title: FL iLS_10h after treatment rep3

source_name: FL iLS_10h after treatment

value: 10h after treatment


title: PFOA3

status: Public on Mar 06 2018

type: SRA

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

country: USA

institute: Michigan State University

description: Perfluorooctanoic acid treated TSCs, repl 3

library_source: transcriptomic

data_processing:
Illumina Real Time Analysis (RTA) v2.7.6
HISAT 2.0.5 alignment to MacaM v7 genome
Trimming 8 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Merging accepted_hits.bam from two alignment step (samtools merge)
Removing "ExAmp" duplicates with distance threshold 2500 using proprietary Python code
Cuffdiff 2.2.1 comparisons of 6 Vehicle libraries to each group of toxicant treated libraries (5 groups, 3-6 libraries per group)
Genome_build: MacaM v7 (Macaca Mulatta)
Supplementary_files_format_and_content: gene_exp.diff files (one for each toxicant) produced by Cuffdiff

molecule: total RNA

organism: Macaca mulatta

source_name: Trophoblast stem cells, Perfluorooctanoic acid

growth_protocol: Trophoblast stem cells (TSCs) (line 119-T) were isolated previously from rhesus monkey blastocysts and characterized using a panel of antibodies to detect TSC biomarkers. TSCs were maintained in DMEM/F- 12 (Invitrogen) supplemented with 15% fetal bovine serum (FBS; Hyclone), 1% minimum essential medium (MEM) nonessential amino acids (Invitrogen), 1 mM glutamine (Sigma), 0.1 mM  β -mercaptoethanol, and 1X  penicillin/streptomycin sulfate (Invitrogen) on plates coated with human placental collagen (Sigma). Medium was changed daily.

extract_protocol:
Cells were detached with 0.25% trypsin-EDTA (Gibco). They were then centrifuged at 3000 x g for 3 min, supernatant removed, and the cell pellet resuspended in 100 µL Picopure lysis buffer (Applied Biosystems).  Lysates were stored at -80°C until shipment.
100 ng of each RNA sample were processed first using a mixture of random and oligo(dT) primers and reverse transcription to generate double stranded cDNA using the Ovation Universal RNA-Seq System (NuGen, San Carlos, CA). This was followed by cDNA fragmentation to an average of 300 bp using a Covaris-2 sonicator, and then a brief S1 nuclease digestion. After purification, the cDNA was processed further through the Ovation Universal RNA-Seq System (NuGen) for end repair, barcoding, InDA-C mediated ribosomal RNA depletion, and final library production with the addition of unique nucleotide barcodes to each library.

treatment_protocol:
The cells were grown to confluence and passaged weekly by rinsing wells with PBS, incubating with 1.0 mL trypsin-EDTA, and transferring 20% of cell suspension to each new well. Treatments began when cells first reached confluence and continued for 4 weeks, including during passage.
Chemicals for testing were made as 1000x stocks in methanol and were added to aliquots of TSC maintenance medium up to 48 hours before use and stored at 4°C until use. Chemicals were obtained from Sigma (DEHP: Bis(2-ethylhexyl) phthalate – 47994; PFOA: Perfluorooctanoic acid – 171468; ATR: Atrazine – 45330; TBT: Tributyltin chloride – 442869; BPA: Bisphenol A – 133027).  In addition to untreated control, treatment groups included a vehicle control (methanol) and each of five EDCs at environmentally relevant doses [10 nM BPA (36 nM fetal serum), 5 uM DEHP (7.7uM pubertal serum), 30 uM ATR (up to 7 uM drinking water reported), 100 nM PFOA (average 94 nM >12 year old serum), and 25 nM TBT (0.17 – 534 adult nM serum).

tag: cell line

tag: treatment

value: Perfluorooctanoic acid

tag: passages


title: FL iLS_12h after treatment rep1

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression (raw counts of mapped reads and FPKM) was obtained using Cufflinks (version 2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

molecule: polyA RNA

organism: Mus musculus

source_name: FL iLS_12h after treatment

growth_protocol: Id3-ERT2-induced hematopoietic multipotent progenitors (induced leukocyte stem, or iLS cells) were co-cultured with TSt-4 feeder cells in IMDM medium supplemented with 20 ng/mL IL-7, 10 ng/mL SCF, 10 ng/mL Flt-3L and 40 nM 4-OHT.

extract_protocol:
Total RNA was isolated using Maxwell 16LEV simplyRNA purification kit.
Poly(A)+ mRNA was isolated from total RNA by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) then library was prepared by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Average size and quantity of each library were measured by Agilent 2100 Bioanalyzer (Agilent Technologies) and KAPA Library Quantification Kit (KAPA Biosystems), respectively. Sequences were read by HiSeq 1500 system (Illumina).

treatment_protocol: To induce B cell differentiation of iLS cells, the cells were co-cultured with TSt-4 cells in IMDM medium supplemented with 5 ng/ml IL-7 in the absence of 4-OHT.

tag: strain

tag: cell type

value: fetal liver induced leukocyte stem cell (FL iLS)

tag: time point

value: 12h after treatment


title: FL iLS_10h after treatment rep2


title: FL iLS_10h after treatment rep1


title: PFOA1

description: Perfluorooctanoic acid treated TSCs, repl 1

value: Trophoblast stem cells (TSCs) (line 119-T)


title: VEH4

description: Vehicle control TSCs, repl 4

source_name: Trophoblast stem cells, Methanol (vehicle control)

value: Methanol (vehicle control)


title: PFOA2

description: Perfluorooctanoic acid treated TSCs, repl 2


title: DEHP5

description: Bis(2-ethylhexyl) phthalate treated TSCs, repl 5

source_name: Trophoblast stem cells, Bis(2-ethylhexyl) phthalate

value: Bis(2-ethylhexyl) phthalate


title: FL iLS_8h after treatment rep3

source_name: FL iLS_8h after treatment

value: 8h after treatment


title: DEHP4

description: Bis(2-ethylhexyl) phthalate treated TSCs, repl 4


title: FL iLS_6h after treatment rep3

source_name: FL iLS_6h after treatment

value: 6h after treatment


title: DEHP1

description: Bis(2-ethylhexyl) phthalate treated TSCs, repl 1


title: DEHP3

description: Bis(2-ethylhexyl) phthalate treated TSCs, repl 3


title: FL iLS_8h after treatment rep2


title: FL iLS_24h after treatment rep2

source_name: FL iLS_24h after treatment

value: 24h after treatment


title: FL iLS_6h after treatment rep2


title: CTRL5

description: Untreated control TSCs, repl 5

source_name: Trophoblast stem cells, Untreated control

value: Untreated control


title: FL iLS_6h after treatment rep1


title: FL iLS_12h after treatment rep2


title: FL iLS_8h after treatment rep1


title: FL iLS_4h after treatment rep2

source_name: FL iLS_4h after treatment

value: 4h after treatment


title: CTRL3

description: Untreated control TSCs, repl 3


title: FL iLS_4h after treatment rep3


title: CTRL4

description: Untreated control TSCs, repl 4


title: CTRL2

description: Untreated control TSCs, repl 2


title: FL iLS_4h after treatment rep1


title: BPA5

description: Bisphenol A treated TSCs, repl 5

source_name: Trophoblast stem cells, Bisphenol A

value: Bisphenol A


title: FL iLS_2h after treatment rep3

source_name: FL iLS_2h after treatment

value: 2h after treatment


title: BPA6

description: Bisphenol A treated TSCs, repl 6


title: BPA4

description: Bisphenol A treated TSCs, repl 4


title: FL iLS_2h after treatment rep1


title: CTRL1

description: Untreated control TSCs, repl 1


title: FL iLS_2h after treatment rep2


title: DEHP2

description: Bis(2-ethylhexyl) phthalate treated TSCs, repl 2


title: BPA3

description: Bisphenol A treated TSCs, repl 3


title: BPA2

description: Bisphenol A treated TSCs, repl 2


title: FL iLS_1h after treatment rep1

source_name: FL iLS_1h after treatment

value: 1h after treatment


title: BPA1

description: Bisphenol A treated TSCs, repl 1


title: FL iLS_1h after treatment rep2


title: FL iLS_1h after treatment rep3


title: FL iLS_0.5h after treatment rep2

source_name: FL iLS_0.5h after treatment

value: 0.5h after treatment


title: ATR6

description: Atrazine treated TSCs, repl 6

source_name: Trophoblast stem cells, Atrazine

value: Atrazine


title: ATR4

description: Atrazine treated TSCs, repl 4


title: ATR5

description: Atrazine treated TSCs, repl 5


title: FL iLS_0.5h after treatment rep1


title: FL iLS_0h after treatment rep3

source_name: FL iLS_0h after treatment

value: 0h after treatment


title: FL iLS_0h after treatment rep2


title: ATR2

description: Atrazine treated TSCs, repl 2


title: FL iLS_0h after treatment rep1


title: ATR1

description: Atrazine treated TSCs, repl 1


title: flashtag-06hr-rep3

status: Public on Mar 05 2018

city: New York

first: Christoph

last: Hafemeister

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
The raw data was processed with the Drop-seq tools pipeline (Drop-seq tools version 1.12 from McCarroll lab). Reads were aligned to the ENSEMBL release 84 Mus musculus genome.
We selected cells for downstream processing in each sample, using the QC metrics output by the Drop-seq tools package, as well as metrics derived from the unique molecular identifier (UMI) matrix. We kept only cells with at least 2,000 unique genes detected. We further removed cells with a z- scored alignment rate < -3, or with an absolute z-scored number of reads (after log10 tranformation) > 3.
Genome_build: ENSEMBL release 84
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are protein coding genes; columns are cells with naming scheme {sample}_{cell barcode}

source_name: Medial ganglionic eminence

extract_protocol:
After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted into 96-well plates and immediately frozen on dry ice. FlashTag: Immediately prior to use 10mM CFSE (Life Technologies, #C34554) CellTrace solution was prepared according to the manufacturer's instructions, and 2-3ul was injected into the lateral ventricle of E13.5 wild type mouse embryos. Embryos were harvested 3, 6, 12 and 24 hours post-injection.
Smart-seq2 protocol was used for cDNA synthesis and libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturers instructions. Cells were immediately lysed and mRNAs were released when single cells were sorted into wells with 5X Maxima reverse transcription buffer, dNTP mixture, RNase inhibitors (SUPERase In RNase Inhibitor, Thermo Fisher Scientific #AM2696) and water. We reverse-transcribed the mRNAs using Superscript II Reverse Transcriptase (Thermo Fisher Scientific #18064071), and amplified cDNAs for each cell in individual wells using the Smart-seq2 protocol, with a custom modification where a 12-base cell barcode was included in the 3’-end RT primer. This allowed us to perform multiplexed pooling before library preparation with the Nextera XT DNA sample prep kit (Illumina), and returned 3’ biased data similar to the Drop-seq protocol. We quantified the cDNA libraries on Agilent BioAnalyzer and sequenced them on HiSeq 2500.

