title: WT2_LV

description: Nppb-KO-RNA-seq-counts.xlsx


title: CMT-077-tumor

status: Public on Jul 22 2019

type: SRA

city: Seoul

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

country: South Korea

institute: Yonsei University College of Medicine

description: processed data file: CMT_222S_FPKM.csv

library_source: transcriptomic

data_processing:
Base-calling process was performed using FastQC version 0.10.1.
Alignment was conducted using Tophat version 2.0.9 with Ensembl gene annotation of CanFam3.1 and fr-firststrand library type. Canine reference genome sequence CanFam3.1 (Ensembl, Canis lupus familiaris) was used in alignment process through Bowtie2 Index.
FPKM values are calculated by Cufflinks version 2.1.1 using bam files. Parameters including fr-firststrand, CanFam3.1 GTF, CanFam3.1 Bowtie2 Index are used.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CMT_222S_FPKM.csv: Comma-separated text file includes FPKM values for each Sample.

molecule: total RNA

organism: Canis lupus familiaris

source_name: canine mammary tumor tissue

extract_protocol:
Fresh tissue samples were transferred in to RNAlater (Thermo Fisher Scientific), refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit (Qiagen).
RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit. Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: dog id

tag: tissue

value: mammary tumor tissue

tag: tumor grade

tag: age

tag: diagnosis

value: Simple carcinoma (Solid type)

tag: Sex

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Beagle

tag: er allred score

tag: er status

value: Negative

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: BRD3_ChIPSeq_IBET151_5000nM_K562_rep2

city: Beirut

first: Pierre

last: Khoueiry

address: Bliss street

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

description:
BRD3_K562_ChIP_BRD3_151_C_5000nM_RPGC_inputSub.bw
K562_ChIP_BRD3_151_C_5000nM.bed

library_source: genomic

data_processing:
Quality check for raw sequencing reads was performed using FastQC
ChIP-seq and Chem-seq reads were aligned to the hg19 genome assembly using bwa with default parameters
Data were filtered for duplicated reads using samtools
Peaks were called using a MACS2 derived pipeline on two replicates for each sample using a combination of lenient and strick p-value largely inspired by the IDR workflow.
Bigwig profiles were created using deeptools normalized using the RPGC method with input subtracted
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include signal files (biwig) and peak files (bed)

molecule: genomic DNA

organism: Homo sapiens

source_name: CML cells

growth_protocol:
MV4;11 and K562 cells were grown in RPMI-1640 supplemented with 10% FBS, in a humidified incubator (37 °C, 5% CO2).
MV4;11 and K562 cells were grown in RPMI-1640 supplemented with 10% FBS, in a humidified incubator (37 °C, 5% CO2).

extract_protocol:
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000

treatment_protocol:
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions

tag: cell type

value: Chronic Myelogenous Leukemia

tag: chip antibody

value: BRD3 (Bethyl Labs #A302-368A)


title: CMT-074-normal

description: processed data file: CMT_222S_FPKM.csv

source_name: canine mammary normal tissue

tag: dog id

value: mammary normal tissue

value: Benign

value: Simple adenoma

value: Neutered

value: Shih Tzu

value: Positive


title: LFD ad lib, mouse 3

type: RNA

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

country: USA

institute: Weill Cornell Medical College

hyb_protocol: Samples were hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Genomics Resources Core Facility at Weill Cornell Medicine.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G (GC30007G) according the manufacturer’s instructions. Affymetrix GeneChip Command Console Software was used for image acquisition.

data_processing: Raw image data were background corrected, normalized and summarized into probeset expression values using the Robust Multichip Average (RMA) algorithm within GeneSpring 12.6 Software (Agilent Technologies). Log2 transformed expression values for within-array replicate probes were condensed by their average. Differential gene expression analyses were carried out using limma package in R 3.5.0 (R Foundation for Statistical Computing, Vienna, Austria). Genes with false discovery rate < 0.05 and fold change > 2 in between-group comparisons were considered significantly differentially expressed.

label: biotin

organism: Mus musculus

source_name: Peri-prostatic fat

label_protocol: Samples were labeled and hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Genomics Resources Core Facility at Weill Cornell Medicine.

growth_protocol: All animals were housed in the Weill Cornell Medicine vivarium under standard temperature controlled conditions with a 12-hour light-dark cycle. Animals had ad libitum access to their respective diets (low fat or high fat).

extract_protocol: Mice were euthanized by CO2 asphyxiation, periprostatic fat was harvested and snap frozen in liquid nitrogen prior to storage at -80C. Total RNA was extracted from frozen tissue using trizol reagent and the RNAeasy Mini Kit (Qiagen). RNA concentration (NanoDrop) and quality (Bioanalyzer) were measured. Only samples with RNA Integrity Number (RIN) >7 were used for microarray analysis.

