title: DUX_OE-2_ASTAR-ATAC-96

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
Duplicates were removed from the libraries using the “MarkDuplicate” module of PICARD
Mapped files were merged using samtools and peaks were called to identify the Highly accessible regions using MACS2 and bedgraphs were generated using makeUCSCfile of HOMER.
Then the deduplicated libraries along with the Highly accessible regions bed file were uploaded to ChromVAR to identify the variable motifs.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs indicating the enrichment of the libraries on the Genome/

source_name: DUX OE mESCs

growth_protocol: mESCs carrying 2c-GFP reporter and inducible DUX ORF constrcts were maintained in DME+4500 mg/l medium (HyClone) supplemented with 15% Fetal Bovine Serum (Gibco), MEM Non-Essential Amino Acids Solution (100X, Gibco), 200mM L-Glutamine (100X, Gibco), 55mM β-mercaptoethanol, 100 U/ml Penicillin-Streptomycin (100X, Gibco), 10^7 unit/ml ESGRO® Recombinant Mouse LIF Protein (10000X, Merck), with addition of antibotics  puromycin (1ug/ml) and G418 (250ug/ml).  Cells were routinely propagated by trypsinization and re-plated onto 0.1% gelatin coated plates every three to four days.

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for ASTAR Scripts run using C1 Fluidigm Open App chips (10-17um).
The open chromatin was transposed by Tn5 transposase. Cell specific barcode was integrated to tagmented DNA of each cell by PCR amplification with indexed primer. The amplified PCR produced was purified by Ampure XP beads and the purified ATACseq library was sent for sequencing.
Single-Cell ATAC-Seq

treatment_protocol: DUX overexpression was induced for 24hrs by adding Dox (1ug/ml) to the culture medium of mESCs carrying 2c-GFP reporter and inducible DUX ORF constrcts


title: 23334_USF1_K562

status: Public on Jun 09 2020

type: SRA

city: Ithaca

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

library_source: genomic

data_processing:
Library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.45 with the following setting: q-value (0.1)
Genome_build: hg19
Supplementary_files_format_and_content: bed format, ChExMix peak calls

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 were grown in suspension using IMDM media and periodically checked for mycoplasma contamination. HepG2 and MCF7 were grown as adherent cells in DMEM media.

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: MCF7 cells were additionally grown in phenol red-free DMEM and treated with Beta-estradiol 30 min prior to cell harvest.

tag: cell line

tag: antibody


title: BJ_STAR_ATAC-seq_17

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Libraries were mapped to hg19 genome using STAR aligner. We allowed up to 2 mismatches and removed reads mapping to more than one region in the genome. The “–alignIntronMax” was set to 1 and the option “--  alignEndsType EndToEnd” was used.
Duplicates were removed using MarkDuplicates module of PICARD.
To determine the highly accessible regions, the de-duplicated mouse ATAC-Seq libraries were merged and peaks were called using MACS2. The following MACS2 options were used: -- nomodel -- nolambda -- keep-dup all – call-summits.
The de-duplicated single cell bam files were uploaded to chromVAR.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs which can be used for visualization in the UCSC genome browser.

source_name: BJ Fibroblasts

growth_protocol: Human neonatal fibroblast cell line, BJ (Stemgent, Cambridge, MA), were maintained in BJ medium, which is composed of DME+4500 mg/l medium (HyClone) supplemented with 10% Fetal Bovine Serum (Gibco), MEM Non-Essential Amino Acids Solution (100X, Gibco), 200mM L-Glutamine (100X, Gibco), 10000 U/ml Penicillin-Streptomycin (100X, Gibco). K562 (ATCC® CCL-243™) were maintained in K562 medium, which is composed of RPMI1640 medium with L- Glutamine (HyClone) supplemented with 10% Fetal Bovine Serum (Gibco), 200mM L-Glutamine (100X, Gibco), 10000 U/ml Penicillin-Streptomycin (100X, Gibco).

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for STAR Scripts run using C1 Fluidigm mRNA-seq chips (10-17um).
The open chromatin was transposed by Tn5 transposase. Cell specific barcode was integrated to tagmented DNA of each cell by PCR amplification with indexed primer. The amplified PCR produced was purified by Ampure XP beads and the purified ATACseq library was sent for sequencing.