value: wild type Swiss Webster

tag: mouse stage

tag: hours post injection

tag: library cell barcode bases

tag: library molecular barcode bases


title: flashtag-03hr-rep2


title: flashtag-12hr-rep3


title: flashtag-24hr-rep4


title: dlx6neg-rep5

value: Dlx6a-Cre; RCEloxP


title: flashtag-24hr-rep5


title: flashtag-24hr-rep3


title: FL iLS_0.5h after treatment rep3

value: fetal liver induced leukocyte stem cell (FL iLS)


title: flashtag-06hr-rep2


title: flashtag-06hr-rep1


title: flashtag-03hr-rep1


title: dlx6neg-rep4


title: flashtag-24hr-rep2


title: dlx6neg-rep2


title: flashtag-24hr-rep1


title: dlx6neg-rep3


title: flashtag-12hr-rep2


title: flashtag-12hr-rep1


title: dlx6neg-rep1


title: ATR3

description: Atrazine treated TSCs, repl 3

value: Trophoblast stem cells (TSCs) (line 119-T)


title: Subcortex_P10

data_processing:
The raw data was processed with the Drop-seq tools pipeline (Drop-seq tools version 1.12 from McCarroll lab). Reads were aligned to the ENSEMBL release 84 Mus musculus genome.
We selected cells for downstream processing in each sample, using the QC metrics output by the Drop-seq tools package, as well as metrics derived from the unique molecular identifier (UMI) matrix. 1) We first removed cells with a low number (< 700) of unique detected genes. From the remaining cells, we filtered additional outliers. 2) We removed cells where the overall alignment rate is less than the mean minus three standard deviations. 3) We removed cells where the total number of reads (after log10 transformation) is not within 3 standard deviations of the mean. 4) We removed cells where the total number of unique molecules (UMIs, after log10 transformation) is not within 3 standard deviations of the mean. 5) We removed cells where the transcriptomic alignment rate (defined by PCT_USABLE_BASES) is not within 3 standard deviations of the mean. 6) We removed cells that show an unusually high or low number of UMIs given their number of reads by fitting a loess curve (f=0.5, degree=2) to the number of UMIs with number of reads as predictor (both after log10 transformation). Cells with a residual more than 3 standard deviations away from the mean are removed. 7) With the same criteria, we removed cells that show an unusually high or low number of genes given their number of UMIs. Of these filter steps, step 1 removed the majority of cells. Steps 2 to 7 removed only a small number of additional cells from each eminence (2% to 4%), and these cells did not exhibit unique or biologically informative patterns of gene expression.
Genome_build: ENSEMBL release 84
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are protein coding genes; columns are cells with naming scheme {sample}_{cell barcode}

source_name: Subcortex

extract_protocol:
After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The CGE, MGE, cortical or subcortical region was dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells from Lhx6(BAC)-GFP brain tissue were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted in bulk.
The Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3' Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V2 User Guide.


title: Subcortex_E18.5


title: Cortex_P10

source_name: Cortex


title: Cortex_E18.5


title: MGE_E13.5_Lhx6pos


title: MGE_4

data_processing:
The raw Drop-seq data was processed with the standard pipeline (Drop-seq tools version 1.12 from McCarroll lab). Reads were aligned to the ENSEMBL release 84 Mus musculus genome.
We selected cells for downstream processing in each Drop-seq run, using the QC metrics output by the Drop-seq tools package5, as well as metrics derived from the unique molecular identifier (UMI) matrix. 1) We first removed cells with a low number (< 700) of unique detected genes. From the remaining cells, we filtered additional outliers. 2) We removed cells where the overall alignment rate is less than the mean minus three standard deviations. 3) We removed cells where the total number of reads (after log10 transformation) is not within 3 standard deviations of the mean. 4) We removed cells where the total number of unique molecules (UMIs, after log10 transformation) is not within 3 standard deviations of the mean. 5) We removed cells where the transcriptomic alignment rate (defined by PCT_USABLE_BASES) is not within 3 standard deviations of the mean. 6) We removed cells that show an unusually high or low number of UMIs given their number of reads by fitting a loess curve (f=0.5, degree=2) to the number of UMIs with number of reads as predictor (both after log10 transformation). Cells with a residual more than 3 standard deviations away from the mean are removed. 7) With the same criteria, we removed cells that show an unusually high or low number of genes given their number of UMIs. Of these filter steps, step 1 removed the majority of cells. Steps 2 to 7 removed only a small number of additional cells from each eminence (2% to 4%), and these cells did not exhibit unique or biologically informative patterns of gene expression.
Genome_build: ENSEMBL release 84
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are protein coding genes; columns are cells with naming scheme {sample}_{cell barcode}

extract_protocol:
After removal from the mother, embryos were stored on ice in Leibovitz`s L-15 Media and 1% Fetal Bovine Serum. Brains were removed from the embryos and imbedded in 1% UltraPure Low Melting Point Agarose and sectioned in 50-micron sections with a vibratome (Leica VT1200S). The MGE, CGE or LGE were dissected from each embryo. Tissue from multiple embryos was pooled together before dissociation. Embryonic brain tissue pooled from multiple embryos was dissociated into a single cell suspension using Papain dissociation system (Worthington Biochemical Corporation) according to the manufacturer’s instructions. Postnatal brain tissue was dissociated with 1mg/mL of pronase (Roche, #10 165 921 001) in ice cold prebubbled aCSF (Artificial Cerebrospinal Fluid) for 25 minutes. Fluorescent cells from Lhx6(BAC)-GFP brain tissue were sorted on a Sony SY3200 sorter with a 100 micron nozzle. Cells were sorted in bulk.
Drop-seq was run on single cells according to the Online-Dropseq-Protocol-v.-3.1 (December 2015) and the methods published in Macosko et al. 20155. Drop-seq flow rates (oil: 6,000 ul/hr, cells: 2,000 ul/hr, beads: 2,000 ul/hr) were optimized based on human-mouse species mixing experiments with a 1-2% doublet rate. Libraries were prepared with the Nextera XT DNA Library Preparation Kit according to the manufacturer's instructions.

tag: age


title: CGE_E13.5_Lhx6neg

source_name: Caudal ganglionic eminence


title: flashtag-03hr-rep3


title: MGE_2


title: MGE_1


title: LGE_3_run2

source_name: Lateral ganglionic eminence


title: LGE_3_run1


title: CGE_3_run2


title: LGE_2


title: LGE_1


title: CGE_2


title: CGE_3_run1


title: CGE_1


title: MOLM13_48H_DMSO_1

city: Boston

first: Nathanael

last: Gray

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

institute: DFCI

data_processing:
FASTQs were aligned using Tophat2.'
Counts were quantified via cuffquant and cuffnorm.
Custom in house r script for differential analyis and ercc normalization
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file containing ERCC spike in normalized FPKM RNA-Seq expression values

organism: Homo sapiens

source_name: AML

growth_protocol: Cells were cultured in their respective growth medium supplemented with PS.

extract_protocol: RNA was prepared from the MOLM13 cell line. Illumina NextSeq 500 with cell count normalized and mixed with ERCC spike in.

treatment_protocol: Cells were treated for 24 or 48 hours with molecule.

tag: agent

value: DMSO

value: 48 hours


title: MOLM13_48H_DTRIM24_1


title: MOLM13_48H_DMSO_3


title: MOLM13_48H_DTRIM24_2


title: MOLM13_48H_DMSO_2


title: MOLM13_24H_DMSO_2

value: 24 hours


title: MOLM13_24H_DMSO_3


title: MOLM13_24H_DTRIM24_1


title: MOLM13_24H_DTRIM24_3


title: THP1_DTRIM24_2


title: THP1_DMSO_2


title: THP1_DTRIM24_1


title: MOLM13_24H_DMSO_1


title: THP1_DMSO_1


title: MV411_DTRIM24_2


title: THP1_DMSO_3


title: MOLM13_48H_DTRIM24_3


title: MV411_DMSO_3


title: MV411_DTRIM24_1


title: MGE_3


title: MV411_DMSO_1


title: NOMO1_DTRIM24_2


title: NOMO1_DMSO_1


title: NOMO1_DMSO_2


title: HL60_DTRIM24_3


title: NOMO1_DMSO_3


title: MOLM13_24H_DTRIM24_2


title: HL60_DTRIM24_2


title: OCIAML5_DTRIM24_3


title: HL60_DTRIM24_1


title: OCIAML5_DTRIM24_1


title: OCIAML5_DTRIM24_2


title: OCIAML5_DMSO_3


title: HL60_DMSO_2


title: KASUMI1_DMSO_3

value: KASUMI


title: HL60_DMSO_1


title: HL60_DMSO_3


title: KASUMI1_DTRIM24_3


title: OCIAML5_DMSO_2


title: KASUMI1_DTRIM24_1


title: KASUMI1_DMSO_1


title: KASUMI1_DMSO_2


title: DTRIM24_2

data_processing:
FASTQs were aligned using Tophat2.
Counts were quantified via cuffquant and cuffnorm.
Custom in house r script for differential analyis and ercc normalization
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM summarized across replicates.

growth_protocol: Cells were cultured in RPMI media 10%FBS with PS.

treatment_protocol: Cells were treated for 24 hours with molecule.

value: acute monocytic leukemia (AML)

value: 24 hour


title: OCIAML5_DMSO_1


title: DTRIM24_1


title: IACS24_3


title: MV411_DMSO_2


title: DTRIM24_3


title: NOMO1_DTRIM24_1


title: IACS24_1


title: DMSO24_1


title: DTRIM4_1

value: 4 hour


title: DMSO24_2


title: DTRIM4_2


title: DMSO24_3


title: KASUMI1_DTRIM24_2


title: IACS4_3


title: IACS4_1


title: nhr1

city: Vancouver

first: Forum

last: Bhanshali

state: BC

address: 950 west 28th avenue

department: Medical genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics, UBC

data_processing:
Single-end reads were aligned to the C. elegans UCSC ce10 reference genome using an RNA-seq alignment app from Illumina, which uses STAR aligner to map reads
we used edgeR to convert raw gene counts into counts per million (CPM) and log2-counts per million (log-CPM).
Weakly expressed genes were removed by only including genes with counts per million (CPM) >1 across two libraries. Gene expression distributions were normalized by the method of trimmed mean of M-values (TMM) in edgeR
Genome_build: C. elegans UCSC ce10
Supplementary_files_format_and_content: tab-delimited text files with raw counts and normalized CPM values for each sample

organism: Caenorhabditis elegans

source_name: nhr-49(nr2041), No treatment

growth_protocol: We allowed N2 and nhr-49(nr2041) worms to grow on OP50 until they reached L4 stage

extract_protocol:
RNA was extracted with Trizol
ribosomal RNA removed using the RiboGone - Mammalian—Low Input Ribosomal RNA Removal Kit for Human, Mouse and Rat Samples (Takara #634847). Ribosomal RNA depletion and RNA integrity were verified on a Bioanalyzer with the RNA 6000 Pico kit (Agilent #5067-1513). We constructed cDNA libraries with the SMARTer Universal Low Input RNA Kit (Takara #634900), and measured adapter-ligated concentrations with the High Sensitivity DNA Analysis Kit (Agilent #5067-4626) and by qPCR standard-curve quantitation using the KAPA Library Quantification Kit Illumina Platforms (KK4824).
RNA-seq was done on an Illumina Nextseq 500 using 76bp x2 paired-end reads, using the NextSeq 500/550 High Output Kit v2 (150 cycles).

treatment_protocol: L4 stage worms were exposed to 7.5 mM tBOOH for 4 hours, while the control remained untreated

tag: genotype

tag: Stage

value: No treatment


title: nhr3


title: N2tbooh3

source_name: N2, tBOOH treated

value: tBOOH treated


title: nhr49tbooh1

source_name: nhr-49(nr2041), tBOOH treated


title: DMSO4_1


title: dTRIM24_input

description: Input

library_source: genomic

data_processing:
FASTQs were aligned to assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1) with parameter '-k 1.'
Wiggles for visualization and peak calling was performed on aligned data using MACS version 1.4.2 using with matched input chromatin as control, with a p-value threshold of 1e-9.
For any genomic region, normalized read density was calculated using Bamliquidator (version 1.0) (https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files of tag pileup