treatment_protocol: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet (LFD, 10 kcal% fat, 12450Bi; Research Diets) or high fat diet (HFD, 60 kcal% fat, D12492i) beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks. After 12 weeks of feeding, the HFD fed mice were divided into two groups. One group was fed ad libitum for an additional 7 weeks until sacrifice while the other group was switched to a 30% CR feeding regimen for 7 weeks until sacrifice. Each day for 7 weeks the CR group received 70% of the amount consumed by the HFD group that was fed ad libitum. The LFD group was fed ad libitum for an additional 7 weeks until sacrifice. All mice were sacrificed at 25 weeks of age and periprostatic fat was harvested and snap frozen.

tag: strain

tag: tissue

value: Peri-prostatic fat

value: 25 weeks

tag: treatment

value: LFD no calorie restriction (ad lib)


title: Frontal_Cortex AD (9344744094_G)

city: London

first: Hamel

last: Patel

address: De Crespigny Park

department: Biostatistics and health informatics

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was Maximum Likelihood Estimation (MLE) background corrected using R package “MBCB” (version 1.18.0), log2 transformed, and Robust Spline Normalisation (RSN) using R package “lumi” (version 2.16.0)

label_protocol: Total RNA (25ng) was prepared for array expression profiling using the Ovation Pico WTA system (NuGEN Technologies, Inc., San Carlos, CA), as described by the manufacturer

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen,74804) and according to manufactures protocol.

treatment_protocol: Tissue blocks, approximately 0.5-1cm3, were obtained and stored in RNAlater RNA Stabilization Reagent (Qiagen) before RNA extraction.

tag: gender

value: MALE

tag: age

tag: individual

value: Subject  9

tag: disease state

value: AD


title: CMT-074-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

tag: Sex

value: Female

tag: neuter status

tag: lymphatic vessel invasion

value: Absent

tag: breed


title: Cerebellum AsymAD (9031356084_K)

source_name: Cerebellum

value: Subject  8

value: Cerebellum

value: AsymAD


title: LFD ad lib, mouse 5


title: LFD ad lib, mouse 4


title: LFD ad lib, mouse 1


title: Temporal_Cortex AsymAD (9031356091_K)


title: High Fat Diet, Mouse 1

treatment_protocol: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet  (10 kcal% fat, 12450Bi; Research Diets), n=4 or high fat diet (60 kcal% fat, D12492i), n=5 beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks before being sacrificed by CO2 asphyxiation at 18 weeks of age. Periprostatic fat was then harvested, snap frozen in liquid nitrogen, and stored at -80C until total RNA extraction.

value: 18 weeks

tag: diet

value: High fat diet, 60 kcal% fat


title: LFD ad lib, mouse 6


title: Entorhinal_Cortex AsymAD (9216457022_K)


title: Temporal_Cortex AD (9031356085_F)

value: Subject  10


title: Entorhinal_Cortex AsymAD (9216457027_K)


title: Entorhinal_Cortex AD (9371242065_B)


title: CMT-072-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Carcinoma in benign mixed tumor

value: Intact

value: Mixed

tag: er allred score

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: KO-IL25

city: Shanghai

first: Tao

last: Yu

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Science

description: Tpl2-KO with IL-25 treatment

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: hepatocytes

growth_protocol: Hepatocytes were isolated from liver of adult WT and Tpl2 totally deficient mice and cultured for 24 hours in a DMEM medium supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stimulated for 8 h with IL-25

tag: strain

tag: genotype

tag: tissue

value: Liver


title: CMT-072-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: age

value: Positive


title: CMT-070-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Benign

tag: diagnosis

value: Benign mixed tumor

value: Pomeranian


title: CMT-063-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: Sex

value: Female

tag: neuter status

value: Absent

value: Shih Tzu


title: HFD ad lib, mouse 5

value: Peri-prostatic fat

value: 25 weeks

tag: treatment

value: HFD no calorie restriction (ad lib)


title: Stat3β TG rep3

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Quality control of the raw sequence reads was carried out with FastQC
Pre-processing  with PRINSEQ-lite
Alignment against the mouse reference genome (GRCm38) using STAR
Normalization and differential gene expression analysis with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes normalized values for each sample

source_name: Bone marrow

extract_protocol: Total RNA from sorted, MLL-AF9+ transplanted blasts (harvested from bone marrow from NSG mice 6 weeks post-transplantation) was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Fetal liver-derived cells from Mx1-Cre/Stat3β transgenic and wild-type mice were transformed with a MLL-AF9-retrovirus. 2x106 FLCs were injected into immunocompromised NSG mice via the tail vein. Four weeks post-transplantation, mice were injected with 100μL polyinosine-polycytidine (2mg/mL), to induce Cre and therefore the Stat3β transgene. Transplanted mice suffering from acute myeloid leukemia were sacrifized 6 weeks post-transplantation, bone marrow was harvested and sorted for MLL-AF9+ blasts. MLL-AF9+ blasts were directly used for total RNA extraction.

