title: CGND-HRA-00377

description: total RNA rRNA depleted


title: CGND-HRA-00381

status: Public on Oct 04 2019

type: SRA

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

description: total RNA rRNA depleted

library_source: transcriptomic

data_processing:
fastq Illumina RNASeq paired-end reads were aligned to the hg19 reference genome using STAR v2.5.2b with the following configurations: --outFilterMultimapNmax 100; --outFilterMismatchNoverReadLmax 0.04
Genes and transposable elements (TE) were quantified using TEcount (from TEtranscripts v2.0.3) with the following configurations: hg19 genic GTF from refGene (Jan 2018), custom hg19 TE GTF generated from repeatMasker; --stranded reverse
Genome_build: hg19
Supplementary_files_format_and_content: Individual count tables (SampleName_counts.txt) were generated as output from TEcount

molecule: total RNA

organism: Homo sapiens

source_name: Motor Cortex

extract_protocol:
Total RNA is extracted from flash frozen post-mortem tissue using Trizol/Chloroform, followed by Qiagen RNeasy minikit column purification. RNA is quantified on a Nanodrop 2000 and Qubit™ 2.0 Fluorometer; the quality and integrity of the RNA are verified on an Agilent Bioanalyzer.
Starting from 500 ng of total RNA, rRNA are depleted and cDNA libraries prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, Roche) and Illumina platform-compatible PCR primers (NEXTflex RNA-seq indexes, BioScientific). Libraries are 500-550bp in length and sequenced PE 125.

treatment_protocol: Flash frozen autopsy tissue

tag: tissue type

value: post-mortem tissue

tag: cns subregion

value: Motor Cortex (Medial)

tag: subject id

tag: sample group

value: ALS Spectrum MND


title: CGND-HRA-00374

description: total RNA rRNA depleted

value: Motor Cortex (Lateral)


title: CGND-HRA-00388

description: total RNA rRNA depleted


title: CGND-HRA-00373

description: total RNA rRNA depleted


title: CGND-HRA-00429

description: total RNA rRNA depleted


title: CGND-HRA-00367

description: total RNA rRNA depleted


title: CGND-HRA-00366

description: total RNA rRNA depleted


title: CGND-HRA-00359

description: total RNA rRNA depleted


title: CGND-HRA-00351

description: total RNA rRNA depleted


title: CGND-HRA-00335

description: total RNA rRNA depleted


title: CGND-HRA-00350

description: total RNA rRNA depleted


title: CGND-HRA-00362

description: total RNA rRNA depleted

source_name: Frontal Cortex

value: Frontal Cortex


title: CGND-HRA-00338

description: total RNA rRNA depleted


title: CGND-HRA-00321

description: total RNA rRNA depleted


title: CGND-HRA-00316

description: total RNA rRNA depleted


title: CGND-HRA-00312

description: total RNA rRNA depleted


title: CGND-HRA-00305

description: total RNA rRNA depleted


title: CGND-HRA-00334

description: total RNA rRNA depleted


title: CGND-HRA-00313

description: total RNA rRNA depleted


title: CGND-HRA-00308

description: total RNA rRNA depleted


title: CGND-HRA-00304

description: total RNA rRNA depleted


title: CGND-HRA-00287

description: total RNA rRNA depleted


title: CGND-HRA-00285

description: total RNA rRNA depleted


title: CGND-HRA-00256

description: total RNA rRNA depleted


title: CGND-HRA-00255

description: total RNA rRNA depleted


title: CGND-HRA-00286

description: total RNA rRNA depleted


title: CGND-HRA-00252

description: total RNA rRNA depleted


title: CGND-HRA-00358

description: total RNA rRNA depleted


title: CGND-HRA-00354

description: total RNA rRNA depleted


title: CGND-HRA-00251

description: total RNA rRNA depleted

value: Non-Neurological Control


title: CGND-HRA-00250

description: total RNA rRNA depleted


title: CGND-HRA-00248

description: total RNA rRNA depleted


title: CGND-HRA-00247

description: total RNA rRNA depleted


title: CGND-HRA-00297

description: total RNA rRNA depleted

value: Other Neurological Disorders


title: CGND-HRA-00242

description: total RNA rRNA depleted


title: CGND-HRA-00245

description: total RNA rRNA depleted


title: CGND-HRA-00244

description: total RNA rRNA depleted


title: CGND-HRA-00243

description: total RNA rRNA depleted


title: CGND-HRA-00296

description: total RNA rRNA depleted


title: CGND-HRA-00288

description: total RNA rRNA depleted

value: Motor Cortex


title: CGND-HRA-00240

description: total RNA rRNA depleted


title: CGND-HRA-01242

description: total RNA rRNA depleted


title: CGND-HRA-00300

description: total RNA rRNA depleted


title: CGND-HRA-00224

description: total RNA rRNA depleted


title: CGND-HRA-00221

description: total RNA rRNA depleted


title: CGND-HRA-00241

description: total RNA rRNA depleted


title: CGND-HRA-00223

description: total RNA rRNA depleted


title: CGND-HRA-00217

description: total RNA rRNA depleted


title: CGND-HRA-00219

description: total RNA rRNA depleted


title: CGND-HRA-00225

description: total RNA rRNA depleted


title: CGND-HRA-00226

description: total RNA rRNA depleted


title: CGND-HRA-00220

description: total RNA rRNA depleted


title: CGND-HRA-00246

description: total RNA rRNA depleted


title: CGND-HRA-00213

description: total RNA rRNA depleted


title: CGND-HRA-00216

description: total RNA rRNA depleted


title: CGND-HRA-00215

description: total RNA rRNA depleted


title: CGND-HRA-00218

description: total RNA rRNA depleted


title: CGND-HRA-00210

description: total RNA rRNA depleted


title: CGND-HRA-00211

description: total RNA rRNA depleted


title: CGND-HRA-00209

description: total RNA rRNA depleted


title: CGND-HRA-00134

description: total RNA rRNA depleted

value: JHU 38


title: CGND-HRA-00212

description: total RNA rRNA depleted


title: CGND-HRA-00092

description: total RNA rRNA depleted


title: CGND-HRA-00214

description: total RNA rRNA depleted


title: CGND-HRA-00084-2

description: total RNA rRNA depleted


title: CGND-HRA-00083

description: total RNA rRNA depleted


title: CGND-HRA-00096

description: total RNA rRNA depleted


title: CGND-HRA-00091

description: total RNA rRNA depleted


title: CGND-HRA-00088

description: total RNA rRNA depleted


title: CGND-HRA-00086

description: total RNA rRNA depleted


title: CGND-HRA-00089-2

description: total RNA rRNA depleted


title: CGND-HRA-00061

description: total RNA rRNA depleted


title: CGND-HRA-00063

description: total RNA rRNA depleted


title: CGND-HRA-00062

description: total RNA rRNA depleted


title: CGND-HRA-00068

description: total RNA rRNA depleted


title: CGND-HRA-00064

description: total RNA rRNA depleted


title: CGND-HRA-00059

description: total RNA rRNA depleted


title: CGND-HRA-00058

description: total RNA rRNA depleted


title: CGND-HRA-00055

description: total RNA rRNA depleted


title: CGND-HRA-00025

description: total RNA rRNA depleted


title: CGND-HRA-00026

description: total RNA rRNA depleted


title: CGND-HRA-00023

description: total RNA rRNA depleted


title: CGND-HRA-00056

description: total RNA rRNA depleted


title: CGND-HRA-00022

description: total RNA rRNA depleted


title: CGND-HRA-00057

description: total RNA rRNA depleted


title: CGND-HRA-00019

description: total RNA rRNA depleted


title: CGND-HRA-00020-2

description: total RNA rRNA depleted


title: CGND-HRA-00021

description: total RNA rRNA depleted


title: CGND-HRA-00015

description: total RNA rRNA depleted


status: Public on Sep 18 2019

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: scRNAseq sample generated from NeuroD Pos Enteroendocrine Cells from Large Intestine Replicate 2

data_processing:
Raw sequence data was processed using 10X Cellranger software version 2.0.0 (mkfastq) to generate fastqs
Cells were detected and gene-level counts were generated using Cellranger software V2.0.0 (count)
Further analyses were performed using Cellranger R kit and Seurat 2.0
Genome_build: mm10
Supplementary_files_format_and_content: raw gene level counts per cells are presented in tsv format

organism: Mus musculus

source_name: NeuroD Pos Enteroendocrine Cells

growth_protocol: mice were kept on a 12h dark/light cycle with ad libitum access to water and standard chow

extract_protocol:
The epithelium was single-cell digested with Collagenase and FACs sorted for positive cells. Two samples, each containing 3500 enteroendocrine cells were loaded on a Chromium system for cDNA generation
Libraries were generated using 10X Genomics Single-Cell 3' V2 system

treatment_protocol: Mice were culled during the light phase in a fed state

tag: strain

tag: tissue

value: Large Intestine epithelium

tag: cell type

value: NeuroD Pos Enteroendocrine Cells

tag: fluorescence

value: GFP Positive


title: CGND-HRA-00013

description: total RNA rRNA depleted


description: scRNAseq sample generated from NeuroD Pos Enteroendocrine Cells from Large Intestine Replicate 1


title: CGND-HRA-00016

description: total RNA rRNA depleted


title: CGND-HRA-00014-2

description: total RNA rRNA depleted


title: CGND-HRA-00060

description: total RNA rRNA depleted


title: CGND-HRA-00018

description: total RNA rRNA depleted


title: CGND-HRA-00017

description: total RNA rRNA depleted


title: 60_Control

status: Public on Jul 10 2019

type: RNA

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 FanninSuite 5270

institute: University of Texas Health Science Center at Houston

description:
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hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BRB ArrayTools

label: biotin

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Whole blood was extracted from Tempus Tubes. RNA quality was checked with Agilent Bioanalyser.

