title: H_0750 (re-analyzed)

status: Public on Apr 09 2019

city: Boston

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

description:
all_norm.csv
H_0750

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
mRNA-Seq reads were aligned against UCSC hg19 genome build with STAR 2.5.3, parameters --runThreadN 8 --runMode alignReads --readFilesCommand zcat --outSAMtype BAM Unsorted
Aligned reads were counted against the Gencode v25 annotation gtf using Salmon 0.8.2
Genes were filtered from further analysis that had more than half of both HD and Control samples with zero counts
Outlier sample counts in individual genes were filtered
Differential expression between HD and Control was assessed using DESeq2 v1.3.34
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains normalized counts for all samples

source_name: BA9 prefrontal cortex

extract_protocol:
QIAzol, Qiagen miRNeasy kit
Illumina TruSeq RNA Sample Prep Kit, mRNA

value: Huntington's Disease

value: brain

tag: tissue region

value: BA9 prefrontal cortex


title: H_0726 (re-analyzed)

type: SRA

state: MA

country: USA

description:
all_norm.csv
H_0726

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: disease state

tag: tissue


title: H_0695 (re-analyzed)

description:
all_norm.csv
H_0695


title: H_0700 (re-analyzed)

description:
all_norm.csv
H_0700


title: H_0681 (re-analyzed)

description:
all_norm.csv
H_0681


title: H_0658 (re-analyzed)

description:
all_norm.csv
H_0658


title: H_0657 (re-analyzed)

description:
all_norm.csv
H_0657


title: H_0539 (re-analyzed)

description:
all_norm.csv
H_0539


title: H_0013 (re-analyzed)

description:
all_norm.csv
H_0013


title: H_0740 (re-analyzed)

description:
all_norm.csv
H_0740


title: H_0010 (re-analyzed)

description:
all_norm.csv
H_0010


title: H_0012 (re-analyzed)

description:
all_norm.csv
H_0012


title: H_0009 (re-analyzed)

description:
all_norm.csv
H_0009


title: H_0007 (re-analyzed)

description:
all_norm.csv
H_0007


title: H_0008 (re-analyzed)

description:
all_norm.csv
H_0008


title: H_0006 (re-analyzed)

description:
all_norm.csv
H_0006


title: H_0005 (re-analyzed)

description:
all_norm.csv
H_0005


title: H_0002 (re-analyzed)

description:
all_norm.csv
H_0002


title: H_0003 (re-analyzed)

description:
all_norm.csv
H_0003


title: C_0087 (re-analyzed)

description:
all_norm.csv
C_0087


title: C_0082 (re-analyzed)

description:
all_norm.csv
C_0082


title: C_0081 (re-analyzed)

description:
all_norm.csv
C_0081


title: C_0083 (re-analyzed)

description:
all_norm.csv
C_0083


title: C_0071 (re-analyzed)

description:
all_norm.csv
C_0071


title: C_0077 (re-analyzed)

description:
all_norm.csv
C_0077


title: C_0076 (re-analyzed)

description:
all_norm.csv
C_0076


title: C_0069 (re-analyzed)

description:
all_norm.csv
C_0069


title: C_0070 (re-analyzed)

description:
all_norm.csv
C_0070


title: C_0065 (re-analyzed)

description:
all_norm.csv
C_0065


title: C_0061 (re-analyzed)

description:
all_norm.csv
C_0061


title: C_0050 (re-analyzed)

description:
all_norm.csv
C_0050


title: C_0062 (re-analyzed)

description:
all_norm.csv
C_0062


title: C_0060 (re-analyzed)

description:
all_norm.csv
C_0060


title: C_0053 (re-analyzed)

description:
all_norm.csv
C_0053


title: C_0038 (re-analyzed)

description:
all_norm.csv
C_0038


title: C_0039 (re-analyzed)

description:
all_norm.csv
C_0039


title: C_0037 (re-analyzed)

description:
all_norm.csv
C_0037


title: H_0001 (re-analyzed)

description:
all_norm.csv
H_0001


title: C_0036 (re-analyzed)

description:
all_norm.csv
C_0036


title: C_0035 (re-analyzed)

description:
all_norm.csv
C_0035


title: C_0033 (re-analyzed)

description:
all_norm.csv
C_0033


title: C_0032 (re-analyzed)

description:
all_norm.csv
C_0032


title: C_0075 (re-analyzed)

description:
all_norm.csv
C_0075


title: C_0021 (re-analyzed)

description:
all_norm.csv
C_0021


title: C_0024 (re-analyzed)

description:
all_norm.csv
C_0024


title: C_0031 (re-analyzed)

description:
all_norm.csv
C_0031


title: C_0029 (re-analyzed)

description:
all_norm.csv
C_0029


title: C_0022 (re-analyzed)

description:
all_norm.csv
C_0022


title: C_0023 (re-analyzed)

description:
all_norm.csv
C_0023


title: C_0019 (re-analyzed)

description:
all_norm.csv
C_0019


title: C_0025 (re-analyzed)

description:
all_norm.csv
C_0025


title: C_0013 (re-analyzed)

description:
all_norm.csv
C_0013


title: C_0014 (re-analyzed)

description:
all_norm.csv
C_0014


title: C_0018 (re-analyzed)

description:
all_norm.csv
C_0018


title: C_0012 (re-analyzed)

description:
all_norm.csv
C_0012


title: C_0015 (re-analyzed)

description:
all_norm.csv
C_0015


title: C_0016 (re-analyzed)

description:
all_norm.csv
C_0016


title: C_0026 (re-analyzed)

description:
all_norm.csv
C_0026


title: C_0017 (re-analyzed)

description:
all_norm.csv
C_0017


title: C_0010 (re-analyzed)

description:
all_norm.csv
C_0010


title: C_0011 (re-analyzed)

description:
all_norm.csv
C_0011


title: C_0006 (re-analyzed)

description:
all_norm.csv
C_0006


title: C_0008 (re-analyzed)

description:
all_norm.csv
C_0008


title: C_0009 (re-analyzed)

description:
all_norm.csv
C_0009


title: C_0004 (re-analyzed)

description:
all_norm.csv
C_0004


title: H_1106_BA9

description:
all_norm.csv
H_1106_BA9_mRNASeq


title: C_0003 (re-analyzed)

description:
all_norm.csv
C_0003


title: C_0002 (re-analyzed)

description:
all_norm.csv
C_0002


title: C_0020 (re-analyzed)

description:
all_norm.csv
C_0020


title: H_1105_BA9

description:
all_norm.csv
H_1105_BA9_mRNASeq


title: H_1104_CAP

description:
all_norm.csv
H_1104_CAP_mRNASeq

source_name: CAU

value: CAU


title: H_0513_BA9

description:
all_norm.csv
H_0513_BA9_mRNASeq


title: H_0656_BA9

description:
all_norm.csv
H_0656_BA9_mRNASeq


title: C_0114_CAP

description:
all_norm.csv
C_0114_CAP_mRNASeq

value: control


title: H_0601_BA9

description:
all_norm.csv
H_0601_BA9_mRNASeq


title: H_0689_BA9

description:
all_norm.csv
H_0689_BA9_mRNASeq


title: H_1104_BA9

description:
all_norm.csv
H_1104_BA9_mRNASeq


title: H_0723_BA9

description:
all_norm.csv
H_0723_BA9_mRNASeq


title: C_0091_BA9

description:
all_norm.csv
C_0091_BA9_mRNASeq


title: H_0709_BA9

description:
all_norm.csv
H_0709_BA9_mRNASeq


title: C_0074_BA9

description:
all_norm.csv
C_0074_BA9_mRNASeq


title: H_1105_CAP

description:
all_norm.csv
H_1105_CAP_mRNASeq


title: C_0005 (re-analyzed)

description:
all_norm.csv
C_0005


title: C_0034_BA9

description:
all_norm.csv
C_0034_BA9_mRNASeq


title: C_0113_CAP

description:
all_norm.csv
C_0113_CAP_mRNASeq


title: ATAC_I-BRD9-4hr

status: Public on Oct 24 2018

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
ATAC-seq: paired‐end 38‐bp sequencing reads were aligned with BWA (version 0.7.10) allowing one mismatch.
bam files were converted to tag align files using gawk and bedtools.
tag alignments were shifted (+4 bp for plus strand and -5bp for minus strand) to account for TN5 insertion
peak calling was done with MACS (version 2.1.0).
ChIP-seq: sequencing reads were aligned with BWA (version 0.7.10) allowing one mismatch.
bam files were converted to tag align files using gawk and bedtools.
peak calling was done with MACS (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq fold change (vs input) signal files in bigwig format and called peaks in bed format. ATAC-seq fold change (vs. background) signal in bigwig format and called pooled peaks in bed format.

molecule: genomic DNA

source_name: HeLa

extract_protocol:
ChIP-seq samples were purified from sonicated nuclei using antibody-based immunoprecipitation. ATAC-seq samples were generated using Nextera transposase (Illumina) on purified nuclei.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to the manufacturer's protocol.  ATAC-seq libraries were prepared using Nextera chemistry (Illumina).

treatment_protocol: HeLa S3 cells were treated with DMSO or I-BRD9 (10 μM ) for 6 h prior to isolating chromatin (ChIP-seq) or induction with EGF (100 ng/ml)  (ATAC-seq).

tag: cell type

value: immortalized cervical cancer cells

tag: treatment

tag: timepoint


title: ATAC_DMSO-4hr

value: DMSO


title: ATAC_DMSO-1hr


title: ATAC_I-BRD9-0min


title: ATAC_DMSO-30min


title: ATAC_I-BRD9-30min


title: H6FiPS2 rep 3

status: Public on Nov 29 2018

type: RNA

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
iPSCs are reprogrammed from the F134 fibroblasts.
Replicate 3

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4 expression BeadChips (Illumina, USA) following the manufacturer’s instructions.

scan_protocol: After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

label: biotin

molecule: total RNA

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

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h).

