title: ChIPSeq_Spt5_Myc_rep1

city: Bronx

first: PABITRA

middle: K

last: PARUA

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
PRO-seq: Adaptor sequences were clipped from read 3' ends.  In cases where inline barcodes were used, they were clipped from 5' ends.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
PRO-seq: Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
PRO-seq: Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
ChIP-seq: Paired-end sequencing (50-nt reads) was performed on an Illumina HiSeq 2000 (Genome Quebec Innovation Centre, McGill University).
ChIP-seq: After adaptor trimming and quality control, processed FASTQ files were aligned to the S. pombe genome using Bowtie2 (Galaxy Version 2.2.6.2).
ChIP-seq: Aligned sequences of each biological replicate were fed into MACS2 (Galaxy Version 2.1.1.20160309.0) to call peaks from alignment results. Generated “bedgraph treatment” files were concatenated (Galaxy Version 1.0.1) to combine replicates of each sample, converted into bigwig using “Wig/BedGraph-to-bigWig converter” (Galaxy Version 1.1.0) and processed using computeMatrix (Galaxy Version 2.3.6.0) in DeepTools to prepare data for plotting a heatmap and/ or a profile of given regions.
Genome_build: PRO-seq: S. pombe: ASM294v2;  S. cerevisiae: S288C_reference_genome_R64-1-1_20110203.
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Supplementary_files_format_and_content: PRO-seq: processed files are in bigwig format. There are two bigwig files for each sample, one for each strand. Each bigwig file contains normalized counts of read 3'-ends.
Supplementary_files_format_and_content: ChIP-seq: processed files are in bedraph format. There are 3 bedgraph files for each sample, two for biological replicates and one combined.

organism: Schizosaccharomyces pombe

source_name: spt5-13myc::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+

growth_protocol:
For PRO-seq, S. pombe cultures were grown in YES media from a starting OD600 of 0.2 to a final OD600 = 0.5 before treatment.
For ChIP-seq: S. pombe cultures were grown in YES media till OD600 ~ 0.4.

extract_protocol:
PRO-seq: Immediately prior to treatments, a fixed amount of spike-in culture (i.e.  S. cerevisaie samples) was added to each sample culture for PRO-seq experiment.  After treatment, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol followed by ethanol precipitation.
ChIP-seq: After HCHO-crosslinking (15 min at 25°C) protein extract was made using Mini-beadbeater (Biospec; 30 sec "ON" and 30 sec "OFF"). Lysates were precleared with IgG and used for IP with respective antibodies.
PRO-seq libraries were prepared according to Mahat et al. Nature Protocols (2016).
ChIP-seq: Multiplexed ChIP-seq libraries were prepared using the Illumina TruSeq DNA Sample Preparation kit v2 with 75 ng of input or IP DNA and barcode adaptors.

treatment_protocol: For PRO-seq, Cells were spun down and resuspended in fresh YES medium, pre-conditioned at the desired temperature (30°C or 18°C) and allowed to incubate for 10 min.  Either 10 uM 3-MB-PP1 or equivalent volume of DMSO was then added to samples for 5 minutes before harvesting.

tag: temperature c

tag: drug (5 minutes)

tag: antibody

value: Anti-Myc epitope (EMD Millipore, 05-724)

tag: assay

value: ChIP-seq


title: ChIPSeq_Spt5_Myc_rep2

status: Public on Jun 07 2018

type: SRA

state: NY

country: USA

library_source: genomic

molecule: genomic DNA


title: ChIPSeq_pSpt5_rep2

value: Anti-pSpt5 antibody (custom made from 21st Century Biochemicals, Marlboro, MA; Sanso et al. 2012)


title: ChIPSeq_pSpt5_rep1


title: ChIPSeq_Input_rep2


title: ChIPSeq_Input_rep1


title: Nrd1-AA MNase-seq +Rap rep2

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

data_processing:
fastq files were processed through the mapping function of HTS EPFL station.PCR duplicates were discarded from the analysis.
bigwig were generated using HTS EPFL station. Strands were merged by 125bp for BrdU-seq.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: Nrd1-AA MNase-seq +Rap

growth_protocol: Nrd1AA strain is pre-cultured and grown to the log phase, half of the culture is fixed by adding 37% formaldehyde (final concentration of 1%) followed by quenching with Glycine (final concentration 125mM) and the other half was treated with rapamycin for 60 minutes before fixation. The cells were harvested using centrifugation and washed twice with H2O.

extract_protocol:
MNase treatment was performed as described in (Weiner et al., 2015).The chromatin was extracted by breaking cells with bead beating in magnalyser (Roche). The chromatin was then collected by centrifugation and then re-suspended in NP-buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2). MNase (Thermo-Scientific) treatment is performed at a previously optimised concentration to have comparable intensity of both mono and di nucleosomes within and between the samples.  MNase treatment was followed by de-crosslinking, protease treatment and DNA was extracted using NucleoSpin gel and PCR extraction columns (Macherey-Nagel).
MNase treatment was performed as described in (Weiner et al., 2015).The chromatin was extracted by breaking cells with bead beating in magnalyser (Roche). The chromatin was then collected by centrifugation and then re-suspended in NP-buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2). MNase (Thermo-Scientific) treatment is performed at a previously optimised concentration to have comparable intensity of both mono and di nucleosomes within and between the samples.  MNase treatment was followed by de-crosslinking, protease treatment and DNA was extracted using NucleoSpin gel and PCR extraction columns (Macherey-Nagel).

tag: strain

tag: treatment

value: +Rap


title: Nrd1-AA MNase-seq -Rap rep2

source_name: Nrd1-AA MNase-seq -Rap

value: -Rap


title: 03

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice given a single bolus dose by oral gavage

library_source: transcriptomic

data_processing:
FASTQC v0.11.3 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v2.1.0 was used for alignment
SAMTools v0.1.2 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Male C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected at 2, 4, 8, 12, 24, 72, and 168h following gavage.

tag: Sex

value: Male

tag: age

tag: age unit

value: days

value: Vehicle

tag: dose

tag: dose unit

value: ug/kg

tag: duration

tag: duration unit

value: hours

tag: replicate


title: 02


title: Delta phi9 phi10 8stop rep10

city: Austin

first: Claus

last: Wilke

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
alignment with hisat2
counting with bedtools multicov
computation of TPMs with R script
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded strains
Supplementary_files_format_and_content: tab-delimitted text file for each sample with four columns: strain, gene start position, gene stop position, gene name, T7 gene number, and TPM (transcripts per million)

organism: Escherichia phage T7

source_name: Ecoli/T7 cell culture

extract_protocol:
RNA was isolated using Trizol reagent (Thermo Fisher Scientific)
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent).

value: wild type

tag: genotype

value: delta phi9 phi10 8stop

tag: host

value: Escherichia coli


title: 08

value: TCDD


title: WT rep8

value: wild type gene 10


title: CHART-seq Smchd1-/- clone 1 input rep2

city: Boston

first: Chen-Yu

last: Wang

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
CHART-seq: Input and CHART-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate input-subtracted coverage profiles using SPP.
Genome_build: mm9
Supplementary_files_format_and_content: CHART-seq: Uniquely mapped reads without PCR duplicates were used to generate input-subtracted coverage profiles by SPP as described in Simon et al., 2013. WT1, WT clone 1. KO1, Smchd1-/- clone 1. Xist: CHART performed using probes that capture Xist RNA. control: CHART performed using probes with sequences antisense to the Xist-capturing probe.  rep1, replicate 1. rep2, replicate 2. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. To compare the distribution of Xist between WT and Smchd1-/-, we scaled the Xist coverage profiles of WT and Smchd1-/- based on the total number of Xmus reads minus the total number of Xcas reads (file names ending in '.scaled.bw').

source_name: neural progenitor cells

growth_protocol: ES cell-derived neural progenitor cell clones were cultured on poly-L-ornithine (0.001%) and laminin (1µg/ml) coated plates with N2 media (DMEM/F-12, GlutaMAX supplement, 1X N2 supplement, 1X B27 supplement, 1X Pen/Strep) supplemented with FGF2 (20ng/ml), EGF (20ng/ml), laminin (1µg/ml), and heparin (10µg/ml). Undifferentiated ES cells were grown on 0.2% gelatin-coated plates with N2B27 media (mixture of 500ml DMEM/F12 media, 500ml Neurobasal media, 5ml N2 supplement, 10ml B27 supplement, 10ml Pen/Strep, 5ml GlutaMAX, and 2ml 55mM β-mercaptoethanol) supplemented with 1µM PD0325901, 3µM CHIR-99021, and 1000U/ml LIF. Embryoid bodies (EBs) were grown with differentiation media (DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS, 25mM HEPES pH 7.2-7.5, 1X MEM non-essential amino acids, 1X Pen/Strep, 0.1mM β-mercaptoethanol) in suspension (D4 EBs) or on gelatin-coated plates (D7 EBs).

