title: P1470

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R02C01

value: Affected


title: 2-080-2-3_S139

status: Public on Apr 01 2020

type: SRA

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

library_source: transcriptomic

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

molecule: total RNA

organism: Homo sapiens

source_name: adipose tisue

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID3

tag: individual


title: 2-080-2-1b_S65

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN116 microRNA

type: RNA

city: Memphis

first: Jeremiah

middle: Ray

last: Holt

state: TN

address: 19 S. Manassas, Room 202

department: Medicine

country: USA

institute: UTHSC

hyb_protocol: Biotin-labeled RNA was hybridized to the Affymetrix GeneChip miRNA-1_0 array overnight at 48℃.

scan_protocol: After hybridization and wash, the arrays were scanned with the GeneChip Scanner 3000

data_processing:
Probe-level intensity files were evaluated for quality using the ‘affy’ R package to process the raw CEL files. PM intensities were log2 transformed and then normalized using the 'affy' expresso() function, and batch effects were corrected for using the ComBat() function in the 'sva' package in R.
Log2 transformed and quantile normalized RMA expression values.

label: biotin

label_protocol: One microgram total RNA was labeled with FlashTaq RNA labeling kit from Genisphere (Genisphere Inc. Hatfield, PA), and then poly-(A) tailing was added to RNA, before ligating a biotinylated signal molecule to the target RNA sample

growth_protocol: not applicable

extract_protocol: RNA was extracted using TRIzol from Invitrogen and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: not applicable

tag: tissue

value: Tumor

tag: age

tag: race

value: Black or African American

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: light or moderate

tag: differentiation

value: Well Differentiated

tag: tumor site

tag: Stage

value: not available

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: negative


title: P1367

type: genomic

city: Bethesda

first: Ariel

middle: Fernando

last: Martinez

state: MD

address: 35 Convent Drive, Room 1B209

institute: National Institutes of Health

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R04C01

hyb_protocol: According to the Infinium HD Assay Ultra protocol

data_processing:
BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
The supplementary file on the series record contains the columns Genotype: AA,AB,BB,or NC (no call), Score, Theta, R, B Allele Freq, Log R Ratio, X Raw and Y Raw for each sample.  There is also a separate file with raw data only. Sample ID can be found in the 'description' field.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Blood

label_protocol: 200ng of genomic DNA were processed following the Infinium HD Assay Ultra protocol

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAGEN's QIAamp DNA Blood Maxi kit (cat No 51194)

value: Blood

value: M

tag: adhd affection status


title: P1049

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R01C01

scan_protocol: According to the Infinium HD Assay Ultra protocol

value: Unaffected


title: 2-079-2-2_S65

value: baseline, cid2 :lcd, cid3 :di):CID2


title: BlastCellhighDXRA3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.13.
FPKM was generated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

organism: Mus musculus

extract_protocol:
1,000 cells per sample were sorted into 96-well plates with 7 ul lysis buffer containing RNase inhibitor (2 U/μl) from BM. First-strand cDNA synthesis and cDNA libraries were constructed using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech) following the manufacturer’s instructions. cDNA quality was determined by Agilent high sensitivity DNA kit on Agilent 2100 BioAnalyzer (Agilent Technologies).
RNA-seq libraries were prepared using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech Nextera)

tag: genotype

value: Bone Marrow

tag: cell type

value: BlastCell

value: Clinical DXR


title: 2-079-2-1_S21

tag: cid (cid1

tag: individual


title: BlastCellhighDXRA2

tag: tissue


title: P1028

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R06C02

value: Affected


title: 2-085-1-1_S219

value: baseline, cid2 :lcd, cid3 :di):CID1


title: BlastCellhighDXRA1


title: P1395

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R05C02


title: Head and neck squamous cell carcinoma HN114 microRNA

value: Tumor

tag: age

tag: race

value: Moderately Differentiated

value: Hypopharynx

value: Concurrent Chemoradiation


title: 2-079-2-1_S117


title: BlastCellhighDXRB1


title: P1841

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R04C02

tag: gender


title: BlastCellChemoB3

source_name: BlastCellChemo

value: Chemotherapy


title: BlastCellChemoB2


title: Head and neck squamous cell carcinoma HN112 microRNA

value: White

value: Male

tag: smoking packyears

tag: alcohol use

value: light or moderate

value: Larynx

value: IVA

value: not available


title: Head and neck squamous cell carcinoma HN115 microRNA

value: Black or African American

tag: differentiation

tag: tumor site

value: negative


title: P1592

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744150_R03C01

value: Blood

value: M

value: Unaffected


title: 2-078-2-3_S179

value: baseline, cid2 :lcd, cid3 :di):CID3


title: Head and neck squamous cell carcinoma HN105 microRNA

value: Tumor

tag: Stage

tag: tumor status

value: Surgery and Radiation


title: P1543

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R03C02

value: F

value: Affected


title: P1420

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R02C02


title: Head and neck squamous cell carcinoma HN109 microRNA

value: Well Differentiated

tag: node status

tag: treatment

value: Surgery and Concurrent Chemoradiation

value: HPV+ (type unknown, not 16 or 18)


title: Head and neck squamous cell carcinoma HN108 microRNA

value: White

value: Female

value: light or moderate

value: Poorly Differentiated

value: Oropharynx

value: Concurrent Chemoradiation

tag: hpv status


title: BlastCellChemoB1

tag: genotype

value: Bone Marrow

value: BlastCell

value: Chemotherapy


title: P1427

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R01C02

value: Blood

tag: adhd affection status

value: Unaffected


title: BlastCellChemoA3

tag: cell type


title: Head and neck squamous cell carcinoma HN098 microRNA

value: Tumor

value: Male

value: heavy use > 6 months ago

value: Moderately Differentiated

value: Larynx

value: III

value: negative


title: 2-078-2-2_S28

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: P1015

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R06C01

tag: tissue

value: M


title: Head and neck squamous cell carcinoma HN095 microRNA

tag: age

tag: race

value: White

value: light or moderate

value: Poorly Differentiated

value: IVA

value: Surgery Alone

value: positive


title: P1032

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R05C01

value: Blood

tag: gender


title: 2-077-2-2_S176


title: P1575

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R04C01

value: F

value: Affected


title: 2-077-2-1_S141

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-077-2-3_S56

value: baseline, cid2 :lcd, cid3 :di):CID3


title: BlastCellChemoA1

value: Bone Marrow

value: BlastCell

value: Chemotherapy


title: Head and neck squamous cell carcinoma HN094 microRNA

value: Tumor

value: Male

tag: smoking packyears

tag: alcohol use

value: heavy use currently:>3 drinks per day

value: Moderately Differentiated

value: Oropharynx

value: not available

value: Surgery and Concurrent Chemoradiation


title: LC2

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

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

country: United Kingdom

institute: Newcastle University

data_processing:
trimmd with Trimmomatic v 0.36
aligned with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 50bp were dropped
counts obtained with HTSEQ v 0.6.1
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files containg HTSEQ counts

source_name: skin LCs emigrated from epidermis

growth_protocol:
migrated from epidermal sections by incubation at 37°C for 72 hours in RF10 Media (RPMI+10%FCS)
3 days culture with GM-CSF and TGF-B on OP9-DLL4 feeder layer in RF10 Media (RPMI+10%FCS)

extract_protocol:
Flow Cytometric Sorting
Nextera XT

tag: source

value: skin


title: 2-077-1-2_S100

value: baseline, cid2 :lcd, cid3 :di):CID2


title: Head and neck squamous cell carcinoma HN089 microRNA

value: White

value: Female

tag: differentiation

value: Poorly Differentiated

tag: tumor site

value: Larynx

tag: Stage

value: III

value: negative


title: LC1


title: P1270

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R03C01

value: Blood

value: M

value: Unaffected


title: 2-078-2-1_S146

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-077-1-1_S160


title: P1675

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R01C01


title: Head and neck squamous cell carcinoma HN087 microRNA

value: Tumor

value: Male

value: light or moderate

value: IVC

tag: tumor status

tag: node status

tag: treatment

value: Concurrent Chemoradiation


title: BlastCellChemoA2

tag: genotype

value: Bone Marrow

value: BlastCell

value: Chemotherapy


title: MCF7_siKAP1_RPB3_Rep1_ChIPSeq

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

description: An antibody specific to Drosophilla H2Av (Active Motif, 61686) and Drosophilla chromatin  (Active Motif, 53083) was added to each sample for normalization.

library_source: genomic

data_processing:
Quality of reads from all experiments was determined with FASTQC v0.11.2 using default parameters.
ChIP-seq: Reads were aligned to hg38 with Bowtie2 v2.3.2 with the --very-sensitive flag. SAM files were converted to BAM and sorted by chromosome with samtools v1.6. The view command with the -q flag set to 25 was used to filter out low quality reads. The sort command was used to convert SAM to BAM and sort by chromosome. Duplicates marked and removed with picard v1.127. Drosophilla spike-in chromatin was aligned to dm6 as described above for hg38. BAM files were generated and de-duplicated as described above for hg38 aligned reads. Drosophilla normalization factors were generated by dividing the Drosophilla read counts from each sample to the sample containing the least read counts. BedGraph tracks were generated with MACS2 v2.1.0 and normalized to Drosophilla spike-in normalization factors. BedGraph then converted to BigWig using bedGraphtoBigWig.
4sU-/RNA-seq: Reads were aligned to hg38 with STAR/2.5.2b. Sorted by coordinate BAM files were created by STAR with the âoutSAMtype BAM flag. RPM normalized bedgraph files were also generated using STAR with the âoutWigType bedGraph and âoutWigNorm RPM flags. ERCC spike-ins were similarly aligned to an ERCC fasta file. Reads for protein coding genes were counted using the Gencode v27 annotation and featureCounts. Differential expression analysis was performed using RUVseq v1.14.0 R package.
Genome_build: hg38 and dm6
Supplementary_files_format_and_content: ChIP-seq: BigWig track files containing Drosophilla normalized aligned read densities
Supplementary_files_format_and_content: RNA-seq: RPM normalized BigWig track files
Supplementary_files_format_and_content: RNA-seq: tab-delimited file containing raw transcript counts

source_name: MCF7 Colorectal Carcinoma Cell Line

growth_protocol: MCF7 cells were cultured in Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum, 1% Pen/Strep, and 0.01 mg/mL of insulin from bovine pancreas (Sigma-Aldrich, I6634). MCF7 cells were grown at 37°C with 5% CO2.

