title: Endothelial cells 1 cell narrow TE1N

description:
gene_counts.csv
mature_miRNA_counts.csv

source_name: TW1 hES cells

value: ES-derived endothelial cells


title: F15B1_1NP

status: Public on Mar 08 2017

type: SRA

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: library strategy: DNA-seq

library_source: genomic

data_processing:
Basecalls were made using RTA version 1.17.21.3, with default filter and quality settings. The reads were demultiplexed (allowing 0 or 1 mismatches in the index sequence) with CASAVA 1.8.2
Reads were mapped to the mm9 genome assembly using bowtie v2.0.5 with all default settings. Non-unique reads or reads with low mapping quality were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command.
Samples were checked for contamination using fastq_screen v0.4.2. Samples with <15% of reads mapped or with more than 20% of reads mapped to the Human hg19 reference were excluded from further processing (but are included in this submission).
Coverage depth of each sample in 30kb windows was calculated using bedtools v2.17 and the command “multiBamCov -bed <(bedtools makewindows -w 30000 -g mm9.chrom.sizes)”. Each 30kb window was then called as positive or negative using a custom python script.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix files (ending .txt.gz) are tab-delimited tables containing one row/column per genomic locus, where the score in each cell of the matrix indicates the strength of the interaction between the corresponding two genomic loci. Segmentation files contain one row for every genomic locus, and one column for every raw data file which passed QC parameters, with the values representing the segmentation score for each sample at that genomic location.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse ES Cells

growth_protocol: Cells were grown at 37°C in a 5% CO2 incubator in Glasgow Modified Eagles Medium, supplemented with 10% fetal bovine serum, 2 ng/ml LIF and 1 mM 2-mercaptoethanol, on 0.1% gelatin-coated dishes. Cells were passaged every other day. After the last passage 24h before harvesting, ES cells were re-plated in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.)

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10

tag: cell type

tag: strain


title: 293FT 100 cells high 293FTH

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

description:
gene_counts.csv
mature_miRNA_counts.csv
MIR_differential_expression_PSCvs293.csv
protein_coding_differential_expression_PSCvs293.csv

library_source: transcriptomic

data_processing:
The raw sequencing data were processed through FASTQ Groomer using the basic options on the Galaxy website (Blankenberg et al., 2010). Reads with more than 8 As at the 3’ ends were selected for further analyses, and the A tails were clipped away using FASTQ/A Clipper (Patel and Jain, 2012). The filtered reads were aligned to human genome assembly version GRCh38 using STAR aligner (Dobin et al., 2013) with the following parameters:  --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterMatchNminOverLread 0.95 --outFilterType BySJout --outFilterMatchNmin 18. The aligned reads were assigned to the GENCODE v22 features and counted with Bedtools (Quinlan and Hall, 2010) while the strandedness was taken into account.
The mature-miRNA reads were defined by those only alingned to mature miRNA but not to primary miRNA transcripts of hsa.gff3 in miRBase 21.
The differential expression was performed with DESeq package for genes with read sums >1 across samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts.csv read counts by gene_id
Supplementary_files_format_and_content: mature_miRNA_counts.csv read counts by accession # of miRNA
Supplementary_files_format_and_content: MIR_differential_expression_PSCvsEND.csv differential expression by DESeq2
Supplementary_files_format_and_content: MIR_differential_expression_PSCvs293.csv differential expression by DESeq2
Supplementary_files_format_and_content: protein_coding_differential_expression_PSCvs293.csv differential expression by DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: 293FT cells

