title: High dose3

city: Suwon

first: Gwang

last: Lee

state: Yeongtong-gu

address: 206 Worldcup-ro

department: Department of Physiology and Department of Biomedical Sciences

institute: Ajou University

description:
0.1 µg/µl MNPs@SiO2(RITC)
TN1603R0720

data_processing:
In the RNA-seq data, low quality reads were filtered according to the following criteria: reads containing more than 10% of skipped bases, reads containing more than 40% of bases whose quality scores are less than 20, and reads whose average quality scores of each read is less than 20.
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell et al., 2012), using the gene annotation database of Ensembl release 77.
To improve the accuracy of measurement, multi-read-correction and fragbias- correct options were applied.
All other options were set to default values.
Differentially expressed genes were identified using Cuffdiff tool with default parameter setting with a significance of p value < 0.05.
Genome_build: The whole filtering process was performed using in-house scripts. Filtered reads were mapped to the mouse reference genome for sequence alignment using the aligner Tophat (Trapnell et al, 2012).
Supplementary_files_format_and_content: FPKM

source_name: in vitro cultured cells

extract_protocol:
BV2 cells were treated with 0.01 and 0.1 µg/µl of MNPs@SiO2(RITC) for 12 h, lysed, and total RNA was isolated with TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA). RNA quality was analyzed by rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA).
cDNA library was constructed from 1 µg of total RNA. Magnetic beads conjugated with Oligo (dT) were used to enrich poly A tailed mRNA. Purified mRNAs were fragmented into short fragments, and double-stranded cDNAs were synthesized. The cDNAs were modified with end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). cDNA fragments were purified with BluePippin (Sage Science, MA) and amplified by PCR.

value: Microglia

tag: cell line

tag: treatment

value: 0.1 microg/microl MNPs@SiO2(RITC)


title: Sample 158

status: Public on Aug 18 2021

type: RNA

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

country: USA

institute: SUNY Upstate Medical University

description: human breast tumor RNA

hyb_protocol: standard

scan_protocol: Labelled cRNAs were fragmented to an average size of approximately 50–100 nucleotides by heating at 60 °C in the presence of 10 mM ZnCl2, added to a hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM MES, pH 6.5, and formamide to a final concentration of 30%, final volume 3 ml at 40 °C. Hu25K microarrays represented the 24,479 biological oligonucleotides plus 1,281 control probes. Sequences for microarrays were selected from RefSeq (a collection of non-redundant mRNA sequences; http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) and from expressed sequence tag (EST) contigs (http://www.phrap.org/est_assembly/human/gene_number_methods.html). Each mRNA or EST contig was represented on the Hu25K microarray by a single 60-polymer oligonucleotide chosen by the oligonucleotide probe design programme. After hybridization, slides were washed and scanned using a confocal laser scanner (Agilent Technologies). Fluorescence intensities on scanned images were quantified, corrected for background noise and normalized.

data_processing:
Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes.
Batch effect correction using the Kolmogorov-Smirnov weighted mean method was used to reduce variability between patients. Patients were first categorized into batches. Then, for each probe, Kolmogorov-Smirnov statistics were calculated for every batch permutation. Weights were calculated by using the sum normalized sums of the KS distance matrix. Weights were used to calculate the weighted mean expression value of the given probe. Weighted average mean correction was then performed on each batch.

molecule: total RNA

organism: Homo sapiens

source_name: pool of individual breast tumors

label_protocol: cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 µg total RNA and labelled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech). Five micrograms of Cy-labelled cRNA from one breast cancer tumour was mixed with the same amount of reverse colour Cy-labelled product from a pool, which consisted of an equal amount of cRNA from each individual sporadic patient

extract_protocol:
The criteria for the sporadic patients (n = 97) were: primary invasive breast carcinoma less than 5 cm (T1 or T2), no axillary metastases (N0), age at diagnosis less than 55 years, calendar year of diagnosis 1983–1996, no previous malignancies; all patients were treated by modified radical mastectomy (n = 35) or breast-conserving treatment (n = 62), including axillary lymph node dissection followed by radiotherapy. Five patients of the metastases group received adjuvant systemic therapy consisting of chemotherapy (n = 3) or hormonal therapy (n = 2), all other patients did not receive additional treatment. All patients were followed at least annually for a period of at least 5 years. The criteria for hereditary patients (n = 20) were: carriers of a germline mutation in BRCA1 or BRCA2, and primary invasive breast carcinoma; no other selection criterion was applied. This study was approved by the Medical Ethical Committee of the Netherlands Cancer Institute.
Tumour material was snap-frozen in liquid nitrogen within 1 h after surgery. A haematoxylin and eosin stained section was prepared before and after cutting slides for RNA isolation for assessment of the percentage of tumour cells. Only samples with greater than 50% tumour cells were selected, mean 67% and median 70% for all groups studied. Formalin-fixed, paraffin-embedded tumour tissue was used to evaluate the following: tumour type (according to the World Health Organisation classification), histological grade (grade 1–3), and the presence of angioinvasive growth and extensive lymphocytic infiltrate. ER expression was determined by immunohistochemical staining (negative when less than 10% of the nuclei showed staining, all others ER positive).
We used 30 sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with RNAzolB, and finally dissolved in RNase-free H2O. Twenty-five micrograms of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 µg µl-1.

tag: tissue

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 249

type: genomic

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description: umbilical cord blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

molecule: genomic DNA

source_name: umbilical cord blood 249

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 246

description: umbilical cord blood sample

source_name: umbilical cord blood 246

value: Female


title: genomic DNA from umbilical cord bood 244

description: umbilical cord blood sample

source_name: umbilical cord blood 244


title: High dose2

type: SRA

country: South Korea

description:
0.1 µg/µl MNPs@SiO2(RITC)
TN1603R0719

library_source: transcriptomic

organism: Mus musculus

tag: cell type

tag: cell line

tag: treatment


title: genomic DNA from umbilical cord bood 245

description: umbilical cord blood sample

source_name: umbilical cord blood 245


title: High dose1

description:
0.1 µg/µl MNPs@SiO2(RITC)
TN1603R0718


title: genomic DNA from umbilical cord bood 243

description: umbilical cord blood sample

source_name: umbilical cord blood 243


title: genomic DNA from umbilical cord bood 241

description: umbilical cord blood sample

source_name: umbilical cord blood 241


title: Sample 156

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: metastatis

value: Meta-

value: Alive

value: ER+


title: Low dose3

description:
0.01 µg/µl MNPs@SiO2(RITC)
TN1603R0717

value: 0.01 microg/microl MNPs@SiO2(RITC)


title: genomic DNA from umbilical cord bood 240

description: umbilical cord blood sample

source_name: umbilical cord blood 240


title: Control BSO rep2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: run0347_lane9_read*_indexN706-S517=Ctrl-BSO-48h-2.fastq.gz

data_processing:
RNA-Seq data were pseudoaligned and quantified (transcript per million estimates) using a call to the software Kallisto within AltAnalyze version 2.1.4 and an Ensembl version 72 reference database.
Genome_build: mm10
Supplementary_files_format_and_content: exp.db-BSO.txt

source_name: SLAM HSC cultured with BSOfor 48hrs

growth_protocol: 1,000 HSC-SLAMs were isolated from db and littermate control mice and cultured for 48h in StemSpan media (StemCell Technologies) with cytokines (SCF 20 ng/mL; TPO 20 ng/mL).

extract_protocol:
After culture, cells were washed with phosphate-buffered saline (PBS), and collected for RNA isolation.
The cDNA synthesis and amplification were done as recommended by Clontech. cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents. Fragmented and tagged libraries were quantified using an agilent bio-analyzer, pooled and sequenced on a HiSeq 2500 platform (Illumina) using the pair-end 75-bp sequencing strategy.

treatment_protocol: Cells were cultured in the presence or absence of BSO (100 µM). After culture, cells were washed with phosphate-buffered saline (PBS), and collected for RNA isolation.

value: SLAM HSC

tag: age

value: 4 months old

tag: treatement

value: buthionine sulfoximine


title: Sample 153

description: human breast tumor RNA

value: LN-

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 242

description: umbilical cord blood sample

source_name: umbilical cord blood 242


title: Low dose2

description:
0.01 µg/µl MNPs@SiO2(RITC)
TN1603R0716

value: Microglia


title: Sample 157

description: human breast tumor RNA

value: breast tumor

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 151

description: human breast tumor RNA

value: LN+

tag: conservflag


title: genomic DNA from umbilical cord bood 233

description: umbilical cord blood sample

source_name: umbilical cord blood 233

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 239

description: umbilical cord blood sample

source_name: umbilical cord blood 239


title: Sample 155

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Meta+


title: Low dose1

description:
0.01 µg/µl MNPs@SiO2(RITC)
TN1603R0715

tag: cell type

tag: cell line

tag: treatment


title: genomic DNA from umbilical cord bood 237

description: umbilical cord blood sample

source_name: umbilical cord blood 237


title: genomic DNA from umbilical cord bood 231

description: umbilical cord blood sample

source_name: umbilical cord blood 231


title: genomic DNA from umbilical cord bood 236

description: umbilical cord blood sample

source_name: umbilical cord blood 236


title: genomic DNA from umbilical cord bood 238

description: umbilical cord blood sample

source_name: umbilical cord blood 238


title: genomic DNA from umbilical cord bood 227

description: umbilical cord blood sample

source_name: umbilical cord blood 227


title: genomic DNA from umbilical cord bood 232

description: umbilical cord blood sample

source_name: umbilical cord blood 232


title: Sample 150

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: metastatis

tag: death

value: Dead

tag: timesurvival(years)


title: genomic DNA from umbilical cord bood 230

description: umbilical cord blood sample

source_name: umbilical cord blood 230


title: Control3

source_name: in vitro cultured cells

value: non-treated control


title: genomic DNA from umbilical cord bood 229

description: umbilical cord blood sample

source_name: umbilical cord blood 229


title: genomic DNA from umbilical cord bood 225

description: umbilical cord blood sample

source_name: umbilical cord blood 225

value: Male


title: Control2


title: genomic DNA from umbilical cord bood 228

description: umbilical cord blood sample

source_name: umbilical cord blood 228

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 235

description: umbilical cord blood sample

source_name: umbilical cord blood 235

value: Female


title: Control1


title: Sample 149

description: human breast tumor RNA

value: Meta-

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

value: ER-


title: Sample 148

description: human breast tumor RNA

value: Alive

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+


title: genomic DNA from umbilical cord bood 226

description: umbilical cord blood sample

source_name: umbilical cord blood 226


title: RNAseq FoxA1-Hnf4a induced rep3

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

data_processing:
We aligned transcripts using Salmon (Patro et al. 2017) with default parameters.
We filtered out any transcripts with fewer than 10 reads.
We called differentially expressed transcripts with DeSeq2 (Love et al. 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Transcript count files from Salmon are in .tar.gz format.

