title: K96243_2

city: Rockville

first: Liliana

last: Losada

address: 9704 Medical Center Dr

institute: JCVI

data_processing:
Reads were mapped to the Burkholderia pseudomallei K96243 genome using CLC Genomics Workbench v 6.0.2, using default settings.
Reads that aligned to the ribosomal RNA loci were removed after mapping, and not accounted in the gene expression analysis.
Genome_build: Burkholderia_pseudomallei_K96243
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Burkholderia pseudomallei

source_name: Wild type

growth_protocol: Burkholderia pseudomallei were gronw in liquid LB broth at 37C for 4 hours, 4 independent times.

extract_protocol:
RNA was extracted using Zymo Research ZR Fungal/Bacterial RNA miniprep kit following manufacturer's instructions.
Sequencing libraries were generating using standard Illumina ScripSeq v2 library preparation kit and sequenced on Illumina HiSeq2000 at Ambry Genetics (Aliso Viejo, CA)

value: Wild type


title: TT-seq_Raji-CDK9as_1NAPP1_rep2

status: Public on Oct 09 2017

type: SRA

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

country: Germany

institute: MPI

description:
Human Black, Burkitt′s lymphoma
4sU-labeled RNA

library_source: transcriptomic

data_processing:
Sequencing data preprocessing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. 2 replicates of TT-Seq with 1-NA-PP1 treatment and 2 replicates of TT-Seq with DMSO treatment. Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts and antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Sequencing depth calculations resulted in no detectable global differences.
Calculation of the number of transcribed bases (coverage). For each sample aligned duplicated fragments were discarded. Of the resulting unique fragment isoforms only those were kept that exhibited a positive inner mate distance. The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38, ~ 98% of all fragments) in addition to the sum of the coverage of non-evident fragment parts (entire fragment).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

molecule: total RNA

organism: Homo sapiens

source_name: Raji B lymphocyte cells (CDK9as)

growth_protocol: Raji B cells were grown in RPMI 1640 medium (Gibco) supplemented with 10 % foetal calf serum (bio-sell), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), and 2 mM L-glutamine (Gibco) at 37 °C and 5 % CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen).

extract_protocol:
Cells were harvested by centrifugation at 3,000 x g for 2 min. Total RNA was extracted using QIAzol according to the manufacturer’s instructions. RNAs were sonicated to generate fragments of <1.5 kb using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris). 4sU-labeled RNA was purified from 150 µg total fragmented RNA. Separation of labeled RNA was performed using streptavidin beads (Miltenyi Biotec). Prior to library preparation, 4sU-labeled RNA was purified and quantified. Enrichment of 4sU-labeled RNA was analyzed by RT-qPCR as described before in (Schwalb et al., 2016). Input RNA was treated with HL-dsDNase (ArcticZymes) and used for strand-specific library preparation according to the Ovation Universal RNA-Seq System (NuGEN). The size-selected and pre-amplified fragments were analyzed on a Fragment Analyzer before clustering and sequencing on the Illumina HiSeq 1500.
NuGEN Ovation Universal RNA-Seq System, starting with 100 ng RNA input

treatment_protocol: Reactions including RNA spike-ins were performed essentially as described before in (Schwalb et al., 2016). Two independent biological replicates were prepared for the present study. Briefly, for TT-seq experiments, 3.3 x 107 Raji B cells were treated for 15 minutes with solvent (DMSO) or 5 µM of 4-Amino-1-tert-butyl-3-(1ʹ-naphthyl)pyrazolo[3,4-d]pyrimidine (1-NA-PP1) (Calbiochem). Labeling was performed with the addition of 500 µM of 4-thiouracil (4sU) (Sigma) for 5 min at 37 °C and 5 % CO2.

tag: treatment conditions

value: 15 min of 5 µM of 1-NA-PP1 (CDK9as inhibitor) (Calbiochem, EMD Millipore); incl. 4sU-labeling during the last 5 minutes.

tag: cell type

value: B lymphocyte cells

tag: genotype

tag: method protocol

value: TT-seq (Schwalb et al., 2016)

tag: antibody


title: K96243_3

state: MD

country: USA

tag: strain


title: K96243_4


title: E1K27

city: Stanford

first: Jared

last: Churko

state: CA

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

library_source: genomic

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.8
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1  was used to generate bigwig files
Genome_build: Ensembl; GRCh38
Supplementary_files_format_and_content: AltAnalyze 2.0.8 was used to generated a table of RPKM values

molecule: genomic DNA

source_name: fibroblasts

growth_protocol: hiPSCs and hESCs were grown in E8 media on  Matrigel

extract_protocol:
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin
RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep

treatment_protocol: no treatment

value: human induced pluripotent stem cells (hiPSCs)

tag: passages

tag: reprogramming method

value: Episomal

tag: clone

tag: chip antibody

value: H3K27me3 (Active Motif, 39155)


title: C1-R

value: Minicircle


title: K96243_1


title: C1K4

value: H3K4me3 (Active Motif, 39159)


title: DDL3431_4

source_name: TctR mutant

value: TctR mutant


title: N2_Tre_3

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210  version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >1 in at least 4 libraries were included in the analysis.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Strains were grown on OP50 plates at 20C, and adults were hypochlorite treated to obtain embryos.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit. 500ng of starting RNA was used and 12 cycles of PCR were used to amplify libraries.

treatment_protocol: Embryos were grown in S-basal (with or without 50mM trehalose) at a density of 1 embryo/uL. After 24 hours, L1 larvae were spun down and flash frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: buffer

value: 50mM trehalose in S-basal

tag: developmental stage

value: L1 larvae


title: N2_Sba_9

value: S-basal


title: C1HDAC2-C

value: HDAC2 (Cell Signaling, 2545S)


title: DDL3431_2


title: C1K27


title: N2_Sba_6


title: EtOH_11hr_Rep2

status: Public on Oct 08 2017

city: Durham

first: Timothy

last: Reddy

state: NC

address: 101 Science Drive

institute: Duke University

data_processing:
RNA-seq reads were aligned to multi-fasta file containing all GENCODE v.19 protein-coding and long non-coding RNA transcript sequences.
Read counts were quantified with samtools idxstats utility.
Genome_build: hg19
Supplementary_files_format_and_content: Each column in the gene expression matrix represents a sample, as indicated in the header, and each row represents a transcript, as indicated in an index column. Values are read counts.

source_name: A549 cell line

growth_protocol: A549 cells (ATCC CCL-185) were grown in F-12K media (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and 1% penicillin-streptomycin (Invitrogen). Cells were harvested at approximately 80% confluence.

extract_protocol:
RNA was extracted with RNeasy Miniprep kit.
Libraries were generated on an Apollo 324 liquid handling platform using the Wafergen poly-A RNA purification.

treatment_protocol: Cells were treated for 1 h with either 100 nM dexamethasone in ethanol or an equal volume (0.02% v/v of media) of ethanol as a vehicle control.

tag: cell line

tag: treatment

value: 0.02% v/v ethanol

tag: duration of treatment

value: 11 hr

tag: biological replicate


title: DDL3431_3


title: DDL3431_1


title: EtOH_11hr_Rep1


title: EtOH_9hr_Rep2

value: 9 hr


title: C1H3

value: H3 (Active Motif, 61475)


title: N2_Sba_3


title: N2_Tre_8


title: EtOH_9hr_Rep1


title: EtOH_3hr_Rep2

value: 3 hr


title: EtOH_7hr_Rep2

value: 7 hr


title: EtOH_1hr_Rep1

value: 1 hr


title: EtOH_3hr_Rep1


title: tps_Tre_8

value: tps-1;tps-2 double mutant


title: EtOH_5hr_Rep1

value: 5 hr


title: N2_Sba_8


title: EtOH_1hr_Rep2


title: DEX_11hr_Rep2

value: 100 nM dexamethasone


title: L2H3

value: human induced pluripotent stem cells (hiPSCs)

value: LentiVirus


title: DEX_11hr_Rep1


title: DEX_9hr_Rep2


title: DEX_7hr_Rep2


title: DEX_9hr_Rep1


title: DEX_7hr_Rep1


title: DEX_5hr_Rep1


title: DEX_5hr_Rep2


title: DEX_3hr_Rep1


title: DEX_1hr_Rep1


title: EtOH_7hr_Rep1


title: DEX_1hr_Rep2


title: Mitoplast RNA

city: Tuscaloosa

first: Carl

middle: A.

last: Pinkert

state: AL

address: 201 Rose Administration Bldg

institute: University of Alabama

description:
Mitochondrial RNA
RNA isolated from purified, nuclease treated liver mitoplasts

data_processing:
Paired end reads were aligned to the M. m. domesticus mitochondrial genome (mm9) using BWA
All reads aligning to the mitochondrial genome were removed.
Remaining reads were then aligned to the M. m. domesticus genome with tophat to identify nuclear RNAs
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is an excel sheet containing the following columns: Chr, Start, End, Seq. length, Max coverage, IntersectBed(overlapping genes), Repeatmasker type, Repeatmasker, Blast #1, Blast #2, Sequence

organism: Mus musculus

source_name: Purified liver mitoplasts

extract_protocol:
Mitoplasts were extracted using Trizol
Libraries were prepared at the HudsonAlpha Genomic Services Lab. RNA was first amplified using an Ovation RNA-seq kit (NuGEN, San Carlos CA) to amplify the RNA and produce a cDNA library. cDNA was electrophoretically separated and gel excision allowed selection of fragments roughly 300 nucleotides in length. The cDNA library was then sequenced.

tag: sample type

tag: tissue

value: liver


title: EtOH_5hr_Rep2


title: Input_GDF15

city: Denver

first: Brian

middle: Patrick

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

data_processing:
ChIP-seq sequencing reads were aligned to the human reference genome using the Ion Torrent Suite software, version 4.0.2 and version 4.4
Peak-calling from aligned reads will be performed using the Model-based Analysis for ChIP-Sequencing (MACS2) software (Zhang, 2008), comparing pSmad IPs to their respective total input controls. Peak significance was determined with a false discovery rate (FDR) cutoff of 0.001.
Peaks found by ChIP-seq will be associated with the nearest gene by genomic location, using both the RefSeq, refGene, and UCSC known gene models. A gene lists based on closest called peaks was generated.
Genome_build: HG19
Supplementary_files_format_and_content: peak.bed files were generated using MACS2 as described above

source_name: Human tracheobronchial epithelial cells (hTBEs)

growth_protocol: Normal human tracheobronchial epithelial cells at passage 2 were seeded onto collagen-coated 60 mm tissue culture dishes (4 x 10^5 cells) in bronchial epithelial cell growth medium (BEGM) with SingleQuots™ supplements (Lonza, Walkersville, MD) at 37°C, 5% CO2. At 80-90% confluence, cells were treated with 0.1% BSA-HCl (control) or 25 ng/ml of recombinant human GDF15 (rhGDF15, R&D Systems, Minneapolis, MN) for 2 h.

extract_protocol:
Chromatin was sheared using the isothermal Covaris S2 to produce approximately 100-300bp fragments for Ion Proton ChIP-seq. DNA-protein complexes were immunoprecipitated with an anti-pSMAD antibody (#11971, Cell Signaling), captured by magnetic beads, cross-links reversed, and the genomic DNA purified (Invitrogen Magnify ChIP Kit #49-2024).
Libraries were made according to the instructions using the Ion Xpress Plus Fragment Library Kit- 4471252

treatment_protocol: We chose 2 h of GDF15 stimulation for ChIP-seq analysis since the maximal activation of Smad1 pathway was observed at this time-point after rhGDF15 (25 ng/ml) stimulation in hTBEs as reported in our previous study (PMID: 27093475).