tag: recipient strain

value: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG)

tag: transplanted cells

value: MLL-AF9+ blasts

tag: transplanted cells (origin)

value: C57BL/6, Mx1-Cre recombinase & Stat3β transgenic


title: Temporal_Cortex AsymAD (9031292037_L)

tag: gender

value: FEMALE

tag: individual

value: Subject  7

tag: disease state

value: AsymAD


title: HFD ad lib, mouse 3


title: HFD ad lib, mouse 6


title: Entorhinal_Cortex AsymAD (9031356094_L)


title: Cerebellum AsymAD (9031356072_L)

value: Cerebellum


title: HFD ad lib, mouse 4


title: LFD ad lib, mouse 2

value: LFD no calorie restriction (ad lib)


title: CMT-060-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Benign

value: Complex adenoma

value: Intact

tag: lymphatic vessel invasion

tag: breed

tag: er allred score

tag: er status

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: Frontal_Cortex AsymAD (9031356097_K)

value: MALE

tag: age

value: Subject  8

tag: tissue


title: Frontal_Cortex AsymAD (9031356077_L)


title: CMT-057-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Female

tag: neuter status

value: Neutered

value: Absent

value: Maltese


title: Stat3β TG rep2

tag: recipient strain

value: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG)

tag: transplanted cells

value: MLL-AF9+ blasts

tag: transplanted cells (origin)

value: C57BL/6, Mx1-Cre recombinase & Stat3β transgenic


title: Stat3β TG rep1


title: Temporal_Cortex AsymAD (9031356081_L)

tag: gender

value: FEMALE

tag: individual

value: Subject  7

tag: disease state

value: AsymAD


title: CMT-053-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Intact

tag: lymphatic vessel invasion

tag: breed

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: WT-IL25

description: WT with IL-25 treatment

tag: strain

tag: genotype

value: Wild type

tag: tissue

value: Liver


title: HFD ad lib, mouse 1

value: Peri-prostatic fat

tag: age

value: 25 weeks

tag: treatment

value: HFD no calorie restriction (ad lib)


title: WT rep3

value: C57BL/6, wild-type littermates


title: CMT-053-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: tumor grade

tag: diagnosis

tag: Sex

value: Female

tag: neuter status

value: Positive

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: CMT-051-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Benign mixed tumor

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Mixed

value: loss to follow-up


title: WT rep1

tag: recipient strain

value: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG)

tag: transplanted cells

value: MLL-AF9+ blasts

tag: transplanted cells (origin)


title: WT rep2


title: CMT-051-normal

description: processed data file: CMT_222S_FPKM.csv

value: Intact

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: HFD+CR, mouse 3

tag: strain

tag: tissue

value: Peri-prostatic fat

tag: age

tag: treatment

value: HFD + 30% calorie restriction


title: Ctl noAB (rep. 1 SPT6 control)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA.
Sequence reads with an alignment score <20 reads were discarded.
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

source_name: AS CDK12 HCT116 cells

growth_protocol: AS CDK12 HCT116 cells were maintained in Dulbecco’s modified Eagle’s medium containing high glucose supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
ChIP was performed with SPT6 antibody. Immunoprecipitated DNA was dissolved in  H2O and DNA concentration was measured by Qubit fluorometer (Thermo Fisher Scientific) and 3.5 ng of immunoprecipitated DNA was used for library preparation.
ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) with KAPA Pure Beads (KK8001), and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 (NEB, E7335S) with 15x PCR cycles for library amplification, as per manufacturer’s instructions. Libraries were run on the fragment analyser (Advanced Analytical Technologies) to check the quality and were sequenced with 50 bp single-end reads on  Illumina HiSeq 2500 (VBCF Vienna).

treatment_protocol: Serum synchronised AS CDK12 HCT116 cells were treated with or without 5 µM 3-MB-PP1 for 4.5 h during the time of release into  DMEM containing 15% FBS

value: DMSO

tag: chip antibody

value: no antibody


title: HFD ad lib, mouse 2

value: 25 weeks

value: HFD no calorie restriction (ad lib)


title: HFD+CR, mouse 2


title: CMT-031-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tumor grade

tag: diagnosis

value: Simple adenoma

tag: Sex

value: Female

tag: neuter status

value: Positive


title: HFD+CR, mouse 4


title: Frontal_Cortex AD (9344744094_L)

tag: gender

value: FEMALE

tag: individual

value: Subject  6

tag: disease state

value: AD


title: HFD+CR, mouse 5


title: Entorhinal_Cortex AD (9371242065_D)


title: HFD+CR, mouse 1


title: 14811X3

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.18.0.
Supplementary_files_format_and_content: FeatureCount output files combined into tab-delimited file

source_name: TMEV-macrophages

extract_protocol:
RNA was extracted using TRYzol,  precipitated using glycogen, and polyA mRNA-enriched with oligo d(T)25 magnetic beads
Smarter Stranded RNA-Seq Kit  (Takara)

