title: singles-20160726-scATAC-BM1214-CMP-LS-76


title: singles-20160726-scATAC-BM1214-CMP-LS-69

status: Public on Apr 26 2018

type: SRA

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

library_source: genomic

data_processing:
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.
Genome_build: hg19
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

source_name: Bone Marrow CD34+

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. All cells described here were FACS sorted prior to performing the assay.
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: tissue

value: CD34+ Bone Marrow

tag: cell type

value: CMP


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title: singles-20160617-scATAC-BM1077-CMP-HYC-33


title: singles-20160617-scATAC-BM1077-CMP-HYC-38


title: singles-20160617-scATAC-BM1077-CMP-HYC-31


title: singles-20160617-scATAC-BM1077-CMP-HYC-32


title: singles-20160617-scATAC-BM1077-CMP-HYC-29


title: singles-20160617-scATAC-BM1077-CMP-HYC-26


title: singles-20160617-scATAC-BM1077-CMP-HYC-22


title: singles-20160617-scATAC-BM1077-CMP-HYC-24


title: singles-20160617-scATAC-BM1077-CMP-HYC-28


title: singles-20160617-scATAC-BM1077-CMP-HYC-30


title: singles-20160617-scATAC-BM1077-CMP-HYC-27


title: singles-20160617-scATAC-BM1077-CMP-HYC-25


title: singles-20160617-scATAC-BM1077-CMP-HYC-21


title: singles-20160617-scATAC-BM1077-CMP-HYC-19


title: singles-20160617-scATAC-BM1077-CMP-HYC-23


title: singles-20160617-scATAC-BM1077-CMP-HYC-17


title: singles-20160617-scATAC-BM1077-CMP-HYC-16


title: singles-20160617-scATAC-BM1077-CMP-HYC-18


title: singles-20160617-scATAC-BM1077-CMP-HYC-20


title: singles-20160617-scATAC-BM1077-CMP-HYC-12


title: singles-20160617-scATAC-BM1077-CMP-HYC-10


title: singles-20160617-scATAC-BM1077-CMP-HYC-11


title: singles-20160617-scATAC-BM1077-CMP-HYC-13


title: singles-20160617-scATAC-BM1077-CMP-HYC-9


title: singles-20160617-scATAC-BM1077-CMP-HYC-15


title: singles-20160617-scATAC-BM1077-CMP-HYC-8


title: singles-20160617-scATAC-BM1077-CMP-HYC-7


title: singles-20160617-scATAC-BM1077-CMP-HYC-5


title: singles-20160617-scATAC-BM1077-CMP-HYC-4


title: singles-20160617-scATAC-BM1077-CMP-HYC-3


title: singles-20160617-scATAC-BM1077-CMP-HYC-6


title: singles-20160617-scATAC-BM1077-CMP-HYC-2


title: singles-160819-BM1137-CMP-LS-95


title: singles-160819-BM1137-CMP-LS-96


title: singles-160819-BM1137-CMP-LS-93


title: singles-160819-BM1137-CMP-LS-94


title: singles-160819-BM1137-CMP-LS-92


title: singles-160819-BM1137-CMP-LS-90


title: singles-20160617-scATAC-BM1077-CMP-HYC-14


title: singles-160819-BM1137-CMP-LS-89


title: singles-160819-BM1137-CMP-LS-91


title: singles-160819-BM1137-CMP-LS-87


title: singles-160819-BM1137-CMP-LS-83


title: singles-160819-BM1137-CMP-LS-88


title: singles-160819-BM1137-CMP-LS-86


title: singles-160819-BM1137-CMP-LS-80


title: singles-160819-BM1137-CMP-LS-82


title: singles-160819-BM1137-CMP-LS-84


title: singles-160819-BM1137-CMP-LS-79


title: singles-160819-BM1137-CMP-LS-77


title: singles-160819-BM1137-CMP-LS-76


title: singles-160819-BM1137-CMP-LS-74


title: singles-160819-BM1137-CMP-LS-72


title: singles-160819-BM1137-CMP-LS-75


title: singles-20160617-scATAC-BM1077-CMP-HYC-1


title: singles-160819-BM1137-CMP-LS-70


title: singles-160819-BM1137-CMP-LS-71


title: singles-160819-BM1137-CMP-LS-69


title: singles-160819-BM1137-CMP-LS-67


title: singles-160819-BM1137-CMP-LS-68


title: singles-160819-BM1137-CMP-LS-66


title: singles-160819-BM1137-CMP-LS-85


title: singles-20160617-scATAC-BM1077-CMP-HYC-54


title: singles-160819-BM1137-CMP-LS-64


title: singles-160819-BM1137-CMP-LS-63


title: singles-160819-BM1137-CMP-LS-81


title: singles-160819-BM1137-CMP-LS-61


title: singles-160819-BM1137-CMP-LS-78


title: singles-160819-BM1137-CMP-LS-59


title: singles-160819-BM1137-CMP-LS-58


title: singles-160819-BM1137-CMP-LS-57


title: singles-160819-BM1137-CMP-LS-56


title: singles-160819-BM1137-CMP-LS-55


title: singles-160819-BM1137-CMP-LS-54


title: singles-160819-BM1137-CMP-LS-53


title: singles-160819-BM1137-CMP-LS-52


title: singles-160819-BM1137-CMP-LS-50


title: singles-160819-BM1137-CMP-LS-73


title: singles-160819-BM1137-CMP-LS-51


title: singles-160819-BM1137-CMP-LS-49


title: singles-160819-BM1137-CMP-LS-47


title: singles-160819-BM1137-CMP-LS-48


title: singles-160819-BM1137-CMP-LS-46


title: singles-160819-BM1137-CMP-LS-45


title: singles-160819-BM1137-CMP-LS-44


title: singles-160819-BM1137-CMP-LS-65


title: singles-160819-BM1137-CMP-LS-43


title: singles-160819-BM1137-CMP-LS-62


title: singles-160819-BM1137-CMP-LS-40


title: singles-160819-BM1137-CMP-LS-42


title: singles-160819-BM1137-CMP-LS-39


title: singles-160819-BM1137-CMP-LS-41


title: singles-160819-BM1137-CMP-LS-37


title: singles-160819-BM1137-CMP-LS-36


title: singles-160819-BM1137-CMP-LS-38


title: singles-160819-BM1137-CMP-LS-34


title: singles-160819-BM1137-CMP-LS-33


title: singles-160819-BM1137-CMP-LS-60


title: singles-160819-BM1137-CMP-LS-35


title: singles-160819-BM1137-CMP-LS-30


title: singles-160819-BM1137-CMP-LS-31


title: singles-160819-BM1137-CMP-LS-27


title: singles-160819-BM1137-CMP-LS-28


title: singles-160819-BM1137-CMP-LS-26


title: singles-160819-BM1137-CMP-LS-25


title: singles-160819-BM1137-CMP-LS-24


title: singles-160819-BM1137-CMP-LS-22


title: singles-160819-BM1137-CMP-LS-32


title: singles-160819-BM1137-CMP-LS-21


title: singles-160819-BM1137-CMP-LS-20


title: singles-160819-BM1137-CMP-LS-19


title: singles-160819-BM1137-CMP-LS-18


title: singles-160819-BM1137-CMP-LS-16


title: singles-160819-BM1137-CMP-LS-15


title: singles-160819-BM1137-CMP-LS-14


title: singles-160819-BM1137-CMP-LS-9


title: singles-160819-BM1137-CMP-LS-13