tag: cell type

value: BJ Fibroblasts


title: BJ_STAR_ATAC-seq_13


title: BJ_STAR_ATAC-seq_11


title: 23332_NKX2_K562


title: 23330_ETS1_K562


title: 23331_SATB1_K562


title: BJ_STAR_ATAC-seq_1


title: DUX_OE-2_ASTAR-ATAC-9

organism: Mus musculus

tag: strain


title: DUX_OE-2_ASTAR-ATAC-94


title: 28315_STAT3-_K562


title: DUX_OE-2_ASTAR-ATAC-95


title: 28314_MAX-_K562


title: 28310_STAT5A-_K562


title: DUX_OE-2_ASTAR-ATAC-92


title: DUX_OE-2_ASTAR-ATAC-88


title: 23080_STAT1_K562


title: DUX_OE-2_ASTAR-ATAC-87


title: 28312_NRF1-_K562


title: DUX_OE-2_ASTAR-ATAC-91


title: DUX_OE-2_ASTAR-ATAC-90


title: DUX_OE-2_ASTAR-ATAC-86


title: 23083_HEY2_K562


title: 28313_YY1-_K562


title: DUX_OE-2_ASTAR-ATAC-8


title: 15412_TGIF1_K562-8M


title: 23087_ZBTB5_K562


title: DUX_OE-2_ASTAR-ATAC-93


title: DUX_OE-2_ASTAR-ATAC-89


title: 23086_PRDM4_K562


title: DUX_OE-2_ASTAR-ATAC-82


title: DUX_OE-2_ASTAR-ATAC-85


title: 23082_YY1_K562


title: 18113_USF1_MCF7


title: 15413_USF1_K562-8M


title: DUX_OE-2_ASTAR-ATAC-84


title: 18111_NRF1_MCF7


title: DUX_OE-2_ASTAR-ATAC-81


title: DUX_OE-2_ASTAR-ATAC-83


title: DUX_OE-2_ASTAR-ATAC-7


title: 18117_GRHL2_MCF7


title: 18110_PAX2_MCF7


title: 23088_USF1_K562


title: DUX_OE-2_ASTAR-ATAC-80


title: DUX_OE-2_ASTAR-ATAC-77


title: 23551_PHF7_K562


title: DUX_OE-2_ASTAR-ATAC-75


title: DUX_OE-2_ASTAR-ATAC-78


title: 23553_NCOA3_K562


title: DUX_OE-2_ASTAR-ATAC-76


title: 23550_SCXA_K562


title: DUX_OE-2_ASTAR-ATAC-74


title: 18116_FOXM1_MCF7


title: 23555_TFAP2B_K562


title: DUX_OE-2_ASTAR-ATAC-73


title: 23556_NFIX_K562


title: 22842_ISL1_K562


title: 23554_Smad4_K562


title: 22843_PPP1R13L_K562


title: 18112_TP73_MCF7


title: DUX_OE-2_ASTAR-ATAC-71


title: DUX_OE-2_ASTAR-ATAC-6


title: DUX_OE-2_ASTAR-ATAC-69


title: DUX_OE-2_ASTAR-ATAC-79


title: DUX_OE-2_ASTAR-ATAC-70


title: 17488_Znf143_K562


title: DUX_OE-2_ASTAR-ATAC-68


title: 23552_ZBTB39_K562


title: 22841_ETV7_K562


title: 22846_RAX_K562


title: DUX_OE-2_ASTAR-ATAC-67


title: 22844_PBX4_K562


title: 22847_CSTF2_K562


title: DUX_OE-2_ASTAR-ATAC-65


title: 17482_ZEB2_K562


title: 17483_THRB_K562


title: DUX_OE-2_ASTAR-ATAC-64


title: DUX_OE-2_ASTAR-ATAC-66


title: DUX_OE-2_ASTAR-ATAC-72


title: DUX_OE-2_ASTAR-ATAC-63


title: 17487_Max_K562


title: DUX_OE-2_ASTAR-ATAC-5


title: DUX_OE-2_ASTAR-ATAC-61


title: 24057_ZFP3-_K562


title: DUX_OE-2_ASTAR-ATAC-56


title: 24056_GTF2H2C-_K562


title: 24055_ZNF830-_K562


title: DUX_OE-2_ASTAR-ATAC-54


title: 17481_ZNF174_K562


title: DUX_OE-2_ASTAR-ATAC-60


title: 24053_ZNF548-_K562


title: 17485_ELF2_K562


title: DUX_OE-2_ASTAR-ATAC-59


title: 17480_YBX1_K562


title: DUX_OE-2_ASTAR-ATAC-53


title: DUX_OE-2_ASTAR-ATAC-51


title: 24059_HMGN5-_K562


title: 24051_ZNF212-_K562


title: DUX_OE-2_ASTAR-ATAC-50


title: 22939_MLX_K562


title: 24050_ZBTB46-_K562


title: DUX_OE-2_ASTAR-ATAC-4


title: DUX_OE-2_ASTAR-ATAC-58


title: 22937_BRPF1_K562


title: 24058_ZNF280D-_K562


title: DUX_OE-2_ASTAR-ATAC-57


title: DUX_OE-2_ASTAR-ATAC-55


title: DUX_OE-2_ASTAR-ATAC-48


title: 24054_RHOXF2-_K562


title: 17465_CLOCK_K562


title: DUX_OE-2_ASTAR-ATAC-45


title: 17466_DEAF1_K562


title: 17467_STAT3_K562


title: DUX_OE-2_ASTAR-ATAC-43


title: DUX_OE-2_ASTAR-ATAC-62


title: 16627_ATF2_MCF7


title: 24052_LCORL-_K562


title: 22845_BRWD1_K562


title: 16629_HMGB1_MCF7


title: 16628_ELK1_MCF7


title: DUX_OE-2_ASTAR-ATAC-49


title: DUX_OE-2_ASTAR-ATAC-47


title: 22053_NRF1_MCF7


title: 17464_ZBTB5_K562


title: DUX_OE-2_ASTAR-ATAC-38


title: DUX_OE-2_ASTAR-ATAC-37


title: DUX_OE-2_ASTAR-ATAC-46


title: DUX_OE-2_ASTAR-ATAC-52


title: DUX_OE-2_ASTAR-ATAC-44


title: DUX_OE-2_ASTAR-ATAC-42


title: 17469_NFATC3_K562


title: DUX_OE-2_ASTAR-ATAC-34


title: DUX_OE-2_ASTAR-ATAC-33


title: DUX_OE-2_ASTAR-ATAC-41


title: DUX_OE-2_ASTAR-ATAC-31


title: 26325_USF2_K562


title: DUX_OE-2_ASTAR-ATAC-40


title: DUX_OE-2_ASTAR-ATAC-3


title: 17460_Esrra_K562


title: 18311_ING1_HepG2


title: DUX_OE-2_ASTAR-ATAC-39


title: 17468_HDGF_K562


title: 26323_HDAC7_K562


title: 26328_USF1-_K562


title: DUX_OE-2_ASTAR-ATAC-36


title: DUX_OE-2_ASTAR-ATAC-2


title: DUX_OE-2_ASTAR-ATAC-27


title: 26322_ZNF358_K562


title: DUX_OE-2_ASTAR-ATAC-35


title: 26321_LCORL-_K562


title: 26320_ELK1_K562


title: DUX_OE-2_ASTAR-ATAC-32


title: 26327_NFYC-_K562


title: 19053_CXXC1_K562


title: DUX_OE-2_ASTAR-ATAC-30


title: 26324_TCEAL8_K562


title: 26326_ZNF81_K562


title: DUX_OE-2_ASTAR-ATAC-29


title: DUX_OE-2_ASTAR-ATAC-28


title: 19056_ATRX_K562


title: 19051_MEIS2_K562


title: DUX_OE-2_ASTAR-ATAC-22


title: 19055_TSC22D1_K562


title: DUX_OE-2_ASTAR-ATAC-26


title: 19058_ZNF583_K562


title: 19054_SHARPIN_K562


title: DUX_OE-2_ASTAR-ATAC-24


title: 19052_DAXX_K562


title: DUX_OE-2_ASTAR-ATAC-25


title: 19050_GLI1_K562


title: DUX_OE-2_ASTAR-ATAC-21


title: 19057_HES1_K562


title: DUX_OE-2_ASTAR-ATAC-20


title: 19059_MAFF_K562


title: 26435_LEUTX_K562


title: DUX_OE-2_ASTAR-ATAC-1


title: DUX_OE-2_ASTAR-ATAC-18


title: DUX_OE-2_ASTAR-ATAC-14


title: DUX_OE-2_ASTAR-ATAC-19


title: 26437_SCXA_K562


title: DUX_OE-2_ASTAR-ATAC-23


title: DUX_OE-2_ASTAR-ATAC-17


title: 26434_MLXIP_K562


title: DUX_OE-2_ASTAR-ATAC-13


title: DUX_OE-2_ASTAR-ATAC-16


title: DUX_OE-2_ASTAR-ATAC-15


title: 26433_THAP9_K562


title: 26430_ZMYM3_K562


title: DUX_OE-2_ASTAR-ATAC-11


title: 26436_ZNF24_K562


title: 26432_GRAMD4_K562


title: 28423_USF1-_kidney

source_name: kidney

value: kidney


title: DUX_OE-2_ASTAR-ATAC-10


title: 26431_TFAP2A_K562


title: DUX_OE-1_ASTAR-ATAC-96


title: DUX_OE-1_ASTAR-ATAC-9


title: 23898_SIRT2-_K562


title: 26439_GBX1_K562


title: 23328_NFKB2_K562


title: 23329_PAX5_K562


title: DUX_OE-1_ASTAR-ATAC-95


title: 23320_HDAC8_K562


title: DUX_OE-1_ASTAR-ATAC-93


title: 26438_ZNF385B_K562


title: 23899_ZNF230-_K562


title: DUX_OE-1_ASTAR-ATAC-94


title: 23897_ID3-_K562


title: DUX_OE-1_ASTAR-ATAC-91


title: 23322_FEZF2_K562


title: DUX_OE-1_ASTAR-ATAC-90


title: 23325_CREBL2_K562


title: DUX_OE-2_ASTAR-ATAC-12


title: DUX_OE-1_ASTAR-ATAC-8


title: DUX_OE-1_ASTAR-ATAC-88


title: DUX_OE-1_ASTAR-ATAC-89


title: 23326_KCMF1_K562


title: DUX_OE-1_ASTAR-ATAC-87


title: 18312_ARID3A_HepG2


title: 23891_IRX5-_K562


title: DUX_OE-1_ASTAR-ATAC-86


title: 23544_ETS2_K562


title: 23545_SOX9_K562


title: DUX_OE-1_ASTAR-ATAC-85


title: DUX_OE-1_ASTAR-ATAC-82


title: DUX_OE-1_ASTAR-ATAC-83


title: DUX_OE-1_ASTAR-ATAC-92


title: DUX_OE-1_ASTAR-ATAC-84


title: 15409_Smad4_K562-8M


title: 23540_USF1_K562


title: 23547_ELF2_K562


title: DUX_OE-1_ASTAR-ATAC-81


title: DUX_OE-1_ASTAR-ATAC-79


title: 23323_MAP3K7_K562


title: 23543_IRX2_K562


title: 23324_PLXNB1_K562


title: DUX_OE-1_ASTAR-ATAC-78


title: DUX_OE-1_ASTAR-ATAC-77


title: 15405_IRF3_K562-8M


title: 15406_KLF1_K562-8M


title: 15407_NFATC1_K562-8M


title: DUX_OE-1_ASTAR-ATAC-76


title: DUX_OE-1_ASTAR-ATAC-75


title: 23548_ZEB2_K562


title: 15401_ATF2_K562-8M


title: DUX_OE-1_ASTAR-ATAC-73


title: 23546_ZNF23_K562


title: DUX_OE-1_ASTAR-ATAC-72


title: 15402_ELK1_K562-8M


title: DUX_OE-1_ASTAR-ATAC-80


title: DUX_OE-1_ASTAR-ATAC-71


title: 15403_HMGB1_K562-8M


title: DUX_OE-1_ASTAR-ATAC-7


title: 18310_PLAG1_HepG2


title: DUX_OE-1_ASTAR-ATAC-70


title: DUX_OE-1_ASTAR-ATAC-6


title: 26443_SYAP1_K562


title: 23542_SRF_K562


title: 23807_ZNF585B-_K562


title: DUX_OE-1_ASTAR-ATAC-68


title: DUX_OE-1_ASTAR-ATAC-69


title: 23806_CC2D1A-_K562


title: 26446_USF1_K562


title: DUX_OE-1_ASTAR-ATAC-67


title: DUX_OE-1_ASTAR-ATAC-66


title: DUX_OE-1_ASTAR-ATAC-65


title: 26449_QKI_K562


title: DUX_OE-1_ASTAR-ATAC-64


title: DUX_OE-1_ASTAR-ATAC-74


title: DUX_OE-1_ASTAR-ATAC-63


title: 26282_TSC22D1_K562


title: 23809_YBX3-_K562


title: DUX_OE-1_ASTAR-ATAC-62


title: 26284_PROX2_K562


title: DUX_OE-1_ASTAR-ATAC-61


title: DUX_OE-1_ASTAR-ATAC-60


title: 26285_NMI_K562


title: 26286_BATF2_K562


title: 26442_ZKSCAN2_K562


title: 26283_HOXB2_K562


title: 26287_DRAP1_K562


title: 26289_SIX5-_K562


title: DUX_OE-1_ASTAR-ATAC-59


title: DUX_OE-1_ASTAR-ATAC-58


title: DUX_OE-1_ASTAR-ATAC-57


title: DUX_OE-1_ASTAR-ATAC-56


title: 26288_ZFAT_K562


title: 19625_USF1_K562


title: DUX_OE-1_ASTAR-ATAC-53


title: DUX_OE-1_ASTAR-ATAC-5


title: 19620_ZNF804a_K562


title: DUX_OE-1_ASTAR-ATAC-55


title: 19622_PHF19_K562


title: DUX_OE-1_ASTAR-ATAC-52


title: DUX_OE-1_ASTAR-ATAC-54


title: 19623_GTF2H1_K562


title: DUX_OE-1_ASTAR-ATAC-50


title: DUX_OE-1_ASTAR-ATAC-4


title: DUX_OE-1_ASTAR-ATAC-51


title: 28665_HSF1-_K562


title: 28664_HSF1-_K562


title: 28667_HSF1-_K562


title: 28669_USF1-_liver

source_name: liver

value: liver


title: DUX_OE-1_ASTAR-ATAC-49


title: 28666_HSF1-_K562


title: 28663_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-47


title: DUX_OE-1_ASTAR-ATAC-48


title: 19119_UBQLN2_K562


title: 19118_IKZF1_K562


title: 19116_Med4_K562


title: DUX_OE-1_ASTAR-ATAC-45


title: DUX_OE-1_ASTAR-ATAC-46


title: 19117_TBX4_K562


title: 19114_RUNX1_K562


title: DUX_OE-1_ASTAR-ATAC-42


title: DUX_OE-1_ASTAR-ATAC-43


title: 28668_HSF1-_K562


title: 19115_JUP_K562


title: DUX_OE-1_ASTAR-ATAC-40


title: DUX_OE-1_ASTAR-ATAC-3


title: 19112_SSBP4_K562


title: 19113_MYOD1_K562


title: 19110_NFkB1_K562


title: DUX_OE-1_ASTAR-ATAC-39


title: DUX_OE-1_ASTAR-ATAC-38


title: DUX_OE-1_ASTAR-ATAC-44


title: 22627_BACH1_K562


title: 22624_MEIS2_K562


title: 22628_PRDM16_K562


title: 22629_ANAPC2_K562


title: 22625_KLF7_K562


title: 22622_RFX2_K562


title: 22623_CEBPE_K562


title: DUX_OE-1_ASTAR-ATAC-34


title: DUX_OE-1_ASTAR-ATAC-33


title: DUX_OE-1_ASTAR-ATAC-37


title: DUX_OE-1_ASTAR-ATAC-41


title: 22621_IRF3_K562


title: DUX_OE-1_ASTAR-ATAC-32


title: DUX_OE-1_ASTAR-ATAC-31


title: DUX_OE-1_ASTAR-ATAC-30


title: 23069_NFIA_K562


title: 23061_FOXN1_K562


title: 23062_USF1_K562


title: DUX_OE-1_ASTAR-ATAC-29


title: DUX_OE-1_ASTAR-ATAC-28


title: 23060_STAT2_K562


title: DUX_OE-1_ASTAR-ATAC-27


title: DUX_OE-1_ASTAR-ATAC-26


title: DUX_OE-1_ASTAR-ATAC-36


title: 22626_IRF9_K562


title: 23065_MIS18BP1_K562


title: DUX_OE-1_ASTAR-ATAC-35


title: 23067_PPP5C_K562


title: 28249_ZEB2_K562


title: 28247_TSC22D1_K562


title: 28248_ZFAT_K562


title: DUX_OE-1_ASTAR-ATAC-25


title: DUX_OE-1_ASTAR-ATAC-21


title: DUX_OE-1_ASTAR-ATAC-20


title: DUX_OE-1_ASTAR-ATAC-2


title: 28240_MXD3_K562


title: 28399_HSF1-_K562


title: 28397_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-24


title: 28404_HSF1-_K562


title: 28398_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-22


title: DUX_OE-1_ASTAR-ATAC-18


title: 28405_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-17


title: 28406_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-16


title: 28407_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-19


title: 28401_HSF1-_K562


title: 28400_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-14


title: DUX_OE-1_ASTAR-ATAC-13


title: DUX_OE-1_ASTAR-ATAC-23


title: DUX_OE-1_ASTAR-ATAC-12


title: 28402_HSF1-_K562


title: DUX_OE-1_ASTAR-ATAC-1


title: DUX_OE-1_ASTAR-ATAC-10


title: 18379_IRF2_K562


title: 28409_USF1-_K562


title: 18370_NFKB2_K562


title: 18378_SOX10_K562


title: DUX_OE-2_ASTAR-RNA-96

library_source: transcriptomic

data_processing:
Libraries were mapped to mm9 genome using STAR allowing up to 2 mismatches. Only uniquely mapped reads were kept for further analysis.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimieted text table containing the FPKM for every gene in every single cell library

molecule: polyA RNA

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for ASTAR Scripts run using C1 Fluidigm Open App chips (10-17um).
The concentration of amplified cDNA was measured by high sensitivity bioanalyzer chips and diluted to required range of cDNA for following library preparation steps. ASTAR-mRNAseq libraries were prepared using Nextera XT DNA Library Preparation Kit (FC-131-1096) following “Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing” manual.
Single-cell RNA-Seq


