title: Organoid 7 derived from patient 19a

description: mRNA


title: Organoid 4 derived from patient 19a

status: Public on May 07 2015

type: SRA

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: mRNA

library_source: transcriptomic

data_processing:
After sequencing, read 1 was aligned to the hg19 RefSeq human transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013) using bwa (Li and Durbin, 2010) with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL-seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Samples with less than 500.000 reads were discarded after which the remaining samples were rpm normalized.
Genome_build: hg19
Supplementary_files_format_and_content: mRNA count data for all samples, each column is a sample each row is a gene

molecule: total RNA

organism: Homo sapiens

source_name: Colonic Adenocarcinoma derived organoid

growth_protocol: Organoids derived from colorectal cancer cases were resuspended in matrigel. Subseqeuntly, droplets of matrigel (10 ul), were put in a dish. After letting the Matrigel solidy, Human Intestinal  Stem Cell medium (HISC) (Basal culture medium with 50% Wnt conditioned medium, 20% R-Spondin conditioned medium, 10% Noggin conditioned medium,  1 x B27, 1,25 mM n-Acetyl Cysteine, 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 500 nM A83-01, 3 uM SB202190, 10 nM Prostaglandine E2 and 1 x Primocin (Vivogen)) minus Wnt was added and the cells were incubated at 37 oC.

extract_protocol:
For single organoid mRNA sequencing, organoids were hand-picked and deposited into trizol (life technologies).
The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.

tag: sample type

value: Organoid culture

tag: tissue

value: Colonic Adenocarcinoma derived organoid

tag: protocol

value: CEL-seq (Hashimshony et al., Cell reports 2012)

tag: subject

value: patient 19a


title: Organoid 5 derived from patient 19a

description: mRNA


title: Organoid 3 derived from patient 19a

description: mRNA


title: Organoid 2 derived from patient 8

description: mRNA

value: patient 8


title: Organoid 2 derived from patient 19a

description: mRNA


title: Organoid 6 derived from patient 19a

description: mRNA


title: Organoid 8 derived from patient 7

description: mRNA

value: patient 7


title: Organoid 10 derived from patient 19a

description: mRNA


title: Organoid 1 derived from patient 19a

description: mRNA


title: Organoid 12 derived from patient 19a

description: mRNA


title: Organoid 7 derived from patient 7

description: mRNA


title: Organoid 8 derived from patient 17

description: mRNA

value: patient 17


title: Organoid 11 derived from patient 19a

description: mRNA


title: Organoid 6 derived from patient 17

description: mRNA


title: Organoid 7 derived from patient 17

description: mRNA


title: Organoid 4 derived from patient 17

description: mRNA


title: Organoid 9 derived from patient 17

description: mRNA


title: Organoid 3 derived from patient 17

description: mRNA


title: Organoid 2 derived from patient 17

description: mRNA


title: Organoid 5 derived from patient 17

description: mRNA


title: Organoid 1 derived from patient 7

description: mRNA


title: Organoid 10 derived from patient 17

description: mRNA


title: Input_ICeChIP-seq_S2_P1000

city: Chicago

first: Alexander

last: Ruthenburg

state: Illinois

address: 920 E 58th St

department: Molecular Genetics and Cell Biology

country: USA

institute: The University of Chicago

description:
Sample 21
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing symmetrically trimethylated lysines-27 on histone H3.
Processed data file(s):
AR8_Input_P1000_mQ20_L190_Genome_Coverage.bigwig
AR8_Input_Padded_mQ20_L190_Genome_Coverage.bigwig

library_source: genomic

data_processing:
Data analysis was performed with Galaxy (Blankenberg et al., 2010; Giardine et al., 2005; Goecks et al., 2010)
Raw reads in FastQ fromat were first submitted to FastQ Groomer
Reads were mapped with Bowtie2 (Langmead et al., 2009) (sensitive preset option, end-to-end alignment), depending on organism of origin, to human (hg19) or mouse (mm10 or mm9) or fly (dm3) reference genomes with sequences of barcodes catenated at the end (each barcode with its own entry)
Resulting SAM files were then filtered using SAMtools (Li et al., 2009). Reads that were unmapped, unpaired (distance >1000 bp) and paired in wrong pair were removed from the set by this data analysis pipeline.
To remove noise coming from low quality reads and contaminants as well to mask repeatable genomic sequences, reads with mapping quality lower than 20 (mQ20) or 13 (mQ13) were removed.
To avoid signal artifacts and not distort Poisson sampling statistics paired reads were merged together into single entries (overlapping fragments were flattened and gaps were filled). To avoid oligonucleosome avidity bias, reads longer than 220 bps (L0-220) or 200bps (L200) or 190 bps (L190) were removed, except where explicitly stated otherwise (L0). When indicated single end reads were extended to the length of 150 bps (e150).
In order to compute barcode IP enrichment, we calculated the ratio of integrated coverage over the whole sequence of each baracode in IP over the input. To calculate Histone Modification Density (HMD) we have divided genome coverage over 1-bp window for IP by genome coverage over 1-bp window in the input, this value was subsequently divided by average barcode IP enrichment and multiplied by 100%.
BEDTools (Quinlan and Hall, 2010) were used to create genome coverage bedgraphs.
Genome_build: hg19, mm10, mm9, dm3
Supplementary_files_format_and_content: bigwig (Score). Score: HMD - histone modification density; min95_CI_HMD -  Lower confidence interval for HMD; max95_CI_HMD - Higher confidence interval for HMD; (Genome_Coverage) - integrated reads depth over 1-bp window; (K4_K9_K27) - HMD linearly decovoluted from H3K4me3, H3K9me3 and H3K27me3); (K4_K9_K27_K36_K79) -  HMD linearly deconvoluted from H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K79me3)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Cell culture

growth_protocol:
HEK293 cells were grown in 37°C, 5% CO2, 95% humidity in high glucose DMEM (Invitrogen) supplemented with 10% (v/v) HyClone FBS Characterized U.S. and 1X Penicillin/Streptomycin (Gibco). HEK293 cultures were grown in 15 cm polystyrene dishes, passaged 1:20 every 5 days, Cells used in ChIP experiments were harvested when 80-90% confluent with media changed at least 3 hours prior harvesting.
Mouse Embryonic Stem Cells (mESC) E14 cell line (129/Ola background) (Hooper et al., 1987) were grown at 37°C, 5% CO2, 95% humidity in ES media high glucose DMEM (Invitrogen) supplemented with 15% (v/v) FBS (Gibco), 2mM L-glutamine (Gibco), 1% (v/v) non-essential amino acids (Gibco), 1X Penicillin/Streptomycin (Gibco), 0.1 mM  2-mercaptoethanol (Gibco), 1000U/mL LIF (ESG1107, Millipore), 3 µM CHIR99021 (04-0004, Stemgent), 1 µM PD0325901 (04-0006, Stemgent), sterile filtered 0.1 µm membrane, stored in 4°C for up to 1 week. E14 cells were cultured on dishes coated with 0.1% gelatin (Sigma) without feeder cells, and passaged daily in 1:3 ratio (media was changed 3 hours prior passage). Cells were harvested at 80-90% confluence, with media changed at least 3 hours prior.
S2 cells were grown in 24°C, 95% humidity in Shneider S2 Drosophila medium(Gibco) supplemented with 1X Insect Media Supplement(Sigma) and 1X Penicillin/Streptomycin (Gibco). S2 cultures were grown in T-175 polystyrene dishes, passaged 1:5 every 5 days, Cells used in ChIP experiments were harvested when 80-90% confluent.