title: singles-160819-BM1137-CMP-LS-10


title: singles-160819-BM1137-CMP-LS-12


title: singles-160819-BM1137-CMP-LS-11


title: singles-160819-BM1137-CMP-LS-6


title: singles-160819-BM1137-CMP-LS-29


title: singles-160819-BM1137-CMP-LS-8


title: singles-160819-BM1137-CMP-LS-5


title: singles-160819-BM1137-CMP-LS-3


title: singles-160819-BM1137-CMP-LS-4


title: singles-160819-BM1137-CMP-LS-1


title: singles-160819-BM1137-CMP-LS-23


title: singles-160819-BM1137-CMP-LS-7


title: BM1077-CMP-Frozen-160106-96


title: singles-160819-BM1137-CMP-LS-2


title: BM1077-CMP-Frozen-160106-95


title: BM1077-CMP-Frozen-160106-92


title: BM1077-CMP-Frozen-160106-88


title: BM1077-CMP-Frozen-160106-90


title: BM1077-CMP-Frozen-160106-91


title: singles-160819-BM1137-CMP-LS-17


title: BM1077-CMP-Frozen-160106-86


title: BM1077-CMP-Frozen-160106-89


title: BM1077-CMP-Frozen-160106-94


title: BM1077-CMP-Frozen-160106-85


title: BM1077-CMP-Frozen-160106-84


title: BM1077-CMP-Frozen-160106-87


title: BM1077-CMP-Frozen-160106-79


title: BM1077-CMP-Frozen-160106-81


title: BM1077-CMP-Frozen-160106-78


title: BM1077-CMP-Frozen-160106-77


title: BM1077-CMP-Frozen-160106-83


title: BM1077-CMP-Frozen-160106-82


title: BM1077-CMP-Frozen-160106-76


title: BM1077-CMP-Frozen-160106-73


title: BM1077-CMP-Frozen-160106-80


title: BM1077-CMP-Frozen-160106-75


title: BM1077-CMP-Frozen-160106-70


title: BM1077-CMP-Frozen-160106-72


title: BM1077-CMP-Frozen-160106-93


title: BM1077-CMP-Frozen-160106-69


title: BM1077-CMP-Frozen-160106-65


title: BM1077-CMP-Frozen-160106-66


title: BM1077-CMP-Frozen-160106-68


title: BM1077-CMP-Frozen-160106-64


title: BM1077-CMP-Frozen-160106-62


title: BM1077-CMP-Frozen-160106-61


title: BM1077-CMP-Frozen-160106-60


title: BM1077-CMP-Frozen-160106-58


title: BM1077-CMP-Frozen-160106-59


title: BM1077-CMP-Frozen-160106-57


title: BM1077-CMP-Frozen-160106-56


title: BM1077-CMP-Frozen-160106-55


title: BM1077-CMP-Frozen-160106-52


title: BM1077-CMP-Frozen-160106-51


title: BM1077-CMP-Frozen-160106-47


title: BM1077-CMP-Frozen-160106-53


title: BM1077-CMP-Frozen-160106-49


title: BM1077-CMP-Frozen-160106-71


title: BM1077-CMP-Frozen-160106-50


title: BM1077-CMP-Frozen-160106-74


title: BM1077-CMP-Frozen-160106-67


title: BM1077-CMP-Frozen-160106-45


title: BM1077-CMP-Frozen-160106-48


title: BM1077-CMP-Frozen-160106-44


title: BM1077-CMP-Frozen-160106-39


title: BM1077-CMP-Frozen-160106-43


title: BM1077-CMP-Frozen-160106-40


title: BM1077-CMP-Frozen-160106-41


title: BM1077-CMP-Frozen-160106-63


title: BM1077-CMP-Frozen-160106-38


title: BM1077-CMP-Frozen-160106-42


title: BM1077-CMP-Frozen-160106-37


title: BM1077-CMP-Frozen-160106-36


title: BM1077-CMP-Frozen-160106-35


title: BM1077-CMP-Frozen-160106-34


title: BM1077-CMP-Frozen-160106-32


title: BM1077-CMP-Frozen-160106-31


title: BM1077-CMP-Frozen-160106-29


title: BM1077-CMP-Frozen-160106-54


title: BM1077-CMP-Frozen-160106-30


title: BM1077-CMP-Frozen-160106-46


title: BM1077-CMP-Frozen-160106-20


title: BM1077-CMP-Frozen-160106-24


title: BM1077-CMP-Frozen-160106-21


title: BM1077-CMP-Frozen-160106-25


title: BM1077-CMP-Frozen-160106-26


title: BM1077-CMP-Frozen-160106-28


title: BM1077-CMP-Frozen-160106-27


title: BM1077-CMP-Frozen-160106-23


title: BM1077-CMP-Frozen-160106-19


title: BM1077-CMP-Frozen-160106-22


title: BM1077-CMP-Frozen-160106-18


title: BM1077-CMP-Frozen-160106-16


title: BM1077-CMP-Frozen-160106-15


title: BM1077-CMP-Frozen-160106-17


title: BM1077-CMP-Frozen-160106-11


title: BM1077-CMP-Frozen-160106-10


title: BM1077-CMP-Frozen-160106-33


title: BM1077-CMP-Frozen-160106-14


title: BM1077-CMP-Frozen-160106-6


title: BM1077-CMP-Frozen-160106-13


title: BM1077-CMP-Frozen-160106-9


title: BM1077-CMP-Frozen-160106-12


title: BM1077-CMP-Frozen-160106-1


title: BM1077-CMP-Frozen-160106-7


title: BM1077-CMP-Frozen-160106-5


title: BM1077-CMP-Frozen-160106-3


title: BM1077-CMP-Frozen-160106-4


title: BM1077-CMP-Frozen-160106-2


title: singles-BM0828-LMPP-frozen-151105-96

value: LMPP


title: singles-BM0828-LMPP-frozen-151105-94


title: singles-BM0828-LMPP-frozen-151105-95


title: singles-BM0828-LMPP-frozen-151105-88


title: singles-BM0828-LMPP-frozen-151105-91


title: singles-BM0828-LMPP-frozen-151105-90


title: singles-BM0828-LMPP-frozen-151105-92


title: singles-BM0828-LMPP-frozen-151105-93


title: singles-BM0828-LMPP-frozen-151105-87


title: singles-BM0828-LMPP-frozen-151105-86


title: singles-BM0828-LMPP-frozen-151105-89


title: singles-BM0828-LMPP-frozen-151105-81


title: BM1077-CMP-Frozen-160106-8


title: singles-BM0828-LMPP-frozen-151105-85


title: singles-BM0828-LMPP-frozen-151105-80


title: singles-BM0828-LMPP-frozen-151105-78


title: singles-BM0828-LMPP-frozen-151105-77


title: singles-BM0828-LMPP-frozen-151105-79


title: singles-BM0828-LMPP-frozen-151105-75


title: singles-BM0828-LMPP-frozen-151105-74


title: singles-BM0828-LMPP-frozen-151105-68


title: singles-BM0828-LMPP-frozen-151105-71


title: singles-BM0828-LMPP-frozen-151105-83


title: singles-BM0828-LMPP-frozen-151105-72


title: singles-BM0828-LMPP-frozen-151105-69


title: singles-BM0828-LMPP-frozen-151105-67


title: singles-BM0828-LMPP-frozen-151105-65


title: singles-BM0828-LMPP-frozen-151105-66


title: singles-BM0828-LMPP-frozen-151105-62


title: singles-BM0828-LMPP-frozen-151105-61


title: singles-BM0828-LMPP-frozen-151105-60


title: singles-BM0828-LMPP-frozen-151105-84


title: singles-BM0828-LMPP-frozen-151105-64


title: singles-BM0828-LMPP-frozen-151105-59


title: singles-BM0828-LMPP-frozen-151105-58


title: singles-BM0828-LMPP-frozen-151105-82


title: singles-BM0828-LMPP-frozen-151105-76


title: singles-BM0828-LMPP-frozen-151105-55


