA-Seq analysis were performed by Theragen Etex (Korea). The libraries were prepared for 100 bp paired-end sequencing using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). The quality of the cDNA libraries was evaluated using the Agilent 2100 BioAnalyzer (Agilent). The cDNA libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer’s instructions. Fibroblasts were isolated from fetus at dpc 30, and RNAs were extracted from fibroblasts at passage 6 in the same manner as the pig ESCs.

value: IVF-derived ESC-11


title: IVF-derived ESC-11 (Rep.3)


title: WT-Ang_25-3

value: Angiotensin II 500ng/kg/min 28 days


title: WT-Ang_43-3

value: WT


title: SAM24358403 DLD1_colon 5

source_name: Human CRC cell line (DLD1) implanted in colon of mice

value: DLD1_colon 5


title: KO-Ang_8-2

value: KO


title: IVF-derived ESC-11 (Rep.1)


title: KO-Ang_62-1


title: SAM24358406 DLD1_Liver 3

value: DLD1_Liver 3

value: Recipient animals:NSG mice (JAX00557)


title: SAM24358402 DLD1_colon 4

value: DLD1_colon 4


title: SAM24358401 DLD1_colon 3

value: DLD1_colon 3


title: Parthenogenetic ESC-7 (Rep.2)

source_name: Parthenogenetic ESC-7

value: Parthenogenetic ESC-7


title: SAM24358400 DLD1_colon 2

value: DLD1_colon 2

value: Colon


title: Col1a1-Pth1r H223R 8

city: Boston

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9

source_name: cortical bone RNA

extract_protocol:
Femur were dissected, epiphyses cut off, and marrow was flushed with PBS until bone appeared white. Bone was flash frozen in TRIzol for RNA isolation. RNA was further purified using Qiagen Rneasy columns prior to library construction
Methods per BGI

tag: genotype/variation

value: Col1a1-Pth1r H223R


title: Parthenogenetic ESC-7 (Rep.1)


title: KO-Ang_52-1


title: KO-Ang_33-1


title: KO-Ang_24-3


title: KO-Ang_22-3


title: SAM24358404 DLD1_Liver 1

value: DLD1_Liver 1

value: Liver

value: Adenocarcinoma Metastatic


title: SAM24358399 DLD1_colon 1

value: DLD1_colon 1

value: Colorectal cancer


title: KO-Ang_1-2

value: Angiotensin II 500ng/kg/min 28 days


title: WT (for Sik2/3 DKO) 1

value: WT (for Sik2/3 DKO)


title: SAM24358398 RKO_Liver 5

source_name: Human CRC cell line (RKO) implanted in liver of mice

value: RKO_Liver 5


title: Parthenogenetic ESC-3 (Rep.3)

source_name: Parthenogenetic ESC-3

value: Parthenogenetic ESC-3


title: MM40592 SCL

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
Library strategy: SCL-seq
SCL-exo fastq files were filtered using SolexaQA to retain high-quality reads only (Q=20, l=17) before being mapped to hg19 genome assembly, forward and reverse strands separately, using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
SCL-exo data reads for which a single CpG was found within 10 bases from their 5’ end were selected to build a single-CpG resolution .wig file in which signal at identified CpGs corresponds to the sum of the reads covering both Cs (two strands) at each given CpG.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: primary MM cells

growth_protocol: XG21 and XG25 cell lines were cultured in RPMI 1640 medium, 10% fetal calf serum, and 2 ng/mL Interleukin-6.

extract_protocol:
MM cells were purified from bone marrow samples using anti-CD138 MACS microbeads (Miltenyi Biotech). Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen, France).
Ten micrograms of genomic DNA from MM patients or cell lines were subjected to the SCL-exo protocol (Sérandour et al., Genome Biol, 2016). Libraries were obtained using the TruSeq ChIP Sample Prep Kit from Illumina and quantified using the KAPA library quantification kit (KAPA Biosystems). Libraries were sequenced (50bp, single end) with HiSeq 1500 (Illumina).

