title: singles-K562-CDKi-well-87


title: singles-K562-CDKi-well-86

status: Public on Jun 17 2015

type: SRA

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

description: processed data file: single-K562.peaks.bed

library_source: genomic

data_processing:
library strategy: Single-cell ATAC-seq (scATAC-seq)
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions. Although we saw little effect on calculations of variability, in the case of K562 data, peaks were additionally filtered to exclude copy number amplifications. Using the filtered peak set, peak summits were extended +/-250 bps. The top 50,000 non-overlapping 500 bp summits are available here and were used for all downstream analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep). K562 cells were treated with 1 µM CDK4/6 inhibitor (PD 0332991, Pfizer) for 24 h.

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: cell line

tag: cell type

value: chronic myeloid leukemia cells

tag: treated with

value: a cell cycle inhibitor


title: singles-K562-CDKi-well-83


title: singles-K562-CDKi-well-84


title: singles-K562-CDKi-well-85


title: singles-K562-CDKi-well-80


title: singles-K562-CDKi-well-81


title: singles-K562-CDKi-well-79


title: singles-K562-CDKi-well-77


title: singles-K562-CDKi-well-82


title: singles-K562-CDKi-well-76


title: singles-K562-CDKi-well-95


title: singles-K562-CDKi-well-75


title: singles-K562-CDKi-well-72


title: singles-K562-CDKi-well-73


title: singles-K562-CDKi-well-74


title: singles-K562-CDKi-well-71


title: singles-K562-CDKi-well-70


title: singles-K562-CDKi-well-65


title: singles-K562-CDKi-well-67


title: singles-K562-CDKi-well-90


title: singles-K562-CDKi-well-64


title: singles-K562-CDKi-well-66


title: singles-K562-CDKi-well-62


title: singles-K562-CDKi-well-63


title: singles-K562-CDKi-well-78


title: singles-K562-CDKi-well-61


title: singles-K562-CDKi-well-58


title: singles-K562-CDKi-well-59


title: singles-K562-CDKi-well-60


title: singles-K562-CDKi-well-53


title: singles-K562-CDKi-well-55


title: singles-K562-CDKi-well-52


title: singles-K562-CDKi-well-50


title: singles-K562-CDKi-well-57


title: singles-K562-CDKi-well-56


title: singles-K562-CDKi-well-54


title: singles-K562-CDKi-well-49


title: singles-K562-CDKi-well-47


title: singles-K562-CDKi-well-46


title: singles-K562-CDKi-well-45


title: singles-K562-CDKi-well-68


title: singles-K562-CDKi-well-42


title: singles-K562-CDKi-well-44


title: singles-K562-CDKi-well-43


title: singles-K562-CDKi-well-48


title: singles-K562-CDKi-well-40


title: singles-K562-CDKi-well-41


title: singles-K562-CDKi-well-36


title: singles-K562-CDKi-well-34


title: singles-K562-CDKi-well-51


title: singles-K562-CDKi-well-31


title: singles-K562-CDKi-well-32


title: singles-K562-CDKi-well-30


title: singles-K562-CDKi-well-35


title: singles-K562-CDKi-well-38


title: singles-K562-CDKi-well-27


title: singles-K562-CDKi-well-39


title: singles-K562-CDKi-well-23


title: singles-K562-CDKi-well-29


title: singles-K562-CDKi-well-24


title: singles-K562-CDKi-well-26


title: singles-K562-CDKi-well-20


title: singles-K562-CDKi-well-33


title: singles-K562-CDKi-well-22


title: singles-K562-CDKi-well-15


title: singles-K562-CDKi-well-16


title: singles-K562-CDKi-well-18


title: singles-K562-CDKi-well-28


title: singles-K562-CDKi-well-25


title: singles-K562-CDKi-well-17


title: singles-K562-CDKi-well-14


title: singles-K562-CDKi-well-19


title: singles-K562-CDKi-well-37


title: singles-K562-CDKi-well-12


title: singles-K562-CDKi-well-13


title: singles-K562-CDKi-well-11


title: singles-K562-CDKi-well-9


title: singles-K562-CDKi-well-10


title: singles-K562-CDKi-well-7


title: singles-K562-CDKi-well-4


title: singles-K562-CDKi-well-6


title: singles-K562-CDKi-well-3


title: singles-K562-CDKi-well-5


title: singles-K562-CDKi-well-21


title: singles-K562-CDKi-well-8


title: singles-K562-CDKi-well-2


title: singles-K562-CDKi-well-1


title: singles-GM-TNFa6h-well-91

description: processed data file: single-GM12878.peaks.bed

growth_protocol: GM12878 lymphoblastoid cells (a kind gift from the Snyder lab) were grown in RPMI 1640 with 2 mmol/L L-glutamine, 15% FBS and 1% Pen/Strep. GM12878 cells were treated with 25 ng/mL rhTNFα (eBiosciences) for 6 h.

value: lymphoblastoid cells

value: TNFa for 6 hours


title: singles-GM-TNFa6h-well-87


title: singles-GM-TNFa6h-well-90


title: singles-GM-TNFa6h-well-92


title: singles-GM-TNFa6h-well-94


title: singles-GM-TNFa6h-well-89


title: singles-K562-CDKi-well-69


title: singles-GM-TNFa6h-well-96


title: singles-GM-TNFa6h-well-88


title: singles-GM-TNFa6h-well-86


title: singles-GM-TNFa6h-well-83


title: singles-GM-TNFa6h-well-84


title: singles-GM-TNFa6h-well-82


title: singles-GM-TNFa6h-well-85


title: singles-GM-TNFa6h-well-95


title: singles-GM-TNFa6h-well-79


title: singles-GM-TNFa6h-well-78


title: singles-GM-TNFa6h-well-73


title: singles-GM-TNFa6h-well-74


title: singles-GM-TNFa6h-well-72


title: singles-GM-TNFa6h-well-93


title: singles-GM-TNFa6h-well-76


title: singles-GM-TNFa6h-well-75


title: singles-GM-TNFa6h-well-71


title: singles-GM-TNFa6h-well-77


title: singles-GM-TNFa6h-well-69


title: singles-GM-TNFa6h-well-68


title: singles-GM-TNFa6h-well-66


title: singles-GM-TNFa6h-well-65


title: singles-GM-TNFa6h-well-63


title: singles-GM-TNFa6h-well-81


title: singles-GM-TNFa6h-well-67


title: singles-GM-TNFa6h-well-80


title: singles-GM-TNFa6h-well-64


title: singles-GM-TNFa6h-well-59


title: singles-GM-TNFa6h-well-58


title: singles-GM-TNFa6h-well-57


title: singles-GM-TNFa6h-well-61


title: singles-GM-TNFa6h-well-56


title: singles-GM-TNFa6h-well-54


title: singles-GM-TNFa6h-well-55


title: singles-GM-TNFa6h-well-70


title: singles-GM-TNFa6h-well-53


title: singles-GM-TNFa6h-well-49


title: singles-GM-TNFa6h-well-52


title: singles-GM-TNFa6h-well-51


title: singles-GM-TNFa6h-well-46


title: singles-GM-TNFa6h-well-50


title: singles-GM-TNFa6h-well-47


title: singles-GM-TNFa6h-well-43


title: singles-GM-TNFa6h-well-44


title: singles-GM-TNFa6h-well-45


title: singles-GM-TNFa6h-well-62


title: singles-GM-TNFa6h-well-41


title: singles-GM-TNFa6h-well-60


title: singles-GM-TNFa6h-well-39


title: singles-GM-TNFa6h-well-38


title: singles-GM-TNFa6h-well-35


title: singles-GM-TNFa6h-well-42


title: singles-GM-TNFa6h-well-37


title: singles-GM-TNFa6h-well-33


title: singles-GM-TNFa6h-well-30


title: singles-GM-TNFa6h-well-31


title: singles-GM-TNFa6h-well-27


title: singles-GM-TNFa6h-well-29


title: singles-GM-TNFa6h-well-28


title: singles-GM-TNFa6h-well-26


title: singles-GM-TNFa6h-well-25


title: singles-GM-TNFa6h-well-48


title: singles-GM-TNFa6h-well-23


title: singles-GM-TNFa6h-well-22


title: singles-GM-TNFa6h-well-24


title: singles-GM-TNFa6h-well-19


title: singles-GM-TNFa6h-well-21


title: singles-GM-TNFa6h-well-20


title: singles-GM-TNFa6h-well-17


title: singles-GM-TNFa6h-well-16


title: singles-GM-TNFa6h-well-18


title: singles-GM-TNFa6h-well-36


title: singles-GM-TNFa6h-well-34


title: singles-GM-TNFa6h-well-40


title: singles-GM-TNFa6h-well-15


title: singles-GM-TNFa6h-well-14


title: singles-GM-TNFa6h-well-13


title: singles-GM-TNFa6h-well-32


title: singles-GM-TNFa6h-well-9


title: singles-GM-TNFa6h-well-10


title: singles-GM-TNFa6h-well-12


title: singles-GM-TNFa6h-well-8


title: singles-GM-TNFa6h-well-7


title: singles-GM-TNFa6h-well-6


title: singles-GM-TNFa6h-well-3


title: singles-GM-TNFa6h-well-5


title: singles-GM-TNFa6h-well-4


title: singles-GM-TNFa6h-well-1


title: singles-GM-rep4-well-96

growth_protocol: GM12878 lymphoblastoid cells (a kind gift from the Snyder lab) were grown in RPMI 1640 with 2 mmol/L L-glutamine, 15% FBS and 1% Pen/Strep.

