title: TAL1 G1E-ER4 0h [Replicate 1]

status: Public on Sep 17 2015

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

description:
Replicate 1
tal1_peakpair.gff
tal1_multiGPS.gff

data_processing:
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.15.
ChIP-exo reads were aligned to the mm9 genome assembly using Bowtie 1.00 for SOLiD(1 mismatch allowed), and BWA (Version: BWA ALN 0.6.2 for HiSeq single end reads and Version: BWA MEM 0.7.9a for NextSeq paired end reads) with default options. Non-uniquely mapped reads were filtered out in order to remove the reads with low mapping quality.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
multiGPS v0.5; http://mahonylab.org/software/multigps/ (--geninfo mm9.info --threads 4 --q 0.05 --d reb1_chipexo.distrib.txt --exclude blacklist.bed --design design_gata1 --verbose --probshared 0.99 --poissongausspb --medianscale --prlogconf -5 --memepath usr/bin --mememinw 6 --mememaxw 16 )
finding the enriched peaks from multiple biological replicates; http://atlas.bx.psu.edu/Han_etal_GATA_Method.htm
Genome_build: mm9
Supplementary_files_format_and_content: gff

extract_protocol:
Lysates were clarified from sonicated nuclei and GATA1(or TAL1)-DNA complexes were isolated with antibody.
ChIP-exo libraries were prepared for sequencing using standard SOLiD & Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: No special treatment or protocol applies

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)


title: TAL1 G1E [Replicate 1]

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: chip antibody

tag: cell type

value: Gata1- erythroid progenitor

tag: strain


title: GATA1 G1E-ER4 24h [Replicate 1]

description:
Replicate 1
gata1_peakpair.gff
gata1_multiGPS.gff

treatment_protocol: 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

value: GATA1 (sc265)


title: GATA1 G1E-ER4 24h [Replicate 2]

description:
Replicate 2
gata1_peakpair.gff
gata1_multiGPS.gff


title: GATA1 G1E-ER4 0h [Replicate 1]


title: GATA1 G1E-ER4 3h [Replicate 1]

treatment_protocol: 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)


title: AP1_Vehicle

status: Public on Sep 18 2015

city: Stanford

first: Xun

last: Lan

state: CA

address: 318 Campus Dr. Room S240

department: Genetics

institute: Stanford University

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
RNA-Seq: Read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using Partek Genomics Suite (v6.6) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.

organism: Homo sapiens

growth_protocol: The TNBC cell line MDA-MB-231 were obtained from the American Type Culture Collection, and cultured in DMEM 10% FBS.

extract_protocol:
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody. MDA-MB-231 cells were treated with 100 nM Dex, or 10 M CpdA for 2h and 4h, respectively. RNA was extracted using the RNeasy Mini Kit.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, libraries were constructed using the Illumina Truseq RNA Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: For hormone responsive experiments, MDA-MB-231 cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with vehicle and different ligands.

tag: cell line

tag: cancer

value: Breast adenocarcinoma

tag: type

value: TNBC

value: c-Jun Antibody (H-79) from Santa Cruz Biotechnology


title: RNA_Compound A 2h_2

description: RNA-seq replicate 2

library_source: transcriptomic

molecule: total RNA

source_name: RNA_Compound A 2h_2


title: GATA1 G1E [Replicate 1]


title: RNA_Dexamethasone 2h_2

description: RNA-seq replicate 2

source_name: RNA_Dexamethasone 2h_2


title: GR_Compound_A_2

description:
TNBC
ChIP-exo replicate 2

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.

source_name: MDA-MB-231 cells

extract_protocol:
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

value: Glucocorticoid Receptor (D8H2) XP® Rabbit mAb #3660 from CST


title: RNA_Dexamethasone 4h_1

description: RNA-seq replicate 1

source_name: RNA_Dexamethasone 4h_1


title: Whole blood_S352

type: genomic

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

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 Illumina's iScan reader using standard recommended Illumina scanner settings

data_processing: GenomeStudio 2009.2 toghether with the minfi, ChAMP, sva and MethylAid packages from Bioconductor.  First, we background corrected the data using NOOB. We removed probes with missing β-values, probes having less than 75% of samples with detection p-value<0.01 and probes located on the sex chromosomes. Using the annotation generated by Chen et al., we also removed cross-reactive probes and probes containing SNPs with minor allele frequency > 1% in European populations. Then, we applied the BMIQ algorithm, to adjust for the two different probe designs.

label: Cy5 and Cy3

source_name: Whole blood, S352

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from pheripheral whole blood