molecule: polyA RNA

source_name: RNAseq FoxA1-Hnf4a induced

growth_protocol: We derived clonal FoxA1, Hnf4a, and FoxA1-Hnf4a lines by transducing K562 lymphoblast cells (ATCC CCL-243) with lentiviral constructs. We then cultured lines in IMDM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% non-essential amino acids at 37C.

extract_protocol:
We extracted RNA from 1e6 cells/sample using the PureLink RNA Mini column extraction kit (Invitrogen #12183020) and completed on-column DNA digestion with PureLink DNase (Invitrogen #12185010).
We generated libraries by following the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7765S) and then size selected the libraries with AmpureXP beads.

treatment_protocol: We induced transgene expression by treating cells for 24 hours with 0.5µg/ml doxycycline.

tag: cell line background

value: Immortalized lymphoblast

tag: genotype

value: FoxA1-Hnf4a doxycycline-inducible clonal line

value: 0.5ug/ml doxycycline for 24 hours


title: Sample 147

description: human breast tumor RNA

tag: nih

tag: stgallen

tag: conservflag


title: Sample 146

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes


title: RNAseq FoxA1-Hnf4a induced rep2

tag: cell type

tag: treatment


title: genomic DNA from umbilical cord bood 224

description: umbilical cord blood sample

source_name: umbilical cord blood 224

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 234

description: umbilical cord blood sample

source_name: umbilical cord blood 234


title: Sample 145

description: human breast tumor RNA

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years


title: genomic DNA from umbilical cord bood 222

description: umbilical cord blood sample

source_name: umbilical cord blood 222


title: genomic DNA from umbilical cord bood 223

description: umbilical cord blood sample

source_name: umbilical cord blood 223


title: genomic DNA from umbilical cord bood 221

description: umbilical cord blood sample

source_name: umbilical cord blood 221


title: RNAseq FoxA1-Hnf4a induced rep1


title: Sample 154

description: human breast tumor RNA

value: LN-

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: RNAseq FoxA1-Hnf4a uninduced rep3

source_name: RNAseq FoxA1-Hnf4a uninduced

tag: cell line background

tag: genotype

value: none (uninduced)


title: Sample 144

description: human breast tumor RNA

value: breast tumor

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: Sample 142

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes


title: genomic DNA from umbilical cord bood 219

description: umbilical cord blood sample

source_name: umbilical cord blood 219

tag: gender

tag: sample type


title: RNAseq FoxA1-Hnf4a uninduced rep1

tag: cell type

tag: treatment


title: genomic DNA from umbilical cord bood 217

description: umbilical cord blood sample

source_name: umbilical cord blood 217


title: genomic DNA from umbilical cord bood 218

description: umbilical cord blood sample

source_name: umbilical cord blood 218


title: Sample 140

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years


title: RNAseq Hnf4a induced rep3

source_name: RNAseq Hnf4a induced

value: Hnf4a doxycycline-inducible clonal line


title: Sample 141

description: human breast tumor RNA

value: Meta+

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 215

description: umbilical cord blood sample

source_name: umbilical cord blood 215


title: Sample 139

description: human breast tumor RNA

tag: estrogen-receptor

tag: nih


title: RNAseq FoxA1-Hnf4a uninduced rep2

tag: cell line background

tag: genotype


title: RNAseq Hnf4a induced rep2


title: Sample 138

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Dead

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 220

description: umbilical cord blood sample

source_name: umbilical cord blood 220

tag: gender

tag: sample type


title: RNAseq Hnf4a induced rep1

tag: cell type

tag: treatment


title: genomic DNA from umbilical cord bood 211

description: umbilical cord blood sample

source_name: umbilical cord blood 211


title: Sample 137

description: human breast tumor RNA

value: LN+

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years


title: RNAseq Hnf4a uninduced rep3

source_name: RNAseq Hnf4a uninduced


title: genomic DNA from umbilical cord bood 209

description: umbilical cord blood sample

source_name: umbilical cord blood 209

value: Male


title: genomic DNA from umbilical cord bood 208

description: umbilical cord blood sample

source_name: umbilical cord blood 208

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 206

description: umbilical cord blood sample

source_name: umbilical cord blood 206


title: RNAseq Hnf4a uninduced rep2


title: genomic DNA from umbilical cord bood 210

description: umbilical cord blood sample

source_name: umbilical cord blood 210


title: genomic DNA from umbilical cord bood 214

description: umbilical cord blood sample

source_name: umbilical cord blood 214


title: genomic DNA from umbilical cord bood 207

description: umbilical cord blood sample

source_name: umbilical cord blood 207

value: Female


title: genomic DNA from umbilical cord bood 205

description: umbilical cord blood sample

source_name: umbilical cord blood 205


title: Sample 136

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 213

description: umbilical cord blood sample

source_name: umbilical cord blood 213


title: genomic DNA from umbilical cord bood 212

description: umbilical cord blood sample

source_name: umbilical cord blood 212


title: RNAseq Hnf4a uninduced rep1

tag: cell line background

tag: genotype


title: Sample 135

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Meta-

tag: estrogen-receptor

tag: nih


title: RNAseq FoxA1 induced rep3

source_name: RNAseq FoxA1 induced

value: FoxA1 doxycycline-inducible clonal line


title: genomic DNA from umbilical cord bood 199

description: umbilical cord blood sample

source_name: umbilical cord blood 199

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 203

description: umbilical cord blood sample

source_name: umbilical cord blood 203


title: Sample 134

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 201

description: umbilical cord blood sample

source_name: umbilical cord blood 201


title: RNAseq FoxA1 induced rep2

tag: cell type

tag: treatment


title: Sample 133

description: human breast tumor RNA

tag: metastatis

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years


title: genomic DNA from umbilical cord bood 202

description: umbilical cord blood sample

source_name: umbilical cord blood 202


title: genomic DNA from umbilical cord bood 204

description: umbilical cord blood sample

source_name: umbilical cord blood 204


title: genomic DNA from umbilical cord bood 200

description: umbilical cord blood sample

source_name: umbilical cord blood 200


title: genomic DNA from umbilical cord bood 196

description: umbilical cord blood sample

source_name: umbilical cord blood 196


title: RNAseq FoxA1 induced rep1


title: Sample 132

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

value: ER+


title: RNAseq FoxA1 uninduced rep3

source_name: RNAseq FoxA1 uninduced

tag: cell line background

value: Immortalized lymphoblast

tag: genotype


title: genomic DNA from umbilical cord bood 198

description: umbilical cord blood sample

source_name: umbilical cord blood 198


title: RNAseq FoxA1 uninduced rep2


title: genomic DNA from umbilical cord bood 195

description: umbilical cord blood sample

source_name: umbilical cord blood 195


title: Sample 130

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: estrogen-receptor

value: ER-

tag: nih


title: Sample 131

description: human breast tumor RNA

tag: stgallen

tag: conservflag


title: RNAseq FoxA1 uninduced rep1

tag: cell type

tag: treatment


title: genomic DNA from umbilical cord bood 216

description: umbilical cord blood sample

source_name: umbilical cord blood 216

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 193

description: umbilical cord blood sample

source_name: umbilical cord blood 193


title: Sample 129

description: human breast tumor RNA

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years


title: Sample 128

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 188

description: umbilical cord blood sample

source_name: umbilical cord blood 188


title: genomic DNA from umbilical cord bood 192

description: umbilical cord blood sample

source_name: umbilical cord blood 192


title: CUTTag FoxA1-Hnf4a induced +Hnf4a ab rep2

library_source: genomic

data_processing:
Library strategy: CUT&Tag
We aligned transcripts with bowtie2 using recommended parameters (Kaya-Okur et al. 2020): --very-sensitive --end-to-end --no-mixed --no-discordant -I 10 -X700.
We used DeepTools bamCoverage (Ramirez et al. 2016) to generate RPKM normalized bigwig coverage files.
We called peaks with macs2 with p=1e-5.
We combined overlapping peaks from replicate samples with bedtools intersect.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files from macs2 are in .narrowPeak format.

source_name: CUTTag FoxA1-Hnf4a induced

extract_protocol:
We isolated 1e5 cells/sample and then followed the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher).
We generated libraries by following the CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher) and then size selected the libraries with AmpureXP beads.