extract_protocol: For ChIP-seq, chromatin was cross-linked with 0.5% formaldehyde for 10 min at room temperature in culture media, and the reaction was stopped by the addition of glycine (150 mM final). Cells were washed twice with PBS and re-suspended in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, protease inhibitor (Roche)) at 10x106 [10 million cells/mL], dounced 15X, and incubated for 30 min at 4Â°C. Cell nuclei were collected by centrifugation at 1000xg for 5 min at 4Â°C, and re-suspended in Szak's RIPA buffer (50 mM Tris-HCl pH 8.0, 1% NP-40, 150 mM NaCl, 0.5% deoxycholate, 0.1% SDS, 5 mM EDTA, 0.5 mM PMSF, protease inhibitor) at 25x106 nuclei/mL. Nuclear pellets were sonicated using the Bioruptor water bath sonicator (Diagenode) using the high setting with 30 sec on 30 sec off for 45 min to generate 100-300 bp DNA fragments. Approximately 20x106 nuclei were used for each ChIP. For the ChIP step, 5-10 ug of antibody was conjugated with 100 uL of protein G dynabeads Thermo Fisher and blocked with 5% bovine serum albumin in RIPA for 1 hr at 4Â°C. An additional 2.5 Âµg of antibody specific for Drosophilla H2Av (Active Motif, 61686) was also conjugated at the same time. Drosophilla spike-in chromatin (Active Motif, 53083) was added to each sample for normalization between samples according to manufacture's instructions. Antibody-conjugated dynabeads were incubated with sheared chromatin suspension overnight at 4Â°C. Then the beads were sequentially washed two times with each of the following buffers: Szak's RIPA buffer (see above), low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 20 mM Tris, pH 8.0), and 1 mM Tris-EDTA pH 8.0. Chromatin immunocomplexes were eluted by incubation for 30 min at 65Â°C with 1% SDS and 100 mM NaHCO3, and cross-linking was reversed by incubation in the solution adjusted to 200 mM NaCl and proteinase K (20 Î¼g) for 1 hr at 65Â°C. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (Zymo Research). Final ChIP DNA was quantified on a Qubit 2.0 Fluorometer (Invitrogen) and approximately 5-10 ng of DNA were submitted (used?) for library preparation.  For 4sU-seq, HCT116 Ctrl and KAP1 KO1 cells were seeded into three 10cm plates per biological replicate and grown to 70% confluency. Cells were pulsed for 10 min with DMEM + 500 ÂµM 4sU (Sigma-Aldrich, T4509). At the 9 min mark the DMEM + 4sU media was removed and cells were washed one time with 1X PBS. The PBS was removed, and cells were lysed on-plate using the standard TRizol protocol (ThermoFisher Scientific, 15596026). RNA samples were DNase treated (NEB, M0303) and then extracted with acid:phenol chloroform (ThermoFisher Scientific, AM9720) followed by an additional chloroform extraction. RNA was then precipitated with 1/10 volume of NaCl (5M), 1 ÂµL glycoblue, and 2.5 volumes of 100% EtOH. RNA pellets were washed with 1 mL of 75% EtOH and air dried. RNA pellets were then resuspended in RNase-free H2O. RNA (300 ug) was brought to a final concentration of 0.4 mg/mL with RNase-free H2O. A separate aqueous master mix (20mM NaOAC pH 5.2, 1 mM EDTA pH 8.0, 0.1% SDS) was added to the diluted RNA mix followed by the addition of 0.2 mg/mL Biotin-HPDP (ThermoFisher Scientific 21341) in DMF. The biotinylation reaction was incubated at room temperature for 2 hrs followed by acid:phenol chloroform extraction. Biotinylated RNA pellets were resuspended in 500 ÂµL RPB buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 300 mM NaCl). Dyna MyOne Strepavidin T1 beads (200 uL/sample; ThermoFisher Scientific, 65601) were blocked at room temperature in beads wash buffer + 1% polyvinylpyrrolidone for 10 min. After blocking, beads were washed 1X with 1 mL beads wash (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 50 mM NaCl) buffer and then resuspended in RPB. Biotinylated, 4sU RNA was denatured at 65Â°C for 5 min and then placed on ice for 2 min. 200 ÂµL of blocked beads were added to each sample and incubated for 30 min with rotation at room temperature. Beads were washed 5X with 4sU wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 1 M NaCl, 0.1% Tween-20). Biotinylated, 4sU RNA was eluted from beads 2 times in 75 ÂµL of 0.1M DTT for 15 min at room temp with rotation, giving a final elution valume of 150 ÂµL. 4sU-RNA was further purified using the Zymo RNA Clean and Concentrator Kit (Zymo Reasearch, R1013). RNA concentration was measured using the Qubit RNA HS assay (ThermoFisher Scientific, Q32852) and quality was determined using the Agilent Tapestation RNA ScreenTape (Agilent, 5067-5576).  For RNA-seq, HCT116 Ctrl and KAP1 gRNA cells were grown in 6-well dishes and total RNA extracted using the Zymo Quick-RNA Miniprep Kit (R1055) according to manufacturer instructions.  For MNase-seq, cells were crosslinked with 0.5% methanol-free formaldehyde for 10 min and reaction was quenched for 5 min with 150 mM glycine before harvesting. Cells were washed twice with PBS buffer and nuclei were gathered by lysing the cells in Franhamâs lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 freshly supplemented with 1mM PMSF and EDTA free-Protease inhibitor cocktail). Nuclei were washed once with cold MNase buffer (20 mM Tris-HCl pH 7.5,15 mM NaCl, 60 mM KCl, 2 mM CaCl2) and resuspended in MNase buffer with concentration of 10x106 cells/mL before digestion. Micrococcal nuclease (New England BioLabs, M0247S) digestion was performed (240 U/106 cells) at 37ï°C to achieve 80% mono-nucleosomes populations and reaction was stopped with 10 mM EDTA, 20 mM EGTA, 0.4% SDS solution. Samples were centrifuged for 5 min at high speed and supernatant was collected. Samples were reverse crosslinked in de-crosslinking buffer (20 mM Tris- HCl pH 6.8, 500 mM NaCl, 2mM EDTA, and 0.5 mg/mL Proteinase K) overnight at 65Â°C. Following phenol-chloroform extraction and ethanol precipitation, DNA samples were run on 1.5% agarose gel and fragments of ~150 bp size were excised and purified. DNA from two biological replicates were analyzed on high sensitivity DNA tape on a 2200 TapeStation and used for library preparation.  For ChIP-seq and MNase-seq, libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8504) according to manufacturerâs instructions. Brielfy, 5-10 ng of either ChIP or MNase digested DNA was end repaired and A-tailed. Illumina adapters (New England BioLabs, E7335L) were then ligated to DNA fragments. ChIP DNA was size selected using the double-sided selection method outlined in the KAPA Hyper Prep Kit instructions. DNA was then amplified using Illumina indexed barcoding primers (New England BioLabs, E7335L) for 8-12 cycles depending on amount of input DNA.  For 4sU-seq and RNA-seq, the KAPA Stranded RNA-seq kit with RiboErase (HMR) (KAPA Biosystems, KK8483) was used to prepare libraries according to manufacturerâs instructions. Briefly, 200 ng of 4sU RNA and 1 ug of total RNA was used to prepare 4sU-seq and RNA-seq libraries, respectively. Libraries were rRNA depleted followed by DNase treatment. RNA was fragmented and primed followed by 1st strand cDNA synthesis. 2nd strand synthesis was then performed with the incorporation of dUTP. Libraries were then A-tailed, adapter ligated, and amplified as described for ChIP-seq.  All libraries were quantified using the Qubit 2.0 fluorometer and library size verified using the Agilent Tapestation DNA D1000 ScreenTape (Agilent, 5067-5582). All libraries were submitted to the McDermott Center Sequencing Core at UTSW. 75 bp paired-end reads were generated for all libraries

treatment_protocol: MCF7 cells were transfected with siRNA’s through a reverse transfection protocol. 150 pmols siNT/siKAP1 (Qiagen, final concentration of ~18 nM) and 30 uL RNAiMAX (Thermo) were added to the bottom of a 10 cm plate and incubated with 5 mL OPTI-MEM (Gibco) for 20 minutes at room temperature. MCF7 Cells were trypsinized and resuspended in complete media, and 3.5E6 cells were added to each OPTIMEM mix in each plate (final volume 10 mls). Cells were collected three days post-transfection for western blotting, RT-qPCR and ChIP-qPCR (after crosslinking).

