title: Thiolutin_rep1

description:
Sample 27
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx

value: 3 ug/mL thiolutin, 45min


title: rsc8-21-37C_rep1

status: Public on Jun 25 2015

type: SRA

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

description:
Sample 70
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx

library_source: genomic

data_processing:
library strategy: Micro-C
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to sacCer3 genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate interaction matrix.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: readme.txt file contains additional description of how each processed data file was generated.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: 100mL yeast culture were grown to midlog phase ~OD 0.55 in YPD media at 30 C.

extract_protocol:
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads.

treatment_protocol: Yeast cells were fixed with 3% formaldehyde for 15 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted, spheroplasted with Zymolyase, and treated with a level of MNase yielding >95% mononucleosom. After stopping MNase, chromatin supernatant was dephosphorylated using Antarctic phosphatase. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Crosslinked chromatin was diluted into 10 mL and treated with T4 DNA ligase. After heat inactivation, chromatin was concentrated to 250uL, and treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated for 65 C overnight.

tag: strain

value: rsc8-21, ts-allele mutant

tag: treatment

tag: media

value: YPD


title: Diamide_rep2

description:
Sample 26
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx

value: 1.5 mM diamide, 30 min


title: Diamide_rep1-2

description:
Sample 25
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H4R23A_rep2-2

description:
Sample 42
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: Thiolutin_rep2

description:
Sample 28
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: W303_rep1-2

description:
Sample 30
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: Diamide_rep1

description:
Sample 24
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-No_crosslinking

description:
Sample 22
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-No_ligation

description:
Sample 23
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741-32C

description:
Sample 21
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep18

description:
Sample 20
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep17

description:
Sample 19
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep16

description:
Sample 18
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: input DNA_+Tam_R2

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: No. 199, Ren'ai Road

country: China

institute: Suzhou Medical College of Soochow University

data_processing:
Basecalls performed using Off-Line Basecaller 1.9.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.1.0 with the following setting: broad, extsize (146), q-value (0.01)
Genome_build: mm9
Supplementary_files_format_and_content: bigwiggle files were generated by MACS2, the score represents number of bp fall into the single base pair region.

organism: Mus musculus

source_name: input DNA_+Tam

growth_protocol: The iKO ES cells were cultured feeder-free in 60 mm or 100 mm tissue culture dishes at 37 C with 5% CO2. The culture surface was pre-coated with 0.1% (w/v) gelatin in PBS. The ES cell culture medium consists of Dulbecco's modified Eagle's medium supplemented with 15% fetal bovine serum, 1 mM glutamine, 0.1 mM β-mercaptoethanol, 0.1 mM non-essential amino acid, 50 U/mL penicillin plus 50 µg/mL streptomycin, and 1000 units ESGRO (LIF).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For ChIP-seq libraries, 10 ng of input chromatin DNA or ChIP DNA were processed using the ChIP-seq sample prep kit (Illumina). Gel-purified ChIP-seq library DNA was further purified by phenol-chloroform extraction and ethanol precipitation, and processed for cluster generation, 15-cycle sequencing, and sequence analysis using Illumina Hiseq.

treatment_protocol: To induce the ablation of Setdb1, cells were treated with 2.5 μM tamoxifen (Tam) (Sigma), with DMSO used as the solvent control

tag: genotype/variation

value: inducible SetDB1 KO

tag: cell type

value: ES cells

tag: treated with

value: 2.5 μM tamoxifen (Tam)

tag: chip antibody


title: BY4741_rep11

description:
Sample 13
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep15

description:
Sample 17
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep10

description:
Sample 12
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep13

description:
Sample 15
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep14

description:
Sample 16
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep12

description:
Sample 14
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep9-2

description:
Sample 11
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H3K27me3_ChIPSeq+Tam_R2

value: H3K27me3 (Millipore:07-449)


title: input DNA_noTam_R3

source_name: input DNA_noTam

value: none (noTam)


title: Pool_Col_Cvi_2_NS

city: Versailles

first: Francisco

middle: A.

last: Cubillos

address: Route de St Cyr

country: France

institute: INRA-IJPB

library_source: transcriptomic

data_processing:
Aligment was peformed using Palmapper v.0.4 using Col-0 and seudo-Cvi-0 genomes as references
Reads were called as either Col or Cvi based on SNP data from the re-sequencing of Cvi-0
Genome_build: TAIR10
Supplementary_files_format_and_content: allele specific expression ASE of Col-0 vs. Cvi-0

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 3-week old plants

growth_protocol: Samples were grown in the Phenoscope platform for 21 days under short day periods.

extract_protocol:
RNeasy Plant mini kit (Qiagen kit #74904)
Libraries were prepared according to Illumina's protocol for HiSeq2000

treatment_protocol: Water was automatically controlled and images were taken every day.

value: Control

tag: sample type

value: pool of plants

tag: age

value: 3 wk

tag: genetic background

value: Pool of equal amounts of cDNA from parental Col-0 and Cvi-0 plants

tag: tissue

value: whole plant


title: input DNA_noTam_R2


title: BY4741_rep6-2

description:
Sample 7
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep7

description:
Sample 8
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep6

description:
Sample 6
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: BY4741_rep9

description:
Sample 10
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H3K27me3_ChIPSeq_noTam_R2


title: BY4741_rep5

description:
Sample 5
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: input, hMSC extract for ChIP-Seq

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
Reads were mapped to the hg19 genome using Bowtie. Ambiguous alignments were excluded for TF ChIP-seq tracks. For H3K27Ac, reads were included with alignment locations of up to 3 possible loci.
Redundant reads were removed from TF ChIP-seq datasets using the makeTagDirectory script in HOMER. Redundant reads were preserved only for the H3K27Ac dataset.
Bed files for TF ChIP-Seq peaks were generated using the FindPeaks script in HOMER.
Bedgraph file for H3K27Ac was generated using the makeUCSCfile script in HOMER.
RNAPII.peaks.bed file was produced using a slope-based feature detection algorithm in Galaxy, see Cohen et al. ELife for details.
Input bias regions were manually curated from genomic regions showing strong ChIP enrichment on the genome browser independently of ChIP antibody.
Genome_build: hg19
Supplementary_files_format_and_content: 1 )TF ChIP-seq peak files in BED format 2) H3K27Ac in BEDGRAPH format

organism: Homo sapiens

source_name: hMSC

growth_protocol: hMSCs were cultured in low glucose DMEM supplemented with 1% glutamine, and 10% FBS. For cell seeding density experiments, low cell density refers to 3000 cells/cm2, and high density to 35000 cells/cm2.

extract_protocol:
Cell pellets were prepared from 1.8x106 cells, crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. Cells were harvested from 10 or 15cm dishes in DPBS using a cell scraper. To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: hMSCs were treated with DMI adipogenic induction medium for 24 hours (RNAPII) or 6 hrs (CEBPb, GR).

value: Human Mesenchymal Stem Cells


title: BY4741_rep3-2

description:
Sample 4
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H3K27me3_ChIPSeq_+Tam

data_processing:
Basecalls performed using Off-Line Basecaller 1.9.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.0.10 with the following setting: broad, shift-size (73), q-value (0.01)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated by MACS2, the score represents number of bp fall into the single base pair region

growth_protocol: The iKO ES cells were cultured feeder-free in 60 mm or 100 mm tissue culture dishes at 37 ºC with 5% CO2. The culture surface was pre-coated with 0.1% (w/v) gelatin in PBS. The ES cell culture medium consists of Dulbecco's modified Eagle's medium supplemented with 15% fetal bovine serum, 1 mM glutamine, 0.1 mM β-mercaptoethanol, 0.1 mM non-essential amino acid, 50 U/mL penicillin plus 50 µg/mL streptomycin, and 1000 units ESGRO (LIF).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For ChIP-seq libraries, 10 ng of input chromatin DNA or ChIP DNA were processed using the ChIP-seq sample prep kit (Illumina). Gel-purified ChIP-seq library DNA was further purified by phenol-chloroform extraction and ethanol precipitation, and processed for cluster generation, 15-cycle sequencing, and sequence analysis using Illumina Hiseq performed at the Beijing Genomics Institute (BGI)

value: inducible SetDB1 KO  ES cell


title: input DNA_+Tam

value: none (input)


title: H3K9me3_ChIPSeq_noTam

value: H3K9me3 (Active Motif:39161)


title: BY4741_rep3-1

description:
Sample 3
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: H3K27me3_ChIPSeq_noTam


title: ChIP-seq, H3K27Ac_HighDensity_noDMI

value: H3K27Ac, ab4729, Abcam


title: BY4741_rep1

description:
Sample 1
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx

value: YPD


title: ChIP-seq, CEBPb_HighDensity_DMI

value: CEBPb, sc-150, Santa Cruz


title: BY4741_rep8

description:
Sample 9
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: ChIP-seq, CEBPb_LowDensity_DMI


title: SpeciesMix_FluidigmC1 Cells 192

status: Public on Jun 24 2015

city: Boston

first: Evan

last: Macosko

state: MA

address: 77 Avenue Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

data_processing:
Base calls performed with bcl2fastq2.15
Read 1was aligned with Star v2.4.0
Genome_build: mm10 and hg19 (dual reference)
Supplementary_files_format_and_content: bam file

organism:
Homo sapiens
Mus musculus

source_name: HEK and 3T3 mix

extract_protocol:
Single cell suspensions were processed through C1 according to manufacturer's instructions
Libraries were prepared from C1-mediated whole transcriptome amplifications using Nextera XT (Illumina)

tag: cell line

value: HEK and 3T3 mix


title: SpeciesMix_FluidigmC1 Cells 191


title: SpeciesMix_FluidigmC1 Cells 190


title: input DNA_noTam


title: SpeciesMix_FluidigmC1 Cells 189


title: SpeciesMix_FluidigmC1 Cells 187


title: SpeciesMix_FluidigmC1 Cells 183


title: SpeciesMix_FluidigmC1 Cells 188


title: SpeciesMix_FluidigmC1 Cells 180


title: SpeciesMix_FluidigmC1 Cells 179


title: SpeciesMix_FluidigmC1 Cells 186


title: SpeciesMix_FluidigmC1 Cells 185


title: SpeciesMix_FluidigmC1 Cells 184


title: ChIP-seq, GR_HighDensity_DMI

value: GR, PA1-511A, Pierce; sc-1004, Santa Cruz


title: SpeciesMix_FluidigmC1 Cells 176


title: SpeciesMix_FluidigmC1 Cells 175


title: SpeciesMix_FluidigmC1 Cells 173


title: SpeciesMix_FluidigmC1 Cells 178


title: BY4741_rep2

description:
Sample 2
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
Boundary calls for wild-type yeast.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for all datasets with multiple replicates.xlsx