value: none (untreated)


title: singles-GM-rep4-well-95


title: singles-GM-rep4-well-92


title: singles-GM-rep4-well-94


title: singles-GM-rep4-well-93


title: singles-GM-rep4-well-90


title: singles-GM-rep4-well-91


title: singles-GM-rep4-well-87


title: singles-GM-rep4-well-88


title: singles-GM-rep4-well-89


title: singles-GM-rep4-well-86


title: singles-GM-rep4-well-85


title: singles-GM-TNFa6h-well-11


title: singles-GM-rep4-well-82


title: singles-GM-rep4-well-84


title: singles-GM-rep4-well-81


title: singles-GM-rep4-well-80


title: singles-GM-rep4-well-83


title: singles-GM-rep4-well-78


title: singles-GM-rep4-well-76


title: singles-GM-rep4-well-79


title: singles-GM-rep4-well-77


title: singles-GM-TNFa6h-well-2


title: singles-GM-rep4-well-74


title: singles-GM-rep4-well-72


title: singles-GM-rep4-well-73


title: singles-GM-rep4-well-75


title: singles-GM-rep4-well-69


title: singles-GM-rep4-well-70


title: singles-GM-rep4-well-67


title: singles-GM-rep4-well-66


title: singles-GM-rep4-well-65


title: singles-GM-rep4-well-64


title: singles-GM-rep4-well-60


title: singles-GM-rep4-well-62


title: singles-GM-rep4-well-61


title: singles-GM-rep4-well-58


title: singles-GM-rep4-well-57


title: singles-GM-rep4-well-56


title: singles-GM-rep4-well-54


title: singles-GM-rep4-well-50


title: singles-GM-rep4-well-52


title: singles-GM-rep4-well-48


title: singles-GM-rep4-well-47


title: singles-GM-rep4-well-55


title: singles-GM-rep4-well-51


title: singles-GM-rep4-well-45


title: singles-GM-rep4-well-46


title: singles-GM-rep4-well-43


title: singles-GM-rep4-well-44


title: singles-GM-rep4-well-71


title: singles-GM-rep4-well-42


title: singles-GM-rep4-well-68


title: singles-GM-rep4-well-41


title: singles-GM-rep4-well-39


title: singles-GM-rep4-well-40


title: singles-GM-rep4-well-63


title: singles-GM-rep4-well-38


title: singles-GM-rep4-well-59


title: singles-GM-rep4-well-37


title: singles-GM-rep4-well-36


title: singles-GM-rep4-well-35


title: singles-GM-rep4-well-53


title: singles-GM-rep4-well-34


title: singles-GM-rep4-well-29


title: singles-GM-rep4-well-28


title: singles-GM-rep4-well-30


title: singles-GM-rep4-well-32


title: singles-GM-rep4-well-24


title: singles-GM-rep4-well-31


title: singles-GM-rep4-well-49


title: singles-GM-rep4-well-22


title: singles-GM-rep4-well-25


title: singles-GM-rep4-well-27


title: singles-GM-rep4-well-23


title: singles-GM-rep4-well-20


title: singles-GM-rep4-well-16


title: singles-GM-rep4-well-18


title: singles-GM-rep4-well-19


title: singles-GM-rep4-well-26


title: singles-GM-rep4-well-15


title: singles-GM-rep4-well-17


title: singles-GM-rep4-well-12


title: singles-GM-rep4-well-11


title: singles-GM-rep4-well-14


title: singles-GM-rep4-well-13


title: singles-GM-rep4-well-8


title: singles-GM-rep4-well-33


title: singles-GM-rep4-well-10


title: singles-GM-rep4-well-6


title: singles-GM-rep4-well-7


title: singles-GM-rep4-well-5


title: singles-GM-rep4-well-3


title: singles-GM-rep4-well-4


title: singles-GM-rep4-well-2


title: singles-GM-rep3-well-96


title: singles-GM-rep4-well-1


title: singles-GM-rep3-well-95


title: singles-GM-rep3-well-94


title: singles-GM-rep3-well-93


title: singles-GM-rep3-well-91


title: singles-GM-rep3-well-92


title: singles-GM-rep3-well-88


title: singles-GM-rep3-well-90


title: singles-GM-rep4-well-9


title: singles-GM-rep3-well-87


title: singles-GM-rep3-well-85


title: singles-GM-rep3-well-86


title: singles-GM-rep3-well-83


title: singles-GM-rep3-well-84


title: singles-GM-rep3-well-78


title: singles-GM-rep3-well-77


title: singles-GM-rep3-well-82


title: singles-GM-rep3-well-80


title: singles-GM-rep3-well-79


title: singles-GM-rep3-well-76


title: singles-GM-rep3-well-75


title: singles-GM-rep3-well-74


title: singles-GM-rep3-well-73


title: singles-GM-rep3-well-72


title: singles-GM-rep3-well-71


title: singles-GM-rep3-well-68


title: singles-GM-rep3-well-69


title: singles-GM-rep3-well-70


title: singles-GM-rep3-well-65


title: singles-GM-rep3-well-89


title: singles-GM-rep3-well-66


title: singles-GM-rep3-well-67


title: singles-GM-rep3-well-81


title: singles-GM-rep3-well-64


title: singles-GM-rep3-well-60


title: singles-GM-rep3-well-59


title: singles-GM-rep3-well-63


title: singles-GM-rep3-well-61


title: singles-GM-rep3-well-62


title: singles-GM-rep3-well-54


title: singles-GM-rep3-well-58


title: singles-GM-rep3-well-53


title: singles-GM-rep3-well-52


title: singles-GM-rep3-well-51


title: singles-GM-rep3-well-50


title: singles-GM-rep3-well-56


title: singles-GM-rep3-well-48


title: singles-GM-rep3-well-49


title: singles-GM-rep3-well-47


title: singles-GM-rep3-well-55


title: singles-GM-rep3-well-46


title: singles-GM-rep3-well-44


title: singles-GM-rep3-well-41


title: singles-GM-rep3-well-42


title: singles-GM-rep3-well-39


title: singles-GM-rep3-well-37


title: singles-GM-rep3-well-38


title: singles-GM-rep3-well-57


title: singles-GM-rep3-well-36


title: singles-GM-rep3-well-35


title: singles-GM-rep3-well-34


title: singles-GM-rep3-well-33


title: singles-GM-rep3-well-32


title: singles-GM-rep3-well-31


title: singles-GM-rep3-well-30


title: singles-GM-rep3-well-28


title: singles-GM-rep3-well-27


title: singles-GM-rep3-well-24


title: singles-GM-rep3-well-23


title: singles-GM-rep3-well-26


title: singles-GM-rep3-well-25


title: singles-GM-rep3-well-22


title: singles-GM-rep3-well-21


title: singles-GM-rep3-well-45


title: singles-GM-rep3-well-43


title: singles-GM-rep3-well-40


title: singles-GM-rep3-well-19


title: singles-GM-rep3-well-20


title: singles-GM-rep3-well-18


title: singles-GM-rep3-well-17


title: singles-GM-rep3-well-16


title: singles-GM-rep3-well-15


title: singles-GM-rep3-well-12


title: singles-GM-rep3-well-13


title: singles-GM-rep3-well-14


title: singles-GM-rep3-well-11


title: singles-GM-rep3-well-10


title: singles-GM-rep3-well-9


title: singles-GM-rep3-well-29


title: singles-GM-rep3-well-7


title: singles-GM-rep3-well-6


title: singles-GM-rep3-well-8


title: singles-GM-rep3-well-5


title: singles-GM-rep3-well-4


title: singles-GM-rep3-well-3


title: singles-H1ESC-well-96

description: processed data file: single-H1ESC.peaks.bed

growth_protocol: The H1 human embryonic stem cells were obtained from WiCell and grown in chemically defined mTeSR1 medium (STEMCELL Technologies) on Matrigel-coated plates.

