title: breast_cancer_primary_sample_352

description: breast cancer primary tumor


title: breast_cancer_primary_sample_349

status: Public on Sep 26 2019

type: RNA

city: Vancouver

first: Laura

last: Chang

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: PFS Genomics

description: breast cancer primary tumor

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE breast cancer

label_protocol: cDNA was amplified using the Ovation FFPE WTA system (NuGEN, San Carlos, CA). Amplified cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN, San Carlos, CA).

extract_protocol: After pathologic review, FFPE tissue was harvested with a 1 mm punch. RNA was extracted from tissue punches using the RNeasy FFPE kit (Qiagen, Hilden, Germany).

tag: grade

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age

tag: Sex

value: female


title: breast_cancer_primary_sample_351

description: breast cancer primary tumor


title: P116_C8 (scRNAseq)

type: SRA

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
CelSeq2 RNA sequencing reads were mapped to the GRCm38 mouse genome and GRCh38 human genome using the Subread aligner and assigned to genes using scPipe with ENSEMBL v86 annotation. Gene counts were exported as a matrix by scPipe with UMI-aware counting and imported into R.
For 100 cell bulk samples, cells were removed from further analysis if they failed to achieve 5000 total counts. In single cell samples, cells were removed using the detect_outlier function from the scPipe. In 100 cell bulk samples, genes were filtered out if they failed to achieve 5 counts per million in 3 samples and in single cells genes were required to be expressed in at least 5 samples and an average of 2 or more counts in those samples.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: comma-separated files containing gene counts accounting for unique moleculat identifiers

molecule: polyA RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Single cell suspensions from mouse and human thymus were obtained by mechanically grinding the organs through a 70mm sieve. Single cell suspensions of mouse thymus were  stained with PE-mouse MR1-5-OP-RU tetramers prior to magnetic bead enrichment using anti-PE microbeads as per manufacturer’s instructions (Miltenyi Biotec). Single cell suspensions of human thymus were enriched for TRAV1.2+ cells by staining for TRAV1.2-PE antibody, followed by magnetic bead enrichment using anti-PE microbeads (Miltenyi Biotec). Human blood cell suspensions were obtained through Ficoll gradient separation. After staining with a panel of flow cytometry surface markers, cells were sorted into a chilled 384-well PCR plate (Greiner #785290) containing 1.2μl of primer/lysis mix.
RNA libraries were prepared and described fully in the methods section of the manuscript..

tag: sample index

value: ATCACGAC

tag: plate number

tag: well position

tag: donor id

tag: cell type

value: CD319+ Spleen Maits

tag: cell number


title: breast_cancer_primary_sample_345

description: breast cancer primary tumor


title: ResB 10 nM DHT b1-rep3

city: Leuven

first: Frank

last: Claessens

address: Herestraat 49, box 901

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

data_processing:
The reads were mapped to hg19 human reference genome using TopHat v1.3.3 with default settings.
The reads were counted with HTSeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *count.txt: Tab-delimited text files include mapped reads per gene counted with HTSeq.

source_name: LNCaP, enzalutamide resistant, subline ResB

growth_protocol: Cells were grown in RPMI 1640 with 4.5 g/l glucose, 10% FCS, 1% Penicillin/Streptomycin, 10 mM HEPES pH 7-7.6, and 1 mM sodium pyruvate, supplemented with 10 µM enzalutamide for the enzalutamide resistant cell lines.

extract_protocol:
RNA isolation was performed with the RNeasy plus mini kit according to the manufacturer's recommendation.
The libraries were generated with the TruSeq RNA Library Prep Kit according to the manufacturer’s recommendations.

treatment_protocol: Cells were plated in medium with 5% dextran-coated charcoal (DCC) treated FCS at a density of 1 million cells/well in 6-well plates. After 24 hours of steroid starvation the cells were treated with 10 nM DHT, 10 µM enzalutamide, a combination of the two, or vehicle (DMSO) for 18 hours.

tag: cell line

value: ResB

tag: treatment

value: 10 nM DHT

tag: batch


title: breast_cancer_primary_sample_348

description: breast cancer primary tumor


title: breast_cancer_primary_sample_355

description: breast cancer primary tumor


title: breast_cancer_primary_sample_347

description: breast cancer primary tumor


title: breast_cancer_primary_sample_342

description: breast cancer primary tumor


title: ResB 10 nM DHT b1-rep2


title: ResB DMSO b1-rep3

value: DMSO


title: P116_C6 (scRNAseq)

value: TACGCTGA


title: ResB 10 nM DHT b1-rep1


title: ResB DMSO b1-rep1


title: ResB DMSO b1-rep2


title: breast_cancer_primary_sample_346

description: breast cancer primary tumor


title: breast_cancer_primary_sample_343

description: breast cancer primary tumor


title: breast_cancer_primary_sample_341

description: breast cancer primary tumor


title: breast_cancer_primary_sample_338

description: breast cancer primary tumor


title: breast_cancer_primary_sample_340

description: breast cancer primary tumor


title: breast_cancer_primary_sample_344

description: breast cancer primary tumor


title: breast_cancer_primary_sample_337

description: breast cancer primary tumor


title: LNCaP 10 nM DHT + 10 µM enz b1-rep3

source_name: LNCaP

value: LNCaP

value: 10 nM DHT + 10 uM enz


title: LNCaP 10 nM DHT + 10 µM enz b1-rep2


title: breast_cancer_primary_sample_335

description: breast cancer primary tumor


title: P116_C3 (scRNAseq)

value: GGACTTAC


title: P116_C24 (scRNAseq)

value: ACTGTGAC


title: P116_E10 (scRNAseq)

value: TACGAGTC


title: LNCaP 10 nM DHT + 10 µM enz b1-rep1


title: P116_C23 (scRNAseq)

value: TCCTCTTC


title: P116_C22 (scRNAseq)

value: GACCATCA


title: P116_C4 (scRNAseq)

value: CTATCGGA


title: LNCaP 10 nM DHT b1-rep3


title: breast_cancer_primary_sample_333

description: breast cancer primary tumor


title: breast_cancer_primary_sample_334

description: breast cancer primary tumor


title: breast_cancer_primary_sample_331

description: breast cancer primary tumor


title: breast_cancer_primary_sample_332

description: breast cancer primary tumor


title: LNCaP 10 nM DHT b1-rep2


title: breast_cancer_primary_sample_339

description: breast cancer primary tumor


title: P116_C21 (scRNAseq)

value: TGACTCAG


title: LNCaP 10 nM DHT b1-rep1


title: breast_cancer_primary_sample_330

description: breast cancer primary tumor


title: LNCaP DMSO b1-rep3


title: breast_cancer_primary_sample_336

description: breast cancer primary tumor


title: P116_C19 (scRNAseq)

value: TGCACGTA


title: P116_C18 (scRNAseq)

value: GGCACTTA


title: breast_cancer_primary_sample_328

description: breast cancer primary tumor

value: female


title: P116_C17 (scRNAseq)

value: CACGGTAT

value: CD319+ Spleen Maits


title: LNCaP DMSO b1-rep1


title: P116_C16 (scRNAseq)

value: AGTCACGT


title: P116_C15 (scRNAseq)

value: CTCACGAA


title: breast_cancer_primary_sample_326

description: breast cancer primary tumor


title: breast_cancer_primary_sample_323

description: breast cancer primary tumor


title: P116_C14 (scRNAseq)

value: GCTAGTGT


title: breast_cancer_primary_sample_320

description: breast cancer primary tumor


title: breast_cancer_primary_sample_321

description: breast cancer primary tumor


title: P116_C13 (scRNAseq)

value: TGCGTAGT


title: breast_cancer_primary_sample_314

description: breast cancer primary tumor


title: breast_cancer_primary_sample_322

description: breast cancer primary tumor


title: breast_cancer_primary_sample_317

description: breast cancer primary tumor


title: breast_cancer_primary_sample_316

description: breast cancer primary tumor


title: breast_cancer_primary_sample_319

description: breast cancer primary tumor


title: breast_cancer_primary_sample_327

description: breast cancer primary tumor


title: breast_cancer_primary_sample_313

description: breast cancer primary tumor


title: breast_cancer_primary_sample_324

description: breast cancer primary tumor


title: breast_cancer_primary_sample_318

description: breast cancer primary tumor


title: breast_cancer_primary_sample_381

description: breast cancer primary tumor


title: P116_C11 (scRNAseq)

value: TCAGTGCA


title: breast_cancer_primary_sample_325

description: breast cancer primary tumor


title: P116_C10 (scRNAseq)

value: ACTGTTGG


title: P116_C12 (scRNAseq)

value: GCGATATC


title: A549 DDP-2 m6A-seq

city: guangzhou

first: Xingyang

last: Li

state: Guangdong

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

country: China

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

description: Lung epithelial cell

data_processing:
m6A-seq and RIP-seq reads were aligned to the hg38 genome assembly using STAR version 020201 with the "twopassMode"  configuration.
m6A peaks were called using MeTPeak version 1.0.0 with the default setting.
Genes expression estimate were calculated using RSEM.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: txt files were generated using RSEM and MeTPeak.

growth_protocol: A549 and A549 DDP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. Then we performed the paired-end 2×150bp sequencing on an Illumina NovaseqTM 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

value: DDP resistant lung cancer cell line

tag: passages

tag: rip antibody

value: m6A-specific antibody(No. 202003, Synaptic Systems, Germany)


title: A549 DDP-1 m6A-seq

description: Lung epithelial cell


title: breast_cancer_primary_sample_311

description: breast cancer primary tumor

tag: grade


title: breast_cancer_primary_sample_315

description: breast cancer primary tumor

tag: systemic therapy


title: breast_cancer_primary_sample_308

description: breast cancer primary tumor

tag: menopause


title: breast_cancer_primary_sample_312

description: breast cancer primary tumor

tag: tumor size (millimeters)


title: breast_cancer_primary_sample_309

description: breast cancer primary tumor

tag: age


title: breast_cancer_primary_sample_305

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_307

description: breast cancer primary tumor


title: breast_cancer_primary_sample_306

description: breast cancer primary tumor


title: A549-1 m6A-seq

description: Lung epithelial cell

value: Lung cancer cell line


title: P116_C1 (scRNAseq)

tag: sample index

value: AGTGTGCT


title: A549-2 m6A-seq

description: Lung epithelial cell


title: P116_B8 (scRNAseq)

value: CGTGTCAA

tag: plate number


title: A549 DDP-2 input

description: Lung epithelial cell

value: DDP resistent lung cancer cell line


title: P116_B7 (scRNAseq)

value: CTCTCCTT

tag: well position


title: breast_cancer_primary_sample_303

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_301

description: breast cancer primary tumor


title: A549-2 input

description: Lung epithelial cell


title: P116_B9 (scRNAseq)

value: GCCTTAAG

tag: donor id


title: P116_B5 (scRNAseq)

value: CCTGTAAG

tag: cell type

value: CD319+ Spleen Maits


title: A549-1 input

description: Lung epithelial cell


title: P116_B3 (scRNAseq)

value: AGCAGCTT

tag: cell number


title: breast_cancer_primary_sample_299

description: breast cancer primary tumor


title: breast_cancer_primary_sample_304

description: breast cancer primary tumor


title: P116_B24 (scRNAseq)