value: whole blood

tag: condition

value: Control

tag: visit number

tag: treatment group

value: Cyclophosphamide


title: 60_Month 8

description:
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value: systemic sclerosis patient

value: g. Month 8


title: 60_Day 0

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value: b. Day 0


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value: Transplant


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value: k. Month 26


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value: a. Pre-Trt


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name in non-normalized data file:
SAMPLE 28


title: 4_Month 26

description:
name in non-normalized data file:
SAMPLE 16


title: 3_Month 8

description:
name in non-normalized data file:
SAMPLE 11


title: 5_Control

description:
name in non-normalized data file:
SAMPLE 17


title: 3_Day 0

description:
name in non-normalized data file:
SAMPLE 10


title: 2_Month 26

description:
name in non-normalized data file:
SAMPLE 8


title: 3_Month 26

description:
name in non-normalized data file:
SAMPLE 12


title: 5_Day 0

description:
name in non-normalized data file:
SAMPLE 18


title: 5_Month 26

description:
name in non-normalized data file:
SAMPLE 19


title: 14_Month 26

description:
name in non-normalized data file:
SAMPLE 49


title: 6_Day 0

description:
name in non-normalized data file:
SAMPLE 21


title: Capture_2.7kb_teto_integrations_pure_clone

status: Public on May 15 2019

city: Basel

first: Luca

last: Giorgetti

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
library strategy: Capture
Reads were trimmed to have 50bps
Reads are mapped to the integration cassette (teto cassette or CTCF+teto cassette) treating paired end as single end
reads where only one of the two reads are mappable to the cassette are kept and only the unmapped reads of the pair are kept
Kept reads are mapped to the mouse genome
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing integration sites position and (if available) the CTCF orientation

molecule: genomic DNA

growth_protocol: Cells were cultured on gelatin-coated culture plates in Dulbecco Modified Eagle’s medium (Sigma) in the presence of 15% foetal calf serum (Eurobio Abcys), 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade) in 8% CO2 at 37°C. After insertion of the rTetR-Dam vector (see below), cells were cultured in the presence of 250 µg/mL hygromycin.

extract_protocol:
2µg of genomic DNA were fragmented to an average of 500bp by sonication (Covaris S220, duty cycle: 5%, peak power: 175W, duration: 25sec).
End-repair, A-tailing and ligation of full-length barcoded Illumina adapters were performed using the TruSeq DNA PCR-free kit (Illumina) according to the manufacturer guidelines with the exception that large DNA fragments were not removed. 750ng of libraries for each sample were pooled together, and fragments of interest were captured using biotinylated probes against the the piggyBac inverted terminal repeats (ITRs) sequence and the xGen Hybridisation Capture kit (IDT) according to the manufacturer protocol (probes concentration of 2.25pmol/µl). Following the capture, libraries were amplified for 12 cycles using the Kapa Hi-fi polymerase and the following primers: 5’-AATGATACGGCGACCACCGAGAT, 5’-CAAGCAGAAGACGGCATACGAGA. Final libraries were purified using AMPure XP beads (1:1 ratio), quality controlled and sequenced on the NextSeq500 platform (paired-end 300 cycles mid-output) for a total of 8x108 paired-end reads per sample on average.

treatment_protocol: no treatment

value: embryonic stem cells (ESCs)

tag: clone

value: 2.7kb teto integrations_pure clone


title: 3_Control

description:
name in non-normalized data file:
SAMPLE 9


title: 1_Day 0

description:
name in non-normalized data file:
SAMPLE 2


title: 4_Control

description:
name in non-normalized data file:
SAMPLE 13


title: Capture_3CTCF_teto_integrations_clone

value: 3 CTCF teto integrations clone


title: 1_Month 26

description:
name in non-normalized data file:
SAMPLE 4


title: 2_Control

description:
name in non-normalized data file:
SAMPLE 5


title: 2_Month 8

description:
name in non-normalized data file:
SAMPLE 7


title: 4_Day 0

description:
name in non-normalized data file:
SAMPLE 14


title: 1_Month 8

description:
name in non-normalized data file:
SAMPLE 3


title: 1_Control

description:
name in non-normalized data file:
SAMPLE 1


title: 8_Control

description:
name in non-normalized data file:
SAMPLE 26


title: 4C_27kb_chr1_reverseCTCF_repl2

description: S19_TetO_4C_Chris_TetO_ES_27_2_Chr1_VP22

data_processing:
library strategy: 4C-seq
Single-end reads from each sample were mapped to the mouse genomes using the QuasR software (v 1.20.0, qAlign function, default settings).
4C signal quantification was done using qAlign (from QuasR, v 1.20.0) using as query a GRanges object containing the position of GATC sites. Library sizes are rescaled to the minimum library size
Running average of the signal was done using 21 steps
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including genomic coordinates and enrichments

extract_protocol:
The initial steps of 4C protocol were performed as published before (Splinter et al., 2012; Methods (PMID: 22929766)).
Briefly, cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme Csp6I. After a second re-ligation step, the sample is purified and a 4C PCR directly on this template for mouse genome viewpoints. In order to PCR amplify the ectopic TetO viewpoint, 4C templates were treated with Cas9 in vitro. Cas9 is targeted into the TetO repeats by using a sgRNA designed in between 4C viewpoint primers.

value: 2.7kb teto integrations


title: Capture_2.7kb_teto_integrations_mixed_population


title: HiC_2.7kb_clone_replicate2

data_processing:
Hi-C paired end datasets were processed using HiC-Pro (version 2.7.10). HiC-Pro covers the whole analysis from fastq files to the interaction matrix
Genome_build: mm9
Supplementary_files_format_and_content: iced and binned matrix (10kb). The format of the matrix is the standard from HiC-Pro, namely, 3 columns: start end interactions. It's a sparce matrix annotation, no zero values are reported.

extract_protocol:
see library construction protocol
6x10^6 mESC were harvested and diluted in 1x PBS to final 1x106 cells/ml, then crosslinked with 1% formaldehyde and quenched with 0,125M glycine for 5 min at RT. After two 1x PBS washes, cells pellets were obtained by centrifugation, snap frozen and stored at -80°C. Pellets were thawed on ice and resuspended in 500 ul lysis buffer (10 nM Tris-HCl pH8.0, 10 nM NaCl, 0.2%NP40, 1x Roche protease inhibitors) and left 30 min on ice. Cells were then pelleted by centrifugation (954 x g, 5 min, 4°C ), washed once with 300 ul 1x NEB2 buffer and nuclei were extracted by 1 h incubation at 37°C in 190 ul 0.5%SDS 1xNEB2 buffer. SDS was neutralized by diluting the sample with 400 ul NEB2 buffer and adding 10% Triton X-100. After 15 min of incubation at 37°C, nuclei were pelleted, washed once in PBS and resuspended in 300 ul NEB2 buffer. 400U of MboI (NEB, 25 000 units/ml) were added and incubated at 37°C overnight. The next day, nuclei were pelleted again, resuspended in 200 ul fresh NEB2 buffer and additional 200U of MboI were added for two more hours before heat inactivation at 65°C for 15 min. 43 ul of end-repair mix (1.5 μL of 10 mM dCTP; 1.5 μL of 10mM dGTP; 1.5 μL of 10 mM dTTP; 37.5 μL of 0.4 mM Biotin-11-dATP (Invitrogen) and 1 μL of 50U/μL DNA Polymerase I Large Klenow fragment (NEB)) were added to the nuclear suspension, incubated at 37°C for 45 min and heat inactivated at 65°C for 15 min. The end repair mix was exchanged with 1.2 ml of ligation mix (120μL of 10X T4 DNA Ligase Buffer; 100 μL of 10% Triton X-100; 6 μL of 20 mg/mL BSA; 969μL of H2O) plus 5 ul of T4 ligase (NEB, 2000 units/ml) and ligation was performed at 16°C overnight. Nuclei were reconstituted in 200 ul fresh NEB2 buffer followed by RNA digestion in 0.5 mg/ml RNAse A for 10 min at 37°C. Samples were de-crosslinked with Proteinase K at 65°C overnight and DNA was purified using phenol/chloroform. 2 ug of DNA sample were sonicated using Diagenode Bioruptor Pico. MyOne Streptavidin T1 (Life Technologies # 65601) magnetic beads were used to capture biotinylated DNA followed by A-tailing. Adapter ligation was performed according to NEB Next Ultra DNA Library prep kit instructions. Two independent PCR reactions with multiplex oligos for Illumina sequencing were performed and pooled for the final PCR clean-up by magnetic AMPure bead (Beckman Coulter) purification. The final libraries were eluted in nuclease-free water, QCed by Bioanalyzer and Qubit