value: induced pluripotent stem cells

tag: pluripotency

value: yes


title: ATAC_DMSO-0min


title: H4FiPS2 rep 3


title: ATAC_I-BRD9-1hr


title: H6FiPS3 rep 3


title: Fibro rep 1

description: Replicate 1

source_name: Fibroblasts

tag: cell line

value: fibroblast cell line

value: no


title: input_iBRD9

tag: chip antibody


title: H4FiPS1 rep 3


title: H1 rep 3

description: Replicate 3

value: embryonic stem cell line


title: H6FiPS2 rep 1

description:
iPSCs are reprogrammed from the F134 fibroblasts.
Replicate 1


title: H4FiPS1 rep 1


title: H9 rep 1

description: Replicate 1


title: HH28_DFL_WT_H3K27ac

status: Public on Nov 27 2018

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: chick HH28 WT distal forelimb H3K27ac

data_processing:
Demultiplexed ChIP-seq reads were mapped onto the galGal5 or mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
By using bamCompare (Version 2.5.0), The ChIP data from H3K27ac, H3K27me3 and H3K4me1 and the input data were normalized and compared to compute the log2 of the number of reads ratio.
The CTCF ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016). Peaks of CTCF were called by using MACS2 (Version 2.1.0.20151222) with q-value (0.01) and used for the CTCF motif orientation analysis as previously described (Rodríguez-Carballo et al. 2017)
All analysis was done with our Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input; bedgraph of the normalized 1x depth of CTCF coverage; bed of CTCF narrow peaks with q-value=0.01

organism: Gallus gallus

source_name: Forelimb

extract_protocol:
Chromatin immunoprecipitated experiment was performed as previously described (Beccari et al. 2016). Micro-dissected limb tissues from mouse and chick embryos were cross-linked with 1% formaldehyde/PBS for 15 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Merck Millipore), anti-H3K4me1 (ab8895, Abcam) and anti-CTCF (61311, Active Motif), respectively.
Libraries were prepared with at least 5 ng of purified DNA following Illumina TruSeq ChIP library preparation guide. Sequencing was performed with 100-bp single-end.

tag: breed

value: White Leghorn

tag: age

tag: tissues

value: Distal forelimb

tag: genotype

value: wild type

tag: antibody


title: HH28_PFL_WT_H3K27ac

description: chick HH28 WT proximal forelimb H3K27ac

value: Proximal forelimb


title: H6FiPS2 rep 2

description:
iPSCs are reprogrammed from the F134 fibroblasts.
Replicate 2


title: H4FiPS1 rep 2


title: H6FiPS3 rep 2


title: H4FiPS2 rep 1


title: H6FiPS3 rep 1


title: H1 rep 2

description: Replicate 2


title: H9 rep 2

description: Replicate 2


title: H9 rep 3

description: Replicate 3


title: H4FiPS2 rep 2


title: input_untreated


title: H1 rep 1

description: Replicate 1


title: BRD9_untreated

value: Rabbit polyclonal anti-BRD9 (Active Motif 61537, 61538)


title: GFP_GLTSCR1L_iBRD9

value: Rabbit polyclonal anti-GFP (Abcam ab290)


title: GFP_GLTSCR1L_untreated


title: I-BRD9_1hr_rep2

status: Public on Oct 17 2018

data_processing:
CAGE-seq: assigned reads were 5′-end trimmed to remove linker sequences (9+2 bp to account for the CAGE protocol G-bias), 3′-end trimmed to a length of 25 bp using FASTX toolkit (version 0.0.13)
Reads matching to reference rRNA sequences were discarded using rRNAdust
mapping to the human genome was performed using BWA (version 0.7.10)
Only the 5’ ends of mapped reads were considered in subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CAGE tag files in bed format.

growth_protocol: HeLa S3 cells were grown on 60 mm plates treated with DMSO or I-BRD9 (10 μM ) 6 h prior to induction with EGF (100 ng/ml) for 30 min

extract_protocol:
Total RNA was isolated using TRI Reagent® (Ambion) according to manufacturer’s recommendations
CAGE libraries were prepared using the protocol by (Takahashi et al. 2012) with an input of 3 μg of total RNA


title: I-BRD9_30min_rep1


title: I-BRD9_4hr_rep3


title: I-BRD9_30min_rep2


title: I-BRD9_30min_rep3


title: I-BRD9_0min_rep3


title: I-BRD9_4hr_rep1


title: I-BRD9_0min_rep1


title: I-BRD9_0min_rep2


title: I-BRD9_4hr_rep2


title: BRD9_iBRD9


title: DMSO_4hr_rep3


title: DMSO_4hr_rep2


title: DMSO_1hr_rep1


title: DMSO_1hr_rep2


title: I-BRD9_1hr_rep3


title: DMSO_4hr_rep1


title: DMSO_30min_rep2


title: DMSO_1hr_rep3


title: DMSO_30min_rep1


title: I-BRD9_1hr_rep1


title: DMSO_0min_rep3


title: DMSO_0min_rep2


title: DMSO_0min_rep1


title: prostate: MSKCC-EF1 ATAC-seq

status: Public on Oct 05 2018

city: Los Angeles

first: Owen

middle: N

last: Witte

state: CA

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

data_processing:
ENCODE processing pipeline (https://www.encodeproject.org/atac-seq/)
Genome_build: hg38 human genome
Supplementary_files_format_and_content: bigwig

source_name: prostate

value: prostate

value: small cell prostate cancer

tag: transplant


title: prostate: PARCB6 ATAC-seq

value: transformed prostate basal epithelial

value: NSG mice


title: prostate: PARCB1 ATAC-seq


title: prostate: PARCB8 ATAC-seq


title: DMSO_30min_rep3

value: immortalized cervical cancer cells


title: prostate: PARCB3 ATAC-seq


title: PFL_E12_Wt_CTCF

status: Public on Dec 22 2017

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Proximal forelimb mouse E12.5_Wt_CTCF_ChIP-seq

data_processing:
adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Then reads were mapped using bowtie2 on the mm10 genome (ref Langmead et al. 2012 version 2.2.4 default parameters).
Bam files were merged when replicates or resequencing were done.
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B). By default, MACS2 only kept one tag at the same location (the same coordinates and the same strand), which would remove all potential contaminants from 4C experiments.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak contains the peak calling; BedGraph contains the coverage from macs2

organism: Mus musculus

source_name: Proximal Forelimbs

growth_protocol: Heterozygous mutant mice were crossed in order to obtain Wt and homozygous mutant embryos.

extract_protocol:
E12.5 limb tissue was micordissected from wild type or HoxD mutants embryos and used for ChIP experiments. Samples were fixed in 1% formaldehyde/PBS for 10 (CTCF, H3K27ac, RAD21) or 25 (RAD21, SMC1) minutes at room temperature, washed three times with cold PBS containing protease inhibitor (and, for H3K27ac, deacetylase inhibitor) and stored at -80°C. For ChIP-seq samples, around, one hundred milligrams of tissue were used. Nuclei were extracted by incubating them in a cell lysis buffer provided in the ChIP IT high sensitivity kit (Active motif) during at least 10 minutes and with the aid of a Dounce homogenizer type B (Active motif). The isolated nuclei were pelleted and lysed in sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH=8.0, protease inhibitor and, for the case of H3K27ac, deacetylase inhibitor) for 10 min on ice, and fragmented to a range of 200-500 bp using a Vibracell tip sonicator or a Diagenode Bioruptor pico waterbath device. DNA concentration was estimated using the Qubit ds DNA HS assay kit following manufacturer instruction and 25-30ug of chromatin were diluted ten times in ChIP dilution buffer (20mM HEPES, 150mM NaCl, 0.1% NP40) and incubated overnight at 4ºC with 4ug of anti-CTCF antibody (Active motif, 61311, 61312), anti-SMC1 (Bethyl, A300-055A), anti-RAD21 (abcam, ab992) or 2ug of anti-H3K27ac (abcam, ab4729) on a rotating platform. For ChIP-seq samples, the next day chromatin-antibody complexes were incubated with protein A/G agarose beads during 3h at 4ºC and successively washed following manufacturer instructions. Finally they were eluted and purified by phenol:chlorophorm extraction and precipitation. Between 5 to 10ng of immunoprecipitated DNA were sequenced with a 50bp single-end Illumina HiSeq flow cell.
For ChIP-seq, 5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: Proximal Forelimbs

tag: strain

tag: embryonic day

value: anti-CTCF (Active motif, 61311, 61312)


title: DFL_E12_Wt_CTCF

description: Distal forelimb mouse E12.5_Wt_CTCF_ChIP-seq

source_name: Distal Forelimbs

value: Distal Forelimbs


title: PFL_E12_Wt_H3K27ac

description: Proximal forelimb mouse E12.5_Wt_H3K27ac_ChIP-seq

data_processing:
adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Then reads were mapped using bowtie2 on the mm10 genome (ref Langmead et al. 2012 version 2.2.4 default parameters).
Bam files were merged when replicates or resequencing were done.
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B). By default, MACS2 only kept one tag at the same location (the same coordinates and the same strand), which would remove all potential contaminants from 4C experiments.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph contains the coverage from macs2

value: anti-H3K27ac (abcam, ab4729)


title: Nd0 rep 3

status: Public on Jun 06 2018

description: replicate 3

hyb_protocol: Agilent mouse whole genome 8x60K oligo microarrays (design 028005) were used for hybridizations. Each microarray displayed 39,430 Entrez Gene RNAs and 16,251 lincRNAs. The Agilent Gene Expression Hybridization Kit was used for hybridization as detailed in the Agilent processing protocol (Agilent technologies). In brief, 600 ng Cy3-labelled fragmented cRNA in hybridization buffer was hybridized overnight at 65C to the microarrays using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed with the Agilent Gene Expression Wash Buffer 1 (1 min at 23C) and then with preheated Agilent Gene Expression Wash Buffer 2 (1 min at 37C).

scan_protocol: The Agilent’s Microarray Scanner Sytem (Agilent Technologies) was used for detecting fluorescence signals on the hybridized microarrays. The microarray image files were processed with the Agilent Feature Extraction Software (FES),

data_processing: The microarray raw data were normalized using the quantile method.

source_name: Nd0, Non-vaccinated day 0

label_protocol:
Each RNA sample was used to produce Cy3-labeled cRNA.
Eqivalents of 100 ng from the individual RNA samples were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies)
according to the manufacturer’s instructions.
Yields of cRNA and dye-incorporation were determined with the ND-1000 Spectrophotometer (NanoDrop Technologies).
The incorporations were between 18 and 23 fmol Cy3/ng cRNA.

extract_protocol:
Livers were aseptically removed from sacrificed mice, rapidly frozen in liquid nitrogen and stored at -80o C until use.
For isolation of total RNA, livers were individually grounded in a mortar under liquid nirogen and aliquots were subjected to the
Trizol standard RNA extraction. An additional cleaning up of  RNA followed using the miRNeasy Kit (Qiagen, Hilden, Germany).
Integrity and quality of RNA was checked with the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
RIN values of all RNA samples ranged beween 8.7 and 9.1.