tag: Sex

value: Male

tag: tissue

value: blood

tag: age

tag: weight category

value: Overweight

value: A/G

value: G/G

value: A/A

value: A/C

value: C/C

value: C/G

value: A/T


title: GR_Vehicle_2

description:
TNBC
ChIP-exo replicate 2


title: Whole blood_S336

source_name: Whole blood, S336

value: Female

value: Normal-weight


title: Whole blood_S334

source_name: Whole blood, S334

value: T/T


title: Whole blood_S332

source_name: Whole blood, S332


title: Whole blood_S350

source_name: Whole blood, S350


title: Whole blood_S347

source_name: Whole blood, S347


title: Whole blood_S351

source_name: Whole blood, S351


title: Whole blood_S333

source_name: Whole blood, S333


title: Whole blood_S341

source_name: Whole blood, S341


title: Whole blood_S349

source_name: Whole blood, S349


title: Whole blood_S340

source_name: Whole blood, S340


title: Whole blood_S331

source_name: Whole blood, S331


title: Whole blood_S353

source_name: Whole blood, S353


title: Whole blood_S355

source_name: Whole blood, S355


title: Whole blood_S344

source_name: Whole blood, S344


title: Whole blood_S339

source_name: Whole blood, S339


title: Whole blood_S343

source_name: Whole blood, S343


title: Whole blood_S342

source_name: Whole blood, S342


title: Whole blood_S346

source_name: Whole blood, S346


title: Whole blood_S329

source_name: Whole blood, S329


title: Whole blood_S330

source_name: Whole blood, S330


title: Whole blood_S337

source_name: Whole blood, S337


title: Whole blood_S335

source_name: Whole blood, S335


title: Whole blood_S345

source_name: Whole blood, S345


title: Whole blood_S354

source_name: Whole blood, S354


title: Whole blood_S338

source_name: Whole blood, S338


title: Whole blood_S348

source_name: Whole blood, S348


title: Whole blood_S327

source_name: Whole blood, S327


title: Whole blood_S328

source_name: Whole blood, S328


title: Whole blood_S326

source_name: Whole blood, S326


title: Whole blood_S323

source_name: Whole blood, S323


title: Whole blood_S325

source_name: Whole blood, S325


title: Whole blood_S324

source_name: Whole blood, S324


title: Whole blood_S318

source_name: Whole blood, S318


title: Whole blood_S320

source_name: Whole blood, S320


title: Whole blood_S319

source_name: Whole blood, S319


title: Whole blood_S317

source_name: Whole blood, S317


title: Whole blood_S315

source_name: Whole blood, S315


title: Whole blood_S305

source_name: Whole blood, S305


title: Whole blood_S314

source_name: Whole blood, S314


title: Whole blood_S306

source_name: Whole blood, S306


title: Whole blood_S308

source_name: Whole blood, S308


title: Whole blood_S307

source_name: Whole blood, S307


title: Whole blood_S297

source_name: Whole blood, S297


title: Whole blood_S304

source_name: Whole blood, S304


title: Whole blood_S321

source_name: Whole blood, S321


title: Whole blood_S316

source_name: Whole blood, S316


title: Whole blood_S312

source_name: Whole blood, S312


title: Whole blood_S300

source_name: Whole blood, S300


title: Whole blood_S299

source_name: Whole blood, S299

value: Obese


title: Whole blood_S310

source_name: Whole blood, S310


title: Whole blood_S296

source_name: Whole blood, S296


title: Whole blood_S309

source_name: Whole blood, S309


title: Whole blood_S302

source_name: Whole blood, S302


title: Whole blood_S313

source_name: Whole blood, S313


title: Whole blood_S298

source_name: Whole blood, S298


title: Whole blood_S303

source_name: Whole blood, S303


title: Whole blood_S311

source_name: Whole blood, S311


title: Whole blood_S301

source_name: Whole blood, S301


title: Whole blood_S322

source_name: Whole blood, S322


title: Whole blood_S295

source_name: Whole blood, S295


title: Whole blood_S293

source_name: Whole blood, S293


title: Whole blood_S291

source_name: Whole blood, S291


title: Whole blood_S292

source_name: Whole blood, S292


title: Whole blood_S288

source_name: Whole blood, S288


title: Whole blood_S289

source_name: Whole blood, S289


title: Whole blood_S286

source_name: Whole blood, S286


title: Whole blood_S290

source_name: Whole blood, S290


title: Whole blood_S285

source_name: Whole blood, S285


title: Whole blood_S294

source_name: Whole blood, S294


title: Whole blood_S281

source_name: Whole blood, S281


title: Whole blood_S282

source_name: Whole blood, S282


title: Whole blood_S283

source_name: Whole blood, S283


title: Whole blood_S279

source_name: Whole blood, S279


title: Whole blood_S277

source_name: Whole blood, S277


title: Whole blood_S273

source_name: Whole blood, S273


title: Whole blood_S278

source_name: Whole blood, S278


title: Whole blood_S284

source_name: Whole blood, S284


title: Whole blood_S276

source_name: Whole blood, S276


title: Whole blood_S275

source_name: Whole blood, S275


title: Whole blood_S287

source_name: Whole blood, S287


title: Whole blood_S270

source_name: Whole blood, S270


title: Whole blood_S280

source_name: Whole blood, S280


title: Whole blood_S271

source_name: Whole blood, S271


title: Whole blood_S265

source_name: Whole blood, S265


title: Whole blood_S272

source_name: Whole blood, S272


title: Whole blood_S266

source_name: Whole blood, S266


title: Whole blood_S263

source_name: Whole blood, S263


title: Whole blood_S267

source_name: Whole blood, S267


title: Whole blood_S274

source_name: Whole blood, S274


title: Whole blood_S268

source_name: Whole blood, S268


title: Whole blood_S258

source_name: Whole blood, S258


title: Whole blood_S262

source_name: Whole blood, S262


title: Whole blood_S264

source_name: Whole blood, S264


title: Whole blood_S256

source_name: Whole blood, S256


title: Whole blood_S257

source_name: Whole blood, S257


title: Whole blood_S255

source_name: Whole blood, S255


title: Whole blood_S261

source_name: Whole blood, S261


title: Whole blood_S259

source_name: Whole blood, S259


title: Whole blood_S249

source_name: Whole blood, S249


title: Whole blood_S250

source_name: Whole blood, S250


title: Whole blood_S260

source_name: Whole blood, S260


title: Whole blood_S247

source_name: Whole blood, S247


title: Whole blood_S244

source_name: Whole blood, S244


title: Whole blood_S241

source_name: Whole blood, S241


title: Whole blood_S251

source_name: Whole blood, S251


title: Whole blood_S245

source_name: Whole blood, S245


title: Whole blood_S254

source_name: Whole blood, S254


title: Whole blood_S253

source_name: Whole blood, S253


title: Whole blood_S235

source_name: Whole blood, S235


title: Whole blood_S252

source_name: Whole blood, S252


title: Whole blood_S236

source_name: Whole blood, S236


title: Whole blood_S269

source_name: Whole blood, S269


title: Whole blood_S243

source_name: Whole blood, S243


title: Whole blood_S242

source_name: Whole blood, S242


title: Whole blood_S246

source_name: Whole blood, S246


title: Whole blood_S240

source_name: Whole blood, S240


title: Whole blood_S233

source_name: Whole blood, S233


title: Whole blood_S239

source_name: Whole blood, S239


title: Whole blood_S237

source_name: Whole blood, S237


title: Whole blood_S248

source_name: Whole blood, S248


title: Whole blood_S238

source_name: Whole blood, S238


title: Whole blood_S231

source_name: Whole blood, S231


title: Whole blood_S230

source_name: Whole blood, S230


title: Whole blood_S232

source_name: Whole blood, S232


title: Whole blood_S227

source_name: Whole blood, S227


title: Whole blood_S228

source_name: Whole blood, S228


title: Whole blood_S229

source_name: Whole blood, S229


title: Whole blood_S224

source_name: Whole blood, S224


title: Whole blood_S234

source_name: Whole blood, S234


title: Whole blood_S223

source_name: Whole blood, S223


title: Whole blood_S225

source_name: Whole blood, S225


title: Whole blood_S221

source_name: Whole blood, S221


title: Whole blood_S220

source_name: Whole blood, S220


title: Whole blood_S209

source_name: Whole blood, S209


title: Whole blood_S217

source_name: Whole blood, S217


title: Whole blood_S226

source_name: Whole blood, S226


title: Whole blood_S222

source_name: Whole blood, S222


title: Whole blood_S218

source_name: Whole blood, S218


title: Whole blood_S219

source_name: Whole blood, S219


title: Whole blood_S210

source_name: Whole blood, S210


title: Whole blood_S212

source_name: Whole blood, S212


title: Whole blood_S208

source_name: Whole blood, S208


title: Whole blood_S200

source_name: Whole blood, S200


title: Whole blood_S206

source_name: Whole blood, S206


title: Whole blood_S202

source_name: Whole blood, S202


title: Whole blood_S201

source_name: Whole blood, S201


title: Whole blood_S204

source_name: Whole blood, S204


title: Whole blood_S214

source_name: Whole blood, S214


title: Whole blood_S215

source_name: Whole blood, S215


title: Whole blood_S205

source_name: Whole blood, S205


title: Whole blood_S198

source_name: Whole blood, S198


title: Whole blood_S211

source_name: Whole blood, S211


title: Whole blood_S216

source_name: Whole blood, S216


title: Whole blood_S207

source_name: Whole blood, S207


title: Whole blood_S194

source_name: Whole blood, S194


title: Whole blood_S197

source_name: Whole blood, S197


title: Whole blood_S213

source_name: Whole blood, S213


title: Whole blood_S203

source_name: Whole blood, S203


title: Whole blood_S193

source_name: Whole blood, S193


title: Whole blood_S189

source_name: Whole blood, S189


title: Whole blood_S195

source_name: Whole blood, S195


title: Solexa-268293

city: Boston

first: Rafael

middle: Machado

last: Rezende

state: MA

address: 77 Avenue Louis Pasteur

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Tuxedo RNA-Seq pipeline; TopHat v2.0.11, Bowtie v2.2.2.0, Cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: cuff diff

source_name: Jackson Laboratory

growth_protocol: 20 mice were eight weeks old when sacraficed; concentrated Gamma-delta cells using anti-TCR Gamma-delta beads. FACS sorted based on LAP expression.

extract_protocol:
Illumina's TruSeq kit with Poly A selection
pooled; twenty C57BL/6 mice were used in two separate experiments (10 mice each), where LAP+ and LAP- Gamma-delta T-cells were isolated. This resulted in three  samples (two LAP- samples and one LAP+ sample (two samples combined))

value: TCRgd+LAP+


title: Whole blood_S192

source_name: Whole blood, S192


title: Whole blood_S199

source_name: Whole blood, S199


title: Whole blood_S190

source_name: Whole blood, S190


title: Solexa-268291

value: TCRgd+LAP-


title: Solexa-268290


title: Whole blood_S178

source_name: Whole blood, S178


title: TAL1 G1E-ER4 24h [Replicate 3]

description:
Replicate 3
tal1_peakpair.gff
tal1_multiGPS.gff

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)


title: Whole blood_S196

source_name: Whole blood, S196


title: Whole blood_S182

source_name: Whole blood, S182

value: Male


title: Whole blood_S188

source_name: Whole blood, S188

value: blood


title: Whole blood_S186

source_name: Whole blood, S186


title: Whole blood_S191

source_name: Whole blood, S191


title: Whole blood_S183

source_name: Whole blood, S183


title: Whole blood_S180

source_name: Whole blood, S180

value: Overweight


title: Whole blood_S177

source_name: Whole blood, S177

value: A/G


title: Whole blood_S172

source_name: Whole blood, S172

value: G/G


title: Whole blood_S175

source_name: Whole blood, S175

value: A/A


title: Whole blood_S171

source_name: Whole blood, S171

value: A/C


title: Whole blood_S185

source_name: Whole blood, S185

value: C/C


title: TAL1 G1E-ER4 3h [Replicate 3]


title: Whole blood_S176

source_name: Whole blood, S176


title: TAL1 G1E-ER4 24h [Replicate 1]


title: Whole blood_S187

source_name: Whole blood, S187

value: C/G


title: Whole blood_S170

source_name: Whole blood, S170

value: A/T


title: TAL1 G1E-ER4 24h [Replicate 2]

description:
Replicate 2
tal1_peakpair.gff
tal1_multiGPS.gff


title: Whole blood_S179

source_name: Whole blood, S179


title: Whole blood_S174

source_name: Whole blood, S174


title: TAL1 G1E-ER4 3h [Replicate 1]


title: TAL1 G1E-ER4 3h [Replicate 2]


title: Whole blood_S184

source_name: Whole blood, S184


title: Whole blood_S181

source_name: Whole blood, S181


title: TAL1 G1E [Replicate 3]

value: Gata1- erythroid progenitor


title: Whole blood_S167

source_name: Whole blood, S167

value: Normal-weight


title: TAL1 G1E-ER4 0h [Replicate 4]

description:
Replicate 4
tal1_peakpair.gff
tal1_multiGPS.gff


title: TAL1 G1E [Replicate 4]


title: Whole blood_S169

source_name: Whole blood, S169


title: Whole blood_S168

source_name: Whole blood, S168


title: TAL1 G1E [Replicate 2]


title: TAL1 G1E-ER4 0h [Replicate 2]


title: TAL1 G1E-ER4 0h [Replicate 3]


title: Whole blood_S166

source_name: Whole blood, S166


title: Whole blood_S173

source_name: Whole blood, S173


title: HD1.1.w2

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: single cell in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.txt file gives the read counts described above for each sample (columns) and gene (rows).

source_name: white blood cell

extract_protocol:
Samples that have “source name” above set to “candidate PCa CTC” or “lineage-confirmed PCa CTC” were extracted as follows. We applied the CTC-iChip (PMID: 23552373) to efficiently deplete normal hematopoietic cells from whole blood specimens. Cell surface staining of remaining unfixed cells for epithelial (EpCAM) and mesenchymal (CDH11) markers (PMID: 23845299), combined with absent staining for the common leukocyte marker CD45, was used to select candidate tumor cells for micromanipulation. Samples that have “source name” set to “primary PCa tumor” were frozen primary prostate cancer tissue samples from patients with localized prostate cancer who underwent prostatectomy, that were then sectioned and microdissected for >70% tumor content. Samples that have “source name” above set to “single cell from PCa cell line” were trypsinized into single-cell suspension and then micromanipulated.  Only samples for which amplification was successful were submitted for sequencing. White blood cell samples from donor Pr23 were processed using the CTC-iChip and micromanipulated after staining for CD45. White blood cells from healthy donor HD1 were isolated from his blood using a micromanipulator, after enrichment of the mononuclear fraction using a BD Vacutainer CPT Cell Preparation Tube with Sodium Citrate and staining for CD45. For all samples RNA was extracted and amplified as in Tang, et. al. (PMID: 20203668).
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