value: CGCATGTA


title: A549 DDP-1 input

description: Lung epithelial cell

tag: cell line


title: breast_cancer_primary_sample_302

description: breast cancer primary tumor


title: P116_C5 (scRNAseq)

value: ACGCGTTA


title: P116_B22 (scRNAseq)

value: CAGTCATG


title: breast_cancer_primary_sample_296

description: breast cancer primary tumor


title: P116_B21 (scRNAseq)

value: TACTGGCA


title: P116_B20 (scRNAseq)

value: ATGCTGAC


title: P116_B2 (scRNAseq)

value: AGTCTTGG


title: Patient 106_lh 68

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 10 HK genes (SF3A3, PPIA, POLR2A, MRPS5, MTMR14, GUSB, G6PD, ERCC3, EIF2B4, COG7). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, ten reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Classical Hodgkin Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of classical Hodgkin Lymphoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Pretreatment diagnostic biopsies from ABVD-treated classical Hodgkin Lymphoma patients

tag: subject status

value: patient affected by Hodgkin Lymphoma

tag: gender

value: M

tag: Stage

value: I A

value: yes

tag: interim pet response


title: breast_cancer_primary_sample_300

description: breast cancer primary tumor

tag: grade


title: Patient 105_lh 93

value: F

value: II B

value: no

value: positive


title: Patient 102_lh 105

value: IV A


title: Patient 103_lh 107

value: III A


title: Patient 104_lh 43

value: IV B


title: breast_cancer_primary_sample_298

description: breast cancer primary tumor

tag: systemic therapy

value: female


title: breast_cancer_primary_sample_310

description: breast cancer primary tumor

tag: menopause


title: breast_cancer_primary_sample_297

description: breast cancer primary tumor

tag: tumor size (millimeters)


title: Patient 101_lh 102

tag: age

value: II A


title: P116_B19 (scRNAseq)

value: ACCGACAT

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_295

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_294

description: breast cancer primary tumor


title: Patient 100_lh 90


title: breast_cancer_primary_sample_293

description: breast cancer primary tumor


title: breast_cancer_primary_sample_290

description: breast cancer primary tumor


title: breast_cancer_primary_sample_289

description: breast cancer primary tumor


title: breast_cancer_primary_sample_288

description: breast cancer primary tumor


title: breast_cancer_primary_sample_287

description: breast cancer primary tumor


title: breast_cancer_primary_sample_284

description: breast cancer primary tumor


title: breast_cancer_primary_sample_286

description: breast cancer primary tumor


title: breast_cancer_primary_sample_285

description: breast cancer primary tumor


title: breast_cancer_primary_sample_282

description: breast cancer primary tumor


title: breast_cancer_primary_sample_279

description: breast cancer primary tumor


title: breast_cancer_primary_sample_283

description: breast cancer primary tumor


title: breast_cancer_primary_sample_280

description: breast cancer primary tumor


title: P116_B17 (scRNAseq)

tag: sample index

value: GTTGCTGA


title: P116_B16 (scRNAseq)

value: GTGGTTGT

tag: plate number


title: Patient 99_lh 83

value: patient affected by Hodgkin Lymphoma


title: breast_cancer_primary_sample_277

description: breast cancer primary tumor


title: breast_cancer_primary_sample_281

description: breast cancer primary tumor


title: Patient 98_lh 78

value: M


title: P116_B18 (scRNAseq)

value: CCTGGATA

tag: well position


title: Patient 96_lh 60


title: Patient 97_lh 74


title: P116_B13 (scRNAseq)

value: TATCCAGG

tag: donor id


title: breast_cancer_primary_sample_278

description: breast cancer primary tumor


title: LNCaP DMSO b1-rep2

value: LNCaP

tag: treatment

value: DMSO

tag: batch


title: P116_B12 (scRNAseq)

value: GCGTACAT

tag: cell type

tag: cell number


title: breast_cancer_primary_sample_276

description: breast cancer primary tumor


title: Patient 95_lh 58

tag: subject status

tag: gender

value: F

value: no

value: positive


title: Patient 94_lh 47

tag: Stage

value: IV B

value: yes

tag: interim pet response


title: P116_B11 (scRNAseq)

value: CAACGTAC


title: P116_B14 (scRNAseq)

value: CCGATATG


title: breast_cancer_primary_sample_273

description: breast cancer primary tumor

tag: grade

tag: systemic therapy

value: female


title: breast_cancer_primary_sample_275

description: breast cancer primary tumor

tag: menopause

tag: tumor size (millimeters)


title: breast_cancer_primary_sample_274

description: breast cancer primary tumor

tag: age

tag: Sex


title: breast_cancer_primary_sample_272

description: breast cancer primary tumor


title: breast_cancer_primary_sample_271

description: breast cancer primary tumor


title: P116_B10 (scRNAseq)

tag: sample index

value: GCACGTAT

tag: plate number

value: CD319+ Spleen Maits


title: breast_cancer_primary_sample_270

description: breast cancer primary tumor


title: breast_cancer_primary_sample_269

description: breast cancer primary tumor


title: breast_cancer_primary_sample_268

description: breast cancer primary tumor


title: Patient 93_lh 36

value: patient affected by Hodgkin Lymphoma

value: II A


title: Patient 92_lh 32


title: breast_cancer_primary_sample_267

description: breast cancer primary tumor


title: P115_M9 (scRNAseq)

source_name: thymus

value: CATTGTGG

tag: well position

tag: donor id

value: CD138+ Thymus Maits


title: breast_cancer_primary_sample_265

description: breast cancer primary tumor


title: breast_cancer_primary_sample_264

description: breast cancer primary tumor


title: Patient 91_lh 30

value: M

value: III A


title: breast_cancer_primary_sample_329

description: breast cancer primary tumor


title: P116_B1 (scRNAseq)

value: GACTACTG


title: breast_cancer_primary_sample_263

description: breast cancer primary tumor


title: P115_M8 (scRNAseq)

value: GGCCAATT


title: P115_M7 (scRNAseq)

value: ACTCTGAG


title: Patient 90_lh 22

value: F

value: IV A

value: no

value: positive


title: breast_cancer_primary_sample_261

description: breast cancer primary tumor


title: breast_cancer_primary_sample_266

description: breast cancer primary tumor


title: P115_M5 (scRNAseq)

value: GGTATCGT


title: breast_cancer_primary_sample_262

description: breast cancer primary tumor

value: female


title: Patient 88_lh 6

value: yes


title: Patient 89_lh 17

value: II B


title: breast_cancer_primary_sample_260

description: breast cancer primary tumor


title: Patient 87_lh 16

value: patient affected by Hodgkin Lymphoma


title: breast_cancer_primary_sample_259

description: breast cancer primary tumor


title: breast_cancer_primary_sample_255

description: breast cancer primary tumor


title: breast_cancer_primary_sample_257

description: breast cancer primary tumor


title: breast_cancer_primary_sample_258

description: breast cancer primary tumor


title: Patient 86_lh 13

value: IV B


title: P115_M3 (scRNAseq)

value: TCAAGCAC


title: Patient 85_lh 11


title: P115_M23 (scRNAseq)

value: ACCAAGCT

value: CD138+ Thymus Maits


title: breast_cancer_primary_sample_256

description: breast cancer primary tumor


title: Patient 83_lh 48

value: negative


title: breast_cancer_primary_sample_253

description: breast cancer primary tumor


title: P115_M21 (scRNAseq)

value: TGCCAGAT


title: P115_M24 (scRNAseq)

value: AGCATGTC


title: Patient 82_lh 46

value: M


title: breast_cancer_primary_sample_251

description: breast cancer primary tumor


title: breast_cancer_primary_sample_252

description: breast cancer primary tumor


title: breast_cancer_primary_sample_249

description: breast cancer primary tumor


title: P115_M20 (scRNAseq)

value: GCCAATTG


title: Patient 81_lh 21

value: II A


title: breast_cancer_primary_sample_244

description: breast cancer primary tumor


title: Patient 80_lh 119

value: F


title: breast_cancer_primary_sample_245

description: breast cancer primary tumor


title: P115_M22 (scRNAseq)

value: TAGCGTCA


title: Patient 84_lh 117

value: no


title: breast_cancer_primary_sample_292

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_250

description: breast cancer primary tumor


title: breast_cancer_primary_sample_254

description: breast cancer primary tumor


title: breast_cancer_primary_sample_248

description: breast cancer primary tumor


title: breast_cancer_primary_sample_247

description: breast cancer primary tumor


title: breast_cancer_primary_sample_240

description: breast cancer primary tumor


title: breast_cancer_primary_sample_246

description: breast cancer primary tumor


title: Patient 79_lh 118

value: yes


title: breast_cancer_primary_sample_243

description: breast cancer primary tumor


title: P115_M16 (scRNAseq)

value: ATTGCCGA


title: breast_cancer_primary_sample_239

description: breast cancer primary tumor


title: Patient 78_lh 116

value: patient affected by Hodgkin Lymphoma

value: II B


title: P115_M15 (scRNAseq)

value: AGCGTATC


title: Patient 76_lh 114


title: Patient 77_lh 115

value: IV A


title: P115_M18 (scRNAseq)

value: TGGCAACT

value: CD138+ Thymus Maits


title: breast_cancer_primary_sample_242

description: breast cancer primary tumor


title: breast_cancer_primary_sample_241

description: breast cancer primary tumor


title: breast_cancer_primary_sample_238

description: breast cancer primary tumor


title: breast_cancer_primary_sample_233

description: breast cancer primary tumor


title: breast_cancer_primary_sample_235

description: breast cancer primary tumor


title: breast_cancer_primary_sample_234

description: breast cancer primary tumor


title: P115_M13 (scRNAseq)

value: GACATGCT


title: breast_cancer_primary_sample_237

description: breast cancer primary tumor


title: P115_M12 (scRNAseq)

value: TGCGGTTA


title: Patient 75_lh 113

value: negative


title: Patient 74_lh 112


title: breast_cancer_primary_sample_232

description: breast cancer primary tumor


title: P115_M10 (scRNAseq)

value: GATTGGTC


title: P115_M11 (scRNAseq)

value: TCAGGCAT


title: breast_cancer_primary_sample_230

description: breast cancer primary tumor


title: breast_cancer_primary_sample_229

description: breast cancer primary tumor


title: breast_cancer_primary_sample_228

description: breast cancer primary tumor


title: breast_cancer_primary_sample_231

description: breast cancer primary tumor


title: P115_L9 (scRNAseq)

value: CGATAGCT


title: P115_M19 (scRNAseq)

value: GCATCTAG


title: Patient 72_lh 110

value: M

value: III B


title: P115_L6 (scRNAseq)

value: AGCTGTTG


title: P115_L8 (scRNAseq)

value: TGGTGATC


title: P115_L3 (scRNAseq)

value: TGCGGATT


title: P115_L5 (scRNAseq)

value: TCGCACAA


title: Patient 73_lh 111

value: patient affected by Hodgkin Lymphoma

value: II B

value: no


title: Patient 71_lh 109

value: F

value: III A


title: Patient 70_lh 108

value: II A


title: P115_L4 (scRNAseq)

