title: EtOH-siCTL_repeat1_GROseq (v.s. EtOH-siNCAPG_GROseq)

description:
nascent RNA
cells were transfected with siCTL, after 1hr treatment with ethanol, subjected to GRO-seq, serves as a control for cells with siNCAPG and EtOH treatment (v.s. EtOH-siNCAPG_GROseq)
library strategy: GRO-seq


title: H3K27Ac-EtOH-siNCAPG_ChIP-Seq

status: Public on Jul 15 2015

type: SRA

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

country: USA

institute: UCSD

description: cells transfected with siNCAPG, and 1hr treatment with ethanol, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

molecule: genomic DNA

organism: Homo sapiens

source_name: beast cancer cell line

growth_protocol: MCF7 obtained from ATCC were cultured in α-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.

extract_protocol:
Lysates were crosslinked with 1% of formaldehyde or double-crosslinked with DSG first followed by 1% of formaldehyde, clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.

treatment_protocol: Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.

tag: cell line

tag: chip antibody

tag: antibody vendor/catalog#

value: Ab4729, Abcam

tag: treatment


title: B3/penetrating Crohn's disease [ncRNA-Seq, 434_CD_NI_B3]

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

department: Genetics

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Small RNA-seq data was aligned using methodology described in Baran-Gale et al. (PLOS ONE, 2012)
Reads were trimmed by cutAdapt to remove adaptor remnants. Trimmed reads of 14-41 nt are first mapped exactly (no mismatches) using Bowtie. Windows are determined using these mapped reads, and the unmapped reads, are realigned to these windows using SHRiMP2 with mismatches allowed (See Baran-Gale et al, 2012), these would be considered edits & isomiRs, and are named based on the canonical miRNA (miRbase).
Reads were normalized using Reads per Million Mapped (RPMM). We pulled out miRNAs and isomiRs with at least 100 RPMM in at least 1 sample for downstream analyses.
Genome_build: Hg19
Supplementary_files_format_and_content: Multiple sample Tab-delimited file with RPMMs of all miRNAs & isomiRs that reached 100 RPMM in at least one sample analyzed.

molecule: total RNA

source_name: Colon

extract_protocol:
RNA was isolated from fresh-frozen human colon tissues using the Qiagen RNeasy Mini Kit
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit

tag: age

tag: Sex

value: male

tag: disease

value: Crohn's Disease

tag: inflamed

value: No

tag: montreal classification


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 433_CD_NI_B1]

value: B1/non-strictuing, non-penetrating


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 431_CD_NI_B1]

value: female


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 429_CD_NI_B1]


title: NCAPG-cyclingMCF7_ChIPSeq

description: MCF7 cells growing in full MEM medium without hormone stripping was subjected to NCAPG ChIPseq

value: NCAPG

value: A300-602A, Bethyl


title: B3/penetrating Crohn's disease [ncRNA-Seq, 424_CD_NI_B3]


title: ERa-E2-siNCAPD3/H2_ChIPSeq

description: cells transfected with siNCAPD3 and H2 together, and 1hr treatment with 100nM E2, double crosslinked, ERa ChIPseq was then performed.

value: ERa

value: SC-543, Santa Cruz Biotech

value: cells transfected with siNCAPD3 and H2 together, and 1hr with 100nM E2, double crosslinked


title: ERa-E2-siNCAPG_ChIPSeq

description: cells transfected with siNCAPG, and 1hr treatment with 100nM E2, double crosslinked, ERa ChIPseq was then performed.

value: cells transfected with siNCAPG, and 1hr with 100nM E2, double crosslinked


title: B2/stricturing Crohn's disease [ncRNA-Seq, 420_CD_NI_B2]


title: RNApolII-E2-siNCAPG_ChIPSeq

description: cells transfected with siNCAPG, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, RNA PolII ChIPseq was then performed.

value: RNApolII

value: SC-899, Santa Cruz Biotech

value: cells transfected with siNCAPG, and 1hr with 100nM E2, crosslinked with 1% formaldehyde


title: RNApolII-EtOH-siNCAPG_ChIPSeq

description: cells transfected with siNCAPG, and 1hr treatment with ethanol, crosslinked with 1% formaldehyde, RNA PolII ChIPseq was then performed.

value: cells transfected with siNCAPG, and 1hr with ethanol, crosslinked with 1% formaldehyde


title: ERa-E2-siCTL_repeat1_ChIPSeq (v.s. ERa-E2-siNCAPG)

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, double crosslinked, ERa ChIPseq was then performed,  serves as the control for ERa ChIPseq in siNCAPG cells (Chipseq-ERa-siNCAPG-MCF7-E2)

value: cells transfected with siCTL, and 1hr with 100nM E2, double crosslinked


title: RNApolII-EtOH-siCTL_ChIPSeq

description: cells transfected with siCTL, and 1hr treatment with ethanol, crosslinked with 1% formaldehyde, RNA PolII ChIPseq was then performed.

value: cells transfected with siCTL, and 1hr with ethanol, crosslinked with 1% formaldehyde


title: B3/penetrating Crohn's disease [ncRNA-Seq, 407_CD_NI_B3]


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 413_CD_NI_B1]


title: H3K27Ac-E2-siCTL_ChIP-Seq

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq

value: Ab4729, Abcam


title: RNApolII-E2-siCTL_ChIPSeq

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, RNA PolII ChIPseq was then performed.

value: cells transfected with siCTL, and 1hr with 100nM E2, crosslinked with 1% formaldehyde


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 408_CD_NI_B1]

value: Crohn's Disease

value: No


title: B2/stricturing Crohn's disease [ncRNA-Seq, 21_CD_NI_B2]

value: female


title: B3/penetrating Crohn's disease [ncRNA-Seq, 29_CD_NI_B3]


title: B2/stricturing Crohn's disease [ncRNA-Seq, 20_CD_NI_B2]

value: male


title: p300-E2-siNCAPG_ChIPSeq

description: cells transfected with siNCAPG, and 1hr treatment with 100nM E2, double crosslinked, p300 ChIPseq was then performed.

tag: cantibody vendor/catalog#

value: SC-585, Santa Cruz Biotech

value: cells transfected with siNCAPG, and 1hr with 100nM E2


title: p300-E2-siCTL-repeat2_ChIPSeq (v.s. p300-E2-siNCAPD3)

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, double crosslinked, p300 ChIPseq was then performed, serves as the control for p300 ChIPseq in siNCAPD3 cells (Chipseq-P300-siNCAPD3-MCF7-E2)


title: p300-E2-siCTL-repeat1_ChIPSeq (v.s. p300-E2-siNCAPG)

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, double crosslinked, p300 ChIPseq was then performed, serves as the control for p300 ChIPseq in siNCAPG cells (Chipseq-P300-siNCAPG-MCF7-E2)


title: ERa-E2-siCTL_repeat2_ChIPSeq (v.s. ERa-E2-siNCAPD3/H2)

description: cells transfected with siCTL, and 1hr treatment with 100nM E2, double crosslinked, ERa ChIPseq was then performed,  serves as the control for ERa ChIPseq in siNCAPD3/H2 cells (Chipseq-ERa-siNCAPD3/H2-MCF7-E2)

value: ERa

value: SC-543, Santa Cruz Biotech


title: Normal colon acquired during surgery for adenoma, male age 62 [ncRNA-Seq, 49_NIBD_NI]

value: Normal, Adenoma


title: Normal colon acquired during surgery for adenoma, male age 70 [ncRNA-Seq, 48_NIBD_NI]


title: p300-EtOH-siCTL-ChIPSeq

description: cells transfected with siCTL, and 1hr treatment with ethanol, double crosslinked, p300 ChIPseq was then performed.

value: cells transfected with siCTL, and 1hr with ethanol, double crosslinked


title: p300-E2-siNCAPD3_ChIPSeq

description: cells transfected with siNCAPD3, and 1hr treatment with 100nM E2, double crosslinked, p300 ChIPseq was then performed.

value: cells transfected with siNCAPD3, and 1hr with 100nM E2, double crosslinked


title: HECTD1-E2_ChIPSeq

description: 1hr treatment with 100nM E2, double crosslinked, HECTD1 ChIPseq was then performed.

value: A302-908A, Bethyl

value: 1hr with 100nM E2, double crosslinked


title: HECTD1-ETOH_ChIPSeq

description: 1hr treatment with ethanol, double crosslinked, HECTD1 ChIPseq was then performed.

value: 1hr with ethanol, double crosslinked


title: B2/stricturing Crohn's disease [ncRNA-Seq, 422_CD_NI_B2]


title: Normal colon acquired during surgery for large polyp, male age 65 [ncRNA-Seq, 42_NIBD_NI]

value: Normal control, large polyp


title: Normal colon acquired during surgery for colonic inertia, female age 45 [ncRNA-Seq, 43_NIBD_NI]

value: Normal, colonic inertia


title: NCAPG-YK-ETOH_ChIPSeq

description: 1hr treatment with ethanol, double crosslinked, NCAPG (antibody from K. Yokomori) ChIPseq was then performed.

value: NCAPG

value: gift from K. Yokomori (UC Irvine)


title: NCAPG-YK-E2_ChIPSeq

description: 1hr treatment with 100nM E2, double crosslinked, NCAPG (antibody from K. Yokomori) ChIPseq was then performed.


title: Normal colon acquired during surgery for colonic inertia, female age 41 [ncRNA-Seq, 36_NIBD_NI]

value: Normal, colonic inertia, TI submucosal hemorrhage (but looked inflamed on macro)

value: No


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 405_CD_NI_B1]

value: female

value: Crohn's Disease

value: B1/non-strictuing, non-penetrating


title: Normal colon acquired during surgery for colon cancer, male age 44 [ncRNA-Seq, 32_NIBD_NI]

value: male

value: Normal, Colon cancer


title: NCAPH2(condensinII)-E2_ChIPSeq

description: 1hr treatment with 100nM E2, double crosslinked, NCAPH2 (condensin II) ChIPseq was then performed.

value: A302-276A, Bethyl


title: NCAPH2(condensinII)-ETOH_ChIPSeq

description: 1hr treatment with ethanol, double crosslinked, NCAPH2 (condensin II) ChIPseq was then performed.


title: Normal colon acquired during surgery for colon cancer, male age 52 [ncRNA-Seq, 39_NIBD_NI]


title: Normal colon biopsy acquired during surgery for colon cancer, male age 44 [ncRNA-Seq, 31_NIBD_NI]


title: Normal colon acquired during surgery for small intestine neuroendocrine tumor, female age 49 [ncRNA-Seq, 50_NIBD_NI]

value: Normal, SI Neuroendocrine tumor


title: NCAPH-E2_ChIPSeq

description: 1hr treatment with 100nM E2, double crosslinked, NCAPH ChIPseq was then performed.

value: A300-603A, Bethyl


title: NCAPH-ETOH_ChIPSeq

description: 1hr treatment with ethanol, double crosslinked, NCAPH ChIPseq was then performed.


title: Normal colon acquired during surgery for diverticulitis, male age 70 [ncRNA-Seq, 27_NIBD_NI]

value: Normal, diverticulitis


title: NCAPG-E2-ICI _ChIPSeq

description: 24hr of 100nM ICI then 1hr treatment with 100nM E2, double crosslinked, NCAPG ChIPseq was then performed.