tag: donor

tag: donor type

value: healthy


title: VCaP.5

description: single cell in lysis buffer

source_name: single cell from PCa cell line

value: VCaP

value: PCa cell line


title: HD1.1.w3

description: single cell in lysis buffer


title: VCaP.4

description: single cell in lysis buffer


title: HD1.1.w1

description: single cell in lysis buffer


title: Pr23.1.w1

description: single cell in lysis buffer

value: CRPC


title: Whole blood_S161

source_name: Whole blood, S161

value: T/T


title: VCaP.3

description: single cell in lysis buffer


title: VCaP.2

description: single cell in lysis buffer


title: Whole blood_S163

source_name: Whole blood, S163

value: Male


title: VCaP.1

description: single cell in lysis buffer


title: PC3.5

description: single cell in lysis buffer


title: Whole blood_S162

source_name: Whole blood, S162

value: blood


title: Whole blood_S160

source_name: Whole blood, S160

value: Overweight


title: PC3.3

description: single cell in lysis buffer


title: PC3.2

description: single cell in lysis buffer


title: PC3.4

description: single cell in lysis buffer


title: Whole blood_S153

source_name: Whole blood, S153

value: A/G


title: Whole blood_S164

source_name: Whole blood, S164

value: G/G


title: PC3.1

description: single cell in lysis buffer


title: Whole blood_S154

source_name: Whole blood, S154

value: A/A


title: Whole blood_S159

source_name: Whole blood, S159

value: A/C


title: Whole blood_S158

source_name: Whole blood, S158

value: Female

value: C/C


title: Pr23.1.w2

description: single cell in lysis buffer


title: Whole blood_S156

source_name: Whole blood, S156


title: LNCaP.R.5

description: single cell in lysis buffer

value: LNCaP


title: Whole blood_S150

source_name: Whole blood, S150

value: A/T

value: C/G


title: Whole blood_S157

source_name: Whole blood, S157

value: Normal-weight


title: LNCaP.R.4

description: single cell in lysis buffer


title: Whole blood_S165

source_name: Whole blood, S165

value: Obese


title: Whole blood_S155

source_name: Whole blood, S155


title: Whole blood_S149

source_name: Whole blood, S149


title: Whole blood_S143

source_name: Whole blood, S143


title: LNCaP.R.3

description: single cell in lysis buffer

source_name: single cell from PCa cell line

value: PCa cell line


title: LNCaP.R.1

description: single cell in lysis buffer


title: Whole blood_S144

source_name: Whole blood, S144


title: Whole blood_S151

source_name: Whole blood, S151


title: Whole blood_S141

source_name: Whole blood, S141


title: Whole blood_S145

source_name: Whole blood, S145


title: Whole blood_S142

source_name: Whole blood, S142


title: LNCaP.D.5

description: single cell in lysis buffer


title: Whole blood_S148

source_name: Whole blood, S148


title: Whole blood_S146

source_name: Whole blood, S146


title: LNCaP.D.2

description: single cell in lysis buffer


title: Whole blood_S152

source_name: Whole blood, S152


title: LNCaP.4

description: single cell in lysis buffer


title: LNCaP.3

description: single cell in lysis buffer


title: Whole blood_S138

source_name: Whole blood, S138


title: LNCaP.2

description: single cell in lysis buffer


title: Whole blood_S147

source_name: Whole blood, S147


title: LNCaP.D.1

description: single cell in lysis buffer


title: LNCaP.1

description: single cell in lysis buffer


title: LNCaP.R.2

description: single cell in lysis buffer


title: Whole blood_S137

source_name: Whole blood, S137


title: DU145.5

description: single cell in lysis buffer


title: Whole blood_S136

source_name: Whole blood, S136


title: Whole blood_S139

source_name: Whole blood, S139


title: DU145.4

description: single cell in lysis buffer


title: DU145.3

description: single cell in lysis buffer


title: DU145.2

description: single cell in lysis buffer


title: DU145.1

description: single cell in lysis buffer


title: PriTum9

description: total RNA

source_name: primary PCa tumor

value: localized PCa Gleason Score 8-10


title: LNCaP.D.4

description: single cell in lysis buffer


title: LNCaP.5

description: single cell in lysis buffer


title: PriTum8

description: total RNA


title: Whole blood_S129

source_name: Whole blood, S129


title: Whole blood_S132

source_name: Whole blood, S132

value: T/T


title: PriTum6

description: total RNA


title: Whole blood_S135

source_name: Whole blood, S135

value: Male


title: PriTum5

description: total RNA


title: Whole blood_S140

source_name: Whole blood, S140

value: blood


title: Whole blood_S131

source_name: Whole blood, S131


title: Whole blood_S128

source_name: Whole blood, S128

value: Overweight


title: PriTum7

description: total RNA


title: Whole blood_S133

source_name: Whole blood, S133

value: A/G


title: PriTum12

description: total RNA


title: LNCaP.D.3

description: single cell in lysis buffer

source_name: single cell from PCa cell line


title: Whole blood_S127

source_name: Whole blood, S127

value: G/G


title: PriTum11

description: total RNA


title: PriTum10

description: total RNA


title: PriTum4

description: total RNA

value: localized PCa Gleason Score 6-7


title: Whole blood_S126

source_name: Whole blood, S126

value: A/A

value: A/C


title: Whole blood_S124

source_name: Whole blood, S124

value: Female

value: C/C


title: Whole blood_S122

source_name: Whole blood, S122

value: A/T


title: PriTum3

description: total RNA


title: Whole blood_S125

source_name: Whole blood, S125

value: C/G


title: PriTum1

description: total RNA


title: Whole blood_S130

source_name: Whole blood, S130


title: Whole blood_S134

source_name: Whole blood, S134

value: Normal-weight


title: Pr6.1.5

description: single cell in lysis buffer

source_name: lineage-confirmed PCa CTC

value: CSPC

tag: enzalutamide

value: enzalutamide-naive (Group A)


title: Whole blood_S121

source_name: Whole blood, S121


title: Whole blood_S115

source_name: Whole blood, S115


title: Pr6.1.2

description: single cell in lysis buffer


title: Pr3.1.1

description: single cell in lysis buffer


title: Pr22.1.9

description: single cell in lysis buffer

value: CRPC

value: progressed on enzalutamide (Group B)


title: Pr22.1.7

description: single cell in lysis buffer


title: Pr22.1.8

description: single cell in lysis buffer


title: Whole blood_S117

source_name: Whole blood, S117

value: Male


title: Pr22.1.6

description: single cell in lysis buffer


title: Whole blood_S118

source_name: Whole blood, S118

value: blood

value: T/T


title: Whole blood_S123

source_name: Whole blood, S123

value: Overweight

value: A/G


title: Whole blood_S114

source_name: Whole blood, S114

value: G/G


title: Whole blood_S112

source_name: Whole blood, S112

value: A/A


title: Pr22.1.5

description: single cell in lysis buffer


title: Pr22.1.4

description: single cell in lysis buffer


title: Whole blood_S116

source_name: Whole blood, S116

value: A/C


title: PriTum2

description: total RNA

source_name: primary PCa tumor

value: localized PCa Gleason Score 6-7


title: Pr22.1.2

description: single cell in lysis buffer


title: Whole blood_S110

source_name: Whole blood, S110

value: Female

value: C/C


title: Pr22.1.12

description: single cell in lysis buffer


title: Pr22.1.11

description: single cell in lysis buffer


title: Whole blood_S109

source_name: Whole blood, S109

value: C/G


title: Whole blood_S111

source_name: Whole blood, S111

value: Normal-weight

value: A/T


title: Whole blood_S105

source_name: Whole blood, S105

value: Obese


title: Pr21.1.8

description: single cell in lysis buffer

value: CRPC


title: Pr21.1.9

description: single cell in lysis buffer

value: progressed on enzalutamide (Group B)


title: Pr22.1.10

description: single cell in lysis buffer


title: Pr21.1.7

description: single cell in lysis buffer


title: Pr6.1.1

description: single cell in lysis buffer

value: CSPC

value: enzalutamide-naive (Group A)


title: Pr21.1.6

description: single cell in lysis buffer


title: Whole blood_S106

source_name: Whole blood, S106

value: blood


title: Whole blood_S100

source_name: Whole blood, S100

value: T/T


title: Whole blood_S102

source_name: Whole blood, S102

value: Male

value: A/G


title: Whole blood_S119

source_name: Whole blood, S119

value: Overweight

value: A/A

value: G/G


title: Whole blood_S120

source_name: Whole blood, S120

value: A/C


title: Whole blood_S107

source_name: Whole blood, S107

value: Female

value: C/C


title: Pr21.1.4

description: single cell in lysis buffer

source_name: lineage-confirmed PCa CTC


title: Whole blood_S104

source_name: Whole blood, S104

value: Normal-weight

value: C/G


title: Pr21.1.3

description: single cell in lysis buffer


title: Pr21.1.5

description: single cell in lysis buffer


title: Pr21.1.12

description: single cell in lysis buffer


title: Pr21.1.2

description: single cell in lysis buffer


title: Whole blood_S103

source_name: Whole blood, S103

value: A/T


title: Whole blood_S97

source_name: Whole blood, S97


title: Whole blood_S98

source_name: Whole blood, S98


title: Pr21.1.11

description: single cell in lysis buffer

value: CRPC


title: Pr21.1.1

description: single cell in lysis buffer

value: progressed on enzalutamide (Group B)


title: Pr21.1.10

description: single cell in lysis buffer


title: Pr20.1.1

description: single cell in lysis buffer


title: Whole blood_S95

source_name: Whole blood, S95


title: Whole blood_S96

source_name: Whole blood, S96


title: Pr19.1.5

description: single cell in lysis buffer


title: Whole blood_S113

source_name: Whole blood, S113


title: Pr19.1.3

description: single cell in lysis buffer


title: Pr19.1.2

description: single cell in lysis buffer


title: Pr19.1.4

description: single cell in lysis buffer


title: Pr18.2.2

description: single cell in lysis buffer


title: Whole blood_S108

source_name: Whole blood, S108


title: Whole blood_S94

source_name: Whole blood, S94


title: Pr18.2.1

description: single cell in lysis buffer


title: Whole blood_S89

source_name: Whole blood, S89


title: Whole blood_S85

source_name: Whole blood, S85


title: Whole blood_S88

source_name: Whole blood, S88


title: Whole blood_S93

source_name: Whole blood, S93


title: Pr18.1.8

description: single cell in lysis buffer


title: Whole blood_S84

source_name: Whole blood, S84


title: Whole blood_S92

source_name: Whole blood, S92


title: Whole blood_S101

source_name: Whole blood, S101


title: Whole blood_S90

source_name: Whole blood, S90


title: Whole blood_S87

source_name: Whole blood, S87

value: Obese


title: Whole blood_S80

source_name: Whole blood, S80


title: Pr18.1.5

description: single cell in lysis buffer

source_name: lineage-confirmed PCa CTC


title: Pr18.1.6

description: single cell in lysis buffer


title: Pr18.2.3

description: single cell in lysis buffer


title: Pr18.1.1

description: single cell in lysis buffer


title: Pr18.1.7

description: single cell in lysis buffer


title: Whole blood_S81

source_name: Whole blood, S81


title: Pr9.3.8

description: single cell in lysis buffer

value: enzalutamide-naive (Group A)