extract_protocol:
The cells were either diluted into phosphate buffer saline (PBS) with 0.1% polyvinyl alcohol (PVA) before lysis or sorted directly into a lysis buffer .
After incubation at 37°C for 30 minutes and inactivating proteinase K, the lysate was polyadenylated in a final 4 µl of 1X PAP mixture (37°C for 15 minutes, 45°C for 5 minutes, 55°C for 5 minutes, and 65°C for 20 minutes). After supplementing 0.5 µl of 20 µM i7T20V oligo, the reaction was heated at 75°C for 1 minute and cooled back to 42°C. 5.5 µl of RT mixture were added to final 1X, and then the mixture was incubated at 42°C for 90 minutes and 70°C for 15 minutes. If further preamplification was required, the cDNA was added to 40 µl of preamplification mixture. The thermal cycling were performed with initial denaturation at 98°C for 1 minute followed by cycles at 98°C for 10 seconds, 65°C for 15 seconds, and 72°C for 1 minute, with a final extension at 72°C for 10 minutes.   The cDNA from RT reaction/preamplification, or eluted DNA from size selection was concentrated with carboxylated beads and PEG/NaCl (Rohland and Reich, 2012). Briefly, 1 µl of magnetic beads and 3 volumes of PEG/NaCl solution were mixed with the solution containing DNA. The mixtures were left at ambient temperature for 15 minutes. After being washed two times with freshly prepared 80% ethanol, the beads were dried at ambient temperature for 15 minutes on a magnetic stand and eluted with 0.1% Triton X-100 for another 15 minutes at ambient temperature.  After preamplification and concentration with PEG/NaCl, the cDNA was run in 6% denaturing PAGE and stained in a 1X TBE buffer containing 1X SYBR GOLD for 20 minutes. After visualization and size-selection, the gel pieces were crushed by spun through a 0.5 ml microtube with a pinhole at the bottom and soaked in 300 µl of 10 mM Tris 8.0, 300 mM NaCl, and 1 mM EDTA at ambient temperature overnight. After concentration with PEG/NaCl, the eluted cDNA was appended with P5 and P7 adapters by 10 cycles of PCR with KAPAHiFi DNA polymerase (conditions identical to preamplification, except P5PCRIIA and N7xx were used as primers). After another round of PEG/NaCl to remove primers, equal amounts of the indexed libraries were mixed for sequencing with the Illumina Hiseq 2500 system.

value: human embyronic kidney cells


title: Endothelial cells 10 cells narrow TE10N

description:
gene_counts.csv
mature_miRNA_counts.csv


title: Endothelial cells 10 cells wide CE10W

description:
gene_counts.csv
mature_miRNA_counts.csv

source_name: Ch8 hES cells


title: F15A8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: Endothelial cells 100 cells wide CE100W

description:
gene_counts.csv
mature_miRNA_counts.csv
MIR_differential_expression_PSCvsEND.csv


title: F15A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: F15B7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: F15A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: F15A7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: Control

city: Shanghai

first: Ji-hang

last: Yuan

address: 800 Xiangyin Road

department: Department of Medical  Genetics

country: China

institute: Naval medical university

data_processing:
The samples were paired-end sequenced with a read length of 100 bp on an Illumina HiSeq 2500 sequencer.
Sequencing reads were mapped against the human reference genome version 19 using the TopHat algorithm version 2.0.9.
After alignment to the genome, the expression level of genes was determined based on the value of FPKM which was calculated by cuffdiff (version: 2.1.1).
Genome_build: human reference genome version 19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values and counts for each Sample.

source_name: Control

extract_protocol:
Total RNA was harvested from the cells using Trizol reagent. TruSeq Stranded Total RNA Library Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SMMC-7721 cells were stably transfected with MBNL3 shRNA expression vector or control.

tag: cell line

value: HCC cells SMMC-7721

tag: genotype/variation

value: Control


title: Endothelial cells 100 cells narrow CE100N


title: Endothelial cells 100 cells narrow TE100N


title: F15A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: F15A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: PSC 10 cells narrow TP10N

description:
gene_counts.csv
mature_miRNA_counts.csv

value: embryonic stem  cells


title: PSC 100 cells wide CP100W

description:
gene_counts.csv
mature_miRNA_counts.csv
MIR_differential_expression_PSCvsEND.csv
MIR_differential_expression_PSCvs293.csv
protein_coding_differential_expression_PSCvs293.csv


title: PSC 100 cells narrow CP100N


title: F12G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 9


title: PSC 100 cells narrow TP100N


title: F12G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 9


title: TGF-b treatment8

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

country: USA

institute: Augusta University

data_processing:
Alignment using SHRiMP version 2.2.3
Differential gene expression analysis was performed using cufflinks version 2.02 (cuffdiff2, run cuffdiff) with an FDR cutoff of 0.05 (95% confidence interval)
Genome_build: NCBI build 37.2
Supplementary_files_format_and_content: Tab delimited .txt file with RPKM for each sample.