tag: infection

value: TMEV

tag: tisue

value: Brain

tag: tissue/cell type

value: macrophages

tag: time point

value: 6 days post-injection


title: Entorhinal_Cortex control (9216457028_I)

value: Subject  5

value: control


title: 14811X4

tag: strain


title: Frontal_Cortex control (9031356076_A)

tag: tissue


title: Inhi SPT6 (rep. 3)

value: 5 uM 3-MB-PP1

value: SPT6 (Novus Biologicals, NB100-2582)


title: Temporal_Cortex control (9031356085_A)

tag: age


title: 14811X1

source_name: PBS-microglia

value: PBS

value: microglia


title: 14811X2

source_name: TMEV-microglia


title: Inhi SPT6 (rep. 2)

tag: treatment


title: CMT-017-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Neutered

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Mixed

tag: er allred score

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: Inhi SPT6 (rep. 1)

tag: chip antibody


title: Cerebellum control (9031356073_A)

tag: gender

value: FEMALE

tag: individual

value: Cerebellum

tag: disease state


title: Entorhinal_Cortex control (9031356088_A)


title: Entorhinal_Cortex control (9216457002_A)


title: CMT-021-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tumor grade

tag: diagnosis

value: Carcinoma in benign mixed tumor

tag: Sex

value: Female

tag: neuter status

value: Maltese

value: Not applicable


title: Ctl SPT6 (rep. 3)

tag: treatment

value: DMSO


title: CMT-013-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

value: Simple carcinoma (Solid type)

tag: lymphatic vessel invasion

value: Present

tag: breed

value: Positive

value: Y


title: Ctl SPT6 (rep. 2)

value: SPT6 (Novus Biologicals, NB100-2582)


title: High Fat Diet + 17[beta]-estradiol mouse 4

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

extract_protocol:
Mice were euthanized by CO2 asphyxiation, periprostatic fat was harvested and snap frozen in liquid nitrogen prior to storage at -80C. Total RNA was extracted from frozen tissue using trizol reagent and the RNAeasy Mini Kit (Qiagen). RNA concentration (NanoDrop) and quality (Bioanalyzer) were measured. Only samples with RNA Integrity Number (RIN) >7 were used for RNAseq.
Sequencing libraries were constructed following the Illumina TrueSeq Stranded Total RNA Library preparation protocol with rRNA depletion

tag: strain

value: Peri-prostatic fat

value: 26 weeks

tag: diet

value: High fat diet, 60 kcal% fat

value: 0.25mg 17[beta]-estradiol pellet


title: Entorhinal_Cortex AD (9371242065_J)

value: MALE

value: Subject  4

value: AD


title: High Fat Diet + 17[beta]-estradiol mouse 3


title: High Fat Diet + 17[beta]-estradiol mouse 2


title: CMT-008-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Benign mixed tumor

value: Intact

value: Absent

value: Chihuahua

tag: er allred score

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: High Fat Diet + 17[beta]-estradiol mouse 1


title: Inhi nuclear (rep. 2)

description: total nuclear RNA

data_processing:
Reads were mapped against the human genome (GRCh38) and rRNA sequences using ContextMap 2.7.9 with BWA as internal alignment program.
Read counts per gene (from Gencode version 27) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCh38
Supplementary_files_format_and_content: read counts for genes

extract_protocol:
After cellular fractionation, nuclear RNA was isolated using Tri-Reagent (MRC, #TR118), and treated with DNase (Sigma, AMPD1). 250 ng of nuclear RNA was used for library preparation after removing ribosomal RNA  with NEBNext rRNA Depletion Kit (NEB, E6310S)
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) and NEBNext Multiplex Oligos for Illumina (NEB, E7500S and E7335S), according to manufacturer's instructions and sequenced with 50 bp single-end reads on Illumina HiSeq 2500 (VBCF Vienna).

value: 5 uM 3-MB-PP1


title: CMT-009-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tumor grade

value: Osteosarcoma

value: Female

value: Maltese

value: Not applicable

value: N

tag: date of death


title: Ctl SPT6 (rep. 1)

value: DMSO

tag: chip antibody

value: SPT6 (Novus Biologicals, NB100-2582)


title: CMT-013-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: diagnosis

value: Simple carcinoma (Solid type)

tag: Sex

tag: neuter status

value: Neutered

value: Present

value: Mixed

value: Positive

value: Y


title: CMT-017-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Benign

tag: age

value: Simple adenoma

tag: lymphatic vessel invasion

value: Absent

value: loss to follow-up


title: High Fat Diet + Placebo mouse 5

tag: strain

value: Peri-prostatic fat

value: 26 weeks

tag: diet

value: High fat diet, 60 kcal% fat

tag: treatment

value: Placebo pellet


title: Inhi nuclear (rep. 3)

description: total nuclear RNA

value: 5 uM 3-MB-PP1


title: High Fat Diet + 17[beta]-estradiol mouse 5

value: 0.25mg 17[beta]-estradiol pellet


title: CMT-003-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Simple carcinoma (Tubulopapillary type)