title: SpeciesMix_FluidigmC1 Cells 177


title: SpeciesMix_FluidigmC1 Cells 171


title: SpeciesMix_FluidigmC1 Cells 181


title: SpeciesMix_FluidigmC1 Cells 182


title: SpeciesMix_FluidigmC1 Cells 167


title: SpeciesMix_FluidigmC1 Cells 172


title: SpeciesMix_FluidigmC1 Cells 162


title: SpeciesMix_FluidigmC1 Cells 166


title: SpeciesMix_FluidigmC1 Cells 174


title: SpeciesMix_FluidigmC1 Cells 164


title: SpeciesMix_FluidigmC1 Cells 170


title: SpeciesMix_FluidigmC1 Cells 158


title: SpeciesMix_FluidigmC1 Cells 160


title: SpeciesMix_FluidigmC1 Cells 154


title: SpeciesMix_FluidigmC1 Cells 169


title: SpeciesMix_FluidigmC1 Cells 168


title: SpeciesMix_FluidigmC1 Cells 165


title: SpeciesMix_FluidigmC1 Cells 151


title: SpeciesMix_FluidigmC1 Cells 161


title: SpeciesMix_FluidigmC1 Cells 150


title: SpeciesMix_FluidigmC1 Cells 159


title: SpeciesMix_FluidigmC1 Cells 163


title: SpeciesMix_FluidigmC1 Cells 148


title: SpeciesMix_FluidigmC1 Cells 146


title: SpeciesMix_FluidigmC1 Cells 155


title: SpeciesMix_FluidigmC1 Cells 145


title: SpeciesMix_FluidigmC1 Cells 157


title: SpeciesMix_FluidigmC1 Cells 156


title: SpeciesMix_FluidigmC1 Cells 141


title: SpeciesMix_FluidigmC1 Cells 153


title: SpeciesMix_FluidigmC1 Cells 139


title: SpeciesMix_FluidigmC1 Cells 152


title: SpeciesMix_FluidigmC1 Cells 140


title: SpeciesMix_FluidigmC1 Cells 147


title: SpeciesMix_FluidigmC1 Cells 144


title: SpeciesMix_FluidigmC1 Cells 143


title: SpeciesMix_FluidigmC1 Cells 135


title: SpeciesMix_FluidigmC1 Cells 133


title: SpeciesMix_FluidigmC1 Cells 134


title: SpeciesMix_FluidigmC1 Cells 138


title: SpeciesMix_FluidigmC1 Cells 132


title: SpeciesMix_FluidigmC1 Cells 142


title: SpeciesMix_FluidigmC1 Cells 137


title: SpeciesMix_FluidigmC1 Cells 136


title: SpeciesMix_FluidigmC1 Cells 149


title: SpeciesMix_FluidigmC1 Cells 127


title: SpeciesMix_FluidigmC1 Cells 130


title: SpeciesMix_FluidigmC1 Cells 126


title: SpeciesMix_FluidigmC1 Cells 129


title: SpeciesMix_FluidigmC1 Cells 124


title: SpeciesMix_FluidigmC1 Cells 125


title: SpeciesMix_FluidigmC1 Cells 121


title: SpeciesMix_FluidigmC1 Cells 122


title: SpeciesMix_FluidigmC1 Cells 128


title: SpeciesMix_FluidigmC1 Cells 118


title: SpeciesMix_FluidigmC1 Cells 115


title: SpeciesMix_FluidigmC1 Cells 117


title: SpeciesMix_FluidigmC1 Cells 123


title: SpeciesMix_FluidigmC1 Cells 113


title: SpeciesMix_FluidigmC1 Cells 131


title: SpeciesMix_FluidigmC1 Cells 120


title: SpeciesMix_FluidigmC1 Cells 116


title: SpeciesMix_FluidigmC1 Cells 119


title: SpeciesMix_FluidigmC1 Cells 114


title: SpeciesMix_FluidigmC1 Cells 108


title: SpeciesMix_FluidigmC1 Cells 112


title: SpeciesMix_FluidigmC1 Cells 107


title: SpeciesMix_FluidigmC1 Cells 110


title: SpeciesMix_FluidigmC1 Cells 106


title: SpeciesMix_FluidigmC1 Cells 111


title: SpeciesMix_FluidigmC1 Cells 104


title: SpeciesMix_FluidigmC1 Cells 109


title: SpeciesMix_FluidigmC1 Cells 105


title: SpeciesMix_FluidigmC1 Cells 103


title: SpeciesMix_FluidigmC1 Cells 101


title: SpeciesMix_FluidigmC1 Cells 100


title: SpeciesMix_FluidigmC1 Cells 102


title: SpeciesMix_FluidigmC1 Cells 97


title: SpeciesMix_FluidigmC1 Cells 95


title: SpeciesMix_FluidigmC1 Cells 98


title: SpeciesMix_FluidigmC1 Cells 93


title: SpeciesMix_FluidigmC1 Cells 94


title: SpeciesMix_FluidigmC1 Cells 90


title: SpeciesMix_FluidigmC1 Cells 96


title: SpeciesMix_FluidigmC1 Cells 87


title: SpeciesMix_FluidigmC1 Cells 89


title: SpeciesMix_FluidigmC1 Cells 88


title: SpeciesMix_FluidigmC1 Cells 86


title: SpeciesMix_FluidigmC1 Cells 91


title: SpeciesMix_FluidigmC1 Cells 84


title: SpeciesMix_FluidigmC1 Cells 82


title: SpeciesMix_FluidigmC1 Cells 81


title: SpeciesMix_FluidigmC1 Cells 80


title: SpeciesMix_FluidigmC1 Cells 77


title: SpeciesMix_FluidigmC1 Cells 79


title: SpeciesMix_FluidigmC1 Cells 76


title: SpeciesMix_FluidigmC1 Cells 83


title: SpeciesMix_FluidigmC1 Cells 99


title: SpeciesMix_FluidigmC1 Cells 74


title: SpeciesMix_FluidigmC1 Cells 72


title: SpeciesMix_FluidigmC1 Cells 73


title: SpeciesMix_FluidigmC1 Cells 71


title: SpeciesMix_FluidigmC1 Cells 92


title: SpeciesMix_FluidigmC1 Cells 68


title: SpeciesMix_FluidigmC1 Cells 67


title: SpeciesMix_FluidigmC1 Cells 70


title: SpeciesMix_FluidigmC1 Cells 69


title: SpeciesMix_FluidigmC1 Cells 61


title: SpeciesMix_FluidigmC1 Cells 58


title: SpeciesMix_FluidigmC1 Cells 85


title: SpeciesMix_FluidigmC1 Cells 63


title: SpeciesMix_FluidigmC1 Cells 78


title: SpeciesMix_FluidigmC1 Cells 62


title: SpeciesMix_FluidigmC1 Cells 65


title: SpeciesMix_FluidigmC1 Cells 60


title: SpeciesMix_FluidigmC1 Cells 56


title: SpeciesMix_FluidigmC1 Cells 55


title: SpeciesMix_FluidigmC1 Cells 75


title: SpeciesMix_FluidigmC1 Cells 57


title: SpeciesMix_FluidigmC1 Cells 51


title: SpeciesMix_FluidigmC1 Cells 64


title: SpeciesMix_FluidigmC1 Cells 59


title: SpeciesMix_FluidigmC1 Cells 49


title: SpeciesMix_FluidigmC1 Cells 53


title: SpeciesMix_FluidigmC1 Cells 48


title: SpeciesMix_FluidigmC1 Cells 50


title: SpeciesMix_FluidigmC1 Cells 66


title: SpeciesMix_FluidigmC1 Cells 43


title: SpeciesMix_FluidigmC1 Cells 46


title: SpeciesMix_FluidigmC1 Cells 45


title: SpeciesMix_FluidigmC1 Cells 44


title: SpeciesMix_FluidigmC1 Cells 47


title: SpeciesMix_FluidigmC1 Cells 41


title: SpeciesMix_FluidigmC1 Cells 39


title: SpeciesMix_FluidigmC1 Cells 30


title: SpeciesMix_FluidigmC1 Cells 34


title: SpeciesMix_FluidigmC1 Cells 40


title: SpeciesMix_FluidigmC1 Cells 37


title: SpeciesMix_FluidigmC1 Cells 27


title: SpeciesMix_FluidigmC1 Cells 52


title: SpeciesMix_FluidigmC1 Cells 26


title: SpeciesMix_FluidigmC1 Cells 28


title: SpeciesMix_FluidigmC1 Cells 24


title: SpeciesMix_FluidigmC1 Cells 54


title: SpeciesMix_FluidigmC1 Cells 23


title: SpeciesMix_FluidigmC1 Cells 22


title: SpeciesMix_FluidigmC1 Cells 38


title: SpeciesMix_FluidigmC1 Cells 36


title: SpeciesMix_FluidigmC1 Cells 32


title: SpeciesMix_FluidigmC1 Cells 31


title: SpeciesMix_FluidigmC1 Cells 29


title: SpeciesMix_FluidigmC1 Cells 16


title: SpeciesMix_FluidigmC1 Cells 33


title: SpeciesMix_FluidigmC1 Cells 35


title: SpeciesMix_FluidigmC1 Cells 14


title: SpeciesMix_FluidigmC1 Cells 20


title: SpeciesMix_FluidigmC1 Cells 21


title: SpeciesMix_FluidigmC1 Cells 15


title: SpeciesMix_FluidigmC1 Cells 19


title: SpeciesMix_FluidigmC1 Cells 7


title: SpeciesMix_FluidigmC1 Cells 17


title: SpeciesMix_FluidigmC1 Cells 6


title: SpeciesMix_FluidigmC1 Cells 5


title: SpeciesMix_FluidigmC1 Cells 4


title: SpeciesMix_FluidigmC1 Cells 3


title: PC3 DAXX K/D - DAXX IP

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: ChIP-Seq: PC3 DAXX K/D - DAXX IP

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-Seq reads were aligned to the human genome (hg19) 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 identify peaks.  Peaks for WT and DAXX K/D conditions were found relative to the condition specific input experiments.  HOMER's findPeaks program was run in "factor" mode for DAXX and DNMT1 peak finding and "histone" mode for DMHH3 (H3K4me2) peak finding.
Genome_build: hg19
Supplementary_files_format_and_content: bed format (peak regions)

source_name: Prostate

growth_protocol: The human prostate cancer cell line PC3 and its DAXX knock-down counterpart were maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine. For the DAXX K/D PC3 cells, the RPMI medium was supplemented with puromycin (Sigma, Cat # P9620; 2 μg/ml).

extract_protocol:
ChIP was performed using the Active Motif’s ChIP-IT High Sensitivity kit (cat # 53040), starting with PC3 and DAXX K/D PC3 cells. The manufacturer’s protocol was followed. The following goat polyclonal antibodies from Santa Cruz Biotechnology Inc. were used for ChIP: anti-DAXX (sc-7001) and anti-DNMT1 (sc-10219). A two-step cross-linking procedure (protein-protein & DNA-protein) preceded ChIP using disuccinimidyl glutarate (DSG) for protein-protein cross-linking (Thermo Scientific, cat # 20593). For ChIP, anti-DAXX or anti-DNMT1 antibodies were used to collect chromatin bound to the respective antibody, and was followed by deep sequencing (ChIP-Seq) using an Illumina HiSeq 2500 system. Non-immunoprecipitated (input) chromatin, subjected to the same treatment, served as a control.
Illumina HiSeq 2500 system and associated protocol was used.

tag: source tissue

value: Prostate

tag: genotype

value: DAXX knock-down

tag: antibody

value: anti-DAXX (sc-7001)


title: PC3 WT - DNMT1 IP

description: ChIP-Seq: PC3 WT - DNMT1 IP

value: wild type

value: anti-DNMT1 (sc-10219)


title: PC3 WT - DAXX IP

description: ChIP-Seq: PC3 WT - DAXX IP


title: PC3_WT_2

description: non-stranded RNA-seq: PC3_WT_2

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: 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 (9-12) FPKM

extract_protocol:
Total RNA was isolated using NucleoSpin RNA kit (Clontech, cat # 740955). The RNA integrity number (RIN) was determined using The Agilent RNA ScreenTape assay (Agilent 2200 TapeStation, Salk Institute’s Next Generation Sequencing core), and high quality RNA was used for RNA-Seq. The RNA-Seq libraries were prepared using Illumina TruSeq RNA v2 non-stranded sample prep kits and sequenced on an Illumina HiSeq 2500 according to the manufacturer’s instructions.
Illumina HiSeq 2500 system and associated protocol was used. Run type: SE50; Run mode: High Output

value: Prostate cancer


title: PC3_WT_1

description: non-stranded RNA-seq: PC3_WT_1


title: PC3_DAXX_KD_2

description: non-stranded RNA-seq: PC3_DAXX_KD_2


title: G2_Exp1.077

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8
Gene expected counts were calculated using RSEM 1.2.3
Normalized expected counts were calculated using EBSeq 1.5.4
Genome_build: hg19

source_name: single H1-Fucci cell sorted from G2/M phase of the cell cycle only

growth_protocol: Undifferentiated H1 or H1-Fucci hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance.

extract_protocol:
Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system.

treatment_protocol: FACS was performed on the FACSAria IIIu instrument and using FACSDiva software version 6.1.3 (Becton Dickinson). Unlabeled H1 cells or cells stained with single fluorochromes were served as controls for fluorescence gating.