extract_protocol:
Total RNA was extracted using standard Trizol protocol. ChIP/CHART-enriched and input DNA were extracted with phenol:chloroform.
RNA-seq libraries were generated by dUTP-mediated directional RNA-seq based on NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: cell type

value: ESC-derived clonal neural progenitor cells


title: Hi-C WT clone 1 rep2

data_processing:
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file.
Genome_build: mm9
Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with '.summary.txt'), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5' end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5' end of read), and strand of read 2 (+ or -), respectively. WT1, WT clone 1. KO1, Smchd1-/- clone 1. rep1, replicate 1. rep2, replicate 2. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Two biological replicates were pooled and principle component analysis was performed on pooled Hi-C data at 200-kb resolution using HiTC. PC1 values were presented as bedGraph files (file names ending with '.PC1.bedGraph'). WT1, WT clone 1. KO1, Smchd1-/- clone 1. D0, undifferentiated ES cells. D4, day4 differentiated embryoid bodies. D7, day7 differentiated embryoid bodies. Xa, PC1 values derived from Xcas reads (WT1, KO1, D4, and D7) or all reads mapped to the X (D0). Xi, Xmus reads. To match sequencing depths, 50% reads from WT1 rep1 and KO1 rep1 Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files and PC1 profiles (file names starting with 'Downsampled'). We also reanalyzed published undifferentiated female ES cells Hi-C data (GSE72697: GSM1868575). Reads were aligned to the mm9 genome using bowtie2 and the PC1 values of the X chromosome at 200-kb resolution were similarly derived using total X chromosomal reads (Giorgetti.D0.HiC.Xa.comp.PC1.bedGraph). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 40-kb resolution as described (Giorgetti et al., 2016) and summarized in X_chromosome.insulation_score.txt.

value: WT


title: CHART-seq WT clone 1 input rep2


title: CHART-seq Smchd1-/- clone 1 sense control probes rep2


title: CHART-seq Smchd1-/- clone 1 Xist capture probes rep2


title: Hi-C Smchd1-/- clone 1 rep2


title: CHART-seq WT clone 1 sense control probes rep2


title: CHART-seq Smchd1-/- clone 1 Xist capture probes rep1


title: CHART-seq WT clone 1 Xist capture probes rep2


title: Hi-C WT clone 1 rep1


title: CHART-seq Smchd1-/- clone 1 sense control probes rep1


title: CHART-seq Smchd1-/- clone 1 input rep1


title: CHART-seq WT clone 1 sense control probes rep1


title: Delta phi9 phi10 8stop rep8


title: CHART-seq WT clone 1 input rep1


title: Delta phi9 phi10 evo rep10

value: delta phi9 phi10 evo


title: Hi-C Smchd1-/- clone 1 rep1


title: CHART-seq WT clone 1 Xist capture probes rep1


title: Delta phi9 phi10 evo rep9


title: ChIP-seq Smchd1-/- clone 1 RAD21 rep2

data_processing:
ChIP-seq: Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. H3K27me3 ChIP-seq tracks were further scaled by total reads mapped to the X chromosome.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT1, WT clone 1. KO1, Smchd1-/- clone 1. rep1, replicate 1. rep2, replicate 2. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. To compare the distribution of H3K27me3 marks between WT and Smchd1-/-, we scaled them based on the number of total uniquely mapped reads on the X chromosome (WT1.ChIP.H3K27me3.rep1.comp.scaled.bw  and KO1.ChIP.H3K27me3.rep1.comp.scaled.bw). Using chromatin signatures and expression profiles, we defined 6 classes of X-linked genes (X-linked.gene.classes.bed): silent genes (black), escapees (pink), Class I genes (red), Class II genes (orange), Class III genes (blue), and unclassified genes (gray). We also compiled a list of escapees reported in the literature (allreportedescapees.bed and all_reported_escapees.xlsx) to investigate the relationship between Class I genes and escapees. For CTCF and RAD21, we called peaks using MACS2, and merged the peaks called in WT and Smchd1-/- for analysis (CTCF.peaks.rep1.bed and RAD21.peaks.rep1.bed).

tag: antibodies

value: anti-RAD21 (Abcam ab992, lot:GR106791-9)


title: ChIP-seq Smchd1-/- clone 1 CTCF rep2

value: anti-CTCF (Cell Signaling, 2899S, lot:2)


title: ChIP-seq Smchd1-/- clone 1 H3K27me3 rep2


title: Delta phi9 phi10 8stop rep9


title: dis2_T316D_rep2

data_processing:
Library strategy: PRO-seq
PRO-seq: Adaptor sequences were clipped from read 3' ends.  In cases where inline barcodes were used, they were clipped from 5' ends.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
PRO-seq: Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
PRO-seq: Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Genome_build: PRO-seq: S. pombe: ASM294v2;  S. cerevisiae: S288C_reference_genome_R64-1-1_20110203.
Supplementary_files_format_and_content: PRO-seq: processed files are in bigwig format. There are two bigwig files for each sample, one for each strand. Each bigwig file contains normalized counts of read 3'-ends.

growth_protocol: PRO-seq, S. pombe cultures were grown in YES media from a starting OD600 of 0.2 to a final OD600 = 0.5.

extract_protocol:
PRO-seq: Immediately prior to treatments, a fixed amount of spike-in culture (i.e.  S. cerevisaie samples) was added to each sample culture for PRO-seq experiment.  After treatment, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol followed by ethanol precipitation. For
PRO-seq libraries were prepared according to Mahat et al. Nature Protocols (2016).

tag: temperature °c

tag: drug

value: PRO-seq (Nascent RNA)


title: Delta phi9 phi10 evo rep8


title: ChIP-seq Smchd1-/- clone 1 H3K4me3 rep2


title: dis2_T316D_rep1

tag: antibody

tag: assay


title: ChIP-seq Smchd1-/- clone 1 input rep2


title: Delta phi10 rep7

tag: strain

value: delta phi10


title: Delta phi9 phi10 rep7

value: delta phi9 phi10


title: ChIP-seq WT clone 1 RAD21 rep2


title: dis2_T316A_rep1


title: Delta phi9 rep7

value: delta phi9


title: dis2Del_rep2

source_name: dis2Del: h- ura4-D18 leu1-32 dis2::ura4+


title: ChIP-seq Smchd1-/- clone 1 RAD21 rep1


title: dis2Del_rep1


title: ChIP-seq WT clone 1 CTCF rep2


title: Delta phi9 8stop rep7

value: delta phi9 8stop


title: ChIP-seq WT clone 1 input rep2


title: dis2_T316A_rep2


title: Deop delta phi10 rep7

value: deoptimized

value: delta phi10, deoptimized gene 10


title: ChIP-seq Smchd1-/- clone 1 H3K27me3 rep1


title: ChIP-seq WT clone 1 H3K27me3 rep2


title: GM12878-DNA-SPRITE11

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM tag, and Read 2 has the remaining tags.
Processed data files:
human.mapq-ge10.clusters.gz
human.mapq-ge30.clusters.gz

data_processing:
Library strategy: DNA SPRITE
SPRITE barcodes were identified by parsing the first DNA tag sequence from the beginning of Read 1 (DPM) and the remainder of the tags were parsed from Read 2. We identified these tag sequences corresponding to the DPM, Odd, Even, and Terminal tags that were added to these samples. The tags and their sequences were identified by software available at: https://github.com/GuttmanLab/sprite-pipeline/wiki/1.-Barcode-Identification. The configuration files required for this software are available on the series record.
We aligned each read to the appropriate reference genome (mm9 for mouse; hg19 for human) using Bowtie2 (v2.3.1). We trimmed the 11 base pair tag sequence (DPM) from Read 1 using the --trim5 11 parameter and used a local alignment search (--local).
We filtered the alignments for low quality reads, multimappers, and repetitive sequences. First, we removed all alignments with a MAPQ score less than 10 or 30. Second, we removed all reads that had >2 mismatches to the reference genome. Third, we removed all alignments that overlapped a region that was masked by Repeatmasker (UCSC, milliDiv < 140) using bedtools (v2.26.0). Fourth, we removed any read that aligned to a non-unique region of the genome by excluding alignments mapping to regions generated by the ComputeGenomeMask program in the GATK package (readLength=35nt mask).
To define SPRITE clusters, all reads that have the same barcode sequence were grouped into a single cluster. To remove possible PCR duplicates, all reads starting at the same genomic position with identical barcodes were removed.
Genome_build: mm9 (mouse), hg19 (human)
Supplementary_files_format_and_content: Cluster files were generated for the F1-21 mES cell and GM12878 lymphoblast DNA-SPRITE samples for all reads with MAPQ scores greater than 10 or 30. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments. When multiple positions are listed, these regions are in physical contact with each other. If only one position is listed, either that fragment exists on its own as a singleton, or the other constituent pieces were not sequenced.

organism: Homo sapiens

source_name: B-lymphoblastoids

growth_protocol: Cell lines were cultured according to manufacturers instructions

extract_protocol: Cells were crosslinked with 3%FA-DSG and then lysed with nuclei isolated. DNA was then lightly sonicated and DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked protein-DNA complexes were isolated on NHS beads, DNA ends were repaired, dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. For DNA-RNA SPRITE, a distinct RNA adaptor was ligated to RNA to flag a molecule as RNA rather than DNA. This adaptor contains a shared overhang that allows for simultaneous tagging of RNA and DNA during the split-and-pool tagging process. Reverse transcription was performed to convert RNA into cDNA. After split-and-pool tagging, crosslinks were reversed, the DNA/RNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (single index), and purified using SPRI beads. Libraries were sequenced on the HiSeq2500 or NextSeq 500 following the manufacturer's protocols.

