title: CTCF_knockout_CTCF_ChIPseq

data_processing:
ChIP-seq libraries were sequenced on an Illumina HiSeq 2000 instrument. Raw single end 50 bp reads were demultiplexed using a custom Python script and then mapped to the mm10 Ensembl reference genome, using Bowtie2 (Langmead and Salzberg, 2012) v2.2.6 with default parameters. Samtools (Li et al., 2009) v0.1.19 was used to convert SAM files to BAM format, and peak calling was performed using the macs2.1.1.2016.0309 callpeak function (Zhang et al., 2008) with default parameters. The CTCF ChIP BAM file was used as the treatment file and input BAM file as the control.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files (output from MACS peak calling software)

extract_protocol:
ChIP for CTCF (Active Motif Cat# 61311) was performed on pooled isolated cardiomyocytes (~10 million total), using the ChIP-IT High Sensitivity Kit as described (Monte et al., 2016). Cardiomyocyte pools were obtained from 3 control and 3 CTCF KO hearts.
ChIP-seq libraries were prepared using the NuGEN Ovation Ultralow System V2 1–16 kit (Cat# 0344).

tag: genotype/variation

value: Left ventricle

value: Isolated cardiac myocytes

value: CTCF (Active Motif Cat# 61311)


title: Control_Input

status: Public on Aug 30 2017

type: SRA

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

country: USA

institute: UCLA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Control

tag: strain

value: control

tag: tissue

tag: cell type

tag: chip antibody

value: none (input)


title: Control_CTCF_ChIPseq


title: TAC_RNAseq_Rep3

library_source: transcriptomic

data_processing:
Raw paired-end 100bp reads were sequenced on two lanes of an Illumina HiSeq 2000, and FASTQ files were demultiplexed using a custom Python script. Reads were mapped to the mm10 genome with TopHat v2.1.0 (Kim et al., 2013), using mm10 bowtie2 indices and a reference GTF provided by iGenomes (Illumina, downloaded from Ensembl release 81 on July 17, 2015). Transcripts were assembled using Cufflinks (Trapnell et al., 2010) v2.2.1 with the -G parameter (using the same GTF), and merged using the Cuffmerge feature of Cufflinks with the -g and -s parameters (using the same GTF and the reference FASTA provided by iGenomes, respectively) (Trapnell et al., 2013; Trapnell et al., 2010). Cuffquant (from Cufflinks v2.2.1) was performed to determine transcript abundances for all samples, using the -b parameter (with reference FASTA from iGenomes), and the --max-bundle-frags 5000000 and -u parameters. Cuffdiff (also from Cufflinks v2.2.1) was used with identical extra parameters as Cuffquant to determine differential gene expression between conditions and assign p-values and q-values for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: transcripts.gtf files (output from Cufflinks)

molecule: polyA RNA

extract_protocol:
Total RNA from isolated adult cardiomyocytes was isolated using the Qiagen RNeasy Mini Kit (Cat# 74104). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Cat# G2940CA).
Ribosomal RNA was then removed using an Illumina Ribo-Zero rRNA Removal Kit (Cat# MRZH11124) and the RNA-seq library was prepared at the UCLA Clinical Microarray Core using the KAPA Stranded RNA-Seq Library Preparation Kit (Cat# KK8401). The average insert size of each library was measured using an Agilent 4200 TapeStation (Cat# G2991AA). All libraries ranged from 200 to 400bp in length. RNA-seq libraries were sequenced on two lanes of an Illumina HiSeq 2000 to obtain 2x100bp (paired-end) reads. On average, ~50 million raw pairs were generated per library.

tag: mouse id


title: CTCF_knockout_Input


title: OSKM_rep2_PolII

city: New York

first: Mark

last: Ptashne

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

description:
Sample 1716
[Processed data files]:
OSKM_avg_PolII_Bin_2000_118.bed.gz
OSKM_avg_PolII_Bin_2000_118.wig.gz
OSKM_rep2_PolII_Bin_2000_1716.bed.gz
OSKM_rep2_PolII_Bin_2000_1716.wig.gz
gene_OSKM_avg_PolII_118.bed.gz
gene_OSKM_avg_PolII_118.bedGraph.gz
gene_OSKM_rep2_PolII_1716.bed.gz
gene_OSKM_rep2_PolII_1716.bedGraph.gz

data_processing:
cutadapt-1.9.1  cutadapt -a AGATCGGAAGAGC
bwa-0.7.13  bwa aln
bwa-0.7.13  bwa sampe
all duplicates eliminated
values at all features are calculated by (number of midpoints of tags / bp of feature) / (total number of unique tags / genome length)
above described values are quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: bed, bedGraph, and wig.

organism: Homo sapiens

extract_protocol: See ChIP-Endo Protocol.pdf

treatment_protocol: About 7-8 x 105 MRC5 fibroblasts were seeded on 10 cm plates on day 0. These cells were grown in EMEM (ATCC) media supplemented with 10% FBS. Twenty-four hours later, two plates were trypsinzed to get an estimate of average number of cells in each 10 cm plate. Cells were then infected with lentiviruses separately encoding either OSKM or OS(v)KM at multiplicities of infections (MOIs) that were determined to be optimal for reprogramming (see Suppl Table 2). Media was changed daily until the time of harvest on day 5. At the time of harvest, cells on plates were washed once with PBS (room temperature) and cross-linked by adding EMEM + 10% FBS containing 1% fomaldehyde. Plates were returned to the incubator and incubated for 10-15 minutes. Cells were washed twice with ice cold PBS containing a cocktail of protease inhibitors (Sigma Cat # P8340; 10ml/ml PBS) and 1mM phenylmethylsulfonyl fluoride (PMSF). Cross-linked cells from each condition (Mock infected MRC5, OSKM or OS(v)KM; all at passage 8) were scraped using a cell scraper, pooled in 15 ml tubes and pelleted. We typically pooled cross-linked cells from at least 4-5, 10cm plates per condition (~ 5 million cells) for each ChIP-Seq assay. As controls, we harvested approximately 5 million cross-linked human ES (H9 hESCs, p. 35) or human iPS cells (an iPSC line derived using OS(v)KM (3S2 hiPSC, p.20) from on 6 cm plates and grown in feeder-free conditions (on vitronectin-coated plates and grown in Essential 8 media).

value: Rpb1 CTD (Cell Signaling 2629S Lot:3)

tag: cell line

value: MRC5 fibroblasts

tag: protocol

value: Oct4, Sox2, Klf4 and Myc addition

tag: time

value: 5 days

tag: passage


title: OSKM_rep1_PolII

description:
Sample 1512
[Processed data files]:
OSKM_avg_PolII_Bin_2000_118.bed.gz
OSKM_avg_PolII_Bin_2000_118.wig.gz
OSKM_rep1_PolII_Bin_2000_1512.bed.gz
OSKM_rep1_PolII_Bin_2000_1512.wig.gz
gene_OSKM_avg_PolII_118.bed.gz
gene_OSKM_avg_PolII_118.bedGraph.gz
gene_OSKM_rep1_PolII_1512.bed.gz
gene_OSKM_rep1_PolII_1512.bedGraph.gz


title: TAC_RNAseq_Rep2


title: TAC_RNAseq_Rep1


title: CTCF_knockout_RNAseq_Rep4


title: MRC5_rep2_PolII

description:
Sample 1705
[Processed data files]:
MRC5_avg_PolII_Bin_2000_117.bed.gz
MRC5_avg_PolII_Bin_2000_117.wig.gz
MRC5_rep2_PolII_Bin_2000_1705.bed.gz
MRC5_rep2_PolII_Bin_2000_1705.wig.gz
gene_MRC5_avg_PolII_117.bed.gz
gene_MRC5_avg_PolII_117.bedGraph.gz
gene_MRC5_rep2_PolII_1705.bed.gz
gene_MRC5_rep2_PolII_1705.bedGraph.gz


title: MRC5_rep1_PolII

description:
Sample 1694
[Processed data files]:
MRC5_avg_PolII_Bin_2000_117.bed.gz
MRC5_avg_PolII_Bin_2000_117.wig.gz
MRC5_rep1_PolII_Bin_2000_1694.bed.gz
MRC5_rep1_PolII_Bin_2000_1694.wig.gz
gene_MRC5_avg_PolII_117.bed.gz
gene_MRC5_avg_PolII_117.bedGraph.gz
gene_MRC5_rep1_PolII_1694.bed.gz
gene_MRC5_rep1_PolII_1694.bedGraph.gz


title: CTCF_knockout_RNAseq_Rep3


title: CTCF_knockout_RNAseq_Rep2


title: CTCF_knockout_RNAseq_Rep1


title: Control_RNAseq_Rep2


title: CC3-C225

city: Nashville

first: Shilin

last: Zhao

state: TN

address: 2200 Pierce Ave, PRB building 571

department: Center for Quantitative Sciences

institute: Vanderbilt University

data_processing:
Library strategy: Exome-seq
Reads were mapped to the hg19 reference genome with BWA (version 0.7.5a). sorted and indexed with SAMtools. Duplicated reads were marked by Picard (http://picard.sourceforge.net/).
SNPs and Indels were called simultaneously on HCA-7, SC and CC samples by SAMtools with base quality≥30, reads with mapping quality ≥30 and mapping quality downgrading coefficient of 50.
SNPs and Indels with strand bias p<0.01 or base quality bias p<0.01 or mapping quality bias p<0.01 or end distance bias p<0.01 were filtered out.
VarScan 2 was used to perform copy number analysis using its recommend workflow. CNV regions were smoothed and segmented by the DNAcopy R package.
Genome_build: hg19

source_name: Cetuximab-resistant CC cell line

growth_protocol: CC and SC cells were grown in 3D collagen in 12 well dishes using 25,000 cells/ml.

extract_protocol:
On day 16, the middle, cell-containing layers were collagenase treated for 1 hr at 37°C, colonies were pelleted and washed and DNA was isolated using the GeneJET Genomic DNA Purification Kit
3 ug of genomic DNA was used to produce exome captured sequencing libraries using NimbleGen SeqCap EZ v3.0 following manufacturer's recommended instructions applying pre-capture multiplexing (http://www.nimblegen.com/products/lit/NimbleGen_SeqCap_EZ_SR_Pre-Captured_Multiplexing.pdf).


title: HCA-7-EKI

source_name: EKI-resistant HCA-7 cell line


title: SC1

source_name: HCA7-derived cell line with spiky colonies


title: SC1-EKI

source_name: EKI-resistant SC cell line


title: CC3

source_name: HCA7-derived cell line with cystic colonies


title: Control_RNAseq_Rep1


title: D7: Chow-Sedentary (C-SED)

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing:
Read quality was determined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed (phred score<30 trimmed) using PRINSEQ (http://prinseq.sourceforge.net/) and processed reads that were <50 bases in length were discarded
Reads were aligned to the rat transcriptome (reference sequence NCBI version Rnor_5.0) using TopHat (version 2.1.0). Differential gene expression was determined using Cuffdiff (Cufflinks version 2.2.1). Cuffdiff command was used with parameters -u (multi read correction algorithm) and -b (bias detection and correction algorithm).
Genome_build: Rattus norvegicus NCBI version Rnor_5.0
Supplementary_files_format_and_content: diff file format with following grouping definitions:
Supplementary_files_format_and_content: #G1 - HF-EEX (High-fat early-exercise)
Supplementary_files_format_and_content: #G2 - HF-LEX (High-fat, late exercise)
Supplementary_files_format_and_content: #G3 - HF-SED (High-fat, sedentary)
Supplementary_files_format_and_content: #G4 - Chow-SED (Chow-sedentary)

molecule: total RNA

organism: Rattus norvegicus

source_name: Femoral mid-diaphysis marrow

growth_protocol: Eighty 21-23 days old male SD rats were kept kept in pairs in cages and had ad libitum access to food and water. They were housed in a temperature controlled room (25oC) with a 12 hour light/dark cycle.