title: DUX_OE-2_ASTAR-RNA-95


title: 28408_HSF1-_K562


title: DUX_OE-2_ASTAR-RNA-92


title: 18375_ZSCAN26_K562


title: 18373_Orc1_K562


title: DUX_OE-2_ASTAR-RNA-94


title: DUX_OE-1_ASTAR-ATAC-15


title: DUX_OE-2_ASTAR-RNA-93


title: DUX_OE-2_ASTAR-RNA-90


title: 18377_MEF2C_K562


title: 18397_CASP8AP2_K562


title: 18374_MAFG_K562


title: 28403_HSF1-_K562


title: 18372_CBX3_K562


title: DUX_OE-2_ASTAR-RNA-87


title: DUX_OE-2_ASTAR-RNA-8


title: 18376_LDB1_K562


title: DUX_OE-2_ASTAR-RNA-89


title: DUX_OE-2_ASTAR-RNA-88


title: DUX_OE-2_ASTAR-RNA-91


title: DUX_OE-1_ASTAR-ATAC-11


title: 18396_TRIM27_K562


title: DUX_OE-2_ASTAR-RNA-9


title: 18391_BATF2_K562


title: 18399_ZNF654_K562


title: 18390_NMI_K562


title: 18395_YEATS2_K562


title: DUX_OE-2_ASTAR-RNA-82


title: DUX_OE-2_ASTAR-RNA-7


title: 18393_ZNF239_K562


title: DUX_OE-2_ASTAR-RNA-84


title: DUX_OE-2_ASTAR-RNA-86


title: 18392_ZNF232_K562


title: DUX_OE-2_ASTAR-RNA-85


title: 18394_BATF_K562


title: DUX_OE-2_ASTAR-RNA-83


title: 28429_USF1-_placenta

source_name: placenta

value: placenta


title: DUX_OE-2_ASTAR-RNA-80


title: 18398_CBX5_K562


title: DUX_OE-2_ASTAR-RNA-78


title: 18429_STAT1_MCF7


title: DUX_OE-2_ASTAR-RNA-79


title: DUX_OE-2_ASTAR-RNA-77


title: 18425_SIRT1_MCF7


title: 18424_SMARCE1_MCF7


title: 18427_Med6_MCF7


title: DUX_OE-2_ASTAR-RNA-75


title: DUX_OE-2_ASTAR-RNA-81


title: DUX_OE-2_ASTAR-RNA-74


title: 18426_SNW1_MCF7


title: DUX_OE-2_ASTAR-RNA-73


title: 18421_PRDM2_MCF7


title: DUX_OE-2_ASTAR-RNA-71


title: 18422_RPS6KA5_MCF7


title: 18423_YBX2_MCF7


title: 18958_HOXB2_K562


title: DUX_OE-2_ASTAR-RNA-72


title: DUX_OE-2_ASTAR-RNA-70


title: DUX_OE-2_ASTAR-RNA-69


title: 18955_ZNF583_K562


title: 18428_POLE3_MCF7


title: 18959_ID3_K562


title: 18420_EDF1_MCF7


title: 18954_HES1_K562


title: DUX_OE-2_ASTAR-RNA-65


title: DUX_OE-2_ASTAR-RNA-76


title: 18957_TFAP2A_K562


title: DUX_OE-2_ASTAR-RNA-66


title: DUX_OE-2_ASTAR-RNA-68


title: 18956_MAFF_K562


title: DUX_OE-2_ASTAR-RNA-6


title: DUX_OE-2_ASTAR-RNA-64


title: 18951_SHARPIN_K562


title: DUX_OE-2_ASTAR-RNA-63


title: DUX_OE-2_ASTAR-RNA-62


title: DUX_OE-2_ASTAR-RNA-61


title: 18952_TSC22D1_K562


title: DUX_OE-2_ASTAR-RNA-60


title: DUX_OE-2_ASTAR-RNA-5


title: 23571_ELK1_K562


title: DUX_OE-2_ASTAR-RNA-59


title: DUX_OE-2_ASTAR-RNA-58


title: DUX_OE-2_ASTAR-RNA-67


title: 23577_POLE3_K562


title: 23929_POU3F2_K562


title: 17491_HINFP_K562


title: DUX_OE-2_ASTAR-RNA-56


title: 23923_BSX_K562


title: DUX_OE-2_ASTAR-RNA-55


title: DUX_OE-2_ASTAR-RNA-57


title: 23920_HMGA1_K562


title: 23924_DBX2_K562


title: 23927_ZNF165_K562


title: 23921_MEIS3_K562


title: DUX_OE-2_ASTAR-RNA-54


title: DUX_OE-2_ASTAR-RNA-53


title: 18950_CXXC1_K562


title: DUX_OE-2_ASTAR-RNA-50


title: DUX_OE-2_ASTAR-RNA-51


title: DUX_OE-2_ASTAR-RNA-52


title: 23925_USF1_K562


title: 17357_USF1_K562


title: DUX_OE-2_ASTAR-RNA-4


title: 17358_YY1_K562


title: 18953_ATRX_K562


title: 23816_RPRD1A_K562


title: 23928_MYCN_K562


title: 23813_USF1_K562


title: DUX_OE-2_ASTAR-RNA-47


title: 23815_CSTF2T_K562


title: DUX_OE-2_ASTAR-RNA-46


title: DUX_OE-2_ASTAR-RNA-48


title: 23810_SMARCC2-_K562


title: 23818_GMEB1_K562


title: 19611_OLIG2_K562


title: 19610_GTF2B_K562


title: DUX_OE-2_ASTAR-RNA-43


title: DUX_OE-2_ASTAR-RNA-45


title: 19613_TDRKH_K562


title: DUX_OE-2_ASTAR-RNA-42


title: 19612_UBR2_K562


title: DUX_OE-2_ASTAR-RNA-44


title: 19615_PRDM13_K562


title: DUX_OE-2_ASTAR-RNA-40


title: DUX_OE-2_ASTAR-RNA-3


title: 19619_UBQLN2_K562


title: 19616_BRPF1_K562


title: DUX_OE-2_ASTAR-RNA-38


title: 19614_Med8_K562


title: DUX_OE-2_ASTAR-RNA-39


title: DUX_OE-2_ASTAR-RNA-49


title: DUX_OE-2_ASTAR-RNA-37


title: 22036_ZNF217-_MCF7


title: DUX_OE-2_ASTAR-RNA-36


title: 22035_WHSC1-_MCF7


title: DUX_OE-2_ASTAR-RNA-35


title: 22032_SOX4-_MCF7


title: 22033_YY1-_MCF7


title: DUX_OE-2_ASTAR-RNA-33


title: 22031_IRX5-_MCF7


title: DUX_OE-2_ASTAR-RNA-32


title: DUX_OE-2_ASTAR-RNA-41


title: 22030_ISL1-_MCF7


title: DUX_OE-2_ASTAR-RNA-30


title: DUX_OE-2_ASTAR-RNA-31


title: DUX_OE-2_ASTAR-RNA-2


title: DUX_OE-2_ASTAR-RNA-29


title: 19169_NINJ2_K562


title: 19162_ZNF189_K562


title: 19163_PAWR_K562


title: DUX_OE-2_ASTAR-RNA-27


title: 19167_SLC30A9_K562


title: DUX_OE-2_ASTAR-RNA-26


title: DUX_OE-2_ASTAR-RNA-25


title: DUX_OE-2_ASTAR-RNA-28


title: DUX_OE-2_ASTAR-RNA-24


title: 19160_ESRRG_K562


title: 19166_ZNF140-_K562


title: 19164_RNF2_K562


title: DUX_OE-2_ASTAR-RNA-34


title: 19165_FoxO3_K562


title: DUX_OE-2_ASTAR-RNA-22


title: DUX_OE-2_ASTAR-RNA-23


title: 23496_MAT2B-_K562


title: DUX_OE-2_ASTAR-RNA-20


title: 23494_SMARCAL1-_K562


title: DUX_OE-2_ASTAR-RNA-19


title: 23495_NR1H2-_K562


title: 23498_HOXB2-_K562


title: DUX_OE-2_ASTAR-RNA-17


title: DUX_OE-2_ASTAR-RNA-18


title: 19168_ZFYVE19_K562


title: DUX_OE-2_ASTAR-RNA-16


title: 19161_NKX3-1_K562


title: DUX_OE-2_ASTAR-RNA-15


title: DUX_OE-2_ASTAR-RNA-14


title: 28232_QKI_K562


title: 28233_ZNF581_K562


title: DUX_OE-2_ASTAR-RNA-13


title: 28238_SIRT2_K562


title: 28231_ZKSCAN2_K562


title: DUX_OE-2_ASTAR-RNA-12


title: 28230_ZFYVE20_K562


title: 28237_FOXM1_K562


title: 23497_HMGXB4-_K562


title: DUX_OE-2_ASTAR-RNA-21


title: DUX_OE-2_ASTAR-RNA-11


title: 28236_MEN1_K562


title: 28235_TADA2A_K562


title: DUX_OE-2_ASTAR-RNA-10


title: DUX_OE-2_ASTAR-RNA-1


title: DUX_OE-1_ASTAR-RNA-96


title: DUX_OE-1_ASTAR-RNA-9


title: 28234_THAP4_K562


title: 23499_HIF3A-_K562


title: 28239_ZNF354B_K562


title: 28431_NRF1-_placenta


title: DUX_OE-1_ASTAR-RNA-93


title: 28436_YY1-_Breast

source_name: Breast

value: Breast


title: DUX_OE-1_ASTAR-RNA-94


title: DUX_OE-1_ASTAR-RNA-92


title: 28430_YY1-_placenta


title: 28433_GABPA-_placenta


title: 28435_USF1-_Breast


title: DUX_OE-1_ASTAR-RNA-91


title: DUX_OE-1_ASTAR-RNA-90


title: 24389_CEBPZ-_K562


title: 24388_ZNF7-_K562


title: DUX_OE-1_ASTAR-RNA-8


title: DUX_OE-1_ASTAR-RNA-89


title: 24387_ZNF385B-_K562


title: 24385_GMEB2-_K562


title: 24386_KLF17-_K562


title: DUX_OE-1_ASTAR-RNA-87


title: DUX_OE-1_ASTAR-RNA-86


title: DUX_OE-1_ASTAR-RNA-88


title: 24384_HMX3-_K562


title: DUX_OE-1_ASTAR-RNA-84


title: 18368_KDM1A_K562


title: DUX_OE-1_ASTAR-RNA-85


title: DUX_OE-1_ASTAR-RNA-83


title: DUX_OE-1_ASTAR-RNA-95


title: 18362_SP140_K562


title: 18369_ZNF202_K562


title: DUX_OE-1_ASTAR-RNA-82


title: 18363_CREB3L1_K562


title: DUX_OE-1_ASTAR-RNA-81


title: DUX_OE-1_ASTAR-RNA-80


title: 18366_Dcp2_K562


title: DUX_OE-1_ASTAR-RNA-7


title: DUX_OE-1_ASTAR-RNA-79


title: 18364_LHX2_K562


title: 18365_MLLT3_K562


title: DUX_OE-1_ASTAR-RNA-78


title: 23074_TFAP2C_K562


title: 23075_USF1_K562


title: DUX_OE-1_ASTAR-RNA-77


title: DUX_OE-1_ASTAR-RNA-76


title: DUX_OE-1_ASTAR-RNA-75


title: 23077_FOSB_K562


title: DUX_OE-1_ASTAR-RNA-74


title: DUX_OE-1_ASTAR-RNA-73


title: 23079_FoxO3_K562


title: 28439_GABPA-_Breast


title: 23078_Bmi1_K562


title: 18380_CBFB_K562


title: 18382_PGBD1_K562


title: DUX_OE-1_ASTAR-RNA-71


title: DUX_OE-1_ASTAR-RNA-70


title: 18381_SETD6_K562


title: 18383_DIS3_K562


title: 18367_CIZ1_K562


title: DUX_OE-1_ASTAR-RNA-6


title: DUX_OE-1_ASTAR-RNA-72


title: DUX_OE-1_ASTAR-RNA-69


title: 18385_IGF2BP1_K562


title: 18384_ATF7_K562


title: DUX_OE-1_ASTAR-RNA-68


title: DUX_OE-1_ASTAR-RNA-66


title: 18387_MLLT10_K562


title: 18386_COPS3_K562


title: 18388_ZNF397_K562


title: 18389_ZBTB37_K562


title: DUX_OE-1_ASTAR-RNA-65


title: 18094_PAX2_K562


title: 18095_NRF1_K562


title: DUX_OE-1_ASTAR-RNA-61


title: DUX_OE-1_ASTAR-RNA-5


title: 18764_ZNF556_HepG2


title: 18097_USF1_K562


title: 18762_T_HepG2


title: DUX_OE-1_ASTAR-RNA-59


title: 18760_PHF10_HepG2


title: DUX_OE-1_ASTAR-RNA-58


title: 18761_AKNA_HepG2


title: DUX_OE-1_ASTAR-RNA-67


title: DUX_OE-1_ASTAR-RNA-56


title: DUX_OE-1_ASTAR-RNA-57


title: 18098_YY1_K562


title: 18763_SFMBT2_HepG2


title: DUX_OE-1_ASTAR-RNA-54


title: 18439_SMARCD1_MCF7


title: 18438_CBX1_MCF7


title: DUX_OE-1_ASTAR-RNA-64


title: DUX_OE-1_ASTAR-RNA-55


title: DUX_OE-1_ASTAR-RNA-53


title: DUX_OE-1_ASTAR-RNA-63


title: DUX_OE-1_ASTAR-RNA-52


title: 18437_ETV6_MCF7


title: DUX_OE-1_ASTAR-RNA-51


title: 18436_HELLS_MCF7


title: DUX_OE-1_ASTAR-RNA-60


title: DUX_OE-1_ASTAR-RNA-62


title: DUX_OE-1_ASTAR-RNA-50


title: 18435_ING4_MCF7


title: 18432_KHDRBS1_MCF7


title: DUX_OE-1_ASTAR-RNA-4


title: DUX_OE-1_ASTAR-RNA-49


title: 18433_DVL2_MCF7


title: 18430_PPP1R10_MCF7


title: DUX_OE-1_ASTAR-RNA-47


title: DUX_OE-1_ASTAR-RNA-48


title: 18431_ARNTL_MCF7


title: 18948_MEIS2_K562


title: DUX_OE-1_ASTAR-RNA-46


title: DUX_OE-1_ASTAR-RNA-44


title: 18949_DAXX_K562


title: DUX_OE-1_ASTAR-RNA-43


title: 18947_GLI1_K562


title: DUX_OE-1_ASTAR-RNA-42


title: 18944_ZNF574_K562


title: DUX_OE-1_ASTAR-RNA-41


title: DUX_OE-1_ASTAR-RNA-40


title: 18942_HOXB6_K562


title: DUX_OE-1_ASTAR-RNA-3


title: 18945_SIRT2_K562


title: DUX_OE-1_ASTAR-RNA-39


title: 18434_WDR5_MCF7


title: DUX_OE-1_ASTAR-RNA-38


title: 18941_SMAD2_K562


title: DUX_OE-1_ASTAR-RNA-37


title: 22811_NR0B1_K562


title: 22810_PRRX2_K562


title: DUX_OE-1_ASTAR-RNA-36


title: DUX_OE-1_ASTAR-RNA-45


title: 22812_USF1_K562


title: 26299_EHMT2_K562


title: 26298_FEZF2_K562


title: DUX_OE-1_ASTAR-RNA-35


title: DUX_OE-1_ASTAR-RNA-32


title: DUX_OE-1_ASTAR-RNA-34


title: 18946_Smad3_K562


title: 19597_SOX8_K562


title: DUX_OE-1_ASTAR-RNA-31


title: 19595_ZFYVE20_K562


title: DUX_OE-1_ASTAR-RNA-2


title: 19598_SIRT6_K562


title: DUX_OE-1_ASTAR-RNA-30


title: DUX_OE-1_ASTAR-RNA-29


title: 18943_ABTB1_K562


title: 26296_ATRX_K562


title: 19599_DDX58_K562


title: DUX_OE-1_ASTAR-RNA-27


title: 23863_USF1_K562


title: DUX_OE-1_ASTAR-RNA-28


title: DUX_OE-1_ASTAR-RNA-26


title: 19594_TRIM28_K562


title: 23862_ZFP92_K562


title: DUX_OE-1_ASTAR-RNA-25


title: 23861_ZNF485_K562


title: DUX_OE-1_ASTAR-RNA-33


title: DUX_OE-1_ASTAR-RNA-23


title: DUX_OE-1_ASTAR-RNA-24


title: 23860_ATAD2_K562


title: DUX_OE-1_ASTAR-RNA-22


title: 23866_NR1H2-_K562


title: 23867_MAT2B-_K562


title: 19596_DVL3_K562


title: DUX_OE-1_ASTAR-RNA-20


title: DUX_OE-1_ASTAR-RNA-21


title: 23865_SMARCAL1-_K562


title: DUX_OE-1_ASTAR-RNA-1


title: 23868_HMGXB4-_K562


title: 19602_ZNFX1_K562


title: DUX_OE-1_ASTAR-RNA-19


title: 23869_HOXB2-_K562


title: DUX_OE-1_ASTAR-RNA-16


title: 19600_BOLA3_K562


title: DUX_OE-1_ASTAR-RNA-17


title: 19601_IRX2_K562


title: DUX_OE-1_ASTAR-RNA-14


title: DUX_OE-1_ASTAR-RNA-13


title: 16656_YY1_MCF7


title: 16655_GRHL2_MCF7


title: 19606_ZBTB3_K562


title: DUX_OE-1_ASTAR-RNA-12


title: DUX_OE-1_ASTAR-RNA-15


title: 19605_POU3F2_K562


title: 19608_PRDM16_K562


title: 19609_ZNF169_K562


title: 16658_USF1_MCF7


title: 22026_ID4-_MCF7


title: DUX_OE-1_ASTAR-RNA-11


title: Wildtype mouse 6

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

data_processing:
Illumina Casava used for basecalling.
Sequenced reads were trimmed with cutadapt(v1.18) for adapter sequences, and masked for low-complexity or low-quality sequence. fastqc was applied to assess for sample quality. Subsequently, an alignment was performed using STAR on the reference genome mm10 provided from UCSC
Results were displayed as bam files sorted by coordinates. Using featureCounts a summary of bam files was created, which contained the amount of mapped reads, chromosomal locations, strand, genes and further additional data. Genes were annotated using the mm10 assembly.
Normalized abundance measurement, output table of Deseq2
The output table was analysed applying the Bioconductor R package Deseq2 (version 1.22.2), that applies negative binomial generalized linear models in order to test for differential expression. Normalized data were further analyzed with ArrayStar (Lasergene 15). Genes were filtered for at least three valid samples per group and to exclude low expression genes. Data were log2 transformed and results displayed as scatter plots and as Volcano plots, the latter showing the log2 difference i.e. fold change (positive for upregulated genes and negative for downregulated genes) versus the –log10 of the ttest P value. The P value was set at 0.05 and adjusted according to Benjamini Hochberg. Hierarchical clustering was employed to assess gene expression patterns using Euclidean distance metrics. Gene set enrichment analyses (GSEA) (http://www.gsea-msigdb.org) were used to further assess functional implications of up- or downregulated genes and to obtain a gene ranking and heat map of the leading edge 50 up- and downregulated genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each sample target length and coordinates, tab-delimited text file with normalized counts of valid genes including gene IDs

molecule: total RNA

source_name: hippocampus

extract_protocol:
Hippocampi were removed, flash frozen on dry ice, and RNA was harvested using Trizol 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.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: naive mice, no treatment

tag: tissue

value: hippocampus

tag: age

tag: gender

value: male

tag: genotype

value: wildtye control


title: Wildtype mouse 7


title: Wildtype mouse 4


title: 22027_RXRA-_MCF7


title: Wildtype mouse 5


title: DUX_OE-1_ASTAR-RNA-18


title: 19170_FOXR1_K562


title: 19603_CELF4_K562


title: 19171_HOPX_K562


title: Wildtype mouse 2


title: LPAR2-/- mouse 7

value: knockout


title: 18121_USF1_MCF7


title: 28228_ZNF385B_K562


title: 19173_USF1_K562


title: 28229_GBX1_K562


title: Wildtype mouse 1


title: LPAR2-/- mouse 4


title: 18096_TP73_K562


title: LPAR2-/- mouse 3


title: 18766_USF1_HepG2


title: LPAR2-/- mouse 5


title: DUX_OE-1_ASTAR-RNA-10


title: 18092_FOXM1_K562


title: LPAR2-/- mouse 2


title: LPAR2-/- mouse 1


title: 24398_ZNF830-_K562


title: mES_STAR_RNA-seq_96

data_processing:
Libraries were mapped to mm9 genome using STAR aligner. We allowed up to 2 mismatches and removed reads mapping to more than one region in the genome.
Cuffquant was used to quantify reads mapping to each gene in every single-cell library
Cuffnorm was used to normalize the values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited tables containing the FPKM values of the genes in each single-cell library.

source_name: E14 Mouse ES Cells grown in Serum LIF Medium

growth_protocol: mES-E14TG2a mouse embryonic stem cells were maintained in DME+4500 mg/l medium (HyClone) supplemented with 15% Fetal Bovine Serum (Gibco), MEM Non-Essential Amino Acids Solution (100X, Gibco), 200mM L-Glutamine (100X, Gibco), 55mM β-mercaptoethanol, 100 U/ml Penicillin-Streptomycin (100X, Gibco), 10^7 unit/ml ESGRO® Recombinant Mouse LIF Protein (10000X, Merck). 2i cells were derived by culturing mES-E14TG2a cells with N2B27 based 2i medium and harvested for STAR at passage 3. The recipe of N2B27 based 2i medium is as follows: DMEM/F12 medium (Gibco), Neurobasal medium (Gibco), N2 Supplement (200X, Gibco), B27 Supplement (100X, Gibco), 200mM L-Glutamine (200X, Gibco), 0.1mM β-mercaptoethanol (Gibco), 7.5% BSA (1500X, HyClone), 3uM CHIR99021 (STEMCELL Technologies), 1uM PD0325901 (STEMCELL Technologies), 10^7 unit/ml ESGRO® Recombinant Mouse LIF Protein (10000X, Merck). Cells were routinely propagated by trypsinization and re-plated onto 0.1% gelatin coated plates every three to four days.