value: tumor plasma cells


title: MM35174 SCL


title: Parthenogenetic ESC-3 (Rep.2)


title: KO-Ang_53-1

value: KO


title: Parthenogenetic ESC-7 (Rep.3)


title: KO-Ang_54-1


title: XG25 SCL-exo

data_processing:
Library strategy: SCL-exo-seq
SCL-exo fastq files were filtered using SolexaQA to retain high-quality reads only (Q=20, l=17) before being mapped to hg19 genome assembly, forward and reverse strands separately, using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
SCL-exo data reads for which a single CpG was found within 10 bases from their 5’ end were selected to build a single-CpG resolution .wig file in which signal at identified CpGs corresponds to the sum of the reads covering both Cs (two strands) at each given CpG.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: MM cell line

value: immortalized tumor plasma cells


title: SAM24358397 RKO_Liver 4

value: RKO_Liver 4

value: Recipient animals:NSG mice (JAX00557)


title: XG25 input


title: Parthenogenetic ESC-3 (Rep.1)


title: XG21 SCL-exo


title: SAM24358396 RKO_Liver 3

value: RKO_Liver 3


title: Somatic cell control (Rep.3)

source_name: Somatic cell control

value: fetal fibroblast


title: E14023 SCL-exo


title: E12196 SCL-exo


title: Liver1-RRBS-wild

first: Dafni

address: Pg. Marítim de la Barceloneta 37-49

institute: Institute of Marine Sciences-CSIC

description: European sea bass

data_processing:
RRBS raw reads were quality trimmed by the Timmomatic v. 0.32 with the following parameters SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18.
RRBS: Trimmed reads were aligned to the reference genome dicLab v1.0c using BSMAP v. 2.90 in RRBS mode with the following parameters -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2.
RRBS: Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
RNA-seq reads were decontaminated by BBDuk (v. 37.61) using the following parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=30 minlen=23.
RNA-seq: Reads were aligned to the genome by HISAT2 (v. 2.1.0) using the core hisat2 function with default parameters.
RNA-seq: Reads were counted at the gene level by feature Counts of the Subread package.
Genome_build: dicLab v1.0c (June 2012); http://seabass.mpipz.mpg.de/
Supplementary_files_format_and_content: *.txt: Output of methratio.py was converted using awk to methylkit input. Tab-delimited files contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered.
Supplementary_files_format_and_content: *-RNAseq-Feature_Counts.txt: For each tissue, one plain text file is provided with the feature counts per gene per sample.

source_name: Liver

extract_protocol:
Phenol-Chloroform DNA extraction.
RRBS library preparation using the Premium RRBS Kit from Diagenode (C02030032).

value: Wild (captured in NE Spain)

value: Adults


title: SAM24358395 RKO_Liver 2

value: RKO_Liver 2

value: Liver


title: Somatic cell control (Rep.2)


title: E12196 input


title: SAM24358394 RKO_Liver 1

value: RKO_Liver 1

value: Adenocarcinoma Metastatic


title: E12144 SCL-exo


title: E14023 input


title: SAM24358393 RKO_Colon 5

source_name: Human CRC cell line (RKO) implanted in colon of mice

value: RKO_Colon 5

value: Colon

value: Colorectal cancer


title: E12097 SCL-exo


title: E12144 input


title: A1_L

data_processing:
Demultiplexed reads were trimmed using FASTX followed by alignment to GRCm38.81 using Tophat (v2.0.13) and generation of reads per gene using htseq-count.
Pairwise comparisons were performed on genes that had a read count of >=33 in at least one replicate sample.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: tab-deliminted text file includes raw read count values for each sample

source_name: Mammary gland

extract_protocol:
Mammary glands were removed, minced, and stored in freezing media prior to single-cell dissociation. Single-cell dissociated mammary cells were pooled from 3 mice prior to sorting on EpCAM and CD49f expression via FACS. RNA was harvested using a combined protocol of Trizol extraction and column-based (Qiagen RNeasy Kit) isolation. NuGEN Ovation V2 system (#7102-32) was used to produce and amplify cDNA from 5 ng of total RNA input, followed by library construction using Illumina TruSeq Nano DNA Kit (#FC-121-4001) from 100 ng of cDNA input.
Standard protocols were used (a) to produce and amplify cDNA using NuGEN Ovation V2 System and (b) for library construction using Illumina system.