extract_protocol:
The left femur was partially sawn at the junction of (1) the distal and the middle thirds and (2) the middle and proximal thirds.The femur was snapped and the resulting mid-diaphysis was centrifuged (10,000 rpm, 4oC, 30s) to obtain the bone marrow. Total RNA was extracted using TRIzol® and cleaned up using RNeasy minikit. A minimum of 1.5 ug of total RNA was sent to Novogene for RNA-seq
After QC, mRNA  is enriched from total RNA by Oligo (dT) beads. The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR

treatment_protocol: Eighty male SD rats were randomised at weaning into chow-fed froup (C-SED; n=20) which obtained 18% of their energy from fat (Diet 2018, Harlan Teklad, USA) or a high-fat fed group (n=60) which obtained 45% of their total energy intake from fat (D12451, Research Diets, USA). The high-fat fed group was further divided into three sub-groups. The high-fat sedentary (HF-SED) group which had only spontaneous movement within the cage, the high-fat late-exercise (HF-LEX) group, which was allowed spontaneous activity upto day 60 after which it had access to a running wheel from day 67 to day 120 and the high-fat early exercise (HF-EEX) group which had access to a running wheel from day 22 to day 60 followed by spontaneous movement for the remainder of the experiment.

value: Sprague-Dawley

tag: age

tag: Sex

value: male

value: Femoral bone marrow

tag: group

value: Chow-Sedentary (C-SED)


title: D9: Chow-Sedentary (C-SED)


title: D6: Chow-Sedentary (C-SED)


title: D5: Chow-Sedentary (C-SED)


title: KIF1Bb_SCG_cKO2

city: Solna

first: Susanne

last: Schlisio

address: Nobels vag 3

country: Sweden

institute: Ludwig Institute for Cancer Research Ltd

data_processing:
base calling Illumina HiSeq 2000, with a 50bp single-end read length, encoding Illumina 1.5, no filtered sequences
Alignment with RNA-star (Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21, doi:10.1093/bioinformatics/bts635 (2013))
relative expression levels estimated with RPKMforgenes (Ramskold, D., Wang, E. T., Burge, C. B. & Sandberg, R. An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data. Plos Computational Biology 5, doi:ARTN e1000598 10.1371/journal.pcbi.1000598 (2009))
Genome_build: mm10
Supplementary_files_format_and_content: data table with raw count data for refseq genes

source_name: superior cervical ganglia

extract_protocol:
Total RNA was isolated from snap-frozen SCGs using a modified Trizol extraction protocol as follows. SCG pairs from each animal were thawed and then suspended in 300 ul Trizol (Invitrogen) containing 20 ug/ml Proteinase K (Invitrogen) and incubated at 55°C with shaking for 10 mins. Samples were then cooled on ice, 2 ul of Pelletpaint (Novagen) added, followed by 60 ul chloroform. Samples were then incubated on ice for 5mins, and centrifuged at 20,000g for 10 minutes to separate phases. The upper (aquaeus) phase was then collected and combined 1:1 with isopropanol, mixed vigorously, incubated for 5 minutes on ice and centrifuged for 30 minutes at 20,000g to precipitate RNA. After aspiration of supernatant, the RNA pellets were then washed with 300 ul 75% ethanol and centrifuged for a further 10 mins. After aspiration of the supernatant, pellets were resuspended in 100 ul of water, 10 μl 3M Sodium acetate was added, followed by 250 μl icecold 100% EtOH. Following incubation for 1 hour at -20°C, and centrifugation for 30 mins, suparnatant was aspirated and 300ul of 75% ethanol added to wash the RNA pellets that were then centrifuged for a further 10 mins. Finally, supernatant was completely aspirated from the pellets that were then briefly left to dry at room temperature in a fumehood, and then resuspended in 20 ul water. RNA was then quantified using a Nanodrop, and quality controlled using RNA PICO chips on an Agilent Bioanalyzer. Only samples with an RNA integrity index greater than 7.5 were used for RNA sequencing
Truseq v2

tag: developmental age

value: post natal day 1

tag: genotype

value: KIF1Bb fl/fl :DBHcre +/-

value: SCG


title: KIF1Bb_SCG_cKO3


title: KIF1Bb_SCG_cKO1


title: KIF1Bb_SCG_cKO4


title: KIF1Bb_SCG_WT4

value: KIF1Bb fl/fl :DBHcre -/-


title: D4: Chow-Sedentary (C-SED)


title: KIF1Bb_SCG_WT3


title: KIF1Bb_SCG_WT1


title: KIF1Bb_SCG_WT2


title: D2: Chow-Sedentary (C-SED)


title: D3: Chow-Sedentary (C-SED)


title: C8: High-Fat Sedentary (HF-SED)

value: High-Fat Sedentary (HF-SED)


title: Control_RNAseq_Rep3

value: Left ventricle

value: Isolated cardiac myocytes


title: C9: High-Fat Sedentary (HF-SED)


title: HCA-7

source_name: HCA-7 cell line


title: D10: Chow-Sedentary (C-SED)


title: C6: High-Fat Sedentary (HF-SED)


title: C5: High-Fat Sedentary (HF-SED)


title: C4: High-Fat Sedentary (HF-SED)


title: C2: High-Fat Sedentary (HF-SED)


title: C3: High-Fat Sedentary (HF-SED)


title: iPS_rep3_PolII

description:
Sample 728
[Processed data files]:
iPS_avg_PolII_Bin_2000_121.bed.gz
iPS_avg_PolII_Bin_2000_121.wig.gz
iPS_rep3_PolII_Bin_2000_728.bed.gz
iPS_rep3_PolII_Bin_2000_728.wig.gz
gene_iPS_avg_PolII_121.bed.gz
gene_iPS_avg_PolII_121.bedGraph.gz
gene_iPS_rep3_PolII_728.bed.gz
gene_iPS_rep3_PolII_728.bedGraph.gz

value: iPS cells

value: iPS R4


title: C1: High-Fat Sedentary (HF-SED)


title: B10: High Fat-Late Exercise (HF-LEX)

value: High Fat-Late Exercise (HF-LEX)


title: B5: High Fat-Late Exercise (HF-LEX)


title: B9: High Fat-Late Exercise (HF-LEX)


title: B8: High Fat-Late Exercise (HF-LEX)


title: B7: High Fat-Late Exercise (HF-LEX)


title: B6: High Fat-Late Exercise (HF-LEX)


title: B3: High Fat-Late Exercise (HF-LEX)


title: D1: Chow-Sedentary (C-SED)


title: A7: High Fat-Early Exercise (HF-EEX)

value: High Fat-Early Exercise (HF-EEX)


title: A9: High Fat-Early Exercise (HF-EEX)


title: A8: High Fat-Early Exercise (HF-EEX)


title: A4: High Fat-Early Exercise (HF-EEX)


title: A3: High Fat-Early Exercise (HF-EEX)


title: C10: High-Fat Sedentary (HF-SED)


title: B4: High Fat-Late Exercise (HF-LEX)


title: B2: High Fat-Late Exercise (HF-LEX)


title: B1: High Fat-Late Exercise (HF-LEX)


title: A10: High Fat-Early Exercise (HF-EEX)


title: C7: High-Fat Sedentary (HF-SED)


title: A1: High Fat-Early Exercise (HF-EEX)


title: A6: High Fat-Early Exercise (HF-EEX)


title: A5: High Fat-Early Exercise (HF-EEX)


title: A2: High Fat-Early Exercise (HF-EEX)


title: WT +Zn 2

city: Emeryville

first: Megan

middle: Elizabeth

last: Garber

address: 5885 Hollis st

department: Department of Energy/ UC Berkeley

institute: ENIGMA

description: tpm.csv

data_processing:
pseudo-alignments done via kallisto v.0.42.5
differential expression, tpm calculated via R package slueth v.0.28.1
Genome_build: Pseudomonas stutzeri rch2.ASM32706v1
Supplementary_files_format_and_content: csv with transcripts per million calculated via slueth

organism: Stutzerimonas stutzeri

source_name: mRNA from bacterial cells

growth_protocol: WT and ∆Czcr P. stutzeri RCH2 were each grown from overnight cultures I 6mL UGA medium (+Kan for the mutant) at 30˚C with shaking. At OD600 of 0.2 three of the WT and ∆CzcR tubes received 100µM zinc chloride. The remaining tubes received nothing. All tubes were incubated for 1 hour at 30˚C

extract_protocol:
qiagen RNAeasy, according to manufacters instructions for gram negative bacteria
rRNA depletion via ThermoFisher RiboMinus. NEBnext RNA library kit, according to maufacturers instructions

value: WT + Zn


title: WT +Zn 3

description: tpm.csv


title: WT +Zn 1

description: tpm.csv


title: WT 1

description: tpm.csv

value: WT


title: WT 2

description: tpm.csv


title: [delta]CzcR + Zn 2

description: tpm.csv

value: [delta]CzcR + Zn


title: WT 3

description: tpm.csv


title: [delta]CzcR + Zn 3

description: tpm.csv


title: [delta]CzcR + Zn 1

description: tpm.csv


title: dCas9-1_4+dCas9-3_2

status: Public on Aug 29 2017

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description:
Site4 dCas9 DNA replicate 1 and FANCF dCas9 DNA replicate 3
eBE_Indels.xlsx

data_processing:
Library strategy: DNA-Seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

source_name: 293FT cells

growth_protocol: 293FT from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination.

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For DNA, cells were seeded in a 6-well plate at a density of 8 × 105 per well and transfected with 500 μl serum-free Opti-MEM that contained 5.4 μl LipofectamineTM 2000 (Thermo Fisher Scientific), 2.5 μg pCMV-BE3 (pCMV-eBE3a or pCMV-eBE-S3), 1.6 μg sgRNA-expressing plasmid without or with 50, 100, 200 ng pUGI-NLS.  After 24 hr, puromycin (ant-pr-1, InvivoGen) and blasticidin (ant-bl-1, InvivoGen) were added to the media at the final concentration of 10 μg/ml,

tag: treatment

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: [delta]CzcR 2

description: tpm.csv

tag: strain

tag: genotype/variation

value: [delta]CzcR


title: dCas9-3_1

description:
EMX1 dCas9 DNA replicate 3
eBE_Indels.xlsx


title: dCas9-3_4

description:
Site4 dCas9 DNA replicate 3
eBE_Indels.xlsx


title: [delta]CzcR 3

description: tpm.csv


title: dCas9-2_2+dCas9-3_3

description:
FANCF dCas9 DNA replicate 2 and Site2 dCas9 DNA replicate 3
eBE_Indels.xlsx


title: dCas9-1_2

description:
FANCF dCas9 DNA replicate 1
eBE_Indels.xlsx


title: eBE-S3-2_2+eBE-S3-2_3+eBE-S3-2_4+eBE-S3-3_5

description:
FANCF eBE-S3 DNA replicate 2 and Site2 eBE-S3 DNA replicate 2 and Site4 eBE-S3 DNA replicate 2 and RNF2 eBE-S3 DNA replicate 3
eBE_Indels.xlsx


title: eBE-S3-3_1+eBE-S3-3_4

description:
EMX1 eBE-S3 DNA replicate 3 and Site4 eBE-S3 DNA replicate 3
eBE_Indels.xlsx


title: eBE-S3-1_2+eBE-S3-1_3+eBE-S3-1_4+eBE-S3-2_1+eBE-S3-2_5

description:
FANCF eBE-S3 DNA replicate 1 and Site2 eBE-S3 DNA replicate 1 and Site4 eBE-S3 DNA replicate 1 and EMX1 eBE-S3 DNA replicate 2 and RNF2 eBE-S3 DNA replicate 2
eBE_Indels.xlsx


title: eBE-S1-3_3

description:
Site2 eBE-S1 DNA replicate 3
eBE_Indels.xlsx


title: eBE-S3-1_5+eBE-S3-3_3

description:
RNF2 eBE-S3 DNA replicate 1 and Site2 eBE-S3 DNA replicate 3
eBE_Indels.xlsx