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for STAR Scripts run using C1 Fluidigm mRNA-seq chips (10-17um).
The concentration of amplified cDNA was measured by high sensitivity bioanalyzer chips and diluted to required range of cDNA for following library preparation steps. STAR mRNAseq libraries were prepared using Nextera XT DNA Library Preparation Kit (FC-131-1096) following “Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing” manual.

value: E14 Mouse ES Cells


title: 24399_ZFP3-_K562


title: 18093_GRHL2_K562


title: 28421_GABPA-_liver


title: mES_STAR_RNA-seq_94


title: Wildtype mouse 3


title: mES_STAR_RNA-seq_95


title: mES_STAR_RNA-seq_93


title: LPAR2-/- mouse 6


title: 28425_NRF1-_kidney


title: 28427_GABPA-_kidney


title: 28424_YY1-_kidney


title: mES_STAR_RNA-seq_9


title: 24390_ZNF324-_K562


title: mES_STAR_RNA-seq_90


title: 24391_ZNF689-_K562


title: mES_STAR_RNA-seq_92


title: 24392_WDHD1-_K562


title: mES_STAR_RNA-seq_91


title: 24393_RBMS2-_K562


title: mES_STAR_RNA-seq_89


title: mES_STAR_RNA-seq_87


title: 24394_ZNF549-_K562


title: mES_STAR_RNA-seq_86


title: 24395_ZBTB46-_K562


title: mES_STAR_RNA-seq_85


title: mES_STAR_RNA-seq_83


title: 24396_ZNF212-_K562


title: 18317_SMAD9_HepG2


title: mES_STAR_RNA-seq_84


title: 24397_ZNF548-_K562


title: 18645_NR1D1_K562


title: 23041_JAZF1_K562


title: mES_STAR_RNA-seq_81


title: mES_STAR_RNA-seq_82


title: mES_STAR_RNA-seq_80


title: 23515_TP53-_K562


title: 23514_ZSCAN2-_K562


title: 23040_UBE3A_K562


title: mES_STAR_RNA-seq_79


title: mES_STAR_RNA-seq_78


title: 23511_RCOR2-_K562


title: mES_STAR_RNA-seq_88


title: 23044_LHX4_K562


title: mES_STAR_RNA-seq_8


title: 23045_ID4_K562


title: 23046_KLF10_K562


title: 18647_ONECUT1_K562


title: mES_STAR_RNA-seq_76


title: mES_STAR_RNA-seq_74


title: mES_STAR_RNA-seq_75


title: 23048_PIKFYVE_K562


title: mES_STAR_RNA-seq_73


title: 23519_ZNF264-_K562


title: 18629_RXRG_K562


title: 23518_ZNF75A-_K562


title: 18628_RELA_K562


title: mES_STAR_RNA-seq_70


title: mES_STAR_RNA-seq_7


title: mES_STAR_RNA-seq_71


title: 18627_ZNF524_K562


title: mES_STAR_RNA-seq_68


title: mES_STAR_RNA-seq_69


title: mES_STAR_RNA-seq_77


title: mES_STAR_RNA-seq_67


title: mES_STAR_RNA-seq_66


title: 18625_GCM2_K562


title: 18624_FOXN1_K562


title: mES_STAR_RNA-seq_65


title: 18626_ZNF697_K562


title: 18621_ETV7_K562


title: 18622_DPRX_K562


title: mES_STAR_RNA-seq_64


title: 18620_JAZF1_K562


title: mES_STAR_RNA-seq_63


title: mES_STAR_RNA-seq_62


title: 18713_HINFP_K562


title: mES_STAR_RNA-seq_72


title: 18710_Znf143_K562


title: mES_STAR_RNA-seq_60


title: mES_STAR_RNA-seq_61


title: 18716_ZNF701_K562


title: 18714_ZIC2_K562


title: 18715_Maz_K562


title: mES_STAR_RNA-seq_59


title: mES_STAR_RNA-seq_58


title: 18718_USF1_K562


title: mES_STAR_RNA-seq_56


title: 18623_KLF14_K562


title: mES_STAR_RNA-seq_57


title: mES_STAR_RNA-seq_55


title: mES_STAR_RNA-seq_54


title: 18443_ZNF165_MCF7


title: 23888_SCML2-_K562


title: mES_STAR_RNA-seq_51


title: mES_STAR_RNA-seq_52


title: 18441_ZMAT2_MCF7


title: 18711_CREB1_K562


title: 18446_RNF20_MCF7


title: 18440_BRD9_MCF7


title: mES_STAR_RNA-seq_6


title: 18447_ZBTB25_MCF7


title: 18445_ATAD2_MCF7


title: mES_STAR_RNA-seq_5


title: mES_STAR_RNA-seq_49


title: 18939_ZNF438_K562


title: mES_STAR_RNA-seq_48


title: 18719_ID1_HepG2


title: mES_STAR_RNA-seq_47


title: 18938_Med1_K562


title: 18932_CTBP1_K562


title: 22200_STAT5A_K562


title: mES_STAR_RNA-seq_46


title: mES_STAR_RNA-seq_45


title: mES_STAR_RNA-seq_44


title: 18931_HMG20B_K562


title: mES_STAR_RNA-seq_43


title: mES_STAR_RNA-seq_53


title: 18930_TAX1BP1_K562


title: mES_STAR_RNA-seq_50


title: mES_STAR_RNA-seq_42


title: 18936_MEF2A_K562


title: mES_STAR_RNA-seq_41


title: mES_STAR_RNA-seq_40


title: mES_STAR_RNA-seq_39


title: 23880_GTF2F2-_K562


title: 23886_TP53-_K562


title: 18934_PRRX2_K562


title: mES_STAR_RNA-seq_4


title: 22208_STAT5B_K562


title: 18933_NR5A2_K562


title: 23085_NEDD4L_K562


title: mES_STAR_RNA-seq_38


title: mES_STAR_RNA-seq_36


title: 22808_TAX1BP1_K562


title: mES_STAR_RNA-seq_37


title: mES_STAR_RNA-seq_35


title: 22809_FOXP4_K562


title: mES_STAR_RNA-seq_34


title: 22806_NR3C2_K562


title: 22807_ZKSCAN2_K562


title: 22804_STAT3_K562


title: mES_STAR_RNA-seq_32


title: mES_STAR_RNA-seq_33


title: 23882_RCOR2-_K562


title: 22805_ARNT_K562


title: mES_STAR_RNA-seq_30


title: mES_STAR_RNA-seq_3


title: 22803_Elf1_K562


title: mES_STAR_RNA-seq_31


title: 22802_ZNF639_K562


title: mES_STAR_RNA-seq_29


title: 22800_GABPA_K562


title: 22801_ETV6_K562


title: mES_STAR_RNA-seq_27


title: mES_STAR_RNA-seq_26


title: 24093_E4F1-_K562


title: mES_STAR_RNA-seq_25


title: mES_STAR_RNA-seq_24


title: 24092_BATF3-_K562


title: 24097_PRDM7-_K562


title: mES_STAR_RNA-seq_23


title: 24094_ZNF24-_K562


title: mES_STAR_RNA-seq_20


title: mES_STAR_RNA-seq_2


title: 26148_PBX1-_K562


title: mES_STAR_RNA-seq_22


title: 26147_FOS-_K562


title: 18118_NRF1_MCF7


title: mES_STAR_RNA-seq_21


title: mES_STAR_RNA-seq_17


title: 18119_PAX2_MCF7


title: mES_STAR_RNA-seq_16


title: 23878_SMARCD1-_K562


title: mES_STAR_RNA-seq_28


title: mES_STAR_RNA-seq_18


title: 24098_ZNF846-_K562


title: 23879_SIN3B-_K562


title: 24096_PROX2-_K562


title: mES_STAR_RNA-seq_15


title: mES_STAR_RNA-seq_14


title: 23874_HDAC6-_K562


title: mES_STAR_RNA-seq_13


title: 23875_ZBTB25-_K562


title: mES_STAR_RNA-seq_11


title: mES_STAR_RNA-seq_12


title: 23877_PKNOX2-_K562


title: 23876_SRY-_K562


title: 26149_GLI1-_K562


title: 23870_HIF3A-_K562


title: mES_STAR_RNA-seq_1


title: 2i_STAR_RNA-seq_96

source_name: E14 Mouse ES Cells grown in 2i Medium


title: 23871_DMRTB1-_K562


title: 23872_TADA2A-_K562


title: 15411_STAT5A_K562-8M


title: 15415_NFATC1_K562-8M


title: 2i_STAR_RNA-seq_95


title: 2i_STAR_RNA-seq_94


title: 15414_TP73_K562-8M


title: 16665_NRF1_MCF7


title: 2i_STAR_RNA-seq_93


title: 2i_STAR_RNA-seq_92


title: 16664_YY1_MCF7


title: 2i_STAR_RNA-seq_91


title: 2i_STAR_RNA-seq_90


title: 2i_STAR_RNA-seq_9


title: 16662_FOXM1_MCF7


title: 2i_STAR_RNA-seq_89


title: 19141_USP7_K562


title: mES_STAR_RNA-seq_10


title: 2i_STAR_RNA-seq_88


title: 19140_NANOGP1_K562


title: 19143_RXRB_K562


title: 19142_FoxC2_K562


title: 2i_STAR_RNA-seq_86


title: 2i_STAR_RNA-seq_85


title: 2i_STAR_RNA-seq_84


title: 19145_SET_K562


title: 19144_HOXB9_K562


title: 2i_STAR_RNA-seq_83


title: 19147_RBBP5_K562


title: 2i_STAR_RNA-seq_82


title: 19149_SIRT5_K562


title: 2i_STAR_RNA-seq_80


title: 19146_FOXA2_K562


title: 2i_STAR_RNA-seq_81


title: 16666_USF1_MCF7


title: 18114_YY1_MCF7


title: 23500_DMRTB1-_K562


title: 19148_HDAC1_K562


title: 2i_STAR_RNA-seq_87


title: 2i_STAR_RNA-seq_8


title: 16663_GRHL2_MCF7


title: 2i_STAR_RNA-seq_77


title: 2i_STAR_RNA-seq_76


title: 2i_STAR_RNA-seq_75


title: 2i_STAR_RNA-seq_78


title: 23050_ZNF81_K562


title: 2i_STAR_RNA-seq_74


title: 23503_HDAC6-_K562


title: 2i_STAR_RNA-seq_73


title: 23057_PPARD_K562


title: 23055_USF1_K562


title: 2i_STAR_RNA-seq_72


title: 2i_STAR_RNA-seq_70


title: 23508_SIN3B-_K562


title: 23509_GTF2F2-_K562


title: 2i_STAR_RNA-seq_69


title: 2i_STAR_RNA-seq_7


title: 2i_STAR_RNA-seq_79


title: 23059_SMARCE1_K562


title: 23053_MEF2A_K562


title: 2i_STAR_RNA-seq_68


title: 23504_ZBTB25-_K562


title: 18631_RORA_K562


title: 18632_OTX2_K562


title: 2i_STAR_RNA-seq_67


title: 18634_ZBTB46_K562


title: 2i_STAR_RNA-seq_66


title: 2i_STAR_RNA-seq_65


title: 18633_RAX_K562


title: 2i_STAR_RNA-seq_64


title: 23054_CEBPB_K562


title: 18635_HOXD9_K562


title: 18708_NCOA1_K562


title: 2i_STAR_RNA-seq_63


title: 2i_STAR_RNA-seq_61


title: 18709_Max_K562


title: 2i_STAR_RNA-seq_62


title: 2i_STAR_RNA-seq_71


title: 2i_STAR_RNA-seq_60


title: 23058_ANAPC2_K562


title: 18700_DR1_K562


title: 2i_STAR_RNA-seq_6


title: 18701_TFCP2_K562


title: 2i_STAR_RNA-seq_59


title: 2i_STAR_RNA-seq_58


title: 18702_YBX1_K562


title: 18927_FOSB_K562


title: 2i_STAR_RNA-seq_57


title: 18928_KLF16_K562


title: 2i_STAR_RNA-seq_56


title: 18929_PRDM1_K562


title: 2i_STAR_RNA-seq_55


title: 22873_SOX4_K562


title: 22872_DMRT2_K562


title: 22879_DAXX_K562


title: 22871_UBE2B_K562


title: 2i_STAR_RNA-seq_52


title: 18707_ELF2_K562


title: 22878_PAX5_K562


title: 2i_STAR_RNA-seq_54


title: 22877_PRKRA_K562


