title: MEF_bc8_PAR_4C-seq_BioRep2

first: Hsueh-Ping

last: Chu

address: 185 Cambridge St

department: molecular biology

institute: MGH, Harvard Medical School

data_processing:
Basecalls performed using Illumina MiSeq software. Our design of the 4C adaptors allows us to filter out several sources of noise in 4C experiments, most notably spurious amplification of off-target sequences and PCR duplicates. Our paired-end sequencing strategy allows us to sequence the viewpoint primer in read 1, and then identify potential interaction reads by sequence that ligated onto the viewpoint in read 2. This allows us to identify library molecules that actually contain the viewpoint, as opposed to library molecules that arise from off-target priming or spurious amplification of from the universal adaptor sequences, thus allowing us to eliminate several sources of noise from our data. To achieve this, we first filtered read pairs so that we include only read pairs with the viewpoint sequence present at the beginning of the read 1. We included a 6 nt random barcode sequence at the beginning of read 2; we stripped this sequence from the beginning of read 2 and appended it to the name of the read in the fastq file. We also removed the FatI sequence next to the barcode. Finally, we trimmed read 2 for sequence beyond the DpnII site, as we are interested in the molecules that ligated onto the DpnII site near the viewpoint primer. All filtering steps were conducted using cutadapt 1.7.1 using its built-in paired-end filtering options. After these filtering steps, read2 was aligned to the mm9 reference genome using the same single-end alignment strategy we have previously used to align Hi-C reads allele-specifically (Minajigi et al., 2015), which is an extension of our pipeline for aligning ChIP-seq reads allele-specifically (Kung et al., 2015; Pinter et al., 2012; Yildirim et al., 2012). Next, we employed a random-barcode strategy to eliminate PCR duplicates. Properly identifying and removing PCR duplicates in 4C experiments is usually not possible using standard methods because the positions of 4C reads are “anchored” by the positions of the 1st and 2nd restriction sites. Thus, genuine interactions will result in multiple reads that align to exactly the same coordinates and have the same sequence; these reads are indistinguishable from PCR duplicates. Since we have included a random barcode sequence, we can properly identify duplicates. If multiple reads at the same coordinates arise from duplication during PCR, then these reads will have the same barcode, whereas if they arise from interactions present multiple times in the population, then the reads will have distinct barcodes. Thus, we collapsed the counts of all reads  with the same barcode aligning to the same coordinates to 1, eliminating PCR duplicates from the data. Read counts were normalized at each position by read depth and represent read counts as reads /million reads (RPM). Only uniquely mapped reads were used in the downstream analysis. Coverage was generated using bedtools and then windowed in sizes of 100 kb using our custom script. The processed bigwig files were produced using the sum coverages of 100 kb bins on chrX.
library strategy: 4C-seq
Genome_build: mm9
Supplementary_files_format_and_content: The processed bigwig files were produced using the sum coverages of 100 kb bins on chrX.

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol:
6-8 million cells were trypsinized and crosslinked in 40 mL of media with 2% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched by adding glycine to a final concentration of 125 mM; cells were then washed twice in 1X PBS, frozen in liquid nitrogen and stored at -80°C. To prepare 3C libraries, we used a method similar to the “in situ Hi-C” method (Nagano et al., 2015). Cells were lysed by resuspending them in 500 ml permabilization buffer (10 mM Tris-HCl pH=8.0, 10 mM NaCl, 0.2% Igepal CA-630) supplemented with 50 ml 100X EDTA-free protease inhibitor cocktail for 30 minutes on ice with occasional agitation to keep them from settling. Cells were spun at 1350g for 5 minutes at room temperature, then resupsended in 358 ml 1.25X DpnII buffer + 11 ml 10% SDS. Cells were rotated for 1 hour at 37°C, then 75 ml 10% Triton X-100 was added and cells were rotated at 37 °C for an additional hour to quench the SDS. To digest the chromatin, we added 5000 units of DpnII (NEB) and rotated the lysate at 37°C overnight. To perform in-situ ligation, we added 820 ml 10X T4 DNA Ligase Buffer (NEB), 82 ml 10 mg/ml BSA (NEB), 7.61 ml water and 50 ml T4 DNA Ligase (Enzymatics) and rotated for 4 hours at room temperature. To purify the DNA, 2 mg Proteinase K was added to the ligation reactions and left at 65°C overnight, then the DNA was cleaned by phenol:cholorform:isoamyl alcohol extraction followed by ethanol precipitation. We then treated the DNA with 40 ug RNaseA for 15 minutes at 37°C and performed a SPRI cleanup using a 1.5:1 bead:DNA ratio.
We converted the 3C libraries into 4C libraries, using a protocol similar to the modified-4C protocol (Apostolou et al., 2013), but with additional modifications. First, we digested 3 mg of each 3C library with 4 units of FatI (NEB) for 4 hours at 55 degrees. We then dephosphorylated the ends of the FatI digested molecules by adding 20 units of Calf Intestinal Phosphotase (NEB) and heating at 37°C for 1 hour. The DNA was then purified using the PCR Purification Kit (Qiagen). To ligate the universal adaptor to the 3C library, we incubated the 3C library with 200 picomoles universal adaptor and 2 ml T4 DNA Ligase (Enzymatics) in 1X T4 DNA Ligase Buffer (NEB) in a volume of 50 ml for 1 hour at 16°C, then 2 hours at 25°C. We then purified the DNA and removed excess adaptor by adding 90 ml Ampure XP SPRI beads and performing a standard SPRI cleanup. Next, we used ligation-mediated PCR (LM-PCR) to selectively amplify molecules containing the viewpoint within the PAR region. We performed LM-PCR using 1.5 mM biotinylated viewpoint primer, 1.5 mM Illumina Index Primer in a 100 ml reaction with Phusion HF buffer as the master mix for 12 cycles. We then performed a SPRI cleanup with a 1:1 bead:PCR reaction ratio to remove unincorporated primers. To enrich for library molecules containing the viewpoint primer, we washed 10 ml MyOne C1 Streptavidin Beads (ThermoFisher) 3 times in 2X Binding and Wash buffer (10 mM Tris-HCl pH-8.0, 2M NaCl, 1 mM EDTA, 0.1% Tween-20), then incubated the washed beads with the purified PCR products for 15 minutes with rotation. We then washed twice with 1X Binding and Wash Buffer (10 mM Tris-HCl pH-8.0, 1M NaCl, 1 mM EDTA, 0.1% Tween-20), and once in TE+Tween (10 mM Tris-HCl pH-8.0 mM EDTA, 0.1% Tween-20). To incorporate full-length Illumina primer sequences, we added the beads to 100 ml PCR reactions, using 2 ml Illumina TruSeq Universal primer and 2 ml Illumina Index primer and Phusion HF master mix for 13 cycles. We then purified and size selected using a 0.85:1 bead:PCR reaction ratio. Library sizes were determined using the High Sensitivity Bioanalyzer (Agilent), and quantifications were determined using Library Quantification Kit (KAPA Biosystems). 2x76 bp paired-end reads were obtained using an Illumina MiSeq. 4C-PAR DpnIIview-point primer: /5Biosg/ccctacacgacgctcttccgatctNNNNCGAGAACGGGTGTCTCGGGGTT

value: CAST/Ei x 129/Sv/Jae

value: Immortalized MEFs

tag: primers


title: 10D

status: Public on Jul 10 2017

type: SRA

city: Barcelona

first: Elena

last: Hidalgo

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

description:
Barcode: CAGATC
f30310D

library_source: transcriptomic

data_processing:
original reads have been inspected by FastQC for their quality
reads have been then aligned to reference genome by using tophat (v2.1.1) and using the annotation as a guide. Annotation was retrieved by iGenomes website,
Annotation was retrieved by iGenomes website,
tophat was run by limiting the size of introns to minimum 20 and maximum 1000 bases.
Htseq-count was used for counting the number of mapped tags
Genome_build: EF2
Supplementary_files_format_and_content: Read count matrix for each gene