title: eBE-S3-1_1

description:
EMX1 eBE-S3 DNA replicate 1
eBE_Indels.xlsx


title: eBE-S1-3_1+eBE-S1-3_4

description:
EMX1 eBE-S1 DNA replicate 3 and Site4 eBE-S1 DNA replicate 3
eBE_Indels.xlsx


title: eBE-S1-2_2+eBE-S1-2_3+eBE-S1-2_4+eBE-S1-3_5

description:
FANCF eBE-S1 DNA replicate 2 and Site2 eBE-S1 DNA replicate 2 and Site4 eBE-S1 DNA replicate 2 and RNF2 eBE-S1 DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-H-2_3

description:
RNF2 BE3_UGI-H-1 DNA replicate 2
eBE_Indels.xlsx


title: eBE-S1-1_2+eBE-S1-1_3+eBE-S1-1_4+eBE-S1-2_1_eBE-S1-2_5

description:
FANCF eBE-S1 DNA replicate 1 and Site2 eBE-S1 DNA replicate 1 and Site4 eBE-S1 DNA replicate 1 and EMX1 eBE-S1 DNA replicate 2 and RNF2 eBE-S1 DNA replicate 2
eBE_Indels.xlsx


title: eBE-S1-1_1+eBE-S1-1_5

description:
EMX1 eBE-S1 DNA replicate 1 and RNF2 eBE-S1 DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-H-3_2+eBE-S3-3_2

description:
Site2 BE3_UGI-H-1 DNA replicate 3 and FANCF eBE-S3 DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-M-2_2

description:
Site2 BE3_UGI-M DNA replicate 2
eBE_Indels.xlsx


title: BE3_UGI-H-1_1+BE3_UGI-H-1_3

description:
FANCF BE3_UGI-H DNA replicate 1 and RNF2 BE3_UGI-H-1 DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-H-3_1+BE3_UGI-H-3_3

description:
FANCF BE3_UGI-H DNA replicate 3 and RNF2 BE3_UGI-H-1 DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-M-2_3

description:
RNF2 BE3_UGI-M DNA replicate 2
eBE_Indels.xlsx


title: BE3_UGI-M-3_2+eBE-S1-3_2

description:
Site2 BE3_UGI-M DNA replicate 3 and FANCF eBE-S1 DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-H-1_2+BE3_UGI-H-2_1

description:
FANCF BE3_UGI-H DNA replicate 2 and Site2 BE3_UGI-H DNA replicate 1
eBE_Indels.xlsx


title: dCas9-2_4

description:
Site4 dCas9 DNA replicate 2
eBE_Indels.xlsx


title: BE3_UGI-M-3_1+BE3_UGI-M-3_3

description:
FANCF BE3_UGI-M DNA replicate 3 and RNF2 BE3_UGI-M DNA replicate 3
eBE_Indels.xlsx


title: dCas9-1_1

description:
EMX1 dCas9 DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-M-1_1+BE3_UGI-M-1_3

description:
FANCF BE3_UGI-M DNA replicate 1 and RNF2 BE3_UGI-M DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-L-2_2

description:
Site2 BE3_UGI-L DNA replicate 2
eBE_Indels.xlsx


title: BE3_UGI-L-3_2

description:
Site2 BE3_UGI-L DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-L-2_3

description:
RNF2 BE3_UGI-L DNA replicate 2
eBE_Indels.xlsx


title: BE3_UGI-L-3_1+BE3_UGI-L-3_3

description:
FANCF BE3_UGI-L DNA replicate 3 and RNF2 BE3_UGI-L DNA replicate 3
eBE_Indels.xlsx


title: BE3_UGI-L-1_1+BE3_UGI-L-1_3

description:
FANCF BE3_UGI-L DNA replicate 1 and RNF2 BE3_UGI-L DNA replicate 1
eBE_Indels.xlsx


title: dCas9-2_1+BE3-3_3

description:
Site2 BE3 DNA replicate 3 and EMX1 dCas9 DNA replicate 2
eBE_Indels.xlsx

value: BE3 or dCas9


title: BE3-1

description:
EMX1, FANCF, Site2, Site4, RNF2 BE3 DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-L-1_2+BE3_UGI-L-2_1

description:
FANCF BE3_UGI-L DNA replicate 2 and Site2 BE3_UGI-L DNA replicate 1
eBE_Indels.xlsx


title: BE3_UGI-M-1_2+BE3_UGI-M-2_1

description:
FANCF BE3_UGI-M DNA replicate 2 and Site2 BE3_UGI-M DNA replicate 1
eBE_Indels.xlsx


title: hESC_wnt3a_12h

city: La Jolla

first: Theresa

last: Gaasterland

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

description: total RNA extracted for RNA-seq

data_processing:
RNA-seq: mapped to human reference genome hg19; bowtie version 0.12.7, seed size 50 bases, up to 3 mismatches, one match site (-l 50 -n 3 -m1); output sam file format
CHIP-seq: mapped to human reference genome hg19; bowtie version 0.12.7, seed size 50 bases, up to 2 mismatches, one match site (-l 50 -n 2 -m 1); output bowtie-output format
converted sam to bam format, sort and index bam files; samtools version 0.1.12a
RNA-seq: generated normalized readcounts; cuffdiff version v1.3.0 (3022)
RNA-seq: merged readcounts into single table; custom perl script
RNA-seq: converted normalized readcounts to "percent of maximum readcount" for each gene
CHIP-seq: convert bowtie mapped reads to bed format; custom perl script (generate_bed_file_from_bowtie.pl)
CHIP-seq: convert bed to wig format; custom perl script (bedGraphToBigWig)
CHIP-seq:convert wig to bigwig for visual display; custom perl script (bedGraphToBigWig)
CHIP-seq: call peaks from control and treatment bed files; MACS version 1.4.2 (-tsize 100 --nomodel --shiftsize 100 --gzize hs)
Genome_build: GRCh37/hg19

source_name: human embryonic stem cells, H1 (WA01/NIH Registration Number 0043)

growth_protocol: grown in Essential 8 (E8) media (as described in Chen et al, Nat. Meth., 8, 424-429, 2011)

extract_protocol:
total RNA: RNeasy Plus, Qiagen; chromatin: as described in Myers Lab ChIP-seq Protocol v041610 (http:hudsonalpha.org/protocols)
RNA-seq: Ribo-Zero Gold rRNA Removal Kit by Epicentre (Illumina) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina / CHIP-seq: NEBNext Ultra DNA Library Prep Kit for Illumina

treatment_protocol: Wnt3a, 1nM concentration (Wnt3a prepared as described in Willert, Methods Mol. Biol., 468, 17-29, 2008)

tag: cell type

value: human embryonic stem cells

value: H1 hESC WA01/NIH Reg. No 0043

tag: cell line name

tag: alternative cell line name

tag: nih registration number


title: hESC_wnt3a_00h

description: total RNA extracted for RNA-seq

tag: cell line


title: BE3-3_5

description:
RNF2 BE3 DNA replicate 3
eBE_Indels.xlsx


title: BE3-3_2

description:
FANCF BE3 DNA replicate 3
eBE_Indels.xlsx


title: BE3-2

description:
EMX1, FANCF, Site2, Site4, RNF2 BE3 DNA replicate 2
eBE_Indels.xlsx


title: BE3-3_4+BE3_UGI-H-2_2

description:
Site4 BE3 DNA replicate 3 and and Site2 BE3_UGI-H DNA replicate 2
eBE_Indels.xlsx

value: BE3 or BE3_UGI-H


title: hESC_wnt3a_24h_SP5_chromatin_IP

description: chromatin extracted for ChIP-seq


title: BE3-3_1

description:
EMX1 BE3 DNA replicate 3
eBE_Indels.xlsx


title: hESC_wnt3a_24h

description: total RNA extracted for RNA-seq


title: hESC_wnt3a_00h_SP5_chromatin_IP

description: chromatin extracted for ChIP-seq


title: 27A_Non-responder

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

data_processing:
Reads were created by CASAVA 1.8.2 from the  HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X and at most 500X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: hg18
Supplementary_files_format_and_content: myCpG.txt = methylation calls; tab delimited file with the following column heades: chrBase chr base strand coverage freqC freqT

source_name: sorted monocytes from peripheral blood

extract_protocol:
Genomic DNA were isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer’s instructions
ERRBS libraries were constructed as described in 44. Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781

tag: response to decitabine

value: Non-responder

tag: gender

value: Male

tag: type of cmml

tag: karyotype

tag: mutation status

value: Mutant


title: 36A_Non-responder

tag: age


title: 6A_Responder

value: Responder


title: 9A_Non-responder


title: 34A_Non-responder


title: 37A_Non-responder

value: Female


title: 2A_Responder


title: 5A_Non-responder


title: 7A_Non-responder


title: 41A_Responder


title: 4A_Responder


title: 3A_Responder


title: 26A_Responder


title: 35A_Non-responder


title: 23A_Responder


title: 30A_Non-responder


title: 22A_Non-responder


title: 32A_Non-responder


title: 15A_Non-responder


title: 13A_Responder


title: 18A_Non-responder

value: Wild type


title: 12A_Responder

value: Not determined


title: 25A_Responder


title: 33A_Responder


title: 39A_Non-responder


title: UGJLR9VW..TS

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: Cell Wall Regeneration JL-R9-53

data_processing:
Alignment to Chlamydomonas reinhardtii genome v5.5 from Phytozome with RNA-Star v2.4.1d
Gene expression determination with cuffdiff v2.2.1
Genome_build: Chlamydomonas reinhardtii genome v5.5 from Phytozome
Supplementary_files_format_and_content: Standard cuffdiff output

organism: Chlamydomonas reinhardtii

source_name: Cell Wall Regeneration JL-R9-53 (mt+/mt-;imp11)

growth_protocol: Vegetative cells were grown in liquid, and all other samples were grown on Agar-plate, of Tris-Acetate-Phosphate (TAP) media under constant light (90 µmole m^-2 s^-1)

extract_protocol:
RNA was extracted by Trizol reagent, and treated with RNAse-free DNAse I, and then Poly(A)+ RNA was isolated using the Dynabeads mRNA purification kit prior to sequencing library preparation.
RNA libraries were prepared for sequencing using standard unstranded Illumina protocols.

treatment_protocol: Gametogenesis is induced by resuspension in nitrogen free-TAP and incubated for 24 hr. Zygotes were produced by mating equal number of plus and minus gametes and harvested at 30 mins and 2 hrs after mixing.