molecule: polyA RNA

source_name: human coronary artery smooth muscle cells (HCASM)

extract_protocol:
miR-easy kit extracted RNA (0.5 ug) was submitted for RNA-seq
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols

tag: cell isolate

value: Human coronary VSMC (Jane isolate)

tag: passage

value: less than passage 8

tag: treatment

value: 2ng/ml  TGFbeta treatment for 24 hrs


title: F12G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 9


title: TGF-b treatment6


title: F15A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 10


title: PSC 1 cell narrow TP1N

description:
gene_counts.csv
mature_miRNA_counts.csv


title: F12F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: F12F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: F12G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 9


title: vehicle control5

value: Vehicle Control


title: F12F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: vehicle control7


title: Ldlr-Mc4r_semi_wt-ko_2

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

data_processing:
reads were mapped using Tophat 2.0.6 and Bowtie2
alignment was filterd for mapping quality (samtools view -q 255) and all reads mapping to the mitochondrial genome were removed
readcounts were retrieved using BEDtools intersectBED
differential gene expression analysis was performed using the R-package Deseq
Genome_build: mm9
Supplementary_files_format_and_content: read counts are provided as matrix for all samples in a space delimited text file

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions

tag: age

value: 6 months

tag: tissue

value: Liver

tag: diet

value: semisynthetic diet


title: 293T 100 cells middle 293TM

source_name: 293T cells

extract_protocol:
The cells were either diluted into phosphate buffer saline (PBS) with 0.1% polyvinyl alcohol (PVA) before lysis or sorted directly into a lysis buffer .
After incubation at 37°C for 30 minutes and inactivating proteinase K, the lysate was polyadenylated in a final 4 µl of 1X PAP mixture (37°C for 15 minutes, 45°C for 5 minutes, 55°C for 5 minutes, and 65°C for 20 minutes). After supplementing 0.5 µl of 20 µM i7T20V oligo, the reaction was heated at 75°C for 1 minute and cooled back to 42°C. 5.5 µl of RT mixture were added to final 1X, and then the mixture was incubated at 42°C for 90 minutes and 70°C for 15 minutes. If further preamplification was required, the cDNA was added to 40 µl of preamplification mixture. The thermal cycling were performed with initial denaturation at 98°C for 1 minute followed by cycles at 98°C for 10 seconds, 65°C for 15 seconds, and 72°C for 1 minute, with a final extension at 72°C for 10 minutes.   The cDNA from RT reaction/preamplification, or eluted DNA from size selection was concentrated with carboxylated beads and PEG/NaCl (Rohland and Reich, 2012). Briefly, 1 µl of magnetic beads and 3 volumes of PEG/NaCl solution were mixed with the solution containing DNA. The mixtures were left at ambient temperature for 15 minutes. After being washed two times with freshly prepared 80% ethanol, the beads were dried at ambient temperature for 15 minutes on a magnetic stand and eluted with 0.1% Triton X-100 for another 15 minutes at ambient temperature.  After preamplification and concentration with PEG/NaCl, the cDNA was run in 6% denaturing PAGE and stained in a 1X TBE buffer containing 1X SYBR GOLD for 20 minutes. After visualization and size-selection, the gel pieces were crushed by spun through a 0.5 ml microtube with a pinhole at the bottom and soaked in 300 µl of 10 mM Tris 8.0, 300 mM NaCl, and 1 mM EDTA at ambient temperature overnight. After concentration with PEG/NaCl, the eluted cDNA was appended with P5 and P7 adapters by 10 cycles of PCR with KAPAHiFi DNA polymerase (conditions identical to preamplification, except P5PCRIIA and N7xx were used as primers). After another round of PEG/NaCl to remove primers, equal amounts of the indexed libraries were mixed for sequencing with the Illumina Hiseq 2500 system.


title: F12F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: F12G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 9


title: PSC 10 cells wide CP10W

description:
gene_counts.csv
mature_miRNA_counts.csv


title: F12F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: I2_HFF_BGT

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: HELP-GT
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software.
Genome_build: hg19
Supplementary_files_format_and_content: A bedgraph of angle values was generated for each sample.

growth_protocol: HFFs were grown to confluency prior to infection using DMEM supplemented with 10% FBS, 1% penicilin streptomycin and 1% L-glutamine.

extract_protocol:
Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight.  The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours.  The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry.
Two custom adapters were created for HELP-GT, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  500 nanograms of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).