tag: cell line

value: ESC


title: 4C_27kb_chr1_CTCF_repl2

description: S19_TetO_4C_Chris_TetO_ES_27_2_Chr1_VP21


title: HiC_3CTCF_clone_replicate1


title: HiC_2.7kb_clone_replicate1


title: HiC_3CTCF_clone_replicate2


title: 4C_noteto_WT_chr1_reverseCTCF

value: 94.1 clone


title: 4C_27kb_chr1_CTCF_repl1

description: S19_TetO_4C_Chris_TetO_ES_27_1_Chr1_VP21


title: 4C_27kb_chr1_reverseCTCF_repl1

description: S19_TetO_4C_Chris_TetO_ES_27_1_Chr1_VP22


title: 4C_noteto_WT_chr1_CTCF


title: 4_Month 8

description:
name in non-normalized data file:
SAMPLE 15


title: 4C_3CTCF_clone_replicate2

description: S16_TetO_4C_Chris_3xCTCF_TetO_ES_C3_2_TetO_VP1_Cas9


title: 500 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X15_1829X16_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F15

data_processing:
library strategy: damC library preparation
Single-end 76bp damC-seq reads from each sample were mapped to the mouse genomes using the QuasR software (v 1.20.0, qAlign function, default settings).
Deduplication based on UMIs was done using a custom script on bam files (UMIs are contained in the readname of each read in each fastq file)
damC signal quantification was done using qAlign (from QuasR, v 1.20.0) using as query a GRanges object containing the position of GATC sites shifted by 5bps upstream (plus strand) and downstream (minus strand). Library sizes are rescaled to have 10M reads mapped to the query and a pseudocount of 0.2 is added
Running average of the signal was done prior enrichment calculation using a custom script and using 21 steps
Enrichment was then calculated as described in the paper
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including genomic coordinates and enrichments

source_name: 500 nM_2.7kb_pure_clone_-dox

extract_protocol:
3x106 cells were harvested using trypsin after 18 hours of induction with tamoxifen +/- doxycyclin. Genomic DNA was extracted using the Qiagen blood and tissue kit adding RNaseA in step 1. Genomic DNA was eluted in 80ul ddH2O. DNA concentration was measured using the Qbit DNA Broad Range kit
Genomic DNA (100ng input) was treated with Shrimp Alkaline Phosphatase treatment (NEB, 1U), followed by DpnI digestion (ThermoFisher Scientific, 10U), A-tailing (0.6mM final dATP, 5U Klenow exo-, ThermoFisher Scientific), and UMI adapters ligation (30U T4 DNA ligase, PEG4000, ThermoFisher Scientific) performed within the same tube and buffer (Tango 1X, ThermoFisher Scientific) by heat inactivating each enzymatic step followed by adjustment with the reagents required for the next step, Ligation reactions were treated with Exonuclease I (20U, ThermoFisher Scientific ) then purified using AMPureXP beads (1:0.8 ratio, Agencourt) and the second sequencing adapter was tagged using heat denaturation and second strand synthesis (5U T4 DNA Polymerase, ThermoFisher Scientific). The tagging reaction was purified using AMPure XP beads (1:1 ratio) followed by a final library amplification (10 cycles) using 1U of Phusion polymerase, 2μl 10 μM DAM_UMIindex_PCR was tagged using heat denaturation and second strand synthesis (5U T4 DNA Polymerase, ThermoFisher Scientific). The tagging reaction was purified using AMPure XP beads (1:1 ratio) followed by a final library amplification (10 cycles) using 1U of Phusion polymerase, 2μl 10 μM DAM_UMIindex_PCR.

treatment_protocol: To induce nuclear translocation of the rTetR-Dam fusion protein to the nuclei, mESC were trypsinized and directly seeded in culture medium containing 4-hydroxy-tamoxifen (4-OHT) at the concentrations indicated for 18 hours. Binding of the Dam fusion protein to the TetO arrays was induced by simultaneously adding 2.5 μg/ml doxycycline (Dox).

value: Embyonic stem cell


title: 100 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X13_1829X14_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F13

source_name: 100 nM_2.7kb_pure_clone_-dox


title: 4C_2.7kb_clone_replicate2


title: 100 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X13_1829X14_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F14

source_name: 100 nM_2.7kb_pure_clone_+dox


title: 50 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X11_1829X12_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F12

source_name: 50 nM_2.7kb_pure_clone_+dox


title: 50 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X11_1829X12_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F11

source_name: 50 nM_2.7kb_pure_clone_-dox


title: 25 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X9_1829X10_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F10

source_name: 25 nM_2.7kb_pure_clone_+dox


title: 5 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X5_1829X6_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F6

source_name: 5 nM_2.7kb_pure_clone_+dox


title: 10 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X7_1829X8_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F8

source_name: 10 nM_2.7kb_pure_clone_+dox


title: 10 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X7_1829X8_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F7

source_name: 10 nM_2.7kb_pure_clone_-dox


title: 500 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp1829X15_1829X16_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F16

source_name: 500 nM_2.7kb_pure_clone_+dox


title: 6_Month 8

description:
name in non-normalized data file:
SAMPLE 22

value: whole blood


title: 5 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X5_1829X6_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F5

source_name: 5 nM_2.7kb_pure_clone_-dox


title: 1 nM_2.7kb_pure_clone_+dox_rp4

description:
processed data file:
Exp1829X3_1829X4_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F4

source_name: 1 nM_2.7kb_pure_clone_+dox


title: 1 nM_2.7kb_pure_clone_-dox_rp4

description:
processed data file:
Exp1829X3_1829X4_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F3

source_name: 1 nM_2.7kb_pure_clone_-dox


title: 0.1 nM_2.7kb_pure_clone_-dox_rp4

description:
processed data file:
Exp1829X1_1829X2_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F1

source_name: 0.1 nM_2.7kb_pure_clone_-dox


title: 0.1 nM_2.7kb_pure_clone_+dox_rp4

description:
processed data file:
Exp1829X1_1829X2_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F2

source_name: 0.1 nM_2.7kb_pure_clone_+dox


title: 500 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X15_1829X16_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F16


title: 500 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X15_1829X16_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F15


title: 100 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X13_1829X14_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F14


title: 50 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X11_1829X12_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F11


title: 50 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X11_1829X12_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F12


title: 25 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X9_1829X10_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F10


title: 4C_3CTCF_clone_replicate1

description: S15_TetO_4C_Chris_3xCTCF_TetO_ES_C3_1_TetO_VP1_Cas9


title: 10 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X7_1829X8_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F8


title: 25 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X9_1829X10_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F9

source_name: 25 nM_2.7kb_pure_clone_-dox


title: 5 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X5_1829X6_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F5


title: 10 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X7_1829X8_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F7


title: 5 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp1829X5_1829X6_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F6


title: 1 nM_2.7kb_pure_clone_-dox_rp3

description:
processed data file:
Exp1829X3_1829X4_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F3


title: 0.1 nM_2.7kb_pure_clone_+dox_rp3

description:
processed data file:
Exp1829X1_1829X2_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F2


title: 1 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F23
barcoded.1930F23


title: 1 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F20
barcoded.1930F20


title: 0.1 nM_2.7kb_pure_clone_-dox_rp3

description:
processed data file:
Exp1829X1_1829X2_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F1


title: 1 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F24
barcoded.1930F24


title: 25 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp1829X9_1829X10_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1859F9


title: 0.1 nM_2.7kb_pure_clone_-dox_rp2

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F21
barcoded.1930F21


title: 0.1 nM_2.7kb_pure_clone_+dox_rp2

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F22
barcoded.1930F22


title: 1 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F19
barcoded.1930F19