tag: genotype/variation

value: Parental

tag: passages

value: Under 15

tag: cell line

tag: chip antibody

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: 2-075-2-2_S7

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: 2-076-2-2_S189


title: Head and neck squamous cell carcinoma HN088 microRNA

tag: tissue

tag: age

tag: race

value: White

tag: gender

value: Moderately Differentiated

value: Oropharynx

value: not available

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: positive


title: P1797

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744104_R02C01

value: Blood

value: M

tag: adhd affection status

value: Unaffected


title: 2-075-2-1_S41

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN084 microRNA

value: Tumor

value: Male

tag: smoking packyears

tag: alcohol use

value: light or moderate

tag: differentiation

tag: tumor site

value: Hypopharynx

tag: Stage

value: Concurrent Chemoradiation

value: negative


title: MCF7_siNT_RPB3_Rep2_ChIPSeq

tag: genotype/variation

value: Parental

value: Under 15

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: Head and neck squamous cell carcinoma HN086 microRNA

value: Black or African American

value: heavy use currently:>3 drinks per day

value: Well Differentiated

value: II

tag: tumor status

tag: node status

value: Nx

tag: treatment

value: Surgery Alone


title: P1216

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R05C02

value: Blood

value: M

value: Unaffected


title: MCF7_siKAP1_RPB3_Rep2_ChIPSeq

tag: passages

tag: cell line

tag: chip antibody


title: 2-074-1-2_S126

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: P1823

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R04C02

tag: tissue

tag: gender


title: Head and neck squamous cell carcinoma HN083 microRNA

value: Tumor

tag: age

tag: race

value: White

value: Male

value: Moderately Differentiated

value: Oropharynx

value: IVA

value: not available

tag: hpv status

value: positive


title: Head and neck squamous cell carcinoma HN082 microRNA

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Concurrent Chemoradiation


title: MCF7_siKAP1_Input_ChIPSeq

tag: genotype/variation

value: Parental

value: Under 15

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: 2-074-1-1_S75

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN081 microRNA

value: Well Differentiated

tag: tumor site

tag: Stage

tag: tumor status

value: Surgery and Radiation

value: negative


title: MCF7_siNT_Input_ChIPSeq

tag: passages


title: P1528

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R02C02

value: Blood

value: F

tag: adhd affection status

value: Unaffected


title: P1862

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R03C02

value: M

value: Affected


title: 2-073-2-3_S46

value: baseline, cid2 :lcd, cid3 :di):CID3


title: KAP1_KO2_RPB3_Rep2_ChIPSeq

source_name: HCT116 Colorectal Carcinoma Cell Line

value: KAP1 KO2

tag: cell line

tag: chip antibody


title: 2-073-2-2_S120

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: MCF7_siNT_RPB3_Rep1_ChIPSeq


title: Head and neck squamous cell carcinoma HN078 microRNA

tag: tissue

value: Tumor

value: White

tag: gender

value: Male

value: heavy use > 6 months ago

value: Poorly Differentiated

value: Larynx

value: IVB

tag: node status

tag: treatment


title: Head and neck squamous cell carcinoma HN079 microRNA

tag: age

tag: race

value: Female

tag: smoking packyears

value: Moderately Differentiated

value: Oropharynx

value: IVA

value: Concurrent Chemoradiation

tag: hpv status

value: positive


title: P1472

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R06C01

value: Blood

value: M

value: Unaffected


title: KAP1_KO2_RPB3_Rep1_ChIPSeq

tag: genotype/variation

value: KAP1 KO2

value: Under 15

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: 2-073-2-1_S113

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN077 microRNA

value: Tumor

value: White

value: Male

value: Unknown

tag: alcohol use

tag: differentiation

value: Not evaluated

tag: tumor site

tag: Stage

value: not available

value: Surgery Alone


title: KAP1_KO2_Input_Rep2_ChIPSeq

tag: passages

tag: cell line


title: 2-073-2-1_S17

tag: cid (cid1


title: Head and neck squamous cell carcinoma HN074 microRNA

value: Black or African American

value: light or moderate

value: Poorly Differentiated

value: Hypopharynx

value: III

tag: tumor status

value: negative


title: 2-072-1-1_S81

tag: individual


title: Ctrl2_RPB3_Rep2_ChIPSeq

tag: chip antibody


title: P1804

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R04C01

tag: tissue

value: Blood

tag: gender

value: M

tag: adhd affection status

value: Affected


title: P1868

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R05C01

value: F


title: Head and neck squamous cell carcinoma HN070 microRNA

value: Tumor

tag: age

tag: race

value: heavy use > 6 months ago

value: Moderately Differentiated

value: Oropharynx

value: II

tag: node status

tag: treatment


title: 2-071-2-1_S102

value: baseline, cid2 :lcd, cid3 :di):CID1


title: KAP1_KO2_Input_Rep1_ChIPSeq

tag: genotype/variation

value: KAP1 KO2

value: Under 15


title: P1818

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R02C01

value: Unaffected


title: 2-070-2-2_S43

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1698

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R03C01


title: Head and neck squamous cell carcinoma HN068 microRNA

value: White

value: Male

tag: smoking packyears

tag: alcohol use

value: light or moderate

tag: differentiation

value: IVA

value: Surgery and Concurrent Chemoradiation

tag: hpv status


title: 2-070-1-3_S191

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1641

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R06C02

value: Blood

value: M

value: Affected


title: P1037

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R01C02


title: P1802

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744074_R01C01


title: Head and neck squamous cell carcinoma HN067 microRNA

value: Tumor

value: Poorly Differentiated

tag: tumor site

tag: Stage

value: III

value: negative


title: Ctrl2_Input_Rep1_ChIPSeq

tag: passages

tag: cell line


title: 2-070-1-2_S94

tag: cid (cid1

tag: individual


title: P1669

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R06C02

tag: tissue

tag: gender

value: F


title: Head and neck squamous cell carcinoma HN063 microRNA

tag: age

value: Unknown

tag: tumor status

value: not available

value: Concurrent Chemoradiation


title: siKAP1_Rep3_RNASeq

description:
featurecounts_siKAP1_RNASeq.txt
ERCC spike-in RNA added.

treatment_protocol: HCT116 cells were seeded into 6-well plates the night before transfection to achieve ~50% confluency. 50 pmol of 4-pooled siRNAs targeting SMAD2 and a single siRNA targeting KAP1 were diluted in 100 µL Opti-MEM media (Thermo Fisher Scientific, 31985062). 10 µL of RNAiMax Transfection Reagent (Thermo Fisher Scientific, 13778030) was diluted in 100 µL of Opti-MEM media. The RNAiMax solution was added to the siRNA solution and incubated at room temperature for 5 min and then added dropwise to cells for a final siRNA concentration of 25 nM. Cells treated with siSMAD2 were incubated for 24 hr, while cells treated with siKAP1 were incubated for 72 hr. Knockdown efficiency was determined by western blot and RT-qPCR analysis. For western blot, whole cell lysates were electrophoresed on an 8% SDS-PAGE and blots were probed with 1:1000 dilution of α-SMAD2, 1:5000 dilution of α-KAP1, and 1:10,000 of α-Rhodamine actin. α-SMAD2 blot was exposed using Super Signal West Femto Luminol Enhancer.

value: Parental

value: Under 15


title: P1537

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R05C02

tag: adhd affection status

value: Unaffected


title: 2-068-2-3_S66


title: Head and neck squamous cell carcinoma HN060 microRNA

tag: race

value: White

value: Male

value: Moderately Differentiated

tag: node status

tag: treatment


title: siKAP1_Rep2_RNASeq

tag: genotype/variation


title: 2-067-2-2_S118

value: baseline, cid2 :lcd, cid3 :di):CID2


title: siKAP1_Rep1_RNASeq


title: Ctrl2_Input_Rep2_ChIPSeq


title: Ctrl2_RPB3_Rep1_ChIPSeq

description: An antibody specific to Drosophilla H2Av (Active Motif, 61686) and Drosophilla chromatin  (Active Motif, 53083) was added to each sample for normalization.