value: CGACCATA

value: CD138+ Thymus Maits


title: Patient 68_lh 104

value: IV A

value: yes

value: negative


title: breast_cancer_primary_sample_227

description: breast cancer primary tumor

value: female


title: Patient 69_lh 106


title: Patient 67_lh 103


title: breast_cancer_primary_sample_222

description: breast cancer primary tumor


title: breast_cancer_primary_sample_219

description: breast cancer primary tumor


title: Patient 66_lh 101


title: breast_cancer_primary_sample_223

description: breast cancer primary tumor


title: breast_cancer_primary_sample_218

description: breast cancer primary tumor


title: breast_cancer_primary_sample_221

description: breast cancer primary tumor


title: breast_cancer_primary_sample_214

description: breast cancer primary tumor


title: breast_cancer_primary_sample_291

description: breast cancer primary tumor


title: breast_cancer_primary_sample_216

description: breast cancer primary tumor


title: breast_cancer_primary_sample_215

description: breast cancer primary tumor


title: breast_cancer_primary_sample_217

description: breast cancer primary tumor


title: breast_cancer_primary_sample_224

description: breast cancer primary tumor


title: breast_cancer_primary_sample_225

description: breast cancer primary tumor


title: P115_L24 (scRNAseq)

value: GTCATGTG


title: breast_cancer_primary_sample_213

description: breast cancer primary tumor


title: breast_cancer_primary_sample_226

description: breast cancer primary tumor


title: P115_L23 (scRNAseq)

value: TGGTCTGA


title: P115_L22 (scRNAseq)

value: GCAATGTC


title: breast_cancer_primary_sample_212

description: breast cancer primary tumor


title: Patient 65_lh 99

value: IV B


title: Patient 64_lh 98

value: M


title: P115_M4 (scRNAseq)

value: GCAAGTTC


title: breast_cancer_primary_sample_236

description: breast cancer primary tumor


title: breast_cancer_primary_sample_211

description: breast cancer primary tumor


title: breast_cancer_primary_sample_207

description: breast cancer primary tumor


title: breast_cancer_primary_sample_210

description: breast cancer primary tumor


title: breast_cancer_primary_sample_206

description: breast cancer primary tumor


title: breast_cancer_primary_sample_220

description: breast cancer primary tumor


title: P115_L20 (scRNAseq)

value: CACACTAG


title: breast_cancer_primary_sample_209

description: breast cancer primary tumor


title: Patient 63_lh 97

value: patient affected by Hodgkin Lymphoma

value: no


title: P115_L19 (scRNAseq)

value: ACCATGTG


title: Patient 62_lh 96

value: II A


title: breast_cancer_primary_sample_208

description: breast cancer primary tumor


title: breast_cancer_primary_sample_205

description: breast cancer primary tumor


title: P115_L18 (scRNAseq)

value: GCGCAATT


title: P115_L17 (scRNAseq)

value: TCGAGTTG

value: CD138+ Thymus Maits


title: Patient 61_lh 95

value: F

value: yes


title: Patient 60_lh 94

value: negative


title: breast_cancer_primary_sample_204

description: breast cancer primary tumor

value: female


title: P115_L13 (scRNAseq)

value: GACCTACA


title: Patient 58_lh 91


title: breast_cancer_primary_sample_201

description: breast cancer primary tumor


title: P115_L11 (scRNAseq)

value: CGCTAGTA


title: Patient 57_lh 89

value: III B


title: breast_cancer_primary_sample_202

description: breast cancer primary tumor


title: Patient 56_lh 88

value: III A


title: breast_cancer_primary_sample_198

description: breast cancer primary tumor


title: breast_cancer_primary_sample_203

description: breast cancer primary tumor


title: breast_cancer_primary_sample_200

description: breast cancer primary tumor


title: breast_cancer_primary_sample_199

description: breast cancer primary tumor


title: breast_cancer_primary_sample_196

description: breast cancer primary tumor


title: Patient 55_lh 87


title: P115_K8 (scRNAseq)

value: ACCACTGA


title: P115_K9 (scRNAseq)

value: GCTCTGAA


title: breast_cancer_primary_sample_195

description: breast cancer primary tumor


title: Patient 59_lh 92

value: patient affected by Hodgkin Lymphoma

value: IV B


title: breast_cancer_primary_sample_194

description: breast cancer primary tumor


title: breast_cancer_primary_sample_192

description: breast cancer primary tumor


title: Patient 53_lh 85

value: II B


title: breast_cancer_primary_sample_197

description: breast cancer primary tumor


title: breast_cancer_primary_sample_191

description: breast cancer primary tumor


title: P115_L12 (scRNAseq)

value: CGCAACAT


title: breast_cancer_primary_sample_190

description: breast cancer primary tumor


title: breast_cancer_primary_sample_188

description: breast cancer primary tumor


title: P115_K7 (scRNAseq)

value: ACTTCAGG


title: breast_cancer_primary_sample_187

description: breast cancer primary tumor


title: breast_cancer_primary_sample_189

description: breast cancer primary tumor


title: breast_cancer_primary_sample_185

description: breast cancer primary tumor


title: Patient 52_lh 84

value: M

value: no


title: Patient 54_lh 86

value: II A


title: P115_K24 (scRNAseq)

value: CCATCGAA

value: CD138+ Thymus Maits


title: Patient 51_lh 82

value: negative


title: breast_cancer_primary_sample_193

description: breast cancer primary tumor

value: female


title: Patient 50_lh 81

value: F


title: breast_cancer_primary_sample_182

description: breast cancer primary tumor


title: P115_K4 (scRNAseq)

value: TCTCAAGG


title: breast_cancer_primary_sample_186

description: breast cancer primary tumor


title: Patient 49_lh 80

value: yes


title: P115_K21 (scRNAseq)

value: CGTAGCAT


title: breast_cancer_primary_sample_178

description: breast cancer primary tumor


title: Patient 48_lh 79


title: P115_K22 (scRNAseq)

value: ACCAAGTC


title: P115_K23 (scRNAseq)

value: CGTGATGT


title: Patient 47_lh 77

value: patient affected by Hodgkin Lymphoma


title: P115_K20 (scRNAseq)

value: TATTGCGG


title: breast_cancer_primary_sample_180

description: breast cancer primary tumor


title: Patient 46_lh 76

value: III A


title: P115_K2 (scRNAseq)

value: ACCAACGT


title: Patient 45_lh 75


title: breast_cancer_primary_sample_176

description: breast cancer primary tumor


title: breast_cancer_primary_sample_175

description: breast cancer primary tumor


title: breast_cancer_primary_sample_183

description: breast cancer primary tumor


title: breast_cancer_primary_sample_179

description: breast cancer primary tumor


title: breast_cancer_primary_sample_173

description: breast cancer primary tumor


title: breast_cancer_primary_sample_172

description: breast cancer primary tumor


title: breast_cancer_primary_sample_177

description: breast cancer primary tumor


title: breast_cancer_primary_sample_181

description: breast cancer primary tumor


title: P115_K18 (scRNAseq)

value: GTGGTCTA


title: breast_cancer_primary_sample_171

description: breast cancer primary tumor


title: P115_K15 (scRNAseq)

value: ACGCACTA


title: breast_cancer_primary_sample_174

description: breast cancer primary tumor


title: breast_cancer_primary_sample_170

description: breast cancer primary tumor


title: breast_cancer_primary_sample_169

description: breast cancer primary tumor


title: Patient 44_lh 73

value: M

value: IV B


title: breast_cancer_primary_sample_168

description: breast cancer primary tumor


title: Patient 43_Lh 71

value: IV A


title: P115_K13 (scRNAseq)

value: ACTACGGT

value: CD138+ Thymus Maits


title: Patient 42_lh 70

value: II A

value: negative


title: breast_cancer_primary_sample_165

description: breast cancer primary tumor

value: female


title: breast_cancer_primary_sample_167

description: breast cancer primary tumor


title: breast_cancer_primary_sample_164

description: breast cancer primary tumor


title: breast_cancer_primary_sample_166

description: breast cancer primary tumor


title: P115_K12 (scRNAseq)

value: GCAGTCAT


title: Patient 41_lh 69

value: F

value: I

value: yes


title: breast_cancer_primary_sample_163

description: breast cancer primary tumor


title: P115_J9 (scRNAseq)

value: TACCGAAC


title: P115_K10 (scRNAseq)

value: CAAGTGTC


title: P115_K1 (scRNAseq)

value: TCTCCTCT


title: Patient 40_lh 66

value: patient affected by Hodgkin Lymphoma

value: II B

value: no


title: P115_K3 (scRNAseq)

value: GTAGTGTC


title: Patient 39_lh 65

value: IV B


title: Patient 38_lh 63

value: III A


title: Patient 37_lh 62

value: M


title: breast_cancer_primary_sample_161

description: breast cancer primary tumor


title: Patient 36_lh 61

value: II A


title: P115_J7 (scRNAseq)

value: TACTGTGG

value: CD138+ Thymus Maits


title: P115_K11 (scRNAseq)

value: TGCATGGT


title: Patient 35_lh 56

value: negative


title: breast_cancer_primary_sample_162

description: breast cancer primary tumor

value: female


title: P115_L2 (scRNAseq)

value: ACACGCAT


title: breast_cancer_primary_sample_159

description: breast cancer primary tumor


title: P115_J6 (scRNAseq)

value: GCCAACTA


title: P115_J4 (scRNAseq)

value: GGTGCATT


title: breast_cancer_primary_sample_160

description: breast cancer primary tumor


title: breast_cancer_primary_sample_156

description: breast cancer primary tumor


title: breast_cancer_primary_sample_153

description: breast cancer primary tumor


title: breast_cancer_primary_sample_157

description: breast cancer primary tumor


title: breast_cancer_primary_sample_154

description: breast cancer primary tumor


title: breast_cancer_primary_sample_184

description: breast cancer primary tumor


title: P115_J3 (scRNAseq)

value: GTGCTCAA


title: breast_cancer_primary_sample_151

description: breast cancer primary tumor


title: breast_cancer_primary_sample_158

description: breast cancer primary tumor


title: P115_J24 (scRNAseq)

value: GCATGTAC


title: breast_cancer_primary_sample_155

description: breast cancer primary tumor


title: P115_J23 (scRNAseq)

value: TATGGCTG


title: breast_cancer_primary_sample_152

description: breast cancer primary tumor


title: breast_cancer_primary_sample_149

description: breast cancer primary tumor


title: breast_cancer_primary_sample_148

description: breast cancer primary tumor


title: breast_cancer_primary_sample_146

description: breast cancer primary tumor


title: breast_cancer_primary_sample_143

description: breast cancer primary tumor


title: Patient 33_lh 52

value: patient affected by Hodgkin Lymphoma

value: F

value: no


title: breast_cancer_primary_sample_150

description: breast cancer primary tumor


title: breast_cancer_primary_sample_145

description: breast cancer primary tumor


title: Patient 34_lh 54

value: IV B

value: yes


title: P115_J21 (scRNAseq)

value: CGCATGAT


title: breast_cancer_primary_sample_144

description: breast cancer primary tumor


title: breast_cancer_primary_sample_147

description: breast cancer primary tumor


title: P115_J20 (scRNAseq)

value: CTCCTCTT


title: breast_cancer_primary_sample_141

description: breast cancer primary tumor


title: breast_cancer_primary_sample_142

description: breast cancer primary tumor


title: breast_cancer_primary_sample_140

description: breast cancer primary tumor


title: breast_cancer_primary_sample_139

description: breast cancer primary tumor


title: Patient 29_lh 45

value: M

value: IV A


title: Patient 32_lh 51

value: II A

value: negative


title: breast_cancer_primary_sample_138

description: breast cancer primary tumor

value: female


title: P115_J19 (scRNAseq)

