title: HTB61_CD123_pos_HHT

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13
ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:25"
PhiX Screen - Bowtie-2.2.1 "-N 1"
MAPPING - SHRiMP_2_2_3 "--qv-offset 33 --all-contigs"
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing fpkm values of all samples

growth_protocol: Cells were culture in serum free conditions with cytokines for 4 hours.

extract_protocol:
Qiagen Rneasy Plus
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer’s protocols.
mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3’-adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

treatment_protocol: 250 nM homoharringtonine for 4 hours

tag: cell type

value: Primary MDS patient specimen

tag: cell population

tag: agent

value: Homoharringtonine


title: HTB61_CD123_pos

status: Public on Aug 01 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: HTB336_CD123_pos_HHT


title: HTB336_CD123_pos


title: 200598350080_R06C01

type: genomic

city: Atlanta

first: Sarah

middle: Whelan

last: Curtis

state: GA

address: 101 Woodruff Circle NE, Ste 42

institute: Emory University

description: HumanMethylationEPIC BeadChip - standard protocol

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing:
non-normalized, background subtracted
beta-values

label: Cy3, Cy5

molecule: genomic DNA

source_name: Peripheral Blood

label_protocol: not provided

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

tag: tissue

value: Peripheral Blood

tag: gender

value: Female

tag: age

tag: ln(totalpbb)


title: 200598360001_R01C01

value: Male


title: 200598350080_R04C01


title: MDS_280_123-


title: MDS_280_123+


title: 200598350079_R07C01


title: 200598350079_R05C01


title: 200598350079_R06C01


title: 200598350079_R04C01


title: 200598350079_R03C01


title: 200598360001_R08C01


title: MDS_268_123+


title: 200598350079_R02C01


title: 200598350079_R01C01


title: MDS_268_Bulk

value: Bulk


title: 200598350078_R08C01


title: 200598350078_R07C01


title: 200598350080_R08C01


title: 200598350080_R01C01


title: 200598350078_R04C01


title: 200598350078_R02C01


title: MDS_314_123-


title: MDS_314_Bulk


title: 200598350078_R03C01


title: 200598350077_R08C01


title: MDS_314_123+


title: MDS_268_123-


title: 200598350078_R01C01


title: MCF7-AA-t96

city: Cambridge

first: Yaara

last: Oren

state: Massachusetts

address: 415 MAIN

department: Cell circuits

institute: Broad

description: 10X Genomics single cell RNAseq data

data_processing:
Reads were aligned to and expression quantified using the 10x pipeline cell ranger-2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with tab delimiters

source_name: MCF7 human cancer cell line

growth_protocol: MCF7 cells were cultured in RPMI-1640 (Life Technologies), with 10% Fetal Bovine Serum (Sigma-Aldrich) and 1% Penicillin-Streptomycin-Glutamine (Life Technologies).

extract_protocol:
DissociateCells were washed, trypsinized, passed through a 40μM cell strainer, centrifuged at 400g, and resuspended at a concentration of 1,000 cells/μL in PBS + 0.5% BSA.
Single cells were processed through the Chromium Single Cell 3′ Solution platform using the Chromium Single Cell 3’ Gel Bead, Chip and Library Kits (10X Genomics), as per the manufacturer’s protocol.

treatment_protocol: MCF7-AA cells were exposed to 500nM of bortezomib (Selleckchem S1013 ) and harvested before treatment, after 12 hours of exposure (t12), after 24 hours of exposure (t48), or after 72 hours of exposure followed by drug wash and 24 hours of recovery (t72+24).

tag: cell line background

value: human cancer cell line

tag: cell line strain

value: AA

tag: treated with

value: bortezomib (500nM)

tag: time point


title: 200598350077_R05C01


title: 200598350077_R07C01


title: MCF7-AA-t48

description: 10X Genomics single cell RNAseq data

value: 48 hours of exposure (t48)


title: 200598350077_R04C01


title: MCF7-AA-t12

description: 10X Genomics single cell RNAseq data

value: 12 hours of exposure (t12)


title: 200598350077_R06C01


title: 200598350077_R01C01


title: MCF7-AA-t0

description: 10X Genomics single cell RNAseq data

value: 0 hr of exposure (t0)


title: 200598350077_R02C01


title: 200598350078_R06C01


title: 200598350078_R05C01


title: MCF7-clone9-Nov

description: 10X Genomics single cell RNAseq data

treatment_protocol: Single cell clones were then isolated by a limiting dilution single cell cloning in 96-well plates

tag: cell line strain/clone

value: strain L/clone9


title: 200598350076_R08C01


title: 200598350077_R03C01


title: 200598350076_R05C01


title: 200598350076_R04C01


title: 200598350076_R01C01


title: MCF7-clone9-May

description: 10X Genomics single cell RNAseq data


title: 200598350075_R08C01


title: 200598350075_R07C01


title: 200598350075_R05C01


title: MCF7-L

description: 10X Genomics single cell RNAseq data

value: strain L


title: 200598350075_R04C01


title: MCF7-SC-WT5

description: 10X Genomics single cell RNAseq data

treatment_protocol: Single cell clones were then isolated by single cell sorting. Single cells were sorted into individual wells of 96-well plates, using BD FACSAriaII SORP Cell Sorter.

tag: clone

value: subclone


title: MCF7-SC-WT4

description: 10X Genomics single cell RNAseq data


title: 200598350075_R06C01


title: 200598350075_R03C01


title: 200598350075_R01C01


title: 200598350075_R02C01


title: 200598350069_R01C01


title: 200598350069_R05C01


title: 200598350069_R03C01


title: 200598350069_R07C01


title: MCF7-Parental

description: 10X Genomics single cell RNAseq data

value: parental


title: 200598350069_R04C01


title: 200598350069_R02C01


title: 200598350067_R08C01


title: 200598350067_R07C01


title: 200598350069_R08C01


title: DICER1*_-DOX_3_c4

city: New York

first: Virginia

last: Teijeiro

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences using TrimGalore (0.4.5).
Reads were aligned to human genome assembly hg19 using STAR (v2.5.3a) with default parameters.
Read count tables were created using HTSeq v0.9.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts

source_name: HUES8 human embryonic stem cells (hESCs)

growth_protocol: HUES8 (NIHhESC-09-0021) hESCs were cultured on irradiated mouse embryonic fibroblasts (iMEFs) feeder layers in DMEM/F12 medium (Life Technologies, 12500-062) supplemented with 20% KnockOut Serum Replacement (Life Technologies, 10828028), 1X MEM Non-Essential Amino Acids (Life Technologies, 11140050), 1X GlutaMAX (Life Technologies, 35050079), 100U/ml Penicillin and 100 μg/ml Streptomycin (Gemini, 15070063), 0.055 mM 2-mercaptoethanol (Life Technologies, 21985023) and 10 ng/ml recombinant human bFGF (EMD Millipore, GF003AF). Cells were incubated at 37 °C with 5% (vol/vol) CO2, and media was changed daily. Cultures were passaged at a 1:6 - 1:12 split ratio every 4 - 6 days using TrypLE (Life Technologies, 12563-029). 5 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells are regularly confirmed to be mycoplasma-free by the MSKCC Antibody & Bioresource Core Facility.

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen, Cat. No. 217004).
After ribogreen quantification and quality control on bioAnalyser,  500ng of total RNA underwent library preparation using the Truseq Stranded Total RNA library preparation chemistry (Illumina), with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 50 million paired reads were generated per sample and the percent of mRNA bases was 72% on average.

treatment_protocol: Cells were culture in doxycycline (2ug/ml) conditions or not (control) for 6 days prior to RNA extraction.

tag: cell line

value: embryonic stem cells

tag: genotype

value: DICER1 knockout


title: DICER1*_+DOX_2_c5

value: wild-type


title: Gp8_RAD+Ner+Ful_N.3

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

description: Gp8 RAD+Ner+Ful replicate 3

data_processing:
Tophat (v2.1) and Cuffdiff (v2.2.1) using default parameters
Genome_build: Human Reference Genome (assembly hg19)
Supplementary_files_format_and_content: Cuffdiff output files

source_name: breast cancer cell line xenograft

growth_protocol: In-vivo studies were carried out in ovariectomized 8- to 12-week old female BALB/c FOX nude mice, in accordance with Home Office guidelines

extract_protocol:
Tumours were snap frozen in liquid nitrogen and RNA was extracted using the RNeasy kit (Qiagen)
Libraries were created after Ribo-zero rRNA removal kit (Illumina) using NEBNext Ultra Directional RNA (NEB) kit

treatment_protocol: Xenograft tumours from three mice per treatment were harvested 6-hours post-final drug following five full days of therapy.