title: singles-BM0828-LMPP-frozen-151105-54


title: singles-BM0828-LMPP-frozen-151105-53


title: singles-BM0828-LMPP-frozen-151105-51


title: singles-BM0828-LMPP-frozen-151105-57


title: singles-BM0828-LMPP-frozen-151105-52


title: singles-BM0828-LMPP-frozen-151105-50


title: singles-BM0828-LMPP-frozen-151105-46


title: singles-BM0828-LMPP-frozen-151105-48


title: singles-BM0828-LMPP-frozen-151105-47


title: singles-BM0828-LMPP-frozen-151105-45


title: singles-BM0828-LMPP-frozen-151105-70


title: singles-BM0828-LMPP-frozen-151105-49


title: singles-BM0828-LMPP-frozen-151105-73


title: singles-BM0828-LMPP-frozen-151105-44


title: singles-BM0828-LMPP-frozen-151105-42


title: singles-BM0828-LMPP-frozen-151105-63


title: singles-BM0828-LMPP-frozen-151105-43


title: singles-BM0828-LMPP-frozen-151105-40


title: singles-BM0828-LMPP-frozen-151105-41


title: singles-BM0828-LMPP-frozen-151105-39


title: singles-BM0828-LMPP-frozen-151105-36


title: singles-BM0828-LMPP-frozen-151105-33


title: singles-BM0828-LMPP-frozen-151105-35


title: singles-BM0828-LMPP-frozen-151105-56


title: singles-BM0828-LMPP-frozen-151105-37


title: singles-BM0828-LMPP-frozen-151105-34


title: singles-BM0828-LMPP-frozen-151105-31


title: singles-BM0828-LMPP-frozen-151105-38


title: singles-BM0828-LMPP-frozen-151105-28


title: singles-BM0828-LMPP-frozen-151105-32


title: singles-BM0828-LMPP-frozen-151105-25


title: singles-BM0828-LMPP-frozen-151105-26


title: singles-BM0828-LMPP-frozen-151105-24


title: singles-BM0828-LMPP-frozen-151105-30


title: singles-BM0828-LMPP-frozen-151105-29


title: singles-BM0828-LMPP-frozen-151105-23


title: singles-BM0828-LMPP-frozen-151105-20


title: singles-BM0828-LMPP-frozen-151105-19


title: singles-BM0828-LMPP-frozen-151105-22


title: singles-BM0828-LMPP-frozen-151105-21


title: singles-BM0828-LMPP-frozen-151105-16


title: singles-BM0828-LMPP-frozen-151105-15


title: singles-BM0828-LMPP-frozen-151105-14


title: singles-BM0828-LMPP-frozen-151105-12


title: singles-BM0828-LMPP-frozen-151105-10


title: singles-BM0828-LMPP-frozen-151105-17


title: singles-BM0828-LMPP-frozen-151105-11


title: singles-BM0828-LMPP-frozen-151105-7


title: singles-BM0828-LMPP-frozen-151105-8


title: singles-BM0828-LMPP-frozen-151105-9


title: singles-BM0828-LMPP-frozen-151105-6


title: singles-BM0828-LMPP-frozen-151105-2


title: singles-BM0828-LMPP-frozen-151105-1


title: singles-BM0828-MPP-frozen-151103-96

value: MPP


title: singles-BM0828-LMPP-frozen-151105-4


title: singles-BM0828-LMPP-frozen-151105-5


title: singles-BM0828-LMPP-frozen-151105-13


title: singles-BM0828-MPP-frozen-151103-95


title: singles-BM0828-MPP-frozen-151103-94


title: singles-BM0828-LMPP-frozen-151105-27


title: singles-BM0828-MPP-frozen-151103-93


title: singles-BM0828-MPP-frozen-151103-91


title: singles-BM0828-MPP-frozen-151103-92


title: singles-BM0828-LMPP-frozen-151105-3


title: singles-BM0828-LMPP-frozen-151105-18


title: singles-BM0828-MPP-frozen-151103-90


title: singles-BM0828-MPP-frozen-151103-88


title: singles-BM0828-MPP-frozen-151103-89


title: singles-BM0828-MPP-frozen-151103-86


title: singles-BM0828-MPP-frozen-151103-84


title: singles-BM0828-MPP-frozen-151103-87


title: singles-BM0828-MPP-frozen-151103-85


title: singles-BM0828-MPP-frozen-151103-83


title: singles-BM0828-MPP-frozen-151103-81


title: singles-BM0828-MPP-frozen-151103-79


title: singles-BM0828-MPP-frozen-151103-80


title: singles-BM0828-MPP-frozen-151103-77


title: singles-BM0828-MPP-frozen-151103-75


title: singles-BM0828-MPP-frozen-151103-76


title: singles-BM0828-MPP-frozen-151103-74


title: singles-BM0828-MPP-frozen-151103-72


title: singles-BM0828-MPP-frozen-151103-69


title: singles-BM0828-MPP-frozen-151103-78


title: singles-BM0828-MPP-frozen-151103-70


title: singles-BM0828-MPP-frozen-151103-68


title: singles-BM0828-MPP-frozen-151103-64


title: singles-BM0828-MPP-frozen-151103-61


title: singles-BM0828-MPP-frozen-151103-66


title: singles-BM0828-MPP-frozen-151103-71


title: singles-BM0828-MPP-frozen-151103-73


title: singles-BM0828-MPP-frozen-151103-63


title: singles-BM0828-MPP-frozen-151103-67


title: singles-BM0828-MPP-frozen-151103-65


title: singles-BM0828-MPP-frozen-151103-56


title: singles-BM0828-MPP-frozen-151103-57


title: singles-BM0828-MPP-frozen-151103-58


title: singles-BM0828-MPP-frozen-151103-59


title: singles-BM0828-MPP-frozen-151103-82


title: singles-BM0828-MPP-frozen-151103-53


title: singles-BM0828-MPP-frozen-151103-55


title: singles-BM0828-MPP-frozen-151103-62


title: singles-BM0828-MPP-frozen-151103-54


title: singles-BM0828-MPP-frozen-151103-51


title: singles-BM0828-MPP-frozen-151103-50


title: singles-BM0828-MPP-frozen-151103-49


title: singles-BM0828-MPP-frozen-151103-47


title: singles-BM0828-MPP-frozen-151103-45


title: singles-BM0828-MPP-frozen-151103-60


title: singles-BM0828-MPP-frozen-151103-48


title: singles-BM0828-MPP-frozen-151103-43


title: singles-BM0828-MPP-frozen-151103-44


title: singles-BM0828-MPP-frozen-151103-39


title: singles-BM0828-MPP-frozen-151103-38


title: singles-BM0828-MPP-frozen-151103-42


title: singles-BM0828-MPP-frozen-151103-36


title: singles-BM0828-MPP-frozen-151103-40


title: singles-BM0828-MPP-frozen-151103-35


title: singles-BM0828-MPP-frozen-151103-31


title: singles-BM0828-MPP-frozen-151103-33


title: singles-BM0828-MPP-frozen-151103-29


title: singles-BM0828-MPP-frozen-151103-32


title: singles-BM0828-MPP-frozen-151103-27


title: singles-BM0828-MPP-frozen-151103-28


title: singles-BM0828-MPP-frozen-151103-26


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title: singles-BM0828-MPP-frozen-151103-21


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title: singles-BM0106-HSC-SIM-160219-31


