title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_384

description:
Protocol described by Buenrostro et al (2015)
FLUIDIGMC1_SCATACSEQ_SENS-GFP_CTXREGIONS.tsv
FLUIDIGMC1_SCATACSEQ_SENS-GFP_AGGREGATE.normalized.bw

data_processing:
ATAC-seq reads were first cleaned for adapters using fastq-mcf. (ea-utils v1.12) and a list of sequencing primers. Cleaned reads (FastQC v0.1) were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using Bowtie2 (v2.2.5) with default parameters, and sorted bam files were produced using using SAMtools (v1.2). The data was deduplicated using picard MarkDuplicates.
Aggregation plots were produced using in-house scripts available at: https://github.com/aertslab/ATAC-seq-analysis, and cells well filtered manually based on the aggregation plot profiles, resulting in 72 and sens-GFP+ single cell ATAC-seq profiles. Single-cell profiles were aggregated using samtools merge. Normalized bigwigs were generated using the Kent software (UCSC). Some of the cells were filtered out based on aggregation plots, so they werent use for the analysis (before counting fragments in the regions).
Downstream analysis was done using cisTopic (v0.2.2)
Genome_build: dm6
Supplementary_files_format_and_content: There are two processed data files: a tab-delimited file containing cell names as columns, ctx regions as rows, and number of fragments as values, and a bigwig file containing the normalized coverage profiles of the aggregated sens-GFP+ cells.

extract_protocol:
Wandering third instar larvae were collected and a total of 200 eye-antennal discs were dissected in ice-cold PBS and placed in SF900 medium. For dissociation, the tissue was placed in 400 µl of trypsin in 0.05% EDTA. The eye–antennal discs were then incubated at 37 °C for 1 h with agitation; being mixed every 20 min with a pipette. After dissociation, cells were centrifuged at 800 g for 5 min at 4 °C and washed with PBS. Finally, the cells were resuspended in 400 µl of PBS, filtered using a 40 µm cell strainer and stained with propidium iodide (PI; final concentration 1 µg/ml) to exclude dead cells. The cells were sorted on a BD Aria I, selecting against the presence of PI and for the presence of GFP.
For single-cell ATAC–seq, as many cells as possible were sorted into a microcentrifuge tube, pelleted by centrifugation at 800 g for 5 min at 4 °C and resuspended at a concentration of 1,000 cells/µl. Single-cell ATAC–seq was performed as previously described12,81, using 5- to 10-µm Open App integrated fluidic circuits (IFCs) on the Fluidigm C1 and with no cell washing step. Briefly, cells were loaded (using a 40:60 ratio of RGT:cells) on a primed Open App IFC (5-10 µm, the protocol for ATAC-seq from the C1 Script Hub was used). After cell loading, the plate was visually checked under a microscope and the number of cells in each of the capture chambers was noted. Next, the sample preparation was performed on the Fluidigm C1 during which the cells underwent lysis and ATAC-seq fragments were prepared. In a 96-well plate, the harvested libraries were amplified in a 25 µl PCR reaction. The PCR products were pooled and purified on a single MinElute PCR purification column for a final library volume of 15 µl. Quality checks were performed using the Bioanalyzer high sensitivity chips. Fragments under 150 bp were removed by bead-cleanup using AMPure XP beads (1.2x bead ratio) (Beckman Coulter).
Single-cell ATAC-seq (Fluidigm C1)

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: Pre-1-B1

status: Public on Apr 08 2020

type: SRA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: experiment: JQ1+paclitaxel in vitro

library_source: genomic

data_processing:
Library strategy: Exome-Seq
Alignment using Picard (http://broadinstitute.github.io/picard)
SNV calling using MuTect v1.1.4 (Cibulskis et al., 2013) and annotation using Varient Effect Predictor (VEP, McLaren et al., 2010). MuTect was run in paired mode pairing the tumor samples to the project normal, CEPH 1408.
Indel calling using GATK
Variant annotation using OncoAnnotate
CNV calling using RobustCNV. RobustCNV relies on localized changes in mapping depth of sequenced reads in order to identify changes in copy number. Observed values are normalized against the mapping depth in a panel of normals (PON) sampled with the same capture bait set. Normalized coverage data are then segmented using Circular Binary Segmentation (Olshen et al., 2004) with the DNAcopy Bioconductor package. Finally, segments are assigned gain, loss, or normal-copy calls using a cutoff derived from the within-segment standard deviation and a tuning parameter set based on comparisons to array-CGH calls in separate validation experiments.
Genome_build: b37
Supplementary_files_format_and_content: SNV and indel report contains variants with genomic coordinates, gene, DNA and protein change, allele fraction, coverage, and annotations from dbSNP, COSMIC, and gnomAD. CNV report contains gene level calls, with genomic coordinates and coverage levels, and chromosome arm-level calls.

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer cells SUM159

growth_protocol: Cells were lentivirally infected with the ClonTracer barcode library (Bhang et al., 2015). Barcoded cells were passaged in vitro in the presence of drug or injected orthotopically into mammary fat pads of NOG mice to produce xenografts.

extract_protocol:
DNA was extracted from frozen cultured cells and xenografts using the AllPrep DNA/RNA Mini Kit or the QIAamp DNA Mini Kit (Qiagen). Equal amounts of DNA were pooled from replicates for library construction.
DNA was fragmented to 250 bp (Covaris ultrasonication) and further purified using Agencourt AMPure XP beads. Size-selected DNA was ligated to sequencing adaptors with sample-specific barcodes using the KAPA Hyper Prep Kit. Libraries were pooled and sequenced on an Illumina MiSeq nano flow cell to estimate the library DNA concentration based on the number of barcode reads per sample. Libraries were pooled and captured using SureSelectXT Human All Exon v5 (Agilent) in 7 x 3-plex and 1 x 2-plex. Captures were performed using the SureSelectXT Reagent Kit (Agilent).

treatment_protocol: Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages. Mice were treated for up to 2 weeks with vehicle, JQ1 (30-50 mg/kg daily), palbociclib (75 mg/kg daily), paclitaxel (10 mg/kg twice weekly), JQ1+palbociclib, or JQ1+paclitaxel, or for 1 week with JQ1 followed by 1 week with paclitaxel, 1 week with paclitaxel followed by 1 week with JQ1, or 1 week with JQ1+paclitaxel followed by 1 week with vehicle, with 5 mice per group.

tag: cell line

tag: treatment

value: pre-treatment


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_383

city: Leuven

first: Carmen

last: Bravo González-Blas

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

organism: Drosophila melanogaster

source_name: L3 Drosophila eye-antennal disc

growth_protocol: All flies were raised and crossed at 25°C on a yeast based medium.

tag: strain

tag: sequencing method


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_382


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_381


title: GMR-GAL4_UAS-FRU2366

description: Omni-ATAC-seq protocol as described by Corces et al. (2017)

data_processing:
ATAC-seq reads were first cleaned for adapters using fastq-mcf. (ea-utils v1.12) and a list of sequencing primers. Cleaned reads (FastQC v0.1) were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using Bowtie2 (v2.2.5) with default parameters, with the single end option (to compare with the WT sample, which was single-end sequenced).
Sorted bam files were produced using using SAMtools (v1.2). Normalized bigwigs were generated using the Kent software (UCSC). Peaks were called on mapped reads using MACS2 (v2.1.2.1) with the following options: -g dm –nomodel –bdg -t Sample/Control -c Sample/Control (depending on whether we want to determine upregulated or downregulated peaks).
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files containing the normalized coverage profiles of each experiment.

extract_protocol:
Briefly, ~10 eye-antennal discs were dissected and lysed using 50 µl of cold ATAC-Resupension Buffer (RSB) (see Corces et al. for composition) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubating the cells for 3 min on ice. The lysis was washed out by adding 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and inverting the tube three times.
Nuclei were pelleted at 500 RCF for 10 min at 4°C, the supernatant was carefully removed and nuclei were resuspended in 50 µl of transposition mixture (25 µl 2x TD buffer (see Corces et al. for composition), 2.5 µl transposase (100 nM), 16.5 µl DPBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) by pipetting six times up and down, followed by 30 minutes incubation at 37°C at 1000 RPM mixing rate. After MinElute clean-up and elution in 21 µl elution buffer, the transposed fragments were pre-amplified with Nextera primers by mixing 20 µl of transposed sample, 2.5 µl of both forward and reverse primers (25 µM) and 25 µl of 2x NEBNext Master Mix (program: 72°C for 5 min, 98°C for 30 sec and 5 cycles of [98°C for 10 sec, 63 °C for 30 sec, 72°C for 1 min] and hold at 4°C). To determine the required number of additional PCR cycles, a qPCR was performed (see Buenrostro et al.83 for the determination of the number of cycles to be added). The final amplification was done with the additional number of cycles, samples were cleaned-up by MinElute and libraries were prepped using the KAPA Library Quantification Kit as previously described82. Samples were sequenced on a NextSeq500 High Output chip, with 50bp single-end reads.
Omni-ATAC-seq (Corces et al., 2017)

value: Omni-ATAC-seq


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_378


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_377


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_379


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_374


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_375


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_370


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_371


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_373


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_376


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_372


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_369


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_367


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_368


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_366


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_363


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_361


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_360


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_359


title: Bladder_tumor_8.5mM_exp1

status: Public on Apr 09 2020

type: RNA

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from MB49-induced bladder cancer mice treated with 8.5mM of alpha1-oleate

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Mouse Genome 430 PM array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas system (Affymetrix).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mice bladder cancer treated with 8.5mM alpha1-oleate

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented (GeneChip 3´IVT Express Kit). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. On day 0, bladders were preconditioned by intravesical instillation of poly-L-lysine followed by instillation of MB49 mouse bladder carcinoma cells.

extract_protocol: Frozen bladder tissue was pulverized using liquid nitrogen, total RNA was extracted (RNeasy Mini kit, Qiagen), according to the manufacturer's instructions.

treatment_protocol: The treatment group received alpha1-oleate by intravesical instillation (1.7 mM, 8.5 mM or 17 mM) on days 3, 5, 7, 9 and 11, sham treated animals received PBS.