tag: cell line

tag: protocol

value: DNA SPRITE


title: Deop delta phi9 rep7

value: delta phi9, deoptimized gene 10


title: dis2_11_rep1


title: ChIP-seq Smchd1-/- clone 1 H3K4me3 rep1


title: WT_rep2

source_name: WT: h+ leu1-32 ura4-D18 his3-D1 ade6-M210


title: ChIP-seq WT clone 1 H3K4me3 rep2


title: ChIP-seq Smchd1-/- clone 1 input rep1


title: Delta phi9 phi10 8stop rep7

value: wild type

value: delta phi9 phi10 8stop

value: Escherichia coli


title: GM12878-DNA-SPRITE09


title: Deop rep7

value: deoptimized gene 10


title: ChIP-seq WT clone 1 RAD21 rep1

value: ESC-derived clonal neural progenitor cells

value: WT


title: ChIP-seq Smchd1-/- clone 1 CTCF rep1


title: WT rep7

value: wild type gene 10


title: dis2_11_rep2


title: WT_rep1


title: dis2cs_Myc_rep2

data_processing:
ChIP-seq: Paired-end sequencing (50-nt reads) was performed on an Illumina HiSeq 2000 (Genome Quebec Innovation Centre, McGill University).
ChIP-seq: Quality control and adapter trimming of the FASTQ (raw sequencing files) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.69) and trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.3) respectively.
ChIP-seq: After adaptor trimming and quality control, processed FASTQ files were aligned to the S. pombe genome using Bowtie2 (Galaxy Version 2.2.6.2).
ChIP-seq: Aligned sequences of each biological replicate were fed into MACS2 (Galaxy Version 2.1.1.20160309.0) to call peaks from alignment results. Generated “bedgraph treatment” files were converted into bigwig using “Wig/BedGraph-to-bigWig converter” (Galaxy Version 1.1.0), concatenated (Galaxy Version 1.0.1) to combine replicates of each sample, subtracted IgG reads from each and processed using computeMatrix (Galaxy Version 2.3.6.0) in DeepTools to prepare data for plotting a heatmap and/ or a profile of given regions.
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format. There are 26-bigWig files in total. 4 for pSpt5, 4 for Myc, 3 for IgG and 2 for Iuput for each strain (wt or dis2cs) including two biological replicates.

source_name: spt5-13myc::kanMX6 dis2-11 leu1-32 ura4-D18 his3-D1 ade6-M210 h+

growth_protocol: ChIP-seq: S. pombe cultures were grown in YES media till OD600 ~ 0.4.

extract_protocol:
ChIP-seq: After HCHO-crosslinking (15 min at 25°C) protein extract was prepared using Mini-beadbeater (Biospec; 30 sec "ON" and 30 sec "OFF"). Lysates were precleared with Protein A agarose beads and used for IP with respective antibodies.
ChIP-seq: Multiplexed ChIP-seq libraries were prepared using the Illumina TruSeq DNA Sample Preparation kit v2 with 75 ng of input or IP DNA and barcode adaptors.

tag: temperature c

value: Anti-Myc epitope (EMD Millipore, 05-724)

value: ChIP-seq


title: GM12878-DNA-SPRITE07


title: Delta phi10 rep6

value: delta phi10


title: GM12878-DNA-SPRITE08


title: GM12878-DNA-SPRITE06


title: Delta phi9 phi10 rep6

value: delta phi9 phi10


title: ChIP-seq WT clone 1 CTCF rep1

value: anti-CTCF (Cell Signaling, 2899S, lot:2)


title: ChIP-seq WT clone 1 H3K27me3 rep1


title: adult human hepatocytes biological rep1

type: RNA

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

description: Gene expression data from fresh hepatocytes isolated from adult human livers

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

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

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

label: biotin

source_name: Primary cells

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

growth_protocol: Cells were either freshly isolated as described by Cho JJ et al. Liver International 2004; 24:361-370.

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

treatment_protocol: Cells were not specifically treated.

tag: tissue

value: liver


title: GM12878-DNA-SPRITE05


title: dis2cs_pSpt5_rep2

value: Anti-pSpt5 antibody (custom made from 21st Century Biochemicals, Marlboro, MA; Sanso et al. 2012)


title: ChIP-seq WT clone 1 H3K4me3 rep1


title: adult human hepatocytes biological rep3


title: dis2cs_Myc_rep1


title: Delta phi9 rep6

value: delta phi9


title: adult human hepatocytes biological rep2


title: ChIP-seq WT clone 1 input rep1


title: GM12878-DNA-SPRITE04

value: DNA SPRITE


title: dis2cs_pSpt5_rep1


title: RNA-seq Smchd1-/- XO clone

data_processing:
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. rep1, replicate 1. rep2, replicate 2. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSE58524:GSM1412989 , dSP27b) in Pinter et al., 2015.


title: dis2cs_IgG_rep2

value: Rabbit-IgG antibody (Santa Cruz Biotechnology, sc-2027)


title: GM12878-DNA-SPRITE03


title: Delta phi9 phi10 8stop rep6

value: wild type


title: dis2cs_IgG_rep1


title: Delta phi9 8stop rep6

value: delta phi9 8stop


title: GM12878-DNA-SPRITE02


title: RNA-seq WT XO clone


title: Deop delta phi10 rep6

value: deoptimized

value: delta phi10, deoptimized gene 10

value: Escherichia coli


title: dis2cs_Input_rep2


title: K562i_CyrKD_3

city: Cambridge

first: David

middle: P

last: Bartel

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute / MIT

description:
21287287
DESeq2_CyrKD_K562i_smallRNA.txt

data_processing:
Reads were trimmed of adaptor sequence using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters "-q 30 -p 100" to ensure that all bases have an accuracy of 99.9%.
To count miRNAs in each library, the first 18 nts of each read were string-matched to a dictionary of miRNA sequences. Mouse and human dictionaries were based on annotations in miRbase_v20 and miRbase_v21, respectively. Matching to the first 18 nt had the advantage of combining all miRNA isoforms into a single count but also can result in ambiguous read assignments for mature miRNAs from distinct loci that are identical for the first 18 nt but differ at one or more positions closer to their 3′ ends (such as let-7a-5p and let-7c-5p). To avoid this ambiguity, these miRNAs (<5% of all annotations) were removed from the dictionary.
Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.10-v1.18 (Love et al, Genome Biol 2014) with the parameter “betaPrior = FALSE” and with no lfcShrink function.
Genome_build: miRbase_v20 (mouse) or miRbase_v21 (human)
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 v1.10-v1.18 contain normalized counts for each library, log2-fold changes, and p-values

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Small-RNA sequencing libraries were prepared as described (Fang and Bartel, 2015), except for size selection, which was for small RNAs from 18–32 nts (instead of 18–30 nts). A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA from K562i cells.

value: K562 expressing dCas9-KRAB

tag: treatment

value: CYRANO sgRNA

tag: rin


title: Deop delta phi9 rep6

value: delta phi9, deoptimized gene 10


title: K562i_CyrKD_2

description:
27129736
DESeq2_CyrKD_K562i_smallRNA.txt


title: dis2cs_Input_rep1

value: ChIP-seq


title: RNA-seq Smchd1-/- clone 2 rep2

value: ESC-derived clonal neural progenitor cells


title: K562i_CyrKD_1

description:
23640561
DESeq2_CyrKD_K562i_smallRNA.txt


title: wt_Myc_rep2

value: Anti-Myc epitope (EMD Millipore, 05-724)


title: WT rep6

value: wild type gene 10


title: K562i_ControlKD_3

description:
21659227
DESeq2_CyrKD_K562i_smallRNA.txt

value: control sgRNA


title: Deop rep6

value: deoptimized gene 10


title: Delta phi10 rep5

value: delta phi10


title: wt_Myc_rep1


title: wt_pSpt5_rep2

value: Anti-pSpt5 antibody (custom made from 21st Century Biochemicals, Marlboro, MA; Sanso et al. 2012)


title: RNA-seq WT clone 2 rep2

value: WT


title: RNA-seq Smchd1-/- clone 1 rep2


title: K562i_ControlKD_2

description:
25605912
DESeq2_CyrKD_K562i_smallRNA.txt


title: RNA-seq WT clone 1 rep2


title: Delta phi9 phi10 rep5

value: wild type

value: delta phi9 phi10


title: RNA-seq Smchd1-/- clone 2 rep1


title: K562i_ControlKD_1

description:
15504958
DESeq2_CyrKD_K562i_smallRNA.txt


title: wt_pSpt5_rep1


title: Delta phi9 rep5

value: delta phi9


title: M397_73d

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

data_processing:
Reads were mapped using TopHat2 v2.0.9 and aligned to the Homo sapiens genome NCBI build 37.2
Expected counts were normalized to FPKM values using Cufflinks v2.2.1  Cuffnorm program using the geometric library normalization method
Genome_build: Homo sapiens NCBI build 37.2
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

source_name: Melanoma

extract_protocol:
AllPrep DNA/RNA Mini kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: M397 melanoma cell line

value: vemurafenib, treated at 2X IC50 (264 nM)

tag: time


title: RNA-seq Smchd1-/- clone 1 rep1


title: M397_21d


title: mES-RNA-DNA-SPRITE02

description:
genomic DNA, nuclear RNA
SPRITE RNA-DNA maps were generated in the pSM33 ES cell line (provided by K. Plath), a male ES cell line derived from the V6.5 ES cell line, which expresses Xist from the endogenous locus under the transcriptional control of a tet-inducible promoter and the Tet transactivator (M2rtTA) from the Rosa26 locus. We induced Xist expression in these cells using doxycycline (Sigma, D9891) at a final concentration of 2 µg/mL for 6-24 hours.
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM or cDNA tag, and Read 2 has the remaining tags.
Processed data files:
RNA_DNA_20160604_5p2.mapq-ge10.clusters.gz
RNA_DNA_20160604_5p2.mapq-ge30.clusters.gz