title: Whole blood_S91

source_name: Whole blood, S91

value: blood


title: Whole blood_S82

source_name: Whole blood, S82

value: T/T


title: Whole blood_S83

source_name: Whole blood, S83


title: Whole blood_S86

source_name: Whole blood, S86


title: Whole blood_S76

source_name: Whole blood, S76


title: Pr9.3.7

description: single cell in lysis buffer


title: Whole blood_S79

source_name: Whole blood, S79

value: Male


title: Whole blood_S78

source_name: Whole blood, S78

value: A/G


title: Pr9.3.6

description: single cell in lysis buffer


title: Whole blood_S75

source_name: Whole blood, S75


title: Whole blood_S74

source_name: Whole blood, S74


title: Whole blood_S99

source_name: Whole blood, S99

value: Overweight


title: Whole blood_S72

source_name: Whole blood, S72

value: A/A


title: Whole blood_S77

source_name: Whole blood, S77

value: G/G


title: Pr9.3.1

description: single cell in lysis buffer


title: Pr9.1.4

description: single cell in lysis buffer


title: Pr9.1.1

description: single cell in lysis buffer


title: Pr17.2.2

description: single cell in lysis buffer


title: Whole blood_S69

source_name: Whole blood, S69

value: A/C


title: Pr9.1.3

description: single cell in lysis buffer


title: Pr9.1.2

description: single cell in lysis buffer


title: Pr17.1.2

description: single cell in lysis buffer


title: Whole blood_S70

source_name: Whole blood, S70


title: Pr17.2.1

description: single cell in lysis buffer


title: Whole blood_S67

source_name: Whole blood, S67


title: Whole blood_S73

source_name: Whole blood, S73


title: Pr17.1.1

description: single cell in lysis buffer

source_name: lineage-confirmed PCa CTC


title: Whole blood_S66

source_name: Whole blood, S66


title: Pr14.3.6

description: single cell in lysis buffer


title: Pr14.3.5

description: single cell in lysis buffer


title: Pr14.3.4

description: single cell in lysis buffer


title: Whole blood_S68

source_name: Whole blood, S68


title: Pr15.1.1

description: single cell in lysis buffer


title: Whole blood_S71

source_name: Whole blood, S71


title: Pr14.2.6

description: single cell in lysis buffer


title: Pr14.3.1

description: single cell in lysis buffer


title: Pr18.1.4

description: single cell in lysis buffer


title: Whole blood_S64

source_name: Whole blood, S64


title: Whole blood_S63

source_name: Whole blood, S63


title: Pr14.2.3

description: single cell in lysis buffer


title: Pr14.2.5

description: single cell in lysis buffer


title: Pr9.1.6

description: single cell in lysis buffer


title: Pr14.2.4

description: single cell in lysis buffer


title: Pr14.2.2

description: single cell in lysis buffer


title: Pr14.2.1

description: single cell in lysis buffer


title: Whole blood_S60

source_name: Whole blood, S60

value: Female


title: Pr14.1.1

description: single cell in lysis buffer


title: Whole blood_S55

source_name: Whole blood, S55

value: C/C


title: Whole blood_S62

source_name: Whole blood, S62

value: Normal-weight


title: Pr11.4.6

description: single cell in lysis buffer


title: Whole blood_S54

source_name: Whole blood, S54


title: Pr11.4.4

description: single cell in lysis buffer


title: Pr11.4.3

description: single cell in lysis buffer


title: Pr11.4.5

description: single cell in lysis buffer


title: Whole blood_S56

source_name: Whole blood, S56

value: C/G


title: Whole blood_S48

source_name: Whole blood, S48


title: Whole blood_S47

source_name: Whole blood, S47

value: A/T


title: Whole blood_S49

source_name: Whole blood, S49


title: Whole blood_S51

source_name: Whole blood, S51


title: Pr11.4.1

description: single cell in lysis buffer

value: CRPC


title: Whole blood_S58

source_name: Whole blood, S58


title: Pr11.3.3

description: single cell in lysis buffer


title: Pr11.3.2

description: single cell in lysis buffer


title: Pr11.3.1

description: single cell in lysis buffer


title: Pr11.2.2

description: single cell in lysis buffer


title: Whole blood_S57

source_name: Whole blood, S57


title: Whole blood_S50

source_name: Whole blood, S50


title: Whole blood_S41

source_name: Whole blood, S41


title: Whole blood_S42

source_name: Whole blood, S42


title: Pr11.1.1

description: single cell in lysis buffer

source_name: lineage-confirmed PCa CTC


title: Whole blood_S43

source_name: Whole blood, S43


title: Whole blood_S45

source_name: Whole blood, S45


title: Pr10.2.2

description: single cell in lysis buffer


title: Pr8.1.2

description: single cell in lysis buffer

source_name: candidate PCa CTC

value: CSPC


title: Whole blood_S52

source_name: Whole blood, S52


title: Whole blood_S39

source_name: Whole blood, S39


title: Whole blood_S44

source_name: Whole blood, S44


title: Whole blood_S36

source_name: Whole blood, S36


title: Pr5.1.3

description: single cell in lysis buffer


title: Whole blood_S40

source_name: Whole blood, S40


title: Pr5.1.2

description: single cell in lysis buffer


title: Pr6.1.3

description: single cell in lysis buffer


title: Whole blood_S38

source_name: Whole blood, S38


title: Whole blood_S35

source_name: Whole blood, S35


title: Pr4.1.2

description: single cell in lysis buffer


title: Pr11.4.2

description: single cell in lysis buffer


title: Pr4.1.1

description: single cell in lysis buffer


title: Whole blood_S33

source_name: Whole blood, S33


title: Pr6.1.4

description: single cell in lysis buffer


title: Whole blood_S65

source_name: Whole blood, S65


title: Whole blood_S61

source_name: Whole blood, S61


title: Pr3.1.2

description: single cell in lysis buffer


title: Whole blood_S32

source_name: Whole blood, S32


title: Pr1.1.1

description: single cell in lysis buffer


title: Whole blood_S59

source_name: Whole blood, S59


title: HeLa miR-17~92 mimics

city: La Jolla

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

description:
small RNA
1_S1

data_processing:
bcl2fastq/2.16.0.10 for base-calling
Raw reads were preprocessed and remove the adaptors using cutadapt (Martin et al., EMBnet. journal 17, pp. 10-12 (2011)). Reads shorter than 15 nucleotide or more than 80 nucleotide in length were discarded
reads were aligned to the pre-built Bowtie indexed human genome, H. Sapiens UCSC hg19, using Bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml), and removed rRNA species.
The remaining non-rRNA reads were examined for quality control using FastQC software and defined highly enriched reads (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ). Candidates for novel miRNAs were typically in very low abundance and constituted less than 1% of the mapped reads in each sample and therefor were excluded from the analysis.
To analyze high molecular weight RNA species, reads sizes between 25nt-74nt were pre-selected and analyzed by ShortRead and Biostrings library from Bioconductor in R (Morgan et al., 2009). To isolate RNA species containing a string of mature miR-17~92 or mutated miR-17~92 sequences, vcountPattern function with max.mismatch=5, with.indels=T option was used. The length distribution plot was generated using custom scripts in R.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with read counts

source_name: small RNA

growth_protocol: In DMEM with glutamax media, supplemented with 10% FBS and 1% of 100units/ml penn/strep.

extract_protocol:
RNA was harvested using Trizol reagent.
Methods for small RNA prep  Approximately 1 µg of total RNA was used for Next Generation Sequencing following the standard Illumina protocol, TruSeq_SmallRNA_SamplePrep_Guide_15004197_C.pdf, using 12 cycles of PCR.  3’ Adapter Ligation. 10 pmol of 3’-adenylated DNA adapter (5’-AppTGGAATTCTCGGGTGCCAAGGddC) is combined with 1 ug total RNA in a 4 ul volume, heated to 70 degrees C for 2 minutes and then placed on ice.  In a separate tube, 2 uL 10X T4 RNA Ligase 2 Truncated reaction buffer(NEB), 2 uL 50% PEG8000 (NEB), 1 uL RNase OUT (Lifetech) and 1 uL T4 RNA Ligase 2 Truncated enzyme (NEB) were combined and added to the RNA/3’adapter mix and incubated at 28 degrees C for one hour. This mixture was then heated to 70 degrees C for 2 minutes.  5’ Adapter Ligation. Next, 1 uL water, 1 uL 10 mM ATP, 1 uL T4 RNA Ligase and 1 uL 5’ RNA adapter (25 pmol, 5’-GUUCAGAGUUCUACAGUCCGACGAUC) were added and incubated at 28°C for 1 hour.  Reverse Transcription. Next, 1 uL of a 10 uM solution of RT primer (5’-GCCTTGGCACCCGAGAATTCCA) was added to 6 uL of the 5’adapter ligation mix above heated to 70 degrees C for 2 minutes and then transferred to ice. This was then combined with a solution containing: 2 uL of 5X First Strand Buffer (Superscript II buffer, Lifetech), 0.5 uL of 12.5 mM dNTPs, 1 uL 0.1 M DTT, 1 uL RNaseOUT (Lifetech), and 1 uL Superscript II (200 U/uL). The reaction was incubated at 50 degrees C for 1 hour and then placed on ice.  PCR. The 12.5 uL reverse transcription reaction above was then added to a tube containing: 30 pmol of Illumina Truseq Universal PCR primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA); 30 pmol of Illumina Truseq Barcoded PCR primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA, where XXXXXX, correspond to standard Illumina Truseq barcodes); and 25 uL of 2X KAPA HiFi HotStart ReadyMix PCR Kit in a 50 uL total volume. The reaction was heated to 98 degrees C for 1 minute, and then cycled 12 times with 98 degrees C for 10 seconds, 60 degrees C for 30 seconds, and 72 degrees C for 15 seconds, followed by a single incubation at 72 degrees C for 5 minutes. The resulting PCR products were isolated using AmpureXp magnetic bead purification (Agencourt, Beckman-Coulter) and then size selected on 4% Agarose gel cutting library products in the 140-190 bps corresponding to insert sizes of 20-70 bps.   The prepared library was then loaded onto an Illumina NextSeq500 V2 flowcell, standard cluster generation was performed on a Cbot and sequenced for 75 bases of the insert and 7 bases of the index read using standard NextSeq500 sequencing reagents. Reads were then processed  and demultiplexed based on index sequences using bcl2fastq 2.0.

treatment_protocol: Half million cells were seeded in 60mm plates a day prior to transfection. Media was replaced with antibiotics-free media 6 to 12 hours before transfection. The miRNA mimics were transfected using Dharmafect1 according to manufacturer's protocol.

value: HeLa

value: Cervical cancer cells

tag: genotype

value: wild type


title: Whole blood_S34

source_name: Whole blood, S34

value: blood


title: Whole blood_S31

source_name: Whole blood, S31

value: Male


title: HeLa

description:
small RNa
2_S2


title: Pr9.3.5

description: single cell in lysis buffer


title: Pr9.3.4

description: single cell in lysis buffer


title: Whole blood_S37

source_name: Whole blood, S37

value: A/G


title: Whole blood_S29

source_name: Whole blood, S29

value: Overweight


title: Pr9.3.3

description: single cell in lysis buffer

source_name: candidate PCa CTC


title: Whole blood_S28

source_name: Whole blood, S28

value: A/A


title: Whole blood_S46

source_name: Whole blood, S46

value: Obese

value: G/G

value: T/T


title: Pr5.1.1

description: single cell in lysis buffer


title: Pr2.1.1

description: single cell in lysis buffer


title: Pr9.3.2

description: single cell in lysis buffer


title: TAL1 G1E-ER4 0h [Replicate 5]

description:
Replicate 5
tal1_peakpair.gff
tal1_multiGPS.gff

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)


title: GATA1 G1E-ER4 24h [Replicate 3]

description:
Replicate 3
gata1_peakpair.gff
gata1_multiGPS.gff

value: GATA1 (sc265)


title: Whole blood_S53

source_name: Whole blood, S53

value: Normal-weight

value: A/C

value: C/C


title: Whole blood_S25

source_name: Whole blood, S25

value: A/T


title: GATA1 G1E-ER4 3h [Replicate 2]


title: GATA1 G1E-ER4 3h [Replicate 3]


title: Whole blood_S20

source_name: Whole blood, S20

value: C/G


title: GATA1 G1E-ER4 0h [Replicate 3]


title: GATA1 G1E-ER4 0h [Replicate 2]


title: Pr9.2.2

description: single cell in lysis buffer

value: CRPC


title: Pr9.2.1

description: single cell in lysis buffer


title: Whole blood_S23

source_name: Whole blood, S23


title: Whole blood_S30

source_name: Whole blood, S30


title: Restim_Input_ChIPSeq

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using Bowtie (Langmead et al., 2009). Duplicated reads were filtered (allowing no more than 2 reads at the same location).
Because the longer DSG crosslinker generated wider enrichments compared to formaldehyde alone, a higher 2 kb cutoff was applied to filter spurious peaks. Intersecting regions (physically overlapping) in all four conditions (OCA-B and Oct1 enriched material from resting and restimulated T cells) were generated using BEDTools (Quinlan and Hall, 2010). Nearest gene analysis and GO enrichment were performed with Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010) using a 100000 bp cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: TDF format; generated with igvtools count program

source_name: CD4 T cells

growth_protocol: WT CD4 T cells were purified from spleens and  stimulated with plate-bound anti-CD3e and anti-CD28 antibodies for 2 days. For rested and restimulated conditions, naïve cells were stimulated for a total of 48 hrs, then rested in absence of any stimulation for 8 days. These cells were again stimulated with plate-bound anti-CD3e and anti-CD28 antibodies for 6 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei and trancription factor-DNA complexes were isolated with antibody.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary mouse splenic CD4+ T cells Cells were stimulated using CD3/CD28 antibodies followed by rest period of 8 days without any stimulation and restimulation with CD3/CD28 antibodies for 6 hrs. The rested and restimulated cells were fixed with DSG and formaldehyde, lysed using cell lysis buffer, sonicated to shear chromosomal DNA to 250-750 bp size, immunoprecipitated using antibodies against Oct1 and OcaB.

value: Spleen

value: postnatal 8 weeks

tag: treatment

value: restimulated

tag: antibody


title: Whole blood_S26

source_name: Whole blood, S26

value: Male

value: blood

value: A/G


title: Pr2.1.2

description: single cell in lysis buffer

value: CSPC


title: Whole blood_S22

source_name: Whole blood, S22

value: Female

value: G/G

value: A/A


title: Whole blood_S21

source_name: Whole blood, S21

value: T/T


title: S2_RNA_Seq_replicate_2_L002

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

data_processing:
Reads were aligned with tophat.
Coverage profiles in bedGraph format were generated using bedtools.
Genome_build: BDGP5/dm3
Supplementary_files_format_and_content: bedgraph