tag: chip antibody

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: P1330

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R03C02

value: Blood

value: M


title: siNT_Rep3_RNASeq


title: P1649

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R04C02


title: 2-067-2-1_S10

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-066-2-2_S94


title: Head and neck squamous cell carcinoma HN055 microRNA

value: Tumor

value: Black or African American

tag: smoking packyears

tag: alcohol use

value: heavy use > 6 months ago

tag: differentiation

value: Larynx

value: III

tag: hpv status

value: positive


title: siNT_Rep2_RNASeq

value: Parental

tag: passages

tag: cell line


title: P1009

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R01C02


title: BlastCellLowDXRA1

source_name: BlastCellLowDXR

tag: genotype

value: Bone Marrow

tag: cell type

value: BlastCell

value: [Low]DXR


title: siNT_Rep1_RNAseq

value: Under 15


title: 2-066-2-1_S85

tag: cid (cid1

tag: individual


title: Head and neck squamous cell carcinoma HN047 microRNA

tag: tissue

tag: age

tag: gender

value: Male

value: heavy use currently:>3 drinks per day

value: Moderately Differentiated

tag: tumor site

tag: Stage

value: IVA

tag: tumor status

value: Concurrent Chemoradiation

value: negative


title: P1824

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R06C01

value: Blood

value: M

tag: adhd affection status

value: Affected


title: Head and neck squamous cell carcinoma HN064 microRNA

value: Tumor

tag: race

value: White

value: Female

tag: smoking packyears

value: Oropharynx

value: IVB

tag: node status

tag: treatment


title: 2-069-2-2_S40

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 2-066-1-2_S114


title: Head and neck squamous cell carcinoma HN057 microRNA

value: Black or African American

tag: alcohol use

tag: differentiation

value: not available

tag: hpv status


title: P1316

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R05C01

value: Unaffected


title: Head and neck squamous cell carcinoma HN043 microRNA

value: light or moderate

value: Poorly Differentiated

value: Hypopharynx


title: KAP1_KO2_Rep1_4sUSeq

extract_protocol:
RNA samples were DNase treated (NEB, M0303) and then extracted with acid:phenol chloroform (ThermoFisher Scientific, AM9720) followed by an additional chloroform extraction. RNA was then precipitated with 1/10 volume of NaCl (5M), 1 µL glycoblue, and 2.5 volumes of 100% EtOH. RNA pellets were washed with 1 mL of 75% EtOH and air dried. RNA pellets were then resuspended in RNase-free H2O. RNA (300 ug) was brought to a final concentration of 0.4 mg/mL with RNase-free H2O. A separate aqueous master mix (20mM NaOAC pH 5.2, 1 mM EDTA pH 8.0, 0.1% SDS) was added to the diluted RNA mix followed by the addition of 0.2 mg/mL Biotin-HPDP (ThermoFisher Scientific 21341) in DMF. The biotinylation reaction was incubated at room temperature for 2 hrs followed by acid:phenol chloroform extraction. Biotinylated RNA pellets were resuspended in 500 µL RPB buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 300 mM NaCl). Dyna MyOne Strepavidin T1 beads (200 uL/sample; ThermoFisher Scientific, 65601) were blocked at room temperature in beads wash buffer + 1% polyvinylpyrrolidone for 10 min. After blocking, beads were washed 1X with 1 mL beads wash (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 50 mM NaCl) buffer and then resuspended in RPB. Biotinylated, 4sU RNA was denatured at 65°C for 5 min and then placed on ice for 2 min. 200 µL of blocked beads were added to each sample and incubated for 30 min with rotation at room temperature. Beads were washed 5X with 4sU wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 1 M NaCl, 0.1% Tween-20). Biotinylated, 4sU RNA was eluted from beads 2 times in 75 µL of 0.1M DTT for 15 min at room temp with rotation, giving a final elution valume of 150 µL. 4sU-RNA was further purified using the Zymo RNA Clean and Concentrator Kit (Zymo Reasearch, R1013). RNA concentration was measured using the Qubit RNA HS assay (ThermoFisher Scientific, Q32852) and quality was determined using the Agilent Tapestation RNA ScreenTape (Agilent, 5067-5576). For RNA-seq, HCT116 Ctrl and KAP1 gRNA cells were grown in 6-well dishes and total RNA extracted using the Zymo Quick-RNA Miniprep Kit (R1055) according to manufacturer instructions.
For 4sU-seq and RNA-seq, the KAPA Stranded RNA-seq kit with RiboErase (HMR) (KAPA Biosystems, KK8483) was used to prepare libraries according to manufacturer’s instructions. Briefly, 200 ng of 4sU RNA and 1 ug of total RNA was used to prepare 4sU-seq and RNA-seq libraries, respectively. Libraries were rRNA depleted followed by DNase treatment. RNA was fragmented and primed followed by 1st strand cDNA synthesis. 2nd strand synthesis was then performed with the incorporation of dUTP. Libraries were then A-tailed, adapter ligated, and amplified as described for ChIP-seq. All libraries were quantified using the Qubit 2.0 fluorometer and library size verified using the Agilent Tapestation DNA D1000 ScreenTape (Agilent, 5067-5582). All libraries were submitted to the McDermott Center Sequencing Core at UTSW. 75 bp paired-end reads were generated for all libraries

tag: strain

value: KAP1 KO2

tag: passages

value: Under 15


title: Ctrl2_Rep2_4sUSeq


title: KAP1_KO2_Rep2_4sUSeq


title: P1477

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R04C01

value: Blood


title: 2-065-2-2_S42

tag: cid (cid1

tag: individual


title: Head and neck squamous cell carcinoma HN041 microRNA

tag: tissue

tag: age

value: Male

value: heavy use currently:>3 drinks per day

value: Moderately Differentiated

value: IVA

value: Surgery and Concurrent Chemoradiation

value: negative


title: P1407

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R02C02

tag: gender

value: M

value: Affected


title: Head and neck squamous cell carcinoma HN040 microRNA

value: Tumor

value: White

tag: tumor site

tag: Stage


title: 2-065-2-1b_S103

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1634

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R02C01

tag: adhd affection status


title: Head and neck squamous cell carcinoma HN037 microRNA

tag: race

value: Black or African American

tag: tumor status

value: Surgery and Radiation


title: Ctrl2_Rep1_4sUSeq


title: P1071

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R03C01

value: Unaffected


title: Head and neck squamous cell carcinoma HN045 microRNA

tag: smoking packyears

value: Unknown

value: light or moderate

value: Larynx

value: not available

tag: node status

value: Concurrent Chemoradiation


title: 2-063-2-3_S60

value: baseline, cid2 :lcd, cid3 :di):CID3


title: x_320_3

first: Fernando

middle: Henrique

last: Martins

address: 6000 Harry Hines Blvd, NL4.110H

institute: University of Texas Southwestern Medical Center

description: actin polymerization via Tir:EspFu

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: wild-type (WT)

growth_protocol: HeLa cells were seeded onto 6-well plates at a density of 1x105 cells/mL and grown at 37 °C and 5% CO2 for 48 hours to 80-90% confluency in Dulbecco’s modified Eagle’s essential medium (DMEM) containing 10% fetal bovine serum, and supplemented with penicillin (100 U/mL), streptomycin (100 μg/mL) and L-glutamine (4 mM). aEPEC strains were grown overnight at 37 °C in Luria-Bertani (LB) broth.

extract_protocol:
After six hours of infection, cells were washed three times with PBS and lysed with RLT buffer (Qiagen). Cell lysates were homogenized and total RNA was then purified using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions. RNA samples were treated with RNAse-free DNAse I (Invitrogen) to remove contaminating DNA, and then purified again using RNeasy Mini Spin columns. The concentration and quality of the samples were evaluated using Qubit fluorimeter and Agilent 2100 Bioanalyzer prior to library prep.
A total of 4 μg of DNAse-treated RNA were prepared with TruSeq Stranded Total RNA LT Sample Prep kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNA were then A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with Ampure XP beads, then validated and quantified again using Agilent 2100 Bioanalyzer and Qubit fluorimeter. Then, cDNA libraries were sequenced on an Illumina HiSeq 2500 platform using SBS v3 reagents.

treatment_protocol: HeLa cells were washed with phosphate-buffer saline (PBS) and then infected with BA320, KOct1, KOct2 or KO strains at a multiplicity of infection (MOI) of 10 in DMEM containing 10% FBS and lacking antibiotics. Control included plates with HeLa cells alone (mock infections). After three hours of incubation at 37°C in 5% CO2, cells were washed with PBS, fresh DMEM was added, and plates were then incubated for additional three hours.

tag: cell type

value: cervical adenocarcinoma epithelial cells

tag: cell line

value: HeLa

tag: infection status

value: infected with BA320 (WT) strain


title: tir_4

description: actin polymerization via Tir:EspFu and Tir:Nck

value: infected with KOct1 strain


title: Head and neck squamous cell carcinoma HN034 microRNA

value: Male

tag: alcohol use

tag: differentiation

value: Moderately Differentiated

tag: treatment

tag: hpv status

value: positive


title: P1007

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R06C02

tag: tissue

value: Blood

value: M


title: tir_3


title: P1751

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744047_R01C01

value: F


title: P1640

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R05C02

value: Unaffected


title: 2-063-1-1b_S150

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: 2-062-2-2_S138

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1827

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R04C02

tag: gender

value: Affected


title: Head and neck squamous cell carcinoma HN056 microRNA

value: Tumor

tag: age

value: White

value: heavy use currently:>3 drinks per day

tag: tumor site

value: Larynx

tag: Stage

value: III

value: Surgery and Concurrent Chemoradiation

value: negative


title: Head and neck squamous cell carcinoma HN031 microRNA

tag: race

value: Female

value: I

tag: tumor status

value: not available

value: Concurrent Chemoradiation


title: P1855

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R03C02

value: Blood

value: M

tag: adhd affection status


title: x_320_4

description: actin polymerization via Tir:EspFu

tag: cell type

value: cervical adenocarcinoma epithelial cells

value: HeLa

value: infected with BA320 (WT) strain


title: Head and neck squamous cell carcinoma HN030 microRNA

value: Black or African American

value: Male

tag: smoking packyears

value: Moderately Differentiated

value: Oropharynx

value: IVB

tag: node status


title: 2-062-2-1b_S69

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN035 microRNA

value: Tumor

value: White

tag: alcohol use

value: heavy use > 6 months ago

value: Well Differentiated

value: Larynx

value: IVA


title: 2-064-2-3_S107

value: baseline, cid2 :lcd, cid3 :di):CID3


title: HeLa_3

description: no actin polymerization

source_name: control

tag: cell line

tag: infection status

value: uninfected (mock)