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: exponential cultures, minimal media

growth_protocol: Cells were grown in MM to an OD600=0.5)

extract_protocol:
RNA was obtained through phenol/chloroform extraction.
RNA was enriched for presence of polyA

treatment_protocol: Cells were treated or not with 1 mM of hydrogen peroxide for 15 min.

tag: genotype

value: [delta]sty1 HA-Atf1.10D

tag: atf1 phosphorylation status

value: phosphomimicking Atf1

tag: treatment

value: untreated


title: MEF_bc12_PAR_4C-seq_BioRep1

city: Boston

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: cell type


title: ESd4_bc16_PAR_4C-seq_BioRep3

growth_protocol: Cells were cultured in regular ES mediun (15% FBS) with LIF

treatment_protocol: ES cells were cultured without LIF for 4 days under non-adherent conditions to form embryonic bodies.

value: Embryonic stem cells


title: E12.5_C21 [single cell RNA-seq]

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz

data_processing:
RNA-seq data was aligned using tophat2, read counts were quantified with HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq read counts for each cell were combined and written out into a csv file

molecule: polyA RNA

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E12.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.

extract_protocol:
Timed-pregnant mice were sacrificed by deep anesthesia followed by cervical dislocation. Dissection of embryos and adrenal anlages was carried out using a stereotactic microscope equipped with a fluorescent light source. Biological materials were transferred into DMEM/F12 medium with 0.05% Trypsin/ 0.02% EDTA (Sigma) and incubated at 37⁰ C for 5 min. Single cells were isolated by gentle trituration using P1000 tips and then added cold 10% FCS to stop the enzymatic reaction. After a double wash procedure using PBS with RNAse inhibitor, cells were filtered through a 40 uM nylon cell strainer and collected into a FACS tube on ice. Samples remained on ice throughout the process and total processing time from adrenal anlages isolation to sorting was limited to 1 hour.
Dissection of Wnt1-Cre/Tomato+ sympatho-adrenal anlages at E12.5 and E13.5 stages was carried out using a stereomicroscope equipped with a fluorescent light source. The dissected fragments were transferred into DMEM/F12 medium with 0.05% Trypsin/ 0.02% EDTA (Sigma) and incubated at 37⁰ C for 5 min. Single cells were released by gentle trituration using P1000 tips, and then ice-cold 10% FCS was added to stop the enzymatic reaction. After a double wash procedure using PBS with RNAse inhibitor, cells were filtered through a 40 uM nylon cell strainer and collected into a FACS tube on ice. After that the samples remained on ice or were kept at +4C throughout the rest of the processing that included single cell FACS sorting of Tomato+ cells into 384-well plates with pre-filled lysis buffer.The sequencing libraries were generated using the published protocol for Smartseq2 sequencing (Picelli et al., Nature Protocols 2014). Resulting libraries were sequenced on the Illumina® HiSeqTM 2000 sequencing platform. The extended analysis is published in Furlan, Dyachuk and Kastriti et al., Science 2016".

value: sympatho-adrenal anlage

tag: age


title: Old_Monkey_02_Methylation

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Library protocol: DREAM
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: rheMac2
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_rheMac2 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

organism: Macaca mulatta

source_name: Rhesus monkey whole blood

extract_protocol:
PAXgene DNA extraction protocol
Five micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: tissue

value: whole blood

tag: gender

value: Female

value: 23.7 years old

tag: caloric status

value: Ad Libitum


title: ESd4_bc1_PAR_4C-seq_BioRep2


title: E12.5_C19 [single cell RNA-seq]


title: Middle_Age_Monkey_46_Methylation

value: Male

value: 11.4 years old


title: Middle_Age_Monkey_43_Methylation


title: ESd4_bc4_PAR_4C-seq_BioRep1


title: E12.5_D3 [single cell RNA-seq]


title: Bs.BsB1.rhomutant.1

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

data_processing:
The raw data quality was controlled using FastQC (v0.11.3) and  low quality ends were removed using Prinseq (0.20.1; options "-trim_ns_left 0 -trim_ns_right 0 -trim_qual_right 20").
Remnant sequencing adaptors identified with FastQC were removed using Cutadapt (1.8.3; option "-b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG").
Reads were trimmed based on sequencing quality using Sickle (1.200; options "-n -x -q 30 -l 30").
Reads were mapped on AL009126.3 reference genome using Bowtie2 (2.0.6; options "-N 1 -L 16 -R 4").
Stranded and reverse stranded read count aggregation was performed using Htseq-count (0.6.0; standard options).
Genome_build: Genbank AL009126.3
Supplementary_files_format_and_content: CSV with tab-separated columns which contains read-counts aggregated on the sense and antisense strand of transcribed segments (annotated genes and S-segments of Nicolas et al., 2012). Each locus is uniquely identified by its coordinates on AL009126.3 (columns "Start.AL009126.3","End.AL009126.3 ","Strand.AL009126.3") and the read count data for reads with forward (sense) and reverse (antisense) directions are reported in two separate rows distinguished by the value in column "Direction.Of.Reads". Columns "Gene.Name" and "Locus.Tag" contains either the information found AL009126.3 (for annotated genes) or the information from Nicolas et al. (2012) for S-segments.

organism: Bacillus subtilis

growth_protocol: Bacteria were grown in LB medium at 37°C under vigorous agitation up to an OD600nm of ~0.5.

extract_protocol:
RNA preparation and DNase treatment were done as described (Nicolas et al., 2012). Quality and quantity of RNA samples was verified on a Bioanalyzer (Agilent, CA).
Library preparation and sequencing was performed by Plate-forme Transcriptome et Epigénome at Pasteur Institut (Paris, France). Ribosomal RNA were depleted using RIBOZero rRNA removal kit Bacteria (Illumina, San Diego, California). The libraries were then prepared with the Truseq Stranded mRNA sample preparation kit (Illumina) according to manufacturer’s instructions. Strand-specific reads with a 6 nt index used for multiplexing and an orientation reverse to the transcripts (first strand cDNA) were obtained on an Illumina Hiseq2500 platform.