tag: gender

value: female

tag: tissue

value: bladder

tag: agent

tag: dose

tag: cancer model

value: MB49 bladder cancer

tag: disease

value: bladder cancer

tag: sacrifice time

tag: experiment


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_380


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_358


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_357


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_356


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_355


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_354


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_353


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_351


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_350


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_348


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_349


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_364


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_365


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_347


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_346


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_362


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_342


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_341


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_340


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_337


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_338


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_336


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_334


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_330


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_332


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_345


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_352


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_344


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_331


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_329


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_343


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_327


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_325


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_324


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_326


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_321


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_323


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_322


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_339


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_318


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_333


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_320


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_319


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_335


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_317


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_315


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_311


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_313


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_314


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_328


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_307


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_309


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_310


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_308


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_306


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_303


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_304


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_305


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_302


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_300


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_301


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_316


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_296


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_294


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_295


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_297


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_298


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_312


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_293


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_292


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_288


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_290


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_291


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_287


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_289


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_285


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_286


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_284


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_282


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_280


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_279


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_278


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_299


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_277


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_276


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_283


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_274


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_271


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_275


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_272


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_268


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_269


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_267


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_266


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_264


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_263


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_265


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_262


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_259


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_281


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_258


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_260


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_256


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_255


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_254


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_252


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_257


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_251


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_248


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_249


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_253


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_270


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_273


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_246


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_244


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_243


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_245


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_241


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_240


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_242


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_261


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_237


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_235


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_239


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_236


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_233


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_230


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_229


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_250


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_232


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_234


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_228


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_231


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_226


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_247


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_227


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_224


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_223


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_225


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_222


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_221


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_219


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_218


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_220


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_217


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_238


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_216


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_215


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_214


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_213


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_209


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_208


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_210


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_204


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_212


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_205


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_207


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_202


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_201


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_203


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_198


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_199


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_206


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_197


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_195


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_200


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_194


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_192


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_193


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_196


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_188


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_186


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_190


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_187


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_211


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_189


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_191


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_185


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_183


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_184


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_178


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_181


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_177


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_179


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_176


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_174


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_180


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_170


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_175


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_171


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_168


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_169


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_172


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_167


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_166


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_164


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_163


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_165


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_159


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_161


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_182


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_160


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_157


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_156


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_155


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_162


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_154


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_153


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_173


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_150


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_149


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_148


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_146


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_143


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_142


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_140


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_144


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_141


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_147


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_158


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_139


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_136


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_138


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_137


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_135


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_132


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_133


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_130


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_134


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_152


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_128


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_129


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_151


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_126


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_127


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_125


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_145


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_124


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_119


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_120


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_122


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_117


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_118


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_121


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_116


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_115


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_114


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_131


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_109


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_112


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_113


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_111


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_107


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_104


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_108


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_106


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_103


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_110


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_123


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_101


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_100


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_105


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_102


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_99


title: NOG-A4

description:
cell line: NOD.Cg-Prkdcscid Il2rgtm1Sug/JicTac (NOG)
experiment: N/A

source_name: xenograft host mouse


title: A549 PIK3CD-AS2 siRNA#1

city: nanjing

first: Rong

last: Yin

state: -- None selected --

address: 42 baiziting

country: China

institute: Jiangsu Cancer Hospital

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to human  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: A549 cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: A549 cells were transfected with PIK3CD-AS2 siRNA or control, respectively.

value: lung

tag: genotype

value: p53 wild-type

tag: cell type


title: A549 Control siRNA#2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_97


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_96


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_95


title: A549 PIK3CD-AS2 siRNA#2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_94


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_93


title: A549 Control siRNA#1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_92


title: WT_H3K4me3ChIP_PFA_rep1

city: Memphis

first: Hans-Martin

last: Herz

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: SJMMNORM050492_C105-mES_WTBRUCE4_rep1-H3K4me3-AB8

data_processing:
Mapping reads and visualizing data:ChIP-seq raw reads were aligned to the mouse and Drosophila melanogaster hybrid reference genomes (mm9+dm3) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’). Mapped reads were then split into two bam files (mapped to mm9 and dm3 respectively). For data quality control and to estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to calculate the relative strand correlation value with support of R (version 3.3.1). To visualize ChIP-seq data on the integrated genome viewer (IGV) (version 2.3.82), we utilized genomeCoverageBed (bedtools 2.25.0) to obtain genome-wide coverage in BEDGRAPH file format and then converted it to bigwig file format by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
Peak calling, annotation and motif analysis:MACS2 (version 2.1.1 20160309) was used to call narrow peaks (Dnttip1, Hdac1, H3K27ac and H3K4me3) with option “nomodel” and “extsize” defined as fragment size estimated by SPP and a FDR corrected p-value cutoff of 0.05. For broad peak/domain calling (H3K4me1 and H3K27me3). SICER (version 1.1, with parameters of redundancy threshold 1, window size 200 bp, effective genome fraction 0.86, gap size 600 bp, FDR 0.00001 with fragment size defined above) was used for broad peak/domain calling (H3K4me1 and H3K27me3). Enriched regions were identified by comparing the ChIP library file to input library file. Peak regions were defined to be the union of peak intervals from two ChIP replicates of WT or KO mESCs, respectively. Promoter regions were defined as ± 1000 bp from a TSS based on the mouse RefSeq annotation. Genomic feature annotation of peaks was carried out by annotatePeaks.pl, a program from HOMER suite (v4.8.3, http://homer.salk.edu/homer/). HOMER software was used to perform de novo motif discovery and to check for enrichment of known motifs from a set of Dnttip1 peaks (associated with up- or downregulated genes in Dnttip1 KO versus WT mESCs) or all Dnttip1 peaks.
Spike-in normalization and differential analysis:ChIP-seq raw read counts were reported for each region/each sample using bedtools 2.25.0. Spike-in normalization was performed by counting Drosophila reads and mouse reads in each ChIP sample and corresponding input sample and using those counts to generate a normalization factor for each sample, which was calculated as (ChIP_dm3.reads/ChIP_mm9.reads)/(Input_dm3.reads/Input_mm9.reads). Raw read counts were voom normalized and statistically contrasted using the pipeline limma in R (version 3.3.1). The normalization factor defined above was used to modify the mouse library size in edgeR (version 3.16.5) for CPM calculation and differential analysis. An empirical Bayes fit was applied to contrast KO samples to WT samples and to generate log2 fold changes, p-values and false discovery rates for each peak region. Histograms showing average ChIP-seq intensity over gene bodies were generated using ngsplot (v2.61).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: Mouse embryonic stem cells

growth_protocol: mESCs were grown in chemically defined 2iL medium (defined naïve culture conditions): 50% DMEM/F-12; 50% Neurobasal Medium (no L-glutamine); B-27 Supplement, minus vitamin A (1:100); N-2 Supplement (1:200); 2 mM L-Glutamine or GlutaMAX (1:100); 0.1 mM β-Mercaptoethanol (1:500); 3 µM CHIR 99021 (GSK3β inhibitor) (1:1000 from 3 mM stock in DMSO); 1 µM PD 0325901 (MEK inhibitor) (1:1000 from 1 mM stock in DMSO); 1000 U/ml LIF (1:10,000 from 107 U/ml stock); 50 U/ml Pen/Strep (1:100).

extract_protocol:
ChIP-seq for non-histone proteins (Dnttip1) was carried out with 5 x 10e7 cells and for histones with 2-2.5 x 10e7 mESCs, using a modified version of Lee et al., Nature Protocols, 2006.
ChIP-seq Library Preparation and Sequencing:DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067-4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067-5584, 5067-5585, 5067-5587, 5067-5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay. Single end 50 cycle sequencing was performed on a HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina).

value: WT

value: Mouse embryonic stem cells

tag: chip antibody


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_91


title: Dnttip1KO2_D1E6_H3K4me3ChIP_PFA_rep1

description: SJMMNORM050492_C113-mES_Dnttip1KOD2E6_rep1-H3K4me3-AB8

value: Dnttip1 KO2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_90


title: WT_H3K27acChIP_PFA_rep1

description: SJMMNORM050492_C130-mES_WTBRUCE4_rep1-H3K27Ac-AB6


title: WT_H3K4me3ChIP_PFA_rep2

description: SJMMNORM050492_C110-mES_WTBRUCE4_rep2d-H3K4me3-AB8


title: WT_H3K27acChIP_PFA_rep2

description: SJMMNORM050492_C132-mES_WTBRUCE4_rep2e-H3K27Ac-AB6


title: Brd4 KO_20hr_REP2

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

description: Sample_20h-ko 2

data_processing:
Paired-end reads were aligned to M.musculus reference genome using bowtie with default parameters.
Transcript abundance was quantified using rpkm for genes (Ramskold et.al 2009)
EdgeR software was used to determine differentially expressed genes  with p-values<0.01 and FDR 0.1
Genome_build: mm9
Supplementary_files_format_and_content: rawcount.txt

source_name: Brd4 KO_20hr

growth_protocol: Brd4f/f ERT2Cre MEFs were cultured in DMEM supernatant with 10% FCS, 1% penicillin-streptomycin, in the presence of 4uM 4-hydroxytamoxifen resulting in Ert2-Cre mediated deletion of Brd4 floxed allele after 96 in culture.

extract_protocol:
RNA-seq:Total RNA was extracted using Quick-RNA Miniprep Kit (ZYMO research).
Library preparation, including ligating barcode, was performed using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). Fragments ranging from 250 to 450 bp were selected and subjected to paired-end sequencing on a HiSeq 2000 sequencing system (Illumina).

treatment_protocol: For synchronization by serum starvation, Brd4 WT or KO cells were incubated in DMEM with 0. 05% FBS, 1% penicillin-streptomycin for 72 hours, released in complete media as above with 5 % CO2 at 37oC, and then collected at indicated times.

