title: WS

city: yangling

first: jianqin

last: zhang

state: shaanxi

address: xinong street No. 22

department: college of animal science and technology

institute: Northwest A&F university

data_processing:
The raw reads were cleaned by removing the adaptors and low quality reads prior to assembly. The unigene assembly was carried out using the short reads assembly program. All assembled unigenes were compared with the proteins in the non-redundant (nr) protein database, using BLAST software with a significance threshold of E-value < 10−5. Functional categorization by gene ontology (GO) terms was carried out according to molecular function, biological process and cellular component ontologies with an E-value threshold of 10−5. The pathway assignments were performed by sequence searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and using the BLASTX algorithm with an E-value threshold of 10−5.  Cuffdiff was used to calculate FPKM and perform differential expression analysis.
Genome_build: Galgal4 release 72 from Ensembl using Gallus-gallus.Galgal14.72.dna.toplevel.fa.gz.
Supplementary_files_format_and_content: excel files containing output from Cuffdiff. gene_exp.xls contains output of all analyzed genes while WSVSBS_gene_diff.xls  contains a subset of selected genes with significance status.

organism: Gallus gallus

source_name: white skin

growth_protocol: A total of 200 eggs were collected at random from the Lueyang chicken core breeding factory. The incubation and care of the birds were completed at the poultry farm. Ten healthy, 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample
RNA libraries were prepared for sequencing using standard Illumina protocols. Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The isolated mRNA was fragmented, followed by first-strand cDNA synthesis using random hexamer primers. The second-strand cDNA was synthesized using buffer ( Invitrogen, 20 ?L ), dNTPs ( 0.25 mM / ?L ), RNaseH ( 0.05 U / ?L ) and DNA polymerase I ( 0.5 U / ?L ). The short cDNA fragments were purified using the QIAQuick PCR extraction kit ( LianChuan Sciences, Hangzhou, China). The fragment ends were repaired, A-tailed and ligated to sequencing adaptors. Suitably sized ( 350 ± 50 bp ) fragments were selected following an agarose gel electrophoresis and used as templates for the PCR amplification to generate an RNA-seq library. The sequencing of the library was performed using an Illumina HiSeq 2000 ( LianChuan Sciences, Hangzhou, China).

treatment_protocol: A piece of skin (8 mm in diameter) from the left back was collected and immediately placed in liquid nitrogen. Total RNA was extracted from the sample using Trizol reagent (Takara, Dalian, China) according to the manufacturer’s instructions.  RNA samples with a RIN value greater than 8.0 and an OD 260/280 ratio greater than 1.9 were selected for deep sequencing.

value: Lueyang

value: skin

tag: tissue location

value: left back

tag: skin color

value: white

tag: age

value: 16 week

tag: gender

value: female


title: BS

status: Public on May 20 2015

type: SRA

country: China

library_source: transcriptomic

data_processing:
The raw reads were cleaned by removing the adaptors and low quality reads prior to assembly. The unigene assembly was carried out using the short reads assembly program. All assembled unigenes were compared with the proteins in the non-redundant (nr) protein database, using BLAST software with a significance threshold of E-value < 10−5. Functional categorization by gene ontology (GO) terms was carried out according to molecular function, biological process and cellular component ontologies with an E-value threshold of 10−5. The pathway assignments were performed by sequence searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and using the BLASTX algorithm with an E-value threshold of 10−5. Cuffdiff was used to calculate FPKM and perform differential expression analysis.
Genome_build: Galgal4 release 72 from Ensembl using Gallus-gallus.Galgal14.72.dna.toplevel.fa.gz.
Supplementary_files_format_and_content: excel files containing output from Cuffdiff. gene_exp.xls contains output of all analyzed genes while WSVSBS_gene_diff.xls  contains a subset of selected genes with significance status.

molecule: total RNA

source_name: black skin

tag: strain

tag: tissue

value: black


title: K0522S

city: Houston

first: Horatiu

last: Voicu

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were trimmed for adaptor sequence, and  aligned to hg19 using TopHat v2.0.8b
HTSeq-0.5.3p9 was used to generate counts for each gene and edgeR Bioconductor package was used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for all samples

organism: Homo sapiens

source_name: Renal Cell Carcinoma

extract_protocol:
Total cellular RNA was isolated from core punches using the Epicentre  MasterPure™ Complete DNA and RNA Purification Kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol following de-paraffinization and proteinase K treatment. RNA was quantified using the  Picogreen assay.
cDNA was made from total RNA using the NuGEN Ovation RNA-Seq FFPE System (Part # 7150-08). Libraries were prepared for sequencing using cDNA into the Illumina TruSeq DNA-seq protocol (Part #: FC-121-2001). Both parts followed the standard NuGEN and Illumina protocols.

tag: sample type

value: S

tag: pretreatment

tag: grade

value: Sarcomatoid

tag: Stage

value: IV


title: healthy cortex cell 458

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: Single cell from healthy human cortex

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: Brain

extract_protocol:
C1 autoprep standard protocol
C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol
Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system.

value: cortex

tag: cell type

value: prenatal 16-18 W

tag: c1 chip id


title: healthy cortex cell 459

description: Single cell from healthy human cortex


title: healthy cortex cell 462

description: Single cell from healthy human cortex


title: healthy cortex cell 463

description: Single cell from healthy human cortex


title: healthy cortex cell 464

description: Single cell from healthy human cortex


title: healthy cortex cell 461

description: Single cell from healthy human cortex


title: healthy cortex cell 465

description: Single cell from healthy human cortex


title: healthy cortex cell 466

description: Single cell from healthy human cortex


title: healthy cortex cell 460

description: Single cell from healthy human cortex


title: healthy cortex cell 457

description: Single cell from healthy human cortex


title: healthy cortex cell 453

description: Single cell from healthy human cortex


title: healthy cortex cell 455

description: Single cell from healthy human cortex


title: healthy cortex cell 454

description: Single cell from healthy human cortex


title: healthy cortex cell 448

description: Single cell from healthy human cortex


title: healthy cortex cell 450

description: Single cell from healthy human cortex


title: healthy cortex cell 456

description: Single cell from healthy human cortex


title: healthy cortex cell 444

description: Single cell from healthy human cortex


title: healthy cortex cell 446

description: Single cell from healthy human cortex


title: healthy cortex cell 451

description: Single cell from healthy human cortex


title: healthy cortex cell 445

description: Single cell from healthy human cortex


title: healthy cortex cell 447

description: Single cell from healthy human cortex


title: healthy cortex cell 443

description: Single cell from healthy human cortex


title: healthy cortex cell 442

description: Single cell from healthy human cortex


title: healthy cortex cell 441

description: Single cell from healthy human cortex


title: healthy cortex cell 440

description: Single cell from healthy human cortex


title: healthy cortex cell 439

description: Single cell from healthy human cortex


title: healthy cortex cell 438

description: Single cell from healthy human cortex


title: healthy cortex cell 452

description: Single cell from healthy human cortex


title: healthy cortex cell 449

description: Single cell from healthy human cortex


title: SpeciesMix_HundredSTAMPs_50cellpermicroliter

city: Boston

first: Evan

last: Macosko

state: MA

address: 77 Avenue Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

description: The "100 STAMPs" experiment was sequenced at a mean depth of 769,000 reads per cell. We estimated 100 STAMPs by counting the beads; the actual number we uncovered in analysis is 83

data_processing:
Base calls performed with bcl2fastq2.15
Read 2 was aligned with Star v2.4.0
Each aligned read was tagged with its mate-pair UMI and cell barcode, and barcodes collapsed by ED=1 using custom software available at the Drop-Seq portal.
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.  Gene expression from each organism is listed in a separate file.
Genome_build: mm10 and hg19 (dual reference)

organism:
Homo sapiens
Mus musculus

source_name: HEK and 3T3 mix

extract_protocol:
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified (estimated 1000 cells for sample 1, or 100 cells for sample 2) by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

value: HEK and 3T3 mix at 50 cells per microliter final concentration in droplets.


title: SpeciesMix_ThousandSTAMPs_50cellspermicroliter

description: This experiment was sequenced at a mean depth of 69,004 reads per cell. We estimated 1000 STAMPs by counting the beads; the actual number we uncovered in analysis is 1020

value: HEK and 3T3 mix at final droplet concentration of 50 cells per microliter.


title: P granule RNAi

city: Salisbury Cove

first: Dustin

middle: Lynn

last: Updike

state: ME

address: 159 Old Bar Harbor Rd.

institute: Mount Desert Island Biological Laboratory

description: QUAD

data_processing:
Base calling was done using Illumina Casava software
Reads were aligned using TopHat (v. 2.0.8b) using -G, -M arguments
samtools (v.0.1.18) used for indexing
HTSeq (v.0.5.4p3) used to generate read counts per gene using '-m union' argument
DESeq (v.1.1.2.1) was used to normalize gene counts across samples; 'method="blind"' was used for dispersion estimation.  Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution.
Genome_build: WBcel215, Ensembl release 70
Supplementary_files_format_and_content: There are 3 included tab delimited text files: the first ('Raw read counts for EV…') include the raw read counts output from HTSeq for EV, P  granule ('QUAD') and CSR-1.  The other two ('CSR1 RNAi…' and 'P granule RNAi…') include base mean, fold change, log2fold change, p value, and adj p value calculations output from DESeq.