tag: genotype/variation

value: rho-deletion mutant

tag: growth stage

value: Cells grown in LB; early exponential phase

tag: replicate

value: replicate 1


title: ESd0_bc10_PAR_4C-seq_BioRep1

data_processing:
Basecalls performed using Illumina MiSeq software. Reads aligned to mouse reference genomes (GRCm38/mm10) using Tophat2 after removal of adaptor sequences by Trim Galore. Due to the low quality after 100 cycles of Miseq runs, it produced less mapped reads using longer reads (300-paired) than shorter reads (100-paired). We presented here using the first 100-paired end reads alignment instead of 300-paired end alignment. After removal of PCR duplicates, unmapped reads were filtered out. Alignments were divided into positive and negative strands, followed by coverage generation. Scaled wig files were generated by dividing these coverages by number of fragments per million (FPM).
library strategy: 4C-seq
Genome_build: mm9
Supplementary_files_format_and_content: The processed bigwig files were produced using the sum coverages of 100 kb bins on chrX.


title: E12.5_C20 [single cell RNA-seq]


title: ESd0_bc3_PAR_4C-seq_BioRep2


title: E12.5_C18 [single cell RNA-seq]


title: E12.5_C24 [single cell RNA-seq]


title: Middle_Age_Monkey_42_Methylation

value: 10.5 years old


title: Bs.BsB1.parental.1

value: parental


title: Old_Monkey_07_Methylation

value: 29.8 years old


title: E12.5_C15 [single cell RNA-seq]


title: Middle_Age_Monkey_40_Methylation

value: 12.1 years old


title: E12.5_C16 [single cell RNA-seq]


title: Caloric_Restriction_Old_Monkey_28_Methylation

value: 25.1 years old

value: Caloric Restriction


title: E12.5_C17 [single cell RNA-seq]


title: Caloric_Restriction_Old_Monkey_04_Methylation


title: E12.5_C12 [single cell RNA-seq]


title: E12.5_C11 [single cell RNA-seq]


title: TERRA capture RNA-Seq_RandomPrimer

description: TERRA RNA

data_processing:
mm10
Basecalls performed using Illumina MiSeq software. Reads aligned to mouse reference genomes (GRCm38/mm10) using Tophat2 after removal of adaptor sequences by Trim Galore. Due to the low quality after 100 cycles of Miseq runs, it produced less mapped reads using longer reads (300-paired) than shorter reads (100-paired). We presented here using the first 100-paired end reads alignment instead of 300-paired end alignment. After removal of PCR duplicates, unmapped reads were filtered out. Alignments were divided into positive and negative strands, followed by coverage generation. Scaled wig files were generated by dividing these coverages by number of fragments per million (FPM).
Alignments were divided into positive and negative strands, followed by coverage generation. Scaled bigwig files were generated by dividing these coverages by number of fragments per million (FPM).

source_name: TERRA capture RNA-Seq

growth_protocol: Cells were cultured in regular ES medium (15% FBS) with LIF

extract_protocol:
Total RNA was extracted by Trizol followed by acid phenol/chloroform extraction. 20 mg of total RNA was treated with 4 units of TURBO DNase at 37°C for 10 min in 100 ml of RNase inhibitor (10 nM of Ribonucleoside Vanadyl Complex(VRC) ) containing buffer. EDTA (final concentration 5 mM) was added to disrupt VRC, and DNase-treated RNA was purified by Trizol. 10 pmol of biotin-labeled oligo probes ((TAACCC)3TA-/3’BioTEG) was added to 20 mg of RNA, and the RNA-probes mixture was denatured at 70°C in 100 ml of 6XSSC hybridization buffer for 10 min. Denatured RNA was directly transferred to 44°C heat block and incubated for 30 min. RNA was then captured by 100 ml of MyOneC1 beads at 37°C for 15 min. RNA-beads were washed with 2XSSC/0.1% NP40 at 37°C for 4 times (5 min each time), 1XSSC/0.1 NP40 at 37°C twice, and then RNA-beads were rinsed once with 1X SSC at room temperature. TERRA-enriched RNA was eluted in 30 ml of DEPC-treated water at 70°C for 5 min.
cDNA libraries were reversed transcribed with random primers using Superscript III (Invitrogen) at 55°C for 60 min. 1.25 mM of dUTP was supplied during second strand synthesis, and then dsDNA was briefly sonicated by covaris E220 in microTUBEs (Duty factor=2%, peak intensity power=140, cycle per burst=200, time=15 second). End repair, dA-tailing, adaptor ligation, and USER enzyme digestion were performed according to NEBUltra Directional RNA library preparation protocol for Illumina (NEB). Larger fragments (~>500 bp) of adaptor-ligated DNA were selected by 0.6x AMpure XP beads. Sequencing of purified libraries was carried out on an Illumina MiSeq instrument for paired 300 nucleotides reads.

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

value: Random Primer


title: Caloric_Restriction_Old_Monkey_01_Methylation

value: whole blood

value: Female

value: 24.9 years old


title: TERRA capture RNA-Seq_TeloPrimer

description: TERRA RNA

extract_protocol:
Total RNA was extracted by Trizol followed by acid phenol/chloroform extraction. 20 mg of total RNA was treated with 4 units of TURBO DNase at 37°C for 10 min in 100 ml of RNase inhibitor (10 nM of Ribonucleoside Vanadyl Complex(VRC) ) containing buffer. EDTA (final concentration 5 mM) was added to disrupt VRC, and DNase-treated RNA was purified by Trizol. 10 pmol of biotin-labeled oligo probes ((TAACCC)3TA-/3’BioTEG) was added to 20 mg of RNA, and the RNA-probes mixture was denatured at 70°C in 100 ml of 6XSSC hybridization buffer for 10 min. Denatured RNA was directly transferred to 44°C heat block and incubated for 30 min. RNA was then captured by 100 ml of MyOneC1 beads at 37°C for 15 min. RNA-beads were washed with 2XSSC/0.1% NP40 at 37°C for 4 times (5 min each time), 1XSSC/0.1 NP40 at 37°C twice, and then RNA-beads were rinsed once with 1X SSC at room temperature. TERRA-enriched RNA was eluted in 30 ml of DEPC-treated water at 70°C for 5 min.
cDNA libraries were reversed transcribed with telomeric repeat primers (TAACCC)4 using Superscript III (Invitrogen) at 55°C for 60 min. 1.25 mM of dUTP was supplied during second strand synthesis, and then dsDNA was briefly sonicated by covaris E220 in microTUBEs (Duty factor=2%, peak intensity power=140, cycle per burst=200, time=15 second). End repair, dA-tailing, adaptor ligation, and USER enzyme digestion were performed according to NEBUltra Directional RNA library preparation protocol for Illumina (NEB). Larger fragments (~>500 bp) of adaptor-ligated DNA were selected by 0.6x AMpure XP beads. Sequencing of purified libraries was carried out on an Illumina MiSeq instrument for paired 300 nucleotides reads.