tag: condition

value: cell wall regeneration


title: 10A_Responder

value: 46, XY sur 25


title: UGJLQUZY..nS

description: Early Zygote of CC-2937(mt+) and CC-621(mt-)

value: zygote


title: UGJLR9VL..TS

description: Vegetative Growth JL-R9-53

source_name: Vegetative Growth JL-R9-53 (mt+/mt-;imp11)

value: vegetative growth


title: 11A_Non-responder


title: UGJLPAZY..nS

description: Early Zygote of CC-125(mt+) and CC-2342(mt-)


title: UGJLI2VW..TS

description: Cell Wall Regeneration JL-I2-152

source_name: Cell Wall Regeneration JL-I2-152 (mt-;iso2)


title: UGJLI2VL..TS

description: Vegetative Growth JL-I2-152

source_name: Vegetative Growth JL-I2-152 (mt-;iso2)


title: NC36h-1

city: Guangzhou

first: Min

last: Feng

address: wushan road

institute: South China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gallus gallus whole genome using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9
To estimate the expression of each gene, the total number of reads mapped to its unigenes were calculated and normalized with FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Gallus_gallus.Galgal4. 76

organism: Gallus gallus

source_name: macrophage

extract_protocol:
Total RNA was extracted from each samples using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit  was used with 3 ug of total RNA for the construction of sequencing libraries.
mRNA and lncRNA libraries were prepared for sequencing using standard Illumina protocols (Novogene (Beijing, China) )

tag: strains

value: White Leghorns

tag: group

value: Uninfected MDM


title: J36h-1

value: J subgroup avian leukosis virus (ALV-J) infected MDM


title: NC36h-2


title: J36h-2


title: hESC_wnt3a_48h

description: total RNA extracted for RNA-seq

value: human embryonic stem cells


title: 16A_Non-responder


title: NC3h-2


title: J-36h

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences, low quality reads (Sanger bases quality < 20), and contaminant reads were removed with the Fastx-Toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were mapped to chicken genome to annotate the location in the chromosomes using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml).
Genome_build: Gallus_gallus.Galgal4.76
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was extracted from each samples using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit  was used with 3 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols (Novogene (Beijing, China) )

value: J subgroup avian leukosis virus (ALV-J) infected MDM at 36 hpi


title: UGJLM2PZ..nS

description: Pseudo-zygotes JL-M2MP-10

source_name: Pseudo-zygotes JL-M2MP-10 (mt-; mid-2)

value: pseudo-zygote


title: C-36h


title: smallRNA_2

city: Chapel Hill

first: Terry

last: Furey

state: North Carolina

address: 5022 Genetic Medicine Bldg, CB#7264

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were quality-filtered, adapters removed, and aligned to appropriate reference genomes (C57BL/6: NCBI Build 37; CAST/EiJ: Build 37 pseudogenome (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo)) using Bowtie (Langmead et al. 2009)
Subsequently, the remaining sequences were aligned to regions with exact match reads allowing a maximum of one mismatch in the body or up to 3 mismatches at the 3’-end of the read (depending on the length of the read) using SHRimP2 (David et al., 2011).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of raw ATAC-seq signal
Supplementary_files_format_and_content: RNA count matrix
Supplementary_files_format_and_content: microRNA count matrix

source_name: CAST/EiJ_Clean-air_small RNA-seq

growth_protocol: Male C57BL/6J and CAST/EiJ mice were purchased from The Jackson Laboratory (Bar Harbor, ME)

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini Kit (Valencia, CA)
TruSeq libraries were constructed as per manufacturer's recommendations.

treatment_protocol: Mice were exposed to clean-air for 6 hours a day, Monday-Friday, across a two week period

value: CAST/EiJ

tag: genotype

value: Wild-type

tag: Sex

value: male

tag: exposed to

value: Clean-air

tag: tissue

value: lung


title: smallRNA_1

tag: strain


title: GRIDseq.mESC_rep1

city: San Diego

first: Bing

last: Zhou

state: CALIFORNIA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

description: total RNA and genomic DNA

data_processing:
Library strategy: GRID-seq
Upon sequencing, individual libraries were segregated according to multiplexing barcodes and then both barcode and residual adapter sequences were removed from each tag to produce tags with non-uniform length, the majority of which ranged from 84 bp to 87 bp in each library. To precisely remove linker sequence from the DNA and cDNA tags, MmeI motifs were used for defining linker boundaries. Linker orientation also dictated whether the tags at each side were originated from genomic DNA or RNA. To minimize the loss of tags due to sequencing errors, tags were first filtered based on the presence of two opposite-orientated MmeI motifs, then aligned to the linker sequence from both directions to determine its orientation. DNA and corresponding RNA tags, most of which ranged from 18 bp to 23 bp, were extracted for alignment.
All processed tags were aligned to their indicated genome build using Bowtie2 with parameter of --local. Human samples were aligned to genome build hg38, mouse samples to genome build mm9 and Drosophila samples to genome build dm3 with parameters -q 2. To estimate the numbers of cross-species-ligated RNA and DNA tags in the mix of MDA-MB-231 and S2 cell nuclei, RNA tags were first aligned independently to the transcriptome builds of hg38 and dm3, with the most stringent parameter of -q 44. Linked DNA tags of those RNA tags that were unambiguously aligned to human transcriptome were then aligned to human genome with the parameter of -q 2. These DNA tags failed to align to the human genome were then aligned to the Drosophila genome, with the parameter of -q 2. Conversely, DNA tags linked to the RNA tags that were unambiguously aligned (-q 44) to the Drosophila transcriptome were first aligned to the Drosophila genome (-q 2), and those unaligned DNA tags were then aligned to the human genome (-q 2)
Genomic regions with enriched GRID-seq RNA reads were detected by MACS2 using the model for broad-peak detection. These mapped regions with significant enrichment (p < 0.001) and overlapping with known-gene annotation (Ensemble genes GRCh38.83 for human, NCBI m37 for mouse and BDGP5.78 for Drosophila) were assigned to their respective largest annotated genes. Enriched regions that did not overlap with any known gene were assigned as “unannotated transcripts”. The RNA read-coverage of genomic regions was calculated by BEDtools and SAMtools. The genes with the tag-coverage above the sliding-window threshold [(Ni+n - Ni) ≥ n, where i was the rank of given RNA, N was the read-counts of this RNA and n was the 1/100 of the total number of ranked RNAs] were selected as abundant chromatin-interacting RNAs. A subset of abundant RNAs with sufficient RNA read-density [RPK (reads per Kb) ≥ 100] or with significant DNA read-densities (RPK ≥ 10) associated at any genomic region was identified as hit RNAs for further analysis (Supplementary Table 1).
To determine the specific RNA-chromatin interaction pattern of each hit RNA, we developed a genome-wide background for non-specific interactions. Ideally, for each library, we could setup mixed nuclei from different species in order to evaluate cross-species RNA-chromatin interactions, which would represent the true background. In practice, it is feasible to generate such background with sufficient density on the Drosophila genome by using RNA reads from human cells because of the much smaller Drosophila genome, but the RNA density on the human genome based on the RNA reads from Drosophila is often too scattered to provide a reliable background. We thus sought to deduce the background in the Drosophila genome based on endogenous RNA reads in comparison with the true background based on cross-species RNA-chromatin interactions. Toward this goal, we selected RNAs from protein-coding genes engaged in trans-chromosomal interactions, and calculated their density on the 1 Kb-binned genome. Such deduced background read-density at each 1 Kb bin was then smoothed by a moving widow of 100 Kb and normalized by the total read number and chromosome size.  The resulting background in the Drosophila genome was highly correlated with the cross-species background. This strategy enabled us to deduce the background on any human cells by using endogenous RNA reads.
To evaluate specific RNA-chromatin interactions of each hit RNA at each genomic bin, we first summarized the DNA reads for each gene at each genomic bin, and then normalized them to 1 million reads followed by further normalization of total number of bins of each chromosome. A ratio was next calculated by dividing the normalized DNA read density with background read density, which represents specific binding of this RNA at the genomic bin.   To construct a robust global binding matrix for all hit RNAs, genomic bins with significant binding level (at least 3 bins with binding level ≥ 2 in every 10 bin-window) were preserved and further smoothed by a moving-widow of 10 bins. All subsequent analyses involving binding levels and patterns were based on such genomic binding matrix.
In the processing of GRO-seq data, multiplexing barcode sequences were removed from each tag after sequecing. All tags were aligned to hg38 genome build using Bowtie2 --local -q2. Due to high variability of small transcripts, only transcripts with lengths larger than 4 Kb were included in the analysis. First, coverages on promoter regions (2 Kb upstream of TSS to 2 Kb downstream of TSS) were compared among transcript isoforms of each gene, and the transcript with highest promoter coverage was selected to represent the gene. To finally estimate the transcription activity for each gene’s representative transcript, normalized read densities (read per Kb per million total reads, RPKM) were calculated within a 2 Kb region that started at 2 Kb downstream of TSS and ended at 4 Kb downstream of TSS. Analysis were applied in all samples, and JQ1/DMSO log-ratio for each gene was calculated as [log2(JQ1_RPKM+1)- log2(DMSO_RPKM+1)].
Genome_build: human genome hg38, mouse mm9 and Drosophila genome dm3
Supplementary_files_format_and_content: The processed GRID-seq data are recorded as tab-delimited text files with 9 columns for each sample , representing RNA_Chrom, RNA_Start, RNA_End, GeneID, RNA_Total_Reads, RNA_Strand, DNA_Chrom, DNA_Bin and Value. The GRID-seq value is normalized interaction density between RNA and DNA. And the processed GRO-seq data are recorded in one tab-delimited text file with 8 columns representing GeneID, DMSO_rep1, DMSO_rep2, JQ1_rep1, JQ1_rep2, DMSO_sum, JQ1_sum, LogRatio_JQ1_vs_DMSO. GRO-seq values represent the densities of genes (RPKM) in each samples, where the DMSO_sum and JQ1_sum are the summarized densities in the two repeats and the LogRatio_JQ1_vs_DMSO is based on the summarized values.

source_name: ES

growth_protocol: MDA-MB-231 breast cancer cells (HTB-26 ATCC) and MM.1S multiple myeloma cells were grown at 37°C and 5% CO2. MDA-MB-231 cells were cultured in Dulbecco's Modified Eagle Medium (Thermo Fisher Sci.) supplemented with 10% fetal bovine serum. MM.1S cells were cultured in RPMI-1640 supplemented with 1% GlutaMAX (Thermo Fisher Sci.) and 10% fetal bovine serum. Mouse ES Cells were maintained in KnockoutTM DMEM supplemented with 15% KnockoutTM Serum Replacement, 2 mM L-glutamine, 1X Non-essential amino acids, 1X Penicillin-Streptomycin, 0.1 mM 2-Mercaptoethanol, 1000 U/ml LIF, 3 µM CHIR99021 and 1 µM PD0325901. Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Sci.) supplemented with 10% fetal bovine serum and 2 mM L-glutamine (Thermo Fisher Sci.), at room temperature in ambient CO2.

extract_protocol:
Approximately 2 million mammalian cells or 10 million Drosophila cells were sequentially crosslinked with 2 mM DSG and 3% formaldehyde. Nuclei were isolated, washed and digested in situ by AluI restriction enzyme. All DNA and RNAs in the nuclei were then treated by T4 PNK. After washing, nuclei were mixed with GRID-seq linkers and T4 RNA Ligase 2-truncated KQ for ssRNA ligation. Shorter strand of the linker was extended by SuperScript III Reverse Transcriptase to generate cDNA. Nuclei were washed again and resuspended in T4 DNA ligase solution for ligation of genomic DNA. By Proteinase K digestion at 65°C, linker-ligated DNA were reverse-crosslinked and extracted, followed by affinity purification by Streptavidin-conjugated beads. By denaturation with 150 mM NaOH solution, the non-biotinylated strand of the linker-ligated-DNA were released, and subjected to second strand synthesis by Klenow Fragment (3' to 5' exo-) enzyme. Newly synthesized dsDNA were then digested by MmeI for paired-end-tag generation, followed by size-selection in 12% native polyacrylamide gel. Recovered dsDNA was further ligated with adapters, PCR amplified to generate libraries for illumina sequencing.   GRO-seq protocol was adapted from (Core, L. J. et al, Science, 2008)
Adapters were prepared by annealing the following two oligonucleotides in 1× NEB Buffer 2 to a final concentration of 25 mM: 5’-/5Phos/AGATCGGAAGAGCACACGTCT-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNN-3’. Purified DNA was dissolved in 10 µl of 1× NEB Buffer CutSmart and 0.5 U Shrimp Alkaline Phosphatase, incubated at 37 °C for 30 min and heat inactivated at 65°C for 5 min. The reaction was diluted with 36 µl H2O, mixed with 10 µl of 10× T4 DNA Ligase Buffer, 32 µl of PEG-6000, 200 pmol of Adapters and 1,600 U T4 DNA Ligase, and incubated at room temperature for 1 h. Unligated nick was phosphorylated by 20 U T4 Polynucleotide Kinase supplemented by 100 pmol ATP and incubated at 37°C for 30 min. Nick was then ligated by addition of 1 µl of 10× T4 DNA Ligase Buffer, 100 pmol ATP and 1,600 U T4 DNA Ligase, and incubation at room temperature for 30 min. DNA along with excessive Adapters were extracted and purified before loading to 10% native PAGE gel for size-selection. The desired band at approximately 185 bp was excised. DNA was extracted and dissolved in 20 µl of H2O. To amplify each library, 20 µl of PCR amplification mix (9.4 µl of H2O, 5 µl of DNA sample, 4 µl of 5× Phusion HF Buffer, 40 pmol dNTP, 5 pmol Primer#1, 5 pmol Primer#2, 0.4 U Phusion High-Fidelity DNA Polymerase was prepared. PCR primers consist of Primer#1 (5’- AATGATACGGCGACCACCGAGATCTACACBBBBBACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’ (BBBBB: 5 nt barcode for multiplexing libraries)) and Primer#2 (5’- CAAGCAGAAGACGGCATACGAGACGTGTGCTCTTCCGATCT -3’).  PCR was performed with an initial 30 sec denaturation at 98°C, followed by 16 cycles of 10 sec denaturation at 98°C, 30 sec annealing at 65°C and 15 sec extension at 72°C. The PCR product was separated on a native 10% PAGE gel and the band at 188 bp was recovered. DNA was subsequently subjected to Illumina HiSeq 2500 for single-end 100 bp sequencing, with the sequencing primer (5’- ACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’).