value: Balb/c

value: Non-vaccinated

tag: infection

value: control

tag: time

value: day 0

value: liver


title: DFL_E12_Wt_H3K27ac

description: Distal forelimb mouse E12.5_Wt_H3K27ac_ChIP-seq

tag: tissue

value: wild type


title: NSC-3

status: Public on Oct 04 2018

description: replicate 1

hyb_protocol: Purified and labeled cRNA was then hybridized for 12 hrs onto MouseRef-8 v2.0 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina)background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: NSC

extract_protocol: 300  µg of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

tag: cell type

value: In vitro Neural Stem Cell (NSC)

tag: clone


title: Vd4 rep 1

description: replicate 1

source_name: Vd4, Vaccinated day 4

tag: treatment

value: Vaccinated

value: P. chabaudi malaria

value: day 4


title: Nd0 rep 2

description: replicate 2


title: ESC NPC-1

description: replicate 1

source_name: ESC NPC

value: Neural Progenitor Cell (NPC) differentiated from Embryonic Stem Cell (ESC)


title: iNSC-1

description: replicate 1

source_name: iNSC

value: Neural Stem Cell (NSC) induced from Mouse Embryonic Fibroblast (MEF)


title: NSC-2

description: replicate 1


title: ESC NPC-2

description: replicate 1


title: ESC (not NSC)

description: replicate 1

source_name: ESC

value: Embryonic Stem Cell (ESC), not Neural Stem Cell (NSC)


title: Vd0 rep 3

description: replicate 3

source_name: Vd0, Vaccinated day 0


title: iNSC-3

description: replicate 1


title: NSC-1

description: replicate 1


title: iNSC-2

description: replicate 1


title: ESC NPC-3

description: replicate 1


title: Vd4 rep 3

description: replicate 3


title: Nd4 rep 1

description: replicate 1

source_name: Nd4, Non-vaccinated day 4


title: NSC-In vivo

description: replicate 1

source_name: NSC-In vivo

value: In vivo Neural Stem Cell (NSC)


title: iNSC-In vivo

description: replicate 1

source_name: iNSC-In vivo

value: In vivo (14 after transplantation into the adult mouse brain) Neural Stem Cell (NSC) induced from Mouse Embryonic Fibroblast (MEF)


title: Nd0 rep 1

description: replicate 1


title: MEF (not NSC)

description: replicate 1

source_name: MEF

value: Mouse Embryonic Fibroblast (MEF), not Neural Stem Cell (NSC)


title: Vd0 rep 1

description: replicate 1


title: Vd0 rep 2

description: replicate 2


title: Nd4 rep 2

description: replicate 2


title: Vd4 rep 2

description: replicate 2


title: Nd4 rep 3

description: replicate 3


title: FTD-2 GC-3

status: Public on Jun 12 2017

description: Replicate 1

source_name: FTD-2 GC-3

value: FTD-2 GC-3

tag: gene corrected

value: Yes


title: Ctrl-2 Astro, rep 3

description: Replicate 3

source_name: Ctrl-2 Astro

value: Ctrl-2 Astro


title: FTD-1, rep 1

description: Replicate 1

value: No


title: FTD-2 GC-1

description: Replicate 1

source_name: FTD-2 GC-1

value: FTD-2 GC-1


title: Ctrl-Neurons on Ctrl Astro, rep 3

description: Replicate 3

source_name: Ctrl-Neurons on Ctrl Astro

value: Ctrl-Neurons on Ctrl Astro


title: Ctrl-1 Astro, rep 3

description: Replicate 3

source_name: Ctrl-1 Astro

value: Ctrl-1 Astro


title: FTD-2, rep 1

description: Replicate 1


title: FTD-1 GC-1

description: Replicate 1

source_name: FTD-1 GC-1

value: FTD-1 GC-1


title: C1 FTD-2, rep 2

description: Replicate 2

source_name: C1 FTD-2

value: C1 FTD-2


title: FTD-2, rep 2

description: Replicate 2


title: Ctrl-1 Astro, rep 1

description: Replicate 1


title: Ctrl-2 Astro, rep 1

description: Replicate 1


title: C1 FTD-2, rep 1

description: Replicate 1


title: FTD-2 GC-2

description: Replicate 1

source_name: FTD-2 GC-2

value: FTD-2 GC-2


title: FTD-2 Astro, rep 2

description: Replicate 2

source_name: FTD-2 Astro

value: FTD-2 Astro


title: C1

description: Replicate 1


title: Ctrl-2 Astro, rep 2

description: Replicate 2


title: Ctrl-1 Astro, rep 2

description: Replicate 2


title: FTD-1 Astro, rep 2

description: Replicate 2

source_name: FTD-1 Astro

value: FTD-1 Astro


title: Ctrl-Neurons on Ctrl Astro, rep 2

description: Replicate 2


title: Ctrl-Neurons on FTD Astro, rep 2

description: Replicate 2

source_name: Ctrl-Neurons on FTD Astro

value: Ctrl-Neurons on FTD Astro


title: FTD-1, rep 2

description: Replicate 2


title: FTD-2 Astro, rep 3

description: Replicate 3


title: Ctrl-Neurons on Ctrl Astro, rep 1

description: Replicate 1


title: C1 FTD-2, rep 3

description: Replicate 3


title: Ctrl-Neurons on FTD Astro, rep 3

description: Replicate 3


title: FTD-1 Astro, rep 3

description: Replicate 3


title: Ctrl-Neurons on FTD Astro, rep 1

description: Replicate 1


title: FTD-1 Astro, rep 1

description: Replicate 1


title: FTD-2 Astro, rep 1

description: Replicate 1


title: PC2FiOPCp25 rep 2

status: Public on May 21 2017

description: replicate 2

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina

scan_protocol: After the recommended washing the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina)
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.

source_name: PC2FiOPCp25 rep 2

extract_protocol:
300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)
The RNA samples from in vivo transplanted and FACS sorted cells
were amplified using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre

value: iOPC


title: PC2FiOPCp5 rep 2

description: replicate 2

source_name: PC2FiOPCp5 rep 2


title: PC2FiOPCp5 rep 1

description: replicate 1

source_name: PC2FiOPCp5 rep 1


title: OPC rep 2

description: replicate 2

source_name: OPC rep 2

value: Oligodendrocyte


title: PC rep 1

description: replicate 1

source_name: PC rep 1

value: Pericyte


title: PC2FiOPCp25 rep 1

description: replicate 1

source_name: PC2FiOPCp25 rep 1


title: PC2FiOPCp15 rep 1

description: replicate 1

source_name: PC2FiOPCp15 rep 1


title: PC2FiOPCp15 rep 2

description: replicate 2

source_name: PC2FiOPCp15 rep 2


title: OPC rep 1

description: replicate 1

source_name: OPC rep 1


title: patient 1 iPS rep1

status: Public on Apr 11 2017

description: Replicate 1

value: induced pluripotent stem cells

tag: pluripotent

value: yes


title: patient 2 iPS rep1

description: Replicate 1


title: H9 rep1

description: Replicate 1

tag: cell line

value: embryonic stem cell line


title: H1 rep1

description: Replicate 1


title: control 2 iPS rep1

description: Replicate 1


title: PC rep 2

description: replicate 2

source_name: PC rep 2


title: F134 rep1

description: Replicate 1

value: fibroblast cell line

value: no


title: CD1 Sdc4- rep1

status: Public on Feb 21 2017

description: replicate 1

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing:
Primary data was processed with GeneSpring 11.0 software (Silicon Genetics, Redwood City, CA).
Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: CD1 Sdc4-, Lineage tracing of mouse CD1 [Fullname strain: Crl:CD1(ICR)] Sdc4-, 1 replicate

label_protocol: Biotinylated cRNA. with the Low Input Quick Amp Labeling Kit (5190-2305, Agilent Technologies), according to manufacturer´s instructions

extract_protocol: Total RNA was extracted from cells by miRNeasy Micro Kit (50) (217084, Qiagen) and a range between 10 ng and 200 ng of total DNA-free RNA was used

value: CD1 Sdc4-


title: Cspg4+ rep1

description: replicate 1

source_name: Cspg4+, Lineage tracing of mouse Cspg4+ [Fullname strain: B6,FVB-Tg(Cspg4-cre)1Akik/J], 1 replicate


title: B195AP+ Sdc4- rep1

description: replicate 1

source_name: B195AP+ Sdc4-, Lineage tracing of mouse B195AP+ [Fullname strain: B195AP-Cre]  Sdc4-, 1 replicate

value: B195AP+ Sdc4-


title: Cspg4- Sdc4+ rep1

description: replicate 1

source_name: Cspg4- Sdc4+, Lineage tracing of mouse Cspg4- [Fullname strain: B6,FVB-Tg(Cspg4-cre)1Akik/J] Sdc4+, 1 replicate

value: Cspg4- Sdc4+


title: CD1 Sdc4+ rep1

description: replicate 1

source_name: CD1 Sdc4+, Lineage tracing of mouse CD1 [Fullname strain: Crl:CD1(ICR)] Sdc4+, 1 replicate

value: CD1 Sdc4+


title: Myf5SOR+ Sdc4+ rep1

description: replicate 1

source_name: Myf5SOR+ Sdc4+, Lineage tracing of mouse Myf5SOR+ [B6.129S4-Myf5tm3(cre)Sor /J] Sdc4+, 1 replicate

value: Myf5SOR+ Sdc4+


title: Cspg4- Sdc4- rep1

description: replicate 1

source_name: Cspg4- Sdc4-, Lineage tracing of mouse Cspg4- [Fullname strain: B6,FVB-Tg(Cspg4-cre)1Akik/J] Sdc4-, 1 replicate

value: Cspg4- Sdc4-


title: S95-2, rep 2

status: Public on Feb 13 2017

description: Replicate 2

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2.0 expression BeadChips (Illumina, USA) following the manufacturer’s instructions. After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare).

scan_protocol: The chips were scanned using the iScan reader (Illumina) and the accompanying software.