value: Telomeric Primer


title: E12.5_C9 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_C8 [single cell RNA-seq]


title: E12.5_C10 [single cell RNA-seq]


title: Prox1_1

city: New York

first: Kelley

last: Yan

state: NY

department: Medicine

institute: Columbia University

description: Chromium, v2

data_processing:
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). For the old Prox1+ samples, UMI=5 was used for the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bam: bam files of individual samples; mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

source_name: small intestine

growth_protocol: primary cell isolates from reporter mice

extract_protocol:
epithelial cell preparation from proximal jejunum of mice
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single-cell GEMs for the "Original Prox1_1" and "Orginal_Prox1_2" samples, which are two technical replicates. Single-cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. 2017.  The remainder of the libraries were made using the Chromium Single Cell Instrument to generate single-cell GEMs using the Chromium Single Cell 3' Gel Bead and Library Kit from 10x Genomics (#120235, 120234, 120236, 120262).
For the "Original_Prox1_1" and "Original_Prox1_2" samples, the sequencing libraries were loaded at 2.1 pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98 bp Read1, 14 bp I7 Index, 8 bp I5 Index and 5 bp Read2. Note that these libraries were generated before the official launch of GemCode Single Cell 3’ Gel Bead and Library Kit. Thus 5bp UMI was used (the official GemCode Single Cell 3’ Gel Bead contains 10 bp UMI).  For the remainder of the samples, the sequencing libraries were loaded at 2.1 pM on an Illumina Hiseq4000 with 2 × 75 paired-end kits using the following read length: 26 bp Read1, 8 bp I7 Index and 98 bp Read2.

value: Prox1-GFP(+) cells

tag: condition

value: sorted Prox1+ cells from Prox1-GFP reporter mouse


title: Lgr5-eGFP+_1

description: Chromium, v2

value: Lgr5-eGFP(+) cells

value: sorted cells from Lgr5-eGFP reporter mouse


title: Lgr5-eGFPneg_2

description: Chromium, v2

value: Lgr5-eGFP(-) cells


title: Lgr5-eGFP+_2

description: Chromium, v2


title: Prox1_2

description: Chromium, v2


title: E12.5_C7 [single cell RNA-seq]


title: Lgr5-eGFPneg_1

description: Chromium, v2


title: E12.5_C6 [single cell RNA-seq]


title: Bmi1_2

description: Chromium, v2

value: Bmi1-GFP(+) cells

value: sorted cells from Bmi1-GFP reporter mouse


title: Middle_Age_Monkey_17_Methylation

value: Male

value: 10.4 years old

value: Ad Libitum


title: Bmi1_1

description: Chromium, v2


title: E12.5_C5 [single cell RNA-seq]


title: E12.5_C14 [single cell RNA-seq]


title: E12.5_C4 [single cell RNA-seq]


title: E12.5_C3 [single cell RNA-seq]


title: E12.5_C13 [single cell RNA-seq]


title: E12.5_C1 [single cell RNA-seq]


title: E12.5_C2 [single cell RNA-seq]


title: ChIP-seq from PC-9 (ENCLB891EJR)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR243INX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR243INX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB891EJR
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

source_name: Homo sapiens PC-9 immortalized cell line

tag: antibody

value: CTCF

tag: line

value: immortalized cell line

tag: description

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

tag: biosample encode accession

tag: dev stage

value: unknown

tag: Sex

value: not collected

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS987JQH at ENCODE; https://www.encodeproject.org/ENCBS987JQH/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: E12.5_B24 [single cell RNA-seq]

tag: genotype

tag: cell type

value: sympatho-adrenal anlage


title: ChIP-seq from stomach (ENCLB742OEJ)

description:
https://www.encodeproject.org/experiments/ENCSR166CNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR166CNR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB742OEJ
size range: 200-600

source_name: Homo sapiens stomach tissue female adult (53 years)

value: stomach

value: tissue

value: adult

tag: age

value: 53 year

value: female

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from spleen (ENCLB055OMO)

description:
https://www.encodeproject.org/experiments/ENCSR161FEJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR161FEJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB055OMO
size range: 200-600

source_name: Homo sapiens spleen tissue female adult (53 years)

value: spleen

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: E12.5_B23 [single cell RNA-seq]


title: ChIP-seq from tibial nerve (ENCLB904CMO)

description:
https://www.encodeproject.org/experiments/ENCSR157ZVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157ZVP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB904CMO
size range: 200-600

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/


title: ChIP-seq from H1-hESC (ENCLB269VHM)

description:
https://www.encodeproject.org/experiments/ENCSR157EOE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR157EOE
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269VHM
size range: 200-600
nucleic acid starting quantity: 45
nucleic acid starting quantity units: ng

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: embryonic

value: male

value: unknown

tag: health state

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS849HZG at ENCODE; https://www.encodeproject.org/ENCBS849HZG/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: E12.5_B21 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from esophagus muscularis mucosa (ENCLB142RBB)

description:
https://www.encodeproject.org/experiments/ENCSR229KWP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR229KWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB142RBB
size range: 200-600

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: esophagus muscularis mucosa

value: tissue

value: EnTEX:Esophagus - Muscularis

value: adult

value: female

value: 53 year

value: ENCBS071FUE at ENCODE; https://www.encodeproject.org/ENCBS071FUE/


title: E12.5_B20 [single cell RNA-seq]


title: E12.5_B19 [single cell RNA-seq]


title: ChIP-seq from esophagus muscularis mucosa (ENCLB817QTL)

description:
https://www.encodeproject.org/experiments/ENCSR229KWP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229KWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817QTL
size range: 200-600

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_B18 [single cell RNA-seq]


title: E12.5_B17 [single cell RNA-seq]


title: ChIP-seq from OCI-LY1 (ENCLB858SVQ)

description:
https://www.encodeproject.org/experiments/ENCSR155XXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR155XXB
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR569IIN
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB858SVQ
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

value: immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from tibial artery (ENCLB558VKV)

description:
https://www.encodeproject.org/experiments/ENCSR233LCT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR233LCT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR950CDM
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB558VKV
size range: 200-600

source_name: Homo sapiens tibial artery tissue female adult (53 years)

value: tibial artery

value: EnTEX:Artery - Tibial

value: Bradley Bernstein, Broad

value: ENCBS826SVC at ENCODE; https://www.encodeproject.org/ENCBS826SVC/


title: E12.5_B16 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_B15 [single cell RNA-seq]


title: E12.5_B14 [single cell RNA-seq]


title: ChIP-seq from tibial nerve (ENCLB490GZK)

description:
https://www.encodeproject.org/experiments/ENCSR154SJE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154SJE
assay title: ChIP-seq
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB490GZK
size range: 200-600

value: Control

value: tibial nerve

value: tissue

value: EnTEX:Nerve - Tibial

value: adult

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/


title: ChIP-seq from sigmoid colon (ENCLB331CFF)

description:
https://www.encodeproject.org/experiments/ENCSR150YAU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR150YAU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR844YME
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB331CFF
size range: 200-600

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 53 year

value: female

value: ENCBS555KUV at ENCODE; https://www.encodeproject.org/ENCBS555KUV/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_B12 [single cell RNA-seq]


title: ChIP-seq from gastrocnemius medialis (ENCLB406STF)

description:
https://www.encodeproject.org/experiments/ENCSR148FWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR148FWR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406STF
size range: 200-600
nucleic acid starting quantity: 148.72
nucleic acid starting quantity units: ng