extract_protocol:
Our ICeChIP protocol is based on input preparation largely following the Dilworth lab native ChIP protocol (Brand et al., 2008). Plate-adhered cells  (~107 cells) were washed twice with 10 mL of PBS, and released by 5 mL Accutase (Millipore) for 5 minutes in 37°C, quenched with 2 mL of complete media, and collected by centrifugation (500 x g, for 5 minutes at 4°C). All subsequent steps were performed on ice with ice-cold buffers. Cells were washed twice with 10 mL PBS, and twice with 5 mL of Buffer N (15 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% (w/v) Sucrose, 5 mM MgCl2, 1 mM CaCl2 1 mM DTT, 200 μM PMSF, 1x RL Protease Inhibitor Cocktail). Cells were resuspended in 1mL of Buffer N and lysed by adding 1 mL of 2x Lysis Buffer (Buffer N supplemented with 0.6% NP-40 substitute (Sigma)) for 10 minutes at 4°C. Nuclei were collected by centrifugation (500 x g for 5 minutes at 4°C) and were resuspended in 6 PCVs (packed cell volumes) of Buffer N. To remove cell debris, resuspended nuclei were overlaid on the surface of 7.5 mL of sucrose cushion (10 mM HEPES pH 7.9, 30%(w/v) sucrose, 1.5 mM MgCl2) in a 50 mL centrifuge tube centrifuged (1300 x g, Sorvall Legend XTR swinging bucket rotor for 12 minutes at 4°C). Most cell debris remained in upper layer while nuclei sedimented through the sucrose cushion and pelleted on the bottom of the tube.  The supernatant was discarded and nuclei were resuspended in 2 PCVs of Buffer N. To measure apparent concentration of chromatin, 2 μL of resuspended nuclei were diluted in 98 μL of 2M NaCl in triplicate, total nucleic acid absorbance was measured at 260 nm by Nanodrop (Thermo Scientific), and the conversion factor assuming 1A260 = 50 ng/μL of chromatin employed. Based on these measurements, apparent concentration of chromatin was adjusted to 1 μg/μL with Buffer N. The quantity and quality of nuclei were also assessed using hemocytometer. Chromatin was sheared through exhaustive MNase digest.  At this stage, a ladder of semisynthetic nucleosomes was doped into the pool of native nucleosomes.  The amount of spiked ladder was comparable to estimated amount of genome copies in the pool based on the nuclei counting times the average DNA content per cell (~2.5 copy of genome per cell).  To remove debris coming from nuclei lysis and MNase digestion as well as strip chromatin bound factors, the pool of nucleosomes was subjected to hydroxyapatite chromatography purification (Brand et al., 2008).  Fragmented chromatin with internal standard ladders were split into 100 μg total nucleic acid fractions and each fraction was mixed with 66 mg of hydroxyapatite (HAP) resin (Bio-Rad Macro-Prep® Ceramic Hydroxyapatite Type I 20 μm) rehydrated with 200 μL of HAP buffer 1(3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 μM PMSF), incubated for 10 minutes at 4°C on rotator and subsequently was applied to the centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 μm). The chromatin-loaded resin in the column was drained and then washed four times with 200 μL HAP buffer 1 and four times with 200 μL of HAP buffer 2 (3.42 mM Na2HPO4 and 1.58 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF) by centrifugation (600 x g, 1 minute at 4°C in fixed angle rotor. Nucleosomes were eluted from the HAP column with three 100 μL washes of HAP elution buffer (342 mM Na2HPO4 and 158 mM NaH2PO4 final pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 μM PMSF). To measure apparent concentration of HAP purified chromatin fragments, 10 μL of HAP elution was diluted in 40 μL of 2M NaCl in triplicate, and absorbance measured at 260 nm averaged and adjusted (1A260 = 50 ng/μL of chromatin). Apparent concentration of chromatin was adjusted to 20 μg/mL with ChIP Buffer 1(25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute). H3K4me3 ChIP was performed with 10 μg of chromatin and 15 μL of AM39159 antibody, H3 and H4 ChIP was performed with 1 μg of chromatin and 15 μL of AM61277 and AM61299 antibody, respectively (Active Motif). 10% of initial chromatin for each IP was set aside to serve as ChIP input. Each IP experiment used 50 μL of Protein A Dynabeads (Invitrogen) that were washed twice with 1mL of ChIP buffer 1 with 1 min collection on magnetic rack after each wash. To prepare the resin, 15 μL of antibody and 85 μL of ChIP buffer 1 was added to Protein A Dynabeads and incubated for 10 minutes at room temperature on a rotator, then washed twice with 1mL of ChIP Buffer 1. Chromatin (10 μg unless otherwise indicated) in 500 μL of ChIP buffer 1 was then added to magnetic beads and incubated for 15 minutes at room temperature on rotator. Beads were washed 3 times with 1 mL of ChIP Buffer 2 (mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% (v/v) glycerol, 0.1% (v/v) NP-40 substitute), then twice with ChIP buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1mM EDTA, 0.5% Na•Deoxycholate, 0.5%(v/v) NP 40 substitute), each wash consisting of a 10 minute rotating incubation and 1 minute collection on magnetic rack at 4ºC.  During the course of washing, at least two tube changes reduced non-specific background.  Beads were then rinsed with 1 mL of ChIP Buffer 1 and 1 mL of TE buffer, followed with two 200 μL ChIP elution buffer steps (50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS). Each elution step consisted of 10 minute incubation at 65ºC in a Thermoshaker (Eppendorf) at 900 rpm. Elutions were combined and ChIP elution buffer was added to inputs to match volume of ChIP elutions. After adjusting the buffer to 200mM NaCl, 100 ng of RNase A was added into the mixture and incubated at 65ºC for 45 minutes in Thermoshaker at 800 rpm, and terminated with 10 mM EDTA. Next, protein digestion was accomplished with 20 ug of proteinase K (Roche) for 2 hrs at 42ºC in the Thermoshaker at 800 rpm. DNA was recovered and purified with Qiaquick columns (Qiagen): 6 volumes of PB buffer were added to the digestion and this solution applied to the column (17900 x g, 30s) followed by 3x 750 μL of PE buffer washes (17900 x g, 30s) with an extra 1 minute spin to remove residual ethanol. DNA was eluted by applying two times 25 μL of TE buffer at 50ºC and centrifuging (17900 x g, 1 min).
For library preparation 10 ng of DNA isolated from IP or input was used. In cases in which the total amount of DNA was below 10 ng, all available DNA was subjected to library preparation.  Ends of DNA were blunted using the End-it™DNA End-Repair Kit (Epicentre) (7μL 10x End-It buffer, 7μL 2.5 mM dNTP Mix, 7μL 10 mM ATP, 1.4μL of  End-Repair Enzyme Mix and 47.6μL of DNA in TE buffer, incubated for 45 minutes at room temperature. DNA was purified with 126μL (1.8 volume) of Ampure XP Beads (Beckman Coulter). Beads were mixed with End repair mixture by pipetting 10 times up and down followed by 5 minutes incubation at room temperature. Magnetic beads were collected on side of the tube by magnet and two 30 sec 250 μL 80% EtOH washes on magnet were performed. Tubes were removed from the magnetic rack and 34 μL of TE buffer was added to beads and pipetted 10 times up and down. Magnetic beads were not removed from elution and remained in the tube during A-tailing. Addition of single adenosine to 3’ ends of DNA was accomplished by adding to 5 μL NEB buffer 2, 10 μL 1 mM dATP, 1 μL Klenow fragment (3’→5’ exo-, NEB) to the End-repaired DNA, and with incubation at 37ºC for 30 minutes. To purify DNA, 110 μL (2.2 volume) of SPRI Buffer (20% PEG6000, 2.5M NaCl) was added to the reaction and was pipetted 10 times up and down followed by 5 minutes incubation at room temperature. Magnetic beads were collected on side of the tube with magnet and two 30 sec 200 μL 80% EtOH washes on magnet were performed. Tubes were then taken out of magnetic rack and 13 μL of TE buffer was added to beads and mixed by pipette. Magnetic beads were not removed from elution and remained in the tube during adaptor liga

tag: cell line

tag: chip antibody

tag: growth protocol

tag: amplification cycles

tag: map quality cut-off

tag: mononucleosome cut-off

tag: reference genome


title: Organoid 1 derived from patient 17

description: mRNA


title: Input_ICeChIP-seq_S2_P500

description:
Sample 20
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing 50:50 mixture of nonmodief nucleosomes and symmetrically trimethylated lysines-27 on histone H3.
Processed data file(s):
AR8_Input_P500_mQ20_L190_Genome_Coverage.bigwig
AR8_Input_Padded_mQ20_L190_Genome_Coverage.bigwig

value: S2 cells were grown in 24°C, 95% humidity in Shneider S2 Drosophila medium(Gibco) supplemented with 1X Insect Media Supplement(Sigma) and 1X Penicillin/Streptomycin (Gibco). S2 cultures were grown in T-175 polystyrene dishes, passaged 1:5 every 5 days, Cells used in ChIP experiments were harvested when 80-90% confluent.


title: Input_ICeChIP-seq_S2_P0

description:
Sample 19
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing nonmodifed nucleosomes.
Processed data file(s):
AR8_Input_P0_mQ20_L190_Genome_Coverage.bigwig
AR8_Input_Padded_mQ20_L190_Genome_Coverage.bigwig


title: H3K27me3_ICeChIP-seq_S2_qChIP_P1000

description:
Sample 18
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing symmetrically trimethylated lysines-27 on histone H3. qChIP is a modification of our ICeChIP protocol meant to test different pull-down conditions. It relies on the same buffers as ICeChIP but it is performed without batch-wash incubations, instead continous fast wash is employed.
Processed data file(s):
AR8_qCHIP_Input_P1000_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_P1000_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_P1000_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_P1000_mq20_L190_Genome_Coverage.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: H3K27me3_ICeChIP-seq_S2_ChIP_P500

description:
Sample 14
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing 50:50 mixture of nonmodief nucleosomes and symmetrically trimethylated lysines-27 on histone H3.
Processed data file(s):
AR8_CHIP_Input_P500_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_P500_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_P500_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_P500_mQ20_L190_Genome_Coverage.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: H3K27me3_ICeChIP-seq_S2_ChIP_P1000

description:
Sample 15
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing symmetrically trimethylated lysines-27 on histone H3.
Processed data file(s):
AR8_CHIP_Input_P1000_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_P1000_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_P1000_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_P1000_mQ20_L190_Genome_Coverage.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: Input_ICeChIP-seq_mESC-E14

description:
Sample 27
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-9_Input_mQ20_L200_c0_Genome_Coverage.bigwig

organism: Mus musculus

source_name: Embryonic stem cells

value: Mouse Embryonic Stem Cells (mESC) E14 cell line (129/Ola background) (Hooper et al., 1987) were grown at 37°C, 5% CO2, 95% humidity in ES media high glucose DMEM (Invitrogen) supplemented with 15% (v/v) FBS (Gibco), 2mM L-glutamine (Gibco), 1% (v/v) non-essential amino acids (Gibco), 1X Penicillin/Streptomycin (Gibco), 0.1 mM  2-mercaptoethanol (Gibco), 1000U/mL LIF (ESG1107, Millipore), 3 µM CHIR99021 (04-0004, Stemgent), 1 µM PD0325901 (04-0006, Stemgent), sterile filtered 0.1 µm membrane, stored in 4°C for up to 1 week. E14 cells were cultured on dishes coated with 0.1% gelatin (Sigma) without feeder cells, and passaged daily in 1:3 ratio (media was changed 3 hours prior passage). Cells were harvested at 80-90% confluence, with media changed at least 3 hours prior.


title: H3K27me3_ICeChIP-seq_S2_ChIP_P0

description:
Sample 13
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing nonmodifed nucleosomes.
Processed data file(s):
AR8_CHIP_Input_P0_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_P0_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_P0_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_P0_mQ20_L190_Genome_Coverage.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_CHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_CHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: Semi-synthetic Nucleosomes Sequencing

description:
Sample 2
This experiment was conducted to check whether quantification of reads using Illumina HiSeq 2500 is linear for DNA fragments wrapped around semi-synthetic nucleosomes. Briefly, the mixture of syntetic dsDNA fragments , the same as in Sample1, was added to non-modified histone octamers in 1:1 ratio to reconstitute nucleosomes, which were than subjected to the same procedure as Sample 1 to generate Illumina library for sequencing.
Processed data file(s):
N/A

data_processing:
Data analysis was performed with Galaxy (Blankenberg et al., 2010; Giardine et al., 2005; Goecks et al., 2010)
Raw reads in FastQ fromat were first submitted to FastQ Groomer
Reads were mapped with Bowtie2 (Langmead et al., 2009) (sensitive preset option, end-to-end alignment), depending on organism of origin, to human (hg19) or mouse (mm10 or mm9) or fly (dm3) reference genomes with sequences of barcodes catenated at the end (each barcode with its own entry)
Resulting SAM files were then filtered using SAMtools (Li et al., 2009). Reads that were unmapped, unpaired (distance >1000 bp) and paired in wrong pair were removed from the set by this data analysis pipeline.
To remove noise coming from low quality reads and contaminants as well to mask repeatable genomic sequences, reads with mapping quality lower than 20 (mQ20) or 13 (mQ13) were removed.
To avoid signal artifacts and not distort Poisson sampling statistics paired reads were merged together into single entries (overlapping fragments were flattened and gaps were filled). To avoid oligonucleosome avidity bias, reads longer than 220 bps (L0-220) or 200bps (L200) or 190 bps (L190) were removed, except where explicitly stated otherwise (L0). When indicated single end reads were extended to the length of 150 bps (e150).
In order to compute barcode IP enrichment, we calculated the ratio of integrated coverage over the whole sequence of each baracode in IP over the input. To calculate Histone Modification Density (HMD) we have divided genome coverage over 1-bp window for IP by genome coverage over 1-bp window in the input, this value was subsequently divided by average barcode IP enrichment and multiplied by 100%.
BEDTools (Quinlan and Hall, 2010) were used to create genome coverage bedgraphs.
Genome_build: hg19, mm10, mm10, dm3
Supplementary_files_format_and_content: bigwig (Score). Score: HMD - histone modification density; min95_CI_HMD -  Lower confidence interval for HMD; max95_CI_HMD - Higher confidence interval for HMD; (Genome_Coverage) - integrated reads depth over 1-bp window; (K4_K9_K27) - HMD linearly decovoluted from H3K4me3, H3K9me3 and H3K27me3); (K4_K9_K27_K36_K79) -  HMD linearly deconvoluted from H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K79me3)