value: breast cancer cell line

tag: source

value: ATCC

tag: estrogen

value: No, LTED (long term estrogen deprived)

tag: treatment

value: RAD + Ner + Ful


title: 200598350067_R05C01

value: Peripheral Blood

value: Male


title: DICER1*_-DOX_2_c3

tag: cell type


title: DICER1*_+DOX_1_c1


title: 200598350066_R08C01


title: 200598350067_R01C01

value: Female


title: 200598360004_R06C01


title: Gp8_RAD+Ner+Ful_N.2

description: Gp8 RAD+Ner+Ful replicate 2


title: MCF7-SC-WT3

description: 10X Genomics single cell RNAseq data

value: human cancer cell line


title: DICER1*_-DOX_1_c2


title: 200598350067_R06C01


title: DICER1*_+DOX_3_c6


title: 200598350067_R03C01


title: 200598350067_R02C01


title: 200598350066_R07C01


title: 200598350066_R06C01


title: 200598350066_R04C01


title: Gp8_RAD+Ner+Ful_N.1

description: Gp8 RAD+Ner+Ful replicate 1


title: Gp7_RAD+Ner_N.3

description: Gp7 RAD+Ner replicate 3

value: RAD + Ner


title: 200598350066_R05C01


title: 200598350065_R08C01


title: Gp7_RAD+Ner_N.2

description: Gp7 RAD+Ner replicate 2


title: 200598350066_R01C01


title: 200598350066_R02C01


title: 200598350065_R06C01


title: 200598350065_R05C01


title: 200598350065_R03C01


title: Gp6_RAD+Ful_N.3

description: Gp6 RAD+Ful replicate 3

value: RAD + Ful


title: Gp6_RAD+Ful_N.2

description: Gp6 RAD+Ful replicate 2


title: 200598350065_R04C01


title: 200598350065_R02C01


title: Gp6_RAD+Ful_N.1

description: Gp6 RAD+Ful replicate 1


title: 200598350065_R01C01


title: 200598350062_R08C01


title: Gp5_Ner+Ful_N.4

description: Gp5 Ner+Ful replicate 4

value: Ner + Ful


title: 200598350062_R07C01


title: Gp7_RAD+Ner_N.1

description: Gp7 RAD+Ner replicate 1


title: Gp5_Ner+Ful_N.3

description: Gp5 Ner+Ful replicate 3


title: 200598350065_R07C01


title: Gp5_Ner+Ful_N.1

description: Gp5 Ner+Ful replicate 1


title: 200598350067_R04C01


title: Gp4_Ful_N.1

description: Gp4 Ful replicate 1

value: fulvestrant ICI182780 (Ful)


title: Gp4_Ful_N.2

description: Gp4 Ful replicate 2


title: 200598350062_R04C01


title: Gp3_RAD_N.3

description: Gp3 RAD replicate 3

value: RAD001 (RAD)


title: 200598350062_R01C01


title: 200598350062_R06C01


title: 200598350054_R08C01


title: 200598350062_R03C01


title: 200598350054_R07C01


title: Gp3_RAD_N.2

description: Gp3 RAD replicate 2


title: 200598350054_R04C01


title: 200598350054_R06C01


title: 200598350054_R05C01


title: 200598350054_R02C01


title: 200598350054_R01C01


title: 200598350053_R08C01


title: Gp3_RAD_N.1

description: Gp3 RAD replicate 1


title: Gp2_Ner_N.4

description: Gp2 Ner replicate 4

value: pan-ERBB inhibitor neratinib (Ner)


title: 200598350053_R07C01


title: 200598350053_R06C01


title: Gp2_Ner_N.3

description: Gp2 Ner replicate 3


title: 200598350054_R03C01


title: Gp2_Ner_N.2

description: Gp2 Ner replicate 2


title: 200598350053_R04C01


title: 200598350053_R03C01


title: 200598350062_R05C01


title: Gp1_Vehicle_N.1

description: Gp1 Vehicle replicate 1

value: vehicle


title: Gp1_Vehicle_N.4

description: Gp1 Vehicle replicate 4


title: 200598350053_R02C01


title: 200598350052_R04C01


title: 200598350052_R05C01


title: 200598350053_R01C01


title: 200598350052_R08C01


title: Chorio_LPS3

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

data_processing:
Trimmomatic was used to trim adapter sequences from the raw reads
The adapter trimmed reads were aligned to the hg19 genome using HISAT2 v2.1.0 using the paired-end option.
Subread v1.6.0 was used to align reads, quantify transcript abundance and assign reads to genomic features.
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated file matrix including raw counts for each exposure/treatment group obtained using featureCounts function in Subread v1.6.0

source_name: Umbilical cord blood purified CD14+ monocytes

extract_protocol:
CD14+ monocytes were isolated from umbilical cord blood using Ficoll-Isopaque density gradient centrifugation and positive magnetic bead selection (Miltenyi Biotec). RNA was extracted using an Rneasy microkit with on column DNAse digestion.
SMARTer stranded total RNA pico kit (Takara) was used for library preparation. After library consruction, samples were pooled in equimolar concentrations and were sequenced on an Illumina HiSeq machine according to the manufacturer's guidelines.

value: Term neonate (37+ weeks gestation)

tag: exposure

value: Chorioamnionitis

value: LPS 100 ng/mL

tag: replicate


title: 200598350052_R07C01

tag: tissue

tag: gender


title: 200598350052_R03C01

tag: age

tag: ln(totalpbb)


title: 200598360001_R02C01


title: 200598350052_R06C01


title: Chorio_LPS2

value: Umbilical cord blood purified CD14+ monocytes


title: 200598350052_R02C01


title: Chorio_LPS1


title: 200598350045_R08C01


title: 200598350052_R01C01


title: 200598350045_R07C01


title: Chorio_unstimulated2


title: 200598350053_R05C01


title: 200598350045_R06C01


title: 200598350045_R05C01


title: Chorio_unstimulated1


title: 200598350045_R02C01


title: Healthy_LPS2


title: 200598350045_R01C01


title: 200598350045_R04C01


title: 200598350044_R08C01


title: 200598350079_R08C01


title: 200598350044_R07C01


title: Healthy_LPS1


title: 200598350044_R03C01


title: 200598350044_R01C01


title: 200598350044_R04C01


title: 200598350044_R06C01


title: Healthy_unstimulated2


title: MDS_280_Bulk

value: Primary MDS patient specimen

tag: cell population

value: Bulk


title: Healthy_unstimulated1


title: 200598350044_R02C01

value: Peripheral Blood


title: Healthy_unstimulated3


title: 200598350043_R08C01

value: Male


title: 200598350043_R07C01


title: 200598350043_R06C01


title: 200598350043_R05C01


title: 200598350043_R04C01

value: Female


title: 200598350045_R03C01


title: Healthy_LPS3


title: TermC3_H3K4me3

library_source: genomic

data_processing:
Scythe was used to trim adapter sequences from the raw reads
The adapter trimmed reads were aligned to the hg19 genome using Bowtie2 v2.0.0 default settings
MACS2 v2.1.1.20160309 was used to call peaks against input samples using the default settings
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using the -B command in MACS2 v2.1.1.20160309

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to the published protocol: Bermick JR, Lambrecht NJ, denDekker AD, Kunkel SL, Lukacs NW, Hogaboam CM, Schaller MA. Neonatal monocytes exhibit a unique histone modification landscape. Clinical Epigenetics, 2016, 8:99. After library consruction, samples were pooled in equimolar concentrations and were sequenced on an Illumina HiSeq machine according to the manufacturer's guidelines.

tag: chip antibody


title: 200598350043_R03C01


title: TermC3_Input


title: 200598350043_R01C01


title: TermC2_Input


title: 200598350042_R08C01


title: TermC2_H3K4me3


title: 200598350042_R06C01


title: 200598350042_R04C01


title: 200598350042_R03C01


title: TermC1_H3K4me3


title: TermC1_Input


title: 200598350041_R08C01


title: 200598350042_R01C01


title: 200598350041_R07C01


title: O30C3_H3K4me3

value: Late preterm neonate (30-36.99 weeks gestation)


title: O30C3_Input


title: 200598350042_R02C01


title: 200598350041_R04C01


title: 200598350041_R06C01


title: 200598350041_R05C01


title: O30C2_H3K4me3


title: 200598350041_R03C01


title: O30C2_Input


title: 200598350043_R02C01


title: O30C1_Input


title: 200598350041_R02C01


title: O30C1_H3K4me3


title: 200598350042_R05C01


title: 200598350066_R03C01


title: 200598350031_R08C01


title: 200598350031_R03C01


title: 200598350042_R07C01


title: 200598350031_R06C01


title: U30C3_Input

value: Extremely preterm neonate (under 30 weeks gestation)


title: 200598350041_R01C01


title: U30C3_H3K4me3


title: 200598350029_R08C01


title: 200598350029_R07C01


title: 200598350031_R01C01


title: U30C2_Input


title: 200598350029_R06C01


title: 200598350029_R04C01


title: U30C2_H3K4me3


title: 200598350029_R05C01


title: 200598350029_R03C01


title: U30C1_Input


title: 200598350029_R02C01


title: 200598350029_R01C01


title: 200598350027_R07C01


title: 200598350027_R08C01


title: U30C1_H3K4me3


title: 200598350027_R06C01


title: 200598350027_R05C01


title: 200598350027_R04C01


title: Non-SCC9

city: Philadelphia

first: Andrew

last: South

state: PA

address: 233 S 10th Street

department: Dermatology and Cutaneous Biology

institute: Thomas Jefferson University

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

extract_protocol:
RNA was extracted using Qiagen Rneasy protocols from fresh forzen tumors where tumor cellularity was determined to be >85% using immunohistochemistry for SCC cases and whole skin used for non-SCC.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: Normal RDEB Skin