tag: cell line background

tag: genotype

value: FoxA1-Hnf4a doxycycline-inducible clonal line

value: 0.5ug/ml doxycycline for 24 hours

tag: primary antibody

value: Mouse anti-human Hnf4a monoclonal (Invitrogen #MA1-199)

tag: secondary antibody

value: Goat anti-mouse (Epicypher #13-0048)


title: CUTTag FoxA1-Hnf4a induced +Hnf4a ab rep1


title: genomic DNA from umbilical cord bood 190

description: umbilical cord blood sample

source_name: umbilical cord blood 190


title: genomic DNA from umbilical cord bood 197

description: umbilical cord blood sample

source_name: umbilical cord blood 197


title: genomic DNA from umbilical cord bood 191

description: umbilical cord blood sample

source_name: umbilical cord blood 191


title: CUTTag FoxA1-Hnf4a induced +FoxA1 ab rep2

value: Rabbit anti-human FoxA1 monoclonal (Cell Signaling #53528)

value: Goat anti-rabbit (Epicypher #13-0047)


title: Sample 126

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: tissue

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

value: LN-

value: Meta+

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: Sample 127

description: human breast tumor RNA

value: LN+

tag: metastatis

tag: death


title: genomic DNA from umbilical cord bood 189

description: umbilical cord blood sample

source_name: umbilical cord blood 189

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: CUTTag FoxA1-Hnf4a induced +FoxA1 ab rep1

tag: cell type

tag: treatment


title: Sample 125

description: human breast tumor RNA

value: Meta-

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 186

description: umbilical cord blood sample

source_name: umbilical cord blood 186

value: Female


title: Sample 124

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Alive

value: ER+


title: genomic DNA from umbilical cord bood 181

description: umbilical cord blood sample

source_name: umbilical cord blood 181


title: genomic DNA from umbilical cord bood 184

description: umbilical cord blood sample

source_name: umbilical cord blood 184


title: genomic DNA from umbilical cord bood 187

description: umbilical cord blood sample

source_name: umbilical cord blood 187


title: CUTTag Hnf4a induced +Hnf4a ab rep1

source_name: CUTTag Hnf4a induced

tag: cell line background

value: Immortalized lymphoblast

tag: genotype

value: Hnf4a doxycycline-inducible clonal line

tag: primary antibody

tag: secondary antibody


title: CUTTag Hnf4a induced +Hnf4a ab rep2

value: 0.5ug/ml doxycycline for 24 hours


title: Sample 123

description: human breast tumor RNA

tag: metastatis

tag: death

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 180

description: umbilical cord blood sample

source_name: umbilical cord blood 180

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 178

description: umbilical cord blood sample

source_name: umbilical cord blood 178


title: CUTTag FoxA1 induced +FoxA1 ab rep2

source_name: CUTTag FoxA1 induced

tag: cell type

value: FoxA1 doxycycline-inducible clonal line

tag: treatment


title: genomic DNA from umbilical cord bood 194

description: umbilical cord blood sample

source_name: umbilical cord blood 194


title: Sample 122

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 182

description: umbilical cord blood sample

source_name: umbilical cord blood 182


title: CUTTag FoxA1 induced +FoxA1 ab rep1

tag: cell line background

tag: genotype

tag: primary antibody

tag: secondary antibody


title: ATACseq FoxA1-Hnf4a induced rep2

data_processing:
We aligned transcripts with bowtie2 with the parameters: --local -X2000.
We used DeepTools bamCoverage (Ramirez et al. 2016) to generate RPKM normalized bigwig coverage files.
We called peaks at low stringency using macs2 with p=0.01.
We called reproducible peaks at an FDR of 0.05 with IDR.
We called differential peaks with DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files from macs2 are in .narrowPeak format.

source_name: ATACseq FoxA1-Hnf4a induced

extract_protocol:
We followed the OMNI-ATAC protocol (Corces et al. 2017) to extract 5e4 nuclei from 2e5 isolated cells/sample.
We generated libraries by following the OMNI-ATAC protocol (Corces et al. 2017) and then size selected the libraries with AmpureXP beads.

value: FoxA1-Hnf4a doxycycline-inducible clonal line


title: Sample 75

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: metastatis

tag: death

value: Dead

tag: estrogen-receptor

value: ER-

tag: nih


title: genomic DNA from umbilical cord bood 185

description: umbilical cord blood sample

source_name: umbilical cord blood 185

tag: gender

tag: sample type


title: Sample 76

description: human breast tumor RNA

value: breast tumor

tag: timesurvival(years)

tag: survival-years

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 183

description: umbilical cord blood sample

source_name: umbilical cord blood 183


title: Adjacent normal skin tissue of patient C

city: Hangzhou

first: Xi

last: Chu

address: 261 Huansha Road

country: China

institute: Hangzhou First People's Hospital

description:
lncRNA/mRNA
EMT-related lncRNA expression data

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing and fixing, the hybridized arrays were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

label_protocol: LncRNAs/mRNAs were purified from total RNA after removal of rRNA (Arraystar rRNA removal kit). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Germany). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions (Invitrogen). The RNA quality was assessed by NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was assessed by denaturing agarose gel electrophoresis.

treatment_protocol: Subcutaneous fat was removed from keloid and adjacent normal skin, and tissues were frozen by liquid nitrogen and stored at -80 ̊C immediate after excision.

value: normal skin

value: female

tag: age

tag: lesion location

value: chest


title: genomic DNA from umbilical cord bood 174

description: umbilical cord blood sample

source_name: umbilical cord blood 174

value: Male


title: genomic DNA from umbilical cord bood 173

description: umbilical cord blood sample

source_name: umbilical cord blood 173

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 172

description: umbilical cord blood sample

source_name: umbilical cord blood 172


title: Sample 73

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

value: LN-

value: Meta+

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: ATACseq FoxA1-Hnf4a uninduced rep2

source_name: ATACseq FoxA1-Hnf4a uninduced

tag: cell line background

tag: cell type

tag: genotype

tag: treatment

value: none (uninduced)


title: genomic DNA from umbilical cord bood 175

description: umbilical cord blood sample

source_name: umbilical cord blood 175

value: Female


title: ATACseq FoxA1-Hnf4a induced rep1

value: Immortalized lymphoblast


title: genomic DNA from umbilical cord bood 167

description: umbilical cord blood sample

source_name: umbilical cord blood 167


title: Sample 72

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: metastatis

tag: death

tag: estrogen-receptor

value: ER+

tag: nih


title: genomic DNA from umbilical cord bood 169

description: umbilical cord blood sample

source_name: umbilical cord blood 169

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 176

description: umbilical cord blood sample

source_name: umbilical cord blood 176


title: genomic DNA from umbilical cord bood 165

description: umbilical cord blood sample

source_name: umbilical cord blood 165


title: genomic DNA from umbilical cord bood 177

description: umbilical cord blood sample

source_name: umbilical cord blood 177


title: ATACseq FoxA1-Hnf4a uninduced rep1


title: Sample 71

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: stgallen

tag: conservflag


title: ATACseq Hnf4a induced rep2

source_name: ATACseq Hnf4a induced

value: Hnf4a doxycycline-inducible clonal line

value: 0.5ug/ml doxycycline for 24 hours


title: Keloid of patient B

source_name: Keloid of patient B

value: keloid

tag: age

tag: lesion location

value: abdomen


title: genomic DNA from umbilical cord bood 171

description: umbilical cord blood sample

source_name: umbilical cord blood 171


title: genomic DNA from umbilical cord bood 168

description: umbilical cord blood sample

source_name: umbilical cord blood 168


title: Trichoplusia ni hemolymph samples [F111]

city: Pomona

first: Peter

last: Arensburger

state: CA

address: 3801 Watkins Avenue

department: Dept. of Biology

institute: California State Polytechnic University Pomona

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

data_processing:
Low sequencing quality and adapter sequences were removed from the libraries using trimmomatic-0.32
ribosomal contaminants were removed with SortMeRNA version 2.0
Sequencing reads were mapped to one or several of the following reference genome assemblies: 1) viral genome of SfAV , 2) viral genome of TnAV , 3) Spodoptera frugiperda genome, SF_CORN_1 assembly (NCBI accession GCA_900240015.1), and bowtie2 and the splice-aware program hisat2 was used for all other genomes.
Library statistics, read counts and RPKMs calculation were determined using the bedtools intersectBed program in conjunction with custom written Perl scripts (available upon request).
Genome_build: GCA_900240015.1 and ASM360422v1
Supplementary_files_format_and_content: RPKM expression levels, .xlsx files

organism: Trichoplusia ni

source_name: hemolymph tissue

extract_protocol:
Hemolymph or combination of other body tissues, which from the standpoint of bulk, consisted primarily of the fat body, epidermis, tracheal matrix and midgutody tissues (referred to as somatic body tissues) were collected and homogenized in Trizol. Samples were DNAse treated and cDNA libraries were constructed.
RNA libraries were prepared for sequencing using NEBNext Utra Directional RNA Library Prep kit.