value: Brd4Floxed :Ert2-Cre

value: Mouse Embryonic Fibroblasts (MEFs)

value: released at 20h


title: Brd4 KO_8hr_REP2

description: Sample_8h-ko 2

source_name: Brd4 KO_8hr

value: released at 8h


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_89

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]


title: Dnttip1KO2_D1E6_H3K4me3ChIP_PFA_rep2

description: SJMMNORM050492_C118-mES_Dnttip1KOD2E6_rep2d-H3K4me3-AB8


title: Brd4 KO_12hr_REP2

description: Sample_12h-ko 2

source_name: Brd4 KO_12hr

value: released at12h


title: Brd4 KO_8hr_REP1

description: Sample_8h-ko 1


title: Brd4 KO_24hr_REP2

description: Sample_24h-ko 2

source_name: Brd4 KO_24hr

value: released at 24h


title: Dnttip1KO2_D1E6_H3K27acChIP_PFA_rep1

description: SJMMNORM050492_C134-mES_Dnttip1KOD2E6_rep1e-H3K27Ac-AB6


title: WT_H3K27me3ChIP_PFA_rep1

description: SJMMNORM050492_C142-mES_WTBRUCE4_rep1-H3K27me3-AB4

value: Cell signaling technology H3K27me3 #9733


title: Dnttip1KO2_D1E6_H3K27acChIP_PFA_rep2

description: SJMMNORM050492_C135-mES_Dnttip1KOD2E6_rep2-H3K27Ac-AB6


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_88

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: WT_H3K27me3ChIP_PFA_rep2

description: SJMMNORM050492_C143-mES_WTBRUCE4_rep2-H3K27me3-AB4


title: Brd4 KO_24hr_REP1

description: Sample_24h-ko 1


title: Brd4 KO_20hr_REP1

description: Sample_20h-ko 1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_87


title: Dnttip1KO2_D1E6_H3K27me3ChIP_PFA_rep1

description: SJMMNORM050492_C146-mES_Dnttip1KOD2E6_rep1-H3K27me3-AB4


title: Dnttip1KO2_D1E6_H3K27me3ChIP_PFA_rep2

description: SJMMNORM050492_C147-mES_Dnttip1KOD2E6_rep2-H3K27me3-AB4


title: Brd4 KO_12hr_REP1

description: Sample_12h-ko 1

value: released at 12h


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_86


title: Brd4 KO_4 hr

description: Sample_4h ko

source_name: Brd4 KO_4 hr

value: released at 4h


title: Dnttip1KO2_D1E6_H3K4me1ChIP_PFA_rep1

description: SJMMNORM050492_C160-mES_Dnttip1KOD2E6_rep1.2b-H3K4me1-AB4


title: Elmsan1KO1_E2E8_Dnttip1ChIP_DCL_rep2

description: SJMMNORM050492_C99-mES_Elmsan1KOE2E8_rep2-DNTTIP1-AB1

value: Elmsan1 KO1

value: Bethyl Dnttip1 #A304-048A


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_85

description:
Protocol described by Buenrostro et al (2015)
FLUIDIGMC1_SCATACSEQ_SENS-GFP_CTXREGIONS.tsv
FLUIDIGMC1_SCATACSEQ_SENS-GFP_AGGREGATE.normalized.bw


title: Elmsan1KO1_E2E8_Dnttip1ChIP_DCL_rep1

description: SJMMNORM050492_C91-mES_Elmsan1KOE2E8_rep1-DNTTIP1-AB1


title: Dnttip1KO2_D1E6_Dnttip1ChIP_DCL_rep2

description: SJMMNORM050492_C83-mES_Dnttip1KOD2E6_rep2-DNTTIP1-AB1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_84


title: Brd4 KO_16hr_REP1

description: Sample_16h-ko 1

source_name: Brd4 KO_16hr

value: released at 16h


title: Brd4 KO_16hr_REP2

description: Sample_16h- ko 2


title: Brd4 KO_0hr_REP2

description: Sample_0h-ko 2

source_name: Brd4 KO_0hr

value: released at 0h


title: Dnttip1KO2_D1E6_H3K4me1ChIP_PFA_rep2

description: SJMMNORM050492_C65-mES_Dnttip1KOD2E6_rep1-H3K4me1-AB4

value: Mouse embryonic stem cells


title: Dnttip1KO2_D1E6_Dnttip1ChIP_DCL_rep1

description: SJMMNORM050492_C75-mES_Dnttip1KOD2E6_rep1-DNTTIP1-AB1

value: Dnttip1 KO2


title: WT_Dnttip1ChIP_DCL_rep1

description: SJMMNORM050492_C59-mES_WTBRUCE4_rep1-DNTTIP1-AB1

value: WT


title: WT_H3K4me1ChIP_PFA_rep2

description: SJMMNORM050492_C57-mES_WTBRUCE4_rep1-H3K4me1-AB4


title: Elmsan1KO1_E2E8_Input_DCL_rep1

description: SJMMNORM050492_C48-mES_Elmsan1KOE2E8_rep1-INPUT


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_82


title: Brd4 KO_0hr_REP1

description: Sample_0h-ko 1

value: Brd4Floxed :Ert2-Cre

value: Mouse Embryonic Fibroblasts (MEFs)


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_81


title: Brd4 WT_24hr_REP2

description: Sample_24h-wt 2

source_name: Brd4 WT_24hr

value: Brd4f/f ERT2Cre


title: WT_H3K4me1ChIP_PFA_rep1

description: SJMMNORM050492_C157-mES_WTBRUCE4_rep1.2b-H3K4me1-AB4


title: Dnttip1KO2_D1E6_Input_DCL_rep2

description: SJMMNORM050492_C38-mES_Dnttip1KOD2E6_rep2-INPUT


title: Elmsan1KO1_E2E8_Input_DCL_rep2

description: SJMMNORM050492_C49-mES_Elmsan1KOE2E8_rep2-INPUT


title: Dnttip1KO2_D1E6_Input_DCL_rep1

description: SJMMNORM050492_C37-mES_Dnttip1KOD2E6_rep1-INPUT


title: Dnttip1KO2_D1E6_Input_PFA_rep1

description: SJMMNORM050492_C35-mES_Dnttip1KOD2E6_rep1-INPUT


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_79

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]


title: WT_Input_PFA_rep2

description: SJMMNORM050492_C32-mES_WTBRUCE4_rep2a-INPUT


title: WT_Dnttip1ChIP_DCL_rep2

description: SJMMNORM050492_C67-mES_WTBRUCE4_rep2-DNTTIP1-AB1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_78


title: WT_Input_DCL_rep2

description: SJMMNORM050492_C29-mES_WTBRUCE4_rep2-INPUT


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_83


title: Brd4 WT_12hr_REP2

description: Sample_12h-wt 2

source_name: Brd4 WT_12hr

value: released at12h


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_77


title: WT_Input_PFA_rep1

description: SJMMNORM050492_C26-mES_WTBRUCE4_rep1-INPUT


title: Input DNA

city: Little Rock

first: PIROON

last: JENJAROENPUN

state: AR

address: 4301 W Markham Slot 782

institute: University of Arkansas for Medical Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Raw sequence reads were preprocessed to ensure that only the high-quality reads will be used for further bioinformatics analysis; adapters trimming and quality filtering were performed using fastp software v0.19.5 with default parameters
The resulting high-quality reads were then aligned to the human genome version hg19, using BWA-MEM v0.7.17 with ‘-M’ as parameter
The PCR duplicate reads were then removed using MarkDuplicates from Picards package v2.9.2 (http://broadinstitute.github.io/picard) with default parameter. The uniquely mapped reads were filtered (mapping quality score MAPQ 30), sorted and converted to BAM files using SAMtools (http://samtools.sourceforge.net/).
The BAM files were subjected to subsequent processing with Model-based Analysis for ChIP-seq (MACS2 v2.1.1, https://pypi.python.org/pypi/MACS2).
Enriched peak regions of the genome were identified by comparing the AID antibody and a rabbit IgG (a mock pull-down) samples to whole cell extract (WCE) samples using callpeak from MACS2 with modified parameters “-f BAMPE --broad --broad-cutoff 0.1”. The AID enriched peaks were filtered out if they overlap with the mock pull-down peaks and the blacklist (ENCODE blacklisted regions), which is combined from a consensus list empirically defined by the Encyclopedia of DNA Elements (ENCODE) consortium, available at https://github.com/kundajelab/HiC-pipeline/blob/master/hic_flexibleWindow-pipeline/data/reference_genomes/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz
Genome_build: hg19
Supplementary_files_format_and_content: Broad Peaks is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format. (https://genome.ucsc.edu/FAQ/FAQformat.html#format13)

growth_protocol: U2932 DLBCL cells obtained from the American Type Culture Collection were grown in RPMI 1640 medium (Corning) supplemented with 10% FBS (Atlanta Biiologicals) and 1% Pen/Strep (Gibco)

extract_protocol:
Exponentially growing cells were cross-linked with 1% formaldehyde and then quenched with glycine for 5 min at RT followed by lysis and MNase digestion. Samples were sonicated for 60 min using the Bioruptor (Diagenode)
For each immunoprecipitation reaction, 4x106 chromatin cell equivalent were incubated overnight with either an AID antibody (Abcam, ab59361) or a rabbit IgG negative control antibody, subjected to protein A/G magnetic bead binding, IP elution and DNA recovery. The ChIP DNA was used to generate ChIPseq libraries with the ChIP-Seq sample preparation kit (Illumina) for sequencing at the Arkansas Children’s Research Institute Genomics Core.

treatment_protocol: cells were not treated, but taken from culture in medium only to identify basal AID targets in untreated growth conditions.

value: Diffuse large B-cell lymphoma activated B-cell type


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_76

description:
Protocol described by Buenrostro et al (2015)
FLUIDIGMC1_SCATACSEQ_SENS-GFP_CTXREGIONS.tsv
FLUIDIGMC1_SCATACSEQ_SENS-GFP_AGGREGATE.normalized.bw