organism: Caenorhabditis elegans

source_name: germline

growth_protocol: RNAi feeding was started in L1 staged worms at 24C; germlines were dissected from their F1 young adult progeny

extract_protocol:
Total RNA was collected from young adult hermpahrodite germlines.  Mouth-pipetting with a pulled capillary needle was used to isolate the gonad at the dorsal-to-ventral bend.  Germlines were dissected in egg buffer and immediately dispensed into Trizol on ice.  400-500 total dissected germlines were collected for each replicate, resulting in total RNA ranging from 1.5 to 4 ug per replicate sample.
Using a TruSeq RNAv2 kit (Illumina), mRNA was polyA-selected, fragmented and   used to create adapter-ligated cDNA for sequencing. One hundred base pair  sequences were obtained on an Illumina HiSeq2500 and processed as single end  reads

tag: RNAi

value: P granule RNAi (Updike et al., 2014)

value: Young adult


title: healthy cortex cell 311

description: Single cell from healthy human cortex

value: neurons

value: postnatal 21 years


title: healthy cortex cell 307

description: Single cell from healthy human cortex


title: healthy cortex cell 305

description: Single cell from healthy human cortex


title: EV

description: EV

value: L4440 plasmid in HT115


title: healthy cortex cell 309

description: Single cell from healthy human cortex

value: oligodendrocytes


title: healthy cortex cell 313

description: Single cell from healthy human cortex

value: hybrid


title: Human-mouse 12.5 cells / ul (~570 STAMPs)

data_processing:
Base calls performed with bcl2fastq2.15
Read 2 was aligned with Star v2.4.0
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.  Gene expression from each organism is listed in a separate file.
Genome_build: mm10 and hg19 (dual reference)
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters

extract_protocol:
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified (estimated 570 cells) by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

value: HEK and 3T3 mix at a final concentration of 12.5 cells / ul in droplets.


title: healthy cortex cell 308

description: Single cell from healthy human cortex


title: CSR-1 RNAi

value: csr-1 RNAi (Ahringer library)


title: healthy cortex cell 310

description: Single cell from healthy human cortex


title: healthy cortex cell 302

description: Single cell from healthy human cortex


title: healthy cortex cell 300

description: Single cell from healthy human cortex


title: healthy cortex cell 301

description: Single cell from healthy human cortex


title: healthy cortex cell 299

description: Single cell from healthy human cortex


title: healthy cortex cell 303

description: Single cell from healthy human cortex


title: healthy cortex cell 298

description: Single cell from healthy human cortex

value: astrocytes


title: healthy cortex cell 297

description: Single cell from healthy human cortex


title: healthy cortex cell 295

description: Single cell from healthy human cortex


title: ERCC at high sequencing depth (84 beads)

description: ERCC spike-ins: external RNA controls developed by the External RNA Controls Consortium (ERCC)

data_processing:
Base calls performed with bcl2fastq2.15
Read 2 was aligned with Star v2.4.0
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.  Gene expression from each organism is listed in a separate file.
Genome_build: ERCC and hg19 (dual reference)
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters

organism: synthetic construct

source_name: ERCC spike-in molecules

extract_protocol:
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified (estimated 84 beads) by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

value: ERCCs at a concentration of 100,000 molecules per droplet were used in Drop-Seq.