treatment_protocol: Cells were infected with T. gondii and harvested 24 hours after the infection for DNA extraction.

value: hff

tag: infection status

value: T. gondii infected


title: U3_HFF_BGT

value: Uninfected


title: I1_HFF_BGT


title: I3_HFF_BGT


title: F12F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 9


title: F12E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: U2_HFF_BGT


title: F12E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: F12E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: F12E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: F12E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: MspI_referenceI_HFF

data_processing:
Library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software.
Genome_build: hg19
Supplementary_files_format_and_content: A bedgraph of angle values was generated for each sample.

extract_protocol:
Genomic DNA was extracted by resuspending the cells in lysis buffer (10 mM TE, 150 mM EDTA and 1% SDS) supplemented with 10 mg/ml of RNase A and 20 mg/ml of Proteinase K, and incubated at 50 °C overnight.  The lysed cells were phenol-chloroform extracted and the resultant DNA was dialyzed in 0.2X SSC buffer (300 mM NaCl and 3 mM Na3C6H5O7, ph 7.0) for 24 hours.  The DNA sample was concentrated in the dialysis bags using polyethylene glycol, following which the quality and concentration of the DNA were measured by Nanodrop spectrophotometry.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  500 ng of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 500 ng of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).


title: I3_HFF_HELP


title: F12D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: I2_HFF_HELP


title: I1_HFF_HELP


title: U3_HFF_HELP


title: F12D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: F12D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: U2_HFF_HELP


title: F12D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: I2_HFF_ATAC

description: Transposase accessible chromatin

data_processing:
Library strategy: ATAC-seq
The fastq files were aligned using bwa-mem
Genome_build: hg19-TgME49v9.0
Supplementary_files_format_and_content: A bed file of peaks for each sample. See Supplemental materials from publication for more details.

extract_protocol:
Each sample was prepared as previously described in Buenrostro J.D. Nature Methods 2013
Each sample was prepared as previously described in Buenrostro J.D. Nature Methods 2013


title: U1_HFF_HELP


title: I3_HFF_ATAC

description: Transposase accessible chromatin


title: I1_HFF_ATAC

description: Transposase accessible chromatin


title: F12D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: U2_HFF_ATAC

description: Transposase accessible chromatin


title: MspI_referenceII_HFF


title: U1_HFF_BGT


title: U1_HFF_ATAC

description: Transposase accessible chromatin


title: U3_HFF_ATAC

description: Transposase accessible chromatin


title: F12C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: F12C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: F12C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: F12D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 9


title: F12C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: F12C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: I3_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA

data_processing:
Sequencing reads were aligned using gsnap.
FASTQ files incorperate Phred quality scores. NOTE: In the raw sequence data fastq file reads failing Illumina's purity filter are removed automatically.
Htseq count was used to obtain count values for each sample.
Genome_build: hg19-TgME49
Supplementary_files_format_and_content: Counts generated by Htseq-count

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and rRNA depleted with Ribozero (Epicentre).
cDNA synthesis was performed by using oligo-dT as well as random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA. During second strand synthesis, a dU/VTP mix was used to create directional libraries. Before library preparation, cDNA samples were Covaris-fragmented to 300 bp fragments. The samples were then end-filled, 3’ terminal A-extended and ligated to pre-annealed TruSeq indexed Illumina adapters.  Uracil-DNA-glycosylase (UDG) treatment preceded the PCR reaction to cleave the uridine-containing strand and therefore identify the orientation of each transcript

treatment_protocol: Cells were infected with T. gondii and harvested 24 hours after the infection for RNA extraction.


title: F12E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 9


title: F12B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: I2_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA


title: F12B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: F12B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: U3_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA


title: F12B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: U1_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA


title: U2_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA


title: pBQ_unamp_K562_3C

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

description: TOP2A-bound DNA (amplification)