tag: cell type

value: Human tracheobronchial epithelial cells


title: ChIP_Psmad_GDF15


title: ChIP_Psmad_BSA


title: 96_A-sr_CD8_day8

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 4.0.2.
Sequence reads of at least 30 nt length were mapped to the hg19 release of the human genome using STAR (version 2.4.0h1) with splice site data from the human Ensembl annotation version 75.
Reads mapping unambiguously to each gene in the Ensembl 75 annotation were quantified using the htseq-count program from the HTSeq package (version 0.6.1) in the “intersection-nonempty” mode.
Genome_build: hg19
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text table (derived from htseq-count)

source_name: Peripheral blood

growth_protocol: Activated (anti-CD3/CD2) CD8+ T cells  were purified from the peripheral blood on day 0 and cultured in the presence of IL-2 for 8 days.  Peripheral blood CD8+ T cells were stimulated with anti-human CD3 monoclonal antibody (2 mg/mL; BD  PharMingen, San Jose, California)/antihuman CD28 monoclonal  antibody (2 mg/mL; BD PharMingen) and human recombinant IL-2  (100 U/mL; Peprotech, Rocky Hill, New Jersey). Cells were cultured for 8 days   at 1x10e6 cells/mL per well. Medium containing IL-2 was changed every other day. Cells were harvested on day 0 and day 8.

extract_protocol:
Total RNA was extracted using the the NucleoSpin II RNA isolation kit (#740955, Macherey-Nagel, Dueren, Germany) following the manufacturer's protocol
Libraries were made out of 200 ng input RNA using the RNA Library Preparation Kit (Kapa Biosystems #KK8420) and modified primers. Libraries were analyzed for size and quality using the High Sensitivity Bioanalyzer Kit (Agilent #5067-4626) and sequenced with on Life Technologies Ion Proton at the NJH Genomics Facility.

treatment_protocol: not applicable

value: CD8+T cells

tag: patient id

tag: disease status

value: steroid-resistant asthma

tag: culturing time

value: 8 days


title: 96_A-sr_CD8_day0


title: 85_control_CD8_day8

value: healthy control


title: 82_A-sr_CD8_day8


title: 77_A-ss_CD8_day8

value: steroid-sensitive asthma


title: 77_A-ss_CD8_day0


title: 82_A-sr_CD8_day0


title: 103_A-ss_CD8_day0


title: 66_A-ss_CD8_day8


title: 66_A-ss_CD8_day0


title: 103_A-ss_CD8_day8


title: 102_control_CD8_day8


title: 102_control_CD8_day0


title: 100_A-sr_CD8_day8


title: 100_A-sr_CD8_day0


title: DEX_3hr_Rep2


title: Input_BSA


title: HELA cell RNA-seq after MED12 knockdown plus Serum stimulation

city: Miami

first: Jingyin

last: Yue

state: FL

address: 1501 NW 10th Ave

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Illumina NextSeq 500 system was used to do sequencing and generate FASTQ files
For RNA-seq, reads were aligned to human hg19 genome assembly using BaseSpace apps_TopHat Alignment (version 1.0.0) by selecting trim TruSeq Adapters option.
For CHIP-seq, Sequenced reads were processed using trimmomatic/0.32 with parameter LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 and also trimmed adaptor sequence; and then were aligned to human hg19 genome assembly using bowtie2/2.2.6.
For both RNA-seq and CHIP-seq, aligned reads were processed with samtools to get .bam and .bam.bai files. Python bam2wig tools were used to generate bigwig files in order to visualize sequencing tracks on UCSC genome browser.
Genome_build: Human hg19
Supplementary_files_format_and_content: bigwig files for UCSC genome browser visualization

source_name: cervix

growth_protocol: The cells were cultured in 37 degree incubator with 5% CO2. The growth medium contains 10% FBS and 1X L-gultamine.

extract_protocol:
Chromatin associate RNA were extracted from cultured cells for RNA-seq. DNA was immuno-precipitated with antibody from sonicated cell lysate.
RNA  and CHIP libraries were prepared with NEBNext Library Prep Kits for Illumina using standard Illumina protocols

treatment_protocol: The inhibitor treatment was carried out by incubating cells with drug containing medium for 3 hours.

value: HeLa

tag: genetic background

value: Harboring inducible shRNA expressing cassette

tag: culture medium

value: Starvation:Culture in 0.5% FBS medium for 2 days

tag: agent

value: Doxycycline for 3 days

tag: egf stimulation

value: Serum stimulation:20 min, 10%


title: HELA cell RNA-seq after MED12 knockdown before serum stimulation


title: HELA cell RNA-seq for MED12 shRNA control before serum stimulation


title: HELA cell RNA-seq after MED12 knockdown plus EGF stimulation

value: EGF stimulation:20 min, 100ng/ml


title: HELA cell RNA-seq for INTS11 shRNA control before serum stimulation


title: HELA cell RNA-seq after MED12 knockdown


title: HELA cell RNA-seq for MED12 shRNA control plus Serum stimulation


title: HELA cell RNA-seq for INTS11 shRNA control plus serum stimulation


title: HELA cell RNA-seq for MED12 shRNA control plus EGF stimulation


title: HELA cell RNA-seq for MED12 shRNA control


title: HELA cell RNA-seq with Flag_INTS11 overexpression plus EGF stimulation


title: HELA cell RNA-seq after MED1 knockdown plus EGF stimulation


title: HELA cell RNA-seq with MEK inhibitor treatment  plus EGF stimulation

value: MEK inhibitor  for 3 hours at 0.2uM


title: HELA cell RNA-seq with Flag_INTS11 overexpression


title: HELA cell RNA-seq with MEK inhibitor treatment


title: Patient 3.3, 72 hour

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode against the Homo_sapiens.GRCh38.79.gtf annotation table from http://www.ensembl.org.
Genome_build: hg38
Supplementary_files_format_and_content: The raw read counts described above are in fastq format tabulated below. The final read counts are provided as an Excel file.

source_name: enriched CTCs_72-hour preserved blood

extract_protocol:
Enriched CTCs from the CTC-iChip were spun down, resuspended in RNAlater, flash-frozen in liquid nitrogen, and stored in -80 deg C. RNA was extracted using the Qiagen RNeasy Plus Micro Kit.
Using the SMARTer Ultra Low Input RNA Kit for Sequencing – v4 kit (Clontech Laboratories), RNA (~1 ng) was converted to cDNA and amplified per the manufacturer’s protocol. After 18 cycles of second strand synthesis and amplification, cDNA was purified with a 1× Agencourt AMPure XP bead cleanup (Beckman Coulter), and the Nextera® XT DNA Library Preparation kit (Illumina) was used for sample fragmentation/barcoding. Fragmentation used 1 ng of purified cDNA, followed by 12 cycles of amplification prior to unique dual-index barcoding. After the PCR product was purified with a 1.8× Agencourt AMPure XP bead cleanup, the eluted cDNA did not undergo the bead-based normalization step in the Nextera XT protocol.

treatment_protocol: Whole blood was preserved at 4 deg C for 24, 48, or 72 hours in the presence of tirofiban. Immediately prior to CTC isolation, blood was warmed to room temperature and supplemented with 3 mM EDTA. CTCs were isolated using the CTC-iChip.

value: patient 3

value: enriched prostate CTCs from patient blood sample

tag: blood storage

value: 72-hour preserved blood


title: Patient 3.1, 0 hour

source_name: enriched CTCs_fresh blood

value: fresh blood


title: Patient 3.2, 0 hour


title: Patient 4, 0 hour

value: patient 4


title: Patient 4, 48 hour

source_name: enriched CTCs_48-hour preserved blood

value: 48-hour preserved blood


title: Patient 2.1, 24 hour

source_name: enriched CTCs_24-hour preserved blood

value: patient 2

value: 24-hour preserved blood


title: Patient 3.1, 24 hour


title: Patient 3.2, 48 hour


title: Patient 3.3, 0 hour


title: HELA cell RNA-seq after INTS11 knockdown plus serum stimulation


title: HELA cell RNA-seq after INTS11 knockdown before serum stimulation


title: Patient 2.1, 0 hour


title: Patient 1, 24 hour

value: patient 1


title: Patient 1, 0 hour


title: HELA cell RNA-seq for MED1 shRNA control plus EGF stimulation


title: HELA cell RNA-seq after MED1 knockdown


title: HELA cell INTS11 CHIP-seq with ERK inhibitor treatment plus EGF stimulation

value: ERK inhibitor 3 hours at 1uM


title: HELA cell INTS11 CHIP-seq with ERK inhibitor treatment

value: HeLa


title: HELA cell RNA PolII CHIP-seq with ERK inhibitor treatment plus EGF stimulation

value: Harboring inducible shRNA expressing cassette


title: A375 cell RNA-seq with ERK inhibitor treatment

source_name: Skin

value: BRAF mutation

value: Starvation:Culture in 0.5% FBS medium for 2 days


title: A375 cell RNA-seq with control siRNA

value: Control siRNA transfection, 3 days


title: A549 cell RNA-seq with MEK inhibitor treatment plus EGF stimulation

source_name: Lung

value: KRAS mutation

value: MEK inhibitor 3 hours at 0.2 uM

value: EGF stimulation:20 min, 100ng/ml


title: A375 cell RNA-seq with vehicle treatment plus EGF stimulation

value: DMSO treatment for 3 hours


title: HELA cell RNA-seq for MED1 shRNA control


title: HELA cell INTS11 CHIP-seq with Vehicle treatment plus EGF stimulation


title: A549 cell RNA-seq with MEK inhibitor treatment


title: HELA cell INTS11 CHIP-seq with Vehicle treatment


title: HELA cell RNA PolII CHIP-seq with ERK inhibitor treatment


title: HELA cell RNA PolII CHIP-seq with Vehicle treatment plus EGF stimulation


title: HELA cell RNA PolII CHIP-seq with Vehicle treatment


title: A375 cell RNA-seq with control siRNA plus EGF stimulation


title: A375 cell RNA-seq after INTS11 knockdown

value: INTS11 siRNA transfection, 3 days


title: A375 cell RNA-seq with ERK inhibitor treatment plus EGF stimulation


title: A549 cell RNA-seq with control siRNA


title: A375 cell RNA-seq with BRAF inhibitor treatment

value: BRAF inhibitor 3 hours at 1uM


title: A375 cell RNA-seq with MEK inhibitor treatment


title: HELA cell RNA-seq with Control shRNA

value: Doxycycline for 3 days


title: A375 cell RNA-seq with BRAF inhibitor treatment plus EGF stimulation


title: A375 cell RNA-seq with vehicle treatment


title: K8 CLIP-seq  in BJAB cells

city: guangzhou

first: Dongcheng

last: Liu

state: guangdong

address: zhongshan 2nd road

department: Institute of Human Virology and Ministry of Education Key Laboratory of Tropical Disease Control

country: China

institute: Sun Yat-sen University

data_processing:
Sequence reads were trimmed for adaptor, then mapped to low-quality sequence hg19 and U75698.1 by  TopHat 1.3.0 or bowtie software
Peak calling was performed by RIPSeeker software.
Genome_build: hg19 and  U75698.1
Supplementary_files_format_and_content: txt file with peak coordinates.

source_name: BJAB cells

growth_protocol: BCBL-1,a primary effusion lymphoma cell line which carries latently infected KSHV and BJAB, a  KSHV-free Burkitt lymphoma B cell line, were maintained in RPMI 1640 medium  with 10% heat-inactivated fetal bovine serum (FBS) contained  penicillin-streptomycin (50 U/ml), amphotericin B (1.25 μg /ml).