title: 100 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp1829X13_1829X14_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F13


title: 1 nM_CTCF_clone_cre_deleted_+dox_rp2

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F16
barcoded.1930F16

source_name: 1 nM_CTCF_clone_cre_deleted_+dox

value: CTCF clone


title: 1 nM_CTCF_clone_cre_deleted_-dox_rp2

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F15
barcoded.1930F15

source_name: 1 nM_CTCF_clone_cre_deleted_-dox


title: 1 nM_CTCF_clone_cre_deleted_+dox_rp1

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F14
barcoded.1930F14


title: 1 nM_CTCF_clone_cre_deleted_-dox_rp1

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F13
barcoded.1930F13


title: 0.1 nM_CTCF_clone_cre_deleted_+dox_rp2

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F12
barcoded.1930F12

source_name: 0.1 nM_CTCF_clone_cre_deleted_+dox


title: 0.1 nM_CTCF_clone_cre_deleted_-dox_rp2

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F11
barcoded.1930F11

source_name: 0.1 nM_CTCF_clone_cre_deleted_-dox


title: 1 nM_CTCF_clone_+dox_rp2

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F8
barcoded.1930F8

source_name: 1 nM_CTCF_clone_+dox


title: 0.1 nM_CTCF_clone_cre_deleted_-dox_rp1

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F9
barcoded.1930F9


title: 0.1 nM_2.7kb_pure_clone_+dox_rp1

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F18
barcoded.1930F18


title: 1 nM_CTCF_clone_+dox_rp1

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F6
barcoded.1930F6


title: 1 nM_CTCF_clone_-dox_rp2

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F7
barcoded.1930F7

source_name: 1 nM_CTCF_clone_-dox


title: 2_Day 0

description:
name in non-normalized data file:
SAMPLE 6

source_name: whole blood

value: Cyclophosphamide


title: 1 nM_CTCF_clone_-dox_rp1

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F5
barcoded.1930F5


title: 0.1 nM_CTCF_clone_-dox_rp2

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F3
barcoded.1930F3

source_name: 0.1 nM_CTCF_clone_-dox


title: 0.1 nM_CTCF_clone_+dox_rp2

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F4
barcoded.1930F4

source_name: 0.1 nM_CTCF_clone_+dox


title: 0.1 nM_CTCF_clone_+dox_rp1

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F2
barcoded.1930F2


title: 2.7kb mixed_population nodox 5nM repl1

description:
processed data file:
Exp1374X7_1374X8_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F8

source_name: 2.7kb mixed_population nodox 5nM


title: 2.7kb mixed_population nodox 1nM repl1

description:
processed data file:
Exp1374X5_1374X6_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F6

source_name: 2.7kb mixed_population nodox 1nM


title: 2.7kb mixed_population dox 1nM repl1

description:
processed data file:
Exp1374X5_1374X6_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F5

source_name: 2.7kb mixed_population dox 1nM


title: 0.1 nM_CTCF_clone_-dox_rp1

description:
processed data file:
ExpC3Nodox0.1_1nm_C3dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F1
barcoded.1930F1


title: 0.1 nM_2.7kb_pure_clone_-dox_rp1

description:
processed data file:
Exp_subclone3_0.1nm_1nm_Enrichment_dedupON_sf_20steps_br.dat
barcoded.1926F17
barcoded.1930F17


title: 2.7kb mixed_population dox 0.5nM repl1

description:
processed data file:
Exp1374X3_1374X4_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F3

source_name: 2.7kb mixed_population dox 0.5nM


title: 2.7kb mixed_population nodox 0.5nM repl1

description:
processed data file:
Exp1374X3_1374X4_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F4

source_name: 2.7kb mixed_population nodox 0.5nM


title: 2.7kb mixed_population nodox 0.1nM repl1

description:
processed data file:
Exp1374X1_1374X2_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F2

source_name: 2.7kb mixed_population nodox 0.1nM


title: 2.7kb mixed_population dox 0.1nM repl1

description:
processed data file:
Exp1374X1_1374X2_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F1

source_name: 2.7kb mixed_population dox 0.1nM


title: 2.7kb mixed_population nodox 500nM repl1

description:
processed data file:
Exp1374X17_1374X18_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F18

source_name: 2.7kb mixed_population nodox 500nM


title: 2.7kb mixed_population nodox 100nM repl1

description:
processed data file:
Exp1374X15_1374X16_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F16

source_name: 2.7kb mixed_population nodox 100nM


title: 0.1 nM_CTCF_clone_cre_deleted_+dox_rp1

description:
processed data file:
ExpA4Nodox0.1_1nm_A4dox0.1_1nm_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1926F10
barcoded.1930F10


title: 2.7kb mixed_population dox 500nM repl1

description:
processed data file:
Exp1374X17_1374X18_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F17

source_name: 2.7kb mixed_population dox 500nM


title: 2.7kb mixed_population dox 100nM repl1

description:
processed data file:
Exp1374X15_1374X16_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F15

source_name: 2.7kb mixed_population dox 100nM


title: 2.7kb mixed_population dox 10nM repl1

description:
processed data file:
Exp1374X9_1374X10_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F9

source_name: 2.7kb mixed_population dox 10nM


title: 2.7kb mixed_population dox 50nM repl1

description:
processed data file:
Exp1374X13_1374X14_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F13

source_name: 2.7kb mixed_population dox 50nM


title: 2.7kb mixed_population dox 25nM repl1

description:
processed data file:
Exp1374X11_1374X12_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F11

source_name: 2.7kb mixed_population dox 25nM


title: 2.7kb mixed_population nodox 25nM repl1

description:
processed data file:
Exp1374X11_1374X12_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F12

source_name: 2.7kb mixed_population nodox 25nM


title: 1 nM_2.7kb_pure_clone_+dox_rp3

description:
processed data file:
Exp1829X3_1829X4_Enrichment_dedupON_lambdaON_singleFragment_20steps_before_ration.dat.txt
barcoded.1829F4

source_name: 1 nM_2.7kb_pure_clone_+dox


title: 2.7kb mixed_population dox 5nM repl1

description:
processed data file:
Exp1374X7_1374X8_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F7

source_name: 2.7kb mixed_population dox 5nM


title: 4C_2.7kb_clone_replicate1


title: 2.7kb mixed_population nodox 50nM repl1

description:
processed data file:
Exp1374X13_1374X14_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F14

source_name: 2.7kb mixed_population nodox 50nM


title: 2.7kb mixed_population nodox 10nM repl1

description:
processed data file:
Exp1374X9_1374X10_Enrichment_dedupON_singleFragment_20steps_before_ration.txt
barcoded.1374F10

source_name: 2.7kb mixed_population nodox 10nM


title: In vivo human muscle [C504]

status: Public on Jul 31 2018

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

description: human skeletal muscle

hyb_protocol: Arrays were washed, stained and scanned following Affymetrix standard procedures.

scan_protocol: Affymetrix Gene Chip Scanner

data_processing: The data was analyzed with a transcript level custom CDF. The CDF file is available on the platform record. We have used aroma.affymetrix to normalise our data (RMA)

source_name: In vivo human muscle

label_protocol: Ambions WT expression kit to produce cDNA. The cDNA was fragmented and labeled with GeneChip WT Terminal labeling kit (Affymetrix). The hybridization of cDNA to exon array was 16h at 45 degrees. The arrays were washed in Affymetrix FS450 wash stations

extract_protocol: Total RNA was isolated by TRIzol (Invitrogen) according to the manufacturers protocol. RNA was dissolved in 20ul of RNAse-free water and quantified using a Nanodrop 2000 (NanoDrop technologies).