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

value: gastrocnemius medialis

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: male

value: 37 year

value: ENCBS263ACC at ENCODE; https://www.encodeproject.org/ENCBS263ACC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: E12.5_B22 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_B10 [single cell RNA-seq]


title: E12.5_B11 [single cell RNA-seq]


title: E12.5_B9 [single cell RNA-seq]


title: ChIP-seq from H1-hESC (ENCLB842RCY)

description:
https://www.encodeproject.org/experiments/ENCSR157EOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157EOE
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842RCY
size range: 200-600

value: stem cell

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from stomach (ENCLB704GCC)

description:
https://www.encodeproject.org/experiments/ENCSR133NBJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133NBJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704GCC
size range: 200-600

value: stomach

value: tissue

value: adult

value: 53 year

value: female

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/


title: E12.5_B7 [single cell RNA-seq]


title: ChIP-seq from tibial artery (ENCLB460WDH)

description:
https://www.encodeproject.org/experiments/ENCSR127ZSP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR127ZSP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR950CDM
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460WDH
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: ENCBS826SVC at ENCODE; https://www.encodeproject.org/ENCBS826SVC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from GM12878 (ENCLB690SLO)

description:
https://www.encodeproject.org/experiments/ENCSR228DTL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR228DTL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB690SLO
size range: 200-600
nucleic acid starting quantity: 39
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

tag: passage number

value: ENCBS155GIM at ENCODE; https://www.encodeproject.org/ENCBS155GIM/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from GM12878 (ENCLB200PBJ)

description:
https://www.encodeproject.org/experiments/ENCSR228DTL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR228DTL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200PBJ
size range: 200-600
nucleic acid starting quantity: 18.19
nucleic acid starting quantity units: ng

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/


title: E12.5_B8 [single cell RNA-seq]

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz

value: sympatho-adrenal anlage


title: E12.5_B5 [single cell RNA-seq]


title: ChIP-seq from hepatocyte (ENCLB291ZMP)

description:
https://www.encodeproject.org/experiments/ENCSR384LYW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR384LYW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB291ZMP
size range: 200-600

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: E12.5_B3 [single cell RNA-seq]


title: E12.5_B13 [single cell RNA-seq]


title: ChIP-seq from GM12878 (ENCLB507VEX)

description:
https://www.encodeproject.org/experiments/ENCSR391IWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR391IWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB507VEX
size range: 200-600
nucleic acid starting quantity: 39
nucleic acid starting quantity units: ng

value: adult

value: Bradley Bernstein, Broad

value: female


title: ChIP-seq from ascending aorta (ENCLB938MZV)

description:
https://www.encodeproject.org/experiments/ENCSR122LOZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR122LOZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007WYC
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938MZV
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: 53 year

value: ENCBS328HPC at ENCODE; https://www.encodeproject.org/ENCBS328HPC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from transverse colon (ENCLB169IZI)

description:
https://www.encodeproject.org/experiments/ENCSR208QRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR208QRN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169IZI
size range: 200-600

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: transverse colon

value: EnTEX:Colon - Transverse

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/


title: E12.5_B4 [single cell RNA-seq]

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E12.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.

value: sympatho-adrenal anlage


title: E12.5_B2 [single cell RNA-seq]


title: ChIP-seq from GM12878 (ENCLB769GWB)

description:
https://www.encodeproject.org/experiments/ENCSR391IWM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR391IWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB769GWB
size range: 200-600
nucleic acid starting quantity: 11.59
nucleic acid starting quantity units: ng

value: immortalized cell line

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from adrenal gland (ENCLB902CFJ)

description:
https://www.encodeproject.org/experiments/ENCSR204DMS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR204DMS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR754WVA
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB902CFJ
size range: 200-600

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: EnTEX:Adrenal Gland

value: adult

value: male

value: 37 year

value: ENCBS137LDS at ENCODE; https://www.encodeproject.org/ENCBS137LDS/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ChIP-seq from esophagus squamous epithelium (ENCLB294SQM)

description:
https://www.encodeproject.org/experiments/ENCSR121RSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121RSS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB294SQM
size range: 200-600

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa

value: female

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS054JUC at ENCODE; https://www.encodeproject.org/ENCBS054JUC/


title: E12.5_B1 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from upper lobe of left lung (ENCLB572ECE)

description:
https://www.encodeproject.org/experiments/ENCSR208WDY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR208WDY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572ECE
size range: 200-600

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: upper lobe of left lung

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_A24 [single cell RNA-seq]


title: ChIP-seq from esophagus muscularis mucosa (ENCLB836RTH)

description:
https://www.encodeproject.org/experiments/ENCSR095YMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR095YMD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB836RTH
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: ENCBS071FUE at ENCODE; https://www.encodeproject.org/ENCBS071FUE/


title: E12.5_A22 [single cell RNA-seq]


title: ChIP-seq from ascending aorta (ENCLB351XJL)

description:
https://www.encodeproject.org/experiments/ENCSR202XTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR202XTW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR494YJW
encode release date: 2016-11-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB351XJL
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (51 year)

value: ascending aorta

value: EnTEX:Artery- Aorta

value: adult

value: 51 year

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from GM12878 (ENCLB082XBO)

description:
https://www.encodeproject.org/experiments/ENCSR120IIK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR120IIK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082XBO
size range: 200-600
nucleic acid starting quantity: 3.46
nucleic acid starting quantity units: ng

value: immortalized cell line

value: female

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: E12.5_A21 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from fibroblast of arm (ENCLB818INI)

description:
https://www.encodeproject.org/experiments/ENCSR124MTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124MTJ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR922FLS
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818INI
size range: 200-600
nucleic acid starting quantity: 146.25
nucleic acid starting quantity units: ng

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: E12.5_B6 [single cell RNA-seq]


title: ChIP-seq from GM12878 (ENCLB818JAF)

description:
https://www.encodeproject.org/experiments/ENCSR120IIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR120IIK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818JAF
size range: 200-600
nucleic acid starting quantity: 18.6
nucleic acid starting quantity units: ng

value: adult

value: Bradley Bernstein, Broad

value: ENCBS330WEW at ENCODE; https://www.encodeproject.org/ENCBS330WEW/


title: ChIP-seq from adrenal gland (ENCLB191XGX)

description:
https://www.encodeproject.org/experiments/ENCSR094VJC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR094VJC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR754WVA
encode release date: 2016-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB191XGX
size range: 200-600
nucleic acid starting quantity: 204.25
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: 37 year

value: ENCBS232HQQ at ENCODE; https://www.encodeproject.org/ENCBS232HQQ/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: E12.5_A20 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_A19 [single cell RNA-seq]


title: E12.5_A17 [single cell RNA-seq]


title: E12.5_A16 [single cell RNA-seq]


title: E12.5_A18 [single cell RNA-seq]


title: ChIP-seq from neutrophil (ENCLB954RWK)

description:
https://www.encodeproject.org/experiments/ENCSR373WCB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR373WCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2017-03-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB954RWK
size range: 200-600

source_name: Homo sapiens neutrophil primary cell

value: neutrophil

value: primary cell

value: Neutrophils were isolated by centrifuging heparinized venous blood over Histopaque 1119 (Sigma-Aldrich) and subsequently over a discontinuous Percoll (Amersham Biosciences) gradient.  Cells provided by Max Planck Institute for Infection Biology, Berlin

value: unknown

value: not collected

value: ENCBS360EQL at ENCODE; https://www.encodeproject.org/ENCBS360EQL/

value: Derived from ENCODE donor ENCDO055UKA; https://www.encodeproject.org/ENCDO055UKA/


title: ChIP-seq from neutrophil (ENCLB889GSB)

description:
https://www.encodeproject.org/experiments/ENCSR373WCB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373WCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2017-03-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB889GSB
size range: 200-600

value: ENCBS462VZJ at ENCODE; https://www.encodeproject.org/ENCBS462VZJ/


title: E12.5_A15 [single cell RNA-seq]