tag: time point

tag: replicate

value: Replicate 3


title: Keloid of patient C

source_name: Keloid of patient C


title: Keloid of patient A

source_name: Keloid of patient A

value: male

value: cheek


title: Adjacent normal skin tissue of patient B

value: normal skin

value: female


title: Sample 62

description: human breast tumor RNA

value: breast tumor

value: Dead

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 164

description: umbilical cord blood sample

source_name: umbilical cord blood 164

value: Umbilical cord blood


title: Adjacent normal skin tissue of patient A

tag: tissue


title: genomic DNA from umbilical cord bood 160

description: umbilical cord blood sample

source_name: umbilical cord blood 160

value: Male


title: ATACseq Hnf4a uninduced rep2

source_name: ATACseq Hnf4a uninduced

tag: cell line background

tag: cell type

tag: genotype

tag: treatment

value: none (uninduced)


title: genomic DNA from umbilical cord bood 163

description: umbilical cord blood sample

source_name: umbilical cord blood 163

tag: gender

tag: sample type


title: Sample 61

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: lypmph-nodes

value: LN-

tag: metastatis

value: Meta+

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 60

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

value: ER+

tag: conservflag


title: Trichoplusia ni hemolymph samples [F110]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

tag: time point

tag: replicate

value: Replicate 2


title: genomic DNA from umbilical cord bood 162

description: umbilical cord blood sample

source_name: umbilical cord blood 162

value: Female


title: genomic DNA from umbilical cord bood 157

description: umbilical cord blood sample

source_name: umbilical cord blood 157


title: Trichoplusia ni hemolymph samples [F109]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

value: Replicate 1


title: ATACseq FoxA1 induced rep2

source_name: ATACseq FoxA1 induced

tag: cell line background

tag: cell type

value: Immortalized lymphoblast

tag: genotype

value: FoxA1 doxycycline-inducible clonal line

tag: treatment

value: 0.5ug/ml doxycycline for 24 hours


title: ATACseq Hnf4a uninduced rep1

value: Hnf4a doxycycline-inducible clonal line


title: Trichoplusia ni hemolymph samples [F108]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

value: Replicate 3


title: genomic DNA from umbilical cord bood 170

description: umbilical cord blood sample

source_name: umbilical cord blood 170

tag: gender

tag: sample type


title: Trichoplusia ni hemolymph samples [F107]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls


title: ATACseq FoxA1 uninduced rep2

source_name: ATACseq FoxA1 uninduced


title: Sample 59

description: human breast tumor RNA

tag: tissue

value: breast tumor

tag: lypmph-nodes

tag: metastatis

tag: death

tag: timesurvival(years)

tag: metastasis-years


title: ATACseq Hnf4a induced rep1

source_name: ATACseq Hnf4a induced


title: genomic DNA from umbilical cord bood 156

description: umbilical cord blood sample

source_name: umbilical cord blood 156


title: Trichoplusia ni hemolymph samples [F106]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls


title: Sample 57

description: human breast tumor RNA

value: Dead

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: estrogen-receptor

value: ER-

tag: nih

tag: stgallen


title: ATACseq FoxA1 uninduced rep1

tag: cell line background

tag: cell type


title: Sample 58

description: human breast tumor RNA

tag: timemeta

tag: conservflag


title: Trichoplusia ni hemolymph samples [F105]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

tag: time point

tag: replicate


title: Sample 56

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes


title: 106_EPDHT_d Sd3

city: Tartu

first: Alvin

last: Meltsov

state: Tartumaa

address: Teaduspargi tn 13

country: Estonia

institute: The Competence Centre on Health Technologies

description:
106_EPDHT_d
Control set

data_processing:
Trimming adapters with Trimmomatic 0.38 with flags “SE CROP:57”
Salmon 0.9.1 in “quant” mode with flags “-l A –gcBias”
FastQC 0.11.5
MultiQC 1.7
Summarized to genes using R 3.5.1 packages tximport 1.10.1 (countsFromAbundance = “no”) and biomaRt 2.38.0 (for downloading Ensembl v95 annotation)
Genome_build: GRCh38 Ensembl release 95 cdna – indexed with Salmon 0.9.1
Supplementary_files_format_and_content: GEO_salmon_counts.tsv – TSV file of summarized Salmon pseudocounts per gene (marked with Ensembl Gene ID)

source_name: Endometrial stromal cells

growth_protocol: Endometrial biopsy samples were collected at the proliferative phase (PE) of the menstrual cycle (cycle days [cd] 6–10) from Ctrl and from women with PCOS and eSCs were isolated as previously described Piltoen TT., Human Reproduction., 2015.

extract_protocol:
For decidualization (DE cells), eSCs from Ctrl (eSCCtrl, n=6) and PCOS (eSCPCOS, n=6) were treated with 8-Br-cAMP (0.5 mM, Sigma-Aldrich, Germany) for 96 h in a low serum medium (3), while pre-decidualised (non-DE cells) were cultured for 96 h using the 0.1% DMSO ( Sigma-Aldrich, Germany) as a vehicle only. Next, DE and non-DE eSCs were treated for 24 h with hormones: non-DE eSCs were post-treated with E2 (10 nM, Sigma-Aldrich, Germany) with or without (±) DHT (100 nM, Sigma-Aldrich, Germany); while the DE eSCs were post-treated with E2 (10 nM, Sigma-Aldrich, Germany) in combination with P4 (E2P4, 1 mM, Sigma-Aldrich, Germany) ± DHT.
Total RNA was extracted using RNeasy Mini Kits (Qiagen, Valencia, USA) and RNA sequencing (RNA-seq) libraries were prepared using the SMART-seq2 protocol with modification (Piselli S., 2014). Instead of single cells and original template-switching oligonucleotide (TSO), 12 ng of total RNA for cDNA synthesis and 1 μM TSO (biotin-AAGCAGTGGTATCAACGCAGAGTrGrGrG, Sigma, Schnelldorf, Germany) in combination with 200 nM anchored oligo-T primer (biotin-TTAAGCAGTGGTATCAACGCAGAGTCGACT30+V, where + is LNA nucleotide, Exiqon, Vedbaek, Denmark) was used. Ten cycles of PCR with Phusion High-Fidelity DNA Polymerase (Thermo Scientific, HL, Finland) compatible with the original protocol were used for pre-amplification. 5 µl of cDNA was applied to single-index library preparation using Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1024, San Diego, CA, USA). AMPure XP beads (Beckman Coulter, San Jose, CA, USA) were used for all clean-up steps. The quality of the resulting libraries was assessed with the 2200 TapeStation system (Agilent, Edinburg, UK). Libraries were pooled and sequenced on NextSeq500 using High Output Flow Cell v2.5 (single-end, 80 bp; Illumina).

treatment_protocol: DE eSCs (0.5 mM 8-Br-cAMP, 96 h), as model of SE, were treated with E2 and P4 (E2P4) with/without (±) DHT; while non-DE eSCs, as model of PE, were subjected to E2 ± DHT (post-treatment). The 24-hour steroid hormone exposure was followed by RNA-seq.

tag: condition

value: control

tag: treatment

value: EPDHT


title: genomic DNA from umbilical cord bood 158

description: umbilical cord blood sample

source_name: umbilical cord blood 158

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: Trichoplusia ni hemolymph samples [F104]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

source_name: hemolymph tissue


title: Sample 48

description: human breast tumor RNA

value: LN-

tag: metastatis

value: Meta+

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: metastasis-years


title: Sample 51

description: human breast tumor RNA

tag: recurrence-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen


title: 106_EP_c Sc3

description:
106_EP_c
Control set

value: EP


title: Trichoplusia ni hemolymph samples [F103]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

tag: time point

tag: replicate

value: Replicate 1


title: 106_E2_b Sb3

description:
106_E2_b
Control set


title: Sample 45

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Alive

tag: timemeta

tag: conservflag


title: genomic DNA from umbilical cord bood 159

description: umbilical cord blood sample

source_name: umbilical cord blood 159

tag: gender

tag: sample type


title: Trichoplusia ni hemolymph samples [F102]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

value: Control


title: genomic DNA from umbilical cord bood 155

description: umbilical cord blood sample

source_name: umbilical cord blood 155

value: Female


title: Trichoplusia ni hemolymph samples [F101]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls

value: Replicate 2


title: genomic DNA from umbilical cord bood 166

description: umbilical cord blood sample

source_name: umbilical cord blood 166


title: genomic DNA from umbilical cord bood 179

description: umbilical cord blood sample

source_name: umbilical cord blood 179


title: genomic DNA from umbilical cord bood 153

description: umbilical cord blood sample

source_name: umbilical cord blood 153


title: 106_V_a Sa3

description:
106_V_a
Control set

tag: condition

tag: treatment

value: V


title: Sample 39

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

tag: metastatis

value: Meta-

tag: death

tag: timesurvival(years)

tag: survival-years


title: Sample 38

description: human breast tumor RNA

source_name: patient sample

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

tag: estrogen-receptor


title: 109_EDHT S59

value: EDHT


title: genomic DNA from umbilical cord bood 161

description: umbilical cord blood sample

source_name: umbilical cord blood 161


title: 109_EPDHT S60

value: control


title: ATACseq FoxA1 induced rep1

tag: cell line background

tag: cell type

value: Immortalized lymphoblast

tag: genotype

value: FoxA1 doxycycline-inducible clonal line

value: 0.5ug/ml doxycycline for 24 hours


title: Sample 36

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN-

tag: timemeta

tag: nih

tag: stgallen


title: Trichoplusia ni somatic samples [F125]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

source_name: somatic body tissues

tag: time point

tag: replicate


title: Sample 29

description: human breast tumor RNA

tag: metastatis

tag: death

tag: conservflag


title: Trichoplusia ni hemolymph samples [F100]

description:
S1B.xls
S1F.xls
S1H.xls
S1L.xls


title: Trichoplusia ni somatic samples [F126]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

value: Replicate 3


title: 109_EP S58

tag: condition

tag: treatment


title: Sample 28

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

value: ER-


title: 109_V S56


title: Trichoplusia ni somatic samples [F124]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls


title: genomic DNA from umbilical cord bood 152

description: umbilical cord blood sample

source_name: umbilical cord blood 152

tag: gender

tag: sample type

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 150

description: umbilical cord blood sample

source_name: umbilical cord blood 150


title: genomic DNA from umbilical cord bood 154

description: umbilical cord blood sample

source_name: umbilical cord blood 154


title: Trichoplusia ni somatic samples [F123]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls


title: 109_E2 S57


title: Sample 27

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: timemeta

tag: estrogen-receptor

value: ER+


title: Sample 26

description: human breast tumor RNA

value: Alive

tag: nih

tag: stgallen


title: 105_EDHT S54

value: PCOS


title: Trichoplusia ni somatic samples [F122]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