tag: diagnosis

value: recessive dystrophic epidermolysis bullosa (RDEB)


title: SCCRDEB_06

value: squamous cell carcinoma (SCC) tumor


title: 200598360006_R02C01


title: 200598350025_R07C01


title: 200598350025_R08C01


title: Non-SCC7


title: Non-SCC8


title: 200598350025_R06C01


title: 200598350025_R05C01


title: 200598350025_R04C01


title: Non-SCC5


title: Non-SCC4


title: Non-SCC3


title: 200598350025_R02C01


title: 200598350025_R03C01


title: 200598350025_R01C01


title: 200598350022_R06C01


title: Non-SCC2


title: 200598350022_R08C01


title: Non-SCC1


title: 200598350022_R04C01


title: 200598350022_R05C01


title: Non-SCC10


title: 200598350027_R01C01


title: 200598350022_R01C01


title: 200598350022_R02C01


title: SCCRDEB_25


title: 200598350018_R08C01


title: 200598350027_R02C01


title: 200598350022_R03C01


title: Non-SCC6


title: 200598350018_R06C01


title: SCCRDEB_20


title: 200598350018_R07C01


title: 200598350018_R04C01


title: 200598350018_R03C01


title: SCCRDEB_15


title: 200598350022_R07C01


title: SCCRDEB_17


title: 200598350018_R02C01


title: 200598350018_R01C01


title: SCCRDEB_12


title: SCCRDEB_19


title: 200598350017_R06C01


title: 200598350017_R08C01


title: 200598350017_R05C01


title: SCCRDEB_18


title: 200598350062_R02C01


title: 200598350017_R03C01


title: 200598350017_R02C01


title: 200598350015_R08C01


title: 200598350015_R03C01


title: 200598350015_R01C01


title: 200598350015_R07C01


title: 200598350012_R06C01


title: 200598350015_R05C01


title: 200598350015_R02C01


title: 200598350012_R08C01


title: 200598350012_R05C01


title: 200598350017_R07C01


title: 200598350012_R03C01


title: 200598350018_R05C01


title: 200598350012_R07C01


title: 200598350011_R07C01


title: 200598350012_R01C01


title: 200598350011_R05C01


title: 200598350012_R02C01


title: 200598350011_R03C01


title: 200598350011_R04C01


title: 200598350017_R04C01


title: 200598350011_R06C01


title: 200598350011_R01C01


title: 200598350011_R02C01


title: 200598350006_R08C01


title: 200598350006_R07C01


title: 200598350006_R06C01


title: 200598350006_R04C01


title: 200598350006_R05C01


title: 200598350006_R03C01


title: 200598350006_R02C01


title: 200598350012_R04C01


title: 200598350005_R07C01


title: 200598350006_R01C01


title: 200598350005_R05C01


title: 200598350005_R04C01


title: 200598350011_R08C01


title: 200598350004_R08C01


title: 200598350004_R06C01


title: 200598350004_R07C01


title: 200598350004_R04C01


title: 200598350004_R05C01


title: 200598350004_R02C01


title: 200598340040_R05C01


title: 200598340040_R06C01


title: 200598340040_R02C01


title: 200598350004_R01C01


title: 200598340040_R04C01


title: 200598340040_R08C01


title: 200598340040_R07C01


title: 200598340040_R03C01


title: 200598340037_R07C01


title: 200598340037_R06C01


title: 200598340040_R01C01


title: 200598340037_R05C01


title: 200598340037_R04C01


title: 200598340037_R03C01


title: 200598340037_R02C01


title: 200598340037_R01C01


title: 200598350005_R01C01


title: 200598340033_R07C01


title: 200598340033_R08C01


title: 200598340033_R06C01


title: 200598340033_R05C01


title: 200598340033_R04C01


title: 200598350004_R03C01


title: 200598340033_R03C01


title: 200598340033_R02C01


title: 200594740086_R08C01


title: 200594740086_R06C01


title: 200594740086_R07C01


title: 200598340032_R07C01


title: 200598340032_R02C01


title: 200594740089_R06C01


title: 200594740087_R06C01


title: 200594740089_R05C01


title: 200594740087_R04C01


title: 200594740087_R03C01


title: 200598340032_R06C01


title: 200598340032_R08C01


title: 200594740087_R07C01


title: 200598340032_R04C01


title: 200594740087_R08C01


title: 200594740089_R08C01


title: 200598340032_R01C01


title: 200594740087_R02C01


title: 200594740087_R01C01


title: 200594740089_R01C01


title: 200594740089_R07C01


title: 200598340032_R05C01


title: 200594740089_R04C01


title: 200594740087_R05C01


title: 200594740089_R03C01


title: 200598340032_R03C01


title: 200598340033_R01C01


title: 200594740089_R02C01


title: 200594740086_R04C01


title: 200594740086_R05C01


title: 200594740086_R02C01


title: 200594740086_R01C01


title: 200594740085_R07C01


title: 200594740084_R06C01


title: 200594740083_R06C01


title: 200594740084_R03C01


title: 200594740083_R05C01


title: 200594740084_R01C01


title: 200594740085_R03C01


title: 200594740083_R04C01


title: 200594740084_R02C01


title: 200594740084_R04C01


title: 200594740084_R08C01


title: 200594740085_R02C01


title: 200594740083_R01C01


title: 200594740083_R07C01


title: 200594740084_R07C01


title: 200594740085_R06C01


title: 200594740080_R06C01


title: 200594740085_R01C01


title: 200594740083_R03C01


title: 200594740085_R05C01


title: Homo_Li_KPDS

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: G4-seq protocol

data_processing:
library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes:  http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)

source_name: purified DNA from Coriell Institute for Medical Research

growth_protocol: Organisms were cultured in standard conditions, withouth any treatment.

extract_protocol:
DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were  sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).

treatment_protocol: All samples were untreated, wild type organisms.

tag: strain or cell type


title: 200594740080_R07C01


title: 200594740080_R08C01


title: Homo_Li_K

description: G4-seq protocol


title: 200594740085_R08C01


title: 200594740085_R04C01


title: 200594740084_R05C01


title: 200594740080_R05C01


title: 200594740083_R08C01


title: 200594740083_R02C01


title: 200594740080_R03C01


title: 200594740080_R02C01


title: 200594740080_R04C01


title: 200594740080_R01C01


title: 200594740079_R04C01


title: 200594740079_R05C01


title: 200594740079_R08C01


title: 200594740079_R01C01


title: 200594740073_R06C01


title: 200594740075_R06C01


title: 200594740073_R04C01


title: 200594740075_R07C01


title: 200594740073_R08C01


title: 200594740079_R03C01


title: 200594740075_R04C01


title: 200594740073_R07C01


title: 200594740075_R03C01


title: 200594740079_R02C01


title: 200594740079_R06C01


title: 200594740079_R07C01


title: 200594740075_R02C01


title: 200594740075_R05C01


title: 200594740073_R05C01


title: 200594740073_R03C01


title: 200594740073_R02C01


title: 200594740073_R01C01


title: 200594740072_R08C01


title: FPCKpP1-4 cell line

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: FPCK p1-4

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: FPCKpP1-4 cell line

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: FPCK-1–1 and FPCKpP1-4 cells were maintained with a mixture of 6052 medium and DM-160 medium (Kyokuto, Japan) supplemented with 1% dialyzed FBS (GIBCO BRL, Grand Island, New York), ITSô premix (Becton Dickinson Labware, Maryland; 10 ng/ml of insulin, transferrin, and 10 pg/ml of selenious acid), and 10 ng/ml epidermal growth factor (Takara, Tokyo, Japan).

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (Qiagen).

tag: cell line

value: developed from nontumorigenic FPCK-1-1 cells and were converted to tumorigenic by chronic inflammation


title: 200594740072_R07C01


title: run183.SB-15perc-ETOH_L006

city: Chapel Hill

first: Abrar

middle: E

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

description:
neural fold-stage embryos
ALL_RUN-182-183.SB_ETOH_SALINE_EXONS-DEXSeq_unstranded-B.counts.txt
15perc-ETOH_NoIndex_L006

data_processing:
Illumina’s Genome Analyzer Pipeline Software v1.8 was used to transform the primary imaging output into fastq files containing sequences of nucleic acids associated with quality scores
Bowtie2 was used for alignment to the reference genome
featureCounts tool under subread package was used for exon level counts (parameters used: -f, -B, -s 0)
DEXSeq was used for generation of normalized abundances and statistics
Genome_build: Gallus gallus 5.0
Supplementary_files_format_and_content: The processed data file is in CSV or txt format with raw counts (ALL_RUN*txt) or all normalized read counts for each sample included, log2 fold changes, BH-output from DEXSeq (DAVID*csv).

organism: Gallus gallus

source_name: cranial headfolds_ETOH

growth_protocol: Embryos were incubated (3-4 somites, 27 hr incubation)

extract_protocol:
RNA was extracted using a RNAqueous-4PCR Kit (Ambion/Applied Biosystems, Carlsbad, CA)
cDNA libraries were constructed using the Illumina RNA Sequencing Sample Preparation kit. mRNA was purified from approximately 8 µg total purified RNA with poly-T oligo-attached magnetic beads. Double-stranded cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA) with random hexamer priming, purified with QIAquick PCR purification columns (Qiagen, Valencia, CA), ligated to Illumina adapters, and size-selected using electrophoresis to approximately 300bp.