tag: strain/background

value: Sox2-null ESCs

tag: type of sox2 mutant

value: Sox2 95 mutant clone 2


title: TSS, rep 2

description: Replicate 2

source_name: TSS

value: Sox2 expressed


title: S95-4, rep 1

description: Replicate 1

value: Sox2 95 mutant clone 4


title: S95-2, rep 1

description: Replicate 1


title: S95-4, rep 2

description: Replicate 2


title: TSS, rep 1

description: Replicate 1


title: S95-1, rep 2

description: Replicate 2

value: Sox2 95 mutant clone 1


title: SWT-4, rep 2

description: Replicate 2

value: Sox2 wild type clone 4


title: SWT-4, rep 1

description: Replicate 1


title: S95-1, rep 1

description: Replicate 1


title: SWT-5, rep 1

description: Replicate 1

value: Sox2 wild type clone 5


title: S113-5, rep 1

description: Replicate 1

value: Sox2 113 mutant clone 5


title: SWT-5, rep 2

description: Replicate 2


title: S113-4, rep 1

description: Replicate 1

value: Sox2 113 mutant clone 4


title: S113-4, rep 2

description: Replicate 2


title: FTDP17-1 Dif rep 3

status: Public on Feb 10 2017

description: replicate 3

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: FTDP17-1 Dif rep 3

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

value: Neurons


title: FTDP17-2 Dif rep 3

description: replicate 3

source_name: FTDP17-2 Dif rep 3


title: Ctrl-1 Dif rep 3

description: replicate 3

source_name: Ctrl-1 Dif rep 3


title: Ctrl 3-I iPSC

description: replicate 1

source_name: Ctrl 3-I iPSC

value: iPSC


title: Ctrl 1-II iPSC

description: replicate 1

source_name: Ctrl 1-II iPSC


title: FTDP17 2-II iPSC

description: replicate 1

source_name: FTDP17 2-II iPSC


title: FTDP17-1 Dif rep 2

description: replicate 2

source_name: FTDP17-1 Dif rep 2


title: Ctrl 2-I iPSC

description: replicate 1

source_name: Ctrl 2-I iPSC


title: Ctrl-1 Dif rep 2

description: replicate 2

source_name: Ctrl-1 Dif rep 2


title: FTDP17-2 Dif rep 2

description: replicate 2

source_name: FTDP17-2 Dif rep 2


title: FTDP17-1 Dif rep 1

description: replicate 1

source_name: FTDP17-1 Dif rep 1


title: FTDP17-2 Dif rep 1

description: replicate 1

source_name: FTDP17-2 Dif rep 1


title: FTDP17 1-II iPSC

description: replicate 1

source_name: FTDP17 1-II iPSC


title: Ctrl-2 Dif rep 3

description: replicate 3

source_name: Ctrl-2 Dif rep 3


title: H9 ESC rep 2

description: replicate 2

source_name: H9 ESC rep 2

value: ESC


title: Ctrl-2 Dif rep 1

description: replicate 1

source_name: Ctrl-2 Dif rep 1


title: FTDP17 1-I iPSC

description: replicate 1

source_name: FTDP17 1-I iPSC


title: H1 ESC rep 2

description: replicate 2

source_name: H1 ESC rep 2


title: H9 ESC rep 1

description: replicate 1

source_name: H9 ESC rep 1


title: Ctrl-1 Dif rep 1

description: replicate 1

source_name: Ctrl-1 Dif rep 1


title: H1 ESC rep 3

description: replicate 3

source_name: H1 ESC rep 3


title: Ctrl-2 Dif rep 2

description: replicate 2

source_name: Ctrl-2 Dif rep 2


title: Ctrl 1-I iPSC

description: replicate 1

source_name: Ctrl 1-I iPSC


title: H9 ESC rep 3

description: replicate 3

source_name: H9 ESC rep 3


title: H1 ESC rep 1

description: replicate 1

source_name: H1 ESC rep 1


title: FTDP17 2-I iPSC

description: replicate 1

source_name: FTDP17 2-I iPSC


title: Fibroblast rep 1

description: replicate 1

source_name: Fib rep 1

value: Fibroblast


title: Fibroblast rep 2

description: replicate 2

source_name: Fib rep 2


title: hiPSC-w/o DAS

status: Public on Feb 09 2017

description:
hiPSCs are derived from fibroblasts.
Replicate 1 of 1.

hyb_protocol: Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 Chip, following the manufacturer’s instructions.

scan_protocol: Arrays scanning was performed with GeneChip Scanner 3000 (Affymetrix). Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal, and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was performed using the Affymetrix Robust Multi-array Analysis (RMA), variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

source_name: hiPSCs grown on uncoated glass

label_protocol: Biotinylated cRNA were prepared for Affymetrix arrays following the manufacturer's instructions.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

value: human induced pluripotent stem cells (hiPSCs)

tag: growth condition

value: uncoated glass


title: hiPSC-DAS/GL

source_name: hiPSCs grown on DAS-NG coated glass

value: diffusion-associated synthesis nanocrystalline graphene (DAS-NG) coated glass


title: MEF rep 1

status: Public on Dec 21 2016

description: replicate 1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method

source_name: MEF rep 1

tag: potency

value: Unipotent


title: O6SKM-iPSC1

description: replicate 1

value: Pluripotent


title: O4SKM-iPSC rep 2

description: replicate 2

source_name: O4SKM-iPSC rep 2


title: MEF rep 2

description: replicate 2

source_name: MEF rep 2


title: O4SK-iPSC1

description: replicate 1


title: O4SKM-iPSC rep 1

description: replicate 1

source_name: O4SKM-iPSC rep 1


title: OG2-ESC rep 1

description: replicate 1

source_name: OG2-ESC rep 1


title: OG2-ESC rep 2

description: replicate 2

source_name: OG2-ESC rep 2


title: O4SK-iPSC2

description: replicate 1


title: hiPSC_MEF

source_name: hiPSCs grown on mitomycin-C treated MEF

value: mitomycin-C treated MEF


title: hESC-MEF

description: Replicate 1 of 1.

source_name: hESCs grown on mitomycin-C treated MEF

value: human embryonic stem cells (hESCs)


title: O6SKM-iPSC2

description: replicate 1


title: Aph+SCNT rep1

status: Public on Dec 17 2016

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: Aph+SCNT rep1

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

extract_protocol: 150 ng of total DNA-free RNA was extrated using ZR RNA MicroPrep kit (ZYMO RESEARCH, R1061) following the manufacturer's instructions (IVT: 17h)

tag: aphidicolin treated

value: Yes

value: Aphidicolin

tag: sample type

value: somatic cell nuclear transfer blastocyst

value: blastocysts


title: e11.5_forelimb_distal_wt_HoxA13

status: Public on Dec 14 2016

city: montreal

first: Rushikesh

last: Sheth

address: 110 avenue des pins ouest

department: Genetics and Development

country: Canada

institute: IRCM

description: Chromatin IP against HoxA13

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS v1.4 (PMID: 18798982) with default parameters and --nomodel. Each IP was compared to experiment-matched input DNA.
In the case of e10.5 forelimb H3K27me3 sample, trimming of 56 bases at the 3' was performed before alignment. All the other samples were trimmed by 6 bases at their 3'.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: embryonic forelmb bud, HoxA13 ChIP

growth_protocol: The Hoxa13 loss of function allele was generated by insertion of neomycine cassette in Hoxa13 coding region (PMID: 8898214). In Hoxd13 loss of function allele, a lacZ reporter transgene is inserted in the first exon of Hoxd13 (PMID: 10652274). The Hoxa13 and Hoxd13 mutant lines were maintained in a mixed background. Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from tail biopsies and yolk sacs, respectively

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 16630818) with some modifications. Briefly, E11.5 ZAP cells from wild type and mutant limbs were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was cross-linked using formaldehyde as previously described except for HOXA13 ChIP for which we performed the cross-linking using a dual method using disuccinimidyl glutarate (DSG) and formaldehyde (PMID: 21123453). Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. Protein A and G Dynabeads (Invitrogen) were incubated 6h at 4 C with 5 µg of antibody. The chromatin was then incubated with the beads overnight at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 65 C overnight. Samples were treated for 15 min RT with RNase A and then with Proteinase K for one hour at 55 C. Finally, the DNA was purified on QIAquick columns (Qiagen) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared by the IRCM functional genomics core facility using Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2000.

tag: strain

value: Mixed C57BL/6 - CD1

tag: developmental stage

value: gestational day e11.5

value: forelimb bud

tag: antibody

value: anti-HoxA13 (in-house, affinity purified)


title: e11.5_forelimb_distal_wt_HoxD13

description: Chromatin IP against HoxD13

source_name: embryonic forelmb bud, HoxD13 ChIP

value: anti-HoxD13 (in-house, affinity purified)


title: Aph-IVF rep1

description: replicate 1

source_name: Aph-IVF rep1

value: No

value: in vitro fertilization


title: B6C3F1-Cum rep2

description: replicate 2

value: B6C3F1 cumulus cells

value: cumulus cell


title: Aph-IVFBla rep1

description: replicate 1

source_name: Aph-IVFBla rep1

value: in vitro fertilization blastocyst


title: B6C3F1-Ooc rep1

description: replicate 1

value: B6C3F1 oocytes

value: oocyte


title: Aph+IVFBla rep1

description: replicate 1

source_name: Aph+IVFBla rep1


title: Aph-SCNTBla rep1

description: replicate 1

source_name: Aph-SCNTBla rep1


title: Aph-SCNT96 rep1

description: replicate 1

source_name: Aph-SCNT96 rep1

value: somatic cell nuclear transfer (96h)


title: Aph+IVF96 rep1

description: replicate 1

source_name: Aph+IVF96 rep1

value: Yes

value: in vitro fertilization (96h)


title: Aph+IVF rep1

description: replicate 1

source_name: Aph+IVF rep1

value: Aphidicolin


title: Aph-IVF96 rep1

description: replicate 1

source_name: Aph-IVF96 rep1

value: blastocysts


title: Aph-SCNT rep1

description: replicate 1

source_name: Aph-SCNT rep1

value: somatic cell nuclear transfer


title: B6C3F1-Cum rep1

description: replicate 1


title: Fgf2-

status: Public on Oct 13 2016

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

value: mouse embryonic fibroblast

tag: gender

value: male

tag: agent


title: Fgf2+

tag: cell type


title: Akata_induced_rep2_DNase

status: Public on Jul 08 2016

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Illumina 1.9 basecalling
Alignment to the Akata EBV genome (NCBI accession number KC207813.1) using STAR version 2.3.0.1 with default parameters
Generation of signalmap files with IGVTools, using reads with primary alignments
Genome_build: KC207813.1
Supplementary_files_format_and_content: Signalmap coverage files for the Akata genome

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 0.5% Penicillin-Streptomycin.

extract_protocol:
TRIzol (Ambion). A portion of each replicate was treated with DNAse (Ambion) and a portion left untreated for a total of 4 samples.
nAnT-iCAGE

treatment_protocol: One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1×106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10 μg/ml anti-IgG or no anti-IgG (uninduced).