tag: time point

tag: replicate


title: 105_EPDHT S55

tag: condition

value: EPDHT


title: Sample 17

description: human breast tumor RNA

tag: metastatis

tag: death

tag: conservflag


title: genomic DNA from umbilical cord bood 149

description: umbilical cord blood sample

source_name: umbilical cord blood 149

value: Female


title: genomic DNA from umbilical cord bood 145

description: umbilical cord blood sample

source_name: umbilical cord blood 145


title: 105_E2 S52

source_name: Endometrial stromal cells

tag: treatment


title: genomic DNA from umbilical cord bood 148

description: umbilical cord blood sample

source_name: umbilical cord blood 148

value: Male


title: 105_EP S53

value: EP


title: Trichoplusia ni somatic samples [F119]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

value: Replicate 2


title: Trichoplusia ni somatic samples [F121]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

value: Replicate 1


title: Sample 12

description: human breast tumor RNA

value: breast tumor

value: Meta-

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: Trichoplusia ni somatic samples [F120]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls


title: Sample 13

description: human breast tumor RNA

tag: tissue

tag: metastasis-years


title: Sample 14

description: human breast tumor RNA

tag: lypmph-nodes

tag: timemeta


title: Trichoplusia ni somatic samples [F118]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls


title: 105_V S51

value: V


title: 97_EPDHT S50

value: control


title: Trichoplusia ni somatic samples [F117]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

value: Control


title: 97_EDHT S49

value: EDHT


title: Sample 11

description: human breast tumor RNA

value: LN-

tag: estrogen-receptor

tag: nih


title: genomic DNA from umbilical cord bood 146

description: umbilical cord blood sample

source_name: umbilical cord blood 146

tag: gender

tag: sample type

value: Umbilical cord blood


title: Sample 8

description: human breast tumor RNA

value: ER-

tag: stgallen


title: Trichoplusia ni somatic samples [F116]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls

tag: time point

tag: replicate


title: Sample 9

description: human breast tumor RNA

tag: metastatis

tag: death

value: Alive

value: ER+

tag: conservflag


title: 97_EP S48

tag: condition

tag: treatment


title: Trichoplusia ni somatic samples [F115]

description:
S1B.xls
S1D.xls
S1G.xls
S1K.xls


title: Sample 7

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 141

description: umbilical cord blood sample

source_name: umbilical cord blood 141


title: 97_E2 S47


title: genomic DNA from umbilical cord bood 143

description: umbilical cord blood sample

source_name: umbilical cord blood 143


title: Sample 6

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: timemeta

tag: metastasis-years


title: 97_V S46


title: CCSBA63

city: New York

first: Fabio

last: Vanoli

address: 1250 1st Avenue

institute: MSKCC

description: CHP file not available for this sample.

hyb_protocol: 10 micrograms of labeled and fragmented cRNA were hybridized onto a human genome U133A expression array.

scan_protocol: Posthybridization staining, washing, and scanning were done according to manufacturers's instruction (Affymetrix).

data_processing: The raw expression data were derived using the Affymetrix Microarray analysis 5.0 (MAS 5.0) software. The data were normalized using a scaling target intensity of 500 to account for differences in the global chip intensity. The expression values were transformed using the logarithm base two.

label: biotin

source_name: Knee

label_protocol: Samples were labeled according to manufacturer's instructions (Affymetrix Santa Clara, CA).

extract_protocol: RNA was extracted from tumor samples using Trizol.

value: solid tumor

tag: sarcoma type

value: Clear Cell Sarcoma (GI-CCS)

tag: fusion type


title: genomic DNA from umbilical cord bood 151

description: umbilical cord blood sample

source_name: umbilical cord blood 151

tag: gender

value: Male

tag: sample type


title: CCSAM49

description: CHP file not available for this sample.

source_name: Hip


title: 96_EPDHT S45

value: PCOS

value: EPDHT


title: genomic DNA from umbilical cord bood 138

description: umbilical cord blood sample

source_name: umbilical cord blood 138

value: Female


title: genomic DNA from umbilical cord bood 144

description: umbilical cord blood sample

source_name: umbilical cord blood 144


title: Sample 4

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

source_name: patient sample

tag: metastatis

tag: estrogen-receptor

tag: nih

tag: stgallen


title: 96_EDHT S44

tag: condition

tag: treatment


title: Sample 120

description: human breast tumor RNA

value: Meta-

tag: death

tag: timesurvival(years)

tag: survival-years

tag: conservflag


title: genomic DNA from umbilical cord bood 140

description: umbilical cord blood sample

source_name: umbilical cord blood 140


title: 96_EP S43

value: EP


title: CCS3409

description: CHP file not available for this sample.

source_name: thigh

tag: tissue


title: Sample 118

description: human breast tumor RNA

tag: lypmph-nodes

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: Sample 117

description: human breast tumor RNA

value: LN+

tag: metastasis-years


title: genomic DNA from umbilical cord bood 139

description: umbilical cord blood sample

source_name: umbilical cord blood 139

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 142

description: umbilical cord blood sample

source_name: umbilical cord blood 142


title: genomic DNA from umbilical cord bood 147

description: umbilical cord blood sample

source_name: umbilical cord blood 147


title: CCS11610

description: CHP file not available for this sample.

source_name: arm

tag: sarcoma type

tag: fusion type


title: genomic DNA from umbilical cord bood 134

description: umbilical cord blood sample

source_name: umbilical cord blood 134


title: Sample 113

description: human breast tumor RNA

tag: metastatis

value: Meta+

value: Dead

tag: estrogen-receptor

tag: nih

tag: stgallen


title: 96_V S41

source_name: Endometrial stromal cells

tag: condition

tag: treatment

value: V


title: genomic DNA from umbilical cord bood 137

description: umbilical cord blood sample

source_name: umbilical cord blood 137

value: Umbilical cord blood


title: 106_EPDHT_d Sd2

description:
106_EPDHT_d
Control set

value: control


title: AFH6

value: Angiomatoid Fibrous Histiocytoma (AFH)


title: Sample 111

description: human breast tumor RNA

value: LN-

tag: death

tag: timesurvival(years)

tag: survival-years

value: ER+

tag: conservflag


title: Sample 110

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Alive

tag: timerecurrence(years)

tag: recurrence-years


title: GICCS11497

source_name: colon

value: solid tumor

value: Clear Cell Sarcoma (GI-CCS)


title: genomic DNA from umbilical cord bood 133

description: umbilical cord blood sample

source_name: umbilical cord blood 133

tag: gender

value: Male

tag: sample type


title: genomic DNA from umbilical cord bood 135

description: umbilical cord blood sample

source_name: umbilical cord blood 135


title: 106_EP_c Sc2

description:
106_EP_c
Control set


title: 106_E2_b Sb2

description:
106_E2_b
Control set


title: genomic DNA from umbilical cord bood 132

description: umbilical cord blood sample

source_name: umbilical cord blood 132


title: 96_E2 S42

value: PCOS


title: genomic DNA from umbilical cord bood 130

description: umbilical cord blood sample

source_name: umbilical cord blood 130


title: 106_V_a Sa2

description:
106_V_a
Control set


title: genomic DNA from umbilical cord bood 131

description: umbilical cord blood sample

source_name: umbilical cord blood 131

value: Female


title: XPO1_rep3

city: Shanghai

first: Lijia

last: Pan

address: Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: text files include raw counts for each Sample

source_name: neuroblastoma

extract_protocol:
cells were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

value: neuroblastoma

tag: strain


title: Sample 107

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

source_name: patient sample

tag: metastatis

tag: timemeta

tag: metastasis-years


title: AFH5

tag: sarcoma type

tag: fusion type


title: XPO1_rep1

institute: Xinhua Hospital, School of Medicine, Shanghai Jiaotong University

tag: treatment


title: AFH4


title: genomic DNA from umbilical cord bood 127

description: umbilical cord blood sample

source_name: umbilical cord blood 127


title: 100_EPDHT S40

tag: condition

value: EPDHT


title: Sample 404

description: human breast tumor RNA

value: LN+

value: Meta-

tag: death

tag: timesurvival(years)

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 109

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Meta+

tag: survival-years

tag: timerecurrence(years)

value: ER-

tag: conservflag


title: 100_EDHT S39

value: control

value: EDHT


title: NC_rep2

value: DMSO

tag: strain


title: NC_rep3


title: Sample 103

description: human breast tumor RNA

value: LN-

tag: metastatis

value: Dead

tag: recurrence-years

tag: timemeta


title: genomic DNA from umbilical cord bood 128

description: umbilical cord blood sample

source_name: umbilical cord blood 128

tag: gender

tag: sample type

value: Umbilical cord blood


title: NC_rep1

tag: treatment


title: Sample 403

description: human breast tumor RNA

tag: death

value: Alive

tag: metastasis-years

value: ER+


title: 100_E2 S37

tag: condition


title: Sample 402

description: human breast tumor RNA

tag: timesurvival(years)

tag: estrogen-receptor

tag: nih


title: XPO1_rep2

tag: tissue


title: 100_V S36

value: V


title: genomic DNA from umbilical cord bood 125

description: umbilical cord blood sample

source_name: umbilical cord blood 125

value: Male


title: 89_EPDHT S35

value: PCOS


title: 100_EP S38

value: EP


title: Sample 401

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

tag: survival-years

tag: stgallen


title: Sample 398

description: human breast tumor RNA

tag: timerecurrence(years)

tag: conservflag


title: genomic DNA from umbilical cord bood 122

description: umbilical cord blood sample

source_name: umbilical cord blood 122

value: Female


title: genomic DNA from umbilical cord bood 126

description: umbilical cord blood sample

source_name: umbilical cord blood 126


title: Sample 397

description: human breast tumor RNA

tag: metastatis

tag: recurrence-years


title: genomic DNA from umbilical cord bood 124

description: umbilical cord blood sample

source_name: umbilical cord blood 124

tag: gender


title: 89_E2 S32

source_name: Endometrial stromal cells


title: 89_EP S33


title: genomic DNA from umbilical cord bood 129

description: umbilical cord blood sample

source_name: umbilical cord blood 129

tag: sample type


title: Sample 395

description: human breast tumor RNA

value: LN+

tag: timemeta


title: Sample 396

description: human breast tumor RNA

value: Meta-

tag: death


title: genomic DNA from umbilical cord bood 123

description: umbilical cord blood sample

source_name: umbilical cord blood 123


title: genomic DNA from umbilical cord bood 136

description: umbilical cord blood sample

source_name: umbilical cord blood 136


title: 89_V S31

tag: treatment


title: Sample 393

description: human breast tumor RNA

tag: metastasis-years


title: Sample 394

description: human breast tumor RNA

tag: timesurvival(years)