data_processing:
Raw reads were aligned to the human genome version hg38 using Bowtie2 (version 2.1.0) in default end-to-end mode reporting 1-2 alignments per read. SAM mapping files were converted to BAM files and sorted with SAMtools (version 0.1.19). The BAM files were converted to BED files, filtering sites with multiple reads, and only retaining reads that mapped uniquely.
The Audic and Claverie test was used to measure the statistical significance of the difference in read frequencies. TOP2A cleavage sites were identified as the most 5’ bases (i.e.+1 position of cleavage sites on plus strand, and +1 position of cleavage sites on minus stand corresponding to plus strand position +4; Figure 1A) of all reads that both mapped uniquely and showed a 4X enrichment compared to input with p-value < 0.05 . Adjacent cleavage sites meeting the criteria above were collapsed if separated by ≤200bp, allowing closely spaced cleavage sites to be combined intoCCRssimilar to SPO11 hotspots(Pan et al., 2011). CCR boundaries were defined by the first and last cleavage sites in each cluster. CCRs were subsequently filtered to require a 25 ntlength minimum and 4X enrichmentoverinput.CCR signals were normalized to hits per 10 million reads (HP10M). CCRs from replicates were merged as a union set for each sample. Further analyses were based on the merged CCR data sets.
Genome_build: hg38
Supplementary_files_format_and_content: BED file; TOP2A cleavage cluster regions (CCRs)

source_name: human K562 cell_pBQ_unamp

growth_protocol: K562 (ATCC CCL 243) cells were grown to 0.5 x 10^6 cells/ml in 20 ml of IMDM-10% FSC in T75 flasks.  Stocks of TOP2 poisons in DMSO were added to a final DMSO concentration of 0.05%.

extract_protocol:
Ten million vehicle or TOP2 poison-treated K562 cells were lysed with RIPA buffer and the lysates sonicated to fragment the DNA to 250-750bp. TOP2A was immunocaptured with anti-TOP2A IgG and Protein G magnetic beads, the bead-bound fraction separated, and immunoprecipitation repeated twice on non-bound fractions. The bead-bound fractions were combined and treated with CIP (NEB) to detach the TOP2A-bound DNA from cleavage complexes.
The released DNA and input DNA from sonicated lysates were purified and used directly for library synthesis with an IlluminaTruSeq ChIP library kitor pre-amplified with a SEQXE kit (Sigma) before library preparation. Sequencing was performed on an Illumina HiSeq2500 (SE50 protocol)

treatment_protocol: The cells in medium were treated with 25 μM etoposide (Sigma E1318), 2 μM mitoxantrone (Sigma M6545)or 50 μM genistein (Sigma G6776) in DMSO (0.05% final concentration)X1 h, with 8 μM p-benzoquinone (Sigma B10358) in DMSO (0.05% final concentration)X 4 h, or with DMSO (vehicle) X 1 or 4 h. The cells were collected by centrifugation and washed once with PBS at room temperature.  Cell pellets were lysed by addition of 1 ml ice-cold RIPA buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Igepal CA-630, 1% Sodium deoxycholate, 0.5% SDS with 1x Roche Complete EDTA-free Protease Inhibitor Cocktail) and transferred to microcentrifuge tubes.  Lysates were incubated on ice X 15 min before being passed 4 times through a 1 ml 25 g needle and then 4 times through a 27 g needle.  Clumps and debris were removed by centrifugation for 20 min at 4°C at 13.2 krpm in an Eppendorf microcentrifuge.  The supernatants were sonicated at high power in a Diagenode Bioruptor to fragment the DNA to peaksizes between 250 and 1000 bp.Fragmentation wasdetermined by electrophoresis in a 1.5 % agarose gel in 1x TAE  buffer (40 mM Tris/31.25 mM sodium acetate/0.1 mM EDTA). The sonicated lysates were frozen overnight at -20°C to enhance subsequent TOP2A immunocapture.

tag: replicate


title: F12B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: F12A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: pBQ_amp_K562_2C

description:
TOP2A-bound DNA (amplification)
processed data file: pBQ_union_CCR.bed

source_name: human K562 cell_pBQ_amp


title: F12A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCTCGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: F12A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: F12C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 9


title: F12A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TAATGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: F12A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: Input_unamp_K562

description: fragmented DNA (un-amplification)

source_name: human K562 cell_input_unamp


title: Mitoxantrone_amp_4

description: TOP2A-bound DNA (amplification)

source_name: human K562 cell_Mitoxantrone_amp


title: F12A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 9


title: Etoposide_unamp_K562_3B

description: TOP2A-bound DNA (un-amplification)

source_name: human K562 cell_Etoposide_unamp


title: F11G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 8


title: Genistein_amp_4_3

description:
TOP2A-bound DNA (amplification)
processed data file: Genistein_union_CCR.bed