value: GCGTTAGT

value: CD138+ Thymus Maits


title: P115_J2 (scRNAseq)

value: CAAGACTC


title: breast_cancer_primary_sample_137

description: breast cancer primary tumor


title: Patient 28_lh 44


title: Patient 26_lh 41


title: Patient 30_lh 49


title: P115_J18 (scRNAseq)

value: TCTTCCTC


title: Patient 31_lh 50


title: P115_J15 (scRNAseq)

value: TCCATGAG


title: P115_J16 (scRNAseq)

value: TCATGGTG


title: breast_cancer_primary_sample_135

description: breast cancer primary tumor


title: P115_J14 (scRNAseq)

value: CGAATCCA


title: Patient 27_lh 42

value: patient affected by Hodgkin Lymphoma


title: Patient 24_lh 39

value: F

value: no


title: Patient 25_lh 40

value: IV B

value: yes


title: Patient 23_lh 38

value: M


title: breast_cancer_primary_sample_132

description: breast cancer primary tumor


title: breast_cancer_primary_sample_131

description: breast cancer primary tumor


title: breast_cancer_primary_sample_136

description: breast cancer primary tumor


title: breast_cancer_primary_sample_129

description: breast cancer primary tumor


title: breast_cancer_primary_sample_128

description: breast cancer primary tumor


title: breast_cancer_primary_sample_134

description: breast cancer primary tumor


title: breast_cancer_primary_sample_130

description: breast cancer primary tumor


title: breast_cancer_primary_sample_127

description: breast cancer primary tumor


title: breast_cancer_primary_sample_125

description: breast cancer primary tumor


title: breast_cancer_primary_sample_133

description: breast cancer primary tumor


title: P115_J13 (scRNAseq)

value: CAGACGTT


title: Patient 22_lh 37

value: II B


title: P115_J12 (scRNAseq)

value: CTGTGAGT


title: Patient 21_lh 35

value: II A

value: negative


title: Patient 20_lh 34

value: IV A


title: breast_cancer_primary_sample_126

description: breast cancer primary tumor

value: female


title: Input-CtrlMO_2

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

country: USA

institute: University of Miami Miller School of Medicine

library_source: genomic

data_processing:
Reads were trimmed (if required) and aligned to the Xenopus laevis 9.1 genome using Novoalign (v3.04.06).
ChIP-Sequencing data was marked for duplicates using Picard (v1.128) and filtered for mapping quality using SAMtools (v1.2).
Bigwig files were created using THOR (10/5 Binning)
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Xenopus laevis

source_name: Input-CtrlMO_whole embryo

growth_protocol: Embryos were obtained by in vitro fertilization of oocytes from 2 different females per condition

extract_protocol:
ChIP-seq was performed on 500  stage 12 embryos , according to a protocol from the Cold Spring Harbor Lab , with 35 minutes of crosslinking. Sodium N-lauroylsacrosine in Buffer E3 was replaced by 0.1% SDS,. Chromatin was sonicated to an average fragment size of 200 bp with a Diagenode Bioruptor® Pico before ChIP.
Libraries were prepared using the NEBNext® Ultra™ kit, and sequenced on the Illumia NextSeq 500 (1x75 bp).

treatment_protocol: Embryos were injected at the 1-cell stage with 15 ng of control MO or MO targeting Bap1 and maintained at 22oC until they reached stage 12.

tag: animal id#

tag: embryonic stage

value: stage 12

tag: frog type

value: pigmented

tag: tissue

value: whole embryo

tag: seq. of mo injected/embryo-ng

tag: genotype/variation

value: control

tag: chip antibody


title: Input-CtrlMO_1


title: Patient 19_lh 33

tag: subject status

value: patient affected by Hodgkin Lymphoma

tag: gender

tag: Stage

value: III B

tag: interim pet response


title: breast_cancer_primary_sample_122

description: breast cancer primary tumor

tag: grade

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age


title: Input-Bap1MO_2

source_name: Input-Bap1MO_whole embryo

tag: Sex

value: Bap1 depleted


title: breast_cancer_primary_sample_123

description: breast cancer primary tumor


title: Patient 18_lh 29

value: F

value: no


title: Input-Bap1MO_1

tag: animal id#


title: breast_cancer_primary_sample_120

description: breast cancer primary tumor


title: breast_cancer_primary_sample_121

description: breast cancer primary tumor


title: breast_cancer_primary_sample_118

description: breast cancer primary tumor


title: H2Aub-CtrlMO_1

source_name: H2Aub-CtrlMO_whole embryo

tag: embryonic stage

value: H2AK199ub (Cell Signaling, D27C4, #8240)


title: breast_cancer_primary_sample_115

description: breast cancer primary tumor


title: Patient 15_lh 25

value: yes


title: Patient 17_lh 27


title: H2Aub-Bap1MO_2

source_name: H2Aub-Bap1MO_whole embryo

tag: frog type


title: breast_cancer_primary_sample_124

description: breast cancer primary tumor


title: breast_cancer_primary_sample_116

description: breast cancer primary tumor


title: H2Aub-CtrlMO_2

tag: tissue


title: H2Aub-Bap1MO_1

tag: seq. of mo injected/embryo-ng


title: breast_cancer_primary_sample_113

description: breast cancer primary tumor


title: Patient 13_lh 23


title: breast_cancer_primary_sample_119

description: breast cancer primary tumor


title: breast_cancer_primary_sample_117

description: breast cancer primary tumor


title: breast_cancer_primary_sample_109

description: breast cancer primary tumor


title: breast_cancer_primary_sample_107

description: breast cancer primary tumor


title: breast_cancer_primary_sample_110

description: breast cancer primary tumor


title: Patient 12_lh 20

value: M

value: I A


title: Patient 16_lh 26

value: II A


title: H3K27me3-CtrlMO_2

source_name: H3K27me3-CtrlMO_whole embryo

tag: genotype/variation

value: H3K27me3 (Cell Signaling, C36B11, 9733BF)


title: H3K27me3-CtrlMO_1

tag: chip antibody


title: breast_cancer_primary_sample_105

description: breast cancer primary tumor


title: breast_cancer_primary_sample_104

description: breast cancer primary tumor


title: Patient 11_lh 19

tag: subject status

value: negative


title: breast_cancer_primary_sample_108

description: breast cancer primary tumor

value: female


title: H3K27Me3-Bap1MO_2

source_name: H3K27Me3-Bap1MO_whole embryo

value: stage 12


title: Patient 10_lh 18

tag: gender

value: II B


title: breast_cancer_primary_sample_112

description: breast cancer primary tumor


title: breast_cancer_primary_sample_102

description: breast cancer primary tumor


title: breast_cancer_primary_sample_103

description: breast cancer primary tumor


title: H3K27Me3-Bap1MO_1

value: pigmented

value: whole embryo


title: Patient 9_lh 9

value: patient affected by Hodgkin Lymphoma

tag: Stage

value: IV A


title: Patient 8_lh 8

tag: interim pet response


title: breast_cancer_primary_sample_100

description: breast cancer primary tumor

tag: grade


title: Patient 7_lh 5


title: H3K4me3-CtrlMO_1

source_name: H3K4me3-CtrlMO_whole embryo

value: control

value: H3K4me3 (Active Motif, #39915)


title: H3K4me3-CtrlMO_2


title: breast_cancer_primary_sample_97

description: breast cancer primary tumor

tag: systemic therapy


title: Patient 6_lh 4


title: breast_cancer_primary_sample_101

description: breast cancer primary tumor

tag: menopause


title: H3K4me3-Bap1MO_1

source_name: H3K4me3-Bap1MO_whole embryo

value: Bap1 depleted


title: breast_cancer_primary_sample_98

description: breast cancer primary tumor

tag: tumor size (millimeters)


title: breast_cancer_primary_sample_95

description: breast cancer primary tumor

tag: age


title: breast_cancer_primary_sample_99

description: breast cancer primary tumor

tag: Sex


title: breast_cancer_primary_sample_93

description: breast cancer primary tumor


title: breast_cancer_primary_sample_92

description: breast cancer primary tumor


title: breast_cancer_primary_sample_96

description: breast cancer primary tumor


title: Patient 5_lh 3

value: F

value: IV B

value: no


title: breast_cancer_primary_sample_94

description: breast cancer primary tumor


title: H3K4me3-Bap1MO_2

tag: animal id#


title: breast_cancer_primary_sample_91

description: breast cancer primary tumor


title: Patient 4_lh 15

value: M


title: breast_cancer_primary_sample_88

description: breast cancer primary tumor


title: H3K27AC-CtrlMO_2

source_name: H3K27AC-CtrlMO_whole embryo

tag: embryonic stage

value: H3K27AC (Active Motif, #39133)


title: breast_cancer_primary_sample_90

description: breast cancer primary tumor


title: breast_cancer_primary_sample_87

description: breast cancer primary tumor


title: breast_cancer_primary_sample_89

description: breast cancer primary tumor


title: breast_cancer_primary_sample_86

description: breast cancer primary tumor


title: Patient 3_lh 14

value: II A

value: yes


title: H3K27AC-CtrlMO_1

value: female

tag: frog type


title: Bap1MO rep3

data_processing:
Next generation sequencing quality was assessed using FastQC (v0.11.3).
Reads were trimmed (if required) and aligned to the Xenopus laevis 9.1 genome (available on Xenbase.org) using STAR (v2.5.2a)
Read counts of RNA-seq data were obtained using HTSeq
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: bigwig

source_name: Bap1MO_whole embryo

growth_protocol: the embryos were obtained by in vitro fertilization

extract_protocol:
RNA was isolated with Trizol/Chloroform, and yolk and pigment were further removed from samples using RNeasy MinElute Cleanup Kit
Libraries were prepared using the NEBNext® Ultra™ kit

value: stage 12

tag: tissue

tag: sequence of mo injected per embryo  - ng


title: Patient 1_lh 55

value: III A

value: negative


title: Rescue Rep3

source_name: Rescue_whole embryo

value: pigmented

value: whole embryo

value: AGCCTTTATTCATGTTGCCTCCTCC-15 + GCCACGATAATTCCACTAGCAATC-7.5 + CCAACTGCATAGCAAGTCTGTGG-7.5

tag: genotype/variation

value: HDAC4 rescue


title: H3K27AC-Bap1MO_1

source_name: H3K27AC-Bap1MO_whole embryo

tag: seq. of mo injected/embryo-ng

tag: chip antibody


title: H3K27AC-Bap1MO_2


title: CtrlMO rep3

source_name: CtrlMO_whole embryo

value: control


title: Rescue Rep2


title: breast_cancer_primary_sample_79

description: breast cancer primary tumor

source_name: FFPE breast cancer


title: breast_cancer_primary_sample_80

description: breast cancer primary tumor


title: Bap1MO rep2

value: Bap1 depleted


title: breast_cancer_primary_sample_81

description: breast cancer primary tumor


title: breast_cancer_primary_sample_78

description: breast cancer primary tumor


title: iPSC3

city: Rochester

first: Patricia

last: Devaux

state: Minnesota

address: 200 First St SW

institute: Mayo Clinic

description: Gene expression data from MV-derived iPSC cells

hyb_protocol: The IVT products were then bead-purified (Affymetrix), fragmented, and hybridized onto Affymetrix U133Plus 2 GeneChips® at 45º C for 16 hours.  Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin,

scan_protocol: GeneChips were scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA).