value: Female

tag: breed

value: Chihuahua

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: High Fat Diet + Placebo mouse 4


title: CMT-008-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

value: Benign mixed tumor

value: Intact

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: Frontal_Cortex control (9031356076_B)

tag: gender

value: FEMALE

tag: individual

value: Subject  3

tag: disease state

value: control


title: Temporal_Cortex control (9031356085_B)

tag: tissue


title: Inhi nuclear (rep. 1)

description: total nuclear RNA


title: Ctl nuclear (rep. 3)

description: total nuclear RNA

value: DMSO


title: CMT-002-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

tag: age

tag: diagnosis

value: Carcinoma in benign mixed tumor

tag: Sex

tag: neuter status

value: Neutered

value: Absent

value: Shih Tzu

value: Negative

value: loss to follow-up


title: Entorhinal_Cortex control (9031356088_B)


title: High Fat Diet + Placebo mouse 3

tag: strain

value: Peri-prostatic fat

value: 26 weeks

tag: diet

value: High fat diet, 60 kcal% fat

tag: treatment

value: Placebo pellet


title: Ctl nuclear (rep. 2)

description: total nuclear RNA


title: High Fat Diet + Placebo mouse 2


title: Ctl nuclear (rep. 1)

description: total nuclear RNA


title: Inhi 3' (rep. 3)

description: polyA-selected total RNA

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from AS CDK12 HCT116 cells by TRIzol reagent (Thermo Fisher Scientific, 15596026) and purified by RNA QiAamp Spin Column (QIAGEN, 52304), according to the manufacturer’s guidelines. RNA quality was assessed by TapeStation 2200 (Agilent Technologies).
PolyA-selected libraries were made from 200 ng of total RNA input using QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.24) and external multiplexing barcodes for Illumina (i7 index primers 7001-7096; Lexogen, 044.96) with 12x PCR cycles for library amplification, according to manufacturer’s instructions. The fragment size and quality of the libraries were assessed by fragment analyzer (Advanced Analytical Technologies) and sequenced with 50 bp single-end reads on a single lane of an Illumina HiSeq 2500 (VBCF Vienna).

treatment_protocol: Serum synchronised AS CDK12 HCT116 cells were treated with or without 5 µM 3-MB-PP1 for 5 h during the time of release into  DMEM containing 15% FBS

value: 5 uM 3-MB-PP1


title: High Fat Diet + Placebo mouse 1


title: gH2A.V on preassembled FlyFos 2 min FseI cut

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Reads were aligned to the reference genome (version dm6) using bowtie2 (version 2.2.9).
Coverage vectors were generated from BAM using R/Bioconductor packages, and were normalized to the total number of reads derived from the uncut fosmid. Tracks were exported as Bedgraph files.
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files of normalized ChIP-seq tracks

organism: Drosophila melanogaster

source_name: cell-free chromatin assembly system

extract_protocol:
Drosophila embryo extract (DREX) was prepared from preblastoderm embryos (within 90 min after egg laying as described {Becker:1992tt}, with modifications. The embryos were dechorionated in 200 ml embryo wash buffer (0.7% NaCl, 0.04% Triton X-100) and 60 ml 13% sodium hypochlorite (VWR) for 3 min at room temperature (RT) while stirring. Embryos were rinsed for 5 min with cold water and transferred into a glass cylinder with embryo wash buffer. Settled embryos, were washed first in 0.7% NaCl and then in extract buffer (10 mM HEPES, pH 7.6, 10 mM KCI, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol, 10 mM 3-glycerophosphate; 1 mM DTT, protease inhibitors added freshly before use (0.2 mM PMSF, 1 mM Aprotinin, 1 mM Leupeptin, 1 mM Pepstatin). Embryos were settled in a homgenplus homogenizer (Schuett-Biotec) the supernatant was decanted and homogenized with one stroke at 3000 rpm and 10 strokes at 1500 rpm. The homogenate was filled up to 5 mM MgCl2 (f.c.) and centrifuged for 15 min at 27,000 g at 4°C. The white lipid layer was discarded and the supernatant was centrifuged for 2 h at 245,000 g at 4°C. The clear extract was collected with a syringe, leaving the lipid layer and pellet behind.
MNase-cleaved DNA after overnight proteinase K digestion was purified with the GenElute PCR clean-up kit (Sigma-Aldrich) and libraries for paired-end sequencing were prepared using the MicroPlex Library Preparation kit (Diagenode). Fifty bp sequencing reads were obained on a HiSeq 1500 (Illumina) instrument.

tag: ChIP

tag: template

tag: assembly

value: DREX, assembly on preassembled H2A.V arrays

tag: cut

tag: time (min)


title: gH2A.V on preassembled FlyFos 10 min FseI cut


title: Inhi 3' (rep. 2)

description: polyA-selected total RNA


title: Low Fat Diet mouse 5

value: Low fat diet, 10 kcal% fat

value: Nothing


title: Low Fat Diet mouse 4


title: 1st and 2nd pharyngeal arches, Kat6a homozygous knockout replicate 4 (RNA-seq)