extract_protocol:
Turbo DNase was added into the cell lysate. Lysate was incubated on ice for 30 min and spun downed at 4°C and 20,000 g for 10 min to clear the lysate. Antibody of interest and 50μl washed protein A Dynabeads was added per 500μl lysates. Samples were rotated for 2 h at 4°C. Discarded the supernatant and washed the beads twice with 900 μl high-salt buffer. Then washed twice with 900 μl wash buffer with different mount of Rnase A (high-RNase concentration: 2μg/ml, moderate-RNase concentration: 1μg/ml and low-RNase concentration: 0.2μg/ml). Beads were washed with 900 μl RNase-free wash buffer twice. Then RNA 3’ ends were dephosphorylated. Linkers were ligated to 3’ ends of RNAs, 32P-γ-ATP labeled linker was ligated to the 5 ’ends of RNAs. The protein-RNA complexes were resolved on a 4-12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane.
K8-RNAs complexes were isolated and subjected to proteinase K digestion and RNA purification by TRIzol. RNAs were subjected to RT-PCR according to TruSeq™ RNA and DNA Sample Prep Kits.

treatment_protocol: BCBL-1 was induced by 20ng/ml TPA for 48h

tag: clip antibody

value: K8 (generated and purified in our lab; Yan Wang, et al.,J Viral, 2011 and Xin Wang, et al., PLOS pathogens, 2015)

value: BJAB

value: KSHV-free Burkitt lymphoma B cell line


title: A375 cell RNA-seq with MEK inhibitor treatment plus EGF stimulation


title: HELA cell RNA-seq after INTS11 knockdown plus EGF stimulation


title: HELA cell RNA-seq after INTS11 knockdown


title: A549 cell RNA-seq with ERK inhibitor treatment plus EGF stimulation


title: A549 cell RNA-seq with vehicle treatment plus EGF stimulation


title: A549 cell RNA-seq with vehicle treatment


title: IgG CLIP-seq in BCBL-1 cells

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: BCBL-1 cells

tag: infected with

value: Human gammaherpesvirus 8

value: IgG (Sigma-Aldrich, Catalog Number I5381)

value: primary effusion lymphoma cell line which carries latently infected KSHV


title: K8 CLIP-seq-1 in BCBL-1 cells

tag: cell line


title: HELA cell RNA-seq with vehicle treatment

value: HeLa

value: Harboring inducible shRNA expressing cassette


title: HELA cell RNA-seq with ERK inhibitor treatment

value: Starvation:Culture in 0.5% FBS medium for 2 days

value: ERK inhibitor 3 hours at 1uM


title: A375 cell RNA-seq after INTS11 knockdown plus EGF stimulation

value: BRAF mutation


title: A549 cell RNA-seq with ERK inhibitor treatment

value: KRAS mutation


title: A549 cell RNA-seq after INTS11 knockdown


title: A549 cell RNA-seq with control siRNA plus EGF stimulation

value: Control siRNA transfection, 3 days

value: EGF stimulation:20 min, 100ng/ml


title: K8 CLIP-seq-2 in BCBL-1 cells


title: HELA cell RNA-seq with control siRNA plus EGF stimulation


title: HELA cell RNA-seq with vehicle treatment plus EGF stimulation

value: DMSO treatment for 3 hours


title: Fasted 24 hrs pCREB ChIP-seq rep#3

status: Public on Oct 07 2017

city: Bethesda

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description:
GH2114
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fasted_24_r13_RC_GH2112xGH2114_FDR0.csv

data_processing:
Illumina Casava 1.8 software was used for basecalling and alignment.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.

source_name: Fasted 24 hrs pCREB ChIP-seq

growth_protocol: mice maintained according to NIH guidelines under 12-hr light-dark cycles (light on at 6:00AM). Hepatocytes isolated by the two-step collagenase perfusion technique

extract_protocol:
crosslinked material was lyzed and sonicated.
Chromatin precipitated with antibody and DNA was purified by ethanol precipitation. All the sequencing data were sequenced on NextSeq 500 using NextSeq High V2 chemistry single end.

treatment_protocol: mice were fasted for 24 or 10 hrs or fed ad lib. Hepatocytes treated with glucagon (10nM) or glucagon (10nM) + corticosterone (1.7uM) for 1hr

tag: strain

value: liver

tag: chip antibody

value: Phospho-CREB (Ser133) (87G3) Rabbit mAb #9198


title: HELA cell RNA-seq with ERK inhibitor treatment plus EGF stimulation


title: A549 cell RNA-seq after INTS11 knockdown plus EGF stimulation

value: INTS11 siRNA transfection, 3 days


title: Fasted 24 hrs pCREB ChIP-seq rep#1

description:
GH2112
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fasted_24_r13_RC_GH2112xGH2114_FDR0.csv


title: Fasted 24 hrs CREB ChIP-seq rep#2

description:
GH2107
processed data file:
hs_RC_mouseliver_ChIP_CREB_fasted_24_r13_RC_GH2106xGH2108_FDR0.csv

source_name: Fasted 24 hrs CREB ChIP-seq

value: CREB (48H2) Rabbit mAb #9197


title: Fed 24 hrs CREB ChIP-seq rep#2

description:
GH2104
processed data file:
hs_RC_mouseliver_ChIP_CREB_fed_24_r13_RC_GH2103xGH2105_FDR0.csv

source_name: Fed 24 hrs CREB ChIP-seq


title: Fasted 24 hrs pCREB ChIP-seq rep#2

description:
GH2113
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fasted_24_r13_RC_GH2112xGH2114_FDR0.csv


title: Fed 24 hrs pCREB ChIP-seq rep#2

description:
GH2110
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fed_24_r13_RC_GH2109xGH2111_FDR0.csv

source_name: Fed 24 hrs pCREB ChIP-seq


title: Fed 24 hrs pCREB ChIP-seq rep#1

description:
GH2109
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fed_24_r13_RC_GH2109xGH2111_FDR0.csv


title: Fasted 24 hrs CREB ChIP-seq rep#1

description:
GH2106
processed data file:
hs_RC_mouseliver_ChIP_CREB_fasted_24_r13_RC_GH2106xGH2108_FDR0.csv


title: ten_infected_6

city: New York

first: Itai

last: Yanai

address: 430 East 29th St., Office 510

department: Biochemistry and Molecular Pharmacology

institute: New York University, School of Medicine

data_processing:
Libraries were sequenced on the Illumina HiSeq2500, paired-end sequencing R1- 15bp, R2- 35bp, Index- 6bp
Conversion from BCL to FASTQ and deumltiplexing using CASAVA
Filter barcode minimum quality of 10.
Demultiplexing using the CEL-Seq2 pipeline (Hashimshony, et a. 2016) of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against mouse and salmonella transcriptome from refseq (Avraham et al., 2015)
Genome_build: Read counting with htseq-count
Supplementary_files_format_and_content: expression matrix

source_name: BMDM

growth_protocol: C57BL/6 WT mice were obtained from Jackson Laboratory. Cultures of Salmonella typhimurium labeled with GFP (pFPV25.1; Addgene) were grown in Luria-Bertani (LB) medium at 37°C, washed in PBS and incubated for 1 hr with pHrodo dye (Life Technologies)

extract_protocol:
From each time-point cells were lifted from plates and sorted using fluorescence activated cell sorting (FACS) into 96-well plates containing 4.5 μl lysis buffer (TE containg 5%NP-40 and RNAse inhibitor) (Avraham et al., 2015).
scDual-Seq

treatment_protocol: BMDMs were infected at an MOI of 50:1. After 30 minutes, cells were washed with media containing 15 μg/ml gentamicin.

tag: cell culture

value: primary cell culture

tag: time point

value: Salmonella typhimurium SL1344


title: ten_unexposed_4

value: unexposed


title: ten_unexposed_3


title: ten_unexposed_5


title: ten_infected_4


title: ten_infected_3


title: ten_infected_5


title: Fed 24 hrs pCREB ChIP-seq rep#3

description:
GH2111
processed data file:
hs_RC_mouseliver_ChIP_pCREB_fed_24_r13_RC_GH2109xGH2111_FDR0.csv

tag: tissue


title: ten_infected_2


title: ten_infected_1


title: singles_unexposed_39

description: cells_singles_cells_unexposed_sample_0039


title: singles_unexposed_40

description: cells_singles_cells_unexposed_sample_0040


title: singles_unexposed_38

description: cells_singles_cells_unexposed_sample_0038


title: Fasted 24 hrs CREB ChIP-seq rep#3

description:
GH2108
processed data file:
hs_RC_mouseliver_ChIP_CREB_fasted_24_r13_RC_GH2106xGH2108_FDR0.csv


title: singles_unexposed_37

description: cells_singles_cells_unexposed_sample_0037


title: Fed 24 hrs CREB ChIP-seq rep#3

description:
GH2105
processed data file:
hs_RC_mouseliver_ChIP_CREB_fed_24_r13_RC_GH2103xGH2105_FDR0.csv


title: singles_unexposed_36

description: cells_singles_cells_unexposed_sample_0036


title: singles_unexposed_33

description: cells_singles_cells_unexposed_sample_0033


title: Fed 24 hrs CREB ChIP-seq rep#1

description:
GH2103
processed data file:
hs_RC_mouseliver_ChIP_CREB_fed_24_r13_RC_GH2103xGH2105_FDR0.csv