data_processing:
Control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated using the GeneChipTM Command ConsoleTM Software
The .cel files were processed using Partek Genomics Suite software, version 6.6 Copyright ©; 2017 Partek Inc., St. Louis, MO, USA
The files were normalized using quantile normalization with a log probes using base 2. The differential expression was performed using the ANOVA method in Partek. The scatter plots was generate using R script version 3.1.1. The heatmap was generated using Excel software

source_name: MV-derived iPSC clone 3

label_protocol: RNA quality was assessed by Agilent Bioanalyzer (Agilent Technologies). Reverse transcription to second strand cDNA was generated from 100ng of high quality total RNA.  Subsequently, the products were in vitro transcribed to generate biotin-labeled cRNA

growth_protocol: iPSC were grown in iPSC media until they reach 70-80% confluency in a 6 well plate. BJ cells were grown T75 flask in DMEM-10%FBS-NEAA

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

treatment_protocol: Cells were detach and wash once with PBS then the pellet was resuspended in a solution of trizol

tag: cell type

value: iPSC


title: breast_cancer_primary_sample_77

description: breast cancer primary tumor


title: iPSC1

source_name: MV-derived iPSC clone 1


title: iPSC2

source_name: MV-derived iPSC clone 2


title: breast_cancer_primary_sample_82

description: breast cancer primary tumor


title: breast_cancer_primary_sample_73

description: breast cancer primary tumor


title: breast_cancer_primary_sample_85

description: breast cancer primary tumor


title: breast_cancer_primary_sample_84

description: breast cancer primary tumor


title: breast_cancer_primary_sample_83

description: breast cancer primary tumor


title: breast_cancer_primary_sample_72

description: breast cancer primary tumor


title: breast_cancer_primary_sample_75

description: breast cancer primary tumor


title: CtrlMO rep2


title: breast_cancer_primary_sample_76

description: breast cancer primary tumor


title: Mouse_Testis_Newborn3

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

country: France

institute: CNRS, Université Claude Bernard Lyon 1

data_processing:
Reads were aligned on the corresponding genomes with HISAT2 version 2.0.5.
We used Ensembl release 94 annotations as a reference and we assembled additional gene models with StringTie 1.3.5.
We estimated gene expression levels with Kallisto 0.45.0 (TPM and estimated read counts).
We normalized per.gene TPM levels among samples with a median scaling approach, using the 100 least-varying genes as a reference (Brawand et al., Nature, 2011)
We also computed uniquely mapped read counts using the Rsubread library in R (featureCounts) version 1.32.4, in R version 3.5.
Genome_build: mm10, rn6, galGal5
Supplementary_files_format_and_content: tab-separated files containing TPM and read count values for each gene and sample. Genes are in rows, samples in columns.

source_name: Testis

extract_protocol:
RNA was extracted using the RNeasy plus kit from Qiagen.
Libraries were constructed using  the Illumina TruSeq Stranded mRNA protocol, with polyA selection.

tag: strain

tag: developmental stage

value: newborn (post-natal day 1-2)


title: breast_cancer_primary_sample_74

description: breast cancer primary tumor

tag: grade


title: Rat_Testis_Newborn2

organism: Rattus norvegicus

value: Wistar


title: Patient 2_lh 10

source_name: Classical Hodgkin Lymphoma

tag: subject status

value: patient affected by Hodgkin Lymphoma

tag: gender

value: F

tag: Stage

tag: interim pet response


title: Rat_Testis_LateEmbryo2

value: embryonic day 18.5-19


title: Mouse_Testis_Newborn2


title: Rat_Testis_Newborn1


title: CtrlMO rep1

tag: Sex


title: Mouse_Testis_Newborn1


title: Bap1MO rep1

tag: animal id#


title: Rescue Rep1

tag: embryonic stage


title: Mouse_Testis_LateEmbryo2

value: embryonic day 17-17.5


title: Rat_Testis_LateEmbryo1


title: breast_cancer_primary_sample_71

description: breast cancer primary tumor

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age

value: female


title: breast_cancer_primary_sample_70

description: breast cancer primary tumor


title: breast_cancer_primary_sample_114

description: breast cancer primary tumor


title: breast_cancer_primary_sample_69

description: breast cancer primary tumor


title: Mouse_Testis_Aged1

value: aged adult (24 months)


title: H99-37_degree-input: ccr4 input 37 C

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main St., Suite 5229

department: Microbiology and Immunology

institute: University at Buffalo SUNY

data_processing:
Basecalling and Demultiplexing using bcl2fastq version 2.17.1.14
QC was preformed using FastQC v0.11.5, Fastq_Screen v0.11.1
Adapters were trimmed using cutadapt v1.16
Alignments using hisat2 v.2.1.0 and samtools v1.7
Quantifcation of transcripts using FeatureCounts v1.6.0
Differential Expression and subsequent analysis in DeSeq2
Genome_build: Cryptococcus_neoformans_var._grubii_H99
Supplementary_files_format_and_content: gene quantification text file

organism: Cryptococcus neoformans

source_name: ccr4Δ mutant

growth_protocol: Cells were grown at 30⁰C in YPD, shaking at 250 rpm, until mid-log phase was reached. Half of the samples were resuspended in 37⁰C YPD and incubated at 37⁰C for one hour while the other half remained incubated at 30⁰C.

extract_protocol:
A portion of celared cell lysate was saved for Input samples. The remaining was subjected to sucrose gradient fractionation and polysome profiling. Polysome associated mRNA, defined as the mRNA associated with the 2n polysome peak and above,  was TRIzol extracted and pooled. Input and polysome RNA was then purified by RNeasy Mini column. mRNA was isolated using NEBNext poly(A) mRNA Magnetic Isolation Module.
Libraries were made using NEBNext mRNA Library Prep Master Mix Set for Illumina according to manufacturer’s protocol.

value: ccr4 mutant

tag: tissue

value: yeast cell

tag: fraction

value: total

tag: temperature

value: 37⁰C for one hour


title: Mouse_Testis_Adult2

tag: strain

value: young adult (8-10 weeks)


title: BJ

description: Gene expression data from BJ cells

source_name: neonatal human fibroblasts

tag: cell type

value: neonatal fibroblast


title: Rat_Testis_Aged2

tag: developmental stage


title: H99-A37-Input_TTAGGC: ccr4 input 37 A


title: Mouse_Testis_Adult1


title: Mouse_Testis_Aged2


title: breast_cancer_primary_sample_66

description: breast cancer primary tumor

tag: grade


title: Rat_Testis_Aged1


title: breast_cancer_primary_sample_68

description: breast cancer primary tumor


title: Rat_Testis_Adult2


title: H99-B37-Input_CAGATC: ccr4 input 37 B


title: breast_cancer_primary_sample_111

description: breast cancer primary tumor


title: Rat_Testis_Adult1


title: Mouse_Liver_Newborn2

source_name: Liver


title: breast_cancer_primary_sample_67

description: breast cancer primary tumor


title: Mouse_Liver_Newborn1


title: Rat_Liver_Newborn2


title: breast_cancer_primary_sample_106

description: breast cancer primary tumor


title: Mouse_Testis_LateEmbryo1


title: Mouse_Liver_Newborn3


title: H99-B30-Input_ACAGTG: ccr4 input 30 B


title: breast_cancer_primary_sample_63

description: breast cancer primary tumor


title: H99-30_degree-polysome: ccr4 polysome 30 C

value: polysome associated


title: Rat_Liver_Newborn1


title: Rat_Liver_LateEmbryo2


title: breast_cancer_primary_sample_65

description: breast cancer primary tumor


title: breast_cancer_primary_sample_64

description: breast cancer primary tumor


title: breast_cancer_primary_sample_60

description: breast cancer primary tumor


title: H99-A30-Input_ATCACG: ccr4 input 30 A


title: Rat_Liver_LateEmbryo1


title: ccr4-C37-polysome_CTTGTA: WT polysome 37 C

source_name: Wild type; H99

value: Wild type; H99


title: breast_cancer_primary_sample_62

description: breast cancer primary tumor


title: Mouse_Liver_EarlyEmbryo2

value: embryonic day 13.5


title: Mouse_Liver_LateEmbryo2


title: H99-30_degree-input: ccr4 input 30 C


title: H99-A30-Polysome_CGATGT: ccr4 polysome 30 A


title: Rat_Liver_EarlyEmbryo2

value: embryonic day 15


title: Rat_Liver_EarlyEmbryo1

value: Wistar


title: breast_cancer_primary_sample_58

description: breast cancer primary tumor


title: Mouse_Liver_Aged3


title: breast_cancer_primary_sample_61

description: breast cancer primary tumor


title: H99-B30-Polysome_GCCAAT: ccr4 polysome 30 B


title: ccr4-C37-input_GGCTAC: WT input 37 C


title: Rat_Liver_Aged4

value: aged adult (12 months)


title: breast_cancer_primary_sample_59

description: breast cancer primary tumor


title: Mouse_Liver_EarlyEmbryo1


title: Rat_Liver_Adult2


title: Mouse_Liver_Aged1


title: Rat_Liver_Adult1


title: Rat_Liver_Aged3


title: breast_cancer_primary_sample_55

description: breast cancer primary tumor


title: breast_cancer_primary_sample_54

description: breast cancer primary tumor


title: Rat_Liver_Aged2


title: ccr4-C30-Polysome_TAGCTT: WT polysome 30 C


title: ccr4-B37-Polysome_ACTTGA: WT polysome 37 B


title: Mouse_Liver_Aged4


title: Mouse_Liver_LateEmbryo1


title: ccr4-A37-Polysome_TGACCA: WT polysome 37 A


title: Rat_Kidney_Newborn1

source_name: Kidney

value: newborn (post-natal day 1-2)


title: Rat_Liver_Aged1


title: Rat_Kidney_LateEmbryo2

value: embryonic day 18.5-19


title: breast_cancer_primary_sample_57

description: breast cancer primary tumor


title: breast_cancer_primary_sample_56

description: breast cancer primary tumor


title: Mouse_Liver_Aged2


title: ccr4-A37-Input_TTAGGC: WT input 37 A


title: Mouse_Liver_Adult2


title: ccr4-A30-Polysome_CGATGT: WT polysome 30 A


title: ccr4-B37-Input_CAGATC: WT input 37 B


title: ccr4-C30-Input_GATCAG: WT input 30 C


title: Rat_Kidney_Newborn2


title: Mouse_Liver_Adult1


title: Mouse_Kidney_LateEmbryo2

value: embryonic day 17-17.5


title: ccr4-B30-Polysome_GCCAAT: WT polysome 30 B


title: ccr4-A30-Input_ATCACG: WT input 30 A


title: breast_cancer_primary_sample_50

description: breast cancer primary tumor

value: female


title: Mouse_Kidney_Newborn3


title: Mouse_Kidney_Newborn1


title: Mouse_Kidney_Newborn2


title: Rat_Kidney_EarlyEmbryo2


title: breast_cancer_primary_sample_52

description: breast cancer primary tumor


title: Rat_Kidney_Aged2


title: breast_cancer_primary_sample_49

description: breast cancer primary tumor


title: ccr4-B30-Input_ACAGTG: WT input 30 B


title: Rat_Kidney_EarlyEmbryo1


title: Mouse_Kidney_LateEmbryo1


title: breast_cancer_primary_sample_48

description: breast cancer primary tumor


title: Rat_Kidney_Aged1


title: breast_cancer_primary_sample_51

description: breast cancer primary tumor


title: Mouse_Kidney_EarlyEmbryo2


title: Rat_Kidney_LateEmbryo1


title: breast_cancer_primary_sample_53

description: breast cancer primary tumor


title: Mouse_Kidney_EarlyEmbryo1


title: enNOS-90-mpw-B

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Low quality reads and adaptor sequences were removed using TrimmomaticPE (v. 0.36). Ribosomal and mitochondrial RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Reads were aligned against the Xenbase Xenopus genome version 9.1 using STAR (version 2.5.2b). Count tables were generated to annotation version 1.8.3.2 using htseq-count (v. 0.6.1p1).
Normalized number of reads was generated by DESeq2 using default parameters.
Genome_build: 9.1
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample

source_name: Wounded tissue collected 90 minutes post wounding in embryos injected with morpholinos against nos1 and nos3

growth_protocol: Embryos were grown at 15 °C for 3 days up to the NF stage 26 in 0.1xMBS with addition of gentamicin.