title: singles-BM0106-HSC-SIM-160219-28


title: singles-BM0106-HSC-SIM-160219-8


title: singles-BM0106-HSC-SIM-160219-13


title: singles-BM0106-HSC-SIM-160219-7


title: singles-BM0106-HSC-SIM-160219-6


title: singles-BM0106-HSC-SIM-160219-33


title: singles-BM0106-HSC-SIM-160219-22


title: singles-BM0106-HSC-SIM-160219-5


title: singles-BM0106-HSC-LS-160219-94


title: singles-BM0106-HSC-LS-160219-93


title: singles-BM0106-HSC-SIM-160219-3


title: singles-BM0106-HSC-SIM-160219-4


title: singles-BM0106-HSC-LS-160219-91


title: singles-BM0106-HSC-SIM-160219-2


title: singles-BM0106-HSC-LS-160219-96


title: singles-BM0106-HSC-LS-160219-86


title: singles-BM0106-HSC-LS-160219-90


title: singles-BM0106-HSC-LS-160219-88


title: singles-BM0106-HSC-SIM-160219-1


title: singles-BM0106-HSC-LS-160219-89


title: singles-BM0106-HSC-LS-160219-87


title: singles-BM0106-HSC-LS-160219-82


title: singles-BM0106-HSC-LS-160219-84


title: singles-BM0106-HSC-LS-160219-83


title: singles-BM0106-HSC-LS-160219-80


title: singles-BM0106-HSC-LS-160219-81


title: singles-BM0828-HSC-fresh-151027-47


title: singles-BM0106-HSC-LS-160219-79


title: singles-BM0106-HSC-LS-160219-78


title: singles-BM0106-HSC-LS-160219-77


title: singles-BM0106-HSC-LS-160219-71


title: singles-BM0106-HSC-LS-160219-92


title: singles-BM0106-HSC-LS-160219-73


title: singles-BM0106-HSC-LS-160219-95


title: singles-BM0106-HSC-LS-160219-74


title: singles-BM0106-HSC-LS-160219-66


title: singles-BM0106-HSC-LS-160219-72


title: singles-BM0106-HSC-LS-160219-68


title: singles-BM0106-HSC-LS-160219-67


title: singles-BM0106-HSC-LS-160219-65


title: singles-BM0106-HSC-LS-160219-64


title: singles-BM0106-HSC-LS-160219-85


title: singles-BM0106-HSC-LS-160219-69


title: singles-BM0106-HSC-LS-160219-63


title: singles-BM0106-HSC-LS-160219-61


title: singles-BM0106-HSC-LS-160219-62


title: singles-BM0828-HSC-fresh-151027-35


title: singles-BM0106-HSC-LS-160219-60


title: singles-BM0106-HSC-LS-160219-76


title: singles-BM0106-HSC-LS-160219-75


title: singles-BM0106-HSC-LS-160219-55


title: singles-BM0106-HSC-LS-160219-53


title: singles-BM0106-HSC-LS-160219-59


title: singles-BM0106-HSC-LS-160219-58


title: singles-BM0106-HSC-LS-160219-56


title: singles-BM0106-HSC-LS-160219-57


title: singles-BM0106-HSC-LS-160219-50


title: singles-BM0106-HSC-LS-160219-70


title: singles-BM0106-HSC-LS-160219-51


title: singles-BM0106-HSC-LS-160219-52


title: singles-BM0106-HSC-LS-160219-47


title: singles-BM0106-HSC-LS-160219-49


title: singles-BM0106-HSC-LS-160219-48


title: singles-BM0106-HSC-LS-160219-45


title: singles-BM0106-HSC-LS-160219-46


title: singles-BM0106-HSC-LS-160219-43


title: singles-BM0106-HSC-LS-160219-41


title: singles-BM0106-HSC-LS-160219-44


title: singles-BM0106-HSC-LS-160219-39


title: singles-BM0106-HSC-LS-160219-42


title: singles-BM0106-HSC-LS-160219-34


title: singles-BM0106-HSC-LS-160219-37


title: singles-BM0106-HSC-LS-160219-35


title: singles-BM0106-HSC-LS-160219-32


title: singles-BM0106-HSC-LS-160219-54


title: singles-BM0106-HSC-LS-160219-33


title: singles-BM0106-HSC-LS-160219-40


title: singles-BM0106-HSC-LS-160219-30


title: singles-BM0106-HSC-LS-160219-28


title: singles-BM0106-HSC-LS-160219-29


title: singles-BM0106-HSC-LS-160219-31


title: singles-BM0106-HSC-LS-160219-26


title: singles-BM0106-HSC-LS-160219-22


title: singles-BM0106-HSC-LS-160219-36


title: singles-BM0106-HSC-LS-160219-24


title: singles-BM0106-HSC-LS-160219-25


title: singles-BM0106-HSC-LS-160219-19


title: singles-BM0106-HSC-LS-160219-23


title: singles-BM0106-HSC-LS-160219-21


title: singles-BM0106-HSC-LS-160219-20


title: singles-BM0106-HSC-LS-160219-16


title: singles-BM0106-HSC-LS-160219-17


title: singles-BM0106-HSC-LS-160219-38


title: singles-BM0106-HSC-LS-160219-18


title: singles-BM0106-HSC-LS-160219-15


title: singles-BM0106-HSC-LS-160219-27


title: singles-BM0106-HSC-LS-160219-14


title: singles-BM0106-HSC-LS-160219-12


title: singles-BM0106-HSC-LS-160219-11


title: singles-BM0106-HSC-LS-160219-9


title: singles-BM0106-HSC-LS-160219-10


title: singles-BM0106-HSC-LS-160219-5


title: singles-BM0106-HSC-LS-160219-6


title: singles-BM0106-HSC-LS-160219-3


title: singles-BM0106-HSC-LS-160219-2


title: singles-BM0106-HSC-LS-160219-7


title: singles-BM0106-HSC-LS-160219-1


title: BM1077-HSC-Frozen-160105-95


title: singles-BM0106-HSC-LS-160219-4


title: BM1077-HSC-Frozen-160105-96


title: BM1077-HSC-Frozen-160105-94


title: BM1077-HSC-Frozen-160105-89


title: BM1077-HSC-Frozen-160105-91


title: BM1077-HSC-Frozen-160105-87


title: singles-BM0106-HSC-LS-160219-13


title: BM1077-HSC-Frozen-160105-90


title: BM1077-HSC-Frozen-160105-88


title: BM1077-HSC-Frozen-160105-86


title: BM1077-HSC-Frozen-160105-84


title: BM1077-HSC-Frozen-160105-81


title: BM1077-HSC-Frozen-160105-80


title: singles-BM0106-HSC-LS-160219-8


title: BM1077-HSC-Frozen-160105-79


title: BM1077-HSC-Frozen-160105-78


title: BM1077-HSC-Frozen-160105-76


title: BM1077-HSC-Frozen-160105-73


title: BM1077-HSC-Frozen-160105-75


title: BM1077-HSC-Frozen-160105-93


title: BM1077-HSC-Frozen-160105-92


title: BM1077-HSC-Frozen-160105-71


title: BM1077-HSC-Frozen-160105-77


title: BM1077-HSC-Frozen-160105-70


title: BM1077-HSC-Frozen-160105-74


title: BM1077-HSC-Frozen-160105-72


title: BM1077-HSC-Frozen-160105-68


title: BM1077-HSC-Frozen-160105-69


title: BM1077-HSC-Frozen-160105-66


title: BM1077-HSC-Frozen-160105-65


title: BM1077-HSC-Frozen-160105-64


title: BM1077-HSC-Frozen-160105-85


title: BM1077-HSC-Frozen-160105-63


title: BM1077-HSC-Frozen-160105-82


title: BM1077-HSC-Frozen-160105-83


title: BM1077-HSC-Frozen-160105-67


title: BM1077-HSC-Frozen-160105-60


title: BM1077-HSC-Frozen-160105-62


title: BM1077-HSC-Frozen-160105-57


title: BM1077-HSC-Frozen-160105-59


title: BM1077-HSC-Frozen-160105-61


title: BM1077-HSC-Frozen-160105-56


title: BM1077-HSC-Frozen-160105-55


title: BM1077-HSC-Frozen-160105-58


title: BM1077-HSC-Frozen-160105-54


title: BM1077-HSC-Frozen-160105-45


title: BM1077-HSC-Frozen-160105-48


title: BM1077-HSC-Frozen-160105-51


title: BM1077-HSC-Frozen-160105-49


title: BM1077-HSC-Frozen-160105-44


title: BM1077-HSC-Frozen-160105-50


title: BM1077-HSC-Frozen-160105-38


title: BM1077-HSC-Frozen-160105-41


title: BM1077-HSC-Frozen-160105-46


title: BM1077-HSC-Frozen-160105-40


title: BM1077-HSC-Frozen-160105-42


title: BM1077-HSC-Frozen-160105-47


title: BM1077-HSC-Frozen-160105-33


title: BM1077-HSC-Frozen-160105-37


title: BM1077-HSC-Frozen-160105-34


title: BM1077-HSC-Frozen-160105-30


title: BM1077-HSC-Frozen-160105-32


title: BM1077-HSC-Frozen-160105-36


title: BM1077-HSC-Frozen-160105-39


title: BM1077-HSC-Frozen-160105-35


title: BM1077-HSC-Frozen-160105-53


title: BM1077-HSC-Frozen-160105-29


title: BM1077-HSC-Frozen-160105-31


title: BM1077-HSC-Frozen-160105-27


title: BM1077-HSC-Frozen-160105-26


title: BM1077-HSC-Frozen-160105-25


title: BM1077-HSC-Frozen-160105-24


title: BM1077-HSC-Frozen-160105-52


title: BM1077-HSC-Frozen-160105-43


title: BM1077-HSC-Frozen-160105-23


title: BM1077-HSC-Frozen-160105-21


title: BM1077-HSC-Frozen-160105-19


title: BM1077-HSC-Frozen-160105-20


title: BM1077-HSC-Frozen-160105-22


title: BM1077-HSC-Frozen-160105-16


title: BM1077-HSC-Frozen-160105-14


title: BM1077-HSC-Frozen-160105-15


title: BM1077-HSC-Frozen-160105-17


title: BM1077-HSC-Frozen-160105-10


title: BM1077-HSC-Frozen-160105-8


title: BM1077-HSC-Frozen-160105-9


title: BM1077-HSC-Frozen-160105-6


title: BM1077-HSC-Frozen-160105-11


title: BM1077-HSC-Frozen-160105-7


title: BM1077-HSC-Frozen-160105-13


title: BM1077-HSC-Frozen-160105-3


title: BM1077-HSC-Frozen-160105-12


title: BM1077-HSC-Frozen-160105-4


title: BM1077-HSC-Frozen-160105-1


title: BM1077-HSC-Frozen-160105-2


title: BM1077-HSC-Frozen-160105-5


title: ML-2 SHARP1 input

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
ChIP-Seq reads aligned to hg19 genome using BWA  (version 0.7.12).
ChIP-Seq peaks with q<0.05 and fold-enrichment between 5 to 30 were called by MACS (version 2.1).
RNA-seq aligned to hg19 genome and UCSC reference transcript using STAR (version 2.4.0).
Expression analysis performed by Featurecounts (version 1.5.0).
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: Commercially available cell line

growth_protocol: ML-2 was maintained in RPMI 1640 supplemented with 10% FBS.