title: healthy cortex cell 294

description: Single cell from healthy human cortex


title: healthy cortex cell 293

description: Single cell from healthy human cortex


title: healthy cortex cell 306

description: Single cell from healthy human cortex


title: healthy cortex cell 296

description: Single cell from healthy human cortex


title: healthy cortex cell 292

description: Single cell from healthy human cortex


title: healthy cortex cell 291

description: Single cell from healthy human cortex


title: healthy cortex cell 304

description: Single cell from healthy human cortex


title: healthy cortex cell 289

description: Single cell from healthy human cortex


title: healthy cortex cell 290

description: Single cell from healthy human cortex


title: healthy cortex cell 288

description: Single cell from healthy human cortex


title: healthy cortex cell 282

description: Single cell from healthy human cortex


title: healthy cortex cell 286

description: Single cell from healthy human cortex


title: healthy cortex cell 280

description: Single cell from healthy human cortex


title: healthy cortex cell 278

description: Single cell from healthy human cortex


title: healthy cortex cell 284

description: Single cell from healthy human cortex


title: healthy cortex cell 276

description: Single cell from healthy human cortex


title: healthy cortex cell 281

description: Single cell from healthy human cortex


title: healthy cortex cell 277

description: Single cell from healthy human cortex


title: healthy cortex cell 287

description: Single cell from healthy human cortex


title: healthy cortex cell 283

description: Single cell from healthy human cortex


title: healthy cortex cell 273

description: Single cell from healthy human cortex


title: healthy cortex cell 275

description: Single cell from healthy human cortex


title: healthy cortex cell 285

description: Single cell from healthy human cortex


title: healthy cortex cell 279

description: Single cell from healthy human cortex


title: healthy cortex cell 272

description: Single cell from healthy human cortex


title: healthy cortex cell 271

description: Single cell from healthy human cortex


title: healthy cortex cell 270

description: Single cell from healthy human cortex


title: healthy cortex cell 269

description: Single cell from healthy human cortex


title: healthy cortex cell 266

description: Single cell from healthy human cortex


title: healthy cortex cell 268

description: Single cell from healthy human cortex


title: healthy cortex cell 265

description: Single cell from healthy human cortex


title: healthy cortex cell 264

description: Single cell from healthy human cortex


title: healthy cortex cell 267

description: Single cell from healthy human cortex


title: healthy cortex cell 263

description: Single cell from healthy human cortex


title: healthy cortex cell 262

description: Single cell from healthy human cortex


title: healthy cortex cell 274

description: Single cell from healthy human cortex


title: healthy cortex cell 312

description: Single cell from healthy human cortex


title: healthy cortex cell 259

description: Single cell from healthy human cortex


title: healthy cortex cell 257

description: Single cell from healthy human cortex


title: healthy cortex cell 260

description: Single cell from healthy human cortex


title: healthy cortex cell 254

description: Single cell from healthy human cortex

value: hippocampus

value: postnatal 63 years


title: healthy cortex cell 252

description: Single cell from healthy human cortex

value: endothelial


title: healthy cortex cell 250

description: Single cell from healthy human cortex


title: healthy cortex cell 256

description: Single cell from healthy human cortex


title: healthy cortex cell 249

description: Single cell from healthy human cortex


title: healthy cortex cell 255

description: Single cell from healthy human cortex


title: healthy cortex cell 248

description: Single cell from healthy human cortex


title: healthy cortex cell 258

description: Single cell from healthy human cortex

value: cortex


title: healthy cortex cell 245

description: Single cell from healthy human cortex


title: healthy cortex cell 251

description: Single cell from healthy human cortex


title: healthy cortex cell 247

description: Single cell from healthy human cortex


title: healthy cortex cell 253

description: Single cell from healthy human cortex


title: healthy cortex cell 246

description: Single cell from healthy human cortex

value: microglia


title: healthy cortex cell 243

description: Single cell from healthy human cortex


title: healthy cortex cell 241

description: Single cell from healthy human cortex


title: healthy cortex cell 238

description: Single cell from healthy human cortex


title: healthy cortex cell 239

description: Single cell from healthy human cortex


title: healthy cortex cell 236

description: Single cell from healthy human cortex


title: healthy cortex cell 261

description: Single cell from healthy human cortex


title: healthy cortex cell 240

description: Single cell from healthy human cortex


title: healthy cortex cell 237

description: Single cell from healthy human cortex


title: healthy cortex cell 235

description: Single cell from healthy human cortex


title: healthy cortex cell 234

description: Single cell from healthy human cortex


title: healthy cortex cell 232

description: Single cell from healthy human cortex


title: healthy cortex cell 233

description: Single cell from healthy human cortex


title: healthy cortex cell 230

description: Single cell from healthy human cortex


title: healthy cortex cell 224

description: Single cell from healthy human cortex


title: healthy cortex cell 225

description: Single cell from healthy human cortex


title: healthy cortex cell 228

description: Single cell from healthy human cortex


title: healthy cortex cell 227

description: Single cell from healthy human cortex


title: healthy cortex cell 229

description: Single cell from healthy human cortex


title: healthy cortex cell 231

description: Single cell from healthy human cortex


title: healthy cortex cell 244

description: Single cell from healthy human cortex


title: healthy cortex cell 222

description: Single cell from healthy human cortex


title: healthy cortex cell 218

description: Single cell from healthy human cortex


title: healthy cortex cell 219

description: Single cell from healthy human cortex


title: healthy cortex cell 217

description: Single cell from healthy human cortex


title: healthy cortex cell 216

description: Single cell from healthy human cortex


title: healthy cortex cell 221

description: Single cell from healthy human cortex


title: healthy cortex cell 214

description: Single cell from healthy human cortex


title: healthy cortex cell 223

description: Single cell from healthy human cortex


title: healthy cortex cell 209

description: Single cell from healthy human cortex

value: postnatal 50 years


title: healthy cortex cell 210

description: Single cell from healthy human cortex


title: healthy cortex cell 212

description: Single cell from healthy human cortex


title: healthy cortex cell 213

description: Single cell from healthy human cortex


title: healthy cortex cell 211

description: Single cell from healthy human cortex


title: healthy cortex cell 208

description: Single cell from healthy human cortex


title: healthy cortex cell 207

description: Single cell from healthy human cortex


title: healthy cortex cell 226

description: Single cell from healthy human cortex


title: healthy cortex cell 206

description: Single cell from healthy human cortex


title: healthy cortex cell 205

description: Single cell from healthy human cortex


title: healthy cortex cell 203

description: Single cell from healthy human cortex


title: healthy cortex cell 204

description: Single cell from healthy human cortex


title: healthy cortex cell 220

description: Single cell from healthy human cortex


title: healthy cortex cell 202

description: Single cell from healthy human cortex


title: healthy cortex cell 200

description: Single cell from healthy human cortex


title: healthy cortex cell 215

description: Single cell from healthy human cortex


title: healthy cortex cell 195

description: Single cell from healthy human cortex


title: healthy cortex cell 194

description: Single cell from healthy human cortex


title: healthy cortex cell 197

description: Single cell from healthy human cortex


title: healthy cortex cell 193

description: Single cell from healthy human cortex


title: healthy cortex cell 196

description: Single cell from healthy human cortex


title: healthy cortex cell 190

description: Single cell from healthy human cortex


title: healthy cortex cell 191

description: Single cell from healthy human cortex


title: healthy cortex cell 188

description: Single cell from healthy human cortex


title: healthy cortex cell 192

description: Single cell from healthy human cortex


title: healthy cortex cell 189

description: Single cell from healthy human cortex


title: healthy cortex cell 187

description: Single cell from healthy human cortex


title: healthy cortex cell 186

description: Single cell from healthy human cortex


title: healthy cortex cell 182

description: Single cell from healthy human cortex


title: healthy cortex cell 183

description: Single cell from healthy human cortex


title: healthy cortex cell 180

description: Single cell from healthy human cortex


title: healthy cortex cell 201

description: Single cell from healthy human cortex


title: healthy cortex cell 179

description: Single cell from healthy human cortex


title: healthy cortex cell 178

description: Single cell from healthy human cortex


title: healthy cortex cell 181

description: Single cell from healthy human cortex


title: healthy cortex cell 176

description: Single cell from healthy human cortex


title: healthy cortex cell 177

description: Single cell from healthy human cortex


title: healthy cortex cell 199

description: Single cell from healthy human cortex


title: healthy cortex cell 174

description: Single cell from healthy human cortex


title: healthy cortex cell 175

description: Single cell from healthy human cortex


title: healthy cortex cell 173

description: Single cell from healthy human cortex


title: healthy cortex cell 172

description: Single cell from healthy human cortex


title: healthy cortex cell 170

description: Single cell from healthy human cortex


title: healthy cortex cell 169

description: Single cell from healthy human cortex


title: healthy cortex cell 168

description: Single cell from healthy human cortex


title: healthy cortex cell 167

description: Single cell from healthy human cortex


title: healthy cortex cell 166

description: Single cell from healthy human cortex


title: healthy cortex cell 165

description: Single cell from healthy human cortex


title: healthy cortex cell 185

description: Single cell from healthy human cortex


title: healthy cortex cell 184

description: Single cell from healthy human cortex


title: healthy cortex cell 164

description: Single cell from healthy human cortex


title: healthy cortex cell 162

description: Single cell from healthy human cortex


title: healthy cortex cell 242

description: Single cell from healthy human cortex


title: healthy cortex cell 161

description: Single cell from healthy human cortex


title: healthy cortex cell 160

description: Single cell from healthy human cortex


title: healthy cortex cell 437

description: Single cell from healthy human cortex

value: prenatal 16-18 W


title: healthy cortex cell 198

description: Single cell from healthy human cortex


title: healthy cortex cell 434

description: Single cell from healthy human cortex


title: healthy cortex cell 436

description: Single cell from healthy human cortex


title: healthy cortex cell 158

description: Single cell from healthy human cortex


title: healthy cortex cell 435

description: Single cell from healthy human cortex


title: healthy cortex cell 433

description: Single cell from healthy human cortex


title: healthy cortex cell 171

description: Single cell from healthy human cortex


title: healthy cortex cell 155

description: Single cell from healthy human cortex


title: healthy cortex cell 156

description: Single cell from healthy human cortex


title: healthy cortex cell 154

description: Single cell from healthy human cortex


title: healthy cortex cell 153

description: Single cell from healthy human cortex


title: healthy cortex cell 432

description: Single cell from healthy human cortex


title: healthy cortex cell 163

description: Single cell from healthy human cortex


title: healthy cortex cell 151

description: Single cell from healthy human cortex


title: healthy cortex cell 152

description: Single cell from healthy human cortex


title: healthy cortex cell 430

description: Single cell from healthy human cortex


title: healthy cortex cell 429

description: Single cell from healthy human cortex


title: healthy cortex cell 149

description: Single cell from healthy human cortex


title: healthy cortex cell 159

description: Single cell from healthy human cortex


title: healthy cortex cell 426

description: Single cell from healthy human cortex


title: healthy cortex cell 148

description: Single cell from healthy human cortex


title: healthy cortex cell 425

description: Single cell from healthy human cortex


title: healthy cortex cell 427

description: Single cell from healthy human cortex


title: healthy cortex cell 147

description: Single cell from healthy human cortex


title: healthy cortex cell 424

description: Single cell from healthy human cortex


title: healthy cortex cell 157

description: Single cell from healthy human cortex


title: healthy cortex cell 146

description: Single cell from healthy human cortex


title: healthy cortex cell 423

description: Single cell from healthy human cortex


title: healthy cortex cell 145

description: Single cell from healthy human cortex


title: healthy cortex cell 143

description: Single cell from healthy human cortex


title: healthy cortex cell 431

description: Single cell from healthy human cortex


title: healthy cortex cell 420

description: Single cell from healthy human cortex


title: healthy cortex cell 422

description: Single cell from healthy human cortex


title: healthy cortex cell 421

description: Single cell from healthy human cortex


title: healthy cortex cell 144

description: Single cell from healthy human cortex


title: healthy cortex cell 419

description: Single cell from healthy human cortex


title: healthy cortex cell 418

description: Single cell from healthy human cortex


title: healthy cortex cell 428

description: Single cell from healthy human cortex


title: healthy cortex cell 142

description: Single cell from healthy human cortex


title: healthy cortex cell 150

description: Single cell from healthy human cortex


title: healthy cortex cell 141

description: Single cell from healthy human cortex


title: healthy cortex cell 140

description: Single cell from healthy human cortex


title: healthy cortex cell 139

description: Single cell from healthy human cortex


title: healthy cortex cell 417

description: Single cell from healthy human cortex


title: healthy cortex cell 138

description: Single cell from healthy human cortex


title: healthy cortex cell 414

description: Single cell from healthy human cortex


title: healthy cortex cell 416

description: Single cell from healthy human cortex


title: healthy cortex cell 121

description: Single cell from healthy human cortex

value: postnatal 37 years


title: healthy cortex cell 136

description: Single cell from healthy human cortex


title: healthy cortex cell 137

description: Single cell from healthy human cortex


title: healthy cortex cell 413

description: Single cell from healthy human cortex


title: healthy cortex cell 120

description: Single cell from healthy human cortex

value: neurons