data_processing:
Library strategy: DNA-RNA SPRITE
SPRITE barcodes were identified by parsing the first DNA tag sequence from the beginning of Read 1 (DPM) and the remainder of the tags were parsed from Read 2. We identified these tag sequences corresponding to the DPM, Odd, Even, and Terminal tags that were added to these samples. The tags and their sequences were identified by software available at: https://github.com/GuttmanLab/sprite-pipeline/wiki/1.-Barcode-Identification. The configuration files required for this software are available on the series record.
We aligned each read to the appropriate reference genome (mm9 for mouse; hg19 for human) using Bowtie2 (v2.3.1). We trimmed the 11 base pair tag sequence (DPM) from Read 1 using the --trim5 11 parameter and used a local alignment search (--local).
We filtered the alignments for low quality reads, multimappers, and repetitive sequences. First, we removed all alignments with a MAPQ score less than 10 or 30. Second, we removed all reads that had >2 mismatches to the reference genome. Third, we removed all alignments that overlapped a region that was masked by Repeatmasker (UCSC, milliDiv < 140) using bedtools (v2.26.0). Fourth, we removed any read that aligned to a non-unique region of the genome by excluding alignments mapping to regions generated by the ComputeGenomeMask program in the GATK package (readLength=35nt mask).
To define SPRITE clusters, all reads that have the same barcode sequence were grouped into a single cluster. To remove possible PCR duplicates, all reads starting at the same genomic position with identical barcodes were removed.
Genome_build: mm9 (mouse), hg19 (human)
Supplementary_files_format_and_content: Cluster files were generated for the F1-21 mES cell and GM12878 lymphoblast DNA-SPRITE samples for all reads with MAPQ scores greater than 10 or 30. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments. When multiple positions are listed, these regions are in physical contact with each other. If only one position is listed, either that fragment exists on its own as a singleton, or the other constituent pieces were not sequenced.

source_name: Mouse Embryonic Stem cells

growth_protocol: Mouse ES cell lines were cultured in serum-free 2i/LIF medium and maintained at an exponential growth phase

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: wt_IgG_rep1

value: Rabbit-IgG antibody (Santa Cruz Biotechnology, sc-2027)


title: RNA-seq WT clone 2 rep1


title: RNA-seq WT clone 1 rep1


title: wt_Input_rep2

value: ChIP-seq


title: wt_Input_rep1


title: Deop delta phi10 rep5

value: deoptimized

value: delta phi10, deoptimized gene 10

value: Escherichia coli


title: M397_3d


title: mES-DNA-SPRITE07

description:
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM tag, and Read 2 has the remaining tags.
Processed data files:
mouse.mapq-ge10.clusters.gz
mouse.mapq-ge30.clusters.gz

value: DNA SPRITE


title: Treated

description: Mice gavaged once and livers collected 2 hours following exposure. Five livers were pooled

data_processing:
MACS 2.1.0 was used for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of ChIP-seq tags

extract_protocol:
ChIP-seq analysis of NRF2 following 2 hrs TCDD exposure was performed using the FactorPath services by Active Motif (Carlsbad, CA) on ~100mg frozen liver sections. livers cut in small pieces were incubated in 1% formaldehyde for 15 min at room temperature. Cross-linking was halted by the addition of 0.125 M glycine and tissue was homogenized by Dounce homogenizer followed by shearing DNA by sonication to achieve an average length of 300 – 500 bp. A total of 30 μg of precleared sheared chromatin with protein A agarose beads was immunoprecipitated using 20 μL of rabbit anti-NRF2 polyclonal IgG (sc-13032; Santa Cruz, Dallas, TX) overnight at 4°C. Chromatin was eluted from the beads with SDS buffer and cross-links reversed by incubation with RNase and Proteinase K followed by an overnight incubation at 65°C.
Libraries for sequencing were prepared by Active Motif and sequenced using NextSeq 500 (1 x 75bp).

treatment_protocol: Male C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected 2 hours following treatment.

value: Liver

tag: Sex

value: Male

tag: age

tag: age unit

value: days

value: TCDD

tag: dose

tag: dose unit

value: ug/kg

tag: duration

tag: duration unit

value: hours

tag: replicate

tag: chip antibody

tag: antibody vendor

value: Santa Cruz


title: 41

tag: strain

value: Vehicle


title: Deop rep5

tag: genotype

value: deoptimized gene 10

tag: host


title: Deop delta phi9 rep5

value: delta phi9, deoptimized gene 10


title: M229_90d

tag: cell line

value: M229 melanoma cell line

value: vemurafenib, treated at 2X IC50 (564 nM)


title: M397_DMSO

value: M397 melanoma cell line

tag: treatment

value: DMSO

value: control


title: 30C_Cdk9as_dis2ts_3MBPP1_rep2

source_name: cdk9as dis2-11: cdk9T120G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210  dis2-11 h+

tag: temperature c

tag: drug (5 minutes)

tag: antibody

tag: assay

value: PRO-seq


title: 30C_Cdk9as_dis2ts_3MBPP1_rep1


title: Input

tag: tissue

tag: Sex

tag: age

tag: age unit

value: Input


title: M229_21d

tag: time


title: Untreated

value: Liver

value: Sesame Oil

tag: dose

tag: dose unit

tag: duration

tag: duration unit

tag: replicate


title: wt_IgG_rep2

value: Rabbit-IgG antibody (Santa Cruz Biotechnology, sc-2027)

value: ChIP-seq


title: Deop delta phi10 rep4

tag: strain

value: deoptimized

tag: genotype

value: delta phi10, deoptimized gene 10

tag: host

value: Escherichia coli


title: M397_11d

tag: cell line

tag: treatment

value: vemurafenib, treated at 2X IC50 (264 nM)


title: Delta phi9 8stop rep5

value: wild type

value: delta phi9 8stop


title: Delta phi9 phi10 8stop rep5

value: delta phi9 phi10 8stop


title: 30C_Cdk9as_dis2ts_DMSO_rep2

tag: temperature c

tag: drug (5 minutes)

tag: antibody


title: 30C_Cdk9as_dis2ts_DMSO_rep1

tag: assay


title: Deop delta phi9 rep4

value: delta phi9, deoptimized gene 10


title: M229_2mo

value: M229 melanoma cell line

value: vemurafenib, treated at 2X IC50 (564 nM)


title: 18C_Cdk9as_dis2ts_3MBPP1_rep2


title: M229_3d


title: WT rep5

value: wild type gene 10


title: Delta phi9 phi10 rep4

value: delta phi9 phi10


title: M229_DMSO

value: DMSO

value: control


title: Delta phi10 rep4

value: delta phi10


title: Detla phi9 rep4

value: delta phi9


title: 18C_Cdk9as_dis2ts_3MBPP1_rep1

value: PRO-seq


title: 18C_Cdk9as_dis2ts_DMSO_rep1


title: 18C_Cdk9as_dis2ts_DMSO_rep2


title: Delta phi9 phi10 8stop rep4


title: 30C_dis2ts_3MBPP1_rep1


title: 30C_dis2ts_3MBPP1_rep2


title: 30C_dis2ts_DMSO_rep2


title: Deop rep4

value: deoptimized

value: deoptimized gene 10


title: WT rep4

value: Escherichia coli


title: 18C_dis2ts_3MBPP1_rep2


title: Delta phi9 8stop rep4


title: Delta phi9 rep3


title: Delta phi9 phi10 rep3


title: iWT.D2.1o RA 1µM d3-6_2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: iWT.D2.1o RA 1ÂµM d3-6_2

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done using fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using STAR v2.4 to Human hg19 genome allowing 2 mismatches
Subsequently, conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (Li et al., 2009) (version 0.1.18) and HTSeq (Anders et al., 2015) (version 0.6.1p1).
Candidate genes were filtered to a minimum of  log2 fold change=0.5 and FDR-corrected p-value<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package Goseq_1.20.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files having raw count values or Candidate genes with stats value

source_name: cardiomyocytes

growth_protocol: Human iPSCs were maintained in feeder-free culture conditions with E8 medium on Geltrex-coated plates. Directed differentiation of iPSCs into ventricular iPSC-CMs was initiated at confluence of 90-100% via WNT signaling modulation with cardio differentiation medium (RPMI1640 HEPES Glutamax, 0.5mg/ml human recombinant albumin and 0.2mg/ml L-ascorbic acid 2-phosphate) and progressive treatment with 4µM CHIR99021 for 48h and 5µM IWP2 for further 48h. Medium was changed to cardio culture medium (RPMI1640 HEPES Glutamax, 10µl/ml B27) at d8. For atrial subtype directed differentiation 1µM retinoic acid was supplemented for 72h on d3 (after 72h) of differentiation. Metabolic cardiomyocytes selection was performed using cardio selection medium (RPMI 1640 minus Glucose, 0.5mg/ml human recombinant albumin and 0.2mg/ml L-ascorbic acid 2-phosphate, 4mM Lactate) for 5 days. Cardiomyocytes were cultured in cardio culture medium at least to d60 for further maturation.

