title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978710110317428272788150


title: WTCHG_388581_253273

status: Public on Aug 01 2020

type: SRA

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

country: United Kingdom

institute: Newcastle University

library_source: transcriptomic

data_processing:
Trimmed with Trimmomatic v 0.36
Aligned reads with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 60bp were dropped
Counts were obtained with HTSEQ v 0.6.1
Further processing was performed in R 3.3.3. The cells were filtered based on precentage of ERCC counts (<30%), mitochondrial percentage (<25%), total features (>2500), total counts (>50000)
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files with HTSEQ counts
Supplementary_files_format_and_content: BM_CD34_flow_channel_values.csv: Channel values produced when sorting the individual cells for scRNA-Seq.

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: primary cells

extract_protocol: Smart-seq2 and Nextera XT

value: CMP 33-

tag: passed cell qc

value: YES


title: WTCHG_388581_253274


title: WTCHG_388581_253276

value: NO


title: WTCHG_388581_254208

value: HSC/MPP CD90-


title: WTCHG_388581_253207

value: HSC/MPP CD90+


title: WTCHG_388581_253206


title: WTCHG_388581_253205


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-IBDu subject-104 biological rep-25

type: RNA

city: Indianapolis

first: Boyd

last: Steere

state: IN

address: Lilly Corporate Center

department: Immunology

country: USA

institute: Lilly

description:
subject-ID_104
@52084400978709110317428272788086

hyb_protocol: 5 μg of biotin-labeled cDNA per HTA2 platform standard procedure

scan_protocol: Scanning performed with Affymetrix GeneChip station under default settings followed by CEL file derivation from Affymetrix GeneChip Command Console (AGCC)

data_processing:
Background correction and quantile normalization of the gene expression data obtained from the Affymetrix Human Transcriptome Array 2.0 (HTA2) platform were performed by the RMA method while controlling for batch.  Summarization was performed with RLM.  Annotations were defined by the Affymetrix NetAffx(TM) NA35 release, which is based on the GRCh37 human reference genome. Differential expression at the gene-level was performed using the empirical Bayes method implemented in LIMMA{Ritchie:ef}controlling for donor in the model.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label: biotin

label_protocol: Minimum RNA input was 100ng with a concentration range of 10 ng/μl to 50 ng ng/μl.  Label molecule was biotin.  Amplification performed using standard protocol from Affymetrix WT Express Kit.

growth_protocol: Whole blood was collected into EDTA-containing tubes. PBMC were purified using Ficoll-Paque density gradient purification. The absolute number of cells was determined using a haemocytometer (Marienfeld).

extract_protocol: Total RNA was extracted from cultured cells, using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA yield was determined by quantifying the samples on an Agilent Bioanalyzer.  Only samples with a 28S/18S ratio of 0.8 to 3.0 and a RIN Score of >= 6.0 passed QC metrics and were accepted for analysis.

treatment_protocol: For stimulation assays, 0.5×10^6 to 1×10^6 PBMC were cultured in 200 μl medium in duplicates in round bottom 96-well plates and exposed to ultrapure 200 ng/ml LPS (Enzo Life Sciences; Cat.# ALX-581-008), 200 ng/ml L18MDP (Invivogen) 10 μg/ml anti-IL-10R (Biolegend; clone: 3F9), and/or anti-CD3/anti-CD28 beads (Invitrogen) for 16 hours in complete RPMI with L-glutamine (Sigma) supplemented with 10 % human serum (Sigma; Cat.# H4522), non-essential amino acids (Gibco); 1 mM Sodium-Pyruvate (Gibco) and 100 U/ml penicillin and 10 μg/ml streptomycin (Sigma).

tag: stimulation

tag: diagnosis

value: IBDu

tag: Sex

value: M

tag: batch

tag: tissue

value: peripheral PBMC


title: WTCHG_388581_253204


title: WTCHG_388581_253203


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-UC subject-429 biological rep-30

description:
subject-ID_429
@52084400978708110317428272788048

value: UC


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1838 biological rep-23

description:
subject-ID_1838
@52084400978710110317428272788154

value: CD


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1600 biological rep-22

description:
subject-ID_1600
@52084400978327102417428100272907

value: F


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400980522112917428617726940


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1045 biological rep-19

description:
subject-ID_1045
@52084400978329102417428100273031


title: WTCHG_388581_253202


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1180 biological rep-20

description:
subject-ID_1180
@52084400978711110317428272788246


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978328102417428100272943


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1018 biological rep-18

description:
subject-ID_1018
@52084400978709110317428272788106


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-891 biological rep-17

description:
subject-ID_891
@52084400978711110317428272788241


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978329102417428100273023

value: Other


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-843 biological rep-16

description:
subject-ID_843
@52084400978328102417428100272944


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1253 biological rep-21

description:
subject-ID_1253
@52084400978710110317428272788187


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-792 biological rep-15

description:
subject-ID_792
@52084400980523112917428617727042


title: WTCHG_388581_253208


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-701 biological rep-14

description:
subject-ID_701
@52084400980525112917428617727143


title: WTCHG_388581_253201


title: WTCHG_388581_252280


title: WTCHG_388581_252279


title: WTCHG_388581_252278


title: WTCHG_388581_252277


title: WTCHG_388581_252275


title: WTCHG_388581_252274


title: WTCHG_388581_252273


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-558 biological rep-10

description:
subject-ID_558
@52084400980524112917428617727088


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-643 biological rep-11

description:
subject-ID_643
@52084400978709110317428272788109


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-670 biological rep-13

description:
subject-ID_670
@52084400978708110317428272788035


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-528 biological rep-9

description:
subject-ID_528
@52084400978710110317428272788176


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-649 biological rep-12

description:
subject-ID_649
@52084400978327102417428100272920


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
@52084400978710110317428272788162