value: human embryonic stem cells

tag: passages

value: FACS sorted


title: G2_Exp1.073


title: SpeciesMix_FluidigmC1 Cells 42


title: SpeciesMix_FluidigmC1 Cells 12


title: SpeciesMix_FluidigmC1 Cells 25


title: PC3 WT - DMHH3(Lys4)

description: ChIP-Seq: PC3 WT - DMHH3(Lys4)


title: SpeciesMix_FluidigmC1 Cells 10


title: SpeciesMix_FluidigmC1 Cells 11


title: SpeciesMix_FluidigmC1 Cells 9


title: G2_Exp1.069


title: G2_Exp1.070


title: SpeciesMix_FluidigmC1 Cells 8


title: G2_Exp1.065


title: SpeciesMix_FluidigmC1 Cells 2


title: G2_Exp1.066


title: G2_Exp1.068


title: G2_Exp1.067


title: PC3 DAXX K/D - INPUT

description: ChIP-Seq: PC3 DAXX K/D - INPUT


title: PC3 WT - INPUT

description: ChIP-Seq: PC3 WT - INPUT


title: G2_Exp1.060


title: SpeciesMix_FluidigmC1 Cells 18


title: SpeciesMix_FluidigmC1 Cells 1


title: G2_Exp1.059


title: G2_Exp1.061


title: PC3 DAXX K/D - DMHH3(Lys4)

description: ChIP-Seq: PC3 DAXX K/D - DMHH3(Lys4)