title: singles_unexposed_34

description: cells_singles_cells_unexposed_sample_0034


title: singles_unexposed_32

description: cells_singles_cells_unexposed_sample_0032


title: ten_unexposed_6


title: singles_unexposed_30

description: cells_singles_cells_unexposed_sample_0030


title: singles_unexposed_31

description: cells_singles_cells_unexposed_sample_0031


title: singles_unexposed_35

description: cells_singles_cells_unexposed_sample_0035


title: ten_unexposed_1


title: ten_unexposed_2


title: singles_unexposed_28

description: cells_singles_cells_unexposed_sample_0028


title: singles_unexposed_27

description: cells_singles_cells_unexposed_sample_0027


title: singles_unexposed_24

description: cells_singles_cells_unexposed_sample_0024


title: singles_unexposed_26

description: cells_singles_cells_unexposed_sample_0026


title: singles_unexposed_23

description: cells_singles_cells_unexposed_sample_0023


title: singles_unexposed_25

description: cells_singles_cells_unexposed_sample_0025


title: singles_unexposed_21

description: cells_singles_cells_unexposed_sample_0021


title: singles_unexposed_22

description: cells_singles_cells_unexposed_sample_0022


title: singles_unexposed_20

description: cells_singles_cells_unexposed_sample_0020


title: singles_unexposed_15

description: cells_singles_cells_unexposed_sample_0015


title: singles_unexposed_18

description: cells_singles_cells_unexposed_sample_0018


title: singles_unexposed_17

description: cells_singles_cells_unexposed_sample_0017


title: singles_unexposed_19

description: cells_singles_cells_unexposed_sample_0019


title: singles_unexposed_14

description: cells_singles_cells_unexposed_sample_0014


title: singles_unexposed_12

description: cells_singles_cells_unexposed_sample_0012


title: singles_unexposed_13

description: cells_singles_cells_unexposed_sample_0013


title: singles_unexposed_11

description: cells_singles_cells_unexposed_sample_0011


title: singles_unexposed_8

description: cells_singles_cells_unexposed_sample_0008


title: singles_unexposed_9

description: cells_singles_cells_unexposed_sample_0009


title: singles_unexposed_2

description: cells_singles_cells_unexposed_sample_0002


title: singles_unexposed_7

description: cells_singles_cells_unexposed_sample_0007


title: singles_unexposed_3

description: cells_singles_cells_unexposed_sample_0003


title: singles_infected_40

description: cells_singles_cells_infected_sample_0088


title: singles_unexposed_5

description: cells_singles_cells_unexposed_sample_0005


title: singles_unexposed_6

description: cells_singles_cells_unexposed_sample_0006


title: singles_unexposed_10

description: cells_singles_cells_unexposed_sample_0010


title: singles_unexposed_29

description: cells_singles_cells_unexposed_sample_0029


title: singles_unexposed_4

description: cells_singles_cells_unexposed_sample_0004


title: singles_unexposed_1

description: cells_singles_cells_unexposed_sample_0001


title: singles_unexposed_16

description: cells_singles_cells_unexposed_sample_0016


title: singles_infected_38

description: cells_singles_cells_infected_sample_0086


title: singles_infected_39

description: cells_singles_cells_infected_sample_0087


title: singles_infected_34

description: cells_singles_cells_infected_sample_0082


title: singles_infected_35

description: cells_singles_cells_infected_sample_0083


title: singles_infected_37

description: cells_singles_cells_infected_sample_0085


title: singles_infected_33

description: cells_singles_cells_infected_sample_0081


title: singles_infected_36

description: cells_singles_cells_infected_sample_0084


title: singles_infected_31

description: cells_singles_cells_infected_sample_0079


title: singles_infected_32

description: cells_singles_cells_infected_sample_0080


title: singles_infected_29

description: cells_singles_cells_infected_sample_0077


title: singles_infected_27

description: cells_singles_cells_infected_sample_0075


title: singles_infected_25

description: cells_singles_cells_infected_sample_0073


title: singles_infected_26

description: cells_singles_cells_infected_sample_0074


title: singles_infected_24

description: cells_singles_cells_infected_sample_0072


title: singles_infected_23

description: cells_singles_cells_infected_sample_0071


title: singles_infected_28

description: cells_singles_cells_infected_sample_0076


title: singles_infected_30

description: cells_singles_cells_infected_sample_0078


title: singles_infected_21

description: cells_singles_cells_infected_sample_0069


title: singles_infected_20

description: cells_singles_cells_infected_sample_0068


title: singles_infected_19

description: cells_singles_cells_infected_sample_0067


title: singles_infected_13

description: cells_singles_cells_infected_sample_0061


title: singles_infected_17

description: cells_singles_cells_infected_sample_0065


title: singles_infected_18

description: cells_singles_cells_infected_sample_0066


title: singles_infected_22

description: cells_singles_cells_infected_sample_0070


title: singles_infected_9

description: cells_singles_cells_infected_sample_0057


title: singles_infected_11

description: cells_singles_cells_infected_sample_0059


title: singles_infected_10

description: cells_singles_cells_infected_sample_0058


title: singles_infected_7

description: cells_singles_cells_infected_sample_0055


title: singles_infected_6

description: cells_singles_cells_infected_sample_0054


title: singles_infected_4

description: cells_singles_cells_infected_sample_0052


title: singles_infected_15

description: cells_singles_cells_infected_sample_0063


title: singles_infected_8

description: cells_singles_cells_infected_sample_0056


title: singles_infected_16

description: cells_singles_cells_infected_sample_0064


title: singles_infected_3

description: cells_singles_cells_infected_sample_0051


title: singles_infected_2

description: cells_singles_cells_infected_sample_0050


title: singles_infected_1

description: cells_singles_cells_infected_sample_0049


title: hundred_unexposed_2

description: cells_hundred_cells_unexposed_sample_0048


title: singles_infected_14

description: cells_singles_cells_infected_sample_0062


title: singles_infected_12

description: cells_singles_cells_infected_sample_0060


title: hundred_unexposed_1

description: cells_hundred_cells_unexposed_sample_0047


title: hundred_infected_2

description: cells_hundred_cells_infected_sample_0096


title: infected_T8_93

data_processing:
Libraries were sequenced on the Illumina HiSeq2500, paired-end sequencing R1- 15bp, R2- 35bp, Index- 6bp
Conversion from BCL to FASTQ and deumltiplexing using CASAVA
Filter barcode minimum quality of 10.
Demultiplexing using the CEL-Seq2 pipeline (Hashimshony, et a. 2016) of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against a combined transcriptome of mouse downaloaded from UCSC genome browser (GRCM38/mm10) and salmonella from NCBI NC_017718.1 (Avraham et al., 2015)
Genome_build: Read counting with htseq-count
Supplementary_files_format_and_content: expression matrix