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400978328102417428100272951


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-508 biological rep-8

description:
subject-ID_508
@52084400980522112917428617726964


title: WTCHG_388581_252206


title: WTCHG_388581_252207


title: WTCHG_388581_252208


title: WTCHG_388581_252205


title: WTCHG_388581_252204


title: WTCHG_388581_252276


title: WTCHG_388581_252203


title: WTCHG_388581_252201


title: WTCHG_388581_252202


title: WTCHG_388581_251280


title: WTCHG_388581_251279


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
@52084400978330102417428100373071


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978709110317428272788083


title: WTCHG_388581_251277


title: WTCHG_388581_251275


title: WTCHG_388581_251278


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-2001 biological rep-36

description:
subject-ID_2001
@52084400978711110317428272788224


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978327102417428100272905


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-1014 biological rep-33

description:
subject-ID_1014
@52084400980524112917428617727092


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400975431121817428781459681


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-1338 biological rep-34

description:
subject-ID_1338
@52084400978328102417428100272956


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-1628 biological rep-35

description:
subject-ID_1628
@52084400978711110317428272788253


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-531 biological rep-31

description:
subject-ID_531
@52084400978329102417428100273021


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-2031 biological rep-37

description:
subject-ID_2031
@52084400980525112917428617727170


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-447 biological rep-30

description:
subject-ID_447
@52084400978326102417428100272851


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-554 biological rep-32

description:
subject-ID_554
@52084400980523112917428617727016


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978710110317428272788171


title: WTCHG_388581_251273


title: WTCHG_388581_251208


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-429 biological rep-29

description:
subject-ID_429
@52084400980524112917428617727091


title: [gene] LPS aCD3-aCD28 diagnosis-Other subject-464 biological rep-26

description:
subject-ID_464
@52084400978328102417428100272976


title: WTCHG_388581_251276


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-369 biological rep-28

description:
subject-ID_369
@52084400978328102417428100272959


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978327102417428100272915


title: [gene] LPS aCD3-aCD28 diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400980522112917428617726968


title: WTCHG_388581_251207


title: WTCHG_388581_251274


title: WTCHG_388581_251206


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1838 biological rep-23

description:
subject-ID_1838
@52084400978711110317428272788235


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1600 biological rep-22

description:
subject-ID_1600
@52084400978327102417428100272880


title: WTCHG_388581_251205


title: [gene] LPS aCD3-aCD28 diagnosis-UC subject-113 biological rep-27

description:
subject-ID_113
@52084400978326102417428100272853


title: WTCHG_388581_251204


title: WTCHG_388581_251203


title: WTCHG_388581_251202


title: WTCHG_388581_250279


title: WTCHG_388581_251201


title: WTCHG_388581_250280


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1253 biological rep-21

description:
subject-ID_1253
@52084400980525112917428617727128


title: WTCHG_388581_250277


title: WTCHG_388581_250278


title: WTCHG_388581_250276


title: WTCHG_388581_250275


title: WTCHG_388581_250274


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1016 biological rep-17

description:
subject-ID_1016
@52084400978711110317428272788242


title: retina_Atoh7 siRNA_rep4

city: Geneva

first: Tania

last: Rodrigues

state: Geneva

address: 30 quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

description: Gene expression data from HH24 chicken retina 16 hours after electroporation with Atoh7 siRNA and a Hes5.3-RFP reporter plasmid

hyb_protocol: 5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Chicken Gene 1.0 ST Array. GeneChips were washed and stained in the Fluidics Stations 450 using the FS450-0002 protocol.

scan_protocol: GeneChips were scanned on the GS300 Affymetrix scanner.

data_processing: The data were analyzed with Affymetrix Expression Console v1.4.1.46 using Affymetrix default analysis settings and RMA as normalization method. The differential expression analysis was done with a one-way unpaired Anova with the Affymetrix transcriptome Analysis Console v3.1.0.5.

organism: Gallus gallus

source_name: HH24 chicken retina, with Atoh7 siRNA

label_protocol: 150 ng of total RNA were used as input for cRNA preparation using the Ambion WT Expression kit from Ambion (Thermofisher Scientific). After cRNA reverse transcription, 5.5 ug single-strand cDNA were fragmented and labelled with the Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: Electroporated retinas were cultured in DMEM (ThermoFisher) supplemented with 10% Fetal Bovine Serum (ThermoFisher) and 1% Penicillin-Streptomycin (ThermoFisher) for 16 hours at 37°C in an incubator with 5% CO2.