title: PC3_DAXX_KD_1

description: non-stranded RNA-seq: PC3_DAXX_KD_1


title: SpeciesMix_FluidigmC1 Cells 13


title: G2_Exp1.055


title: PC3 DAXX K/D - DNMT1 IP

description: ChIP-Seq: PC3 DAXX K/D - DNMT1 IP


title: G2_Exp1.064


title: G2_Exp1.052


title: G2_Exp1.075


title: G2_Exp1.048


title: G2_Exp1.049


title: G2_Exp1.072


title: G2_Exp1.071


title: G2_Exp1.076


title: G2_Exp1.046


title: G2_Exp1.074


title: G2_Exp1.043


title: G2_Exp1.062


title: G2_Exp1.042


title: G2_Exp1.040


title: G2_Exp1.057


title: G2_Exp1.054


title: G2_Exp1.038


title: G2_Exp1.056


title: G2_Exp1.050


title: G2_Exp1.036


title: G2_Exp1.033


title: G2_Exp1.063


title: G2_Exp1.032


title: G2_Exp1.051


title: G2_Exp1.053


title: G2_Exp1.047


title: G2_Exp1.045


title: G2_Exp1.041


title: G2_Exp1.044


title: G2_Exp1.058


title: G2_Exp1.037


title: G2_Exp1.022


title: G2_Exp1.034


title: G2_Exp1.021


title: G2_Exp1.019


title: G2_Exp1.029


title: G2_Exp1.027


title: G2_Exp1.026


title: G2_Exp1.031


title: G2_Exp1.030


title: G2_Exp1.025


title: G2_Exp1.024


title: G2_Exp1.013


title: G2_Exp1.023


title: G2_Exp1.020


title: G2_Exp1.011


title: G2_Exp1.009


title: G2_Exp1.015


title: G2_Exp1.014


title: G2_Exp1.006


title: G2_Exp1.007


title: G2_Exp1.018


title: G2_Exp1.016


title: G2_Exp1.039


title: G2_Exp1.017


title: G2_Exp1.028


title: G2_Exp1.008


title: G2_Exp1.005


title: G2_Exp1.004


title: G2_Exp1.002


title: G2_Exp1.001


title: S_Exp1.081

source_name: single H1-Fucci cell sorted from S phase of the cell cycle only


title: G2_Exp1.003


title: S_Exp1.080


title: S_Exp1.074


title: G2_Exp1.010


title: S_Exp1.076


title: S_Exp1.079


title: S_Exp1.073


title: S_Exp1.078


title: S_Exp1.072


title: S_Exp1.069


title: G2_Exp1.012


title: S_Exp1.075


title: S_Exp1.067


title: S_Exp1.071


title: S_Exp1.065


title: S_Exp1.066


title: S_Exp1.070


title: S_Exp1.068


title: S_Exp1.064


title: S_Exp1.063


title: S_Exp1.062


title: S_Exp1.060


title: S_Exp1.061


title: S_Exp1.058


title: S_Exp1.057


title: S_Exp1.059


title: S_Exp1.053


title: S_Exp1.054


title: S_Exp1.056


title: S_Exp1.055


title: S_Exp1.052


title: S_Exp1.077


title: S_Exp1.050


title: S_Exp1.049


title: S_Exp1.048


title: S_Exp1.047


title: S_Exp1.043


title: S_Exp1.046


title: S_Exp1.045


title: S_Exp1.042


title: S_Exp1.044


title: S_Exp1.040


title: S_Exp1.036


title: S_Exp1.037


title: S_Exp1.035


title: S_Exp1.038


title: S_Exp1.033


title: S_Exp1.034


title: S_Exp1.028


title: S_Exp1.032


title: S_Exp1.029


title: S_Exp1.027


title: S_Exp1.031


title: S_Exp1.026


title: S_Exp1.030


title: S_Exp1.022


title: S_Exp1.021


title: S_Exp1.025


title: S_Exp1.020


title: S_Exp1.041


title: S_Exp1.019


title: S_Exp1.039


title: S_Exp1.018


title: S_Exp1.013


title: S_Exp1.014


title: S_Exp1.016


title: S_Exp1.015


title: S_Exp1.017


title: S_Exp1.011


title: S_Exp1.010


title: S_Exp1.008


title: S_Exp1.007


title: S_Exp1.023


title: S_Exp1.005


title: G1_Exp1.091

source_name: single H1-Fucci cell sorted from G1 phase of the cell cycle only


title: S_Exp1.004


title: S_Exp1.001


title: S_Exp1.003


title: S_Exp1.002


title: G1_Exp1.086


title: G1_Exp1.089


title: G1_Exp1.085


title: G1_Exp1.088


title: G1_Exp1.087


title: G1_Exp1.090


title: G1_Exp1.083


title: G1_Exp1.084


title: S_Exp1.012


title: G1_Exp1.082


title: G1_Exp1.081


title: S_Exp1.051


title: G1_Exp1.080


title: G1_Exp1.079


title: S_Exp1.009


title: G1_Exp1.078


title: G1_Exp1.075


title: G1_Exp1.076


title: G1_Exp1.074


title: G1_Exp1.071


title: S_Exp1.006


title: G1_Exp1.073


title: G1_Exp1.072


title: G1_Exp1.064


title: G1_Exp1.070


title: G1_Exp1.068


title: G1_Exp1.069


title: G1_Exp1.062


title: G1_Exp1.066


title: G1_Exp1.063


title: G1_Exp1.060


title: G1_Exp1.058


title: G1_Exp1.057


title: G1_Exp1.061


title: G1_Exp1.059


title: G1_Exp1.067


title: G1_Exp1.056


title: G1_Exp1.055


title: G1_Exp1.050


title: G1_Exp1.053


title: G1_Exp1.054


title: G1_Exp1.077


title: G1_Exp1.051


title: G1_Exp1.044


title: G1_Exp1.047


title: G1_Exp1.052


title: G1_Exp1.049


title: G1_Exp1.045


title: G1_Exp1.065


title: G1_Exp1.042


title: G1_Exp1.043


title: G1_Exp1.038


title: G1_Exp1.037


title: G1_Exp1.039


title: G1_Exp1.041


title: G1_Exp1.035


title: G1_Exp1.036


title: G1_Exp1.034


title: G1_Exp1.040


title: G1_Exp1.048


title: G1_Exp1.032


title: G1_Exp1.029


title: G1_Exp1.027


title: G1_Exp1.046


title: G1_Exp1.030


title: G1_Exp1.025


title: G1_Exp1.028


title: G1_Exp1.026


title: G1_Exp1.021


title: G1_Exp1.017


title: G1_Exp1.023


title: G1_Exp1.019


title: G1_Exp1.022


title: G1_Exp1.024


title: G1_Exp1.016


title: G1_Exp1.020


title: G1_Exp1.014


title: G1_Exp1.015


title: G1_Exp1.033


title: G1_Exp1.013


title: G1_Exp1.031


title: G1_Exp1.010


title: G1_Exp1.012


title: G1_Exp1.008


title: G1_Exp1.006


title: G1_Exp1.007


title: G1_Exp1.003


title: G1_Exp1.001


title: G1_Exp1.005


title: G1_Exp1.009


title: G1_Exp1.002


title: H1_Exp3.291

source_name: single H1 hESC

value: not sorted


title: H1_Exp3.290


title: H1_Exp3.289


title: G1_Exp1.004


title: H1_Exp3.288


title: H1_Exp3.286


title: H1_Exp3.287


title: H1_Exp3.284


title: H1_Exp3.285


title: G1_Exp1.011


title: H1_Exp3.283


title: H1_Exp3.279


title: H1_Exp3.281


title: H1_Exp3.282


title: H1_Exp3.280


title: H1_Exp3.277


title: H1_Exp3.278


title: H1_Exp3.275


title: G1_Exp1.018


title: H1_Exp3.273


title: H1_Exp3.262


title: H1_Exp3.263


title: H1_Exp3.274


title: H1_Exp3.260


title: H1_Exp3.272


title: H1_Exp3.271


title: H1_Exp3.259


title: H1_Exp3.258


title: H1_Exp3.256


title: H1_Exp3.276


title: H1_Exp3.270


title: H1_Exp3.268


title: H1_Exp3.269


title: H1_Exp3.267


title: H1_Exp3.264


title: H1_Exp3.266


title: H1_Exp3.265


title: H1_Exp3.246


title: H1_Exp3.244


title: H1_Exp3.261


title: H1_Exp3.257


title: H1_Exp3.243


title: H1_Exp3.242


title: H1_Exp3.255


title: H1_Exp3.254


title: H1_Exp3.253


title: H1_Exp3.240


title: H1_Exp3.239


title: H1_Exp3.235


title: H1_Exp3.248


title: H1_Exp3.250


title: H1_Exp3.249


title: H1_Exp3.252


title: H1_Exp3.247


title: H1_Exp3.241


title: H1_Exp3.233


title: H1_Exp3.251


title: H1_Exp3.228


title: H1_Exp3.238


title: H1_Exp3.223


title: H1_Exp3.232


title: H1_Exp3.234


title: H1_Exp3.231


title: H1_Exp3.236


title: H1_Exp3.237


title: H1_Exp3.229


title: H1_Exp3.230


title: H1_Exp3.227


title: H1_Exp3.226


title: H1_Exp2.149


title: H1_Exp2.152


title: H1_Exp3.225


title: H1_Exp2.147


title: H1_Exp3.224


title: H1_Exp3.222


title: H1_Exp3.221


title: H1_Exp2.154


title: H1_Exp2.145


title: H1_Exp2.148


title: H1_Exp2.150


title: H1_Exp2.141


title: H1_Exp2.153


title: H1_Exp3.220


title: H1_Exp3.218


title: H1_Exp2.144


title: H1_Exp2.142


title: H1_Exp3.219


title: H1_Exp2.136


title: H1_Exp2.133


title: H1_Exp2.130


title: H1_Exp2.132


title: H1_Exp2.139


title: H1_Exp2.126


title: H1_Exp2.138


title: H1_Exp2.129


title: H1_Exp2.128


title: H1_Exp2.135


title: H1_Exp2.151


title: H1_Exp2.127


title: H1_Exp2.125


title: H1_Exp2.137


title: H1_Exp2.123


title: H1_Exp2.124


title: H1_Exp2.140


title: H1_Exp2.146


title: H1_Exp2.122


title: H1_Exp2.121


title: H1_Exp2.134


title: H1_Exp2.113


title: H1_Exp2.114


title: H1_Exp2.120


title: H1_Exp2.116


title: H1_Exp2.115


title: H1_Exp2.110


title: H1_Exp2.109


title: H1_Exp2.106


title: H1_Exp2.105


title: H1_Exp2.108


title: H1_Exp2.111


title: H1_Exp2.104


title: H1_Exp2.103


title: H1_Exp2.102


title: H1_Exp2.107


title: H1_Exp2.101


title: H1_Exp2.097


title: H1_Exp2.094


title: H1_Exp2.093


title: H1_Exp2.117


title: H1_Exp2.118


title: H1_Exp2.098


title: H1_Exp2.100


title: H1_Exp2.112


title: H1_Exp2.096


title: H1_Exp2.091


title: H1_Exp2.090


title: H1_Exp2.092


title: H1_Exp2.089


title: H1_Exp2.087


title: H1_Exp2.086


title: H1_Exp2.084


title: H1_Exp2.083


title: H1_Exp2.088


title: H1_Exp2.081


title: H1_Exp2.099


title: H1_Exp2.082


title: H1_Exp2.078


title: H1_Exp2.080


title: H1_Exp2.076


title: H1_Exp2.079


title: H1_Exp2.077


title: H1_Exp2.075


title: H1_Exp2.074


title: H1_Exp2.073


title: H1_Exp1.065


title: H1_Exp1.070


title: H1_Exp1.066


title: H1_Exp1.062


title: H1_Exp1.061


title: H1_Exp1.068


title: H1_Exp2.085


title: H1_Exp1.069


title: H1_Exp1.064


title: H1_Exp1.060


title: H1_Exp1.063


title: H1_Exp1.058


title: H1_Exp1.053


title: H1_Exp1.055


title: H1_Exp1.050


title: H1_Exp1.051


title: H1_Exp1.049


title: H1_Exp1.048


title: H1_Exp1.052


title: H1_Exp1.057


title: H1_Exp1.042


title: H1_Exp1.054


title: H1_Exp1.047


title: H1_Exp1.040


title: H1_Exp1.044


title: H1_Exp1.045


title: H1_Exp1.041


title: H1_Exp1.039


title: H1_Exp1.038


title: H1_Exp1.033


title: H1_Exp1.032


title: H1_Exp1.029


title: H1_Exp1.035


title: H1_Exp1.036


title: H1_Exp1.024


title: H1_Exp1.030


title: H1_Exp1.025


title: H1_Exp1.026


title: H1_Exp1.031


title: H1_Exp1.059


title: H1_Exp1.027


title: H1_Exp1.043


title: H1_Exp1.023


title: H1_Exp1.022


title: H1_Exp1.016


title: H1_Exp1.017


title: H1_Exp1.021


title: H1_Exp1.018


title: H1_Exp1.019


title: H1_Exp1.015


title: H1_Exp1.020


title: H1_Exp1.014


title: H1_Exp1.012


title: aged_SH_biological_rep3

city: Chicago

first: C. Sehwan

last: Park

state: IL

address: 375 East Chicago Ave

department: Pritzker School of Law

institute: Northwestern University

data_processing:
base-calling performed using Applied Biosystems Bioscope version 1.31
alignment performed using Applied Biosystems SOLID SAGE perl script version 1.10 (1 mismatch)
comparative counts performed using R/Bioconductor statistical package, EdgeR
Genome_build: NCBI37/mm9 (July 2007)
Supplementary_files_format_and_content: excel file containing summaries of comparative counts performed using EdgeR, group x over group y (x|y)

extract_protocol:
TRIzol total RNA extraction
SAGE-Seq: Total RNA was extracted from hippocampus using the TRIzol procedure (Invitrogen). RNA quality was assessed using an Agilent Bioanalyser 2100 and quantified using a Qubit 2.0 Fluorometer (Invitrogen). SAGE tag library preparation was performed according to the SOLiD SAGE kit with Barcoding Adaptor Module (Invitrogen). Approximately 3 µg of RNA was used to isolate polyadenylated RNA using poly-dT Dynabeads and converted to cDNA using Superscript III Reverse Transcriptase. Samples were digested with sequence specific Endonuclease Nla III restriction enzyme, the restriction site of which is known to occur approximately every 250 bp, and ligated to barcoded adaptor A which has cohesive a 4 bp overhang complementary to the Nla III digested cDNA and an EcoP151 restriction enzyme recognition site. The fragments were then released from the Oligo (dT) EcoP magnetic beads using EcoP15I restriction enzyme, which cleaves cDNA 27 bp downstream of the barcoded adaptor A. The resulted fragments were then ligated to adapter B which contains the P1 sequence for the SOLiD emulsion PCR. 130 bp ligation products were PCR-amplified and purified using PureLink PCR Micro Kit (Invitrogen). Barcoded libraries were then quantified using a Qubit Fluorometer and pooled in equimolar volumes before emulsion PCR and sequenced on one full SOLiD4 slide (Applied Biosystems). From six groups - aged EE, aged SH, young EE, young SH, aged I1 transgenic mice, and aged wild type littermates - three samples from each group were run in parallel as biological replicates.

treatment_protocol: environmental enrichment (EE) or standard housing (SH)

tag: strain background

value: 14-17 months (aged)

tag: housing group

value: standard housing (SH)

value: hippocampus


title: young_SH_biological_rep1

value: 5-6 months (young)


title: H1_Exp1.009

tag: treatment


title: young_SH_biological_rep2


title: aged_SH_biological_rep2


title: 1133S_RRBS

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: DNA methylation analysis using bisulfite sequencing

data_processing:
To map the sequencing reads from RRBS, the human genome (hg18) was indexed by converting all C’s and G’s to T’s and A’s, respectively, i.e., two different reference databases. Bowtie was used to map the cleaned reads to each of the two reference databases after converting all C’s to T’s.
For each read, an in-house script computed the best of all alignments for the different loci using two different reference databases based on the number of mismatches after realigning the original read and reference sequences. The script also determined the methylation status of each cytosine residue by comparing the bisulfite-converted sequence to the reference sequence.
Another in-house script piled reads for each cytosine in the reference genome and counted the numbers of reads that contained methylated and unmethylated cytosines, respectively. Finally the methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined. CpGs with < 5 reads were filtered out for further analyses.
Genome_build: hg18
Supplementary_files_format_and_content: BED format, Total number of reads and methylation level ( a value between 0 and 1) at each CpG sites.

source_name: GBM stem cells

growth_protocol: To establish the neurosphere or tumor sphere cultures, primary tissue samples were mechanically dissociated and washed with PBS; red blood cells were removed with Histopaque (Sigma, USA). The single-cell suspensions were then grown as non-adherent cultures (spheres) in un-coated petri dishes with serum-free defined medium containing DMEM-F12 supplemented with 20 ng/mL epidermal growth (EGF; Invitrogen, USA), 20 ng/mL basic fibroblast growth factor (bFGF; Invitrogen), 1:50 B27 supplement (Invitrogen), 1:100 N2 supplement (Invitrogen), 10 ng/mL leukemia inhibitory factor (LIF; Millipore, USA), as a stem-cell permissive medium to facilitate the growth of neurospheres and tumor spheres.

extract_protocol: RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications. For each sample, 1  g genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20  l reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2  l premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20  l reaction containing 1  l concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 ?m of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

tag: tissues

value: Brain

tag: cell types

value: GBM stem cells

tag: tumorgenecity

value: Tumor


title: mayo59_RRBS

source_name: GBM xenograft tumor tissue

value: GBM xenograft tumor tissue


title: mayo39_RRBS


title: mayo22_RRBS


title: aged_SH_biological_rep1

tag: genotype/variation


title: H1_Exp1.007

tag: cell type


title: H1_Exp1.008


title: young_EE_biological_rep3

value: environmental enrichment (EE)


title: young_SH_biological_rep3


title: H1_Exp1.004


title: 1133T_RRBS

source_name: Primary GBM tissue

value: Brain tissue


title: young_EE_biological_rep1


title: H1_Exp1.011


title: NB_RRBS

source_name: Normal brain tissue

value: Normal


title: H1_Exp1.006


title: young_EE_biological_rep2

value: wild type


title: H1_Exp1.003


title: H1_Exp1.010


title: aged_EE_biological_rep3


title: 1063T_RRBS


title: NSC_RRBS

source_name: Normal neural stem cells

value: Neural Stem cells


title: H1_Exp1.002


title: 1063S_RRBS


title: 1142S_RRBS


title: aged_EE_biological_rep2


title: 1142T_RRBS


title: Ribosome profiling SiControl-input-poly(A)

first: Chuan

last: He

state: Illinois

address: 929 E. 57th. Street

department: Chemistry

institute: The University of Chicago

description:
poly(A)+ mRNA
D-METTL3-Ribosome profiling.xlsx

data_processing:
General: Illumina Casava 1.8.2 software were used for basecalling.
General: Reads were aligned to the hg19 genome assembly using bowtie version 1.0 with at most 2 mismatch allowed -n 2 -g 1.
Ribosome profiling were mapped by Tophat version 2.0 and analyzed by cuffdiff to generate RPKM
All other following calculation steps were illustrated in processed files.
Genome_build: hg19
Supplementary_files_format_and_content: The results were organized in the Microsoft Excel format

source_name: HeLa cell

extract_protocol:
Extract by trizol, then poly(A) selection
TruSeq Small RNA Library Preparation Kits (Illumina)

value: HeLa

tag: transfection

value: siControl

tag: cell treatment

value: 40nM siRNA knock-down for 48h


title: Ribosome profiling SiMETTL3-input-poly(A)


title: Ribosome profiling SiControl-RPF

description:
Ribosome-protected mRNA
D-METTL3-Ribosome profiling.xlsx

extract_protocol:
Isolate from surcrose gradient, recovered by trizol
TruSeq Small RNA Library Preparation Kits (Illumina)

value: siControl-RPF


title: H1_Exp1.001

value: human embryonic stem cells

value: not sorted


title: Ribosome profiling SiMETTL3-RPF


title: Adelman_Bl6_macrophage_startRNA-seq_5pr_2hr_LPS_rep2

status: Public on Jun 23 2015

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

description:
processed data file:
Adelman_Bl6_macrophage_startRNA-seq_5pr_2hr_LPS_rep1and2_forward_normalized.wig.gz
Adelman_Bl6_macrophage_startRNA-seq_5pr_2hr_LPS_rep1and2_reverse_normalized.wig.gz

data_processing:
Base calling and generation of FASTQ files performed by MiSeq Control Software 2.2.0 (MEF samples), standard Illumina GAIIx pipeline (macrophage samples)
Reads trimmed for adapter sequence using cutadapt 1.2.1, pairs containing reads shorter than 15 nt excluded (-q 10 -m 15, otherwise default), reads further trimmed to maximum length of 36 nt, MEF paired-end startRNA-seq only
Reads 3' trimmed to 36 nt (all macrophage data)
Reads aligned using bowtie 0.12.8 (-m1 -v2, -X1000 for paired-end alignments)
Technical and biological replicates merged
Counts normalized such that totals across all time points are equivalent (macrophage startRNA-seq, RNA PolII ChIP-seq)
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph: 5' ends of uniquely aligned pairs (MEF samples); wig: normalized 5' ends of uniquely aligned single-end reads (macrophage samples), normalized center-shifted (65 nt), strand merged, and binned (25) RNA PolII ChIP-seq read counts; bigWig: 25 nt binned MNase-seq fragment centers

growth_protocol: For each biological replicate, macrophages were derived from female C57BL/6 mice (age 8-12 weeks). Day 7 bone marrow-derived macrophages were incubated at 37°C with 5% CO2. MEFs were derived from e13.5 female C57BL/6 embryos as follows: body tissue from e13.5 embryos was minced and incubated at 37°C with 0.5% Trypsin, followed by quenching with DMEM (10% FBS, 1X Penn/Strep, 1X Glutamine), and passage through a 100 micron mesh filter. Cells in suspension were plated, incubated at 37°C with 5% CO2, and passaged as necessary.

extract_protocol:
Total RNA was extracted from nuclei using Trizol reagent (Invitrogen)
Start-RNA libraries were prepared as described in (PMID:20007866) except reads were size selected in the range 20-80 nt to exclude full length snRNA species.

treatment_protocol: BMDMs were incubated with 0 or 100ng/ml LPS (Sigma L6529) for the time indicated.