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in Schneider’s media (Invitrogen) supplied with 10% Fetal Calf Serum (Life Technologies) at 27°C.

extract_protocol:
RNA from Drosophila S2 cells was extracted using Promega's SV Total RNA Isolation System (Z3100) according to manufacturer’s protocol.
The Illumina® mRNA-Seq Sample Prep Kit was used to process the sample(s). The sample preparation was performed according the Illumina protocol "Preparing Samples for Sequencing of mRNA" (1004898 Rev. D). Briefly, mRNA was isolated from total RNA using the poly-T-oligo-attached magnetic beads. After fragementation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with a DNA 1000 Lab-on-a-Chip (see appendices). The size of the resulting products was consistent with the expected size of approximately 300 bp. Clustering and DNA sequencing using the Illumina HiSeq 2000 (Solexa) were performed according manufacturer’s protocols. A total of 6.5 pmol of DNA was used. Two sequencing reads of 100 cycles each using the Read 1 sequencing and Read 2 sequencing primers were performed with the flow cell.

value: S2 cells


title: Pr9.1.7

description: single cell in lysis buffer


title: Whole blood_S19

source_name: Whole blood, S19

value: Normal-weight

value: A/C


title: S2_RNA_Seq_replicate_1_L002


title: Pr22.1.3

description: single cell in lysis buffer


title: Pr9.1.5

description: single cell in lysis buffer


title: Restim_Oct1_ChIPSeq

tag: antibody vendor/catalog

value: SantaCruz, catalog# sc-232X


title: Pr22.1.1

description: single cell in lysis buffer


title: Pr20.1.2

description: single cell in lysis buffer


title: S2_RNA_Seq_replicate_1_L001


title: Rest_Input_ChIPSeq

value: rest


title: Restim_OcaB_ChIPSeq

value: OcaB

value: SantaCruz, catalog# sc-955X


title: Pr18.2.4

description: single cell in lysis buffer

value: CRPC


title: Rest_OcaB_ChIPSeq

value: Spleen

value: postnatal 8 weeks


title: Dm_S2_cells_18C_MNase_HIGH_rep1

description: Drosophila S2 cells 18°C chromatin MNase-HIGH-seq 1n (mononucl.) replicate 1

data_processing:
Reads were aligned to the dm3 genome assembly using bowtie2 (default parameters).
Occupancy profiles in bedGraph format were generated using bedtools.
For further analyses the aligned reads were size selected as described in the article.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph

growth_protocol: Flies of Oregon-R strain were reared at 25°C under standard conditions in population cages. Embryos were collected overnight (~12 hours) on grape juice plates supplied with yeast paste. S2 cells were grown in Schneider’s media (Invitrogen) supplied with 10% Fetal Calf Serum (Life Technologies) at 27°C. To assess the temperature effects on nucleosome sensitivity/accessibility to MNase, S2 cells were incubated overnight (~16 hours) at 18°C and fixed with formaldehyde prior to MNase digestion.

extract_protocol:
1) Differential MNase-seq:  MNase digestion of chromatin of Drosophila embryos was performed as described (Petesch SJ and Lis JT, Cell 2008, 134:74-84) with few modifications. In brief, 2 g of embryos collected overnight were homogenized in 5 ml of buffer A1 (60mM KCl, 15 mM NaCl2, 4mM MgCl2, 15 mM HEPES pH7.6, 0.5 mM DTT, 0.5% Triton X-100, protease inhibitors) containing 2% of formaldehyde and crosslinked for 15’ at room temperature. Reaction was stopped by adding 1M of glycine to a final concentration of 225 mM followed by 5’ incubation. Cross-linked nuclei were filtered through Miracloth (475855, EMD Millipore), loaded on top of the sucrose cushion (0.3 M sucrose in buffer A1) and centrifuged at 700 g, 4°C for 5’. Nuclei were washed 2X in buffer A1, 2X in buffer D (25% glycerol, 5 mM Mg Acetate, 50 mM Tris pH 8.0, 0.1 mM EDTA, 5 mM DTT) and re-suspended in 1 ml of buffer MN (60 mM KCl, 15 mM NaCl, 15 mM Tris pH 7.4, 0.5 mM DTT, 0.25 M sucrose, 1.0 mM CaCl2).    Micrococcal nuclease (MNase) digestion of chromatin was performed by the addition of 10 (MNase-LOW) to 250 (MNase-HIGH) total units of MNase (70196Y, Affymetrix) to 200 mkl of isolated nuclei. Following 10’ of incubation at 25°C, the reactions were stopped with EDTA and SDS added to final concentrations of 12.5 mM and 0.5% respectively. MNase digested DNA was decrosslinked by incubation in elution buffer containing 1% SDS, 0.5 mg/ml Proteinase K, 0.1 M NaHCO3 for 2 h at 37°C and 16 h at 65°C, purified with QIAquick PCR Purification kit (28106, QIAgen) and analysed on 2% agarose gel. DNA fragments corresponding to mono-nucleosome (~147 bp) were excised from the gel and purified for further analysis.    A similar protocol was used for MNase digestion of chromatin from 2 ×10^8 Drosophila S2 cells. For S2 cells, DNA fragments corresponding to mono- (~147 bp) and di- (~300-350 bp) nucleosomes were gel-isolated.    2) Differential MNase-ChIP-seq:  For MNase-HIGH-ChIP-seq, 1 ml of nuclei was prepared from 2 g of Drosophila embryos as described above followed by the complete digestion of chromatin to mono-nucleosomes with 250 U of MNase per 200 mkl of nuclei for 10’ at 25°C. After that, nuclei were lysed immediately for 10’ at 4°C by the addition of equal volume of 2X ChIP lysis buffer (2% SDS, 20 mM EDTA, 100 mM Tris-HCl pH 8.1, 0.2 mM PMSF) and stored at -80°C before use.    For MNase-LOW-ChIP-seq, 12 ml of nuclei was prepared from 50 g of Drosophila embryos followed by the digestion of chromatin with 10 U of MNase per 200 μl of nuclei for 10’ at 25°C. After the reaction was stopped, nuclei were collected by centrifugation at 9000 g for 10’ at 4°C and lysed for 1 hour at 4°C in 6 ml of a buffer containing 0.5 M NaCl, 10 mM HEPES pH 7.6, 1 mM EDTA and 0.2 mM of protease inhibitor PMSF. Lysed nuclei were spun at 15000 g for 15’ at 4°C and supernatant containing soluble chromatin was loaded onto 5-30% sucrose gradient prepared on Gradient Master (Biocomp). Molecular weight fractions were formed by centrifugation at 26000 rpm for 16 h at 4°C in SW 40 Ti swing rotor. 1ml fractions were collected and 200 μl aliquots were decrosslinked and analysed on 2% agarose gel. Fractions containing mono-nucleosomes were used for ChIP.    Chromatin immune-precipitations (ChIPs) were performed as described (Moshkin YM, et al., Mol Cell Biol 2012, 32:675-688). In brief, lysed nuclei from MNase-HIGH digestion or isolated mono-nucleosomes from MNase-LOW digestion experiments were diluted with 10 volumes of ChIP dilution buffer (1% Triton X-100, 150 mM NaCl, 2 mM EDTA, 20mM Tris-HCl pH 8.1, 0.2 mM PMSF), incubated with ChIP-grade antibodies against histone H3 (ab1791, Abcam) or H2B (Moshkin YM, et al., Mol Cell Biol 2012, 32:675-688) overnight at 4°C and precipitated with pre-blocked protein A agarose (16-157, EMD Millipore). Following extensive washes: 3 times with a buffer containing 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1 and 150 mM NaCl and once with the similar buffer containing 500 mM NaCl, DNA was decrosslinked and purified with QIAquick PCR Purification kit (28106, QIAgen).
Libraries for Illumina sequencing were prepared from 10 ng of DNA by Service XS (Netherlands) with Illumina kits, or in-house with SureSelect kit (G9691A, Agilent) starting from the end-repair step. For the input controls, libraries from sonicated or MNase digested genomic DNA were prepared. Libraries’ quality was assessed on Bioanalyzer using DNA1000 kit (5067-1504, Agilent). Libraries were paired-end sequenced (2x25 bp or 2x50 bp) on Illumina HiSeq 2000.

tag: mnase conc.

value: LOW

tag: mono- (1n), di- (2n) nucleosome


title: Rest_Oct1_ChIPSeq

tag: strain


title: Whole blood_S16

source_name: Whole blood, S16

value: Male

value: blood

value: A/G

value: A/T

value: C/C

value: C/G


title: Whole blood_S14

source_name: Whole blood, S14

value: A/A

value: G/G


title: S2_RNA_Seq_replicate_2_L001

tag: cell type

value: S2 cells


title: S2_cells_MNase_LOW_2n_rep_2

description: Drosophila S2 cells chromatin MNase-HIGH-seq 2n (dinucl.) replicate 2

tag: cell line


title: Whole blood_S18

source_name: Whole blood, S18

value: Female

value: Normal-weight

value: A/C


title: Whole blood_S17

source_name: Whole blood, S17

value: T/T


title: Whole blood_S27

source_name: Whole blood, S27

value: Overweight


title: S2_cells_MNase_LOW_2n_rep_1

description: Drosophila S2 cells chromatin MNase-HIGH-seq 2n (dinucl.) replicate 1


title: Pr18.1.3

description: single cell in lysis buffer

source_name: candidate PCa CTC

value: CRPC


title: S2_cells_MNase_LOW_1n_rep_1

description: Drosophila S2 cells chromatin MNase-LOW-seq 1n (mononucl.) replicate 1


title: Pr18.1.2

description: single cell in lysis buffer


title: Whole blood_S15

source_name: Whole blood, S15


title: S2_cells_MNase_HIGH_1n_rep_2

description: Drosophila S2 cells chromatin MNase-HIGH-seq 1n (mononucl.) replicate 2

value: HIGH


title: Pr16.1.4

description: single cell in lysis buffer


title: Pr16.1.3

description: single cell in lysis buffer


title: Pr18.1.9

description: single cell in lysis buffer


title: Pr16.1.2

description: single cell in lysis buffer


title: Whole blood_S9

source_name: Whole blood, S9


title: Whole blood_S12

source_name: Whole blood, S12


title: Whole blood_S11

source_name: Whole blood, S11


title: S2_cells_MNase_LOW_1n_rep_2

description: Drosophila S2 cells chromatin MNase-LOW-seq 1n (mononucl.) replicate 2

value: LOW


title: 12h_embryo_MNase_LOW_H2B_ChIP_rep1

description: Drosophila 0-12h embryo chromatin MNase-LOW-H2B-ChIP-seq replicate 1

source_name: 0-12h embryo

value: Oregon-R

tag: developmental stage

value: 0-12h embryo

tag: chip antibody

value: anti-H2B (Moshkin et al., 2012)


title: Whole blood_S24

source_name: Whole blood, S24

tag: Sex

value: Male

tag: tissue

value: blood

value: A/G


title: Whole blood_S13

source_name: Whole blood, S13

tag: age

tag: weight category

value: A/A

value: A/T

value: C/C


title: Whole blood_S10

source_name: Whole blood, S10

value: G/G

value: C/G


title: Pr16.1.6

description: single cell in lysis buffer

tag: donor

tag: donor type


title: T20

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

country: China

institute: Chinese Academy of Sciences

description: OSK treated with LSD1 inhibitor Tranylcypromine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Mouse embryonic fibroblast