molecule: other

organism: synthetic construct

source_name: Synthetic

growth_protocol:
HEK293 cells were grown in 37°C, 5% CO2, 95% humidity in high glucose DMEM (Invitrogen) supplemented with 10% (v/v) HyClone FBS Characterized U.S. and 1X Penicillin/Streptomycin (Gibco). HEK293 cultures were grown in 15 cm polystyrene dishes, passaged 1:20 every 5 days, Cells used in ChIP experiments were harvested when 80-90% confluent with media changed at least 3 hours prior harvesting.
Mouse Embryonic Stem Cells (mESC) E14 cell line (129/Ola background) (Hooper et al., 1987) were grown at 37°C, 5% CO2, 95% humidity in ES media high glucose DMEM (Invitrogen) supplemented with 15% (v/v) FBS (Gibco), 2mM L-glutamine (Gibco), 1% (v/v) non-essential amino acids (Gibco), 1X Penicillin/Streptomycin (Gibco), 0.1 mM  2-mercaptoethanol (Gibco), 1000U/mL LIF (ESG1107, Millipore), 3 µM CHIR99021 (04-0004, Stemgent), 1 µM PD0325901 (04-0006, Stemgent), sterile filtered 0.1 µm membrane, stored in 4°C for up to 1 week. E14 cells were cultured on dishes coated with 0.1% gelatin (Sigma) without feeder cells, and passaged daily in 1:3 ratio (media was changed 3 hours prior passage). Cells were harvested at 80-90% confluence, with media changed at least 3 hours prior.

value: not performed


title: H3K27me3_ICeChIP-seq_S2_qChIP_P0

description:
Sample 16
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing nonmodifed nucleosomes. qChIP is a modification of our ICeChIP protocol meant to test different pull-down conditions. It relies on the same buffers as ICeChIP but it is performed without batch-wash incubations, instead continous fast wash is employed.
Processed data file(s):
AR8_qCHIP_Input_P0_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_P0_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_P0_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_P0_mQ20_L190_Genome_Coverage.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: H3K27me3_ICeChIP-seq_mESC-E14

description:
Sample 24
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-4_IP_Input_mQ20_L200_c0_HMD.bigwig
AR9-4_IP_Input_mQ20_L200_c0_maxCI95.bigwig
AR9-4_IP_Input_mQ20_L200_c0_minCI95.bigwig
AR9-4_IP_mQ20_L200_c0_Genome_Coverage.bigwig
AR9-4_IP_Input_mQ20_L200_c0_HMD(K4_K9_K27_Corrected).bigwig


title: H3K9me3_ICeChIP-seq_mESC-E14

description:
Sample 23
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-3_IP_Input_mQ20_L200_c0_HMD.bigwig
AR9-3_IP_Input_mQ20_L200_c0_maxCI95.bigwig
AR9-3_IP_Input_mQ20_L200_c0_minCI95.bigwig
AR9-3_IP_mQ20_L200_c0_Genome_Coverage.bigwig
AR9-3_IP_Input_mQ20_L200_C0_HMD(K4_K9_K27_Corrected).bigwig

value: H3K9me3 (Hattori T. et al. 309M3A, lot 3)


title: Barcoded DNA Sequencing

description:
Sample 1
This experiment was conducted to check whether quanitification of reads using Illumina HiSeq 2500 is linear over meaningful concentration range. To test that known amounts (measured by densitometry)  of synthetic dsDNA (203 bp long) were used to prepare Illumina library which was than sequenced. Sequences of syntheitc dsDNA used are as follows: >601_0708 ggcggcatatcgcgcgtcgtatcgcggtCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTtcgtatcgcgccgcgtattcgggccgcc >601_0304 ggcggcgtatcgcgtcgcgcgtaatcgaCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTgcgcgacgttacgctcgacgtagccgcc >601_1920 ggcggctacgctcggactcgcgcgatgaCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTcgatcgtcgcatcggtacgctagccgcc >601_0916 ggcggcccgcgcgatattacgcgcgaatCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTcgacgttaacgcgttacgcgtcgccgcc >601_2122 ggcggctattatgcgcgacccgcgtacgCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTcgtaccgcgatccgacgatcgagccgcc >601_1112 ggcggccgacgaacggttcgtacgcgagCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTtcgcgtacgaatcgcgtaatcggccgcc >601_1314 ggcggccgcgtaatacgccgcgatacgaCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTaacgcgtatcgcgcgtaacgcggccgcc >601_1510 ggcggccgtacgacgctcgcgatatccgCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTcgacgttaacgcgttacgcgtcgccgcc >601_2324 ggcggctcgcgaccgtacgaatttcgcgCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTcgcgtcaatcgcgattacgcgagccgcc
Processed data file(s):
N/A


title: H3K36me3_ICeChIP-seq_mESC-E14

description:
Sample 25
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-6_IP_Input_mQ20_L200_c0_HMD.bigwig
AR9-6_IP_Input_mQ20_L200_c0_maxCI95.bigwig
AR9-6_IP_Input_mQ20_L200_c0_minCI95.bigwig
AR9-6_IP_mQ20_L200_c0_Genome_Coverage.bigwig
AR9-6_IP_Input_mQ20_L200_c0_HMD(K4_K9_K27_K36_K79_Corrected).bigwig


title: H3K4me3_ICeChIP-seq_mESC-E14

description:
Sample 22
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-1_IP_Input_mQ20_L200_c0_HMD.bigwig
AR9-1_IP_Input_mQ20_L200_c0_maxCI95.bigwig
AR9-1_IP_Input_mQ20_L200_c0_minCI95.bigwig
AR9-1_IP_mQ20_L200_c0_Genome_Coverage.bigwig
AR9-1_IP_Input_mQ20_L200_c0_HMD(K4_K9_K27_Corrected).bigwig


title: H3K79me2_ICeChIP-seq_mESC-E14

description:
Sample 26
Samples 22, 23, 24, 25, 26, 27 make a set. It was calibrated using Second generation barcodes assembled on H3K4me3 (C-α3 set), H3K9me3(C-α4 set), H3K27me3(C-α5 set), H3K36me3(C-α6 set), H3K79me2(C-α7 set), nonmodifed(C-α9 set), H3K4me3K27me3(C-α1 set) semi-synthetic nucleosomes.
Processed data file(s):
AR9-8_IP_Input_mQ20_L200_c0_HMD.bigwig
AR9-8_IP_Input_mQ20_L200_c0_maxCI95.bigwig
AR9-8_IP_Input_mQ20_L200_c0_minCI95.bigwig
AR9-8_IP_mQ20_L200_c0_Genome_Coverage.bigwig
AR9-8_IP_Input_mQ20_L200_c0_HMD(K4_K9_K27_K36_K79_Corrected).bigwig


title: Input_ICeCHIP-seq_mESC-E14_S1

description:
Sample 10
Samples 9, 10, 11, 12 make a set. Sample 9, 10 are replicate 1, sample 11, 12 are replicate 2. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S1_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S1.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S1.bigwig
AR7_INPUT-7c_mQ20_L0_S1(Genome_Coverage).bigwig
AR7_INPUT-7c_mQ20_L0-220_S1(Genome_Coverage).bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_maxCI95_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_minCI95_HMD.bigwig


title: Organoid 12 derived from patient 17

description: mRNA


title: H3K4me3_ICeCHIP-seq_mESC-E14_S2

description:
Sample 11
Samples 9, 10, 11, 12 make a set. Sample 9, 10 are replicate 1, sample 11, 12 are replicate 2. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S2_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S2.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S2.bigwig


title: Input_ICeCHIP-seq_mESC-E14_S2

description:
Sample 12
Samples 9, 10, 11, 12 make a set. Sample 9, 10 are replicate 1, sample 11, 12 are replicate 2. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S2_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S2.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S2.bigwig


title: Input_DNA_SOLiD

city: Uppsala

first: Marcin

last: Kruczyk

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
ChIP-seq reads were aligned to rn4 genome using Bioscope software with the default settings.
Peaks were called using MACS software using default settings and the Input file was used as control.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: The bed file reports peaks called using MACS software.

organism: Rattus norvegicus

source_name: C6 rat glioma cells_input DNA

growth_protocol: The rat C6 glioma cells purchased from ATCC were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Sigma) and antibiotics (50 U/ml penicillin, 50 μg/ml streptomycin). Cells were grown in 6-cm diameter culture plates (Corning) in a humidified atmosphere of CO2/air (5%/95%) at 37°C.

extract_protocol:
For ChIP-chip experiments, 5 x 107 C6 glioma cells were cultured to 90% confluence. Cells were treated with 1% formaldehyde, and the cross-linked chromatin was sonicated (average size, 300 bp). Immunoprecipitation were performed with components of the ChIP IT kit according to the manufacturer’s instructions (Active Motif, Carlsbad, CA). Each sample was immunoprecipitated with 1 µg of anti-H3K4me3 antibody (Millipore). The amount and quality of immunoprecipitated DNA were determined by capillary electrophoresis with a Bioanalyzer 2100 and a High Sensitivity DNA LabChip kit from Agilent Technologies (Santa Clara, CA).
Samples were amplified using the ChIP-Seq DNA sample prep kit from Illumina, following the manufacturer's instructions, and sequenced using Solid 5500xl platform (University of Uppsala Genomic Center).

tag: cell type

value: C6 glioma cells


title: Organoid 11 derived from patient 17

description: mRNA


title: Input_DNA_Illumina

description: Input_DNA for H3K4me3_Ilumina_ChIP-seq and for H3ac_Ilumina_ChIP-seq.

data_processing:
ChIP-seq reads were aligned to rn4 genome using BWA software.
Peaks were called using MACS software using default settings and the Input file was used as control.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: The bed file reports peaks called using MACS software.