extract_protocol: Retina fragments encompassing the peripheral fluorescent domain were micro-dissected under a stereoscopic microscope 16 hours after electroporation. For each biological replicate, RNA was isolated from fragments dissected from four retinas. Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: We designed the Atoh7 and Hes5.3 siRNAs (Chiodini et al., 2013). siRNA synthesis was performed under contract with Thermo Scientific Dharmacon. siSTABLE nontargeting siRNAs are from Thermo Scientific Dharmacon. Chick embryos from a White Leghorn strain were staged according to Hamburger and Hamilton (1951). Embryonic eyes were positioned in an electroporation chamber (BT 640, BTX, Genetronics) filled with 0.1 ml PBS (pH 7.4) containing the reporter plasmid (0.5 μg/μl) and siRNAs (0.1 μg/μl each). Electroporation consisted in five 12.5 V/cm pulses of 50 ms duration spaced 1 second apart.

tag: developmental stage

value: Hamburger and Hamilton (HH) Stage 24

value: retina

tag: rna interference

value: Atoh7 siRNA


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-792 biological rep-15

description:
subject-ID_792
@52084400980525112917428617727150


title: WTCHG_388581_250273


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1018 biological rep-18

description:
subject-ID_1018
@52084400980522112917428617726965


title: retina_Atoh7 siRNA_rep3


title: retina_Hes5.3 siRNA_rep4

description: Gene expression data from HH24 chicken retina 16 hours after electroporation with Hes5.3 siRNA and a Hes5.3-RFP reporter plasmid

source_name: HH24 chicken retina, with Hes5.3 siRNA

value: Hes5.3 siRNA


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-643 biological rep-11

description:
subject-ID_643
@52084400978708110317428272788061


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1045 biological rep-19

description:
subject-ID_1045
@52084400978709110317428272788089


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-701 biological rep-14

description:
subject-ID_701
@52084400978326102417428100272859


title: retina_Atoh7 siRNA_rep2


title: retina_Hes5.3 siRNA_rep3


title: retina_Atoh7 siRNA_rep1


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-649 biological rep-12

description:
subject-ID_649
@52084400978709110317428272788076


title: retina_Hes5.3 siRNA_rep2


title: retina_nt siRNA_rep1

description: Gene expression data from HH24 chicken retina 16 hours after electroporation with non-targeting siRNA and a Hes5.3-RFP reporter plasmid

source_name: HH24 chicken retina, non-targeting siRNA

value: non-targeting siRNA


title: WTCHG_388581_250208


title: retina_nt siRNA_rep3


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-670 biological rep-13

description:
subject-ID_670
@52084400978327102417428100272894


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-843 biological rep-16

description:
subject-ID_843
@52084400978329102417428100272998


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-423 biological rep-7

description:
subject-ID_423
@52084400978329102417428100273001


title: retina_Hes5.3 siRNA_rep1


title: WTCHG_388581_250207


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-558 biological rep-10

description:
subject-ID_558
@52084400980525112917428617727153


title: WTCHG_388581_250206


title: retina_nt siRNA_rep2


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-508 biological rep-8

description:
subject-ID_508
@52084400980525112917428617727168


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-528 biological rep-9

description:
subject-ID_528
@52084400978708110317428272788054


title: retina_nt siRNA_rep4


title: WTCHG_388581_250204


title: WTCHG_388581_250205


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-372 biological rep-6

description:
subject-ID_372
@52084400978326102417428100272832


title: 6 hr 50 mg/kg CYC065 treatment-tumors from the Th-MYCN GEMM (T17)

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

institute: Institute of Cancer Research

hyb_protocol: Following fragmentation, 5.5 ug of ss c-DNA were hybridized for 16 hr at 45C on Gene Chip® human or mouse transcriptome expression array. GeneChips were washed and stained in the Gene Chip®  Fluidics station 450

scan_protocol: GeneChips were scanned using the Gene Chip® Scanner

data_processing: Samples were RMA normalized using the “limma” package from R and differentially expressed genes were called using a linear model and empirical Bayes statistics from the “affy” package

organism: Mus musculus

source_name: 6 hr CYC065 50 mg/kg treatment-tumors from the Th-MYCN GEMM

label_protocol: cRNA were prepared according to the standard Affymetrix GeneChip® WT PLUS Reagent Kit protocol from 100 ng total RNA and labeled (Gene Chip® human or mouse transcriptome expression array)

growth_protocol: Kelly, SKNAS, BE(2)C AND SH-SY-5Y cell lines were maintained in DMEM as recommended by the suppliers, supplemented with 10% fetal calf serum (FCS) (Gibco), and were maintained at 37°C under 5% CO2 in air.

extract_protocol: Cells or tissue were harvested using Qiagen mRNeasy Plus Kit

treatment_protocol: Kelly, BE(2)C AND SH-SY-5Y were treated with 1 µM CYC065 for 1 hour and SKNAS was treated with 5 µM CYC065 for 1 hour.  Mice were treated with CYC065 50 mg/kg or vehicle for 6 hours.