value: vastus lateralis

tag: developmental stage

value: young adult


title: In vivo human muscle [C498]

description: human skeletal muscle

value: middle aged adult


title: In vivo human muscle [C375]

description: human skeletal muscle


title: In vivo human muscle [C57]

description: human skeletal muscle


title: In vivo human muscle [C330]

description: human skeletal muscle


title: In vivo human muscle [C459]

description: human skeletal muscle


title: In vivo human muscle [C402]

description: human skeletal muscle


title: In vivo human muscle [C378]

description: human skeletal muscle


title: In vivo human muscle [C141]

description: human skeletal muscle


title: In vivo human muscle [C486]

description: human skeletal muscle


title: In vivo human muscle [C51]

description: human skeletal muscle


title: In vivo human muscle [C54]

description: human skeletal muscle


title: In vivo human muscle [C354]

description: human skeletal muscle


title: In vivo human muscle [C282]

description: human skeletal muscle


title: In vivo human muscle [C117]

description: human skeletal muscle


title: In vivo human muscle [C102]

description: human skeletal muscle


title: In vivo human muscle [C237]

description: human skeletal muscle


title: In vivo human muscle [C126]

description: human skeletal muscle


title: In vivo human muscle [C39]

description: human skeletal muscle


title: In vivo human muscle [C195]

description: human skeletal muscle


title: In vivo human muscle [C165]

description: human skeletal muscle


title: In vivo human muscle [C222]

description: human skeletal muscle


title: In vivo human muscle [C168]

description: human skeletal muscle


title: In vivo human muscle [C297]

description: human skeletal muscle


title: In vivo human muscle [C321]

description: human skeletal muscle


title: In vivo human muscle [C48]

description: human skeletal muscle


title: In vivo human muscle [C30]

description: human skeletal muscle


title: In vivo human muscle [C81]

description: human skeletal muscle


title: In vivo human muscle [C78]

description: human skeletal muscle


title: In vivo human muscle [C120]

description: human skeletal muscle


title: In vivo human muscle [C99]

description: human skeletal muscle


title: In vivo human muscle [C27]

description: human skeletal muscle


title: In vivo human muscle [C6]

description: human skeletal muscle


title: In vivo human muscle [B595]

description: human skeletal muscle


title: In vivo human muscle [C15]

description: human skeletal muscle


title: In vivo human muscle [C9]

description: human skeletal muscle


title: In vivo human muscle [B550]

description: human skeletal muscle


title: In vivo human muscle [B466]

description: human skeletal muscle


title: In vivo human muscle [B565]

description: human skeletal muscle


title: In vivo human muscle [B559]

description: human skeletal muscle


title: In vivo human muscle [B556]

description: human skeletal muscle


title: In vivo human muscle [B586]

description: human skeletal muscle


title: In vivo human muscle [B538]

description: human skeletal muscle


title: In vivo human muscle [B589]

description: human skeletal muscle


title: In vivo human muscle [B499]

description: human skeletal muscle


title: In vivo human muscle [B547]

description: human skeletal muscle


title: In vivo human muscle [B376]

description: human skeletal muscle


title: In vivo human muscle [B361]

description: human skeletal muscle


title: In vivo human muscle [B424]

description: human skeletal muscle


title: In vivo human muscle [B202]

description: human skeletal muscle


title: In vivo human muscle [B574]

description: human skeletal muscle


title: In vivo human muscle [B325]

description: human skeletal muscle


title: In vivo human muscle [B295]

description: human skeletal muscle


title: In vivo human muscle [B196]

description: human skeletal muscle


title: In vivo human muscle [B220]

description: human skeletal muscle


title: In vivo human muscle [B274]

description: human skeletal muscle


title: In vivo human muscle [B313]

description: human skeletal muscle


title: In vivo human muscle [B244]

description: human skeletal muscle


title: In vivo human muscle [B298]

description: human skeletal muscle


title: In vivo human muscle [B193]

description: human skeletal muscle


title: In vivo human muscle [B175]

description: human skeletal muscle


title: In vivo human muscle [B166]

description: human skeletal muscle


title: In vivo human muscle [B187]

description: human skeletal muscle


title: In vivo human muscle [B190]

description: human skeletal muscle


title: In vivo human muscle [B106]

description: human skeletal muscle


title: In vivo human muscle [B181]

description: human skeletal muscle


title: In vivo human muscle [B163]

description: human skeletal muscle


title: In vivo human muscle [A566]

description: human skeletal muscle


title: In vivo human muscle [B136]

description: human skeletal muscle


title: In vivo human muscle [B7]

description: human skeletal muscle


title: In vivo human muscle [B103]

description: human skeletal muscle


title: In vivo human muscle [B43]

description: human skeletal muscle


title: In vivo human muscle [A590]

description: human skeletal muscle


title: In vivo human muscle [B31]

description: human skeletal muscle


title: In vivo human muscle [B19]

description: human skeletal muscle


title: In vivo human muscle [A587]

description: human skeletal muscle


title: In vivo human muscle [A584]

description: human skeletal muscle


title: In vivo human muscle [B85]

description: human skeletal muscle


title: In vivo human muscle [A551]

description: human skeletal muscle


title: In vivo human muscle [B130]

description: human skeletal muscle


title: In vivo human muscle [A548]

description: human skeletal muscle


title: In vivo human muscle [B127]

description: human skeletal muscle


title: In vivo human muscle [A530]

description: human skeletal muscle


title: In vivo human muscle [A503]

description: human skeletal muscle


title: In vivo human muscle [A494]

description: human skeletal muscle


title: In vivo human muscle [A536]

description: human skeletal muscle


title: In vivo human muscle [A500]

description: human skeletal muscle


title: In vivo human muscle [A437]

description: human skeletal muscle


title: In vivo human muscle [A524]

description: human skeletal muscle


title: In vivo human muscle [A353]

description: human skeletal muscle


title: In vivo human muscle [A485]

description: human skeletal muscle


title: In vivo human muscle [A455]

description: human skeletal muscle


title: In vivo human muscle [A305]

description: human skeletal muscle


title: In vivo human muscle [A395]

description: human skeletal muscle


title: In vivo human muscle [A287]

description: human skeletal muscle


title: In vivo human muscle [A347]

description: human skeletal muscle


title: In vivo human muscle [A326]

description: human skeletal muscle


title: In vivo human muscle [A299]

description: human skeletal muscle


title: In vivo human muscle [A377]

description: human skeletal muscle


title: In vivo human muscle [A275]

description: human skeletal muscle


title: In vivo human muscle [A146]

description: human skeletal muscle


title: In vivo human muscle [A176]

description: human skeletal muscle


title: In vivo human muscle [A164]

description: human skeletal muscle


title: In vivo human muscle [A143]

description: human skeletal muscle


title: In vivo human muscle [A203]

description: human skeletal muscle


title: In vivo human muscle [A107]

description: human skeletal muscle


title: In vivo human muscle [A239]

description: human skeletal muscle


title: In vivo human muscle [A8]

description: human skeletal muscle


title: In vivo human muscle [A116]

description: human skeletal muscle


title: In vivo human muscle [A137]

description: human skeletal muscle


title: In vivo human muscle [A68]

description: human skeletal muscle


title: In vivo human muscle [A98]

description: human skeletal muscle


title: In vivo human muscle [A5]

description: human skeletal muscle


title: In vivo human muscle [A140]

description: human skeletal muscle


title: In vivo human muscle [C600]

description: human skeletal muscle


title: In vivo human muscle [C576]

description: human skeletal muscle


title: CGND-HRA-00730

status: Public on Jul 13 2018

description:
CGND-HRA-00730_ACCACTGT_BCB4F2ANXX_L005_001
CGND-HRA-00730

data_processing:
fastq Illumina RNASeq paired-end reads were aligned using STAR (2.5.2a).
We used Leafcutter (0.2.6) to perform differential splicing analyses of each of four defined groups of ALS cases (ALSlow, ALShigh, C9, FTD grouped samples for a total of 54 samples referred to as the training set) against the Control group (all groups are described in: link to manuscript here). In each differential splicing analysis, Leafcutter outputs a file listing the set of cluster padj values, and a second file listing the splice junctions that reside within those clusters and their delta PSIs as a result of the differential analysis.
Clusters with a padj value <0.1 were selected for further analysis; we aggregated splice junctions and their corresponding delta PSIs across the 4 analyses into a single matrix. Differentially spliced events are ordered by the max delta PSI across the 4 analyses (file: sig.junctions.padj01.sorted_by_max_deltapsi_Conlon_et_al_2018.txt).
Splice junction coordinates are intersected with Gencode release 25 annotations.
PSI ratios across all samples in Conlon et al. 2018 (77 training and test samples, see link to manuscript here) were computed using the leafcutter_quantify_psi.R  script starting from the splice junction counts (see https://github.com/davidaknowles/leafcutter/issues/34)
Genome_build: GRCh38
Supplementary_files_format_and_content: sig.junctions.padj01.sorted_by_max_deltapsi_Conlon_et_al_2018.txt : Differentially spliced events, coordinates and gene names are ordered by the max delta PSI across the 4 analyses of 54 ALS and Control samples.
Supplementary_files_format_and_content: DS_leafcutter.ratios_Conlon_et_al_2018.txt : PSI ratios across all samples (77 training and test samples in Conlon et al. 2018, link to manuscript here) were computed using the leafcutter_quantify_psi.R  script starting from the splice junction counts (see https://github.com/davidaknowles/leafcutter/issues/34)

tag: sample type

value: post-mortem tissue

value: Cerebellum

value: Cerebellum, BA4


title: CGND-HRA-00729

description:
CGND-HRA-00729_AGTGGTCA_BCB4F2ANXX_L004_001
CGND-HRA-00729


title: In vivo human muscle [C573]