title: infected_T8_91


title: infected_T8_96


title: infected_T8_89


title: hundred_infected_1

description: cells_hundred_cells_infected_sample_0095


title: infected_T8_90


title: infected_T8_94


title: infected_T8_86


title: infected_T8_87


title: infected_T8_88


title: infected_T8_85


title: infected_T8_95


title: infected_T8_83


title: infected_T8_84


title: infected_T8_82


title: infected_T8_80


title: infected_T8_78


title: infected_T8_81


title: infected_T8_77


title: infected_T8_79


title: infected_T8_75


title: infected_T8_74


title: infected_T8_76


title: infected_T8_73


title: infected_T8_72


title: infected_T8_92


title: infected_T8_70


title: infected_T8_71


title: infected_T8_69


title: infected_T8_68


title: infected_T8_66


title: infected_T8_67


title: infected_T8_65


title: infected_T8_64


title: infected_T8_62


title: infected_T8_60


title: infected_T8_61


title: infected_T8_63


title: infected_T8_55


title: infected_T8_58


title: infected_T8_59


title: infected_T8_57


title: infected_T8_56


title: infected_T8_54


title: infected_T8_51


title: infected_T8_50


title: infected_T8_53


title: infected_T8_49


title: infected_T8_46


title: infected_T8_47


title: infected_T8_48


title: infected_T8_44


title: infected_T8_45


title: infected_T8_43


title: infected_T8_42


title: infected_T8_41


title: infected_T8_39


title: infected_T8_33


title: infected_T8_35


title: infected_T8_34


title: infected_T8_32


title: infected_T8_38


title: infected_T8_52


title: infected_T8_30


title: infected_T8_36


title: infected_T8_31


title: infected_T8_37


title: infected_T8_25


title: infected_T8_24


title: infected_T8_28


title: infected_T8_26


title: infected_T8_19


title: infected_T8_27


title: infected_T8_20


title: infected_T8_23


title: infected_T8_16


title: infected_T8_18


title: infected_T8_15


title: infected_T8_22


title: infected_T8_17


title: infected_T8_14


title: infected_T8_40


title: infected_T8_12


title: infected_T8_21


title: infected_T8_29


title: singles_infected_5

description: cells_singles_cells_infected_sample_0053


title: infected_T8_13


title: infected_T8_9


title: infected_T8_3


title: infected_T8_2


title: infected_T8_5


title: infected_T8_6


title: infected_T8_4


title: infected_T8_8


title: infected_T8_7


title: infected_T8_1


title: infected_T4_95


title: infected_T4_94


title: infected_T4_93


title: infected_T4_90


title: infected_T4_92


title: infected_T4_96


title: infected_T4_89


title: infected_T4_86


title: infected_T4_84


title: infected_T4_85


title: infected_T4_83


title: infected_T4_82


title: infected_T4_87


title: infected_T8_11


title: infected_T8_10


title: infected_T4_81


title: infected_T4_80


title: infected_T4_79


title: infected_T4_91


title: infected_T4_77


title: infected_T4_69


title: infected_T4_68


title: infected_T4_76


title: infected_T4_74


title: infected_T4_71


title: infected_T4_70


title: infected_T4_78


title: infected_T4_67


title: infected_T4_88


title: infected_T4_73


title: infected_T4_72


title: infected_T4_66


title: infected_T4_64


title: infected_T4_63


title: infected_T4_61


title: infected_T4_65


title: infected_T4_59


title: infected_T4_62


title: infected_T4_56


title: infected_T4_60


title: infected_T4_55


title: infected_T4_57


title: infected_T4_58


title: infected_T4_75


title: infected_T4_52


title: infected_T4_54


title: infected_T4_53


title: infected_T4_51


title: infected_T4_50


title: infected_T4_49


title: infected_T4_46


title: infected_T4_47


title: infected_T4_45


title: infected_T4_43


title: infected_T4_44


title: infected_T4_40


title: infected_T4_39


title: infected_T4_41


title: infected_T4_42


title: infected_T4_38


title: infected_T4_37


title: infected_T4_30


title: infected_T4_33


title: infected_T4_34


title: infected_T4_29


title: infected_T4_36


title: infected_T4_28


title: infected_T4_32


title: infected_T4_26


title: infected_T4_25


title: infected_T4_24


title: infected_T4_22


title: infected_T4_23


title: infected_T4_21


title: infected_T4_48


title: infected_T4_18


title: infected_T4_17


title: infected_T4_20


title: infected_T4_35


title: infected_T4_16


title: infected_T4_14


title: infected_T4_31


title: infected_T4_15


title: infected_T4_13


title: infected_T4_12


title: infected_T4_10


title: infected_T4_11


title: infected_T4_9


title: infected_T4_7


title: infected_T4_27


title: infected_T4_6


title: infected_T4_3


title: infected_T4_2


title: infected_T4_4


title: infected_T4_1


title: infected_T2_96


title: infected_T2_94


title: infected_T2_93


title: infected_T2_95


title: infected_T4_19


title: infected_T2_91


title: infected_T2_92


title: infected_T2_90


title: infected_T2_86


title: infected_T2_87


title: infected_T2_88


title: infected_T2_85


title: infected_T2_83


title: infected_T2_81


title: infected_T2_82


title: infected_T4_8


title: infected_T4_5


title: infected_T2_84


title: infected_T2_76


title: infected_T2_80


title: infected_T2_72


title: infected_T2_78


title: infected_T2_74


title: infected_T2_75


title: infected_T2_77


title: infected_T2_79


title: infected_T2_63


title: infected_T2_73


title: infected_T2_69


title: infected_T2_70


title: infected_T2_62


title: infected_T2_68


title: infected_T2_67


title: infected_T2_66


title: infected_T2_57


title: infected_T2_65


title: infected_T2_53


title: infected_T2_60


title: infected_T2_89


title: infected_T2_61


title: infected_T2_54


title: infected_T2_56


title: infected_T2_51


title: infected_T2_71


title: infected_T2_50


title: infected_T2_49


title: infected_T2_48


title: infected_T2_46


title: infected_T2_45


title: infected_T2_44


title: infected_T2_64


title: infected_T2_59


title: infected_T2_41


title: infected_T2_40


title: infected_T2_39


title: infected_T2_38


title: infected_T2_37


title: infected_T2_58


title: infected_T2_36


title: infected_T2_55


title: infected_T2_35


title: infected_T2_52


title: infected_T2_33


title: infected_T2_43


title: infected_T2_34


title: infected_T2_30


title: infected_T2_31


title: infected_T2_32


title: infected_T2_28


title: infected_T2_27


title: infected_T2_26


title: infected_T2_29


title: infected_T2_47


title: infected_T2_24


title: infected_T2_25


title: infected_T2_20


title: infected_T2_42


title: infected_T2_22


title: infected_T2_19


title: infected_T2_17


title: infected_T2_14


title: infected_T2_18


title: infected_T2_15


title: infected_T2_13


title: infected_T2_16


title: infected_T2_12


title: infected_T2_11


title: infected_T2_4


title: infected_T2_9


title: infected_T2_5


title: infected_T2_7


title: infected_T2_6


title: infected_T2_10


title: infected_T2_2


title: infected_T2_3


title: unexposed_T0_96


title: unexposed_T0_95


title: infected_T2_23


title: infected_T2_8


title: infected_T2_1


title: infected_T2_21


title: unexposed_T0_93


title: unexposed_T0_94


title: unexposed_T0_90


title: unexposed_T0_91


title: unexposed_T0_88


title: unexposed_T0_89


title: unexposed_T0_87


title: unexposed_T0_85


title: unexposed_T0_83


title: unexposed_T0_86


title: unexposed_T0_84


title: unexposed_T0_82


title: unexposed_T0_80


title: unexposed_T0_79


title: unexposed_T0_77


title: unexposed_T0_76


title: unexposed_T0_75


title: unexposed_T0_67


title: unexposed_T0_78


title: unexposed_T0_73


title: unexposed_T0_66


title: unexposed_T0_69


title: unexposed_T0_74


title: unexposed_T0_64


title: unexposed_T0_68


title: unexposed_T0_71


title: unexposed_T0_65


title: unexposed_T0_60


title: unexposed_T0_81


title: unexposed_T0_61


title: unexposed_T0_72


title: unexposed_T0_57


title: unexposed_T0_55


title: unexposed_T0_54


title: unexposed_T0_59


title: unexposed_T0_63


title: unexposed_T0_53


title: unexposed_T0_58


title: unexposed_T0_56


title: unexposed_T0_51


title: unexposed_T0_52


title: unexposed_T0_70


title: unexposed_T0_92


title: unexposed_T0_50


title: unexposed_T0_49


title: unexposed_T0_48


title: unexposed_T0_46


title: unexposed_T0_45


title: unexposed_T0_62


title: unexposed_T0_43


title: unexposed_T0_42


title: unexposed_T0_44


title: unexposed_T0_47


title: unexposed_T0_41


title: unexposed_T0_39


title: unexposed_T0_38


title: unexposed_T0_40


title: unexposed_T0_37


title: unexposed_T0_36


title: unexposed_T0_35


title: unexposed_T0_33


title: unexposed_T0_34


title: unexposed_T0_28


title: unexposed_T0_31


title: unexposed_T0_29


title: unexposed_T0_25


title: unexposed_T0_32


title: unexposed_T0_30


title: unexposed_T0_27


title: unexposed_T0_26


title: unexposed_T0_23


title: unexposed_T0_22


title: unexposed_T0_20


title: unexposed_T0_24


title: unexposed_T0_21


title: unexposed_T0_17


title: unexposed_T0_14


title: HiC 120min_rep2

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

data_processing:
Library strategy: HiC-seq
HiC-seq: The 76 bp paired reads were separately aligned to the fission yeast genome (version ASM294v2.19) using Bowtie2.2.5. Partial alignment was judged by the CIGAR string. Unaligned bases were trimmed, and a remaining sequence was realigned. If alignable locations were not identified across the genome, either upstream or downstream 5 bases were trimmed. Reads were again evaluated by the CIGAR string, and the trimming step was repeated until the truncated reads became less than 25 bp. Mapped reads were assigned to MboI fragments.
HiC-seq: Redundant paired reads mapped to exactly the same genomic positions were discarded to remove a potential PCR bias. When reads were aligned to repetitive sequences or have low mapping quality (MAPQ < 30), they were also removed. Subsequently, paired reads aligned to two loci positioned less than 20 kb apart and potentially derived from self-ligation and undigested products were discarded.
HiC-seq: Contact matrices were generated at three resolutions such as 5, 10, and 20 kb. The entire fission yeast genome was divided into 5, 10, or 20 kb sections. A raw contact matrix was first constructed by counting paired reads assigned to two genomic sections. Note that reads belong to MboI fragments.
Biases in distance-normalized contact matrices were corrected by ICE method (Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012)). The ICE normalization was repeated 10 times, and an average score was adjusted to 1 , resulting in contact scores.
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: HiC-seq: tab-deliminated text files of normalized scores. First row and column indicate the location of the genome in following format, "<chromosome name>:<start position>:<end position>"

organism: Schizosaccharomyces pombe

growth_protocol: The fission yeast Schizosaccharomyces pombe strains were cultured in Yeast-Extract Adenine.

extract_protocol:
The in situ Hi-C experiment was performed as previously reported (Rao et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159, 1665–80 (2014).) Total RNA was extracted from cells as previously described (Alfa et al. Experiments with fission yeast. (Cold Spring Harbor Laboratory Press, 1993).)
Hi-C samples were prepared for sequencing using NEBNext Multiplex Oligos for Illumina kit. RNA libraries were prepared for sequencing using NEBNext ultra NDA library prep kit

tag: culture condition

tag: mutation


title: unexposed_T0_19


title: unexposed_T0_18


title: unexposed_T0_16


title: unexposed_T0_15


title: unexposed_T0_13


title: unexposed_T0_11


title: unexposed_T0_12


title: HiC 80min_rep2


title: unexposed_T0_10


title: dilution_1_to_1000_rep5

description:
clean RNA
AS_sens_AS_sens_sample_0020

source_name: RNA from mESC and Salmonella

extract_protocol:
Mouse RNA was isolated from CGR8 embryonic stem cell (ESC) line and prepared using a TRIzol extraction and treated with RQ1 RNase-free DNase (Promega) according to the manufacturers’ protocols. RNA cleanup was done with AMPure RNAClean beads. To extract Salmonella RNA, Salmonella were grown in LB and lysed by bead beating and RNA was extracted by the Qiagen RNeasy kit
scDual-Seq

tag: dilution

value: 10pg of mouse RNA and 0.01pg of Salmonella typhimurium SL1344

tag: cell type

value: mESC


title: RNAseq WT

data_processing:
Genome_build: ASM294v2.19
RNA-seq: Sequenced reads were mapped to the fission yeast reference genome (version ASM294v2.30) using STAR v2.5.2 program
RNA-seq: htseq-count 0.6.1 software was used to estimate read numbers assigned to exons, and the read numbers were normalized using the TMM method
RNA-seq: Differentially expressed genes between wild-type and cut14-208 condensin mutant cells were identified by edgeR package using the dispersion value of 0.029, which was estimated from the cut3-477 and cut14-208 condensin mutant samples treated as biological replicas
RNA-seq: FDR < 0.05 were used as a threshold to define significantly up- or down-regulated genes.
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each transcript

source_name: WT

value: 36C 2hour

value: wild type


title: dilution_1_to_1000_rep4

description:
clean RNA
AS_sens_AS_sens_sample_0019


title: HiC 60min_rep2


title: unexposed_T0_9


title: unexposed_T0_1


title: HiC WT1

data_processing:
Library strategy: HiC-seq
HiC-seq: The 76 bp paired reads were separately aligned to the fission yeast genome (version ASM294v2.19) using Bowtie2.2.5. Partial alignment was judged by the CIGAR string. Unaligned bases were trimmed, and a remaining sequence was realigned. If alignable locations were not identified across the genome, either upstream or downstream 5 bases were trimmed. Reads were again evaluated by the CIGAR string, and the trimming step was repeated until the truncated reads became less than 25 bp. Mapped reads were assigned to MboI fragments.
HiC-seq: Redundant paired reads mapped to exactly the same genomic positions were discarded to remove a potential PCR bias. When reads were aligned to repetitive sequences or have low mapping quality (MAPQ < 30), they were also removed. Subsequently, paired reads aligned to two loci positioned less than 20 kb apart and potentially derived from self-ligation and undigested products were discarded.
HiC-seq: Contact matrices were generated at three resolutions such as 5, 10, and 20 kb. The entire fission yeast genome was divided into 5, 10, or 20 kb sections. A raw contact matrix was first constructed by counting paired reads assigned to two genomic sections. Note that reads belong to MboI fragments.
Biases in *raw *contact matrices were corrected by *ICE* method (*Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999 1003 (2012)*). The *ICE* normalization was repeated 10 times, and an average score of bias corrected matrix was adjusted to 1 , resulting in contact scores.
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: HiC-seq: tab-deliminated text files of normalized scores. First row and column indicate the location of the genome in following format, "<chromosome name>:<start position>:<end position>"


title: dilution_1_to_1000_rep3

description:
clean RNA
AS_sens_AS_sens_sample_0018


title: HiC double -1 and -2

source_name: double


title: RNAseq cut3


title: dilution_1_to_1000_rep1

description:
clean RNA
AS_sens_AS_sens_sample_0016


title: RNAseq cut14


title: unexposed_T0_8


title: dilution_1_to_1000_rep2

description:
clean RNA
AS_sens_AS_sens_sample_0017


title: unexposed_T0_5


title: HiC WT2


title: HiC rad21 -1 and -2


title: unexposed_T0_6


title: unexposed_T0_4


title: unexposed_T0_2


title: unexposed_T0_7


title: dilution_1_to_100_rep3

description:
clean RNA
AS_sens_AS_sens_sample_0013

value: 10pg of mouse RNA and 0.1pg of Salmonella typhimurium SL1344


title: dilution_1_to_100_rep4

description:
clean RNA
AS_sens_AS_sens_sample_0014


title: dilution_1_to_100_rep2

description:
clean RNA
AS_sens_AS_sens_sample_0012


title: dilution_1_to_100_rep5

description:
clean RNA
AS_sens_AS_sens_sample_0015


title: unexposed_T0_3


title: HiC cut14

value: 36C 1hour


title: HiC cut3


title: dilution_1_to_100_rep1

description:
clean RNA
AS_sens_AS_sens_sample_0011


title: dilution_1_to_10_rep5

description:
clean RNA
AS_sens_AS_sens_sample_0010

value: 10pg of mouse RNA and 1pg of Salmonella typhimurium SL1344


title: dilution_1_to_10_rep2

description:
clean RNA
AS_sens_AS_sens_sample_0007


title: dilution_1_to_10_rep4

description:
clean RNA
AS_sens_AS_sens_sample_0009


title: dilution_1_to_10_rep3

description:
clean RNA
AS_sens_AS_sens_sample_0008


title: HiC 80min -1 and -2


title: HiC 70min -1 and -2


title: dilution_1_to_10_rep1

description:
clean RNA
AS_sens_AS_sens_sample_0006


title: HiC 60min -1 and -2


title: dilution_1_to_1_rep2

description:
clean RNA
AS_sens_AS_sens_sample_0002

value: 10pg of mouse RNA and 10pg of Salmonella typhimurium SL1344


title: dilution_1_to_1000_rep5 [CEL-Seq2]

organism:
Mus musculus
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

extract_protocol:
Mouse RNA was isolated from CGR8 embryonic stem cell (ESC) line and prepared using a TRIzol extraction and treated with RQ1 RNase-free DNase (Promega) according to the manufacturers’ protocols. RNA cleanup was done with AMPure RNAClean beads. To extract Salmonella RNA, Salmonella were grown in LB and lysed by bead beating and RNA was extracted by the Qiagen RNeasy kit
CEL-Seq2

value: embryonic stem cell (ESC) line


title: dilution_1_to_1_rep5

description:
clean RNA
AS_sens_AS_sens_sample_0005


title: dilution_1_to_1000_rep4 [CEL-Seq2]


title: dilution_1_to_1_rep3

description:
clean RNA
AS_sens_AS_sens_sample_0003


title: Salmonella_stat_rep3

description:
SL_stat_SL_sample_0003
clean RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: RNA from Salmonella grown in liquid culture

extract_protocol:
To extract Salmonella RNA, Salmonella were grown in LB ON. 1ml was washed with PBS, and RNA was extracted using phenol chlorophorm
scDual-Seq

tag: growth phase

value: stationary


title: dilution_1_to_1_rep1

description:
clean RNA
AS_sens_AS_sens_sample_0001


title: dilution_1_to_1000_rep1 [CEL-Seq2]