extract_protocol:
ChIP were performed as described in (Milne et al., 2009) with the following modifications: The cells were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 45 min, 2mM disuccinimidyl glutarate (DSG) and a 30 min 1% FA double fixation protocol was used for all other antibodies. The antibodies used included SHARP1 (a mixture of H-72 Santa-Cruz, 12688-1-AP Proteintech, and ab175544 Abcam), H3K79me2 (Millipore, 04-835), H3K79me3 (Diagenode, pAb-068-050), MLL1 (Bethyl, A300-086A), H3K4me3 (Active Motif, 39159), H3K27me3 (Millipore, 07-499), H3K27ac (Millipore, 07-360), LEDGF (Bethyl, A300-848A), MEN1 (Bethyl, A300-105A). Fixed chromatin samples were fragmented using a Bioruptor sonicator (Diagenode) for 30 min at high in a constantly circulating 4C water bath to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 2X with a solution of 50mM HEPES-KOH, pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. RNA was extracted using RNeasy kit (QIAGEN).
ChIP-seq libraries were prepared using Next ChIP-Seq library prep reagent set (New England Biolabs), and multiplexed (New England Biolabs). RNA-seq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol, according to the manufacturer’s instructions (Illumina, San Diego, California, USA).

treatment_protocol: ML-2 cells were transduced with lentivrial shRNA and selected by puromycin.

value: Human leukemia cell


title: ML-2 shSHARP1 #1

library_source: transcriptomic

molecule: total RNA


title: ML-2 shGFP, rep1


title: ML-2 shSHARP1 #2


title: ML-2 shGFP, rep2


title: ML-2 SHARP1


title: BM1077-HSC-Frozen-160105-18


title: ML-2 LEDGF


title: ML-2 LEDGF input


title: ML-2 H3K79me3 input


title: ML-2 H3K79me3


title: ML-2 H3K79me2 input


title: ML-2 MEN1 input


title: ML-2 H3K79me2


title: ML-2 MEN1


title: ML-2 H3K27ac


title: ML-2 H3K27me3 input


title: ML-2 H3K27me3


title: ML-2 H3K4me3/ H3K27ac input


title: PacBio full-length isoform sequencing of total RNA

city: Beijing

first: Minghong

last: Jiang

address: 5 Dong Dan San Tiao

country: China

institute: Chinese Academy of Medical Sciences

description:
Sample 4
Peritoneal macrophages upon VSV infection for 12 hr.
Processed data file: Total_RNA.subreads_distri.txt

data_processing:
Sequence data were processed using the SMRTlink 4.0 software.
Circular consensus sequence (CCS) was generated from subread BAM files.
Additional nucleotide errors in consensus reads were corrected using the Illumina RNA-seq data with the software proovread.
Aligning consensus reads to reference using GMAP.
Samtools software was then used to perform the transcription analysis.
IGVtools software was used  to view different transcriptions.
The length of the reads in bam was summed in the txt file.
Genome_build: mm10
Supplementary_files_format_and_content: Total_RNA.subreads_distri.txt: Tab-delimited text file includes the sum results of the distribution of the read length in the bam files.

organism: Mus musculus

source_name: Peritoneal macrophages

growth_protocol: Peritoneal macrophages were isolated and cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted by TRIzol reagent and the isolated RNA was further assessed by PacBio-seq analysis.
RNA libraries were prepared for sequencing using standard PacBio-seq protocols.

treatment_protocol: Peritoneal macrophages were infected with VSV for 12 hr.

value: Peritoneal macrophages

tag: passages

value: Primary

tag: strain/background

tag: infection

value: VSV for 12 hr

tag: rip antibody


title: PacBio full-length isoform sequencing of RIG-I RIPed RNA

description:
Sample 3
RAW264.7 cells upon VSV infection for 12 hr.
Processed data file: RIP.subreads_distri.txt

data_processing:
Sequence data were processed using the SMRTlink 4.0 software.
Circular consensus sequence (CCS) was generated from subread BAM files.
Additional nucleotide errors in consensus reads were corrected using the Illumina RNA-seq data with the software proovread.
Aligning consensus reads to reference using GMAP.
Samtools software was then used to perform the transcription analysis.
IGVtools software was used  to view different transcriptions.
The length of the reads in bam was summed in the txt file.
Genome_build: mm10
Supplementary_files_format_and_content: RIP.subreads_distri.txt: Tab-delimited text file includes the sum results of the distribution of the read length in the bam files.

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RIP experiment was performed with anti-RIG-I antibody according to the manufacturer’s instructions. The isolated RNA was further assessed by PacBio-seq analysis.
RNA libraries were prepared for sequencing using standard PacBio-seq protocols.

treatment_protocol: RAW264.7 cells were infected with VSV for 12 hr.

tag: cell line

value: macrophage cell line

value: RIG-I (Cell Signaling Technology, D14G6, 3743BC)


title: ML-2 MLL-N


title: NpA+ rep2

status: Public on Apr 25 2018

city: Los Angeles

first: Xinshu

last: Xiao

state: California

address: 610 Charles E. Young Drive S, Terasaki Life Sciences Building, Room 2000B

institute: University of California Los Angeles

description: Polyadenylated RNA

data_processing:
The RNA-Seq datasets were mapped to the hg19 genome and Ensembl (Release 75) transcriptome using a stringent mapping method named RASER, which was described in (Ahn and Xiao 2015). RASER parameters were specified as m = 0.05 and b = 0.03. Uniquely mapped reads were retained for further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: Glioblastoma cells

extract_protocol:
Total RNA was extracted from each fractionated sample using TRIzol LS, and ribosomal RNA was depleted using the RiboMinus™ Transcriptome Isolation Kit according to manufacturer’s instructions. Polyadenylated RNA was then selected by Oligo (dT)25 Dynabeads following the instructions provided by manufacturer. The flow through was collected, and the RNA was extracted using TRIzol LS as non-polyadenylated RNA. Three biological replicates (independent cell culture) were obtained for each fraction.
To prepare for RNA-Seq libraries, 50ng of RNA was extracted from each sample. Paired-end strand-specific RNA-Seq was performed with the NEBNext Ultra Directional RNA Library Prep Kit with the following adjustments to the manufacturer’s instructions: fragmentation was performed for 12 minutes at 94°C and PCR cycling was set to 12 cycles. Unique index was ligated to each sample RNA library construct using the NEBNext® Multiplex Oligos for Illumina® Index Primers Sets 1&2.

value: Glioblastoma (Astrocytoma) cells

tag: subcellular fraction

value: Nucleoplasmic

tag: replicate


title: NpA+ rep3

description: Polyadenylated RNA


title: CpA+ rep1

description: Polyadenylated RNA

value: Cytoplasmic


title: CpA+ rep2

description: Polyadenylated RNA


title: CpA+ rep3

description: Polyadenylated RNA


title: NpA+ rep1

description: Polyadenylated RNA


title: ChA+ rep2

description: Polyadenylated RNA

value: Chromatin


title: ChA+ rep1

description: Polyadenylated RNA


title: ChA− rep3

description: Non-polyadenylated RNA


title: UV-RIP-seq 2

description:
Sample 2
RAW264.7 cells upon VSV infection for 12 hr.
Processed data file: 3-10.txt

data_processing:
Primary sequencing data produced by Illumina HiSeq 4000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by Trimmomatic and Fastx-toolkit.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into lncmm10 transcripts was processed by Stringtie.
Differential expression analysis between sample1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: txt

growth_protocol: RAW264.7 cells stably expressing Flag-tagged RIG-I were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
UV-RIP was performed with anti-Flag antibody. The isolated RNA was further assessed by RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells stably expressing Flag-tagged RIG-I were treated with VSV 4-SU at 100μM for 12hr and crosslinked with UV at 365 nm for 300 mJ/cm2. RIP experiment was performed using anti-Flag antibody, and then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing.