title: 2i_STAR_RNA-seq_50


title: 2i_STAR_RNA-seq_49


title: 2i_STAR_RNA-seq_53


title: 2i_STAR_RNA-seq_5


title: 2i_STAR_RNA-seq_48


title: 2i_STAR_RNA-seq_47


title: 22875_Med1_K562


title: 22870_KLF5_K562


title: 2i_STAR_RNA-seq_46


title: 2i_STAR_RNA-seq_45


title: 18454_EIF4A2_MCF7


title: 22874_RXRG_K562


title: 18455_NR2F2_MCF7


title: 2i_STAR_RNA-seq_44


title: 18457_USF1_MCF7


title: 2i_STAR_RNA-seq_43


title: 2i_STAR_RNA-seq_42


title: 2i_STAR_RNA-seq_51


title: 18451_DACH1_MCF7


title: 2i_STAR_RNA-seq_4


title: 28411_USF1-_liver


title: 18453_EEA1_MCF7


title: 22876_NFKB2_K562


title: 2i_STAR_RNA-seq_40


title: 2i_STAR_RNA-seq_41


title: 26158_YY1-_K562


title: 2i_STAR_RNA-seq_39


title: 2i_STAR_RNA-seq_37


title: 26150_ZNF143-_K562


title: 2i_STAR_RNA-seq_38


title: 26159_MAX-_K562


title: 2i_STAR_RNA-seq_36


title: 26151_NFIA-_K562


title: 26152_NAB2-_K562


title: 26153_GTF2H2C-_K562


title: 26154_GABPA-_K562


title: 2i_STAR_RNA-seq_32


title: 2i_STAR_RNA-seq_33


title: 26155_STAT5A-_K562


title: 2i_STAR_RNA-seq_35


title: 18450_TERF2IP_MCF7


title: mES_STAR_RNA-seq_19


title: 2i_STAR_RNA-seq_31


title: 26156_STAT5B-_K562


title: 18452_GABPB1_MCF7


title: 26157_NRF1-_K562


title: 2i_STAR_RNA-seq_28


title: 2i_STAR_RNA-seq_27


title: 17385_HMGB1-4F10_MCF7


title: 2i_STAR_RNA-seq_26


title: 2i_STAR_RNA-seq_30


title: 2i_STAR_RNA-seq_24


title: 2i_STAR_RNA-seq_34


title: 17384_ZIC1-1E3_MCF7


title: 2i_STAR_RNA-seq_3


title: 2i_STAR_RNA-seq_29


title: 17380_GRHL2_MCF7


title: 2i_STAR_RNA-seq_23


title: 2i_STAR_RNA-seq_25


title: 17382_PRDM7-3D3_MCF7


title: 17383_BRD3-1C12_MCF7


title: 23841_ZNF232_K562


title: 23848_GTF2IRD2_K562


title: 2i_STAR_RNA-seq_22


title: 23843_ZNF354A_K562


title: 23842_ZFP28_K562


title: 2i_STAR_RNA-seq_21


title: 2i_STAR_RNA-seq_20


title: 23845_GRAMD4_K562


title: 2i_STAR_RNA-seq_2


title: 2i_STAR_RNA-seq_19


title: 23844_ZNF341_K562


title: 23847_ZNF98_K562


title: 23846_GTF2I_K562


title: 2i_STAR_RNA-seq_18


title: 23849_ZNF783_K562


title: 2i_STAR_RNA-seq_17


title: 19152_MESP2_K562


title: 2i_STAR_RNA-seq_15


title: 19151_HEYL_K562


title: 2i_STAR_RNA-seq_14


title: 19153_MYCL1_K562


title: 2i_STAR_RNA-seq_13


title: 2i_STAR_RNA-seq_12


title: 19150_CBX2_K562


title: 2i_STAR_RNA-seq_10


title: 2i_STAR_RNA-seq_16


title: 19154_RGCC_K562


title: 2i_STAR_RNA-seq_11


title: mES_STAR_ATAC-seq_96

data_processing:
Libraries were mapped to mm9 genome using STAR aligner. We allowed up to 2 mismatches and removed reads mapping to more than one region in the genome. The “–alignIntronMax” was set to 1 and the option “--  alignEndsType EndToEnd” was used.
Duplicates were removed using MarkDuplicates module of PICARD.
To determine the highly accessible regions, the de-duplicated mouse ATAC-Seq libraries were merged and peaks were called using MACS2. The following MACS2 options were used: -- nomodel -- nolambda -- keep-dup all – call-summits.
The de-duplicated single cell bam files were uploaded to chromVAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs which can be used for visualization in the UCSC genome browser.


title: 19159_EIF4E_K562


title: 2i_STAR_RNA-seq_1


title: mES_STAR_ATAC-seq_95


title: LMS20_cell line RNA-seq

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq of a human leiomyosarcoma cell line.

data_processing:
RNA-seq data were aligned using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM values are in text format

source_name: Leiomyosarcoma cell line

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Libraries for Illumina NextSeq 500 sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced with single-end 75 bp reads.

tag: sample type

value: cell line


title: 19157_HDGFRP2_K562


title: mES_STAR_ATAC-seq_93


title: mES_STAR_ATAC-seq_92


title: LMS_82588 RNA-seq

description: RNA-seq of a human leiomyosarcoma tumor.

source_name: LMS tumor sample

value: tumor


title: LMS_7 RNA-seq


title: mES_STAR_ATAC-seq_91


title: mES_STAR_ATAC-seq_94


title: LMS_64043 RNA-seq


title: LMS_57897 RNA-seq


title: mES_STAR_ATAC-seq_90


title: 19156_PCGF6_K562


title: LMS_52278 RNA-seq


title: mES_STAR_ATAC-seq_9


title: LMS_4449 RNA-seq


title: mES_STAR_ATAC-seq_88


title: 19155_VDR_K562


title: LMS_4 RNA-seq


title: mES_STAR_ATAC-seq_89


title: mES_STAR_ATAC-seq_87


title: LMS_38 RNA-seq


title: 19158_ZBTB17_K562


title: mES_STAR_ATAC-seq_84


title: mES_STAR_ATAC-seq_86


title: mES_STAR_ATAC-seq_82


title: LMS_26726 RNA-seq


title: LMS_27736 RNA-seq


title: mES_STAR_ATAC-seq_83


title: LMS_23120 RNA-seq


title: mES_STAR_ATAC-seq_81


title: LMS_20 RNA-seq


title: mES_STAR_ATAC-seq_80


title: LMS_19066 RNA-seq


title: LMS_21506 RNA-seq


title: mES_STAR_ATAC-seq_79


title: LMS_19 RNA-seq


title: LMS_18591 RNA-seq


title: mES_STAR_ATAC-seq_77


title: LMS_33 RNA-seq


title: mES_STAR_ATAC-seq_76


title: Sox9_GFP_Hi_ATAC_2

city: Bronx

first: John

middle: Robert

last: Christin

state: NY

address: 1301 Morris Park Avenue, Room 108/114

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
FASTQC Checked
Sequencing reads were mapped to the mouse genome (mm9) with Bowtie (Langmead et al., 2009), with these parameters: -m 1 -S -n 2 -l 30
Duplicated reads were removed and peak calling was done with MACS2 (Zhang et al., 2008) with these parameters: --nolambda --nomodel --shift -100 --extsize 200
Bedgraph files generated were then quantile normalized using the R package “preprocessCore” and converted into BigWig format
Genome-wide average signal profile at genes was checked for each sample to ensure similar signal-to-noise level. Signal profiling was performed using deepTools
Differential peaks were called with SICER-df-rb (Zang et al., 2009), with these parameters: window size: 100, gap size: 100, E-value: 0.01, FDR: 0.05
Genome_build: Mm9
Supplementary_files_format_and_content: BigWig quantile normalized

extract_protocol:
Nuclei were isolated from 1.4x10^4 from sorted Sox9-GFP-high and Sox9-GFP-low C3(1)/Tag cells and described in Buenrostro et al., 2015
Nuclei were incubated in a 20 μl of transposition mix (10 μl 2x TD, 0.5 μl TDE1, 6.6 ul PBS, 2.9 μl H2O; Illumina Nextera FC-121-1030) and incubated at 37°C for 30 minutes with shaking. The library was amplified with 12 cycles of PCR as determined by qPCR to be the optimal cycle number (25% library saturation).

tag: genotype/variation

value: Sox9-GFP; C3(1)/Tag

value: mammary glands

tag: sorted cells

value: Luminal Sox9-GFP high mammary epithelial cells

tag: molecule subtype

value: Transpoase Accesible DNA


title: mES_STAR_ATAC-seq_85


title: LMS_28826 RNA-seq


title: LMS_31 RNA-seq


title: Sox9_GFP_Lo_ATAC_1

value: Luminal Sox9-GFP low mammary epithelial cells


title: mES_STAR_ATAC-seq_78


title: mES_STAR_ATAC-seq_73


title: Sox9_GFP_Hi_ATAC_1


title: mES_STAR_ATAC-seq_72


title: mES_STAR_ATAC-seq_70


title: mES_STAR_ATAC-seq_71


title: subclone_SLP#114_129_T2

city: Dallas

first: Joseph

middle: S

last: Takahashi

state: TX

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Illumina bcl2fastq version 2.15 for base calling and demultiplexing.
Raw reads were tested for quality using FastQC, and low-quality reads were trimmed using Seqtk
The resulting reads were mapped to mm10 annotation from UCSC using TopHat
The output BAM file was then filtered for uniquely mapped reads using Samtools.
RPKM calculations were performed using analyzeRepeats.pl of HOMER suite.
Genome_build: mm10
Supplementary_files_format_and_content: Comma delimited CSV file include RPKM values for all samples

source_name: Immortalized ear fibroblast clone#114-129

growth_protocol: Immortalized mouse ear fibroblast cells from male mice carrying Per2::luc bioluminescence reporter were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
Sequencing libraries were made following the protocol described in: Takahashi, J.S., Kumar, V., Nakashe, P., Koike, N., Huang, H.C., Green, C.B., and Kim, T.K. (2015). ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals. Methods Enzymol 551, 285-321.

treatment_protocol: Confluent cells were synchronized with 100 nM dexamethasone for 2 hr, then changed to medium with 2% FBS. Cells were collected at 2 timepoints after synchronization: the first peak (T1) and the following trough (T2) based on Per2::luc bioluminescence signal. At each timepoint, we collected 2 replicates for 10 clonal cell lines and 1 replicate for 24 subclones.