value: mammary gland

value: Luminal

value: 12 mo

value: wild type


title: E11240 SCL-exo

value: tumor plasma cells


title: E12097 input


title: SAM24358391 RKO_Colon 3

value: RKO_Colon 3

value: Recipient animals:NSG mice (JAX00557)


title: E11240 input


title: SAM24358390 RKO_Colon 2

value: RKO_Colon 2


title: E10061 SCL-exo


title: XG21 input

value: immortalized tumor plasma cells


title: Somatic cell control (Rep.1)

value: fetal fibroblast


title: E10025 input


title: E7060 SCL-exo


title: E7060 input


title: SAM24358409 Ls180_colon 1

value: Ls180_colon 1


title: E6068 SCL-exo


title: SAHA-treated HeLa cells, replicate 2

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

label: biotin

source_name: HeLa cells, treated with SAHA for 24 hours

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: HeLa cells were grown  at 37°C in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 2 mM GlutaMAX, penicillin (100 U/ml), and streptomycin (100 μg/ml) in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using the PureLink RNA kit (LifeTechnologies) according to manufacturer’s protocol.

treatment_protocol: HeLa cells were treated for 24 h with 20 uM of SAHA

value: HeLa


title: SAM24358392 RKO_Colon 4

value: RKO_Colon 4


title: E6068 input


title: SAHA-treated HeLa cells, replicate 3


title: A549_12h_0.2MOI

city: New York

first: Gregory

middle: Robert

last: Smith

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

data_processing:
Cell Ranger 2.0.1 used for data demultiplexing and alignment to the hg19 and PR8-NS1-GFP genomes
Seurat 2.3 used for filtering cells with less than 200 discovered genes and filtering genes expressed in fewer than 3 cells. Cells were further filtered to remove those with high mitochondrial gene counts
Matlab used to normalize total cell UMI counts to 10k host cell gene UMIs
Genome_build: hg19+PR8-NS1-GFP
Supplementary_files_format_and_content: csv files of normalized UMI counts per sample

source_name: Lung Epithelial Cells

extract_protocol:
A549 H2B-mCherry infected or MOCK infected cells were detached from the cell culture plates using trypsin-EDTA 0.05% (Gibco), washed with cell culture media and passed through a 40 mM cell strainer to prepare single-cell suspensions, and the final concentration was set at 1,000 cells/ml.
Single-cell gel beads in emulsion (GEMs) were generated using the 10X Genomics Chromium system following the Single Cell 3’ Reagents Kits V2 recommendations. The 10X chip was loaded to target 5,000 cells final. Reverse-transcription was performed in the emulsion and cDNA was amplified for 12 cycles before library construction. Each library was tagged with a different index for multiplexing. Quality control and quantification of the amplified cDNA were assessed by Bioanalyzer. Library quality control were evaluated by Bioanalyzer, Qubit and Kappa assays.

value: Lung Epithelial Cells

tag: infection

value: PR8-NS1-GFP MOI 0.2

tag: time post infection

value: 12 Hours

tag: molecule subtype

value: Genomic and Viral RNA


title: E10061 input

tag: cell type


title: SAHA-treated HeLa cells, replicate 1


title: A549_4h_Mock

value: Mock

value: 4 Hours

value: Genomic DNA


title: A549_4h_0.2MOI


title: E10025 SCL-exo


title: A549_4h_2.0MOI

value: PR8-NS1-GFP MOI 2.0


title: SW480_lncRNA-AF339830 siRNA3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: SW480_lncRNA-AF339830 siRNA

growth_protocol: The human SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of SW480 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human lncRNA-AF339830 siRNA were introduced into the SW480 colorectal cells, while nonspecific siRNA was used as negative controls.

value: human colorectal cancer cells

tag: passage

value: lncRNA-AF339830 siRNA1


title: SAM24358389 RKO_Colon 1

value: RKO_Colon 1

value: Recipient animals:NSG mice (JAX00557)

value: Colon

value: Colorectal cancer


title: A549_12h_Mock


title: Aortas, Mymsl WT  rep1

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment - STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.6.1, featurecounts, -s 1 -t exon -g gene_name
Genome_build: GRCm38 + gencode M17
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: aorta

extract_protocol:
Aortas were isolated from WT versus Mymsl knockout mice and total RNA was extracted from purifed medial layer aortic smooth muscle cells for RNA-seq.
Illumina TruSeq Stranded mRNA