extract_protocol:
RNA was isolated using TRIreagent (Sigma) following the manufacturer's protocol. Diluted RNA was treated with DNAse I solution (Sigma), followed by an overnight reprecipitation during incubation at -20 °C using a 4 M final concentration of  LiCl solution .
RNA-Seq was performed using biological duplicates. Kit from NewEnglandBiolabs (NEB #E7490S) was used for poly-A selection of RNA using 500 ng of total RNA. Libraries were prepared by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7420S) according to manufacturer's protocol and sequenced on the NextSeq 550 in 2x75bp HighOutput mode.

treatment_protocol:
We removed the vitelline membrane one hour before wounding and incubated embryos in 0.1xMBS with gentamicin and TRIM (1-(2-Trifluoromethylphenyl) imidazole, Sigma). TRIM solution was prepared as 1 M stock solution in DMSO and 2 µL per mL were used in final solution.
A 2:1 mix of morpholino-oligonucleotides targeting against nos3 (eNOS) and nos1 (nNOS) was prepared at a final concentration of 17 ng/µL. Two nanolitres of this mix was then injected into the fertilized oocytes.

tag: time after injury

value: 90 min

tag: biological replicate

value: B

tag: treatment

value: nos1 + nos3 morpholino

value: embryo


title: Mouse_Kidney_Aged4

value: aged adult (24 months)


title: enNOS-90-mpw-A

value: A


title: Rat_Kidney_Adult1

value: young adult (8-10 weeks)


title: Rat_Kidney_Adult2


title: Mouse_Kidney_Aged3


title: breast_cancer_primary_sample_45

description: breast cancer primary tumor

tag: Sex


title: Rat_Brain_Newborn2

source_name: Brain


title: enNOS-60-mpw-A

source_name: Wounded tissue collected 60 minutes post wounding in embryos injected with morpholinos against nos1 and nos3

value: 60 min


title: breast_cancer_primary_sample_47

description: breast cancer primary tumor


title: enNOS-30-mpw-B

source_name: Wounded tissue collected 30 minutes post wounding in embryos injected with morpholinos against nos1 and nos3

value: 30 min


title: breast_cancer_primary_sample_46

description: breast cancer primary tumor


title: Mouse_Kidney_Aged1


title: enNOS-30-mpw-A


title: breast_cancer_primary_sample_44

description: breast cancer primary tumor


title: Rat_Brain_Newborn1


title: breast_cancer_primary_sample_43

description: breast cancer primary tumor


title: enNOS-0-mpw-A

source_name: Wounded tissue collected immediately after injury in embryos injected with morpholinos against nos1 and nos3

value: 0 min


title: enNOS-0-mpw-B


title: Rat_Brain_LateEmbryo1


title: Mouse_Kidney_Adult1


title: Rat_Brain_EarlyEmbryo2

value: embryonic day 15


title: Mouse_Brain_Newborn2


title: Rat_Brain_EarlyEmbryo1

value: Wistar


title: Mouse_Brain_Newborn1


title: TRIM-90-mpw-A

source_name: Wounded tissue collected 90 minutes post wounding in embryos treated with TRIM

value: TRIM


title: Rat_Brain_Aged2


title: Mouse_Brain_LateEmbryo2


title: breast_cancer_primary_sample_41

description: breast cancer primary tumor

source_name: FFPE breast cancer


title: Rat_Brain_LateEmbryo2


title: Mouse_Kidney_Aged2


title: Mouse_Kidney_Adult2


title: breast_cancer_primary_sample_37

description: breast cancer primary tumor


title: breast_cancer_primary_sample_38

description: breast cancer primary tumor


title: breast_cancer_primary_sample_42

description: breast cancer primary tumor


title: TRIM-60-mpw-B

source_name: Wounded tissue collected 60 minutes post wounding in embryos treated with TRIM


title: breast_cancer_primary_sample_39

description: breast cancer primary tumor


title: breast_cancer_primary_sample_40

description: breast cancer primary tumor


title: Rat_Brain_Adult2


title: breast_cancer_primary_sample_36

description: breast cancer primary tumor


title: Mouse_Brain_LateEmbryo1


title: Mouse_Brain_EarlyEmbryo2

value: embryonic day 13.5


title: TRIM-60-mpw-A


title: TRIM-30-mpw-B

source_name: Wounded tissue collected 30 minutes post wounding in embryos treated with TRIM


title: Rat_Brain_Adult1


title: TRIM-90-mpw-B


title: TRIM-30-mpw-A


title: breast_cancer_primary_sample_34

description: breast cancer primary tumor


title: breast_cancer_primary_sample_33

description: breast cancer primary tumor


title: breast_cancer_primary_sample_35

description: breast cancer primary tumor


title: Mouse_Brain_Aged1


title: TRIM-0-mpw-A

source_name: Wounded tissue collected immediately after injury in embryos treated with TRIM


title: Mouse_Brain_EarlyEmbryo1


title: delCSSRS, replicate3

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
From each library 4M reads were selected for downstream analysis
Reads were trimmed from their adapter with cutadapt
Alignment to the genome (NCIB 3610, NZ_CM000488.1) was done with Bowtie2 version 2.3.4.1
The number of uniquely mapped reads per gene was calculated with HT-seq
Genome_build: NZ_CM000488.1
Supplementary_files_format_and_content: bam files

organism: Bacillus subtilis

source_name: Biofilms colony

growth_protocol: Biofilms colonies were grown on MSgg solid medium for 24 hours, and colonies (n=3) were collected for RNA extraction.

extract_protocol:
RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) according to the manufacturer’s instructions. RNA levels and integrity were determined by Qubit RNA BR Assay Kit (Life Technologies, Q10210) and Tapestation, respectively.
The samples were snap-frozen in liquid nitrogen and stored at -80°C until extraction. Frozen pellets were lysed by incubation with lysozyme (20 mg/ml) for 10 min at 37°C, and RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) according to the manufacturer’s instructions. RNA levels and integrity were determined by Qubit RNA BR Assay Kit (Life Technologies, Q10210) and Tapestation, respectively. A total of 5 ug RNA was treated with Illumina Ribo-Zero rRNA Removal Kit  (Illumina, RZMB123), according to the manufacturers’ protocols. RNA quantity and quality post-depletion was assessed as described above. RNA-seq libraries were contracted with NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, E7420) according to the manufacturer’s instructions. Libraries concentrations and sizes were evaluated as above, and were sequenced as multiplex indexes in one lane using the Illumina Hiseq1500 platform.

tag: genotype/variation

value: CSSRS gene deletion


title: Mouse_Brain_Adult1


title: delCSSRS, replicate2


title: Mouse_Brain_Adult2


title: Mouse_Brain_Aged2


title: WT, replicate2

value: wild type


title: WT, replicate1


title: WT-90-mpw-B

source_name: Wounded tissue collected 90 minutes post wounding in control embryos

value: control


title: breast_cancer_primary_sample_32

description: breast cancer primary tumor

value: female


title: TRIM-0-mpw-B

value: B


title: breast_cancer_primary_sample_29

description: breast cancer primary tumor


title: delTASA, replicate3

value: TASA gene deletion


title: breast_cancer_primary_sample_30

description: breast cancer primary tumor


title: WT-90-mpw-A

value: 90 min

value: embryo


title: delTASA, replicate2


title: WT-60-mpw-A

source_name: Wounded tissue collected 60 minutes post wounding in control embryos

value: A


title: delTASA, replicate1


title: delCSSRS, replicate1


title: WT-30-mpw-B

source_name: Wounded tissue collected 30 minutes post wounding in control embryos


title: WT-30-mpw-A


title: WT-0-mpw-B

source_name: Wounded tissue collected immediately after injury in control embryos


title: WT-60-mpw-B


title: Wild type 3

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

data_processing:
Reads were trimmed using cutadapt versin 1.17 to remove the Illumina adaptor sequence
The reads were mapped against the Sulfolobus Acidocaldarius DSM639 reference genome using STAR version 2.5.3a
Count tables were generated by RSEM version 1.2.21
Genome_build: Sulfolobus Acidocaldarius DSM639 GCA_000012285.1
Supplementary_files_format_and_content: comma separated values files including  Gene ID, transcript ID, Gene length, predicted length, Expected counts and normalized counts

organism: Sulfolobus acidocaldarius

growth_protocol: cultured in 20 ml Basic Brock supplemented with 0.1 % NZ amine and 0.2 % Sucrose, grown shaking at 75°C

extract_protocol:
At OD 0.4 cells were havested/treated with RNAprotect Bacteria Reagent (Qiagen) and peletted/ total RNA is extracted with RNeasy Mini Kit (Qiagen) in combination with RNase-free DNase Set (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: breast_cancer_primary_sample_28

description: breast cancer primary tumor


title: WT-0-mpw-A


title: breast_cancer_primary_sample_26

description: breast cancer primary tumor


title: breast_cancer_primary_sample_31

description: breast cancer primary tumor


title: breast_cancer_primary_sample_27

description: breast cancer primary tumor


title: breast_cancer_primary_sample_24

description: breast cancer primary tumor


title: 90_mpw_C

source_name: Wounded tissue collected 90 minutes post wounding

extract_protocol:
RNA was isolated using TRIreagent (Sigma) following the manufacturer's protocol. Diluted RNA was treated with DNAse I solution (Sigma), followed by an overnight reprecipitation during incubation at -20 °C using a 4 M final concentration of  LiCl solution .
Libraries were prepared from 200 ng of total RNA using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing (Agilent, G9691) according to the manufacturer's protocol, which includes a polyA selection of RNA. Sequencing was performed on the NextSeq 550 in 2x75bp HighOutput mode.