value: Ear


title: subclone_SLP#114_125_T2

source_name: Immortalized ear fibroblast clone#114-125


title: mES_STAR_ATAC-seq_75


title: mES_STAR_ATAC-seq_74


title: mES_STAR_ATAC-seq_8


title: mES_STAR_ATAC-seq_7


title: mES_STAR_ATAC-seq_69


title: subclone_SLP#114_125_T1


title: subclone_SLP#114_65_T1

source_name: Immortalized ear fibroblast clone#114-65


title: mES_STAR_ATAC-seq_68


title: mES_STAR_ATAC-seq_67


title: Sox9_GFP_Lo_ATAC_2


title: mES_STAR_ATAC-seq_65


title: mES_STAR_ATAC-seq_66


title: subclone_SLP#114_65_T2


title: subclone_SLP#114_62_T2

source_name: Immortalized ear fibroblast clone#114-62


title: subclone_SLP#114_62_T1


title: subclone_SLP#114_57_T1

source_name: Immortalized ear fibroblast clone#114-57


title: mES_STAR_ATAC-seq_64


title: mES_STAR_ATAC-seq_63


title: subclone_SLP#114_31_T1

source_name: Immortalized ear fibroblast clone#114-31


title: mES_STAR_ATAC-seq_62


title: subclone_SLP#114_31_T2


title: mES_STAR_ATAC-seq_61


title: subclone_SSP#33_141_T2

source_name: Immortalized ear fibroblast clone#33-141


title: subclone_SLP#114_57_T2


title: mES_STAR_ATAC-seq_6


title: mES_STAR_ATAC-seq_60


title: subclone_SSP#33_141_T1


title: subclone_SSP#33_123_T2

source_name: Immortalized ear fibroblast clone#33-123


title: subclone_SSP#33_123_T1


title: mES_STAR_ATAC-seq_59


title: subclone_SSP#33_117_T2

source_name: Immortalized ear fibroblast clone#33-117


title: mES_STAR_ATAC-seq_57


title: subclone_SSP#33_117_T1


title: mES_STAR_ATAC-seq_56


title: mES_STAR_ATAC-seq_58


title: subclone_SSP#33_112_T1

source_name: Immortalized ear fibroblast clone#33-112


title: mES_STAR_ATAC-seq_55


title: mES_STAR_ATAC-seq_54


title: mES_STAR_ATAC-seq_53


title: subclone_SSP#33_3_T2

source_name: Immortalized ear fibroblast clone#33-3


title: subclone_SSP#33_26_T2

source_name: Immortalized ear fibroblast clone#33-26


title: subclone_SSP#33_3_T1


title: mES_STAR_ATAC-seq_51


title: subclone_SSP#33_26_T1


title: subclone_LLP#114_96_T2

source_name: Immortalized ear fibroblast clone#114-96


title: mES_STAR_ATAC-seq_52

source_name: E14 Mouse ES Cells grown in Serum LIF Medium


title: mES_STAR_ATAC-seq_50


title: mES_STAR_ATAC-seq_49


title: mES_STAR_ATAC-seq_5


title: mES_STAR_ATAC-seq_48


title: subclone_LLP#114_96_T1


title: subclone_LLP#114_82_T2

source_name: Immortalized ear fibroblast clone#114-82


title: mES_STAR_ATAC-seq_47


title: subclone_LLP#114_91_T1

source_name: Immortalized ear fibroblast clone#114-91


title: subclone_LLP#114_82_T1


title: mES_STAR_ATAC-seq_46


title: subclone_SSP#33_112_T2


title: subclone_LLP#114_80_T2

source_name: Immortalized ear fibroblast clone#114-80


title: mES_STAR_ATAC-seq_43


title: mES_STAR_ATAC-seq_44


title: subclone_LLP#114_80_T1


title: subclone_LLP#114_49_T2

source_name: Immortalized ear fibroblast clone#114-49


title: mES_STAR_ATAC-seq_45


title: subclone_LLP#114_49_T1


title: mES_STAR_ATAC-seq_42


title: mES_STAR_ATAC-seq_41


title: subclone_LLP#114_41_T1

source_name: Immortalized ear fibroblast clone#114-41


title: subclone_LLP#114_41_T2


title: subclone_LLP#114_91_T2


title: mES_STAR_ATAC-seq_40


title: subclone_LSP#33_84_T2

source_name: Immortalized ear fibroblast clone#33-84


title: subclone_LSP#33_84_T1


title: subclone_LSP#33_53_T2

source_name: Immortalized ear fibroblast clone#33-53


title: mES_STAR_ATAC-seq_4


title: subclone_LSP#33_53_T1


title: mES_STAR_ATAC-seq_38


title: mES_STAR_ATAC-seq_37


title: mES_STAR_ATAC-seq_39


title: subclone_LSP#33_51_T2

source_name: Immortalized ear fibroblast clone#33-51


title: mES_STAR_ATAC-seq_35


title: mES_STAR_ATAC-seq_36


title: mES_STAR_ATAC-seq_34


title: mES_STAR_ATAC-seq_33


title: subclone_LSP#33_49_T1

source_name: Immortalized ear fibroblast clone#33-49


title: subclone_LSP#33_49_T2


title: mES_STAR_ATAC-seq_32


title: mES_STAR_ATAC-seq_31


title: subclone_LSP#33_27_T1

source_name: Immortalized ear fibroblast clone#33-27


title: subclone_LSP#33_22_T2

source_name: Immortalized ear fibroblast clone#33-22


title: mES_STAR_ATAC-seq_30


title: mES_STAR_ATAC-seq_3


title: clone_SP#137_rep2_T2

source_name: Immortalized ear fibroblast clone#137


title: mES_STAR_ATAC-seq_29


title: mES_STAR_ATAC-seq_28


title: mES_STAR_ATAC-seq_27


title: clone_SP#137_rep1_T2


title: subclone_LSP#33_22_T1


title: clone_SP#128_rep2_T2

source_name: Immortalized ear fibroblast clone#128


title: mES_STAR_ATAC-seq_26


title: subclone_LSP#33_51_T1


title: mES_STAR_ATAC-seq_25


title: clone_SP#128_rep2_T1


title: mES_STAR_ATAC-seq_24


title: clone_SP#128_rep1_T2


title: subclone_LSP#33_27_T2


title: clone_SP#128_rep1_T1


title: mES_STAR_ATAC-seq_22


title: mES_STAR_ATAC-seq_20


title: mES_STAR_ATAC-seq_21


title: clone_LP#114_rep1_T2

source_name: Immortalized ear fibroblast clone#114


title: clone_LP#114_rep2_T1


title: mES_STAR_ATAC-seq_2


title: mES_STAR_ATAC-seq_19


title: clone_LP#108_rep2_T2

source_name: Immortalized ear fibroblast clone#108


title: clone_SP#137_rep2_T1


title: clone_SP#137_rep1_T1


title: clone_LP#108_rep2_T1


title: mES_STAR_ATAC-seq_18


title: clone_LP#108_rep1_T2


title: mES_STAR_ATAC-seq_16


title: mES_STAR_ATAC-seq_15


title: mES_STAR_ATAC-seq_17


title: mES_STAR_ATAC-seq_23


title: clone_LP#108_rep1_T1


title: clone_LP#114_rep2_T2


title: clone_LP#86_rep1_T2

source_name: Immortalized ear fibroblast clone#86


title: clone_LP#86_rep2_T2


title: mES_STAR_ATAC-seq_12

source_name: E14 Mouse ES Cells grown in Serum LIF Medium


title: mES_STAR_ATAC-seq_11


title: clone_LP#86_rep2_T1


title: clone_LP#86_rep1_T1


title: mES_STAR_ATAC-seq_10


title: clone_SP#80_rep2_T1

source_name: Immortalized ear fibroblast clone#80


title: mES_STAR_ATAC-seq_1


title: clone_LP#114_rep1_T1


title: mES_STAR_ATAC-seq_13


title: clone_SP#80_rep1_T2


title: clone_SP#80_rep2_T2


title: 2i_STAR_ATAC-seq_95

source_name: E14 Mouse ES Cells grown in 2i Medium


title: mES_STAR_ATAC-seq_14


title: 2i_STAR_ATAC-seq_93


title: clone_LP#74_rep1_T2

source_name: Immortalized ear fibroblast clone#74


title: clone_LP#74_rep1_T1


title: 2i_STAR_ATAC-seq_91


title: clone_LP#74_rep2_T1


title: 2i_STAR_ATAC-seq_92


title: clone_SP#44_rep2_T2

source_name: Immortalized ear fibroblast clone#44


title: clone_SP#44_rep2_T1


title: 2i_STAR_ATAC-seq_94


title: 2i_STAR_ATAC-seq_9


title: clone_SP#44_rep1_T1


title: clone_SP#44_rep1_T2


title: 2i_STAR_ATAC-seq_90


title: 2i_STAR_ATAC-seq_88


title: 2i_STAR_ATAC-seq_96


title: 2i_STAR_ATAC-seq_87


title: 2i_STAR_ATAC-seq_89


title: 2i_STAR_ATAC-seq_86


title: clone_LP#34_rep2_T1

source_name: Immortalized ear fibroblast clone#34


title: clone_LP#34_rep2_T2


title: clone_LP#34_rep1_T2


title: 2i_STAR_ATAC-seq_85


title: clone_LP#34_rep1_T1


title: clone_LP#74_rep2_T2


title: clone_SP#80_rep1_T1


title: 2i_STAR_ATAC-seq_84


title: clone_SP#33_rep2_T1

source_name: Immortalized ear fibroblast clone#33


title: 2i_STAR_ATAC-seq_82


title: clone_SP#33_rep1_T1


title: 2i_STAR_ATAC-seq_81


title: 2i_STAR_ATAC-seq_80


title: 2i_STAR_ATAC-seq_8


title: Mouse8_liver_AAVrh.10Null_sc

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Technical R1 read length: 20 (positions of cell_barcodes are bases 1 - 12 and UMIs are 13 - 20). Biological R2 read length: 72.
The clustering algorithm was performed using Seurat, a R package for single cell analysis. Raw digital expression matrices that contain integer counts of number of transcripts for each gene in each cell were generated separately for each sequence.
All the genes expressed in at least 10 cells and all the cells with at least 200 detected genes were analyzed. Cells were filtered out that had unique gene counts over 10,000 and the percentage of mitochondrial genes over 0.5.
A multi-set canonical correlation analysis (CCA) was performed using the Seurat RunMultiCCA function to defined a shared correlation space to produce an integrated gene expression matrix.
The filtered gene expression matrix from a total of 17,251 genes across 46,500 cells from 9 samples was then normalized by the total number of UMIs per cells, multiplying by a scale factor (10,000) and then log transformed. Cell-cell variation were regressed out in gene expression driven by number of UMI as well as the percentage of mitochondrial gene content.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include UMI values for each cell; column headers are cell_barcodes.

source_name: Liver

extract_protocol:
Single cells were isolated from mouse livers, and RNA from individual cells was harvested using the Drop-seq technique.
RNA libraries were prepared for sequencing using standard Illumina protocols
The single cell libraries were sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

treatment_protocol: PBS, AAVrh.10Null and AAVrh.10mCherry were intravenously injected.

value: 8 weeks

tag: treatment


title: 2i_STAR_ATAC-seq_78


title: Mouse7_liver_PBS_sc

value: liver

value: PBS


title: Mouse6_liver_AAVrh.10mCherry_sc


title: 2i_STAR_ATAC-seq_77


title: 2i_STAR_ATAC-seq_79


title: Mouse5_liver_AAVrh.10Null_sc


title: clone_SP#33_rep2_T2


title: Mouse4_liver_PBS_sc


title: subclone_SLP#114_129_T1

source_name: Immortalized ear fibroblast clone#114-129


title: 2i_STAR_ATAC-seq_74


title: 2i_STAR_ATAC-seq_76


title: 2i_STAR_ATAC-seq_75


title: Mouse2_liver_AAVrh.10Null_sc


title: 2i_STAR_ATAC-seq_73


title: 2i_STAR_ATAC-seq_83


title: Mouse3_liver_AAVrh.10mCherry_sc


title: Mouse9_liver_AAVrh.10mCherry_sc


title: Mouse1_liver_PBS_sc


title: clone_SP#33_rep1_T2


title: 2i_STAR_ATAC-seq_72


title: 2i_STAR_ATAC-seq_71


title: 2i_STAR_ATAC-seq_70


title: 2i_STAR_ATAC-seq_7


title: P38_d10_rep2

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

data_processing:
Illumina RTA v1.18.66.3 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star v2.4.2a with parameters as default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using R. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The raw read counts were generated using subread v.1.4.6
The normalization was used TMM and differential expression analysis was used DeSeq2, R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalization values for each Sample ...

source_name: Day 10 stim mouse Pmel T cell + BIRB796 500nM

extract_protocol:
Qiagen RNeasy micro kit (following manufacturer instructions)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: C57BL/6J pmel-1 Tg. Mice

value: Pmel CD8+ T cells


title: Vehicle_d10_rep1

source_name: Day 10 stim mouse Pmel T cell + Vehicle


title: 2i_STAR_ATAC-seq_69


title: P38_d10_rep3


title: 2i_STAR_ATAC-seq_68


title: P38_d10_rep1


title: Vehicle_d10_rep2


title: Vehicle_d10_rep3


title: Vehicle_d5_rep4

source_name: Day 5 stim mouse Pmel T cell + Vehicle


title: 2i_STAR_ATAC-seq_67


title: Cyclo rep3

type: RNA

city: miki

first: kenji

last: gomi

state: kagawa

country: Japan

institute: Kagawa University

description: gene expression after 24 hr in beta-cyclocitral-treated rice leaf blades

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays for 17 hours at 65 ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: Rice leaf blades treated with 10 μM beta-cyclocitral, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rice plants were grown from seed in growthchamber [25 ºC, 60 - 80% relative humidity (RH)].

extract_protocol: Total RNA from rice was extracted from leaf blades after each treatment using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Five-leaf-stage rice plants were treated with 10μM beta-cyclocitral for 1 day at 25 ºC.

tag: cultivar

value: Japonica cultivar Hinohikari

tag: Stage

value: five- leaf-stage

value: fifth-leaf blade

value: beta-cyclocitral


title: 2i_STAR_ATAC-seq_66

value: E14 Mouse ES Cells


title: Vehicle_d5_rep3


title: 2i_STAR_ATAC-seq_64


title: Vehicle_d5_rep2


title: Vehicle_d5_rep1


title: 2i_STAR_ATAC-seq_63


title: Cyclo rep4

source_name: Rice leaf blades treated with 10 μM beta-cyclocitral, replicate4


title: Mock rep2

description: gene expression after 24 hr in mock-treated rice leaf blades

source_name: Rice leaf blades without treatment, replicate2

value: mock


title: 2i_STAR_ATAC-seq_65


title: Mock rep1

source_name: Rice leaf blades without treatment, replicate1


title: P38_d5_rep4

source_name: Day 5 stim mouse Pmel T cell + BIRB796 500nM


title: 2i_STAR_ATAC-seq_62


title: Cyclo rep2

source_name: Rice leaf blades treated with 10 μM beta-cyclocitral, replicate2


title: Cyclo rep1

source_name: Rice leaf blades treated with 10 μM beta-cyclocitral, replicate1


title: Mock rep3

source_name: Rice leaf blades without treatment, replicate3


title: Mock rep4

source_name: Rice leaf blades without treatment, replicate4


title: 2i_STAR_ATAC-seq_61

source_name: E14 Mouse ES Cells grown in 2i Medium


title: P38_d5_rep3


title: P38_d5_rep2


title: 2i_STAR_ATAC-seq_60


title: 2i_STAR_ATAC-seq_6


title: 2i_STAR_ATAC-seq_59


title: 2i_STAR_ATAC-seq_55


title: 2i_STAR_ATAC-seq_56


title: Du145 siControl

city: Shenzhen

first: Yeqing

last: Yuan

address: Dongmen Road

country: China

institute: Shenzhen People's Hospital

data_processing:
bwa 0.7.17-r1188 was used to do the alignment
samtools 1.7 was used to sort the sam file and convert the bam file
picard.jar 2.9.0 was used to mark the duplicate reads
macs2 2.1.2 was used to all the peaks
htseq-count 0.8.0 was used to count reads for each gene
Genome_build: library edgeR 3.5 was used to calculate rpkm and normalized reads count
Supplementary_files_format_and_content: gemone build hg19
Supplementary_files_format_and_content: processed data: rpkm and normalized reads count (.txt)

source_name: prostate

growth_protocol: PCa cell lines were maintained in RPMI 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (10 ng/ml penicillin and 10 U/ml streptomycin), and 2.5 mM glutamine at 37 °C in a humidified 5% CO2 incubator. Prostate RNA was purchased from Clontech.

extract_protocol: RNAeasy Mini kit (QIAGEN) was used for high quality RNA extraction

value: siControl


title: 2i_STAR_ATAC-seq_57


title: 2i_STAR_ATAC-seq_58


title: 2i_STAR_ATAC-seq_54


title: P38_d5_rep1


title: Du145 siCDCA2


title: AV_1 dpi Mouse 3

city: Saint Louis

first: Emma

middle: Suening

last: Winkler

state: Missouri

address: 660 S. Euclid Ave, Campus Box 8051

department: DOM-ID

institute: Washington University in St. Louis

hyb_protocol: Hybridization with Nanostring codeset reagents, sample, and buffer for 12 hours

scan_protocol: Analysis on the nCounter MAX/FLEX system

data_processing: The gene expression data were normalized to a set of 6 internal positive and 8 internal negative controls and then 14 internal reference genes. Values above the threshold (mean + 2SD of the negative controls) were considered for analysis. Normalized log2-transformed values were analyzed and unbiased hierarchical clustering was used to generate heatmaps in nSolver analysis software 4.0.

source_name: sorted splenic pDCs

label_protocol: nCounter Barcodes

growth_protocol: Mice were maintained under SPF conditions in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health after approval by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (Assurance number A3381-01).

extract_protocol: Total RNA was extracted from sorted pDCs using the MagMAX™ mirVana™ Total RNA Isolation Kit as per manufacturer’s instructions.

treatment_protocol: Mice were treated with oral antibiotics prior to infection Mayaro virus. Splenic pDCs were isolated using SiglecH-APC, B220-BV711, and PDCA-1 FITC.