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for base-calling
Reads were aligned to the mouse genome by Rsubread version 1.14.2
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Technical replicates were aggreated following read counting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene for the combined technical replicates.

source_name: 1st and 2nd pharyngeal arches

extract_protocol:
For RNA sequencing and RT-qPCR, total RNA was isolated from the maxillary component of the 1st pharyngeal arch at E10.5 and E11.5, the palatal shelves at E13.5 and E14.0 and E10.5 1st and 2nd pharyngeal arches (RNAeasy, Qiagen) from embryos on a C57BL/6 background.
Uniquely indexed libraries were generated per sample with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), according to manufacturer's instructions.

tag: kat6a genotype

tag: dlx5 genotype

tag: batch

tag: developmental stage

value: 1st and 2nd pharyngeal arches


title: Low Fat Diet mouse 3

tag: tissue


title: Inhi 3' (rep. 1)

description: polyA-selected total RNA


title: Cerebellum control (9031356073_B)

tag: gender

value: FEMALE

tag: age

tag: individual

value: Subject  3

value: Cerebellum

tag: disease state

value: control


title: 1st and 2nd pharyngeal arches, Kat6a homozygous knockout replicate 3 (RNA-seq)

tag: strain


title: gH2A.V on preassembled FlyFos 0.5 min RsrII cut


title: Temporal_Cortex control (9344744089_I)

value: Subject  2


title: Low Fat Diet mouse 2

tag: diet


title: Ctl 3' (rep. 3)

description: polyA-selected total RNA

tag: treatment

value: DMSO


title: Frontal_Cortex AD (9345344027_D)

value: Subject  1

value: AD


title: Cerebellum AD (9344744094_C)


title: Entorhinal_Cortex control (9216457002_B)


title: Frontal_Cortex control (9344744043_I)


title: 1st and 2nd pharyngeal arches, Kat6a homozygous knockout replicate 2 (RNA-seq)


title: Entorhinal_Cortex AD (9371242082_K)


title: gH2A.V on preassembled FlyFos 10 min RsrII cut

tag: ChIP


title: gH2A.V on preassembled FlyFos 0.5 min FseI cut

tag: template


title: Temporal_Cortex AD (9371242065_I)


title: Ctl 3' (rep. 1)

description: polyA-selected total RNA


title: gH2A.V on preassembled FlyFos 10 min control

tag: assembly


title: gH2A.V on preassembled FlyFos 2 min control

tag: cut


title: 1st and 2nd pharyngeal arches, Kat6a homozygous knockout replicate 1 (RNA-seq)


title: Inhi noAB (rep. 1)

extract_protocol:
ChIP was performed with RNAPII, P-Ser2 and P-Ser5 antibodies. Immunoprecipitated DNA was dissolved in  H2O and DNA concentration was measured by Qubit fluorometer (Thermo Fisher Scientific) and 4 ng of immunoprecipitated DNA was used for library preparation.
ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) with KAPA Pure Beads (KK8001), and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2 (NEB, E7335S, E7500S) with 13x PCR cycles for library amplification, as per manufacturer’s instructions. Libraries were run on the fragment analyser (Advanced Analytical Technologies) to check the quality and were sequenced with 50 bp single-end reads on 2 lanes of an Illumina HiSeq 2500 (VBCF Vienna).

tag: chip antibody

value: no antibody


title: gH2A.V on preassembled FlyFos 2 min RsrII cut

tag: time (min)


title: gH2A.V on preassembled FlyFos 0.5 min control


title: 1st and 2nd pharyngeal arches, Dlx5 homozygous knockout replicate 4 (RNA-seq)

tag: kat6a genotype

tag: dlx5 genotype


title: H2A.V on preassembled FlyFos 10 min FseI cut


title: 1st and 2nd pharyngeal arches, Dlx5 homozygous knockout replicate 3 (RNA-seq)

tag: batch

tag: developmental stage


title: Ctl 3' (rep. 2)

description: polyA-selected total RNA


title: Infarct zone-7.2

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
RNA-MI-counts.xlsx
IZ-7.2

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10 (RNA-seq)
Supplementary_files_format_and_content: RNA-seq: MI-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

source_name: Infarct zone left ventricular tissue post myocardial infarction

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

extract_protocol:
Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen).
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads.

treatment_protocol: Tamoxifen (20 mg/kg) was administrated i.p. one week prior to t=0 and repeated the two following days. Myocardial infarction was performed as described previously in Sergeeva et al., 2013.