value: NB tumors

tag: treatment

value: 6 hr CYC065 50 mg/kg


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-280 biological rep-5

description:
subject-ID_280
@52084400980522112917428617726979


title: 6 hr 50 mg/kg CYC065 treatment-tumors from the Th-MYCN GEMM (T15)


title: WTCHG_388581_250203

value: NO


title: 6 hr 50 mg/kg CYC065 treatment-tumors from the Th-MYCN GEMM (T14)


title: 6 hr 50 mg/kg CYC065 treatment-tumors from the Th-MYCN GEMM (T18)


title: untreated-tumors from the Th-MYCN GEMM (V6)

source_name: untreated-tumors from the Th-MYCN GEMM

value: Untreated


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-243 biological rep-4

description:
subject-ID_243
@52084400978708110317428272788056


title: WTCHG_388581_250202

value: HSC/MPP CD90+

value: YES


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-232 biological rep-3

description:
subject-ID_232
@52084400978711110317428272788207


title: WTCHG_388581_250201


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-138 biological rep-1

description:
subject-ID_138
@52084400978708110317428272788027

value: M


title: untreated-tumors from the Th-MYCN GEMM (V5)


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-186 biological rep-2

description:
subject-ID_186
@52084400973515011718428996209132

value: peripheral PBMC


title: WTCHG_388581_249280

value: CMP 33-


title: untreated-tumors from the Th-MYCN GEMM (V3)


title: untreated-tumors from the Th-MYCN GEMM (V4)


title: untreated-tumors from the Th-MYCN GEMM (V2)


title: WTCHG_388581_249279


title: WTCHG_388581_249278


title: [gene] LPS diagnosis-UC subject-2031 biological rep-37

description:
subject-ID_2031
@52084400980525112917428617727156

source_name: LPS

value: LPS

value: UC


title: [gene] LPS diagnosis-UC subject-2001 biological rep-36

description:
subject-ID_2001
@52084400980525112917428617727169

value: F


title: untreated-tumors from the Th-MYCN GEMM (V1)


title: WTCHG_388581_249277


title: WTCHG_388581_249275


title: [gene] LPS diagnosis-UC subject-1338 biological rep-34

description:
subject-ID_1338
@52084400980524112917428617727067


title: [gene] LPS diagnosis-UC subject-1628 biological rep-35

description:
subject-ID_1628
@52084400973514011718428996209093


title: WTCHG_388581_249276


title: [gene] LPS diagnosis-UC subject-447 biological rep-31

description:
subject-ID_447
@52084400973515011718428996209134


title: [gene] LPS diagnosis-UC subject-1014 biological rep-33

description:
subject-ID_1014
@52084400978708110317428272788050


title: WTCHG_388581_249274


title: WTCHG_388581_249273


title: [gene] LPS diagnosis-UC subject-531 biological rep-32

description:
subject-ID_531
@52084400978710110317428272788160


title: [gene] LPS diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978327102417428100272922


title: [gene] LPS diagnosis-UC subject-429 biological rep-30

description:
subject-ID_429
@52084400980523112917428617727048


title: [gene] LPS diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978708110317428272788032


title: WTCHG_388581_249208


title: [gene] LPS diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978327102417428100272876

value: Other


title: [gene] LPS diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400980522112917428617726975

value: IBDu


title: [gene] LPS aCD3-aCD28 diagnosis-CD subject-1180 biological rep-20

description:
subject-ID_1180
@52084400978711110317428272788214

value: CD


title: WTCHG_388581_249207

value: HSC/MPP CD90-


title: [gene] LPS diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400980525112917428617727166


title: WTCHG_388581_249206


title: [exon] PBMC-control diagnosis-UC subject-2031 biological rep-34

description:
subject-ID_2031
@52084400980524112917428617727087

source_name: PBMC-control

value: PBMC-control


title: [exon] PBMC-control diagnosis-UC subject-2001 biological rep-33

description:
subject-ID_2001
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title: [exon] PBMC-control diagnosis-IBDu subject-104 biological rep-23

description:
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title: [exon] PBMC-control diagnosis-CD subject-1018 biological rep-18

description:
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title: [exon] PBMC-control diagnosis-UC subject-369 biological rep-27

description:
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description:
subject-ID_429
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title: [exon] PBMC-control diagnosis-UC subject-1628 biological rep-32

description:
subject-ID_1628
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title: [exon] PBMC-control diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
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title: [exon] PBMC-control diagnosis-UC subject-113 biological rep-26

description:
subject-ID_113
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title: WTCHG_388581_249204


title: [exon] PBMC-control diagnosis-Other subject-464 biological rep-25

description:
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title: WTCHG_388581_249203


title: [exon] PBMC-control diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
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title: [gene] LPS diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
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title: [exon] PBMC-control diagnosis-CD subject-1253 biological rep-20

description:
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title: WTCHG_388581_249201


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description:
subject-ID_643
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description:
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description:
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description:
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description:
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description:
subject-ID_649
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description:
subject-ID_1253
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subject-ID_129
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description:
subject-ID_508
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subject-ID_423
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title: GeCKO-B_Olaparib-2, Day 14