tag: gender

value: female

tag: age

value: 8-12 weeks

value: bone marrow-derived macrophages

tag: treated with

value: LPS for 2hr

tag: molecule subtype

value: short capped RNA isolated from macrophage nuclei


title: Adelman_Bl6_macrophage_MNase-seq_rep3

description:
processed data file:
Adelman_Bl6_macrophage_MNase-seq_allReps_binned.bw

extract_protocol:
Nuclei were pelleted at 1000 X G for 5 minutes and 5 × 106 nuclei were resuspended in 400 μl digest buffer (15 mM Tris pH 8, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.25 M sucrose, 0.5 mM DTT), and incubated with varying concentrations of MNase (Worthington) for 5 minutes. 400 μl stop solution (1% SDS, 0.1 M sodium bicarbonate, 20 mM EDTA) was added and digested nuclei were incubated at 65°C for 90 minutes. 24 μl Tris pH 7.6, 3 μl Proteinase K (Life Technologies), and 3 μl GlycoBlue (Life Technologies) were added and digestions were incubated for 12 hours at 65°C. DNA was extracted and mono-nucleosome fragments were gel-purified from fractions digested to ~60% mono-nucleosome, ~30% di-nucleosome, and ~10% tri-nucleosome- sized fragments.
MNase-seq libraries were prepared as described in (Gilchrist et al., 2010)

value: none (untreated)

value: MNase-digested chromatin mononucleosomal fragments


title: Adelman_Bl6_macrophage_MNase-seq_rep1


title: Adelman_Bl6_macrophage_MNase-seq_rep2


title: Adelman_Bl6_macrophage_startRNA-seq_5pr_2hr_LPS_rep1


title: Adelman_Bl6_macrophage_startRNA-seq_5pr_30min_LPS_rep2

description:
processed data file:
Adelman_Bl6_macrophage_startRNA-seq_5pr_30min_LPS_rep1and2_forward_normalized.wig.gz
Adelman_Bl6_macrophage_startRNA-seq_5pr_30min_LPS_rep1and2_reverse_normalized.wig.gz

value: LPS for 30min


title: Adelman_Bl6_macrophage_startRNA-seq_5pr_30min_LPS_rep1


description:
processed data file:
Adelman_Bl6_macrophage_startRNA-seq_5pr_untreated_rep1and2_forward_normalized.wig.gz
Adelman_Bl6_macrophage_startRNA-seq_5pr_untreated_rep1and2_reverse_normalized.wig.gz


title: Adelman_Bl6_macrophage_startRNA-seq_5pr_untreated_rep2


title: Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_30min_LPS_rep2

description:
processed data file:
Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_30min_LPS_rep1and2_binned_normalized.wig.gz

extract_protocol:
Pol II ChIP material was prepared as described previously (Muse et al., 2007). Immunoprecipitations were carried out with 25 μl total anti-Pol II antibody
ChIP material was purified using the Qiaquick PCR purification kit and ChIP-seq libraries were prepared using the Illumina ChIP-seq kit according to manufacturer's instructions

tag: chip antibody

value: Pol II Antibody (H-224)

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #

value: anti-Pol II immunoprecipitated chromatin fragments


title: Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_2hr_LPS_rep2

description:
processed data file:
Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_2hr_LPS_rep1and2_binned_normalized.wig.gz

tag: strain background


description:
processed data file:
Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_untreated_rep1and2_binned_normalized.wig.gz


title: Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_30min_LPS_rep1


title: Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_2hr_LPS_rep1


title: Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_untreated_rep2


title: 4C-KO2-SOX17

city: Athens

first: Stephen

last: Dalton

state: Georgia

address: Paul D. Coverdell Center, Rm. 245/276, 500 DW Brooks Drive

department: Department of Biochemistry and Molecular Biology

institute: Univ. of Georgia

data_processing:
chip-seq reads were mapped to reference genome mm9 using bowtie 0.12.7. After reads mapping, Peaks were called using HPeak version 3.
4C-seq reads were processed to be separated into 8 samples with different viewpoint and cell-cycle stages by recognizing sample-specific primer and barcode below:  Gata6_AZH AAGGTAATGGTTGGGTGTGAAGCTT  Gata6_AZL TTGGTAATGGTTGGGTGTGAAGCTT  Gata6_KO2 CCGGTAATGGTTGGGTGTGAAGCTT  Gata6_DN GAGGTAATGGTTGGGTGTGAAGCTT  Sox17_AZH AATGGTTTTCTAACTGTTGAATCATAAGCTT  Sox17_AZL TGTGGTTTTCTAACTGTTGAATCATAAGCTT  Sox17_KO2 CCTGGTTTTCTAACTGTTGAATCATAAGCTT  Sox17_DN GGTGGTTTTCTAACTGTTGAATCATAAGCTT  A customized reference genome composed of sequence around all HindIII cutting sites through hg19 were built. Then reads were mapped to the customized genome using bowtie version 0.12.7. Mapping frequency at each cutting site were calculated and given in site_ocp.txt.
Genome_build: hg19
Supplementary_files_format_and_content: Column header for *.hpeak.out: chromosome start end width summit reads posterior. Column header for site_ocp.txt: chromosome_sn site Gata6_AZH Gata6_AZL Gata6_DN Gata6_KO2 Sox17_AZH Sox17_AZL Sox17_DN Sox17_KO2

source_name: KO2-Late G1

growth_protocol: Fucci hESCs were grown in a serum/feeder free, fully defined media, consisting of Heregulin b1 (10 ng/ml), Activin a (10 ng/ml), Longr3 IGF-1 (200 ng/ml) and FGF2 (8 ng/ml).

extract_protocol:
For ChIP-seq, lysates were isolated from sonicated nuclei and histone-DNA complexes were purified with antibody. For 4C, lysates were purified from restriction digested nuclei.
ChIP-seq libraries were prepared by HudsonAlpha by first performing end-repair and adapter ligation of Chip'd DNA fragments, followed by size selection and PCR amplifcation to generate the library for sequencing.  Library was prepared using the Illumina DNA Library Construction Kit.  DNA barcodes were introduced to permit multiple samples per flowcell lane.  4C-libaries were prepared by first digesting nuclei with HindIII, followed by ligation and crosslink reversal.  Chromatin was re-digested with NlaIII and re-ligated to generate DNA libraries by PCR using the Expand Long Template Polymerase Kit from Roche.

tag: cell line

value: Fucci human embryonic stem cell


title: 4C-AzH-SOX17


title: aged_EE_biological_rep1

value: wild type

value: 14-17 months (aged)

tag: housing group

value: environmental enrichment (EE)

tag: tissue

value: hippocampus


title: Input-AzH


title: 4C-AzL-GATA6

source_name: AzL-S phase


title: 4C-KO2-GATA6


title: 4C-AzH-GATA6


title: Input-DN

source_name: DN-Early G1


title: H3K4me1_ChIPSeq-AzH

tag: antibody


title: 4C-DN-GATA6


title: 4C-DN-SOX17


title: Input-KO2


title: 4C-AzL-SOX17


title: H3K4me1_ChIPSeq-KO2


title: H3K4me3 _ChIP-seq

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using Strand NGS software version 1.6 with default parpemters.
Duplicated reads were filted. Peaks for SOX6, SOX9 and histone modifications were identified using MACS software (version 1.4.5) with default settings
Genome_build: rn5

organism: Rattus norvegicus

source_name: RCS cells

extract_protocol:
RCS cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP-seq DNA libraries wereprepared for sequencing using standard Illumina protocols

value: Rat chondrosarcoma cell

tag: chip-seq antibody

value: H3K4me3 (ab8580, Abcam)


title: H3K9me3 _ChIP-seq

value: H3K9me3 (ab8889, Abcam)


title: H3K4me1_ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: Input-AzL


title: H3K4me1_ChIPSeq-AzL


title: H3K4me1_ChIPSeq-DN


title: Input_me1me3K9me3


title: H3K27ac_ChIPSeq-AzH


title: H3K27ac_ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Input_H3K27ac


title: H3K27ac_ChIPSeq-AzL


title: H3K27ac_ChIPSeq-DN


title: SOX6_ChIP-seq

value: SOX6 (ab30455, Abcam)


title: H3K27me3_ChIPSeq-AzH


title: Input_SOX6


title: SOX9_ChIP-seq

value: SOX9 (AB5535, Millipore)


title: Input_SOX9


title: H3K27me3_ChIPSeq-AzL


title: H3K4me3_ChIPSeq-AzH


title: Rib_3_RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using Strand NGS software version 1.6 with default parpemters.
Duplicated reads were filted and reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using DESeq.
Genome_build: rn5

source_name: neonatal rib samples

extract_protocol: RNA-Seq libraries were prepared for sequencing using standard Illumina protocols

value: rib tissue

value: rib


title: H3K27me3_ChIPSeq-DN


title: Rib_1_RNA-seq


title: H3K27me3_ChIPSeq-KO2


title: RCS_2_RNA-seq


title: H3K4me3_ChIPSeq-KO2


title: H3K4me3_ChIPSeq-AzL


title: H3K4me3_ChIPSeq-DN


title: Donor6_Day38_Rep1

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Library strategy: ATAC-Seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in-house generated script, and data matrix was normalized using R.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Bed files: Peak files are in tab-separated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand.

source_name: human CD4+ T cells, normal donor

growth_protocol: Donors were recruited under a Stanford University IRB-approved protocol. Informed consent was obtained. Standard blood draws in green-top tube were obtained for each time point. 1-5mL of whole blood was enriched for CD4+ cells using RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCell Technology).

extract_protocol:
CD4+ T cells were isolated from 5 ml of blood using negative selection. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: For T cell activation time course, CD4+ cells from donor 1 isolated as above were stimulated with ionomycin (1 ug/mL) and PMA (20 ng/mL) and collected at 0, 1, 2, 4 hours in duplicate.

tag: donor identifier

tag: disease state

value: healthy

value: CD4+ T cells


title: Donor9_Day38_Rep1

value: female

tag: cell type


title: Donor31_Day192_Rep2

value: male


title: Donor7_Day38_Rep1


title: Donor8_Day38_Rep1


title: Donor31_Day192_Rep1


title: H3K27ac_ChIPSeq-KO2

value: Fucci human embryonic stem cell


title: Donor5_CTCL_Rep3

source_name: human CD4+ T cells, patient with CTCL

value: cutaneous T cell leukemia (CTCL)


title: Donor5_CTCL_Rep2


title: Donor5_CTCL_Rep4


title: Donor5_CTCL_Rep1


title: Donor4_Day37_Rep1


title: Donor4_Day224_Rep1


title: Donor4_Day224_Rep2


title: Rib_2_RNA-seq


title: Donor4_Day107_Rep2


title: RCS_3_RNA-seq


title: Donor20_CTCL_Rep4


title: Donor4_Day107_Rep1


title: Donor33_Day224_Rep2


title: Donor20_CTCL_Rep3


title: Donor32_Day224_Rep2


title: RCS_1_RNA-seq


title: Donor33_Day224_Rep1


title: Donor3_Day37_Rep1


title: Donor32_Day224_Rep1


title: Donor20_CTCL_Rep2


title: Donor20_CTCL_Rep1


title: Donor2_Day37_Rep1


title: Donor2_Day224_Rep2


title: Donor2_Day224_Rep1


title: Donor11_CTCL_Rep5


title: Donor11_CTCL_Rep6


title: Donor11_CTCL_Rep7


title: Donor11_CTCL_Rep4


title: Donor11_CTCL_Rep2


title: Donor11_CTCL_Rep1


title: Donor10_Day224_Rep2


title: Donor11_CTCL_Rep3


title: Donor10_Day224_Rep1


title: Donor1_TCA4hrs_Rep2

source_name: human CD4+ T cells, normal donor, T cell activation at 4hrs

tag: treatment

value: T cell activation

tag: time point


title: Donor1_TCA1hrs_Rep2

source_name: human CD4+ T cells, normal donor, T cell activation at 1hrs

tag: gender


title: Donor1_TCA2hrs_Rep2

source_name: human CD4+ T cells, normal donor, T cell activation at 2hrs


title: Donor1_TCA1hrs_Rep1


title: Donor1_TCA4hrs_Rep1


title: Donor1_TCA2hrs_Rep1


title: Donor1_Day39_Rep1


title: Donor1_Day37_Rep2


title: Donor1_Day224_Rep2


title: Donor1_Day38_Rep1


title: Donor1_Day2_Rep2


title: Donor1_Day37_Rep1


title: Donor1_TCA0hrs_Rep2

source_name: human CD4+ T cells, normal donor, T cell activation at 0hrs


title: Donor1_Day38_Rep2


title: Adelman_Bl6_MEF_startRNA-seq_rep1

description:
processed data file:
Adelman_Bl6_MEF_startRNA-seq_5pr_rep1and2_forward.bedgraph.gz
Adelman_Bl6_MEF_startRNA-seq_5pr_rep1and2_reverse.bedgraph.gz