description: human skeletal muscle


title: CGND-HRA-00727

description:
CGND-HRA-00727_ATAGCGAC_BCB4F2ANXX_L008_001
CGND-HRA-00727

value: ALSlow


title: In vivo human muscle [C582]

description: human skeletal muscle


title: In vivo human muscle [A92]

description: human skeletal muscle


title: CGND-HRA-00725

description:
CGND-HRA-00725_CAATGGAA_BCB4F2ANXX_L008_001
CGND-HRA-00725

value: ALShigh


title: In vivo human muscle [C570]

description: human skeletal muscle


title: CGND-HRA-00722

description:
CGND-HRA-00722_CCTCCTGA_BCB4F2ANXX_L003_001
CGND-HRA-00722

source_name: ungrouped ALS_Cerebellum

value: ungrouped ALS


title: CGND-HRA-00726

description:
CGND-HRA-00726_TTCACGCA_BCB4F2ANXX_L008_001
CGND-HRA-00726


title: In vivo human muscle [C558]

description: human skeletal muscle


title: In vivo human muscle [A53]

description: human skeletal muscle


title: In vivo human muscle [A11]

description: human skeletal muscle


title: CGND-HRA-00724

description:
CGND-HRA-00724_ACCTCCAA_BCB4F2ANXX_L008_001
CGND-HRA-00724


title: In vivo human muscle [C561]

description: human skeletal muscle


title: In vivo human muscle [C510]

description: human skeletal muscle


title: CGND-HRA-00721

description:
CGND-HRA-00721_CCGACAAC_BCB4F2ANXX_L002_001
CGND-HRA-00721

value: Control


title: CGND-HRA-00720

description:
CGND-HRA-00720_CTAAGGTC_BCB4F2ANXX_L007_001
CGND-HRA-00720


title: In vivo human muscle [C549]

description: human skeletal muscle


title: CGND-HRA-00753

description:
CGND-HRA-00753_CAGCGTTA_ACBDBDANXX_L008_001
CGND-HRA-00753-b38


title: CGND-HRA-00717

description:
CGND-HRA-00717_CCTCTATC_BCB4F2ANXX_L004_001
CGND-HRA-00717


title: CGND-HRA-00710

description:
CGND-HRA-00710_AGCCATGC_BCB4F2ANXX_L006_001
CGND-HRA-00710

source_name: ungrouped FTD_Cerebellum

value: ungrouped FTD


title: CGND-HRA-00723

description:
CGND-HRA-00723_CATCAAGT_BCB4F2ANXX_L008_001
CGND-HRA-00723


title: In vivo human muscle [C528]

description: human skeletal muscle


title: CGND-HRA-00714

description:
CGND-HRA-00714_AATGTTGC_BCB4F2ANXX_L001_001
CGND-HRA-00714


title: In vivo human muscle [C540]

description: human skeletal muscle


title: In vivo human muscle [C546]

description: human skeletal muscle


title: In vivo human muscle [C543]

description: human skeletal muscle


title: In vivo human muscle [C534]

description: human skeletal muscle


title: CGND-HRA-00719

description:
CGND-HRA-00719_CGGATTGC_BCB4F2ANXX_L006_001
CGND-HRA-00719


title: CGND-HRA-00705

description:
CGND-HRA-00705_CTCAATGA_BCB4F2ANXX_L007_001
CGND-HRA-00705


title: In vivo human muscle [A194]