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
B3
processed data file: my_counts_anno_merged.txt

library_source: genomic

data_processing:
Library strategy: CRISPR Screen
50 bp single reads were trimmed using cutadapt (version 1.16) by removing the adapter sequence (-g GGACGAAACACCG) and setting the read length to 20 bp (-l 20).
Trimmed reads were separately aligned to Human GeCKOv2 Library A or B using bowtie2 (version 2.3.4.1) with parameter --norc.
Aligned reads were filtered by samtools (version 1.7) using the parameter -q 2.
Reads were subsampled to 5 million reads with replacement and counted for each sgRNA, annotated with gene information and library A and B from the same sample were merged into a table.
Genome_build: Human_GeCKOv2
Supplementary_files_format_and_content: my_counts_anno_merged.txt: Tab-delimited text file with annotated read counts subsampled to 5 million reads.

molecule: genomic DNA

source_name: Hela cells

extract_protocol:
HeLa cells were collected and gDNA was extracted from samples using NucleoSpin® Blood XL from MACHEREY-NAGEL GmbH & Co. according to the manufacturer's instructions. The sgRNA cassette was initially amplified according to Shalem et al. 2014 (doi:10.1126/science.1247005). Illumina primers were added through a second PCR as described. The amplicon was purified using AMPure XP beads and DNA was quantified using a Qubit dsDNA HS Assay Kit.
The library was constructed as in Sanjana et al. 2014 (doi:10.1038/nmeth.3047).

treatment_protocol: Knockout populations were treated with 3 μM olaparib or DMSO for 14 days.

tag: cell line

value: Hela

value: Olaparib

tag: library

value: B


title: GeCKO-B_DMSO-1, Day 14

description:
B4
processed data file: my_counts_anno_merged.txt

value: DMSO


title: GeCKO-B_DMSO-2, Day 14

description:
B5
processed data file: my_counts_anno_merged.txt


title: WTCHG_388581_230276

value: NO


title: WTCHG_388581_230275

value: YES


title: GeCKO-B_Olaparib-1, Day 14

description:
B2
processed data file: my_counts_anno_merged.txt


title: WTCHG_388581_230274


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
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value: M


title: GeCKO-B input control, Day 0

description:
B1
processed data file: my_counts_anno_merged.txt

value: Input


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-792 biological rep-15

description:
subject-ID_792
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value: peripheral PBMC


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1045 biological rep-19

description:
subject-ID_1045
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title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
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title: GeCKO-A_DMSO-1, Day 14

description:
A5
processed data file: my_counts_anno_merged.txt

value: A


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-670 biological rep-13

description:
subject-ID_670
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title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-843 biological rep-16

description:
subject-ID_843
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title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-643 biological rep-11

description:
subject-ID_643
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title: GeCKO-A_Olaparib-1, Day 14

description:
A3
processed data file: my_counts_anno_merged.txt


title: GeCKO-A_Olaparib-2, Day 14

description:
A4
processed data file: my_counts_anno_merged.txt


title: WTCHG_388581_230273


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-701 biological rep-14

description:
subject-ID_701
@52084400980525112917428617727143


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-558 biological rep-10

description:
subject-ID_558
@52084400980524112917428617727088


title: [gene] L18MDP aIL10R diagnosis-CD subject-701 biological rep-16

description:
subject-ID_701
@52084400980525112917428617727154


title: [gene] L18MDP aIL10R diagnosis-CD subject-792 biological rep-17

description:
subject-ID_792
@52084400980524112917428617727085


title: WTCHG_388581_230208

value: HSC/MPP CD90+


title: GeCKO-A input control, Day 0

description:
A1
processed data file: my_counts_anno_merged.txt


title: GeCKO-A_DMSO-2, Day 14

description:
A2
processed data file: my_counts_anno_merged.txt


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1018 biological rep-18

description:
subject-ID_1018
@52084400978709110317428272788106


title: WTCHG_388581_230207


title: [gene] L18MDP aIL10R diagnosis-CD subject-670 biological rep-15

description:
subject-ID_670
@52084400978328102417428100272977

value: F


title: MCF7_gc10bza_R7

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
MCF7_gc10_merged_norm_pos.bw
MCF7_gc10_merged_norm_neg.bw

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim 10bp from 5'end. (FASTQ Trimmer 1.0.0)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v21). Genes with very low expression (< 10 counts) were removed from the analysis.
Strand specific read depth normalized bigwigs created by UCSC's genomeCoverageBed (specifying scale 10^6/readcount and strand) and bedGraphToBigWig
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the normalized counts from the HTSeq-count quantification.  Bigwig tracks, strand specific and normalized for read depth (UCSC's genomeCoverageBed -bg -split -scale 10^6/$read_count -strand + or -).

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10A cells were grown in DMEM: F12 (Hyclone-SH30272 without phenol red), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies).  MCF7 were grown in DMEM: F12 (Hyclone-SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals).  )  Prior to treatment cells were plated in serum containing media for 24hrs to establish a monolayer.  Media was removed and replaced with 2% charcoal-stripped serum for 48hrs prior to 24hr treatment with each pharmaceutical agent.  Cells were  harvested for ChIP-seq analysis 24 hrs post-treatment as previously described (Messier, et al.  Oncotarget  2016).