treatment_protocol: 0.43 mmol USP grade ethanol or isotonic saline

tag: strain

value: Special black

tag: developmental stage

value: Hamburger-Hamilton stage 8-9

value: cranial headfolds


title: 200594740072_R06C01


title: 200594740072_R05C01


title: run183.SB-15perc-ETOH_L005

description:
neural fold-stage embryos
ALL_RUN-182-183.SB_ETOH_SALINE_EXONS-DEXSeq_unstranded-B.counts.txt
15perc-ETOH_NoIndex_L005


title: 200594740072_R04C01


title: 200594740072_R03C01


title: FPCK-1-1 cell line

description: FPCK 1-1

source_name: FPCK-1-1 cell line

value: human colonic adenoma cell line


title: run182.SB-Saline_L006

description:
neural fold-stage embryos
ALL_RUN-182-183.SB_ETOH_SALINE_EXONS-DEXSeq_unstranded-B.counts.txt
Saline_NoIndex_L006

source_name: cranial headfolds_saline


title: 200594740070_R01C01


title: 200594740072_R01C01


title: 200594740070_R03C01


title: 200594740070_R07C01


title: 200594740070_R04C01


title: 200594740069_R08C01


title: 200594740070_R02C01


title: 200594740072_R02C01


title: 200594740069_R07C01


title: 200594740070_R08C01


title: Resident fibroblast transfected with stealth WT1 siRNA, V6

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
VS6
processed data file: countsTable.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
Fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using DESeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: countsTable.txt: Tab-delimited text file includes raw counts with genes in rows and samples in columns.

organism: Mus musculus

source_name: Lung resident fibroblasts

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Fibrotic lung resident fibroblasts were isolated from TGFα mice and treated with Control or WT1-specific siRNA.

tag: genotype/variation

value: TGF-alpha transgenic

value: Cultured fibrotic lung resident fibroblasts

tag: sirna


title: Resident fibroblast transfected with stealth WT1 siRNA, V4

description:
VS4
processed data file: countsTable.txt

tag: cell type


title: 200594740069_R06C01


title: 200594740069_R05C01


title: 200594740069_R04C01


title: Resident fibroblast transfected with stealth control siRNA, VS3

description:
VS3
processed data file: countsTable.txt

value: Control


title: Resident fibroblast transfected with stealth control siRNA, VS2

description:
VS2
processed data file: countsTable.txt


title: 200594740069_R03C01


title: run182.SB-Saline_L007

description:
neural fold-stage embryos
ALL_RUN-182-183.SB_ETOH_SALINE_EXONS-DEXSeq_unstranded-B.counts.txt
Saline_NoIndex_L007


title: 200594740069_R01C01


title: 200594740057_R08C01


title: 200594740057_R07C01


title: H226 anti-CD26

description: H226 anti-CD26/H226 Cont

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: H226 Cont

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: H226 and JMN cells were maintained with RPMI-1640 supplemented with 10%FCS at 37ºC, 5% CO2.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen)

treatment_protocol: H226 and JMN cells (2.5 x 10^5 ) were seed into 24 well culture plate, add anti-CD26Ab (10µg/ml), and at 16hr total RNA was isolated.

tag: agent

value: control

source_name: H226 anti-CD26


title: Resident fibroblast transfected with stealth control siRNA, VS1

description:
VS1
processed data file: countsTable.txt


title: 200594740070_R06C01

value: Peripheral Blood


title: Resident fibroblast transfected with stealth WT1 siRNA, V5

description:
VS5
processed data file: countsTable.txt


title: 200594740057_R06C01


title: 200594740057_R05C01


title: 200594740057_R04C01


title: 200594740052_R07C01

value: Male


title: 200594740057_R02C01


title: 200594740052_R08C01


title: 200594740057_R03C01


title: 200594740057_R01C01

value: Female


title: 200594740052_R06C01


title: 200594740052_R05C01


title: 200594740069_R02C01


title: 200594740052_R03C01


title: JMN anti-CD26

description: JMN anti-CD26/JMN Cont

source_name: JMN Cont

value: JMN

source_name: JMN anti-CD26


title: 200594740052_R02C01


title: 200594740052_R01C01


title: 200594740051_R08C01


title: 200594740051_R06C01


title: 200594740051_R05C01


title: 200594740052_R04C01


title: 200594740051_R03C01


title: 200594740051_R01C01


title: CD19-MS-ZM

first: Renato

last: Umeton

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

hyb_protocol: Labeled cDNA was hybridized to GeneChip® Human Exon 1.0 ST Arrays according to the manufacturer’s protocols.

scan_protocol: All arrays were stained in the Fluidics Station 450 and then scanned on the GeneChip® Scanner 3000 (Affymetrix, USA) according to the manufacturer's instructions.

data_processing:
Affymetrix Power Tools: http://www.affymetrix.com/support/developer/powertools/index.affx using RMA-sketch
Gene-level and exon-level analyses were performed. The output from the RMA-sketch script (for both analyses) is available on the series record. The sample data tables include the gene-level RMA-sketch values.

label: biotin

source_name: CD19 cells

label_protocol: RNA quality and purity were assessed by RNA 6000 Nano assay on Agilent 2100 Bioanalyzer (Agilent). RNA was processed for use on GeneChip® Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Single stranded cDNA was fragmented and end-labeled following the GeneChip WT Terminal Labeling Kit- Affymetrix.

growth_protocol: CD19 cells were obtained from fresh peripheral blood mononuclear cells of healthy donors and multiple sclerosis patients

extract_protocol: Highly purified CD19+ B cells were lysed and frozen in QIAzol Lysis Reagent (Qiagen, Hilden, Germany). Total RNA, including small RNA, was extracted by miRNeasyMini Kit® (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Fresh peripheral blood mononuclear cells (PBMCs) were obtained by density gradient centrifugation over Ficoll–Hypaque according to standard procedure. B cells were purified by positive sorting using anti-CD19 conjugated magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) following the recommended protocol

value: peripheral blood

value: CD19+ B cell

value: multiple sclerosis (MS)


title: 200594740051_R02C01


title: 200594740047_R08C01


title: CD19-MS-NB


title: 200594740051_R04C01


title: 200594740051_R07C01


title: 200594740047_R07C01


title: CD19-MS-GP


title: CD19-MS-TF


title: CD19-MS-MD


title: CD19-MS-MIV


title: CD19-MS-MV-bis


title: CD19-MS-GAL


title: 200594740047_R06C01


title: CD19-MS-GF


title: 200594740047_R04C01


title: 200594740047_R03C01


title: 200594740047_R05C01


title: CD19-MS-BM


title: CD19-H-VD

value: healthy


title: CD19-H-SF


title: CD19-H-CG


title: 200594740047_R02C01


title: CD19-H-TMS


title: CD19-H-CD


title: CD19-H-OA


title: CD19-H-AM-bis


title: CD19-H-EN


title: CD19-H-AL


title: 200594740047_R01C01


title: CD19-H-BC


title: 200594740046_R08C01


title: 200594740046_R07C01


title: 200594740046_R05C01


title: 200594740046_R06C01


title: SHC_2

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

hyb_protocol: After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, then placed in a humidified container for a minimum of 16 h at 48°C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: After staining was complete, the slides were washed with low salt wash buffer (PB1), immediately coated with XC4, and then imaged on the Illumina iScan Reader which is a two-color (532 nm/658 nm) confocal fluorescent scanner with 0.53 m pixel resolution. The image intensities are extracted using Illumina’s iScan Control software

data_processing:
Raw data were extracted as beta values for each CpG for each sample using R watermelon package. Beta values were calculated by subtracting background using negative controls on the array and taking the ratio of the methylated signal intensity against the sum of both methylated and unmethylated signals. Array CpG probes that have detection p-value ≥ 0.05 (similar to signal to noise) in over 25% samples were filtered out. And then filtered data was background correction & dye bias equalization by R methylumi & lumi package. To reduce Infinium I and Infinium II assay bias, corrected signal value was normalized by BMIQ (Beta Mixture Quantile) method.
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). Beta values were calculated by subtracting background using negative controls on the array and taking the ratio of the methylated signal intensity against the sum of both methylated and unmethylated signals. A beta value of 0.0-1.0 was reported significant percent methylation, from 0% to 100%, respectively, for each CpG site. Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0) and R 3.0.2
Array CpG probes that have detection p-value ≥ 0.05 (similar to signal to noise) in over 25% samples were filtered out. And then filtered data was background correction & dye bias equalization by R methylumi & lumi package. To reduce Infinium I and Infinium II assay bias, corrected signal value was normalized by BMIQ (Beta Mixture Quantile) method. Differentially expressed methylation list were determined using |delta_mean| ≥ 0.2 (the difference of methylation signal, avg beta of Case – avg beta of Control) and p-value < 0.05 of independent t-test in which the null hypothesis was that no difference exists among 2 groups.

source_name: Human umbilical cord blood-derived mesenchymal stem cells(MSCs)

label_protocol: The HumanMethylation 450 BeadChip employs both infinium I and infinum II assay, enhancing the breadth of coverage it is able to include.