value: Mymsl WT

value: aorta


title: SW480_lncRNA-AF339830 siRNA2


title: Aortas, Mymsl WT  rep3


title: Aortas, Mymsl WT  rep2


title: Aortas, Mymsl KO rep1

value: Mymsl KO


title: DMSO-treated HeLa cells, replicate 3

source_name: HeLa cells, treated with vehicle DMSO for 24 hours

value: HeLa


title: Aortas, Mymsl KO rep3


title: DMSO-treated HeLa cells, replicate 2


title: A549_12h_2.0MOI

value: Lung Epithelial Cells


title: SW480_Control siRNA3

description: Sample_SW480_AF123_3_20160323_CTTGTA_L007

source_name: SW480_Control siRNA

value: Control siRNA1


title: SW480_lncRNA-AF339830 siRNA1


title: Aortas, Mymsl KO rep2


title: SW480_Control siRNA1

description: Sample_SW480_AF123_1_20160323_TAGCTT_L007


title: SW480_Control siRNA2

description: Sample_SW480_AF123_2_20160323_GGCTAC_L007


title: DMSO-treated HeLa cells, replicate 1


title: SJMMBRCA050608_C1-Col-4T1-Wisp1-1

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files were mapped with internal pipeline that employs bwa and STAR
reads were counted using HTSEQ
raw counts are provided, DE was found using limma voom in R 3.2.4
Genome_build: mm9
Supplementary_files_format_and_content: each count txt file has raw count for each gene symbol  for one sample

source_name: 4T1 breast cancer cells

growth_protocol: 4T1 breast cancer cells were cultivated in RPMI 10% FCS, 1% Penicillin/Streptomycin.

extract_protocol:
RNA was isolated from total cell lysates with the Rneasy Plus Mini kit (Qiagen).
Total RNA was polyA enriched and prepared for RNA sequencing with TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: 4T1 cells were transduced with a lentiviral vector expressing Wisp1 and selected with puromycin to establish a stable cell line. The stable cell line was grown in Collagen type I-coated plastic dishes. RNA was collected from subconfluent cultures.

value: 4T1 breast cancer cells

tag: treatment class

value: Col I-4T1-Wisp1


title: SJMMBRCA050608_C3-Col-4T1-Wisp1-3


title: SJMMBRCA050607_C1-Col-4T1-EV-1

treatment_protocol: 4T1 cells were transduced with an empty lentiviral vector and selected with puromycin to establish a stable cell line. The stable cell line was grown in Collagen type I-coated plastic dishes. RNA was collected from subconfluent cultures.

value: Col I-4T1-EV


title: SCC25_shETS1_3_Rep2

city: Buffalo

first: Satrajit

last: Sinha

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

description: featureCounts_SCC25_shETS1_vs_shCON.Counts

data_processing:
Reads were mapped to the Homo sapiens genome (GRCH37 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the Ensembl GRCH37 build were quantified with featureCounts (v1.5.0).
Gene-level counts were normalized and used to calculate TPM values.
Genome_build: GRCH37
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample

growth_protocol: Cells were grown in DMEM/F12 Media containg 10% FBS, 1% Pen/Strep and 400 ng/ml hydrocortisone.  Cells infected with shRNA were selected using Puromycin treatment at a concentration of 2 μg/ml.

extract_protocol:
RNA was extracted from SCC25 cells using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.


title: SCC25_shETS1_3_Rep1


title: SJMMBRCA050608_C2-Col-4T1-Wisp1-2


title: SJMMBRCA050607_C2-Col-4T1-EV-2


title: SJMMBRCA050503_C3-4T1-WISP1-3

treatment_protocol: 4T1 cells were transduced with a lentiviral vector expressing Wisp1 and selected with puromycin to establish a stable cell line. The stable cell line was grown in tissue culture-treated plastic dishes. RNA was collected from subconfluent cultures.


title: SJMMBRCA050503_C2-4T1-WISP1-2


title: SCC25_shCON_Rep1

value: shCON


title: SCC25_shCON_Rep2


title: SJMMBRCA050503_C1-4T1-WISP1-1


title: SCC25_ETS1_siRNA_KD_Rep2

description: featureCounts_SCC25_siRNA_ETS1_vs_Control.Counts


title: SCC25_ETS1_siRNA_KD_Rep1


title: SJMMBRCA050502_C1-4T1-EV-1

treatment_protocol: 4T1 cells were transduced with an empty lentiviral vector and selected with puromycin to establish a stable cell line. The stable cell line was grown in tissue culture-treated plastic dishes. RNA was collected from subconfluent cultures.