value: sorted splenic pDCs

value: 1 day-post MAYV infection, oral antibiotic-treated


title: AV_1 dpi Mouse 2


title: AV_1 dpi Mouse 1


title: KA_1 dpi Mouse 3

value: 1 day post-MAYV infection, vehicle-treated


title: A549 TRIB3-shRNA cells-2

city: Beijing

first: Jiaojiao

last: Yu

address: 1 Xian Nong Tan Street

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

description: Gene expression data from A549 cells stably expressing TRIB3-shRNA

hyb_protocol: 3.5ug of cRNA were hybridized on Affymetrix Human Gene 2.0 ST Array at 45 degree C for 16 hours. Cartridge arrays were washed and stained using GeneChip Fluidic Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner with 7G upgrade.

data_processing: Intensity signals were normalized by RMA algorithm using Expression Console v1.4.1, Affymetrix. Statistical significant was determined by t-test. GO and KEGG analysis were performed by WebGestalt (updated on 1/30/2013). Heatmap was generated by R.

label: biotin

source_name: A549 TRIB3-shRNA cells

label_protocol: 5.5 ug ss-cDNA was fragmented and labeled according to the standard Affymetrix protocol.

growth_protocol: A549 cells were cultured in RPMI-1640 media.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: To generate cell populations stably expressing TRIB3-shRNA or Control-shRNA, plasmids were transfected into cells. After 24 hr of transfection, stable transfectants were selected in medium containing hygromycin for 14 days. After 2-3 passages in the presence of hygromycin, the cultured cells were used for experiments without cloning.

value: lung cancer cell line

value: stably expressing TRIB3-shRNA


title: 2i_STAR_ATAC-seq_53


title: A549 TRIB3-shRNA cells-3


title: KA_1 dpi Mouse 1


title: 2i_STAR_ATAC-seq_51


title: KA_1 dpi Mouse 2


title: Placenta_T1_6_PAC035

type: genomic

city: Adelaide

first: Claire

last: Roberts

state: SA

address: AHMS building

department: Adelaide Medical School

country: Australia

institute: The University of Adelaide

description: Placenta sample from terminated pregnancy

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Using R version 3.5.3. Array probes targeting sex chromosomes, with evidence of cross-hybridization, rs probes, polymorphic probes, poor quality probes (detection p value >0.01 or <3 bead replicates in >5 % of samples) were eliminated.

label: Cy5 and Cy3

source_name: Placenta chorionic vill, first trimester, 6 weeks

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 10 placental tissue samples using a modified version of the TES protocol (10mM Tris(T), 2mM Na2EDTA(E), 10% SDS(S)).

value: Placenta

tag: fetal sex

value: Female

tag: gestational age

tag: outliers

value: Outlier

tag: sample id


title: GlcNAc-UA159-2

city: Gainesville

first: Lin

last: Zeng

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: Bacterial batch culture

growth_protocol: Bacterial strains UA159 and DL1 were first cultivated overnight, each with 3 individual cultures, on a TV medium supplemented with 20 mM of glucose, GlcN, or GlcNAc, then diluted at 1:20 ratio into a fresh TV medium containing the same carbohydrate. When the optical density (OD600) of an individual culture reached around 0.5, a portion of the culture was placed on ice temporarily before use. The rest of the culture was harvested by centrifugation, treated with the RNAprotect Bacteria Reagent (Qiagen, Germantown, MD) and stored at -80°C. Once all cultures were ready on ice, UA159 and DL1 grown on the same carbohydrates were mixed at 20:1 ratio based on their OD600, before diluted again at 1:50 ratio into the same medium. After the mixed-species co-culture reached OD600 ≈ 0.5, cells were harvested as before and stored at -80°C.

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-end short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: parental strain

value: Wild type

tag: media

value: TV-GlcNAc


title: AV_0 dpi Mouse 1

tag: cell type

value: uninfected, oral antibiotic-treated


title: AV_0 dpi Mouse 3


title: GlcNAc-UA159-1


title: KA_0 dpi Mouse 2

value: uninfected, vehicle-treated


title: AV_0 dpi Mouse 2


title: 2i_STAR_ATAC-seq_50


title: 2i_STAR_ATAC-seq_52


title: Placenta_T1_9_PAC008

source_name: Placenta chorionic vill, first trimester, 9 weeks

tag: tissue


title: GlcNAc-Co-3

organism:
Streptococcus gordonii
Streptococcus mutans

value: UA159 and DL1

tag: genotype


title: A549 TRIB3-shRNA cells-1

tag: cell line


title: Placenta_T1_7_PAC037

source_name: Placenta chorionic vill, first trimester, 7 weeks

value: Pure


title: GlcNAc-Co-2


title: Placenta_T1_6_PAC036


title: Placenta_T1_9_PAC038


title: A549 Control-shRNA cells-2

description: Gene expression data from A549 cells stably expressing Control-shRNA

source_name: A549 Control-shRNA cells

tag: genotype/variation

value: stably expressing Control-shRNA


title: Placenta_T1_6_PAC039


title: 2i_STAR_ATAC-seq_49

value: E14 Mouse ES Cells


title: GlcNAc-Co-1


title: KA_0 dpi Mouse 1


title: 2i_STAR_ATAC-seq_5


title: GlcNAc-UA159-3


title: GlcN-UA159-3

value: TV-GlcN


title: GlcN-UA159-1


title: GlcN-Co-2


title: GlcN-Co-1


title: Placenta_T1_9_PAC006


title: KA_0 dpi Mouse 3

value: sorted splenic pDCs


title: 2i_STAR_ATAC-seq_47


title: Placenta_T1_8_PAC042

source_name: Placenta chorionic vill, first trimester, 8 weeks

value: Male


title: Placenta_T1_9_PAC016


title: Placenta_T1_8_PAC010


title: Glc-Co-2

value: TV-glucose


title: 2i_STAR_ATAC-seq_46


title: Glc-UA159-3


title: Glc-UA159-2


title: Glc-UA159-1


title: 2i_STAR_ATAC-seq_45


title: 2i_STAR_ATAC-seq_44


title: ChIP-Seq_CtrA_NA1000∆divJ∆pleC∆cckN

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

data_processing:
Around 2 x 10^7 single-end sequence reads (1 x 50) were first mapped on the genome of C. crescentus NA1000 (NC_011916.1) and converted to SAM using BWA and SAM tools from the sourceforge server (https://sourceforge.net/)
MACS2 algorithm was used to model the length of DNA fragment as well as the shift size.
The number of reads overlapping each genomic position was computed using custom Python scripts and the previously modeled DNA fragment and shift sizes.
A peak was defined as the genomic region where each position has more reads than the 97th percentile. The candidate peaks were annotated using custom Python scripts.
In the purpose to compare strains, the total number of reads was normalized by the ratio of the number of reads between the two strains.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: The xls files report CtrA ChIP-Seq peaks in the WT and mutant strains of Caulobacter. The  different columns are organized as follows: column 1: Start_Coord (coordinates for the start of the peak); column 2: End_Coord (coordinates for the end of the peak); column 3: Summit (highest number of reads of peak); column 4:  Summit_Coord (coordinates for the highest number of reads of peak); column 5: Reads (number of reads in the peak); column 6: Reads Norm (number of reads / total number of alignedreads ); column 7: GeneUp (CCNA_number of gene upstream of the peak based on the summit); column 8: GeneUpName (name of gene upstream of the peak); column 9: GeneDown ( CCNA_number of gene downstream of the peak based on the summit); column 10: GeneDownName (name of gene downstream of the peak); column 11: OperonUp (Operon in which gene upstream of the peak belongs); column 12: OperonDowncolumn (Operon in which gene downstream of the peak belongs).

organism: Caulobacter vibrioides

growth_protocol: C. crescentus strains grown overnight at 30°C in complex media (PYE) to saturation before being diluted in fresh PYE media and grown at 30°C to mid-exponential phase (OD660~0.5-0.6).

extract_protocol:
Resuspended pellets were lysed with 2 µl of Ready-lyse lysozyme solution (Epicentre)  for 5 min at RT. Protease inhibitors (Roche) was added and incubated for 10 min. Then, 550 µl of ChIP buffer (1.1% triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, plus protease inhibitors) was added to the lysate and incubated at 37 °C for 10 min before sonication (2 x 8 bursts of 30 sec on ice using a Diagenode Bioruptor) to shear DNA fragments to a length of 300 to 500 bp. Lysate was cleared by centrifugation for 10 min at 12,500 rpm at 4 °C and protein content was evaluated by measuring OD280. Then, 7.5 mg of proteins were diluted in ChIP buffer supplemented with 0.01% SDS and precleared 1 h at 4 °C with 50 µl of protein A agarose beads (BioRad) and 100 µg BSA. Two µl of polyclonal anti-CtrA antibodies were added to the supernatant before overnight incubation at 4 °C under gentle agitation. Eighty µl of BSA pre-saturated protein A agarose beads were added to the solution for 2 h at 4 °C with rotation, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), once with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA) at 4 °C and a second wash with TE buffer at RT. The DNA-protein complexes were eluted twice in 250 µl freshly prepared elution buffer (0.1 M NaHCO3, 1% SDS). NaCl was added at a concentration of 300 mM to the combined eluates (500 µl) before overnight incubation at 65 °C to reverse the crosslink. The samples were treated with 20 µg of proteinase K in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5) for 2 h at 45 °C. DNA was extracted using Nucleospin PCR clean-up kit (Macherey-Nagel) and resuspended in 50 µl elution buffer (5 mM Tris-HCl pH 8.5). Sample libraries of immunoprecipitated chromatin and deep-sequencing were performed at the Genomicscore KULeuven (Belgium).
ChIP-Seq libraries were prepared at the Genomicscore KULeuven (Belgium) using the Illumina TruSeq DNA library  according to the manufacturer's instructions.

treatment_protocol: 80 ml of mid-log phase cells (OD660~ 0.5-0.6) were cross-linked in 1% formaldehyde and 10 mM sodium phosphate (pH 7.6) at room temperature for 10 min and 30 min on ice thereafter. Crosslinking was stopped by addition of 125 mM glycine and incubated for 5 min on ice. Cells were washed thrice in PBS resuspended in 450 µl in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl)

value: {delta}divJ{delta}pleC{delta}cckN


title: ChIP-Seq_CtrA_NA1000

value: WT


title: BC22 8

city: Shanghai

first: Peizhan

last: Chen

institute: Ruijin Hospital North

data_processing:
Cell Ranger
R preprocessing for doublets removal
mitochondrial genes proportion (≦ 10%) and the numer of detected genes (≧300 features)
Genome_build: GRCH38
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every single cell in the specific patients

source_name: Osteosarcoma patients

extract_protocol:
The tissue pieces were digested with 2 mL of GEXSCOPETM tissue dissociation solution (Singleron Bio Com, Nanjing, China) at 37 °C for 15 min with sustained agitation. After digestion, the samples were filtered through 40-µm sterile strainers and centrifuged at 1,000 rpm for 5 min. Then the supernatants were discarded, and the cell pellets were suspended in 1 mL phosphate-buffered saline (PBS; HyClone). To remove red blood cells, 2 mL of GEXSCOPETM red blood cell lysis buffer (Singleron) was added, and cells were incubated at 25 °C for 10 min. The solution was then centrifuged at 500 g for 5 min and resuspended in PBS.  Single cells were encapsulated into emulsion droplets using the Chromium Controller (10 x Genomics).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit (10x Genomics)

tag: tumor type

value: Chondroblastic


title: 2i_STAR_ATAC-seq_43

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for STAR Scripts run using C1 Fluidigm mRNA-seq chips (10-17um).
The open chromatin was transposed by Tn5 transposase. Cell specific barcode was integrated to tagmented DNA of each cell by PCR amplification with indexed primer. The amplified PCR produced was purified by Ampure XP beads and the purified ATACseq library was sent for sequencing.


title: BC22 7


title: Assay_NegativeControl

type: other

city: Houston

first: Sujith

middle: K

last: Joseph

state: Texas

address: 1102 Bates Avenue Suite 1770

department: Pediatrics Hematology-Oncology

institute: Baylor College of Medicine

description: Negative Control

hyb_protocol: Microarray slides were blocked in blocking buffer (50 mM HEPES, 200 mM NaCl, 0.01% Triton X-100, 25% glycerol, 20 mM reduced glutathione, 1.0 mM DTT, 1X Synthetic Block) at 4 °C for 1 hour. After blocking, arrays were rinsed once with freshly prepared PBST buffer (1X PBS, 0.1% Tween 20, and 1 X Synthetic Block). Arrays were then probed with a 1:500 dilution of each sample diluted in 5 mL of PBST buffer. Arrays were incubated for 90 minutes at 4°C in QuadriPERM 4-well trays (Greiner) with gentle agitation. After incubation, slides were washed five times (5 minutes per wash) in 5 ml PBST Buffer in 4-well trays.   An Alexa Fluor™647-conjugated goat anti-human IgG antibody diluted in 5 ml PBST buffer to a 1.0 ug/ml final concentration was added to each array and allowed to incubate with gentle shaking at 4°C for 90 minutes. After incubation, the secondary antibody was removed, and arrays were washed as described above. Arrays were briefly rinsed in water and then dried by spinning in a table top centrifuge equipped with a plate rotor at 200x gravity for 2 minutes. In the negative control assay, a ProtoArray™ Human Protein Microarray was treated in an identical manner to the experimental assays, except that it was incubated with buffer containing no serum prior to incubation with the Alexa Fluor™647-anti-human IgG detection reagent.

scan_protocol: Arrays were scanned using a GenePix 4000B fluorescent microarray scanner. GenePix 7 software was used to overlay the mapping of human proteins in the array list file to each array image with a fixed feature size of 130 μm (diameter). After aligning each of the 48 subarrays using spots from the AlexaFluor™-conjugated and antibodies printed in each subarray, the features were resized by the GenePix software to best fit the feature. Pixel intensities for each spot on the array were determined from the software and saved to a text file formatted for use in GenePix (.gpr file).

data_processing:
Thermo Fisher Scientific’s proprietary ProtoArray™ Prospector software was used to analyze data resulting from immune response profiling studies, with the goal of identifying proteins interacting with serum autoantibodies. For each protein on each array, a series of values are calculated including background subtracted signals, Z-Score, Z-Factor, CI-P value, and replicate spot coefficient of variation.
In conducting the analyses comparing selected individual serum samples, the data from one sample were filtered to remove proteins that were bound by the anti-human IgG detection reagent alone and compared in pairwise fashion to a second sample. Proteins were defined as eliciting increased signal from serum autoantibody binding if they met the following criteria:
• The Signal Used value, or background-subtracted signal, on the array probed with one sample under comparison was at least 5,000 RFU.
• The ratio of the Signal Used value on the array probed with one sample under comparison to the Signal Used value on the other array under comparison was greater than 2.
• The Z-Score, or normalized signal intensity, was less than 1.0 on the negative control array. The Z-Score indicates the number of standard deviations above or below the median signal value for all human protein features on the array.
• The Z-Factor, or signal-to-noise ratio, was greater than 0.5 on the corresponding array, indicating a signal greater than 2-fold above the noise.
• The coefficient of variation (CV) was less than 50% for the adjacent replicate spots on the corresponding array
Additional values calculated by the ProtoArray® Prospector software that were incorporated into the data analysis included the CI P-Value. The CI P-Value assigns a probability that an observed signal is derived from the distribution of signals arising from a set of defined negative controls. Typically, a CI P-Value <0.05 correlates with a visually confirmable signal on the array and was used.