extract_protocol:
For ChIP-chip experiments, 5 x 107 C6 glioma cells were cultured to 90% confluence. Cells were treated with 1% formaldehyde, and the cross-linked chromatin was sonicated (average size, 300 bp). Immunoprecipitation were performed with components of the ChIP IT kit according to the manufacturer’s instructions (Active Motif, Carlsbad, CA). Each sample was immunoprecipitated with 1 µg of anti-H3K4me3 antibody (Millipore). The amount and quality of immunoprecipitated DNA were determined by capillary electrophoresis with a Bioanalyzer 2100 and a High Sensitivity DNA LabChip kit from Agilent Technologies (Santa Clara, CA).
Samples were amplified using the ChIP-Seq DNA sample prep kit from Illumina, following the manufacturer's instructions, and sequenced using the Ilumina HiSeq 2000 (University of Uppsala Genomic). Center).


title: H3K4me3_Illumina_ChIP-seq

source_name: C6 rat glioma cells_ChIP DNA

value: anti-H3K4me3 antibody (Millipore, catalog# 07-473, lot# JBC1888194)


title: H3K27me3_ICeChIP-seq_S2_qChIP_P500

description:
Sample 17
Samples 13, 14, 15, 16, 17, 18, 19, 20, 21 make a set. It was calibrated using Second generation barcodes (C001-C100) assembled on semisynthetic nucleosomes bearing 50:50 mixture of nonmodief nucleosomes and symmetrically trimethylated lysines-27 on histone H3. qChIP is a modification of our ICeChIP protocol meant to test different pull-down conditions. It relies on the same buffers as ICeChIP but it is performed without batch-wash incubations, instead continous fast wash is employed.
Processed data file(s):
AR8_qCHIP_Input_P500_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_P500_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_P500_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_P500_mQ20_L190_Genome_Coverage.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_maxCI95.bigwig
AR8_qCHIP_Input_PAvg_mQ20_L190_HMD_minCI95.bigwig
AR8_qCHIP_Padded_mQ20_L190_Genome_Coverage.bigwig


title: H3K4me3_SOLiD_ChIP-seq


title: Drosha KD #2 (48h MSC treatment)

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

data_processing:
Reads quality was estimated using FastQC v0.10.1. Positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads mapping was performed using TopHat v2.0.10 (http://tophat.cbcb.umd.edu/, parameters: -a 5 --bowtie1). Wiggle file were generated from BAM alignment using the Wiggles v1.2.0 tool.
Genome_build: mm9

molecule: polyA RNA

source_name: Male SCID mouse kidney

growth_protocol: Studies were approved by the Ethic Committee of Turin University and conducted in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals. A model of rhabdomyolisis-induced acute kidney injury (AKI) was performed in male SCID mice as previous described. On day 3 after glycerol administration, mice received an intravenous injection into the tail vein of 75.000 MSC-CTRL or MSC-Dsh cells; and EV-CTRL or EV-Dsh in 150 μl saline, or saline alone. The number of particles injected (2.2x108 particles/mice) corresponds to an average of the amount of EVs released overnight by 75.000 MSCs (average of 2.900 EVs/cell), which showed a therapeutic effect on this AKI model. Mice were killed at day 5 (n =8 per group) after glycerol administration and blood samples for BUN determination and kidney specimens were collected. For gene expression, RNA was extracted using TRIzol from small pieces of the kidney cortical regions.

extract_protocol:
Total RNA from kidney was extracted using TRIzol (Invitrogen). RNA extraction was performed following manufacturer protocol.
For RNA-Seq library preparation, approximately 2 μg of TRIzol (Invitrogen) isolated total RNA from whole kidney was subjected to polyA+ selection and library preparation using the TruSeq RNA Sample Prep Kit (Illumina), following manufacturer instructions

tag: strain

value: SCID

value: Kidney

tag: treatment

value: 48h MSC treatment


title: Drosha KD (48h MV treatment)

value: 48h MV treatment


title: Ctrl #2 (48h MSC treatment)


title: Ctrl (48h MV treatment)


title: Drosha KD #1 (48h MSC treatment)


title: Whole Genome Bisulfite Sequencing from v6.5 embryonic stem cells

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were aligned to a C->T converted version of the mm9 reference genome using a proprietary script wrapping the bowtie2 aligner.
Aligned reads were filtered. Only reads where both ends were aligned concordantly, without indels and with a mapping quality of 10 or more were kept. Duplicate reads (identified by alignment positions) were removed.
For each CpG, a methylation call was extracted according to the sequenced base. Sequenced bases with a Phred score lower than 10 were ignored.
For each CpG, only the first methylation call was kept for processing.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-separated text files containing CpG methylation values. The files' columns are: Column1: chromosome. Column 2: position of CpG. Column 3: seen count. Column 4: methylation count. Note that each CpG's coverage is given by column 3, and its methylation value by column4/column3.

source_name: mouse embryonic stem cells

growth_protocol: Intermediate cells at day 9 (IES9): Reprogramming of reporter Nanog-CreER MEFs was done in media containing: knock-out DMEM (Invitrogen) with supplemented 15% FBS and 5% KSR with added JAK1 inhibitor (Calbiochem 420099, 0.5ϻM) for 6 days, followed by switching to 1% FBS and 14% KSR and JAK1 inhibitor for 3 days. The medium was supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 0.1 mM β-mercaptoethanol. Doxycycline hyclate (Dox) and 4-Hydroxytamoxifen (4OHT) were added to the medium at day 1 and continuously kept in the medium until day 9. At day 9 cells were sorted for tdTomato and taken for DNA isolation.   Intermedaite cells at day 6 (IES6): Reprogramming of Nnaog-CreER MEFS was carried out in knock-out DMEM medium (Gibco 10829-018) with 10% KSR, 5% FBS, 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin, 0.05 mM β-mercaptoethanol and with Dox+4OHT for 6 days. At day 6 ells were sorted for tdTomato and taken for DNA isolation.

extract_protocol:
Nanog-CreER reporter MEFs were reprogrammed in for 6 or 9 days, and sorted for tdTomato+ the end of OSKM induction step, at day 6 and 9 respectively. DNA was isolated from snap-frozen intermediate sorted cells using the Quick-gDNA mini prep kit (Zymo). DNA was then bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo). Sequencing libraries were created using the EpiGnome Methyl-Seq (Epicentre) and sequenced on an Illumina HiSeq 1500 system. The sequencing reads were aligned to the Mouse Genome Build 37 (mm9) using a proprietary script based on Bowtie 2. Due to the low sequencing depth of some of the samples, the methylation calls were down-sampled so that each CpG was covered by a single call (being either ‘methylated’ or ‘non-methylated’). Mean methylation was then calculated over all CpGs that had calls in all samples (either methylated “1” or non-methylated “0”)
EpiGnome Methyl-Seq (Epicentre)

treatment_protocol: IES9 sample was generated by addting dox and 4OHT to the medium from day 1- 9. IES6 sample was generated by addting dox and 4OHT to the medium from day 1- 6


title: Ctrl #1 (48h MSC treatment)


title: Healthy #2 (48h MSC treatment)


title: Healthy #1 (48h MV treatment)


title: Treated sample 3

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format
We map the reads to a reference genome using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default setting
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: expression levels (fpkm); text files

source_name: CUTLL1 cell line_perhexiline

growth_protocol: CUTLL1 cells were cultured in standard conditions in RPMI 1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit
Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: 3x10^5 leukemic cells were plated with 2x10^4 MS5-DL1 stroma cells into 24-well plates and treated after 24 hr with vehicle only (DMSO) or Perhexiline for 3 days

value: leukemia


title: Whole Genome Bisulfite Sequencing from from day 6 of OSKM trans-differentiation to Neural Stem Cells

description: Sorted tdTomato positive cells. No  MEF feeders

source_name: day 6 of OSKM-trans differentiation to Neural Stem Cells

tag: transgene

value: Rosa26-TdTomato B6 female + Col1a-OSKM 129 male


title: Control sample 3

source_name: CUTLL1 cell line_control


title: Whole Genome Bisulfite Sequencing from Mouse Embryonic Fibroblasts

source_name: mouse embryonic fibroblasts


title: Treated sample 2


title: H3K4me3_ICeCHIP-seq_mESC-E14_S1

description:
Sample 9
Samples 9, 10, 11, 12 make a set. Sample 9, 10 are replicate 1, sample 11, 12 are replicate 2. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR7_IP-7c_INPUT-7c_mQ20_L0-220_c0_S1_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_maxCI95_HMD_S1.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0-220_minCI95_HMD_S1.bigwig
AR7_IP-7c_mQ20_L0_S1(Genome_Coverage).bigwig
AR7_IP-7c_mQ20_L0-220_S1(Genome_Coverage).bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_maxCI95_HMD.bigwig
AR7_IP-7c_INPUT-7c_mQ20_L0_c0_S1_minCI95_HMD.bigwig


title: GM12878 and Patski Mixture

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

data_processing:
library strategy: ATAC-seq
qseq files generated with OLB v1.9.3
barcodes updated and fastq files generated with custom perl script
Adapters trimmed with Trimmomatic v0.32
Reads mapped with BWA v0.7.8-r749-dirty
Unmapped reads and mitochondrial reads filtered out.
Duplicate fragments removed with picard v1.105
Reads overlapping known hypersensitive sites were counted for each barcode to generate DHS matrix with custom python script
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: tab-separated vector - first 4 columns contain location information for each hypersensitivity site, remaining columns include counts of reads overlapping that site assigned to each barcode. Please see 'readme.txt' for detailed description.
Note: the full 32 base pair barcode ([8bp transposome index 1][8bp PCR index 1][8bp PCR index 2][8bp transposome index 2]) for each read is available as the readname from SRA, but the fastq files need to be extracted with a command like the following:
fastq-dump --split-files --origfmt --defline-seq '$sg:$sn'

organism:
Homo sapiens
Mus musculus

source_name: Mixture of GM12878 and Patski mouse embryonic kidney fibroblast cell line

growth_protocol: Cells grown under standard conditions. Patski and HEK293T were cultured in DMEM supplemented with 10% FBS. GM12878 and HL-60 were grown in RPMI 1640 supplemented with 15% FBS.

extract_protocol:
Intact nuclei were isolated with ATAC-seq cold lysis buffer suplemented with protease inhibitors.
Genomic DNA in intact nuclei was simultaneously molecularly tagged and fragmented with barcoded transposome complexes. Nuclei tagged with 1 of 96 barcodes (8 base pairs (bp)) were pooled and then redistributed into wells of a PCR plate (15 nuclei per well) using a cell sorter.  A second 8 base pair barcode was introduced during library amplification.

value: Patski mouse embryonic kidney fibroblast cell line and GM12878 human lymphoblastoid cell line

tag: molecule subtype

value: Accessible genomic DNA


title: Control sample 2


title: YBX1_CLIP_r3

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: library strategy: HITS-CLIP