value: C


title: breast_cancer_primary_sample_25

description: breast cancer primary tumor


title: breast_cancer_primary_sample_23

description: breast cancer primary tumor


title: Overexpression strain 3


title: enNOS-60-mpw-B

value: 60 min

value: nos1 + nos3 morpholino


title: 90_mpw_B


title: Overexpression strain 2


title: Wild type 2


title: 90_mpw_A


title: breast_cancer_primary_sample_22

description: breast cancer primary tumor


title: Wild type 1


title: Control-PC

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

data_processing:
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Strand NGS v2.8 Software.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.25.0; tab-delimited text files include RPKM values for each gene;

source_name: parietal cells

extract_protocol:
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I. Ribosomal RNA (rRNA) was removed from total RNA using Low Input RiboMinus Eukaryote System v2 (Life Technologies).
RNA-seq libraries were prepared for sequencing using Ion Total RNA-Seq Kit v2 and multiplexed by using Ion Xpress™ RNA-seq Barcoding 01-16 Kit according to the manufacturer’s instructions.

value: stomach

value: parietal


title: breast_cancer_primary_sample_21

description: breast cancer primary tumor


title: 60_mpw_C

source_name: Wounded tissue collected 60 minutes post wounding


title: Overexpression strain 1


title: Rat_Brain_Aged1

source_name: Brain

value: Wistar

value: aged adult (24 months)


title: Isomorphic diffuse glioma, sample 25

type: genomic

city: Regensburg

first: Annika

middle: K

last: Wefers

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

description: Methylation data from brain tumor sample

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

label: Cy3 and Cy5

source_name: brain tumor

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE


title: breast_cancer_primary_sample_20

description: breast cancer primary tumor

tag: systemic therapy


title: Mock sample 3

description:
ES1_MS3_peaks.txt
ES2_MS3_peaks.txt
ES3_MS3_peaks.txt

data_processing:
Reads were trimmed using cutadapt versin 1.17 to remove the Illumina adaptor sequence
The reads were mapped against the Sulfolobus Acidocaldarius DSM639 reference genome using Bowtie2 version 2.2.5
The findPeaks program, in the homer suite version 4.10, was used to call the peaks
Genome_build: Sulfolobus Acidocaldarius DSM639 GCA_000012285.1
Supplementary_files_format_and_content: comma separated values files including  generic peak id, chromosome number, start, end, strand and peak intensities parameters

extract_protocol:
Cell lysate clarified for the cells was precipitated with Dynabeads M-280 sheep anti-rabbit IgG beads (Life technologies) and DNA was purified with IPURE DNA extraction kit (Diagenode)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: polyclonal anti- YtrASa rabbit antibodies (Innovagen)


title: HFD-PC


title: Isomorphic diffuse glioma, sample 22


title: 60_mpw_A


title: Mock sample 1

description:
ES1_MS1_peaks.txt
ES2_MS1_peaks.txt
ES3_MS1_peaks.txt


title: Mock sample 2

description:
ES1_MS2_peaks.txt
ES2_MS2_peaks.txt
ES3_MS2_peaks.txt


title: Isomorphic diffuse glioma, sample 19


title: breast_cancer_primary_sample_18

description: breast cancer primary tumor

extract_protocol: After pathologic review, FFPE tissue was harvested with a 1 mm punch. RNA was extracted from tissue punches using the RNeasy FFPE kit (Qiagen, Hilden, Germany).

tag: menopause

tag: tumor size (millimeters)


title: breast_cancer_primary_sample_19

description: breast cancer primary tumor

tag: age


title: 60_mpw_B

tag: tissue


title: breast_cancer_primary_sample_17

description: breast cancer primary tumor


title: 30_mpw_C

source_name: Wounded tissue collected 30 minutes post wounding

value: 30 min


title: Enriched sample 3

description:
ES3_MS1_peaks.txt
ES3_MS2_peaks.txt
ES3_MS3_peaks.txt


title: Enriched sample 2

description:
ES2_MS1_peaks.txt
ES2_MS2_peaks.txt
ES2_MS3_peaks.txt


title: Isomorphic diffuse glioma, sample 16


title: 30_mpw_B


title: 30_mpw_A


title: Enriched sample 1

description:
ES1_MS1_peaks.txt
ES1_MS2_peaks.txt
ES1_MS3_peaks.txt


title: 0_mpw_C

source_name: Wounded tissue collected immediately after injury

value: 0 min


title: Isomorphic diffuse glioma, sample 12


title: EpiDerm FT (RHE), CTL, replicate 1, strip 3

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description:
Gene expression data from CTL-treated RHE cultures.
CTL_S3_3

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Gene 2.1 ST arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by using the Affymetrix GeneTitan system (software version 3.2.4.1515) according to the Affymetrix Expression Analysis Technical Manual.

data_processing: Robust multichip average (RMA) was used to generate expression intensity estimates (R package: oligo; function: rma).

source_name: RHE tissue cultures

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module following the manufacturer's protocol.

growth_protocol: EpiDerm FT (RHE) tissues prepared from neonatal keratinocytes and fibroblasts were obtained from Mattek (Ashland, MA; Cat. No. EFT-412; Lot No. 21452). EpiDerm FT tissues were handled according to the manufacturer’s instructions.

extract_protocol: RNA was extracted and purified with the NucleoSpin RNA kit from Macherey-Nagel (Cat. No. 740955.240C; Bethlehem, PA), using QiaCube robotic station (Qiagen, Germantown, MD).

treatment_protocol: Z test material was purchased from Sigma Aldrich (Cat. No. MKBQ9931; St. Louis, MO) and stored at room temperature. It was dissolved in DMSO at 20 mg/ml on the day of the experiment and further dilutions were made in water. The test concentration was 50 μg/ml. Following a 24 hour equilibration period, RHE tissue culture medium was changed and 50 μg/ml zingerone or water control (CTL) were topically applied in triplicates (25 μl per sample). Following a 24 hour incubation period, tissues were rinsed, collected and preserved in RNAlater solution (Thermo Fisher Scientific, Waltham, MA).

value: CTL

tag: tissue culture

value: EpiDerm FT (RHE)


title: breast_cancer_primary_sample_14

description: breast cancer primary tumor

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE breast cancer

value: female


title: breast_cancer_primary_sample_15

description: breast cancer primary tumor


title: EpiDerm FT (RHE), Z, replicate 1, strip 2

description:
Gene expression data from Z-treated RHE cultures.
Z_S2_2

value: Z


title: Isomorphic diffuse glioma, sample 3


title: breast_cancer_primary_sample_16

description: breast cancer primary tumor


title: EpiDerm FT (RHE), Z, replicate 1, strip 1

description:
Gene expression data from Z-treated RHE cultures.
Z_S1_1


title: Isomorphic diffuse glioma, sample 18


title: 0_mpw_B

value: B

value: embryo


title: Rep3 - gB-CD8 Tim-3-PD-1- [NS3-8]

city: Pittsburgh

first: Anthony

last: St. Leger

state: PA

address: 203 Lothrop St.

institute: University of Pittsburgh

hyb_protocol: Samples were hybridized according to Nanostring protocol.

scan_protocol: Samples were scanned according to Nanostring protocol.

data_processing:
Using the nCounter 4.0 software, the data set was normalized using the included positive controls and housekeeping genes using the default software settings. Also using the nCounter 4.0 software, fold change analysis was performed for each of the three replicates with the reference samples being averaged among the three replicates.
nCounter 4.0 software was used to normalize samples to positive controls and housekeeping genes and perform fold change analysis.

label: nCounter reporter and capture probes

source_name: Trigeminal ganglion 8dp HSV-1 infection

label_protocol: Probes were labeled by Nanostring Technologies (Mouse PanCancer Immune Panel)

extract_protocol: Trigeminal ganglion (TG) from 8dpi mice were excised and digested in 0.2 U/ml Liberase for 50 minutes at 37°C. Digested TGs were triturated into a single cell suspension and filtered through a 35µm filter top flow tube before being stained with a viability dye and antibodies for CD45, CD8, gB Tetramer, PD-1 and, Tim-3. Cells were then FACS sorted into the indicated populations on a BD FACSAria. Sorted populations were pelleted and resuspended in iScript for a concentration of 250 cells/µl followed by vortexing to lyse cells. 1 µl of this cell lysate was amplified by using the nCounter® Low RNA Input Kit (Nanostring) according to manufacturer protocol, using 10 cycles of amplification.

treatment_protocol: 8 week old female C57BL/6 mice were anesthetized and corneas were infected by scarifying the cornea with a 30G needle and administering 1x105 pfu/eye of HSV-1 strain RE.

tag: mouse strain

value: Female

value: 8 weeks

tag: hsv-1 strain

value: RE

tag: infection method

value: Corneal scarification

tag: source of rna

value: Cell Lysates

tag: cell population

value: gB-CD8 Tim-3-PD-1-


title: sin3_B6

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description: Replicate 2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Mapping & QC-mapped with rna-STAR (2.4.1d) & Samtools (0.1.19)
Gene expression analysis with HTSeq-count (Version 0.7.2) & package DESeq2 (1.10.1 using R version 3.2.4)
Genome_build: WS254
Supplementary_files_format_and_content: 4 CSV files containing genes differentially (cfp1 vs WT, set2 vs WT, sin3 vs WT) and raw counts

organism: Caenorhabditis elegans

source_name: The material is RNA extracted from C. elegans embryos using the Nucleozol preparation protocol from Macherey Nagel.

growth_protocol: Nematode strain maintenance was as described previously (Brenner, 1974).

extract_protocol:
RNAs were extracted with NucleoZol [Macherey-Nagel] according to manufacturer’s instructions and treated with DNAse [Turbo-free DNAse, Ambion]. Integrity of RNA was assessed on Tape Station 4200 [Agilent].
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: RNA were extracted from frozen early stage embryos prepared by hypochlorite treatment of young adults

value: embryos

tag: genotype

value: mutant sin3


title: breast_cancer_primary_sample_13

city: Vancouver

first: Laura

last: Chang

institute: PFS Genomics

description: breast cancer primary tumor

tag: grade


title: Rep3 - gB-CD8 Tim-3+PD-1- [NS3-5]

tag: Sex

value: gB-CD8 Tim-3+PD-1-


title: EpiDerm FT (RHE), CTL, replicate 1, strip 2

description:
Gene expression data from CTL-treated RHE cultures.
CTL_S2_2

tag: treatment


title: H99-37_degree-polysome: ccr4 polysome 37 C

source_name: ccr4Δ mutant

tag: strain

value: ccr4 mutant

value: yeast cell

tag: fraction

value: polysome associated

tag: temperature

value: 37⁰C for one hour


title: Isomorphic diffuse glioma, sample 2

tag: material

value: FFPE


title: EpiDerm FT (RHE), CTL, replicate 1, strip 1

description:
Gene expression data from CTL-treated RHE cultures.
CTL_S1_1

value: CTL

value: EpiDerm FT (RHE)


title: H99-B37-Polysome_ACTTGA: ccr4 polysome 37 B


title: cfp1_B4

description: Replicate 2

value: mutant cfp1


title: 0_mpw_A

tag: time after injury

value: 0 min

tag: biological replicate

value: A

value: embryo


title: sin3_B4

description: Replicate 1

tag: tissue


title: breast_cancer_primary_sample_12

description: breast cancer primary tumor

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age

value: female


title: breast_cancer_primary_sample_11

description: breast cancer primary tumor


title: breast_cancer_primary_sample_9

description: breast cancer primary tumor


title: set2_B2

description: Replicate 3

value: mutant set2


title: Rep2 - gB-CD8 Tim-3-PD-1- [NS2-8]

tag: mouse strain

value: Female

value: 8 weeks

tag: hsv-1 strain

value: RE

tag: infection method

value: Corneal scarification

tag: source of rna

value: Cell Lysates

value: gB-CD8 Tim-3-PD-1-


title: Rep3 - Subdom-CD8 Tim-3-PD-1- [NS3-4]

tag: Sex

tag: cell population

value: Subdom-CD8 Tim-3-PD-1-


title: EpiDerm FT (RHE), Z, replicate 1, strip 3

description:
Gene expression data from Z-treated RHE cultures.
Z_S3_3

tag: treatment

value: Z

tag: tissue culture


title: set2_B5

description: Replicate 2

value: embryos

tag: genotype


title: Rep2 - Subdom-CD8 Tim-3-PD-1- [NS2-4]


title: cfp1_B5

description: Replicate 3


title: breast_cancer_primary_sample_10

description: breast cancer primary tumor

tag: grade


title: S_pneumo_dVP1_study_mutant_rep3

first: Rolando

middle: A.