extract_protocol:
Total RNA for experiments was isolated using the SV Total RNA Isolation System by Promega according to manufacturer’s instructions (Promega #Z3100).After immunopurification of the ribosome-associated RNAs, RNA quality was assessed on a Fragment analyzer and RNA amounts were quantified using the The RNA integrity value (RIN) of the samples were above 7.5
RNA-samples were prepared using "TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301, RS-122-2302, and RS-122-2303) according to the manufacturer's protocol (Illumina). Accurate quantitation of cDNA libraries was performed using the DeNovix QFX Fluorometer. Samples were sequenced using the HiSeq 2000 (Illumina) (SE, 50 bp)

tag: cell type

value: iPSC-derived cardiomyocytes

tag: cardiomyocyte type

value: atrial

tag: maturity


title: iBM76.3 RA 1µM d3-6_1

description: iBM76.3 RA 1ÂµM d3-6_1


title: iWT.D2.1o RA 1µM d3-6_1

description: iWT.D2.1o RA 1ÂµM d3-6_1


title: 30C_dis2ts_DMSO_rep1

data_processing:
PRO-seq: Adaptor sequences were clipped from read 3' ends.  In cases where inline barcodes were used, they were clipped from 5' ends.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
PRO-seq: Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
PRO-seq: Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
ChIP-seq: Paired-end sequencing (50-nt reads) was performed on an Illumina HiSeq 2000 (Genome Quebec Innovation Centre, McGill University).
ChIP-seq: After adaptor trimming and quality control, processed FASTQ files were aligned to the S. pombe genome using Bowtie2 (Galaxy Version 2.2.6.2).
ChIP-seq: Aligned sequences of each biological replicate were fed into MACS2 (Galaxy Version 2.1.1.20160309.0) to call peaks from alignment results. Generated “bedgraph treatment” files were concatenated (Galaxy Version 1.0.1) to combine replicates of each sample, converted into bigwig using “Wig/BedGraph-to-bigWig converter” (Galaxy Version 1.1.0) and processed using computeMatrix (Galaxy Version 2.3.6.0) in DeepTools to prepare data for plotting a heatmap and/ or a profile of given regions.
Genome_build: PRO-seq: S. pombe: ASM294v2;  S. cerevisiae: S288C_reference_genome_R64-1-1_20110203.
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Supplementary_files_format_and_content: PRO-seq: processed files are in bigwig format. There are two bigwig files for each sample, one for each strand. Each bigwig file contains normalized counts of read 3'-ends.
Supplementary_files_format_and_content: ChIP-seq: processed files are in bedraph format. There are 3 bedgraph files for each sample, two for biological replicates and one combined.


title: Delta phi9 phi19 8stop rep3

value: wild type

value: delta phi9 phi19 8stop


title: 18C_dis2ts_3MBPP1_rep1


title: 18C_dis2ts_DMSO_rep2


title: KO4

city: Leuven

first: Rik

last: Lories

address: O&N1 Herestraat 49

department: Skeletal Biology and Engineering Research Center

country: Belgium

institute: KU Leuven

description: gene expression data

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450¬† (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)

data_processing: Data were normalized using RMA and called using Mas5 as implemented in Bioconductor.  Data are presented as RMA logfold differences between ANP32A KO and wildtypes in the file normalized_data_with_statisics.xlsx.

source_name: dissected cartilage

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction.  Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: ex vivo mouse tissue analysis

extract_protocol: Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in Trizol. RNA was isolated using a manual phenol/chloroform extraction protocol.

treatment_protocol: tissue dissection immediately after sacrifice

tag: tissue

value: cartilage

value: ANP32A KO

tag: age

value: 8 weeks


title: 18C_dis2ts_DMSO_rep1


title: WT3

description: gene expression data

value: Wild-type


title: Delta phi9 8stop rep3

value: delta phi9 8stop


title: Delta phi10 rep3


title: KO1

description: gene expression data


title: isWT1.Bld2 RA 1µM d3-6_1

description: isWT1.Bld2 RA 1ÂµM d3-6_1


title: KO2

description: gene expression data


title: WT1

description: gene expression data


title: 18C_Cdk9as_3MBPP1_rep2

source_name: cdk9as: cdk9T120G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: iWT.D2.1o control_2

description: iWT.D2.1o control_2

value: ventricular


title: WT4

description: gene expression data


title: iBM76.3 control_2


title: WT2

description: gene expression data


title: KO3

description: gene expression data


title: WT rep3

value: wild type gene 10


title: iWT.D2.1o control_1

description: iWT.D2.1o control_1


title: Deop delta phi10 rep3

value: delta phi10, deoptimized gene 10


title: 18C_Cdk9as_3MBPP1_rep1


title: isWT1.Bld2 control_1

description: isWT1.Bld2 control_1


title: 18C_Cdk9as_DMSO_rep2

value: DMSO


title: Deop delta phi9 rep3

value: delta phi9, deoptimized gene 10


title: 18C_Cdk9as_DMSO_rep1

value: PRO-seq


title: Delta phi9 rep2

value: delta phi9


title: Delta phi9 phi10 rep2

value: delta phi9 phi10

value: Escherichia coli


title: Deop rep3

value: deoptimized

value: deoptimized gene 10


title: Deop delta phi10 rep2


title: Deop delta phi9 rep2


title: Delta phi9 phi10 8stop rep2

value: wild type

value: delta phi9 phi10 8stop


title: Delta phi10 rep 2

value: delta phi10


title: WT rep2


title: RNAseq_SCer_8603_Async_23C_rep2

city: New York City

first: Matthew

middle: R

last: Paul

address: 1230 York Ave

department: Bioinformatics Resource Center

institute: Rockefeller University

description:
2018_01_25_corrected_cpm.csv.gz
sample name in processed data file:
corrected_ycg1_23

data_processing:
RNA-seq mapping: Mapping was conducted using tophat version 2.1.0 to the SacCer3 genome and S. pombe ASM294v2. Mapping paraeters used are: --no-novel-juncs --library-type fr-firststrand. Reads with unique mapping to a organism were kept for further analysis.
RNA-seq counts and correction: Read counts per gene was calculated using featureCounts of the subread package version 1.4.6-p3. Parameters used are -s 2 -t CDS. Linear correction was used to corerect for differeces in spike-in data. To this end a linear curve was plotted between CPM for each gene between each spike-in S. pombe data set and the baseline (i.e. untreated wild-type cells). The slope of the curve was compared to the expected 1:1 ratio. The transformation required to move the spike-in data set on to the 1:1 line was then applied to the expeirmental S . cerevisiae dataset for the same comparison.
Genome_build: SacCer3 (S. cerevisiae) and  ASM294v2 (S. pombe)
Supplementary_files_format_and_content: RNA-seq corrected counts

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: 90% S. cerevisiae cells, 10% S.pombe cells

growth_protocol: Overnight cultures were prepared for cells. They were reseeded in the morning and grown to OD1.

extract_protocol:
RNA-seq: Cells were counted and 10% S. pombe cells were added. Total RNA was extracated with Qiagen Rneasy columns. mRNA was selected with oligo-dT bead. cDNA was prepared based on the incorporation of dUTPs using reverse transcription.
DNA was ligated to Illumina or home-made multiplexed adapters and amplified by PCR. For 3C-seq library DNA between 400-1Kb was gel purified. For ChIP Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Temperature-senstive strains were either shifted to 37C or maintained at 23C for 2 hrs.

value: 8603 - ycg1-2 strain

value: Growth at restrictive 37C


title: RNAseq_SCer_8603_Async_37C_rep2

description:
2018_01_25_corrected_cpm.csv.gz
sample name in processed data file:
corrected_ycg1_37

value: 90% S. cerevisiae cells, 10% S.pombe cells


title: RNAseq_SCer_12_Async_23C_8603control_rep2

description:
2018_01_25_corrected_cpm.csv.gz
sample name in processed data file:
corrected_wt_23

value: 12 - wild type strain

value: Growth at restrictive 23C


title: RNAseq_SCer_12_Async_37C_8603control_rep2

description:
2018_01_25_corrected_cpm.csv.gz
sample name in processed data file:
corrected_wt_37

value: Growth at permissive 23C


title: RNAseq_SCer_8603_Async_37C_rep1


title: Delta phi9 8stop rep2

data_processing:
alignment with hisat2
counting with bedtools multicov
computation of TPMs with R script
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded strains
Supplementary_files_format_and_content: tab-delimitted text file for each sample with four columns: strain, gene start position, gene stop position, gene name, T7 gene number, and TPM (transcripts per million)

value: delta phi9 8stop


title: Delta phi9 phi10 8stop rep1


title: Deop rep2


title: WT rep1

value: wild type gene 10


title: RNAseq_SCer_8603_Async_23C_rep1


title: RNAseq_SCer_12_Async_37C_8603control_rep1


title: Deta phi9 8stop rep1


title: RNAseq_SCer_12_Async_23C_8603control_rep1


title: Imatinib mesylate, replicate 3

status: Public on Jun 06 2018

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

data_processing:
Raw reads were converted to FASTQ files using Illumina CASAVA_v1.8.0, then Illumina adapters were trimmed and reads were QC-filtered with Trim galore software (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters except that stringency = 3 and error rate = 0.
Tophat v.2.0 (Trapnell et al. 2009)  with bowtie2 v.2.1  was used to map reads to the D. magna genome using the parameters described in Rozenberg et al. to account for the small intron size in Daphnia spp. (min_segment_intron =10; max_segment_intron = 5000, min_coverage_intron = 10; max_coverage_intron = 2000) (Rozenberg et al. 2015).
The Cufflinks v.2.2.1 suite (Trapnell et al. 2012) was then used to assemble transcripts and determine differentially expressed transcripts. First, aligned reads were assembled with cufflinks using default options, with a mask file consisting of D. magna rRNA sequences in fasta format and no GTF guide file.  Transcripts from all samples were merged into a single transcriptome using cuffmerge. Cuffquant was used to count transcripts abundances across the samples, and finally cuffdiff with bias correction and multi-read correction options was used to identify transcripts that were differentially expressed between each treatment and the corresponding control exposure. The default false discovery rate, set to 0.05, was used to determine differentially expressed transcripts.
Genome_build: The D. manga assembly v2.4 was downloaded from wfleabase.org
Supplementary_files_format_and_content: tab delimited GEO_cytotoxin_FPKM.txt provides a matrix table of the fragments per kilobase transcript per million reads (FPKM) for each transcript (isoform) in each replicate sample

organism: Daphnia magna

source_name: whole organism

growth_protocol: D. magna Straus was obtained from a laboratory culture originally purchased from Aquatic Research Organisms, Inc. (Hampton, NH, USA) and maintained according to U.S. EPA (USEPA 2002) at 24±1 °C with a 16:8 light-dark cycle.  D. magna were cultured in moderately hard fresh water according to ISO 10706, 2000. Organisms were fed with YCT mix (Yeast Saccharomyces cerevisiae, Cereal leaves, Trout chow) and the unicellular green alga Pseudokirchneriella subcapitata.