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
CIMS was then used to identify the YBX1 CLIP tags (Zhang & Darnell, 2001, Nat. Biotech. 29:607). Tags between the replicates were then overlapped between the two biological replicates.
YBX1 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model, for motif comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: Fasta file with the identified TARBP2 tags along with their shuffled controls

source_name: MDA-shID

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
48 hours post-transfection, cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

value: MDA

tag: rep


title: AKI #2a (48h MSC treatment)


title: H4_ICeChIP-seq_HEK293

description:
Sample 8
Samples 7, 8 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR6_H3vsH4_HMD.bigwig

value: HEK 293

value: HEK293 cells were grown in 37°C, 5% CO2, 95% humidity in high glucose DMEM (Invitrogen) supplemented with 10% (v/v) HyClone FBS Characterized U.S. and 1X Penicillin/Streptomycin (Gibco). HEK293 cultures were grown in 15 cm polystyrene dishes, passaged 1:20 every 5 days, Cells used in ChIP experiments were harvested when 80-90% confluent with media changed at least 3 hours prior harvesting.


title: H3ac_Illumina_ChIP-seq

data_processing:
ChIP-seq reads were aligned to rn4 genome using Bowtie software with the default settings.
Peaks were called using MACS software using default settings and the Input file was used as control.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: The bed file reports peaks called using MACS software.

extract_protocol:
For ChIP-chip experiments, 5 x 107 C6 glioma cells were cultured to 90% confluence. Cells were treated with 1% formaldehyde, and the cross-linked chromatin was sonicated (average size, 300 bp). Immunoprecipitation were performed with components of the ChIP IT kit according to the manufacturer’s instructions (Active Motif, Carlsbad, CA). Each sample was immunoprecipitated with 1 µg of anti-H3ac antibody (Millipore). The amount and quality of immunoprecipitated DNA were determined by capillary electrophoresis with a Bioanalyzer 2100 and a High Sensitivity DNA LabChip kit from Agilent Technologies (Santa Clara, CA).
Samples were amplified using the ChIP-Seq DNA sample prep kit from Illumina, following the manufacturer's instructions, and sequenced using the Ilumina HiSeq 2000 (University of Uppsala Genomic). Center).

value: anti-acetyl-Histone H3 antibody (Millipore, catalog# 06-599, lot# JBC1924319)


title: YBX1_CLIP_r2

description: library strategy: HITS-CLIP


title: Input_ICeChIP-seq_HEK293_2

description:
Sample 6
Samples 5, 6 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR5_INPUT_mQ0_e150(Genome_Coverage).bigwig
AR5_IP_INPUT_L0_mQ0_c0_e150_HMD.bigwig


title: YBX1_CLIP_r1

description: library strategy: HITS-CLIP


title: Whole Genome Bisulfite Sequencing from from day 9 of OSKM trans-differentiation to Neural Stem Cells

source_name: day 9 of OSKM-trans differentiation to Neural Stem Cells


title: H3K4me3_ICeChIP-seq_HEK293_2

description:
Sample 5
Samples 5, 6 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR5_IP_mQ0_e150(Genome_Coverage).bigwig
AR5_IP_INPUT_L0_mQ0_c0_e150_HMD.bigwig


title: root LN

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cucumis sativus L. whole genome using bowtie v0.12.9 with parameters -t -k 2 -v 1 -p 16 --sam --quiet  --solexa-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol of in house. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Cucumis sativus L. v1.0/CucSat_1.0
Supplementary_files_format_and_content: he reads and RPKM number for each expressed genes of cucumber ,and for all samples (phytozome at JGI)

organism: Cucumis sativus

source_name: cucumber root

growth_protocol: cucumber seeds were germinated and grown in plastic pots containing clean sand. Plants were grown in a growth chamber under a 14/10h photoperiod at 25℃(day)and 18℃(night), and 65% humidity.

extract_protocol:
roots and leaves from plants of CK and LN were taken, a total of 0.1g tissue for each sample was frozen in liquid nitrogen and stored at -80℃ prior to use,and RNA was harvested using Trizol reagent. Illumina Gene Expression Sample Prep Kit was used with 6 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the low N stress condition (LN), plants were fed a 1 mM nitrogen solution (0.8 mM KNO3, 0.1 mM Ca(NO3)2,0.25 mM KH2PO4, 0.25 mM MgSO4,1.2 mM K2SO4, 0.8 mM KCl,0.4 mM CaCl2, 0.2 mM NaCl). Control plants (CK)were fed a complete nutrient solution containing 5 mM nitrate as nitrogen source (4 mM KNO3, 0.5 mM Ca(NO3)2, 0.25 mM MgSO4, 0.25 mM KH2PO4, 0.2 mM NaCl). All nutrient solutions contained oligoelements (24 μM H3BO3, 10 μM MnSO4, 3 μM ZnSO4, 0.9 μM CuSO4, 0.04 μM (NH4)6Mo7O24), and iron-EDTA 10 mg /L

tag: age

value: 28-day after sowing

value: root

value: low nitrogen


title: leaf LN

source_name: cucumber leaf

tag: tissue

value: leaf


title: AKI #2b (48h MSC treatment)


title: Input_ICeChIP-seq_HEK293_1

description:
Sample 4
Samples 3, 4 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR3andAR4_IP_INPUT_mQ13_c0_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_min95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_max95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_min95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_max95_CI_HMD.bigwig
AR3andAR4_INPUT_mQ13(Genome_Coverage).bigwig
AR3andAR4_INPUT_mQ13_e150(Genome_Coverage).bigwig

value: not performed


title: Treated sample 1


title: H3K4me3_ICeChIP-seq_HEK293_1

description:
Sample 3
Samples 3, 4 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR3andAR4_IP_INPUT_mQ13_c0_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_min95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_max95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_min95_CI_HMD.bigwig
AR3andAR4_IP_INPUT_mQ13_c0_e150_max95_CI_HMD.bigwig
AR3_IP_mQ13(Genome_Coverage).bigwig
AR3_IP_mQ13_e150(Genome_Coverage).bigwi


title: YBX1-LMW-CLIP-r2

description: library strategy: HITS-CLIP

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
The number of reads overlapping tRNA loci were counted and combined for the three replicates.
Genome_build: hg19
Supplementary_files_format_and_content: tRNA loci with the number of YBX1 tags mapped to each across the replicates.

extract_protocol:
48 hours post-transfection, cells were UV cross-linked and prepared as described previously (Chi SW, et al. 2009, Nature 460:479).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).


title: YBX1-LMW-CLIP-r3

description: library strategy: HITS-CLIP


title: YBX1-LMW-CLIP-r1

description: library strategy: HITS-CLIP


title: H9 rsESC

status: Public on May 06 2015

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
Region selective Human embryonic stem cell RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.primates.txt.gz

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) or human (hg19) genomes with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis.
Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file. Columns: (1) RefSeq acc, (2) chr, (3) start, (4) end, (5) strand, (6) length, (7) copies, (8) annotation, (9 to the end) FPKM.

source_name: rsESCs

growth_protocol: EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A supplemented with 20% KSR; rsEpiSCs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM; Human ESCs (H1 & H9) were grown on matrigel-coated dishes in mTeSR1 media; Human rsESCs (H1 & H9) and Chimp rsiPSCs were grown on Matrigel-coated plates in modified mTeSR1 media containing 20ng/ml FGF2 and 2.5uM IWR1; Rhesus ORMES23 rsESCs were grown on MEFs in modified N2B27 media containing 20ng/ml FGF2 and 2.5uM IWR1, MEFs were removed before RNA isolation.

extract_protocol:
Total RNA of all samples was extracted using RNeasy Mini Kit (Qiagen) per manufacturer's instructions.
RNA libraries were prepared for sequencing using strand-specific Illumina TruSeq kits per the manufacturer's instructions.

value: H9 ESC

tag: passages


title: AKI #1 (48h MV treatment)

value: SCID

value: Kidney


title: Control sample 1


title: H3_ICeChIP-seq_HEK293

description:
Sample 7
Samples 7, 8 make a set. It was calibrated using First generation barcodes (601_0708, 601_1920, 601_0102, 601_0916, 601_2122, 601_2324)
Processed data file(s):
AR6_H3vsH4_HMD.bigwig

source_name: Cell culture


title: H9 ESC

description:
Human embryonic stem cell RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.primates.txt.gz

source_name: ESCs


title: rsH1-input

description: Input for ChIP-Seq in rsH1 ESCs

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-Seq reads were aligned to the mouse (mm9) and human (hg19) genomes using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigWigs for the UCSC Genome Browser and quantify H3K4me3 and H3K27me3 levels at promoters.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig format. Initial reads were extended to approximately 150 bp and normalized coverage bedGraphs were generated using HOMER. The bedGraphToBigWig utility from the UCSC Genome Browser was then used to generate the bigWig files.

growth_protocol: Mouse EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A supplementated with 20% KSR; rsEpiSCs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM; Human H1 ESCs were grown on Matrigel-coated plates in mTeSR1 media, Human H1 rsESCs were grown on Matrigel-coated plates in customized mTeSR1 media containing 20ng/ml FGF2 and 2.5uM IWR1.

extract_protocol:
Cells were fixed with 1% formaldehyde at 37C for 10min, quenched with glycine at 37C for 5 min. Fixed cells were sonicated using Epishear (Active Motif) to achieve 200-700 size chromatin fragments. Solubilized chromatin was immunoprecipiated with antibody against H3K4me3 (Abcam 8580) and H3K27me3 (Millipore 07-449). Antibody-chromatin complexes were pulled down using Dynabeads protein A (Invitrogen), washed and then eluted. After cross-linking reversal, RNase and proteinase K treatment, immunoprecipiated DNA was purified using AMPure beads (Beckman Coulter).
ChIP DNA were end-repaired and 5' phosphorylated using T4 DNA Polymerase, Klenow and T4 Polynucleotide Kinase (Enzymatics). A single Adenine was added to 3' ends by Klenow (3-->5' exo-), and double-stranded Bioo Illumina Adapters (Bioo Scientific) were ligated to the ends of the ChIP fragments. Adapter-ligated ChIP DNA fragments were subjected to 15 cycles of PCR amplification using Q5 polymerase (NEB). AMPure beads were used to purify DNA after each step (Beckman Coulter). Pooled libraries were sequenced on the NextSeq 500 for single-end 75bp using high-output flowcell or on the HiSeq 2000 for single-end 36bp according to manufacturer’s instructions.

value: H1 derived rsESCs

value: OCT4-deltaPE-GFP x C57BL/6


title: rsH1-H3K27me3

description: ChIP-Seq for H3K27me3 in rsH1 ESCs


title: H1 ESC

value: H1 ESC


title: H1 rsESC


title: H1-H3K27me3

description: ChIP-Seq for H3K27me3 in H1 ESCs

source_name: Embryonic stem cells

value: H1 ESCs


title: rsH1-H3K4me3

description: ChIP-Seq for H3K4me3 in rsH1 ESCs


title: mESC_ChIPseq_IgG

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: J1 mESCs with ectopic 3xFlag-Tex10 transgene expression (T10F10 ESC) by transfecting piggybac transposon vectors

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome (NCBI build 37, mm9) using the bowtie (v1.0.0) program, with parameters -m 1 -v 2 --best --strata.
The duplicated reads of the aligned data were removed, then filtered reads were sorted with samtools (v0.1.19)
Tex10 ChIP-seq peaks were determined by MACS program (v.1.4.2), using input ChIP-seq as the control data, and all other parameters followed the default settings.
Bedgraph files were converted from bam files by Bedtools suite (v2.18.1) genomecov component with -bg parameter
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files of ChIP-seq reads and bed file of MACS called peaks.

growth_protocol: mESCs were grown in DMEM (GIBCO) supplemented with 15% Serum (Corning), 10^3 units/ml recombinant murine Leukemia Inhibitory Factor (LIF) (ESGRO, Millipore), 2mM L- alanyl-L-glutamine dipeptide (Glutamax; Invitrogen), 1x non-essential amino acids (Invitrogen), and 0.1mM 2-mercaptoethanol (Sigma). mESCs were passaged every two day as a single cell suspension using 0.05% trypsin/EDTA and seeded at 3.0x10^4 cells/cm^2 for routine culture. All cells were grown on 0.1% (w/v) gelatin coated tissue culture dish.