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and Trim24-DNA complexes were isolated with antibody.
Sonicated in bioruptor. Library prep with Rubicon Thruplex DNA-seq.

tag: chip antibody

value: none (input)


title: IACS-9571

description: ChIP-seq

value: TRIM24 (Bethyl A300-851A)


title: nhr49tbooh3


title: DMSO4_2


title: IACS-9571_input

description: Input


title: DMSO

description: ChIP-seq


title: DMSO_input

description: Input


title: N21

data_processing:
Single-end reads were aligned to the C. elegans UCSC ce10 reference genome using an RNA-seq alignment app from Illumina, which uses STAR aligner to map reads.
we used edgeR to convert raw gene counts into counts per million (CPM) and log2-counts per million (log-CPM).
Weakly expressed genes were removed by only including genes with counts per million (CPM) >1 across two libraries. Gene expression distributions were normalized by the method of trimmed mean of M-values (TMM) in edgeR.
Genome_build: C. elegans UCSC ce10
Supplementary_files_format_and_content: tab-delimited text files with raw counts and normalized CPM values for each sample

source_name: N2, No treatment

growth_protocol: We allowed N2 and nhr-49(nr2041) worms to grow on OP50 until they reached L4 stage.

extract_protocol:
RNA was extracted with Trizol.
ribosomal RNA removed using the RiboGone - Mammalian—Low Input Ribosomal RNA Removal Kit for Human, Mouse and Rat Samples (Takara #634847). Ribosomal RNA depletion and RNA integrity were verified on a Bioanalyzer with the RNA 6000 Pico kit (Agilent #5067-1513). We constructed cDNA libraries with the SMARTer Universal Low Input RNA Kit (Takara #634841), and measured adapter-ligated concentrations with the High Sensitivity DNA Analysis Kit (Agilent #5067-4626) and by qPCR standard-curve quantitation using the KAPA Library Quantification Kit Illumina Platforms (KK4824).
RNA-seq was done on an Illumina Nextseq 500 using 76bp x2 paired-end reads, using the NextSeq 500/550 High Output Kit v2 (150 cycles).

treatment_protocol: L4 stage worms were exposed to 7.5 mM tBOOH for 4 hours, while the controls remained untreated.


title: N2tbooh1


title: N23


title: DTRIM4_3


title: IACS24_2


title: C6KNFANXX_8_18

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description: AA3323 (FOXO76.001)

data_processing:
Sequence reads were mapped against the human reference genome (hg19) with the GEM split-mapper software (Marco-Sola et al., 2012) using the gencode_v21 annotation, and genes quantified with flux capacitor (Montgomery et al-. 2010).
The differential expression analysis was performed with the DESeq2 package using P Wald test, and considering the gender of the samples as a covariate of the generalized linear model
DESeq2: regularized log transformation of normalized RNA seq counts and further variance stabilizing transformation
Supplementary_files_format_and_content: Excell files data log and  variance stabilizing transformed for each Sample

source_name: fibroblasts

growth_protocol: Arm surface skin biopsies of 3 mm of diameter were obtained from subjects. Primary cultures of fibroblasts  were cultured in 25 mM DMEM medium (Gibco, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin following standard culture conditions. Cells were cultured in parallel in successive passes until the same cell pass number and, at confluence, cultures were trypsinized with 2.5% Trypsin (Gibco, Life Technologies) and harvested by centrifugation 8 minutes at 500g. Cell pellets were kept dry at -80 C° until RNA extracction.

extract_protocol:
RNA was extracted using the Allprep DNA RNA Protein Minikit from Qiagen following manufacter instructions. Resulting RNA samples were assayed for quantity and quality using the  Qubit® RNA HS (Life Technologies) and RNA 6000 Nano assays on a Bioanalyzer 2100.
RNA sequencing (RNA-seq) was performed at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona, Catalonia. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,) with minor modifications.

treatment_protocol: Fibroblasts were cultured in two conditions in standard culture conditions: 25 mM DMEM medium (Gibco, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin following standard culture conditions.

tag: status

value: healthy control

tag: glucose

value: Control

tag: gender

value: female


title: C6KNFANXX_8_19

description: AA3324 (SP-17 )

value: male


title: dTRIM24

description: ChIP-seq

tag: cell line


title: C6KNFANXX_6_13

description: AA3319 (MF011)

value: Parkin Parkinson's disease (PRKN mutation)

value: Patient


title: C6KNFANXX_6_14

description: AA3320 (MF013)


title: IACS4_2


title: C6KNFANXX_7_16

description: AA3322 (FOXO73.001)


title: Fermentor N°3 Sample 24h (G5)

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description: barcode: ATGTCA

data_processing:
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads. In a second step, reads were mapped onto the C. beijerinckii DSM6423 genome sequence using the SSAHA2 package that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained. To lower false positives discovery rate, the SAMtools (v.0.1.8, [22]) are then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome is subsequently computed with the Bioconductor GenomicFeatures package. If reads matching several genomic objects, the count number is weighted in order to keep the same total number of reads.
Finally, the Bioconductor-DESeq package with default parameters is used to analyze raw counts data and test for differential expression between conditions
Genome_build: chromosome (circular DNA) LN908213.1 GI: 1188447636; bacteriophage (linear DNA) LN908215.1 GI: 1188453697; plasmid (circular DNA) LN908214.1 GI: 1188453683
Supplementary_files_format_and_content: The csv files report abundance measurements.  Column header names: Label (Feature ID), Type (features include CDS, tRNA, rRNA, misc_RNA, fCDS), Name, Product (Putative Function), Begin (start location of feature), End (end location of feature), Frame (frame of feature), sense (Raw Count), antisense (Raw Count)

organism: Clostridium beijerinckii

growth_protocol: Actively growing culture was inoculated at 5% into a fermentation medium (GAPES). In order to get 3 biological replicates, the same procedure was repeated 3 times on 3 different weeks. Each week, a fresh preculture was used to inoculate 2 identical bioreactors. Samples were taken over the early exponential, late exponential and stationary phases (samples at 3, 6, 8, 11, and 24h). Following centrifugation of the samples, cell pellets were immediately frozen in liquid nitrogen and supernatants were used for HPLC analysis. For each timepoint, the RNA samples of the 2 bioreactors were pooled, leading to 1 RNA sample per week and timepoint.

extract_protocol:
Cell lysis and RNA isolation was done with the TRIzol Plus RNA purification kit (AMbion). 5 mL TRIzol reagent is added to the frozen pellet followed by 1 mL chloroform after cell lysis. After shacking and centrifugation, the upper phase is mixed with an equal volume of 70% ethanol before transfer to PureLink RNA Spin Cartridges furnished with the kit. Kit instructions allow to obtain purified total RNA which is further processed by cleanup with the RNeasy mini kit (Qiagen).  DNA is eliminated after DNAse I treatment (AM1906, Invitrogen). 20µL RNA is treated with 2 µL DNAse in 50 µL nuclease free water for 30 min at 37°C before addition of another 1.5 µL DNAse and 30 min extra incubation. Treatment is done twice and is followed by RNA cleanup with the RNeasy kit. A full quality assessment of the RNA, quantification using Nanodrop, PCR to check for residual DNA and migration on 1% agarose gel is done before depletion of ribosomal RNA with MicrobExpress kit (ThermoFischer). Depletion uses 2-10 µg total RNA in 15 µL water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: fermentor

value: no. 3

tag: time


title: C6LE0ANXX_8_12

description: AA3318 (MF014)


title: C6KNFANXX_7_15

description: AA3321 (FOXO69.001)


title: DMSO4_3

tag: cell type


title: Fermentor N°3 Sample 11h (G4)

description: barcode: AGTTCC

tag: strain


title: C6LE0ANXX_8_11/ C6KNFANXX_5_11

description: AA3317 (MF009)


title: Fermentor N°3 Sample 6h (G2)

description: barcode: CTTGTA


title: Fermentor N°3 Sample 3h (G1)

description: barcode: GGCTAC


title: Fermentor N°2 Sample 11h (E4)

description: barcode: GATCAG

value: no. 2


title: Fermentor N°2 Sample 8h (E3)

description: barcode: ACTTGA


title: Fermentor N°3 Sample 8h (G3)

description: barcode: AGTCAA


title: Fermentor N°2 Sample 24h (E5)

description: barcode: TAGCTT


title: Fermentor N°1 Sample 3h (D1)

description: barcode: ATCACG

value: no. 1


title: Fermentor N°2 Sample 3h (E1)

description: barcode: GCCAAT


title: brat RNAi larval tumor neuroblasts - replicate2

status: Public on Mar 04 2018

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Basecalling RTA 1.18.64.0
The reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44). snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked for downstream analysis.
Reads arising from duplication events are marked as such in the alignment (SAM/BAM files) as follows. The different tags (i7 random octameres) are counted at each genomic position. Thereafter, the diversity of tags at each position is examined. First, tags are sorted descending by their count. If several tags have the same occurrence, they are further sorted alphanumerically. Reads sharing the same tag, are sorted by the average PHRED quality. Again if several reads have the same quality, they are further sorted alphanumerically. Now the tags are cycled through by their counts. Within one tag, the read with the highest average PHRED quality is the unique correct read and all subsequent reads with the same tag are marked as duplicates. Furthermore, all reads which have tags with one mismatch difference compared the pool of valid read tags are also marked as duplicates.
The aligned and deduplicated reads were counted with HTSeq.
The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.10.1).
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample (Standard output Htseq); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Flies expressing UAS-dcr2; wor-GAL4, ase-GAL80; UAS-stinger::RFP were crossed to w1118 (wild-type) or brat RNAi (VDRC, TID105054) and raised at 29C. Wandering L3 larval brains were collected and prepared for FACS-sorting.

extract_protocol: Type II neuroblasts were FACS sorted and total RNA was isolated using TRIzol LS reagent. Total RNA was converted to first strand (using oligo-(dT)20 primers) and second strand cDNA. Library preparation was done using Illumina's protocol with Nextera DNA Library Preparation Kit using a modified Index primer 1 (i7), which included random octamere sequences for molecular barcoding.

value: Type II neuroblasts

tag: developmental stage

value: third instar larva

tag: marker

value: cells express nuclear RFP marker (UAS-stinger::RFP )

tag: genotype/variation

value: brat RNAi-triggered tumor type II


title: Fermentor N°1 Sample 6h (D2)

description: barcode: CGATGT


title: brat RNAi larval tumor neuroblasts - replicate3


title: Fermentor N°1 Sample 8h (D3)

description: barcode: TTAGGC


title: wild type larval type II neuroblasts - replicate1

value: wild type


title: Fermentor N°1 Sample 11h (D4)

description: barcode: TGACCA


title: Fermentor N°2 Sample 6h (E2)

description: barcode: CAGATC


title: brat RNAi larval tumor neuroblasts - replicate1


title: wild type larval type II neuroblasts - replicate2


title: wild type larval type II neuroblasts - replicate3


title: Fermentor N°1 Sample 24h (D5)

description: barcode: ACAGTG


title: Aconitum_carmichaelii_Leaf

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

institute: Chiba University

description: Plant Material No. 0871-09TS in NIBIOHN

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
The Trinity program ver 2.5 was used for the de novo transcriptome assembly using clean reads from all the samples. De novo assembly resulted in 182,928 unigenes, with a N50 value of 905. Trinity program derived de novo transcriptome assembly was further processed through CD-HIT-EST program (Li and Godzik 2006) to remove transcripts redundancies, resulting in our final assembly of 128,183 unigenes with N50 value as 830bps
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 and RSEM respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were aligned on Aconitum carmichaelii de novo transcriptome assembly that were generated using Trinity, and abundace were measured using RSEM. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM, and IsoPct for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: tab-delimited text file includes contig_id, unigene_id, and FPKM values for each tissues. FPKM values were calculated using RSEM program. results files for all tissues were used to extract FPKM values for each tissues, and were combind/alligned against transcript_id and gene_id

organism: Aconitum carmichaelii

source_name: Leaf

growth_protocol: All four tissues, namely flower, bud, leaf and root were harvested from A. carmichaelii growing in the natural conditions at the Tsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN, Tsukuba, Japan) in the month of September, 2014.