growth_protocol: Human UCB-MSCs used in the present study were grown in Minimum Essential Medium-a (MEM-a, Gibco, Carlsbad, Grand Island, NY)  supplemented with 2mM L-glutamine, 20mM 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) (pH7.3), minimum essential medium(MEM) nonessential amino acid solution, penicillin/streptomycin(Corning Cellgro; Thermo Fisher Scientific, Inc., Waltham, MA, USA), 1mg/ml ascorbic acid (Sigma-Aldrich), 10% heat-inactivated fetal bovine serum(FBS) (Hyclone) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Genomic DNA (gDNA) were isolated using the DNeasy Blood & Tissue Kit (Qiagen Inc, Valencia, CA, USA). Next, 500 ng of gDNA were used in bisulfite conversion with Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA). For sample amplification and hybridization for BeadChips, 200ng of input bisulfite-converted DNA (MA1) was required to create a sufficient quantity of DNA (1000  amplification) on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM)

treatment_protocol: MSCs cultured under SHC procedure (SHC) were cultivated under 3 % hypoxic condition in MEM-a medium supplemented with 1.8 mM calcium and 10% fetal bovine serum (FBS, Gibco). For control, normally cultured naïve MSCs were used.

value: Umbilical cord blood

value: Mesenchymal stem cell


title: eFHLC, day 13 biological rep1

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Gene expression data from early stage fetal hepatocyte-like cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy Gene Chip Scanner 3000 7G.

data_processing: The probe level intensities were adjusted by quantile normalization and gene expression measures were summarized by the robust multi-array analysis (RMA) approach with Bioconductor software

source_name: Cultured cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in condition medium from fetal human hepatocytes

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

treatment_protocol: No treatment

tag: cells

value: Differentiated HESC

tag: time point

value: day 13


title: 200594740046_R04C01

source_name: Peripheral Blood

tag: tissue

tag: gender


title: eFHLC, day 3 biological rep1

value: day 3


title: 200594740046_R02C01

tag: age

tag: ln(totalpbb)


title: eFHLC, day 13 biological rep2


title: eFHLC, day 3 biological rep2


title: NT_2

description: control replicate#2


title: eFHLC, day 3 biological rep3


title: SHC_3


title: 200594740046_R03C01


title: inhi

city: BEIJING

first: WEI

last: TIAN

address: FUCHENG ROAD 52#

country: China

institute: BEIJING CANCER HOSPITAL

description: Gene expression data from human colon cancer cell HCT116's total RNA ater treated by inhibitor ctrl

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45℃ on Affymetrix U133 Plus 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HCT116 cells with transfection of single-stranded scrambled RNA  as ctrl

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HCT116 cell lines were cultured in RPMI 1640 medium containing 10% FBS and 100 U/mL penicillin/streptomycin at 37℃ in a humidiﬁed incubator with 5% CO2.

treatment_protocol: HCT116 cells were transfected with plasmids pcDNA3.1or pcDNA3.1-pri-miR663a, or single-stranded  RNA ctrl and inhibitor for miR663a.


title: SHC_1


title: eFHLC, day 13 biological rep3


title: AEC 16d

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

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

scan_protocol: Arrays were scanned using Illumina iScan using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: ddCTP with biotin; ddATP, ddUTP and ddGTP with 2,4-dinitrophnenol

source_name: Primary feto-placental endothelial cells

label_protocol: Standard Illumina Protocol

growth_protocol: Primary arterial (AEC) and venous endothelial cells (VEC) were isolated from third trimester human placentas after healthy and GDM (dAEC, dVEC) complicated pregnancies following a standard protocol (Lang I et. al,  Differentiation. 76:1031-1043, 2008)

extract_protocol: genomic DNA was extracted and purified using trizol according to standard instructions

value: arterial

tag: fetal sex

value: female


title: VEC 21d

value: venous


title: NT_1

description: control replicate#1


title: 200594740039_R08C01

data_processing:
non-normalized, background subtracted
beta-values


title: 200594740039_R07C01


title: ctrl

description: Gene expression data from human colon cancer cell HCT116's total RNA ater treated by miR663a inhibitor

source_name: HCT116 cells with transfection of single-stranded miR663a inhibitor


title: 200594740046_R01C01


title: 200594740039_R06C01


title: AEC 20d

value: male


title: NT_3

description: control replicate#3


title: 663

description: Gene expression data from human colon cancer cell HCT116's total RNA ater treated by miR663a overexpression

source_name: HCT116 cells with pcDNA3.1-pri-miR663a overexpression

value: pcDNA3.1-pri-miR663a overexpression


title: VEC 10d


title: 3.1

description: Gene expression data from human colon cancer cell HCT116's total RNA ater treated by vector ctrl

source_name: HCT116 cells with pcDNA3.1 vector overexpression

value: pcDNA3.1 vector overexpression


title: 200594740039_R05C01

value: Peripheral Blood

value: Female


title: 200594740039_R03C01

value: Male


title: recurrence 5

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip S.canner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: colonosphere L145

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 200ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Human Tissue

extract_protocol: Total RNA was isolated using RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Not Applicable

value: liver metastasis

value: KRAS mutant p.G12D

value: Recurrence


title: recurrence 3


title: VEC17d


title: 200594740039_R02C01

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)


title: VEC 25d


title: recurrence 4


title: AEC 11d


title: AEC110


title: VEC 110


title: 200594740039_R01C01


title: recurrence 2


title: VEC 11d


title: VEC107


title: VEC 20d


title: 200594740035_R08C01


title: pre-treatment 5

value: Pre-treatment


title: AEC 107


title: 200594740035_R07C01


title: 200594740035_R06C01


title: 200594740035_R05C01


title: pre-treatment 3


title: pre-treatment 4


title: 200594740035_R04C01


title: recurrence 1


title: VEC 98


title: 200594740035_R03C01


title: pre-treatment 1


title: post-treatment 5

value: Post-treatment


title: AEC 98


title: pre-treatment 2


title: AEC 8d


title: post-treatment 3


title: 200594740035_R01C01


title: VEC 2d


title: 200594740035_R02C01


title: VEC 9d


title: VEC 92


title: CS2: ChIP_seq_RPA_aB_28h_HU_28h_10mM_rep2

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
mouse ChIP-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
Genome_build: GRCm38p2/mm10 for mouse
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Activated primary B cells

extract_protocol:
20 million fixed B-cells were washed twice with cold PBS and pellets were snap frozen in dry ice and stored at −80°C. Fixed cell pellets of 20 million cells were thawed on ice and resuspended in 1 mL of cold RIPA buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using the Covaris S220 sonicator at duty cycle 20%, peak incident power 175, cycle/burst 200 for 30 min. Chromatin were clarified by centrifugation at 21,000 g at 4°C for 10 min and precleared with 80 μL prewashed Dynabeads protein A (ThermoFisher) for 30 min at 4°C. 40 μL prewashed Dynabeads protein A were incubated with 10 μg of Anti-RPA32/RPA2 antibody (Abcam, ab10359) in 100 μL of PBS for 20 min at room temperature in continuous mixing, washed twice in PBS for 5 min and added to 1 mL of chromatin followed by overnight incubation at 4°C on a rotator. Beads were then collected in a magnetic separator (DynaMag-2 Invitrogen), washed twice with cold RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (10 mM Tris pH 8.0, 1mM EDTA) plus 0.2% Triton X-100, and once with TE. Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1mg/ml of Proteinase K (Ambion). DNA was purified by standard phenol-chloroform method and eluted in 20 μl. 100ng ChIP DNA was used to prepare Illumina sequencing libraries.
libraries were prepared and sequenced following standard Illumina protocols

value: Activated primary B cells

tag: genotype

value: WT


title: AEC 105


title: post-treatment 4


title: post-treatment 1


title: 200594740034_R07C01

first: Sarah

last: Curtis

address: 101 Woodruff Circle NE, Ste 42

institute: Emory University


title: 14285x5

city: Salt Lake City

first: Frank

middle: B

last: Sachse

state: Utah

department: CVRTI

institute: University of Utah

data_processing:
Reads were aligned to the Oryctolagus cuniculus genome assembly OryCun2.0 (GCA_000003625.1) with Spliced Transcripts Alignment to a Reference (STAR) software
DESeq2 was used to normalize counts.
Genome_build: OryCun2.0 (GCA_000003625.1)
Supplementary_files_format_and_content: ReadsPerGene.out.tab

organism: Oryctolagus cuniculus

source_name: Left ventricle

extract_protocol:
Total RNA was isolated and purified from 20-30 mg of tissue with either Zymo Direct-zol RNA Miniprep Kit (R2061) or Qiagen RNeasy Mini Kit (74104).
Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2301 and RS-122-2302).

treatment_protocol: The animals had undergone sham surgery where a suture was loosely tied around a coronary artery without occluding it. After 3 weeks the hearts were harvested and perfused with Ca2+-free solution for 5 min to wash out the blood in the heart. Tissue samples were snap frozen in liquid nitrogen and stored at -80 ̊C.