value: Akata cells

tag: treatmemt

value: DNAse


title: Induced BZLT12-22 GapmeR 2

data_processing:
Illumina 1.9 basecalling
Alignment to the Akata EBV genome (NCBI accession number KC207813.1) using STAR version 2.3.0.1 with default parameters
Generation of signalmap files using IGVTools
Genome_build: KC207813.1
Supplementary_files_format_and_content: Signalmap coverage files for the Akata genome

source_name: Induced BZLT12-22 GapmeR 2

extract_protocol:
TRIzol reagent (Ambion) followed byb DNase (Ambion) treatment
Illumina TruSeq Stranded protocol

treatment_protocol: One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1×106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10 μg/ml anti-IgG or no anti-IgG (uninduced). For GapmeR treatment, 3 × 106 cells in RPMI (with 10% FBS) were nucleofected (Lonza) with 600 pmol of either negative control GapmeR A or targeted GapmeR. On the following day an equal volume of RPMI (with 10% FBS) was added with either 20 μg/ml anti-IgG or no anti-IgG (uninduced).


title: Akata_induced_rep1_noDNase

value: untreated


title: Akata_induced_rep1_DNase


title: Induced BZLT12-22 GapmeR 1

source_name: Induced BZLT12-22 GapmeR 1


title: micromanipulation control rep1

status: Public on Aug 25 2016

description: replicate 1

source_name: micromanipulation control

extract_protocol: 150 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumna TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

value: micromanipulation control


title: Induced BZLT12-22 GapmeR 3

source_name: Induced BZLT12-22 GapmeR 3


title: oviduct rep1

description: replicate 1

source_name: oviduct

value: oviduct


title: Blastocyst/KSOM(aa) rep1

description: replicate 1

source_name: Blastocyst/KSOM(aa)


title: Uninduced negative control GapmeR 3

source_name: Uninduced negative control GapmeR 3


title: Uninduced negative control GapmeR 2

source_name: Uninduced negative control GapmeR 2


title: oviduct rep3

description: replicate 3


title: micromanipulation control rep3

description: replicate 1


title: Blastocyst/KSOM(aa) rep2

description: replicate 2


title: Induced negative control GapmeR 2

source_name: Induced negative control GapmeR 2


title: Induced negative control GapmeR 3

source_name: Induced negative control GapmeR 3


title: Induced negative control GapmeR 1

source_name: Induced negative control GapmeR 1


title: Akata_induced

data_processing:
Library strategy: Iso-Seq
SMRTportal RS_IsoSeq v.1 with ICE to obtain full-length consensus isoforms
Alignment to the EBV genome (NCBI accession number KC207813.1) using GMAP 2014-07-21 with the parameter -n 1
TRIMD end validator and TRIMD start validator to produce bedgraph files of isoform 5' and 3' ends
Genome_build: KC207813.1
Supplementary_files_format_and_content: BedGraph files of isoform 5' and 3' ends

extract_protocol:
TRIzol reagent (Ambion)
Iso-Seq

treatment_protocol: One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1 x 106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus 10 μg/ml anti-IgG.


title: Akata_induced_rep2_noDNase


title: Blastocyst/ISM1/ISM2 rep3

description: replicate 3


title: MultiBlast/HTF rep2

description: replicate 2

source_name: MultiBlast/HTF

value: multiblastocyst


title: MultiBlast/HTF rep3

description: replicate 3


title: MultiBlast/HTF rep1

description: replicate 1


title: Blastocyst/ISM1/ISM2 rep1

description: replicate 1


title: S113-5, rep 2

description: Replicate 2

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h).

value: Sox2-null ESCs

value: Sox2 113 mutant clone 5


title: oviduct rep2

description: replicate 2


title: Blastocyst/ISM1/ISM2 rep2

description: replicate 2


title: micromanipulation control rep2

description: replicate 1


title: Uninduced negative control GapmeR 1

source_name: Uninduced negative control GapmeR 1


title: Poly(A)-selected 24h

source_name: Poly(A)-selected 24h


title: Poly(A)-selected 48h

source_name: Poly(A)-selected 48h


title: Poly(A)-selected 30m

source_name: Poly(A)-selected 30m


title: Poly(A)-selected 1h

source_name: Poly(A)-selected 1h


title: Poly(A)-selected 2h

source_name: Poly(A)-selected 2h


title: Poly(A)-selected 4h

source_name: Poly(A)-selected 4h


title: Poly(A)-selected 5m

source_name: Poly(A)-selected 5m


title: Poly(A)-selected 8h

source_name: Poly(A)-selected 8h


title: Poly(A)-selected 0

source_name: Poly(A)-selected 0


title: PFL_E12_WT_H3K27me3_rep1

status: Public on May 19 2016

description: Proximal forelimb mouse E12.5 WT_H3K27me3 ChIPseq

data_processing:
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed ChIP-seq reads were mapped onto the GRCm38 (mm10) using Bowtie (Galaxy Tool Version 1.1.2) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al., 2014). Both unmapped regions containing adaptors and contamination, and PCR duplicates were removed from mapped reads.
These analyses were performed on the public server of the Galaxy Project (https://usegalaxy.org/) (Hillman-Jackson et al., 2012).
By using bamCompare (Galaxy Tool Version 1.5.9.1.0) from the Galaxy deepTools webserver (http://deeptools.ie-freiburg.mpg.de/), ChIP and input data were normalized and compared to compute the log2 of the number of reads ratio (Ramirez et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input.

source_name: Forelimb

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 forelimbs from wild type mice were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 18 minutes at room temperature, washed at least three times with cold PBS containing protease inhibitor and stored at -80°C. Pools of ten pairs of wild type proximal or distal forelimbs were used for each experiment. The samples were treated with lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl and protease inhibitor) for 10 min on ice, followed by RIPA buffer (TE with 140 mM NaCl, 0.1% deoxycholate, 0.1% SDS, 1% TritonX-100 and protease inhibitor) and fragmented to a range of 200-500 bp by a Biorupter sonication device (Diagenode). PierceTM Protein A/G magnetic beads (88803, Thermo Scientific) were conjugated with each antibody in blocking buffer (PBS, 0.5% Tween20, 0.5% BSA and protease inhibitor) for 4 hrs at 4°C and washed with blocking buffer. Chromatin was incubated with the prepared protein A/G beads overnight at 4°C with rotation. 3 µg of H3K27ac (ab4729, Abcam) and 3 µg of H3K27me3 (07-449, Millipore) were used for each immunoprecipitation. Samples were washed 6 times with RIPA buffer, twice with RIPA/500 mM NaCl buffer, twice with LiCl wash buffer (TE, 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholate) and twice with TE, followed by eluted in direct elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl and 0.1% SDS). Cross-links were reversed overnight at 65°C and ChIPed DNA was treated with RNase A and proteinase K, and purified by phenol chloroform extraction.
For ChIP-seq, at least 5 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

tag: age

tag: tissues

value: Proximal forelimb

tag: genotype

value: wild type


title: DFL_E12_WT_H3K27me3_rep2

description:
Distal forelimb mouse E12.5 WT_H3K27me3 ChIPseq
Processed for replicates have been combined into one file. Processed data for this sample can be found on GSM2061124

value: Distal forelimb


title: ARF_ecoli-ZmARF5_col_4

status: Public on May 25 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: A. thaliana Col-0 input DNA library

data_processing:
library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Reads were aligned by bowtie2 version 2.0.0-beta7 against the Arabidopsis TAIR10 genome assembly or Zea mays genome assembly B73 with default parameters, and additionally filter for highest scoring MAPQ alignments only (score=254).
Peaks were called using GEM peak caller version 2.3 with the default version 2.3 read distribution, TAIR10 genome sequences and parameters " --k_min 6 --k_max 20 --k_seqs 250 --outNP --k_neg_dinu_shuffle".
Genome_build: Arabidopsis TAIR10 or maize B73
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

organism: Zea mays

source_name: young leaf

extract_protocol:
Genomic DNA is extracted from Arabidopsis young leaves by phenol:chloroform:isoamyl alchohol (25:24:1) followed by a chloroform  extraction, ethanol precipitation and resuspension in Tris/EDTA buffer.  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing an affinity-tagged transcription factor (GST or HALO) is translated by either heterologous (E. coli) or in vitro (wheat germ) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina HiSeq 2500.

tag: protein

tag: gene id

tag: protein family

value: ARF

tag: protein source

value: Zea mays

tag: protein affinity tag

value: GST

tag: expression system

value: ecoli

tag: dna source

value: col

tag: replicate

tag: subset

value: motif+TFBS


title: ARF_ecoli.MP_col_v31

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-ARF_ecoli-MP_col-chr1-5_GEM_events.narrowPeak

organism: Arabidopsis thaliana

value: MP

value: Arabidopsis thaliana


title: ARF_ecoli.MP_col_v35


title: In-vitro iHep mHSC, rep 1

status: Public on Feb 22 2016

description: Replicate 1

hyb_protocol: The cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent's One-Color Microarray-Based Gene Expression Analysis Protocol V5.7 except that 500ng of each labelled cRNA sample were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565 CA (pixel resolution 5 micrometers, bit depth 20). Data extraction was performed with the Feature Extraction Software V10.7.3.1.

data_processing: Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

label: Alexa Fluor 555

source_name: In-vitro iHep mHSC

label_protocol: 100 ng of total DNA-free RNA was used as input to prepare the aminoallyl-UTP-modified (aaUTP) cRNAs (Amino Allyl MessageAmp II Kit, #AM1753, Life Technologies) as directed by the company. The aaUTP-cRNAs were labelled with Alexa Fluor 555 Reactive Dye (#A32756, LifeTechnologies). Prior to the reverse transcription reaction, 1μl of a 1:5000 dilution of Agilent's One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100ng of total RNA of each analyzed sample.

extract_protocol: Total RNA was extracted from the cells.

tag: strain/background

value: Balb/c AnNCrl

value: in-vitro myofibroblasts-derived induced hepatocytes

tag: reprogrammed

value: yes


title: GSC[neonatal] rep1

status: Public on Dec 17 2015

description: replicate 1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina). Background correction was performed using the Affymetrix robust multiarray analysis (RMA) background correction model. Variance stabilization was performed by log2 scaling, and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: GSC[neonatal] rep1

extract_protocol: 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 14h)

tag: strain

tag: pluripotent

value: No


title: aNPCwm rep 1

status: Public on Jun 10 2016

description: aNPCwm replicate 1

hyb_protocol: cRNA was hybridized to HG-U133A GeneChip expression arrays (Affymetrix).

scan_protocol: The arrays were washed and stained and stained automatically on a GeneChip Fluidics station 450 (Affymetrix) and scanned in a GeneChip scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA. Scatter plots were performed using in-house developed functions in Matlab.