last: Cuevas

state: Pennsylvania

address: 4400 Fifth Avenue, Mellon Institute, Room 217

department: Biological Sciences

institute: Carnegie Mellon University

description: This sample is of dVP1 deletion mutant Streptococcus pneumoniae PN4595-T23. It is the third of three biological deletion mutant  replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen hybridization kit components as per the NimbleGen Arrays User's Guide, Gene Expression Analysis Version 6.0

scan_protocol: Scanning was performed using manufacrturer's array software, NimbleScan as per the user's guide

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package

organism: Streptococcus pneumoniae

source_name: Clinical strain PN4594-T23

label_protocol: Labeling was performed using NimbleGen One Color DNA Labeling Kit as per the NimbleGen Arrays User's Guide, Gene Expression Analysis Version 6.0

growth_protocol: Streptococcus pneumoniae was grown to mid-log phase (O.D.600nm 0.3) in CDM media supplemented with 55.5 mM of glucose at 37 degrees C with 5% CO2, without shaking.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by Turbo DNase digestion (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Streptococcus pneumoniae vp1 deletion mutant was grown to mid-log phase (O.D.600nm 0.3) in CDM media supplemented with 55.5 mM of glucose at 37 degrees C with 5% CO2, without shaking.

tag: media

value: CDM-Glucose

value: Liquid culture

value: Deletion of vp1 (SPN23F_01520)


title: Rep3 - Subdom-CD8 Tim-3+PD-1- [NS3-1]

value: Subdom-CD8 Tim-3+PD-1-


title: S_pneumo_dVP1_study_mutant_rep1

description: This sample is of dVP1 deletion mutant Streptococcus pneumoniae PN4595-T23. It is the first of three biological deletion mutant  replicates used in this experiment, each from separate cultures.


title: H99-A37-Polysome_TGACCA: ccr4 polysome 37 A

tag: strain

value: ccr4 mutant

value: yeast cell

tag: fraction

value: polysome associated

tag: temperature

value: 37⁰C for one hour


title: WT_B3

description: Replicate 3

tag: tissue

value: WT


title: cfp1_B2

description: Replicate 1

value: mutant cfp1


title: Rep1 - gB-CD8 Tim-3-PD-1- [NS1-8]

value: Female

value: 8 weeks

value: RE


title: Rep2 - gB-CD8 Tim-3+PD-1- [NS2-5]

value: Corneal scarification

value: Cell Lysates

value: gB-CD8 Tim-3+PD-1-


title: set2_B1

description: Replicate 1

value: embryos

value: mutant set2


title: Rep2 - Subdom-CD8 Tim-3+PD-1- [NS2-1]


title: S_pneumo_dVP1_study_mutant_rep2

description: This sample is of dVP1 deletion mutant Streptococcus pneumoniae PN4595-T23. It is the second of three biological deletion mutant  replicates used in this experiment, each from separate cultures.

value: CDM-Glucose

value: Liquid culture


title: Rep1 - gB-CD8 Tim-3+PD-1- [NS1-5]


title: Col_Light_2

status: Public on Sep 25 2019

city: Austin

first: Enamul

last: Huq

state: TX

address: 205 West 24th

department: IB

institute: University of Texas at Austin

description: rRNA depleted RNA lib

data_processing:
tophat2 to align the reads to the genome
Cufflink2 to calculate the differential gene expression
ASpli to calculate the splicing activities: https://bioconductor.org/packages/release/bioc/vignettes/ASpli/inst/doc/ASpli.pdf
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM to quantify the gene expression; PSI/PIR(percentages) to quantify the splicing activities
Supplementary_files_format_and_content: Supplemental_dataset1_DGE.xlsx: excel file including the gene differential expression analysis from cufflink2. Ⅰ. CR_D_DGE: differential gene expression analysis between Col-0 wild type and rrc1 mutant in the dark condition. Ⅱ. GO_CR_D_DGE: Go term enrichment analysis of  CR_D_DGE. Ⅲ. CR_L_DGE: differential gene expression analysis between Col-0 wild type and rrc1 mutant in the light condition. Ⅳ. GO_CR_L_DGE: Go term enrichment analysis of  CR_L_DGE. Ⅴ. R_DL_DGE: differential gene analysis between rrc1 dark and rrc1 light samples.VI. phenotypic_genes_D: The genes related to rrc1  phenotype in the gene list  CR_D_DGE. VII. phenotypic_genes_L: The genes related to rrc1  phenotype in the gene list  CR_L_DGE.
Supplementary_files_format_and_content: Supplemental_dataset2_AS.xlsx: excel file including the gene differential  splicing analysis using Aspli (Including the raw counts of the splicing junction reads and PSI(percentage of exon splicing in)/PIR(percentage of intron retention. More details are included in the documents of ASpli): Ⅰ. CR_D_AS: differential splicing analysis between Col-0 wild type and rrc1 dark sample. Ⅱ. GO_CR_D_AS.agri_go: go term enrichment analysis based on gene list in CR_D_AS. Ⅲ. CR_L_AS: differential splicing analysis between Col-0 wild type and rrc1 light sample. Ⅳ. GO_CR_L_AS.agri_go: go term enrichment analysis based on gene list in CR_L_AS. Ⅴ. R_DL_AS: differential splicing analysis between rrc1 dark and rrc1 light sample. Ⅵ. CR_D_AS_pathway：pathway enrichment analysis based on gene list in CR_D_AS. Ⅶ. CR_L_AS_pathway: pathway enrichment analysis based on gene list in CR_L_AS. Ⅷ. phenotypic_genes_D: genes related to the rrc1 phenotype in gene list in CR_D_AS. Ⅸ. phenotypic_genes_L: genes related to the rrc1 phenotype in gene list in CR_L_AS.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 1/2 MS media, grew under dark conditions for 4 days

extract_protocol:
Based on the commercial protocol of the RNA extraction kit (RNeasy Mini Kit (50) from QIAGEN)
based on the commercial protocol of NEB RNA library construction kit(NEBNext® Ultra™ DNA Library Prep Kit for Illumina)

treatment_protocol: 4 days dark grown seedling, irradiated with 7 μmolm-2s-1 red light for 3hrs

value: seedlings

tag: developmental stage

value: 4 days

tag: growth/treatment

value: Grown under dark conditions for 4 days, then irradiated with red light for 3hrs

tag: genotype/variation

value: wild type

tag: cultivar/background


title: WT_B1

description: Replicate 1


title: S_pneumo_dVP1_study_wildtype_rep1

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the first of three biological wild-type replicates used in this experiment, each from separate cultures.

value: wild-type


title: S_pneumo_dVP1_study_wildtype_rep2

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the second of three biological wild-type replicates used in this experiment, each from separate cultures.


title: Rep1 - Subdom-CD8 Tim-3-PD-1- [NS1-4]

tag: mouse strain

tag: age

tag: hsv-1 strain

tag: infection method

value: Subdom-CD8 Tim-3-PD-1-


title: Col_Dark_2

description: rRNA depleted RNA lib

value: Grown under dark conditions for 4 days


title: Col_Light_3

description: rRNA depleted RNA lib


title: breast_cancer_primary_sample_3

address: 1152 Mainland St, Suite 430

description: breast cancer primary tumor

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: Sex

value: female


title: breast_cancer_primary_sample_7

description: breast cancer primary tumor

tag: grade


title: breast_cancer_primary_sample_6

description: breast cancer primary tumor


title: breast_cancer_primary_sample_5

description: breast cancer primary tumor


title: S_pneumo_dVP1_study_wildtype_rep3

description: This sample is of wild-type Streptococcus pneumoniae PN4595-T23. It is the third of three biological wild-type replicates used in this experiment, each from separate cultures.

tag: media

tag: genotype


title: breast_cancer_primary_sample_4

description: breast cancer primary tumor


title: Col_Light_1

description: rRNA depleted RNA lib


title: Rep1 - Subdom-CD8 Tim-3+PD-1- [NS1-1]

value: Female

value: 8 weeks

tag: source of rna

tag: cell population

value: Subdom-CD8 Tim-3+PD-1-


title: breast_cancer_primary_sample_1

description: breast cancer primary tumor


title: Col_Dark_1

description: rRNA depleted RNA lib

tag: tissue

tag: developmental stage


title: HeLa_nonCSC, miRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: HeLa, nonCSC

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HeLa cells transfected with ZsGreen-cODCdegron were cultured in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol: ISOGEN was used for extracting total RNA

tag: cell line

value: HeLa

tag: cell type

value: non-cancer stem cells

tag: transfection

value: ZsGreen-cODCdegron


title: Col_Dark_3

description: rRNA depleted RNA lib

tag: growth/treatment

tag: genotype/variation

tag: cultivar/background


title: WT_B2

description: Replicate 2

value: embryos

value: WT


title: 1030

city: Paris

first: ROBERTA

last: CODATO

address: 35 rue Hélène Brion

institute: Paris Diderot University - UMR 7216 Epigenetics and Cell Fate

data_processing:
Illumina Nextseq 500 instrument
Quality of FASTQ files was assessed using FASTQC software (version FastQC-v0.11.5)
Reads were aligned using hisat2 to the Mus_musculus.GRCm38.dna (version hisat2-2.1.0) . no multialignment
Reads were then count using Featurecount (version subread-1.6.3)
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count

extract_protocol:
Total RNA was harvested using NucleoSpin RNA Kit (Machery Nagel) or TRIzol (Invitrogen). The quality of the RNA (RNA integrity number) was determined on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
TruSeq Stranded mRNA kit (Illumina) was used with 100 to 200ng of total RNA for the construction of sequencing libraries.

tag: differentiation timepoint

tag: treatment

tag: rna extraction protocol

value: NucleoSpin RNA Kit


title: 847

value: TRIzol


title: 1033


title: 910

value: SMYD3 overexpression (pREV-SMYD3 CL5)


title: 872


title: 1024


title: 917


title: 868


title: 841


title: 1021


title: 1029


title: HeLa_CSC, miRNA

source_name: HeLa, CSC

value: cancer stem cells


title: 1020


title: breast_cancer_primary_sample_8

description: breast cancer primary tumor

tag: systemic therapy

tag: menopause

tag: tumor size (millimeters)

tag: age

tag: Sex


title: 1023


title: breast_cancer_primary_sample_2

description: breast cancer primary tumor

tag: grade


title: 1032


title: 1022

value: siCtrl


title: 940

value: Empty vector (pREV)


title: 843


title: 1031


title: 1028


title: 849


title: 1019


title: 937


title: 842


title: 870


title: 848


title: 867