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz


title: E12.5_A14 [single cell RNA-seq]


title: ChIP-seq from A549 (ENCLB668FPF)

description:
https://www.encodeproject.org/experiments/ENCSR368ZHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368ZHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB668FPF
size range: 200-600
nucleic acid starting quantity: 6.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: immortalized cell line

value: adult

value: Bradley Bernstein, Broad

value: 58 year

value: male

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: E12.5_A23 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from A549 (ENCLB661RGE)

description:
https://www.encodeproject.org/experiments/ENCSR368ZHR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR368ZHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB661RGE
size range: 200-600
nucleic acid starting quantity: 9.38
nucleic acid starting quantity units: ng

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/


title: ChIP-seq from thoracic aorta (ENCLB617YGS)

description:
https://www.encodeproject.org/experiments/ENCSR083MAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR083MAZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB617YGS
size range: 200-600
nucleic acid starting quantity: 25.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: 37 year

value: ENCBS543OJU at ENCODE; https://www.encodeproject.org/ENCBS543OJU/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: E12.5_A13 [single cell RNA-seq]


title: E12.5_A12 [single cell RNA-seq]


title: ChIP-seq from Peyer's patch (ENCLB894AZQ)

description:
https://www.encodeproject.org/experiments/ENCSR363CJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR363CJF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB894AZQ
size range: 200-600

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: female

value: 53 year

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_A11 [single cell RNA-seq]


title: ChIP-seq from hepatocyte (ENCLB929LYK)

description:
https://www.encodeproject.org/experiments/ENCSR384LYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR384LYW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929LYK
size range: 200-600
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from spleen (ENCLB251HSM)

description:
https://www.encodeproject.org/experiments/ENCSR105URN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105URN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251HSM
size range: 200-600

source_name: Homo sapiens spleen tissue female adult (53 years)

value: spleen

value: tissue

value: adult

value: Bradley Bernstein, Broad

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: E12.5_A10 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_A9 [single cell RNA-seq]


title: ChIP-seq from stomach (ENCLB244ZME)

description:
https://www.encodeproject.org/experiments/ENCSR357ROS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR357ROS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB244ZME
size range: 200-600

source_name: Homo sapiens stomach tissue female adult (53 years)

value: stomach

value: 53 year

value: female

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/


title: E12.5_A8 [single cell RNA-seq]


title: ChIP-seq from GM12878 (ENCLB671RMZ)

description:
https://www.encodeproject.org/experiments/ENCSR330EXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330EXS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB671RMZ
size range: 200-600
nucleic acid starting quantity: 26.6
nucleic acid starting quantity units: ng

value: immortalized cell line

value: unknown

value: ENCBS155GIM at ENCODE; https://www.encodeproject.org/ENCBS155GIM/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: E12.5_A7 [single cell RNA-seq]


title: ChIP-seq from GM12878 (ENCLB069XOY)

description:
https://www.encodeproject.org/experiments/ENCSR330EXS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR330EXS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069XOY
size range: 200-600
nucleic acid starting quantity: 6.89
nucleic acid starting quantity units: ng

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/


title: ChIP-seq from body of pancreas (ENCLB743IWD)

description:
https://www.encodeproject.org/experiments/ENCSR348TQM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348TQM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099LGH
encode release date: 2016-10-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB743IWD
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: male

value: 54 year

value: ENCBS209WBW at ENCODE; https://www.encodeproject.org/ENCBS209WBW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: ChIP-seq from ascending aorta (ENCLB067AYN)

description:
https://www.encodeproject.org/experiments/ENCSR103QHX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR103QHX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR494YJW
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB067AYN
size range: 200-600

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: Bradley Bernstein, Broad

value: 51 year

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from esophagus squamous epithelium (ENCLB726TPD)

description:
https://www.encodeproject.org/experiments/ENCSR078ZGC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR078ZGC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726TPD
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: female

value: 53 year

value: ENCBS054JUC at ENCODE; https://www.encodeproject.org/ENCBS054JUC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_A3 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from gastrocnemius medialis (ENCLB616PJK)

description:
https://www.encodeproject.org/experiments/ENCSR101NFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101NFY
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001UFN
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB616PJK
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue female adult (53 years)

value: gastrocnemius medialis

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: ENCBS866HOM at ENCODE; https://www.encodeproject.org/ENCBS866HOM/


title: E12.5_A2 [single cell RNA-seq]


title: E12.5_A1 [single cell RNA-seq]


title: E12.5_A5 [single cell RNA-seq]


title: ChIP-seq from gastrocnemius medialis (ENCLB027ICU)

description:
https://www.encodeproject.org/experiments/ENCSR201OSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR201OSX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001UFN
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB027ICU
size range: 200-600

value: tissue


title: Extra_Cross_ rep2

city: Cambridge

first: Ilaria

last: Falciatori

address: Robinson Way

department: GH Lab

country: United Kingdom

institute: CRUK-CI

description: Barcode CTTGTA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Libraries were clipped using FASTX toolkit version 0.0.13 (adapter: TGGAATTCTCGGGTGCCAAGG).
Reads longer than 18 nucleotides were mapped using Bowtie version1.1.2 to either a FASTA file containing the floxed version of Kdm1a or to mm10,using parameters: -q -v 1 -a --best --al.
Reads mapping to mm10 were sequentially mapped using Bowtie version1.1.2 (parameters: -q -v 1 -a --best --al) to FASTA files containing rRNAs (Ensembl), miRNAs (hairpin from miRBase), tRNAs (GtRNA db), repeats (Repbase), piRNA clusters (Li et al., 2013) and Refseq (NCBI). To avoid duplications only non mappers from one class were used to map to the following class.
Genome_build: mm10
Supplementary_files_format_and_content: Csv files iincluding the RPM values for the different features in the Original Cross and Extra Cross per each Replicate. For multimappers, the RPM was divided across all the mapping locations with perfect match.

source_name: Sperm

extract_protocol:
Trizol was used to extract RNA from the sperm samples with slight modificatiosn retain small RNAs. Sperm from each mouse was processed separately and treated as a replicate. Two biological replicates per condition were produced. For each sample, 250-1500ng of RNA were used for size-selection on a polyacrylamide gel. After elution from the gel we proceeded to library preparation.
The Truseq small RNA library preparation kit from Illumina was used for library production according to Manufacturer's instructions. Samples (4 in total) were barcoded (Sample 1 GATCAG, Sample 2 TAGCTT, Sample 3 GGCTAC, Sample4 CTTGTA) and run in the same sequencing lane.