description: human skeletal muscle


title: CGND-HRA-00716

description:
CGND-HRA-00716_CCTAATCC_BCB4F2ANXX_L003_001
CGND-HRA-00716


title: CGND-HRA-00709

description:
CGND-HRA-00709_TGGTGGTA_BCB4F2ANXX_L007_001
CGND-HRA-00709


title: CGND-HRA-00702

description:
CGND-HRA-00702_TGGAACAA_BCB4F2ANXX_L005_001
CGND-HRA-00702


title: CGND-HRA-00708

description:
CGND-HRA-00708_GGTGCGAA_BCB4F2ANXX_L007_001
CGND-HRA-00708


title: CGND-HRA-00707

description:
CGND-HRA-00707_TGGCTTCA_BCB4F2ANXX_L006_001
CGND-HRA-00707


title: CGND-HRA-00706

description:
CGND-HRA-00706_AGCACCTC_BCB4F2ANXX_L005_001
CGND-HRA-00706


title: CGND-HRA-00697

description:
CGND-HRA-00697_ACAGATTC_BCB4F2ANXX_L003_001
CGND-HRA-00697


title: CGND-HRA-00715

description:
CGND-HRA-00715_GCCACATA_BCB4F2ANXX_L002_001
CGND-HRA-00715


title: CGND-HRA-00704

description:
CGND-HRA-00704_GACTAGTA_BCB4F2ANXX_L007_001
CGND-HRA-00704


title: CGND-HRA-00703

description:
CGND-HRA-00703_GGAGAACA_BCB4F2ANXX_L006_001
CGND-HRA-00703


title: CGND-HRA-00692

description:
CGND-HRA-00692_AGCAGGAA_BCB4F2ANXX_L002_001
CGND-HRA-00692


title: CGND-HRA-00693

description:
CGND-HRA-00693_TCTTCACA_BCB4F2ANXX_L003_001
CGND-HRA-00693


title: CGND-HRA-00686

description:
CGND-HRA-00686_TATCAGCA_BCB4F2ANXX_L001_001
CGND-HRA-00686


title: CGND-HRA-00687

description:
CGND-HRA-00687_AAACATCG_BCB4F2ANXX_L002_001
CGND-HRA-00687


title: CGND-HRA-00696

description:
CGND-HRA-00696_GCTCGGTA_BCB4F2ANXX_L005_001
CGND-HRA-00696


title: CGND-HRA-00700

description:
CGND-HRA-00700_AGATGTAC_BCB4F2ANXX_L004_001
CGND-HRA-00700


title: CGND-HRA-00685

description:
CGND-HRA-00685_GATAGACA_BCB4F2ANXX_L001_001
CGND-HRA-00685


title: CGND-HRA-00459

description:
EC51_AATCCGTC_ACAVVFANXX_L008_001
EC51

value: FTD


title: CGND-HRA-00701

description:
CGND-HRA-00701_CGCATACA_BCB4F2ANXX_L006_001
CGND-HRA-00701


title: CGND-HRA-00698

description:
CGND-HRA-00698_GCTAACGA_BCB4F2ANXX_L004_001
CGND-HRA-00698


title: CGND-HRA-00695

description:
CGND-HRA-00695_CAACCACA_BCB4F2ANXX_L006_001
CGND-HRA-00695


title: CGND-HRA-00458

description:
EC50_AAGGACAC_ACAVVFANXX_L008_001
EC50


title: CGND-HRA-00454

description:
EC43_CATCAAGT_ACAVVFANXX_L008_001
EC43


title: CGND-HRA-00694

description:
CGND-HRA-00694_CGAACTTA_BCB4F2ANXX_L004_001
CGND-HRA-00694


title: CGND-HRA-00691

description:
CGND-HRA-00691_CGACTGGA_BCB4F2ANXX_L005_001
CGND-HRA-00691


title: CGND-HRA-00690

description:
CGND-HRA-00690_AACGCTTA_BCB4F2ANXX_L003_001
CGND-HRA-00690


title: CGND-HRA-00453

description:
EC42-C9_CAATGGAA_ACAVVFANXX_L008_001
EC42-C9


title: CGND-HRA-00452

description:
EC40_GAACAGGC_ACAVVFANXX_L007_001
EC40


title: CGND-HRA-00451

description:
EC34-internal-k_CTAAGGTC_ACAVVFANXX_L007_001
EC34-internal-k


title: CGND-HRA-00689

description:
CGND-HRA-00689_ATGCCTAA_BCB4F2ANXX_L003_001
CGND-HRA-00689


title: CGND-HRA-00688

description:
CGND-HRA-00688_AACCGAGA_BCB4F2ANXX_L002_001
CGND-HRA-00688


title: CGND-HRA-00457

description:
EC49_AAGAGATC_ACAVVFANXX_L008_001
EC49


title: CGND-HRA-00456

description:
EC48_GCCAAGAC_ACAVVFANXX_L008_001
EC48


title: CGND-HRA-00684

description:
CGND-HRA-00684_CCGAAGTA_BCB4F2ANXX_L001_001
CGND-HRA-00684


title: CGND-HRA-00455

description:
EC47_GACAGTGC_ACAVVFANXX_L007_001
EC47


title: CGND-HRA-00445

description:
EC13_TGAAGAGA_ACAVVFANXX_L006_001
EC13


title: CGND-HRA-00444

description:
EC11_TTCACGCA_ACAVVFANXX_L007_001
EC11


title: CGND-HRA-00450

description:
EC24_CGGATTGC_ACAVVFANXX_L007_001
EC24


title: CGND-HRA-00446

description:
EC16_CCGACAAC_ACAVVFANXX_L006_001
EC16


title: CGND-HRA-00319

description:
CGND-HRA-00319_CTGTAGCC-_ACBCFHANXX_L004_001
CGND-HRA-00319-b38


title: CGND-HRA-00447

description:
EC19_CCTAATCC_ACAVVFANXX_L006_001
EC19


title: CGND-HRA-00197

description:
CGND-HRA-00197_GATAGACA_ACB00PANXX_L005_001
CGND-HRA-00197-b38


title: CGND-HRA-00441

description:
EC08_TCTTCACA_ACAVVFANXX_L006_001
EC08


title: CGND-HRA-00440

description:
EC03_TCCGTCTA_ACAVVFANXX_L006_001
EC03


title: CGND-HRA-00442

description:
EC09_TGGCTTCA_ACAVVFANXX_L007_001
EC09


title: CGND-HRA-00449

description:
EC22-internal-k_CGACACAC_ACAVVFANXX_L006_001
EC22-internal-k


title: CGND-HRA-00206

description:
CGND-HRA-00206_GTCGTAGA_BCAYDHANXX_L004_001
CGND-HRA-00206


title: CGND-HRA-00295

description:
CGND-HRA-00295_CAGATCTG_ACB20PANXX_L007_001
CGND-HRA-00295-b38


title: CGND-HRA-00104

description:
CGND-HRA-00104_GCCACATA_BCB60AANXX_L002_001
CGND-HRA-00104-b38


title: CGND-HRA-00170

description:
CGND-HRA-00170_AGGCTAAC_ACB00PANXX_L003_001
CGND-HRA-00170-b38


title: CGND-HRA-00110

description:
CGND-HRA-00110_CCAGTTCA_BCAYDHANXX_L008_001
CGND-HRA-00110


title: CGND-HRA-00076

description:
CGND-HRA-00076_CGCTGATC_BCAKTHANXX_L005_001
CGND-HRA-00076


title: CGND-HRA-00077

description:
CGND-HRA-00077_AGATGTAC_ACB00PANXX_L006_001
CGND-HRA-00077-b38


title: CGND-HRA-00074

description:
CGND-HRA-00074_AAGAGATC_BCAKTHANXX_L006_001
CGND-HRA-00074


title: CGND-HRA-00448

description:
EC21_CCTCTATC_ACAVVFANXX_L006_001
EC21


title: AHRR_TCDD_24h_ChIPSeq

status: Public on Jul 08 2017

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

data_processing:
Basecalls performed on Illumina HiSeq 2500 platform
Raw reads were aligned to hg19 genome assembly using Bowtie2 with default settings
Replicates of aligned reads were pooled using SAMTools
Peaks were called using MACS2 with default settings; Control input: DMSO, ChIP input: TCDD
Peak annotation was performed using HOMER Analysis Suite
Overlaps were performed with BEDTools
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files with peak location, score and annotation

source_name: MCF-7 breast cancer cells

growth_protocol: MCF-7 human breast cancer cells were cultured in low-glucose (1 g/L) DMEM (Dulbecco’s modified Eagle’s media) supplemented with 1% (v/v) penicillin/streptomycin (P/S) and 5% dextran coated charcoal (DCC)-treated FBS.

extract_protocol:
Cells were sonicated using Diagenode Bioruptor sonicator and protein-DNA complexes were isolated with antibody and beads
MicroPlex Library Preparation Kit using the manufacturer recommended protocol

treatment_protocol: Cells were treated with either DMSO (vehicle) or 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD) for either 45min or 24h

value: epithelial cells

value: mammary gland, breast

tag: chip-antibody

value: anti-AHRR (Sigma, HPA019614)


title: AHR_DMSO_24h_ChIPSeq

value: anti-AHR (Santa Cruz, H-211)


title: AHR_TCDD_45min_ChIPSeq


title: AHRR_DMSO_24h_ChIPSeq


title: AHR_DMSO_45min_ChIPSeq


title: CGND-HRA-00357

description:
CGND-HRA-00357-b38_AGATGTAC-_BCBDKPANXX_L001_001
CGND-HRA-00357-b38


title: CGND-HRA-00443

description:
EC10_TGGTGGTA_ACAVVFANXX_L007_001
EC10


title: CGND-HRA-00196

description:
CGND-HRA-00196_GATGAATC_ACB00PANXX_L004_001
CGND-HRA-00196-b38


title: P47_WT_HFSC_3

status: Public on Feb 05 2016

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

description: processed data file: P47_HTseq_count.txt

data_processing:
Libraries are sequenced by Illumina HiSeq 2000 and 2500.
Raw reads are alligned to mouse genome version mm10 though Tophat 2.
Gene count data are generated using Htseq count function.
Genome_build: mm10
Supplementary_files_format_and_content: column names are sample names, and sample names are gene symbols.

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension. Stem cells are purified through FACS by antibody staining and gating of H2BGFP(+), Sca-1(-), CD34(+) and CD49f(+) cells.
NEBNext® Ultra™ Directional RNA Library Prep Kit

tag: genotype/variation

value: K14-H2BGFP, Foxc1 fl/fl

tag: age

value: postnatal day 47

tag: gender

value: female

value: hair follicle stem cells (HFSC)

tag: molecule subtype

value: Oligo(dT) selected RNA


title: P47_WT_HFSC_4

value: male


title: P47_WT_HFSC_1


title: CGND-HRA-00728

description:
CGND-HRA-00728_GAACAGGC_BCB4F2ANXX_L008_001
CGND-HRA-00728

tag: sample group

tag: subject id

value: post-mortem tissue

value: Cerebellum

tag: cns subregion

value: Cerebellum, BA4


title: P30_WT_HFSC

description: processed data file: P30_HTseq_count.txt

value: postnatal day 30

tag: cell type


title: P29_WT_HFSC

value: postnatal day 29


title: P31_WT_HFSC

value: postnatal day 43


title: AHR_TCDD_24h_ChIPSeq

tag: tissue


title: Tiparp knockout, corn oil treated, biological rep3

status: Public on May 14 2015

description: corn oil treated C57BL/6;129Sv Tiparp-/- mice

hyb_protocol: standard protocols for Affymetrix GeneChip® Mouse Exon 1.0 ST Array

scan_protocol: scanning of microarrays were preformed on Affymetrix GCS3000 platform

data_processing:
Data were processed using Affymetrix® Expression Console with the RMA-Gene Core algorithm. Background adjustment were applied to probe intensities, gene level expression were quantile normalized and then were summarized from the corrected intensities.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Knockout, liver

extract_protocol: RNA was extraced with Trizol and purified with RNAeasy (Qiagen)

treatment_protocol: Mice were intraperitoneal injection with 30 ug/kg/bodyweight 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

value: 8 weeks

value: liver

tag: genotype

value: Tiparp -/-

tag: treatment

value: corn oil treated

tag: genetic background

value: C57BL/6;129Sv Tiparp-/- mice


title: Tiparp knockout, TCDD treated, biological rep1

description: 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv Tiparp-/- mice

label_protocol: standard protocols for Affymetrix GeneChip® Mouse Exon 1.0 ST Array


title: Wild-type corn oil treated, biological rep2

description: corn oil treated C57BL/6;129Sv mice

source_name: wild-type, liver

value: Tiparp +/+

value: C57BL/6;129Sv mice


title: Tiparp knockout, TCDD treated, biological rep2


title: Wild-type TCDD treated, biological rep1

description: 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv mice


title: Wild-type corn oil treated, biological rep1

description: corn oil treated C57BL/6;129Sv mice


title: AML Sample 60

status: Public on Jan 01 2015

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description: 140726and31_TRGRG78_1and2_GTCCGC_L00x_STARout

data_processing:
Basecalling with Illumina Casava version 1.8.2
Read demultiplexing done with bcl2fastq version 1.8.4
Adapter and quality trimming reads with CutAdapt  version 1.6
Alignment with STAR version 2.4.0b
Quantified and annotated LncRNAs with HTSeq framework version 0.6.1
Raw data transformed into Reads Per Million (RPM) and quantiles normalized prior to statistical analysis; RNA-seq data were not thresholded
Hugo Gene Nomenclature Committee (HGNC) gene symbols were used to cross-reference RNA-seq and Arraystar lncRNAs measures.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseqwithArraystarSymbols.NormalizedMatrix.xls; contains normalized expression data for LncRNAs

source_name: BM

extract_protocol:
Total RNA was extracted from patient samples using the Trizol method
Total RNA (200 ng in 10 uL volume; RIN >4) was treated by Ribo-Zero Gold Subtraction reagents from TruSeq stranded total RNA (Illumina; RS-122-2201) to remove human cytoplasmic and mitochondrial rRNAs and for the subsequent construction of the RNA-seq library according to the manufacturer's instructions.