label: Alexa Fluor 647

molecule: other

organism: other sequences

source_name: NegativeControl

extract_protocol: Serum was isolated from peripheral blood samples and stored in aliquots at -80 °C till use.

tag: disease state

value: NegativeControl

value: blank

tag: time point

value: Negative control


title: BC22 6


title: Serum_Recurrence_wk78fromstart

description:
HEROS UPN002F
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody

source_name: Serum peripheral blood

value: metastatic rhabdomyosarcoma

value: Serum peripheral blood


title: BC22 5


title: 2i_STAR_ATAC-seq_42


title: BC22 4


title: Glc-Co-3

value: Wild type


title: A549 Control-shRNA cells-3

value: lung cancer cell line


title: Serum_Remission_wk61fromstart

description:
HEROS UPN002E
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody


title: BC22 3


title: Glc-Co-1

value: UA159 and DL1


title: 2i_STAR_ATAC-seq_41


title: BC22 2


title: ChIP-Seq_CtrA_NA1000∆divJ∆pleC

value: {delta}divJ{delta}pleC


title: BC22 1


title: 2i_STAR_ATAC-seq_40

value: E14 Mouse ES Cells


title: Serum_6wkafterCAR-Tcells_Infusion#2

description:
HEROS UPN002C
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody


title: BC20 8


title: 2i_STAR_ATAC-seq_4


title: BC20 7


title: BC20 6


title: Serum_6wkafterCAR-Tcells_Infusion#1

description:
HEROS UPN002B
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody


title: BC20 5


title: Serum_PreCAR-Tcells

description:
HEROS UPN002A
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody

value: PreCAR-Tcells


title: BC20 4


title: 2i_STAR_ATAC-seq_39


title: 2i_STAR_ATAC-seq_38


title: BC20 3


title: BC20 2


title: CTCF

city: Durham

first: Bryan

middle: J

last: Venters

state: NC

address: 6 Davis Drive

institute: EpiCypher

description: CUT&RUN CTCF 500K Nuclei

data_processing:
Library strategy: CUT&RUN
Base-calling: illumina software
Adapter Trimming: TBD
Alignment: TBD
Filtering: TBD
Peak Calliing: TBD
Genome_build: hg19
Supplementary_files_format_and_content: PCRP_Metadata.xlsx: contains one excel sheet

source_name: K562 human immortalised myelogenous leukemia cell line

growth_protocol: K562 cells were maintained (1–10 × 10^5 cell/ml) in T25 flasks in IMDM + 10% FBS  +  1% Pen/Strep

extract_protocol:
Nuclei were extracted by incubating cells on ice for 10 min in Nuclei Extraction buffer (NE: 20 mM HEPES–KOH, pH 7.9; 10 mM KCl; 0.1% Triton X-100; 20% Glycerol; 0.5mM spermidine; 1x complete protease inhibitor [Roche # 11836170001]), collecting by centrifugation (600 g, 3 min, 4ºC), discarding the supernatant, and resuspending at [100 µl / 500K nuclei] sample in NE buffer. CUTANA protocol v1.5.1; optimized version of PMID: 29651053
NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7645S)
Cleavage under targets and Release using nuclease

treatment_protocol: Native cells used for Nuclei extraction

tag: antibody

value: anti-CTCF Millipore Cat # 07-729, lot 3205452


title: 2i_STAR_ATAC-seq_37

city: Singapore

first: Chadi

last: El Farran

institute: Institute of Molecular and Cell Biology


title: Rabbit IgG 2

description: CUT&RUN Rabbit IgG 500K Nuclei

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody EpiCypher 13-0042, lot 20036001-52


title: Serum_6wkafterCAR-Tcells_Infusion#3

description:
HEROS UPN002D
male, 7 yrs, metastatic rhabdomyosarcoma
serum antibody


title: BC21 7

value: Osteoblastic


title: 2i_STAR_ATAC-seq_36


title: BC21 5


title: 2i_STAR_ATAC-seq_35


title: BC20 1


title: Rabbit IgG 1

description: CUT&RUN Rabbit IgG 500K Nuclei


title: BC21 4


title: BC21 8


title: BC21 3


title: BC21 6


title: USF1

description: CUT&RUN USF1 500K Nuclei


title: BC21 2


title: 2i_STAR_ATAC-seq_34


title: BATF2

description: CUT&RUN BATF2 500K Nuclei


title: 2i_STAR_ATAC-seq_33


title: BC17 8


title: BC17 7


title: DCP2

description: CUT&RUN DCP2 500K Nuclei


title: 2i_STAR_ATAC-seq_32


title: BC17 6


title: DRAP1

description: CUT&RUN DRAP1 500K Nuclei


title: BC17 5


title: 2i_STAR_ATAC-seq_31


title: BC17 3


title: BC17 4


title: GlcN-Co-3

value: TV-GlcN


title: 2i_STAR_ATAC-seq_30


title: BC17 2


title: FEZF2

description: CUT&RUN FEZF2 500K Nuclei


title: FOS

description: CUT&RUN FOS 500K Nuclei


title: BC17 1


title: 2i_STAR_ATAC-seq_3


title: GABPA

description: CUT&RUN GABPA 500K Nuclei

value: PCRP-GABPA-2G3-s (anti-GABPA, lot #:11.22.2017)


title: BC16 8


title: 2i_STAR_ATAC-seq_29


title: BC16 7


title: BC21 1


title: Prostate

description: prostate-cell panel for submission-V1.xls

value: prostate tissue


title: 2i_STAR_ATAC-seq_28


title: PC3


title: MAFG

description: CUT&RUN MAFG 500K Nuclei

value: PCRP-MAFG-1H7-s  (anti-MAFG, lot #:8.13.2015)


title: BC16 5


title: 2i_STAR_ATAC-seq_27


title: Du145


title: BC16 4


title: MEF2D

description: CUT&RUN MEF2D 500K Nuclei

value: PCRP-MEF2D-3A4-s  (anti-MEF2D, lot #:9.7.2017)


title: BC16 3


title: MLLT3

description: CUT&RUN MLLT3 500K Nuclei


title: 22RV1


title: 2i_STAR_ATAC-seq_25


title: LNCaP

value: LNCaP


title: 2i_STAR_ATAC-seq_26


title: NAB2

description: CUT&RUN NAB2 500K Nuclei


title: BC16 2


title: 2i_STAR_ATAC-seq_23


title: BC16 1


title: BC16 6


title: PC4


title: BC11 4


title: NRF1

description: CUT&RUN NRF1 500K Nuclei


title: NFIA

description: CUT&RUN NFIA 500K Nuclei

value: PCRP-NFIA-1B8-s (anti-NFIA, lot #:9.1.2016)


title: 2i_STAR_ATAC-seq_22


title: MPC1 KO-8 15948X18

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description:
MPC1 KO-8
total RNA (post-rRNA subtraction)

data_processing:
CUTADAPT v 1.16: CUTADAPT -j $NCPU -O 6 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT  -o $OUT.1.fq -p $OUT.2.fq $OUT.clump1.fq.gz $OUT.clump2.fq.gz
FASTQ: $FASTQC -T $NCPU -f fastq $OUT.1.fq
: $FASTQC -T $NCPU -f fastq $OUT.2.fq
STAR: $STAR --genomeDir $INDEX --readFilesIn $OUT.1.fq $OUT.2.fq --runThreadN $NCPU --twopassMode Basic --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outWigType bedGraph --outWigStrand Unstranded
RSEM: $RSEM --paired-end -p $NCPU --alignments --strandedness reverse --no-bam-output Aligned.toTranscriptome.out.bam $RSEM_INDEX $OUT
featureCounts: $FEATCOUNT -T $NCPU -p -s 2 --largestOverlap -a $GTF -o $OUT.counts $OUT.bam
: $FEATCOUNT -T $NCPU -p -s 2 --largestOverlap -a $GTF -o $OUT.biotypes -g gene_biotype $OUT.bam
Samtools: $SAMTOOLS index $OUT.bam
: $SAMTOOLS idxstats $OUT.bam | sort -V > $OUT.idxstats
Genome_build: Ensembl Mus musculus Build GRCm38 version 96
Supplementary_files_format_and_content: tab-delimited file

source_name: Mouse heart tissue

extract_protocol:
RNA was isolated from ventricular tissue samples usingmiRNeasyMini Kit. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.
Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).  Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 51 cycle paired end sequence run was performed using a NovaSeq S1 reagent Kit (20027465).

value: MPC1 knockout

tag: timepoint

value: 8 weeks post-knockout


title: MPC1 KO-8 15948X20


title: STAT3

description: CUT&RUN STAT3 500K Nuclei


title: MEIS2

description: CUT&RUN MEIS2 500K Nuclei


title: 2i_STAR_ATAC-seq_21

data_processing:
Libraries were mapped to mm9 genome using STAR aligner. We allowed up to 2 mismatches and removed reads mapping to more than one region in the genome. The “–alignIntronMax” was set to 1 and the option “--  alignEndsType EndToEnd” was used.
Duplicates were removed using MarkDuplicates module of PICARD.
To determine the highly accessible regions, the de-duplicated mouse ATAC-Seq libraries were merged and peaks were called using MACS2. The following MACS2 options were used: -- nomodel -- nolambda -- keep-dup all – call-summits.
The de-duplicated single cell bam files were uploaded to chromVAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs which can be used for visualization in the UCSC genome browser.


title: BC11 3


title: MPC1 KO-8 15948X17


title: BC11 2


title: A549 Control-shRNA cells-1

value: lung cancer cell line

value: stably expressing Control-shRNA


title: 2i_STAR_ATAC-seq_20


title: 2i_STAR_ATAC-seq_24


title: MPC1 KO-8 15948X16


title: 2i_STAR_ATAC-seq_2


title: BC11 1


title: THAP4

description: CUT&RUN THAP4 500K Nuclei


title: BC10 4


title: WT-8 15948X15

description:
WT-8
total RNA (post-rRNA subtraction)

value: wild type


title: 2i_STAR_ATAC-seq_19

value: E14 Mouse ES Cells


title: THAP5

description: CUT&RUN THAP5 500K Nuclei


title: BC10 3


title: WT-8 15948X14

description:
WT-8
total RNA (post-rRNA subtraction)


title: 2i_STAR_ATAC-seq_18


title: BC10 2


title: GlcN-UA159-2

value: Wild type


title: 2i_STAR_ATAC-seq_17


title: WT-8 15948X13

description:
WT-8
total RNA (post-rRNA subtraction)


title: USF2

description: CUT&RUN USF2 500K Nuclei


title: THAP7

description: CUT&RUN THAP7 500K Nuclei

value: PCRP-THAP7-3H4-s (anti-THAP7, lot #:2.7.2019)


title: STAT5A

description: CUT&RUN STAT5A 500K Nuclei

value: PCRP-STAT5A-1A11-s (anti-STAT5A, lot #:2.9.2017)


title: BC10 1

value: Osteoblastic


title: 2i_STAR_ATAC-seq_16


title: WT-8 15948X12

description:
WT-8
total RNA (post-rRNA subtraction)


title: WT-8 15948X11

description:
WT-8
total RNA (post-rRNA subtraction)


title: YY2

description: CUT&RUN YY2 500K Nuclei


title: YY1

description: CUT&RUN YY1 500K Nuclei


title: BC6 4


title: 2i_STAR_ATAC-seq_15


title: BC6 3


title: 2i_STAR_ATAC-seq_14


title: BC6 2


title: ZNF143

description: CUT&RUN ZNF143 500K Nuclei


title: MPC1 KO-16 15948X9

description:
MPC1 KO-16
total RNA (post-rRNA subtraction)

value: 16 weeks post-knockout


title: 2i_STAR_ATAC-seq_13


title: MPC1 KO-16 15948X8


title: BC6 1


title: ZNF354B

description: CUT&RUN ZNF354B 500K Nuclei


title: 2i_STAR_ATAC-seq_12


title: MPC1 KO-16 15948X7


title: KLF1

description: CUT&RUN KLF1 500K Nuclei


title: 2i_STAR_ATAC-seq_11


title: BC5 3


title: MPC1 KO-16 15948X6


title: KLF14

description: CUT&RUN KLF14 500K Nuclei


title: 2i_STAR_ATAC-seq_10


title: KLF16

description: CUT&RUN KLF16 500K Nuclei


title: WT-16 15948X5

description:
WT-16
total RNA (post-rRNA subtraction)


title: 2i_STAR_ATAC-seq_1


title: 2i_STAR_ATAC-seq_48


title: BC5 2


title: MPC1 KO-16 15948X10


title: KLF7

description: CUT&RUN KLF7 500K Nuclei


title: WT-16 15948X4

description:
WT-16
total RNA (post-rRNA subtraction)


title: ZFAT

description: CUT&RUN ZFAT 500K Nuclei

value: PCRP-ZFAT-2D2-s  (anti-ZFAT, lot #:12.27.2018)


title: BC5 1


title: WT-16 15948X3

description:
WT-16
total RNA (post-rRNA subtraction)


title: BCL11A

description: CUT&RUN BCL11A 500K Nuclei


title: WT-16 15948X2

description:
WT-16
total RNA (post-rRNA subtraction)


title: BC3 8


title: BC3 7


title: BC5 4


title: FOXM1

description: CUT&RUN FOXM1 500K Nuclei

value: PCRP-FOXM1-1H4-s (anti-FOXM1, lot #:6.8.2017)


title: BC3 6


title: FOXO3

description: CUT&RUN FOXO3 500K Nuclei

value: PCRP-FOXO3-1G5-s (anti-FOXO3, lot #:6.8.2017)


title: FOXP3

description: CUT&RUN FOXP3 500K Nuclei


title: HOXB2

description: CUT&RUN HOXB2 500K Nuclei


title: BC3 3