extract_protocol:
Frozen samples of A. carmichaelii were powdered using a Multi Beads Shocker (Yasui Kikai, Japan) for subsequent RNA extraction. Total RNA for each of the four tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

treatment_protocol: Not applicable

tag: tissue

value: Leaf


title: X07133

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

country: China

institute: institute of biochemistry and cell biology

data_processing:
Illumina Casava1.7 software was used for basecalling.
Alignment to genome reference sequence was carried on Hisat2（version:2.0.4）using spliced mapping algorithm and Genome mapping algorithm
Seqtk was used to filter the Raw data to removes the sequence of links contained in reads, short reads and the low quality reads
Tophat v2.1.0 was used to map the cleaned reads to the hg38 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff
Genome_build: hg38
Supplementary_files_format_and_content: .xls file contaning the Ensemble Geneid, FPKM and counts for every sample

source_name: Normal diploid ESCs from PB2 transfer reconstructed embryos

growth_protocol: human ESCs were cultured on feeder in human ES medium supplemented with 10μM Y-27635

extract_protocol:
The total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA,US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies), RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea,   CA,USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) were used to purify total RNA
RNA-seq libraries were prepared using TruSeq RNA Sample Pre Kit v2 –Set A/ B (Illumina).

treatment_protocol: When ESCs conlonies achieved its maximum size and 80% coverage, aspirate spent medium followed by adding 1 ml Trizol to lysis the cell with pipetting with 1 ml nuclease free insulin syringe to help release the contents. The sample was stored at -80℃.

value: embryonic stem cells

tag: passage


title: X06277


title: Aconitum_carmichaelii_Bud

description: Plant Material No. 0871-09TS in NIBIOHN

source_name: Bud

value: Bud

tag: age


title: Aconitum_carmichaelii_Root

description: Plant Material No. 0871-09TS in NIBIOHN

source_name: Root

value: Root


title: Aconitum_carmichaelii_Flower

description: Plant Material No. 0871-09TS in NIBIOHN

source_name: Flower

value: Flower


title: X07138

value: female


title: X061427

source_name: Normal diploid ESCs from PB1 transfer reconstructed embryos

value: male


title: X061422


title: TRPC2_2

status: Public on Mar 03 2018

city: PHILADELPHIA

first: Puneet

last: Dang

state: PA

address: 3610 Hamilton Walk

department: Neuroscience

institute: University of Pennsylvania

description: biological replicate

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped tozebrafish GRCz10 whole genome.
Reads per million(rpm) values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads (in million) for that sample.
Alignment – STAR algorithm
Gene counts – VERSE
Genome_build: Ensemble zebrafish assembly GRCz10
Supplementary_files_format_and_content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample

organism: Danio rerio

source_name: TRPC2 expressing olfactory sensory neurons

growth_protocol: Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.

extract_protocol:
Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7-oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one (for OMP neurons) two rounds (for TRPC2 neurons).
Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.

treatment_protocol: Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting (FACS) was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.

value: Tubingen/TLF

tag: embryo stage

value: olfactory sensory neurons

tag: neuron subtype


title: OMP_2

description: biological replicate

source_name: OMP expressing olfactory sensory neurons

value: OMP


title: TRPC2_1

description: biological replicate


title: OMP_1

description: biological replicate


title: B32

city: Guangzhou

first: Haibin

last: Sun

state: Guangdong

address: 7 Jinying Road

department: Plant Protection Research Institute

institute: Guangdong Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Transcriptome assembly: The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011).
Quantification of gene expression levels：Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample: 1. Clean data were mapped back onto the assembled transcriptome; 2. Readcount for each gene was obtained from the mapping results.
Genome_build: de novo assembly transcriptome
Supplementary_files_format_and_content: files with read counts and FPKM values

organism: Conopomorpha sinensis

source_name: larvae

extract_protocol:
extract total RNA from 5 instar larvae of the litchi fruit borer
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNaseH- Clustering and sequencing (Novogene Experimental Department) ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μlUSER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCRproducts were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: larvae

value: 5 instar

tag: background

value: pesticide


title: BR_5week

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

data_processing:
Align to reference gene models (Ensembl; Pmarinus_7.0) using RSEM
Calculate raw transcript expression for each time point using RSEM
Calculate expression fold change and probability of differential expression using EBseq
Genome_build: RNA-Seq reads were mapped against gene models from the publicly available lamprey genome (Ensembl; Pmarinus_7.0)
Supplementary_files_format_and_content: "genes.results" files contain transcript abundance generated by RSEM in the standard RSEM output format. ".appended" files contain differential expression estimates generated by Ebseq in the standard EBseq output format.

organism: Petromyzon marinus

source_name: brain

extract_protocol:
Brains (whole brains without the olfactory lobes) and spinal cords (1cm surrounding the lesion), were  harvested from uninjured lampreys, and at 10 time points from 6 hours to 12 weeks post injury. Tissue was stored in RNALater and then homogenized, pooled by time point (n=6 animals per time point), and total RNA (RIN >9) extracted using Trizol.
RNA-Seq libraries (~250bp) were created using TruSeq RNA Sample Prep Kit v2 (Illumina Inc.; San Diego, CA), + Ribo-Zero Gold (Epicentre).

treatment_protocol: Spinal cord transection

tag: post-injury time point

value: 5 week

value: brain


title: BR_2week

value: 2 week


title: BR_3dpi

value: 3 days


title: BR_1dpi

value: 1 day


title: B11

value: no-pesticide


title: BR_4week

value: 4 week


title: BR_3week

value: 3 week


title: BR_12week

value: 12 week


title: BR_6hpi

value: 6 hours


title: SC_12week

source_name: spinal cord

value: spinal cord


title: SC_6week

value: 6 week


title: SC_4week


title: SC_1week

value: 1 week


title: BR_6week


title: SC_5week


title: SC_3dpi


title: SC_3week


title: BR_Uninjured

value: Uninjured


title: SC_6hpi


title: SC_1dpi


title: SC_Uninjured


title: X06144

value: embryonic stem cells

value: female


title: BR_1week


title: 20d_r3

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
All RNA-seq reads were aligned to the human genome (hg19) using TopHat (v2.0.12) with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene.

source_name: reprogramming cells

growth_protocol: hiF-Ts were cultured in hESM with dox for 6 days followed by changing to 5iLAF medium with dox for 14 days, which were then maintained in 5iLAF medium without dox for additional 4 days before picking-up colonies to estabish niPSC.

extract_protocol:
RNAs were extracted using Trizol reagent. KAPA Stranded mRNA-Seq Kit(KK8420) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to KAPA Stranded mRNA-Seq Kit(KK8420).

treatment_protocol: Reprogrammed cells were dissociated by Accutase and enriched by magnetic beads to deplete feeder.

tag: reprogramming stage


title: 8d_r3


title: SC_2week


title: piPSC-T H3K27me3 ChIP-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
All ChIP-seq reads were aligned to the human genome (hg19) using bowtie2(v 2.2.3) with default parameters. Then reads signal for each sample were generated using the MACS2 (v2.1.0.20140616) pileup function and were normalized to 1 million reads for visualization.
Chromatin states were identified and characterized using ChromHMM (v1.11).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: induced pluripotent stem cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA DNA Library Preparation Kits.

value: piPSC-T

tag: chip antibody


title: n24d+dox H3K27me3 ChIP-seq


title: hiF-T H3K27me3 ChIP-seq

source_name: embryonic fibroblast

value: hiF-T


title: hiF-T H3K9me3 ChIP-seq


title: 6d H3K9me3 ChIP-seq


title: 6d H3K27me3 ChIP-seq


title: p24d+dox H3K27me3 ChIP-seq


title: p24d+dox_r1_1_2

data_processing:
Illumina Casava1.8 software used for basecalling.
All RRBS reads were aligned to human genome (hg19) using BSMAP(v 2.89) with the parameter ‘-D C-CGG -w 100 -s 12 -v 0.1 -n 1 -m 32 -x 1000 -R’
Methylation ratio of each C site was calculated using methratio.py from BSMAP. Bisulfite conversion ratio for each sample was calculated using unmethyalted CpGs divided by total CpGs detected in lambda genome.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

extract_protocol:
Genomic DNAs were extracted from reprogramming cells and iPSCs using DNeasy Blood & Tissue Kits (QIAGEN).
Genomic DNAs was digested by MspI(Fermentas,ER0541),the digested DNA was then end-repaired and tailed with an extra A to the 3'blunted ends.Illumina standard premethylated indexed adaptors were ligated with the dA-tailed DNA fragments. Bisulfite conversion was then performed using the MethyCode bisulfite conversion kit (Invitrogen,MECOV-50).Libraries were prepared according to KAPA DNA Library Preparation Kits.


title: 8d H3K9me3 ChIP-seq


title: piPSC-T


title: niPSC-T_1_2

value: niPSC-T


title: n24d+dox_r1


title: p20d_r1


title: n24d+dox_r2


title: hiF-T


title: n20d


title: 6d


title: 14d_r3


title: piPSC-T H3K4me2 ChIP-seq


title: p24d+dox H3K4me3 ChIP-seq


title: piPSC-T H3K4me3 ChIP-seq


title: niPSC-T H3K9me3 ChIP-seq


title: 14d H3K9me3 ChIP-seq


title: p24d+dox H3K4me2 ChIP-seq


title: niPSC-T H3K4me3 ChIP-seq


title: niPSC-T H3K4me2 ChIP-seq


title: niPSC-T H3K27me3 ChIP-seq


title: p24d+dox_r2


title: p20d_r2


title: n24d+dox H3K4me3 ChIP-seq


title: n24d+dox H3K4me2 ChIP-seq


title: hiF-T H3K4me3 ChIP-seq


title: 6d H3K4me2 ChIP-seq


title: hiF-T H3K4me2 ChIP-seq


title: 6d H3K4me3 ChIP-seq


title: 20d_r1


title: niPSC-T_r1


title: 14d_r1


title: niPSC-T_r2


title: 24d+dox_r2


title: 24d-dox_r1


title: 12d_r2


title: 6d_r1


title: 2d_r1


title: 2d_r2


title: 12d_r1


title: 8d_r2


title: 6d_r2


title: 0d_r2


title: 0d_r1


title: hiF-T_r2


title: 8d_r1


title: 24d+dox_r1


title: hiF-T_r1


title: 24d-dox_r2


title: 14d_r2


title: 12 hour untreated bulk [Sample_D_2]

status: Public on Mar 02 2018

city: San Antonio

first: Tim

middle: Hui-Miing

last: Huang

state: TX

address: 8403 Floyd Curl Dr.