value: Flag-tag (Millipore, MAB3118, clone 2EL-1B11)


title: MDAMB231_MMS_Srfnb_24hr

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Breast cancer MDA-MB231

growth_protocol: Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator

extract_protocol:
Total RNA was extracted from sub-confluent 10cm dishes using Qiagen RNeasy kit
RNA libraries were prepared for sequencing using Illumina TruSeq protocols

treatment_protocol: Samples were treated with either vehicle (DMSO) or indicated doses of drug for indicated amout of time before extraction of RNA

value: Breast cancer

tag: growth protocol

value: Cells were grown in DMEM supplemented with 10%FBS

tag: treatment prototcol

value: 1μM Sorafenib followed by 40μM MMS for 24 hours


title: MDAMB231_MMS_Srfnb_8hr

value: 1μM Sorafenib followed by 40μM MMS for 8 hours


title: ChA− rep2

description: Non-polyadenylated RNA


title: ML-2 H3K4me3


title: MDAMB231_MMS_8hr

value: 40μM MMS for 8 hours


title: MDAMB231_Srfnb_24hr

value: 1μM Sorafenib for 24 hours


title: UV-RIP-seq 1

description:
Sample 1
RAW264.7 cells without VSV infection.
Processed data file: 3-10.txt

treatment_protocol: RAW264.7 cells stably expressing Flag-tagged RIG-I were treated with 4-SU at 100μM for 12hr and crosslinked with UV at 365 nm for 300 mJ/cm2. RIP experiment was performed using anti-Flag antibody, and then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing.


title: MDAMB231_MMS_24hr

value: 40μM MMS for 24 hours


title: ML-2 MLL-N input

value: Human leukemia cell


title: MDAMB231_Ctrl_24hr

value: DMSO for 24 hours


title: MDAMB231_Ctrl_8hr

value: DMSO for 8 hours


title: MDA231_MMS_Srfnb_8hr


title: MDA231_MMS_Srfnb_24hr


title: MDA231_Srfnb_24hr


title: ChA+ rep3

description: Polyadenylated RNA


title: MDA231_MMS_24hr


title: MDA231_Srfnb_8hr

value: 1μM Sorafenib for 8 hours


title: MDA231_Ctrl_24hr


title: ChA− rep1

description: Non-polyadenylated RNA


title: MDA231_MMS_8hr


title: MDAMB231_Srfnb_8hr


title: ChIP-HNF1b, reChIPseq-ERRg (sample set 3)

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

data_processing:
Alignment:  Sequence reads were obtained and mapped to the mouse mm9 genome using Bowtie 1.2 with --best and -m 1  parameters.
Peaks:  Peak detection was performed using the HOMER software package http://homer.salk.edu/homer/ngs/index.html.  Consensus peak lists were defined as peaks present in both biological replicate datasets.  Peaks were annotated to the nearest gene.
Tag directories were generated in HOMER using the -tbp 1 command to remove  clonal reads.  Peak calling stringency settings were used (FDR 0.01, Poisson p-value < 1e-4 for ChIP-seq or <1e-3 for ChIP-reChIP-seq). Peaks were called by comparing ChIP and ChIP-reChIP DNA samples to control DNA derived from sonicated kidney input chromatin and requiring a minimum of 4-fold enrichment of ChIP DNA over control DNA.   ChIP-reChIP-seq peaks were further filtered to also require at least 2-fold enrichment over the reChIP IgG sample.
Colocalization:  A 200 base pair window was used to assess for overlap between peaks.
Visualization: bedGraph files were generated using HOMER which were viewed on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists and bed graphs for ChIP-seq visualization.

source_name: kidney

extract_protocol:
Kidneys were dissected from 2-3-month-old WT mice and chopped into fine pieces.  After digestion with 0.5 mg/ml collagenase I (Worthington) for 15 min at 37 °C, the kidney/collagenase mixture was pushed through a 70 µm cell strainer.  ACK lysis buffer was then used to remove red blood cells. Yields were ~8 million cells per mouse.  Cells were cross-linked with disuccinimidyl glutarate for 30 minutes followed by 1% formaldehyde for 10 minutes, then glycine quenched.  The samples were sonicated and subjected to immunoprecipitation.  Precipitates were washed and DNA was purified.
KAPA Hyper Prep Kit (Kapa Biosciences)

tag: strain

tag: primary antibody

value: HNF1b antibody

tag: secondary antibody

value: ERRg antibody

tag: age

value: 2-3 months


title: HNF1b ChIP-seq replicate 2 (sample set 3)


title: ChIP-HNF1b, reChIPseq-IgG (sample set 3)

value: pre-immune IgG antibody


title: input for "No primary Control for Lamin A/C TSA-Seq"

city: Urbana

first: Andrew

middle: S

last: Belmont

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

data_processing:
Library strategy: TSA-Seq
The raw .bcl files were converted into demultiplexed compressed fastq files using the bcl2fastq v1.8.2 and later v2.17.1.14 conversion software (Illumina).
Raw sequencing reads were first mapped to the human genome (UCSC hg19) using Bowtie 2 version 2.0.2 with default parameters. Chromosome Y was excluded in the reference genome to reduce mapping bias since the K562 cell line was derived from a female.
PCR duplicates reads were removed using samtools version 0.1.19 with default parameters.
We normalized and processed the TSA-Seq data using a sliding window approach as follows. The normalized SON-TSA score was calculated as the log 2 ratio of  (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). This approach can be interpreted as the fold change between the pulldown sample and the input corrected by the total number of mapped reads in each sample. The window slides on the genome with a step size of 100 bp.
We partitioned the genome into non-overlapping 20 kb bins, averaging the TSA-Seq score over the 100 bp intervals within this bin for the new TSA-Seq 20 kb score.  The values for these 20 kb bins were then smoothed by convolution using a Hanning window of length 21 (21 x 20 kb or 420 kb).  This new smoothed TSA-Seq score with 20 kb sampling was used for SON TSA-Seq decile calculations and comparisons with other genome features
Genome_build: hg19
Supplementary_files_format_and_content: normalized TSA signals were in bigWig format, and the 10 deciles are in BED format. Other data files from analyzing public datasets are in bigWig or bigBed formats.

source_name: bone marrow

growth_protocol: K562 Cells were grown according to the ENCODE protocol, in RPMI with 10% FBS (Sigma-Aldrich) and Antibiotic-antimycotic (GIBCO) at density of 0.4 x 10^6-0.75 x 10^6 /ml

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-16 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

treatment_protocol: TSA labeling was done in independent cell batches.  For each batch, cells were divided equally and stained according to four labeling protocols: “Condition 1”, “Condition 2”, “Condition 3”, and “No 1o control”.  Identical staining conditions were used except that 50% sucrose was included in the TSA staining buffer for the “Condition 2” protocol, 0.75mM DTT in addition to 50% sucrose was added in the TSA staining buffer for the “Condition 3” protocol, and the anti-SON primary antibody was omitted for the “No 1o control” protocol.  Cells were fixed by adding 10 ml of 8% paraformaldehyde (Sigma-Aldrich) freshly prepared in CMF-PBS (calcium, magnesium-free phosphate buffered saline) to 40 ml of cells in culture media, incubating for 20 min at room temperature (RT), and quenching aldehydes by addition of 5.6 ml of 1.25 M glycine (Fisher Scientific) and incubation for 5 min at RT.  All incubation steps used a rotating platform to mix the cell suspension.  Cells were then pelleted by centrifugation and resuspended in CMF-PBS buffer with 0.5% Triton-X100 (Sigma-Aldrich) for 30 min at RT.  All centrifugations were for 5 min at 100-200g.  Cells were centrifuged at RT and resuspended in 1.5% H2O2 (Fisher Scientific) in CMF-PBS for 1h at RT to quench endogenous peroxidases, followed by 3 washes at RT in PBST (0.1%Triton-X100/CMF-PBS) by repeated centrifugation and cell pellet resuspension.  Cells were resuspended in IgG Blocking Buffer (5% Normal Goat Serum (Sigma-Aldrich) in PBST) at a concentration of 10^7 cells/ml for 1 hr, followed by centrifugation and resuspension in primary antibody solution (Rabbit-anti-SON primary antibodies (Ab1, Atlas antibodies cat # HPA023535) diluted 1:1000 or 1:2000 in IgG Blocking buffer, or rabbit polyclonal-anti-SON primary antibodies (Ab2) diluted 1:2000 in IgG Blocking buffer, or mouse-anti-phosphorylated SC35 primary antibodies (Sigma-Aldrich cat # S4045) diluted 1:500 in IgG Blocking buffer, or mouse monoclonal anti-lamin A/C primary antibody (Clone 5G4) diluted 1:1000 in IgG Blocking buffer, or mouse monoclonal anti-lamin B primary antibodies (Clone 2D8) diluted 1:1000 in IgG Blocking buffer) at 10^7 cells/ml, or mouse monoclonal anti-RNA polymerase II primary antibodies (clone 4H8) (Millipore cat # 05-623) at 0.5 x 107 cells/ml and incubated 20-24 hrs at 4°C (See METHODS for more information about anti-lamin antibodies). For the no primary control, cells were incubated in IgG Blocking buffer only.  Cells were then washed 3x with PBST, resuspended in IgG Blocking buffer with secondary antibodies at 10^7 cells/ml, and incubated 20-24 hrs at 4°C.  Secondary antibodies (Jackson, ImmunoResearch) used were HRP conjugated, goat-anti-rabbit secondary antibody diluted 1:1000 or HRP conjugated goat-anti-mouse secondary antibody diluted 1:200 or 1:1000. Cells then were washed 3x in PBST and resuspended in reaction buffer A (CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Condition 2, or CMF-PBS with 50% sucrose and 1.5mM DTT for Condition 3) at 2 x 10^7 cells/ml.  Equal volumes of buffer B (8mM tyramide-biotin stock solution diluted 1:5000 with 0.003% H2O2 in CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Conditions 2 and 3) were then added.  Cells were incubated for 10 min and then washed 3x in PBST at RT.  Validation of TSA labeling is done by biotin immunostaining.