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_80


title: Brd4 WT_24hr_REP1

description: Sample_24h-wt 1

value: released at 24h


title: JQ1+Pal

description: experiment: JQ1+palbociclib

data_processing:
Demultiplex, alignment, barcode counting, UMI counting, and aggregation using CellRanger (10X Genomics)
Filter out cells with less than 200 genes detected and genes detected in less than 3 cells using Seurat (Butler et al., 2018)
Genome_build: hg19
Supplementary_files_format_and_content: Rdata contains Seurat object with gene counts and treatment groups for single cells. TXT files contain table of gene counts for single cells and table of treatment groups, number of genes, and number of UMIs for single cells

growth_protocol: Cells were lentivirally infected with the ClonTracer barcode library (Bhang et al., 2015). Barcoded cells were passaged in vitro in the presence of drug.

extract_protocol:
Equal numbers of cells from triplicates were combined, washed twice in PBS with 0.04% RNase-free BSA, diluted to 700 cells/µL, and filtered through a 35 µm nylon mesh prior to library preparation.
Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 and Single Cell A Chip (10X Genomics).

treatment_protocol: Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages.

tag: index


title: IgG_ChIPSeq

value: a rabbit IgG negative control antibody


title: JQ1-B

description: experiment: JQ1+palbociclib


title: Brd4 WT_20hr_REP1

description: Sample_20h-wt 1

source_name: Brd4 WT_20hr

value: released at 20h


title: Dnttip1KO2_D1E6_Input_PFA_rep2

description: SJMMNORM050492_C43-mES_Dnttip1KOD2E6_rep2a-INPUT


title: AID_ChIPSeq

value: anti-AID antibody (ab59361, Abcam; 1:2000 dilution)


title: Brd4 WT_20hr_REP2

description: Sample_20h-wt 2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_74

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: Pal

description: experiment: JQ1+palbociclib

value: palbociclib


title: WT_Input_DCL_rep1

description: SJMMNORM050492_C28-mES_WTBRUCE4_rep1-INPUT


title: JQ1+Tax

description: experiment: JQ1+paclitaxel


title: JQ1-A

description: experiment: JQ1+paclitaxel


title: Tax

description: experiment: JQ1+paclitaxel

value: paclitaxel


title: Brd4 WT_8hr_REP2

description: Sample_8h-wt 2

source_name: Brd4 WT_8hr

value: released at 8h


title: Brd4 WT_12hr_REP1

description: Sample_12h-wt 1

value: released at 12h


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_73


title: DMSO

description: experiment: JQ1+paclitaxel

source_name: breast cancer cells SUM159

value: DMSO


title: Brd4 WT_4 hr

description: Sample_4h wt

source_name: Brd4 WT_4 hr

value: released at 4h


title: Brd4 WT_8hr_REP1

description: Sample_8h-wt 1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_75

source_name: L3 Drosophila eye-antennal disc


title: Brd4 WT_16hr_REP2

description: Sample_16h- wt 2

source_name: Brd4 WT_16hr

value: released at 16h


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_71


title: JT_JQ1Tax_r2

description: experiment: JQ1+paclitaxel

data_processing:
Alignment using STAR (Dobin et al., 2013)
Reads per gene were counted using HTSeq-count (Anders et al., 2015)
Genome_build: hg19
Supplementary_files_format_and_content: TSV files contain gene counts.

molecule: polyA RNA

extract_protocol:
RNA was extracted from duplicate samples using the AllPrep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit, and 16-18 samples were multiplexed per lane for NGS.

tag: replicate


title: JT_JQ1Tax_r1

description: experiment: JQ1+paclitaxel

tag: cell line


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_70


title: Brd4 WT_16hr_REP1

description: Sample_16h-wt 1

value: Mouse Embryonic Fibroblasts (MEFs)

tag: treatment


title: JT_Tax_r2

description: experiment: JQ1+paclitaxel


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_69

tag: strain


title: JT_JQ1_r2

description: experiment: JQ1+paclitaxel


title: Brd4 WT_0hr_REP1

description: Sample_0h-wt 1

source_name: Brd4 WT_0hr

value: Brd4f/f ERT2Cre

value: released at 0h


title: JT_Tax_r1

description: experiment: JQ1+paclitaxel


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_98

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]

tag: sequencing method


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_68


title: JT_JQ1_r1

description: experiment: JQ1+paclitaxel


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_72


title: JT_DMSO_r1

description: experiment: JQ1+paclitaxel


title: JP_JQ1Pal_r1

description: experiment: JQ1+palbociclib


title: Pre

description: experiment: parental

value: pre-treatment


title: JT_DMSO_r2

description: experiment: JQ1+paclitaxel


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_67


title: Spleen CD8 rep1

city: New Haven

first: Ping-Min

state: CT

address: 333 Cedar Street

department: Immunobiology

institute: Yale University

description: Kidney_Spleen_T_cells_normalized_counts.txt

data_processing:
PartekFlow software
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using STAR 2.5.3 and TOPHAT 2.1.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen CD8+ T cells

extract_protocol:
CD44hi CD4+ and CD8+ T cells from kidney and spleens of 14-week-old MRL/lpr mice were sorted, and mRNA isolated by Qiagen RNeasy Plus Micro Kit.
Library was constructed by using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa, 634893)

value: Spleen

value: CD8+ T cells

tag: genotype/variation

value: MRL/lpr


title: Spleen CD8 rep2

tag: tissue


title: JP_JQ1Pal_r2

description: experiment: JQ1+palbociclib


title: Spleen CD4 rep2

source_name: Spleen CD4+ T cells

value: CD4+ T cells


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_66

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: JP_Pal_r2

description: experiment: JQ1+palbociclib

value: palbociclib


title: JP_Pal_r1

description: experiment: JQ1+palbociclib


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_65


title: JP_JQ1_r2

description: experiment: JQ1+palbociclib


title: JP_JQ1_r1

description: experiment: JQ1+palbociclib


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_64


title: Spleen CD4 rep1


title: Brd4 WT_0hr_REP2

description: Sample_0h-wt 2


title: Kidney CD8 rep2

source_name: Kidney CD8+ T cells

value: Kidney


title: JP_DMSO_r2

description: experiment: JQ1+palbociclib


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_63


title: Pre_r2

description: experiment: parental


title: Kidney CD8 rep1


title: JP_DMSO_r1

description: experiment: JQ1+palbociclib


title: Pre_r1

description: experiment: parental


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_62


title: JT_JQ1Tax_P14_2

description: experiment: JQ1+paclitaxel in vitro

data_processing:
Remove 3' adapter and discard reads shorter than 30 bp using fastx_clipper
Filter for reads matching the barcode pattern (alternating A/T and C/G) and with a Phred quality score of at least 10 for all base pairs and an average Phred score of 30
Genome_build: N/A
Supplementary_files_format_and_content: TSV files contain unique barcode sequences with corresponding number of reads.

extract_protocol:
DNA was extracted from frozen cultured cells and xenografts using the AllPrep DNA/RNA Mini Kit or the QIAamp DNA Mini Kit (Qiagen).
PCR was used to amplify barcodes and introduce Illumina adaptors along with a 5 bp index sequence for multiplexing as described (Bhang et al., 2015). 2 µg of genomic DNA was used as template, and 15-16 samples were multiplexed. PCR products were run on 0.8% agarose NGS E-Gels (Invitrogen) to verify the correct library size, and bands were purified using the MinElute Gel Extraction Kit (Qiagen).

treatment_protocol: Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages. Mice were treated for up to 2 weeks with vehicle, JQ1 (30-50 mg/kg daily), palbociclib (75 mg/kg daily), paclitaxel (10 mg/kg twice weekly), JQ1+palbociclib, or JQ1+paclitaxel, with 5 mice per group.

tag: time point

value: passage 14


title: JT_JQ1Tax_P14_1

description: experiment: JQ1+paclitaxel in vitro


title: Kidney CD4 rep1

source_name: Kidney CD4+ T cells


title: Kidney CD4 rep2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_60


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_59


title: C2

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

data_processing:
base calling bcl2fastq 2.19.0.316
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the read needing a quality phred score > 20. Homertools 4.7 33 were used for PolyA-tail trimming, and reads with a length < 17 were removed.
With STAR 2.3 34, the filtered reads were mapped against mouse genome 38 (mm10) using default parameters
Count data were generated using featureCounts 35(parameters --minReadOverlap 3 -T 3 -M -O) for the genes annotated in the gencode.vM16.gtf file.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: skeletal muscle

extract_protocol: SmarTer Ultra Low Input RNA and Illumina Trueseq Stranded RNA-Kit was used for library construction. libraries were pooled with five samples in each lane and sequenced (Illumina HiSeq 2000 v4 Single-Read 50 bp)

treatment_protocol: Quadriceps muscle from LCMV Armstrong- and LCMV clone 13-infected C57BL/6 mice was collected and homogenized. We extracted RNA from the skeletal muscle using the QIAGEN RNeasy Mini Kit and removed genomic DNA using the QIAGEN RNase-Free DNase Set.

value: skeletal muscle

tag: age

tag: agent

value: infected with LCMV Clone 13


title: C3


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_58


title: JT_JQ1Tax_P7_3

description: experiment: JQ1+paclitaxel in vitro

value: passage 7


title: JT_JQ1Tax_P9_1

description: experiment: JQ1+paclitaxel in vitro

value: passage 9


title: JT_JQ1Tax_P7_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1Tax_P7_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1Tax_P9_2

description: experiment: JQ1+paclitaxel in vitro


title: C1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_57


title: JT_JQ1Tax_P4_2

description: experiment: JQ1+paclitaxel in vitro

value: passage 4


title: JT_JQ1Tax_P4_3

description: experiment: JQ1+paclitaxel in vitro


title: A3

value: infected with LCMV Armstrong


title: JT_JQ1Tax_P14_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1Tax_P2_3

description: experiment: JQ1+paclitaxel in vitro

value: passage 2


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_56

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_61


title: A1


title: JT_JQ1Tax_P9_3

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_55


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_54


title: JT_JQ1Tax_P2_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_Tax_P14_2

description: experiment: JQ1+paclitaxel in vitro

value: paclitaxel


title: JT_Tax_P14_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_Tax_P7_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_Tax_P7_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_53


title: A2


title: JT_Tax_P7_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1Tax_P4_1

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_50


title: 31_H929 KO AB alone, biological rep2

city: Houston

first: Ram Kumar

last: Singh

state: Texas

address: 1515 Holcombe Blvd

department: Lymphoma and Myeloma

institute: MD Anderson Cancer Centre

description: Differential gene expression data with HDP-101 Traetment at 200 pM compared with respective controls

hyb_protocol: Hybridization of samples to Affymetrix Human GeneChip arrays was performed according to Affymetrix manual instructions.