tag: disease

value: Acute Myeloid Leukemia


title: AML Sample 63

description: 140726_TRGRG86_V1T_1_GTTTCG_L005_STARout


title: AML Sample 67

description: 140726_TRGRG93_V1T_1_ATTCCT_L002_STARout

tag: Sex

value: female

tag: race

value: White

value: Intermediate


title: AML Sample 62

description: 140726_TRGRG83_V1T_1_GTGAAA_L006_STARout

value: male


title: AML Sample 59

description: 140726_TRGRG76_V1T_1_CAGATC_L003_STARout


title: Wild-type TCDD treated, biological rep3


title: Wild-type corn oil treated, biological rep3

description: corn oil treated C57BL/6;129Sv mice


title: AML Sample 61

description: 140726_TRGRG79_V1T_1_ACTGAT_L007_STARout

value: Adverse


title: AML Sample 70

description: 140731_TRGRG98_1and2_CTTGTA_L00x_STARout


title: AML Sample 65

description: 140731_TRGRG90_1and2_GGCTAC_L00x_STARout


title: AML Sample 66

description: 140726_TRGRG92_V1T_1_GTGGCC_L006_STARout


title: AML Sample 58

description: 140726_TRGRG74_V1T_1_ATCACG_L003_STARout


title: AML Sample 71

description: 140731_TRGRG99_V1T_1_TTAGGC_L007_STARout


title: AML Sample 57

description: 140726_TRGRG73_V1T_1_GGCTAC_L004_STARout

source_name: PB

value: Favorable


title: AML Sample 64

description: 140731_TRGRG88_1and2_TAGCTT_L00x_STARout


title: AML Sample 68

description: 140726_TRGRG95_V1T_1_CGTACG_L006_STARout


title: Tiparp knockout, corn oil treated, biological rep2

description: corn oil treated C57BL/6;129Sv Tiparp-/- mice


title: Tiparp knockout, corn oil treated, biological rep1


title: Tiparp knockout, TCDD treated, biological rep3

description: 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv Tiparp-/- mice


title: Wild-type TCDD treated, biological rep2

description: 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv mice


title: AML Sample 56


title: AML Sample 69

description: 140726_TRGRG96_V1T_1_GTTTCG_L001_STARout


title: CGND-HRA-00718

description:
CGND-HRA-00718_CGACACAC_BCB4F2ANXX_L005_001
CGND-HRA-00718

tag: sample type

value: post-mortem tissue

value: Cerebellum

value: Cerebellum, BA4


title: AML Sample 55

description: 140726_TRGRG71_V1T_1_CCGTCC_L005_STARout


title: AML Sample 54

description: 140726_TRGRG70_V1T_1_TTAGGC_L001_STARout


title: AML Sample 52

description: 140731_TRGRG68_V1T_1_ACTTGA_L008_STARout


title: AML Sample 53

description: 140726_TRGRG69_V1T_1_CGATGT_L003_STARout


title: AML Sample 51

description: 140726_TRGRG67_V1T_1_GTGGCC_L002_STARout


title: AML Sample 33

value: Unclassifiab


title: AML Sample 34


title: AML Sample 43

description: 140726_TRGRG59_V1T_1_ATTCCT_L007_STARout


title: AML Sample 36


title: AML Sample 31


title: AML Sample 44

description: 140731_TRGRG60_V1T_1_CGATGT_L007_STARout


title: AML Sample 50

description: 140726_TRGRG66_V1T_1_GTCCGC_L005_STARout


title: AML Sample 41

description: 140731_TRGRG54_V1T_1_CCGTCC_L002_STARout


title: AML Sample 30

description: 140731_TRGRG37_V1T_1_GCCAAT_L008_STARout


title: AML Sample 49

description: 140726_TRGRG65_V1T_1_GTGAAA_L002_STARout


title: AML Sample 32

description: 140731_TRGRG40_V1T_1_ATTCCT_L004_STARout


title: AML Sample 46

description: 140726_TRGRG62_V1T_1_AGTCAA_L007_STARout

value: Hispanic


title: CGND-HRA-00713

description:
CGND-HRA-00713_CCATCCTC_BCB4F2ANXX_L001_001
CGND-HRA-00713


title: AML Sample 39

description: 140731_TRGRG49_V1T_1_TAGCTT_L001_STARout


title: AML Sample 42

description: 140726_TRGRG57_V1T_1_ACTGAT_L001_STARout


title: AML Sample 29


title: AML Sample 48

description: 140726_TRGRG64_V1T_1_TAGCTT_L004_STARout


title: AML Sample 38

description: 140731_TRGRG48_V1T_1_GATCAG_L001_STARout


title: AML Sample 35


title: AML Sample 28


title: AML Sample 37


title: AML Sample 40


title: AML Sample 27


title: AML Sample 47

description: 140726_TRGRG63_V1T_1_ATGTCA_L005_STARout

value: Black


title: AML Sample 26


title: AML Sample 45

description: 140731_TRGRG61_V1T_1_TGACCA_L008_STARout


title: AML Sample 25

description: 140731_TRGRG31_V1T_1_ACTGAT_L004_STARout


title: AML Sample 24


title: AML Sample 23


title: AML Sample 17


title: AML Sample 19

description: 140731_TRGRG21_V1T_1_GAGTGG_L002_STARout


title: AML Sample 20

description: 140731_TRGRG23_V1T_1_CAGATC_L008_STARout


title: AML Sample 22


title: AML Sample 15


title: AML Sample 13

description: 140711and26_TRGRG12_1and2_AGTTCC_L00x_STARout


title: AML Sample 12

description: 140711and26_TRGRG11_1and2_CCGTCC_L00x_STARout


title: AML Sample 21

description: 140731_TRGRG24_V1T_1_ATGTCA_L002_STARout

value: Native American


title: AML Sample 11


title: AML Sample 10


title: AML Sample 8


title: AML Sample 6

description: 140711and26_TRGRG04_1and2_ATCACG_L00x_STARout


title: AML Sample 18

description: 140731_TRGRG20_V1T_1_GTTTCG_L003_STARout


title: AML Sample 4

description: 140711and26_TRGRG02_1and2_ATGTCA_L00x_STARout


title: AML Sample 2

description: 140726and31_TRGR103_1and2_GAGTGG_L00x_STARout


title: AML Sample 9


title: AML Sample 3


title: AML Sample 7

description: 140711and26_TRGRG05_1and2_CGATGT_L00x_STARout


title: AML Sample 1

description: 140731_TRGR102_1and2_GATCAG_L00x_STARout


title: AML Sample 16

description: 140711and26_TRGRG15_1and2_AGTCAA_L00x_STARout


title: AML Sample 14


title: IgG_negative_control [reps 1 and 2]

status: Public on Oct 24 2012

description: IgG Replicates 1 and 2

data_processing:
Basecalling were performed using CASAVA
ChIP-Seq reads were aligned to the human genome version 19 using Short Oligo Analysis Package 2.21 (BGI, Shenzhen, China) (Li et al. 2009).
AHR Replicates 1 and 3 were compared against IgG Replicate 1 and 3. ARNT Replicates 1 and 2 were compared against IgG Replicate 1 and 2.
Peaks were called using CisGenome v2.0 with the following settings: Read Extension = 150 bp; Bin Size = 50 bp; Max Gap = 50 bp; Min Peak Length = 100 bp
Genome_build: hg19
Supplementary_files_format_and_content: BED

source_name: MCF-7 Breast Cancer Cells

growth_protocol: MCF-7 cells were grown in low glucose DMEM supplemented by steroid-free serum.

extract_protocol:
Cell extracts were sonicated and AHR/ARNT-DNA complexes are immunoprecipitated. Immunoprecipitated DNA was amplified using sigma aldrich SeqPlex whole-genome amplification kit.
Library was prepared according to Illumina's instruction by BGI (Shenzhen, China).

treatment_protocol: 10 nM dioxin for 45 min

tag: cell line

tag: chip antibody

value: IgG from rabbit serum (Sigma Aldrich, I5006)


title: AHR_ChIP-Seq

description: AHR Replicates 1 and 3

value: AHR antibody (Santa Cruz, H-211, catalog# sc-5579, lot# K1010)


title: AML Sample 5

tag: age


title: ARNT_ChIP-Seq

description: ARNT Replicates 1 and 2

value: ARNT antibody (Santa Cruz, H-172, catalog# sc-5580, lot# G3010)


title: IgG_negative_control [reps 1 and 3]

description: IgG Replicates 1 and 3