title: Salmonella_log_rep2

description:
SL_log_SL_sample_0023
clean RNA

value: log


title: Salmonella_log_rep1

description:
SL_log_SL_sample_0022
clean RNA


title: mHP2_S1_R1_001.fastq.gz

status: Public on Oct 06 2017

city: Cambridge

first: Naomi

last: Habib

address: 75 Ames st

department: Zhang

institute: Broad Institute

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
mHP2_S1_R1_001.fastq.gz

data_processing:
The left read was used to infer both the cell of origin, based on the first 12 bases (the Nucleus Barcode), and the molecule of origin (the UMI), based on the next 8 bases
The right mate of each read pair was trimmed and aligned to the genome (mouse mm10 UCSC) using STAR v2.4.0a24
The expression count (or number of transcripts) for a given gene in a given nucleus was determined by merging and counting unique UMIs, into a DGE matrix. The matrix was scaled by total UMI counts, multiplied by the mean number of transcripts (calculated for each dataset separately) and the values were log transformed.
To reduce the effects of library quality and complexity on cluster identity, a linear model was used to regress out effects of the number of transcripts and genes detected per nucleus (using the ‘RegressOut’ function in the Seurat software package).
Nuclei were classified into clusters based on a PCA analysis followed by tSNE 2-D embedding on the top PCs (using R)
Genome_build: mouse mm10 UCSC
Supplementary_files_format_and_content: Tab delimited log transformed DGE matrix (UMI counts per gene and nuclei)

source_name: Mouse Brain

extract_protocol:
Mouse hippocampus and PFC were Microdissections under stereomicroscope, then flash frozen on dry ice and stored at -80°C until processed for nuclei isolation. Tissue samples were cut into pieces < 0.5 cm and homogenized using a glass dounce tissue grinder in 2ml of EZ PREP buffer, and incubated on ice for 5 minutes, with additional 2 ml ice-cold EZ PREP. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, washed with 4 ml ice-cold EZ PREP and incubated on ice for 5 minutes. After centrifugation, the nuclei were washed in 4 ml buffer (1x PBS, 0.01% BSA and 0.1% RNAse inhibitor).
DroNc-seq libraraies were constructed following the step by step protocol: http://dx.doi.org/10.1038/protex.2017.094

value: brain

tag: region

value: Hippocampus


title: HiC 50min -1 and -2


title: dilution_1_to_1000_rep3 [CEL-Seq2]


title: HP1_S1_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
HP1_S1_R1_001.fastq.gz


title: Salmonella_stat_rep1

description:
SL_stat_SL_sample_0001
clean RNA


title: HiC 120min -1 and -2


title: HiC 40min -1 and -2


title: KNI1766A288

city: Oxford

first: Mohammad Hussein

last: Al-Mossawi

address: Botnar Research Centre

department: Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal sciences

country: United Kingdom

institute: University of Oxford

description:
replicate 2
blood bank-derived PBMC samples (lymphocyte cone)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to human genome reference sequence GRCh37 with tophat2
deduplication was performed using samtools version 1.2
gene counts were retrieved using htseq-count
differential gene expression was carried out using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content:  tab-delimited text files include raw and normalised gene counts for each sample

growth_protocol: PBMCs were isolated by density centrifugation and CD4 isolation was carried out using negative magnetic separation

extract_protocol: AllPrep DNA/RNA/miRNA kit (Qiagen) was used for RNA extraction in accordance with the maufactiurers instructions. Quality Control was peeformed with Bioanalyser. Only samples with more than 5,000,000 reads were taken forward for analysis

treatment_protocol: Cells were treated with PMA/Ionomycin and cytokine capture assay was used to sort cells based on cytokine production

value: blood

value: PBMC CD4

tag: cell subtype

tag: replicate number


title: KNI1766A286

description:
replicate 1
blood bank-derived PBMC samples (lymphocyte cone)

source_name: IFN+

value: IFN+


title: KNI1766A287

description:
replicate 3
blood bank-derived PBMC samples (lymphocyte cone)


title: 0_2b_S2_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
0_2b_S2_R1_001.fastq.gz

value: Cortex


title: Salmonella_stat_rep2

description:
SL_stat_SL_sample_0002
clean RNA


title: KNI1766A284

description:
replicate 4
blood bank-derived PBMC samples (lymphocyte cone)

source_name: CSF+

value: CSF+


title: dilution_1_to_1000_rep2 [CEL-Seq2]

value: 10pg of mouse RNA and 0.01pg of Salmonella typhimurium SL1344


title: Salmonella_log_rep3

description:
SL_log_SL_sample_0024
clean RNA


title: HiC 30min -1 and -2


title: KNI1766A281


title: PFC1_S2_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
PFC1_S2_R1_001.fastq.gz


title: mPFC2_S2_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
mPFC2_S2_R1_001.fastq.gz


title: dilution_1_to_1_rep4

description:
clean RNA
AS_sens_AS_sens_sample_0004

value: mESC


title: PFC3_S2_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
PFC3_S2_R1_001.fastq.gz


title: KNI1766A285


title: 0_1b_S2_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
0_1b_S2_R1_001.fastq.gz


title: 0_2a_S1_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
0_2a_S1_R1_001.fastq.gz


title: KNI1766A283


title: 0_1a_S1_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
0_1a_S1_R1_001.fastq.gz


title: HP3_S1_R1_001.fastq.gz

description:
DroNc-seq single nuclei RNA-seq on archived mouse brain tissue
HP3_S1_R1_001.fastq.gz


title: KNI1766A282


title: KNI1766A280


title: KNI1766A278


title: HiC 20min -1 and -2


title: KNI1766A277


title: KNI1766A279

description:
replicate 5
blood bank-derived PBMC samples (lymphocyte cone)


title: KNI1766A276


title: UC06 Caput HEE cells HNF1A&B siRNAs Rep 1

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

data_processing:
Sequences were mapped back to human genome using TopHat (v2.0.9) (Trapnell et al., 2012 Nat Protoc 2012;7:562-578).
Aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation and to estimate expression levels for each transcript.
Assembly files for each of the samples were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff. Samples were then normalized and expressed as FPKM and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
FPKM values were subject to principle component analysis.
Biological processes associated with differentially expressed genes were identified using DAVID.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: Caput Human Epididymis Epithelial Cells

growth_protocol: Adult Caput human epididymis epithelial (HEE) cells were cultured as previously described (Leir et al., 2015 Fertil Steril. 103: 647-54).

extract_protocol:
Confluent adult Caput HEE cells transiently transfected with siRNA (targeting both HNF1alpha and HNF1beta or a non-targeting control) for 72h, were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

tag: transfection

value: HNF1alpha and HNF1beta siRNA


title: UC06 Caput HEE cells HNF1A&B siRNAs Rep 2


title: UC06 Caput HEE cells NC siRNA Rep 3

value: negative control


title: UC06 Caput HEE cells HNF1A&B siRNAs Rep 3


title: KNI1766A275


title: KNI1766A272


title: KNI1766A274


title: UC-05_HNF1_ChIP-seq

data_processing:
FASTQ files were aligned to the hg19 version of the human genome using Bowtie and ChIP-seq peaks were identified using HOMER with a false discovery rate of 0.1%.
Peaks from both replicates were intersected using BEDTools and only the 10,480 sites found in both replicates were used for further analysis.
Identification of transcription factor motifs in the data set and peak annotation based on the nearest gene were also performed using HOMER.
GO terms enriched among the nearest genes in the ChIP-seq data were determined using the Database for Annotation, Visualization, and Integrated Discovery (DAVID).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the HNF1 antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

tag: antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody lot #


title: KNI1766A270


title: UC-05_input


title: KNI1766A271


title: KNI1766A269


title: UC-01_input


title: UC-01_HNF1_ChIP-seq


title: LA42_3

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

department: Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
Lactic acid treated at 42 h rep3
Sample_12

data_processing:
The datasets were generated from a hybrid organism. The genome of this organism contains two similar copies for almost every gene originated from the two parental strains. Some of these genes are identical duplicated genes whose predicted functions are important for the phenotype analysed in this study. In order to analyse their expression profiles, the alignments reported by bowtie were filtered from the SAM files by the "multimapping" XM:i:2 for which the mapping quality (MAPQ) is artificially set to 0. Those alignments were used to produce counts only for the duplicated genes by setting the htseq-count quality filter to 0 (-a 0). These are referred as "Dups".
Setting the htseq-count quality filter to 0 using the full set of alignments over the full genome would have produced counts from low quality alignments which do not necessarily include the tag XM:i:2. To avoid that, a second run was performed with the default htseq-count quality filter (MAPQ >= 10) and produced the "Full" datasets which have 0 counts for the above mentioned duplicated genes.
Full and Dup: Read mapping using bowtie v1.1.2 ; parameters -v 0 -k 10 --best -M 1
Full: htseq-count v0.6.0
Full: edgeR v. 3.18.1 trimmed means of M-values (TMM) normalization and counts per million (CPM) calculation; removed genes with less than 1 CPM in at least 3 samples from the same condition.
Dups: Read mapping using bowtie v1.1.2 ; parameters -v 0 -k 10 --best -M 1
Dups: samtools v0.1.19-44428cd ; parameters view -bF 4 - | grep XM:i:2
Dups: htseq-count v0.6.0 -a 0
Dups: edgeR v. 3.18.1 trimmed means of M-values (TMM) normalization and counts per million (CPM) calculation; removed genes with less than 1 CPM in at least 3 samples from the same condition.
Dups: edgeR v. 3.18.1 Reads Per Kilobase of transcript per Million mapped reads (RPKM) calculation using the normalized and filtered "Dups" dataset.
Genome_build: Zygosaccharomyces parabailii (assembly ASM198439v2)
Supplementary_files_format_and_content:
Zpar_Full_counts.map.txt: Merged htseq-count text file
Zpar_Full_matrix.txt: Filtered and normalized Zpar_Full CPMs
Zpar_Dups_counts.map.txt: Merged htseq-count text file
Zpar_Dups_matrix.txt: Filtered and normalized Zpar_Dups CPMs
Zpar_Dups_RPKMs.txt: RPKMs for the filtered and normalized Zpar_Dups set

organism: Zygosaccharomyces parabailii

source_name: yeast cells

growth_protocol: Batch bioreactor fermentation was performed in Verduyn medium at pH 3 with addition of 40 g L^ -1 lactic acid or without lactic acid. The samples for RNA sequencing were taken at 18 h and 42 h, corresponding to exponential phase and post diauxic shift

extract_protocol:
The total RNA was then extracted using Zymo Research Fungal/Bacterial RNA MiniPrep™ kit (Irvine, USA) and the quality of RNA samples were evaluated with Agilent Bioanalyzer. The RNA samples were sequenced using the Illumina HiSeq2000 platform with 100 nt-long paired-end reads
Library construction using Illumina Truseq RNA protocol after rRNA depletion.

tag: strain

tag: condition

value: Lactic acid treated

tag: timepoint, hours


title: LA18_2

description:
Lactic acid treated at 18 h rep2
Sample_8


title: LA18_3

description:
Lactic acid treated at 18 h rep3
Sample_9


title: LA42_2

description:
Lactic acid treated at 42 h rep2
Sample_11


title: LA18_1

description:
Lactic acid treated at 18 h rep1
Sample_7


title: C42_3

description:
Control at 42 h rep3
Sample_6

value: Control


title: C42_2

description:
Control at 42 h rep2
Sample_5


title: KNI1766A273

description:
replicate 1
blood bank-derived PBMC samples (lymphocyte cone)


title: UC06 Caput HEE cells NC siRNA Rep 1


title: MtrB-20h-1

city: Norwich

first: John

middle: Tyson

last: Munnoch

address: Norwich Research Park

department: Schol of Biological Sciences

institute: University of East Anglia

description: Ribodepleted total RNA converted to cDNA

data_processing:
1. Alignment of reads to reference genome (SVEN2015 genome, carried out at the JIC, no accession number yet available) using Bowtie2 version 2.2.9
2. A perl script was used to calculate the number of reads covering each gene from the SAM files produced in step 1.
3. The counts-per-gene files produced in step 2 were used as input to the Bioconductor package edgeR of R (version 3.3.1) and analysed as described in the edgeR user guide.  Briefly, after the estimation of common and tagwise dispersion, the exactTest function was used to make comparisons between pairs of groups and arrive at log fold change and associated FDR estimates for each gene.  The same data structure was used to arrive at RPKM values for each gene for each counts per gene file using the RPKM function.
Genome_build: SVEN2015 - currently no published accession number is available at this date in preperation of a robust annotation set.  Available on request to the JIC.
Supplementary_files_format_and_content: .txt files containing RPKM values for each condition and an excel file containing comparison of gene expression between conditions.