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions.

data_processing: The data were analyzed by Genome Explorations (GenEx).

label: Biotin

source_name: H929 p53 KO cells treated with AB ALONE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Multiple myeloma cell lines (H929 and MM1.S either p53 WT or p53 KO) were maintained in RPMI 1640 medium (Corning Cellgro; Manassas, VA) supplemented with L‐glutamine, 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with HDP-101 at 200 pM concentration for 24 hours

value: Multiple Myeloma Cell Line


title: 30_H929 KO NTC, biological rep2

source_name: H929 p53 KO cells treated with NTC


title: JT_Tax_P6_3

description: experiment: JQ1+paclitaxel in vitro

value: passage 6


title: 29_H929 KO ctr, biological rep2

source_name: H929 p53 KO cells treated with PBS ctrl


title: 32_H929 KO HDP 101, biological rep2

source_name: H929 p53 KO cells treated with HDP 101


title: JT_Tax_P4_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1Tax_P2_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_Tax_P6_1

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_51


title: JT_Tax_P6_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_49


title: JT_Tax_P4_2

description: experiment: JQ1+paclitaxel in vitro


title: 28_H929 KO HDP 101, biological rep1


title: JT_Tax_P4_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_Tax_P2_3

description: experiment: JQ1+paclitaxel in vitro


title: 27_H929 KO AB alone, biological rep1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_48


title: carbon starvation in Aspergillus nidulans cultures

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

country: Hungary

institute: University of Debrecen

hyb_protocol: Fragmented cRNA samples (825 ng each) were applied to the individual arrays. The slides were placed in an Agilent hybridization oven and hybridized at 65 C and 10 r.p.m. for 17 h.

scan_protocol: Slides were scanned with an Agilent MicroArray Scanner.

data_processing: Intensities were extracted using Agilent’s Feature Extraction software (version 9.1). The log2 ratios of the pre-normalized data were normalized by local regression (LOESS) intensity-dependent blockby-block normalization using the SAS for Windows software.

organism: Aspergillus nidulans

source_name: cultures growing on glucose

label_protocol: Agilent’s Two-Colour Microarray-Based Gene Expression Analysis protocol (Version 5.7) using Cy3 and Cy5 cyanine dyes

growth_protocol: in Barratt’s minimal nitrate medium (either containing or not containing glucose) at 37 C and 3.7 Hz shaking frequency

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: culturing conditions

value: Minimal nitrate medium (100 ml) supplemented with 5 g/l yeast extract was inoculated with 5x10exp7 conidia and incubated for 20 h at 37 C and 3.7 Hz shaking frequency. Mycelia from these, exponential growth phase cultures were separated and were transferred into 100 ml minimal nitrate medium containing 10 g/l glucose. The starting dry cell masses were approximately 4 g/l. Cultures were cultivated at 37 C and 3.7 Hz shaking frequency and samples were taken at 4 h.

source_name: carbon starving cultures

value: Minimal nitrate medium (100 ml) supplemented with 5 g/l yeast extract was inoculated with 5x10exp7 conidia and incubated for 20 h at 37 C and 3.7 Hz shaking frequency. Mycelia from these, exponential growth phase cultures were separated and were transferred into 100 ml glucose-free minimal nitrate medium. The starting dry cell masses were approximately 4 g/l. Cultures were cultivated at 37 C and 3.7 Hz shaking frequency and samples were taken at 4 h.


title: JT_Tax_P2_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_52

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: JT_Tax_P2_1

description: experiment: JQ1+paclitaxel in vitro


title: 26_H929 KO NTC, biological rep1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_47


title: JT_JQ1_P14_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_46


title: 25_H929 KO ctr, biological rep1


title: JT_JQ1_P14_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P7_3

description: experiment: JQ1+paclitaxel in vitro


title: 24_H929 WT HDP 101, biological rep2

source_name: H929 p53 wt cells treated with HDP 101


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_45


title: JT_JQ1_P7_1

description: experiment: JQ1+paclitaxel in vitro

source_name: breast cancer cells SUM159


title: 23_H929 WT AB alone, biological rep2

source_name: H929 p53 wt cells treated with AB ALONE


title: JT_JQ1_P6_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P6_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P7_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P6_2

description: experiment: JQ1+paclitaxel in vitro


title: 22_H929 WT NTC, biological rep2

source_name: H929 p53 wt cells treated with NTC


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_43

source_name: L3 Drosophila eye-antennal disc


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_42


title: JT_JQ1_P4_3

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_44


title: 21_H929 WT ctr, biological rep2

source_name: H929 p53 wt cells treated with PBS ctrl


title: 20_H929 WT HDP 101, biological rep1


title: JT_JQ1_P4_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P2_3

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_41


title: JT_JQ1_P14_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P4_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P2_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_JQ1_P2_1

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_39


title: JT_DMSO_P14_3

description: experiment: JQ1+paclitaxel in vitro

value: DMSO


title: 19_H929 WT AB alone, biological rep1


title: JT_DMSO_P14_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_40


title: JT_DMSO_P14_1

description: experiment: JQ1+paclitaxel in vitro


title: 18_H929 WT NTC, biological rep1


title: JT_DMSO_P7_3

description: experiment: JQ1+paclitaxel in vitro


title: 17_H929 WT ctr, biological rep1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_38


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_36


title: JT_DMSO_P7_2

description: experiment: JQ1+paclitaxel in vitro


title: 16_MM.1S KO HDP 101, biological rep2

source_name: MM1.S p53 KO cells treated with HDP 101


title: 15_MM.1S KO AB alone, biological rep2

source_name: MM1.S p53 KO cells treated with AB ALONE


title: JT_DMSO_P7_1

description: experiment: JQ1+paclitaxel in vitro


title: JT_DMSO_P2_3

description: experiment: JQ1+paclitaxel in vitro


title: JT_DMSO_P2_1

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_37


title: JT_DMSO_P2_2

description: experiment: JQ1+paclitaxel in vitro


title: JT_DMSO_P1_2

description: experiment: JQ1+paclitaxel in vitro

value: passage 1


title: 14_MM.1S KO NTC, biological rep2

source_name: MM1.S p53 KO cells treated with NTC


title: JT_DMSO_P1_3

description: experiment: JQ1+paclitaxel in vitro


title: 778 R Tunicamycin 03/01/2014

city: Melbourne

first: David

last: Goode

state: Victoria

address: 305 Grattan Street

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing: RNA sequencing data consisted of 50bp paired-end reads generated from an Illumina HiSeq 2500 instrument (Illumina, CA, USA). Reads were mapped to hg19 (GRCh37.73) using HISAT2 v2.04 (62).  Transcript counts were obtained using HTSeq v0.6.1 (63) and the GENCODE v7 transcript models (64) from the Ensembl annotation database v62(65). Normalised values and log2 ratios relative to parental lines were obtained by using limma-voom v3.34.9.

source_name: Human well differentiated liposarcoma

growth_protocol: Untreated cells were cultured in  in RPMI 1640 Gibco supplemented with penicillin, streptomycin, L-glutamine and 10% fetal bovine serum

extract_protocol: Qiagen RNeasy midi kit

treatment_protocol: 94T778 cells were exposed to nutlin-3a 2.5µM, palbociclib 7µm and tunicamycin 0.14 µM. Cells were harvested during the early phase of the adaptive evolution in 94T778 cells exposed to palbociclib (P), nutlin-3a (N) and tunicamycin (T) sampled at 10 weeks for P and N and at 9 weeks post-bottleneck for T condition.

value: 94T778 cells

value: tunicamycin 0.14 uM


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_35


title: 13_MM.1S KO ctr, biological rep2

source_name: MM1.S p53 KO cells treated with PBS ctrl


title: JT_DMSO_P1_1

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_33


title: 12_MM.1S KO HDP 101, biological rep1


title: JT_Pre_1

description: experiment: JQ1+paclitaxel in vitro

value: pre-treatment

value: passage 0


title: JT_Pre_2

description: experiment: JQ1+paclitaxel in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_32


title: JP_JQ1Pal_P18_3

description: experiment: JQ1+palbociclib in vitro

value: passage 18


title: 11_MM.1S KO AB alone, biological rep1


title: 10_MM.1S KO NTC, biological rep1


title: 9_MM.1S KO ctr, biological rep1


title: JP_JQ1Pal_P11_3

description: experiment: JQ1+palbociclib in vitro

value: passage 11


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_31


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_30


title: JP_JQ1Pal_P7_1

description: experiment: JQ1+palbociclib in vitro

value: passage 7


title: JP_JQ1Pal_P6_3

description: experiment: JQ1+palbociclib in vitro


title: 8_MM.1S WT HDP 101, biological rep2

source_name: MM1.S p53 wt cells treated with HDP 101


title: 7_MM.1S AB alone, biological rep2

source_name: MM1.S p53 wt cells treated with AB ALONE


title: JP_JQ1Pal_P6_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1Pal_P4_2

description: experiment: JQ1+palbociclib in vitro

value: passage 4


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_34

value: F2-B(sens)-GFP [w;F2-B/CyO (ato-targeted intronic sens enhancer)]


title: JP_JQ1Pal_P6_2

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1Pal_P4_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_28


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_27


title: 6_MM.1S WT NTC, biological rep2

source_name: MM1.S p53 wt cells treated with NTC


title: JT_Pre_3

description: experiment: JQ1+paclitaxel in vitro


title: JP_JQ1Pal_P4_1

description: experiment: JQ1+palbociclib in vitro


title: 5_MM.1S WT ctr, biological rep2

source_name: MM1.S p53 wt cells treated with PBS ctrl


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_26


title: JP_JQ1Pal_P2_2

description: experiment: JQ1+palbociclib in vitro

value: passage 2


title: JP_JQ1Pal_P2_3

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1Pal_P18_2

description: experiment: JQ1+palbociclib in vitro


title: JT_Tax_P14_1

description: experiment: JQ1+paclitaxel in vitro

value: paclitaxel

value: passage 14


title: JP_JQ1Pal_P2_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1Pal_P11_2