title: healthy cortex cell 411

description: Single cell from healthy human cortex


title: healthy cortex cell 412

description: Single cell from healthy human cortex


title: healthy cortex cell 410

description: Single cell from healthy human cortex


title: healthy cortex cell 118

description: Single cell from healthy human cortex


title: healthy cortex cell 119

description: Single cell from healthy human cortex


title: healthy cortex cell 409

description: Single cell from healthy human cortex


title: healthy cortex cell 116

description: Single cell from healthy human cortex


title: healthy cortex cell 406

description: Single cell from healthy human cortex


title: healthy cortex cell 117

description: Single cell from healthy human cortex


title: healthy cortex cell 407

description: Single cell from healthy human cortex


title: healthy cortex cell 115

description: Single cell from healthy human cortex


title: healthy cortex cell 408

description: Single cell from healthy human cortex


title: healthy cortex cell 114

description: Single cell from healthy human cortex


title: healthy cortex cell 112

description: Single cell from healthy human cortex


title: healthy cortex cell 405

description: Single cell from healthy human cortex


title: healthy cortex cell 404

description: Single cell from healthy human cortex


title: healthy cortex cell 415

description: Single cell from healthy human cortex


title: healthy cortex cell 403

description: Single cell from healthy human cortex


title: healthy cortex cell 402

description: Single cell from healthy human cortex


title: healthy cortex cell 113

description: Single cell from healthy human cortex


title: healthy cortex cell 110

description: Single cell from healthy human cortex


title: healthy cortex cell 400

description: Single cell from healthy human cortex


title: healthy cortex cell 109

description: Single cell from healthy human cortex


title: healthy cortex cell 108

description: Single cell from healthy human cortex


title: healthy cortex cell 107

description: Single cell from healthy human cortex


title: healthy cortex cell 398

description: Single cell from healthy human cortex


title: healthy cortex cell 106

description: Single cell from healthy human cortex


title: healthy cortex cell 397

description: Single cell from healthy human cortex


title: healthy cortex cell 105

description: Single cell from healthy human cortex


title: healthy cortex cell 396

description: Single cell from healthy human cortex


title: healthy cortex cell 104

description: Single cell from healthy human cortex


title: healthy cortex cell 395

description: Single cell from healthy human cortex


title: healthy cortex cell 103

description: Single cell from healthy human cortex


title: healthy cortex cell 394

description: Single cell from healthy human cortex


title: healthy cortex cell 101

description: Single cell from healthy human cortex


title: healthy cortex cell 102

description: Single cell from healthy human cortex


title: healthy cortex cell 392

description: Single cell from healthy human cortex


title: healthy cortex cell 111

description: Single cell from healthy human cortex


title: healthy cortex cell 391

description: Single cell from healthy human cortex


title: healthy cortex cell 390

description: Single cell from healthy human cortex


title: healthy cortex cell 99

description: Single cell from healthy human cortex


title: healthy cortex cell 98

description: Single cell from healthy human cortex


title: healthy cortex cell 389

description: Single cell from healthy human cortex


title: healthy cortex cell 97

description: Single cell from healthy human cortex


title: healthy cortex cell 401

description: Single cell from healthy human cortex


title: healthy cortex cell 100

description: Single cell from healthy human cortex


title: healthy cortex cell 399

description: Single cell from healthy human cortex


title: healthy cortex cell 388

description: Single cell from healthy human cortex


title: healthy cortex cell 96

description: Single cell from healthy human cortex


title: healthy cortex cell 386

description: Single cell from healthy human cortex


title: healthy cortex cell 93

description: Single cell from healthy human cortex


title: healthy cortex cell 387

description: Single cell from healthy human cortex


title: healthy cortex cell 385

description: Single cell from healthy human cortex


title: healthy cortex cell 91

description: Single cell from healthy human cortex


title: healthy cortex cell 384

description: Single cell from healthy human cortex


title: healthy cortex cell 383

description: Single cell from healthy human cortex


title: healthy cortex cell 92

description: Single cell from healthy human cortex


title: healthy cortex cell 90

description: Single cell from healthy human cortex


title: healthy cortex cell 381

description: Single cell from healthy human cortex


title: healthy cortex cell 393

description: Single cell from healthy human cortex


title: healthy cortex cell 89

description: Single cell from healthy human cortex


title: healthy cortex cell 380

description: Single cell from healthy human cortex


title: healthy cortex cell 88

description: Single cell from healthy human cortex


title: healthy cortex cell 378

description: Single cell from healthy human cortex


title: healthy cortex cell 87

description: Single cell from healthy human cortex


title: healthy cortex cell 377

description: Single cell from healthy human cortex


title: healthy cortex cell 379

description: Single cell from healthy human cortex


title: healthy cortex cell 86

description: Single cell from healthy human cortex


title: healthy cortex cell 95

description: Single cell from healthy human cortex


title: healthy cortex cell 85

description: Single cell from healthy human cortex


title: healthy cortex cell 375

description: Single cell from healthy human cortex


title: healthy cortex cell 83

description: Single cell from healthy human cortex


title: healthy cortex cell 374

description: Single cell from healthy human cortex


title: healthy cortex cell 82

description: Single cell from healthy human cortex


title: healthy cortex cell 373

description: Single cell from healthy human cortex


title: healthy cortex cell 84

description: Single cell from healthy human cortex


title: healthy cortex cell 94

description: Single cell from healthy human cortex


title: healthy cortex cell 376

description: Single cell from healthy human cortex


title: healthy cortex cell 372

description: Single cell from healthy human cortex


title: healthy cortex cell 371

description: Single cell from healthy human cortex


title: healthy cortex cell 382

description: Single cell from healthy human cortex


title: healthy cortex cell 80

description: Single cell from healthy human cortex


title: healthy cortex cell 78

description: Single cell from healthy human cortex


title: healthy cortex cell 369

description: Single cell from healthy human cortex


title: healthy cortex cell 370

description: Single cell from healthy human cortex


title: healthy cortex cell 81

description: Single cell from healthy human cortex


title: healthy cortex cell 76

description: Single cell from healthy human cortex


title: healthy cortex cell 77

description: Single cell from healthy human cortex


title: healthy cortex cell 367

description: Single cell from healthy human cortex


title: healthy cortex cell 75

description: Single cell from healthy human cortex


title: healthy cortex cell 74

description: Single cell from healthy human cortex


title: healthy cortex cell 366

description: Single cell from healthy human cortex


title: healthy cortex cell 365

description: Single cell from healthy human cortex


title: healthy cortex cell 73

description: Single cell from healthy human cortex


title: healthy cortex cell 72

description: Single cell from healthy human cortex


title: healthy cortex cell 364

description: Single cell from healthy human cortex


title: healthy cortex cell 70

description: Single cell from healthy human cortex


title: healthy cortex cell 363

description: Single cell from healthy human cortex


title: healthy cortex cell 69

description: Single cell from healthy human cortex


title: healthy cortex cell 71

description: Single cell from healthy human cortex


title: healthy cortex cell 362

description: Single cell from healthy human cortex


title: healthy cortex cell 68

description: Single cell from healthy human cortex


title: healthy cortex cell 361

description: Single cell from healthy human cortex


title: healthy cortex cell 360

description: Single cell from healthy human cortex


title: healthy cortex cell 79

description: Single cell from healthy human cortex


title: healthy cortex cell 66

description: Single cell from healthy human cortex


title: healthy cortex cell 359

description: Single cell from healthy human cortex


title: healthy cortex cell 65

description: Single cell from healthy human cortex


title: healthy cortex cell 357

description: Single cell from healthy human cortex


title: healthy cortex cell 368

description: Single cell from healthy human cortex


title: healthy cortex cell 67

description: Single cell from healthy human cortex


title: healthy cortex cell 356

description: Single cell from healthy human cortex


title: healthy cortex cell 64

description: Single cell from healthy human cortex


title: healthy cortex cell 354

description: Single cell from healthy human cortex


title: healthy cortex cell 63

description: Single cell from healthy human cortex


title: healthy cortex cell 353

description: Single cell from healthy human cortex


title: healthy cortex cell 62

description: Single cell from healthy human cortex


title: healthy cortex cell 60

description: Single cell from healthy human cortex


title: healthy cortex cell 352

description: Single cell from healthy human cortex


title: healthy cortex cell 61

description: Single cell from healthy human cortex


title: healthy cortex cell 351

description: Single cell from healthy human cortex


title: healthy cortex cell 350

description: Single cell from healthy human cortex


title: healthy cortex cell 57

description: Single cell from healthy human cortex

value: postnatal 54 years


title: healthy cortex cell 358

description: Single cell from healthy human cortex


title: healthy cortex cell 347

description: Single cell from healthy human cortex


title: healthy cortex cell 348

description: Single cell from healthy human cortex


title: healthy cortex cell 54

description: Single cell from healthy human cortex

value: OPC


title: healthy cortex cell 355

description: Single cell from healthy human cortex


title: healthy cortex cell 349

description: Single cell from healthy human cortex


title: healthy cortex cell 56

description: Single cell from healthy human cortex


title: healthy cortex cell 59

description: Single cell from healthy human cortex


title: healthy cortex cell 345

description: Single cell from healthy human cortex


title: healthy cortex cell 55

description: Single cell from healthy human cortex


title: healthy cortex cell 343

description: Single cell from healthy human cortex


title: healthy cortex cell 346

description: Single cell from healthy human cortex


title: healthy cortex cell 51

description: Single cell from healthy human cortex


title: healthy cortex cell 342

description: Single cell from healthy human cortex


title: healthy cortex cell 341

description: Single cell from healthy human cortex


title: healthy cortex cell 53

description: Single cell from healthy human cortex


title: healthy cortex cell 52

description: Single cell from healthy human cortex


title: healthy cortex cell 344

description: Single cell from healthy human cortex


title: healthy cortex cell 49

description: Single cell from healthy human cortex


title: healthy cortex cell 48

description: Single cell from healthy human cortex


title: healthy cortex cell 340

description: Single cell from healthy human cortex


title: healthy cortex cell 50

description: Single cell from healthy human cortex


title: healthy cortex cell 339

description: Single cell from healthy human cortex


title: healthy cortex cell 47

description: Single cell from healthy human cortex


title: healthy cortex cell 45

description: Single cell from healthy human cortex


title: healthy cortex cell 46

description: Single cell from healthy human cortex


title: healthy cortex cell 337

description: Single cell from healthy human cortex


title: healthy cortex cell 58

description: Single cell from healthy human cortex


title: healthy cortex cell 336

description: Single cell from healthy human cortex


title: healthy cortex cell 44

description: Single cell from healthy human cortex


title: healthy cortex cell 332

description: Single cell from healthy human cortex

value: postnatal 47 years


title: healthy cortex cell 41

description: Single cell from healthy human cortex


title: healthy cortex cell 334

description: Single cell from healthy human cortex


title: healthy cortex cell 333

description: Single cell from healthy human cortex


title: healthy cortex cell 335

description: Single cell from healthy human cortex


title: healthy cortex cell 39

description: Single cell from healthy human cortex


title: healthy cortex cell 331

description: Single cell from healthy human cortex


title: healthy cortex cell 43

description: Single cell from healthy human cortex


title: healthy cortex cell 42

description: Single cell from healthy human cortex

value: hybrid


title: healthy cortex cell 37

description: Single cell from healthy human cortex


title: healthy cortex cell 328

description: Single cell from healthy human cortex


title: healthy cortex cell 40

description: Single cell from healthy human cortex


title: human K562 pure RNA control (953 samples)

first: Allon

middle: M

last: Klein

address: 200 Longwood Avenue

department: Systems Biology

data_processing:
Reads were first filtered based on presence in read 1 of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT)
Read 2 was then trimmed using Trimomatic (5) (version 0.30; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:19).
Barcodes for each read were matched against a list of the 3842 pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 0.12.0, parameters: -n 1 -l 15 -e 300 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using all annotated transcripts (extended with a 125bp poly-A tail) from the UCSC mm10 genome assembly.
We used a custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene.
Genome_build: mm10 for ES cells; hg19 for K562 cells.
Supplementary_files_format_and_content: Columns = cells; rows = genes. Column 1 contains gene symbols. Values show unique molecular identifier (UMI)-filtered counts per cell detected in the raw data. No normalization is performed.

molecule: polyA RNA

source_name: human lymphoblastoma culture ATCC® CCL-243

growth_protocol: The ES cells were maintained in ESC base media inside culture flasks pre-coated with gelatin at 37°C in 5% CO2 and 60-80% humidity at density ~3 × 10^5 cells ml–1. The ESC media contained phenol red free DMEM (Gibco), supplemented with 15% (v/v) fetal bovine serum (Gibco), 2 mM L-glutamine, 1x MEM non-essential amino acids (Gibco), 1% (v/v) penicillin-streptomycin antibiotics, 110 µM b-mercaptoethanol, 100 µM sodium pyruvate.

extract_protocol:
Cells were encapsulated into droplets on ice and lysed  in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA.
Cells were barcoded using the db-Seq platform, which makes use of the CEL-Seq protocol for library construction (Hashimshony et al., Cell Reports 2011).

treatment_protocol: In the undifferentiated state the ESC base media was supplemented with Leukemia Inhibitory Factor (LIF) at final concentration 1000 U/mL and for unguided mES differentiation the media was without LIF. Within 2 days of LIF withdrawal the culture experienced significant morphological changes indicating the differentiation of mES cells.