title: genomic DNA from umbilical cord bood 118

description: umbilical cord blood sample

source_name: umbilical cord blood 118


title: 84_EDHT S29

tag: condition


title: 84_EP S28


title: 84_E2 S27


title: 84_EPDHT S30

value: EPDHT


title: genomic DNA from umbilical cord bood 120

description: umbilical cord blood sample

source_name: umbilical cord blood 120


title: 89_EDHT S34


title: Sample 389

description: human breast tumor RNA

value: Meta+

tag: estrogen-receptor

tag: nih


title: Sample 390

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes


title: Sample 392

description: human breast tumor RNA

tag: survival-years

tag: stgallen


title: genomic DNA from umbilical cord bood 119

description: umbilical cord blood sample

source_name: umbilical cord blood 119


title: Sample 391

description: human breast tumor RNA

tag: timerecurrence(years)

tag: conservflag


title: 84_V S26

value: control


title: 77_EPDHT S25


title: 77_EDHT S24

value: EDHT


title: genomic DNA from umbilical cord bood 117

description: umbilical cord blood sample

source_name: umbilical cord blood 117


title: 77_EP S23


title: Sample 387

description: human breast tumor RNA

tag: metastatis

tag: recurrence-years


title: Sample 385

description: human breast tumor RNA


title: 77_E2 S22


title: Sample 381

description: human breast tumor RNA


title: Sample 383

description: human breast tumor RNA


title: 77_V S21


title: genomic DNA from umbilical cord bood 121

description: umbilical cord blood sample

source_name: umbilical cord blood 121

tag: gender

tag: sample type


title: 106_EPDHT_d Sd

description:
106_EPDHT_d
Control set


title: Sample 379

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: LN-

tag: death

tag: timemeta


title: TL-14d rep3

city: Kumamoto

first: Tomokazu

last: Fujimoto

address: 1-1-1 Honjo

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

data_processing:
Samples were analyzed on a NovaSeq 6000.
The reads were mapped to the rabbit genome sequence using OryCun2.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000003625.3/) and STAR (ver. 2.6.0c).
The expression level was calculated as the FPKM and count per milion (CPM) value for each gene and each transcript based on the mapping information and the gene locus using GeneData Profiler Genome (ver. 13.0.11).
Genome_build: OryCun2.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM and CPM values for each Sample

organism: Oryctolagus cuniculus

source_name: Conjunctiva

extract_protocol:
RNA was isolated from rabbit filtration bleb using Trizol reagent, Phasemaker Tubes, and PureLink RNA Mini Kit (Thermo Fisher Scientific).
For library preparation, TruSeq Stranded mRNA Library Prep (Illumina), IDT for Illumina TruSeq RNA UD Indexes (Illumina), and Agilent XT Auto System (Agilent Technologies) were used according to the manual, TruSeq Standard mRNA Reference Guide v00.

treatment_protocol: Female Japanese white rabbits underwent trabeculectomy with mitomycin C in the right eye. The conjunctiva including filtration bleb was collected 3 hours, 3days, or 14 days after the operation. The conjunctiva in the left eye was also collected as a control.

tag: strain

value: Japanease White

value: conjunctiva

tag: group

value: trabeclectomy after 14-day


title: 106_EP_c Sc

description:
106_EP_c
Control set

tag: condition

tag: treatment


title: genomic DNA from umbilical cord bood 115

description: umbilical cord blood sample

source_name: umbilical cord blood 115

value: Umbilical cord blood


title: Sample 388

description: human breast tumor RNA

source_name: patient sample

value: Alive

tag: timesurvival(years)

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih


title: E. coli cells transformed with fosmids containing Thermococcus kodakarensis genomic DNA.

city: Ipswich

first: Paul

last: Caffrey

state: MA

address: 240 County Road

department: Molecular Enzymology

institute: New England Biolabs

data_processing:
Trimmomatic using Galaxy
HISAT2 using Galaxy
HT-Seq using Galaxy
Genome_build: Thermococcus kodakarensis KOD1
Supplementary_files_format_and_content: Tabular data, contains number of reads mapping to each gene. Available link: ftp://dmk-brain.ecn.uiowa.edu/ATGC/data/ATGC280/genomes/Thermococcus_kodakarensis_KOD1.GCF_000009965.1.html or https://www.genome.jp/dbget-bin/www_bget?refseq+NC_006624

organism: Thermococcus kodakarensis

source_name: E. coli

extract_protocol:
NEB Monarch RNA MiniPrep Kit
NEBNext rRNA depeltion (bacterial), and NEBNext Ultra II Directional library prep kit

value: EPI300 strain


title: TL-14d rep2

tag: tissue


title: 106_E2_b Sb

description:
106_E2_b
Control set


title: genomic DNA from umbilical cord bood 108

description: umbilical cord blood sample

source_name: umbilical cord blood 108


title: genomic DNA from umbilical cord bood 112

description: umbilical cord blood sample

source_name: umbilical cord blood 112

value: Male


title: genomic DNA from umbilical cord bood 111

description: umbilical cord blood sample

source_name: umbilical cord blood 111


title: Sample 377

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: Dead

tag: survival-years

tag: timerecurrence(years)

value: ER-

tag: stgallen


title: Sample 378

description: human breast tumor RNA

value: LN+

tag: metastatis

value: Meta-

tag: recurrence-years

tag: conservflag


title: 106_V_a Sa

description:
106_V_a
Control set

source_name: Endometrial stromal cells

value: V


title: genomic DNA from umbilical cord bood 113

description: umbilical cord blood sample

source_name: umbilical cord blood 113

tag: gender

value: Female

tag: sample type


title: TL-14d rep1

tag: strain

tag: group


title: Sample 375

description: human breast tumor RNA

tag: death

tag: timemeta


title: TL-3d rep3

value: trabeclectomy after 3-day


title: Sample 380

description: human breast tumor RNA

value: LN-

tag: timesurvival(years)

tag: metastasis-years


title: 169_EPDHT S20

tag: condition

value: PCOS

tag: treatment

value: EPDHT


title: genomic DNA from umbilical cord bood 105

description: umbilical cord blood sample

source_name: umbilical cord blood 105


title: TL-3d rep2

value: Japanease White

tag: tissue

value: conjunctiva


title: Sample 374

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: survival-years

tag: estrogen-receptor

tag: nih


title: 169_EDHT S19

value: EDHT


title: Sample 373

description: human breast tumor RNA

tag: metastatis

value: Alive

tag: timerecurrence(years)

tag: recurrence-years

value: ER+

tag: stgallen


title: Sample 371

description: human breast tumor RNA

value: breast tumor

tag: conservflag


title: TL-3d rep1

tag: strain

tag: group


title: 169_EP S18

value: EP


title: genomic DNA from umbilical cord bood 109

description: umbilical cord blood sample

source_name: umbilical cord blood 109

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 103

description: umbilical cord blood sample

source_name: umbilical cord blood 103


title: TL-3h rep3

value: trabeclectomy after 3-hour


title: 169_E2 S17


title: Sample 370

description: human breast tumor RNA

value: LN+

tag: death

value: Dead

tag: timesurvival(years)

tag: timemeta

tag: metastasis-years


title: TL-3h rep2

tag: tissue


title: genomic DNA from umbilical cord bood 106

description: umbilical cord blood sample

source_name: umbilical cord blood 106

value: Female


title: genomic DNA from umbilical cord bood 99

description: umbilical cord blood sample

source_name: umbilical cord blood 99


title: genomic DNA from umbilical cord bood 100

description: umbilical cord blood sample

source_name: umbilical cord blood 100


title: 169_V S16

tag: condition

tag: treatment

value: V


title: genomic DNA from umbilical cord bood 114

description: umbilical cord blood sample

source_name: umbilical cord blood 114


title: TL-3h rep1


title: 116_EPDHT S15

value: PCOS


title: Sample 369

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: lypmph-nodes

value: LN-

tag: survival-years

tag: estrogen-receptor

value: ER-

tag: nih


title: cont rep3

source_name: Conjunctiva

value: Japanease White

value: conjunctiva

value: control


title: Sample 368

description: human breast tumor RNA

tag: metastatis

value: Meta+

value: Alive

tag: timerecurrence(years)

tag: recurrence-years

tag: stgallen


title: cont rep2

tag: strain

tag: group


title: genomic DNA from umbilical cord bood 104

description: umbilical cord blood sample

source_name: umbilical cord blood 104

tag: gender

tag: sample type


title: Sample 367

description: human breast tumor RNA

value: breast tumor

source_name: patient sample

tag: death

tag: timesurvival(years)

tag: timemeta

value: ER+

tag: conservflag


title: 116_EP S13

tag: condition

tag: treatment

value: EP


title: 116_EDHT S14

value: EDHT


title: genomic DNA from umbilical cord bood 116

description: umbilical cord blood sample

source_name: umbilical cord blood 116

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 102

description: umbilical cord blood sample

source_name: umbilical cord blood 102

value: Male


title: 116_E2 S12


title: genomic DNA from umbilical cord bood 97

description: umbilical cord blood sample

source_name: umbilical cord blood 97


title: genomic DNA from umbilical cord bood 110

description: umbilical cord blood sample

source_name: umbilical cord blood 110


title: genomic DNA from umbilical cord bood 107

description: umbilical cord blood sample

source_name: umbilical cord blood 107


title: Sample 366

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: Meta-

tag: survival-years

tag: metastasis-years


title: 116_V S11

source_name: Endometrial stromal cells


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep6

city: Wuhan

first: fang

last: chen

state: Hubei

address: No1, Nanhu Road

institute: Hubei Academy of Agricultural Sciences

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCg6a
Supplementary_files_format_and_content: txt file include FPKM values for each Sample…
Supplementary_files_format_and_content: text file include novel genes…

organism: Gallus gallus

source_name: ileum flora of broiler

growth_protocol: A total of 360 one-day-old broilers were selected and randomly divided into four groups with six replicates: the negative control group (CTL), S. pullorum-infected group (SP), and the S. pullorum-infected group supplemented with 300 mg/kg honokiol (SPH) or magnolol (SPM).