title: HeLa_4

description: no actin polymerization

value: cervical adenocarcinoma epithelial cells


title: P1453

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R02C02

value: Blood

value: M

value: Unaffected


title: Head and neck squamous cell carcinoma HN028 microRNA

value: Unknown

value: Male

tag: differentiation

value: not available

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status

value: negative


title: espFutir_2

description: actin polymerization via Tir:Nck

value: HeLa

value: infected with KOct2 strain


title: 2-066-1-1_S174

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1

tag: individual


title: 2-063-2-2_S136

value: baseline, cid2 :lcd, cid3 :di):CID2


title: Head and neck squamous cell carcinoma HN027 microRNA

tag: tissue

value: Tumor

tag: age

value: White

tag: gender

value: Female

value: Well Differentiated

value: Oropharynx

value: Surgery Alone


title: P1521

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R01C02

value: Blood

value: M


title: 2-062-1-1b_S64


title: espFu_4

description: no robust actin polymerization

source_name: espFu mutant (KO)

value: cervical adenocarcinoma epithelial cells

value: infected with espFu (KO) strain


title: Head and neck squamous cell carcinoma HN026 microRNA

tag: race

value: Black or African American

value: heavy use > 6 months ago

value: Poorly Differentiated

tag: tumor site

value: Larynx

tag: Stage

value: I


title: P1809

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R06C01

tag: adhd affection status

value: Unaffected


title: 2-061-2-1b_S87

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Head and neck squamous cell carcinoma HN033 microRNA

value: Tumor

value: Male

tag: smoking packyears

value: light or moderate

value: IVA

tag: tumor status

value: Concurrent Chemoradiation

value: negative


title: P1655

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R05C01

value: Blood

value: Affected


title: espFu_3

description: no robust actin polymerization

tag: cell type

value: cervical adenocarcinoma epithelial cells

value: HeLa


title: Head and neck squamous cell carcinoma HN025 microRNA

value: Black or African American

tag: alcohol use

value: Moderately Differentiated

value: Oropharynx

value: not available

tag: node status


title: 2-060-2-2_S57

value: baseline, cid2 :lcd, cid3 :di):CID2


title: Experiment2

city: Seattle

first: Douglas

middle: M

last: Fowler

state: WA

address: Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: RPE-1 NLS-Dendra2x3/H2B-miRFP/NES-mBeRFP Clone 3 cells were plated at 50,000 cells per well in a 6-well plate. After 24 hours, cells were treated with paclitaxel at a final concentration of 0.25 nM. After 30 hours of treatment, cells were placed on the microscope and imaged, analyzed, and activated across 2,204 sites (~75% coverage, avoided well edges) in 2 wells. At each site, Dendra2 was imaged with 1x1 binning; a custom nuclear segmentation pipeline that optimized detection of nuclear blebs, herniations, and other abnormalities was employed; Metamorph’s MDA analysis was used to compute shape factors for nuclear binaries. Cells with nuclear shape factor < 0.65 were activated for 200 ms, and cells with nuclear shape factor > 0.65 were activated for 800 ms. Cells from each well were trypsinized and resuspended in DPBS supplemented with 1% BSA and 2% FBS. Using FACS,  cells corresponding to 200 ms and 800 ms photoactivation were sorted using FACS  into a 1.5 mL tube containing 1mL DPBS supplemented with 1% BSA. In Experiment 1, cells were sorted according to their nuclear phenotype (i.e. 200 ms cells in bin 1, 800 ms cells in bin 2).

data_processing:
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.
Genome_build: hg19
Supplementary_files_format_and_content: cell_bulk_RNAseq.annotations: Sample annotations; tab-delimited
Supplementary_files_format_and_content: gene_bulk_RNAseq.annotations: Gene annotations; tab-delimited
Supplementary_files_format_and_content: UMI.count_bulk_RNAseq.matrix: Matrix of gene counts (rows) across samples (columns)
Supplementary_files_format_and_content: processed_nls_counts.csv: Comma separated file with variant identity, replicate, bin number, and count
Supplementary_files_format_and_content: matrix_exp1.mtx: Expression matrix from Experiment 1, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp1.tsv: Gene annotations from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1.tsv: Cell barcodes from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp2.mtx: Expression matrix from Experiment 2, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp2.tsv: Gene annotations from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: features_exp2.tsv: Cell barcodes from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp1_unfiltered.mtx: Expression matrix from Experiment 1, no UMI filtering
Supplementary_files_format_and_content: features_exp1_unfiltered.tsv: Gene annotations from Experiment 1, no UMI filtering; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1_unfiltered.tsv: Cell barcodes from Experiment 1, no UMI filtering; tab-delimited

growth_protocol: hTERT RPE-1 cells (ATCC CRL-4000) and derivatives thereof were cultured in F12/DMEM supplemented with 10% FBS, 1 mM PenStrep, and 0.01 mg/mL hygromycin B.  For Visual Cell Sorting experiments, DMEM without phenol red was used to reduce background fluorescence. Cells were passaged by detachment with trypsin–EDTA 0.25%.

extract_protocol:
After sorting, cells were spun at 1,000 x g at 4 °C for 5 minutes, then all but 50-100 uL of supernatant was removed.
Cells were counted and subjected to 10X Single-Cell RNA sequencing v2 (10x Genomics, cat. no. 120236, 12037) according to the manufacturer’s instructions.

treatment_protocol: Treated with paclitaxel 24 hours after plating and 30 hours before imaging and activation

tag: activated

value: TRUE

tag: activation_time (ms)

value: paclitaxel 0.25nM

tag: molecule subtype

value: single cell RNA


title: P1237

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R04C01

value: F

value: Unaffected


title: Head and neck squamous cell carcinoma HN024 microRNA

value: Tumor

value: White

value: Male

value: heavy use currently:>3 drinks per day

tag: differentiation

value: Poorly Differentiated

value: IVA

tag: treatment

value: Surgery and Radiation

tag: hpv status


title: 2-062-1-2_S167

tag: cid (cid1

tag: individual


title: 2-060-2-1b_S189

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Experiment1_200ms

source_name: RPE-1 NLS-Dendra2x3/H2B-miRFP/NES-mBeRFP Clone 3


title: espFutir_4

description: actin polymerization via Tir:Nck

value: cervical adenocarcinoma epithelial cells

tag: cell line

value: HeLa

tag: infection status

value: infected with KOct2 strain


title: P1034

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R03C01

tag: tissue

value: Blood

tag: gender

value: M


title: P1262

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R02C01

tag: adhd affection status


title: Experiment1_800ms

value: TRUE

value: paclitaxel 0.25nM


title: 2-059-1-3_S137

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 2-058-2-1b_S68


title: Head and neck squamous cell carcinoma HN012 microRNA

tag: age

tag: race

tag: smoking packyears

value: light or moderate

value: Moderately Differentiated

tag: tumor site

tag: Stage

value: not available

tag: tumor status

value: Concurrent Chemoradiation

value: negative


title: R2T3_800ms_lib

description: Eighteen hours before imaging, 300,000 U-2 OS LLP-Blast/H3-Dendra2 Clone 4 cells with the attB-NLS-CMPK-miRFP library recombined into the landing pad were seeded into each well of a 6-well plate. The next day, cells were placed onto the microscope and imaged, analyzed, and activated across 2,949 sites (~100% well coverage) across two wells. At each site, Dendra2 and miRFP were imaged with 2x2 binning; Metamorph’s Count Nuclei module was used on the Dendra2 image to identify nuclei and create a nuclear binary image; cytoplasm binaries were created by subjecting the nuclear binary to a dilate function and subtracting away the nuclear binary; each nucleus-cytoplasm binary pair was superimposed on the miRFP image and average pixel intensities were measured for each compartment; cells with an average nuclear or cytoplasmic miRFP pixel intensity of less than 11,000 were filtered out; a nucleus-to-cytoplasm  (N:C) ratio was calculated by dividing the average nuclear pixel intensity by the average cytoplasmic pixel intensity; nuclei with N:C < 0.964 were not activated at all, N:C 0.964 – 1.079 were activated for 50 ms, N:C 1.079 – 1.244 were activated for 200 ms, and N:C > 1.244 were activated for 800 ms. Once all sites were imaged, analyzed, and activated, the cells were subject to FACS and unactivated Dendra2 (FITC), activated Dendra2 (PE-YG), and miRFP (AlexaFluor-700) fluorescence intensities assessed. Cells were then sorted into four photoactivation bins.

data_processing:
Library strategy: Targeted DNA sequencing
Base calls were trimmed and merged using PEAR. Sequences were quality-filtered and variants were called and counted by using Enrich2 (the Enrich2 configuration file is available on the GitHub repository; https://github.com/FowlerLab/vcs_2019.git). The raw_variants_counts.tsv file from each sample output was then concatenated into a single counts file (processed_nls_counts.csv) using Jupyter running Python3.
Genome_build: hg19
Supplementary_files_format_and_content: cell_bulk_RNAseq.annotations: Sample annotations; tab-delimited
Supplementary_files_format_and_content: gene_bulk_RNAseq.annotations: Gene annotations; tab-delimited
Supplementary_files_format_and_content: UMI.count_bulk_RNAseq.matrix: Matrix of gene counts (rows) across samples (columns)
Supplementary_files_format_and_content: processed_nls_counts.csv: Comma separated file with variant identity, replicate, bin number, and count
Supplementary_files_format_and_content: matrix_exp1.mtx: Expression matrix from Experiment 1, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp1.tsv: Gene annotations from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1.tsv: Cell barcodes from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp2.mtx: Expression matrix from Experiment 2, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp2.tsv: Gene annotations from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: features_exp2.tsv: Cell barcodes from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp1_unfiltered.mtx: Expression matrix from Experiment 1, no UMI filtering
Supplementary_files_format_and_content: features_exp1_unfiltered.tsv: Gene annotations from Experiment 1, no UMI filtering; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1_unfiltered.tsv: Cell barcodes from Experiment 1, no UMI filtering; tab-delimited

source_name: U-2 OS LLP-Blast/H3-Dendra2 Clone 4

growth_protocol: U-2 OS cells (ATCC HTB-96), and derivatives thereof were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 1 ug/mL doxycycline (Sigma), unless otherwise noted.