value: lymphoblastoma

tag: cell line

tag: days post-lif

tag: number cells in sample


title: healthy cortex cell 36

description: Single cell from healthy human cortex


title: healthy cortex cell 38

description: Single cell from healthy human cortex


title: healthy cortex cell 327

description: Single cell from healthy human cortex


title: healthy cortex cell 330

description: Single cell from healthy human cortex


title: healthy cortex cell 325

description: Single cell from healthy human cortex


title: healthy cortex cell 35

description: Single cell from healthy human cortex


title: healthy cortex cell 338

description: Single cell from healthy human cortex


title: healthy cortex cell 34

description: Single cell from healthy human cortex


title: healthy cortex cell 326

description: Single cell from healthy human cortex


title: healthy cortex cell 33

description: Single cell from healthy human cortex


title: healthy cortex cell 324

description: Single cell from healthy human cortex


title: healthy cortex cell 32

description: Single cell from healthy human cortex

value: oligodendrocytes


title: healthy cortex cell 323

description: Single cell from healthy human cortex

value: astrocytes


title: healthy cortex cell 31

description: Single cell from healthy human cortex


title: healthy cortex cell 322

description: Single cell from healthy human cortex


title: healthy cortex cell 329

description: Single cell from healthy human cortex


title: healthy cortex cell 29

description: Single cell from healthy human cortex


title: healthy cortex cell 320

description: Single cell from healthy human cortex


title: healthy cortex cell 27

description: Single cell from healthy human cortex


title: healthy cortex cell 28

description: Single cell from healthy human cortex


title: healthy cortex cell 321

description: Single cell from healthy human cortex


title: healthy cortex cell 318

description: Single cell from healthy human cortex


title: healthy cortex cell 30

description: Single cell from healthy human cortex


title: healthy cortex cell 317

description: Single cell from healthy human cortex


title: healthy cortex cell 24

description: Single cell from healthy human cortex


title: healthy cortex cell 314

description: Single cell from healthy human cortex


title: healthy cortex cell 315

description: Single cell from healthy human cortex


title: healthy cortex cell 23

description: Single cell from healthy human cortex


title: healthy cortex cell 316

description: Single cell from healthy human cortex


title: healthy cortex cell 22

description: Single cell from healthy human cortex


title: healthy cortex cell 134

description: Single cell from healthy human cortex

value: postnatal 22 years


title: healthy cortex cell 20

description: Single cell from healthy human cortex


title: healthy cortex cell 135

description: Single cell from healthy human cortex


title: healthy cortex cell 25

description: Single cell from healthy human cortex


title: healthy cortex cell 133

description: Single cell from healthy human cortex


title: healthy cortex cell 19

description: Single cell from healthy human cortex


title: healthy cortex cell 21

description: Single cell from healthy human cortex


title: healthy cortex cell 17

description: Single cell from healthy human cortex


title: healthy cortex cell 130

description: Single cell from healthy human cortex


title: healthy cortex cell 26

description: Single cell from healthy human cortex


title: healthy cortex cell 16

description: Single cell from healthy human cortex


title: healthy cortex cell 129

description: Single cell from healthy human cortex


title: healthy cortex cell 15

description: Single cell from healthy human cortex


title: healthy cortex cell 128

description: Single cell from healthy human cortex


title: healthy cortex cell 127

description: Single cell from healthy human cortex


title: healthy cortex cell 14

description: Single cell from healthy human cortex


title: healthy cortex cell 126

description: Single cell from healthy human cortex


title: healthy cortex cell 13

description: Single cell from healthy human cortex


title: healthy cortex cell 12

description: Single cell from healthy human cortex


title: healthy cortex cell 319

description: Single cell from healthy human cortex


title: healthy cortex cell 124

description: Single cell from healthy human cortex


title: healthy cortex cell 10

description: Single cell from healthy human cortex


title: healthy cortex cell 122

description: Single cell from healthy human cortex


title: healthy cortex cell 4

description: Single cell from healthy human cortex


title: healthy cortex cell 123

description: Single cell from healthy human cortex


title: healthy cortex cell 7

description: Single cell from healthy human cortex


title: healthy cortex cell 8

description: Single cell from healthy human cortex


title: healthy cortex cell 131

description: Single cell from healthy human cortex


title: healthy cortex cell 18

description: Single cell from healthy human cortex


title: healthy cortex cell 3

description: Single cell from healthy human cortex


title: healthy cortex cell 5

description: Single cell from healthy human cortex


title: healthy cortex cell 6

description: Single cell from healthy human cortex


title: healthy cortex cell 1

description: Single cell from healthy human cortex


title: human K562 cells (239 cells)


title: healthy cortex cell 9

description: Single cell from healthy human cortex


title: phoP::Tn, DMSO, pH 5.7, Rep A

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.30)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie  was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determine counts per gene feature in the M. tuberculosis CDC1551 genome
DESeq was used to normalize data by estimating effective library sizes using robust regression
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the DESeq package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as text files and represents genes that are induced or repressed >2 fold, with a p-value <0.05.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell_phoP::Tn_dmso_pH5.7

growth_protocol: Mtb strain CDC1551 was grown at 37C in T-25 vented, standing tissue culture flasks in 8 ml of buffered 7H9 medium seeded an initial OD of 0.2  Cultures were incubated at 37C for 6 days.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were resuspended in  medium and examined under four conditions: 1) DMSO treated, pH 7.0, 2) DMSO treated, pH 5.7, 3) 40 µM ethoxzolamide treated, pH 7.0, and 4) 40 µM ethoxzolamide treated, pH 5.7. The CDC1551(phoP::Tn) mutant was grown in a similar manner and treated with DMSO at pH 7.0 and 5.7. Following six days incubation, total bacterial RNA was extracted. Two biological replicates were performed.

tag: genotype

tag: ph

tag: treatment

value: DMSO


title: phoP::Tn, DMSO, pH 5.7, Rep B


title: healthy cortex cell 11

description: Single cell from healthy human cortex

tag: age


title: healthy cortex cell 2

description: Single cell from healthy human cortex


title: WT, DMSO, pH 5.7, Rep A

source_name: Bacterial cell_wildtype_dmso_pH5.7

value: wildtype


title: WT

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
mtl1 tagged with flag in C-terminal
rRNA depleted RNA

data_processing:
fastq files were mapped using tophat-2.0.13
coverage was calculated for fw and rev strand separately
median coverage was calculated for all non-intron containing genes, and the median non-intron coding gene coverage was calculated for each dataset
datasets were normalized using the median non-intron containing gene coverage (set to 100)
Genome_build: Schizosaccharomyces_pombe_Ensembl_EF2
Supplementary_files_format_and_content: fw.BigWig and rev.BigWig files for each dataset describe the normalized RNA coverage at the fw/rev strand

organism: Schizosaccharomyces pombe

source_name: rRNA depleted RNA of WT

growth_protocol: WT and gene deletion strains were grown in YEA at 30°C to OD 0.5~0.8. Temperature sensitive strains were grown in YEA at 23°C to OD 0.3~0.4 and then moved to 37°C and grown for 4 h to OD<0.8.

extract_protocol:
RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
Ribosomal RNAs were depleted from Turbo DNase-treated total RNAs using a Ribo-zero Magnetic Gold Kit (Epicentre). The cDNA libraries were prepared using NEBNext Ultra RNA Directional Library Prep Kit (NEB) according to the manufacturer’s instructions. The libraries were purified with Agencourt AMPure XP beads (Beckman Coulter) and assessed on a Bioanalyzer (Agilent). Subsequently, 2x100 bp paired-end sequencing was performed on an Illumina HiSeq 2000 sequencer at BGI Tech (Hong Kong).

value: wildtype strain (p931)


title: WT, DMSO, pH 7.0, Rep B

source_name: Bacterial cell_wildtype_dmso_pH7


title: WT, DMSO, pH 5.7, RepB


title: WT, DMSO, pH 7.0, Rep A


title: nrl1Δ

description: rRNA depleted RNA

source_name: rRNA depleted RNA of nrl1Δ

value: deletion strain:nrl1-delta (p1365)


title: WT, Ethoxzolmaide, pH 5.7, Rep B

value: Ethoxzolamide


title: ctr1Δ

description: rRNA depleted RNA

source_name: rRNA depleted RNA of ctr1Δ

value: deletion strain:ctr1-delta (p1135)


title: mtl1-17

description:
Tagged strain with flag in C-terminal
rRNA depleted RNA

source_name: rRNA depleted RNA of mtl1-17

value: mutant strain:mtl1-17 (p936)


title: healthy cortex cell 125

description: Single cell from healthy human cortex

value: cortex

value: endothelial


title: red1Δ

description: rRNA depleted RNA

source_name: rRNA depleted RNA of red1Δ

value: deletion strain:red1-delta (p934)


title: rrp6Δ

description: rRNA depleted RNA

source_name: rRNA depleted RNA of rrp6Δ

value: deletion strain:rrp6-delta (p74)


title: FOXP1_B-cell

status: Public on May 19 2015

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

library_source: genomic

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome was used for peak-calling from the ChIP-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: peak coordinates file : number_chromosome_start_end_length_fold-enrichment

molecule: genomic DNA

source_name: B-cell

growth_protocol: DLBCLs cell lines OCI-LY-1, -3, -7 and -10 were cultured in Iscove’s medium (Life Technologies, Breda, The Netherlands) supplemented with 10 % fetal calf serum (FCS) (Hyclone Laboratories, Logan, UT), penicillin (50 U/ml), streptomycin (50 mg/ml) (both from Life Technologies). DLBCLs cell line OCI-LY-10 was cultured in the presence of 20% FCS, penicillin, streptomycin and b-mercaptoethanol (55 mM).

extract_protocol:
ChIP-seq was performed essentially as described (van Boxtel et al., 2013;van Keimpema et al., 2014), using 5 ug of anti-FOXP1 (ab16645) from Abcam.
immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD WF sequencer in multiplexed way.

value: primary human memory B cells (MBCs)