value: human embryonic stem cell line


title: singles-H1ESC-well-94


title: singles-H1ESC-well-92


title: singles-H1ESC-well-95


title: singles-H1ESC-well-93


title: singles-GM-rep3-well-2


title: singles-H1ESC-well-90


title: singles-H1ESC-well-89


title: singles-H1ESC-well-85


title: singles-H1ESC-well-84


title: singles-H1ESC-well-88


title: singles-H1ESC-well-86


title: singles-H1ESC-well-83


title: singles-H1ESC-well-91


title: singles-H1ESC-well-82


title: singles-H1ESC-well-80


title: singles-H1ESC-well-81


title: singles-H1ESC-well-77


title: singles-H1ESC-well-79


title: singles-H1ESC-well-78


title: singles-H1ESC-well-76


title: singles-H1ESC-well-75


title: singles-H1ESC-well-73


title: singles-GM-rep3-well-1


title: singles-H1ESC-well-72


title: singles-H1ESC-well-74


title: singles-H1ESC-well-71


title: singles-H1ESC-well-70


title: singles-H1ESC-well-69


title: singles-H1ESC-well-67


title: singles-H1ESC-well-68


title: singles-H1ESC-well-65


title: singles-H1ESC-well-66


title: singles-H1ESC-well-64


title: singles-H1ESC-well-87


title: singles-H1ESC-well-63


title: singles-H1ESC-well-61


title: singles-H1ESC-well-60


title: singles-H1ESC-well-59


title: singles-H1ESC-well-62


title: singles-H1ESC-well-57


title: singles-H1ESC-well-56


title: singles-GM-rep4-well-21


title: singles-H1ESC-well-55


title: singles-H1ESC-well-53


title: singles-H1ESC-well-51


title: singles-H1ESC-well-50


title: singles-H1ESC-well-49


title: singles-H1ESC-well-52


title: singles-H1ESC-well-46


title: singles-H1ESC-well-45


title: singles-H1ESC-well-54


title: singles-H1ESC-well-47


title: singles-H1ESC-well-43


title: singles-H1ESC-well-42


title: singles-H1ESC-well-48


title: singles-H1ESC-well-37


title: singles-H1ESC-well-58


title: singles-H1ESC-well-38


title: singles-H1ESC-well-39


title: singles-H1ESC-well-35


title: singles-H1ESC-well-40


title: singles-H1ESC-well-36


title: singles-H1ESC-well-34


title: singles-H1ESC-well-33


title: singles-H1ESC-well-30


title: singles-H1ESC-well-27


title: singles-H1ESC-well-28


title: singles-H1ESC-well-26


title: singles-H1ESC-well-44


title: singles-H1ESC-well-22


title: singles-H1ESC-well-23


title: singles-H1ESC-well-24


title: singles-H1ESC-well-20


title: singles-H1ESC-well-25


title: singles-H1ESC-well-41


title: singles-H1ESC-well-18


title: singles-H1ESC-well-19


title: singles-H1ESC-well-16


title: singles-H1ESC-well-15


title: singles-H1ESC-well-17


title: singles-H1ESC-well-11


title: singles-H1ESC-well-9


title: singles-H1ESC-well-12


title: singles-H1ESC-well-13


title: singles-H1ESC-well-14


title: singles-H1ESC-well-31


title: singles-H1ESC-well-29


title: singles-H1ESC-well-6


title: singles-H1ESC-well-8


title: singles-H1ESC-well-7


title: singles-H1ESC-well-4


title: singles-H1ESC-well-2


title: singles-H1ESC-well-3


title: singles-H1ESC-well-1


title: GLU rep2

city: Beijing

first: Shan

last: Li

address: No.38 Xueqing Road, Haidian Distric

country: China

institute: Novogene institute

library_source: transcriptomic

data_processing:
Quality control: clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Transcriptome assembly:The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (r20140413p1) with min_kmer_cov set to 2 by default and all other parameters set default.
Quantification of gene expression levels: RSEM (v1.2.15, bowtie2 mismatch 0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Thermomyces lanuginosus

source_name: mycelia

extract_protocol: none provided by the submitter of this dataset

tag: strain

tag: treatment

value: mycelia cultured on glucose

tag: age

value: 2-day old mycelia


title: GLU rep1


title: MCC rep2

value: mycelia cultured on Avicel


title: MCC rep1


title: singles-H1ESC-well-21


title: BxPc3exo 1

city: New York

first: David

last: Lyden

state: NY

department: Departments of Pediatrics, Cell & Developmental Biology

institute: Weill Medical College of Cornell University

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Number of raw counts was calculated using the htseq-count script in the HTSeq package v0.6.1 with parameters "--stranded=no --mode=union --minaqual=10"; Genes with statistically significant changes in expression were selected by using the edgeR package v3.8.2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file including gene name, RefSeq id, raw counts and normalized counts of each sample, for each gene

source_name: Human Kupffer cells

growth_protocol: RPMI + 10% exosome free FBS

extract_protocol:
RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated in 6 wells plates with 5ug/mL of exosomes every other day for 14 days

value: Kupffer cells (Primary culture (Life technologies))

value: BxPC-3 exosomes


title: Control 2

value: PBS


title: singles-H1ESC-well-10


title: BxPc3exo 2


title: BxPc3 Beta5 integrin KD exo 2

value: BxPc3 Beta5KD exosomes


title: singles-H1ESC-well-5


title: singles-mESC-well-93

description: processed data file: single-mESC.peaks.bed

organism: Mus musculus

source_name: singles-mESC

growth_protocol: V6.5 mouse embryonic stem cells were grown in Glasgow Minimum Essential Medium (GMEM) supplemented with 10% FBS, 2 mM glutamine, 1% Pen/Strep, 1 mM sodium pyruvate, 1000 units/ml Leukemia Inhibitory Factor (LIF, Millipore), 1X Minimum Essential Medium NonEssential Amino Acids (MEM NEAA, Invitrogen) and 50 uM β-Mercaptoethanol. Cells were maintained on gelatin-coated dishes without feeders.

value: mouse embryonic stem cells


title: FAIRE_Dvir_EA

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by  Bowtie2 (default parameters)
Species alignments were converted to D.melanogaster coordinates by liftOver tool from UCSC (minMatch=0.1)
F-Seq (Boyle et al. 2008) was used to detect nucleosome-free regions in relation to background signal (parameters l=200)
HT-Seq was used to count the number of reads falling within a called peak
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: Peak position and original as well as normalized counts

organism: Drosophila virilis

source_name: eye-antennal imaginal disc

growth_protocol: All flies were raised at 25 degrees Celsius on standard fly food

extract_protocol:
Nucleosome-depleted regions were extracted with phenol/chloroform followed by ethanol precipitation and RNAse A treatment.
Libraries were prepared for sequencing using standard Illumina Truseq protocols

treatment_protocol: FAIRE-Seq was perfomed in accordance to (Giresi et al. 2007). Eye-antennal imaginal discs were dissected in PBT and cross-linked in 4% formaldehyde for 10 min. Chromatin was isolated using a 3-step lysis protocol and next it was subjected to a ten-cycle sonication (30 seconds on/off).

tag: developmental time point

value: third instar wandering larvae

tag: tissue

value: eye-antennal imaginal disc

tag: genotype

value: Dvir\wild-type

tag: stock


title: singles-mESC-well-95


title: singles-mESC-well-92


title: singles-mESC-well-90


title: singles-mESC-well-96


title: singles-mESC-well-89


title: singles-mESC-well-91


title: BxPc3 Beta5 integrin KD exo 1


title: singles-mESC-well-94


title: singles-H1ESC-well-32


title: singles-mESC-well-88


title: singles-mESC-well-86


title: BxPc3exo 3


title: singles-mESC-well-84


title: singles-mESC-well-83


title: singles-mESC-well-80


title: singles-mESC-well-79


title: Control 1


title: singles-mESC-well-85


title: singles-mESC-well-82


title: singles-mESC-well-87


title: singles-mESC-well-78


title: Control 3


title: singles-mESC-well-81


title: singles-mESC-well-77


title: singles-mESC-well-76


title: singles-mESC-well-73


title: singles-mESC-well-74


title: singles-mESC-well-75


title: singles-mESC-well-70


title: singles-mESC-well-71


title: singles-mESC-well-72


title: singles-mESC-well-67


title: singles-mESC-well-68


title: singles-mESC-well-69


title: singles-mESC-well-66


title: singles-mESC-well-64


title: singles-mESC-well-63


title: singles-mESC-well-61


title: singles-mESC-well-60


title: singles-mESC-well-62


title: singles-mESC-well-57


title: singles-mESC-well-59


title: singles-mESC-well-53


title: singles-mESC-well-54


title: singles-mESC-well-55


title: singles-mESC-well-56


title: singles-mESC-well-51


title: singles-mESC-well-49


title: singles-mESC-well-50


title: singles-mESC-well-52


title: singles-mESC-well-65


title: singles-mESC-well-47


title: singles-mESC-well-48


title: singles-mESC-well-46


title: singles-mESC-well-44


title: RNA-seq JQ1 TNF 2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: RNA.JQ1.counts.txt (JT2)

data_processing:
RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
Total RNA-seq coverage within exons were quantified  using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40). Log2 (Reads pr. kilobase pr. mio reads) are provided in RNA.JQ1.counts.txt
Genome_build: hg19

source_name: Adipocyte

growth_protocol: SGBS cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham’s supplemented with 10% fetal bovine serum, 33 µM biotin, 17 µM pantothenate, 100 µg/ml streptomycin, 62.5 µg/ml penicillin, 1ng/µl fibroblast growth factors (FGF) 1, and 90 µg/µl heparin. At two days postconfluency, SGBS cells were stimulated to differentiate with serum-free growth medium supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM BRL 49653, 0.115 mg/ml MIX, 0.25 mmol/L DEX, and 0.01 mg/ml human transferrin. After 3 days, the medium was replaced with the differentiation medium without FGF1 and heparin, and after 6 days Rosiglitazone/BRL49653, MIX, and DEX was removed from the medium.

extract_protocol:
Following Isol extraction and column purification of total RNA, ribosomal RNAs were removed using the Ribo-Zero Human/Mouse/Rat kit (Epicentre).
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Mature SGBS adipocyte D10 were treated with 10ng/ml TNF or vehicle for 90/60 min before harvest of total RNA or chromatin for ChIP-seq respectively. p65 knockdown was achieved by transduction of SGBS adipocytes at day 6 of differentiation with shRNA-expressing lentivira. For JQ1 experiments, vehicle and TNF treated adipocytes were cotreated with 500nM JQ1 or DMSO for 90 min.

value: SGBS adipocyte D10


title: BRD4 ChIP-seq Vehicle

data_processing:
ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
BedGraph files were created using HOMER for visualization of binding profiles.
Genome_build: hg19

extract_protocol:
ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

tag: chip antibody

value: BRD4 (A301-985A, Bethyl)


title: RNA-seq JQ1 TNF 1

description: RNA.JQ1.counts.txt (JT1)


title: RNA-seq DMSO TNF 2

description: RNA.JQ1.counts.txt (DT2)


title: RNA-seq JQ1 Vehicle 2

description: RNA.JQ1.counts.txt (JV2)


title: RNA-seq JQ1 Vehicle 1

description: RNA.JQ1.counts.txt (JV1)


title: RNA-seq DMSO Vehicle 1

description: RNA.JQ1.counts.txt (DV1)


title: singles-mESC-well-41


title: BRD4 ChIP-seq TNF


title: singles-mESC-well-39


title: singles-mESC-well-40


title: RNA-seq shp65 TNF 3

data_processing:
RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
Total RNA-seq coverage within introns were quantified using the iRNA-seq pipeline (Madsen et al, Nucl. Acids Res. 43 (6): e40), to asses primary transcript levels. Log2 (Reads pr. kilobase pr. mio reads) are provided in RNA.KD.counts.txt
hg19


title: RNA-seq shp65 Vehicle 2


title: singles-mESC-well-38


title: RNA-seq shp65 TNF 1


title: RNA-seq Preadipocyte 1

data_processing:
RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
Total RNA-seq coverage within exons were quantified using the iRNA-seq pipeline (Madsen et al, in review). Log2 (Reads pr. kilobase pr. mio reads) are provided in RNA.Pre.counts.txt
hg19

source_name: Preadipocyte

value: SGBS preadipocyte D0


title: RNA-seq Preadipocyte 2


title: RNA-seq shp65 Vehicle 3


title: RNA-seq shScr TNF 2


title: RNA-seq shp65 Vehicle 1


title: RNA-seq shScr TNF 3


title: RNA-seq shp65 TNF 2


title: singles-mESC-well-45


title: RNA-seq DMSO TNF 1

description: RNA.JQ1.counts.txt (DT1)


title: RNA-seq shScr TNF 1


title: RNA-seq DMSO Vehicle 2

description: RNA.JQ1.counts.txt (DV2)


title: singles-mESC-well-37


title: singles-mESC-well-43


title: RNA-seq shScr Vehicle 3


title: singles-mESC-well-36


title: RNA-seq shScr Vehicle 2


title: singles-mESC-well-35


title: RNA-seq shScr Vehicle 1


title: DHS-seq TNF

data_processing:
Library strategy: DHS-seq
Paired-end DHS-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default paired-end parameters. Prior to data processing, aligned paired-end sequencing reads were processed by unix awk commands to convert paired-end reads to single-end reads.
BedGraph files were created using HOMER for visualization of binding profiles.
hg19

extract_protocol:
DHS-seq was performed on ~10 mill. nuclei essentially as described in (Siersbaek et al. 2011).
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).