value: Left ventricle

value: adult


title: 200594740034_R06C01


title: 14285x4


title: NS4: nRNA_seq_aT_28h_NT_rep1

data_processing:
Library strategy: nRNA-seq
mouse nRNA-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), pre-B cells (40 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), neurons (5 million per agarose plug), MCF7 (5 million per agarose plug) and Nalm6 (15 million per agarose plug) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols

tag: molecule subtype

value: nascent RNA


title: AEC 92

value: arterial


title: 200594740034_R08C01


title: post-treatment 2


title: AEC 103

value: male


title: 200594740039_R04C01


title: NS3: nRNA_seq_aB_28h_NT_rep1


title: 200594740034_R05C01


title: 14285x3


title: VEC 103

value: venous


title: 200594740034_R04C01


title: VEC 105

value: female


title: NS2: nRNA_seq_aT_28h_HU_28h_6mM_rep1


title: 200594740034_R03C01

value: Peripheral Blood


title: NS1: nRNA_seq_aB_28h_HU_28h_10mM_rep1


title: 13872x5


title: EC1: EdC_seq_aB_28h_HU_28h_10mM_rep1

description: Control: EdU_seq_aB_28h_NT_rep1

data_processing:
Library strategy: EdU-seq
mouse nRNA-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   -l 50 -n 2 --best --all --strata -m 1
EdU-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Cells were incubated with 20 uM EdU for 28 hours (B cells, T Cells).  For Click-IT reaction, cell pellets were resuspended in PBS, 10 M Biotin Azide (ThermoFisher Cat# B10184), 200 uM CuSO4 (Sigma), and 10 mM sodium ascorbate (Sigma) for 2 hours, at room temperature,in the dark for 2 hours. Biotin-EdU labeled DNA fragments were puriﬁed using MyOne Streptavidin C1 Beads (ThermoFisher #650-01).  35 L of Dynabeads were washed twice with 1 mL Binding and Wash Buffer (1xBWB) (10 mM Tris-HCl pH8.0, 1 mM EDTA, 1 M NaCl, 0.1% Tween20). Beads were recovered using a DynaMag-2 magnetic separator (12321D, Invitrogen). Supernatants were discarded.
libraries were prepared and sequenced following standard Illumina protocols


title: 13872x3


title: 200594740034_R01C01

value: Female


title: 200594740033_R08C01

value: Male


title: EU4: EdU_seq_aB_28h_NT_rep1

description: Control: NA


title: 200594740033_R07C01


title: 200594740033_R06C01


title: RanBP9D1  /BSC469_3

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
data sets were aligned using TopHat2 Drosophila genome dm6
Counting aligned reads per genes were performed with HTSeq
Differential expression analysis was performed with DESeq2
Genome_build: dm6 (BDGP6.87)
Supplementary_files_format_and_content: text file of expression values per sample in RPKM format

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: All flies were maintained at +25°C.

extract_protocol:
Total RNA was extracted from dissected ovaries with TRIzol (15596026, Thermofisher) according to the manufacturer’s protocol
NEBNext Ultra II Directional RNA Library after purification with polyA binding beads

value: RanBP9D1  /BSC469

tag: replicate


title: VEC 53


title: w1118/BSC469_1


title: RanBP9D1  /BSC469_2


title: w1118/BSC469_3


title: AEC 112


title: VEC 112


title: VEC 84


title: 200594740033_R05C01

city: Atlanta


title: RanBP9D1  /BSC469_1


title: EU1: EdU_seq_aB_28h_HU_28h_10mM_rep1

description: Control: EdU_seq_aB_28h_NT_rep1


title: w1118/BSC469_2


title: CS1: ChIP_seq_RPA_aB_28h_HU_28h_10mM_rep1


title: EU2: EdU_seq_aB_28h_HU_28h_10mM_rep2

description: Control: EdU_seq_aB_28h_NT_rep1


title: w1118_input

data_processing:
ChIP-Seq data sets were aligned using Bowtie2
Peak calling was performed in R using BayesPeak package
Genome_build: dm6 (BDGP6.87)
Supplementary_files_format_and_content: bigwig files were generated using DeepTools

source_name: overies

extract_protocol:
ovaries dissected from fly strains were fixed in 1% PFA for 10 min at RT, homogenized using a pestle in 300 ml of RIPA buffer, and sonicated with Bioruptor (Diagenode).At least 100 ovaries were used per one IP. Immunoprecipitations were carried out with 5 µg antibody overnight at 4°C in a rotating wheel.
ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.

tag: strain background

tag: chip antibody


title: AEC 84


title: 200594740033_R03C01


title: EU3: EdU_seq_aB_28h_HU_28h_10mM_rep3

description: Control: EdU_seq_aB_28h_NT_rep1

tag: strain


title: ES14: END_seq_aB_28h_HU_28h_0.5mM_CAST_eij_rep1

description: Control: END_seq_aB_28h_NT_rep1

data_processing:
Library strategy: END-seq
mouse and human reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), HCT116 (7.5 million per agarose plug)were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols

value: CAST


title: AEC 53


title: 200594740033_R02C01


title: w1118-Pol2-S5P-3

value: 4H8; ab5408, Abcam


title: ES12: END_seq_aB_28h_ATRi_28h_rep1

description: Control: END_seq_aB_28h_NT_rep1


title: ES13: END_seq_aB_28h_HU_28h_0.5mM_BL6_eij_rep1

description: Control: END_seq_aB_28h_NT_rep1


title: w1118-Pol2-S5P-2


title: ES11: END_seq_aB_28h_CDC2i_CDC7i_0.5h_HU_6h_0.5mM_rep1

description: Control: END_seq_aB_28h_NT_rep1


title: 200594740033_R01C01


title: 200594740033_R04C01


title: 200594740031_R08C01


title: w1118-Pol2-S5P-1


title: 200594740031_R07C01


title: w1118-Pol2-S2P-1

value: ab5095, Abcam


title: ES10: END_seq_aB_28h_CDC2i_CDC7i_0.5h_HU_6h_10mM_rep1

description: Control: END_seq_aB_28h_NT_rep1


title: w1118-normal_mIgG-3

value: sc-2025, Santa Cruz Biotechnology


title: ES6: END_seq_aB_28h_HU_28h_0.5mM_rep1

description: Control: END_seq_aB_28h_NT_rep1

value: Activated primary B cells


title: w1118-normal_mIgG-2


title: 200594740031_R06C01


title: ES5: END_seq_aB_28h_NT_rep2

description: Control: N/A

value: WT


title: 200594740031_R05C01


title: 200594740031_R04C01


title: w1118-histoneH3K4me3-2

value: ab8580, Abcam


title: w1118-normal_mIgG-1


title: 200594740031_R03C01


title: w1118-histoneH3K4me3-1


title: 200594740031_R01C01


title: 200594720089_R08C01


title: w1118-AC-74-3


title: ES3: END_seq_aB_28h_HU_6h_10mM_rep1

description: Control: END_seq_aB_28h_NT_rep1


title: ES2: END_seq_aB_28h_HU_28h_10mM_rep2

description: Control: END_seq_aB_28h_NT_rep2


title: w1118-AC-74-2


title: 200594720089_R07C01


title: ES7: END_seq_aT_28h_HU_28h_2mM_rep1

description: Control: N/A

source_name: Activated primary T cells

value: Activated primary T cells


title: 200594720089_R05C01


title: 200594720089_R06C01


title: w1118-AC-74-1


title: 200594720089_R04C01


title: w1118-AC-15-1


title: MAL-GFP_Pol2S5P

value: tub mal-d3xGFP


title: MAL-GFP_normal-mIgG


title: 200594720089_R03C01


title: MAL-GFP_AC-74


title: 200594720089_R02C01


title: MAL-GFP_GFP

value: GFP-Trap ChromoTek


title: 200594720089_R01C01


title: MAL-GFP-input


title: 200594720075_R08C01


title: 200594720075_R06C01


title: 200594720075_R07C01


title: delMAL_AC-74


title: delMAL_Pol2S5P


title: delMAL_normal_mIgG


title: 200594720075_R03C01


title: del-MAL_GFP


title: shiyan30__L7

city: Shanghai

first: Xue

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
The software btrim was utilized to discard low qulity reads whose insert size were less than 30, or average quality score within a moving window were less than 20
The clean data were mapped to the Mus musculus reference genome (GRCm38) using TopHat2 (v2.0.14), with options ‘-N 3 --read-gap-length 3 --read-edit-dist 3’.
Gene expression levels and differential expression were got through the Cufflinks and Cuffdiff program, respectively, in the Cufflinks tool suite (v2.2.1) using the default parameters.
Using the database for annotation, visualization and integrated discovery (DAVID v6.8), the functional annotation of differentially expressed genes was performed.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: abundance measurements

source_name: FACS prostate epithelial cells

growth_protocol: Tempreture is 25℃ and the humidity is 50%, 14h lights on/ 10h lights off.

extract_protocol:
3-month old mouse prostate tissues were got and digested with collagenase type I and 0.25% trypsin/EDTA. Single cell suspension was obtained from passing through a 40µm cell strainer and then FACS sorting for prostate epithelial cells before processing to total RNA extraction, quantification, qualification and finally library preparation. 3ug RNA  were used for the construction of sequencing libraries.
Libraries were constructed following the instruction of the Chromium single cell 3’ solution (10x Genomics). The libraries were sequenced on Illumina Hiseq X Ten platform.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: Normal growth condtion

value: prostate tissue cells

value: 3-month old

tag: genotype/variation

value: E-cadherin conditional knockout


title: del-MAL-input


title: Plasmodium_Li_K

city: Cambridge

description: G4-seq protocol

data_processing:
library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes:  http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)

organism: Plasmodium falciparum

source_name: whole cell

extract_protocol:
DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were  sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).