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

tag: strain background

value: ICR

value: Mouse embryonic fibroblast

tag: passages

tag: infected with

value: Oct4 Klf4 and Sox2

tag: treated with

value: LSD1 inhibitor Tranylcypromine


title: S2_cells_MNase_HIGH_1n_rep_1

description: Drosophila S2 cells chromatin MNase-HIGH-seq 1n (mononucl.) replicate 1

source_name: S2 cells

tag: mnase conc.

value: HIGH


title: Whole blood_S6

source_name: Whole blood, S6

value: Normal-weight

value: A/C


title: 12h_embryo_MNase_HIGH_H3_ChIP_rep1

description: Drosophila 0-12h embryo chromatin MNase-HIGH-H3-ChIP-seq replicate 1

value: Oregon-R

value: 0-12h embryo

tag: mono- (1n), di- (2n) nucleosome

value: anti-H3 (ab1791, Abcam)


title: Pr16.1.1

description: single cell in lysis buffer

value: CRPC


title: 12h_embryo_MNase_LOW_H3_ChIP_rep1

description: Drosophila 0-12h embryo chromatin MNase-LOW-H3-ChIP-seq replicate 1

tag: strain

value: LOW


title: 12h_embryo_MNase_LOW_H2B_ChIP_rep2

description: Drosophila 0-12h embryo chromatin MNase-LOW-H2B-ChIP-seq replicate 2

value: anti-H2B (Moshkin et al., 2012)


title: Whole blood_S5

source_name: Whole blood, S5

value: Male

value: blood

value: Overweight

value: A/G

value: A/A

value: A/T


title: Pr15.1.2

description: single cell in lysis buffer


title: MEF

value: ICR

tag: cell type

value: Mouse embryonic fibroblast


title: 12h_embryo_MNase_LOW_H3_ChIP_rep2

description: Drosophila 0-12h embryo chromatin MNase-LOW-H3-ChIP-seq replicate 2


title: Whole blood_S2

source_name: Whole blood, S2

value: G/G

value: C/C

value: T/T


title: Pr14.3.3

description: single cell in lysis buffer


title: Whole blood_S3

source_name: Whole blood, S3

value: Normal-weight

value: A/C


title: 12h_embryo_MNase_HIGH_H3_ChIP_rep2

description: Drosophila 0-12h embryo chromatin MNase-HIGH-H3-ChIP-seq replicate 2

value: Oregon-R

value: 0-12h embryo

value: HIGH

value: anti-H3 (ab1791, Abcam)


title: 12h_embryo_MNase_LOW_rep2

description: Drosophila 0-12h embryo chromatin MNase-LOW-seq replicate 2

value: LOW


title: Pr14.3.2

description: single cell in lysis buffer

value: CRPC


title: O


title: Whole blood_S4

source_name: Whole blood, S4

value: Female

value: blood


title: KS

value: Klf4 and Sox2


title: 12h_embryo_MNase_LOW_rep1

description: Drosophila 0-12h embryo chromatin MNase-LOW-seq replicate 1


title: Whole blood_S1

source_name: Whole blood, S1

value: Male

value: A/G

value: A/A


title: 12h_embryo_MNase_HIGH_H2B_ChIP_rep2

description: Drosophila 0-12h embryo chromatin MNase-HIGH-H2B-ChIP-seq replicate 2

value: anti-H2B (Moshkin et al., 2012)


title: Pr13.1.2

description: single cell in lysis buffer

source_name: candidate PCa CTC


title: Pr11.2.3

description: single cell in lysis buffer


title: Pr13.1.1

description: single cell in lysis buffer


title: Pr12.1.2

description: single cell in lysis buffer


title: 12h_embryo_MNase_HIGH_H2B_ChIP_rep1

description: Drosophila 0-12h embryo chromatin MNase-HIGH-H2B-ChIP-seq replicate 1


title: Ocab KO rested

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq (Pruitt et al., 2007).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files output by the scripture software (Guttman et al. 2010);  columns: (1--3) genomic location (4) gene name (5) RPKM

source_name: CD4 T cells

growth_protocol: WT and Ocab KO CD4 T cells were purified from spleens. Total RNA was extracted from either Naïve cells, or cells stimulated with plate-bound anti-CD3e and anti-CD28 antibodies for 6 hours. For rested and restimulated conditions, naïve cells were stimulated for a total of 48 hrs, then rested in absence of any stimulation for 8 days. These cells were again stimulated with plate-bound anti-CD3e and anti-CD28 antibodies for 6 hours.

extract_protocol:
RNA was extracted from CD4 T cells using RNA extraction kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary mouse splenic CD4+ T cells Cells were stimulated using CD3/CD28 antibodies. RNA was isolated from naïve cells, 6 hr stimulated cells, or cells rested in culture or restimulated for 6 hr

tag: genotype

value: Ocab KO

tag: treatment

value: rested

value: CD4 T cells

value: postnatal 8 weeks


title: Pr11.2.1

description: single cell in lysis buffer


title: 12h_embryo_MNase_HIGH_rep2

description: Drosophila 0-12h embryo chromatin MNase-HIGH-seq replicate 2

value: Oregon-R

tag: developmental stage


title: Pr11.1.2

description: single cell in lysis buffer


title: OSK

value: ICR

value: Mouse embryonic fibroblast

value: Oct4 Klf4 and Sox2


title: Ocab KO Naïve

value: Naïve


title: Ocab KO restim 6hr

value: restim 6hr


title: Whole blood_S7

source_name: Whole blood, S7

tag: Sex

value: Female

value: Overweight

value: G/G

value: A/T

value: C/C

value: A/C

value: C/G


title: WT rested

value: WT

tag: tissue


title: Pr12.1.1

description: single cell in lysis buffer

value: CRPC


title: Ocab KO 6hr stim

value: Ocab KO

value: 6hr stim

value: CD4 T cells

tag: age


title: Pr10.1.2

description: single cell in lysis buffer


title: S2_cells_genomic_DNA_MNase_rep2

description: Drosophila genomic DNA MNase-seq replicate 2

tag: cell line


title: Pr10.2.1

description: single cell in lysis buffer

tag: donor


title: 12h_embryo_MNase_HIGH_rep1

description: Drosophila 0-12h embryo chromatin MNase-HIGH-seq replicate 1

value: Oregon-R

value: 0-12h embryo

value: HIGH


title: S2_cells_genomic_DNA_MNase_rep1

description: Drosophila genomic DNA MNase-seq replicate 1


title: WT Naïve

value: Naïve

value: postnatal 8 weeks


title: 20121015_control

status: Public on Sep 16 2015

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Control

data_processing:
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Lifescope 2.5.1 software smallRNAs pipeline using default parameters.
Annotation process has been performed within home made pipeline. Alignment bam files with primary alignments (lowest MAPQV) were annotated with .GFF files with genomic coordinates of smallRNAs such as miRNAs (mirbase release 18), tRNAs (UCSC tracks), yRNAs, snoRNAs and piRNAs (fRNAdb) and ensembl ncRNAs tracks (release 69).
Processed data file submitted is a matrix file containning counts for each sample without normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular text-file with feature name, feature type, feature description, feature genomic coordinates and counts associated within each samples, ordered by expression decreasing

source_name: primary macrophages, Control

growth_protocol: Human primary macrophages were prepared from peripheral blood monocytes obtained from healthy donors in agreement with the French legislation on human biomedical research

extract_protocol:
Qiagen miRNeasy mini kit
NEBNext Small RNA Library Prep Set for SOLiD. Libraries were size selected on acrylamide gels (Library size: 110 to 150 nt).

treatment_protocol: Human primary macrophages were treated  with 1 µM staurosporine (STS). After 0, 4 and 6 hours, total RNA was extracted and submitted to small RNA sequencing.

value: primary macrophages


title: 20121015_STS4h

description: STS 4h

source_name: primary macrophages, STS 4h


title: S2_cells_sonicated_genomic_DNA_rep_1

description: Drosophila genomic DNA sonication-seq replicate 1


title: WT restim 6hr

value: restim 6hr


title: 20121015_STS6h

description: STS 6h

source_name: primary macrophages, STS 6h


title: Pr10.1.3

description: single cell in lysis buffer

tag: donor type


title: 40h rep2 barcode3

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

data_processing:
Cluster generation was performed using a TruSeq Single Read Cluster Kit (v3) and the Illumina cBot, with libraries multiplexed in three HiSeq2000 lanes (barcodes 1,2,3).
Images were analyzed using CASAVA version 1.8.2 and FASTQ files generated.
RPKM generated. DNAStar Inc (Madison, WI) modules SeqNGen and Qseq were used for mapping reads and statistical analysis.
Final fastq files processed using DNASTAR modules SeqNGen and Qseq
Genome_build: DoE Joint Genome Institute version 2.2 at http://genome.jgi-psf.org/pages/dynamicOrganismDownload.jsf?organism=Phchr2
Supplementary_files_format_and_content: RPKM values for each Sample. Values for 13602 transcript models (Seq_ID column) predicted by the DoE JGI automated pipeline. Ratios and probabilites computed for 40 hour versus 96 hour expression levels. Corresponding protein models and InterPro domains also listed.

organism: Phanerodontia chrysosporium

source_name: fungal colonized wood section_40hrs

growth_protocol: Phanerochaete. chrysosporium (strain RP-78) was grown as described previously on microtomed tangential sections of spruce sapwood (Picea glauca, 40 mm long, 10 mm wide, 40 µm thick, dry wt approx. 7 mg) that were embedded on glass cover slips in 90 µl of agar containing  a nitrogen/mineral salts medium without nutrient carbon

extract_protocol:
RNA was extracted from fungal colonized wood sections prepared as described above. Samples, comprised of 20 sections each, were harvested after 40h (3 samples) and 96 hr (3 samples), immersed in liquid nitrogen and stored at -80C until extraction. For total RNA purification, wood sections were ground in prechilled mortar and pestle in liquid nitrogen. Autoclaved and prechilled glass beads (0.5mm) were used during the grinding to make the wood sections into fine powder. Following repeated phenol;chloroform extractions, RNA was ethanol precipitated at -20°C overnight and further purified using the RNeasy mini kit (Qiagen, Valencia, CA). Total RNA was DNAase treated according to the manufacture’s protocol.
Messenger RNA was purified from 1μg total RNA using poly-T oligo-attached magnetic beads. Double-stranded cDNAs were synthesized using SuperScript II (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified using Agencourt AMPure XP beads (Qiagen, Valencia, California, USA) as recommended in the TruSeq RNA Sample Prep Guide. cDNAs were end-repaired by T4 DNA polymerase and Klenow DNA polymerase and phosphorylated with T4 polynucleotide kinase. The blunt ended cDNA was purified using Agencourt AMPure XP beads. The cDNA products were incubated with Klenow DNA polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments and then purified using Agencourt AMPure XP beads. DNA fragments were ligated to Illumina adapters having a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated products were purified using Agencourt AMPure XP beads. Adapter ligated DNA was amplified in a Linker Mediated PCR reaction (LM-PCR) for 15 cycles using PhusionTM DNA polymerase and Illumina's PE genomic DNA primer set and then purified using Agencourt AMPure XP beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit HS Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries standardized to 2 μM.