title: singles-mESC-well-58


title: singles-mESC-well-42


title: Input TNF

data_processing:
ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
BedGraph files were created using HOMER for visualization of binding profiles.
hg19


title: p65 ChIP-seq TNF 2

data_processing:
ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
Regions enriched for p65 ChIP-seq signal in TNF treated adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting and a 0.1% FDR threshold. Merged peak files were generated from the individual p65 peak files if the center of two or more peaks were within 200 bp. Peaks from these merged peak files were only included if having more than 10 tags per 10 M tags in a 400 bp window around the center of each merged peak in both replicates of the TNF condition. BedGraph files were created using HOMER for visualization of binding profiles.
hg19

value: RELA (C-20, sc-372, Santa Cruz)


title: singles-mESC-well-34

value: none (untreated)


title: singles-mESC-well-33


title: p65 ChIP-seq Vehicle 2


title: Input Veh


title: MED1 ChIP-seq TNF Rep2

data_processing:
ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
Regions enriched for MED1 ChIP-seq signal in vehicle or TNF treated adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting and a 0.1% FDR threshold. Merged peak files were generated from the individual MED1 peak files if the center of two or more peaks were within 200 bp. Peaks from these merged peak files were only included if having more than 8 tags per 10 M tags in a 400 bp window around the center of each merged peak in both replicates of one or both conditions. Differential signal intensity in MED1 binding regions in white and brite hMADS adipocytes was determined using paired analyses with EdgeR (Robinson et al. 2010, Bioinformatics 26: 139-140). BedGraph files were created using HOMER for visualization of binding profiles.
hg19

value: MED1 (M-255, sc-8998, Santa Cruz)


title: MED1 ChIP-seq Vehicle Rep2


title: singles-mESC-well-30


title: p65 ChIP-seq TNF 1


title: MED1 ChIP-seq Vehicle Rep1

data_processing:
ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
Regions enriched for MED1 ChIP-seq signal in vehicle or TNF treated adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting and a 0.1% FDR threshold. Merged peak files were generated from the individual MED1 peak files if the center of two or more peaks were within 200 bp. Peaks from these merged peak files were only included if having more than 8 tags per 10 M tags in a 400 bp window around the center of each merged peak in both replicates of one or both conditions. Differential signal intensity in MED1 binding regions in white and brite hMADS adipocytes was determined using paired analyses with EdgeR (Robinson et al. 2010, Bioinformatics 26: 139-140). Bigwig files for visualization of binding profiles were created using HOMER.
hg19


title: p65 ChIP-seq Vehicle 1


title: MED1 ChIP-seq TNF Rep1


title: singles-mESC-well-31


title: singles-HL60-well-96

description: processed data file: single-HL60.peaks.bed

growth_protocol: The promyelocytic leukemia cells HL-60 were grown in IMDM containing 20% FBS and 1% Pen/Strep.

value: promyelocytic leukemia cells


title: singles-HL60-well-95


title: singles-mESC-well-28


title: singles-mESC-well-27


title: singles-mESC-well-29


title: singles-mESC-well-26


title: singles-HL60-well-94


title: DHS-seq Veh


title: singles-HL60-well-91


title: singles-HL60-well-89


title: singles-HL60-well-90


title: singles-HL60-well-93


title: singles-HL60-well-87


title: singles-mESC-well-24


title: singles-mESC-well-25


title: singles-HL60-well-86


title: singles-HL60-well-85


title: singles-HL60-well-84


title: singles-HL60-well-83


title: singles-HL60-well-80


title: singles-HL60-well-81


title: singles-HL60-well-82


title: singles-mESC-well-32


title: singles-mESC-well-22


title: singles-HL60-well-92


title: singles-HL60-well-78


title: singles-HL60-well-88


title: singles-mESC-well-19


title: singles-HL60-well-77


title: singles-HL60-well-74


title: singles-mESC-well-20


title: singles-mESC-well-18


title: singles-mESC-well-21


title: singles-mESC-well-17


title: singles-HL60-well-73


title: singles-HL60-well-70


title: singles-HL60-well-75


title: singles-HL60-well-72


title: singles-HL60-well-71


title: singles-mESC-well-14


title: singles-mESC-well-16


title: singles-HL60-well-68


title: singles-mESC-well-23


title: singles-HL60-well-76


title: singles-HL60-well-69


title: singles-HL60-well-66


title: singles-HL60-well-67


title: singles-HL60-well-65


title: singles-mESC-well-13


title: singles-HL60-well-63


title: singles-HL60-well-62


title: singles-HL60-well-64


title: singles-mESC-well-12


title: singles-HL60-well-60


title: singles-HL60-well-57


title: singles-HL60-well-79


title: singles-HL60-well-61


title: singles-mESC-well-9


title: singles-HL60-well-59


title: singles-mESC-well-11


title: singles-HL60-well-55


title: singles-mESC-well-10


title: singles-mESC-well-8


title: singles-HL60-well-54


title: singles-HL60-well-53


title: singles-HL60-well-52


title: singles-mESC-well-15


title: singles-HL60-well-56


title: singles-HL60-well-49


title: singles-mESC-well-6


title: singles-HL60-well-47


title: singles-HL60-well-48


title: singles-HL60-well-50


title: singles-HL60-well-46


title: singles-mESC-well-5


title: singles-HL60-well-44


title: singles-HL60-well-45


title: singles-HL60-well-42


title: singles-HL60-well-41


title: singles-mESC-well-3


title: singles-mESC-well-1


title: singles-HL60-well-38


title: singles-HL60-well-39


title: singles-HL60-well-43


title: singles-HL60-well-36


title: singles-EML-well-95

description: processed data file: single-EML.peaks.bed

source_name: singles-EML

growth_protocol: The mouse EML hematopoietic cells were grown in IMDM containing 20% horse serum, 2 mM L-Glutamine, 1% Pen/Strep and 100 ng/mL recombinant SCF (Peprotech).