title: SCC25_siRNA_Control_Rep2

value: siRNA control


title: SCC25_siRNA_Control_Rep1


title: SCC4_Rep2

description: featureCounts_HNSCC_Cell_Lines_RNA_Seq.Counts

extract_protocol:
RNA was extracted from HNSCC Cell Lines using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.


title: SJMMBRCA050502_C2-4T1-EV-2


title: SJMMBRCA050502_C3-4T1-EV-3


title: SJMMBRCA050607_C3-Col-4T1-EV-3


title: SJMMBRCA054935_C3-HJ510_2-4T1_TGFb

treatment_protocol: Medium was changed to fresh RPMI + 2 ng/mL recombinant human TGFb1 (R&D systems) and RNA was extracted after 24h


title: Female_8_weeks_2

city: Dunedin

first: Megan

last: Wilson

address: 270 Great King St

country: New Zealand

institute: University of Otago

data_processing:
Sequence reads were aligned to the mouse reference genome (mm9) using TopHat (Galaxy version 2.1.0) with default settings
FeatureCount (Galaxy version 1.6.03), as used to map reads to gene features, with a minimum mapping quality per read of 12
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files, reads per gene, GeneID is ENTREZ gene ID

source_name: Spinal cord

extract_protocol:
Spinal cords were removed,and RNA was harvested using Trizol reagent.  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spinal cord

tag: age

value: 8 weeks

tag: gender

value: female


title: Female_8_weeks_3


title: SJMMBRCA054935_C2-HJ497_2-4T1_TGFb


title: SCC4_Rep1


title: Female_8_weeks_1


title: lncRNA-AF339830 siRNA (c-myc antibody treatment)

data_processing:
The FASTQ files were aligned to hg19 using Bowtie2. Enriched regions were determined by the MACS1.4 program
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: DLD1 cells

growth_protocol: The human DLD1 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
DNA were extracted by Phenol chloroform
chip-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRC cells were cross-linked with 1% formaldehyde, isolated with SDS lysis buffer. Subsequently, the chromatin was sonicated and immunoprecipitated with c-myc antibody .

value: human colorectal cancer cells


title: SCC47_Rep2


title: SJMMBRCA054934_C2-HJ497_1-4T1

treatment_protocol: Medium was changed to fresh RPMI and RNA was extracted after 24h


title: Male_8_weeks_3

value: male


title: Control siRNA (c-myc antibody treatment)


title: SJMMBRCA054934_C3-HJ510_1-4T1


title: MDA-MB-231 shSETD1A rep3

city: Charlestown

last: Morris

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

data_processing:
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to analyses using LifeScope software package (Life Technologies), which provided a ChIP-seq module. LifeScope aligned color space read data to the hg19 human genome reference sequence to generate BAM files.
BAM files were subjected to peak calling using MACS2, which generated .narrowPeak files.
R/Bioconductor packages "ChIPseeker" and "clusterProfiler" were used to perform tertiary analyses.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text format matrix of ChIP peak genomic locations

source_name: MDA-MB-231 breast cancer cell line

growth_protocol: Human breast cell line, MDA-MB231, was grown in Dulbeccco’s modified medium supplemented with 10% female fetal bovine serum, glutamine and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA fragments enriched for association with HeK4me3 were subjected to deep sequencing library construction using the SOLiD fragment library core kit (Thermo Fisher) and the EZ Bead emulsion PCR system (Life Technologies).

treatment_protocol: Lentiviral short hairpin RNA constructs were obtained from the RNAi Consortium shRNA Library at the Broad Institute. Conditioned medium containing infective lentiviral particles was generated by co-transfecting 3 µg of lentiviral vector, 3 µg of pCMV ∂8.91 and 1 µg pHCMV-VSV-G into 2×106 293T human embryonic kidney cells using FuGENE 6 transfection reagent (Roche Applied Science). Supernatants were collected 48 hours after transfection and filtered through a 0.45 um membrane (Millipore). The cells were directly infected using 8 µg/mL of polybrene.