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit (Qiagen #74134).  RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina #RS-122-2301). Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.
RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina #RS-122-2301). Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

tag: cell type

value: mammary gland/breast epithelial cell

tag: neoplasia type

value: metastatic site derived

tag: atcc id

value: adenocarcinoma; ATCC HTB-22


title: MCF7_gc10_R3

description:
MCF_gc10bza_merged_norm_pos.bw
MCF_gc10bza_merged_norm_neg.bw

treatment_protocol: Prior to treatment cells were plated in serum containing media for 24hrs to establish a monolayer.  Media was removed and replaced with 2% charcoal-stripped serum for 48hrs prior to 24hr treatment with each pharmaceutical agent.  Cells were  harvested for ChIP-seq analysis 24 hrs post-treatment as previously described (Messier, et al.  Oncotarget  2016).


title: [gene] L18MDP aIL10R diagnosis-CD subject-649 biological rep-14

description:
subject-ID_649
@52084400978710110317428272788188

value: CD


title: WTCHG_388581_230206


title: MCF7_gc10bza_R6


title: WTCHG_388581_230205

value: HSC/MPP CD90-


title: MCF7_gc10bza_R5


title: MCF7_e2_R3

description:
MCF7_e2_merged_norm_pos.bw
MCF7_e2_merged_norm_neg.bw


title: [gene] L18MDP aIL10R diagnosis-CD subject-558 biological rep-12

description:
subject-ID_558
@52084400980523112917428617727038


title: [gene] L18MDP aIL10R diagnosis-CD subject-843 biological rep-18

description:
subject-ID_843
@52084400978708110317428272788025


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1180 biological rep-20

description:
subject-ID_1180
@52084400978711110317428272788246


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-649 biological rep-12

description:
subject-ID_649
@52084400978327102417428100272920


title: MCF7_gc10_R1


title: MCF7_e2_R2


title: [gene] L18MDP aIL10R diagnosis-CD subject-643 biological rep-13

description:
subject-ID_643
@52084400978709110317428272788101


title: MCF7_e2_R1


title: WTCHG_388581_230203


title: [gene] L18MDP aIL10R diagnosis-CD subject-528 biological rep-11

description:
subject-ID_528
@52084400980524112917428617727106


title: MCF7_e2bza_R6

description:
MCF7_e2bza_merged_norm_pos.bw
MCF7_e2bza_merged_norm_neg.bw


title: MCF7_e2bza_R5


title: WTCHG_388581_230202


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400978328102417428100272951


title: MCF7_e2bza_R4


title: MCF7_ctrl_R6

description:
MCF7_ctrl_merged_norm_pos.bw
MCF7_ctrl_merged_norm_neg.bw

value: control


title: [gene] L18MDP aIL10R diagnosis-CD subject-508 biological rep-10

description:
subject-ID_508
@52084400978709110317428272788090


title: WTCHG_388581_230201


title: [gene] L18MDP aIL10R diagnosis-CD subject-423 biological rep-9

description:
subject-ID_423
@52084400978329102417428100273034


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-528 biological rep-9

description:
subject-ID_528
@52084400978710110317428272788176


title: [gene] L18MDP aIL10R diagnosis-CD subject-372 biological rep-8

description:
subject-ID_372
@52084400980524112917428617727076


title: MCF7_ctrl_R2


title: [gene] L18MDP aIL10R diagnosis-CD subject-1016 biological rep-19

description:
subject-ID_1016
@52084400978326102417428100272854


title: MCF7_gc10_R2

description:
MCF_gc10bza_merged_norm_pos.bw
MCF_gc10bza_merged_norm_neg.bw


title: WTCHG_388581_229280


title: MCF7_bza_R6

description:
MCF7_bza_merged_norm_pos.bw
MCF7_bza_merged_norm_neg.bw

value: bza


title: MCF7_bza_R5


title: MCF7_ctrl_R5


title: WTCHG_388581_229279


title: MCF7_bza_R2


title: MCF10A_gc10_R2

description:
MCF10A_gc10_merged_norm_pos.bw
MCF10A_gc10_merged_norm_neg.bw

value: luminal ductal cells

value: fibrocystic disease;ATCC CRL-10317


title: WTCHG_388581_229278

value: NO


title: MCF10A_gc10_R1


title: WTCHG_388581_229277

value: YES


title: [gene] L18MDP aIL10R diagnosis-CD subject-280 biological rep-7

description:
subject-ID_280
@52084400978711110317428272788248

value: M


title: WTCHG_388581_230204


title: MCF10A_gc10_R5


title: MCF10A_gc10bza_R6

description:
MCF10A_gc10bza_merged_norm_pos.bw
MCF10A_gc10bza_merged_norm_neg.bw


title: [gene] L18MDP aIL10R diagnosis-CD subject-232 biological rep-5

description:
subject-ID_232
@52084400978709110317428272788103


title: [gene] L18MDP aIL10R diagnosis-CD subject-243 biological rep-6

description:
subject-ID_243
@52084400980524112917428617727070


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
@52084400978710110317428272788162


title: MCF10A_gc10bza_R1


title: WTCHG_388581_229276

value: CMP 33-


title: MCF10A_gc10bza_R4


title: MCF10A_e2_R8

description:
MCF10A_e2_merged_norm_pos.bw
MCF10A_e2_merged_norm_neg.bw


title: MCF10A_e2_R7


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-508 biological rep-8

description:
subject-ID_508
@52084400980522112917428617726964

value: peripheral PBMC


title: [gene] L18MDP aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978709110317428272788117