value: A300-602A, Bethyl

value: 24hr of 100nM ICI then 1hr with 100nM E2


title: Normal colon biopsy acquired during surgery for diverticulitis,female age 60 [ncRNA-Seq, 25_NIBD_NI]


title: Normal colon biopsy acquired during surgery for colon cancer, female age 82 [ncRNA-Seq, 30_NIBD_NI]


title: Normal colon acquired during Hartmann reversal after colon cancer, male age 52 [ncRNA-Seq, 23_NIBD_NI]

value: Normal, Hartmann reversal after colon cancer


title: Normal colon biopsy, female age 53 [ncRNA-Seq, 22_NIBD_NI]

value: Normal


title: Normal colon acquired during surgery for small intestine neuroendocrine tumor, female age 49 [RNA-Seq, 50_NIBD_NI]

data_processing:
Reads were trimmed to 50 bp
Reads were filtered on the criteria that 90% of bases within the read have quality >= 20
Potential artifactual reads from Truseq library were filtered using tagdust with an fdr cutoff of 0.001
Reads were aligned to personal genomes using GSNAP alignment software, taking into account known heterozygous sites within each individual.
Raw gene counts were derived using a custom perl script and exon annotation gtf file downloaded from UCSC Table Browser
Normalized gene counts were obtained using the varianceStabilizingTransformation function in the R package "DEseq", with default parameters
genome build: hg19
Supplementary_files_format_and_content: Raw/Normalized read counts

extract_protocol:
RNA was isolated from fresh-frozen human colon tissues using the Qiagen RNeasy Mini Kit
mRNA libraries were generated using Illumina TruSeq polyA+ Sample Prep Kit


title: NCAPG-E2_repeat1_ChIPSeq

description: 1hr treatment with 100nM E2, double crosslinked, NCAPG ChIPseq was then performed.

value: NCAPG

value: 1hr with 100nM E2, double crosslinked


title: Normal colon acquired during surgery for adenoma, male age 62 [RNA-Seq, 49_NIBD_NI]

value: Normal, Adenoma


title: Normal colon acquired during surgery for colonic inertia, female age 45 [RNA-Seq, 43_NIBD_NI]

value: Normal, colonic inertia

value: No


title: Input-E2

description: 1hr treatment with 100nM E2, double crosslinked


title: NCAPG-ETOH_repeat2 (v.s. EtOH-ICI)_ChIPSeq

description: 24hr of ethanol pretreatment then 1hr treatment with ethanol, double crosslinked, NCAPG ChIPseq was then performed, serves as the control group for [ICI and ETOH] treated sample

value: 24hr of ethanol pretreatment then 1hr with ethanol, double crosslinked


title: Normal colon acquired during surgery for adenoma, male age 70 [RNA-Seq, 48_NIBD_NI]


title: NCAPG-E2_repeat2 (v.s. E2-ICI)_ChIPSeq

description: 24hr of ethanol pretreatment then 1hr treatment with 100nM E2, double crosslinked, NCAPG ChIPseq was then performed, serves as the control group for [ICI and E2] treated sample

value: 24hr of ethanol pretreatment then 1hr with 100nM E2


title: NCAPG-ETOH_repeat1_ChIPSeq

description: 1hr treatment with ethanol, double crosslinked, NCAPG ChIPseq was then performed.

value: 1hr with ethanol, double crosslinked


title: ERa-E2_repeat1_ChIPSeq

description: 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, ERa ChIPseq was then performed.

value: ERa

value: SC-543, Santa Cruz Biotech

value: 1hr with 100nM E2, crosslinked with 1% formaldehyde


title: ERa-EtOH_repeat1_ChIPSeq

description: 1hr treatment with ethanol, crosslinked with 1% formaldehyde, ERa ChIPseq was then performed.

value: 1hr with ethanol, crosslinked with 1% formaldehyde


title: S3

city: Ji'nan

first: Xingjun

last: Wang

state: Shandong

address: 202#, Gongye Bei Road

department: Biotechnology Research Center

country: China

description: LJ

data_processing:
Illumina HiSeq™ 2000 sequencing
Remove reads with adaptors
Remove reads in which unknown bases are more than 10%
Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arachis hypogaea

source_name: gynophores

growth_protocol: Plants of “Luhua 14”, a widespread cultivar in Northern China, were sown in early May and harvested in early October in the experimental farm of Shandong Academy of Agricultural Sciences. The S1, S2, and S3 gynophores were collected from the farm-grown plants. The tip-most 1 cm was excised from the S1, S2, and S3 gynophores and immediately frozen in liquid nitrogen for protein extraction.

extract_protocol:
Total RNA was isolated from the frozen gynophore by using Trizol Reagent (TaKaRa, Inc., Dalian, China) according to the manufacturer’s instructions. The quality and quantity of the purified RNA from each sample was determined by Agilent 2100. Beads with Oligo(dT) were used to enrich polyA mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Luhua 14

tag: developmental stage

tag: phenotype

value: dark-grown gynophores with 2-3 mm long pods

tag: tissue

value: gynophores


title: S2

institute: Shandong Academy of Agricultural Sciences

value: gynophores that have been buried in the soil for about 3 days


title: S1

value: aerial gynophores that are green or purple and 3-5 cm long


title: Normal colon acquired during surgery for colon cancer, male age 44 [RNA-Seq, 32_NIBD_NI]

value: male

value: Normal, Colon cancer


title: Normal colon acquired during surgery for colon cancer, male age 52 [RNA-Seq, 39_NIBD_NI]


title: Input-EtOH

description: 1hr treatment with ethanol, double crosslinked


title: NCAPG-ETOH-ICI_ChIPSeq

description: 24hr of 100nM ICI then 1hr treatment with ethanol , double crosslinked, NCAPG ChIPseq was then performed.

value: NCAPG

value: A300-602A, Bethyl

value: 24hr of 100nM ICI then 1hr with ethanol


title: ino4-2

city: New York

first: Xuan

last: Zhu

state: NY

address: 430 East 67th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were mapped to the S. cerevisiae sacCer2 genome assembly using the Spliced Transcripts Alignment to a Reference (STAR) software.
Transcriptome assembly and differential expression analysis were performed using the Cufflinks software.
Genome_build: The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: Text files of coverage maps

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.

extract_protocol:
15 OD units of cells were collected for each sample from meiosis 4 hr. Cells were resuspended in 500 μl Complete Buffer A (50 mM NaAc pH 5.2, 10 mM EDTA, 1% SDS). 750 μl equilibrated RNA phenol was added. Cells were disrupted by incubating at 65°C for 5 minutes with vortex for 10 seconds every minute and a half and placing on ice for 3 minutes. After spinning in a mini centrifuge at 13,000 rpm for 6 min, the bottom layer was removed. Phenol incubation and vortex were repeated, but the top layer was transfer to a new 1.5 ml tube this time. RNA was purified by two rounds of phenol/chloroform extraction, one round of chloroform extraction and ethanol precipitation. After ethanol precipitation, the pellets were resuspended in 100 μl TE (10 mM Tris-HCl pH 6.8, 1 mM EDTA).
The RNA-seq library was prepared following Illumina standard protocol. We used Trueseq RNA sample prep kit.

tag: timing

value: time in meiosis:time = 4 hr in meiosis

tag: genotype


title: ino4-1


title: bas1-1


title: Normal colon biopsy acquired during surgery for colon cancer, female age 82 [RNA-Seq, 30_NIBD_NI]

value: female

value: No


title: Normal colon biopsy acquired during surgery for diverticulitis,female age 60 [RNA-Seq, 25_NIBD_NI]

value: Normal, diverticulitis


title: WT-2

value: WT


title: bas1-2


title: Normal colon acquired during surgery for diverticulitis, male age 70 [RNA-Seq, 27_NIBD_NI]


title: WT-1


title: B3/penetrating Crohn's disease [RNA-Seq, 450_CD_NI_B3]

value: Crohn's Disease


title: Normal colon acquired during surgery for large polyp, male age 65 [RNA-Seq, 42_NIBD_NI]

value: Normal control, large polyp


title: Normal colon biopsy, female age 53 [RNA-Seq, 22_NIBD_NI]

value: Normal


title: B2/stricturing Crohn's disease [RNA-Seq, 440_CD_NI_B2]


title: Normal colon acquired during Hartmann reversal after colon cancer, male age 52 [RNA-Seq, 23_NIBD_NI]

value: Normal, Hartmann reversal after colon cancer


title: B2/stricturing Crohn's disease [RNA-Seq, 420_CD_NI_B2]


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 408_CD_NI_B1]

value: B1/non-strictuing, non-penetrating


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 431_CD_NI_B1]


title: B3/penetrating Crohn's disease [RNA-Seq, 434_CD_NI_B3]


title: B3/penetrating Crohn's disease [RNA-Seq, 413_CD_NI_B1]


title: B3/penetrating Crohn's disease [RNA-Seq, 424_CD_NI_B3]


title: Normal colon acquired during surgery for colonic inertia, female age 41 [RNA-Seq, 36_NIBD_NI]

value: Normal, colonic inertia, TI submucosal hemorrhage (but looked inflamed on macro)


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 405_CD_NI_B1]


title: B3/penetrating Crohn's disease [RNA-Seq, 64_CD_NI_B3]


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 63_CD_NI_B1]


title: 8 - H298-24-Hr

city: East Melbourne

first: Paul

middle: James

last: Wood

state: Victoria

address: 2 St. Andrews Place

department: Translational Research Laboratory

country: Australia

institute: Peter MacCallum Cancer Centre

description: 8 - H298-24-Hr

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm10) using Tophat2 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf. Counts were normalised using the limma-voom method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample

organism: Mus musculus

growth_protocol: 8 homozygous TH-MYCN neuroblastoma mice were monitored for neuroblastoma development by ultrasound, treatment was started when tumours were between 200-300mm3 (about 6 weeks of age)

extract_protocol:
Cells were lysed and total RNA was extracted using the Qiagen miRNAeasy kit and quality assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared using the IlluminaTruSeq V2 RNA-Seq sample preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 2 doses (24hr apart) of 5mg/kg panobinostat or vehicle

value: neuroblastoma

tag: cell type

value: entire tumor composition:tumor cells+ stroma cells

tag: origin

value: Transgenic TH-MYCN neuroblastoma

tag: strain

value: TH-MYCN


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 54_CD_NI_B1]

value: male


title: 7 - H297-24-Hr

description: 7 - H297-24-Hr


title: 6 - H296-24-Hr

description: 6 - H296-24-Hr


title: 5 - H282-24-Hr

description: 5 - H282-24-Hr


title: B3/penetrating Crohn's disease [RNA-Seq, 62_CD_NI_B3]


title: B3/penetrating Crohn's disease [RNA-Seq, 29_CD_NI_B3]


title: 4 - H83-Control

description: 4 - H83-Control

source_name: intra-abdominal neuroblastoma_vehicle


title: 3 - H59-Control

description: 3 - H59-Control


title: B2/stricturing Crohn's disease [RNA-Seq, 21_CD_NI_B2]


title: B2/stricturing Crohn's disease [RNA-Seq, 20_CD_NI_B2]


title: B2/stricturing Crohn's disease [RNA-Seq, 51_CD_NI_B2]


title: 1 - H17-Control

description: 1 - H17-Control


title: 2 - H43-Control

description: 2 - H43-Control


title: B1/non-strituring, non-penetrating Crohn's disease [RNA-Seq, 429_CD_NI_B1]


title: B2/stricturing Crohn's disease [RNA-Seq, 422_CD_NI_B2]


title: HITSCLIP-HIVJR-FL+ (3 donor mix)

status: Public on Jul 14 2015

first: Pejman

last: Mohammadi

address: 101 Av. of the Americas

institute: New York Genome Center

description:
HITS-CLIP
Argonaut2 immunoprecipitation
Processed data file: HITSCLIP-Summary.xlsx

data_processing:
Adapters sequences removed from all samples using fastX toolkit.
All samples were aligned to human and HIV genomes simultaneously using Bowtie 1.0.
PAR-CLIP samples were analyzed using Paralyzer tool.
Gene expression was quantified using HTseq count tool for sRNA-seq samples.
HITS-CLIP samples were used for checking the reads on HIV genome using manual scripts.
Genome_build: Human: GRCh37.72
Genome_build: HIV-1: HIV-1JR-FL (GenBank: U63632.1) and the LTR sequences derived from HIV-1JRCSF (GenBank: M38429.1).
Supplementary_files_format_and_content: Tab-delimited text files containing Paralyzer output (PAR-CLIP samples), raw gene expressions (sRNA-seq), and coverage on HIV genome (HITS-CLIP).