value: whole cell


title: shiyan28__L7


title: 200594720026_R08C01

value: Peripheral Blood


title: 200594720075_R01C01

value: Male


title: shiyan13__L7


title: Sample_90170: Het_2

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description: FACS-sorted, tamoxifen at P8

data_processing:
We downloaded the reads files and  concatenated those into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC [1] (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10)  [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran two different, popular techniques for differential expression analysis: Cufflinks/CuffDiff and HTSeq/DESeq2 [9], using UCSC mm10.fa as the reference genome sequence.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

source_name: Dental follicle (mandibular molars)

extract_protocol:
Mandibular molars were extracted, dental follicle cells were enzymatically dissociated and tdTomato+ cells were FACS-isolated. Total RNA was isolated using PicoPure RNA isolation kit and cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA kit for Sequencing.
Nextera XT DNA Library Preparation Kit

value: Dental follicle (mandibular molars)

value: PTHrP+ dental follice cells (tdTomato+)

value: Postnatal day 8


title: Sample_90171: KO-2

description: FACS-sorted, tamoxifen at P8


title: CTL46__L2

value: control


title: 200594720075_R02C01


title: 200594740034_R02C01

value: Female


title: Sample_90169: KO_1

description: FACS-sorted, tamoxifen at P8


title: Sample_90168: Het_1

description: FACS-sorted, tamoxifen at P8


title: 200594720026_R06C01


title: 200594720075_R04C01


title: Sample_90167: KO_0

description: FACS-sorted, tamoxifen at P8


title: 200594720075_R05C01


title: Plasmodium_Li_KPDS

description: G4-seq protocol


title: CTL14__L2


title: 200594720026_R03C01


title: Sample_90166: Het_0

description: FACS-sorted, tamoxifen at P8


title: Menin 4-OHT rep1

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

data_processing:
Quality trim to a minimum of Q15
Map to the mm10 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20141217_250/gsnap -d mm10_total -v mm10_total.snp138 --use-splicing=mm10_total.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $file > ./${j}.sam
sort and index using SAMTOOLS
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing FPKM values

source_name: MLL-AF9-transformed cells from LSK+ bone marrow cells

growth_protocol: Bone marrow cells were transformed by MLL-AF9 in M3434 methylcellulose, then grown in liquid culture using IMDM-based medium supplemented with 50 ng/mL SCF, 10 ng/mL IL-3 and 10 ng/mL IL6

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Illumina directional mRNA prep

treatment_protocol: Cells were treated with ethanol or 100 nM 4-OHT for 24 hours. The drug was washed out for an additional culture period of 2 days.

value: 72 hours since initiating the treatment

value: 100 nM 4-OHT


title: 200594720026_R04C01


title: 200594720026_R02C01


title: Menin 4-OHT rep2


title: 200590500076_R08C01


title: Menin EtOH rep1

value: EtOH


title: ΔMSN1 22h after lights off [dMSN1_22]

city: Heidelberg

first: Michael

last: Brunner

state: Baden-Württemberg

address: Im Neuenheimer Feld 328

department: Biochemistry Center

country: Germany

institute: Heidelberg University

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms166_sequence

data_processing:
Base calling using HiSeq Control Software (HCS) v2.2.38.
Transcript-level quantification using the pseudoalignment approach of kallisto (v 0.43.1) using kallisto quant -b 50 --single --rf-stranded -l 175 -s 20 --bias.
Counts extracted using tximport (v 1.4.0) with the gene level summarization with countsFromAbundance set to "scaledTPM".
Genome_build: NC12
Supplementary_files_format_and_content: comma-separated text file  of read counts from scaled TPM values (unnormalized)

organism: Neurospora crassa

source_name: ΔMSN circadian time series

growth_protocol: Vogel's medium (1 X) supplemented with 2% glucose, 0.5% L-arginine and 10 ng/ml biotin was used as a standard growth medium. 200 ml medium in 500 ml flasks were inoculated with approximately 106 conidia and grown in light for six hours for conidial germination. Afterwards cultures were entrained in 11 hour/11 hour light/dark cycles for 2 days and released to constant dark for 22 hours. Cultures were transferred in a staggered manner, so harvesting of the cultures was performed within 10 hours.

extract_protocol:
Total RNA was extracted by Triazol reagent and mRNA libraries were prepared with NEBNext Ultra RNA Library Prep Kit for Illumina in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBnext multiplex module.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: msn-1 (NCU02671) knockout

value: 22h after lights off


title: ΔMSN1 20h after lights off [dMSN1_20]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms164_sequence

value: 20h after lights off


title: 200594720026_R07C01

description: HumanMethylationEPIC BeadChip - standard protocol

source_name: Peripheral Blood


title: 200590500076_R07C01


title: CTL29__L2

value: prostate tissue cells


title: 200594720026_R01C01


title: L3_cKO_3

city: Hong Kong

first: Yin

last: Xia

address: LKIBSB

institute: The Chinese University of Hong Kong

data_processing:
Basecalls performed using bcl2fastq2 version 2.16
Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read) are discarded and then mapped to mm10 whole genome using HISAT2 v2.0.4 with parameters:  --phred64 --sensitive --no-discordant --no-mixed -I  1 -X 1000, mapped to gene reference using Bowtie2 v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
DEGs (Differentially expression genes) between samples were identified using PossionDis based on the poisson distribution (Filtering parameters: Fold Change >= 2.00 and FDR <= 0.001), performed as described at Audic S, et al. DEGs between groups were identified using DEseq2 with parameters: Fold Change >= 1.50 and Adjusted Pvalue <= 0.05; DEseq2 is based on the negative binomial distribution described at Michael I, et al.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include expected count and FPKM values for each Sample.

source_name: Testis

extract_protocol:
Total RNA was extracted from control and L3mbtl2 cKO testes at 8 months of age using RNA extraction kit (Takara, Cat#9767) with DNase I treatment. Then mRNAs are isolated from total RNA with oligo(dT) method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: L3mbtl2 cKO

value: testis

value: 8 month


title: ΔMSN1 18h after lights off [dMSN1_18]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms162_sequence

value: 18h after lights off


title: 200594720026_R05C01

value: Peripheral Blood

value: Male


title: 200590500076_R06C01


title: 200590500076_R05C01


title: L3_cKO_1


title: 200590500076_R04C01


title: L3_Ctrl_3


title: ΔMSN1 14h after lights off [dMSN1_14]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms158_sequence

value: 14h after lights off


title: 13872x2

value: Left ventricle

value: adult


title: L3_Ctrl_2

value: control


title: Menin EtOH rep2

value: 72 hours since initiating the treatment


title: ΔMSN1 12h after lights off [dMSN1_12]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms156_sequence

value: 12h after lights off


title: 200590500076_R03C01


title: ΔMSN1 10h after lights off [dMSN1_10]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms154_sequence

value: 10h after lights off


title: 200590500076_R02C01


title: 200590500076_R01C01

value: Female


title: L3_Ctrl_1


title: ΔMSN1 8h after lights off [dMSN1_8]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms152_sequence

value: msn-1 (NCU02671) knockout

value: 8h after lights off


title: 200590490074_R08C01


title: ΔMSN1 6h after lights off [dMSN1_6]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms150_sequence

value: 6h after lights off


title: 200590490074_R07C01


title: ΔMSN1 0h after lights off [dMSN1_0]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms144_sequence

value: 0h after lights off


title: ΔMSN1 4h after lights off [dMSN1_4]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms148_sequence

value: 4h after lights off


title: 200590490074_R05C01


title: ΔMSN1 2h after lights off [dMSN1_2]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms146_sequence

value: 2h after lights off


title: ΔMSN1 16h after lights off [dMSN1_16]

description:
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms160_sequence

value: 16h after lights off


title: L3_cKO_2

value: L3mbtl2 cKO

value: testis

value: 8 month


title: wt 22h after lights off [WT_new_66]

description:
processed data file: WT_counts.csv
C5703ACXX_WT66_DD

source_name: wt circadian time series

value: wild type

value: 22h after lights off


title: 200590490074_R03C01

value: Peripheral Blood


title: wt 20h after lights off [WT_new_64]

description:
processed data file: WT_counts.csv
C5703ACXX_WT64_DD

value: 20h after lights off


title: 200590490074_R01C01


title: 200590490074_R02C01

value: Male


title: 200590490062_R08C01


title: wt 16h after lights off [WT_new_60]

description:
processed data file: WT_counts.csv
C5703ACXX_WT60_DD


title: wt 14h after lights off [WT_new_58]

description:
processed data file: WT_counts.csv
C5703ACXX_WT58_DD

value: 14h after lights off


title: 200590490062_R07C01


title: wt 18h after lights off [WT_new_62]