department: Molecular Medicine

institute: University of Texas Health San Antonio

description:
processed data file:
raw.txt
rpkm.txt

data_processing:
Raw fastq is mapped to human genome by TopHat using default parameters for paired end sequencing
Multiple-mapped reads are removed using samtools
HOMER is used to generate text file for rpkm and raw reads using default parameters
Collected the average read value for genes with mulitple transcript variants per cell
R package SCDE is used to detect differentially expressed genes between each two of the three groups of cell population
Genome_build: hg19
Supplementary_files_format_and_content: Raw.txt contains the raw reads generated by HOMER using default parameter. The rpkm.txt contains rpkm reads generated by HOMER using default parameter. The 'results_de12_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 0hr and 12hr untreated cells. The 'results_de23_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 12hr untreated and androgen-treated cells. The 'results_de13_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 0hr untreated and 12hr androgen-treated cells.

source_name: LNCaP_12 hour untreated bulk

growth_protocol: LNCaP cells were cultured (typically 1–2 × 106 cells into a T75 flask ) in RPMI 1640 media (Gibco) supplemented fetal bovine serum and penecillin/streptomycin, 10% and 1% final concentrations respectively.

extract_protocol:
Single cells were hand picked with a micromanipulator and ejected into SMARTseq2 cell lysis buffer. Reverse transcription and PCR amplification occured according to the SMARTseq2 protocol as described by Picelli et al. 2014. The Illumina Nextera XT DNA Library Prep Kit (Cat#FC-131-1096) and the Index Kit v2 set A (Cat#FC-131-2001) were used with 0.3 ng of amplified DNA per cell for the construction of sequencing libraries.
RNA libraries were manually prepared for sequencing. We created equimolar solutions from 96 uniquely indexed cells.

treatment_protocol: Cell were seeded at 4 x 105 per well of a 6-well dish, synchronized  to the G1/S phase with double thymidine block and androgen deprived (in RPMI 1640 -phenol red and substituted charcoal-stripped fetal bovine serum) for ~24 hours. Treatment groups 2 and 3 were cultured in the absence and presence of androgen (1 nM R1881) for 12 hours, respectively. Treatment group 1 was a baseline comparison treatment group and was collected right after cell synchronization and androgen deprivation (considered 0 hour).

value: LNCaP

value: prostate cancer cells

tag: time point

value: 12 hour untreated bulk


title: 12 hour androgen-treated cell 44 [Sample_3_44]

description:
processed data file:
raw.txt
rpkm.txt
results_de13_pvalues_beganwithGeneNames.txt
results_de23_pvalues_beganwithGeneNames.txt

source_name: LNCaP_12 hour androgen-treated cell

value: 12 hour androgen-treated cell


title: 0 hour untreated bulk [Sample_D_1]

description:
processed data file:
raw.txt
rpkm.txt

source_name: LNCaP_0 hour untreated bulk

value: 0 hour untreated bulk


title: 12 hour androgen-treated cell 47 [Sample_3_47]


title: 12 hour androgen-treated cell 48 [Sample_3_48]


title: 12 hour androgen-treated cell 46 [Sample_3_46]


title: 12 hour androgen-treated cell 42 [Sample_3_42]


title: 12 hour androgen-treated cell 41 [Sample_3_41]


title: 12 hour androgen-treated cell 43 [Sample_3_43]


title: 12 hour androgen-treated cell 45 [Sample_3_45]


title: 12 hour androgen-treated cell 37 [Sample_3_37]


title: 12 hour androgen-treated cell 38 [Sample_3_38]


title: 12 hour androgen-treated cell 34 [Sample_3_34]


title: 12 hour androgen-treated cell 35 [Sample_3_35]


title: 12 hour androgen-treated cell 36 [Sample_3_36]


title: 12 hour androgen-treated bulk [Sample_D_3]

description:
processed data file:
raw.txt
rpkm.txt

source_name: LNCaP_12 hour androgen-treated bulk

value: 12 hour androgen-treated bulk


title: 12 hour androgen-treated cell 32 [Sample_3_32]


title: 12 hour androgen-treated cell 33 [Sample_3_33]


title: 12 hour androgen-treated cell 31 [Sample_3_31]


title: 12 hour androgen-treated cell 30 [Sample_3_30]


title: 12 hour androgen-treated cell 39 [Sample_3_39]


title: 12 hour androgen-treated cell 27 [Sample_3_27]


title: 12 hour androgen-treated cell 25 [Sample_3_25]


title: 12 hour androgen-treated cell 24 [Sample_3_24]


title: 12 hour androgen-treated cell 26 [Sample_3_26]


title: 20d_r2


title: 12 hour androgen-treated cell 23 [Sample_3_23]


title: 12 hour androgen-treated cell 22 [Sample_3_22]


title: 12 hour androgen-treated cell 19 [Sample_3_19]


title: 12 hour androgen-treated cell 40 [Sample_3_40]


title: 12 hour androgen-treated cell 21 [Sample_3_21]


title: 12 hour androgen-treated cell 18 [Sample_3_18]


title: 12 hour androgen-treated cell 15 [Sample_3_15]


title: 12 hour androgen-treated cell 14 [Sample_3_14]


title: 12 hour androgen-treated cell 20 [Sample_3_20]


title: 12 hour androgen-treated cell 12 [Sample_3_12]


title: 12 hour androgen-treated cell 9 [Sample_3_9]


title: 12 hour androgen-treated cell 29 [Sample_3_29]


title: 12 hour androgen-treated cell 6 [Sample_3_6]


title: 12 hour androgen-treated cell 7 [Sample_3_7]


title: 12 hour androgen-treated cell 8 [Sample_3_8]


title: 12 hour androgen-treated cell 4 [Sample_3_4]


title: 12 hour androgen-treated cell 5 [Sample_3_5]


title: 12 hour androgen-treated cell 3 [Sample_3_3]


title: 12 hour androgen-treated cell 1 [Sample_3_1]


title: 12 hour androgen-treated cell 10 [Sample_3_10]


title: 12 hour untreated cell 48 [Sample_2_48]

description:
processed data file:
raw.txt
rpkm.txt
results_de12_pvalues_beganwithGeneNames.txt
results_de23_pvalues_beganwithGeneNames.txt

source_name: LNCaP_12 hour untreated cell

value: 12 hour untreated cell


title: 12 hour untreated cell 47 [Sample_2_47]


title: 12 hour untreated cell 46 [Sample_2_46]


title: 12 hour untreated cell 45 [Sample_2_45]


title: 12 hour untreated cell 44 [Sample_2_44]


title: 12 hour untreated cell 43 [Sample_2_43]


title: 12 hour androgen-treated cell 2 [Sample_3_2]


title: 12 hour androgen-treated cell 16 [Sample_3_16]


title: 12 hour untreated cell 41 [Sample_2_41]


title: 12 hour untreated cell 42 [Sample_2_42]


title: 12 hour androgen-treated cell 13 [Sample_3_13]


title: 12 hour androgen-treated cell 17 [Sample_3_17]


title: 12 hour untreated cell 40 [Sample_2_40]


title: 12 hour androgen-treated cell 11 [Sample_3_11]


title: 12 hour untreated cell 36 [Sample_2_36]


title: 12 hour untreated cell 35 [Sample_2_35]


title: 12 hour untreated cell 34 [Sample_2_34]


title: 12 hour untreated cell 33 [Sample_2_33]


title: 12 hour untreated cell 28 [Sample_2_28]


title: 12 hour untreated cell 29 [Sample_2_29]


title: 12 hour untreated cell 27 [Sample_2_27]


title: 12 hour untreated cell 26 [Sample_2_26]


title: 12 hour untreated cell 32 [Sample_2_32]


title: 12 hour untreated cell 25 [Sample_2_25]


title: 12 hour androgen-treated cell 28 [Sample_3_28]


title: 12 hour untreated cell 38 [Sample_2_38]


title: 12 hour untreated cell 30 [Sample_2_30]


title: 12 hour untreated cell 23 [Sample_2_23]


title: 12 hour untreated cell 22 [Sample_2_22]


title: 12 hour untreated cell 24 [Sample_2_24]


title: 12 hour untreated cell 20 [Sample_2_20]


title: 12 hour untreated cell 18 [Sample_2_18]


title: 12 hour untreated cell 39 [Sample_2_39]


title: 12 hour untreated cell 31 [Sample_2_31]


title: 12 hour untreated cell 16 [Sample_2_16]


title: 12 hour untreated cell 14 [Sample_2_14]


title: 12 hour untreated cell 11 [Sample_2_11]


title: 12 hour untreated cell 13 [Sample_2_13]


title: 12 hour untreated cell 12 [Sample_2_12]


title: 12 hour untreated cell 10 [Sample_2_10]


title: 12 hour untreated cell 21 [Sample_2_21]


title: 12 hour untreated cell 9 [Sample_2_9]


title: 12 hour untreated cell 7 [Sample_2_7]


title: 12 hour untreated cell 8 [Sample_2_8]


title: 12 hour untreated cell 15 [Sample_2_15]


title: 12 hour untreated cell 5 [Sample_2_5]


title: 12 hour untreated cell 2 [Sample_2_2]


title: 12 hour untreated cell 3 [Sample_2_3]


title: 12 hour untreated cell 1 [Sample_2_1]


title: 0 hour untreated cell 45 [Sample_1_45]

description:
processed data file:
raw.txt
rpkm.txt
results_de12_pvalues_beganwithGeneNames.txt
results_de13_pvalues_beganwithGeneNames.txt

source_name: LNCaP_0 hour untreated cell

value: 0 hour untreated cell


title: 0 hour untreated cell 48 [Sample_1_48]


title: 0 hour untreated cell 47 [Sample_1_47]


title: 12 hour untreated cell 17 [Sample_2_17]


title: 12 hour untreated cell 19 [Sample_2_19]


title: 0 hour untreated cell 44 [Sample_1_44]


title: 0 hour untreated cell 43 [Sample_1_43]


title: 0 hour untreated cell 41 [Sample_1_41]


title: 0 hour untreated cell 40 [Sample_1_40]


title: 0 hour untreated cell 37 [Sample_1_37]


title: 0 hour untreated cell 38 [Sample_1_38]


title: 0 hour untreated cell 39 [Sample_1_39]


title: 0 hour untreated cell 36 [Sample_1_36]


title: 12 hour untreated cell 4 [Sample_2_4]


title: 0 hour untreated cell 35 [Sample_1_35]


title: 12 hour untreated cell 6 [Sample_2_6]


title: 0 hour untreated cell 33 [Sample_1_33]


title: 0 hour untreated cell 32 [Sample_1_32]


title: 0 hour untreated cell 31 [Sample_1_31]


title: 0 hour untreated cell 34 [Sample_1_34]


title: 0 hour untreated cell 30 [Sample_1_30]


title: 0 hour untreated cell 42 [Sample_1_42]


title: 0 hour untreated cell 29 [Sample_1_29]


title: 0 hour untreated cell 46 [Sample_1_46]


title: 0 hour untreated cell 27 [Sample_1_27]


title: 0 hour untreated cell 26 [Sample_1_26]


title: 0 hour untreated cell 25 [Sample_1_25]


title: 0 hour untreated cell 23 [Sample_1_23]


title: 0 hour untreated cell 24 [Sample_1_24]


title: 0 hour untreated cell 20 [Sample_1_20]


title: 0 hour untreated cell 19 [Sample_1_19]


title: 0 hour untreated cell 18 [Sample_1_18]


title: 0 hour untreated cell 16 [Sample_1_16]


title: 0 hour untreated cell 15 [Sample_1_15]


title: 0 hour untreated cell 17 [Sample_1_17]


title: 0 hour untreated cell 13 [Sample_1_13]


title: 0 hour untreated cell 14 [Sample_1_14]


title: 0 hour untreated cell 12 [Sample_1_12]


title: 0 hour untreated cell 11 [Sample_1_11]


title: 0 hour untreated cell 10 [Sample_1_10]


title: 0 hour untreated cell 8 [Sample_1_8]


title: 0 hour untreated cell 5 [Sample_1_5]


title: 0 hour untreated cell 28 [Sample_1_28]


title: 0 hour untreated cell 9 [Sample_1_9]


title: 0 hour untreated cell 7 [Sample_1_7]


title: 0 hour untreated cell 3 [Sample_1_3]


title: 0 hour untreated cell 2 [Sample_1_2]


title: 0 hour untreated cell 1 [Sample_1_1]


title: IA7_shSUZ12_2

first: Ingrid

middle: M

last: Aries

state: MA

address: 1 Blackfan circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
Sequence alignments were performed with STAR aligner (version 2.3.1z4) against the hg19 w ERCC92 genome (ftp://ftp.ensembl.org/pub/release-75/ fasta/homo_sapiens/dna/). The RUV-Seq package was used to normalize to spike-in controls.
FeatureCounts software was used to produce integer counts for all genes in the supplied genome annotation file, which were then normalized using DESeq package.
Genome_build: hg19 w ERCC92 genome (ftp://ftp.ensembl.org/pub/release-75/ fasta/homo_sapiens/dna/)
Supplementary_files_format_and_content: normalized gene counts

source_name: T-ALL cell line CCRF-CEM

growth_protocol: CCRF-CEM cells were infected with infection with shGFP, shLuciferase, shEZH2#1, shEZH2#4, shEED#2, shEED#5, shSUZ12#2, or shSUZ12#3 and selected with puromycin, 8 days after infection RNA was isolated.