extract_protocol:
After sorting, cells in each Dendra2 photoactivation bin were grown in the absence of doxycycline until confluent in one well of a 6-well plate (~ 7 days), then pelleted and stored at -20 °C.  DNA was extracted from cell pellets with the DNEasy kit (Qiagen 69504) using RNAse according to the manufacturer’s instructions.
gDNA was amplified using SV40_NLS_seq_f and SV40_NLS_seq_r (Supplementary Table 8) primers using Kapa Hifi (Kapa Biosystems KK2602) according to the manufacturer’s instructions. Amplicons were cleaned using Ampure XP beads (Beckman Coulter A63880), then subjected to an indexing PCR step using KAPA2G Robust (Kapa Biosystems KK5705) with primers P5 and an indexing primer. Amplicons were then run on a 1.5% agarose gel at 130 V for 40 min and the DNA in the 235bp band extracted using Freeze’N Squeeze DNA Gel Extraction Spin Columns (BioRad 7326165). Extracted DNA was sequenced on an Illumina NextSeq500 using SV40_NLS_Read1, SV40_NLS_Read2, and SV40_NLS_Index1 primers.

treatment_protocol: Treated with doxycycline for a week prior to starting the experiment

tag: cell type

value: U-2 OS

tag: activated

tag: activation_time (ms)

value: doxycycline 2ug/mL

tag: molecule subtype

value: NLS amplicon DNA


title: Head and neck squamous cell carcinoma HN010 microRNA

value: Tumor

value: Black or African American

value: Male

tag: alcohol use

tag: differentiation

value: IVA

tag: node status

tag: treatment

value: Surgery and Radiation

tag: hpv status


title: Head and neck squamous cell carcinoma HN023 microRNA

tag: tissue

value: White

tag: gender

value: Poorly Differentiated

value: Surgery and Concurrent Chemoradiation


title: 2-057-2-3_S58

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID3

tag: individual


title: 2-057-2-2_S169

value: baseline, cid2 :lcd, cid3 :di):CID2


title: R2T3_200ms_lib

value: TRUE


title: P1645

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R06C02

value: Blood

value: M

tag: adhd affection status

value: Affected


title: Head and neck squamous cell carcinoma HN009 microRNA

tag: age

tag: race

tag: smoking packyears

value: Unknown

value: light or moderate

value: Moderately Differentiated

tag: tumor site

value: III

value: negative


title: P1849

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R05C02


title: R2T3_50ms_lib

tag: cell type

value: U-2 OS

tag: activated

value: doxycycline 2ug/mL

value: NLS amplicon DNA


title: P1840

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R04C02


title: R2T3_0ms_lib

value: FALSE

tag: activation_time (ms)

tag: molecule subtype


title: 2-057-2-1_S4

value: baseline, cid2 :lcd, cid3 :di):CID1


title: R2T2_800ms_lib


title: 2-056-2-1_S141


title: 2-059-1-1_S164


title: P1767

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R03C02


title: R2T2_200ms_lib


title: Head and neck squamous cell carcinoma HN018 microRNA

value: Tumor

value: White

value: Female

tag: alcohol use

tag: differentiation

tag: Stage

value: II

tag: tumor status

value: Surgery and Radiation


title: P1232

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R02C02

tag: tissue

value: Blood

value: M

value: Unaffected


title: P1765

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571726060_R01C01

tag: gender

value: Affected


title: 2-056-1-1_S26

tag: cid (cid1


title: P1819

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R06C01


title: P1098

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R01C02


title: 2-054-2-1_S108

tag: individual


title: 2-052-1-3_S98

value: baseline, cid2 :lcd, cid3 :di):CID3


title: R2T2_50ms_lib

value: TRUE

tag: treatment


title: R2T2_0ms_lib


title: 2-052-1-2_S164

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1549

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R04C01

value: F

tag: adhd affection status


title: Head and neck squamous cell carcinoma HN008 microRNA

tag: age

tag: race

value: Moderately Differentiated

tag: node status

value: Surgery Alone

tag: hpv status


title: P1340

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R03C01


title: 2-052-1-1_S90


title: R2T1_50ms_lib

tag: cell type

value: U-2 OS

tag: activated

value: doxycycline 2ug/mL

value: NLS amplicon DNA


title: R2T1_200ms_lib

tag: activation_time (ms)

tag: molecule subtype


title: P1603

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R02C01


title: 2-049-1-3_S94


title: R2T1_0ms_lib

value: FALSE


title: 2-049-1-3_S190


title: 8D_TLR4-/-_Sham

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 transformed, using the oligo package of Bioconductor

source_name: microglia from ipsilateral cortex

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer, and NanoDrop 1000 spectrophotometer, respectively.

tag: strain

tag: Sex

value: male

tag: genotype

value: Sham


title: 7D_TLR4-/-_IPC

value: Ischemia/reperfusion


title: 8A_TLR4-/-_Sham


title: 7C_TLR4-/-_IPC


title: R1T2_800ms_lib


title: 7B_TLR4-/-_IPC


title: P1754

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R01C01

tag: tissue

value: Blood


title: 2-049-1-2_S192


title: P1830

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925065_R05C01

tag: gender

value: M


title: P1313

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R06C02

value: Unaffected


title: R2T1_800ms_lib


title: R1T2_200ms_lib


title: 2-049-1-1b_S21

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1


title: R1T2_50ms_lib


title: P1174

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R05C02


title: 6D_Wt_Sham

value: Wildtype


title: 2-048-2-3_S75

value: baseline, cid2 :lcd, cid3 :di):CID3

tag: individual


title: P1516

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R04C02


title: 2-047-2-2_S138

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 6C_Wt_Sham

tag: treatment


title: R1T1_800ms_lib

description: Eighteen hours before imaging, 300,000 U-2 OS LLP-Blast/H3-Dendra2 Clone 4 cells with the attB-NLS-CMPK-miRFP library recombined into the landing pad were seeded into each well of a 6-well plate. The next day, cells were placed onto the microscope and imaged, analyzed, and activated across 2,949 sites (~100% well coverage) across two wells. At each site, Dendra2 and miRFP were imaged with 2x2 binning; Metamorph’s Count Nuclei module was used on the Dendra2 image to identify nuclei and create a nuclear binary image; cytoplasm binaries were created by subjecting the nuclear binary to a dilate function and subtracting away the nuclear binary; each nucleus-cytoplasm binary pair was superimposed on the miRFP image and average pixel intensities were measured for each compartment; cells with an average nuclear or cytoplasmic miRFP pixel intensity of less than 11,000 were filtered out; a nucleus-to-cytoplasm  (N:C) ratio was calculated by dividing the average nuclear pixel intensity by the average cytoplasmic pixel intensity; nuclei with N:C < 0.964 were not activated at all, N:C 0.964 – 1.079 were activated for 50 ms, N:C 1.079 – 1.244 were activated for 200 ms, and N:C > 1.244 were activated for 800 ms. Once all sites were imaged, analyzed, and activated, the cells were subject to FACS and unactivated Dendra2 (FITC), activated Dendra2 (PE-YG), and miRFP (AlexaFluor-700) fluorescence intensities assessed. Cells were then sorted into four photoactivation bins.

value: TRUE


title: 8B_TLR4-/-_Sham


title: 2-047-2-1b_S3


title: R1T2_0ms_lib


title: R1T1_200ms_lib


title: P1653

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R06C01

tag: adhd affection status

value: Affected


title: P1373

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R02C02


title: P1853

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R01C02

value: F


title: R1T1_50ms_lib

value: U-2 OS


title: R1T1_0ms_lib

value: doxycycline 2ug/mL


title: 5D_Wt_IPC


title: 2-044-2-1b_S26


title: 6B_Wt_Sham


title: 6A_Wt_Sham


title: 5C_Wt_IPC


title: P1724

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R05C01


title: 2-044-2-2_S85


title: 2-043-1-1_S228


title: P1777

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R04C01


title: P1511

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R03C02


title: U2OS_AAVS-LP_C11_800ms_4.5h

description: U2OS cells activated for 800ms

data_processing:
Reads were converted to a fastq format and demultiplexed using bcl2fastq. Adaptors were clipped using trim_galore with default settigngs and trimmed reads aligned to the human reference genome. Mapped reads were split into sample indices by using the RT index.
Genome_build: hg19
Supplementary_files_format_and_content: cell_bulk_RNAseq.annotations: Sample annotations; tab-delimited
Supplementary_files_format_and_content: gene_bulk_RNAseq.annotations: Gene annotations; tab-delimited
Supplementary_files_format_and_content: UMI.count_bulk_RNAseq.matrix: Matrix of gene counts (rows) across samples (columns)
Supplementary_files_format_and_content: processed_nls_counts.csv: Comma separated file with variant identity, replicate, bin number, and count
Supplementary_files_format_and_content: matrix_exp1.mtx: Expression matrix from Experiment 1, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp1.tsv: Gene annotations from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1.tsv: Cell barcodes from Experiment 1, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp2.mtx: Expression matrix from Experiment 2, UMIs filtered for droplets containing cells
Supplementary_files_format_and_content: features_exp2.tsv: Gene annotations from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: features_exp2.tsv: Cell barcodes from Experiment 2, UMIs filtered for droplets containing cells; tab-delimited
Supplementary_files_format_and_content: matrix_exp1_unfiltered.mtx: Expression matrix from Experiment 1, no UMI filtering
Supplementary_files_format_and_content: features_exp1_unfiltered.tsv: Gene annotations from Experiment 1, no UMI filtering; tab-delimited
Supplementary_files_format_and_content: barcodes_exp1_unfiltered.tsv: Cell barcodes from Experiment 1, no UMI filtering; tab-delimited

source_name: U-2 OS AAVS-LP Clone 11

extract_protocol:
RNA was extracted from each sample using a Trizol/RNeasy Mini Kit (ThermoFisher 15596026, Qiagen 74104).
RNA was subjected to SuperScript IV First-Strand Synthesis (Thermo Fisher 18091050) and NEBNext Ultra II Directional RNA Second Strand Synthesis (NEB E7550), according to the manufacturer’s instructions. cDNA was then tagmented with Nextera Tn5 (Illumina FC-131-1024) and amplified/indexed by PCR with the NEBNext DNA Library Prep Kit (NEB E6040). Samples were sequenced using a NextSeq 500/550 75 cycle kit (Illumina TG-160-2005).