organism: Streptomyces venezuelae ATCC 10712

source_name: Mutant

growth_protocol: 5-7 ul of current spore stock (OD600 ~0.35 after 8h) was innoculated into 35 ml of MYM-tap growth media, and grown for the defined time frame.

extract_protocol: Carried out as above by vertis Biotech using commercially available but confidential kits.

treatment_protocol: RNA isolation and library constructions: Mycelium was harvested at experimentally appropriate time points and immediately transferred to 2 ml round bottom tubes, flash frozen in liquid N2, stored at -80oC or used immediately.  All apparatus used was treated with RNaseZAP (Sigma) to remove RNases for a minimum of 1 hour before use.  RNaseZAP treated mortar and pestles were used, the pestle being placed and cooled on a mixture of dry ice and liquid N2 with liquid N2 being poured into the bowl and over the mortar.  Once the bowl had cooled the mycelium samples were added directly to the liquid N2 and thoroughly crushed using the mortar leaving a fine powder of mycelium.  Grindings were transferred to a pre-cooled 50 ml Falcon tube and stored on dry ice.  Directly to the tube, 2 ml of TRI reagent (Sigma) was added to the grindings and mixed.  Samples are then thawed while vortexing intermittently at room temperature for 5-10 minutes until the solution cleared.   To 1 ml of TRI reagent resuspension, 200 µl of chloroform was added and vortexed for 15 seconds at room temperature then centrifuged for 10 minutes at 13,000 rpm.  The upper, aqueous phase (clear colourless layer) was removed into a new 2 ml tube.  The remainder of the isolation protocol follows the RNeazy Mini Kit (Qiagen) instructions carrying out both on and off column DNase treatments.  On column treatments were carried out following the first RW1 column wash.  DNaseI (Qiagen) was added (10 µl enzyme, 70 µl RDD buffer) to the column and stored at RT for 1 hour.  The column was washed again with RW1 then treated as described in the manufacturer’s instructions.  Once eluted from the column. Ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). The yields of the depleted RNAs were around 1 % of the total RNA samples. The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (15 cycles expect for MtrB-20h-2 which was 14). The TruSeq barcode sequences which are part of the 5' TruSeq sequencing adapter (WT-14h-1 - TCTACTCT, WT-14h-2 - ATCCTGTG, MtrB-14h-1 - TACAGGTC, MtrB-14h-2 - AGTCCAAC, WT-20h-1 - GGCAGCTA, WT-20h-2 - GCAGCATA, MtrB-20h-1 - AAGGTTCA, MtrB-20h-2 – ACTTAGCA). The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

tag: genotype/variation

tag: treatment

value: ribodepeletion, cDNA synthesis

tag: growth time point (hours from innuculation)


title: MtrB-20h-2


title: UC06 Caput HEE cells NC siRNA Rep 2


title: C42_1

description:
Control at 42 h rep1
Sample_4


title: MtrB-14h-2


title: C18_3

description:
Control at 18 h rep3
Sample_3


title: WT-20h-1

value: WT


title: C18_2

description:
Control at 18 h rep2
Sample_2


title: WT-14h-1


title: MtrB-14h-1


title: C18_1

description:
Control at 18 h rep1
Sample_1


title: WT-14h-2


title: RNAPol2_TL-Om1_THZ1_ChipSeq

status: Public on Oct 05 2017

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
Single end ChIP-seq reads of TL-Om1 were aligned to the hg19 human reference genome using Bowtie (version 1.1.1) with the following parameters: -e 70 -k 1 -m 1 -n 2 -l 49 –best
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq). A p-value threshold of enrichment of 10-9 was used for all of the datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph output files of MACS2 wer converted into bigwig file. Counts were normalized to reads per million.

source_name: TL-Om1 cells

growth_protocol: TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and RNA Pol II-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
Library construction and sequencing by Illumina Hiseq 4000 were performed by BGI Tech Solutions Co., Limited (Hongkong).

treatment_protocol: TL-Om1 cells were treated with control DMSO or THZ1 (100 nM) for 3 hours.

tag: cell line

value: adult T-cell leukemia/lymphoma (ATL) cell line

tag: treated with

value: THZ1 for 3 hrs

tag: chip antibody

value: RNA Pol II (Abcam, ab817:8WG16)


title: RNAPol2_TL-Om1_DMSO_ChipSeq

tag: cell type

value: control DMSO  for 3 hrs


title: WCE_TL-Om1_THZ1_ChipSeq


title: LA42_1

description:
Lactic acid treated at 42 h rep1
Sample_10


title: ATL10_WCE_ChIPSeq

data_processing:
Single end ChIP-seq reads of TL-Om1 were aligned to the hg19 human reference genome using Bowtie (version 1.1.1) with the following parameters: -e 70 -k 1 -m 1 -n 2 –best
Paired-end ChIP-seq datasets of the primary ATL samples were aligned to the hg19 human reference genome using Bowtie2 with --no-mixed, --no-unal and default other parameters
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq). A p-value threshold of enrichment of 10-9 was used for all of the datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph output files of MACS2 wer converted into bigwig file. Counts were normalized to reads per million.

source_name: Primary ATL cells (ATL10)

growth_protocol: TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.  Cryopreserved primary leukemia cells were thawed and immediately washed by PBS.

extract_protocol:
TL-Om1 cells and primary ATL cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and histone H3K27Ac-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
Library construction and sequencing by Illumina Hiseq 4000 were performed by BGI Tech Solutions Co., Limited (Hongkong).

treatment_protocol: Not applicable.

tag: sample id

value: Primary leukemia cells derived from ATL patients


title: ATL10_H3K27Ac_ChIPSeq

value: anti-H3K27ac (Abcam, ab4729)


title: ATL9_WCE_ChIPSeq

source_name: Primary ATL cells (ATL9)


title: WT-20h-2


title: ATL8_WCE_ChIPSeq

source_name: Primary ATL cells (ATL8)


title: ATL9_H3K27Ac_ChIPSeq


title: ATL7_WCE_ChIPSeq

source_name: Primary ATL cells (ATL7)


title: ATL8_H3K27Ac_ChIPSeq


title: ATL6_WCE_ChIPSeq

source_name: Primary ATL cells (ATL6)


title: ATL6_H3K27Ac_ChIPSeq


title: ATL5_WCE_ChIPSeq

source_name: Primary ATL cells (ATL5)


title: ATL4_WCE_ChIPSeq

source_name: Primary ATL cells (ATL4)


title: ATL5_H3K27Ac_ChIPSeq


title: ATL4_H3K27Ac_ChIPSeq


title: ATL3_WCE_ChIPSeq

source_name: Primary ATL cells (ATL3)


title: ATL3_H3K27Ac_ChIPSeq


title: ATL2_WCE_ChIPSeq

source_name: Primary ATL cells (ATL2)


title: TL-Om1_WCE_ChIPSeq


title: TL-Om1_H3K27Ac_ChIPSeq


title: WCE_TL-Om1_DMSO_ChipSeq


title: ATL1_H3K27Ac_ChIPSeq

source_name: Primary ATL cells (ATL1)


title: ATL1_WCE_ChIPSeq


title: ATL2_H3K27Ac_ChIPSeq


title: Dengue_Fever_Group_C Sample_77

city: Faridabad

first: ABHAY

middle: DEEP

last: PANDEY

state: HARYANA

address: 3RD MILE STONE, FARIDABAD GURGAON EXPRESSWAY, NCR BIOTECH CLUSTER

department: VIROLOGY

country: India

institute: Translational Health Science and Technology Institute

data_processing:
Inbuilt Illumina Casava 1.8.2 software used for basecalling.
QC of sequenced reads were done by FASTQC.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using protocol from Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
Genome_build: hg19

source_name: PBMC

growth_protocol: growth protocol

extract_protocol:
Total RNA was isolated from PBMC using TRIZOl and purelink RNA mini kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Total RNA samples with RNA Integrity Number (RIN) ≥ 8 were selected for library preparation. extract protocol
RNA-seq library preparation was performed using TruSeq® RNA library Prep Kit v2 (Illumina). library construction protocol

treatment_protocol: treatment protocol

value: Dengue Fever Group C

tag: disease

value: Dengue shock syndrome


title: Dengue_Fever_Group_C Sample_207


title: Dengue_Fever_Group_C Sample_92


title: Dengue_Fever_Group_C Sample_147


title: Dengue_Fever_Group_C Sample_20156


title: Dengue_Fever_Group_C Sample_20258


title: Dengue_Fever_Group_C Sample_144


title: Dengue_Fever_Group_C Sample_20261


title: ATL7_H3K27Ac_ChIPSeq


title: Dengue_Fever_Group_C Sample_139


title: Dengue_Fever_Group_C Sample_135


title: Dengue_Fever_Group_C Sample_110


title: Dengue_Fever_Group_C Sample_113


title: Dengue_Fever_Group_C Sample_124


title: Dengue_Fever_Group_C Sample_130


title: Dengue_Fever_Group_B Sample_513

value: Dengue Fever Group B

value: Dengue hemorrhagic fever


title: Dengue_Fever_Group_B Sample_357


title: Dengue_Fever_Group_B Sample_401


title: Dengue_Fever_Group_B Sample_462


title: Dengue_Fever_Group_B Sample_20157


title: Dengue_Fever_Group_B Sample_150


title: Dengue_Fever_Group_B Sample_131


title: Dengue_Fever_Group_C Sample_83


title: Dengue_Fever_Group_B Sample_120


title: Dengue_Fever_Group_A Sample_20125

value: Dengue Fever Group A

value: Dengue fever


title: Dengue_Fever_Group_A Sample_20079


title: Dengue_Fever_Group_A Sample_20133


title: Dengue_Fever_Group_A Sample_20077


title: Dengue_Fever_Group_A Sample_20048


title: Other_Febrile_Illness Sample_20089

value: Other Febrile Illness


title: Other_Febrile_Illness Sample_20058


title: Other_Febrile_Illness Sample_20071


title: Other_Febrile_Illness Sample_20068


title: Other_Febrile_Illness Sample_20053


title: Other_Febrile_Illness Sample_20059


title: Other_Febrile_Illness Sample_20034


title: PF14_ON treatment

city: Stockholm

first: Moataz

last: Dowaidar

state: Stockholm

address: S.Arrheniusv. 16B

department: Neurochemistry

institute: Dpt. Neurochemistry Stockholm University

data_processing:
Trimming of reads by quality, FastX Toolkit v0.0.13: fastq_quality_trimmer -Q33 -t 20 -l 20 -i <input fastq> -o <output fastq>
Mapping fastq with Bowtie/Tophat: Bowtie v2.1.0.0 Tophat v2.0.11 Samtools v0.1.16.0
Differential expression analysis with Cuffdiff (Cufflinks) v2.2.1. Annotation used: Homo_sapiens.GRCh37.72.gtf - http://ftp.ensembl.org/pub/release-72/gtf/homo_sapiens/
extracting values for raw-read and normalized expression (fpkm) values for annotates genomic regions from cuffdiff output genes.read_group_tracking
Genome_build: Human hg19/grhc37
Supplementary_files_format_and_content: Abundance matrixes of annotated genomic regions for raw reads and normalized expression (fpkm) levels

source_name: HeLa cells

growth_protocol: HeLa cells were sustained in Dulbecco's modified Eagle's medium (DMEM, Life Technologies). DMEM was supplemented with 1 mM sodium pyruvate, glutamate, 10% fetal bovine serum (FBS, Life Technologies), 100 μg/ml streptomycin, with 100 U/ml penicillin, in a water-jacketed incubator at 37 °C and 5% CO2.