value: EML

value: hematopoietic cells


title: singles-HL60-well-37


title: singles-EML-well-96


title: singles-HL60-well-35


title: singles-EML-well-94


title: singles-HL60-well-51


title: singles-HL60-well-33


title: singles-mESC-well-4


title: singles-mESC-well-7


title: singles-HL60-well-34


title: singles-EML-well-93


title: singles-HL60-well-31


title: singles-HL60-well-30


title: singles-EML-well-92


title: singles-HL60-well-29


title: singles-HL60-well-32


title: singles-EML-well-91


title: singles-HL60-well-58


title: singles-HL60-well-27


title: singles-HL60-well-28


title: singles-HL60-well-26


title: singles-HL60-well-40


title: singles-EML-well-89


title: singles-HL60-well-25


title: singles-EML-well-90


title: singles-HL60-well-23


title: singles-EML-well-88


title: singles-HL60-well-20


title: singles-HL60-well-21


title: singles-EML-well-87


title: singles-HL60-well-19


title: singles-HL60-well-22


title: singles-HL60-well-18


title: singles-EML-well-86


title: singles-HL60-well-16


title: singles-HL60-well-17


title: singles-EML-well-85


title: singles-HL60-well-13


title: singles-HL60-well-12


title: singles-EML-well-83


title: singles-EML-well-84


title: singles-HL60-well-14


title: singles-EML-well-82


title: singles-HL60-well-11


title: singles-HL60-well-10


title: singles-HL60-well-9


title: singles-HL60-well-8


title: singles-EML-well-81


title: singles-HL60-well-24


title: singles-HL60-well-7


title: singles-EML-well-80


title: singles-HL60-well-5


title: singles-HL60-well-4


title: singles-EML-well-79


title: singles-EML-well-78


title: singles-HL60-well-3


title: singles-HL60-well-2


title: singles-GM-rep2-well-96

value: lymphoblastoid cells


title: singles-EML-well-77


title: singles-HL60-well-1


title: singles-GM-rep2-well-95


title: singles-HL60-well-15


title: singles-GM-rep2-well-93


title: singles-EML-well-76


title: singles-EML-well-75


title: singles-EML-well-74


title: singles-GM-rep2-well-90


title: singles-GM-rep2-well-91


title: singles-GM-rep2-well-92


title: singles-GM-rep2-well-94


title: singles-GM-rep2-well-89


title: singles-GM-rep2-well-88


title: singles-GM-rep2-well-87


title: singles-EML-well-73


title: singles-GM-rep2-well-86


title: singles-EML-well-72


title: singles-GM-rep2-well-85


title: singles-GM-rep2-well-84


title: singles-EML-well-71


title: singles-EML-well-70


title: singles-EML-well-69


title: singles-GM-rep2-well-81


title: singles-GM-rep2-well-80


title: singles-GM-rep2-well-79


title: singles-EML-well-68


title: singles-mESC-well-2


title: singles-GM-rep2-well-78


title: singles-HL60-well-6


title: singles-EML-well-67


title: singles-GM-rep2-well-77


title: singles-GM-rep2-well-74


title: singles-EML-well-66


title: singles-GM-rep2-well-76


title: singles-GM-rep2-well-72


title: singles-EML-well-65


title: singles-GM-rep2-well-83


title: singles-GM-rep2-well-71


title: singles-GM-rep2-well-69


title: singles-GM-rep2-well-82


title: singles-GM-rep2-well-70


title: singles-EML-well-62


title: singles-EML-well-61


title: singles-GM-rep2-well-64


title: singles-GM-rep2-well-66


title: singles-GM-rep2-well-63


title: singles-GM-rep2-well-67


title: singles-GM-rep2-well-62


title: singles-EML-well-60


title: singles-GM-rep2-well-65


title: singles-GM-rep2-well-73


title: singles-GM-rep2-well-60


title: singles-GM-rep2-well-75


title: singles-GM-rep2-well-59


title: singles-EML-well-59


title: singles-GM-rep2-well-58


title: singles-EML-well-58


title: singles-GM-rep2-well-57


title: singles-EML-well-57


title: singles-EML-well-64


title: singles-GM-rep2-well-68


title: singles-EML-well-63


title: singles-EML-well-56


title: singles-GM-rep2-well-56


title: singles-GM-rep2-well-54


title: singles-GM-rep2-well-53


title: singles-EML-well-55


title: singles-GM-rep2-well-51


title: singles-GM-rep2-well-50


title: singles-GM-rep2-well-48


title: singles-EML-well-54


title: singles-GM-rep2-well-49


title: singles-GM-rep2-well-47


title: singles-GM-rep2-well-46


title: singles-EML-well-53


title: singles-GM-rep2-well-61


title: singles-EML-well-52


title: singles-EML-well-51


title: singles-GM-rep2-well-42


title: singles-GM-rep2-well-43


title: singles-EML-well-50


title: singles-GM-rep2-well-40


title: singles-GM-rep2-well-55


title: singles-GM-rep2-well-39


title: singles-EML-well-49


title: singles-GM-rep2-well-37


title: singles-EML-well-48


title: singles-GM-rep2-well-36


title: singles-GM-rep2-well-52


title: singles-EML-well-47


title: singles-GM-rep2-well-38


title: singles-GM-rep2-well-34


title: singles-EML-well-46


title: singles-GM-rep2-well-33


title: singles-GM-rep2-well-35


title: singles-GM-rep2-well-45


title: singles-GM-rep2-well-28


title: singles-GM-rep2-well-30


title: singles-GM-rep2-well-32


title: singles-GM-rep2-well-29


title: singles-EML-well-45


title: singles-EML-well-44


title: singles-EML-well-43


title: singles-GM-rep2-well-44


title: singles-GM-rep2-well-27


title: singles-EML-well-42


title: singles-GM-rep2-well-26


title: singles-GM-rep2-well-31


title: singles-GM-rep2-well-25


title: singles-EML-well-41


title: singles-GM-rep2-well-23


title: singles-GM-rep2-well-22


title: singles-EML-well-40


title: singles-GM-rep2-well-21


title: singles-EML-well-39


title: singles-EML-well-38


title: singles-GM-rep2-well-41


title: singles-EML-well-37


title: singles-GM-rep2-well-17


title: singles-GM-rep2-well-16


title: singles-GM-rep2-well-20


title: singles-GM-rep2-well-19


title: singles-GM-rep2-well-12


title: singles-GM-rep2-well-14


title: singles-EML-well-36


title: singles-GM-rep2-well-11


title: singles-GM-rep2-well-9


title: singles-EML-well-34


title: singles-GM-rep2-well-10


title: singles-GM-rep2-well-8


title: singles-EML-well-31


title: singles-EML-well-30


title: singles-GM-rep2-well-15


title: singles-GM-rep2-well-4


title: singles-GM-rep2-well-1


title: singles-GM-rep2-well-7


title: singles-GM-rep2-well-18


title: singles-GM-rep1-well-94


title: singles-GM-rep1-well-93


title: singles-EML-well-35


title: singles-EML-well-33


title: singles-EML-well-32


title: singles-GM-rep2-well-5


title: singles-GM-rep2-well-2


title: singles-GM-rep1-well-92


title: singles-EML-well-29


title: singles-GM-rep2-well-13


title: singles-EML-well-28


title: singles-GM-rep1-well-88


title: singles-GM-rep1-well-95


title: singles-GM-rep1-well-96


title: singles-GM-rep2-well-3


title: singles-GM-rep2-well-24


title: singles-EML-well-27


title: singles-GM-rep1-well-87


title: singles-GM-rep2-well-6


title: singles-GM-rep1-well-90


title: singles-GM-rep1-well-89


title: singles-EML-well-26


title: singles-GM-rep1-well-86


title: singles-EML-well-25


title: singles-GM-rep1-well-85


title: singles-GM-rep1-well-84


title: singles-EML-well-23


title: singles-GM-rep1-well-83


title: singles-GM-rep1-well-91


title: singles-GM-rep1-well-82


title: singles-EML-well-21


title: singles-EML-well-22


title: singles-GM-rep1-well-80


title: singles-GM-rep1-well-81


title: singles-EML-well-20


title: singles-GM-rep1-well-78


title: singles-GM-rep1-well-79


title: singles-GM-rep1-well-77


title: singles-EML-well-19


title: singles-EML-well-18


title: singles-GM-rep1-well-76


title: singles-GM-rep1-well-74


title: singles-GM-rep1-well-73


title: singles-EML-well-17


title: singles-EML-well-16


title: singles-GM-rep1-well-72


title: singles-GM-rep1-well-71


title: singles-EML-well-15


title: singles-GM-rep1-well-69


title: singles-EML-well-14


title: singles-GM-rep1-well-70


title: singles-GM-rep1-well-68


title: singles-GM-rep1-well-66


title: singles-GM-rep1-well-64


title: singles-EML-well-13


title: singles-EML-well-12


title: singles-GM-rep1-well-65


title: singles-GM-rep1-well-63


title: singles-GM-rep1-well-62


title: singles-GM-rep1-well-61


title: singles-GM-rep1-well-60


title: singles-GM-rep1-well-59


title: singles-GM-rep1-well-75


title: singles-GM-rep1-well-58


title: singles-EML-well-10


title: singles-GM-rep1-well-57


title: singles-GM-rep1-well-56


title: singles-GM-rep1-well-55


title: singles-GM-rep1-well-54


title: singles-EML-well-8


title: singles-GM-rep1-well-67


title: singles-GM-rep1-well-53


title: singles-EML-well-7


title: singles-GM-rep1-well-52


title: singles-GM-rep1-well-50


title: singles-EML-well-6


title: singles-EML-well-9


title: singles-EML-well-11


title: singles-GM-rep1-well-46


title: singles-GM-rep1-well-44


title: singles-GM-rep1-well-48


title: singles-EML-well-5


title: singles-GM-rep1-well-43


title: singles-EML-well-3


title: singles-GM-rep1-well-49


title: singles-GM-rep1-well-40


title: singles-EML-well-1


title: singles-EML-well-2


title: singles-EML-well-4


title: singles-GM-rep1-well-42


title: singles-EML-well-24


title: singles-GM-rep1-well-39


title: singles-GM-rep1-well-41


title: singles-GM-rep1-well-51


title: singles-GM-rep1-well-37


title: singles-GM-rep1-well-38


title: singles-GM-rep1-well-36


title: singles-GM-rep1-well-35


title: LNK-/- sham 2

city: Framingham

first: Daniel

last: Levy

address: 73 Mt. Wayte Avenue, Suite 2

department: Framingham Heart Study

institute: NHLBI

data_processing:
Quality control (QC) of the RNA-Seq reads from FASTQ files was performed by Fastxtoolkit package (http://hannonlab.cshl.edu/fastx_toolkit/).
The RNA-Seq reads passing QC were mapped to the mouse reference genome (UCSC mm10) using Tophat v2.0 (Trapnell et al, 2009).
Duplicated reads with identical external coordinates were further removed from the output binary sequence alignment (BAM) format files using samtools (samtools rmdup command) (Li et al, 2009).
Cufflinks v2.2 was used to estimate and normalize mRNA abundances in the form of FPRM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) values (Trapnell et al, 2010). Cuffdiff (Trapnell et al, 2010) was used to identify differentially expressed genes between WT and Sh2b3-/- groups.
Genome_build: mm10

source_name: Total RNA from whole blood

growth_protocol: Sh2b3-deficient mice (Sh2b3-/-) were provided by Dr. Satoshi Takaki (International Medical Center of Japan, Tokyo, Japan) and generated as previously described (Takaki et al, 2000). Exons 3-8 of the gene were knock-out by a genetic recombination technology. These mice were backcrossed with C57Bl/6J for >10 generations.

extract_protocol: cDNA library construction and RNA Sequencing was performed by VANTAGE (Vanderbilt Technologies for Advanced Genomics, Vanderbilt University Medical Center, Nashville, TN). Library prepration was performed using the Illumina TruSeq stranded mRNA Sample Preparation Kit, and Rev. D of the protocol. Samples were sequenced on the Illumina HiSeq 2500 using v3 SBS chemistry.  Libraries were sequenced on a Single Read 50bp run at 30 million passing filter reads/sample. Details of RNA Sequencing protocols were available on: http://vantage.vanderbilt.edu/resources/grant-text/.