description:
processed data file: WT_counts.csv
C5703ACXX_WT62_DD

value: 18h after lights off


title: wt 12h after lights off [WT_new_56]

description:
processed data file: WT_counts.csv
C5703ACXX_WT56_DD

value: 12h after lights off


title: 200590490074_R04C01

description: HumanMethylationEPIC BeadChip - standard protocol


title: 200590490074_R06C01

value: Female


title: Zebrafish_Li_KPDS

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: G4-seq protocol

organism: Danio rerio

source_name: whole embryo

value: whole embryo


title: Zebrafish_Li_K

description: G4-seq protocol


title: 200590490056_R08C01


title: 200590490062_R03C01


title: 200590490062_R01C01


title: 200590490062_R04C01


title: 200590490062_R05C01


title: 200590490056_R06C01


title: wt 10h after lights off [WT_new_54]

description:
processed data file: WT_counts.csv
C5703ACXX_WT54_DD

value: 10h after lights off


title: 200590490062_R02C01


title: 200590490056_R05C01


title: wt 8h after lights off [WT_new_52]

description:
processed data file: WT_counts.csv
C5703ACXX_WT52_DD

value: 8h after lights off


title: wt 0h after lights off [WT_new_44]

description:
processed data file: WT_counts.csv
C5703ACXX_WT44_DD

value: 0h after lights off


title: wt 6h after lights off [WT_new_50]

description:
processed data file: WT_counts.csv
C5703ACXX_WT50_DD

value: 6h after lights off


title: wt 4h after lights off [WT_new_48]

description:
processed data file: WT_counts.csv
C5703ACXX_WT48_DD

value: 4h after lights off


title: wt 2h after lights off [WT_new_46]

description:
processed data file: WT_counts.csv
C5703ACXX_WT46_DD

value: 2h after lights off


title: 200590490056_R04C01


title: 200590490056_R03C01


title: 200590490056_R02C01


title: 200590490062_R06C01


title: EU5: EdU_seq_aB_28h_HU_28h_0.5mM_rep1

description: Control: EdU_seq_aB_28h_NT_rep1

value: Activated primary B cells

value: WT


title: 200590490056_R01C01


title: 200590490052_R08C01


title: Ecoli_Li_K

description: G4-seq protocol

organism: Escherichia coli

source_name: purified DNA from Zymo Research

tag: strain or cell type

value: ER2925 strain, D5016


title: Ecoli_Li_KPDS

description: G4-seq protocol


title: 200590490052_R07C01

value: Peripheral Blood


title: 200590490052_R06C01


title: 200590490052_R04C01


title: 200590490052_R03C01


title: 200590490021_R07C01


title: 200590490052_R01C01


title: 200590490052_R02C01


title: 200590490021_R06C01


title: 200590490021_R04C01


title: 200590490052_R05C01


title: 200590490021_R08C01


title: 200590490021_R05C01


title: 200590490021_R01C01


title: 200590490017_R08C01


title: 200590490017_R07C01


title: 200590490021_R02C01


title: Dissociated whole-worms

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

institute: Oregon Health and Science University

description: 30, 1-week starved, whole animals were used for this dataset

data_processing:
Cellular and molecular barcode extraction was performed using the Drop-seq tools softare version 1.13
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.
A digital expression matrix was extracted using the Drop-seq tools software version 1.13
Downstream clustering and gene enrichment analyses were performed using the Seurat R package version 2.1.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: UMI counts

organism: Schmidtea mediterranea

source_name: Wildtype animals (30 animals)

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol: RNA extraction and subsequent library preparation were performed using the Drop-seq protocol.

treatment_protocol: Animals were rinsed with ice cold CMF prior to dissociation in CMF.  Buffer was exchanged to CMF with 0.01% BSA prior to Dropseq.

value: Asexual CIW4

value: All  Tissues

tag: treatment

value: Dissociation


title: Granulosa cells cultured at normal oxygen level (21% O2) rep4

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

institute: Leibniz institute for farm animal biology

description: GC_21% O2_d

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the TAC 4.0 software (Affymetrix) and RMA method was used for normalization.

label: Biotin

organism: Bos taurus

source_name: Cultured granulosa cells, normal oxygen level

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: Granulosa cells were cultured serum-free in alpha-MEM supplemented with FSH, IGF-1 and androstenedione for 8 days.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Granulosa cells were subjected to different oxygen levels from 6th day to 8th day of culture.

tag: cell type

value: cultured granulosa cells

tag: stress

value: control


title: SC1_6h_rep1

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description: Gene expression after 6h in SC1 treated J1 mESCs

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene  Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer  Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were processed using Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: J1 mESC, SC1, 6h, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,  One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 1 μΜ SC1 for 6h.

tag: mouse strain

value: Inner Cell Mass

tag: cell line

value: Embryonic Stem Cell


title: Granulosa cells cultured at normal oxygen level (21% O2) rep2

description: GC_21% O2_b


title: SC1_6h_rep3

source_name: J1 mESC, SC1, 6h, replicate 3

tag: tissue


title: Granulosa cells cultured at normal oxygen level (21% O2) rep3

description: GC_21% O2_c


title: Granulosa cells cultured at normal oxygen level (21% O2) rep1

description: GC_21% O2_a


title: #28-Lenti-shNT

city: Seoul

first: Eun Hee

last: Yi

state: Seoul

address: 103 Daehangno, Jongno-gu

department: Pharmacology

institute: Seoul National University College of Medicine

hyb_protocol: 12 ug of aRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 200 % of controls for upregulated genes and lower than 50% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 12.6.1 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA

growth_protocol: GBM primary cells were cultured under nomal cancer cell culture conditions (DMEM containing 10% FBS and 1% Penicillin/streptomycin)

extract_protocol: Total RNA was extracted from GBM primary cells transduced with either lentiviral vector or shBST-2 using TRIzol reagent.

treatment_protocol: GBM primary cells were infected with shNT or shBST-2 -lentivirus and selected by treating puromycin

value: glioblastoma (GBM) primary cells

tag: infected with

value: shNT-lentivirus


title: 200590490017_R06C01

state: GA

data_processing:
non-normalized, background subtracted
beta-values

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

tag: gender

value: Male

tag: age

tag: ln(totalpbb)


title: Granulosa cells cultured at low oxygen level (1% O2) rep1

description: GC_1% O2_a

source_name: Cultured granulosa cells, low oxygen level

value: low oxygen


title: 200590490017_R05C01

value: Female


title: 200590490021_R03C01


title: 200590490017_R03C01


title: Granulosa cells cultured at low oxygen level (1% O2) rep3

description: GC_1% O2_c


title: 200590490017_R02C01


title: SC1_6h_rep2

source_name: J1 mESC, SC1, 6h, replicate 2


title: Healthy Population Control sample 3 (HIV and HPV Negative cases)

city: trivandrum

first: Radhakrishna

middle: Madhavan

last: Pillai

state: KERALA

address: poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Centre for Biotechnology

description: microRNA expression from human cervical cells

hyb_protocol: The labeled RNA was quantified, fractionated and hybridized to the miRNA microarray according to the standard procedures provided by the manufacture.The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, California, United States).

scan_protocol: The chips were then scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, California, United States).

data_processing: The Data generated from the scan was then analyzed using the Affymetrix GeneChip® Command Console™ Software, v1.1, and the Affymetrix GeneChip® Expression Console software, v 1.1

source_name: Human cervical smear collected with cyto brush

label_protocol: The RNA samples were labeled with the Genisphere FlashTag Biotin HSR RNA labeling kit (Genisphere, Hatfield, United Kingdom).

growth_protocol: The Cervical cells were collected from the subjects in preservecyt medium

extract_protocol: Total RNA was isolated using Ambion MiRVAna Kit according to the manufacturer's instructions.

treatment_protocol: The cervical cells were pelleted down at approximately 6000 rpm and used for isolating Total RNA

value: Cervical cells

value: female

value: 34 years


title: 200590490017_R04C01


title: DMSO_rep3

description: Gene expression after 6h in DMSO(control) treated J1 mESCs

source_name: J1 mESC, DMSO, 6h, replicate 3


title: Granulosa cells cultured at low oxygen level (1% O2) rep2

description: GC_1% O2_b


title: 200590490017_R01C01


title: DMSO_rep2

source_name: J1 mESC, DMSO, 6h, replicate 2


title: #28-Lenti-shBST2


title: HPV 16 positive and HIV negative cases Sample2

value: 40 years


title: DMSO_rep1

source_name: J1 mESC, DMSO, 6h, replicate 1


title: HPV 16 positive and HIV negative cases Sample1

value: 60 years


title: HPV 16 positive and HIV positive cases Sample3


title: 200590490002_R08C01

value: Peripheral Blood


title: HPV 16 positive and HIV positive cases Sample2

value: 30 years


title: Granulosa cells cultured at low oxygen level (1% O2) rep4

description: GC_1% O2_d


title: HPV 16 positive and HIV positive cases Sample1

value: 38 years


title: 200590490002_R07C01


title: HPV 16 positive and HIV negative cases Sample3

value: 45 years


title: 200590490002_R06C01


title: 200590490002_R05C01


title: 200590490002_R02C01


title: 200590490002_R01C01


title: HPV 16 Negative and HIV positive cases Sample3

value: 35 years