treatment_protocol: For JQ1 treatment, MDA-MB-231 cells were resuspended in fresh media containing 500 nM JQ1 or 0.05% DMSO as vehicle for a duration of 6 h.

tag: cell type

value: ES cells


title: GRIDseq.mESC_rep2

description:
total RNA and genomic DNA
Processed data for merged replicates is available on GSM2396700.


title: UGJLN7PZ..nS

description: Pseudo-zygotes JL-N7RM-110


title: smallRNA_101


title: J-3h

value: J subgroup avian leukosis virus (ALV-J) infected MDM at 3 hpi


title: smallRNA_103


title: J3h-1


title: smallRNA_7

source_name: CAST/EiJ_BD_small RNA-seq

treatment_protocol: Mice were exposed to BD for 6 hours a day, Monday-Friday, across a two week period

value: 1,3-Butadiene (BD)


title: smallRNA_10


title: smallRNA_102


title: smallRNA_104


title: smallRNA_8


title: smallRNA_9


title: smallRNA_106

source_name: C57BL/6J_Clean-air_small RNA-seq


title: smallRNA_5


title: NC3h-1


title: smallRNA_6


title: smallRNA_4


title: J3h-2


title: smallRNA_3


title: C-3h


title: smallRNA_17

source_name: C57BL/6J_BD_small RNA-seq


title: smallRNA_18


title: smallRNA_15


title: smallRNA_16


title: smallRNA_105


title: RNA_2

data_processing:
Reads were quality-filtered, adapters removed, and aligned to appropriate reference genomes (C57BL/6: NCBI Build 37; CAST/EiJ: Build 37 pseudogenome (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo)) using GSNAP software (Wu and Nacu, 2010) with and RefSeq splice site annotations
Transcript abundance was estimated using RefSeq gene models aggregated by gene symbol.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of raw ATAC-seq signal
Supplementary_files_format_and_content: RNA count matrix
Supplementary_files_format_and_content: microRNA count matrix


title: RNA_105


title: RNA_1


title: RNA_104


title: RNA_6


title: RNA_9


title: RNA_101


title: RNA_4


title: RNA_10


title: RNA_7


title: RNA_12


title: RNA_103


title: RNA_106


title: RNA_18


title: RNA_8


title: RNA_11


title: RNA_102


title: RNA_17


title: H1 Ribominus sup replicate 1

city: Boston

first: Chan

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

description: The supernatant sample after m6A immunoprecipitation of ribosome-depleted total RNA

data_processing:
Raw RNA-seq data were mapped to the human reference genome (hg19) with bowtie2 (v:2.2.5). All mapped reads in bam files were converted into bigwig files. The unmapped reads were used to identify the back-splice junctions of ciircRNAs with AutoCirc  (https://github.com/chanzhou/AutoCirc).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; Bed
*.minus.bw: all the reads from supernatant RNA-seq mapped into the anti-sense strand of the genome
*.plus.bw: all the reads from supernatant RNA-seq mapped into the sense strand of the genome
*circ.2reads.track.bed: Circular RNAs identified from the samples

source_name: H1 hESC WT_Ribominus sup

growth_protocol: H1 (WA01) cells (WiCell) were cultured in mTeSR1 (Stem Cell Technologies) in feeder-free conditions as previously described (Sigova et al., 2013). Hela cells were grown using DMEM supplemented with 10% heat inactivated FBS, 1% GlutaMAX and 1% Pen/Strep (penicillin/Streptomycin).

extract_protocol:
Both H1 and HeLa cells were extracted as follows: 1.The media was removed; 2. The Cell were washed twice with PBS; 3. TRIZol was added directly to the plate; 4. RNA was extracted by TRIZol; 5. The total RNA was treated with DNASe I; 6 The RNA was once again extracted by acid Phenol/Chloroform followed by Chloroform extraction; 7. The RNA was NaCl precipitated; 8. 80% ethanol washed twice; 9. Resuspended in Ultra pure H2O; 10. The desire amount of RNA was ribosome-depleted twice using a RiboMinus Kit.
RNA-seq libraries were prepared according to Ilumina instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing.

treatment_protocol: No treatment

value: human Embryonic stem cells (hESC)


title: H1 Ribominus sup replicate 2


title: ATAC_2

data_processing:
Library strategy: ATAC-seq
Reads were quality-filtered, adapters removed, and aligned to appropriate reference genomes (C57BL/6: NCBI Build 37; CAST/EiJ: Build 37 pseudogenome (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo)) using GSNAP software (Wu and Nacu, 2010) with and RefSeq splice site annotations
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of raw ATAC-seq signal
Supplementary_files_format_and_content: RNA count matrix
Supplementary_files_format_and_content: microRNA count matrix

extract_protocol:
Flash frozen tissue was pulverized in liquid nitrogen using the BioPulverizer (Biospec). This mechanical process breaks open the cells and allows even exposure of intact chromatin to transposase. Pulverized material was thawed in glycerol containing nuclear isolation buffer to stabilize nuclear structure (Zhang et al.; Masuda et al., 1991), and then filtered through Miracloth (Calbiochem) to remove large tissue debris. Nuclei were washed and directly used for treatment with Tn5 transposase.
TruSeq libraries were constructed as per manufacturer's recommendations.


title: RNA_16


title: RNA_14


title: HeLa Ribominus sup replicate 1

source_name: HeLa_WT_Ribominus sup

value: HeLa


title: dCas9-3_5

description:
RNF2 dCas9 DNA replicate 3
eBE_Indels.xlsx

tag: treatment

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: RNA_15


title: ATAC_105


title: RNA_3


title: RNA_5


title: ATAC_1


title: dCas9-2_3+dCas9-2_5

description:
Site2 dCas9 DNA replicate 2 and RNF2 dCas9 DNA replicate 2
eBE_Indels.xlsx

tag: cell line


title: dCas9-1_5

description:
RNF2 dCas9 DNA replicate 1
eBE_Indels.xlsx


title: dCas9-1_3

description:
Site2 dCas9 DNA replicate 1
eBE_Indels.xlsx


title: ATAC_9


title: RNA_13


title: Sample 9 [MUT 1 d21]

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to h19 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg19 whole genome using tophat2 with parameters  -g 1 -p 8  --library-type fr-firststrand.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth. Kallisto was used to 1) build a transcript index from the Ensembl GRC38 release 85 Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100 --single -l 275 -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: electrically immature motor neurons

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15].Details of the lines used in thus study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM). All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
1 ug of total RNA was subjected to Ribo-Zero treatment TruSeq Stranded mRNA preparation Kit (Illumina).

treatment_protocol: Motor neuron (MN)differentiation was carried out using an adapted version of a previously published protocol [Gupta et al. 2012]. Briefly, iPSCs were first differentiated to neuroepithelium by plating to 100% confluency in chemically defined medium consisting of DMEM/F12 Glutamax, Neurobasal, L-Glutamine, N2 supplement, non essential amino acids, B27 supplement, β-mercaptoethanol (all from Life Technologies) and insulin (Sigma). Treatment with small molecules from day 0-7 was as follows: 1μM Dorsomorphin (Millipore), 2μM SB431542 (TocrisBioscience), and 3μM CHIR99021 (MiltenyiBiotec) for 7 days. At day 8, the neuroepithelial layer was enzymatically dissociated using dispase(GIBCO, 1 mg/ml), plated onto laminin coated plates and next patterned for 7days with 0.5μM retinoic acid and 1μMPurmorphamine. At day 14 spinal cord MN precursors were treated with 0.1μM Purmorphamine for a further 4 days before being terminally differentiated in 0.1 mM Compound E (Enzo Life Sciences) to promote cell cycle exit.

value: electrically immature motor neurons

tag: diagnosis

value: amyotrophic lateral dystrophy (ALS)

tag: patient id

value: Patient 1

tag: cell line id

value: MUT 1

tag: days of differentiation


title: Participant anonymized number 6 at day 1

city: Bordeaux

first: Hadrien

last: Lorenzo

address: 32 rue de Nerac

department: Biostatistiques

country: France

institute: INSERM/INRIA

description: Sample name: X106_d1

data_processing:
Illumina 1.9/Sanger encoding; single end, not strand-specific sequenzing; 50 base sequence
demultiplexed using Illumina configureBCLToFastq.pl command
visual quality control with FASTQC Q coding version recognized automatically. If poor quality, this usually concerns the end of the sequence if necessary read trimming is then performed;i.e. exluding read end
mapping and summary count data with STAR software  (v2.4.2a; option '--quantMode GeneCounts')
output file from STAR software : counts.tsv
DESeq2 TMM library.size adjustment
DESeq2 TMM library.size adjustment
VOOM logcpm normalization
Limma Differential Expression
P-value adjustment with Benjamini Hochberg method
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: counts.tsv count matrix with the 56 samples, aligned with STAR. Can be opened with the R command read.table("counts.tsv",header=TRUE, sep="\t", fileEncoding="windows-1252")
Supplementary_files_format_and_content: countsNormalized.RData : (18,4*18301) matrix (after TMM lib.size adjustment and logCPM computation). Can be opened with the R command load("countsNormalized.RData")

source_name: Full Blood

extract_protocol:
NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs (NEB))
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)  as per manufacturer's instructions

treatment_protocol: Participants received one dose of rVSV ZEBOV vaccination (3x10^6 pfu or 20x10^6 pfu) at D0

value: blood

tag: anonymized participant number

tag: dose group (pfu)