extract_protocol:
RNA was isolated according to the TriReagent manufacturer’s methods, then precipitated on an RNAeasy spin column and treated with DNAse I to remove potential contaminating gDNA (Qiagen).
cDNA libraries were constructed from 320 ng of total RNA using the Illumina TruSeq stranded mRNA kit (Illumina, San Diego, CA) with 12 different indices to label each of the samples.

treatment_protocol: Drug concentrations (Table 1) were chosen according to the genotoxic lowest observed adverse effective concentrations (LOAECs) equal to 10, 300, 2000 ng/L for CDDP, ETP, IMA respectively. These concentrations were selected because they are close to or within environmentally relevant concentrations and are also effective at causing molecular damage. Twenty to twenty-five daphnids were placed in 25 mL of the chemical exposure ISO media or non-exposed control ISO media for 24 h. Daphnids were not fed during the exposure and were held in same conditions as the stock cultures (e.g., 24±1 °C with a 16:8 light-dark cycle).

value: lab strain from  Aquatic Research Organisms

value: neonate

value: 2000 ng/L IMA


title: Cisplatinum, replicate 3

value: 10 ng/L for CDDP


title: control B, replicate 1


title: Cisplatinum, replicate 2


title: Cisplatinum, replicate 1


title: control B, replicate 3


title: Phlda2 TG E16.5 Hypothalamus, Biological Rep1

city: Cardiff

first: Rosalind

middle: M

last: John

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: 1-5 micro grams of good quality total RNA. Affymetrix genechip platform hybridication, washing and scanning of chip, along with QC of all samples and data on a CD-R.

data_processing: Data was initially analyzed at the genome wide level using the Bioconductor packages such as Limma (Linear Model for Microarray data Analysis) written in R statistical software to identify differentially expressed genes between all pair-wise comparisons of the groups.Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to generate molecular function and biological processes pathway data on the unselected dataset highlighting significant changes in genes.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Sigma GenElute™ Mammalian Total RNA Miniprep Kit.

value: Hypothalamus

tag: developmental stage

value: adult

tag: placenta genotype

value: Phlda2 TG


title: Phlda2 WT E16.5 Hippocampus, Biological Rep4

value: Hippocampus

value: Phlda2 WT


title: Phlda2 WT E16.5 Hypothalamus, Biological Rep4


title: Phlda2 TG E16.5 Hippocampus, Biological Rep3


title: Phlda2 WT E16.5 Hypothalamus, Biological Rep2


title: Phlda2 WT E16.5 Hypothalamus, Biological Rep1


title: Phlda2 KO E16.5 Hypothalamus, Biological Rep4

value: Phlda2 KO


title: Phlda2 WT E16.5 Hippocampus, Biological Rep2


title: Phlda2 TG E16.5 Hypothalamus, Biological Rep2


title: control B, replicate 2


title: Phlda2 WT E16.5 Hippocampus, Biological Rep3


title: Phlda2 WT E16.5 Hippocampus, Biological Rep1


title: Phlda2 TG E16.5 Hypothalamus, Biological Rep4


title: Phlda2 WT E16.5 Hypothalamus, Biological Rep3


title: Phlda2 KO E16.5 Hypothalamus, Biological Rep1


title: Phlda2 KO E16.5 Hypothalamus, Biological Rep3


title: Phlda2 TG E16.5 Hippocampus, Biological Rep4


title: Phlda2 KO E16.5 Hypothalamus, Biological Rep2


title: Phlda2 TG E16.5 Hippocampus, Biological Rep1


title: Phlda2 KO E16.5 Hippocampus, Biological Rep3


title: Phlda2 KO E16.5 Hippocampus, Biological Rep4


title: Phlda2 TG E16.5 Hippocampus, Biological Rep2


title: Phlda2 KO E16.5 Hippocampus, Biological Rep2


title: siLRP6-8-48h-rep2

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

country: France

institute: Institut Curie

hyb_protocol: Following fragmentation, 4,7µg of cDNA were hybridized for 16hr at 48°C onto Affymetrix Human Gene 2.1 array plate. Array plate was hybridized, washed and stained using an an Affymetrix Genetitan 4C device.

scan_protocol: Array plate was scannned using the Affymetrix Genetitan 4C device.

data_processing: Raw data were treated, controlled and normalized using Affymetrix Expression Console

source_name: 48h after LRP6#8 siRNA transfection

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Plus protocol from 100ng total RNA

growth_protocol: HCC38 cells were obtained from the American Type Culture Collection and authenticated in 2013 by short tandem repeat profiling. HCC38 cells were cultured in RPMI-1640 with Glutamax containing 10% FBS, 1.5g/L sodium bicarbonate, 10mM Hepes (Invitrogen) and 1mM sodium pyruvate. Antibiotics were added to the media (100U/mL penicillin and 100µg/mL streptomycin). Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit from Qiagen following the manufacturer recommendations.

treatment_protocol: Cells were transiently transfected with 20nM siRNA (Qiagen) using the LipofectamineTM RNAiMax reagent (Invitrogen). Total RNA was then extracted 24, 48 and 72 hours post-transfection.

value: triple negative breast cancer cell line HCC38

tag: disease state

value: human breast cancer

tag: transfection

value: LRP6#8 siRNA

tag: time


title: Phlda2 TG E16.5 Hypothalamus, Biological Rep3

tag: strain


title: siLRP6-8-48h-rep1

tag: cell line


title: siLRP6-8-72h-rep1

source_name: 72h after LRP6#8 siRNA transfection


title: siLRP6-8-72h-rep2


title: siLRP6-7-72h-rep2

source_name: 72h after LRP6#7 siRNA transfection

value: LRP6#7 siRNA


title: Phlda2 KO E16.5 Hippocampus, Biological Rep1


title: siLRP6-8-24h-rep2

source_name: 24h after LRP6#8 siRNA transfection


title: siLRP6-7-48h-rep2

source_name: 48h after LRP6#7 siRNA transfection


title: siLRP6-7-72h-rep1


title: siLRP5-4-72h-rep2

source_name: 72h after LRP5#4 siRNA transfection

value: LRP5#4 siRNA


title: Hei193-TEW10uM-24hr

city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

country: South Korea

institute: Pusan National University

description: Gene expression data from TEW7197 treated Hei193 cells. (10uM, 24hr)

hyb_protocol: Following fragmentation, 50-500 ng of cRNA were hybridized on Affymetrix GeneChip® Human Gene 2.0 ST Array X 4. GeneChips were washed and stained in the Genechip Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip® Command Console® Software (AGCC).

source_name: Hei193-TEW7197 10uM-24hr treatment

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

growth_protocol: HEI-193 cells were cultured in liquid DEME medium containing 10% FBS and 1% antibiotics.

extract_protocol: Total cellular RNA was extracted using the Qiagen (Hilden, Germany) RNA extraction kit.

treatment_protocol: For NF2 transfection, transfection was performed using Jetpei transfection agent (Polyplus New York, USA) for mammalian expression of NF2 vectors. And for TEW7197 treatment, TEW7197 (10 μΜ) was treated for 12 hr or 24 hr in SF condition.

value: human vestibular schwannoma cells


title: Hei193-NF2

description: Gene expression data from NF2 transfected Hei193 cells.

source_name: Hei193-NF2 transfection


title: Control cells expressing random RNA, biological rep 2

city: Montreal

first: Naghmeh

last: Nikpoor

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Gene expression data from flp-in HEK293 cells expressiong random RNA.

hyb_protocol: Labeled DNA was hybridized on Human Gene 2.0 ST (Affymetrix) and incubated at 45° in the GeneChip® Hybridyzation oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip® scanner 3000 (Affymetrix).

data_processing: We used flexArray 1.6.3 software package. Normalization were perfomed using Affymetrix Power Tools (APT) and RMA for ST which are implemented in FlexArray. Differential expression analysis was performed using SAM (Significance Analysis of Microarray) also implemented in FlexArray.

source_name: Flp-in HEK293 cells expressing random RNA

label_protocol: 5.5 μg of the cDNA was fragmented and labeled with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer's instruction (Affymetrix).

growth_protocol: Cells were grown in high glucose DMEM supplemented with 10% FBS, 2mM L-glutamine, 1% Pen-Strep, 100 μg/ml Zeocin (Life Technologies) and 15 μg/ml blasticidin. After transfection we replaced Zeocin with 50 μg/ml Hygromycin (Invitrogene).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA purification and DNase I digestion were performed using RNeasy Qiagen columns.