tag: age

value: 8-12 weeks

value: mouse embryonic fibroblasts

tag: treated with

value: none (untreated)

value: short capped RNA isolated from MEF nuclei


title: Adelman_Bl6_MEF_startRNA-seq_rep2

tag: molecule subtype


title: Donor1_4hrsControl_Rep2

source_name: human CD4+ T cells, normal donor, control of T cell activation at 4hrs

value: control of T cell activation


title: Donor1_4hrsControl_Rep1


title: Donor1_Day1_Rep1


title: Donor10_Day38_Rep1


title: Donor1_Day1_Rep2


title: Donor1_Day224_Rep1


title: LSK-SLAM GFP- BM

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: BM adult LSK-SLAM BRE-GFP-

data_processing:
Mapping of reads to mouse genome (mm10/UCSC ) using Tophat
Calculation and normalization of FPKMs using cufflinks (v2.2.1) and cuffnorm/cuffquant
Genome_build: mm10
Supplementary_files_format_and_content: text file with FPKMs

source_name: Bone marrow

extract_protocol: mirVana miRNA Kit according to SMARTER protocol (Ramskold et al., 2012)

treatment_protocol: sorted by flow cytometry in PBS/FCS and RNA was directly extracted as described in publication

value: LSK-SLAM

tag: marker

value: GFP-

tag: genotype

value: BRE-GFP transgenic


title: LSK-SLAM GFP+ BM

description: BM adult LSK-SLAM BRE-GFP+

value: GFP+


title: LSK-SLAM GFP- FL

description: FL e14 LSK-SLAM BRE-GFP-

source_name: Fetal liver


title: Donor1_TCA0hrs_Rep1


title: LSK-SLAM GFP+ FL

description: FL e14 LSK-SLAM BRE-GFP+


title: Donor1_Day2_Rep1


title: E16.5_Cortex_3_ACAGTG_L008_R1_001

status: Public on Jun 22 2015

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: processed data file: cellRev.rpkm.E16.5.mean.Cortex.csv

data_processing:
Bowtie2 v.2.1.0 defults
TopHat2 v.2.0.9 --no-novel-juncs --b2-very-sensitive
Cuffdiff v.2.0.2. -b path_to/mm9.fa -u
HTSeq v.0.6.0 -stranded=no
DESeq v.1.16.0
Genome_build: NCBIM37
Supplementary_files_format_and_content: csv file of gene mean RPKM values
Supplementary_files_format_and_content: Spreadsheet of DESeq differential analysis result

source_name: Embryonic Cortical Tissue (E16.5)

extract_protocol:
Samples were homogenized in Trizol and processed according to the manufacturer’s instructions. RNA was further purified with RNeasy Micro columns
RNA-seq libraries were prepared according to the Illumina TruSeq protocol and were sequenced on the HiSeq 2000

tag: strain

tag: developemental stage

tag: tissue/cell type

value: Embryonic Cortical Tissue

value: Control (no stimulation)


title: E16.5_Cortex_1_CGATGT_L008_R1_001


title: Astrocyte_miR_AB_plus_H3_3_2_TGACCA_L003_R1_001

description: processed data file: Supplementary_Spreadsheet_S5_Neuron_Re-resubmission_Final.xls

source_name: Primary Cortical Astrocytes (P1)

value: Primary Cortical Astrocytes

value: Lenti-miR (H3f3a/b) + H3.3 (no stimulation)


title: Candida albicans in Streptococcus gordonii media R3

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

institute: University of Aberdeen

description: C. albicans in hypha inducing conditions for two hours before one hour in S. gordonii media

data_processing:
Base calling was carried out using CASAVA v1.8.2
Reads were filtered for quality and adapters removed using fastq-mcf with the parameters -q 20 -l 35 -p 15 -m 3
ERCC transcripts were removed by alignment to the ERCC reference using Bowtie v 1.0.0
Remaining reads were aligned to the C. albicans and S. gordonii reference genomes using Tophat v 2.0.8 with the following parameters: -G <gff> --library-type fr-secondstrand -l 10000 -r 50 --mate-std-dev 100 -p 8
Bedtools multicov was used to quantify the number of reads aligned at each annotated feature.
Differential expression comparisons were carried out using DESeq v.1.12.1 with default parameters.
Genome_build: Ca21_C_albicans_SC5314 genome
Genome_build: NC_009785 S gordonii CH1 genome
Supplementary_files_format_and_content: Tab delimited matrix containing the number of reads aligned to each feature in each sample.

organism: Candida albicans

source_name: Candida albicans hyphal cells

growth_protocol: C. albicans wild-type strain SC5314 was grown aerobically for 16 h in YPD medium (2% yeast extract, 1% Bacto peptone, 2% glucose) at 37 degrees, with shaking at 220-rpm. Cells were then harvested by centrifugation (5000 x g for 5 min), washed twice in YPT medium (1 x Difco yeast nitrogen base, 20 mM phosphate buffer pH 7.1, 0.1% Bacto tryptone) by alternate centrifugation (5000 x g for 5 min) and suspension, and finally suspended at optical density 600 nm (OD600) = 1.0 (approximately 1 x 107 cells ml-1) in YPT medium. Aliquots (10 ml; 1 x 107 cells ml-1) were transferred into conical flasks containing YPT medium (90 ml) supplemented with 0.4% glucose (YPT-Glc). The cultures were then incubated at 37 degrees for 2 h with shaking at 50-rpm to induce hypha formation. S. gordonii cells were grown anaerobically for 16 h in 10 ml BHY medium (per litre: 37g Brain Heart infusion broth, 5 g yeast extract) and then harvested by centrifugation (5000 x g for 7 min). The bacterial cells were washed twice with YPT (no glucose) and finally suspended at OD600 = 0.5 (2 x 108 cells ml-1) in YPT-Glc medium.

extract_protocol:
Cells were harvested by centrifugation, flash frozen and stored at -70 °C. RNA was extracted using a Qiagen RNeasy Mini Kit following the manufacturer's instructions for yeast using mechanical disruption. An on-column DNase digest using RNase-free DNase (Qiagen) was performed.
ERCC RNA Spike-In Control Mix (Ambion) was mixed with 2.5 µg RNA. Riobsomal RNA was depleted with RiboZero Magnetic Gold Kit (Epicentre) and Illumina sequencing libraries were prepared using ScriptSeq v2 (Epicentre).

tag: sample type


title: Candida albicans alone R2

description: C. albicans in hypha inducing conditions for two hours


title: MDA parental cell line rep2

last: Soong

address: 1305 York Avenue

department: Institute for Computational Biomedicine

institute: Weill Cornell Medical College

description: Sample 2

data_processing:
RNA-seq: For read alignment, the quality of the reads generated by high-throughput sequencing was first examined using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The reads were then trimmed and filtered by quality and aligned against the human genome (release hg18) using the TopHat aligner, which builds exon models de novo from the RNA-seq data and aligns reads across splice junctions. PCR duplicates that might interfere with SNV calling were removed using an in-house program.
SNV calling: SNVs were identified using our in-house progam SNVseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNVseeqer_Install). P-values were further corrected for multiple hypotheses using the Benjamini-Hochberg method and the false discovery rate was controlled to 1%. SNVs identified in less than 10 unique reads were removed from further analysis. The SNVs were also filtered to remove known single nucleotide polymorphisms (SNPs) reported in dbSNP (v130) and annotated with our in-house programs. SNV allelic ratios were calculated by dividing the number of unique reads containing a given variant by the total number of unique reads at each position.
Genome_build: hg18
Supplementary_files_format_and_content: SNV: xlsx file containing SNVs and annotations

source_name: MDA parental cell line

extract_protocol:
Total RNA was extracted using the MiRvana kit (Ambion) and reverse transcribed using the cDNA First-Strand Synthesis kit (Invitrogen).
cDNA libraries were generated using the mRNA Sequencing Sample Preparation Kit (Illumina, 2009) according to the manufacturer’s instructions and sequencing-by-synthesis was performed using the GAIIx sequencer (Illumina).

tag: tissue

value: human metastatic pleural effusion

tag: cell line

value: MDA-MB-231; Human breast carcinoma cell line

tag: passage

value: low passage (<15X)

tag: tumor stage

value: Stage IV


title: MDA parental cell line rep1

description: Sample 1


title: CN34 parental cell line rep1

description: Sample 5

source_name: CN34 parental cell line

value: CN34; Human breast carcinoma cell line


title: Candida albicans in Streptococcus gordonii media R1

value: C. albicans in hypha inducing conditions for two hours before one hour in S. gordonii media


title: CN34 LM1a cell line rep2

description:
Sample 8
these are breast cancer cells grown in mice which then metastasized to the lung.

source_name: CN34 LM1a cell line

value: in vivo selected lung metastasic sub-line

value: CN34 LM1a; in vivo selected highly metastatic human breast cancer cell line

value: low passage (<20X)

value: N/A - derivitive line


title: Candida albicans alone R3

value: C. albicans in hypha inducing conditions for two hours


title: Candida albicans in Streptococcus gordonii media R2


title: Astrocyte_miR_AB_+_H3.1_2_TAGCTT_L007_R1_001

value: Lenti-miR (H3f3a/b) + H3.1 (no stimulation)


title: MDA LM2 cell line rep1

description:
Sample 3
these are breast cancer cells grown in mice which then metastasized to the lung.

source_name: MDA LM2 cell line

value: MDA-LM2; in vivo selected highly metastatic human breast cancer cell line


title: CN34 parental cell line rep2

description: Sample 6


title: Astrocyte_miR_AB_plus_H3_3_1_CGATGT_L003_R1_001


title: MDA LM2 cell line rep2

description:
Sample 4
these are breast cancer cells grown in mice which then metastasized to the lung.


title: Astrocyte_miR_AB_plus_H3_3_2_ACAGTG_L003_R1_001


title: Candida albicans alone R1


title: Astrocyte_miR_AB_+_H3.1_2_GTGGCC_L007_R1_001


title: CN34 LM1a cell line rep1

description:
Sample 7
these are breast cancer cells grown in mice which then metastasized to the lung.


title: OV3/COX1KD, rep 1

city: Nashville

first: Dineo

last: Khabele

address: 1161 21st Avenue South

institute: Vanderbily University

description: Sample name: 2903-DK-4

data_processing:
Illumina CASAVA used for basecalling.
Quality control checks before read mapping with FastQC and after mapping with RSeQC.
Sequenced reads were mapped to the hg19 whole human genome using Tophat 2.0. Aligned reads were assembled and transcript expression quantified using Cufflinks.
The number of reads mapped to each gene was calculated by HTseq (http://www-huber.embl.de/users/anders/HTSeq/).
Differentially expressed genes between the OV3/COX1KD and OV3/SCR cells were detected by DESeq2 and P values were corrected for multiple testing using the Benjamini-Hochberg procedure (Benjamini Y: J Roy Stat Soc B Met 1995; 57: 289-300).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file.

growth_protocol: OV3/SCR and OV3/COX1KD cells were propagated in RPMI-1640 with 10% FBS. 3 independent cell populations were harvested at 60-70% confluence for each cell line. In total, 3 replicate pairs were harvested.

extract_protocol:
Cell monolayers were washed and harvested with PBS, snap-frozen in liquid nitrogen and RNA extracted using Qiagen RNeasy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina TruSeq.