treatment_protocol: U-2 OS AAVS-LP Clone 11 cells with attB-H3-Dendra2 recombined into the landing pad were seeded at 20,000 cells per well in 8 wells of a 24-well plate.  Eighteen hours later, cells across 6 wells (678 sites per well; ~100% well coverage) were activated and then incubated for 0.5, 1.5, 2.5, 3.5, 4.5, or 6 hours (1 well each). Two wells were left unactivated. Dendra2 photoactivation was verified by flow cytometry, with the two unactivated samples were used as negative controls.

value: total RNA


title: 2-043-1-1_S150


title: U2OS_AAVS-LP_C11_800ms_3.5h

description: U2OS cells activated for 800ms


title: P1139

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R03C01


title: 2-044-2-3_S139


title: 2-041-2-3_S88


title: 5A_Wt_IPC


title: U2OS_AAVS-LP_C11_800ms_2.5h

description: U2OS cells activated for 800ms


title: U2OS_AAVS-LP_C11_800ms_6h

description: U2OS cells activated for 800ms


title: P1671

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R02C01


title: KTO3, CflarF/F;Tnfrsf1a+/-

city: Tokyo

first: Ryodai

last: Shindo

state: Ota-ku

address: 5-21-16 Omori-Nishi

country: Japan

institute: Toho univercity

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45℃ on Affymetrix GeneChip Whole Transcript (WT) Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using  a G2565BA Microarray Scanner System (Affymetrix).

data_processing: Data were analyzed using GeneSpring GX software (Agilent).

label: Biotin

source_name: skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2011, Affymetrix).

extract_protocol: Total RNAs were extracted from the skin of mice of the indicated genotype using Trizol according to the manufacturer’s instructions

value: skin


title: 2-041-2-2_S181


title: FEX8-12

city: Cambridge

first: Lucas

last: Pantaleao

address: 11A Glisson Road

institute: University of Cambridge

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v1.2.3
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Placenta

extract_protocol:
Placentas were dissected, weighed, snap frozen and stored at −80 °C. Total liver RNA was extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany) including a DNAse digestion protocol.
Four high quality samples from each group were randomly selected and subjected to a cDNA library preparation using TruSeq RNALibrary Preparation kit, following the manufacturer’s protocol.

treatment_protocol: C57BL/6J mice were fed either a standard control diet, RM1 [7% simple carbohydrates/3% lipids (w/w)] or an energy-rich obesogenic diet [10% simple carbohydrates/20% lipids (w/w)] plus sweetened condensed milk [55% simple carbohydrates, 8% lipids, 8% protein (w/w), Nestle (Nestle, UK), supplemented with mineral and vitamin mix AIN93G]. Female mice were mated, and Pregnant mice were housed individually and maintained on their respective diets until sacrafice.  A subset of the mice on the Obesegenic diet were exercised until E17 of pregnancy. Placenta tissue was collected at embryonic day 19.

value: Placenta

tag: age

value: Embryonic day 19

value: wild type

tag: maternal diet

value: Obesogenic

tag: maternal exercise

value: Yes


title: KTO6, CflarF/F;K5-Cre;Tnfrsf1a+/-


title: U2OS_AAVS-LP_C11_800ms_1.5h

description: U2OS cells activated for 800ms


title: P1016

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571925026_R01C01

value: Blood

value: M

value: Unaffected


title: KTO2, CflarF/F;K5-Cre;Tnfrsf1a+/-


title: 2-041-2-1b_S63

value: baseline, cid2 :lcd, cid3 :di):CID1


title: KTO1, CflarF/+;Tnfrsf1a+/-


title: U2OS_AAVS-LP_C11_800ms_0.5h

description: U2OS cells activated for 800ms


title: P1362

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R05C02


title: FEX8


title: 2-040-2-3_S13

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 5B_Wt_IPC

value: male

value: Wildtype

value: Ischemia/reperfusion


title: U2OS_AAVS-LP_C11_0ms_Rep2

description: U2OS cells unactivated

value: U-2 OS

value: FALSE


title: FEX6-1


title: F136

value: No


title: U2OS_AAVS-LP_C11_0ms_Rep1

description: U2OS cells unactivated

value: doxycycline 2ug/mL

value: total RNA


title: FEX GAMMA

value: Placenta

value: Embryonic day 19


title: F120

value: wild type

value: Obesogenic


title: 2-039-2-2_S148

value: baseline, cid2 :lcd, cid3 :di):CID2


title: H1299 cells, Methyl-paraben rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

description: MtylPB

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using systempipeR.
Alignment to GRCh38.95 whole genome with Rsubread 1.34.6 and read feature counting with DESeq2.
Normalized by voom function from limma and edgeR.
FPKM were calculated using a fpkm function from DESeq2 and differential gene expression by edgeR.
Genome_build: GRCh38.95
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

treatment_protocol: 0.5 mM of methylparaben was treated in H1299 cells for 48 hours.

tag: cell line

value: methylparaben


title: P1848

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R04C02

value: Blood

value: M

value: Affected


title: 2-036-1-3_S34

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1718

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R03C02


title: 2-036-1-1_S18

value: baseline, cid2 :lcd, cid3 :di):CID1


title: H1299 cells, Methyl-paraben rep1

description: MtylPA


title: F112


title: P1812

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R01C02


title: P1156

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R02C02

value: Unaffected


title: H1299 cells, EtOH rep2

description: EtOHB

value: control


title: RC74

value: Control


title: H1299 cells, EtOH rep1

description: EtOHA


title: 2-032-2-3_S92


title: P1132

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R05C01


title: 2-033-2-2_S56


title: P1393

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R06C01

value: F


title: 2-032-2-1b_S94


title: F117

value: No


title: 2-040-2-2_S79


title: P1834

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R06C02


title: TC-797_washout_BRD4-NUT_input_replicate2 (ChIP-seq)

city: Houston

first: Kyle

last: Eagen

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using using bowtie2 v2.3.1 with option --very-sensitive.
Reads with a MAPQ ≥ 30 were retained using samtools v1.3.1.
PCR duplicates were removed with picard MarkDuplicates v2.9.2.
MACS2 (Zhang et al., 2008) was used to compute signal tracks by first running macs2 callpeak with parameters -B --SPMR --keep-dup all -g hs -f BAM and then running macs2 bdgcmp with parameter -m FE.
Histone H3K27ac ChIP-seq profiles were calibrated using spike-in normalization with D. melanogaster as the calibration genome, as previously described (Hu et al., 2015). As the NUT epitope is not expressed in Drosophila Kc167 cells, BRD4-NUT ChIP-seq profiles were not spike-in normalized.
The epic v0.2.12 implementation of the SICER algorithm (Xu et al., 2014) was used to identify broadly enriched domains from histone H3K27ac ChIP-seq data setting the window size to 2500 bp and gap size to 1 with parameters -w 2500 -g 1, respectively. Input libraries were used as controls for domain annotation.
Often, we observed closely spaced enriched regions and to span these regions and capture the entire domain, SICER/epic-identified domains within 25 kb of one another were combined using bedtools v2.27.1 with command bedtools merge.
To identify megadomains, the list of called domains was filtered by signal strength and by domain size. Signal strength was determined by subtracting the rpm normalized input reads from rpm normalized sample reads for each called domain and subsequently ranked in increasing order of counts. The ROSE algorithm (Rank Ordering of Super-Enhancers) (Whyte et al., 2013) was applied to the ranked dataset to determine the cutoff threshold for signal strength by sliding a diagonal line and finding the point along the abscissa where the diagonal line was tangent to the rank-ordered curve. The cutoff for feature size was determined in a similar manner by ranking the domain length in base pairs and applying ROSE. Domains that exceeded both the signal cutoff and the size threshold were retained using bedtools intersect with default parameters.
The above was performed for each biological replicate, and, then, to create the highest confidence domain list, domains identified in both replicates were merged using bedtools intersect with default parameters. The resulting domains were considered “megadomains”.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.bw file of ChIP-seq track in bigWig format.
Supplementary_files_format_and_content: *.bed file of megadomain locations in bed format.