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_25


title: JP_Pal_P18_3

description: experiment: JQ1+palbociclib in vitro

value: palbociclib


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_29


title: 1_MM1S WT HDP 101, biological rep1

value: Multiple Myeloma Cell Line


title: JP_Pal_P18_2

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_24

value: Single-cell ATAC-seq protocol with the Fluidigm C1 device as described by Buenrostro et al (2015)


title: JP_Pal_P18_1

description: experiment: JQ1+palbociclib in vitro


title: 1_MM1S WT AB ALONE, biological rep1


title: 1_MM1S WT NTC, biological rep1


title: JP_Pal_P11_2

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P11_1

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_22


title: 1_MM1S WT CTR, biological rep1


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_23


title: JP_Pal_P6_3

description: experiment: JQ1+palbociclib in vitro

value: passage 6


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_20


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_21


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_18


title: JP_Pal_P6_1

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_19


title: JP_Pal_P6_2

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P4_2

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P2_1

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P2_3

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P2_2

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P4_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_17


title: JP_JQ1_P18_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P18_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_16


title: JP_JQ1_P11_3

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P18_2

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_15


title: JP_Pal_P11_3

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P11_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P11_2

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P6_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_14


title: JP_JQ1_P6_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P4_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_12


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_13


title: JP_JQ1_P4_1

description: experiment: JQ1+palbociclib in vitro


title: JP_Pal_P4_1

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P6_2

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P2_3

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P4_2

description: experiment: JQ1+palbociclib in vitro


title: JP_JQ1_P2_1

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_10


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_11


title: JP_JQ1_P2_2

description: experiment: JQ1+palbociclib in vitro


title: JP_DMSO_P18_2

description: experiment: JQ1+palbociclib in vitro

value: DMSO


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_8


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_7


title: JP_DMSO_P11_3

description: experiment: JQ1+palbociclib in vitro


title: JP_DMSO_P18_3

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_9


title: JP_DMSO_P18_1

description: experiment: JQ1+palbociclib in vitro


title: JP_DMSO_P11_2

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_5


title: JP_DMSO_P11_1

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_4


title: T47D_Oesterreich_WT_clone2_E2_ATACseq

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 0.05 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Differential binding sites were identified by using DESeq2 to compare counts per million.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

source_name: mammary gland ductal carcinoma

growth_protocol: WT and mutant T-47D cells were grown in RPMI 1640 media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1% penicillin-streptomycin (Thermo Fisher Scientific) (full media). MCF-7 WT and mutant cells were grown in Minimum Essential Media (MEM, Thermo Fisher Scientific) with 5% fetal bovine serum, 1% penicillin-streptomycin, 1x final concentration non-essential amino acids (NEAA, Thermo Fisher Scientific), and 1nM final concentration insulin (Sigma-Aldrich) (full media). Cells were grown at 37°C with 5% CO2. Five days before all experiments requiring a 17beta-estradiol (E2) induction, cells were placed in hormone-depleted media. Hormone-depleted media consisted of phenol-red free MEM (Thermo Fisher Scientific), 5% charcoal-stripped fetal bovine serum (Thermo Fisher Scientific), 1% penicillin-streptomycin, and NEAA and insulin as described above for MCF-7 cells and phenol-red free RPMI (Thermo Fisher Scientific), 10% charcoal-stripped fetal bovine serum, and 1% penicillin-streptomycin for T-47D cells. Hormone-depleted media was changed twice during each 5-day estrogen-deprivation period in order to ensure complete removal of estrogens from the media.

extract_protocol:
For each of the clones, approximately 250,000 cells were lysed and nuclei were harvested for transposition as described previously (Buenrostro et al., 2013). Tn5 transposase with Illumina adapters was assembled as previously described (Picelli et al., 2014).
ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013).

treatment_protocol: After 5 days of estrogen deprivation, cells were treated with 0.1% DMSO as a vehicle control (Fisher Scientific) or 10nM E2 (Sigma-Aldrich) for 1 hour.

tag: parental cell line

tag: esr1 genotype

value: WT

value: 10 nM E2 1hr

tag: lab of origin

value: Oesterreich


title: T47D_Oesterreich_Y537S_clone1_E2_ATACseq


title: T47D_Oesterreich_D538G_clone2_E2_ATACseq


title: T47D_Oesterreich_Y537S_clone2_E2_ATACseq


title: T47D_Oesterreich_D538G_clone3_E2_ATACseq


title: T47D_Oesterreich_D538G_clone1_E2_ATACseq


title: JP_DMSO_P6_3

description: experiment: JQ1+palbociclib in vitro


title: T47D_Oesterreich_WT_clone1_E2_ATACseq


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_3

data_processing:
ATAC-seq reads were first cleaned for adapters using fastq-mcf. (ea-utils v1.12) and a list of sequencing primers. Cleaned reads (FastQC v0.1) were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using Bowtie2 (v2.2.5) with default parameters, and sorted bam files were produced using using SAMtools (v1.2). The data was deduplicated using picard MarkDuplicates.
Aggregation plots were produced using in-house scripts available at: https://github.com/aertslab/ATAC-seq-analysis, and cells well filtered manually based on the aggregation plot profiles, resulting in 72 and sens-GFP+ single cell ATAC-seq profiles. Single-cell profiles were aggregated using samtools merge. Normalized bigwigs were generated using the Kent software (UCSC). Some of the cells were filtered out based on aggregation plots, so they werent use for the analysis (before counting fragments in the regions).
Downstream analysis was done using cisTopic (v0.2.2)
Genome_build: dm6
Supplementary_files_format_and_content: There are two processed data files: a tab-delimited file containing cell names as columns, ctx regions as rows, and number of fragments as values, and a bigwig file containing the normalized coverage profiles of the aggregated sens-GFP+ cells.

extract_protocol:
Wandering third instar larvae were collected and a total of 200 eye-antennal discs were dissected in ice-cold PBS and placed in SF900 medium. For dissociation, the tissue was placed in 400 µl of trypsin in 0.05% EDTA. The eye–antennal discs were then incubated at 37 °C for 1 h with agitation; being mixed every 20 min with a pipette. After dissociation, cells were centrifuged at 800 g for 5 min at 4 °C and washed with PBS. Finally, the cells were resuspended in 400 µl of PBS, filtered using a 40 µm cell strainer and stained with propidium iodide (PI; final concentration 1 µg/ml) to exclude dead cells. The cells were sorted on a BD Aria I, selecting against the presence of PI and for the presence of GFP.
For single-cell ATAC–seq, as many cells as possible were sorted into a microcentrifuge tube, pelleted by centrifugation at 800 g for 5 min at 4 °C and resuspended at a concentration of 1,000 cells/µl. Single-cell ATAC–seq was performed as previously described12,81, using 5- to 10-µm Open App integrated fluidic circuits (IFCs) on the Fluidigm C1 and with no cell washing step. Briefly, cells were loaded (using a 40:60 ratio of RGT:cells) on a primed Open App IFC (5-10 µm, the protocol for ATAC-seq from the C1 Script Hub was used). After cell loading, the plate was visually checked under a microscope and the number of cells in each of the capture chambers was noted. Next, the sample preparation was performed on the Fluidigm C1 during which the cells underwent lysis and ATAC-seq fragments were prepared. In a 96-well plate, the harvested libraries were amplified in a 25 µl PCR reaction. The PCR products were pooled and purified on a single MinElute PCR purification column for a final library volume of 15 µl. Quality checks were performed using the Bioanalyzer high sensitivity chips. Fragments under 150 bp were removed by bead-cleanup using AMPure XP beads (1.2x bead ratio) (Beckman Coulter).
Single-cell ATAC-seq (Fluidigm C1)


title: JP_DMSO_P6_2

description: experiment: JQ1+palbociclib in vitro


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_6


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_2


title: T47D_Oesterreich_D538G_clone3_DMSO_ATACseq

value: 0.1% DMSO 1hr


title: T47D_Oesterreich_D538G_clone2_DMSO_ATACseq


title: FLUIDIGMC1_SCATACSEQ_SENS-GFP_CELL_1


title: T47D_Oesterreich_D538G_clone1_DMSO_ATACseq


title: JP_DMSO_P4_3

description: experiment: JQ1+palbociclib in vitro


title: Colon organ explant, Salmonella_20

city: Saint Paul

first: Matheus

last: Costa

address: 1988 Fitch avenue

institute: University of Minnesota

data_processing:
GenPipes (https://doi.org/10.1093/gigascience/giz037)
Star
Cuffdiff
DeSEq2
Genome_build: SSc 10.2
Supplementary_files_format_and_content: Raw read counts csv table

organism: Sus scrofa

source_name: Colon organ explant

growth_protocol: Salmonella cultured using LB broth - 37C for 2h30min.