tag: cell line origin

value: derived from parental OVCAR-3 ovarian carcinoma cells

tag: type of shrna

value: COX-1 pRS shRNA HuSH-29 plasmid (OriGene)

tag: cox-1 status

value: COX-1 knockdown


title: OV3/COX1KD, rep 2

description: Sample name: 2903-DK-5


title: OV3/COX1KD, rep 3

description: Sample name: 2903-DK-6


title: OV3/SCR, rep 3

description: Sample name: 2903-DK-3

value: scrambled pRS shRNA HuSH-29 plasmid (OriGene)

value: wild-type


title: OV3/SCR, rep 2

description: Sample name: 2903-DK-2


title: Astrocyte_miR_AB_3_ACAGTG_L002_R1_001

value: Primary Cortical Astrocytes

tag: treatment

value: Lenti-miR (H3f3a/b) (no stimulation)


title: OV3/SCR, rep 1

description: Sample name: 2903-DK-1


title: E16.5_Cortex_2_TGACCA_L008_R1_001

value: Embryonic Cortical Tissue

value: Control (no stimulation)


title: Astrocyte_miR_AB_2_TGACCA_L002_R1_001


title: 30_min_KCl_1_CGATGT_L004_R1_001

description: processed data file: Supplementary_Spreadsheet_S2_Neuron_Re-resubmission_Final.xls

source_name: Primary Cortical Neurons (E16.5 – DIV8)

value: E16.5 – DIV8

value: Primary Cortical Neurons

value: KCl 30 min


title: 30_min_Control_2_TGACCA_L003_R1_001

value: Control (no stimulation) 30 min


title: 2_hr_Control_3_ACAGTG_L005_R1_001

value: Control (no stimulation) 2 hr


title: 2_hr_KCl_1_CGATGT_L006_R1_001

value: KCl 2 hr


title: 2_hr_KCl_2_TGACCA_L006_R1_001


title: rnaseq_K1_Seq_RNA_CGATGT_L007_R1_001

value: KCl 5 hr


title: 30_min_Control_1_CGATGT_L003_R1_001


title: Astrocyte_miR_AB_1_CGATGT_L002_R1_001


title: 30_min_KCl_2_TGACCA_L004_R1_001


title: Astrocyte_miR_AB_+_H3.1_1_ATCACG_L007_R1_001

value: Lenti-miR (H3f3a/b) + H3.1 (no stimulation)


title: 2_hr_Control_1_CGATGT_L005_R1_001


title: 2_hr_Control_2_TGACCA_L005_R1_001


title: rnaseq_EE1_ATCACG_L007_R1_001

description: processed data file: Supplementary_Spreadsheet_S4_Neuron_Re-resubmission_Final.xls

source_name: Adult Hippocampus (~7 weeks)

value: ~7 weeks

value: Adult Hippocampus

value: Environmental Enrichment


title: rnaseq_C2_Seq_RNA_TGACCA_L006_R1_001

value: Control (no stimulation) 5 hr


title: rnaseq_EE3_ACTTGA_L007_R1_001


title: rnaseq_C3_Seq_RNA_ACAGTG_L006_R1_001


title: rnaseq_C1_Seq_RNA_CGATGT_L006_R1_001


title: rnaseq_AF1_ATCACG_L006_R1_001

value: Normally Housed


title: miR_minus_plus_2_merged_R1

description: processed data file: Supplementary_Spreadsheet_S3_Neuron_Re-resubmission_Final.xls

source_name: Primary Cortical Neurons (E16.5 – DIV11)

value: Lenti-miR (-) KCl 5 hr


title: rnaseq_AF2_TTAGGC_L006_R1_001


title: 30_min_Control_3_ACAGTG_L003_R1_001


title: miR_minus_plus_1_merged_R1


title: rnaseq_EE2_TTAGGC_L007_R1_001


title: miR_minus_minus_2_merged_R1

value: Lenti-miR (-) (no stimulation)


title: miR_minus_minus_1_merged_R1


title: 30_min_KCl_3_ACAGTG_L004_R1_001


title: 2_hr_KCl_3_ACAGTG_L006_R1_001


title: rnaseq_K3_Seq_RNA_ACAGTG_L007_R1_001


title: rnaseq_K2_Seq_RNA_TGACCA_L007_R1_001


title: miR_H3f3a_b_KD_plus_2_TGACCA_L003_R1_001

value: Lenti-miR (H3f3a/b) KCl 5 hr


title: miR_H3f3a_b_KD_minus_1_ATCACG_L002_R1_001

value: Lenti-miR (H3f3a/b) (no stimulation)


title: miR_H3f3a_b_KD_minus_2_CGATGT_L002_R1_001


title: miR_AB_H3_3_Control_2_CGATGT_L003_R1_001

value: Lenti-miR (H3f3a/b) + H3.3 (no stimulation)


title: miR_AB_H3_1_Control_2_CGATGT_L002_R1_001

value: Primary Cortical Neurons


title: rnaseq_AF3_ACTTGA_L006_R1_001


title: miR_H3f3a_b_KD_plus_1_TGACCA_L002_R1_001


title: Astrocyte_miR_minus_1_CGATGT_L001_R1_001

value: Primary Cortical Astrocytes

value: Lenti-miR (-)


title: miR_AB_H3_1_Control_1_ATCACG_L002_R1_001


title: Astrocyte_miR_minus_3_ACAGTG_L001_R1_001


title: NM1_IP_ChIP_seq_NoIndex_L003_R1_001.bowtie.mono

description: processed data file: diff.H3.3.Env.w200.fc3.txt

data_processing:
Bowtie version 0.12.7, -v 3 -q -p 3 -a -m 1 -k 1 --best --strata
diffReps v.1.54, --mode n, filter by fold change >3
BedTools v.2.16.2, coverge
Genome_build: mm9
Supplementary_files_format_and_content: TAB delimited text file of chromatin differential sites
Supplementary_files_format_and_content: text file of read counts at TSS+/-1Kb regions

source_name: Adult Hippocampal NeuN+ Cells (~7 weeks postnatal)

extract_protocol:
Crosslinking and Sonicated ChIPs (H3.1/2, H3.3 and HA): Crosslinking ChIP assays were performed with approximately 2x107 neurons per sample (all in vitro experiments analyzed in biological triplicates/group, and in vivo experiments were analyzed in biological duplicates/group). Primary cortical neurons +/- isotonic KCl stimulation (30 min, 2 hrs or 5 hrs) or FACS sorted hippocampal NeuN+ nuclei from adult mice +/- EE (4 wks) were crosslinked with 1% paraformaldehyde (PFA) for 12 minutes at room temperature and then quenched for five minutes with 0.125 M glycine. Pelleted cells/nuclei were washed 5X with 1X PBS containing protease inhibitors before being subjected to lysis and sonication as previously described (Lee et al., 2006). Briefly, crosslinked cell/nuclear pellets were re-suspended and rotated for 10 minutes in 1 mL LB1 buffer [50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X 100, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors] at 4°C. Following pelleting, cells were then re-suspended in 1 mL LB2 buffer [10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors] and rocked at room temperature for 10 minutes. Pelleted cells/nuclei were then re-suspended in 600 µl LB3 buffer [10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors], passed through a 27-gauge needle 3X and split into 300 µl aliquots for sonication using a Bioruptor (Diagenode) for 50 minutes (30 seconds on/30 seconds off; setting = high) at 4°C. All samples were sonicated to approximately 150-300 bp prior to further processing. Following sonication, chromatin was pooled/sample, 1/10 volume of 10% Triton-X 100 was added and samples were spun at 20,000 x g for 10 minutes at 4°C to crack nuclei. Supernatants were then collected and incubated with antibody (7.5 µg/sample) bound sheep anti-rabbit IgG M-280 Dynabeads (Invitrogen, 11203D) on a rotator at 4°C overnight. The following day, immunoprecipitates were washed 8X with 1 mL RIPA buffer [50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors], rinsed 1X with 1 mL TE + 50 mM NaCl buffer and then eluted at 65°C for 30 minutes (shaking) in 210 µl elution buffer [50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS]. After centrifugation, samples, and respective inputs, were reversed crosslinked in elution buffer 65°C overnight. Next, RNA and protein were digested with RNAse (one hour at 37°C; Roche, 11119915001) and proteinase K (two hours at 55°C; Roche, 03115887001), respectively, prior to DNA fragment purification using a Qiagen PCR purification kit.    Covalent Attachment of Tags to Capture Histones and Identify Turnover (CATCH-IT)    For CATCH-IT analyses, primary cortical neurons were cultured as described above for 7 DIV before being switched to conditioned specialty media lacking methionine (AthenaES) but substituted with 4 mM L-Azidohomoalanine-HCl (Aha; Medchem Source) for 24 hours. On DIV 8, neurons (~35x106/sample, analyzed in biological triplicates/condition) were treated +/- KCl (five hours), pelleted and washed 2X with 1X PBS. CATCH-IT processing was then performed and validated as previously described (Deal et al., 2010). Briefly, cells were re-suspended and lysed in 1 mL of ice-cold TM2 buffer [10 mM Tris-HCl, pH 7.0, 2 mM MgCl2, 1% NP-40, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors] with vortexing (5X) for five seconds. Following collection of neuronal nuclei by centrifugation at 1,700 x g for five minutes at 4°C, samples were washed 2X with TM2 buffer minus NP-40 and then re-suspended in 200 µl HB125 buffer [15 mM Tris-HCl, pH 7.5, 125 mM sucrose, 15 mM NaCl, 40 mM KCl, 0.5 mM Spermidine, 0.15 mM Spermine, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors]. Next, cycloaddition reagents were added as follows: biotin alkyne (final concentration of 0.5 mM), a freshly prepared mixture of CuSO4 (final concentration of 1 mM) and ascorbic acid (final concentration of 5 mM). Nuclei were then placed on a rocking platform at 4°C for 30 minutes and pelleted at 17,000 x g for five minutes at 4°C. Re-suspension in HB125 plus cycloaddition reagents (all fresh) was repeated 1X, after which nuclei were re-suspended in 250 µl HB125 with 1 mM EDTA and 2 mM CaCl2 and warmed to 37°C. Next, 15 U MNase was added and samples were further incubated at 37°C for 3.5 minutes with occasional gentle mixing. Digestions were stopped by adding EDTA to a final concentration of 2 mM and nuclei were pelleted at 100 x g for five minutes at 4°C. Nulcei were then re-suspended in 300 µl CSB 350 buffer [1X PBS, 350 mM NaCl, 2 mM EDTA, 0.1% Triton-X 100, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors] and rocked at 4°C for ~16 hours to extract chromatin. Following centrifugation and removal of supernatants (including inputs), 25 µl of packed M280 streptavidin Dynabeads (Invitrogen, 11205D) were added to the solubilized chromatin and samples were rotated at 4°C for 1.5 hours. Magnetic beads were further collected and re-suspended in 1 mL of urea wash buffer [20 mM Tris-HCl, pH 8.0, 4 M urea, 300 mM NaCl, 1 mM EDTA, 10 mM sodium butyrate, plus EDTA-free protease inhibitors and PhosSTOP phosphatase inhibitors] for five minutes at 4°C with gentle rocking. Following urea wash buffer removal, beads were re-suspended in 1 mL of CSB 350 buffer with rocking for five minutes at 4°C. Finally, beads were re-suspended in 100 µl CSB 350 buffer plus 1% SDS, treated with RNAse A (10 minutes at 37°C) and proteinase K (10 minutes at 70°C). DNA fragments associating with newly made H3/H4 proteins were then purified with Qiagen MinElute DNA purification columns and processed for ChIP-seq as described below.
Following DNA purification, ChIP-seq libraries were prepared according to the Illumina protocol and sequenced with the HiSeq 2000. Reads were mapped to the mouse genome (build 37, mm9) using the Bowtie alignment software (Langmead et al., 2009).