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006) by using FLAG antibody (Sigma, F1804) based IP in T10F10 ESCs.
20 µl of 435 ng/µl input and 33.8 ng/µl FLAG-ChIPed DNA were prepared for input and Tex10 ChIP-seq libraries. Massively parallel sequencing was performed with the Illumina HiSeq 2500 according to the manufactory protocol. All libraries were sequenced as 100 bp single-end reads.

tag: antibody

value: Normal Mouse IgG (Millipore 12-371)


title: mESC_ChIPseq_Input

tag: cell line


title: H1-input

description: Input for ChIP-Seq in H1 ESCs

tag: chip antibody


title: leaf CK

value: control


title: Namalwa_anti-mH2A1+NRF1_replicate1+2

city: Athens

first: Dimitris

last: Thanos

address: 4 Soranou Ephessiou

department: Basic Research II

country: Greece

institute: BIOMEDICAL RESEARCH FOUNDATION ACADEMY OF ATHENS (BRFAA)

description:
anti-mH2A1+NRF1_ChIP-seq (Re-ChIP)
Processed data file: Namalwa_anti-mH2A1+NRF1_replicate1+2.bed

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were aligned to the hg18 genome assembly using ELAND or Bowtie
Data were filtered using FastQC.
RNA-seq RPKM data were calculated by counting the  number of reads inRefSeq annotated exons.
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq: bed files were generated using in-house unix scripts.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited .txt file reporting RPKM exons values.

source_name: Namalwa B lymphoblasts

growth_protocol: HeLa and Namalwa cell lines (purchased from ATCC) were maintained in DMEM and RPMI respectively, containing 10% FBS,

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP-seq. RNA was harvested using Trizol reagent and mRNA isolated with polydT dynabeads. Strand-specific protocol was used with 5 ug of mRNA for the construction of the library.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment  and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for a controlled (qPCR estimated) cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (GA), GAIIx, or Hiseq2000) following the manufacturer's protocols.

value: Namalwa B lymphoblasts

value: anti-mH2A1 + anti-NRF1 [in house antibodies]


title: root CK


title: mESC_RNAseq_shTex10-rep2

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

extract_protocol:
RNA was extracted from ~2x10^6 cells with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the RNAeasy Plus kit (Qiagen) according to the manufacturer’s protocol.
PolyA+ RNA was prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. We prepared 20 µl of 100 ng/µl total RNA for each sample to do massively parallel sequencing with the Illumina HiSeq 2500, followed by the manufactory instructions, with a poly-A selection protocol. 100-bp single end reads were generated for each sample.

treatment_protocol: CCE mESCs were treated with control luciferase depletion (shLuci) or Tex10 depletion (shTex10) shRNAs

value: CCE

tag: knockdown


title: mESC_ChIPseq_Flag(Tex10)

value: Flag (Sigma F1804)


title: HeLa_Input_Replicate1+2

description:
Input-seq
Processed data file: HeLa_Input_Replicate1+2.bed.gz

source_name: HeLa epithelial cells

value: HeLa epithelial

value: none (input)


title: mESC_RNAseq_shTex10-rep1


title: mESC_RNAseq_shLuci-rep2

value: shLuci


title: mESC_RNAseq_shLuci-rep1


title: ORMES23 rsESC

description:
Region selective Rhesus macaque embryonic stem cells
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.primates.txt.gz

organism: Macaca mulatta

value: ESC


title: H1-H3K4me3

description: ChIP-Seq for H3K4me3 in H1 ESCs


title: HeLa_anti-mH2A1_replicate1

description:
anti-mH2A1_ChIP-seq
Processed data file: HeLa_anti-mH2A1_replicate1+2.bed

value: anti-mH2A1 [in house antibody]


title: Namalwa_anti-NRF1_replicate1+2

description:
anti-NRF1_ChiP-seq
Processed data file: Namalwa_anti-NRF1_replicate1+2.bed

value: anti-NRF1 [in house antibody]


title: rsEpiSCs Rep #2 [methylC-Seq]

data_processing:
Sequencing reads were first trimmed for adapter sequence using Cutadapt.
All cytosines in the trimmed reads were then computationally converted to thymines and mapped twice, to a converted forward strand reference and to a converted reverse strand reference both based on the mm10 reference genome.
A converted reference is created by replacing all cytosines with thymines (forward strand) or all guanines with adenines (reverse strand) in the reference FASTA file.
For mapping, we used Bowtie3 with the following options: "-S","-k 1","-m 1","--chunkmbs 3072","--best","--strata","-o 4","-e 80","-l 20", and "-n 0".
Any read that mapped to multiple locations was removed and one read from each starting location on each strand from each library was kept (i.e., clonal reads were removed).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: The processed data for the allc_<sample>_<chr>.tsv files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. These are tab-delimited files.

source_name: Region selective epiblast stem cells

extract_protocol: One µg of genomic DNA was spiked with 5 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: E5.75 derived rsEpiSCs

tag: strain/variation

value: CR x  Oct4  PE-GFP transgenic


title: EpiSCs Rep #1 [methylC-Seq]

source_name: Epiblast stem cells

value: E5.75 derived EpiSCs


title: EpiSCs Rep #2 [methylC-Seq]


title: Namalwa_anti-mH2A1_replicate2

description:
anti-mH2A1_ChIP-seq
Processed data file: Namalwa_anti-mH2A1_replicate1+2.bed


title: rsEpiSCs Rep #1 [methylC-Seq]


title: rsEpiSCs Rep #2

description:
rsEpiSCs RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-EpiSC.txt.gz

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) or human (hg19) genomes with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis.
Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text file. Columns: (1) RefSeq acc, (2) chr, (3) start, (4) end, (5) strand, (6) length, (7) copies, (8) annotation, (9 to the end) FPKM.

source_name: rsEpiSCs cells

value: E5.75 derived IS-EPIs

value: OCT4-deltaPE-GFP x C57BL/6


title: Epiblast-PP

description:
E6.5 epiblast tissue posterior-proximal RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-invivo.txt.gz

source_name: E6.5 epiblast tissue posterior-proximal

value: E6.5 epiblast

value: ICRxICR


title: Epiblast-PD

description:
E6.5 epiblast tissue posterior-distal RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-invivo.txt.gz

source_name: E6.5 epiblast tissue posterior-distal


title: EpiSCs Rep #2

description:
Epblast stem cells RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-EpiSC.txt.gz


title: Epiblast-AD

description:
E6.5 epiblast tissue anterior-distal RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-invivo.txt.gz

source_name: E6.5 epiblast tissue anterior-distal


title: rsEpiSCs Rep #1


title: EpiSCs Rep #1


title: Namalwa_anti-mH2A1_replicate1

value: Namalwa B lymphoblasts


title: Dicer WT Pach RNA

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: RNA

data_processing:
Aligned each raw file to genome using BWA v0.7.8
Used HTSeq v0.6.1 to count reads aligning to my .gtf file (annotation file)
Used edgeR v3.6.8 to assess fold change and differential expression
Genome_build: UCSC mm9, gtf transcriptome file from: https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn; used pre-built BWA indexes from https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn; miRBase v20
Supplementary_files_format_and_content: RNA-Seq: output from exact test function, with WT and cKO CPM values added in columns 6 and 7; miRNA-Seq: Normalized number of reads matching to each hairpin to the total number of reads per library (Counts Per Million = CPM).  Showed the most highly expressed miRNA isoform for each hairpin in final ouptut file.

source_name: purified pachytene spermatocytes

growth_protocol: All mice were fed ad libitum with standard laboratory rodent chow, and were maintained under controlled conditions of light and temperature, according to the strict regulations outlined and approved by the Cornell Institutional Care and Use Committee (IACUC).   Spermatocytes were isolated from adult mice about 70-80 days after birth.

extract_protocol:
Testes from adult Dgcr8 and Dicer cKOs, together with WT control littermates (day 70-80 pp) were removed, weighed and decapsulated prior to enrichment of specific spermatogenic cell types using the STA-PUT method based on separation by cell diameter/density at unit gravity (Bellvé, 1993). Purity of resulting fractions was determined by microscopy based on cell diameter and morphology. Pachytene cells were approximately 90% pure, with residual possible contamination from spermatocytes of slightly earlier or later developmental stages. Leptotene and zygotene cells were isolated in combination, and were >90% pure. Neither pachytene nor leptotene/zygotene fractions exhibited evidence of any contaminating somatic cells. RNA was extracted from these STA-PUT purified cells using TRIzol (Life Technologies), and was used as the source material for mRNA sequencing, small RNA sequencing, and qRT-PCR.
Illumina kits were used for preparation of both RNA-Seq (Illumina TruSeq RNA Seq)and Small RNA-Seq libraries (Illumina TruSeq Small RNA Seq).