tag: day

tag: lanes


title: ATAC_104

tag: genotype

tag: Sex


title: Participant anonymized number 6 at day 7

description: Sample name: X106_d7

tag: tissue


title: ATAC_101

tag: strain

tag: exposed to


title: Participant anonymized number 6 at day 0

description: Sample name: X106_d0


title: ATAC_102


title: ATAC_12


title: HeLa Ribominus sup replicate 2


title: ATAC_8


title: ATAC_7


title: ATAC_103


title: Participant anonymized number 3 at day 3

description: Sample name: X103_d3


title: Participant anonymized number 3 at day 7

description: Sample name: X103_d7


title: Participant anonymized number 3 at day 1

description: Sample name: X103_d1


title: ATAC_11


title: ATAC_10


title: Participant anonymized number 11 at day 7

description: Sample name: X111_d7


title: Participant anonymized number 3 at day 0

description: Sample name: X103_d0


title: Participant anonymized number 11 at day 1

description: Sample name: X111_d1


title: ATAC_3


title: ATAC_5


title: Participant anonymized number 6 at day 3

description: Sample name: X106_d3


title: ATAC_4


title: Participant anonymized number 11 at day 3

description: Sample name: X111_d3


title: ATAC_6


title: Participant anonymized number 11 at day 0

description: Sample name: X111_d0


title: Participant anonymized number 18 at day 1

description: Sample name: X118_d1


title: ATAC_18


title: ATAC_106


title: ATAC_16


title: Participant anonymized number 8 at day 7

description: Sample name: X108_d7


title: Participant anonymized number 18 at day 0

description: Sample name: X118_d0


title: Participant anonymized number 8 at day 3

description: Sample name: X108_d3


title: ATAC_14


title: Participant anonymized number 16 at day 7

description: Sample name: X116_d7


title: Participant anonymized number 8 at day 0

description: Sample name: X108_d0


title: Participant anonymized number 16 at day 1

description: Sample name: X116_d1


title: ATAC_13


title: Participant anonymized number 16 at day 3

description: Sample name: X116_d3


title: Participant anonymized number 17 at day 7

description: Sample name: X117_d7


title: Participant anonymized number 17 at day 3

description: Sample name: X117_d3


title: Participant anonymized number 17 at day 0

description: Sample name: X117_d0


title: Participant anonymized number 17 at day 1

description: Sample name: X117_d1


title: Participant anonymized number 12 at day 0

description: Sample name: X112_d0


title: Participant anonymized number 12 at day 1

description: Sample name: X112_d1


title: Participant anonymized number 13 at day 3

description: Sample name: X113_d3


title: Participant anonymized number 2 at day 3

description: Sample name: X102_d3


title: Participant anonymized number 2 at day 1

description: Sample name: X102_d1


title: Participant anonymized number 2 at day 0

description: Sample name: X102_d0


title: Participant anonymized number 4 at day 7

description: Sample name: X104_d7


title: Participant anonymized number 4 at day 3

description: Sample name: X104_d3


title: Participant anonymized number 14 at day 7

description: Sample name: X114_d7


title: Participant anonymized number 10 at day 3

description: Sample name: X110_d3


title: ATAC_17


title: ATAC_15


title: Participant anonymized number 4 at day 0

description: Sample name: X104_d0


title: Participant anonymized number 10 at day 1

description: Sample name: X110_d1


title: Participant anonymized number 4 at day 1

description: Sample name: X104_d1


title: Participant anonymized number 15 at day 3

description: Sample name: X115_d3


title: Participant anonymized number 15 at day 1

description: Sample name: X115_d1


title: Participant anonymized number 14 at day 1

description: Sample name: X114_d1


title: Participant anonymized number 15 at day 7

description: Sample name: X115_d7


title: Participant anonymized number 15 at day 0

description: Sample name: X115_d0


title: Participant anonymized number 10 at day 0

description: Sample name: X110_d0


title: Participant anonymized number 1 at day 3

description: Sample name: X101_d3


title: Participant anonymized number 1 at day 7

description: Sample name: X101_d7


title: Participant anonymized number 16 at day 0

description: Sample name: X116_d0


title: Participant anonymized number 2 at day 7

description: Sample name: X102_d7


title: Participant anonymized number 9 at day 7

description: Sample name: X109_d7


title: Participant anonymized number 1 at day 1

description: Sample name: X101_d1


title: Participant anonymized number 14 at day 3

description: Sample name: X114_d3


title: Participant anonymized number 5 at day 7

description: Sample name: X105_d7


title: Participant anonymized number 5 at day 3

description: Sample name: X105_d3


title: dZF2_wnt3a_12h

description: total RNA extracted for RNA-seq

source_name: human embryonic stem cells, H1 (WA01/NIH Registration Number 0043)

tag: cell type

value: human embryonic stem cells

value: H1 hESC WA01/NIH Reg. No 0043

tag: cell line name

tag: alternative cell line name

tag: nih registration number


title: Participant anonymized number 7 at day 3

description: Sample name: X107_d3


title: dZF2_wnt3a_48h

description: total RNA extracted for RNA-seq

tag: cell line


title: Participant anonymized number 7 at day 7

description: Sample name: X107_d7


title: Participant anonymized number 10 at day 7

description: Sample name: X110_d7


title: Participant anonymized number 7 at day 0

description: Sample name: X107_d0


title: dZF2_wnt3a_24h

description: total RNA extracted for RNA-seq


title: dZF1_wnt3a_48h

description: total RNA extracted for RNA-seq


title: dZF2_wnt3a_00h

description: total RNA extracted for RNA-seq


title: dZF1_wnt3a_24h

description: total RNA extracted for RNA-seq


title: hESC_wnt3a_48h_rep2

description: total RNA extracted for RNA-seq


title: dZF1_wnt3a_12h

description: total RNA extracted for RNA-seq


title: H1 Ribominus eluate replicate 2

description: Ribodepleted total RNA plus m6A immunoprecipitation

data_processing:
Raw RNA-seq data were mapped to the human reference genome (hg19) with bowtie2 (v:2.2.5). All mapped reads in bam files were converted into bigwig files. The unmapped reads were used to identify the back-splice junctions of ciircRNAs with AutoCirc pipeline (https://github.com/chanzhou/AutoCirc).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; Bed
*.minus.bw: all the reads from supernatant RNA-seq mapped into the anti-sense strand of the genome
*.plus.bw: all the reads from supernatant RNA-seq mapped into the sense strand of the genome
*circ.2reads.track.bed: Circular RNAs identified from the samples

growth_protocol: H1 (WA01) cells (WiCell) were cultured in mTeSR1 (Stem Cell Technologies). Hela cells were cultured in DMEM supplemented with 10% fetal calf serum, 1% GlutaMAX and 1% penicillin/streptomycin.

extract_protocol:
Both H1 and Hela cells were extracted as follows: 1.The media was removed; 2. The cells were washed twice with PBS; 3. TRIZol was added directly to the plate; 4. RNA was extracted by TRIZol; 5. The total RNA was treated with DNASe I; 6 The RNA was once again extracted by acid Phenol/Chloroform followed by Chloroform extraction; 7. The RNA was NaCl precipitated; 8. 80% ethanol washed twice; 9. Resuspended in Ultra pure H2O; 10. The desire amount of RNA was ribosome-depleted twice using a RiboMinus Kit.
RNA-seq libraries were prepared according to Ilumina instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing.

value: human embryonic stem cells (hESC)


title: HeLa Ribominus input replicate 2

description: Ribodepleted total RNA

source_name: Hela cells


title: dZF1_wnt3a_00h

description: total RNA extracted for RNA-seq


title: HeLa Ribominus eluate replicate 1


title: hESC_wnt3a_00h_rep2

description: total RNA extracted for RNA-seq


title: HeLa Ribominus input replicate 1

description: Ribodepleted total RNA


title: H1 Ribominus eluate replicate 1


title: H1 Ribominus input replicate 2

description: Ribodepleted total RNA


title: hESC_wnt3a_12h_rep2

description: total RNA extracted for RNA-seq


title: HeLa Ribominus eluate replicate 2


title: GROseq.MDA231_JQ1_2

description:
library strategy: GRO-seq
nascent RNA
processed data file: gene2k_mask2k.cov_ratio

data_processing:
Upon sequencing, individual libraries were segregated according to multiplexing barcodes and then both barcode and residual adapter sequences were removed from each tag to produce tags with non-uniform length, the majority of which ranged from 84 bp to 87 bp in each library. To precisely remove linker sequence from the DNA and cDNA tags, MmeI motifs were used for defining linker boundaries. Linker orientation also dictated whether the tags at each side were originated from genomic DNA or RNA. To minimize the loss of tags due to sequencing errors, tags were first filtered based on the presence of two opposite-orientated MmeI motifs, then aligned to the linker sequence from both directions to determine its orientation. DNA and corresponding RNA tags, most of which ranged from 18 bp to 23 bp, were extracted for alignment.
All processed tags were aligned to their indicated genome build using Bowtie2 with parameter of --local. Human samples were aligned to genome build hg38, mouse samples to genome build mm9 and Drosophila samples to genome build dm3 with parameters -q 2. To estimate the numbers of cross-species-ligated RNA and DNA tags in the mix of MDA-MB-231 and S2 cell nuclei, RNA tags were first aligned independently to the transcriptome builds of hg38 and dm3, with the most stringent parameter of -q 44. Linked DNA tags of those RNA tags that were unambiguously aligned to human transcriptome were then aligned to human genome with the parameter of -q 2. These DNA tags failed to align to the human genome were then aligned to the Drosophila genome, with the parameter of -q 2. Conversely, DNA tags linked to the RNA tags that were unambiguously aligned (-q 44) to the Drosophila transcriptome were first aligned to the Drosophila genome (-q 2), and those unaligned DNA tags were then aligned to the human genome (-q 2)
Genomic regions with enriched GRID-seq RNA reads were detected by MACS2 using the model for broad-peak detection. These mapped regions with significant enrichment (p < 0.001) and overlapping with known-gene annotation (Ensemble genes GRCh38.83 for human, NCBI m37 for mouse and BDGP5.78 for Drosophila) were assigned to their respective largest annotated genes. Enriched regions that did not overlap with any known gene were assigned as “unannotated transcripts”. The RNA read-coverage of genomic regions was calculated by BEDtools and SAMtools. The genes with the tag-coverage above the sliding-window threshold [(Ni+n - Ni) ≥ n, where i was the rank of given RNA, N was the read-counts of this RNA and n was the 1/100 of the total number of ranked RNAs] were selected as abundant chromatin-interacting RNAs. A subset of abundant RNAs with sufficient RNA read-density [RPK (reads per Kb) ≥ 100] or with significant DNA read-densities (RPK ≥ 10) associated at any genomic region was identified as hit RNAs for further analysis (Supplementary Table 1).
To determine the specific RNA-chromatin interaction pattern of each hit RNA, we developed a genome-wide background for non-specific interactions. Ideally, for each library, we could setup mixed nuclei from different species in order to evaluate cross-species RNA-chromatin interactions, which would represent the true background. In practice, it is feasible to generate such background with sufficient density on the Drosophila genome by using RNA reads from human cells because of the much smaller Drosophila genome, but the RNA density on the human genome based on the RNA reads from Drosophila is often too scattered to provide a reliable background. We thus sought to deduce the background in the Drosophila genome based on endogenous RNA reads in comparison with the true background based on cross-species RNA-chromatin interactions. Toward this goal, we selected RNAs from protein-coding genes engaged in trans-chromosomal interactions, and calculated their density on the 1 Kb-binned genome. Such deduced background read-density at each 1 Kb bin was then smoothed by a moving widow of 100 Kb and normalized by the total read number and chromosome size.  The resulting background in the Drosophila genome was highly correlated with the cross-species background. This strategy enabled us to deduce the background on any human cells by using endogenous RNA reads.
To evaluate specific RNA-chromatin interactions of each hit RNA at each genomic bin, we first summarized the DNA reads for each gene at each genomic bin, and then normalized them to 1 million reads followed by further normalization of total number of bins of each chromosome. A ratio was next calculated by dividing the normalized DNA read density with background read density, which represents specific binding of this RNA at the genomic bin.   To construct a robust global binding matrix for all hit RNAs, genomic bins with significant binding level (at least 3 bins with binding level ≥ 2 in every 10 bin-window) were preserved and further smoothed by a moving-widow of 10 bins. All subsequent analyses involving binding levels and patterns were based on such genomic binding matrix.
In the processing of GRO-seq data, multiplexing barcode sequences were removed from each tag after sequecing. All tags were aligned to hg38 genome build using Bowtie2 --local -q2. Due to high variability of small transcripts, only transcripts with lengths larger than 4 Kb were included in the analysis. First, coverages on promoter regions (2 Kb upstream of TSS to 2 Kb downstream of TSS) were compared among transcript isoforms of each gene, and the transcript with highest promoter coverage was selected to represent the gene. To finally estimate the transcription activity for each gene’s representative transcript, normalized read densities (read per Kb per million total reads, RPKM) were calculated within a 2 Kb region that started at 2 Kb downstream of TSS and ended at 4 Kb downstream of TSS. Analysis were applied in all samples, and JQ1/DMSO log-ratio for each gene was calculated as [log2(JQ1_RPKM+1)- log2(DMSO_RPKM+1)].
Genome_build: human genome hg38, mouse mm9 and Drosophila genome dm3
Supplementary_files_format_and_content: The processed GRID-seq data are recorded as tab-delimited text files with 9 columns for each sample , representing RNA_Chrom, RNA_Start, RNA_End, GeneID, RNA_Total_Reads, RNA_Strand, DNA_Chrom, DNA_Bin and Value. The GRID-seq value is normalized interaction density between RNA and DNA. And the processed GRO-seq data are recorded in one tab-delimited text file with 8 columns representing GeneID, DMSO_rep1, DMSO_rep2, JQ1_rep1, JQ1_rep2, DMSO_sum, JQ1_sum, LogRatio_JQ1_vs_DMSO. GRO-seq values represent the densities of genes (RPKM) in each samples, where the DMSO_sum and JQ1_sum are the summarized densities in the two repeats and the LogRatio_JQ1_vs_DMSO is based on the summarized values.