value: FVB/N

tag: stress

value: myocardial infarction

tag: tissue

value: infarct zone left ventricular tissue

tag: time

value: 7 days post-stress

tag: sample type


title: Inhi Ser5P (rep. 3)

value: 5 uM 3-MB-PP1

value: Phospho-RNAPII (Ser5) - 3E8 (Active motif, 61085)


title: Ctl noAB (rep. 1)


title: Low Fat Diet mouse 1

tag: strain

value: Peri-prostatic fat

tag: age

value: 26 weeks

value: Low fat diet, 10 kcal% fat

value: Nothing


title: Border zone-14.6

description:
RNA-MI-counts.xlsx
BZ-14.6

source_name: Border zone left ventricular tissue post myocardial infarction

value: border zone left ventricular tissue post myocardial infarction

value: 14 days post-stress


title: H2A.V on preassembled FlyFos 2 min FseI cut

value: DREX, assembly on preassembled H2A.V arrays


title: Infarct zone-7.1

description:
RNA-MI-counts.xlsx
IZ-7.1


title: 1st and 2nd pharyngeal arches, Dlx5 homozygous knockout replicate 1 (RNA-seq)

value: 1st and 2nd pharyngeal arches


title: H2A.V on preassembled FlyFos 0.5 min FseI cut


title: Inhi Ser5P (rep. 2)

tag: treatment


title: Border zone-14.2

description:
RNA-MI-counts.xlsx
BZ-14.2


title: Infarct zone-7.5

description:
RNA-MI-counts.xlsx
IZ-7.5


title: Border zone-14.1

description:
RNA-MI-counts.xlsx
BZ-14.1


title: 1st and 2nd pharyngeal arches, Kat6a and Dlx5 heterozygous knockout replicate 3 (RNA-seq)


title: Inhi Ser5P (rep. 1)


title: 1st and 2nd pharyngeal arches, Kat6a and Dlx5 heterozygous knockout replicate 4 (RNA-seq)


title: Inhi Ser2P (rep. 3)

value: Phospho-RNAPII (Ser2) - 3E10 (Active motif, 61083)


title: H2A.V on preassembled FlyFos 2 min RsrII cut

tag: ChIP


title: Border zone-7.9

description:
RNA-MI-counts.xlsx
BZ-7.9


title: 1st and 2nd pharyngeal arches, Kat6a and Dlx5 heterozygous knockout replicate 2 (RNA-seq)


title: H2A.V on preassembled FlyFos 0.5 min RsrII cut

tag: template


title: Border zone-7.8

description:
RNA-MI-counts.xlsx
BZ-7.8


title: Inhi Ser2P (rep. 1)


title: 1st and 2nd pharyngeal arches, Dlx5 homozygous knockout replicate 2 (RNA-seq)


title: 1st and 2nd pharyngeal arches, Kat6a and Dlx5 heterozygous knockout replicate 1 (RNA-seq)


title: H2A.V on preassembled FlyFos 10 min control

tag: assembly


title: 1st and 2nd pharyngeal arches, Dlx5 heterozygous knockout replicate 4 (RNA-seq)


title: Inhi PolII (rep. 3)

value: RNAPII (Santa Cruz, sc-899)


title: Border zone-7.6

description:
RNA-MI-counts.xlsx
BZ-7.6


title: H2A.V on preassembled FlyFos 2 min control

tag: cut


title: Border zone-3.3

description:
RNA-MI-counts.xlsx
BZ-3.3

value: 3 days post-stress


title: 1st and 2nd pharyngeal arches, Dlx5 heterozygous knockout replicate 3 (RNA-seq)


title: Inhi PolII (rep. 2)

tag: chip antibody


title: 1st and 2nd pharyngeal arches, Dlx5 heterozygous knockout replicate 2 (RNA-seq)


title: H2A.V on preassembled FlyFos 10 min RsrII cut

tag: time (min)


title: Inhi PolII (rep. 1)


title: input Covaris 120 min FseI cut

value: covaris input

value: DREX assembly on FlyFosmid


title: 1st and 2nd pharyngeal arches, Dlx5 heterozygous knockout replicate 1 (RNA-seq)

tag: kat6a genotype


title: Remote zone-14.6

description:
RNA-MI-counts.xlsx
RM-14.6

source_name: Remote zone left ventricular tissue post myocardial infarction

value: FVB/N

value: myocardial infarction

value: remote zone left ventricular tissue post myocardial infarction


title: input Covaris 10 min FseI cut


title: 1st and 2nd pharyngeal arches, Kat6a heterozygous knockout replicate 4 (RNA-seq)

tag: dlx5 genotype


title: Ctl Ser5P (rep. 3)

value: DMSO

value: Phospho-RNAPII (Ser5) - 3E8 (Active motif, 61085)


title: Border zone-3.1

description:
RNA-MI-counts.xlsx
BZ-3.1


title: Inhi Ser2P (rep. 2)

value: 5 uM 3-MB-PP1


title: Remote zone-14.2

description:
RNA-MI-counts.xlsx
RM-14.2


title: Ctl Ser5P (rep. 2)


title: Ctl Ser5P (rep. 1)


title: 1st and 2nd pharyngeal arches, Kat6a heterozygous knockout replicate 2 (RNA-seq)