treatment_protocol: Female mice carrying homozygous floxed alleles for either Dgcr8Fl/Fl (Dr. Rui Yi, University of Colorado, Boulder) or DicerFl/Fl (B6;129S7-Dicer1tm1Smr/J, Jax Stock: 012284) were first crossed to male mice carrying the Ddx4-cre transgene (FVB-Tg(Ddx4-cre)1Dcas/J, Jax Stock: 006954) to generate the desired Dgcr8Fl/+cre+ and DicerFl/+ cre+ breeder males, which were then crossed to Dgcr8Fl/+cre- and  DicerFl/+ cre- breeder females, respectively. These crosses generated the experimental cohorts, which included male mice displaying the Dgcr8Fl/Δ cre+ and DicerFl/Δ cre+ genotypes, which were homozygous knockouts in the targeted germline cell types (referred to as conditional knockouts, cKO, Dgcr8Δ/Δ cre+ and DicerΔ/Δ cre+), together with wild-type (WT: +/+ cre+, +/+ cre-, or Fl/+ cre-) littermates. Genotypes were confirmed using genomic DNA isolated from tail snips and PCR assays specific to the wild-type, floxed, and deleted alleles.

value: testis

value: C57BL/6 X FVB

value: pachytene spermatocytes

tag: genotype

value: wild-type littermate

tag: library prep method

value: Illumina TruSeq RNA Seq


title: Dgcr8 cKO Pach RNA

description: RNA

value: Dgcr8 germline conditional knockout


title: Dicer cKO L/Z RNA

description: RNA

value: leptotene/zygotene spermatocytes

value: Dicer germline conditional knockout


title: Dgcr8 WT Pach RNA

description: RNA


title: Epiblast-AP

description:
E6.5 epiblast tissue anterior-proximal RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-invivo.txt.gz

source_name: E6.5 epiblast tissue anterior-proximal


title: Dicer cKO Pach RNA

description: RNA


title: HeLa_anti-mH2A1_replicate2

value: HeLa epithelial

value: anti-mH2A1 [in house antibody]


title: Dicer WT L/Z RNA

description: RNA


title: Dgcr8 cKO L/Z RNA

description: RNA


title: Dgcr8 WT L/Z RNA

description: RNA


title: Dgcr8 cKO Pach SMALL RNA

description: small RNA

data_processing:
Trimmed off adapters and filtered out low-quality reads (ones with too many N's, or which failed Illumina's Y/N overall quality metric) - custom python script.
Aligned reads to genome using Bowtie 0.12.7
Aligned reads to miRNA hairpin sequences from miRBase v20 using a custom script.
Genome_build: UCSC mm9, gtf transcriptome file from: https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn; used pre-built BWA indexes from https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn; miRBase v20
Supplementary_files_format_and_content: RNA-Seq: output from exact test function, with WT and cKO CPM values added in columns 6 and 7; miRNA-Seq: Normalized number of reads matching to each hairpin to the total number of reads per library (Counts Per Million = CPM).  Showed the most highly expressed miRNA isoform for each hairpin in final ouptut file.

value: Illumina TruSeq Small RNA Seq


title: Dicer WT Pach SMALL RNA

description: small RNA


title: Dicer cKO Pach SMALL RNA

description: small RNA


title: Dicer WT L/Z SMALL RNA

description: small RNA


title: Dicer cKO L/Z SMALL RNA

description: small RNA


title: Dgcr8 WT Pach SMALL RNA

description: small RNA


title: Dgcr8 WT L/Z SMALL RNA

description: small RNA


title: Namalwa_RNA-seq

description:
RNA-seq
Processed data file: Namalwa_RNA-seq_RPKM.txt.gz


title: rsEpiSCs-H3K27me3

description: ChIP-Seq for H3K27me3 in rsEpiSCs

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-Seq reads were aligned to the mouse (mm9) and human (hg19) genomes using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigWigs for the UCSC Genome Browser and quantify H3K4me3 and H3K27me3 levels at promoters.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig format. Initial reads were extended to approximately 150 bp and normalized coverage bedGraphs were generated using HOMER. The bedGraphToBigWig utility from the UCSC Genome Browser was then used to generate the bigWig files.

source_name: rsEpiSCs

value: E5.75 derived rsEpiSCs


title: EpiSCs-input

description: Input for ChIP-Seq in Epiblast stem cells

value: E5.75 derived EpiSCs


title: QKI5

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5

department: Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

data_processing:
Torrent Suite and Ion Reporter™ software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mirBase release 19 hsa miRNA library using bowtie v0.12.3 with parameters -v 2 -M 1 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: K562 cells transduced with QKI5-overexpressing lentivirus

growth_protocol: K562 cells are maintained in 1640 medium with 10% FBS

extract_protocol:
Small RNA was isolated from total RNA with the mirVana™ miRNA Isolation Kit
Small RNA libraries were prepared with the Ion Total RNA-Seq Kit v2 (Life Technologies), and then were sequenced on the Ion Torrent Proton™ System using Ion PI™ Chips.

treatment_protocol: lentivirus transduction

value: erythroleukemia


title: EpiSCs-H3K4me3

description: ChIP-Seq for H3K4me3 in Epiblast stem cells

value: OCT4-deltaPE-GFP x C57BL/6


title: Con

source_name: K562 cells transduced with GFP lentivirus


title: rsEpiSCs-input

description: Input for ChIP-Seq in rsEpiSCs


title: Namalwa_Input_Replicate1

description:
Input-seq
Processed data file: Namalwa_Input_Replicate1+2.bed

value: none (input)


title: B3_S1

city: Pretoria

first: Oleg

last: Reva

address: Lynnwood Rd., Hillcrest

department: Biochemistry

country: South Africa

institute: University of Pretoria

data_processing:
Basecalls performed using IB MiSeq
Using CLC Genomics Workbench 7.0.3 software, MiSeq 500 reads were aligned against DNA sequences of all predicted CDS in the complete genome sequence of Bacillus atrophaues UCMB-5137 (APIW01000000)
Differential gene expression statistics was calculated for experiment-versus-control samples using EDGE, Baggerley's and t-test algorithms implemented in CLC Genomics Workbench 7.0.3
Supplementary_files_format_and_content: Tab separated text file (locus_tag read_count)

organism: Bacillus atrophaeus

source_name: Bacterial cells

growth_protocol: Bacterial cultures were inoculated from a frozen stock culture and incubated at 37°C overnight on solid LB medium. A colony from overnight culture was inoculated in 1C medium (with 0.1% glucose) at 24°C for 14 hours with shaking at 180 rpm. An aliquot from the overnight culture was added to a new 1C medium (with 0.1% glucose), in control and supplemented with 0.25 mg/ml maize root exudate in experiment. Composition of 1 C medium (0.7%w/v pancreatic digest of casein [MERCK], 0.3%w/v papain digest of soya flour[MERCK], 0.5%w/v NaCl [MERCK],) 0.1% glucose [MERCK]. Conical flasks with cultures in control and experiment were grown at 24°C for 14.30 h to achieve a transition to stationary  phase characterized by culture medium density (or opacity) of OD600= 1.0 units.

extract_protocol:
RNA was isolated using ZR Fungal/ Bacteria RNA Mini Prep kit from Zymo research Corp. according to manufacturer’s instruction. The concentration and quality of RNA was checked by NanoDrop then Ribolock Ribonuclease inhibitor [Thermo Scientific] was added to prevent RNA degradation.
cDNA was extracted from total RNA and sequenced using MiSeq 500 Illumina platform in Inqaba (Pretoria, South Africa). Library was prepared by MiSeq Library Prep protocol. rRNA reduction per library was performed with Ribo-Zero.
IB MiSeq 500 cycles, approx. 6 GB data

treatment_protocol: Bacterial cells were collected for total RNA extraction by mixing with killing buffer that has been previously frozen. Killing buffer was kept on ice during mixing with bacteria culture, 15 ml of the bacteria culture was mixed with 7.5 ml killing buffer. Composition of killing buffer (20 mM Tris-HCl [BDH Laboratory supplies], 5 mM MgCl2[MERCK], 20 mM NaN3[SIGMA], pH 7.5). The mixture was centrifuged at 5,000 rpm for 3 minutes at room temperature. The pellet was washed with 1 ml killing buffer and immediately frozen at -80°C until RNA extraction.

tag: condition

value: experiment

tag: media

value: 1C liquid medium with maize root exudate


title: C3_S3

tag: strain

value: control

value: 1C control medium


title: B_S4


title: EpiSCs-H3K27me3

description: ChIP-Seq for H3K27me3 in Epiblast stem cells

tag: cell type


title: C_S5


title: C2_S2


title: ESC_ESETWT_Input (ctrl for ESET KO)

status: Public on May 05 2015

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: unknown

data_processing:
Raw were aligned to the mouse genome version mm9 with Bowtie using -M 1 --best parameters for inclusive alignment of non-unique reads
Wig files were created from BAM files using IGVTools count function
Wig files were scaled to a genome-wide average read density of 1 using java-genomic-toolkit wigmath.Scale function  made using igvtools and normalized based on read counts
Genome_build: mm9
Supplementary_files_format_and_content: wig files of normalized read density including non-uniquely mappable reads

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina protocol.

value: unknown

value: no antibody

tag: ChIP

value: crosslink

value: ESC

tag: genotype/variation

value: ESET WT


title: ESC_ESETWT_H33-H3K9me3 (ctrl for ESET KO)

description: unknown


title: ESC_ESETKO_Input

description: unknown

value: ESET KO


title: ESC_ESETKO_H33-H3K9me3

description: unknown


title: ESC_DAXXnull_Input-2

description:
SVEV DAXX KO
biological replicate of GSM1429930

value: SVEV

value: native

value: DAXX KO


title: Dgcr8 cKO L/Z SMALL RNA

description: small RNA

value: testis

value: C57BL/6 X FVB

value: leptotene/zygotene spermatocytes

value: Dgcr8 germline conditional knockout

value: Illumina TruSeq Small RNA Seq


title: ESC_ESETWT_H33 (ctrl for ESET KO)

description: unknown


title: ESC_KAP1WT_Input (ctrl for KAP1 KO)

description: C57Bl/6 KAP1 loxP/loxP

value: KAP1 WT


title: ESC_KAP1KO_Input

description: C57Bl/6 KAP1 KO

value: KAP1 KO


title: Chimp rsiPSC

description:
Region selective Chimpanzee induced pluripotent stem cells
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.primates.txt.gz

organism: Pan troglodytes

source_name: rsiPS

value: iPS


title: ESC_KAP1KO_H33

description: C57Bl/6 KAP1 KO


title: rsEpiSCs-H3K4me3

description: ChIP-Seq for H3K4me3 in rsEpiSCs

value: E5.75 derived rsEpiSCs

value: OCT4-deltaPE-GFP x C57BL/6


title: ESC_KAP1WT_H33 (ctrl for KAP1 KO)

description: C57Bl/6 KAP1 loxP/loxP

value: crosslink


title: ESC_ATRXnull_Input

description: 129/C57Bl/6 ATRX KO

value: no antibody

value: ESC

value: ATRX KO


title: ESC_ATRXWT_Input (ctrl for ATRX KO)