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Vegetal cap replicate2

city: Beijing

first: Xiaopeng

last: Ma

state: Outside US and Canada

address: HaiDian district

department: Biology

institute: Tsinghua Univeristy

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to Xenopus laevis RefSeq genes using bowtie with parameters --chunkmbs 300 -a -m 5 -l 40 -p 8 -I 0 -X 350 -S -t --phred64-quals
Different expressed genes was calculated by  R/Bioconductor package DESeq with the default parameters. Genes with FDR  < 0.05 were declared significant
Genome_build: Xenopus laevis RefSeq genes
Supplementary_files_format_and_content: tab-delimited text files include reads count for each sample and DESeq normalized expression and p-value and adjusted p-value(FDR)

organism: Xenopus laevis

source_name: Vegetal cap_8-cell embryo

extract_protocol:
RNA of animal and vegetal blastomeres was isolated respectively using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing according to NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB #E6110)

treatment_protocol: For the dissociation of blastomeres, Xenopus laevis embryos were transferred to 80% phosphate-buffered saline lacking calcium and magnesium at 2-cell stage. The embryos were manually demembranated and the animal and vegetal blastomeres were collected respectively at 8-cell stage.

tag: tissue

value: Vegetal cap

tag: developmental stage

value: 8-cell stage


title: FOXP1_OCI-Ly10

value: diffuse large B cell lymphoma (DLBCL) cell line


title: FOXP1_OCI-Ly3


title: FOXP1_OCI-Ly1


title: WT, Ethoxzolamide, pH 5.7, Rep A

tag: strain


title: Animal cap replicate1

source_name: Animal cap_8-cell embryo

value: Animal cap


title: Vegetal cap replicate1


title: As_mRNASeq

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Illumina mRNA-seq

data_processing:
mRNA-seq reads were aligned to TAIR9 genome and cDNA sequence using BFAST-0.7.0a
Transcript levels were quantified by counting Reads Per Kilobase of exon model per Million mapped reads (RPKM)
Allelic expression was identified by assigning the reads in an allotetraploids into A. thaliana and A. arenosa reads using two or more distinct SNPs between A. thaliana and A. arenosa.
Genome_build: TAIR9 genome and cDNA sequence
Supplementary_files_format_and_content: matrix listing of transcripts and RPKM

organism: Arabidopsis suecica

source_name: Rosette leaves

growth_protocol: All plants were grown under a 16/8-hour light/dark cycle with temperatures of 22oC (light) and 20oC (dark).

extract_protocol: Total RNA was isolated from mature leaves (3-4 weeks old A. thaliana; 6-7 weeks old A. arenosa or allotetraploids plants) prior to bolting using plant RNA purification reagent (Invitrogen, Carlsbad, CA). The integrity of extracted RNA was verified by resolving 1 µg RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10 µg total RNA was used to prepare mRNA-seq libraries using Illumina mRNA-seq sample preparation kit (Illumina Inc., San Diego, CA). Libraries with a range of 200bp} 25 bp were excised and amplified for subsequent cluster generation and massively parallel sequencing using the Illumina Genome Analyzer with read lengths ranged from 60 to 83 bp.

tag: Stage

value: before bolting

tag: ploidy

value: allotetraploids


title: AlloF8_mRNASeq

description: Illumina mRNA-seq

organism: Arabidopsis thaliana x Arabidopsis arenosa

tag: sample type

value: F8 resynthesized allotetraploids between Arabidopsis thaliana and Arabidopsis arenosa


title: Subject20_PBMC

city: Cambridge

first: Melis

last: Anahtar

address: 400 Technology Sq

department: Ragon Institute of MGH, MIT, Harvard

institute: Massachusetts General Hospital

data_processing:
Mapping of read2 on mRNA refseq using BWA
Parsing the output based on cell barcode stored in read1 (first 6bp)
Gene expression computation based on Unique Molecular Identifier (UMI) counts stored in read1 (base 7 to 16)
Concatenation of single cell gene expression in gene expression matrices (processed data files)
DGE file was imported into R. Cervical samples were analyzed separately from PBMC samples. Genes with less than a total of 10 reads across all samples were eliminated from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix

source_name: Peripheral blood

growth_protocol: n/a, samples are ex vivo

extract_protocol:
Cells were sorted directly into TriZOL on a FACS Aria III and frozen at -80C. Gen-Elute linear polyacrylamide (Sigma) was added to the RNA in TRIzol, followed by the addition of 0.2 volumes of chloroform and vortexing. After centrifuging at 14,000xg for 5 minutes, the aqueous phase was transferred to a clean tube. Nucleic acid was precipitated with isopropanol and 3M sodium acetate pH 5.5 (Ambion) at -20°C overnight and then centrifuged at maximum speed for 30 minutes at 4°C. The supernatant was discarded and the pellet was washed by adding 0.5mL of 100% ethanol, centrifuging for 15 minutes at 4°C, and discarding the supernatant. The nucleic acid pellet was allowed to dry and was resuspended in 5 μL of molecular grade water.
RNA-DGE derived from the Single Cell RNA Barcoding and Sequencing (SCRB-Seq) strategy
3’ Digital Gene Expression (3’ DGE)

treatment_protocol: n/a, samples are ex vivo

tag: collection site and cell type

value: PBMC APC

tag: bacterial community type

value: Prevotella dominant

tag: cell type

value: Antigen presenting cells


title: Subject19_PBMC

value: Gardnerella dominant


title: Subject18_PBMC


title: Subject19_Cervical

source_name: Cervical cytobrush

value: Cervical APC


title: Subject16_PBMC

value: Lactobacillus dominant


title: Subject18_Cervical


title: Subject17_Cervical


title: Subject16_Cervical


title: Subject20_Cervical


title: Subject14_PBMC


title: Subject13_Cervical


title: Subject15_Cervical


title: Subject17_PBMC


title: Subject14_Cervical


title: input_OCI-Ly10

tag: cell line


title: FOXP1_OCI-Ly7


title: Subject13_PBMC


title: Animal cap replicate2


title: Subject8_PBMC


title: Subject10_Cervical


title: Subject11_Cervical


title: Subject12_Cervical


title: Subject10_PBMC


title: Subject9_Cervical


title: Subject11_PBMC


title: Subject7_PBMC


title: Subject9_PBMC


title: Subject6_Cervical


title: Subject2_Cervical


title: Subject5_PBMC


title: siScr replicat3

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

description: processed data file: DESeq2_siInt11_vs_siscr_ALLp-value.xls, DESeq2_siNE_vs_siscr_ALLp-value.xls

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data quality was assessed using fastqc from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
De-multiplexing and alignment were performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
TopHat 2.0.9, all subsequent analyses were done in R 3.0.2 (www.r-project.org) with Bioconductor packages (www.bioconductor.org), including GenomicRanges 1.14.432, Rsamtools 1.14.3 and Homo.sapiens 1.1.2.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data files are directly from the DESeq2 output, with .xls files containing all p-values without filters.

source_name: siScr

growth_protocol: Exponentially growing HeLa-LTR-Luciferase cells were treated with si RNAs against Integrator 11 or NELF or control (scrambled). Briefly, knockdowns were performed using Interferin (Polyplus Transfection) as transfection reagent according to manufacturer’s instructions. HeLa-LTR-Luciferase cells were transfected for 5h and then the medium was exchanged.

extract_protocol:
Total RNAs whole-cell RNAs were depleted for ribosomal RNAs using the Ribo-ZeroTM Magnetic Gold Kit following manufacturer’s instructions.For total RNA samples (siInt11_1/2/3, SiNELF-1/2-3; Siscrambled-1/2/3), 100 ng of ribosomal RNA depleted whole cell RNA was used for library construction following Illumina’s instructions. cDNA libraries of poly-adenylated RNAs ('Int11-1/2-3' NELF-1/2/3; scr/Scrambled-1/2/3) were generated using 1 µg of whole-cell RNAs following Illumina’s instructions.
Librairies were prepared using Illumina Tru-Seq stranded mRNA sample prep kit TruSeq Sample Prep Kit (multiplexed libraries) according to manufacturer’s instructions.(Illumina).

treatment_protocol: RNAs were isolated from ~20 x 10^6 HeLa-LTR-Luciferase cells using the mirVana Paris kit (Life Technologies) following manufacturer's instructions. Contaminating DNA was digested by TURBO DNAse (Life Technologies)

value: HeLa-LTR-Luciferase cells

tag: treated with

value: si RNAs against control (scrambled)

tag: molecule subtype

value: ribosomal RNA depleted whole cell RNA


title: siScr replicat2


title: siNELF replicat3

description: processed data file: DESeq2_siNE_vs_siscr_ALLp-value.xls

source_name: siNELF

value: si RNAs against NELF


title: siNELF replicat2


title: siScr replicat1


title: healthy cortex cell 132

description: Single cell from healthy human cortex

source_name: Brain

value: cortex

value: neurons

value: postnatal 22 years

tag: c1 chip id


title: siInt11 replicat3

description: processed data file: DESeq2_siInt11_vs_siscr_ALLp-value.xls

value: si RNAs against Integrator 11


title: siNELF replicat1


title: siInt11 replicat2


title: siInt11 replicat1


title: Scr replicat3

description: processed data file: DESeq2_11_vs_S_ALLp-value.xls, DESeq2_N_vs_S_ALLp-value.xls

source_name: Scr

value: whole-cell RNA


title: Subject7_Cervical


title: AlloTTTA_mRNAseq

description: Illumina mRNA-seq

value: F1 resynthesized allotetraploids between Arabidopsis thaliana and AlloF8

value: before bolting

value: allotetraploids


title: NELF replicat2

description: processed data file: DESeq2_N_vs_S_ALLp-value.xls

source_name: NELF


title: NELF replicat1


title: Scr replicat1


title: NELF replicat3


title: Scr replicat2


title: AlloAATA_mRNAseq

description: Illumina mRNA-seq

value: F1 resynthesized allotetraploids between Arabidopsis arenosa and AlloF8


title: AlloTATT_mRNAseq

description: Illumina mRNA-seq

value: F1 resynthesized allotetraploids between AlloF8 and Arabidopsis thaliana


title: Subject4_Cervical

value: Prevotella dominant

value: Antigen presenting cells


title: AlloTAAA_mRNAseq

description: Illumina mRNA-seq

value: F1 resynthesized allotetraploids between AlloF8 and Arabidopsis arenosa


title: STT6649_Leiomyoma

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: 3SEQ

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

source_name: Leiomyoma

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx and HiSeq machines.