tag: disease

value: chronic myelogenous leukemia (CML)

tag: tsa-seq target


title: No primary Control for Lamin A/C TSA-Seq


title: Input chromatin control DNA for sample set 1


title: MDA231_Ctrl_8hr


title: Input chromatin control DNA for sample set 2


title: ERRg ChIP-seq replicate 1 (sample set 1)


title: HNF1b ChIP-seq replicate 1 (sample set 3)


title: input for "No primary Control for Lamin B TSA-Seq"


title: Sox9CreErt2:TdTomato collection 2 TdTomato-

middle: P

last: McMahon

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description: Sorted TdTomato negative cells

data_processing:
Sequence reads were mapped by the Star aligner
Mapped sequence reads were quantified within the Partek Genomics Suite software (http://www.partek.com) to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: text file with statistical analysis

source_name: hind limb

growth_protocol: Double heterozygous mice, carrying one allele of Sox9CreErt2 driver and one allele of Td-Tomato reporter, were generated by crossing heterozygous Sox9CreErt2 (Sox9tm1(cre/ERT2)Haak) with homozygous Td-Tomato (Gt(ROSA)26Sortm14(CAG-tdTomato)Hze) mice.

extract_protocol:
Femoral diaphyses were digested in a liberase solution (100ug/mL in PBS) for 2 hours in a fast shaking rocker at 37 oC, 100 rpm to obtain diaphyseal periosteum cells. Digested cells were filtered and single cell suspensions were subjected to FACS sorting to collect Td-Tomato positive and negative cells. About 10,000 Td-Tomato positive cells and 10,000 Td-Tomato negative control cells were isolated after two collections from 18 femora (9 mice). Total RNA was extracted from each cell population separately with Qiagen RNAasy micro kit with DNaseI digestion according to the manufacturer’s instructions.
Duplicated experimental RNA sequencing libraries were made with a SMARTer Universal Low Input RNA Kit

treatment_protocol: The mice received 3 intraperitoneal injections of 100µL tamoxifen (TM) solution (20 mg/mL diluted in corn oil), at 48-hour intervals. Intact mouse femora were harvested 2 weeks after the last tamoxifen injection and analyzed with RNA sequencing to determine the gene expression profile of periosteal cells of the femur.

tag: tissue

value: periosteum

tag: facs

value: TdTomato-


title: ERRg ChIP-seq replicate 1 (sample set 2)


title: input_for_SON TSA-Seq Condition 1 (TSA only) and SON TSA-Seq Condition 1 (TSA only) Second pull down

description:
Sample 5
processed data file: SON_TSA-Seq_Score_Condition1.bw
processed data file: SON_TSA-Seq_Score_Condition1_Replicate_2nd_pulldown.bw
processed data file: Speckle_distance_Condition1.bw

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-15 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

value: SON

value: none (input control)


title: input_for_SON TSA-Seq Condition 2 (TSA+Sucrose)

description:
Sample 7
processed data file: SON_TSA-Seq_Score_Condition2.bw
processed data file: hg19F_Sucrose_v_input_10_deciles_WithColor.bed
processed data file: Speckle_distance_Condition2.bw


title: 3T3_KRAS_Trametinib_8hr_rep3

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
FKBP12F36V-KRASG12V_Trametinib_8hr_replicate3
Processed file sample name: X3T3_kras_tram_8h_rep_2

data_processing:
Fastq files were aligned to mouse genome build mm9 using HiSat with default parameters.
Transcripts were assembled and FPKM values were generated using cuff quant and cuffnorm from the cufflinks pipeline (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: dTAG_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

molecule: polyA RNA

growth_protocol: NIH/3T3 cells (ATCC, DMEM supplemented with 10% bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin) cells were cultured at 37 ºC and 5% CO2. Cells that were transduced with lentivirus were additionally cultured with 2 mg/mL puromycin.

extract_protocol:
NIH/3T3 cells were treated in triplicate with DMSO, 1 µM dTAG-13 for four and eight hours, 10 nM of Trametinib for four and eight hours, lysed, homogenized using Qiashredder columns (Qiagen), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cell count normalized RNA samples were mixed with the ERCC RNA Spike-In Mix #1 (Life Technologies) prior to library preparation.
Libraries for Illumina sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced on an Illumina NextSeq 500 (single end 75 bp reads) .

treatment_protocol: Cells were treated with DMSO, 1 μM dTAG-13, or 10 nM Trametinib for the times indicated.

tag: associated experiment

value: KRAS-related experiment

tag: stable transduction

tag: culture condition

value: DMEM + 10% Bovine Serum + 1% Pen/Strep + 2 μg/mL Puromycin

tag: treatment

value: 10 nM Trametinib

tag: time

value: 8 hours


title: input_for_No Primary Control_for_SON TSA-Seq

description:
Sample 2
processed data file: NoPrimaryCtrl_for_SON_TSA-Seq.bw

tag: cell line


title: 3T3_KRAS_Trametinib_4hr_rep2

description:
FKBP12F36V-KRASG12V_Trametinib_4hr_replicate2
Processed file sample name: X3T3_kras_tram_4h_rep_1

value: 4 hours


title: 3T3_KRAS_Trametinib_8hr_rep2

description:
FKBP12F36V-KRASG12V_Trametinib_8hr_replicate2
Processed file sample name: X3T3_kras_tram_8h_rep_1


title: 11X_HSC_WGBS

city: Houston

first: Hyun Jung

last: Park

state: TX

address: One Baylor Plaza

department: Dan L. Duncan Cancer Center

institute: Baylor College of Medicine

data_processing:
use BSMAP-2.87 to align bisulfite-treated sequencing reads to the mouse genome mm9 of bisulfite treated data
use moabs to compute the methylation ratio of single base level
Genome_build: mm9
Supplementary_files_format_and_content: chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand

source_name: 11 times transplanted Dnmt3a KO HSCs

growth_protocol: 11 times transplanted mouse HSCs

extract_protocol:
DNA extraction by Purelink DNA extraction kit
WGBS library was made using Illumina TruSeq DNA methylation kit

treatment_protocol: LSK CD48- CD150+ HSCs were isolated from 11 times transplanted mouse

tag: genotype

value: Dnmt3a knockout

tag: cell type

value: Hematopoietic stem cells


title: 3T3_KRAS_Trametinib_4hr_rep1

description:
FKBP12F36V-KRASG12V_Trametinib_4hr_replicate1
Processed file sample name: X3T3_kras_tram_4h_rep_0


title: 3T3_KRAS_Trametinib_4hr_rep3

description:
FKBP12F36V-KRASG12V_Trametinib_4hr_replicate3
Processed file sample name: X3T3_kras_tram_4h_rep_2


title: 3T3_KRAS_Trametinib_8hr_rep1

description:
FKBP12F36V-KRASG12V_Trametinib_8hr_replicate1
Processed file sample name: X3T3_kras_tram_8h_rep_0


title: 3T3_KRAS_dTAG13_8hr_rep3

description:
FKBP12F36V-KRASG12V_dTAG-13_8hr_replicate3
Processed file sample name: X3T3_kras_dTAG13_8h_rep_2