organism:
Homo sapiens
Human immunodeficiency virus 1

source_name: monocyte-derived macrophages, HIV-1 infected, Ago2 IP

growth_protocol: Primary human monocytes from HIV-1 negative blood donors were isolated with anti-CD14 coated magnetic beads (Miltenyi Biotech) from buffy coats and cultured one week in RPMI supplemented with 1% penicillin/streptomycin, 10% human serum (Sigma) and 0.02 µg/ml M-CSF (macrophage colony stimulating factor). Seven days after isolation, the macrophages were washed in PBS supplemented with 2% FCS to remove not adherent and dead cells and the medium was replaced and cultured in RPMI supplemented with 1% penicillin/streptomycin and 10% FCS.

extract_protocol:
Ago2 immunoprecipitation and PAR-CLIP (as described in Hafner et al., 2010; Kishore et al., 2012; Imig et al., 2015). Small RNA sequencing: Trizol-based total RNA isolation.
According to Kishore et al., Nat Meth, 2011.
Single end reads, 5'-3' adapter, multiplexed barcoded.

treatment_protocol: After another week, the differentiated macrophages were infected with HIV-1JR-FL with a multiplicity of infection (MOI) of 0.1. The cells were washed the next day with PBS supplemented with 2% FCS.

tag: donor

value: mix of 3 donors

value: monocyte-derived macrophages

tag: infection

tag: antibody

value: anti-AGO2, clone 11A9 (Sigma)


title: B3/penetrating Crohn's disease [RNA-Seq, 407_CD_NI_B3]

tag: age

tag: Sex

value: female

value: No


title: sRNAseq-D3JR-FL+

description: Processed data file: ST3_Full_sRNA_RawData.xlsx

source_name: monocyte-derived macrophages, HIV-1 infected


title: sRNAseq-D4JR-FL+


title: sRNAseq-D1JR-FL+


title: sRNAseq-D2JR-FL+


title: PARCLIP-D4HIV-1JR-FL+

description:
PAR-CLIP
Argonaut2 immunoprecipitation
Processed data file: PARCLIP_Clusters_annotated.xlsx


title: PARCLIP-D2JR-FL+


title: TRA00030014_umi_9

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
demultiplex by cell barcode (custom scripts)
tophat2 alignment
Details:
Raw data were processed using custom scripts. Read 1 contains the transcript sequence, and Read 2 contains the single cell barcode and unique molecular identifiers. Raw reads were first trimmed using the FASTX-Tollkit v0.0.13 (fastx_trimmer –Q 33). Read 2 was trimmed in order to extract the single cell barcode (8bp) and the UMI (4-8bp), and Read 1 was trimmed to 30bp get rid of a potential oligo-dT sequence. After merging the different parts (barcode, umi and transcript sequence), reads were filtered for quality (more than 80% of the sequence having a Sanger Phred+33 quality score > 33) using fastq_quality_filter -v -Q 33 -q 20 -p 80. Then the reads were assigned to each single cell by using the 8bp barcode and the fastx_barcode_splitter.pl tool script for a maximum of 2 mismatches. Reads assigned to each single cell were then trimmed again to retrieve the transcript sequence using fastx_trimmer.
Mapping was performed using Tophat2 to the mm10 mouse transcriptome and keeping the strand information with the following options : tophat -p 2 --library-type fr-firststrand --read-mismatches 5 --read-gap-length 5 --read-edit-dist 5 --no-coverage-search --segment-length 15 --transcriptome-index. Duplicated mapping reads were filtered out using the unique molecular barcodes as follows. First duplicated mapped reads were marked using picard-tools-1.79/MarkDuplicates.jar. Then the genomic position of the duplicated reads were extracted and for each of these positions, only reads having unique molecular identifiers were then kept. Reads that mapped to multiple positions were filtered out using samtools 0.1.19 flag 256. Finally reads were assigned to genes using htseq-count, biomart_mm10_gene.gff and the following options : -s yes -m intersection-nonempty. The script was modified in order to assign reads that overlapped in several genes to the one closest to a 3’ end.
Genome_build: mm10
Supplementary_files_format_and_content: SCS_MEC.csv: Raw read counts.
Supplementary_files_format_and_content: SCS_MEC_metadata_table.txt: Metadata, including genotype information for the single cells.

source_name: thymus

growth_protocol: Sorted live cells from thymi of Aire wildtype or KO mice. All mice carried Aire-GFP transgene as marker for Aire expression.

extract_protocol:
Thymi were removed and digested in collagenase/dispase to single cell suspensions. Medullary thymic epithelial cells were sorted by FACS as CD45-Ly51-MHCII+GFP+. Single cells were sorted into water in wells of 96well plate and lysed by freeze-thaw.
mRNA was reverse transcribed using adapters containing oligo dT and ArrayScript (Ambion), second strand synthesis was performed using Second strand synthesis module (NEBNext #E6111L), and linear amplification was performed by in vitro transcription using MEGAshortscript T7 transcription kit (Ambion AM1354). Illumina RNA adapters were ligated onto transcripts using T4 RNA Ligase 2, truncated (Enzymatics L6070L) and processed according to standard Illumina protocols.

value: MEC

value: Female

value: 5 week-old

tag: sorting markers

tag: primer

tag: genotype/variation

value: Aire KO; AireGFP


title: TRA00030014_umi_15

value: WT; AireGFP


title: TRA00030014_umi_14


title: TRA00030014_umi_13


title: TRA00030014_umi_12


title: TRA00030014_umi_11


title: TRA00030014_umi_10


title: TRA00030014_ls_6


title: TRA00030014_ls_7


title: TRA00030014_ls_9


title: TRA00030014_ls_8


title: TRA00030014_ls_3


title: TRA00030014_ls_4


title: TRA00030014_ls_22


title: TRA00030014_ls_5


title: TRA00030014_ls_23


title: TRA00030014_ls_18


title: TRA00030014_ls_2


title: CD34_iPSC_RRBS_3

city: Saarbrücken

first: Fabian

last: Müller

address: Campus A 2.4

country: Germany

institute: Saarland University

description: Reduced Representation Bisulfite Sequencing

data_processing:
Alignment: Sequencing reads were mapped to reference genomes hg19 and mm9 for human and mouse samples respectively using RRBSmap (or BSMAP in case of the CD34 iPS cells).
methylation calling was done using BisSNP with default parameters.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: methylation calls: bed-like format as output by BisSNP (see http://epigenome.usc.edu/publicationdata/bissnp2011/ for details)

growth_protocol: hES, and all LiPS and iPS cells were grown in ES KO DMEM supplemented with 15% KSR serumn in presence of 5ng/ml FGF, at 37 °C in a humidified atmosphere with 5% CO2. K562 and KBM7cells were grown in  DMEM supplemented with 10% FBS , at 37 °C in a humidified atmosphere with 5% CO2. CML primary cells and CD34+ derived from healty donor were grown in QBSF60 medium, 20% FBS, SCF 50µg/ml, TPO 20µg/ml,Flt3 10µg/ml, IL3 10µg/ml.

extract_protocol:
Murine hematopoietic stem cells (LSK) were isolated using cell sorting (FACS ARIA II, BD) using fluorochrome-conjugated antibodies against Sca1 and cKit. After sorting samples were immeditaley processed for methylation analysis
DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected before subjecting to sequencing.

treatment_protocol: Genomic DNA was isolated from the cell lines. DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected, and sequenced on the Illumina GA IIxat a reading length of 36 bp.

tag: digestion

value: MspI

tag: treatment

value: bisulfite


title: CD34_iPSC_RRBS_1


title: CD34_iPSC_RRBS_2


title: TRA00030014_ls_17


title: TRA00030014_ls_15


title: TRA00030014_ls_16


title: TRA00030014_ls_13


title: TRA00030014_ls_14


title: RRBS_K562_12.21

data_processing:
Alignment: Sequencing reads were mapped to reference genomes hg19 and mm9 for human and mouse samples respectively using RRBSmap.
methylation calling was done using BisSNP with default parameters.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: methylation calls: bed-like format as output by BisSNP (see http://epigenome.usc.edu/publicationdata/bissnp2011/ for details)

growth_protocol: hES, and all LiPS cells were grown in ES KO DMEM supplemented with 15% KSR serumn in presence of 5ng/ml FGF, at 37 °C in a humidified atmosphere with 5% CO2. K562 and KBM7cells were grown in  DMEM supplemented with 10% FBS , at 37 °C in a humidified atmosphere with 5% CO2. CML primary cells were grown in QBSF60 medium, 20% FBS, SCF 50µg/ml, TPO 20µg/ml,Flt3 10µg/ml, IL3 10µg/ml.

extract_protocol:
Murine hematopoietic stem cells (LSK) were isolated using cell sorting (FACS ARIA II, BD) using fluorochrome-conjugated antibodies against Sca1 and cKit. After sorting samples were immeditaley processed for methylation analysis.
DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected before subjecting to sequencing.

treatment_protocol: Genomic DNA was isolated from the cell lines. DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected, and sequenced on the Illumina GA IIx at a reading length of 36 bp.