treatment_protocol: Clinical tissue samples were formalin-fixed and paraffin-embedded (FFPE).

value: Soft Tissue

tag: tissue archive method

value: FFPE

tag: source

value: Stanford Surgical


title: Subject3_Cervical

value: Cervical APC

value: Gardnerella dominant


title: Subject6_PBMC

value: PBMC APC


title: Subject1_Cervical

value: Lactobacillus dominant


title: FNY01_2_2_BU_NS_Ery

city: Bronx

first: Eric

middle: E

last: Bouhassira

state: NY

address: 1300 Morris PArk Ave

department: Cell Biology

institute: Albert Einstein College Of Medicine

description: library strategy: Nascent strand sequencing

data_processing:
Base called using CASAVA
read aligned using bwa
variant calling using GATK
Phasing using GenPLay multi-Genome
peak calling using MACS 1.42 and Genomic control as base line (see file genomic control 1-4)
Genome_build: hg19
Supplementary_files_format_and_content: Files labeled P1 or P2 contain allele specific data;  Data were produced from cultured primary human basophilic erythroblasts.

source_name: basophilic erythroblasts

growth_protocol: Mononuclear cells were isolated from peripheral blood by density gradient centrifugation on Histopaque and were expanded and differentiated into basophilic erythroblasts in culture for two weeks in serum-free condition as described in    PMID 18024790

extract_protocol:
Genomic DNA was extracted using standard procedure
Illumina standard single-end protocol was used.Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of various sizes (300 to 500 depending on libraries)  were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Short, newly replicated DNA were extracted using either the lambda exonuclease procedure or using immunoprecipitation with anti-BrdU antibodies

tag: disease state

value: Healthy control


title: STT6648_Myometrium

description: Experiment type: 3SEQ

source_name: Myometrium


title: Int11 replicat3

description: processed data file: DESeq2_11_vs_S_ALLp-value.xls

value: HeLa-LTR-Luciferase cells

value: si RNAs against Integrator 11

value: whole-cell RNA


title: chilling rep2

city: Shanghai

first: Lan

last: Yang

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

description: chilling (4°C, 12h) treated replicate2

data_processing:
Clean reads were acquired from initial pair-end reads after trimming low quality (Q < 20), PCR duplicates and adaptor sequences by SeqPrep virsion 1.1
We pooled together all high quality reads  from four samples to perform the de novo transcriptome assembly use Trinity program(trinityrnaseq_r20140717)  with the default K-mer parameter and minimum K-mers coverage of three, and only transcripts whose length is no less than three hundred base pair were remained for continue analysis.
Unigenes were firstly annotated by searching against the protein databases including NCBI Nr protein database (NCBI non-redundant sequence database), SwissProt and KEGG through BLASTX with an expectation value of 10-5
Differentially expressed genes were identified with the edgeR package.Classic model of edgeR was used for the differential expression analysis with false discovery rate (FDR) of 0.01 and two-fold change of Fragments Per Kilobase of gene per Millon mapped reads (FPKM) as significant cutoffs.
Functional enrichment analyses were then performed on identified DEGs by using GOstats for Gene Ontology and KEGG pathway with Hypergeometric test function (p value < 0.001 )
Genome_build: No genome
Supplementary_files_format_and_content: txt file of FPKM value for each sample

organism: Ocimum americanum

source_name: 30-day-old leaves

growth_protocol: Seeds of the Ocimum americanum var. pilosum plants were surface-sterilized and planted on 0.5xMS medium agar plates supplemented with 2% sucrose. Four days after being incubated at 21 ± 1 ºC in the chamber, germinated seeds will be transferred into moistured soil and continue to grow at 21 ± 1 ºC.

extract_protocol:
Total RNA was isolated with the Universal Plant Total RNA Extraction Kit (Cat#RP3302, BioTeke) and treated with TURBO DNA-free™ Kit (Cat#AM1907, Ambion) to remove any genomic DNA contaminants.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One-month-old plants were transferred into a chamber with a temperature of 4 ºC for 12 hours. Leaves from treated and untreated plants were harvested for RNA extraction.

tag: variety

value: pilosum

value: leaves

tag: age

value: 30 days-old


title: Int11 replicat2


title: Int11 replicat1


title: chilling rep1

description: chilling (4°C, 12h) treated replicate1

tag: tissue


title: STT6645_Leiomyoma

description: Experiment type: 3SEQ


title: STT6647_Myometrium

description: Experiment type: 3SEQ


title: control rep2

description: control (untreated) replicate2


title: control rep1

description: control (untreated) replicate1


title: STT6643_Leiomyoma

description: Experiment type: 3SEQ


title: IP RNAPII (Int11-KD)

description:
Sample 15
processed data file: Profile_RNAPII_Int11_KD_TES.tar.gz, Profile_RNAPII_Int11_KD_TSS.tar.gz

data_processing:
Basecalls performed using CASAVA version 1.8.2
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
ChIP peaks were analyzed using MACS (Feng et al., 2012) or MACS2 with respect to input control (MACS14* processed data files).
For RNAPII, rMAT package was utilized by counting normalized (RPM) ChIP-Seq reads in the indicated windows with respect to transcription start sites  (TSS; -200 to +2000) or to termination sites  (TES; -2000 to + 200) using bioconductor  transcript database of UCSC (BSgenome.Hsapiens.UCSC.hg19; Profile_RNAPII*.tar.gz)
Processed Files were normalized to the corresponding input as followed: H3K4me3 (MACS14_BN_H3K4me3_vs_Input.tar.gz= sample 2 normalized to sample 1 ); Int3:  (MACS14_7A_Int3_vs_Input.tar.gz= sample 4 normalized to sample 3) ; Asun/Int13  (MACS14_7A_Asun_vs_Input.tar.gz= sample 7 normalized to sample 3); NELF:  (MACS14_7A_NELF_vs_Input.tar.gz= sample 5 normalized to sample 3); RNAPII: (MACS14_BN2_PolII_vs_Input.tar.gz= sample 9 normalized to sample 8); SPT5:  (MACS14_7A_Spt5_vs_Input.tar.gz= sample 6 normalized to sample 3); Int11:  (MACS14_X_Int11_vs_Input.tar.gz= sample11 normalized to sample 10)
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data files are directly from the MACS output, with .bed and .xls files.

source_name: HeLa-LTR-Luciferase cells

growth_protocol: Exponentially growing HeLa-LTR-Luciferase cells

extract_protocol:
Chromatin immuno-precipitations (ChIPs) were performed as described in Whyte et al. 201228 using ~100 x 106 HeLa-LTR-Luciferase cells as starting material with the exception of an additional nuclei purification step. Briefly, cells were thawed and resuspended in 1ml Buffer A (0.3M SUCROSE, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF), 1ml Buffer B (0.3M SUCROSE, 0.2% NP40, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF) was then added and incubated for 7min on ice, laid over a 8ml cushion of Buffer C (1.2M SUCROSE, 0.2% NP40, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1 mM EGTA, Tris-HCl pH=7.5, 0.2mM PMSF) and spinned for 20min at 3000rpm on 4  C. Pelleted nuclei were resuspended in 3ml Lysis buffer, incubated for 1 hour, sonicated (Misonix sonicator with the following settings: micro tip, 30sec on, 2min off, amplitude 70, 7min total sonication time). 10ng, as quantified by Qubit   dsDNA HS Assay Kit (Life Technologies), of input and of immuno-precipitated-material was used for library preparation.
Librairies were prepared using Illumina ChIP-Seq sample prep kit (non-multiplexed libraries) or TruSeq ChIP Sample Prep Kit (multiplexed libraries) according to manufacturer’s instructions. Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Data quality was assessed using fastqc from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). De-multiplexing and alignment were performed using Illumina's sequencing analysis software (CASAVA 1.8.2).

treatment_protocol:
Chromatin was purified from 100 millions HeLa-LTR-Luciferase cells for each sample
Chromatin immunoprecipitation (ChIP) was performed using 10 µg antibody resulting in the following amounts of DNA pellets:
Anti-RNAPII total (Santa Cruz) Replicate A: 53.7ng. Replicate B: 71.1ng.
Anti-H3K4me3  (Abcam): Replicate A: 1290ng. Replicate B: 1251ng.
Anti-NELF-E (Millipore): Replicate A: 21ng. Replicate B: 27ng.
Anti-Spt5 (BD Transduction Laboratories): Replicate A: 18ng. Replicate B: 24ng.
Anti-INTS3 (Bethyl Laboratories): Replicate A: 81ng. Replicate B: 81ng.
Anti-INTS11:(Bethyl Laboratories) Replicate A: 10.8ng. Replicate B: 13.2ng.
Anti-INTS13 (Bethyl Laboratories): Replicate A: 33ng. Replicate B: 43.5ng.

tag: genotype/variation

value: depleted of Int11

tag: chip antibody

value: Anti-RNAPII total

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat.#


title: STT6644_Myometrium

description: Experiment type: 3SEQ

value: Soft Tissue


title: Input control (siScrambled)

description:
Sample 16
processed data file: Profile_RNAPII_Scr_control_TES.tar.gz, Profile_RNAPII_Scr_control_TSS.tar.gz

value: mock-treated


title: Input RNAPII (Int11-KD)

description:
Sample 14
processed data file: Profile_RNAPII_Int11_KD_TES.tar.gz, Profile_RNAPII_Int11_KD_TSS.tar.gz


title: IP RNAPII (Int3-KD)

description:
Sample 13
processed data file: Profile_RNAPII_Int3_KD_TES.tar.gz, Profile_RNAPII_Int3_KD_TSS.tar.gz

value: depleted of Int3


title: IP Int11

description:
Sample 11
processed data file: MACS14_X_Int11_vs_Input.tar.gz

value: Bethyl Laboratories


title: Input BN2

description:
Sample 8
processed data file: MACS14_BN2_PolII_vs_Input.tar.gz


title: IP RNAPol II

description:
Sample 9
processed data file: MACS14_BN2_PolII_vs_Input.tar.gz


title: Input RNAPII (Int3-KD)

description:
Sample 12
processed data file: Profile_RNAPII_Int3_KD_TES.tar.gz, Profile_RNAPII_Int3_KD_TSS.tar.gz


title: STT6624_UPS

description: Experiment type: 3SEQ

source_name: Undifferentiated pleomorphic sarcoma

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx machines.