extract_protocol:
RNA was isolated from an equal number of CCRF-CEM cells using RNeasy kit (Qiagen). Samples were then treated with Ambion’s Turbo DNAse (Thermo Fisher Scientific) to yield DNA contamination below 10%.  3 μl of 1:10 ERCC spike-in controls (Ambion, Thermo Fisher Scientific) were added to 5000 ng of RNA. Quality of RNA was assessed using the Agilent 2100 Bioanalyzer.
Using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA), 50-100 ng of total RNA was converted into a DNA library following the manufacturer’s protocol. Libraries passing quality control were diluted to 2nM using sterile water and then sequenced on the HiSeq 2000 (Illumina, San Diego, CA) at a final concentration of 12pM on a single read flowcell with 50 sequencing cycles, following all manufacturer protocols.

tag: cell line

value: T-ALL cell line CCRF-CEM

tag: infection


title: IA8_shSUZ12_3


title: 0 hour untreated cell 21 [Sample_1_21]

tag: cell type


title: 0 hour untreated cell 6 [Sample_1_6]


title: IA4_shEZH2_4


title: IA3_shEZH2_1


title: IA6_shEED_5


title: 0 hour untreated cell 22 [Sample_1_22]


title: IA2_shGFP

value: shGFP


title: IA1_shLuc

value: shLuc


title: CHIP.CARM1-KO.input

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: CHIPseq: CARM1 KO DNA input

data_processing:
Fastq files were generated by Illumina HiSeq 2000 and aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with HOMER software between WT and KO conditions using -style histone -fdr 0.01 parameters
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains Homer peak calling output

source_name: A1847 cell line, CARM1 CRISPR

growth_protocol: A1847 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin  at 37°C supplied with 5% CO2.

extract_protocol:
cells were cross-linked with 1% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min. Fixed cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) once and incubated for 20 minutes at 37 °C in the presence of 1,000 Gel units of MNase (NEB, M0247S) in 250 L reaction volume. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysates were sonicated for 5 min (30 sec-on / 30 sec-off) in a Diagenode bioruptor and centrifuged at 15,000 rpm for 10 min
Ovation Ultralow DR Multiplex system (NuGEN)

treatment_protocol: pLentiCRISPR-CARM1 was constructed by inserting the CARM1 guide RNA (gRNA; 5′-AGCACGGAAAATCTACGCGG-3′). pLentiCRISPR v2 (Addgene) was digested and dephosphorylated with BsmBI restriction enzyme (Fermentas) for 30 min at 37°C. The digested plasmid was run on a 1% agarose gel, cut out, and purified using the Wizard SV Gel and PCR Clean Up kit (Promega). The oligonucleotides were phosphorylated using T4 PNK (M0201S) with T4 Ligation Buffer (New England Biolabs, Inc.). Samples were annealed in a thermocycler at 37°C for 30 min and then at 95°C for 5 min and then were ramped down to 25°C at 5°C/min. Annealed oligonucleotides were diluted 1:200 in RNase/DNase-free water. Ligation of the annealed oligonucleotide and digested pLentiCRISPR v2 plasmid was performed using Quick Ligase (New England Biolabs, Inc.)

value: CARM1 knockout

tag: antibody

value: input


title: CHIP.CARM1-KO.H3K27me3

description: CHIPseq: CARM1 KO H3K27me3 binding

value: anti-H3K27Me3 (Cell Signaling, Cat. No. 9733)


title: CHIP.CARM1-KO.EZH2

description: CHIPseq: CARM1 KO EZH2 binding

value: anti-EZH2 (Cell Signaling, Cat. No. 5246)


title: CHIP.CARM1-WT.input

description: CHIPseq: CARM1 WT DNA input

source_name: A1847 cell line

value: CARM1 wild type


title: 0 hour untreated cell 4 [Sample_1_4]


title: CHIP.CARM1-WT.H3K27me3

description: CHIPseq: CARM1 WT H3K27me3 binding


title: CHIP.CARM1-WT.EZH2

description: CHIPseq: CARM1 WT EZH2 binding


title: Organoids Day 12, LIS1+/-, Repeat #3

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: barcode: GGCGATT

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg38 whole genome using Cutadapt  -a $adapter -q 20 fastqf  ($adapter= sequence of adapter Fastqf= fastqfile) and STAR.
Raw counts were processed, and normalized reads were obtained by DESeq2.
Genome_build: GRCh37/hg38
Supplementary_files_format_and_content: tab-delimited text files include read values for each sample.

source_name: WIBR3 hESC Cerebral Organoids

extract_protocol:
Total RNA was extracted from samples using RNEASY mini-kit (Qiagen)
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014).]

tag: developmental stage

value: Organoids Day 12

tag: genotype


title: Organoids Day 12, LIS1+/-, Repeat #2

description: barcode: CCTAAGG


title: Organoids Day 12, LIS1+/-, Repeat #1

description: barcode: TAGCGCA


title: Organoids Day 12, wild-type, Repeat #1

description: barcode: GGAGACT


title: Organoids Day 5, LIS1+/-, Repeat #3

description: barcode: TACCAGT

value: Organoids Day 5


title: Organoids Day 12, wild-type, Repeat #3

description: barcode: ACTTGGC


title: IA5_shEED_2


title: Organoids Day 5, LIS1+/-, Repeat #2

description: barcode: GGATCTA


title: Organoids Day 5, wild-type, Repeat #2

description: barcode: ATAACCG


title: Organoids Day 5, wild-type, Repeat #3

description: barcode: TGTCACG


title: Organoids Day 5, LIS1+/-, Repeat #1

description: barcode: TTCCTGA


title: Organoids Day 5, wild-type, Repeat #1

description: barcode: AGCTCAA


title: Stem cells, LIS1+/-, Repeat #3

description: barcode: CGTAACT

source_name: WIBR3 hESC

value: hESC


title: Stem cells, wild-type, Repeat #3

description: barcode: GCAGTAG


title: Stem cells, wild-type, Repeat #2

description: barcode: ATCTGCA


title: Stem cells, LIS1+/-, Repeat #1

description: barcode: CAGTACG


title: Stem cells, LIS1+/-, Repeat #2

description: barcode: TGCACAA


title: Stem cells, wild-type, Repeat #1

description: barcode: GTATGCG


title: Quantseq_MV-4-11-B_NA_JQ1_200nM_4h_NA_NA_NA_rep1_J11976_R1

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim RCV GmbH & Co KG

description:
Quant-seq
Quantseq_MV-4-11-B_NA_JQ1_200nM_4h_NA_NA_NA_NA_J11976-J11977-J11978-J11974-J11975_dge.tsv.gz

data_processing:
Base calling was performed using Illumina RTA 1.18.64, afterwards multiplexed samples were converted to FASTQ files using CASAVA 1.8.2 allowing for 1 mismatch in the index sequence. Technical replicates were merged in a single FASTQ files.
Quant-seq: Reads were filtered using BBMap version 36.27 and mapped to hg38 (hs38d1) with STAR version 2.5.2b. Raw read counting over genes loci was also performed using STAR. Differential gene expression was computed using limma+voom filtering out genes with less than 10 reads across the tested samples.
Genome_build: hg38
Supplementary_files_format_and_content: Differential gene expression files list all genes and attach associated statistics from limma+voom.

growth_protocol: The cell lines were cultured with the media suggested by ATCC at 37 degree Celsius incubators with 5% CO2.

extract_protocol:
Cells were lysed in TRI lysis reagent (Sigma-Aldrich, T9424, St. Louis, US-MO), with tissue grinders.
Quant-seq libraries were prepared based on 500 ng of RNA for each library. The QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used from Lexogene (# 015.96.) according to manufacturer's instructions.

treatment_protocol: The corresponding compounds (dissolved in DMSO) were added directly into cell culture media, and cells were kept at normal growth conditions for the treatment duration.

tag: method

value: QUANT-seq

tag: treatment

tag: replicate

tag: internal id


title: Quantseq_MV-4-11-B_NA_JQ1_200nM_4h_NA_NA_NA_rep3_J11978_R1


title: Quantseq_MV-4-11-B_NA_JQ1_200nM_4h_NA_NA_NA_rep2_J11977_R1


title: Quantseq_MV-4-11-B_NA_JQ1_2000nM_4h_NA_NA_NA_rep3_J11981_R1

description:
Quant-seq
Quantseq_MV-4-11-B_NA_JQ1_2000nM_4h_NA_NA_NA_NA_J11979-J11980-J11981-J11974-J11975_dge.tsv.gz


title: Quantseq_MV-4-11-B_NA_JQ1_2000nM_4h_NA_NA_NA_rep1_J11979_R1


title: Quantseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep1_J11974_R1

description: Quant-seq

value: DMSO


title: Quantseq_MV-4-11-B_NA_BI00894999_10nM_4h_NA_NA_NA_rep2_J11983_R1

description:
Quant-seq
Quantseq_MV-4-11-B_NA_BI00894999_10nM_4h_NA_NA_NA_NA_J11982-J11983-J11984-J11974-J11975_dge.tsv.gz


title: Quantseq_MV-4-11-B_NA_BI00894999_10nM_4h_NA_NA_NA_rep3_J11984_R1


title: Quantseq_MV-4-11-B_NA_BI00894999_10nM_4h_NA_NA_NA_rep1_J11982_R1


title: Quantseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_rep2_J11986_R1

description:
Quant-seq
Quantseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_NA_J11985-J11986-J11987-J11974-J11975_dge.tsv.gz


title: Quantseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep2_J11975_R1

description: Quant-seq


title: Quantseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_rep3_J11987_R1


title: Quantseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_rep1_J11985_R1


title: Organoids Day 12, wild-type, Repeat #2

description: barcode: AGCTAGT


title: YU2-C1

city: Sao Paulo

first: Israel

middle: Tojal da

last: Silva

state: SP

address: Tagua, 440

country: Brazil

institute: HOSPITAL A C CAMARGO

description: CD4+ T cell isolated from healthy donor infected in vitro with HIV-1(YU2) for 48h. Cells were then isolated based on anti-Env antibody staining.