title: RRBS_Lips3_p13


title: RRBS_K562_11.05


title: RRBS_Lips1_p3


title: RRBS_Lips3_p3


title: RRBS_Lips1_p13


title: TRA00030014_ls_12


title: RK2.L1.KLIP2p-2


title: RK2.L1.KLIP1p-2


title: TRA00030014_ls_10


title: RK1.L1.KLIP2p-1


title: RK2.KBM7p-2


title: RK1.L1.KLIP1p-1


title: RK1.KBM7p-1


title: TRA00030014_ls_1


title: TRA00030013_umi_9


title: CML_GP


title: CML-iPS_5_Passage_8


title: CML-iPS_5_Passage_1


title: TRA00030013_umi_15


title: CML-iPS_6_Passage_8


title: TRA00030013_umi_14


title: CML_Gilli


title: TRA00030013_umi_13


title: TRA00030013_umi_16


title: TRA00030013_umi_12


title: TRA00030013_umi_10


title: TRA00030013_ls_7


title: TRA00030013_ls_9


title: TRA00030013_ls_5


title: TRA00030013_ls_3


title: TRA00030013_ls_8


title: TRA00030014_ls_11


title: TRA00030013_ls_24


title: CML-iPS_6_Passage_1


title: TRA00030013_ls_6


title: TRA00030013_ls_4


title: TRA00030013_ls_23


title: TRA00030013_ls_22


title: TRA00030013_ls_2


title: TRA00030013_ls_18


title: TRA00030013_ls_17


title: TRA00030013_ls_16


title: TRA00030013_ls_15


title: TRA00030013_umi_11


title: TRA00030013_ls_14


title: TRA00030013_ls_12


title: TRA00030013_ls_13


title: TRA00030013_ls_11


title: TRA00030012_ls_8


title: TRA00030012_ls_9


title: TRA00030012_ls_6


title: TRA00030012_ls_7


title: TRA00030013_ls_1


title: TRA00030012_umi_11


title: TRA00030012_umi_14


title: TRA00030012_ls_23


title: TRA00030012_ls_2


title: TRA00030012_umi_16


title: TRA00030012_umi_13


title: TRA00030012_ls_18


title: TRA00030012_umi_15


title: TRA00030012_umi_12


title: TRA00030012_umi_10


title: TRA00030012_umi_9


title: TRA00030013_ls_21


title: TRA00030012_ls_16


title: TRA00030012_ls_15


title: TRA00030012_ls_14


title: TRA00030012_ls_13


title: TRA00030012_ls_12


title: TRA00030013_ls_10


title: TRA00030012_ls_24


title: TRA00030012_ls_5


title: TRA00030012_ls_4


title: TRA00030012_ls_22


title: TRA00030012_ls_10


title: TRA00030012_ls_21


title: TRA00030012_ls_17


title: TRA00030011_ls_9


title: TRA00030011_umi_16


title: TRA00030012_ls_1


title: TRA00030011_ls_22


title: TRA00030011_ls_6


title: TRA00030011_ls_24


title: TRA00030011_umi_9


title: TRA00030011_ls_12


title: TRA00030011_ls_18


title: TRA00030011_ls_1


title: TRA00030011_umi_11


title: TRA00030010_umi_12


title: TRA00030010_ls_9


title: TRA00030010_ls_7


title: TRA00030010_ls_5


title: TRA00030011_umi_12


title: TRA00030011_ls_23


title: TRA00030010_umi_10


title: TRA00030010_ls_24


title: TRA00030010_ls_2


title: TRA00030010_ls_17


title: TRA00030010_ls_18


title: TRA00030010_ls_15


title: TRA00030010_ls_14


title: TRA00030011_umi_14


title: TRA00030010_ls_13


title: TRA00030010_umi_14


title: TRA00030010_umi_15


title: TRA00030010_ls_12


title: TRA00030010_ls_1


title: TRA00030010_ls_11


title: TRA00030009_umi_13


title: TRA00030010_ls_6


title: TRA00030009_ls_24


title: TRA00030009_ls_23


title: TRA00030009_ls_21


title: TRA00030009_ls_2


title: axons control replicate 2

first: Ulrich

last: Hengst

institute: Columbia University

data_processing:
Basecalls performed by MiSeq Reporter Software
Sequenced reads were trimmed for quality and adapters using Trim-Galore. Reads that lost their paired read were collected and separately aligned.
Reads were mapped to Rn5 using Tophat2
Mapped reads from paired-end and inpaired mapping were combined using Samtools
mapped reads were counted using the summarizeOverlaps function of the GenomicAlignments package, and differential mRNA localization was determined using DESeq2.
Genome_build: Rn5
Supplementary_files_format_and_content: comma separated values files of DESeq2 output for differential expression analysis, separately for axons and cell bodies.

organism: Rattus norvegicus

source_name: axons of hippocampal neurons

growth_protocol: Rat embryonic hippocampal neurons were grown in microfluidic chambers for 10-14 days.

extract_protocol:
RNA sequencing was performed using RNA purified from the cell body and axonal compartments of microfluidic chambers using the PrepEase RNA isolation kit (Affymetrix, Santa Clara, CA) and concentrated with RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA).
cDNA libraries were created from total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA).

treatment_protocol: Axons only were treated for 24 h with soluble oligomeric Aebta(1-42) or vehicle control.

tag: developmental stage

value: embryonic

value: control

value: axons of hippocampal neurons


title: soma Abeta replicate 1

source_name: soma and neurites of hippocampal neurons

value: Abeta

tag: tissue


title: soma control replicate 2

value: soma and neurites of hippocampal neurons


title: axons control replicate 1


title: soma Abeta replicate 2


title: TRA00030009_ls_13


title: TRA00030009_ls_18


title: axons Abeta replicate 2


title: TRA00030009_ls_1


title: TRA00030009_ls_10


title: axons Abeta replicate 1


title: TRA00028928_umi_15


title: TRA00028928_umi_13


title: TRA00028928_ls_8


title: TRA00028928_ls_5


title: TRA00030009_umi_14


title: TRA00030009_umi_10


title: TRA00028928_ls_6


title: TRA00030009_ls_22


title: soma control replicate 1


title: TRA00028928_ls_22


title: TRA00028928_ls_18


title: TRA00028928_ls_4


title: TRA00028928_ls_15


title: TRA00028928_ls_23


title: TRA00028928_ls_16


title: TRA00028928_ls_14


title: TRA00028928_ls_12


title: TRA00028928_ls_10


title: TRA00028928_ls_11


title: TRA00028927_umi_15


title: TRA00028927_umi_12


title: TRA00028927_ls_8


title: TRA00028927_umi_13


title: TRA00028927_ls_6


title: No_JO1_1015C

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

description: Nascent RNA

data_processing:
Nascent RNA-Seq reads were first aligned to the human reference genome using Bowtie (version 0.12.5) with the maximum insert size (-X) set to 100,000, keeping only uniquely mapped reads.
HTSeq (Anders et al. 2015) was used to count reads mapped to genes (using GENCODE v21 annotation).
DESeq (Anders and Huber 2010) was subsequently employed to estimate nascent transcription levels, and analyze differential expression between TC-797 following and prior to JQ1 treatment, and between 293TRex following and before BRD4-NUT induction.
tdf files were generated by converting wig files using igvtools
Genome_build: hg38
Supplementary_files_format_and_content: TDF files (for IGV browser) containing smoothed read density
Supplementary_files_format_and_content: RNASeq.counts.txt reports the read count estimates per gene for each sample

growth_protocol: 293TRex Flag-BRD4-NUT-HA cell lines were generated by recombination with the plasmid  Flag-Brd4-NUT-HA  using the Flp-In technology manufacturer’s instructions (Invitrogen). The resulting cell lines were maintained in medium (above) supplemented with Blasticidin (Invitrogen) and Hygromycin (Sigma).  293TRex cells were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta Biologicals), 1% pen-strep and 1X GlutaMAX (Invitrogen). PER-403 (Kees et al. 1991) were maintained in DMEM with 20% FBS and supplemented as above.  NMC cell lines, TC-797 (Toretsky et al. 2003), 1015 (Grayson et al. 2014), 10326 (French et al. 2008) were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta Biologicals), 1% pen-strep and 1X GlutaMAX (Invitrogen). PER-403 (Kees et al. 1991) were maintained in DMEM with 20% FBS and supplemented as above.

extract_protocol:
Nascent RNA purification was based on the Nascent-seq protocol (Khodor et al. 2011; Ferrari et al. 2013). Briefly, cells were harvested and homogenized 3 times with a 25G needle in 1ml buffer CSK buffer (15mM HEPES pH 7.8; 100mM NaCl; 3mM MgCl2; 1mM EGTA; 500mM Sucrose; 0.5% Triton X-100; Complete protease inhibitor (Roche) and 0.5x SUPERaseIN (Life technologies) to isolate the nuclei. Nuclei were collected by centrifugation and resuspended in 80ul of CF buffer (10mM Tris pH 8.0; 100mM NaCl; 25mM EDTA; 1x SUPERaseIN (Life technologies). Immediately afterwards, 1ml of NUN buffer (1.5M UREA; 20mM HEPES pH 7.8; 300mM NaCl; 7.5mM MgCl2; 500mM EDTA; 1% NP40) was added, and the sample was vortexed to lyse the nuclei. The mixture was incubated on ice with occasional agitation for 10 min to allow precipitation of genomic DNA and core histones together with engaged RNA Pol II and nascent transcripts. After spinning the sample at 20000g for 10 min at 4°C, the pellet was washed twice with NUN buffer. Next, the pellet was resuspended in 700 ul of CF buffer supplemented with 1% SDS and 1 mg/ml Proteinase K using a 25G needle and incubated at 55°C for 60 min. The lysate was extracted with Phenol/Chloroform. Nucleic acids were precipitated, dissolved in H2O and treated with Turbo DNaseI (Ambion) for 60 min at 37°C to eliminate DNA contamination.
50 ng of nascent RNA was used to make the RNA library for Illumina following the instructions provided by manufacture for NEBNext Ultra directional RNA library prep kit (New England BioLabs).

treatment_protocol: 2 × 106  293Trex cells were grown in 100 mm dishes.  Tetracycline was added to the media to a final concentration of 1ug/ml.  2 × 106 TC-797 and 1015 cells were grown in 100 mm dishes. JQ1 was added to the media to a final concentration of 500 nM for TC-797 cells, or 2 uM for 1015 cells.

value: NMC

tag: cell line

value: 1015 (Grayson et al. 2014)

value: JQ1 was not added to the medium


title: TRA00028927_ls_5


title: TRA00028927_ls_4


title: 7hTET_293TB4Nf

description: Nascent RNA

value: 293Trex (cells originating from embryonic kidney)

value: 7h -incubation time period  with Tetracycline (final concentration of 1ug/ml).


title: AAV_Cebpa_rep2

city: Philadelphia

first: Robert

middle: C

last: Bauer

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: ChIP-Seq, C/EBPa, 4-hour fasted

data_processing:
Reads were mapped to the mm9 genome using Bowtie. Ambiguous alignments were excluded for C/EBPa ChIP-seq tracks.
Redundant reads were removed from C/EBPa ChIP-seq datasets using the makeTagDirectory script in HOMER.
Bed files for C/EBPa ChIP-Seq peaks were generated using the FindPeaks script in HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: C/EBPa ChIP-seq peak files in BED format

growth_protocol: Mice were maintained on chow diet and fed ad libitum, and fasted for 4 hours prior to tissue harvest.