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978327102417428100272916

value: UC


title: MCF10A_e2_R6


title: [gene] L18MDP aIL10R diagnosis-CD subject-225 biological rep-4

description:
subject-ID_225
@52084400978710110317428272788170


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
@52084400978330102417428100373071


title: MCF10A_e2bza_R6

description:
MCF10A_e2bza_merged_norm_pos.bw
MCF10A_e2bza_merged_norm_neg.bw


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978327102417428100272905


title: MCF10A_e2bza_R5


title: WTCHG_388581_229274


title: [gene] L18MDP aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978326102417428100272855


title: MCF10A_e2bza_R2


title: MCF10A_ctrl_R6

description:
MCF10A_ctrl_merged_norm_pos.bw
MCF10A_ctrl_merged_norm_neg.bw


title: WTCHG_388581_229273


title: WTCHG_388581_229208

value: HSC/MPP CD90+


title: MCF10A_ctrl_R4


title: WTCHG_388581_229207


title: [gene] L18MDP aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978711110317428272788254

value: F


title: MCF10A_bza_R6

description:
MCF10A_bza_merged_norm_pos.bw
MCF10A_bza_merged_norm_neg.bw

value: mammary gland/breast epithelial cell


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-891 biological rep-17

description:
subject-ID_891
@52084400978711110317428272788241


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978709110317428272788083


title: MCF10A_bza_R4


title: MCF10A_ctrl_R2


title: WTCHG_388581_229205


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-1600 biological rep-22

description:
subject-ID_1600
@52084400978327102417428100272907


title: MCF10A_bza_R3


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-1628 biological rep-35

description:
subject-ID_1628
@52084400978709110317428272788092


title: WTCHG_388581_229204


title: MCF7_gc10bza_H3K4ME3_R1_and_R2

description:
peaks_passing_IDR.tar.gz
chromHMM_7states.tar.gz

data_processing:
Sequencing base calls were generated on the HiSeq 1500 instrument in the Advanced Genome Technologies Core Massively Parallel Sequencing Facility.
Fastq conversion and demultiplexing were done using bcl2fastq (Illumina, v1.8.4)
Adapters were cut by cutadapt and reads were trimmed for quality by FASTQ Trimmer (Galaxy utility)
Enriched regions (narrowPeak calls) for each replicate were generated using MACS2 (Feng, et al.  Nat Protoc  2012) and a weak p-value cutoff e-2.  Replicates were then evaluated using IDR to determine maximum number of peaks in pooled samples, e-5.
A representative 7 state chromHMM model was determined by running chromHMM with 30 states and then reducing to the minimum representative number of states.
MACS2 bdgcmp FE -m FE was using to compare pooled treatment to input bedgraphs and then bedgraphs were converted to bigwig (UCSC bedGraphToBigWig)
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeaks - areas of enrichment passing a reproducibility requirement via IDR; bigwigs - tracks of fold-enrichment of pooled pulldown over input samples; chromHMM - segmentation and model files.

extract_protocol:
Nuclei extraction was performed using a protocol modified from Dignam et al (Dignam, et al.  Nucleic Acids Res  1983). Isolated nuclei were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin with an average peak size of 500 bp.  A total of 20 g of sheared chromatin was used for ChIP immunoprecipitation with either 6.5 ug of anti-H3K4me3  anti-H3K27ac, or anti-H3K4ac (Abcam, ab1012 lot#GR80367-1) or 8 ug of anti-H3K27me3 (Millipore -07-449 lot#1764447 or 2475696 ) used at a ratio of 3:1 or  2.5:1 chromatin to antibody, respectively.  Immunoprecipitated complexes were purified using Protein-G Dynabeads (Life Technologies 10004D lot#123085320).  DNA fragments were isolated by uncross-linking the protein-DNA complex overnight at 65°C. The eluted ChIP-DNA were treated with RNase A (0.2mg/ml final concentration-Life Technologies Cat # AM2269), proteinase K treatment (Life Technologies cat # AM2548) and then phenol extracted, precipitated with ethanol, then resuspended in 10mM Tris.  DNA was quantified using a Qubit fluorimeter (Life Technologies) prior to the library preparation.
Sequencing libraries were prepared using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following instructions provided by the manufacturer.  Libraries were then size selected, purified and quantified prior to sequencing by automated DNA sequencing performed in the University of Vermont Cancer Center Advanced Genome Technologies Core (Messier, et al.  Oncotarget  2016) .