extract_protocol:
After 1 h treatment with the peptide or peptide/oligonucleotide, the media was aspirated and the cells harvested by trypsinization before resuspension in 2 ml media. The suspension was transferred to a 15ml tube and centrifuged at 300 rpm for 5 min. Media was then aspirated, and the cell pellet was frozen at -80°C. The RNA extraction was performed by using RNeasy kit. The RNA samples have shown a good purity according to A260/280 and A260/230 ratios. A portion of the samples was kept for RNA sequencing, and the rest was then converted to cDNA sample using a RevertAid Minus First Strand cDNA Synthesis Kit with random hexamer primers.
One µg of total RNA was used as an input to prepare next-generation sequencing libraries according to the Illumina TruSeq Stranded mRNA sample preparation protocol (Illumina, San Diego, USA).

treatment_protocol: For experiments that examined the RNA levels, 5 × 1000000 HeLa cells were seeded into tissue culture-treated, 6-well plates (Corning) 24 h before treatment. On the day of treatment, the cell culture medium was displaced with two ml new FBS-free media before treatment with two µM peptides or peptide/oligonucleotide molar ratio ten complexes then the cells were incubated for 1 h before removing from the media and cell harvesting.

value: HeLa

value: peptide/oligonucleotide


title: PF14 treatment

value: peptide


title: ESC_ATAC_seq_rep2

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Raw ATAC-seq reads were aligned to the hg19 genome using Novoalign (v2.8, Novocraft) using the following options: -o Sam -r Random.
Sam files were then combined due to high correlation between technical and biological replicates.
Peak calling was performed using callpeak application (v2.1.1.20160309, macs2) using the following parameters: -g 2.7e9 --call-summit –f BAMPE –nomodel –B –SPMR –extsize 200
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using macs2, yielding single-base pair peak summits

source_name: hESCs (H9)

growth_protocol: hESCs were grown on matrigel with StemMACS iPS-Brew XF, human (130-104-368, Miltenyl Biotec) on matrigel coated plates (Corning® Matrigel® Growth Factor Reduced (GFR) Basement Membrane Matrix, *LDEV-Free, 10mL (Product #354230)) and passaged with ReLeSR (Catalog # 05872, StemCell technologies) every 5-6 days at a 1:6 ratio. hESC H9 was used (from WiCell) at passage 38-42.

extract_protocol:
Collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Transposase buffer. The Tn5 enzyme was made in house and the transposition reaction was carried out for 30 minutes at 37°C.
Following purification, the Nextera libraries were amplified for 12 cycles using the NEBnext PCR master mix and purified using the Qiagen PCR cleanup kit. All libraries were sequenced on a 125-cycle paired-end run on an Illumina HiSeq 2500 instrument.

value: Embryonic Stem Cells

tag: marker

tag: passage


title: SSEA4+_SSC_ATAC_seq_patient1_rep2

source_name: Human SSCs

value: Spermatogonial Stem Cells


title: SSEA4+_SSC_ATAC_seq_patient1_rep1


title: SSEA4+_SSC_ATAC_seq_patient2_rep1


title: SSEA4+_SSC_ATAC_seq_patient2_rep2


title: Dengue_Fever_Group_B Sample_119


title: SSEA4+_SSCs_WGBS_rep2

data_processing:
Raw sequencing reads were aligned to the hg19 genome using Novoalign (v2.8, Novocraft) in 'bisulfite' mode with the following parameters: -0 SAM -h 120 -t 240 -b 2 -R 3.
An in silico chrLambda sequence was used to align the fully methylated lambda sequence that was spiked into the samples in order to measure the bisulfite conversion efficiency.
Aligned sequencing reads (sam files) were combined using MergeSamFiles application (v1.80, Picard) considering their high correlation. Bisulfite alignment and parsing was done using NovoalignBisulfiteParser (v8.8.8, USeq package) application and the point data was then parsed into mCG context using the ParsePointDataContexts application (v8.8.8, USeq package). Then BisStat(v8.8.8, USeq package) was used to calculate per base fraction methylation scores for bases with five or more reads from both strands and generate tracks in useq format. Those useq files can be converted into bigwig files for visualization in IGV using the USeq2UCSCBig application (v8.8.8, USeq package).
For further analysis, those bigwig files can be converted into bedgraph format using UCSC bigWigToBedGraph application.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using USeq package (v8.8.8); Scores represent fraction of CpG methylation.

source_name: human SSCs

extract_protocol:
Genomic DNA was extracted from pooled SSEA4+ germline stem cells using AllPrep RNA/DNA/Protein Mini Kit (QIAGEN cat # 80004).
Library construction was performed using the Epicentre EpiGnome Methyl-Seq Kit (EGMsK89312) as described below. Briefly, genomic DNA (50-100 ng) was denatured and bisulfite converted using the Zymo Research EZ DNA Methylation-Gold Kit (cat# D5005) in a reaction containing 0.5 ng of unmethylated lambda DNA (Promega cat# D1521) as a control.  Following purification, the bisulfite converted DNA was hybridized with oligonucleotides consisting of random hexamers linked to Illumina P5 adapter sequence and strand replication was accomplished using EpiGnome polymerase.  Double-stranded DNA was heat denatured to enable ligation of the EpiGnome Terminal Tagging Oligo which adds Illumina P7 adapter sequence to the 3% 2019 end of the replicated strand.  Adapter-ligated DNA molecules were enriched by 10 cycles of pcr and the amplified library was subsequently purified using Agencourt AMPure XP beads (Beckman Coulter Genomics cat#A63881).  The concentration of the library was measured using the Qubit dsDNA HS Assay (Invitrogen cat#Q32854) and an aliquot of the library is resolved on an Agilent 2200 Tape Station using a D1000 (cat# 5067-5582 and 5067-5583) or a High Sensitivity D10000 (cat# 5067-5584 and 5067-5587) assay to define the size distribution of the sequencing library.  Libraries were adjusted to a concentration of approximately 10 nM and quantitative PCR was performed using the Kapa Biosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter-ligated DNA molecules.  The concentration was further adjusted following qPCR to prepare the library for Illumina sequence analysis. Sequencing libraries were then sequenced on a 125-cycle paired-end run on an Illumina HiSeq 2500 instrument.

tag: tissue

value: testis


title: Dengue_Fever_Group_A Sample_20143


title: SSEA4-/KIT+_SSCs_patient3_rep1

data_processing:
Raw RNA sequencing reads (fastq files) were aligned to a custom genome index using Novoalign (v2.8, Novocraft) using the following parameters: -o SAM –r ALL 50. Index was generated using MakeTranscriptome application (USeq package v8.8.8), accounting for splicing junctions. The raw splice juction alignments were converted to genomic cooradinates using SamTranscriptomeParser (USeq package v8.8.8).
FPKMs were counted across all individual exons and subsequently merged by corresponsing ensembl gene annotation using DefinedRegionDifferentialSeq application (USeq package v8.8.8) with default options.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
RNA was extracted from pooled SSEA4+ or Kit+ germline stem cells using AllPrep RNA/DNA/Protein Mini Kit (QIAGEN cat # 80004). Total RNA was then subjected to RiboZero Gold (Illumina cat # MRZG126) to substantially deplete cytoplasmic and mitochondrial rRNA.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2301 and RS-122-2302).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis. Libraries were then sequenced on a 50-cycle single end run on an Illumina HiSeq 2500 instrument.

value: Testis


title: SSEA4-/KIT+_SSCs_patient3_rep2


title: SSEA4+_SSCs_WGBS_rep1


title: KIT-/SSEA4+_SSCs_patient3_rep1


title: SSEA4+_SSCs_patient3_rep2


title: Dengue_Fever_Group_A Sample_20045


title: Other_Febrile_Illness Sample_20135


title: SSEA4+_SSCs_patient3_rep1


title: KIT+_SSCs_patient3_rep1

value: KIT+


title: KIT+_SSCs_patient3_rep2


title: Untreated cells (control)

value: Untreated (control)


title: KIT-/SSEA4+_SSCs_patient1_rep2


title: SSEA4-/KIT+_SSCs_patient2_rep2


title: ESC_ATAC_seq_rep1


title: KIT-/SSEA4+_SSCs_patient1_rep1


title: SSEA4-/KIT+_SSCs_patient1_rep2


title: SSEA4+_SSCs_patient2_rep1


title: SSEA4-/KIT+_SSCs_patient2_rep1


title: SSEA4+_SSCs_patient2_rep2


title: SSEA4+_SSCs_patient1_rep2


title: SSEA4+_SSCs_patient1_rep1


title: KIT-/SSEA4+_SSCs_patient3_rep2


title: Kit+_SingleCells_SSCs_72

data_processing:
Raw RNA sequencing reads (fastq files) were aligned to a custom genome index using Novoalign (v2.8, Novocraft) using the following parameters: -o SAM –r ALL 50. Index was generated using MakeTranscriptome application (USeq package v8.8.8), accounting for splicing junctions.  The raw splice juction alignments were converted to genomic cooradinates using SamTranscriptomeParser (USeq package v8.8.8).
Raw reads were counted across all individual exons and subsequently merged by corresponsing ensembl gene annotation using DefinedRegionDifferentialSeq application (USeq package v8.8.8) with default options. FPKMs were then counted based on reads mapped to genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Isolated SSEA4+ or Kit+ germline stem cells were diluted into 15,000-20,000 cells/ml and loaded into 5-10 μm integrated fluidic circuits (IFCs) using Fluidigm C1 instrument. Single cells captured in IFCs were scored under microscope. Only cells with normal morphology were scored high for sequencing. Single cells in IFCs were lysed and total RNA was harvested for polyadenylation selection, reverse transcription and PCR amplification.
Library constructions were performed according to Fluidigm Library preparation with Nextera XT protocol and sequenced on a 50-cycle single end run on an Illumina HiSeq 2500 instrument.


title: Kit+_SingleCells_SSCs_73


title: Kit+_SingleCells_SSCs_74


title: Kit+_SingleCells_SSCs_67


title: Kit+_SingleCells_SSCs_62


title: Kit+_SingleCells_SSCs_68


title: Kit+_SingleCells_SSCs_58


title: Kit+_SingleCells_SSCs_61


title: Kit+_SingleCells_SSCs_64


title: Kit+_SingleCells_SSCs_60


title: Kit+_SingleCells_SSCs_71


title: Kit+_SingleCells_SSCs_70


title: Kit+_SingleCells_SSCs_65


title: SSEA4-/KIT+_SSCs_patient1_rep1


title: Kit+_SingleCells_SSCs_57


title: Kit+_SingleCells_SSCs_56


title: Kit+_SingleCells_SSCs_55


title: Kit+_SingleCells_SSCs_54


title: Kit+_SingleCells_SSCs_59


title: Kit+_SingleCells_SSCs_53


title: Kit+_SingleCells_SSCs_66