extract_protocol:
Rneasy Qiagen total RNA extraction kit
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: subject

value: Pig 20

tag: in vivo antibiotic group

value: Placebo

tag: in vitro inoculum group

value: Salmonella e. Typhimurirum

value: colon explant


title: Colon organ explant, Control_20

value: PBS


title: T47D_Oesterreich_Y537S_clone2_DMSO_ATACseq


title: JP_DMSO_P4_1

description: experiment: JQ1+palbociclib in vitro

value: passage 4

tag: replicate


title: JP_DMSO_P4_2

description: experiment: JQ1+palbociclib in vitro

tag: cell line


title: T47D_Oesterreich_Y537S_clone1_DMSO_ATACseq

tag: treatment


title: JP_DMSO_P2_3

description: experiment: JQ1+palbociclib in vitro

value: passage 2


title: DGRP-55030

data_processing:
Adapter sequences were trimmed from the raw reads using fastq-mcf (ea-utils v1.1.2, with default parameters and using a list containing the common Illumina adapters) and the quality of the cleaned reads was checked with FastQC (v0.1). All experiments were mapped using Bowtie2 (v2.2.5) to their personalized version on 3rd 2017 FlyBase release (D. melanogaster r6.16) genome. Briefly, called variants in this genome assembly were retrieved from ftp://ftp.hgsc.bcm.edu/DGRP/freeze2_Feb_2013/liftover_data_for_D.mel6.0_from_William_Gilks_Oct_2015/ and for each of the 50 DGRP lines we adapted the consensus genome (r6.16) using seqtk mutfa (seqtk (v1.0)), each time including their SNPs (previously called from whole genome sequencing). After the first mapping round, additional SNPs were called on the ATAC reads using SAMtools (v1.2), with the command samtools mpileup -B –f r6.16.fasta DGRP_lineX.bam | varscan.sh mpileup2snp --output-vcf 1. Newly called homozygous SNPs (several thousands per line) were added to the existing vcf files using VCFtools (v0.1.14). The genomes were again updated to obtain a final personalized genome for every DGRP line, strongly reducing mapping errors and increasing the sensitivity of subsequent analyses. Cleaned reads were mapped onto the final genomes using Bowtie2 (v2.2.5) again and SAMtools (v1.2) was used for sorting and indexing.
Peaks were called on the mapped reads using MACS2 (v2.1.2.1), with the command macs2 callpeak -g dm –nomodel–keep-dup all –call-summits. The narrow peak files (bed format) for all the DGRP lines were merged into a single file that contained a total of 39,879 regions accessible in at least one DGRP line. After filtering out chrU, chrUextra, chrHet and chrM regions and removing regions enriched in repeats (>25% of the sequence) using bedtools (v2.28.0) with the command intersectBed -v -f 0.25, we obtained 38,179 accessible regions across this DGRP panel. For every ATAC-seq sample we counted the number of reads falling into each accessible region using featureCounts (Subread v2.0.0). Normalized bigwig files were generated using the Kent software from UCSC.
Genome_build: dm6
Supplementary_files_format_and_content: There are two types of processed data files: a tab-delimited file containing cell names as columns, bulk called regions as rows, and normalized number of fragments as values, and bigwig files containing the normalized coverage profiles of each DGRP line.

extract_protocol:
For the DGRP panel samples, ~10 eye-antennal discs were dissected and lysed in 50 µl ice-cold ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630). Lysed discs were then centrifuged at 800 g for 10 minutes at 4°C and the supernatant was discarded.
The rest of the ATAC-seq protocol was performed as described previously, using the following primers: Fwd:- ‘AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG’ and Rev:- ‘CAAGCAGAAGACGGCATACGAGATXXXXXXGTCTCGTGGGCTCGGAGATGT’ (where X indicates barcode nucleotides). The final library was purified using a Qiagen MinElute kit (Qiagen) and Ampure XP beads (Ampure) (1:1.2 ratio) were used to remove remaining adapters. The final library was first checked on an Agilent Bioanalyzer 2000 for the average fragment size. Resulting successful libraries were sequenced with 50bp, single end reads on the Illumina HiSeq 2000 platform. ATAC-seq (Buenrostro et al., 2013)

tag: strain

value: ATAC-seq protocol


title: DGRP-55018

tag: sequencing method


title: Colon organ explant, Control_19

value: Pig 19

value: Amoxicillin


title: JP_DMSO_P2_2

description: experiment: JQ1+palbociclib in vitro


title: Colon organ explant, Control_18

value: Pig 18


title: T47D_Oesterreich_WT_clone1_DMSO_ATACseq


title: JP_DMSO_P2_1

description: experiment: JQ1+palbociclib in vitro


title: DGRP-55015


title: JP_DMSO_P6_1

description: experiment: JQ1+palbociclib in vitro

value: passage 6


title: T47D_D538G_clone2_E2_ATACseq

value: Gertz


title: T47D_Oesterreich_WT_clone2_DMSO_ATACseq

value: WT


title: DGRP-29658


title: Colon organ explant, Salmonella_17

value: Pig 17


title: DGRP-29652


title: DGRP-28250


title: T47D_D538G_clone1_E2_ATACseq

value: 10 nM E2 1hr


title: DGRP-28239


title: Colon organ explant, Salmonella_19


title: DGRP-55028


title: Colon organ explant, Salmonella_16

value: Pig 16


title: T47D_Y537S_clone1_E2_ATACseq


title: T47D_Y537S_clone2_E2_ATACseq


title: DGRP-28238


title: Colon organ explant, Salmonella_18


title: JP_Pre_1

description: experiment: JQ1+palbociclib in vitro

value: pre-treatment

value: passage 0


title: DGRP-28235


title: Colon organ explant, Control_16

value: Placebo


title: Colon organ explant, Salmonella_15

value: Pig 15

value: Salmonella e. Typhimurirum

value: colon explant


title: JQ1Tax-2wk_2

description: experiment: JQ1+paclitaxel in vivo

value: 2 wk


title: JQ1Tax-2wk_5

description: experiment: JQ1+paclitaxel in vivo


title: JQ1Tax-2wk_1

description: experiment: JQ1+paclitaxel in vivo


title: JP_Pre_3

description: experiment: JQ1+palbociclib in vitro


title: DGRP-28233

value: ATAC-seq protocol


title: JP_Pre_2

description: experiment: JQ1+palbociclib in vitro


title: DGRP-28229


title: DGRP-28212


title: Colon organ explant, Control_14

value: Pig 14

value: PBS


title: Colon organ explant, Salmonella_14


title: T47D_WT_clone1_E2_ATACseq


title: Colon organ explant, Control_17

value: Amoxicillin


title: T47D_D538G_clone2_DMSO_ATACseq

value: 0.1% DMSO 1hr


title: DGRP-28198


title: T47D_Y537S_clone2_DMSO_ATACseq

value: Gertz


title: Tax_2wk_3

description: experiment: JQ1+paclitaxel in vivo

value: paclitaxel


title: T47D_D538G_clone1_DMSO_ATACseq


title: T47D_WT_clone2_E2_ATACseq

value: WT


title: Tax_2wk_2

description: experiment: JQ1+paclitaxel in vivo


title: DGRP-28189


title: T47D_WT_clone2_DMSO_ATACseq


title: Colon organ explant, Control_13

value: Pig 13


title: Colon organ explant, Control_15


title: T47D_Y537S_clone1_DMSO_ATACseq


title: Tax_2wk_5

description: experiment: JQ1+paclitaxel in vivo


title: Colon organ explant, Salmonella_12

value: Pig 12


title: Tax_2wk_1

description: experiment: JQ1+paclitaxel in vivo


title: JQ1Tax-2wk_3

description: experiment: JQ1+paclitaxel in vivo


title: T47D_WT_clone1_DMSO_ATACseq


title: JQ1-2wk_3

description: experiment: JQ1+paclitaxel in vivo


title: JQ1-2wk_5

description: experiment: JQ1+paclitaxel in vivo


title: Colon organ explant, Salmonella_11

value: Pig 11


title: JQ1-2wk_2

description: experiment: JQ1+paclitaxel in vivo


title: DGRP-28185


title: MCF7_WT_input_ChIPseq

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 1*10-10 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Differential binding sites were identified by using DESeq2 to compare counts per million.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

source_name: mammary gland adenocarcinoma

extract_protocol:
Fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors.
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with either Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1, Anti-CTCF (sc-5916, Santa Cruz Biotechnology), or Anti-OCT1 (A301-716A and A301-717A, Bethyl Laboratories Inc.) antibodies.

tag: chip antibody


title: DGRP-28194


title: JQ1-2wk_1

description: experiment: JQ1+paclitaxel in vivo

source_name: breast cancer cells SUM159


title: MCF7_D538G_input_ChIPseq


title: DGRP-28141


title: Colon organ explant, Control_12

tag: tissue


title: DGRP-28176


title: Veh_2wk_5

description: experiment: JQ1+paclitaxel in vivo

value: vehicle

tag: time point


title: MCF7_Y537S_input_ChIPseq


title: Colon organ explant, Salmonella_13


title: DGRP-28177


title: Colon organ explant, Control_11


title: Colon organ explant, Salmonella_10

value: Pig 10

value: Placebo


title: T47D_D538G_clone1_CTCF_ChIPseq

value: Anti-CTCF


title: T47D_input_ChIPseq


title: DGRP-28140


title: T47D_Y537S_clone1_CTCF_ChIPseq


title: Veh_2wk_3

description: experiment: JQ1+paclitaxel in vivo


title: Veh_2wk_1

description: experiment: JQ1+paclitaxel in vivo


title: DGRP-28129


title: DGRP-28138


title: Colon organ explant, Control_8

value: Pig 8

value: colon explant


title: JQ1Tax-1wk_5

description: experiment: JQ1+paclitaxel in vivo

value: 1 wk


title: T47D_D538G_clone2_OCT1_ChIPseq


title: T47D_D538G_clone1_OCT1_ChIPseq


title: DGRP-28136

value: ATAC-seq protocol


title: Colon organ explant, Salmonella_9

value: Pig 9

value: Salmonella e. Typhimurirum


title: Veh_2wk_2

description: experiment: JQ1+paclitaxel in vivo

value: 2 wk


title: T47D_Y537S_clone2_OCT1_ChIPseq


title: DGRP-25194


title: Colon organ explant, Salmonella_8


title: JQ1Tax-1wk_2

description: experiment: JQ1+paclitaxel in vivo


title: JQ1Tax-1wk_1

description: experiment: JQ1+paclitaxel in vivo


title: DGRP-25191


title: Colon organ explant, Control_9

value: Amoxicillin

value: PBS


title: Tax_1wk_5

description: experiment: JQ1+paclitaxel in vivo

value: paclitaxel


title: DGRP-25201


title: DGRP-25198


title: Tax_1wk_3

description: experiment: JQ1+paclitaxel in vivo


title: Colon organ explant, Salmonella_5

value: Pig 5


title: MCF7_D538G_clone2_E2_ChIPseq

value: 10 nM E2 1hr

value: Anti-FLAG


title: LIC-Hi-C-3

city: Shenzhen

first: Qing

last: Li

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

data_processing:
Reads were quality filtered according to the Illumina pipeline
The reads mapping and filtering procedures of LIC-Hi-C-1, LIC-Hi-C-2, LIC-Hi-C-3,GSM1718027 were performed by HiCUP (v0.5.9).
The reads mapping and filtering procedures of Exo-Hi-C,GSM862720,GSM862721 were performed by HiC-Pro (v2.10.0).
.hic file was generated by Juicebox command  line tool and displayed in Juicebox.
Genome_build: mm9
Supplementary_files_format_and_content: The archive *_HiCUP_summary_report.txt contains the report of HiCUP. *_allValidPairs.hic, a highly compressed binary file that provides rapid random access to the matrices.Statistics about read pairs filtering are available in *.mRSstat.txt. *_allValidPairs.mergestat.txt contains the fraction of dplicates and the fraction of intra and inter-chromosomal interactions.