extract_protocol:
Liver tissue isolated from sacrificed mice was immediately frozen in liquid nitrogen. To process for ChIP, the tissue was thawed, minced and crosslinked in 1 % formaldehyde/PBS. Cells were disrupted and nuclei purified by dounce homogenization in a hypotonic buffer (20 mM HEPES/NaOH pH 7.5, 0.25 M sucrose, 3 mM MgCl2, 0.2% NP-40, 3 mM 2-mercaptoethanol, Complete protease inhibitor cocktail). To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: All AAVs were administered via IP injection. WT and LSKO mice were treated with 1.5e11 gc of AAV_Null or AAV_Cre, respectively. Null and C/EBPa animals were treated with 1e12 gc of AAV_Null or AAV_Cebpa.

tag: chip antibody

value: C/EBPa, sc-61, Santa Cruz

value: liver


title: 3hTET_293TB4Nf

description: Nascent RNA

tag: cell type

value: 3h -incubation time period  with Tetracycline (final concentration of 1ug/ml).


title: AAV_Cebpa_rep1

description: ChIP-Seq, C/EBPa, 4-hour fasted


title: TRA00028927_ls_3

value: MEC

value: Female

value: 5 week-old

value: Aire KO; AireGFP


title: TRA00028927_ls_23

value: WT; AireGFP


title: AAV_Null_rep1

description: ChIP-Seq, C/EBPa, 4-hour fasted


title: AAV_Null_rep2

description: ChIP-Seq, C/EBPa, 4-hour fasted


title: 2hTET_293TB4Nf

description: Nascent RNA

value: 2h -incubation time period  with Tetracycline (final concentration of 1ug/ml).


title: 2h30_JQ1_797R2

description: Nascent RNA

value: TC-797 (Toretsky et al. 2003)

value: 2h30min-incubation time period  with JQ1  ( final concentration of 500 nM)


title: 4h_JQ1_797R2

description: Nascent RNA

value: 4h - incubation time period  with JQ1  ( final concentration of 500 nM)


title: TRA00028927_ls_21


title: TRA00028927_ls_22


title: Trib1_LSKO_rep1

description: ChIP-Seq, C/EBPa, 4-hour fasted


title: TRA00028928_ls_13


title: noTET_293TB4Nf

description: Nascent RNA

value: No Tetracycline was added to the media


title: TRA00028927_ls_18


title: Trib1_LSKO_rep2

description: ChIP-Seq, C/EBPa, 4-hour fasted


title: 1h_JQ1_797R2

description: Nascent RNA

value: NMC

value: 1h-incubation time period  with JQ1  ( final concentration of 500 nM)


title: 4h_JO1_1015C

description: Nascent RNA

value: 1015 (Grayson et al. 2014)

value: 4h - incubation time period  with JQ1  ( final concentration of 2 uM)


title: 2h30_JQ1_797R1

description: Nascent RNA


title: TRA00028927_ls_14


title: TRA00028927_ls_16


title: 1h_JQ1_797R1

description: Nascent RNA

value: 1h -incubation time period  with JQ1  ( final concentration of 500 nM)


title: Trib1_WT_rep1

description: ChIP-Seq, C/EBPa, 4-hour fasted

value: C/EBPa, sc-61, Santa Cruz

value: liver


title: 4h_JQ1_797R1

description: Nascent RNA


title: TRA00028927_ls_12

value: MEC


title: TRA00028927_ls_13

value: Female


title: TRA00028927_ls_15

value: 5 week-old


title: Sample_15220

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Because of biased GC content in the 5’ end, the first 12 bases of each read in all 4 samples were trimmed off.
RNA-Seq libraries were processed by RSEM Li et al., BMC Bioinformatics to estimate expression levels of all genes. The expression level of a gene is expressed as a gene-level FPKM (Fragments Per Kilobase of transcripts per Million mapped reads) value.  UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
EBSeq Leng et al., Bioinformatics was used to identify differentially expressed genes (FDR = 0.01).
Genome_build: mm9
Supplementary_files_format_and_content: Wig file and FPKM values for each Sample

source_name: control GC-Tfh

extract_protocol:
GC-Tfh cells were sorted from the spleens and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: genotype

value: wild type

value: spleen

value: GC-Tfh

tag: cell phenotype

value: PD-1+ CXCR5+ CD4+ T cells


title: Sample_15221

source_name: Tcf1/Lef1-deficient GC-Tfh


title: Sample_15222


title: TRA00028927_ls_11

tag: strain

value: Aire KO; AireGFP


title: No_JQ1_797R1

description: Nascent RNA

value: TC-797 (Toretsky et al. 2003)

value: JQ1 was not added to the medium


title: IP_H3K27Ac_293Trex_3hB4Nflag_Dec2014

data_processing:
Reads were aligned to the human reference genome (GRCh38 assembly) using Bowtie (version 0.12.5), retaining only uniquely mapped reads.
Smoothed enrichment profiles were generated using the SPP package (Kharchenko et al. 2008), using smoothing bandwidth of 5kb.
tdf files were generated by converting wig files using igvtools
Genome_build: GRCh38
Supplementary_files_format_and_content: TDF files (for IGV browser) containing conservative estimates of smoothed enrichment

growth_protocol: 293Trex cells and NMC cell lines, TC-797 (Toretsky et al. 2003), 1015 (Grayson et al. 2014), 10326 (French et al. 2008) were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta Biologicals), 1% pen-strep and 1X GlutaMAX (Invitrogen). PER-403 (Kees et al. 1991) were maintained in DMEM with 20% FBS and supplemented as above. 293TRex-Flag-BRD4NUT cells were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta Biologicals), 1% pen-strep and 1X GlutaMAX (Invitrogen).

extract_protocol:
Formaldehyde cross-linked chromatin for ChIP-seq experiments with antibodies against proteins and histone modifications were prepared from 1.5 × 108 cells of each NMC cell line and 293TRex-Flag-BRD4NUT-HA as described (Alekseyenko et al. 2015). Chromatin from 0.8g of 1015 patient tissue ((Grayson et al. 2014) was prepared as follows: frozen tissue was ground to a powder with a ceramic mortar and pestle chilled with liquid N2. The powder was immediately transferred into a 50 ml Falcon tube filled with 9mL of NEB buffer (10% sucrose, 20 mM HEPES at pH 7.6, 10 mM NaCl, 3 mM MgCl2, 0.5% Triton, 0.1 mM PMSF). The mixture was vortexed for 15sec to brake-up the clumps, and immediately after, 45 mL of PBS and 0.5mL of 37% formaldehyde were added to the tube. The resulting mixture was incubated for 25 min at 25°C on an orbital shaker platform with gentle mixing (150 rpm). Washing and chromatin shearing steps were performed as described (Alekseyenko et al. 2015). Affinity purification was performed as described (Kharchenko et al. 2011). Input and IP DNA recovery and ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015). The following antibodies against proteins and histone modifications were used for ChIP-seq experiments: anti-H3K27ac (10 ul per IP, Active Motif, catalog no. 39133); anti-H3K9ac (15 ul per IP, Abcam, catalog no. ab12179); anti-H3K14ac (2 ul per IP, Abcam , catalog no. ab52946), anti-H3K36me3 (3 ul per IP, Abcam , catalog no. ab9050) anti-P300 (10 ul, Bethyl, catalog no. A300-358A); anti-BRD4-SL (against short and long isoforms of BRD4, 5 ul per IP, Bethyl, catalog no. A301-985A), anti-BRD4-L (against long isoforms of BRD4, 15 ul per IP, Active Motif, catalog no. 39909); anti-NUT (15 ul per IP; Cell Signaling, catalog no. 3625).
ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015).

treatment_protocol: 293TRex cells, which contain a single genomic FRT recombination site, were maintained with Blasticidin (Invitrogen). Flag-BRD4-NUT-HA cell line was generated by recombination with the plasmid Flag-Brd4-NUT-HA using the Flp-In technology manufacturer’s instructions (Invitrogen). The resulting cell lines were maintained in medium supplemented with Blasticidin (Invitrogen) and Hygromycin (Sigma). pEGFPC1-BRD4-NUT was created as described (French et al. 2008) and transfected into 293T cells using Lipofectamine 2000 according to the manufacturer's instructions (Life Technologies). Tetracycline was added (1 μg/mL) to 60-70 % confluent culture to induce transcription Flag-BRD4NUT for 2h, 3h and 7h. JQ1 was added to the media to a final concentration of 500 nM for TC-797 cells

value: H3K27ac (anti-H3K27ac , 10 ul per IP, Active Motif, catalog no. 39133)

value: 293Trex (cells originating from embryonic kidney)

value: 3h -incubation time period with Tetracycline (final concentration of 1ug/ml).


title: Sample_15226


title: Pax6alpha-Cre:Ezh2fl/+_2

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

address: 20 South, 2030 East Rm. 320 BPRB

department: Neurobiology & Anatomy

institute: University of Utah

data_processing:
reads were aligned to mm10 plus extended splice junctions using novoalign (2.08.01). Splice  Up to 50 alignments were reported and adapter sequences were trimmed by novoalign.
splice junction alignments were converted back to genomic space using the USeq (8.8.1) SamTranscriptomeParser application (default settings).
the final alignment files were used in the USeq (8.8.1) DefinedRegionDifferentialSeq application to generate counts per gene, FPKM values and to determine differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files contain raw read counts, FPKM values, log2ratio (DESeq2) and -10*log10(adjusted p-value) (DESeq2)

extract_protocol:
Peripherial retina was dissected at E16.5. The tissue was homogenized and RNA was purified by using Rneasy Plus Mini Kit from Qiagen (cat#74134). 1 ug of total RNA was used for RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Embryonic 16.5

value: retina


title: Pax6alpha-Cre:Ezh2fl/+_3


title: Trib1_WT_rep2

description: ChIP-Seq, C/EBPa, 4-hour fasted

value: C/EBPa, sc-61, Santa Cruz


title: Pax6alpha-Cre:Ezh2fl/+_4


title: IP_B4N_NUT_293Trex_3hB4Nflag_Dec2014

value: BRD4-NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)


title: No_JQ1_797R2

description: Nascent RNA

value: NMC


title: TRA00028926_ls_8

value: MEC

value: Female

value: WT; AireGFP


title: IP_Brd4_SaL_293Trex_3hB4Nflag_Dec2014

value: BRD4 short and long forms (anti-BRD4-SL , against short and long isoforms of BRD4, 5 ul per IP, Bethyl, catalog no. A301-985A)


title: Input_293Trex_3hB4Nflag_Dec2014


title: TRA00028926_umi_10

value: 5 week-old


title: IP_H3K27Ac_293Trex_7hB4Nflag_Oct2014

value: 7h -incubation time period with Tetracycline (final concentration of 1ug/ml).


title: Pax6alpha-Cre:Ezh2fl/null_4


title: Pax6alpha-Cre:Ezh2fl/+_1


title: Pax6alpha-Cre:Ezh2fl/null_3


title: TRA00028926_ls_6


title: IP_Brd4_SaL_293Trex_7hB4Nflag_Oct2014


title: TRA00028926_umi_13


title: Pax6alpha-Cre:Ezh2fl/null_1


title: TRA00028926_ls_22

value: Aire KO; AireGFP


title: TRA00028926_umi_12


title: TRA00028926_ls_4


title: Input_293Trex_2hB4Nflag_Oct2014

value: 2h -incubation time period with Tetracycline (final concentration of 1ug/ml).