treatment_protocol: Vehicle through osmotic minipumps

value: whole blood

tag: genotype/variation


title: LNK-/- sham 4


title: LNK-/- sham 3


title: singles-GM-rep1-well-47


title: singles-GM-rep1-well-33


title: singles-GM-rep1-well-34


title: LNK-/- sham 1


title: singles-GM-rep1-well-45


title: singles-GM-rep1-well-32


title: singles-GM-rep1-well-30


title: Wild type sham 4

value: wild type


title: singles-GM-rep1-well-29


title: Wild type sham 3


title: singles-GM-rep1-well-28


title: singles-GM-rep1-well-27


title: singles-GM-rep1-well-31


title: singles-GM-rep1-well-26


title: singles-GM-rep1-well-23


title: Wild type sham 1


title: singles-GM-rep1-well-21


title: singles-GM-rep1-well-22


title: singles-GM-rep1-well-20


title: singles-GM-rep1-well-24


title: ChIP-seq_input_excitatory_neurons_rep3

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
ChIP-seq: Reads were aligned to the mm10 genome, keeping only uniquely aligning reads (BOWTIE v0.12.7 -m 1)
ChIP-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
ChIP-seq: Peaks were called with SICER_V1.1 (redundancy threshold = 1; fragment size=150; W=200, G=200 for H3K27ac, H3K4me1, and H3K4me3; W=200, G=1000 for H3K27me3). Overlapping peaks from the 2 replicates were merged (BEDTOOLS merge) to generate 1 set of peaks for each histone modification.
sample_supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq, ATAC-seq, and ChIP-seq datasets for each histone modification.
sample_supplementary_files_format_and_content: tab delimited text files of ChIP-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end
Genome_build: mm10

source_name: Excitatory pyramidal neurons from mouse neocortex

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, amplified, and sequenced on an Illumina HiSeq 2500 for 50 cycles. Image analysis and base calling were performed with the standard Illumina pipeline version RTA 1.17.20.

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc

value: brain (neocortex)

value: excitatory pyramidal neurons

value: 8 to 11 weeks

tag: Sex

value: male


title: ChIP-seq_input_excitatory_neurons_rep1


title: singles-GM-rep1-well-14


title: ChIP-seq_input_excitatory_neurons_rep2

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). Amplified nucleosomal cDNA was fragmented, end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.


title: singles-GM-rep1-well-19


title: singles-GM-rep1-well-13


title: ChIP-seq_H3K4me3_excitatory_neurons_rep2


title: ChIP-seq_H3K4me3_excitatory_neurons_rep1


title: singles-GM-rep1-well-12


title: singles-GM-rep1-well-15


title: Wild type sham 2


title: singles-GM-rep1-well-25


title: singles-GM-rep1-well-18


title: singles-GM-rep1-well-11


title: ChIP-seq_H3K4me1_excitatory_neurons_rep2


title: singles-GM-rep1-well-8


title: singles-GM-rep1-well-9


title: singles-GM-rep1-well-10


title: singles-GM-rep1-well-6


title: singles-GM-rep1-well-5


title: ChIP-seq_H3K27me3_excitatory_neurons_rep2


title: ChIP-seq_H3K4me1_excitatory_neurons_rep1


title: ChIP-seq_H3K27me3_excitatory_neurons_rep1


title: singles-GM-rep1-well-4


title: singles-GM-rep1-well-2


title: singles-GM-rep1-well-16


title: singles-GM-rep1-well-3


title: singles-GM-rep1-well-17


title: ChIP-seq_H3K27ac_excitatory_neurons_rep2


title: ChIP-seq_H3K27ac_excitatory_neurons_rep1


title: C5_input

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

institute: University of Chicago

description: ChIP-seq input

data_processing:
Mapping with BWA 0.7.9
Removal of reads that did not map uniquely to the genome, had poor mapping quality or originated from PCR duplicates.
Peak calling with MACS or RSEG
Genome_build: hg19/PanTro3
Supplementary_files_format_and_content: MACS peaks and RSEG peaks bed files, summary table

organism: Pan troglodytes

source_name: induced pluripotent stem cell line

growth_protocol: Standard iPSC and precursor cell line conditions as described in text

extract_protocol:
Cells were lysed and chromatin sheared with a Covaris S2 (settings: 4 minutes, duty cycle 10%, 5 intensity, 200 cycles per burst in 4 6x16mm tubes per individual). H3K27ac- and H3K27me3-enriched regions were isolated using 5 ug of either H3K27ac antibody (ab4729, Abcam, Cambridge, MA, USA) or H3K27me3 antibody (07-449, Millipore, Billerica, MA, USA).
ChIP and input DNA from each individual were end-repaired, A-tailed and ligated to Illumina Truseq sequencing adapters before 18 cycles of PCR amplification. 200-300 bp DNA fragments were selected for sequencing.
Single end 50 bp; Input libraries were multiplexed and sequenced on one lane of an Illumina HiSeq2500 using the rapid run mode, ChIP libraries were multiplexed and sequenced on three lanes of an Illumina HiSeq2500 using the rapid run mode.

value: induced pluripotent stem cell line

tag: passage

value: Male

tag: antibody

value: input


title: ATAC-seq_VIP_neurons_rep2

data_processing:
Library strategy: ATAC-seq
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
ATAC-seq: Adapter sequences were trimmed from ATAC reads (cutadapt v1.3 -a CTGTCTCTTATACACATCT -q 30 --minimum-length 36 --paired-output)
ATAC-seq: Trimmed reads were aligned to the mm10 genome (BOWTIE2 v2.1.0 -t -X2000 --no-mixed --no-discordant)
ATAC-seq: Redundant reads were removed (picard MarkDuplicates).
ATAC-seq: Fragment ends were offset by 4nt towards the center of each fragment.
ATAC-seq: Peaks were called with HOMER (findPeaks -region -size 500 -minDist 50 -o auto -tbp 0) using sub-nucleosomal (<100bp) fragments, and overlapping peaks from the 2 replicates were merged (BEDTOOLS merge) to yield a peak set for each cell type.
ATAC-seq: Visualization tracks were generated by counting genome-wide coverage of all fragments (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
ATAC-seq: Visualization tracks were also generated by counting genome-wide coverage of sub-nucleosomal (<100bp) fragments (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
sample_supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq, ATAC-seq, and ChIP-seq datasets
sample_supplementary_files_format_and_content: tab delimited text files of ATAC-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end
Genome_build: mm10

source_name: Vasoactive intestinal peptide-positive inhibitory neurons from mouse neocortex

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei.
Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described [Buenrostro J.D. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013)], with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.

value: VIP-cre; R26-LSL-CAG-Sun1-GFP-myc

value: vasoactive intestinal peptide-positive (VIP) inhibitory neurons


title: ATAC-seq_VIP_neurons_rep1


title: C5_H3K27ac

description: H3K27ac-crosslinked DNA

value: H3K27ac (ab4729, Abcam, Cambridge, MA, USA)


title: C7_H3K27me3

description: H3K27me3-crosslinked DNA

value: Female

value: H3K27me3 (07-449, Millipore, Billerica, MA, USA)


title: ATAC-seq_PV_neurons_rep2

source_name: Parvalbumin-positive inhibitory neurons from mouse neocortex

value: PV-cre; R26-LSL-CAG-Sun1-GFP-myc

value: parvalbumin-positive (PV) inhibitory neurons


title: C2_input

description: ChIP-seq input


title: C7_H3K27ac

description: H3K27ac-crosslinked DNA


title: singles-GM-rep1-well-7

data_processing:
library strategy: Single-cell ATAC-seq (scATAC-seq)
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions. Although we saw little effect on calculations of variability, in the case of K562 data, peaks were additionally filtered to exclude copy number amplifications. Using the filtered peak set, peak summits were extended +/-250 bps. The top 50,000 non-overlapping 500 bp summits are available here and were used for all downstream analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

value: lymphoblastoid cells

value: none (untreated)


title: C2_H3K27me3

description: H3K27me3-crosslinked DNA


title: ATAC-seq_PV_neurons_rep1


title: ATAC-seq_excitatory_neurons_rep2

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc


title: C2_H3K27ac

description: H3K27ac-crosslinked DNA


title: ATAC-seq_excitatory_neurons_rep1

value: brain (neocortex)


title: Nicotiana benthamiana miR173

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

description: small RNA

data_processing:
Quality filtering and adaptor removal were driven with UEA small RNA Workbench with default values.
Raw Read counting with in-house-developed scripts (no mismatches were allowed)
Raw abundances were transformed to reads per million (RPM)
Supplementary_files_format_and_content: Tab-separated text files.COLUMN1: sequence,COLUMN2:RAW count, COLUMN3:RPM

organism: Nicotiana benthamiana

source_name: Nicotiana benthamiana sRNAs with CP and 3NCR sequences from Plum Pox Virus in presence of miR173

growth_protocol: Nicotiana benthamiana plants were grown in a greenhouse maintained at 16 h light and 8 h dark photoperiod, temperature range 19-23ºC. Plants with 5-6 true leaves were used for agroinfiltration as described. Culture concentration was adjusted to OD600 = 1 for each construct, when two constructs were agroinfilrated a mixed 1:1 (v/v) culture was prepared.

extract_protocol:
Total RNA from leaves was extracted using TRIZOL reagent (Bio-Rad Laboratories). Low-molecular-weight RNA was isolated with RNA/DNA Midi kits (QIAGEN) according to the manufacturer's instructions.
sRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The synthetic tasiRNA constructs targeting the PPV genome were made using a 150 bp fragment including 2 nt from TAS1c, the miR173 target site (22 nt), and either the antisense strand of the CP region (9242-9367) (syn-tasiR-CP) or the 3’NCR region (9529-9654) (syn-tasiR-3NCR) of PPV.All the purified PCR fragments were introduced between the CaMV 35S promoter and the NOS terminator sequences into the pMDC32 binary vector by Gateway recombination and termed syn-tasiR-3NCR, syn-tasiR-CP, MIR173 and MIR159..Two or three agroinfiltrated N. benthamiana leaves were dusted with carborundum and inoculated with 150 ng or 450 ng of purified GFP-tagged PPV .