value: ~7 weeks postnatal

value: Adult Hippocampal NeuN+ Cells

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: miR_H3f3a_b_KD_minus_3_star_ATCACG_L003_R1_001


title: NM2_Input_ChIP_seq_NoIndex_L001_R1_001.bowtie.mono


title: K3_H3.1_2_ChIP_seq_NoIndex_L003_R1_001.bowtie.mono

description: processed data file: diff.H3.1_2.w200.fc3.txt

value: E16.5 – DIV8

value: KCl 5 hr


title: K3_H3.3_Ab_LB_NoIndex_L008_R1_001.bowtie.mono

description: processed data file: diff.H3.3.Ab.w200.f.txt


title: K2_H3.3_Inp_LB_NoIndex_L003_R1_001.bowtie.mono


title: K1_H3_1_2_Chip_seq_NoIndex_L002_R1_001.bowtie.mono


title: K2_H3.1_2_ChIP_seq_NoIndex_L008_R1_001.bowtie.mono


title: K1_H3.3_Ab_LB_NoIndex_L006_R1_001.bowtie.mono


title: NM1_Input_ChIP_seq_NoIndex_L008_R1_001.bowtie.mono


title: NM2_IP_ChIP_seq_NoIndex_L005_R1_001.bowtie.mono


title: EE_Input_Hipp_NeuN-_TTAGGC_L003_R1_001.fastq_rmdup

description: processed data file: diff.H3.3.Astro.w200.fc3.txt

source_name: Adult Hippocampal NeuN- Cells (~7 weeks postnatal)

value: Adult Hippocampal NeuN- Cells


title: EE2_IP_ChIP_seq_NoIndex_L007_R1_001.bowtie.mono

value: Environmental Enrichment


title: EE2_Input_ChIP_seq_NoIndex_L003_R1_001.bowtie.mono


title: EE3_H3_3_Hipp_NeuN-_TTAGGC_L002_R1_001.fastq_rmdup


title: EE1_IP_ChIP_seq_NoIndex_L006_R1_001.bowtie.mono


title: EE2_H3_3_Hipp_NeuN-_ACTTGA_L002_R1_001.fastq_rmdup


title: Astrocyte_miR_minus_2_TGACCA_L001_R1_001


title: E16_5_Cortex_NeuN_plus_2_H3_3_IP_TAGCTT_L008_R1_001.fastq_rmdup

description: processed data file: Mus_musculus.NCBIM37.62.tss1k.gid.Cortex_H3_3_IP.cnt

source_name: Embryonic Cortical NeuN+ Cells (E16.5)

value: No treatment

value: Embryonic Cortical NeuN+ Cells


title: E16.5_Cortex_NeuN+_Input_GCCAAT_L002_R1_001.fastq_rmdup

description: processed data file: Mus_musculus.NCBIM37.62.tss1k.gid.Cortex_Input.cnt


title: Con3_HA_IP_Lib_NoIndex_L005_R1_001.bowtie.mono

description: processed data file: Mus_musculus.NCBIM37.62.tss1k.gid.HA.cnt

value: Control (no stimulation) 5 hr

value: Covance

value: Clone 16B12


title: miR_AB_H3_3_Control_1_ATCACG_L003_R1_001

description: processed data file: Supplementary_Spreadsheet_S5_Neuron_Re-resubmission_Final.xls


title: K2_H3.3_Ab_LB_NoIndex_L007_R1_001.bowtie.mono


title: E16_5_Cortex_NeuN_plus_3_H3_3_IP_GTGGCC_L008_R1_001.fastq_rmdup


title: Con3_HA_Input_Lib_NoIndex_L003_R1_001.bowtie.mono

description: processed data file: Mus_musculus.NCBIM37.62.tss1k.gid.HA.inp.cnt


title: Con1_HA_IP_Lib_NoIndex_L002_R1_001.bowtie.mono


title: Con2_HA_IP_Lib_NoIndex_L003_R1_001.bowtie.mono


title: CATCH-IT_KCl_2_Input_TAGCTT_L003_R1_001.bowtie

description: processed data file: diff.catch-it.dup6.seprep.w200.normByLib.fc3.txt


title: CATCH-IT_KCl_3_IP_GTGGCC_L001_R1_001.bowtie

value: M280 streptavidin Dynabeads

value: Invitrogen


title: CATCH-IT_KCl_3_Input_GTGGCC_L003_R1_001.bowtie

value: Primary Cortical Neurons


title: CATCH-IT_KCl_1_Input_ATCACG_L003_R1_001.bowtie


title: CATCH-IT_KCl_2_IP_TAGCTT_L001_R1_001.bowtie


title: CATCH-IT_Control_3_Input_GTGGCC_L002_R1_001.bowtie


title: CATCH-IT_Control_3_IP_GTGGCC_L005_R1_001.bowtie


title: CATCH-IT_KCl_1_IP_ATCACG_L001_R1_001.bowtie


title: CATCH-IT_Control_1_IP_ATCACG_L005_R1_001.bowtie


title: CATCH-IT_Control_2_Input_TAGCTT_L002_R1_001.bowtie


title: CATCH-IT_Control_1_Input_ATCACG_L002_R1_001.bowtie


title: miR_H3f3a_b_KD_minus_4_star_CGATGT_L003_R1_001

value: Lenti-miR (H3f3a/b) (no stimulation)


title: C3_H3.3_Ab_LB_NoIndex_L008_R1_001.bowtie.mono


title: C3_H3.1_2_ChIP_seq_NoIndex_L007_R1_001.bowtie.mono


title: EE1_H3_3_Hipp_NeuN-_ATCACG_L002_R1_001.fastq_rmdup


title: EE1_Input_ChIP_seq_NoIndex_L002_R1_001.bowtie.mono


title: C2_H3.3_Inp_LB_NoIndex_L002_R1_001.bowtie.mono


title: C2_H3.3_Ab_LB_NoIndex_L007_R1_001.bowtie.mono


title: C2_H3.1_2_ChIP_seq_NoIndex_L006_R1_001.bowtie.mono


title: AF2_H3_3_IP_Hipp_NeuN-_TTAGGC_L001_R1_001.fastq_rmdup

value: Normally Housed


title: C1_H3.3_Ab_LB_NoIndex_L006_R1_001.bowtie.mono


title: AF3_H3_3_IP_Hipp_NeuN-_ACTTGA_L001_R1_001.fastq_rmdup

value: ~7 weeks postnatal


title: C1_H3_1_2_ChIP_seq_NoIndex_L001_R1_001.bowtie.mono


title: AF_Input_Hipp_NeuN-_ATCACG_L003_R1_001.fastq_rmdup


title: 30_min_KCl_Input_TTAGGC_L005_R1_001.fastq_rmdup

description: processed data file: diff.H3.3.30min.w200.fc3.txt

value: KCl 30 min


title: AF1_H3_3_IP_Hipp_NeuN-_ATCACG_L001_R1_001.fastq_rmdup

value: Millipore


title: 30_min_KCl_2_H3_3_IP_TTAGGC_L004_R1_001.fastq_rmdup

value: E16.5 – DIV8


title: CATCH-IT_Control_2_IP_TAGCTT_L005_R1_001.bowtie


title: 30_min_Control_Input_ATCACG_L005_R1_001.fastq_rmdup

value: Control (no stimulation) 30 min


title: 30_min_Control_1_H3_3_IP_Repeat_ATCACG_L008_R1_001.fastq_rmdup

value: Control (no stimulation) 30 min (repeat of #1)


title: 30_min_Control_2_H3_3_IP_TTAGGC_L008_R1_001.fastq_rmdup


title: 2_hr_KCl_3_H3_3_IP_ACTTGA_L007_R1_001.fastq_rmdup

description: processed data file: diff.H3.3.2hr.w200.fc3.txt

value: KCl 2 hr


title: 30_min_Control_3_H3_3_IP_ACTTGA_L008_R1_001.fastq_rmdup


title: 2_hr_KCl_Input_TTAGGC_L008_R1_001.fastq_rmdup


title: 2_hr_KCl_2_H3_3_IP_TTAGGC_L007_R1_001.fastq_rmdup


title: 2_hr_Control_Input_ATCACG_L008_R1_001.fastq_rmdup

value: Control (no stimulation) 2 hr


title: 2_hr_KCl_1_H3_3_IP_ATCACG_L007_R1_001.fastq_rmdup


title: Sperm_VD2_rep1

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired
We aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 4 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0
Genome_build: mm10
Supplementary_files_format_and_content: We provide .igv files containing methylation scores calculated for all CGs with at least 8x sequencing depth.

source_name: Adult sperm

extract_protocol:
Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction.
We prepared RRBS libraries using a published protocol (Gu et al., Nat Protoc 6:468-81, 2011) with some modifications. Briefly, we digested 100 ng of genomic DNA 5 hours with MspI (Fermentas), followed by end-repair and A-tailing (Klenow fragment, Fermentas), and ligation to methylated adapters (T4 DNA ligase, Fermentas) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 17 cycles of PCR.

value: Vinclozolin

tag: cell type

value: Sperm

tag: embryo stage

value: Adult

tag: group

value: high dose

tag: gender

value: male


title: 2_hr_Control_3_H3_3_IP_ACTTGA_L006_R1_001.fastq_rmdup

tag: strain

tag: developemental stage

tag: tissue/cell type


title: Sperm_VD2_rep3


title: Sperm_control_rep4

value: control

value: unexposed


title: 2_hr_Control_1_H3_3_IP_ATCACG_L006_R1_001.fastq_rmdup

value: Primary Cortical Neurons


title: Sperm_VD2_rep2


title: Sperm_control_rep1


title: Sperm_control_rep5


title: PGCs_VD2

source_name: E13.5 PGCs

value: PGCs


title: 2_hr_Control_2_H3_3_IP_TTAGGC_L006_R1_001.fastq_rmdup


title: Sperm_control_rep3


title: 30_min_KCl_3_H3_3_IP_ACTTGA_L004_R1_001.fastq_rmdup


title: PGCs_VD1

value: low dose


title: PGCs_control_rep2


title: Sperm_control_rep2


title: 30_min_Control_1_H3_3_IP_ATCACG_L008_R1_001.fastq_rmdup


title: PGCs_control_rep1


title: 30_min_KCl_1_H3_3_IP_ATCACG_L004_R1_001.fastq_rmdup

value: KCl 30 min


title: R_2_RRBS

city: Houston

first: Hyunjae

middle: R

last: Kim

state: TX

address: 1102 Bates Ave

department: Pediatric Oncology

institute: Baylor College of Medicine

data_processing:
Reads were aligned to the mouse genome using the Bismark alignment software with a maximum of 2 mismatches and only those reads that mapped to a unique location were retained. Bisulfite converted reads were aligned to in silico bisulfate converted MspI fragments using ELAND aligner.
In order to assign a methylation score for a base position, read bases that aligned to a position were required to have at least 20 phred quality score and 10x coverage. Only CpG dinucleotides that satisfied these coverage and quality criteria were used in the subsequent analysis.
Percent methylation for individual Cs in the genome were calculated as the ratio of the number of alignments with C (methylated), over the number of alignments with either C (methylated) or T (unmethylated).
RRBS data analyses were done with methylKit, a multi-threaded R package.
Genome_build: mm9

source_name: Dnmt TKO ESCs

growth_protocol: WT/mutant Dnmt3a2 expressing Dnmt TKO mouse ESCs were cultured using standard conditions.

extract_protocol:
Genomic DNA was digested with MspI (New England Biolabs, NEB), which cuts DNA at CCGG sequences regardless of the cytosine methylation status, and purified using standard phenol chloroform extraction and ethanol precipitation.
The DNA was end repaired a single dA was added and the DNA was ligated to pre-annealed 5-methylcytosine-containing Illumina adapters according to the manufacturer protocols. Fragments of 150–250 and 250–400 bp were isolated from a 1.5% agarose gel (Biorad, low range ultra agarose) using the Qiaquick Gel Extraction kit, and bisulfite treatment was performed using the EZ DNA Methylation Kit (Zymo Research). PCR amplification was performed for each library with FastStart Hifidelity DNA Polymerase (Roche) and Illumina primers PE1.0 and 2.0, and the PCR products were isolated using AMPure XP beads (Agencort).

tag: passages

value: ESC

tag: construct

value: R Dnmt3a2

tag: cell line

value: J1 ES


title: WWD_2_RRBS

value: WWD Dnmt3a2


title: C_1_RRBS


title: WWD_1_RRBS


title: C_2_RRBS


title: TKO_RRBS


title: TKO_set2_RNAseq

data_processing:
Reads for mRNA-seq were mapped to the mouse genome mm9 using Bowtie and Tophat  allowing one mismatch and tracking up to 50 best alignments per read and default parameter values.
Expression levels were quantified using Cufflinks (http://cufflinks.cbcb.umd.edu/) that measures transcript abundances in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: mm9

extract_protocol:
Total RNA was extracted from TKO and wild-type/mutant Dnmt3a2 expressing TKO ESCs.
5 μg of RNA was subjected to mRNA selection, fragmentation, and cDNA synthesis following the TruSeq RNA Sample Preparation guide (Illumina). End repair, addition of a single dA, ligation with indexed adaptors, and 15 cycles of PCR with Illumina primers were performed also following the TruSeq RNA Sample Preparation guide.


title: R_1_set2_RNAseq


title: WT_2_RRBS

value: WT Dnmt3a2


title: WWD_2_set2_RNAseq