source_name: human K562 cell_Genistein_amp


title: pBQ_amp_K562_1C


title: Input_amp_K562

description: fragmented DNA (amplification)

source_name: human K562 cell_input_amp


title: F11G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 8


title: Etoposide_amp_K562_1B

description:
TOP2A-bound DNA (amplification)
processed data file: Etoposide_union_CCR.bed

source_name: human K562 cell_Etoposide_amp


title: Genistein_amp_4_5


title: Etoposide_amp_K562_2B


title: F11G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 8


title: F11G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 8


title: I1_HFF_RNA

description: DNase-treated, rRNA-depleted mRNA

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and rRNA depleted with Ribozero (Epicentre).
cDNA synthesis was performed by using oligo-dT as well as random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA. During second strand synthesis, a dU/VTP mix was used to create directional libraries. Before library preparation, cDNA samples were Covaris-fragmented to 300 bp fragments. The samples were then end-filled, 3’ terminal A-extended and ligated to pre-annealed TruSeq indexed Illumina adapters.  Uracil-DNA-glycosylase (UDG) treatment preceded the PCR reaction to cleave the uridine-containing strand and therefore identify the orientation of each transcript


title: F12B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGGCTATG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 9


title: Etoposide_amp_4_4


title: F11G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 8


title: F11F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: DMSO_amp_K562_2A

description:
TOP2A-bound DNA (amplification)
processed data file: DMSO_union_CCR.bed

source_name: human K562 cell_DMSO_amp

extract_protocol:
Ten million vehicle or TOP2 poison-treated K562 cells were lysed with RIPA buffer and the lysates sonicated to fragment the DNA to 250-750bp. TOP2A was immunocaptured with anti-TOP2A IgG and Protein G magnetic beads, the bead-bound fraction separated, and immunoprecipitation repeated twice on non-bound fractions. The bead-bound fractions were combined and treated with CIP (NEB) to detach the TOP2A-bound DNA from cleavage complexes.
The released DNA and input DNA from sonicated lysates were purified and used directly for library synthesis with an IlluminaTruSeq ChIP library kitor pre-amplified with a SEQXE kit (Sigma) before library preparation. Sequencing was performed on an Illumina HiSeq2500 (SE50 protocol)


title: F11F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: DMSO_amp_4_1


title: DMSO_amp_K562_1A


title: F11F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: V6.5_96 rep1

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
Reads were aligned and assigned to Gencode Mouse released M4 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: GenCode Mouse released M4
Supplementary_files_format_and_content: tab-delimited text files include raw counts and  RPKM values for each Sample

source_name: embryonic stem cells

growth_protocol: ESCs were grown in DMEM, 15% FBS, LIF, and 2i (PD0325901 and CHIR99021)

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit

treatment_protocol: Cells were transfected using Dhamafect 1 transfection reagent  (Dharmacon, GE Health) following manaufacturer's instructions

value: embryonic stem cells

tag: genotype

value: Wild type


title: V6.5_92 rep1


title: F11F2_1NP

description: library strategy: DNA-seq

source_name: Mouse ES Cells

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: V6.5_95 rep1


title: F11E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: F11F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: V6.5_91 rep1


title: V6.5_87 rep1


title: V6.5_90 rep1


title: V6.5_80 rep2


title: F11E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: F11E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: V6.5_80 rep1


title: DMSO_unamp_K562_3A

description: TOP2A-bound DNA (un-amplification)

source_name: human K562 cell_DMSO_unamp


title: V6.5_77 rep1


title: F11D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: F11E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: F11E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: F11F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 8


title: V6.5_51 rep1


title: V6.5_43 rep1


title: F11D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: F11D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: V6.5_39 rep1


title: F11E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 8


title: F11D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: F11D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: V6.5_37 rep1


title: V6.5_32 rep2


title: V6.5_32 rep1


title: V6.5_31 rep1


title: F11D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 8


title: F11C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: F11C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: F11C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: F11C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: Mock_94 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: Mock_96 rep1


title: F11B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: Mock_96 rep2


title: Mock_93 rep1


title: F11B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: Mock_92 rep2


title: F11B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: Mock_92 rep1


title: F11B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: Mock_91 rep1


title: F11C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: V6.5_25 rep1


title: Mock_84 rep1


title: F11A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: F11A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: F11A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: Mock_81 rep1