value: leaves

tag: sample type


title: RNA-seq_PV_neurons_rep1

description: nuclear RNA

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
RNA-seq: Five base pairs were trimmed from the 5'-end of all reads to remove possible adaptor contamination (seqtk trimfq -b 5)
RNA-seq: Trimmed reads were aligned to the mm10/ERCC92 combined index using TOPHAT v1.4.0 (--GTF --no-novel-juncs) guided by protein coding gene annotation from iGenomes
RNA-seq: Gene expression levels were estimated using RSEM v1.1.20 (--fragment-length-mean 250 --fragment-length-sd 50)
RNA-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -split -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
sample_supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq, ATAC-seq, and ChIP-seq datasets
sample_supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.1.20
Genome_build: mm10

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.

value: 8 to 11 weeks


title: RNA-seq_neocortex_rep2

description: nuclear RNA

source_name: Neocortex

extract_protocol:
For preparation of nuclei from the whole neocortex, the neocortex was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.

value: WT

value: all cells in neocortex

value: male


title: RNA-seq_excitatory_neurons_rep2

description: nuclear RNA

value: excitatory pyramidal neurons


title: Nicotiana benthamiana control

description: small RNA

source_name: Nicotiana benthamiana sRNAs with CP and 3NCR sequences from Plum Pox Virus.

value: control


title: RNA-seq_VIP_neurons_rep1

description: nuclear RNA

value: VIP-cre; R26-LSL-CAG-Sun1-GFP-myc

value: vasoactive intestinal peptide-positive (VIP) inhibitory neurons


title: RNA-seq_excitatory_neurons_rep1

description: nuclear RNA


title: RNA-seq_VIP_neurons_rep2

description: nuclear RNA


title: SETD2 KO using zinc finger nuclease

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

data_processing:
Illumina Casava1.9 software used for basecalling.
Paired-end reads are aligned by TopHat 2.0.6 (3) against the hg19 genome build using the bowtie1 aligner option.
Gene counts are generated using HTseq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and gene annotation files are obtained from Illumina.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include GeneCount and RPKM values for each Sample

source_name: Renal cell carcinoma cell line

growth_protocol: RPMI1640 medium supplemented with 10% FBS

extract_protocol:
RNA extraction using conventional protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Medium

value: 786-O SETD2 ZFN KO cell line


title: singles-GM-rep1-well-1


title: C5_H3K27me3

description: H3K27me3-crosslinked DNA

value: induced pluripotent stem cell line

value: Male

value: H3K27me3 (07-449, Millipore, Billerica, MA, USA)


title: C7_input

description: ChIP-seq input

value: Female

value: input


title: WT SETD2

value: 786-O RCC cell line


title: RNA-seq_PV_neurons_rep2

description: nuclear RNA

value: PV-cre; R26-LSL-CAG-Sun1-GFP-myc

value: brain (neocortex)

value: parvalbumin-positive (PV) inhibitory neurons


title: RNA-seq_neocortex_rep1

description: nuclear RNA

value: WT

value: 8 to 11 weeks


title: HMLER_siMBD2_2

city: LYON cedex

first: Robert

last: Dante

address: Centre Léon Bérard 28, rue Laennec

department: Tumoral escape

country: France

institute: Cancer Research Center of Lyon

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HMLER_siMBD2_vs_siCtrl_edgeR_filtred.txt

data_processing:
Reads were aligned on the UCSC Homo sapiens hg19 genome using TopHat2.
Differential expression analysis was performed as described in Anders et al. Nature Protocols 2013.
Only genes with at least 1 read per million (RPM) in at least 2 of the samples were kept for subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: The tab file is a text matrix containing gene expression (row) in RPM for each sample (column). edgeR txt files contain log2 of the fold change, log10 of the mean CPM and Pvalue for each studied pairs of conditions.

molecule: polyA RNA

source_name: cell line

growth_protocol: HMEC-hTERT and HMLER cell lines were kindly provided by Anne-Pierre Morel (CRCL, Lyon, France). They were cultivated as previously described (Morel et al. PLoS One 2008).

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel, Hoerdt, France) following the manufacturer's instructions. RNA purity and integrity were examined on agarose gel, and quantified with a NanoDrop 1000 (Thermo Scientific, Wilmington, DE).
Illumina TruSeq RNA sample preparation Kit.

treatment_protocol: Cells were seeded at 1.105 per well in six-well plates. The day after plating, cells were either transfected with 100 pmol of siRNA targeting MBD2 (sense: 5'-GGAGGAAGUGAUCCGAAAdTdT-3') or of siRNA control (Sigma-Aldrich, Saint Louis, MO, MISSION siRNA Universal Negative Controls #1) using Lipofectamine-2000 (Sigma-Aldrich) as specified by the manufacturer's instructions, or treated every day with 10 µM of 5-aza-2'-deoxycytidine (Sigma-Aldrich). Cells were collected 72 h after the start of the treatments.

value: HMLER


title: BAT13

city: Koeln

first: Gertrud

last: Steger

address: Fuerst-Pueckler-Str. 56

department: Institute for Virology

country: Germany

institute: Universitaet zu Koeln

description: Brown Adipose Tissue, untreated, Sample 13

data_processing:
Illumina Casava 1.7 and 1.8.2 software used for basecalling
Analysis with QuickNGS, version 1.1.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files with FPKM for each sample

source_name: Brown Adipose Tissue, untreated

extract_protocol:
Total RNA was extracted from whole brown adipose tissue using Trizol reagent according to standard procedures
Sequencing libraries were generated according to the Illumina protocol for total RNA library preparation and loaded onto Illumina flow cells (Illumina, San Diego, CA)

tag: tissue type

value: Brown Adipose Tissue


title: BAT15

description: Brown Adipose Tissue, untreated, Sample 15


title: HMLER_DAC_2

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HMLER_DAC_vs_siCtrl_edgeR_filtred.txt

tag: cell line


title: BAT33

description: Brown Adipose Tissue, RO5508887-treated, Sample 33

source_name: Brown Adipose Tissue, RO5508887-treated


title: HMLER_siMBD2_1


title: Abl1_H3K27me3_ChIPSeq

city: Boston

first: Sebastien

last: Vigneau

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Cell line is described in Zwemer et al. (Genome Biol. 2012 Feb 20;13(2):R10).

data_processing:
The H3K27me3, H3K36me3 and input control reads were mapped to the mm9 genome using Bowtie 2 with default parameters (Langmead B, Salzberg SL.  Nat Methods. 2012 Mar 4;9(4):357-9). Library sizes were of 32, 46 and 57 million unique reads, respectively, with alignment rate of 92% in each case.
Duplicate reads were removed.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: B-lymphoid clonal cell line Abl1 / S1Cs-A5

growth_protocol: Cells were grown at 37°C in presence of 5% CO2, in RPMI complemented with 20% FBS, 1X Penicillin-Streptomycin-Glutamine (Gibco 10378-016) and 1X GlutaMAX Supplement (Gibco 35050-061).

extract_protocol:
Chromatin immunoprecipitation (ChIP) on clonal cell line Abl.1 was performed as previously described (Nag et al. Elife. 2013 Dec 31;2:e01256). Briefly, cells were fixed with 1% formaldehyde for 5 minutes at 37°C. Fragmentation was performed using Covaris sonicator. An aliquot of sheared chromatin was saved as input control. Immunoprecipitation was performed with Anti-H3K27me3 antibody (ABE44 Millipore, Billerica, MA) and anti-H3K36me3 antibody (AB9050, Abcam, Cambridge, MA and UK), using Protein-A Sepharose beads.
ChIP-Seq libraries were prepared using NEBNext ChIP-Seq library prep reagent set for Illumina (NEB E6200S) following manufacturer’s instructions. Barcoded libraries were sequenced using Illumina HiSeq platform (SE50).

treatment_protocol: No treatment.

value: 129S1/SvImJ x CAST/EiJ F1

value: female

tag: cell type

value: B-lymphoid immortalized with Abelson murine leukemia virus

value: Anti-H3K27me3 (ABE44 Millipore, Billerica, MA)


title: BAT35

description: Brown Adipose Tissue, RO5508887-treated, Sample 35


title: HMLER_siCtrl_2

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HMEC-hTERT_vs_HMLER_siCtrl_edgeR_filtred.txt

value: siControl


title: BAT14

description: Brown Adipose Tissue, untreated, Sample 14


title: HMEC-hTERT_2

description: processed data file: RNAseq_rpm_hg19.tab

value: HMEC-hTERT


title: HMLER_siCtrl_1


title: Fib1_polyA_RNASeq

data_processing:
A SNP-masked reference for 129CASTF1 transcriptome was generated from mm9 mouse genome assembly using an in-house pipeline implemented in Awk, by removing non-transcribed regions based on GTF annotation, and masking SNP loci imputed from parental strain genome. The libraries from Abl.1 and Abl.2 lines yielded 43 million and 28.4 million reads, respectively, while the libraries from Fib.1 and Fib.2 lines had 41 million and 61 million reads. All reads were mapped against the SNP-masked reference using Bowtie 2, with default parameters (Langmead and Salzberg. Nat Methods. 2012 Mar 4;9(4):357-9).
To counteract disparities in duplication rate and potential allele-specific artifacts, only unique reads were used.
Mapped read counts for the maternal and paternal allele of each SNP were obtained using Samtools (Li et al. Bioinformatics. 2009 Aug 15;25(16):2078-9) and custom Perl scripts. Allelic bias was statistically identified from the resulting SNP allelic counts with in-house Matlab analysis pipeline (Nag et al. Elife. 2013 Dec 31;2:e01256). Briefly, binomial p-value with FDR-correction lower than 0.05 together with 2:1 bias were considered evidence for monoallelic expression, while a positive equivalence test was evidence for biallelic expression.
Relative expression was calculated using Rsem software (Li and Dewey. BMC Bioinformatics. 2011 Aug 4;12:323).
Genome_build: mm9
Supplementary_files_format_and_content: Files with name ending in “abundance.tsv” are output from the Rsem software indicating relative expression for each transcript isoform. Values are as described in the Rsem documentation (http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html). In particular, TPM (“Transcripts Per Million”) and FPKM (“Fragments Per Kilobase Per Million”) are two measures of relative expression; “IsoPct” is the percentage of a transcript's abundance over its parent gene's abundance.  Files with name ending in “allelic.tsv” indicate allele-specific expression of the longest transcript for each gene. Generic information for each transcript is indicated in columns 1-6 (parent gene symbol, transcript Refseq id, chromosome, start coordinate, end coordinate, and strand, respectively). Allele-specific expression data are in the following columns, labelled as follows: "SNP_count", read count per SNP; "Equivalence", result of equivalence test, with value of 1 if equivalent, -1 if not equivalent, and 0 if undetermined; "Bias", allelic bias across all SNPs of the same transcript; "Binom_p", binomial test p-value for differential allelic expression; "isMAE", whether the gene is called MAE, with value of 1 if called MAE and 0 otherwise; "isBAE", ", whether the gene is called BAE, with value of 1 if called BAE and 0 otherwise.