data_processing:
alignment with STAR 2.4.1d
gene counts with htseq-count 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: plain text gene counts, annotated with UCSC refGene table

source_name: CD4+ T cell

growth_protocol: Activated CD4+ T cells were expanded in basal media (RPMI with 10% heat-inactivated fetal bovine and antibiotics) containing IL-2 (350U ml-1) for 5 days, then infected with HIV(YU2) via spinoculation.

extract_protocol:
Single cells were sorted into 96-well plates containing guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA was extracted using Ampure RNAClean SPRI beads.
RNA was converted to full-length cDNA using oligo(dT) priming and SMART template switching technology followed by 24 cycles of PCR preamplification of cDNA. We used the amplified cDNA to construct standard Illumina sequencing libraries Nextera XT library preparation kit. Samples were sequenced by Illumina NextSeq.

treatment_protocol: 48h after infection, cells were labeled with 5ug/mL each of biotinylated 3BNC117, 10-1074, PG16 followed by Streptavidin PE (1:500, BD) and sorted on Env positive, CD4 low cells.

tag: condition

tag: patient

value: Healthy donor


title: YU2-B7


title: YU2-B3


title: YU2-C5


title: YU2-C3


title: YU2-B5


title: YU2-C9


title: YU2-C7


title: YU2-C10


title: YU2-C6


title: YU2-B6


title: YU2-C4


title: YU2-C2


title: YU2-B9


title: Quantseq_MV-4-11-B_NA_JQ1_2000nM_4h_NA_NA_NA_rep2_J11980_R1


title: YU2-B4


title: YU2-B12


title: YU2-B2


title: YU2-B11


title: YU2-B10


title: YU2-A6


title: YU2-A8


title: YU2-A7


title: YU2-B1


title: YU2-C8


title: YU2-A4


title: YU2-A9


title: YU2-A5


title: YU2-B8


title: c-Jun_ChIPseq_E2

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: c-Jun antibody used in MCF-7/c-Jun -Tet cells treated with E2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 and HOMER peak analysis software was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated

source_name: MCF-7/c-Jun -Tet cells

growth_protocol: Cells  were maintained in DMEM supplemented with 10% FBS containing media in absence of tetracycline.

extract_protocol:
Lysates were clarified from sonicated nuclei, c-Jun and ERα complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in steroid depleted media for 72 h and treated with ethanol, 10 nM 17β-estradiol or 1μM Tamoxifen for 1 h. Cells were fixed with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested

value: ERalpha-positive breast cancer cells

value: c-Jun (H-79, Santa Cruz)


title: ERα_ChIPseq_Vehicle

description: ERalpha antibody used in MCF-7/c-Jun -Tet cells treated with vehicle

value: ERalpha (H-20, Santa Cruz)


title: B207-3_I1_B12

description: Recently reactivated latent cell from patient B207 collected by anti-Env antibody capture 36h after PHA activation. Cells were confirmed HIV+ by gag qPCR.

growth_protocol: CD4+ T cells were isolated from 0.8-1x109 PBMCs by negative selection using the Miltenyi CD4+ T isolation kit. Cells were cultured for 36h at 2x10e6/mL in RPMI supplemented with 10% heat inactivated FCS, 10mM HEPES, 100U/mL PenStrep, and 25% volume conditioned media. 100U/mL IL-2 (Peprotech), 1ug/mL PHA (Sigma), 10uM Z-VAD-FKM (R&D), 10uM Ritonavir, 10uM Dolutegravir, 10uM Emtricitabine, 5uM Tenofovir, and 10uM Maraviroc (all Selleckchem) were added to the media.

treatment_protocol: After 36h in culture, cells were labeled with 5ug/mL each of biotinylated 3BNC117, 10-1074, PG16 followed by Streptavidin PE (1:500, BD) and anti-PE magnetic beads (Miltenyi Biotech). Cells were then passed over a magnetic column and bound cells were eluted for downstream analysis. Cells were gated on live, CD1c, CD8, CD14, CD20, and CD56 negative, CD3 positive and sorted based on Env staining.

value: Gag+Env+


title: YU2-A12


title: ERα_ChIPseq_E2

description: ERalpha antibody used in MCF-7/c-Jun -Tet cells treated with E2


title: YU2-A10


title: B207-3_I1_A8


title: B207-3_I1_A6


title: B207-3_I1_B6


title: YU2-A2


title: B207-3_I1_B3


title: ERα_ChIPseq_Tamoxifen

description: ERalpha antibody used in MCF-7/c-Jun -Tet cells treated with Tamoxifen


title: B207-3_I1_A3


title: c-Jun_ChIPseq_Vehicle

description: c-Jun antibody used in MCF-7/c-Jun -Tet cells treated with vehicle


title: YU2-A3


title: B207-3_I1_A12


title: YU2-A11


title: RNAseq_OCI-AML3_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4234

data_processing:
Base calling was performed using Illumina RTA 1.18.64, afterwards multiplexed samples were converted to FASTQ files using CASAVA 1.8.2 allowing for 1 mismatch in the index sequence. Technical replicates were merged in a single FASTQ files.
ChIP-seq: Reads were mapped to hg19 (canoncial chromosomes) using bowtie2 version 2.2.9, peaks calls were perfomed with MACS2 version 2.1.0. and HOMER HOMER version 4.7 on uniquely mapping reads by using the intersection of calls. Parameters for calling super-enhancers were set as described in the HOMER manual. Note, biological replicates were merged for all analysis reported in the paper.
RNA-seq: Reads were mapped to hg19 (hs37d5) with gsnap version 2012-12-20. The ENSEMBL 70 gene annotation was used for further expression estimations. Raw counts were computed using HTSeq version 0.5.3p9, FPKM expression values were estimated using Cufflinks version 2.0.2. Differential gene expression was computed using DESeq filtering out genes with less than 10 reads across the tested samples.
Quant-seq: Reads were filtered using BBMap version 36.27 and mapped to hg38 (hs38d1) with STAR version 2.5.2b. Raw read counting over genes loci was also performed using STAR. Differential gene expression was computed using DESeq2 filtering out genes with less than 10 reads across the tested samples.
Genome_build: hg19/hg38
Supplementary_files_format_and_content: All processed data files contain tab-separated values. Peaks call files contain positions of all peaks with associated statistics from HOMER. Differential gene expression files list all genes and attach associated statistics from DESeq/DESeq2.

source_name: OCI-AML3 cells

extract_protocol:
Cells were lysed in TRI lysis reagent (Sigma-Aldrich, T9424, St. Louis, US-MO), with tissue grinders.
RNA-seq sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit v2.

value: RNA-seq

value: Not applicable


title: B207-3_I1_B9


title: DNA input

description: DNA from T47D cells treated with vehicle


title: B207-2-Pre-C9

description: Unselected CD4 T cells from patient B207 collected 36h after PHA activation in vitro.

treatment_protocol: After 36h in culture, cells were labeled with 5ug/mL each of biotinylated 3BNC117, 10-1074, PG16 followed by Streptavidin PE (1:500, BD) and anti-PE magnetic beads (Miltenyi Biotech). Cells were gated on live, CD1c, CD8, CD14, CD20, and CD56 negative and sorted on CD3 positive cells.

value: Control


title: RNAseq_OCI-AML3_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J4239

description: RNAseq_OCI-AML3_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J4235-J4239-J4234-J4238_dge.tsv.gz


title: B207-2-Pre-C7


title: B207-3_I1_A11


title: B207-2-Pre-C8


title: c-Jun_ChIPseq_Tamoxifen

description: c-Jun antibody used in MCF-7/c-Jun -Tet cells treated with Tamoxifen


title: B207-2-Pre-C5


title: RNAseq_NCI-H2171_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4154

source_name: NCI-H2171 cells


title: B207-2-Pre-B9


title: RNAseq_OCI-AML3_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4238


title: B207-2-Pre-C3


title: B207-2-Pre-C2


title: B207-2-Pre-B7


title: B207-2-Pre-C10


title: B207-2-Pre-C4


title: B207-2-Pre-B8


title: RNAseq_NCI-H2171_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4146


title: RNAseq_NCI-H2171_NA_BI00894999_100nM_4h_NA_NA_NA_rep1_J4147

description: RNAseq_NCI-H2171_NA_BI00894999_100nM_4h_NA_NA_NA_NA_J4146-J4154-J4147-J4155_dge.tsv.gz


title: B207-2-Pre-B2


title: B207-2-Pre-B5


title: RNAseq_MV-4-11-B_NA_EX00101218_5uM_4h_NA_NA_NA_rep1_J4196

description: RNAseq_MV-4-11-B_NA_EX00101218_5uM_4h_NA_NA_NA_NA_J4196-J4204-J4194-J4202_dge.tsv.gz

source_name: MV-4-11-B cells


title: B207-2-Pre-B3


title: RNAseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4202


title: B207-2-Pre-B10


title: 12 hour untreated cell 37 [Sample_2_37]

description:
processed data file:
raw.txt
rpkm.txt
results_de12_pvalues_beganwithGeneNames.txt
results_de23_pvalues_beganwithGeneNames.txt

value: LNCaP

value: prostate cancer cells

value: 12 hour untreated cell


title: B207-2-Pre-B4


title: YU2-A1


title: RNAseq_MV-4-11-B_NA_EX00101218_5uM_4h_NA_NA_NA_rep2_J4204


title: B207-2-Pre-B1


title: RNAseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep2_J3915


title: B207-2-Pre-A8


title: RNAseq_OCI-AML3_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J4235


title: B207-2-Pre-A7


title: RNAseq_NCI-H2171_NA_BI00894999_100nM_4h_NA_NA_NA_rep2_J4155


title: B207-2-Pre-B6


title: RNAseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4194


title: B207-2-Pre-B12


title: B207-2-Pre-A4


title: B207-2-Pre-A5


title: B207-2-Pre-A3


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J4203

description: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J4195-J4203-J4194-J4202_dge.tsv.gz


title: B207-2-Pre-A2


title: RNAseq_MV-4-11-B_NA_DMSO_NA_NA_NA_NA_NA_rep1_J3910


title: B207-2-Pre-A6


title: B207-2-Pre-A12


title: B207-2-Pre-A9


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J3917

description: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J3912-J3917-J3910-J3915_dge.tsv.gz


title: B207-2-Pos-H7


title: B207-2-Pre-A1


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J3912


title: B207-2-Pos-H11


title: B207-2-Pre-A10


title: B207-2-Pos-G6


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_EX00101218_5uM_4h_rep2_J4205

description: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_EX00101218_5uM_4h_NA_J4197-J4205-J4194-J4202_dge.tsv.gz


title: B207-2-Pos-G4


title: RNAseq_MV-4-11-B_NA_BI00894999_1nM_4h_NA_NA_NA_rep2_J3916

description: RNAseq_MV-4-11-B_NA_BI00894999_1nM_4h_NA_NA_NA_NA_J3911-J3916-J3910-J3915_dge.tsv.gz


title: B207-2-Pos-G3


title: B207-2-Pos-G2


title: B207-2-Pos-G10


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_EX00101218_5uM_4h_rep1_J4197


title: B207-2-Pos-F5


title: B207-2-Pos-F1


title: B207-2-Pos-F2


title: B207-2-Pre-A11


title: RNAseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_rep1_J3913

description: RNAseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_NA_J3913-J3918-J3910-J3915_dge.tsv.gz


title: B207-2-Pos-E3


title: B207-2-Pos-E9


title: B207-2-Pos-E7


title: RNAseq_MV-4-11-B_NA_BI00894999_100nM_4h_NA_NA_NA_rep2_J3918


title: RNAseq_MV-4-11-B_NA_BI00894999_1nM_4h_NA_NA_NA_rep1_J3911


title: B207-2-Pos-D9


title: RNAseq_MV-4-11-B_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J4195


title: B207-2-Pos-H4


title: B207-2-Pos-G5


title: RNAseq_MV-4-11-B_NA_BI00894999_1000nM_4h_NA_NA_NA_rep1_J3914

description: RNAseq_MV-4-11-B_NA_BI00894999_1000nM_4h_NA_NA_NA_NA_J3914-J3919-J3910-J3915_dge.tsv.gz


title: B207-2-Pos-D12

description: Recently reactivated latent cell from patient B207 collected by anti-Env antibody capture 36h after PHA activation. Cells were confirmed HIV+ by gag qPCR.