source_name: aNPCwm rep1

label_protocol: Biotin labeling and fragmentation were performed according to the Affymetrix user manual.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

tag: origin

value: White matter

tag: cell type

value: adult neural progenitor cells isolated from white matter


title: In-vivo eHep, rep 2

description: Replicate 2

source_name: In-vivo eHep

value: in-vivo endogenous hepatocytes

value: no


title: In-vivo eHep, rep 1

description: Replicate 1


title: MEF rep1

description: replicate 1

source_name: MEF rep1


title: iPSC[MEF] rep2

description: replicate 2

source_name: iPSC[MEF] rep2

value: Yes


title: In-vivo eHep, rep 3

description: Replicate 3


title: In-vivo iHep, rep 3

description: Replicate 3

source_name: In-vivo iHep

value: in-vivo myofibroblasts-derived induced hepatocytes


title: aNPCwm rep 2

description: aNPCwm replicate 2

source_name: aNPCwm rep2


title: MEF rep2

description: replicate 2

source_name: MEF rep2


title: GSC[neonatal] rep2

description: replicate 2

source_name: GSC[neonatal] rep2


title: In-vivo iHep, rep 1

description: Replicate 1


title: OG2 ESC rep1

description: replicate 1

source_name: OG2 ESC rep1


title: fNSC rep 2

description: fNSC replicate 2

source_name: fNSC rep2

value: Fetal

value: fetal neural stem cells


title: aNPChip rep 1

description: aNPChip replicate 1

source_name: aNPChip rep1

value: Hippocampus

value: adult neural progenitor cells isolated from hippocampus


title: fNSC rep 1

description: fNSC replicate 1

source_name: fNSC rep1


title: Pr-mHSC, rep 3

description: Replicate 3

source_name: Pr-mHSC

value: primary myofibroblasts derived from hepatic stellate cells


title: PH24h

description: Replicate 1

value: primary hepatocytes cultured for 24 hours


title: In-vitro iHep mHSC, rep 2

description: Replicate 2


title: gPSC[GSCadult]#2 rep2

description: replicate 2

source_name: gPSC[GSCadult]#2 rep2


title: GSC[adult] rep1

description: replicate 1

source_name: GSC[adult] rep1


title: In-vivo iHep, rep 2

description: Replicate 2


title: GSC[adult] rep2

description: replicate 1

source_name: GSC[adult] rep2


title: In-vitro iHep mHSC, rep 3

description: Replicate 3

source_name: In-vitro iHep mHSC


title: aNPChip rep 2

description: aNPChip replicate 2

source_name: aNPChip rep2


title: OG2 ESC rep2

description: replicate 2

source_name: OG2 ESC rep2


title: aNPChip rep 3

description: aNPChip replicate 3

source_name: aNPChip rep3


title: Pr-mHSC, rep 2

description: Replicate 2


title: iPSC[MEF] rep1

description: replicate 1

source_name: iPSC[MEF] rep1


title: gPSC[GSCadult]#1 rep1

description: replicate 1

source_name: gPSC[GSCadult]#1 rep1


title: gPSC[GSCneonatal]#2 rep2

description: replicate 2

source_name: gPSC[GSCneonatal]#2 rep2


title: iPSC[GSCadult]#2 rep2

description: replicate 2

source_name: iPSC[GSCadult]#2 rep2


title: iPSC[GSCadult]#1 rep2

description: replicate 2

source_name: iPSC[GSCadult]#1 rep2


title: gPSC[GSCadult]#1 rep2

description: replicate 2

source_name: gPSC[GSCadult]#1 rep2


title: gPSC[GSCneonatal]#2 rep1

description: replicate 1

source_name: gPSC[GSCneonatal]#2 rep1


title: iPSC[GSCneonatal]#1 rep2

description: replicate 2

source_name: iPSC[GSCneonatal]#1 rep2


title: gPSC[GSCneonatal]#1 rep2

description: replicate 2

source_name: gPSC[GSCneonatal]#1 rep2


title: iPSC[GSCneonatal]#2 rep1

description: replicate 1

source_name: iPSC[GSCneonatal]#2 rep1


title: iPSC[GSCneonatal]#1 rep1

description: replicate 1

source_name: iPSC[GSCneonatal]#1 rep1


title: iPSC[GSCadult]#2 rep1

description: replicate 1

source_name: iPSC[GSCadult]#2 rep1


title: gPSC[GSCadult]#2 rep1

description: replicate 1

source_name: gPSC[GSCadult]#2 rep1


title: iPSC[GSCadult]#1 rep1

description: replicate 1

source_name: iPSC[GSCadult]#1 rep1


title: iPSC[GSCneonatal]#2 rep2

description: replicate 2

source_name: iPSC[GSCneonatal]#2 rep2


title: gPSC[GSCneonatal]#1 rep1

description: replicate 1

source_name: gPSC[GSCneonatal]#1 rep1


title: MSC rep 3

status: Public on Nov 03 2015

description: replicate 3

hyb_protocol: The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer’s procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression 3’ Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip® Hybridization, Wash and Stain Kit and mixed with amplified cDNA samples. Affymetrix U133A were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450 and scanning with GeneChip® Scanner 3000 (Affymetrix).

scan_protocol: Data generation was controlled by the Affymetrix GeneChip® Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing:
CEL files were processed using the BioConductor software package (www.bioconductor.org).
Normalization was done employing GCRMA
(Wu et al., Journal of American Statistical Association, 99(468), 909-917, 2004).
Scatter plots were performed using in-house developed functions in Matlab®.

source_name: MSC rep 3

label_protocol: Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.).

extract_protocol: RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel).

value: Mesenchymal


title: ABPMC-wm rep 1

description: replicate 1

source_name: ABPMC-wm rep 1

value: Perivascular


title: ANPC-wm rep 3

description: replicate 3

source_name: ANPC-wm rep 3

value: Neuroprogenitor


title: MSC rep 1

description: replicate 1

source_name: MSC rep 1


title: MSC rep 2

description: replicate 2

source_name: MSC rep 2


title: ABPMC-hip rep 1

description: replicate 1

source_name: ABPMC-hip rep 1


title: ABPMC-wm rep 3

description: replicate 3

source_name: ABPMC-wm rep 3


title: ANPC-wm rep 2

description: replicate 2

source_name: ANPC-wm rep 2


title: ANPC-hip rep 2

description: replicate 2

source_name: ANPC-hip rep 2


title: ABPMC-wm rep 2

description: replicate 2

source_name: ABPMC-wm rep 2


title: ABPMC-hip rep 3

description: replicate 3

source_name: ABPMC-hip rep 3


title: ANPC-hip rep 1

description: replicate 1

source_name: ANPC-hip rep 1


title: ANPC-wm rep 1

description: replicate 1

source_name: ANPC-wm rep 1


title: ABPMC-hip rep 2

description: replicate 2

source_name: ABPMC-hip rep 2


title: ANPC-hip rep 3

description: replicate 3

source_name: ANPC-hip rep 3


title: iOPC-C2 rep1

status: Public on Nov 02 2015

description: iOPC-C2: Induced Oligodendrocyte Progenitor Cells, clon 2, 1 replicate

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol. Chips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G

data_processing: RMA

label_protocol: 10X fragmentation buffer (GeneChip WT Terminal labeling kit Affymetrix P/N900670)

growth_protocol: Mouse fibroblasts were seeded at 30000 cells on 6-well plates and infected with retroviruses for 24 hr in culture medium. Cells were cultivated in OPC medium (DMEM/F12 supplemented with N2, penicillin/streptomycin, 20ng/ml PDGF-aa, 10ng/ml FGF-2) from 3 days after infection. iOPC-like cells were mechanically isolated and expanded into stable iOPC clones.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Ambion WT Expression Kit Affymetrix  P/N 4411973) following the manufacturer's instructions

value: induced oligodendrocyte progenitor cells


title: iOPC-C1 rep1

description: iOPC-C1: Induced Oligodendrocyte Progenitor Cells, clon 1, 1 replicate


title: Mock rep1

description: Mock: Regular mouse embryonic fibroblasts, cultured in OPC medium for 10 days without infection, 1 replicate

source_name: Mock

value: embryonic fibroblasts


title: OPC rep1

description: OPC: Oligodendrocyte Progenitor Cells, 1 replicate

source_name: OPC

value: oligodendrocyte progenitor cells


title: fNSC rep 2 reanalysis

description: replicate 2

source_name: fNSC rep 2

value: NSC


title: MEF rep1

description: MEF: Regular mouse embryonic fibroblasts, 1 replicate

source_name: MEF


title: MEF-D3 rep1

description: MEF-3D: Regular mouse embryonic fibroblasts, after 3 days of infection, 1 replicate


title: iTSC4F8, rep 1

status: Public on Oct 01 2015

description: Replicate 1

hyb_protocol: According to Whole-Genome Gene Expression Direct Hybridization by Illumina.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina).
Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

label_protocol: Illumina total PrepTM 96 RNA amplification kit.

extract_protocol: RNeasy Minikit (Qiagen) according to manufacturer's recommendations.

value: induced trophoblast stem (TS) cells


title: iTSC4F8, rep 2

description: Replicate 2

scan_protocol: According to Whole-Genome Gene Expression Direct Hybridization by Illumina.


title: iTSC4F8, rep 3

description: Replicate 3


title: MEF4F, rep 3

description: Replicate 3

value: mouse embyronic fibroblasts (mEFs)


title: MEF4F, rep 1

description: Replicate 1


title: iTSC4F5, rep 2

description: Replicate 2


title: iTSC4F5, rep 1

description: Replicate 1


title: MEF-D10 rep1

description: MEF-10D: Regular mouse embryonic fibroblasts, after 10 days of infection, 1 replicate


title: iTSC4F5, rep 3

description: Replicate 3


title: TS, rep 1

description: Replicate 1

source_name: TS

value: trophoblast stem cells


title: MEF4F, rep 2

description: Replicate 2


title: TS, rep 2

description: Replicate 2


title: OldNSC rep 1

status: Public on Sep 22 2015

hyb_protocol: Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip® Hybridization, Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip® Arrays Mouse Genome 430 2.0  were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450 and scanning with GeneChip® Scanner 3000 (Affymetrix).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al., Journal of American Statistical Association, 99(468), 909-917, 2004). Scatter plots were performed using in-house developed functions in Matlab®.