treatment_protocol: Sperm was isolated from the cauda epidydimis and washed with PBS.

tag: strain

value: Adult

value: Spermatozoa

tag: cross type

value: Extra cross to wildtype


title: ChIP-seq from right lobe of liver (ENCLB679IKV)

description:
https://www.encodeproject.org/experiments/ENCSR080QVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR080QVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR276SJT
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679IKV
size range: 200-600

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: adult

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/


title: Original_Cross_ rep2

description: Barcode GGCTAC

value: Original cross


title: Extra_Cross_ rep1

description: Barcode TAGCTT


title: Original_Cross_ rep1

description: Barcode GATCAG


title: ChIP-seq from thoracic aorta (ENCLB797IGL)

description:
https://www.encodeproject.org/experiments/ENCSR318HUC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR318HUC
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB797IGL
size range: 200-600
nucleic acid starting quantity: 16.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (54 years)

value: thoracic aorta

value: EnTEX:Artery- Aorta

value: male

value: 54 year

value: ENCBS703OTV at ENCODE; https://www.encodeproject.org/ENCBS703OTV/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Cab10 ES d0 input CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10

source_name: CHIRT-seq

extract_protocol:
CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion. Chromatin was incubated with biotinylated capture oligonucleotides that were complementary to PAR-TERRA RNA, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion.
CHIRT-seq: Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

tag: capture oligos

tag: molecule subtype

value: input DNA


title: ChIP-seq from tibial nerve (ENCLB897YCH)

description:
https://www.encodeproject.org/experiments/ENCSR314SPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314SPW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897YCH
size range: 200-600

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

tag: antibody

value: tibial nerve

value: tissue

value: EnTEX:Nerve - Tibial

value: 53 year

value: female

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from bipolar neuron (ENCLB863GNC)

description:
https://www.encodeproject.org/experiments/ENCSR066BZZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR066BZZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001KCX
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB863GNC
size range: 200-600

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: CTCF

value: bipolar neuron

value: in vitro differentiated cells

tag: description

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: E12.5_A6 [single cell RNA-seq]

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E12.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.

value: sympatho-adrenal anlage


title: Cab10 ES d0 noRNaseH CHIRT-seq

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

value: TERRA-AS,noRNaseH

value: no RNaseH control DNA


title: Cab10 ES d0 TERRA CHIRT-seq

value: TERRA-AS

value: TERRA enriched DNA


title: ChIP-seq from bipolar neuron (ENCLB109JJP)

description:
https://www.encodeproject.org/experiments/ENCSR066BZZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR066BZZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001KCX
encode release date: 2016-11-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB109JJP
size range: 200-600

tag: biosample encode accession

value: 53 year

value: male

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/


title: Cab10 ES d0 Sense CHIRT-seq

value: TERRA-sense

value: Sense control DNA


title: ChIP-seq from adrenal gland (ENCLB909PBO)

description:
https://www.encodeproject.org/experiments/ENCSR043UWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR043UWF
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB909PBO
size range: 200-600

source_name: Homo sapiens adrenal gland tissue female adult (53 years)

value: Control

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

tag: dev stage

value: Bradley Bernstein, Broad

value: female

value: ENCBS130NHB at ENCODE; https://www.encodeproject.org/ENCBS130NHB/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E12.5_A4 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: ChIP-seq from esophagus squamous epithelium (ENCLB836RKS)

description:
https://www.encodeproject.org/experiments/ENCSR057YVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057YVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB836RKS
size range: 200-600

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: adult

tag: Sex

value: ENCBS054JUC at ENCODE; https://www.encodeproject.org/ENCBS054JUC/


title: ChIP-seq from breast epithelium (ENCLB987VXJ)

description:
https://www.encodeproject.org/experiments/ENCSR034ZKE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034ZKE
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR247XFQ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB987VXJ
size range: 200-600

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue

value: 53 year

tag: lab

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/


title: ChIP-seq from esophagus squamous epithelium (ENCLB512MLZ)

description:
https://www.encodeproject.org/experiments/ENCSR057BFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057BFO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB512MLZ
size range: 200-600

tag: link


title: ketamine_3

city: Miami

first: Eleonore

last: Beurel

state: FL

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

data_processing:
Paired-ends reads generated from sequencing on the Illumina Hiseq2000 were trimmed off the adaptor sequences using a custom script.
Trimmed reads were aligned to the human genome reference GRCh37 using TopHat 2.0.9.
Transcriptome for each sample was assembled using Cufflinks, which also provided transcripts abundance in fragments per kilobase of exon per million fragments mapped (FPKM)
Transcripts assemblies were merged using Cuffmerge.
Genes were annotated according to the ENSEMBL classification, and genes that were not annotated as protein coding genes, lincRNA or antisense RNA were filtered out.
Genome_build: Differential gene expression analysis was performed using Cuffdiff.
Supplementary_files_format_and_content: NCBIM37
Supplementary_files_format_and_content: Excel file including RPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA were extracted using the TRIzol methodl
1mg of RNA was used to prepare poly-A selected directional libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs)

treatment_protocol: mice were treated intranasally with 10 ug siRNA for GSK3b, or 60 ug L808mts every other day  for 3 days, or with 10 mg/kg ketamine ip  for 24 h and sacrificed, RNA were extracted from hippocampus and sequenced

tag: treatment

value: ketamine

tag: dose, route, time

value: 10 mg/kg, ip, 24 h


title: ketamine_2


title: ChIP-seq from A549 (ENCLB543CKY)

description:
https://www.encodeproject.org/experiments/ENCSR321BJQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321BJQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB543CKY
size range: 200-600
nucleic acid starting quantity: 2.78
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

tag: line

value: immortalized cell line

tag: age

value: 58 year

value: male

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB031DEJ)

description:
https://www.encodeproject.org/experiments/ENCSR321BJQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR321BJQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB031DEJ
size range: 200-600
nucleic acid starting quantity: 7.7
nucleic acid starting quantity units: ng

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/


title: ChIP-seq from OCI-LY7 (ENCLB506TNR)

description:
https://www.encodeproject.org/experiments/ENCSR027HML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR027HML
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB506TNR
size range: 200-600

source_name: Homo sapiens OCI-LY7 immortalized cell line

value: CTCF

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

tag: health state

value: B cell lymphoma

value: ENCBS699NWP at ENCODE; https://www.encodeproject.org/ENCBS699NWP/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: L803mts_2

tag: strain

value: 60 ug, 5 uL/nostril, in, every other day for 3 days


title: ChIP-seq from ascending aorta (ENCLB140VAC)

description:
https://www.encodeproject.org/experiments/ENCSR069UMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR069UMW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007WYC
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140VAC
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 53 year

value: female

value: ENCBS328HPC at ENCODE; https://www.encodeproject.org/ENCBS328HPC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from OCI-LY7 (ENCLB787KKC)

description:
https://www.encodeproject.org/experiments/ENCSR027HML/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR027HML
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB787KKC
size range: 200-600

value: immortalized cell line

value: male

value: Bradley Bernstein, Broad

value: ENCBS304FAI at ENCODE; https://www.encodeproject.org/ENCBS304FAI/


title: ketamine_1

value: ketamine

value: 10 mg/kg, ip, 24 h


title: ChIP-seq from gastroesophageal sphincter (ENCLB341HGL)

description:
https://www.encodeproject.org/experiments/ENCSR025CGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025CGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178MWD
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341HGL
size range: 200-600