value: Flp-in HEK293


title: siLRP6-7-24h-rep2

source_name: 24h after LRP6#7 siRNA transfection


title: Hei193-TEW10uM-12hr

description: Gene expression data from TEW7197 treated Hei193 cells. (10uM, 12hr)

source_name: Hei193-TEW7197 10uM-12hr treatment


title: Control cells expressing random RNA, biological rep 3


title: Hei193-Control

description: Gene expression data from control Hei193 cells.


title: siLRP6-7-48h-rep1


title: siLRP6-8-24h-rep1


title: Cells expressing TDNC1, biological rep 1

description: Gene expression data from flp-in HEK293 cells stably overexpressiong TDNC1.

source_name: Flp-in HEK293 cells stably overexpressing TDNC1


title: siLRP6-7-24h-rep1


title: siLRP5-4-48h-rep2

source_name: 48h after LRP5#4 siRNA transfection


title: Myo 31

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Early Secretory

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: myometrium, Early Secretory Phase 31

label_protocol: According to Illumina protocol.

extract_protocol:
Permission to work with human tissue specimens was obtained from the Institutional Review Board (H-22119, Approved 5/27/2008). Flash frozen specimens of myometrium and leiomyoma were obtained from Gynecologic Tissue Biorepository at Baylor College of Medicine. All leiomyoma specimens were collected from tumors between 3 and 6 cm in largest transverse diameter at sites >1 cm deep to the pseudocapsule. Myometrial specimens were collected at least 1 cm from the nearest leiomyoma. Any specimens collected from women treated with oral contraceptives or medroxyprogesterone in the 4 months prior to surgery were excluded. Menstrual dating was performed using established histologic criteria to evaluate each patient’s endometrium using corresponding hysterectomy specimens. All histologic assessments were made by experienced board-certified anatomic pathologists (RM). Written informed consent was available for all specimens used.
Total RNA was isolated from flash-frozen tissue specimens using the mirVANA Kit (Ambion, Austin, TX). Transcriptional profiles were generated by the Genomics and Proteomics Core Laboratory at Texas Children's Hospital using Human WG-6 (v3) BeadChip (Illumina, San Diego, CA). Prior to profiling, RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

tag: phase

value: Early Secretory


title: siLRP5-4-72h-rep1


title: Myo 16

description: Early Secretory

source_name: myometrium, Early Secretory Phase 16


title: Myo 11

description: Early Secretory

source_name: leiomyoma, Early Secretory 11


title: Cells expressing TDNC1, biological rep 3


title: Cells expressing TDNC1, biological rep 2


title: Control cells expressing random RNA, biological rep 1


title: siLRP5-4-48h-rep1


title: Fib 31

description: Early Secretory

source_name: leiomyoma, Early Secretory 31


title: siLRP5-4-24h-rep2

source_name: 24h after LRP5#4 siRNA transfection


title: Myo 37

description: Late Secretory

source_name: myometrium, Late Secretory Phase 37

value: Late Secretory


title: siLRP5-2-48h-rep2

source_name: 48h after LRP5#2 siRNA transfection

value: LRP5#2 siRNA


title: siLRP5-2-72h-rep1

source_name: 72h after LRP5#2 siRNA transfection


title: siLRP5-2-48h-rep1


title: Fib 11

description: Early Secretory


title: Myo 32

description: Late Secretory

source_name: myometrium, Late Secretory Phase 32


title: Myo 14

description: Late Secretory

source_name: myometrium, Late Secretory Phase 14


title: sictrl-24h-rep1

source_name: 24h after control siRNA transfection

value: control siRNA


title: Fib 16

description: Early Secretory

source_name: leiomyoma, Early Secretory 16


title: Myo 36

description: Late Secretory

source_name: myometrium, Late Secretory Phase 36


title: Myo 33

description: Late Secretory

source_name: myometrium, Late Secretory Phase 33


title: 8-26-08 #1

description: Late Secretory

source_name: myometrium, Late Secretory Phase6-08 #1


title: sictrl-24h-rep2


title: sictrl-72h-rep2

source_name: 72h after control siRNA transfection


title: siLRP5-4-24h-rep1


title: sictrl-48h-rep2

source_name: 48h after control siRNA transfection


title: Myo 18

description: Late Secretory

source_name: myometrium, Late Secretory Phase 18


title: siLRP5-2-24h-rep1

source_name: 24h after LRP5#2 siRNA transfection


title: siLRP5-2-72h-rep2


title: Fib 36

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase 36


title: siLRP5-2-24h-rep2


title: sictrl-48h-rep1


title: 8-26-08 #2

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase6-08 #2


title: Fib 32

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase 32


title: Fib 33

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase 33


title: sictrl-72h-rep1


title: Imatinib mesylate, replicate 1

source_name: whole organism

value: lab strain from  Aquatic Research Organisms

value: neonate

tag: treatment

value: 2000 ng/L IMA


title: Etoposide, replicate 2

value: 300 ng/L ETP


title: Etoposide, replicate 3


title: Etoposide, replicate 1


title: Fib 18

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase 18


title: control A, replicate 2


title: control A, replicate 1


title: control A, replicate 3


title: Imatinib mesylate, replicate 2


title: La Sota [miRNA]

city: Yangling

first: Yanqing

last: Jia

state: Shaanxi

address: Xinong Road 22#

country: China

institute: Northwest A&F University

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 analyzed the length distribution, mapped to chicken reference genome (Gallus Gallus reference genome Galgal 4.73) using bowtie.
miRNAs were obtained after blast with miRBase, and novel miRNAs were analyzed using miREvo and mirdeep2.
To detect differentially expressed miRNA, the number of clean reads assigned known miRNA and novel miRNA was counted, and then normalized into the values of transcripts per million reads (TPM).
The differential expressions among groups were analysed using DEGseq. Corrected p-value (q-value) < 0.01 and |log2 (foldchange)| > 1 were set as the threshold parameters for significant differentially expressed miRNA.
Genome_build: ftp://ftp.ensembl.org/pub/release-76/fasta/gallus_gallus/dna/
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Gallus gallus

source_name: chicken embryo

extract_protocol:
Visceral tissue were obtained, flash frozen on dry ice, and RNA was extracted using Trizol reagent. NEB Next UltraTM RNA Library PrepKit for Illumina (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: visceral tissue

tag: development stage

value: chicken embryo

tag: agent

value: La Sota


title: Myo 35

description: Proliferative

source_name: myometrium, Proliferative Phase 35

value: Proliferative


title: Fib 37

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase 37


title: 10-15-08 #5

description: Proliferative

source_name: myometrium, Proliferative Phase15-08 #5


title: Fib14 reprep

description: Late Secretory

source_name: leiomyoma, Late Secretory Phase14 reprep


title: Control

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 to chicken reference genome (Gallus Gallus reference genome Galgal 4.73) using TopHat v2.0.12.
Duplicated reads were marked and the bam alignment results of each sample were sorted and reordered using picard-tools v1.96 and samtools v0.1.18.
To detect differentially expressed genes (DEGs), the number of clean reads assigned to a gene was counted using HTSeq v0.6.1, and then normalized into the values of fragments per kilobase of exon per million fragments mapped (FPKM).
The differential expressions among groups were analysed using DEGSeq R package (1.20.0). Corrected p-value (q-value) < 0.005 and |log2 (foldchange)| > 1 were set as the threshold parameters for significant DEGs.
Genome_build: ftp://ftp.ensembl.org/pub/release-81/fasta/gallus_gallus/dna/Gallus_gallus.Galgal4.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: Control


title: F48E9


title: F48E9 [miRNA]


title: Myo 3

description: Proliferative

source_name: myometrium, Proliferative Phase 3


title: MYO #1 10-3-08

description: Proliferative

source_name: myometrium, Proliferative Phase #1 10-3-08


title: Control [miRNA]


title: Myo 17

description: Proliferative

source_name: myometrium, Proliferative Phase 17


title: Myo 22

description: Proliferative

source_name: myometrium, Proliferative Phase 22


title: La Sota


title: Myo 34

description: Proliferative

source_name: myometrium, Proliferative Phase 34


title: Myo 2

description: Proliferative

source_name: myometrium, Proliferative Phase 2


title: Fib 35

description: Proliferative

source_name: leiomyoma, Proliferative Phase 35


title: Fib 34

description: Proliferative

source_name: leiomyoma, Proliferative Phase 34


title: 10-15-08 #3

description: Proliferative

source_name: leiomyoma, Proliferative Phase15-08 #3


title: FIB #2 10-3-08

description: Proliferative

source_name: leiomyoma, Proliferative Phase #2 10-3-08


title: Fib 3

description: Proliferative

source_name: leiomyoma, Proliferative Phase 3


title: Myo 1

description: Proliferative

source_name: myometrium, Proliferative Phase 1


title: Fib 1

description: Proliferative

source_name: leiomyoma, Proliferative Phase 1


title: Fib 17

description: Proliferative

source_name: leiomyoma, Proliferative Phase 17


title: Fib 22

description: Proliferative

source_name: leiomyoma, Proliferative Phase 22


title: Fib 2

description: Proliferative

source_name: leiomyoma, Proliferative Phase 2


title: OGT_SCKO 1

city: st. Louis

first: sungsu

last: kim

address: 600 S. euclid ave

institute: washington university

description: gene expression

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications. Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies)

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). Raw data was quantile normalized and log2 signal intensities reported.