value: 1 μM dTAG-13


title: 3T3_KRAS_dTAG13_8hr_rep1

description:
FKBP12F36V-KRASG12V_dTAG-13_8hr_replicate1
Processed file sample name: X3T3_kras_dTAG13_8h_rep_0


title: 3T3_KRAS_dTAG13_8hr_rep2

description:
FKBP12F36V-KRASG12V_dTAG-13_8hr_replicate2
Processed file sample name: X3T3_kras_dTAG13_8h_rep_1


title: 3T3_KRAS_dTAG13_4hr_rep3

description:
FKBP12F36V-KRASG12V_dTAG-13_4hr_replicate3
Processed file sample name: X3T3_kras_dTAG13_4h_rep_2


title: 3T3_KRAS_DMSO_rep3

description:
FKBP12F36V-KRASG12V_DMSO_replicate3
Processed file sample name: X3T3_kras_DMSO_rep_2

value: DMSO


title: 3T3_KRAS_dTAG13_4hr_rep1

description:
FKBP12F36V-KRASG12V_dTAG-13_4hr_replicate1
Processed file sample name: X3T3_kras_dTAG13_4h_rep_0


title: 3T3_KRAS_DMSO_rep2

description:
FKBP12F36V-KRASG12V_DMSO_replicate2
Processed file sample name: X3T3_kras_DMSO_rep_1


title: 3T3_KRAS_dTAG13_4hr_rep2

description:
FKBP12F36V-KRASG12V_dTAG-13_4hr_replicate2
Processed file sample name: X3T3_kras_dTAG13_4h_rep_1


title: 3T3_KRAS_DMSO_rep1

description:
FKBP12F36V-KRASG12V_DMSO_replicate1
Processed file sample name: X3T3_kras_DMSO_rep_0


title: 3T3_Control_DMSO_rep3

description:
Control_DMSO_replicate3
Processed file sample name: X3T3_control_DMSO_rep_2

value: Untransduced control

value: DMEM + 10% Bovine Serum + 1% Pen/Strep


title: 3T3_Control_DMSO_rep1

description:
Control_DMSO_replicate1
Processed file sample name: X3T3_control_DMSO_rep_0


title: M5_INTS13_shLUC

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: INTS13 was profiled in bone marrow CD34+ derived monocytes (day5), infected with an shRNA against shLUC

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq): BWA
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: in vitro differentiated monocytes (from bone marrow CD34+ cells)

growth_protocol: Monocytes were differentiated from CD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3, 50 ng/ml M-SCF and 25 ng/ml GM-CSF, and collected at day 5

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

tag: chip antibody

value: Bethyl A303-575A

tag: infection

value: shRNA against shLUC


title: Input DNA [H19101]

first: Michelle

middle: C

last: Ward

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
Processed data file: H3K9me3_counts_hg19.txt
Processed data file: H3K9me3_counts_panTro3.txt

data_processing:
Paired-end ChIP-seq reads from each species were mapped to their respective genome (hg19 or panTro3) using BWA (version 0.7.12) (Li and Durbin 2009) and a mapping quality filter of MAQ >10. PCR duplicates were removed by samtools (version 0.1.19)(Li et al. 2009). Properly-paired reads only were selected for further analysis.
ChIP and Input reads from each individual were used to call peaks using MACS2 (Zhang et al. 2008) with the broadpeak option at various qvalue cut-offs. A lenient threshold of qvalue=0.1 was used in subsequent analysis to maximize the number of regions in each species. Peaks called in each species were concatenated to generate a final peak set across both species.
Peak coordinates in each species were then converted to the alternative genome using liftOver (Speir et al. 2016) and the best reciprocal chain (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/reciprocalBest/) between hg19 and panTro3. Peak regions that could be reciprocally and uniquely mapped between the two genomes were kept to generate a list of orthologous peaks.
The number of reads falling into these orthologous peak regions was determined using HTSeq (Anders et al. 2015).
Genome_build: hg19 (GRCh37), panTro3 (Pan_troglodytes-2.1.3)
Supplementary_files_format_and_content: *txt: H3K9me3 ChIP-seq read counts for all orthologous regions in all samples with region coordinates on both the human genome (hg19) and the chimpanzee genome (panTro3).

source_name: induced pluripotent stem cells, input

growth_protocol: Human and chimpanzee feeder-independent induced pluripotent stem cell lines were maintained at 70% confluence on Matrigel hESC-qualified Matrix (354277, Corning, Bedford, MA, USA) at a 1:00 dilution. Cells were cultured in Essential 8 Medium (A1517001, ThermoFisher Scientific, Waltham, MA, USA) at 37°C with 5% (vol/vol) CO2 with daily media changes. Cells were passaged by enzyme-free dissociation (0.5 mM EDTA, 300 mM NaCl in PBS), and seeded with ROCK inhibitor Y-27632 (ab120129, Abcam, Cambridge, MA, USA).

extract_protocol:
ChIP-seq experiments were largely performed according to a published protocol (Schmidt et al. 2009). Briefly, 30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature followed by quenching with 2.5 M glycine. Following cell lysis and sonication (Covaris S2: 4 min, duty cycle 10%, 5 intensity, 200 cycles per burst in 4x 6 x 16 mm tubes per individual), lysates were incubated with 5 μg H3K9me3 antibody (8898, Abcam) overnight.
Libraries were prepared using the Illumina TruSeq ChIP Sample Preparation kit. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

value: induced pluripotent stem cells

tag: Sex

value: Male

tag: population

value: Yoruba


title: QKI eCLIP size-matched input

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

data_processing:
FastQC quality check
Extraction of unique molecular index (UMI) from 5' end of read using UMI Tools (command parameters: umi_tools extract --bc-pattern=NNNNN)
Adapters were trimmed using cutadapt (command parameters: cutadapt --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Trimmed reads were aligned to the human repetitive elements database (RepBase) using STAR (v2.5.2b) (command parameters: STAR --runMode alignReads --runThreadN 8 --genomeDir /path/to/RepBase --readFilesCommand zcat --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd)
Reads not mapping to RepBase were then mapped to the human reference genome (hg19 with Gencode V19 annotations) using STAR (v2.5.2b) (command parameters: STAR --runMode alignReads --genomeDir /path/to/hg19 --readFilesIn --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outStd BAM_Unsorted --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd)
PCR duplicates were removed using UMI Tools (command parameters: umi_tools dedup --method directional-adjacency --spliced-is-unique)
Bigwig files were generated using make_bigwig_files.py (ENCODE gscripts)
CLIP peaks were called using CLIPper
Identified peaks were normalized to the appropriate size-matched input control using Peak_input_normalization_wrapper.pl (ENCODE gscripts)
Genome_build: hg19

source_name: HME_QKI eCLIP size-matched input

extract_protocol:
Immunoprecipitation of RNA-protein complexes and purification of RNA were done as described in the ENCODE eCLIP protocol (Van Nostrand et al. 2016, PMID: 27018577 and ENCODE).
Libraries were constructed as described in the ENCODE eCLIP protocol (Van Nostrand et al  2016, PMID: 27018577), with slight modifications as described in Li et al (submitted).

treatment_protocol: UV crosslinking (254nm) at 400mJ/cm^2

value: Immortalized mammary epithelial cells (HME)

tag: genotype/variation

value: stably overexpressing V5-tagged QKI

tag: treated with

value: UV crosslinking at 254nm with 400mJ/cm^2


title: RBFOX1 eCLIP replicate 1

source_name: HME_RBFOX1 eCLIP

value: stably overexpressing V5-tagged RBFOX1


title: RBFOX1 eCLIP size-matched input

source_name: HME_RBFOX1 eCLIP size-matched input


title: Input DNA [H18511]

value: Female


title: Input DNA [H21194]

value: Caucasian


title: Input DNA [H28126]


title: Input DNA [H21792]


title: Input DNA [H18489]


title: Input DNA [H28815]


title: Input DNA [H19098]


title: Input DNA [H20682]


title: RBFOX1 eCLIP replicate 2


title: Input DNA [H20961]


title: Input chromatin control DNA for sample set 3

tag: strain

tag: primary antibody

tag: secondary antibody

tag: age

value: 2-3 months


title: QKI eCLIP replicate 2

source_name: HME_QKI eCLIP


title: QKI eCLIP replicate 1


title: H3K9me3_ChIPSeq [H19101]

source_name: induced pluripotent stem cells, H3K9me3 ChIP


title: H3K9me3_ChIPSeq [H19098]