tag: time point

value: 40 hrs after inoculation


title: 40h rep2 barcode2


title: 40h rep1 barcode3


title: WT 6hr stim


title: 40h rep1 barcode1


title: S2_cells_sonicated_genomic_DNA_rep_2

description: Drosophila genomic DNA sonication-seq replicate 2


title: 40h rep3 barcode2


title: 40h rep3 barcode3


title: 40h rep3 barcode1


title: 96h rep3 barcode2

source_name: fungal colonized wood section_96hrs

value: 96 hrs after inoculation


title: 96h rep3 barcode3


title: 96h rep3 barcode1


title: 96h rep2 barcode3


title: 40h rep2 barcode1


title: 96h rep2 barcode1


title: 96h rep2 barcode2


title: 96h rep1 barcode3


title: Sample7 (RPL)

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Data processing was performed by ArrayStar Inc., Rockville MA, USA.  Details copied below:
Sequence reads were generated from Genome Analyzer IIx, image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human genome (UCSC Hg19) using BOWTIE software (V0.12.7).
To quantify the DNA methylation level of any specific region, each uniquely mapped read was extended to 200 bp in length. A methylation score for any region in the genome was defined as number of extended reads per kb.
To compare the DNA methylation profiles between multiple samples, the total number of uniquely mapped read of each sample must be normalized by the total number of reference reads (median number of uniquely mapped reads of all samples or total number of uniquely mapped reads of specific sample), the raw extended read counts were normalized accordingly.
Genome_build: hg19
Supplementary_files_format_and_content: .xls Excel spreadsheets containing MeDIP scores as calculated by Arraystar Inc.

source_name: Human Endometrial Stromal Cells

growth_protocol: Human Endometrial Stromal Cells were prepared and maintained in culture as described (Brosens 1999).

extract_protocol:
Sub-confluent cultures were harvested in Shorty Lysis Buffer and DNA was purified from the lysate by phenol-chloroform extraction and ethanol precipitation.
Library preparation and sequencing was performed by ArrayStar Inc., Rockville MA, USA.  Briefly, DNA was fragmented to 100-500bp fragments by sonication using a Bioruptor (Diagenode).  About 1 µg DNA was used for end repair and adapter ligation, then immunoprecipitated using anti-5-methylcytosine antibody (Diagenode).  After PCR amplification for enrichment of precipitated fragment, 200 – 300 nt DNA fragments were gel-extracted and quantitated using Agilent 2100 Bioanalyzer.  Libraries were denatured and sequenced on the Genome Analyzer IIx following the TruSeq SBS Kit v5 protocol.

value: Endometrial Stromal Cells

tag: patient group

value: recurrent pregnancy loss

tag: live births

tag: first trimester losses

tag: day of cycle


title: Sample6 (RPL)


title: Sample3 (control)

value: control


title: Sample8 (RPL)


title: Sample2 (control)


title: 96h rep1 barcode1


title: 40h rep1 barcode2


title: I40 (37C, 40g/L itaconic acid)

city: Jinan

first: Mei

last: Chen

state: Shandong

address: No.3501,Daxue Road

department: Qilu University of Technology

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Aspergillus terreus NIH2624 coding sequences using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Aspergillus terreus NIH2624 sequences (NCBI Reference Sequence: NZ_AAJN00000000.1)
Supplementary_files_format_and_content: One matrix table includes unique reads numbers, coverage and RPKM values for each genes.

organism: Aspergillus terreus

source_name: Fungal mycelia

growth_protocol: The mycelia cultivated in itaconic acid production medium (IPM) at 37°C was considered as a reference. IPMs with 5 g/L and 40 g/L itaconic acid (pH 3.25)  were used for high-acid culture respectively. High-temperature condition was possesed at 42°C in IPM. All samples were cultured on a rotary shaker at 220 rpm  for 36 h.

extract_protocol:
Total RNA were extracted using Trizol reagents (Invitrogen, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelia were collected and filtered by nylon fabric.

tag: culture temperature

tag: initial itaconic acid


title: 96h rep1 barcode2

tag: strain


title: Sample4 (control)

tag: cell type


title: C (37C, 0g/L itaconic acid)

value: 0 g/L


title: T (42C, 0g/L itaconic acid)


title: Stag2-1 [RNA-seq]

city: New York

first: Jasper

last: Mullenders

state: NY

address: 550 1st ave

department: Pathology

institute: NYU School of Medicine

description:
PolyA-RNA
Processed data file: RNA-seq-LSK.txt

data_processing:
Reads aligned with TopHat.
tophat --no-coverage-search --library-type fr-firststrand
Cuffdiff to find FPKM.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs.

source_name: LSK cells, Stag2 knockdown

growth_protocol: LSK cells were sorted from Ren(shRNA/+), Smc1a(shRNA/+) and Stag2(shRNA/+) mice.

extract_protocol:
RNA was isolated with RNeasy mini columns.
Library was constructed with polyA RNA using a strand specific protocol.

tag: genotype/variation

tag: doxycycline

value: 10 days

value: LSK (Lin(neg)/c-Kit(+)/Sca-1(+)) cells from bone marrow


title: Sample1 (control)


title: Smc1a-3 [RNA-seq]

source_name: LSK cells, Smc1a knockdown


title: Smc1a-1 [RNA-seq]


title: Stag2-2 [RNA-seq]


title: Ren-4 [RNA-seq]

source_name: LSK cells, Renilla knockdown

value: Ren(shRNA/+)/ROSA(rtTA/+)


title: Smc1a-2 [RNA-seq]


title: I5 (37C, 5g/L itaconic acid)

value: 5 g/L


title: Stag2-3 [RNA-seq]


title: Sample5 (RPL)


title: Ren-3 [RNA-seq]


title: Ren-1 [RNA-seq]


title: P5_Smc3_1 [RNA-seq]

description:
PolyA-RNA
Processed data file: RNA-Seq-CFU-P5.txt

data_processing:
Reads aligned with TopHat.
tophat --no-coverage-search --library-type fr-firststrand
Cuffdiff to find FPKM.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text files include FPKMs.

source_name: CFU P5 cells, LMP-Smc3

growth_protocol: c-Kit cells were infected with LMP-Renilla or -Cohesin and grown in M3434 methylcellulose for either 1 (P1) or 5 (P5) passages.

value: c-Kit

tag: virus

tag: passage


title: P5_Stag2_0 [RNA-seq]

source_name: CFU P5 cells, LMP-Stag2


title: P5_Smc1a_0 [RNA-seq]

source_name: CFU P5 cells, LMP-Smc1a


title: P5_Smc1a_1 [RNA-seq]


title: P1_Stag2-2 [RNA-seq]

description:
PolyA-RNA
Processed data file: RNA-Seq-CFU-P1.txt

source_name: CFU P1 cells, LMP-Stag2


title: P1_Smc3-1 [RNA-seq]

source_name: CFU P1 cells, LMP-Smc3


title: P1_Smc3-2 [RNA-seq]


title: P1_Smc1a-1 [RNA-seq]

source_name: CFU P1 cells, LMP-Smc1a


title: P1_Stag2-1 [RNA-seq]


title: P1_Rad21-1 [RNA-seq]

source_name: CFU P1 cells, LMP-Rad21


title: P1_Smc1a-0 [RNA-seq]


title: P1_Smc3-0 [RNA-seq]


title: P5_Rad21_0 [RNA-seq]

source_name: CFU P5 cells, LMP-Rad21


title: Ren-2 [RNA-seq]


title: P1_Ren-2 [RNA-seq]

source_name: CFU P1 cells, LMP-Renilla

value: LMP-Renilla


title: P5_Rad21_1 [RNA-seq]


title: P1_Ren-1 [RNA-seq]


title: Stag2-2 [ATAC-seq]

description: Processed data file: Stag2.bw

data_processing:
Library strategy: ATAC-Seq
Reads were aligned with Bowtie.
Reads were filtered at q 30.
Reads were slopped by 250.
Normalization is reads/million.
Bedtools was used to generate a bedGraph which was converted to bigWig.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig

growth_protocol: LSK cells were sorted from Ren(shRNA/+) and Stag2(shRNA/+) mice.

extract_protocol:
Genomic DNA was extracted.
ATAC-sequencing as described in Buenrostro et al. 2013 (PMID 24097267).


title: P1_Ren-0 [RNA-seq]


title: P5_Smc3_0 [RNA-seq]


title: P1_Rad21-0 [RNA-seq]


title: Whole blood_S8

source_name: Whole blood, S8

tag: Sex

value: Female

tag: tissue

value: blood

tag: age

tag: weight category

value: Normal-weight

value: A/G

value: G/G

value: A/A

value: A/C

value: C/C

value: C/G

value: A/T


title: Stag2-1 [ATAC-seq]

description: Processed data file: Stag2.bw


title: Ren-2 [ATAC-seq]

description: Processed data file: Ren.bw


title: Ren-1 [ATAC-seq]

description: Processed data file: Ren.bw


title: P1_Stag2-0 [RNA-seq]


title: Batch 4 iCPC_low passage_rep2

first: Pratik

middle: Arvind

last: Lalit

state: Wi

address: 1111 highland Ave, WIMR2 8th floor

department: Medicine

institute: UW-Madison

data_processing:
Illumina's CASAVA version 1.8.2 was used for basecalling.
Sequenced reads were filtered for presence of sequencing adapters and low quality.
Alignment to the mm9 transcriptome and gene expression quantitation (expected counts and transcripts per million) was done with RSEM version 1.2.3 (alignment with bowtie-0.12.9), input parameters: --bowtie-m 200 --bowtie-n 2 --keep-intermediate-files --no-bam-output --forward-prob 0.5 -p 10 --seed-length 28.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files, two per sample, one with expected count (EC) values and one with transcripts per million (TPM values) as calcuated by RSEM

source_name: low passage iCPCs

extract_protocol:
Ambion RNAqueous kit was used for isolation of total RNA. RNA was subjected to DNAase treatment before performing RNA-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: unknown

value: 1 to 3


title: Cardiac fibroblasts_rep2

source_name: adult cardiac fibroblasts

value: female

value: 1 to 2


title: Batch 3 iCPC_high passage_rep2

source_name: high passage iCPCs


title: P1_Rad21-2 [RNA-seq]


title: Cardiac fibroblasts_rep3

value: male


title: P1_Smc1a-2 [RNA-seq]

value: c-Kit


title: Batch 1 iCPC_low passage_rep1


title: Cardiac fibroblasts_rep1


title: H3K79me3_KO_ChIPSeq

city: Shanghai

first: Gang

last: Wang

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology,

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
CASAVA version 1.6 used for base-calling
Sequencing reads were alligned to mouse genome by Bowtie version 0.12. 8 and parameters are followings:-v1, --best, --strata, -k2, -m1
Peak calling was performed independently for each sample using MACS software version 1.4.2 by p-value threshold of 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files were generated using MACS version 1.4.2. Scores represent fragments pileup at every 10 bps of ChIP-seq.

source_name: MEFs cells knockout MED23

growth_protocol: MEFs cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (vol/vol) FBS (Hyclone)

extract_protocol:
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (anti-H3K79me3, Abcam, ab2621).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic fibroblast

value: MED23 knockout

tag: chip antibody


title: H3K4me3_KO_ChIPSeq

extract_protocol:
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (anti-H3K4me3, Abcam, ab8580).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols


title: H3K4me3_WT_ChIPSeq

source_name: MEFs cells wildtype

extract_protocol:
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (anti-H3K4me3, Abcam, ab8580)
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype


title: P1_Ren-3 [RNA-seq]

value: LMP-Renilla


title: H3K79me3_WT_ChIPSeq


title: mastoparan-D8

city: guangzhou

first: zhongfu

last: ying

state: guangdong

address: kaiyuan

department: stem cell research

institute: chinese academy of sciences

data_processing:
Illumina Miseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2-2.2.5  with parameters  -p 8 --bowtie2 -sensitivity-level very_sensitive
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...