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

extract_protocol: not provided

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: ENCBS783BYN at ENCODE; https://www.encodeproject.org/ENCBS783BYN/


title: ChIP-seq from ACC112 (ENCLB569TOC)

description:
https://www.encodeproject.org/experiments/ENCSR311DQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR311DQO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR836XKP
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB569TOC
size range: 200-600

source_name: Homo sapiens ACC112 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

value: adenoid cystic carcinoma cell line supplied by Lurdes Queimado, M.D., Ph.D.Phone:405-271-4232 (office); 405-271-4279 (lab); cells immortalized by infection with a retrovirus expressing HPV16 E6 and E7

value: 70 year

value: submaxillar tumor

value: ENCBS827JIC at ENCODE; https://www.encodeproject.org/ENCBS827JIC/

value: Derived from ENCODE donor ENCDO085ZKK; https://www.encodeproject.org/ENCDO085ZKK/

value: ENCODE dbxrefs Cellosaurus CVCL_Y492; http://web.expasy.org/cellosaurus/CVCL_Y492


title: siGSK3b_3

value: siRNA GSK3beta

value: 10 ug, 5 uL/nostril, in, every other day for 3 days


title: siGSK3b_2


title: ChIP-seq from ascending aorta (ENCLB390DIM)

description:
https://www.encodeproject.org/experiments/ENCSR007WYC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR007WYC
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB390DIM
size range: 200-600

value: Control

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 53 year

value: female

value: ENCBS328HPC at ENCODE; https://www.encodeproject.org/ENCBS328HPC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: siGSK3b_1


title: ChIP-seq from heart left ventricle (ENCLB522ZXV)

description:
https://www.encodeproject.org/experiments/ENCSR000XAA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000XAA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR526EXI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB522ZXV
size range: 200-600

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: Bradley Bernstein, Broad

value: ENCBS861XCF at ENCODE; https://www.encodeproject.org/ENCBS861XCF/


title: control_3

value: vehicle

value: 5 uL/nostril, in, every other day for 3 days


title: control_1


title: ChIP-seq from Peyer's patch (ENCLB397XWC)

description:
https://www.encodeproject.org/experiments/ENCSR005UXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005UXZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB397XWC
size range: 200-600

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/


title: L803mts_3

value: 60 ug, 5 uL/nostril, in, every other day for 3 days


title: Adult blood O_9 DNA methylation

data_processing:
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: Human whole blood

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: gender

value: Female


title: Adult blood O_102 DNA methylation

value: Male


title: Adult blood O_14 DNA methylation


title: Adult blood O_39 DNA methylation


title: Adult blood O_58 DNA methylation


title: Adult blood M_36 DNA methylation


title: Adult blood M_74 DNA methylation


title: ChIP-seq from ascending aorta (ENCLB583DWI)

description:
https://www.encodeproject.org/experiments/ENCSR007WYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007WYC
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB583DWI
size range: 200-600

value: Control

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult


title: Adult blood O_8 DNA methylation


title: Phf6KO_sg4_rep3

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

description: pre-B cell leukemia cells with indicated genotype

data_processing:
Illumina pipeline version 1.8 used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: BCR-ABL1 transformed p19 null preB-ALL

growth_protocol: RPMI-1640 supplemented with 10% FBS, 4mM L-glutamine, 50µM 2-mercaptoethanol, 100U/mL penicillin and 100ug/mL streptomycin.

extract_protocol:
RNA from preB-ALL cells was prepared using Qiagen RNeasy Mini Kit.
cDNA for RNA-Seq libraries was prepared using Illumina TruSeq mRNA library Prep Kit.

tag: cell type

value: pre-B cell leukemia

tag: genotype

value: BCR-ABL1 overexpressed p19 null

tag: phf6 genotype


title: Phf6KO_sg1_rep2


title: Phf6KO_sg1_rep1


title: Phf6KO_sg4_rep1


title: L803mts_1


title: Phf6KO_sg1_rep3


title: Phf6KD_rep3

value: shRNA


title: Adult blood M_14 DNA methylation


title: Cord blood CB9671 DNA methylation

source_name: Human cord blood mononuclear cells

value: Unknown


title: control_2

value: vehicle


title: Phf6KD_rep1


title: Cord blood CB9524 DNA methylation


title: Phf6WT_rep3

value: Wild-type


title: Phf6WT_rep2


title: Phf6KO_sg4_rep2


title: Degradome_dark

city: Taipei

first: Meng-Chun

last: Lin

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology

data_processing:
Sequence reads were adaptor-trimmed. Only reads with over 18 nt after adaptor removal were used for mapping.
Mapping were conducted using Bowtie (v1.0.0), with parameters set as: –f –n 0 –e 80 –l 18 –a –m 5 –best –strata
Transcripts per million reads (TPM, 20 - 24 nt) were calculated for normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: Degradome analysis of sRNA-mediated cleavage under dark

organism: Arabidopsis thaliana

source_name: 4d-old de-etiolating seedling

growth_protocol: Surface steriled seeds were stratified at 4 °C for 4 days on 1/2 MS medium. The stratified seeds were them applled 1 h of white light exposure to synchronize germination, then placed in dark for 4 days at 22 °C.

extract_protocol:
Total RNA was isolated from seedlings grown under the conditions listed above, and were isolated by using PureLink Plant RNA Reagent (Invitrogen), following manufacturer's instructions. Small RNAs sized between 17 - 30 bp were resolved by TBE-UREA gel and were sliced for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Tru-seq small RNA for sRNA sequencing replicate 1 and 2. sm ll RNA v1.5 for replicate 3. Degradome library construction has followed the protocol puclished in Methods. 2014 1;67(1):84-90.

treatment_protocol: The 4-d-old seedlings were applied for whilte light (100 mE) exposure for 0, 1, 3, 6, 12 and 24 h.

tag: ecotype

tag: time point

tag: genotype/variation

value: wild type

tag: light intensity


title: Phf6WT_rep1


title: W6h_rep3

data_processing:
Sequence reads were adaptor-trimmed. Only reads with over 18 nt after adaptor removal were used for mapping.
Mapping were conducted using Bowtie (v1.0.0), with parameters set as: –f –n 0 –e 80 –l 18 –a –m 5 –best –strata
Transcripts per million reads (TPM, 20 - 24 nt) were calculated for normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel tables for the TPM of the sRNAs are attached.


title: W12h_rep3


title: Adult blood M_34 DNA methylation


title: W3h_rep3


title: W24h_rep2


title: W24h_rep3


title: W1h_rep3


title: W0h_rep3