value: FFPE

value: Stanford Surgical


title: STT6619_UPS

description: Experiment type: 3SEQ


title: STT6623_UPS

description: Experiment type: 3SEQ


title: IP Asun

description:
Sample 7
processed data file: MACS14_7A_Asun_vs_Input.tar.gz


title: STT6625_UPS

description: Experiment type: 3SEQ


title: STT6630_UPS

description: Experiment type: 3SEQ


title: IP Int3

description:
Sample 4
processed data file: MACS14_7A_Int3_vs_Input.tar.gz


title: STT6622_UPS

description: Experiment type: 3SEQ


title: STT6780_LMS

description: Experiment type: 3SEQ

source_name: Leiomyosarcoma

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously [1-3]. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx machines.

tag: subtypes

value: III


title: STT6806_LMS

description: Experiment type: 3SEQ

value: II


title: STT6805_LMS

description: Experiment type: 3SEQ


title: IP RNAPII control (siScrambled)

description:
Sample 17
processed data file: Profile_RNAPII_Scr_control_TES.tar.gz, Profile_RNAPII_Scr_control_TSS.tar.gz

value: HeLa-LTR-Luciferase cells


title: STT6646_Myometrium

description: Experiment type: 3SEQ


title: IP NELF-E

description:
Sample 5
processed data file: MACS14_7A_NELF_vs_Input.tar.gz

value: Anti-NELF-E

value: Millipore


title: IP Spt5

description:
Sample 6
processed data file: MACS14_7A_Spt5_vs_Input.tar.gz

value: BD Transduction Laboratories


title: STT6803_LMS

description: Experiment type: 3SEQ


title: Input 7A

description:
Sample 3
processed data file: MACS14_7A_Int3_vs_Input.tar.gz, MACS14_7A_Asun_vs_Input.tar.gz, MACS14_7A_NELF_vs_Input.tar.gz, MACS14_7A_Spt5_vs_Input.tar.gz


title: Input BN

description:
Sample 1
processed data file: MACS14_BN_H3K4me3_vs_Input.tar.gz


title: STT6799_LMS

description: Experiment type: 3SEQ

value: I


title: STT6798_LMS

description: Experiment type: 3SEQ


title: STT6801_LMS

description: Experiment type: 3SEQ


title: STT6795_LMS

description: Experiment type: 3SEQ


title: STT6864_cellline_LMS676

description: Experiment type: 3SEQ

source_name: LMS cell line


title: STT6794_LMS

description: Experiment type: 3SEQ


title: Input X

description:
Sample 10
processed data file: MACS14_X_Int11_vs_Input.tar.gz


title: STT6863_cellline_LMS05

description: Experiment type: 3SEQ


title: STT6789_LMS

description: Experiment type: 3SEQ


title: STT6788_LMS

description: Experiment type: 3SEQ


title: STT6652_LMS

description: Experiment type: 3SEQ


title: STT6862_cellline_LMS04

description: Experiment type: 3SEQ


title: STT6784_LMS

description: Experiment type: 3SEQ


title: STT6651_LMS

description: Experiment type: 3SEQ


title: STT6650_LMS

description: Experiment type: 3SEQ


title: STT6783_LMS

description: Experiment type: 3SEQ


title: STT6785_LMS

description: Experiment type: 3SEQ


title: STT6779_LMS

description: Experiment type: 3SEQ


title: STT6782_LMS

description: Experiment type: 3SEQ


title: STT6781_LMS

description: Experiment type: 3SEQ


title: STT6778_LMS

description: Experiment type: 3SEQ


title: IP H3K4me3

description:
Sample 2
processed data file: MACS14_BN_H3K4me3_vs_Input.tar.gz

value: Anti-Histone H3 (tri methyl K4) antibody

value: Abcam


title: STT6776_LMS

description: Experiment type: 3SEQ


title: STT6802_LMS

description: Experiment type: 3SEQ


title: STT6804_LMS

description: Experiment type: 3SEQ


title: STT6620_LMS

description: Experiment type: 3SEQ


title: STT6796_LMS

description: Experiment type: 3SEQ


title: STT6096_LMS

description: Experiment type: 3SEQ

value: Not assigned


title: STT6050_LMS

description: Experiment type: 3SEQ


title: STT6049_LMS

description: Experiment type: 3SEQ


title: STT6048_LMS

description: Experiment type: 3SEQ


title: STT6047_LMS

description: Experiment type: 3SEQ


title: STT6046_LMS

description: Experiment type: 3SEQ


title: STT6045_LMS

description: Experiment type: 3SEQ


title: STT6039_LMS

description: Experiment type: 3SEQ


title: STT6044_LMS

description: Experiment type: 3SEQ


title: STT6093_LMS

description: Experiment type: 3SEQ


title: STT6038_LMS

description: Experiment type: 3SEQ


title: STT6040_LMS

description: Experiment type: 3SEQ


title: STT6043_LMS

description: Experiment type: 3SEQ


title: STT6777_LMS

description: Experiment type: 3SEQ


title: STT6775_LMS

description: Experiment type: 3SEQ


title: STT5986_LMS

description: Experiment type: 3SEQ


title: STT6021_LMS

description: Experiment type: 3SEQ


title: STT6022_LMS

description: Experiment type: 3SEQ


title: STT5980_LMS

description: Experiment type: 3SEQ


title: STT6037_LMS

description: Experiment type: 3SEQ


title: STT6034_LMS

description: Experiment type: 3SEQ


title: STT5979_LMS

description: Experiment type: 3SEQ


title: STT6035_LMS

description: Experiment type: 3SEQ


title: STT6036_LMS

description: Experiment type: 3SEQ


title: STT5985_LMS

description: Experiment type: 3SEQ


title: STT5978_LMS

description: Experiment type: 3SEQ


title: STT5976_LMS

description: Experiment type: 3SEQ


title: STT5977_LMS

description: Experiment type: 3SEQ


title: STT5975_LMS

description: Experiment type: 3SEQ


title: STT5863_LMS

description: Experiment type: 3SEQ


title: STT6041_LMS

description: Experiment type: 3SEQ


title: STT5860_LMS

description: Experiment type: 3SEQ


title: STT5861_LMS

description: Experiment type: 3SEQ


title: STT5859_LMS

description: Experiment type: 3SEQ


title: STT5856_LMS

description: Experiment type: 3SEQ


title: STT5857_LMS

description: Experiment type: 3SEQ


title: STT5855_LMS

description: Experiment type: 3SEQ


title: STT5852_LMS

description: Experiment type: 3SEQ


title: STT5858_LMS

description: Experiment type: 3SEQ


title: STT5854_LMS

description: Experiment type: 3SEQ


title: STT5981_LMS

description: Experiment type: 3SEQ


title: STT5853_LMS

description: Experiment type: 3SEQ


title: STT5848_LMS

description: Experiment type: 3SEQ


title: STT5846_LMS

description: Experiment type: 3SEQ


title: STT5851_LMS

description: Experiment type: 3SEQ


title: STT5849_LMS

description: Experiment type: 3SEQ


title: STT5841_LMS

description: Experiment type: 3SEQ


title: STT5845_LMS

description: Experiment type: 3SEQ


title: STT5844_LMS

description: Experiment type: 3SEQ


title: STT5840_LMS

description: Experiment type: 3SEQ


title: STT5842_LMS

description: Experiment type: 3SEQ


title: STT5843_LMS

description: Experiment type: 3SEQ


title: STT5862_LMS

description: Experiment type: 3SEQ


title: STT5839_LMS

description: Experiment type: 3SEQ


title: STT5838_LMS

description: Experiment type: 3SEQ


title: STT5836_LMS

description: Experiment type: 3SEQ


title: STT5834_LMS

description: Experiment type: 3SEQ


title: STT5835_LMS

description: Experiment type: 3SEQ


title: STT5528_LMS

description: Experiment type: 3SEQ


title: STT5837_LMS

description: Experiment type: 3SEQ


title: STT1220_LMS

description: Experiment type: 3SEQ


title: STT516_LMS

description: Experiment type: 3SEQ


title: STT6030_LMS

description: Experiment type: 3SEQ


title: STT6032_LMS

description: Experiment type: 3SEQ


title: STT6029_LMS

description: Experiment type: 3SEQ


title: STT5847_LMS

description: Experiment type: 3SEQ


title: STT6024_LMS

description: Experiment type: 3SEQ


title: STT6025_LMS

description: Experiment type: 3SEQ


title: STT6028_LMS

description: Experiment type: 3SEQ


title: STT6033_LMS

description: Experiment type: 3SEQ


title: STT6023_LMS

description: Experiment type: 3SEQ


title: KO_mTEC_lo_3

city: Montreal

first: Charles

last: St-Pierre

state: Quebec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

organism: Mus musculus

source_name: Thymic epithelial cells

extract_protocol:
Thymi were isolated and stromal cell enrichment was performed. Briefly, thymi were mecanically disrupted, digested and thymic stromal cells were sorted by multicolour flow cytometry.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Aire KO

value: mTEC

tag: strain

value: Thymus

value: 6-8 week old


title: KO_mTEC_lo_1

tag: cell type


title: WT_mTEC_lo_1

value: wild type


title: WT_mTEC_lo_2


title: WT_mTEC_hi_3


title: WT_mTEC_lo_3


title: WT_cTEC_1

value: cTEC


title: WT_cTEC_2


title: KO_mTEC_hi_2