source_name: MEF

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: ICR

value: Mouse Embryo Fibroblast (MEF)

value: expressing CypD

tag: treated with

value: mastoparan

tag: time point

value: at day 8 of reprogramming


title: control-D8

value: none (control)


title: paraquat-D8

value: paraquat


title: input_KO_ChIPSeq

extract_protocol:
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (Millipore, Cat. #05-1312, Lot #DAM1567819); Pol II (N20, Santa Cruz, Cat. sc-899).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols


title: input_WT_ChIPSeq


title: pol2_KO_ChIPSeq

value: Pol II


title: pol2_WT_ChIPSeq


title: Flag-D4

value: expressing Flag

value: at day 4 of reprogramming


title: control18

city: South San Francisco

first: Tiffany

last: hung

address: 1 DNA Way

department: Human Genetics

institute: Genentech

description:
SAM8750176
Processed data file: SLE_Alu_counts.txt

data_processing:
Illumina software CASAVA used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for rRNA contamination, filtered for low-complexity or low-quality sequence, then mapped to hg19 whole genome using GSNAP.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: SLE_RPKMs.txt: Tab-delimited text file includes RPKM values for each patient and control.

source_name: PAXgene blood, healthy control

extract_protocol:
RNA was extracted from PAXgene tubes.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease status

value: healthy

value: whole blood

tag: anti-ro

value: control

tag: ism


title: Batch 1 iCPC_high passage_rep1

value: unknown


title: control17

description:
SAM8750189
Processed data file: SLE_Alu_counts.txt


title: control15

description:
SAM8750185
Processed data file: SLE_Alu_counts.txt


title: control16

description:
SAM8750180
Processed data file: SLE_Alu_counts.txt


title: control14

description:
SAM8750186
Processed data file: SLE_Alu_counts.txt


title: control13

description:
SAM8750174
Processed data file: SLE_Alu_counts.txt


title: control12

description:
SAM8750188
Processed data file: SLE_Alu_counts.txt


title: control11

description:
SAM8750182
Processed data file: SLE_Alu_counts.txt


title: control6

description:
SAM8750187
Processed data file: SLE_Alu_counts.txt


title: control10

description:
SAM8750191
Processed data file: SLE_Alu_counts.txt


title: control7

description:
SAM8750178
Processed data file: SLE_Alu_counts.txt


title: control5

description:
SAM8750177
Processed data file: SLE_Alu_counts.txt


title: control3

description:
SAM8750192
Processed data file: SLE_Alu_counts.txt


title: control8

description:
SAM8750184
Processed data file: SLE_Alu_counts.txt


title: control2

description:
SAM8750175
Processed data file: SLE_Alu_counts.txt


title: CypD-D4

tag: cell type


title: SLE98

description:
SAM8750163
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, no anti-Ro, ISM_high

value: systemic lupus erythematosus (SLE)


title: SLE99

description:
SAM8750057
Processed data file: SLE_Alu_counts.txt


title: control1

description:
SAM8750193
Processed data file: SLE_Alu_counts.txt


title: SLE89

description:
SAM8749997
Processed data file: SLE_Alu_counts.txt


title: SLE93

description:
SAM8749964
Processed data file: SLE_Alu_counts.txt


title: SLE88

description:
SAM8750122
Processed data file: SLE_Alu_counts.txt


title: SLE94

description:
SAM8750095
Processed data file: SLE_Alu_counts.txt


title: SLE91

description:
SAM8750172
Processed data file: SLE_Alu_counts.txt


title: SLE92

description:
SAM8750153
Processed data file: SLE_Alu_counts.txt


title: SLE97

description:
SAM8749916
Processed data file: SLE_Alu_counts.txt


title: SLE87

description:
SAM8750113
Processed data file: SLE_Alu_counts.txt


title: control9

description:
SAM8750181
Processed data file: SLE_Alu_counts.txt


title: control4

description:
SAM8750179
Processed data file: SLE_Alu_counts.txt


title: SLE85

description:
SAM8750035
Processed data file: SLE_Alu_counts.txt


title: SLE95

description:
SAM8750081
Processed data file: SLE_Alu_counts.txt


title: SLE90

description:
SAM8750032
Processed data file: SLE_Alu_counts.txt


title: SLE86

description:
SAM8749994
Processed data file: SLE_Alu_counts.txt


title: SLE83

description:
SAM8750150
Processed data file: SLE_Alu_counts.txt


title: SLE84

description:
SAM8750007
Processed data file: SLE_Alu_counts.txt


title: SLE78

description:
SAM8749975
Processed data file: SLE_Alu_counts.txt


title: SLE82

description:
SAM8750104
Processed data file: SLE_Alu_counts.txt


title: SLE76

description:
SAM8749933
Processed data file: SLE_Alu_counts.txt


title: SLE77

description:
SAM8750135
Processed data file: SLE_Alu_counts.txt


title: SLE80

description:
SAM8749936
Processed data file: SLE_Alu_counts.txt


title: SLE81

description:
SAM8749890
Processed data file: SLE_Alu_counts.txt


title: SLE96

description:
SAM8749904
Processed data file: SLE_Alu_counts.txt


title: SLE75

description:
SAM8749924
Processed data file: SLE_Alu_counts.txt


title: SLE74

description:
SAM8750054
Processed data file: SLE_Alu_counts.txt


title: SLE72

description:
SAM9103792
Processed data file: SLE_Alu_counts.txt


title: SLE73

description:
SAM8750129
Processed data file: SLE_Alu_counts.txt


title: SLE71

description:
SAM8750169
Processed data file: SLE_Alu_counts.txt


title: SLE64

description:
SAM8750065
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, med anti-Ro, ISM_high

value: med


title: SLE66

description:
SAM8749939
Processed data file: SLE_Alu_counts.txt


title: SLE62

description:
SAM8750140
Processed data file: SLE_Alu_counts.txt


title: SLE79

description:
SAM8750010
Processed data file: SLE_Alu_counts.txt


title: SLE67

description:
SAM8750073
Processed data file: SLE_Alu_counts.txt


title: SLE56

description:
SAM8750160
Processed data file: SLE_Alu_counts.txt


title: SLE70

description:
SAM8750060
Processed data file: SLE_Alu_counts.txt


title: SLE59

description:
SAM8749991
Processed data file: SLE_Alu_counts.txt


title: SLE61

description:
SAM8749970
Processed data file: SLE_Alu_counts.txt


title: SLE60

description:
SAM8750106
Processed data file: SLE_Alu_counts.txt


title: SLE69

description:
SAM8749950
Processed data file: SLE_Alu_counts.txt


title: SLE58

description:
SAM8750051
Processed data file: SLE_Alu_counts.txt


title: SLE51

description:
SAM8750100
Processed data file: SLE_Alu_counts.txt


title: SLE52

description:
SAM8750084
Processed data file: SLE_Alu_counts.txt


title: SLE57

description:
SAM8750157
Processed data file: SLE_Alu_counts.txt


title: SLE54

description:
SAM8750132
Processed data file: SLE_Alu_counts.txt


title: SLE48

description:
SAM8750020
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, high anti-Ro, ISM_high

value: high


title: SLE49

description:
SAM8750119
Processed data file: SLE_Alu_counts.txt


title: SLE46

description:
SAM8749927
Processed data file: SLE_Alu_counts.txt


title: SLE45

description:
SAM8750076
Processed data file: SLE_Alu_counts.txt


title: SLE68

description:
SAM8750048
Processed data file: SLE_Alu_counts.txt


title: SLE43

description:
SAM8749930
Processed data file: SLE_Alu_counts.txt


title: SLE63

description:
SAM8749893
Processed data file: SLE_Alu_counts.txt


title: SLE65

description:
SAM8750025
Processed data file: SLE_Alu_counts.txt


title: SLE42

description:
SAM8750090
Processed data file: SLE_Alu_counts.txt


title: SLE55

description:
SAM8750067
Processed data file: SLE_Alu_counts.txt


title: SLE41

description:
SAM8750138
Processed data file: SLE_Alu_counts.txt


title: SLE37

description:
SAM8750028
Processed data file: SLE_Alu_counts.txt


title: SLE40

description:
SAM8749973
Processed data file: SLE_Alu_counts.txt


title: SLE34

description:
SAM8750023
Processed data file: SLE_Alu_counts.txt


title: SLE50

description:
SAM8750116
Processed data file: SLE_Alu_counts.txt


title: SLE47

description:
SAM8749919
Processed data file: SLE_Alu_counts.txt


title: SLE36

description:
SAM8750124
Processed data file: SLE_Alu_counts.txt


title: SLE31

description:
SAM8750017
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 4 [D3-2_S6_L004]

city: Gainesville

first: Stephen

last: Sugrue

address: 1600 SW Archer Road

institute: University of Florida

data_processing:
Distinct reads were aligned as single-ended reads to sequences corresponding to splicing junctions and intron retention events using Bowtie (v0.12.9; --best –tryhard –strata -v3 -m 1)
Distinct reads were aligned as single-ended reads to the hg19 build of the human genome (GRCh37/hg19) using BWA-MEM (0.7.2) for genomic alignments
Using AceView annotations (August 2010 release), overlapping exons were combined into the maximum exonic region in a strand-dependent manner
Expression was quantified using average depth per nucleotide (APN)
Genome_build: GRCh37/hg19

source_name: Doxycycline-treated sample 4, technical replicate

growth_protocol: Doxycycline-inducible PNN knockdown HCET cell were grown in a modified DMEM media (Joo et al., 2005. Mol Vis 11:133-42)

extract_protocol:
Total RNA was extracted using Rneasy Plus Mini Kit (Qiagen) using their standard protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce shRNA expression, the cells were treated with doxycycline at a concentration of 1 μg/ml with daily change of fresh doxycycline medium for 48 to 72h.

value: HCET

tag: shRNA

value: doxycycline-inducible shRNA against PNN

tag: treatment

value: Doxycycline treated


title: SLE33

description:
SAM9103789
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 4 [D3-2_S6_L003]


title: SLE32

description:
SAM8750111
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 4 [D3-2_S6_L001]


title: SLE27

description:
SAM8749986
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, no anti-Ro, ISM_low


title: SLE30

description:
SAM8750070
Processed data file: SLE_Alu_counts.txt


title: SLE38

description:
SAM8749958
Processed data file: SLE_Alu_counts.txt


title: SLE53

description:
SAM8749901
Processed data file: SLE_Alu_counts.txt


title: SLE39

description:
SAM8750063
Processed data file: SLE_Alu_counts.txt


title: SLE29

description:
SAM8750166
Processed data file: SLE_Alu_counts.txt


title: SLE23

description:
SAM8749948
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 3 [D2-2_S5_L002]

source_name: Doxycycline-treated sample 3, technical replicate


title: SLE24

description:
SAM8749956
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 4 [D3-2_S6_L002]


title: SLE26

description:
SAM8749907
Processed data file: SLE_Alu_counts.txt


title: SLE44

description:
SAM8750040
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 3 [D2-2_S5_L004]


title: SLE25

description:
SAM8749942
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 3 [D2-2_S5_L003]