source_name: OGT_SCKO 1

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Quaigen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer

extract_protocol: Total RNA was isolated from sciatic nerves of control and OGT-KO mice using Trizol (Invitrogen).Both control and KO mice are on a C56 BL6 background.

value: sciatic nerves

value: C56 BL6


title: Q398

first: Kinji

last: Asahina

address: 1333 San Pablo Street

department: Pathology

institute: University of Southern California

hyb_protocol: Following fragmentation, 3.75 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array in the GeneChip Hybridization Oven 640. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymerix GeneArray® Scanner.

data_processing: The data were normalized by RMA algorithm with Partek Genomics Suite software.

source_name: ALCAM+ ITGA8+ cells

label_protocol: Biotinylated probes were synthesized from 20 ng total RNA using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen).

extract_protocol: Total RNA was extracted with RNAqueous Micro (Ambion).

value: E12.5 embryonic mouse liver

tag: genotype

value: wild type

value: E12.5 embryo


title: OGT_SCKO 2

description: gene expression

source_name: OGT_SCKO 2


title: OGT_SCKO 3

description: gene expression

source_name: OGT_SCKO 3


title: Ctrl 1

description: gene expression

source_name: Ctrl 1


title: Q399

source_name: ALCAM+ ITGA8- cells


title: Ctrl 3

description: gene expression

source_name: Ctrl 3


title: Q401

source_name: ALCAM+ PDPN- cells


title: Ctrl 2

description: gene expression

source_name: Ctrl 2


title: Q400

source_name: ALCAM+ PDPN+ cells


title: M993

source_name: Liver cells


title: O829

source_name: ALCAM+ cells


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 6 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: BCpcEMT primary culture of human BC epithelial cells

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Respective untreated cell lines, were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: Healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures, were collected after 24 hours post treatments with 9Gy and 23Gy of ionizing radiation (IR) doses.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast

source_name: BCpcEMT

tag: reference

value: BCpcEMT breast cancer primary cell line no exposed to IR tratments


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

source_name: BCpc7 primary culture of human BC epithelial cells

value: BCpc7 breast cancer primary cell line no exposed to IR tratments


title: BCpcEMT primary BC cells treated with 23 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: BCpc7 primary BC cells treated with 23 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: Normal_9124

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Copy number values are estimated total copy number (e.g. 2~wild-type). Additional analysis details are as follows: "We fit a linear model to the normalized intensities stratified by the diallic genotype call. The intercept and slope from the linear model are both SNP- and batch-specific. Raw total copy number were estimated using crlmm package in Bioconductor (R 3.0., Bioconductor 2.12), using the default settings. At allele k, marker i, sample j, and batch p, the estimate of allelespecific copy number is computed by subtracting the estimated background from the normalized intensity and scaling by the slope coefficient.

source_name: Normal sample from prostate cancer patient 9124

label_protocol: According to Affymetix protocol.

growth_protocol: Tissue samples were obtained from the Human Tissue Acquisition and Pathology Core of the Dan L. Duncan Cancer Center and were collected from fresh radical prostatectomy specimens after obtaining informed consent under an Institutional Review Board approved protocol. Cancer tissues include at least 70% tumor tissue and benign tissues were free of cancer on pathological examination.

extract_protocol: DNAs extracted using a Qiagen DNA/RNA mini kit following the manufacturer’s protocol.

tag: subject status

value: prostate cancer patient

tag: subject id

value: patient 9124

tag: ethnic background

value: African American (AA)

tag: tissue type

value: normal; matched benign prostate tissue


title: Normal_9090

source_name: Normal sample from prostate cancer patient 9090

value: patient 9090


title: Cancer_9124

source_name: Cancer sample from prostate cancer patient 9124

value: highly tumor-enriched primary prostate cancer (PCa)


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

source_name: HMEC primary culture of normal human mammary epithelial cells

source_name: HMEC

value: HMEC primary culture of normal human mammary epithelial cell line no exposed to IR tratments


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: Cancer_9061

source_name: Cancer sample from prostate cancer patient 9061

value: patient 9061


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: Cancer_9045

source_name: Cancer sample from prostate cancer patient 9045

value: patient 9045


title: Cancer_9090

source_name: Cancer sample from prostate cancer patient 9090


title: Cancer_8869

source_name: Cancer sample from prostate cancer patient 8869

value: patient 8869


title: Normal_9061

source_name: Normal sample from prostate cancer patient 9061


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: Cancer_8941

source_name: Cancer sample from prostate cancer patient 8941

value: patient 8941


title: Normal_8867

source_name: Normal sample from prostate cancer patient 8867

value: patient 8867


title: Normal_8941

source_name: Normal sample from prostate cancer patient 8941


title: Cancer_8867

source_name: Cancer sample from prostate cancer patient 8867


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

source_name: BCpcEMT primary culture of human BC epithelial cells

growth_protocol: Non tumorigenic (MCF10A) and tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines; and healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures, were collected after 24 hours post treatments.

value: BCpcEMT

value: 9 Gy of IR

value: no exposure to IR treatments


title: Cancer_9014

source_name: Cancer sample from prostate cancer patient 9014

value: patient 9014


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6

value: 24 hours

value: breast

source_name: BCpcEMT


title: Normal_9014

source_name: Normal sample from prostate cancer patient 9014

value: prostate cancer patient


title: Normal_8367

source_name: Normal sample from prostate cancer patient 8367

value: patient 8367

value: African American (AA)


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: Normal_8869

source_name: Normal sample from prostate cancer patient 8869

value: normal; matched benign prostate tissue


title: Cancer_8686

source_name: Cancer sample from prostate cancer patient 8686

value: patient 8686

value: highly tumor-enriched primary prostate cancer (PCa)


title: Normal_9045

source_name: Normal sample from prostate cancer patient 9045


title: Cancer_8418

source_name: Cancer sample from prostate cancer patient 8418

value: patient 8418


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: Normal_8418

source_name: Normal sample from prostate cancer patient 8418


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6

source_name: BCpc7 primary culture of human BC epithelial cells


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: HMEC primary healthy cells treated with 23 Gy of IR dose - replicate2

description: Biological replicate 2 of 6

source_name: HMEC primary culture of normal human mammary epithelial cells

source_name: HMEC

value: HMEC primary culture of normal human mammary epithelial cell line no exposed to IR tratments


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: Cancer_8343

source_name: Cancer sample from prostate cancer patient 8343

value: patient 8343


title: Normal_8686

source_name: Normal sample from prostate cancer patient 8686


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: Normal_8343

source_name: Normal sample from prostate cancer patient 8343


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

value: HMEC


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: BCpcEMT primary BC cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: HMEC primary healthy cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: Normal_8326

source_name: Normal sample from prostate cancer patient 8326

value: patient 8326


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6

source_name: Human breast cancer MCF7 cell line


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: MCF7 tumorigenic BC cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6

source_name: Human non-tumorigenic breast epithelial MCF10A cell line


title: Cancer_8305

source_name: Cancer sample from prostate cancer patient 8305

value: patient 8305


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6

value: 9 Gy of IR


title: BCpc7 primary BC cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

value: no exposure to IR treatments


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: Normal_8305

source_name: Normal sample from prostate cancer patient 8305


title: Cancer_7695

source_name: Cancer sample from prostate cancer patient 7695

value: patient 7695


title: MCF10A non tumorigenic cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6

value: 24 hours


title: RGCs overexpressing mCherry-5

city: Palo Alto

first: Jeffrey

middle: L

last: Goldberg

address: 2452 Watson Ct

institute: Stanford University

hyb_protocol: not provided

scan_protocol: Scanning was performed on a GeneChip® Scanner

data_processing: .CEL files were normalized using Genespring GX 12 software

organism: Rattus norvegicus

source_name: RGCs overexpressing mCherry-5

label_protocol: Biotin

growth_protocol: P4 retinal ganglion cells were purified and transduced with lentivirus.

extract_protocol: Total RNA was extracted using RNEase (Qiagen), following the manufacturer's standard protocol.

treatment_protocol: For microarray analysis of RGCs, the open reading flames of KLF9, -16, -7 and -11 were cloned from plasmids obtained from Open Biosystems. All 4 KLFs and FLAG-tagged mCherry were cloned into pLenti-MP2 expression vector.

tag: cell type

value: retinal ganglion cells (RGC)


title: RGCs overexpressing mCherry-6

source_name: RGCs overexpressing mCherry-6


title: Normal_7695

source_name: Normal sample from prostate cancer patient 7695

value: prostate cancer patient


title: Cancer_8367

source_name: Cancer sample from prostate cancer patient 8367

value: patient 8367


title: RGCs overexpressing mCherry-4

source_name: RGCs overexpressing mCherry-4


title: Cancer_7653

source_name: Cancer sample from prostate cancer patient 7653

value: patient 7653

value: African American (AA)


title: Cancer_8220

source_name: Cancer sample from prostate cancer patient 8220

value: patient 8220


title: Yellow Fever

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq v2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using tophat-2.0.11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel include RPKM values for each Sample

source_name: Germ Cells

extract_protocol:
Cells were lysed using the RNAeasy mini kit from Qiagen and purified
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary Testicular Germ Cells


title: Normal_7599

source_name: Normal sample from prostate cancer patient 7599

value: patient 7599

value: normal; matched benign prostate tissue


title: Cancer_7546

source_name: Cancer sample from prostate cancer patient 7546

value: patient 7546

value: highly tumor-enriched primary prostate cancer (PCa)