extract_protocol:
Approximately 2 million mammalian cells or 10 million Drosophila cells were sequentially crosslinked with 2 mM DSG and 3% formaldehyde. Nuclei were isolated, washed and digested in situ by AluI restriction enzyme. All DNA and RNAs in the nuclei were then treated by T4 PNK. After washing, nuclei were mixed with GRID-seq linkers and T4 RNA Ligase 2-truncated KQ for ssRNA ligation. Shorter strand of the linker was extended by SuperScript III Reverse Transcriptase to generate cDNA. Nuclei were washed again and resuspended in T4 DNA ligase solution for ligation of genomic DNA. By Proteinase K digestion at 65°C, linker-ligated DNA were reverse-crosslinked and extracted, followed by affinity purification by Streptavidin-conjugated beads. By denaturation with 150 mM NaOH solution, the non-biotinylated strand of the linker-ligated-DNA were released, and subjected to second strand synthesis by Klenow Fragment (3' to 5' exo-) enzyme. Newly synthesized dsDNA were then digested by MmeI for paired-end-tag generation, followed by size-selection in 12% native polyacrylamide gel. Recovered dsDNA was further ligated with adapters, PCR amplified to generate libraries for illumina sequencing. GRO-seq protocol was adapted from (Core, L. J. et al, Science, 2008).
Adapters were prepared by annealing the following two oligonucleotides in 1× NEB Buffer 2 to a final concentration of 25 mM: 5’-/5Phos/AGATCGGAAGAGCACACGTCT-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNN-3’. Purified DNA was dissolved in 10 µl of 1× NEB Buffer CutSmart and 0.5 U Shrimp Alkaline Phosphatase, incubated at 37 °C for 30 min and heat inactivated at 65°C for 5 min. The reaction was diluted with 36 µl H2O, mixed with 10 µl of 10× T4 DNA Ligase Buffer, 32 µl of PEG-6000, 200 pmol of Adapters and 1,600 U T4 DNA Ligase, and incubated at room temperature for 1 h. Unligated nick was phosphorylated by 20 U T4 Polynucleotide Kinase supplemented by 100 pmol ATP and incubated at 37°C for 30 min. Nick was then ligated by addition of 1 µl of 10× T4 DNA Ligase Buffer, 100 pmol ATP and 1,600 U T4 DNA Ligase, and incubation at room temperature for 30 min. DNA along with excessive Adapters were extracted and purified before loading to 10% native PAGE gel for size-selection. The desired band at approximately 185 bp was excised. DNA was extracted and dissolved in 20 µl of H2O. To amplify each library, 20 µl of PCR amplification mix (9.4 µl of H2O, 5 µl of DNA sample, 4 µl of 5× Phusion HF Buffer, 40 pmol dNTP, 5 pmol Primer#1, 5 pmol Primer#2, 0.4 U Phusion High-Fidelity DNA Polymerase was prepared. PCR primers consist of Primer#1 (5’- AATGATACGGCGACCACCGAGATCTACACBBBBBACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’ (BBBBB: 5 nt barcode for multiplexing libraries)) and Primer#2 (5’- CAAGCAGAAGACGGCATACGAGACGTGTGCTCTTCCGATCT -3’).  PCR was performed with an initial 30 sec denaturation at 98°C, followed by 16 cycles of 10 sec denaturation at 98°C, 30 sec annealing at 65°C and 15 sec extension at 72°C. The PCR product was separated on a native 10% PAGE gel and the band at 188 bp was recovered. DNA was subsequently subjected to Illumina HiSeq 2500 for single-end 100 bp sequencing, with the sequencing primer (5’- ACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’).

value: MDA-MB-231 breast cancer cells (HTB-26 ATCC)

tag: treatment


title: GROseq.MDA231_JQ1_1


title: GROseq.MDA231_DMSO_2

value: DMSO


title: HeLa_dCas9-3_2

description:
HeLa RNF2 dCas9 DNA replicate 3
eBE_Indels_update.xlsx

source_name: HeLa cells

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: GROseq.MDA231_DMSO_1


title: HeLa_BE3_UGI-H-1_2

description:
HeLa RNF2 BE3_UGI-H DNA replicate 1
eBE_Indels_update.xlsx


title: GRIDseq.MM1S_rep2

description:
library strategy: GRID-seq
total RNA and genomic DNA
Processed data for merged replicates is available on GSM2188868.

value: MM.1S multiple myeloma cells


title: dCas9-c_1+dCas9-c_4

description:
EMX1 dCas9 DNA replicate c and Site4 dCas9 DNA replicate c
eBE_Indels_update.xlsx

source_name: 293FT cells


title: HeLa_dCas9-2_2

description:
HeLa RNF2 dCas9 DNA replicate 2
eBE_Indels_update.xlsx


title: HeLa_dCas9-1_2+dCas9-a_4+dCas9-b_1

description:
HeLa RNF2 dCas9 DNA replicate 1 and Site4 dCas9 DNA replicate a and EMX1 dCas9 DNA replicate b
eBE_Indels_update.xlsx

source_name: HeLa cells and 293FT cells

value: HeLa and 293FT

value: HeLa_dCas9 or dCas9


title: GRIDseq.MDA231_rep2

description:
library strategy: GRID-seq
total RNA and genomic DNA
Processed data for merged replicates is available on GSM2188866.


title: H1 Ribominus input replicate 1

description: Ribodepleted total RNA


title: HeLa_BE3-1_1+dCas9-b_4

description:
HeLa FANCF BE3 DNA replicate 1 and Site4 dCas9 DNA replicate b
eBE_Indels_update.xlsx

value: HeLa_BE3 or dCas9


title: hESC_wnt3a_24h_rep2

description: total RNA extracted for RNA-seq


title: HeLa_BE3-2_2

description:
HeLa RNF2 BE3 DNA replicate 2
eBE_Indels_update.xlsx


title: HeLa_BE3-1_2+HeLa_BE3-2_1

description:
HeLa RNF2 BE3 DNA replicate 1 and HeLa FANCF BE3 DNA replicate 2
eBE_Indels_update.xlsx


title: GRIDseq.MDA231_rep1

description:
library strategy: GRID-seq
total RNA and genomic DNA


title: HeLa_BE3-3_1+BE3-deltaUGI-b_1+BE3-deltaUGI-b_4

description:
HeLa FANCF BE3 DNA replicate 3 and EMX1 BE3-detalUGI DNA replicate b and Site4 BE3-detalUGI DNA replicate b
eBE_Indels_update.xlsx

value: HeLa_BE3 or BE3-detalUGI


title: HeLa_eBE-S3-2_1+BE3-deltaUGI-a_1+BE3-deltaUGI-a_4

description:
HeLa FANCF eBE-S3 DNA replicate 2 and EMX1 BE3-detalUGI DNA replicate a and Site4 BE3-detalUGI DNA replicate a
eBE_Indels_update.xlsx

value: HeLa_eBE-S3 or BE3-detalUGI


title: HeLa_eBE-S3-1_1+HeLa_BE3-3_2+BE3-deltaUGI-c_1+BE3-deltaUGI-c_4

description:
HeLa FANCF eBE-S3 DNA replicate 1 and HeLa RNF2 BE3 DNA replicate 3 and EMX1 BE3-detalUGI DNA replicate c and Site4 BE3-detalUGI DNA replicate c
eBE_Indels_update.xlsx

value: HeLa_eBE-S3 or HeLa_BE3 or BE3-detalUGI


title: HeLa_eBE-S3-2_2+HeLa_BE3_UGI-H-3_1+BE3-b_1+BE3-b_4

description:
HeLa RNF2 eBE-S3 DNA replicate 2 and HeLa FANCF BE3_UGI-H DNA replicate 3 and EMX1 BE3 DNA replicate b and Site4 BE3 DNA replicate b
eBE_Indels_update.xlsx

value: HeLa_eBE-S3 or HeLa_BE3_UGI-H or BE3


title: HeLa_eBE-S3-3_2+HeLa_dCas9-3_1+BE3-c_1+BE3-c_4

description:
HeLa RNF2 eBE-S3 DNA replicate 3 and HeLa FANCF dCas9 DNA replicate 3 and EMX1 BE3 DNA replicate c and Site4 BE3 DNA replicate c
eBE_Indels_update.xlsx

value: HeLa_eBE-S3 or HeLa_dCas9 or BE3


title: HeLa_dCas9-2_1+HeLa_BE3_UGI-H-3_2+BE3-a_1+BE3-a_4

description:
HeLa FANCF dCas9 DNA replicate 2 and HeLa RNF2 BE3_UGI-H DNA replicate 3 and EMX1 BE3 DNA replicate a + Site4 BE3 DNA replicate a
eBE_Indels_update.xlsx

value: HeLa_dCas9 or HeLa_BE3_UGI-H or BE3


title: HeLa_dCas9-1_1

description:
HeLa FANCF dCas9 DNA replicate 1
eBE_Indels_update.xlsx

value: HeLa


title: HeLa_eBE-S3-1_2+dCas9-a_1

description:
HeLa RNF2 eBE-S3 DNA replicate 1 and EMX1 dCas9 DNA replicate a
eBE_Indels_update.xlsx

value: HeLa_eBE-S3 or dCas9


title: HeLa_BE3_UGI-H-2_1+HeLa_BE3_UGI-H-2_2

description:
HeLa FANCF BE3_UGI-H DNA replicate 2 and HeLa RNF2 BE3_UGI-H DNA replicate 2
eBE_Indels_update.xlsx


title: Day 3 activated B cells_Input

city: Rennes

first: Nicolas

last: HIPP

state: France

address: 2 Av. du Pr Léon Bernard

institute: INSERM-

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using BWA algorithm with default setting. RNA sequencing data were aligned to GRCh38 using STAR aligner (outFilterMultimapNmax 20 ; outFilterMismatchNmax 2 ;alignIntronMin 10 and default setting)
For Chip-seq : Data were filtered using the following specifications : Pass Illumin'as purity filter, align with no more than 2 missmatches, and map uniquely on the genome, duplicated are removed. For RNA sequencing data were filtered using STAR filter and aligned reads quality was performed with HTS filter before DEsEQ2 analyses. PCR duplicates were removed.
Peaks were called using MACS 2.1.0 with the Standard normalization method. DEseQ2 was used to defined differentially expressed genes. (default setting)
Genome_build: Chip-seq : hg19/ RNAsequencing : GRCh38
Supplementary_files_format_and_content: Bigwig files were generated by ActiveMotif society. Scores shows the fragment density for 32-nt bins along the genome (“signal map”). For RNAsequencing, table content raw read-counst after featureCount