title: TRA00028926_ls_14


title: Pax6alpha-Cre:Ezh2fl/null_2


title: Input_293Trex_7hB4Nflag_Oct2014


title: TRA00028926_ls_16


title: TRA00028926_ls_11


title: TRA00028926_ls_18


title: IP_H3K27Ac_293Trex_2hB4Nflag_Oct2014


title: IP_B4N_NUT_293Trex_2hB4Nflag_Oct2014


title: IP_B4N_NUT_293Trex_NoB4Nflag_Oct2014

value: No Tetracycline was added to the media


title: Input_293Trex_NoB4Nflag_Oct2014


title: TRA00028926_ls_13


title: IP_Brd4_SaL_293Trex_2hB4Nflag_Oct2014


title: TRA00028925_ls_23


title: TRA00028925_ls_5


title: IP_Brd4_SaL_293Trex_NoB4Nflag_Oct2014


title: IP_H3K27ac_CL1015c_Oct2014

source_name: 1015c cells

value: H3K27ac (anti-H3K27ac , 10 ul per IP, Active Motif, catalog no. 39133)

value: 1015 (Grayson et al. 2014)


title: IP_H3K27Ac_293Trex_NoB4Nflag_Oct2014

value: 293Trex (cells originating from embryonic kidney)


title: TRA00028925_ls_24


title: TRA00028925_ls_18


title: IP_Brd4_SaL_JQ1_4h_797Trex_Oct2014

value: TC-797 (Toretsky et al. 2003)

value: 4h - incubation time period with JQ1 (final concentration of 500 nM)


title: TRA00028925_ls_4


title: IP_B4N_Brd3NUT_Jul2014

source_name: 10326 cells

value: BRD3-NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)


title: TRA00028925_ls_16


title: IP_B4N_CL1015c_Jul2014

value: BRD4-NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)


title: IP_B4N_PT1015c_Jul2014

value: NMC


title: IP_B4N_797Trex_Jul2014


title: TRA00028924_ls_22

value: MEC


title: TRA00028924_ls_5

value: Female


title: IP_B4N_NUT_293Trex_7hB4Nflag_Oct2014


title: TRA00028925_ls_11


title: Input_Brd3NUT_Jul2014


title: TRA00028924_umi_14

value: WT; AireGFP


title: TRA00028925_umi_15


title: Input_JQ1_4h_797Trex_Oct2014


title: TRA00028924_ls_18


title: IP_B4N_Per403_Jul2014

source_name: Per403 cells

value: PER-403 (Kees et al. 1991)


title: IP_H3K27ac_JQ1_4h_797Trex_Oct2014


title: TRA00028924_ls_7

value: 5 week-old


title: TRA00028924_ls_15


title: TRA00028924_ls_24


title: Input_Per403_Jul2014


title: IP_H3K27ac_PT1015c_Oct2014


title: TRA00028923_umi_12


title: TRA00028924_ls_10


title: TRA00028923_umi_16


title: Input_797Trex_Jul2014


title: Input_PT1015c_Jul2014


title: IP_P300_797_Rep1_Jun2014

value: P300 (anti-P300 , 10 ul, Bethyl, catalog no. A300-358A)


title: IP_H3K36me3_797_Rep2_Jun2014

value: H3K36me3 (anti-H3K36me3, 3 ul per IP, Abcam , catalog no. ab9050)


title: TRA00028923_ls_7


title: IP_H3K36me3_797_Rep1_Jun2014


title: TRA00028923_ls_15


title: TRA00028923_ls_3

value: Aire KO; AireGFP


title: TRA00028924_ls_12


title: IP_H3K27ac_797_Rep2_Jun2014


title: TRA00028923_ls_8


title: IP_H3K9ac_797_Rep2_Jun2014

value: H3K9ac (anti-H3K9ac , 15 ul per IP, Abcam, catalog no. ab12179)


title: IP_H3K14ac_797_Rep2_Jun2014

value: H3K14ac (anti-H3K14ac , 2 ul per IP, Abcam , catalog no. ab52946)


title: IP_H3K27ac_797_Rep1_Jun2014

value: H3K27ac (anti-H3K27ac , 10 ul per IP, Active Motif, catalog no. 39133)


title: TRA00028923_ls_14


title: Input_CL1015c_Jul2014

value: 1015 (Grayson et al. 2014)


title: IP_H3K9ac_797_Rep1_Jun2014

value: TC-797 (Toretsky et al. 2003)


title: CR_15_4

city: Orangeburg

first: Stephen

middle: D

last: Ginsberg

address: 140 Old Orangeburg Road

department: Center for Dementia Research

institute: Nathan Kline Institute

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (UCSC build mm10) using the TopHat aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
Mapped reads were analyzed using the Cufflinks package (using fragment bias and multi-read correction).
Genome_build: mm10
Supplementary_files_format_and_content: CSV file contains FPKM values for each sample.

source_name: hippocampal CA1 region

extract_protocol:
RNA was isolated from frozen hippocampal CA1 microdissections using the miRNAeasy Micro Kit.
300 ng of total RNA with an average RIN value of 9 was applied to the TruSeq RNA Sample Preparation Kit v2 to construct mRNA sequencing libraries.

value: hippocampal CA1 region

value: 15 months

tag: diet

value: calorie-restricted


title: TRA00028923_ls_18

tag: age


title: IP_H3K14ac_797_Rep1_Jun2014

value: NMC


title: CR_15_5


title: IP_P300_797_Rep2_Jun2014


title: IP_Brd4_NUT_Rep1_Mar2014

value: BRD4-NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)


title: CR_15_1


title: AL_15_4

value: normal


title: Input_797_Rep1_Jun2014


title: IP_Brd4_NUT_Rep2_Mar2014


title: CR_15_2


title: AL_15_5


title: IP_Brd4_L_797_Rep1_Mar2014

value: BRD4 long form (anti-BRD4-L, against long isoforms of BRD4, 15 ul per IP, Active Motif, catalog no. 39909)


title: CR_15_3


title: AL_15_3


title: IP_Brd4_SaL_797_Rep2_Mar2014

value: BRD4 short and long forms (anti-BRD4-SL , against short and long isoforms of BRD4, 5 ul per IP, Bethyl, catalog no. A301-985A)


title: CR_15_0


title: AL_15_1


title: Input_797_Rep2_Mar2014


title: IP_Brd4_SaL_797_Rep1_Mar2014


title: CR_05_3

value: 5 months


title: IP_H3K27me3_797_Mar2014

value: H3K27me3 (anti-H3K27me3, Abcam ab6002; 5 ul per IP)


title: CR_05_4


title: IP_293T_B4N_N

growth_protocol: 293Trex cells and TC-797 (Toretsky et al. 2003) were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta)

extract_protocol:
1.5 × 109 cells grown as monolayer cultures in 150mm dishes (100 plates total) were used for BioTAP-XL purification. Tetracycline was added (1 μg/mL) to 60-70 % confluent culture to induce transcription of the N- or C-BioTAP tagged BRD4-NUT cDNA clones for 16h. The main steps of BioTAP-XL procedure: harvesting cells, formaldehyde cross-linking, chromatin preparation, affinity purification, input and IP DNA recovery, and ChIP-seq library preparation, were performed as described (Alekseyenko et al. 2014a; Alekseyenko et al. 2015)
ChIP-seq library preparation, were performed as described (Alekseyenko et al. 2014a; Alekseyenko et al. 2015)

treatment_protocol: 797TRex and 293TRex cells, which contain a single genomic FRT recombination site, were maintained as above with Blasticidin (Invitrogen). TC-797 and 293-TRex /N- and C- BioTAP-BRD4-NUT lines were generated by recombination with the plasmids pcDNA5 FRT/TO/N- or C-BioTAP BRD4NUT using the Flp-In technology manufacturer’s instructions (Invitrogen). The resulting cell lines were maintained in medium supplemented with Blasticidin (Invitrogen) and Hygromycin (Sigma).

value: 293Trex (cells originating from embryonic kidney)

tag: pulldown with biotap_tag

value: N- BioTAP-BRD4-NUT


title: Input_797_Rep2_Jun2014


title: Input_797_Rep1_Mar2014


title: IP_293T_B4N_C

value: C- BioTAP-BRD4-NUT


title: Input_293T_B4N_N


title: AL_05_3


title: CR_05_1


title: CR_05_0


title: CR_05_2


title: AL_15_0


title: Input_293T_B4N_C


title: Input_797_B4N_C

description: TC-797 (Toretsky et al. 2003)


title: AL_05_4


title: IP_797_B4N_N

description: TC-797 (Toretsky et al. 2003)


title: AL_05_2


title: AL_15_2


title: PBMCs sample_TR125

city: Atlanta

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

data_processing:
The raw RNA-Seq reads for each sample were aligned to the reference human genome (hg19) using Bowtie as the short read aligner, and splice junctions were identified using TopHat
Raw sequence read depths were converted to estimated transcript abundance measures as fragments per kilobase of exons per million (FPKM) values using Cufflinks
All genes with an FPKM greater than 2.5 averaged across all 24 samples were retained, representing 6,154  genes
FPKM values were transformed to logarithm base 2 and normalized using the supervised normalization of microarray (SNM) procedure with the R package from Bioconductor
Supplementary_files_format_and_content: excel file include normalize expession values matrix for all samples

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
Whole blood mRNA was extracted using TempusTM Blood RNA Tube isolation kits provided by the manufacturer Applied Biosystems, and the quality was determined based on the Agilent Bioanalyzer 2100 RNA Integrity score (RIN).
Illumina RNA seq kit was used for sequence library preparation using the Illumina TruSeq RNA Sample Prep Guide: Low Throughput (LT) Protocol.