title: F11B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: F11B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 8


title: Mock_80 rep2


title: F11A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: F10G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F11C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 8


title: Mock_88 rep1


title: Mock_75 rep2


title: Mock_80 rep1


title: Mock_8 rep2


title: F10G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: F11A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: Mock_8 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F10F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F11A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTACTCG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 8


title: F10F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CTGAAGCT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_74 rep2


title: F10F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: Mock_79 rep1


title: Mock_78 rep1


title: F10G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGCGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_73 rep2


title: Mock_76 rep2


title: Mock_77 rep1


title: F10F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_76 rep1


title: Mock_70 rep1


title: F10G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: V6.5_89 rep1


title: Mock_75 rep1


title: Mock_7 rep1


title: Mock_69 rep1


title: F10E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_74 rep1


title: F10E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_7 rep2


title: F10E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: F10E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_73 rep1


title: Mock_65 rep1


title: Mock_64 rep1


title: F10E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_63 rep2


title: Mock_63 rep1


title: F10D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_62 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F10D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_61 rep1


title: Mock_60 rep1


title: F10D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_6 rep1


title: Mock_6 rep2


title: F10D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_57 rep2


title: F10C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: F10C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 7


title: Mock_57 rep1


title: F10C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_55 rep1


title: Mock_55 rep2


title: F10C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_53 rep1


title: Mock_49 rep2


title: Mock_5 rep1


title: F10B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_5 rep2


title: F10C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_49 rep1


title: F10B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_48 rep1


title: Mock_45 rep1


title: F10A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_40 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: Mock_42 rep1


title: F10A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F6. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: Mock_41 rep1


title: Mock_39 rep1


title: F9G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 6


title: Mock_4 rep1


title: F10A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F10A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: F9G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 6


title: F10B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Mock_36 rep1


title: Mock_35 rep1


title: F9G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 6


title: F9G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 6


title: F9F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: Mock_50 rep1


title: Mock_32 rep1


title: Mock_34 rep1


title: F9F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: F9F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: Mock_38 rep1


title: F9F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: F9G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 6


title: Mock_26 rep1


title: Mock_30 rep1


title: Mock_3 rep1


title: Mock_29 rep2


title: Mock_29 rep1


title: F9E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: F9E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: F9E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: F9E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: Mock_30 rep2

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F9D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: F9F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: F9D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: Mock_33 rep1


title: Mock_2 rep1


title: Mock_18 rep2


title: Mock_24 rep2


title: Mock_17 rep2


title: Mock_18 rep1


title: F10A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F4. AGCGATAG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 7


title: Mock_17 rep1


title: F9D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: F9E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: Mock_16 rep2


title: Mock_24 rep1


title: Mock_16 rep1


title: Mock_23 rep1


title: Mock_15 rep2


title: Mock_15 rep1


title: F9D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: F9C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: F9C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: Mock_11 rep2


title: F9C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: Mock_12 rep1


title: F9C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: F9B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: F9C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: Mock_11 rep1


title: F9B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: F9B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: F9B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: F9D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: F9A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. AGCGATAG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: F9A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: miRNA294_89 rep2

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit

value: Dgcr8-/- plus miR-294


title: miRNA294_79 rep1


title: miRNA294_81 rep1


title: miRNA294_85 rep1


title: miRNA294_91 rep1


title: miRNA294_72 rep1


title: F9A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: F9A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TAATGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: miRNA294_96 rep1


title: miRNA294_71 rep1


title: F9A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: F9E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCCGCGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 6


title: miRNA294_69 rep1


title: F9B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: miRNA294_7 rep1


title: Mock_10 rep1


title: miRNA294_89 rep1


title: F8G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. ATTCAGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 5


title: miRNA294_8 rep1


title: F8G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. GAGATTCC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 5


title: miRNA294_67 rep1


title: miRNA294_68 rep1


title: F9B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CTGAAGCT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 6


title: F9F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 6


title: F8G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. ATTACTCG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 5


title: miRNA294_61 rep2


title: F8F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. ATTCAGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5


title: miRNA294_6 rep1


title: F8F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F3. CGCTCATT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5


title: miRNA294_59 rep2


title: miRNA294_59 rep1


title: miRNA294_79 rep2