title: B207-2-Pos-D11


title: B207-2-Pos-D10


title: RNAseq_MOLM-13_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4245

source_name: MOLM-13 cells


title: RNAseq_MOLM-13_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4249


title: RNAseq_MOLM-13_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J4246

description: RNAseq_MOLM-13_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J4242-J4246-J4249-J4245_dge.tsv.gz


title: B207-2-Pos-B5


title: B207-2-Pos-B8


title: B207-2-Pos-C2


title: B207-2-Pos-C12


title: B207-2-Pos-B12


title: B207-2-Pos-B11


title: RNAseq_MOLM-13_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J4242


title: B207-2-Pos-B1


title: RNAseq_MV-4-11-B_NA_BI00894999_1000nM_4h_NA_NA_NA_rep2_J3919


title: RNAseq_KASUMI-1_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4230

source_name: KASUMI-1 cells


title: B207-2-Pos-A5


title: RNAseq_KASUMI-1_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J4231

description: RNAseq_KASUMI-1_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J4227-J4231-J4226-J4230_dge.tsv.gz


title: 605Pre_B6

description: Unselected CD4 T cells from patient 605 collected 36h after PHA activation in vitro.


title: 605Pre_B3


title: 605Pre_B7


title: 605Pre_B4


title: 605Pre_B5


title: RNAseq_KASUMI-1_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J4227


title: 605Pre_B12


title: 605Pre_B10


title: 605Pre_B1


title: 605Pre_A9


title: 605Pre_A8


title: 605Pre_B9


title: RNAseq_HL-60_NA_BI00894999_35nM_4h_NA_NA_NA_rep2_J4255

description: RNAseq_HL-60_NA_BI00894999_35nM_4h_NA_NA_NA_NA_J4251-J4255-J4250-J4254_dge.tsv.gz

source_name: HL-60 cells


title: B207-2-Pos-C6


title: 605Pre_B8


title: 605Pre_A6


title: QUANTseq_MV-4-11-B_NA_Natrosol_NA_NA_NA_NA_NA_rep3_J5800

source_name: MV-4-11-B CDX

growth_protocol: Mice were housed under pathogen-free conditions (AAALAC accredited facility) and treated according to the institutional, governmental and European Union guidelines (Austrian Animal Protection Laws, GV-SOLAS, FELASA). After arrival, mice were allowed to adjust to conditions for 5 days before they were used for the experiment. They were housed in Macrolon type III cages, soiled with bedding, in groups of 5 to 10 under standardized conditions at 21.5 ± 1.5 °C temperature and 55 ± 10 % humidity. Standardized diet and autoclaved tap water were provided ad libitum.

treatment_protocol: BI00894999 was suspended in Natrosol (0.5%) and perorally administered with a volume of 10 ml/kg. Flavopiridol (Selleckchem) was suspended in 1% DMSO and diluted with water and administered intraperitoneally with a volume of 10 ml/kg.

value: Natrosol


title: 605Pre_A3


title: RNAseq_HL-60_NA_BI00894999_35nM_4h_NA_NA_NA_rep1_J4251


title: 605Pre_A4


title: 605Pre_A12


title: 605Pre_A5


title: RNAseq_KASUMI-1_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4226


title: 605Pre_A2


title: 605Pre_A10


title: QUANTseq_MV-4-11-B_NA_Natrosol_NA_NA_NA_NA_NA_rep1_J5714


title: QUANTseq_MV-4-11-B_NA_Natrosol_NA_NA_NA_NA_NA_rep2_J5746


title: 605pre8


title: RNAseq_HL-60_NA_DMSO_NA_NA_NA_NA_NA_rep2_J4254


title: 605pre9


title: RNAseq_HL-60_NA_DMSO_NA_NA_NA_NA_NA_rep1_J4250


title: 605Pre_A1


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_6h_NA_NA_NA_rep2_J5760

description: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_6h_NA_NA_NA_NA_J5701-J5760-J5814-J5868_dge.tsv.gz

value: Flavopiridol, 2.5mg/kg, 6h


title: 605pre4


title: 605pre5


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_6h_NA_NA_NA_rep1_J5701


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_6h_NA_NA_NA_rep3_J5814


title: 605pre3


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_2h_NA_NA_NA_rep4_J5863

description: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_2h_NA_NA_NA_NA_J5696-J5755-J5809-J5863-J5714-J5746-J5800_dge.tsv.gz

value: Flavopiridol, 2.5mg/kg, 2h


title: 605pre2


title: 605pre18


title: 605pre17


title: 605pre19


title: 605pre16


title: 605pre15


title: 605pre14


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_2h_NA_NA_NA_rep2_J5755


title: 605pre12


title: 605pre13


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_2h_NA_NA_NA_rep1_J5696


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_6h_NA_NA_NA_rep4_J5868


title: 605pre11


title: 605pre6


title: QUANTseq_MV-4-11-B_NA_Flavopiridol_2.5mgkg_2h_NA_NA_NA_rep3_J5809


title: 605pre7


title: 605pre1


title: 605posG9

description: Recently reactivated latent cell from patient 605 collected by anti-Env antibody capture 36h after PHA activation. Cells were confirmed HIV+ by gag qPCR.


title: 605posH7


title: 605posE1


title: 605pre10


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_NA_NA_NA_rep3_J5812

description: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_NA_NA_NA_NA_J5699-J5758-J5812-J5866-J5714-J5746-J5800_dge.tsv.gz


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_NA_NA_NA_rep2_J5758


title: 605posA8


title: 605posB12


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_NA_NA_NA_rep1_J5699


title: 605Pos_6_H7


title: 605Pos_6_A8


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_Flavopiridol_2.5mgkg_6h_rep4_J5870

description: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_Flavopiridol_2.5mgkg_6h_NA_J5703-J5762-J5816-J5870-J5714-J5746-J5800_dge.tsv.gz

value: BI00894999, 1mg/kg, 6h and Flavopiridol, 2.5mg/kg, 6h


title: 605Pos_5_E2


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_Flavopiridol_2.5mgkg_6h_rep3_J5816

value: QUANT-seq


title: 605Pos_1_C11


title: 605Pos_1_D7


title: 605Pos_1_D12


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_Flavopiridol_2.5mgkg_6h_rep2_J5762


title: 603Pre_C9

description: Unselected CD4 T cells from patient 603 collected 36h after PHA activation in vitro.


title: 603Pre_C8


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_Flavopiridol_2.5mgkg_6h_rep1_J5703


title: 603Pre_C6


title: 603Pre_C7


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_NA_NA_NA_rep4_J5861

description: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_NA_NA_NA_NA_J5694-J5753-J5807-J5861-J5714-J5746-J5800_dge.tsv.gz


title: 603Pre_C5


title: 603Pre_C4


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_NA_NA_NA_rep2_J5753


title: 603Pre_C3


title: 603Pre_B9


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_NA_NA_NA_rep3_J5807


title: 603Pre_C2


title: 603Pre_B8


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_Flavopiridol_2.5mgkg_2h_rep3_J5811

description: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_Flavopiridol_2.5mgkg_2h_NA_J5698-J5757-J5811-J5865-J5714-J5746-J5800_dge.tsv.gz

value: BI00894999, 1mg/kg, 2h and Flavopiridol, 2.5mg/kg, 2h


title: 603Pre_C1


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_NA_NA_NA_rep1_J5694


title: 603Pre_B4


title: 603Pre_B7


title: 603Pre_B5


title: 603Pre_B6


title: 603Pre_B3


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_Flavopiridol_2.5mgkg_2h_rep2_J5757


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_Flavopiridol_2.5mgkg_2h_rep4_J5865


title: 603Pre_B12


title: 603Pre_B1


title: 603Pre_B11


title: ChIPseq_OCI-AML3_INPUT_NA_NA_NA_NA_NA_NA_rep1_J4774

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 10 ng of ChIP material per sample. NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB #E6240L) and for the quantity measurement KAPA Library Quantification Kit (KapaBiosystems, #KK4824) was used according to the manufacturer’s instructions. 2 nM samples were multiplexed for sequencing.

value: ChIP-seq


title: ChIPseq_OCI-AML3_H3K27ac_NA_NA_NA_NA_NA_NA_rep1_J4772

description: ChIPseq_OCI-AML3_H3K27ac_NA_NA_NA_NA_NA_NA_NA_J4772-J4774_peaks.tsv.gz


title: 603Pre_A8


title: 603Pre_A6


title: 603Pre_B2


title: ChIPseq_NCI-H2171_INPUT_NA_NA_NA_NA_NA_NA_rep1_J2374-J2385


title: 603Pre_A5


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_2h_Flavopiridol_2.5mgkg_2h_rep1_J5698


title: 603Pre_A4


title: ChIPseq_NCI-H2171_H3K27ac_NA_NA_NA_NA_NA_NA_rep1_J2377-J2388

description: ChIPseq_NCI-H2171_H3K27ac_NA_NA_NA_NA_NA_NA_NA_J2377-J2388-J2374-J2385_peaks.tsv.gz


title: 603Pre_A2


title: 603Pre_A3


title: ChIPseq_NCI-H2171_BRD4_NA_NA_NA_NA_NA_NA_rep1_J2386

description: ChIPseq_NCI-H2171_BRD4_NA_NA_NA_NA_NA_NA_NA_J2386-J2374_peaks.tsv.gz


title: ChIPseq_MV-4-11-B_POLII_EX00101218_5uM_4h_NA_NA_NA_rep1_J5931

description: ChIPseq_MV-4-11-B_POLII_EX00101218_5uM_4h_NA_NA_NA_NA_J5931-J2596-J2605-J3766_peaks.tsv.gz

value: RNA Polymerase II (abcam, #ab5095)


title: 603Pre_A10


title: 603Pre_A11


title: 603Pre_A1


title: ChIPseq_MV-4-11-B_POLII_BI00894999_35nM_4h_NA_NA_NA_rep1_J5929

description: ChIPseq_MV-4-11-B_POLII_BI00894999_35nM_4h_NA_NA_NA_NA_J5929-J2596-J2605-J3766_peaks.tsv.gz


title: QUANTseq_MV-4-11-B_NA_BI00894999_1mgkg_6h_NA_NA_NA_rep4_J5866


title: 603pre7


title: 603pre9


title: 603pre2


title: ChIPseq_MV-4-11-B_POLII_BI00894999_35nM_4h_EX00101218_5uM_4h_rep1_J5933

description: ChIPseq_MV-4-11-B_POLII_BI00894999_35nM_4h_EX00101218_5uM_4h_NA_J5933-J2596-J2605-J3766_peaks.tsv.gz


title: 603Pre_A7


title: 603pre11


title: 603pre12


title: 603pre1