source_name: OldNSC rep 1

tag: age

value: 9 months (old)

value: neural stem cells (NSCs)


title: OldNSC rep 3

source_name: OldNSC rep 3


title: YoungNSC rep 3

source_name: YoungNSC rep 3

value: 6 weeks (young)


title: YoungNSC rep 1

source_name: YoungNSC rep 1


title: OldNSC rep 2

source_name: OldNSC rep 2


title: YoungNSC rep 2

source_name: YoungNSC rep 2


title: MSC-0H-GFP_rep2

status: Public on May 14 2015

description: MSC0HGFP rep2

hyb_protocol: Duplicated samples were hybridized to Whole human Genome 8x60K Microarray (G4851A) following Manufacturer’s instructions (Agilent Technologies, CA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: Primary data was examined using GeneSpring 11.0 software (Silicon Genetics, Redwood City, CA). Gene expression in the control and experimental groups was compared using Student's t test and a Benjamini Hochberg multi-testing correction. Only genes satisfying the threshold of P value < 0.05 and a fold change expression> 2 were included and assigned as significant. Analysis of pathways significantly altered was performed using the Ingenuity Pathway software 8.0 (IPA; Ingenuity Systems, Inc., Redwood City, CA).

source_name: BM-derived hMSCs_control (GFP)

label_protocol: Total RNA samples were labeled with Cy3 using the Quick-Amp Labeling kit following Manufacturer’s instructions (Agilent Technologies, CA)

growth_protocol: All cell cultures were maintained in complete MSC growth medium (DMEM-Advanced, 10% FBS, 1% Pen/Strep and 1% Glutamax).

extract_protocol: Duplicate independent cultures of MSCs (MSC-0H-GFP and MSC-5H-GFP) were collected during the exponential cell growth and stabilized in RNA later (Ambion, Austin, TX) solution until RNA extraction. RNA was isolated using the Agilent Total RNA Isolation Kit (Agilent Technologies, Palo Alto, CA) and its quality (RNA integrity ≥ 9 ) checked in the Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment

tag: tissue

value: bone marrow

value: Human Mesenchymal Stem Cells (hMSCs)

tag: transduced with

value: control (GFP) lentiviral vector

value: MSCs from BM

tag: tumor stage

value: non tumorogenic


title: MSC-5H-GFP_rep1

description: MSC5HGFP rep1

source_name: BM-derived hMSCs_5 oncogenic hits+control (GFP)

value: 5 oncogenic hits and control (GFP) lentiviral vector

value: tumorogenic


title: MSC-0H-GFP_rep1

description: MSC0HGFP rep1


title: MSC-5H-GFP_rep2

description: MSC5HGFP rep2


title: d2 rep2

status: Public on Apr 06 2015

description: replicate 2

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: d2 rep2

extract_protocol: Total RNAs were used as input into a linear amplification protocol (Ambion) which involved synthesis of T7-linked double-stranded cDNA and 12 hours of in vitro transcription incorporating biotin-labelled nucleotides

tag: pgc like cell

value: No

value: induced Pluripotent Stem Cells

value: 2 d


title: ESC rep1

description: replicate 1

source_name: ESC rep1

value: ESC


title: D15--

status: Public on May 08 2015

description: replicate 1

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

scan_protocol: After the recommended washing,the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 14h)

value: PGC

tag: gcnf double ko

value: Yes


title: D15++

description: replicate 1


title: D12--

description: replicate 1


title: H9

status: Public on Feb 20 2015

description: H9 rep1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

source_name: embryonic stem cell (ESC)

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

tag: cell line

value: embryonic stem cell (ESC)


title: d6PGCLC rep2

description: replicate 2

source_name: d6PGCLC rep2

value: 6 d


title: CD34 OSKMiPS 2

description: CD34 OSKMiPS 2 rep1

source_name: CD34 OSKMiPS

value: Human four factors (POU5F1, SOX2, KLF4, CMYC) induced Pluripotent Cell (iPSC) reprogrammed from CD34+ Cord blood CD34+ Hematopoyetic Stem Cell(HSC) induced Pluripotent Cell (iPSC) population 2


title: H1

description: H1 rep1


title: D12++

description: replicate 1


title: EpiSC rep 1

description: replicate 1

source_name: EpiSC rep 1


title: ESC++

description: replicate 1

source_name: ESC++


title: d2 rep1

description: replicate 1

source_name: d2 rep1


title: EpiSC rep 2

description: replicate 2

source_name: EpiSC rep 2


title: d6PGCLC rep1

description: replicate 1

source_name: d6PGCLC rep1


title: CD34 OSiPS 2

description: CD34 OSiPS 2 rep1

source_name: CD34 OSiPS

value: Human two factors (POU5F1, SOX2) induced Pluripotent Cell (iPSC) reprogrammed from CD34+ Cord blood CD34+ Hematopoyetic Stem Cell(HSC) induced Pluripotent Cell (iPSC) population 2


title: CD34 2

description: CD34 2 rep1

value: CD34+ Cord blood CD34+ Hematopoyetic Stem Cell (HSC) population 2


title: CD34 OSiPS 1

description: CD34 OSiPS 1 rep1

value: Human two factors (POU5F1, SOX2) induced Pluripotent Cell (iPSC) reprogrammed from CD34+ Cord blood CD34+ Hematopoyetic Stem Cell(HSC) induced Pluripotent Cell (iPSC) population 1


title: EpiT9

status: Public on Sep 18 2014

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina). Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model. Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the method implemented in the lumi package of RBioconductor. Data post-processing and graphics were performed with in-house developed functions in Matlab. Hierarchical clustering of genes and samples was performed with one minus correlation metric and the unweighted average distance (UPGMA) (also known as group average) linkage method.

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h). The RNA samples were used as input into a linear maplification protocol (Tetu-Bio) which involved synthesis of T7-linked double-stranded cDNA and 12 hours of in vitro transcription incorporating biotin-labelled nucleotides.

tag: strain background

value: Epiblast Stem Cells T9

tag: cultured in hypoxia conditions


title: EpiE3

value: Epiblast Stem Cells E3


title: ESCm rep 2

source_name: ESCm

value: pluripotent embryonic germ cells (EGCs)


title: ESCf rep 2

source_name: ESCf


title: PGC11.5 rep 2

value: unipotent primordial germ cells (PGCs)


title: PGC11.5 rep 1


title: ESCf rep 1


title: hiEGL2 rep 1

value: hypoxia-induced EGC-like cells (hiEGL)


title: CD34 1

description: CD34 1 rep1

value: CD34+ Cord blood CD34+ Hematopoyetic Stem Cell (HSC) population 1


title: ESCm rep 1

value: No


title: hiEGL2 rep 2


title: hiEGL1 rep 2


title: fNSC rep 1  reanalysis

description: replicate 1

source_name: fNSC rep 1

value: NSC


title: EG rep 1

source_name: EG

value: pluripotent Embryonic Germ Cells (EGCs)


title: CD34 OSKMiPS 1

description: CD34 OSKMiPS 1 rep1

value: Human four factors (POU5F1, SOX2, KLF4, CMYC) induced Pluripotent Cell (iPSC) reprogrammed from CD34+ Cord blood CD34+ Hematopoyetic Stem Cell(HSC) induced Pluripotent Cell (iPSC) population 1


title: hiEGL1 rep 1

value: Yes


title: EG rep 2


title: fNSC-1FiPSCa-NSC-In Vivo rep 2

status: Public on Sep 12 2014

description: fNSC-1FiPSCa-NSC-In Vivo rep2

source_name: fNSC-1FiPSCa-NSC-In Vivo

extract_protocol:
300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)
The RNA samples from in vivo transplanted and FACS sorted cells were amplified using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre, USA) from 100 pg to 50 microg.

value: Human one factor (POU5F1) fetal Neural Stem Cell (NSC) induced reprogrammed cell (iPSC) clone a, in vivo differentiated to NSC


title: fNSC-1FiPSCa-NSC-In Vivo rep 1

description: fNSC-1FiPSCa-NSC-In Vivo rep1


title: ESC--

description: replicate 1

source_name: ESC--

value: PGC


title: HUESC6-ESC rep 1

description: HUESC6-ESC rep1

value: HUESC6-ESC, Human HUESC6 embryonic stem cell (ESC) , 2 replicates


title: Fib-4FiPSCa-NSC-In Vivo rep 2

description: Fib-4FiPSCa-NSC-In Vivo rep2

source_name: Fib-4FiPSCa-NSC-In Vivo

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone a, in vivo differentiated to NSC


title: fNSC-1FiPSCa-NSC-In Vivo rep 4

description: fNSC-1FiPSCa-NSC-In Vivo rep4


title: HUESC6-ESC rep 2

description: HUESC6-ESC rep2


title: Fib-4FiPSCa-NSC-In Vivo rep 1

description: Fib-4FiPSCa-NSC-In Vivo rep1


title: fNSC-1FiPSCa-NSC-In Vivo rep 3

description: fNSC-1FiPSCa-NSC-In Vivo rep3


title: H1-ESC rep 2

description: H1-ESC rep2

value: H1-ESC, Human H1 embryonic stem cell (ESC), 3 replicates


title: H1-ESC rep 1

description: H1-ESC rep1

value: Human H1 embryonic stem cell (ESC)


title: H1-ESC rep 3

description: H1-ESC rep3

value: Human HUESC6 embryonic stem cell (ESC)


title: Fib-4FiPSCb

description: Fib-4FiPSCb rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone b


title: Fib-4FiPSCa-NSC rep 1

description: Fib-4FiPSCa-NSC rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone a, in vitro differentiated to NSC


title: Fib-4FiPSCb-NSC rep 1

description: Fib-4FiPSCb-NSC rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone b, in vitro differentiated to NSC


title: Fib-4FiPSCb-NSC rep 2

description: Fib-4FiPSCb-NSC rep2


title: CD34-2FiPSCa

description: CD34-2FiPSCa rep1

value: Human two factors (POU5F1, KLF4) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone a


title: CD34-4FiPSCa

description: CD34-4FiPSCa rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone a


title: fNSC-2FiPSCa

description: fNSC-2FiPSCa rep1

value: Human two factors (POU5F1, KLF4) fetal Neural Stems Cell (NSC) induced reprogrammed cell (iPSC) clone a


title: Fib-4FiPSCa

description: Fib-4FiPSCa rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone a


title: H1-ESC-NSC rep 2

description: H1-ESC-NSC rep2

value: Human H1 embryonic stem cell (ESC), in vitro differentiated to NSC


title: HUES6-ESC-NSC

description: HUES6-ESC-NSC rep1

value: Human HUES6 embryonic stem cell (ESC), in vitro differentiated to NSC


title: Fib-4FiPSCc-NSC

description: Fib-4FiPSCc-NSC rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) fibroblast induced reprogrammed cell (iPSCs) clone c, in vitro differentiated to NSC