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

treatment_protocol: Chicks in the SP, SPH, and SPM groups were orally treated with a 0.5 ml S. pullorum solution at 5 days of age, while chicks in the control (CTL)  group received the same amount of sterilized PBS at the same age.At 14 and 21 days of age, one chick from each replicate was randomly selected to be weighed and slaughtered by jugular exsanguination after a 12-h fasting period.  The  ileum samples were collected to analyze the gene expression.

tag: age

value: ileum

tag: agent

value: S. pullorum

tag: supplement

value: 300 mg/kg magnolol


title: genomic DNA from umbilical cord bood 96

description: umbilical cord blood sample

source_name: umbilical cord blood 96

value: Female


title: 114_EPDHT S10

value: EPDHT


title: genomic DNA from umbilical cord bood 101

description: umbilical cord blood sample

source_name: umbilical cord blood 101


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep4


title: 114_EDHT S9


title: genomic DNA from umbilical cord bood 94

description: umbilical cord blood sample

source_name: umbilical cord blood 94


title: genomic DNA from umbilical cord bood 98

description: umbilical cord blood sample

source_name: umbilical cord blood 98


title: Sample 365

description: human breast tumor RNA

value: LN-

tag: metastatis

tag: timerecurrence(years)

tag: recurrence-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep3


title: 114_EP S8


title: genomic DNA from umbilical cord bood 95

description: umbilical cord blood sample

source_name: umbilical cord blood 95

tag: gender

tag: sample type


title: Sample 364

description: human breast tumor RNA

tag: death

tag: timesurvival(years)

tag: timemeta

value: ER-

tag: conservflag


title: genomic DNA from umbilical cord bood 93

description: umbilical cord blood sample

source_name: umbilical cord blood 93


title: cont rep1

tag: strain

value: Japanease White

tag: tissue

value: conjunctiva

tag: group

value: control


title: genomic DNA from umbilical cord bood 92

description: umbilical cord blood sample

source_name: umbilical cord blood 92


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep2

tag: age

tag: agent


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep5

tag: supplement


title: 114_E2 S7

tag: condition

tag: treatment


title: Sample 361

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Alive

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

tag: estrogen-receptor


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg magnolol, rep1


title: Sample 363

description: human breast tumor RNA

value: Meta+

tag: death

tag: timesurvival(years)

tag: timemeta

value: ER+

tag: nih

tag: stgallen


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep6

tag: age

tag: tissue

value: 300 mg/kg honokiol


title: Sample 362

description: human breast tumor RNA

value: Meta-

tag: conservflag


title: 106_EPDHT S5

tag: condition


title: Sample 360

description: human breast tumor RNA


title: 106_EDHT S4

tag: treatment

value: EDHT


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep5

value: ileum

tag: agent

value: S. pullorum

tag: supplement


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep4


title: Sample 359

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: survival-years


title: 106_EP S3

value: EP


title: Sample 358

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years


title: Sample 357

description: human breast tumor RNA

tag: death

tag: timesurvival(years)

tag: estrogen-receptor


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep3


title: Sample 356

description: human breast tumor RNA

tag: timemeta

tag: nih

tag: stgallen


title: genomic DNA from umbilical cord bood 89

description: umbilical cord blood sample

source_name: umbilical cord blood 89

tag: gender

value: Female

tag: sample type

value: Umbilical cord blood


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep2

tag: age

tag: tissue


title: 106_V S1

tag: condition

tag: treatment

value: V


title: Sample 355

description: human breast tumor RNA

source_name: patient sample

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: conservflag


title: genomic DNA from umbilical cord bood 87

description: umbilical cord blood sample

source_name: umbilical cord blood 87


title: ileum flora in broiler at 14 d,  S. pullorum-infected group supplemented with 300 mg/kg honokiol, rep1

tag: agent

tag: supplement


title: genomic DNA from umbilical cord bood 86

description: umbilical cord blood sample

source_name: umbilical cord blood 86

value: Male


title: 106_E2 S2

value: control


title: Sample 354

description: human breast tumor RNA

value: breast tumor

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years


title: Sample 353

description: human breast tumor RNA

value: LN+

tag: timesurvival(years)

tag: timemeta

tag: estrogen-receptor

tag: nih

tag: stgallen


title: genomic DNA from umbilical cord bood 91

description: umbilical cord blood sample

source_name: umbilical cord blood 91

tag: gender

tag: sample type


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep6

tag: age

tag: tissue


title: BEAS-2B-EV2

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

data_processing:
Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt.
Reads with less than 16 bp insert sequences or with less than 10 bp Unique Molecular Index (UMI) were discarded.
Alignment of reads was performed using bowtie.
miRBase Release 21 was used for miRNAs.
The StrandNGS was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed miRNAs between groups.
.xlsx file was generated by Qiagen online primary data analyzing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).
Genome_build: hg19
Supplementary_files_format_and_content: miRNA normalized values, counts

source_name: Extracellular vesicles collected from BEAS-2B cells

growth_protocol: Freshly isolated HBECs were plated onto Rat Tail and collagen type I-coated dishes in Bronchial Epithelial Growth Medium (BEGM, Lonza) with a 1% antibiotic–antimycotic solution (AA, Invitrogen) at 37 °C in 5% CO2. HBECs were used until passage 4. Bronchial epithelial cell line BEAS-2B was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with a 10% fetal bovine serum (FBS, Gibco Life Technologies, 26140-079) supplemented with a 1% AA at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).
The miRNA sequencing library was prepared using the QIAseq miRNA Library Kit (Qiagen, 331502)

treatment_protocol: HBECs and BEAS-2B cells were washed with phosphate-buffered saline (PBS), and the culture medium was replaced with BEGM (for HBECs) or serum-free advanced RPMI 1640 medium (for BEAS-2B) with a AA. After incubation for 48 h, the conditioned medium (CM) was collected and centrifuged at 2,000 x g for 10 min at 4°C. To thoroughly remove cellular debris, the supernatant was filtered through a 0.22-mm filter (Millipore). The CM was then used for EV isolation. To prepare EVs, CM was ultracentrifuged at 35,000 rpm using a SW41Ti rotor for 70 min at 4°C. The pellets were washed with PBS, ultracentrifuged at 35,000 rpm using the SW41Ti rotor for 70 min at 4°C and resuspended in PBS.

tag: cell type

value: Human bronchial epithelial cell line BEAS-2B


title: Sample 352

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

value: Alive

tag: conservflag


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep5

tag: agent


title: BEAS-2B-EV1


title: genomic DNA from umbilical cord bood 90

description: umbilical cord blood sample

source_name: umbilical cord blood 90


title: 114_V S6

source_name: Endometrial stromal cells

tag: condition

tag: treatment


title: Sample 351

description: human breast tumor RNA

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

value: ER+


title: HBEC-EV2

source_name: Extracellular vesicles collected from human primary bronchial epithelial cells

value: Primary human bronchial epithelial cell line HBEC


title: HBEC-EV1


title: HMGA2-OE MKN-45- input

city: Hohhot

first: zhouying

last: Wu

state: Inner Mongolia Autonomous Region

address: No. 20 Zhaowuda Road, Saihan District

department: Clinical Medical Research Center

institute: Inner Mongolia People’s Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with -p 4
Data were filtered using Homer version 4.8.2, "makeTagDirectory" subroutine
Peaks were called using Homer version 4.8.2 "findPeaks" subroutine, with parameters:  -style histone -L 0 -localSize 10000 -C 3 -size 1000 -minDist 1000 -tbp 3
Called peaks were annotated using Homer version 4.8.2 "annotatePeaks.pl" subroutine with  "gencode.vM13.annotation.gtf" reference file
Genome_build: hg19
Supplementary_files_format_and_content: peak txt file
Supplementary_files_format_and_content: peak with gene annotation txt file
Supplementary_files_format_and_content: peak with transcripts annotation txt file

source_name: Gastric cancer cells (MKN-45)

growth_protocol: The cells were cultured in RPMI Medium 1640 (Gibco, 11875-093) and DMEM (Gibco, 11965-092) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10091-148) and 1% penicillin streptomycin (Gibco, 15140-122), and were maintained at 37℃ with 5% CO2.

extract_protocol:
HMGA2-OE MKN-45 cells (4x106 cells per ChIP) were protein-DNA cross-linked with 1% formaldehyde at 37°C for 10 minutes and then the reactions were ceased with glycine (125mM). The cells were lysed and the chromatins were enzymatic digested with Micrococcal Nuclease (0.0125mL/mL) at 37°C for 20min. The nuclear membranes were disrupted using a Uitrasonic Homogenizer (JY92-IIN) for 10min. The size and the concentration of the purified DNA from the digested chromatins were measured for the quality control via electrophoresis and NanoDrop 2000, respectively. The digested chromatins were then performed the immunoprecipitation with the HMGA2 rabbit mAb (CST, #5269S). Histone H3 (D2B12) XP® Rabbit mAb (CST, #4620) acted as the positive control, and Normal Rabbit IgG (CST, #2729) acted as the negative control correspondingly. After immunoprecipitation, the precipitated protein-DNA were de-crosslinked, purified and checked by qPCR to verify the results of the immunoprecipitation, and the primer we used was SimpleChIP® Human RPL30 Exon 3 Primers 1(CST, #7014). IP efficiency was calculated with the Percent Input Method. SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads, CST, #9005) was used in the experiments.
The DNA was quality evaluated through NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). After the DNA was convinced qualified, the cDNA library was prepared and sequenced on Illumina's Novaseq platform to generate 150 bases pair-end reads.