value: PBMC

tag: gender

value: Female

tag: time

value: DX

tag: location

value: Buenaventura

tag: individual


title: PBMCs sample_TR132

growth_protocol: Peripheral blood mononuclear cells (PBMCs)

value: PRE


title: LSK_BCR-ABL_mice_Sick_2

tag: digestion

value: MspI

tag: treatment

value: bisulfite

tag: background strain


title: TRA00028926_ls_21

value: MEC

tag: Sex

value: 5 week-old

tag: sorting markers

tag: primer

tag: genotype/variation

value: Aire KO; AireGFP


title: LSK_BCR-ABL_mice_Sick_1

tag: cell type


title: LSK_BCR-ABL_mice_Rescued_2


title: PBMCs sample_TR099

value: Cali


title: LSK_BCR-ABL_mice_Rescued_1


title: IP_797_B4N_C

description: TC-797 (Toretsky et al. 2003)

value: NMC

tag: cell line


title: AL_05_0

tag: tissue

value: hippocampal CA1 region

value: 5 months

value: normal


title: IP_Brd4_L_797_Rep2_Mar2014

tag: chip antibody

value: BRD4 long form (anti-BRD4-L, against long isoforms of BRD4, 15 ul per IP, Active Motif, catalog no. 39909)

value: TC-797 (Toretsky et al. 2003)


title: PBMCs sample_TR105

value: PBMC

value: Male

tag: age


title: LSK_BCR-ABL_mice_control_2


title: PBMCs sample_TR080

value: DX


title: PBMCs sample_TR093


title: Input_797_B4N_N

description: TC-797 (Toretsky et al. 2003)

tag: pulldown with biotap_tag


title: sRNAseq-D4-

tag: donor

value: monocyte-derived macrophages

tag: infection


title: LSK_BCR-ABL_mice_control_1


title: PBMCs sample_TR050

tag: gender

value: Female

tag: time

tag: location

value: Buenaventura


title: HITSCLIP-HIV- (3 donor mix)

source_name: monocyte-derived macrophages, noninfected, Ago2 IP

value: mix of 3 donors

tag: antibody

value: anti-AGO2, clone 11A9 (Sigma)


title: PBMCs sample_TR067

tag: individual


title: PBMCs sample_TR049

value: PRE


title: PBMCs sample_TR055


title: sRNAseq-D3-


title: PARCLIP-D2-


title: sRNAseq-D1-


title: PBMCs sample_TR038


title: PBMCs sample_TR035


title: PBMCs sample_TR077


title: PARCLIP-D4-


title: PBMCs sample_TR029


title: PBMCs sample_TR027


title: 7_H526-DMSO_Input

city: Collegeville

first: David

last: Soong

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline

description: input DNA from DMSO treated H526 cells

data_processing:
Sequence reads were aligned to the reference human genome (hg19) using BWA with default parameters
We filtered out reads mapping to multiple locations and removed PCR duplicates using Picard MarkDuplicates
Enriched ChIP-seq regions were identified using MACS 2.0 (q-value < .01)
Read density tracks were calculated using in-house programs and visualized using the UCSC and IGV genome browsers
Genome_build: hg19
Supplementary_files_format_and_content: BED - enriched ChIP-seq regions; Definition of columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue
Supplementary_files_format_and_content: bigWig - genome browser track - tag density

source_name: NCI-H526 small cell lung cancer cell line

extract_protocol: SDS buffer after crosslinking

treatment_protocol: 1 uM GSK2879552 for 24 hours

value: epithelial

tag: passages

value: multiple


title: PBMCs sample_TR022


title: PBMCs sample_TR011

value: Cali


title: 2_H526-GSK552_LSD1

description: LSD1 ChIP-seq in GSK552 treated H526 cells


title: sRNAseq-D2-


title: 5_H526-DMSO_H3K4me1

description: H3K4me1 ChIP-seq in DMSO treated H526 cells


title: PBMCs sample_TR008


title: 8_H526-GSK552_Input

description: input DNA from GSK552 treated H526 cells


title: PBMCs sample_TR007


title: 1_H526-DMSO_LSD1

description: LSD1 ChIP-seq in DMSO treated H526 cells


title: HEMn-LP_miRNA

status: Public on Jul 13 2015

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

data_processing:
Sequenced reads were firsly transformed to fasta file
Fasta files wer aligned to the UCSC reference human genome using miRDeep2 software by default setting (3' adaptor is TCGTATGCCGTCTTCTGCTTGT)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values and normalized values for each Sample

extract_protocol:
Total RNA was extracted from HEMn-LP, A375, and A2058 cell lines using TRIzol® Reagent (Invitrogen, Carlsbad, CA) per manufacturer’s instruction
cDNA library was constructed using Small RNA Sample Preparation Kit (Illumina)

value: HEMn-LP


title: A2058_miRNA


title: A375_miRNA


title: PBMCs sample_TR003


title: CD34_EET

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: rRNA depleted RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

source_name: CD34+cells from cord blood

growth_protocol: Human CD34+ cells were isolated from fresh cord blood by Ficoll separation of mononuclear cells and subsequent positive selection of CD34+ cells using magnetic beads (Miltenyi). U937 cells were cultured in RPMI-1640 Medium (Sigma-Aldrich) and 10% FBS at 5% CO2 in air atmosphere according to seller’s protocol (ATCC).

extract_protocol:
Treated CD34+ and U937 cells were washed with PBS, then total RNA was extracted with the RNeasy mini plus kit from Qiagen.
Total RNA was depleted of ribosomal RNA with the RiboZero gold kit (Epicentre). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

treatment_protocol: Human CD34+ cells were treated in serum free IMDM media (Sigma-Aldrich) with either DMSO or 5 uM 11,12-EET for 2hrs at 37C. U937 cells were serum starved for one hour and then treated with either DMSO or 5 μM 11,12-EET for 2 hrs at 37C.

tag: sample type

value: CD34+ cell

tag: treatment

value: 5uM 11,12-EET for 2 hrs


title: CD34_DMSO

description: rRNA depleted RNA

value: DMSO


title: EMT TC 7d JNKi R1

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

data_processing:
For all the sequenced samples low complexity reads were filtered out and remaining reads were aligned to Mouse genome (mm9) using TopHat with default parameters. The aligned reads were then provided as an input to HTSeq_count utility from HTSeq package. The raw read count files obtained from HTSeq-count were then processed for differential expression using DESeq package. The raw read counts were normalized for library size differences using estimateSizeFactors function from DESeq package.
Genome_build: mm9
Supplementary_files_format_and_content: NormalizedReadCount.txt: Normalized Read Count Per Transcript

source_name: EMT TC 7d JNKi R1

growth_protocol: All cells were cultured at 37°C with 7% CO2 in a humid incubator.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For TGF-β timecourse experiments, cells were treated with 2ng/ml TGF-β for indicated time points with TGF-β replenishment and medium change every 2 days.

value: NmuMG

value: Mammary Gland

tag: genotype

value: WT

tag: strain

value: JNKi

tag: time point


title: EMT TC 7d JNKi R2

source_name: EMT TC 7d JNKi R2

tag: cell type

tag: tissue


title: EMT TC 96h JNKi R1

source_name: EMT TC 96h JNKi R1


title: EMT TC 72h JNKi R2

source_name: EMT TC 72h JNKi R2


title: EMT TC 72h JNKi R1

source_name: EMT TC 72h JNKi R1


title: PBMCs sample_TR021

value: PBMC

value: Male

tag: age

value: DX


title: PBMCs sample_TR018


title: EMT TC 48h JNKi R2

source_name: EMT TC 48h JNKi R2


title: EMT TC 48h JNKi R1

source_name: EMT TC 48h JNKi R1


title: PBMCs sample_TR006


title: 3_H526-DMSO_H3K4me2

description: H3K4me2 ChIP-seq in DMSO treated H526 cells

tag: cell line

tag: chip antibody


title: EMT TC 24h JNKi R2

source_name: EMT TC 24h JNKi R2


title: EMT TC 7d DMSO R1

source_name: EMT TC 7d DMSO R1


title: EMT TC 48h DMSO R1

source_name: EMT TC 48h DMSO R1


title: EMT TC 24h DMSO R2

source_name: EMT TC 24h DMSO R2


title: PBMCs sample_TR005

value: Female

value: Buenaventura


title: EMT TC 24h JNKi R1

source_name: EMT TC 24h JNKi R1


title: EMT TC 7d DMSO R2

source_name: EMT TC 7d DMSO R2


title: IP_B4N_NUT_JQ1_4h_797Trex_Oct2014

value: BRD4-NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)

value: NMC

value: TC-797 (Toretsky et al. 2003)

value: 4h - incubation time period with JQ1 (final concentration of 500 nM)


title: EMT TC 96h DMSO R1

source_name: EMT TC 96h DMSO R1


title: EMT TC 72h DMSO R2

source_name: EMT TC 72h DMSO R2


title: EMT TC 72h DMSO R1

source_name: EMT TC 72h DMSO R1


title: EMT TC 96h JNKi R2

source_name: EMT TC 96h JNKi R2


title: EMT TC 48h DMSO R2

source_name: EMT TC 48h DMSO R2


title: EMT TC 24h DMSO R1

source_name: EMT TC 24h DMSO R1


title: EMT TC 7d R3

source_name: EMT TC 7d R3

value: untreated


title: EMT TC 4d R4

source_name: EMT TC 4d R4


title: EMT TC 10d R1

source_name: EMT TC 10d R1


title: EMT TC 1d R4

source_name: EMT TC 1d R4


title: EMT TC 1d R3

source_name: EMT TC 1d R3


title: EMT TC 96h DMSO R2

source_name: EMT TC 96h DMSO R2


title: EMT TC 7d R4

source_name: EMT TC 7d R4


title: EMT TC 7d R1

source_name: EMT TC 7d R1


title: EMT TC 4d R3

source_name: EMT TC 4d R3


title: EMT TC 4d R1

source_name: EMT TC 4d R1


title: EMT TC 1d R1

source_name: EMT TC 1d R1


title: EMT TC 0h R4

source_name: EMT TC 0h R4


title: EMT TC 0h R3

source_name: EMT TC 0h R3


title: EMT TC 0h R1

source_name: EMT TC 0h R1


title: CLL37

city: Los Angeles

first: Sanjai

last: Sharma

state: CA

department: Hematology Oncology

institute: UCLA West LA VA Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality score of RNA-seq reads was obtained by using the FastQC Version 0.11.1.
Reads were then processed and aligned to the UCSC H. sapiens reference genome (build hg19) using TopHat v1.3.3 with default parameter.
The aligned read BAM files were assembled into transcripts, their abundance estimated and tests for differential expression processed by Cufflinks v2.0.1.
The expression testing was done at the level of transcripts and genes and pairwise comparisons of expression between normal and CLL samples. Only the comparisons with “q-value” less than 0.05 and expression fold change greater than two fold in the Cuffdiff output were regarded as showing significant differential expression.
Downstream analysis for Cuffdiff output was done using CummeRbund.
For splicing analysis, MATS 3.0.8 (Multivariate Analysis of Transcript Splicing) was used to determine junctional reads within ENSEMBL human gene annotations. This software implements a Bayesian approach that detects differential AS (alternative splicing) under two conditions by examining whether the difference in the exon-inclusion levels between two samples exceeds a given user-defined threshold. To identify these events, we used the following criteria, 1. Splicing events were labeled significant if the sum of the reads supporting a specific event exceeded 10 reads, 2. P-value was <0.05, and 3. Minimum inclusion level difference as determined by MATS was >0.1 (10% difference).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including average FPKM values, log2 fold changes for all genes and differential expressions analysis from comparisons among Normal, CLL (IGVH mutated and IGVH unmutated) samples.

source_name: CLL leukemic cells

extract_protocol:
For library preparation, the Illumina TruSeq RNA sample Prep Kit v2 (San Diego, CA) was used according to the manufacturer’s protocol. Briefly, 1 µg of total mRNAs from five normal B and ten CLL cells was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers.
Following second-strand cDNA synthesis, end repair, addition of a single A base, adaptor ligation, and PCR amplification, the enriched cDNA libraries were sequenced using the Illumina HiSeq 2000 at the UCLA Broad Stem Cell Research Center High Throughput Sequencing Core.