title: fNSC-1FiPSCa

description: fNSC-1FiPSCa rep1

value: Human one factor (POU5F1) fetal Neural Stem Cell (NSC) induced reprogrammed cell (iPSC) clone a


title: H1-ESC-NSC rep 1

description: H1-ESC-NSC rep1


title: CD34-4FiPSCb-NSC rep 1

description: CD34-4FiPSCb-NSC rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone b, in vitro differentiated to NSC


title: Fib-4FiPSCa-NSC rep 2

description: Fib-4FiPSCa-NSC rep2


title: CD34-4FiPSCb

description: CD34-4FiPSCb rep1

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone b


title: fNSC-1FiPSCb

description: fNSC-1FiPSCb rep1

value: Human one factor (POU5F1) fetal Neural Stem Cell (NSC) induced reprogrammed cell (iPSC) clone b


title: fNSC-1FiPSCb-NSC rep 2

description: fNSC-1FiPSCb-NSC rep2

value: Human one factor (POU5F1) fetal Neural Stem Cell (NSC) induced reprogrammed cell (iPSC) clone b, in vitro differentiated to NSC


title: CD34-2FiPSCa-NSC rep 1

description: CD34-2FiPSCa-NSC rep1

value: Human two factors (POU5F1, KLF4) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone a, in vitro differentiated to NSC


title: CD34-2FiPSCa-NSC rep 2

description: CD34-2FiPSCa-NSC rep2


title: fNSC-2FiPSCa-NSC rep 2

description: fNSC-2FiPSCa-NSC rep2

value: Human two factors (POU5F1, KLF4) fetal Neural Stems Cell (NSC) induced reprogrammed cell (iPSC) clone a, in vitro differentiated to NSC


title: d4PGCLC rep1

description: replicate 1

source_name: d4PGCLC rep1

value: Yes

value: induced Pluripotent Stem Cells

value: 4 d


title: CD34-4FiPSCa-NSC rep 2

description: CD34-4FiPSCa-NSC rep2

value: Human four factors (POU5F1, KLF4, SOX2, CMYC) cord blood CD34+ Hematopoyetic Stem Cell (HSC) induced reprogrammed cell (iPSC) clone a, in vitro differentiated to NSC


title: fNSC-1FiPSCb-NSC rep 1

description: fNSC-1FiPSCb-NSC rep1


title: CD34-4FiPSCb-NSC rep 2

description: CD34-4FiPSCb-NSC rep2


title: CD34-4FiPSCa-NSC rep 1

description: CD34-4FiPSCa-NSC rep1


title: fNSC-2FiPSCa-NSC rep 1

description: fNSC-2FiPSCa-NSC rep1


title: fNSC

description: fNSC rep1

source_name: fNSC

value: Human fetal Neural Stem Cells (NSC)


title: fNSC-1FiPSCa-NSC rep 1

description: fNSC-1FiPSCa-NSC rep1

value: Human one factor (POU5F1) fetal Neural Stem Cell (NSC) induced reprogrammed cell (iPSC) clone a, in vitro differentiated to NSC


title: ARF6 ChIP-Seq

status: Public on Jun 03 2014

city: Stanford

first: Eunkyoo

last: Oh

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

description: Chromatin IP against ARF6 transcription factor

data_processing:
ARF6 binding peaks were identified using ChIP-Seq analysis R (CSAR) software with parameters (backg=10, norm=-1, test="Ratio", times=1e6, digits=2) (Muino et al., 2011)
Genome_build: TAIR9

source_name: Etiolated ARF6p::ARF6-Myc in arf6;arf8 seedlings

growth_protocol: Transgenic plants expressiong ARF6-Myc driven by native ARF6 promoter (ARF6p::ARF6-Myc) are grown in the dark for 5 days.

extract_protocol: Lysates were clarified from sonicated nuclei and ARF6-Myc-DNA complexes were isolated with anti-Myc antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

value: Etiolated seedlings

tag: antibody

value: anti-myc antibody


title: CD34+

description: CD34+ rep1

value: Human Cord Blood CD34+ Hematopoyetic Stem Cell (HSC)


title: fNSC-1FiPSCa-NSC rep 2

description: fNSC-1FiPSCa-NSC rep2


title: iPSC rep1

description: replicate 1

source_name: iPSC rep1

value: No

value: iPSC


title: Colon+ rep1

status: Public on Aug 11 2014

description: replicate 1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: Col+ rep1

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumna TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

tag: nanog overexpression


title: Fib rep 2

description: Fib rep2

source_name: Fib

value: Human fibroblast F134


title: Fib rep 1

description: Fib rep1


title: Colon- rep1

description: replicate 1

source_name: Col- rep1


title: Colon+ rep2

description: replicate 2

source_name: Col+ rep2


title: Intestine- rep2

description: replicate 2

source_name: Int- rep2


title: Colon- rep2

description: replicate 2

source_name: Col- rep2


title: Intestine+ rep2

description: replicate 2

source_name: Int+ rep2


title: TO_BMC_0

status: Public on May 13 2014

description: replicate 1

value: bone marrow cell

tag: time

tag: treated


title: Intestine- rep1

description: replicate 1

source_name: Int- rep1


title: Ctrl_MEF_24

description: replicate 1

value: mouse embryonic fibroblast


title: Intestine+ rep1

description: replicate 1

source_name: Int+ rep1


title: TO_BMC_12

description: replicate 1


title: TO_BMC_6

description: replicate 1


title: Ctrl_MEF_0

description: replicate 1


title: TO_MEF_12

description: replicate 1


title: TO_NSC_24

description: replicate 1

value: neural stem cell


title: TO_NSC_12

description: replicate 1


title: TO_NSC_6

description: replicate 1


title: TO_BMC_24

description: replicate 1


title: TO_MEF_24

description: replicate 1


title: Ctrl_NSC_0

description: replicate 1


title: TO_NSC_0

description: replicate 1


title: TO_MEF_0

description: replicate 1


title: TO_MEF_6

description: replicate 1


title: ESC rep 1

description: replicate 1

source_name: ESC

value: mouse embryonic stem cell


title: iNdiPSC-4

status: Public on Mar 28 2014

description: replicate 1

tag: background strain


title: NSC2FiPSC

description: replicate 1

tag: pluripotent


title: MEF4FiPSC

description: replicate 1


title: MEF

description: replicate 1

source_name: MEF


title: ESC

description: replicate 1


title: iNdiPSC-1

description: replicate 1


title: iPS1 OSK1

status: Public on Mar 23 2014

description: (OCT4, SOX2, KLF4 from Human) Human iPS line D1OSK1, grown on MEFs

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina) background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor

source_name: iPS1 OSK1

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

value: Human iPS line D1OSK1, grown on MEFs

tag: potency, inductors

value: Pluripotent, (OCT4, SOX2, KLF4 from Human)


title: iPS1 osK1

description: (Oct4, Sox2 from Axolotl)-(KLF4 from Human) Human iPS line D1osK1, grown on MEFs

source_name: iPS1 osK1

tag: cell type

value: Human iPS line D1osK1, grown on MEFs

value: Pluripotent, (Oct4, Sox2 from Axolotl)-(KLF4 from Human)


title: iPS1 OsK2

description: (Sox2 from Axolotl)-(OCT4, KLF4 from Human) Human iPS line D1OsK2, grown on MEFs

source_name: iPS1 OsK2

value: Human iPS line D1OsK2, grown on MEFs

value: Pluripotent, (Sox2 from Axolotl)-(OCT4, KLF4 from Human)


title: iPS1 osK2

description: (Oct4, Sox2 from Axolotl)-(KLF4 from Human) Human iPS line D1osK2, grown on MEFs

source_name: iPS1 osK2

value: Human iPS line D1osK2, grown on MEFs


title: iPS2 osKM1

description: (Oct4, Sox2 from Axolotl)-(KLF4, MYC from Human) Human iPS line D2osKM1, grown on MEFs

source_name: iPS2 osKM1

value: Human iPS line D2osKM1, grown on MEFs

value: Pluripotent, (Oct4, Sox2 from Axolotl)-(KLF4, MYC from Human)


title: HUES6

description: Human ESC6 grown on low-density MEFs, harvested bulk culture at subconfluence after cleaning

value: Pluripotent


title: Shef3

description: Human Sheffield-3 grown on low-density MEFs, harvested bulk culture at subconfluence after cleaning

value: Human Sheffield-3 ESC on low-density MEFs, harvested bulk culture at subconfluence after cleaning


title: iPS1 oSK2

description: (Oct4 from Axolotl)-(SOX2, KLF4 from Human) Human iPS line D1oSK2, grown on MEFs

source_name: iPS1 oSK2

value: Human iPS line D1oSK2, grown on MEFs

value: Pluripotent, (Oct4 from Axolotl)-(SOX2, KLF4 from Human)


title: NSC

description: replicate 1

source_name: NSC

value: No


title: HUES2

description: Human ESC2 grown on low-density MEFs, harvested bulk culture at subconfluence after cleaning


title: hFib2

description: Human parental D2 fibroblast

value: Human parental D2 fibroblast

value: Unipotent


title: iPS1 osKM2

description: (Oct4, Sox2 from Axolotl)-(KLF4, MYC from Human) Human iPS line D1osKM2, grown on MEFs

source_name: iPS1 osKM2

value: Human iPS line D1osKM2, grown on MEFs


title: iPS2 osKM2

description: (Oct4, Sox2 from Axolotl)-(KLF4, MYC from Human) Human iPS line D2osKM2, grown on MEFs

source_name: iPS2 osKM2

value: Human iPS line D2osKM2, grown on MEFs


title: NCL4

description: Human Newcastle-4 grown on low-density MEFs, harvested bulk culture at subconfluence after cleaning

value: Human Newcastle-4 ESC on low-density MEFs, harvested bulk culture at subconfluence after cleaning


title: iNSC

description: replicate 1

source_name: iNSC

value: Yes


title: iPS1 osKM1

description: (Oct4, Sox2 from Axolotl)-(KLF4, MYC from Human) Human iPS line D1osKM1, grown on MEFs

source_name: iPS1 osKM1

value: Human iPS line D1osKM1, grown on MEFs


title: NCL3

description: Human Newcastle-3 grown on low-density MEFs, harvested bulk culture at subconfluence after cleaning

value: Human Newcastle-3 ESC on low-density MEFs, harvested bulk culture at subconfluence after cleaning