source_name: TC-797 cultured cells

growth_protocol: 293TRex-Flag-BRD4-NUT-HA cells were a kind gift from Christopher A. French (Brigham and Women’s Hospital, Boston, MA). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 15 µg/mL blasticidin (Gibco #A1113903) + 100 µg/mL hygromycin (Corning #30240CR) at 37° C with 5% CO2. TC-797 cells were a kind gift from Jeffrey A. Toretsky (Georgetown University, Washington, DC). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) at 37° C with 5% CO2. Kc167 cells were obtained from the Drosophila Genomics Resource Center (#1; Bloomington, IN). Cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde. Cells were lysed with detergent and chromatin solubilized by shearing (for H3K27ac IP) or shearing and enzymatic digestion (for BRD4-NUT IP). An aliquot was removed as the input control and the samples then immunoprecipitated with the respective antibody. DNA-protein cross-links were reversed and the DNA then purified.
DNA was prepared for next-generation sequencing using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO.  TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

tag: cell type

value: NUT carcinoma

tag: chip antibody

value: none (input control)

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: RC73

value: Placenta

value: Embryonic day 19

value: wild type


title: RC61


title: TC-797_washout_BRD4-NUT_input_replicate1 (ChIP-seq)


title: P1561

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R04C01


title: 2-031-2-1_S69

source_name: adipose tisue


title: RC60


title: TC-797_MZ1_BRD4-NUT_input_replicate2 (ChIP-seq)


title: P1104

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R03C01

source_name: Blood


title: 2-031-1-1_S13


title: NFIBX-dKO_M16

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: processed data file: NFIDKO_ATAC_mm10_peaks.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
Duplicates were removed using Picard. ATAC-seq signal tracks were presented by Integrative Genomics Viewer (IGV) software.
Peaks were called using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_ATAC_mm10_peaks.txt: Tab-delimited text files containing peak calling results.

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen and immediately subjected to ATAC-seq library generation.
FACS-sorted cells were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were subjected to a transposition reaction at 37°C for 30 min with 10μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10-15 cycles. Library concentration and quality were assayed by D1000 Tape Station (Agilent) prior to sequencing. The samples were sequenced on Illumina HiSeq 2000 using a 50bp paired-end-reads setting.

value: Male

value: Hair follicle stem cells

tag: sorting markers

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos), YFP (pos)


title: TC-797_MZ1_BRD4-NUT_input_replicate1 (ChIP-seq)


title: P1663

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R02C01

value: Blood

value: M

value: Affected


title: 2-031-1-1_S109

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

value: baseline, cid2 :lcd, cid3 :di):CID1


title: P1661

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744147_R01C01

value: Unaffected


title: NFIBX-dKO_M14

tag: strain


title: TC-797_DMSO_BRD4-NUT_input_replicate2 (ChIP-seq)


title: NFI-WT_M15

description: processed data file: NFIWT_ATAC_mm10_peaks.txt

tag: Sex

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos)


title: 2-028-2-3_S190

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1150

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R06C02


title: NFI-WT_M13


title: P1123

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R05C02


title: TC-797_washout_H3K27ac_input_replicate1 (ChIP-seq)


title: Spi-C B

city: London

first: Rodney

middle: Peter

last: DeKoter

state: Ontario

address: 1151 Richmond St

department: Microbiology and Immunology

country: Canada

institute: Western University

data_processing:
Illumina HiSeq2000 .bam files provided by the sequencing core were processed using rmdup (version 1.0.0) to remove duplicate reads
Files were converted to FASTQ format using Bam-to-FASTA/Q (version 1.0.0) and reads groomed to remove Illumina adapter sequences with TrimGalore!(Krueger 2015) in Galaxy Suite (Giardine, Riemer et al. 2005; Blankenberg, Von Kuster et al. 2010; Goecks, Nekrutenko et al. 2010).
Single-end reads aligned to reference MGSCv37 (MM10) using Bowtie (Langmead, Trapnell et al. 2009).
Bowtie reported only the best alignment for each fragment (--best) with a maximum number of 2 mismatches with an average quality score of at least 70. Peaks called in MACS 1.4.1 with an mfold of (10,30) (Zhang, Liu et al. 2008).
Peak-calling was conducted for two biological replicates for each condition, and replicate region files were used for determining differential peaks between the experimental conditions.
Genome_build: MM9
Supplementary_files_format_and_content: .bigwig files represinging ChIP-signal were generated using using MACS1.4.1.

source_name: 38B9 cells

growth_protocol: 38B9 cells were grown in RPMI-1640 media (Wisent) supplemented with 10% fetal bovine serum (Wisent) , 100 U/mL penicillin–streptomycin + 2 mM L-glutamine, and 5 × 10−5 mol/L 2-mercaptoethanol.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes with rocking at room temperature, and cross-linking was terminated by addition of 125 mM glycine. Pellets were washed in cold PBS and snap frozen in liquid nitrogen. Cell pellets were lysed in buffer (50 mM Tris-HCl [pH 8.1], 10 mM EDTA, 1% SDS) containing Halt™ protease inhibitor mixture (Thermo Scientific). Chromatin fragmentation was conducted using 30 cycles of sonication on a Bioruptor (Diagenode). Chromatin was immunoprecipitated overnight at 4°C with anti-FLAG M2 beads (Sigma-Aldrich) on 300 ug of chromatin per sample. Bound beads were washed once in low salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl[pH 8.0], 150 mM NaCl), once with high salt wash buffer (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCL[pH 8.0], 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Na-deoxycholate, 1mM EDTA, 10 mM Tris-HCl [pH 8.0]), and twice with Tris-EDTA buffer at pH 8.0. Immunocomplexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and the buffer adjusted to 200 mM NaCl. Cross-linking was reversed at 65°C overnight and DNA isolated using a Wizard SV Gel and PCR purification kit (Promega).
Libraries were generated robotically with 10 ng of fragmented DNA (100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold, the size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LaChip GX (PerkinElmer) instrument. Libraries were sequenced on a single-end 100bp read length run on a HiSeq2000 (Illumina).

treatment_protocol: Chromatin was prepared from cells in early to mid log-phase growth.

tag: chip-antibody

value: Anti-FLAG M2 Magnetic Beads (Sigma-Aldrich M8823)


title: 2-028-2-1b_S108

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)


title: TC-797_washout_H3K27ac_input_replicate2 (ChIP-seq)

value: NUT carcinoma


title: 2-028-2-2_S40

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1005

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R04C02

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAGEN's QIAamp DNA Blood Maxi kit (cat No 51194)

tag: tissue


title: TC-797_MZ1_H3K27ac_input_replicate2 (ChIP-seq)

value: none (input control)

value: Drosophila melanogaster Kc167 cells


title: 2-028-1-1_S172


title: P1551

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R03C02

tag: gender


title: 2-027-1-2_S16

tag: cid (cid1


title: Spi-C Input


title: TC-797_MZ1_H3K27ac_input_replicate1 (ChIP-seq)


title: P1594

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R02C02


title: 2-025-2-2_S126

tag: individual


title: TC-797_DMSO_H3K27ac_input_replicate2 (ChIP-seq)


title: 2-025-2-1b_S12


title: TC-797_DMSO_H3K27ac_input_replicate1 (ChIP-seq)


title: P1142

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R06C01

value: F


title: 2-024-2-3_S73


title: P1600

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R05C01


title: 293TRex_induced_BRD4-NUT_input_replicate2 (ChIP-seq)

source_name: 293TRex-Flag-BRD4-NUT-HA cultured cells

value: Human embryonic kidney


title: 2-024-2-1_S183


title: Spi-C A


title: 293TRex_induced_BRD4-NUT_input_replicate1 (ChIP-seq)


title: P1426

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R04C01


title: 293TRex_uninduced_BRD4-NUT_input_replicate2 (ChIP-seq)


title: P1691

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R03C01


title: 2-020-2-3_S16


title: 2-022-2-1_S25


title: P1415

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R02C01


title: P1454

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R06C02


title: 293TRex_induced_H3K27ac_input_replicate2 (ChIP-seq)


title: 2-022-1-1_S89


title: P1215

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R01C01


title: 293TRex_induced_H3K27ac_input_replicate1 (ChIP-seq)


title: 2-020-2-3_S112


title: P1257

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R05C02


title: 293TRex_uninduced_H3K27ac_input_replicate2 (ChIP-seq)


title: 293TRex_uninduced_BRD4-NUT_input_replicate1 (ChIP-seq)


title: 2-020-2-2_S4


title: P1229

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744144_R01C02


title: 2-020-2-1_S235


title: P1526

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R04C02


title: 293TRex_uninduced_H3K27ac_input_replicate1 (ChIP-seq)


title: 2-020-2-1_S152


title: P1177

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R03C02


title: TC-797_washout_BRD4-NUT_replicate2 (ChIP-seq)

value: NUT (C52B1) Rabbit mAb (Cell Signaling Technology Signaling #3625S, lot 4 RRID:AB_2066833)


title: 2-020-1-2_S10


title: P1258

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R02C02


title: TC-797_washout_BRD4-NUT_replicate1 (ChIP-seq)


title: 2-020-1-2_S106


title: P1434

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R01C02


title: TC-797_MZ1_BRD4-NUT_replicate2 (ChIP-seq)


title: 2-018-1-2_S188


title: P1822

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R04C01


title: TC-797_DMSO_BRD4-NUT_input_replicate1 (ChIP-seq)


title: TC-797_DMSO_BRD4-NUT_replicate2 (ChIP-seq)


title: 2-018-2-2_S103


title: TC-797_MZ1_BRD4-NUT_replicate1 (ChIP-seq)


title: P1794

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R06C01


title: P1576

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R05C01