source_name: B cells

growth_protocol: Cells were cultured with anti-BCR/CpG/CD40L in RPMI completed with SVF and Penistromiscin. If indicated IL2 or siRNA agains BACH2 was added

extract_protocol:
Chip-Sequencing were performed by ActiveMoitf society. For RNA sequencing, after sorting , RNA were extracted (NucleoSpin® RNA XS), measured (Qubit® 2.0 Thermo Fisher Scientific), and library were constructed using TruSeq® Stranded mRNA Sample Preparation
Chip-Sequencing libraries and RNAsequencing librairies were performed according to illumina's instruction

value: Activated B cells

tag: passages

value: Primary Cells

tag: chip antibody


title: Day 3 activated B cells not driven by IL2

value: BACH2 (D3T3G)


title: Day 4 CFSElow population not driven by IL2 with siBACH2 rep 3

description: ReadCountfeatureCount.csv

tag: transfection


title: Day 3 activated B cells not driven by IL2 with siBACH2


title: HeLa_BE3_UGI-H-1_1

description:
HeLa FANCF BE3_UGI-H DNA replicate 1
eBE_Indels_update.xlsx


title: Day 4 CFSElow population not driven by IL2 with siBACH2 rep 2

description: ReadCountfeatureCount.csv


title: Day 4 CFSElow population not driven by IL2 priming rep 3

description: ReadCountfeatureCount.csv

tag: sample type

value: uncommitted


title: Day 4 CFSElow population not driven by IL2 priming rep 2

description: ReadCountfeatureCount.csv


title: WT

city: Stanford

first: Humsa

last: Venkatesh

address: 265 Campus Drive - Monje Lab

department: Neurology

institute: Stanford University

data_processing:
We generate 179.62M reads (clusters) (passing filter) with one lane of 50bp paired-end read
libraries were then sequenced on Illumina HiSeq2500
Reads were mapped to whole genome HG19 (UCSC) using TopHat
For data analysis, we use Cufflinks for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks output

source_name: SU-pcGBM2 primary tumor cells

extract_protocol:
RNA was isloated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary cell mechanically dissociated from patient brain tumor

value: SU-pcGBM2 primary tumor cells


title: Day 4 CFSElow population not driven by IL2 priming rep 1

description: ReadCountfeatureCount.csv


title: Day 4 CFSElowCD25hi population driven by IL2 priming rep 3

description: ReadCountfeatureCount.csv

value: committed


title: BloodWT5

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Illumina bcl2fastq application used for base-calling, adapter trimming, and FASTQ generation
Alignment and quantification performed in BaseSpace using Cufflinks with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Whole Mouse Blood

extract_protocol:
Total RNA was isolated from frozen aliquots of whole blood or a frozen powder created from grinding one whole brain hemisphere in liquid nitrogen using Qiazol reagent followed by clean up with the RNeasy Mini Kit (Qiagen, Germantown, MD).
Stranded RNA-seq libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina)

tag: age

value: male

tag: devolopmental stage

value: Young adult

value: Whole Blood


title: HeLa_eBE-S3-3_1

description:
HeLa FANCF eBE-S3 DNA replicate 3
eBE_Indels_update.xlsx

data_processing:
Library strategy: DNA-Seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.


title: Day 4 CFSElowCD25hi population driven by IL2 priming rep 1

description: ReadCountfeatureCount.csv


title: BloodWT3

tag: Sex

tag: tissue


title: Day 4 CFSElowCD25hi population driven by IL2 priming rep 2

description: ReadCountfeatureCount.csv


title: BloodWT2

tag: strain


title: BloodWT1


title: BloodWT4


title: BloodHET5


title: BloodHET4


title: ChR2

tag: cell type


title: BloodHET3


title: BrainWT5

source_name: Whole Mouse Brain

value: Whole Brain


title: BloodHET1


title: BrainWT4


title: Day 4CFSElow population not driven by IL2 with siBACH2 priming rep 1

description: ReadCountfeatureCount.csv


title: neuron ALN-reprogrammed_mice2_rep2

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

institute: Stockholm University

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the mouse genome (mm10) performed using STAR version 2.4.1 with parameter outSAMstrandField set to intronMotif.
Raw read counts were extracted using the function featureCounts (version 1.4.6) using default parameters
Normalized abundance measurements (RPKMs) were generated using the Cufflinks version 2.2.1 with the parameter library-norm-method set to geometric.
Genome_build: mm10 (Ensembl version 78)
Supplementary_files_format_and_content: One processed data file is added providing normalized abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).

source_name: reprogrammed -striatal NG2 glia

growth_protocol: For in vivo conversion experiments, 1 mL of vector mix (AAV5) was injected into the striatum of each animal at a rate of 0,4 mL/min with a diffusion time of 2 minutes at the following coordinates: AP = +1,0 ML = -2,0 and D/V = -2,7 relative to bregma, tooth bar = flat.

extract_protocol:
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagmentation.

treatment_protocol: LCM-seq was conducted 12 weeks post-injection.

value: Male

tag: in vivo reprogramming

value: using the transcription factors Ascl1, Lmx1a and Nurr1

value: striatum

value: reprogammed NG2 glia


title: BrainWT3


title: neuron ALN-reprogrammed_mice2_rep1


title: BrainWT2


title: BrainWT1


title: neuron ALN-reprogrammed_mice1_rep3

value: Female


title: neuron ALN-reprogrammed_mice1_rep2


title: BrainHET4


title: neuron ALN-reprogrammed_mice1_rep1


title: BrainHET5


title: BrainHET3


title: ATAC granule cells r3

city: NYC

first: Marian

last: Mellen

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
100 bp paired-end reads were aligned using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) with default parameters in a sensitive-local configuration with a minimum alignment score of G,20,8
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS, transcripts and regions of interest (enhancers)
BAM files from triplicates were merged and BED file created with BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts are divided according to H3K4m3 coverage levels. For each group, ATAC-Seq RPM were calculated in contiguous 100 bp bins from 10 Kb upstream to TSS, from TTS to 10 Kb downstream and gene bodies (dividing each individual transcript in 100 fragments) using HOMER scripts.

source_name: Cerebellar Granule Cells

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets.
After sorting,  50,000 nuclei were resuspended in 22.5 μL of reaction mix: 25 μL 2X TD Buffer, 2.5 μL Tn5 Transposes and 22.5 μL nuclease free water (Nextera DNA Library Preparation Kit). The reaction was incubated for 30 min at 37 °C. Immediately following transposition, DNA was purified using Qiagen MinElute Kit and DNA eluted in 10 μL of elution buffer. Transposed DNA fragments were then amplified a total of 8 cycles using Nextera PCR Primer 1 and Nextera PCR Primer 2 and Thermo HF Phusion polymerase. Library was purified using Qiagen PCR Cleanup Kit and resuspended in 20 μL of resuspension buffer for HiSeq 2000 Illumina sequencing.

tag: facs condition

value: GFP+


title: ATAC granule cells r2


title: GRIDseq.MM1S_rep1

value: MM.1S multiple myeloma cells


title: BloodHET2


title: BrainHET2


title: ATAC granule cells r1


title: H3K27ac H3K4me1 IN2 granule cells r1 IP

description:
GC_E1_Promoters.txt
GC_E2_Non_regulatory.txt
GC_E3_Primed_Enhancers.txt
GC_E4_Active_Enhancers.txt
Chromatin_ratio_GC_MellenM_genes.bed.txt
Barcode: ACAGTG

data_processing:
50 bp single-end reads were aligned using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) with default parameters in a sensitive-local configuration with a minimum alignment score of G,20,8
Duplicates removed using  SAMtools (Li et al., 2009)
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS and transcripts.
We used ChromHMM for the analysis of chromatin states using a combination of marks. We used H3K4me3, H3K4me1 and H3K27Ac bam files and defined a learning model of four chromatin states with a resolution of 200 bp bins.
Genome_build: mm10
Supplementary_files_format_and_content: Chromatin accessibility ratio (EC/HC). To obtain this ratio, we first calculated the normalized (RPM) enrichment as follows:EC=((H3K27Ac ChIP /mean [H3K27Ac ChIP]))/(( input /mean [input])) HC=((H3K9me3 ChIP /mean [H3K9me3 ChIP]))/(( input /mean [input])). These values were then used to obtain the ratio EC/HC and an estimation of euchromatic and heterochromatic DNA. ChromHMM released four chromatin states. After confirmation of genomic localization and ATAC-Seq peak correlation in the genome browser, we defined emitted state 1 as active promoters, state 2 as non-regulatory DNA, state 3 as primed enhancers and state 4 as active enhancers. Genomic coordinates of each state are shown.

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Throughout the protocol buffers were supplemented with EDTA-free protease inhibitor cocktail and 10 mM of sodium butyrate. For ChIP-Seq homogenates were fixed prior to the addition of 50% iodixanol by adding 1% paraformaldehyde (PFA) for 8 minutes end-to-end rotation.  PFA was then quenched by adding 125 μL of glycine for 5 min. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets. Alternatively, for H3K27Ac and H3K4me1 ChIP-Seq, granule cell nuclei from C57BL/6J were sorted by selecting a specific FSC/SSC population identified from GC EGFP+ mice. We observed that this FSC/SSC gated population in granule cell EGFP+ animals resulted > 92% of the sorted nuclei being EGFP positive. Thus, the gate selected allows us to enrich the sample from 65%–70% to 92%–96% on granule cells, as described in (Mellen et al., 2012).
After sorting, nuclei were processed using LowCell# ChIP kit. 105 Nuclei were sonicated in a Bioruptor water bath sonicator for 15 min at intervals of 30s on and 30 s off to obtain ~350 bp fragments and chromatin frozen in liquid nitrogen and kept at -80 °C. Each immunoprecipitation (IP) was performed in chromatin aliquots of 5x10e5 nuclei. Immunoprecipitation was performed following LowCell# ChIP kit manufacturer’s instructions, mixing 50:50 IgA and IgG coated beads to 3 μg of antibodies. 1:10 of resuspended chromatin per sonicated nuclei was saved as input sample of the procedure. Immunoprecipitation was performed at 4 °C overnight in an end-to-end rotator. After washing beads with IP DNA, both input and IP samples were digested with Proteinase K 100 μg/ml in the presence of SDS 1% for 2 hr at 50 °C. Then, the lysate was treated with RNase A/T1 mix for 1h at 37 °C to and DNA was extracted with phenol: chloroform: isoamyl alcohol (25:24:1), precipitated in 70% ethanol and dissolved in TruSeq DNA Sample kit resuspension buffer.

value: GC size


title: BrainHET1


title: neuron ALN-reprogrammed_mice2_rep3


title: YL-M-9

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  low-quality sequence, then mapped to mm 10 whole genome using TopHat 2
Read density as Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following a method of Mortazavi et al 2008, Nature Methods 2008 using an exon model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each wt and mutant mouse is attached as File 1 Normlaized RPKM values

source_name: tooth germ

extract_protocol:
First mandibular molars at PN4 from Nfic-/- and littermate Nfic+/- control mice were dissected out, and the apical half was cut with a fine blade and transferred to RNA stabilization reagent (Qiagen, 76104). Total RNA was extracted with an RNeasy Mini Kit (Qiagen, 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: apical half of tooth germ

value: post natal day 4

tag: genotype

value: Nfic-/-


title: YL-M-10


title: YL-C-9

value: Control Nfic+/-


title: YL-C-10


title: H3K9me3 granule cells r1 IP

description:
Chromatin_ratio_GC_MellenM_genes.bed.txt
Barcode: GATCAG


title: H3K4me3 H3K9me3 IN1 granule cells r1 IP

description:
GC_E1_Promoters.txt
GC_E2_Non_regulatory.txt
GC_E3_Primed_Enhancers.txt
GC_E4_Active_Enhancers.txt
Chromatin_ratio_GC_MellenM_genes.bed.txt
Barcode: GATCAG


title: YL-M-8