treatment_protocol: HMGA2-overexpressed MKN-45 were established using pCMV6-Entry-HMGA2 (OriGene Technologies, RC210804, China)

value: Poorly Differentiated Adenocarcinoma  Derived from liver metastases

tag: overexpression

value: HMGA2-exogenous overexpression

tag: chip antibody

value: HMGA2 rabbit mAb (CST, #5269S)


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep4

source_name: ileum flora of broiler

value: ileum

value: S. pullorum


title: Sample 350

description: human breast tumor RNA

value: Meta-

tag: timesurvival(years)

tag: timemeta

tag: estrogen-receptor

value: ER-

tag: nih

tag: stgallen


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep3

tag: age

tag: tissue


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep2

tag: agent


title: genomic DNA from umbilical cord bood 85

description: umbilical cord blood sample

source_name: umbilical cord blood 85

tag: gender

tag: sample type

value: Umbilical cord blood


title: ileum flora in broiler at 14 d,  S. pullorum-infected group, rep1


title: genomic DNA from umbilical cord bood 88

description: umbilical cord blood sample

source_name: umbilical cord blood 88

value: Female


title: HMGA2-OE MKN-45-HMGA2 ChIP


title: 0399; 39 weeks; Male

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

description: Male placenta at gestational age 39 weeks

data_processing:
Alignemnt to GRCh38 using STAR run in the 2-pass mode
Reads uniquely mapping to the sense strand of known genes were counted
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level read counts in tab-delimited text format

source_name: Term male

extract_protocol:
Total RNA was extracted from frozen placenta using TRIzol® Reagent (Invitrogen), followed by Qiagen RNeasy® Mini Columns following manufacturer’s instructions.
Multiplexed libraries were created using Agilent SureSelect strand-specific RNA library preparation kit following manufacturer’s instructions

tag: ethnicity

value: African American

tag: experimental group

value: Term male

tag: gestation age

value: 39 weeks

tag: placenta sex

value: Male

value: Placenta


title: Sample 349

description: human breast tumor RNA

extract_protocol:
The criteria for the sporadic patients (n = 97) were: primary invasive breast carcinoma less than 5 cm (T1 or T2), no axillary metastases (N0), age at diagnosis less than 55 years, calendar year of diagnosis 1983–1996, no previous malignancies; all patients were treated by modified radical mastectomy (n = 35) or breast-conserving treatment (n = 62), including axillary lymph node dissection followed by radiotherapy. Five patients of the metastases group received adjuvant systemic therapy consisting of chemotherapy (n = 3) or hormonal therapy (n = 2), all other patients did not receive additional treatment. All patients were followed at least annually for a period of at least 5 years. The criteria for hereditary patients (n = 20) were: carriers of a germline mutation in BRCA1 or BRCA2, and primary invasive breast carcinoma; no other selection criterion was applied. This study was approved by the Medical Ethical Committee of the Netherlands Cancer Institute.
Tumour material was snap-frozen in liquid nitrogen within 1 h after surgery. A haematoxylin and eosin stained section was prepared before and after cutting slides for RNA isolation for assessment of the percentage of tumour cells. Only samples with greater than 50% tumour cells were selected, mean 67% and median 70% for all groups studied. Formalin-fixed, paraffin-embedded tumour tissue was used to evaluate the following: tumour type (according to the World Health Organisation classification), histological grade (grade 1–3), and the presence of angioinvasive growth and extensive lymphocytic infiltrate. ER expression was determined by immunohistochemical staining (negative when less than 10% of the nuclei showed staining, all others ER positive).
We used 30 sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with RNAzolB, and finally dissolved in RNase-free H2O. Twenty-five micrograms of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 µg µl-1.

value: breast tumor

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: death

value: Alive

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

tag: conservflag


title: Sample 348

description: human breast tumor RNA

tag: timesurvival(years)

tag: timemeta

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen


title: ileum flora in broiler at 14 d, control group, rep6

tag: age

tag: tissue

tag: agent

value: control


title: genomic DNA from umbilical cord bood 84

description: umbilical cord blood sample

source_name: umbilical cord blood 84

extract_protocol: genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions

tag: gender

tag: sample type


title: 0398; 39 weeks; Male

tag: ethnicity

tag: experimental group

tag: gestation age

tag: placenta sex


title: Sample 347

description: human breast tumor RNA

tag: lypmph-nodes

value: LN+

tag: metastatis

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 82

description: umbilical cord blood sample

source_name: umbilical cord blood 82


title: 0389; 39 weeks; Male


title: Sample 346

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: timesurvival(years)

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: conservflag


title: ileum flora in broiler at 14 d, control group, rep5

tag: age

tag: tissue

value: ileum

tag: agent


title: genomic DNA from umbilical cord bood 78

description: umbilical cord blood sample

source_name: umbilical cord blood 78

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 76

description: umbilical cord blood sample

source_name: umbilical cord blood 76


title: genomic DNA from umbilical cord bood 80

description: umbilical cord blood sample

source_name: umbilical cord blood 80


title: ileum flora in broiler at 14 d, control group, rep4


title: 0387; 39 weeks; Male

tag: ethnicity

tag: experimental group

tag: gestation age

tag: placenta sex


title: genomic DNA from umbilical cord bood 81

description: umbilical cord blood sample

source_name: umbilical cord blood 81


title: Sample 345

description: human breast tumor RNA

source_name: patient sample

tag: lypmph-nodes

tag: metastatis

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: stgallen


title: ileum flora in broiler at 14 d, control group, rep3


title: genomic DNA from umbilical cord bood 83

description: umbilical cord blood sample

source_name: umbilical cord blood 83


title: Sample 344

description: human breast tumor RNA

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih


title: genomic DNA from umbilical cord bood 75

description: umbilical cord blood sample

source_name: umbilical cord blood 75

tag: gender

tag: sample type


title: 0386; 39 weeks; Male

tag: ethnicity

tag: experimental group

tag: tissue


title: ileum flora in broiler at 14 d, control group, rep2

tag: age

tag: agent


title: 0356; 39 weeks; Male

tag: gestation age

tag: placenta sex


title: ileum flora in broiler at 14 d, control group, rep1


title: 0351; 39 weeks; Male


title: 0336; 39 weeks; Male


title: Sample 342

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: conservflag


title: Sample 343

description: human breast tumor RNA

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: stgallen


title: Sample 341

description: human breast tumor RNA

tag: tissue

value: Meta+

value: Dead

tag: nih


title: genomic DNA from umbilical cord bood 79

description: umbilical cord blood sample

source_name: umbilical cord blood 79

tag: gender

tag: sample type


title: 0417; 30 weeks; Male

description: Male placenta at gestational age 30 weeks

source_name: SPTB male

tag: ethnicity

tag: experimental group

value: spontaneous preterm birth (SPTB) male

tag: gestation age

value: 30 weeks

tag: placenta sex


title: PBMC of RSA patients,replicate 3

city: Jinan

first: Xiaoxiao

last: Zhu

address: 18877 Jingshi Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: miRNA expression of URSA patients

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-ColorLow RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/nAM1556 ) following the manufacturer's instructions.

treatment_protocol: Venous blood samples were obtained after overnight fasting at study inclusion. Samples were processed within 4 h of collection.  PBMCs were isolated by Ficoll density-gradient centrifugation.

tag: subject status

value: unexplained recurrent spontaneous abortion (URSA) patient

tag: tissue/cell type

value: PBMC


title: PBMC of RSA patients,replicate 2

description: miRNA expression of URSA patients


title: Sample 340

description: human breast tumor RNA

data_processing:
Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes.
Batch effect correction using the Kolmogorov-Smirnov weighted mean method was used to reduce variability between patients. Patients were first categorized into batches. Then, for each probe, Kolmogorov-Smirnov statistics were calculated for every batch permutation. Weights were calculated by using the sum normalized sums of the KS distance matrix. Weights were used to calculate the weighted mean expression value of the given probe. Weighted average mean correction was then performed on each batch.

tag: lypmph-nodes

tag: metastatis

tag: death

tag: survival-years

tag: timerecurrence(years)

tag: conservflag


title: genomic DNA from umbilical cord bood 73

description: umbilical cord blood sample

source_name: umbilical cord blood 73

value: Female

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 77

description: umbilical cord blood sample

source_name: umbilical cord blood 77

value: Male


title: Sample 339

description: human breast tumor RNA

value: Meta-

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: stgallen


title: 0402; 30 weeks; Male

tag: ethnicity

value: African American

tag: experimental group

tag: tissue

value: Placenta


title: 0360; 30 weeks; Male

tag: gestation age

tag: placenta sex


title: PBMC of RSA patients,replicate 1

description: miRNA expression of URSA patients

tag: subject status

tag: tissue/cell type


title: PBMC of control subjects,replicate 3

description: miRNA expression of control subjects


title: genomic DNA from umbilical cord bood 68

description: umbilical cord blood sample

source_name: umbilical cord blood 68

tag: gender

tag: sample type


title: PBMC of control subjects,replicate 2

description: miRNA expression of control subjects


title: 0354; 30 weeks; Male


title: Sample 338

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: death

value: Alive

tag: survival-years

tag: timerecurrence(years)

value: ER-

tag: nih


title: genomic DNA from umbilical cord bood 72

description: umbilical cord blood sample

source_name: umbilical cord blood 72