value: IGVH mutated CLL

value: CLL leukemic cells


title: EMT TC 10d R3

source_name: EMT TC 10d R3


title: EMT TC 10d R4

source_name: EMT TC 10d R4


title: CLL39


title: CLL9

value: IGVH non-mutated CLL


title: CLL25


title: B5

source_name: Purified normal B cells

value: Normal

value: Purified normal B cells


title: CLL44


title: CLL40


title: CLL6


title: CLL26


title: B4


title: B1


title: AL_05_1

source_name: hippocampal CA1 region

value: hippocampal CA1 region

value: 5 months

tag: diet

value: normal


title: KCNK1 4

city: La Jolla

first: Don

middle: W.

last: Cleveland

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
Sequenced using an Illumina HiSeq 2000 sequencer with four biological replicates sequenced per condition using single read, 50 cycle runs
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using tophat v2.0.10 with parameters --no-coverage-search -G genes.gtf --transcriptome-index=transcriptome_data/known --prefilter-multihits --max-multihits 1 --library-type fr-firststrand -o *_thout genome *.fastq.bz2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks version v2.1.1 with parameters -N -F 0 -G genes.gtf -o *_clout *_thout/accepted_hits.bam
Significant gene expression change between groups has been detected using T-test with FDR adjusted p-value in R
Genome_build: hg19
Supplementary_files_format_and_content: excel files include FPKM values for each sample, mean of FPKM values for each group, fold change, t-test p-value, FDR adjusted p-value (q-value) for pair-wise group comparison

source_name: RKO_KCNK1 siRNA

growth_protocol: Standard culture conditions

extract_protocol:
TRIzol-extracted RNA
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit

treatment_protocol: siRNA-transfected or mock-transfected

value: RKO

value: colon carcinoma cell line

tag: tansfected with

value: KCNK1 siRNA


title: B2


title: KCNK1 1


title: KCNK1 3


title: CLL28


title: B3


title: Myc 3

source_name: RKO_Myc siRNA

value: Myc siRNA


title: SNTA1 4

source_name: RKO_SNTA1 siRNA

value: SNTA1 siRNA


title: SNTA1 3


title: SNTA1 2


title: CLL32


title: SNTA1 1


title: Mock 5

value: none (mock-transfected)


title: Mock 3


title: Mock 4


title: Mock 2


title: Myc 4


title: Mock 1


title: Non-Targeting 1

source_name: RKO_non-targeting siRNAs

value: non-targeting siRNAs


title: U937_EET

description: rRNA depleted RNA

source_name: Leukemic cell line

value: 5uM 11,12-EET for 2 hrs


title: Non-Targeting 3


title: Myc 2


title: U937_DMSO

description: rRNA depleted RNA

value: DMSO


title: Myc 1


title: KCNK1 2


title: infected BM-PMN 1

first: William

middle: Evan

last: Goldman

address: 130 Mason Farm Rd.

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls performed using CASAVA version 1.8
Alignment to mm9 reference genome with fusion detection using MapSplice version 2.0.1.9
Translate sorted genome alignment file (reordered) to transtriptome coordinates
Filter large indels and inserts greater than 10K bases from transcript file
Gene and isoform expression were calculated with RSEM version 1.1.13
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file represents normalized gene expression of all 12 samples (rsem.genes.normalized_results)

source_name: infected-mouse bone marrow neutrophils

extract_protocol:
For bone marrow neutrophils: femurs of C57BL/6J mice were collected and flushed with 5 mL of cold PBS to extract marrow. Marrow cells were disaggregated by repetitive passes through and 18 gauge needle. Bone marrow neutrophils (BM-PMNs) were then isolated using a MACS Neutrophil isolation kit (Miltenyi Biotec) per the manufacturer’s instructions. The final volume of BM-PMNs was resuspended in TRIzol® Reagent (Ambion®) and total RNA was isolated per the manufacturer’s instructions.
For laser capture microdissection lesion regions: After laser capture microdissection microscopy total RNA was isolated from the LCM-isolated lesion pieces using an RNeasy FFPE Isolate kit (Qiagen™). Total RNA isolation was performed as per the manufacturers instructions with the exception of a 3 h incubation at 56°C after the addition of proteinase K.
Libraries were prepared in an attempt to acquire both eukaryotic and prokaryotic RNA. Ribosomal-RNA was removed using an Epidemiology Ribo-Zero™ Magnetic Gold Kit (Epicentre®). Complementary-DNA was generated using a SMARTer® Universal Low Input RNA Kit (Clontech®) followed by RNAseq library sequencing template preparation using a Low Input Library Prep Kit (Clontech®). Samples were diluted and barcoded for paired end amplification and clustered (TruSeq® SBS Kit v2 (200cycles) and TruSeq® PE Cluster Kit v2 (Illumina®)) using a cBot™ (Illumina®) for running on a HiSeq® 2000 system (Illumina®).

value: 4-6 weeks old

value: bone marrow neutrophils

tag: infection

value: intranasal Yersinia pestis infection

tag: time

value: 48 hours post infection


title: uninfected BM-PMN 1

source_name: uninfected-mouse bone marrow neutrophils


title: uninfected BM-PMN 2


title: infected BM-PMN 3


title: lesion center 2

source_name: center cells of lung lesions, pneumonic plague 48hpi

value: center cells of lung lesions (lung immune infiltrate)


title: infected BM-PMN 2


title: lesion center 3


title: lesion center 1


title: uninfected BM-PMN 3


title: mesenteric artery replicate 1

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Rat Rnor5.72 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Genome_build: R. norvegicus (Rnor5.72)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Mesenteric Arterial Arcade

extract_protocol:
Tissue homogenization and RNA extraction by Qiagen mini-column
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mesenteric artery


title: lesion periphery 2

city: Chapel Hill

source_name: periphery cells of lung lesions, pneumonic plague 48hpi

value: periphery cells of lung lesions (lung immune infiltrate)


title: lesion periphery 3


title: lesion periphery 1


title: Non-Targeting 4


title: aortic tissue replicate 1

source_name: Aorta

value: aorta


title: mesenteric artery replicate 2


title: aortic tissue replicate 2


title: naïve SET2 cells replicate 3

status: Public on Jul 11 2015

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
All sequenced library were mapped to the human genome (hg19) using rnaStar. Unmapped reads were mapped again to the same genome using BWA MEM (version 0.7.5.1)
HTSeq v0.5.3p3 (options -s y -m intersection-strict) is used for feature counting using the Homo_sapiens.GRCh37.69_ENSEMBL gene model also used at the mapping stage
DESeq (v1.10.1) is used for the normalization of count table.
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized count tables from each experiment

source_name: SET2 cell line

growth_protocol: SET2 cells were cultured in RPMI1640 media + 20% FCS. For persistent cell lines, the respective type I JAK inhibitor was added to the culture media for continuous growth in presence of inhibitor. For acute exposures with inhibitor, DMSO was used as a control

extract_protocol:
SET2 cells were lysed in Trizol and processed according to instructions with reagent.
poly(A) RNA was isolated using Dynabeads® mRNA DIRECTTM Micro Kit (Life Technologies) from 1 μg of total RNA. mRNA was then fragmentated using RNaseIII and purified. The fragmented samples’ quality and yield were evaluated using Agilent BioAnalyzer. Subsequently, the fragmented material underwent whole transcriptome library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR.  Samples were barcoded, template-positive Ion PITM Ion SphereTM Particles (ISPs) were prepared using the ion one touch system II and Ion PITMTemplate OT2 200kit v2 Kit (Life Technologies). Enriched particles were sequenced on a Proton sequencing system using 200 bp version 2 chemistry.

tag: inhibitor exposure


title: Non-Targeting 2

value: RKO


title: naïve SET2 cells replicate 1


title: naïve SET2 cells replicate 2


title: MLGB

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed reads with 3′ adapter reads, 5′ adapter contaminants, the poly-A tail, and sequences <18 nt. After this preprocessing, the sequenced raw data were transferred into clean reads. Modified sequences from 18 nt to 30 nt were used for further analyses.
Further analysis began with SOAP 2.0 software (Li et al. 2009) to map the clean reads from mature G. biloba leaves onto entries in the Michigan State University transcriptome database. The GenBank and Rfam (version 10.1) databases were used to annotate the rRNA, scRNA, snoRNA, snRNA, and tRNA in the sRNA library (Gardner et al. 2011). the remaining sRNA sequences were retained for miRNA identification.
Previously known miRNAs were identified in these sRNA sequences by alignment to sequences in miRBase (Release 20.0) with no mismatches (Griffiths-Jones et al. 2008).
Reads remaining without annotation were used to predict potentially novel miRNAs using MIREAP software, followed by a prediction of secondary structure using MFOLD  software (Zuker 2003)
We used the Web-based psRNATarget program to identify putative targets for known and novel miRNAs.
Normalize the expression of miRNA in both female leaves and male leaves to get the expression of transcript per million (TPM). We used  fold-change(log2) < −1 or fold-change(log2) > 1 and p-value < 0.05 as thresholds to determine a significant difference in miRNA expression.
Genome_build: miRNA_target.fa.gz (miRNA target candidates)
Supplementary_files_format_and_content: The compressed files include miRNA read counts (.txt and .fa),TPM values (.txt) and target prediction (.table.txt).

organism: Ginkgo biloba

source_name: Male leaf

growth_protocol: Mature male and female leaves were obtained from healthy G. biloba trees (approximately 30 years old) growing under natural conditions in the Institute of Botany, Chinese Academy of Sciences.

extract_protocol:
Samples were collected in June 2012. Total RNAs of male and female leaves were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sex type

value: male tree

value: leaf

tag: developmental stage

value: mature


title: SET2 cells persistent to SAR302503_replicate 2

city: New York

value: chronic


title: FLGB

source_name: Female leaf

value: female tree


title: SET2 cells persistent to INC424_replicate 3

description:
s_SET2_INC_per3
library run again to get enough reads


title: SET2 cells persistent to SAR302503_replicate 1

description:
s_SET2_SAR_per1
library run again to get enough reads


title: SET2 cells persistent to INC424_replicate 1


title: naïve SET2 cells, 4h INC424 replicate 3

value: acute


title: naïve SET2 cells, 48h INC424 replicate 3


title: naïve SET2 cells, 4h INC424 replicate 1

description:
s_SET2_INC_4h1
library run again to get enough reads


title: naïve SET2 cells, 4h INC424 replicate 2

description:
s_SET2_INC_4h2
library run again to get enough reads


title: SET2 cells persistent to SAR302503_replicate 3

description:
s_SET2_SAR_per3
library run again to get enough reads


title: naïve SET2 cells, 4h DMSO replicate 2

description:
s_SET2_DMSO_4h2
library run again to get enough reads


title: naïve SET2 cells, 4h DMSO replicate 1


title: naïve SET2 cells, 48h INC424 replicate 2

description:
s_SET2_INC_48h2
library run again to get enough reads


title: SET2 cells persistent to CYT387_replicate 3


title: naïve SET2 cells, 4h DMSO replicate 3

description:
s_SET2_DMSO_4h3
library run again to get enough reads


title: SET2 cells persistent to CYT387_replicate 2


title: SET2 cells persistent to CYT387_replicate 1


title: SET2 cells persistent to BMS911543_replicate 3