value: metastatic site derived

tag: antibody


title: WTCHG_388581_229203


title: MCF7_gc10bza_H3K4AC_R1_and_R2

value: adenocarcinoma; ATCC HTB-22


title: WTCHG_388581_229202


title: MCF7_gc10bza_H3K27ME3_R1_and_R2


title: MCF7_gc10_input


title: MCF7_gc10_H3K4ME3_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-1338 biological rep-34

description:
subject-ID_1338
@52084400980525112917428617727122


title: WTCHG_388581_229201


title: MCF7_gc10_H3K4AC_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-531 biological rep-31

description:
subject-ID_531
@52084400978711110317428272788217


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-554 biological rep-32

description:
subject-ID_554
@52084400978710110317428272788182


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-1014 biological rep-33

description:
subject-ID_1014
@52084400978711110317428272788227


title: WTCHG_388580_256208


title: MCF7_gc10_H3K27ME3_R1_and_R2


title: MCF7_gc10_H3K27AC_R1_and_R2


title: WTCHG_388580_256207


title: MCF7_e2bza_input


title: MCF7_e2bza_H3K4ME3_R1_and_R2


title: MCF7_e2bza_H3K4AC_R1_and_R2


title: MCF7_e2bza_H3K27ME3_R1_and_R2


title: MCF7_gc10bza_H3K27AC_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-447 biological rep-30

description:
subject-ID_447
@52084400978710110317428272788178


title: WTCHG_388580_256206


title: WTCHG_388580_256205


title: MCF7_e2_input


title: MCF7_e2bza_H3K27AC_R1_and_R2


title: [exon] LPS aCD3-aCD28 aIL10R diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400975431121817428781459681

value: CD


title: MCF7_e2_H3K4AC_R1_and_R2


title: WTCHG_388580_256204


title: MCF7_e2_H3K4ME3_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400978329102417428100273015

value: IBDu


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400978709110317428272788081


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978710110317428272788138


title: MCF7_e2_H3K27ME3_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978329102417428100273020


title: WTCHG_388580_256203


title: MCF7_e2_H3K27AC_R1_and_R2


title: WTCHG_388580_256202


title: MCF7_ctrl_input

value: control


title: WTCHG_388580_255208


title: MCF7_ctrl_H3K27ME3_R1_and_R2


title: MCF7_ctrl_H3K4AC_R1_and_R2


title: MCF7_gc10bza_input


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978326102417428100272836


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978326102417428100272861

value: Other


title: MCF7_bza_input

value: bza


title: WTCHG_388580_255206


title: MCF7_ctrl_H3K4ME3_R1_and_R2


title: WTCHG_388580_255205


title: MCF10A_gc10bza_input

value: luminal ductal cells

value: fibrocystic disease;ATCC CRL-10317


title: MCF7_bza_H3K27AC_R1_and_R2


title: WTCHG_388580_255204

value: YES


title: MCF7_bza_H3K4AC_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400978710110317428272788159


title: MCF7_ctrl_H3K27AC_R1_and_R2


title: MCF7_bza_H3K27ME3_R1_and_R2


title: WTCHG_388580_255207

value: NO


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978710110317428272788168


title: MCF10A_gc10bza_H3K4ME3_R1_and_R2


title: MCF10A_gc10bza_H3K4AC_R1_and_R2


title: MCF10A_gc10bza_H3K27ME3_R1_and_R2


title: MCF7_bza_H3K4ME3_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1016 biological rep-18

description:
subject-ID_1016
@52084400978326102417428100272819


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
@52084400978709110317428272788105

value: M


title: WTCHG_388580_255202


title: MCF10A_gc10bza_H3K27AC_R1_and_R2

description:
peaks_passing_IDR.tar.gz
chromHMM_7states.tar.gz


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400980525112917428617727158

value: peripheral PBMC


title: MCF10A_gc10_input


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400980524112917428617727095


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978326102417428100272848


title: MCF10A_gc10_H3K4ME3_R1_and_R2


title: WTCHG_388580_255201


title: MCF10A_gc10_H3K4AC_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-1045 biological rep-20

description:
subject-ID_1045
@52084400978711110317428272788237


title: MCF10A_gc10_H3K27ME3_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400978710110317428272788172


title: WTCHG_388580_255203


title: MCF10A_e2bza_input


title: MCF10A_e2bza_H3K4ME3_R1_and_R2


title: WTCHG_388580_254206


title: WTCHG_388580_254207


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978326102417428100272845


title: MCF10A_e2bza_H3K27ME3_R1_and_R2


title: WTCHG_388580_254205


title: MCF10A_e2bza_H3K27AC_R1_and_R2


title: WTCHG_388580_254204


title: MCF10A_e2_input


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400980525112917428617727121


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400978710110317428272788158


title: MCF10A_gc10_H3K27AC_R1_and_R2


title: WTCHG_388580_254208


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400980523112917428617727022


title: MCF10A_e2_H3K27ME3_R1_and_R2


title: MCF10A_e2_H3K4AC_R1_and_R2


title: [gene] L18MDP_aCD3-aCD28 aIL10R diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400980524112917428617727080


title: WTCHG_388580_254203


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