growth_protocol: For mouse E14 embryonic stem cells (ATCC® CRL-1821™), they were cultured under the specific condition (KO-DMEM complete medium) in KO-DMEM (Invitrogen Life Technologies, 10829-018) supplemented with 15% fetal bovine serum (FBS, Invitrogen Life Technologies, 10099-141), 1% penicillin/streptomycin (GIBCO, 15140), 1% MEM nonessential amino acids (NEAA) (Invitrogen Life Technologies,  11140-122), 1% 2-Mercaptoethanol (BME) (Sigma, M-7522), 1% GlutaMAXTM (GIBCO, 35050061), 1‰ Vitamin C (L-ascorbicacid 2-phosphate, Sigma, A8960), 1 ‱ LIF (Chemicon, ESG-1107), 1 ‱ PD0325901 (Selleck), 3 ‱ CHIR-99021 (Selleck). Before the cells were thawed or passaged, firstly, 37°C warmed 0.1% gelatin was covered the bottom of the dish. Then, gelatin solution was removed and 0.5 million cells per 60 mm dish were seeded in the KO-DMEM complete medium. In subculture, the cell colony morphology, density, and size were initially observed. If average distribution of colonies were in size of 200–400 μm in diameter and space was around 400 μm apart in a 60-mm dish, the ESC cells would be split. After the cell clones were washed with 1 x DPBS (Invitrogen Life Technologies, 14190-144), the digestive enzyme Accutase (Invitrogen Life Technologies, A1110501) instead of trypsin was used.

extract_protocol:
Confluence of the cell should be around (80-90%).  Add HCHO to 1% the plate (280ul 37% HCHO to 10 ml medium) and incubate at 37°C for 10 min; Stop the cross linking by adding 0.89 ml 2.5M glycine to medium (final concentration 0.2M) at RT for 5 mins, aspirate the medium. Wash the cells twice with 10 ml of 1xPBS.Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the plate once with 0.5% BSA/PBS. Combine the cells from the plates. Spin down the cells at 500-1000g, 5 min, 4℃.
Following the proximity-ligation and linear noise elimination(exonuclease combination treatment), the chromosome conformation capture library was used for sonication and immunomagnetic interaction capturing of biotin labeled joint DNA. Hi-C library was submitting for next-generation sequencing.

treatment_protocol: MEFs were isolated from E13.5 embryos carrying the Oct4-GFP transgene. “Flag/Jmjd3 treating day3” means MEFs transduced with the virus of Flag/Jmjd3 and OSKM, after cultured in mES medium including Vc for 3 days, cells were cross-linked with 2% formaldehyde for 10 min at room temperature and quenched by glycine at a final concentration of 0.125 M. Then, they were conducted with Hi-C library construction.

tag: cell type

value: Induced pluripotent stem cell

value: Flag treating day3 (MEF--derived)

tag: Stage

value: 3 day


title: Exo-Hi-C (LRC-Hi-C-1)

source_name: mESC E14

value: Mouse embryonic stem cell

value: Wild type

value: 0 day


title: Tax_1wk_2

description: experiment: JQ1+paclitaxel in vivo

value: 1 wk


title: Colon organ explant, Control_5

value: colon explant


title: JQ1Tax-1wk_3

description: experiment: JQ1+paclitaxel in vivo


title: Colon organ explant, Salmonella_7

value: Pig 7


title: Colon organ explant, Control_10

value: Pig 10

value: Placebo


title: Colon organ explant, Control_7

value: Amoxicillin


title: T47D_Y537S_clone1_OCT1_ChIPseq


title: MCF7_Y537S_clone1_E2_ChIPseq


title: T47D_WT_clone1_OCT1_ChIPseq

value: WT


title: Colon organ explant, Salmonella_6

value: Pig 6

value: Salmonella e. Typhimurirum


title: T47D_WT_clone1_CTCF_ChIPseq

value: Anti-CTCF


title: Colon organ explant, Control_6

value: PBS


title: DGRP-25189

value: ATAC-seq protocol


title: Tax_1wk_1

description: experiment: JQ1+paclitaxel in vivo

value: paclitaxel


title: Colon organ explant, Salmonella_4

value: Pig 4


title: MCF7_Y537S_clone2_E2_ChIPseq

value: 10 nM E2 1hr

value: Anti-FLAG


title: JQ1-1wk_5

description: experiment: JQ1+paclitaxel in vivo


title: LIC-Hi-C-1

source_name: MEF

value: Mouse embryonic fibroblast

value: Wild type

value: 0 day


title: JQ1-1wk_2

description: experiment: JQ1+paclitaxel in vivo

value: 1 wk


title: Colon organ explant, Salmonella_2

value: Pig 2

value: colon explant


title: in situ Hi-C 12

data_processing:
Reads were quality filtered according to the Illumina pipeline
The reads mapping and filtering procedures were performed by HiC-Pro (v2.10.0).
Genome_build: mm9

value: Mouse embryonic stem cell


title: Colon organ explant, Control_4

value: Amoxicillin


title: T47D_WT_clone2_OCT1_ChIPseq

value: WT


title: MCF7_D538G_clone1_DMSO_ChIPseq

value: 0.1% DMSO 1hr


title: in situ Hi-C 14


title: LIC-Hi-C-2

value: Induced pluripotent stem cell

value: Jmjd3 treating day3 (MEF--derived)

value: 3 day


title: MCF7_D538G_clone1_E2_ChIPseq


title: in situ Hi-C 13


title: Colon organ explant, Control_3

value: Pig 3

value: Placebo

value: PBS


title: MCF7_WT_clone1_E2_ChIPseq

value: 10 nM E2 1hr

value: Anti-FLAG


title: MCF7_Y537S_clone2_DMSO_ChIPseq


title: JQ1-1wk_3

description: experiment: JQ1+paclitaxel in vivo


title: Veh_1wk_2

description: experiment: JQ1+paclitaxel in vivo

value: vehicle


title: JQ1-1wk_1

description: experiment: JQ1+paclitaxel in vivo


title: LIC-in situ Hi-C 11

value: Wild type

value: 0 day


title: Veh_1wk_1

description: experiment: JQ1+paclitaxel in vivo

value: 1 wk


title: Veh_1wk_5

description: experiment: JQ1+paclitaxel in vivo


title: MCF7_D538G_clone2_DMSO_ChIPseq


title: MCF7_WT_clone2_E2_ChIPseq


title: MCF7_Y537S_clone1_DMSO_ChIPseq


title: IIIIC-in situ Hi-C 10


title: Colon organ explant, Salmonella_1

value: Pig 1

value: Salmonella e. Typhimurirum

value: colon explant


title: LIC-in situ Hi-C 10

value: Mouse embryonic stem cell


title: Pre_0wk_4

description: experiment: JQ1+paclitaxel in vivo

value: pre-treatment

value: 0 wk


title: Colon organ explant, Control_2

value: Pig 2


title: Veh_1wk_3

description: experiment: JQ1+paclitaxel in vivo


title: MCF7_WT_clone1_DMSO_ChIPseq

value: WT

value: 0.1% DMSO 1hr


title: Colon organ explant, Salmonella_3

value: Pig 3

value: Placebo


title: IIIIC-in situ Hi-C 12


title: Colon organ explant, Control_1

value: Amoxicillin

value: PBS


title: Pre_0wk_3

description: experiment: JQ1+paclitaxel in vivo


title: BI16_66

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1, F. acuminatum GGXD00000000, R. stolonifer GGWM00000000
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Solanum lycopersicum

extract_protocol:
At 1 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, wounded, and infected fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as single-end 50-bp reads on an Illumina HiSeq 4000 platform by the DNA Technologies Core at the UC Davis Genome Center.

tag: genotype

value: rin

tag: ripening stage

value: RR-like

value: Wounded


title: in situ Hi-C 2

data_processing:
Reads were quality filtered according to the Illumina pipeline
The reads mapping and filtering procedures were performed by HiC-Pro (v2.10.0) or HiCUP (v0.5.9).
Genome_build: mm9
Supplementary_files_format_and_content: The *_allValidPairs.txt file cotains uniquely mapped and non-redundent valid interactions. HiCPro_statics.xlsx cotains the mapping results and the noises distribution of different Hi-C libraries

extract_protocol:
Confluence of the cell should be around (80-90%).  Add HCHO to 1% the plate (280ul 37% HCHO to 10 ml medium) and incubate at 37°C for 10 min; Stop the cross linking by adding 0.89 ml 2.5M glycine to medium (final concentration 0.2M) at RT for 5 mins, aspirate the medium. Wash the cells twice with 10 ml of 1xPBS.Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the plate once with 0.5% BSA/PBS. Combine the cells from the plates. Spin down the cells at 500-1000g, 5 min, 4℃.
Following the proximity-ligation and linear noise elimination(exonuclease combination treatment), the chromosome conformation capture library was used for sonication and immunomagnetic interaction capturing of biotin labeled joint DNA. Hi-C library was submitting for next-generation sequencing.
Dilution Hi-C and in situ Hi-C

value: Wild type

value: 0 day


title: IIIIC-in situ Hi-C 11


title: BI16_114

value: fruit pericarp and epidermal tissue of the blossom end halves


title: MCF7_WT_clone2_DMSO_ChIPseq

tag: parental cell line

tag: esr1 genotype

value: Anti-FLAG


title: BI16_90


title: in situ Hi-C 3

value: Mouse embryonic stem cell


title: BI16_42