description: 129/C57Bl/6 ATRX loxP

value: ATRX WT


title: ESC_ATRXnull_nInput

description: 129/C57Bl/6 ATRX KO

value: native


title: ESC_ATRXWT-H33BHA_HA (ctrl for ATRX KO)

description: 129/C57Bl/6 H3.3B-HA

value: anti-HA (12CA5)

value: ATRX WT-H3.3BHA_HA


title: ESC_ATRXnull_H3K9me3

description: 129/C57Bl/6 ATRX KO

value: anti-H3K9me3 (ab8898)


title: ESC_ATRXWT_H3K9me3 (ctrl for ATRX KO)

description: 129/C57Bl/6 ATRX loxP


title: ESC_ATRXnull-H33BHA_H33

description: 129/C57Bl/6 H3.3B-HA ATRX KO

value: ATRX KO-H3.3BHA


title: ESC_ATRXWT-H33BHA_H33 (ctrl for ATRX KO)

description: 129/C57Bl/6 H3.3B-HA

value: ATRX WT-H3.3BHA


title: ESC_ATRXWT_nInput (ctrl for ATRX KO)

description: 129/C57Bl/6 ATRX loxP


title: ESC_ATRXnull-H33BHA_HA

description: 129/C57Bl/6 H3.3B-HA ATRX KO

value: ATRX KO-H3.3BHA_HA


title: ESC_DAXXWT_Input (ctrl for DAXX KO)

description: SVEV

value: SVEV

value: DAXX WT


title: ESC_ATRXWT_H33 (ctrl for ATRX KO)


title: ESC_DAXXWT_H3K9me3 (ctrl for DAXX KO)

description: SVEV


title: ESC_ATRXnull_H33

description: 129/C57Bl/6 ATRX KO


title: ESC_ESETKO_H33

description: unknown

value: unknown

value: ESET KO


title: ESC_H33KO1_nH3K9me3

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO2_nH3K9me3

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO2_nInput

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO1_nInput

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33WT_nH3K9me3  (ctrl for KO)

value: H3.3 WT


title: ESC_H33KO1-H32-HA (addback)

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO2_KAP1-2

description: 129/C57Bl/6 H3.3 KO

value: anti-KAP1 (ab10483)

value: crosslink


title: ESC_H33KO1_KAP1-1

description: 129/C57Bl/6 H3.3 KO

value: anti-KAP1 (ab22553)

value: ESC


title: ESC_H33WT_KAP1-1 (ctrl for KO)


title: ESC_H33KO2_KAP1-1

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33WT_KAP1-2 (ctrl for KO)


title: ESC_H33KO1-H33-HA (addback)

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO1_gDNA

description: 129/C57Bl/6 H3.3 KO

value: no antibody


title: ESC_H33KO1_H33 (ctrl for H3.3 Ab)

description: 129/C57Bl/6 H3.3 KO


title: ESC_DAXXnull_H3K9me3

description: SVEV DAXX KO

value: native

value: DAXX KO


title: ESC_H33WT_H33


title: ESC_H33WT_gDNA (ctrl for KO)


title: ESC_DAXXWT_H33-HA (ctrl for DAXXnull)

description: SVEV

value: anti-HA (12CA5)

value: DAXXWT


title: ESC_DAXXnull_H33-HA

description: SVEV DAXX KO


title: ESC_H33KD1-H32-HA (addback)

description: C57Bl/6 H3.3B-KO + H3.2-HA


title: ESC_H33KO2_DAXX

description: 129/C57Bl/6 H3.3 KO

value: anti-DAXX (sc-7512)

value: H3.3 KO


title: ESC_H33KO1_DAXX

description: 129/C57Bl/6 H3.3 KO


title: ESC_DAXXnull_Input

description:
SVEV DAXX KO
biological replicate of GSM1555211


title: ESC_H33KO2_Input

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33WT_Input (ctrl for KO)


title: ESC_H33WT_nInput (ctrl for KO)


title: ESC_H33KO1_Input

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33WT_DAXX (ctrl for KO)


title: ESC_H33KD1-H33-HA (addback)

description: C57Bl/6 H3.3B-KO + H3.3-HA


title: ESC_H33KO2_H3

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO1_H3

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33WT_H3 (ctrl for KO)


title: ESC_H33KO1_KAP1-2

description: 129/C57Bl/6 H3.3 KO


title: ESC_H33KO1_H3K9me3

description: 129/C57Bl/6 H3.3 KO

value: anti-H3K9me3 (ab8898)


title: ESC_H33KO2_H3K9me3

description: 129/C57Bl/6 H3.3 KO


title: ESC_Control_Input (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_H33WT_H3K9me3  (ctrl for KO)


title: ESC_H33KD1_nInput

description: C57Bl/6 H3.3B-KO


title: ESC_H33KD1_H312

description: C57Bl/6 H3.3B-KO

value: anti-H3.1/2 (antiserum)


title: ESC_Control_nInput (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_Control_H3 (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_H33KD1_H3

description: C57Bl/6 H3.3B-KO


title: ESC_Control_H312 (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_H33KD1_H33

description: C57Bl/6 H3.3B-KO

value: anti-H3.3 (antiserum)


title: ESC_Control_H33 (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_H33KD1_H3K9me3

description: C57Bl/6 H3.3B-KO


title: ESC_Control_H3K9me3 (ctrl for KD1)

description: C57Bl/6 H3.3B-HA


title: ESC_H33KO1_RNA-seq

data_processing:
for gene expression analysis, reads were aligned to mm10 using TopHat v2.0.9 (-T -G --no-novel-juncs) and Bowtie v2.1.0 using 100bp segment length
differential gene expression analysis was performed using cufflinks/cuffdiff v2.2.0
for coverage file, reads were aligned to mm9 using bowtie 4.1.2 using –M 1 --best
wig file was created from bam file using igvtools
Genome_build: mm9
Supplementary_files_format_and_content: coverage file in wiggle format

growth_protocol: ESCs (129xC57Bl/6J background) were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Total RNA was extracted from embryonic stem cells using the Qiagen Rneasy kit. 4 ug of RNA was used for library preparation.
Libraries were constructed according to the Illumina Tru-Seq protocol

value: Embryonic stem cells


title: ESC_WT_RNA-seq (control for KO)

value: WT


title: ESC_H33KO2_RNA-seq


title: cDC 1

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

description: DCs were obtained ex vivo from collagenase-digested spleens. The cDC population was defined as CD11c+ CD4+ SiglecH-.

data_processing:
Base calling
Barcode deconvolution and stripping
Alignment to mature miRNA database (miRBase)
Alignment of remaining reads to miRNA precursor database (miRBase)
Read abundance counting and normalization to library read size
Genome_build: Genome_build: miRBase 17
Supplementary_files_format_and_content: miRNA_processed_expression_atlas.xls containing miRNA identity and counts

source_name: Conventional dendritic cell

extract_protocol:
Chloroform (1:5 vol/vol) was added to cell suspensions in TRI homogenate (thawed on ice) before vigorously mixing.  This was allowed to settle for 15 minute at 4oC. Phases were then separated by centrifugation 15 minutes at 4oC. An ethanol precipitation was then performed by adding co-precipitate (e.g. glycoblue (Invitrogen)) to the removed aqueous phase prior to addition of two times volume of ethanol. The solution is then precipitated at -80oC for 25 minutes before centrifugation for 15 minutes at 4oC. The supernatant is then discarded and the pellet washed in 70% ethanol. All supernatant is removed following a final centrifugation step and the pellet resuspended in RNase-free water.
microRNA libraries were constructed as previously described (Chong et al., 2010), adapted from (Hafner et al, 2008). Briefly, total RNA was resolved on a polyacrylamide/urea gel and the 19- to 24- nt small RNA fraction was isolated after each of two adaptor ligations. This fraction was tracked on the gel by the inclusion of radiolabeled 19- and 24-nt synthetic oligoribonucleotides. The first ligation, to the 3’ end of the RNA library, ligated a 5’ preadenylated and 5’-hydroxyl-blocked universal adaptor (miRNA cloning linker 1; Integrated DNA Technologies) facilitated by an RNA ligase 2 truncated mutant (1–249) K227Q (Hafner et al. 2008) in the absence of ATP. An Illumina-compatible adapter was then ligated to the 5’ end of the library, which subsequently allowed for deep sequencing on the Illumina GAII platform. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5’ end of each library. The nature of these two ligations dictate that only small RNAs with 5’ phosphate and 3’ hydroxyl termini were cloned.

treatment_protocol: Progenitor populations were sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. The HSC population was defined as Lin- c-Kit+ Sca-1+ Flt3R-. CMPs were defined as c-Kit- Sca-1+ FcR- CD34+, while CLPs were c-Kitint Sca-1+ IL7R+ Flt3R+. CDPs were identified by expression of c-Kitint Sca-1- M-CSFR+ Flt3R+. Mature DCs were obtained ex vivo from collagenase-digested spleens. The cDC population was defined as CD11c+ CD4+ SiglecH- while pDCs were CD11c int SiglecH+ CD11b-.

tag: tissue origin

value: Spleen

value: Conventional dendritic cell

tag: barcode label

value: AGCCTAAGCT

tag: molecule subtype

value: 19-24nt RNA


title: pDC 1

description: DCs were obtained ex vivo from collagenase-digested spleens. pDCs were CD11c int SiglecH+ CD11b-.

source_name: Plasmacytoid dendritic cell

value: Plasmacytoid dendritic cell

value: TCAACGGTAG


title: cDC 2


title: CLP 1

description: Sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. CLPs were c-Kitint Sca-1+ IL7R+ Flt3R+.

source_name: Common Lymphoid Precursor

value: Bone marrow

value: Common Lymphoid Precursor


title: Flt3L cDC 2

description: cDCs derived by culturing whole bone marrow with 200ng/mL Flt3L (in house) for 8 days. The cDC population was defined as CD11c+ CD4+ SiglecH-.

source_name: Flt3L generated whole bone marrow cDC

value: Flt3L culture

value: Flt3L generated whole bone marrow cDC


title: pDC 2


title: CDP 2

description: Sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. CDPs were identified by expression of c-Kit int Sca-1- M-CSFR+ Flt3R+

source_name: Common dendritic cell precursor

value: Common dendritic cell precursor

value: GTGCATCCTA


title: CMP 1

description: Sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. CMPs were defined as c-Kit- Sca-1+ FcR- CD34+

source_name: Common Myeloid Precursor

value: Common Myeloid Precursor

value: CATTGTTAGC


title: CDP 1


title: HSC 2

description: Sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. The HSC population was defined as Lin- c-Kit+ Sca-1+ Flt3R-.

source_name: Bone marrow stem cell

value: Bone marrow stem cell


title: CMP 2


title: Flt3L cDC 1


title: CLP 2