source_name: Fibroblast clonal cell line Fib1 / S1Cs-F1

growth_protocol: Cells were grown at 37°C in presence of 5% CO2. Abl.1 and Abl.2 lines were cultured in RPMI complemented with 20% FBS, 1X Penicillin-Streptomycin-Glutamine (Gibco 10378-016) and 1X GlutaMAX Supplement (Gibco 35050-061). Fib.1 and Fib.2 lines were cultured in DMEM complemented with 10% FBS, 1X Penicillin-Streptomycin-Glutamine and GlutaMAX Supplement.

extract_protocol: PolyA purified RNA was reverse transcribed using random primers to prepare strand-specific Illumina compatible libraries, following methods described in (Parkhomchuk et al. Nucleic Acids Res. 2009 Oct;37(18):e123) and (Nag et al. Elife. 2013 Dec 31;2:e01256). Libraries were sequenced using Illumina Hi-Seq platform (SE50).

value: SV40-immortalized fibroblast


title: BAT17

description: Brown Adipose Tissue, RO5508887-treated, Sample 17


title: Abl2_polyA_RNASeq

source_name: B-lymphoid clonal cell line Abl2 / S1Cs-A7


title: HME-shP53-RAS_siMBD2_2

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HME-shP53-RAS_siMBD2_vs_siCtrl_edgeR_filtred.txt


title: HME-shP53-RAS_siMBD2_1


title: Abl1_K3K36me3_ChIPSeq

value: Anti-H3K36me3 (AB9050, Abcam, Cambridge, MA and UK)


title: Abl1_WCE


title: Syn_ESC_H3S10p_ChIPseq_1

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

institute: DKFZ

description: ChIP DNA

data_processing:
alignment to the mouse genome assembly mm9 with bowtie
peak calling with MACS for ChIP-seq
genome build: mm9
processed data files format and content: MACS enrichment file (ChIP)

source_name: Embryonic stem cells

growth_protocol: For ChIP-seq mESC were cultured in STEMPan medium (Pan Biotech) and synchronized for 20 hours with aphidicolin and released for three hours.  For RNA-seq cells were treated with ZM-447439 for 48 hours and RNA was extracted and rRNA was depleted with RiboZero.

extract_protocol:
For each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifiacations,  chromatin was sheared to mononucleosomal fragments. For RNA-seq RNA was extracted and treated with RiboZero followed by DNaseI digestion.
Libraries were prepared according to Illumina standard protocols with internal barcodes.

value: Embryonic stem cells

value: ab14955, abcam


title: ESC_RNAseq_wt1

description:
RNA
wildtype

data_processing:
alignment to the mouse genome assembly mm9 with bowtie
read counting for RNA-seq; Normalization and differential expression analysis with Deseq
genome build: mm9
processed data files format and content: table for differential expression (RNA)


title: ESC_RNAseq_wt2

description:
RNA
wildtype


title: Syn_ESC_H3S10p_ChIPseq_2

description: ChIP DNA


title: HMEC-hTERT_1


title: ESC_RNAseq_ZM2

description:
RNA
treated with ZM-447439


title: HMLER_DAC_1


title: Fib2_polyA_RNASeq

source_name: Fibroblast clonal cell line Fib2 / S1Cs-F2


title: ESC_RNAseq_ZM1

description:
RNA
treated with ZM-447439


title: HME-shP53-RAS_siCtrl_2

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HMEC-hTERT_vs_HME-shP53-RAS_siCtrl_edgeR_filtred.txt


title: HME-shP53-RAS_siCtrl_1


title: HME-ZEB1-RAS_siMBD2_2

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HME-ZEB1-RAS_siMBD2_vs_siCtrl_edgeR_filtred.txt


title: MethylC-seq_VIP_neurons_rep2

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2018
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Lister R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013)], except that samples were PCR amplified with KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems KK2802) using the following PCR conditions: 2 minutes at 95°C, 4 cycles of [15 seconds at 98°C, 30 seconds at 60°C, 4 minutes at 72°C], and 10 minutes at 72°C. Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.

value: VIP-cre; R26-LSL-CAG-Sun1-GFP-myc

value: vasoactive intestinal peptide-positive (VIP) inhibitory neurons

value: male


title: HME-ZEB1-RAS_siMBD2_1


title: MethylC-seq_PV_neurons_rep2

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2016
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

value: PV-cre; R26-LSL-CAG-Sun1-GFP-myc

value: brain (neocortex)

value: parvalbumin-positive (PV) inhibitory neurons


title: MethylC-seq_PV_neurons_rep1

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2015
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

value: 8 to 11 weeks


title: HME-ZEB1-RAS_siCtrl_1

description:
processed data file: RNAseq_rpm_hg19.tab
processed data file: HMEC-hTERT_vs_HME-ZEB1-RAS_siCtrl_edgeR_filtred.txt


title: HME-ZEB1-RAS_siCtrl_2


title: Abl1_polyA_RNASeq

value: 129S1/SvImJ x CAST/EiJ F1


title: MethylC-seq_excitatory_neurons_rep2

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2014
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc

value: excitatory pyramidal neurons


title: HMLER_Input

data_processing:
Reads were aligned on the UCSC Homo sapiens hg19 genome using Bowtie (0.12.7).
Duplicate reads were filtered using SAMTools rmdup.
Preliminary peak detection was performed using MACS 1.4.2.
Over sequenced regions were defined as 500 bp regions containing more than 3 times the median number of reads in at least 1 of the 2 inputs. Peaks were filtered against these over sequenced regions, as they represent suspicious false positive regions.
Peaks in HMEC-hTERT and HMLER were compared using MAnorm, and final peak lists were build as peaks common to both cell lines and cell line specific peaks (p value ≤ 0.01).
Reads were extended to 300 bp using Bedtools slop.
Bedgraph coverage files were obtained using Betools genomecov. Coverage value were converted in FPM using -scale.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks bed files contain 3 columns (chr, start, end). Begraph coverage files contain 4 columns (chr, start, end, FPM)

extract_protocol:
Genomic DNA was sheared to a mean fragment length of 300-500 bp through sonication. Methylated-DNA precipitation (MeDP) was carried out using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies) from 1µg of sheared DNA. Pools of 5 independent experiments, library preparation and high throughput sequencing (single-end 50 bp sequencing on Illumina HiSeq 2000) were performed at Beijing Genomics Institute (Hong-Kong, China). MBD2 Chromatin Immunoprecipitations (ChIP) were performed as previously described (Auriol et al. Nucleic Acids Research 2005). Briefly, sheared chromatin (with a mean fragment length between 300 and 500 bp) was obtained by sonication of formaldehyde cross-linked nuclei. ChIP was then performed with a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013) using the ChIP Assay Kit (Merck Millipore, Saint-Quentin-en-Yvelines, France) as specified by the manufacturer’s instruction. Precipitated DNA was finally purified using NucleoSpin Gel and PCR Clean-up kit, (Macherey-Nagel) according to the manufacturer’s protocol “DNA clean-up of samples containing SDS”.
DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

treatment_protocol: No treatments.

value: HMLER

tag: protocol

value: sonication

value: none (input)


title: MethylC-seq_excitatory_neurons_rep1

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2013
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

tag: strain


title: HMEC-hTERT_Input

value: HMEC-hTERT


title: HMLER_Bound_MBD2

value: sonication, MBD2 ChIP

value: a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013)


title: HMEC-hTERT_Bound_MBD2


title: Test2

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
Illumina HiSeq 2000 and Off-Line Basecaller software(OLB V1.8.0) were used for basecalling.
Subsequently, 3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and any reads shorter than 15nt were discarded. Next the 3’-adapter-trimmed-reads (≥ 15nt) were aligned to the latest known human reference miRNA precursor set (Sanger miRBase 19) using Novoalign (v2.07.11). Reads (counts < 2) were discarded when calculating miRNA expression. In order to characterize the isomiR variability, any sequences that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
For piRNAs, the 3’-adapter-trimmed reads (length ≥ 15nt) were aligned to the latest piRNA set in piRNAbank using Novoalign software (v2.07.11). Expression of each piRNA was defined as the mapped tag counts.
Genome_build: n/a
Supplementary_files_format_and_content: counts

source_name: Testis

extract_protocol:
Testes were removed, flash frozen on dry ice, and RNA was harvested using the mirVana™ miRNA Isolation Kit reagent. 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 protocols

value: testis

value: post natal 6 months

value: Mtdh-/-


title: Control 1

value: wild type


title: Test3


title: Test1