value: Triple negative breast cancer

tag: shRNA

value: SETD1A knockdown

tag: antibody


title: SCC29_Rep2

tag: cell line


title: MDA-MB-231 shSETD1A rep2


title: SCC29_Rep1


title: Male_8_weeks_1

tag: strain


title: SJMMBRCA054934_C1-HJ496_1-4T1


title: Female_4_weeks_2

value: 4 weeks


title: MDA-MB-231 shSETD1A rep1


title: SCC23_Rep2


title: SCC23_Rep1


title: HEK293, input DNA

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
Trim Galore (version 0.6.1) was used for adapter trimming and quality filter for all reads.
Then, these reads were mapped to the human genome (hg19) using the STAR (version 2.7.1a) alignment software.
Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard (version 2.20.1) and Samtools(version 1.9).  These files are converted into bed format with bedtools (version 2.28.0).
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and  the Integrative Genomics Browser (IGB, Affymetrix).
The MACS2 software was used for peak identification with data from input as controls with the following setting : mappable genome size (hs),  nomodel (on),  read extension (250), flag (--broad).
Genome_build: hg19
Supplementary_files_format_and_content: The bedGraph files, which were generated by deepTools software (version 3.2.1), report the number of ChIP-Seq sequencing reads in a genomic interval (normalized to a read depth of 1 million reads).

source_name: HEK293, Input DNA

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% FBS, 1% antibiotics.

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

tag: chip antibody


title: HEK293, H3K27me3_ChIPSeq

source_name: HEK293, ChIP DNA

value: H3K27me3 abcam ab6002


title: SJMMBRCA054935_C1-HJ496_2-4T1_TGFb

tag: tissue


title: Female_4_weeks_1


title: larva3_rep3

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 2.0.1
Single cell analysis by Seurat (v2.3.4) and URD (v1.0.0)
Genome_build: Genome used was (Ciona intestinalis (KH2012, Ghost Database) plus mchsv40 and cfpsv40 inserts
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files

organism: Ciona intestinalis

source_name: larva_whole embryo

extract_protocol:
For each sample, 100 to 500 morphologically normal embryos were transferred into tubes pre-coated with 5% BSA in Ca2+-free artificial sea water (Ca2+-free ASW, 10mM KCl, 40mM MgCl2, 15mM MgSO4, 435 mM NaCl, 2.5mM NaHCO3, 7mM Tris base, 13mM Tris-HCl). Embryos were immediately dissociated with 0.5 to 1% trypsin in Ca2+-free ASW with 5 mM EGTA (ASW-EGTA) for 2min (gastrula and neurula stages) to 10min (tailbud stages). Embryos were pipetted 5min on ice to complete dissociation of individual cells.  Then, the digestion was inhibited with 0.2% BSA in Ca2+-free ASW or quenched by 20% FBS. Cells were collected by centrifugation at 4°C at 500g for 2 to 5min and then resuspended in ice-cold Ca2+-free ASW containing 0.5% BSA. For the swimming larva stage, the embryos were either homogenized (H100, Waverly) and dissociated using 1% trypsin or dissociated with 1% trypsin, 1mg/ml collagenase, 0.5% pronase and 0.5mg/ml cellulase in ASW EGTA. Once dissociated, the enzymes were inhibited by 20% FBS and 2mg/ml Glycine.
For all the samples, cells were lysed, cDNAs were barcoded and amplified with Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics, CA) following the instructions of the manufacturer. Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina, CA). All the libraries were sequenced on Illumina HiSeq 2500 Rapid flowcells (Illumina Inc., CA) with paired-end 26nt + 125nt reads following standard Illumina protocols.

tag: developmental stage

value: larva

value: whole embryo

tag: replicates

value: biological replicate 3


title: MDA-MB-231 shGFP rep3

state: Massachusetts

value: Negative control


title: SCC103_Rep2


title: MDA-MB-231 shGFP rep2


title: Male_4_weeks_2


title: SCC103_Rep1


title: Male_4_weeks_1


title: MDA-MB-231 shGFP rep1


title: Male_8_weeks_2


title: larva1_rep1

value: biological replicate 1


title: larva2_rep2

value: biological replicate 2