tag: batch


title: input Covaris 10 min control


title: Ctl Ser2P (rep. 3)


title: 1st and 2nd pharyngeal arches, Kat6a heterozygous knockout replicate 3 (RNA-seq)

tag: developmental stage


title: input Covaris 120 min control


title: Remote zone-14.1

description:
RNA-MI-counts.xlsx
RM-14.1

tag: stress


title: Ctl Ser2P (rep. 2)


title: Remote zone-7.9

description:
RNA-MI-counts.xlsx
RM-7.9

tag: tissue

value: 7 days post-stress


title: Remote zone-7.8

description:
RNA-MI-counts.xlsx
RM-7.8

tag: time


title: Border zone-3.2

description:
RNA-MI-counts.xlsx
BZ-3.2

tag: sample type


title: 1st and 2nd pharyngeal arches, Kat6a heterozygous knockout replicate 1 (RNA-seq)

tag: strain


title: gH2A.V 120 min FseI cut


title: 1st and 2nd pharyngeal arches, Wild type replicate 4 (RNA-seq)


title: Ku 120 min FseI cut

value: Ku


title: H2A.V on preassembled FlyFos 0.5 min control


title: Remote zone-7.6

description:
RNA-MI-counts.xlsx
RM-7.6


title: Ctl Ser2P (rep. 1)


title: H2A.V 120 min FseI cut


title: 1st and 2nd pharyngeal arches, Wild type replicate 3 (RNA-seq)


title: Ctl PolII (rep. 3)


title: input 120 min FseI cut

value: input


title: Remote zone-3.3

description:
RNA-MI-counts.xlsx
RM-3.3


title: Remote zone-3.2

description:
RNA-MI-counts.xlsx
RM-3.2


title: Ctl PolII (rep. 2)


title: Ku 120 min control


title: 1st and 2nd pharyngeal arches, Wild type replicate 2 (RNA-seq)


title: 1st and 2nd pharyngeal arches, Wild type replicate 1 (RNA-seq)


title: Ctl PolII (rep. 1)


title: Remote zone-3.1

description:
RNA-MI-counts.xlsx
RM-3.1

extract_protocol:
Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen).
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads
Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen). For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). Samples were gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. A total of 50.000 nuclei per sample was collected and successively washed with PBS and used as input for ATAC-seq. Prior to sequencing, a quality check was performed to assure cardiomyocyte-specific open chromatin
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads.


title: gH2A.V 120 min control


title: H2A.V 120 min control


title: R728T1-shTaz-2

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trim_galore. Then mapped to  whole genome using TopHat (Trapnellet al.,   2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Mortazaviet al., 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: mouse small cell lung cancer from R728T1 (non-SMCs derived from Rb/P53 mouse model)

growth_protocol: Nude mice were transplanted subcutaneously by R728T1 with or without Taz knockdown

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: subcutaneous tumor

tag: cell type

value: small cell lung cancer


title: R728T1-shTaz-1


title: Sham-14.2

description:
RNA-MI-counts.xlsx
S-14.2

source_name: Sham operated left ventricular tissue

extract_protocol:
Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen).
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads

value: sham operation

value: sham operated left ventricular tissue

value: 14 days post-stress


title: input 120 min control


title: R728T1-shLuciferace_2


title: Sham-14.1

description:
RNA-MI-counts.xlsx
S-14.1


title: Ku 10 min FseI cut


title: R728T1-shLuciferace_1


title: Sham-7.5

description:
RNA-MI-counts.xlsx
S-7.5


title: gH2A.V 10 min FseI cut


title: H2A.V 10 min FseI cut


title: input 10 min FseI cut


title: Sham-7.3

description:
RNA-MI-counts.xlsx
S-7.3


title: Sham-14.3

description:
RNA-MI-counts.xlsx
S-14.3


title: Ku 10 min control


title: gH2A.V 10 min control


title: shRNA#1, stimulation with WNT3A, for 8 hours

city: Milan

first: Giovanni

last: Tonon

state: MI

address: Via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description:
MM1.144 cell lines transduced with an shRNA targeting ROR2 (shRNA#1)
MM1.144_Sh3_3a_8h

data_processing:
The software Illumina®GenomeStudio v.2011.1 was used to assess fluorescent hybridization signals and to perform the quality controls, which includes the biological specimen control, hybridization controls, signal generation controls and negative controls.
Data were normalized using the Cubic spline algorithm embedded in the Illumina®GenomeStudio v.2011.1 software.

source_name: MM1.144 multiple myeloma human cell line

label_protocol: An amount of 500 ng of total RNA was reverse transcribed into cRNA and biotin-UTP labelled using the IlluminaTotalPrep RNA Amplification Kit (Applied Biosystems) according to the manufacturer’s protocol.

growth_protocol: MM1.144 cells were grown in RPMI1640 medium supplemented with 10% FBS

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were starved overnight in RPMI1640 medium without FBS, then stimulated with 100ng/ml of either recombinant WNT3A or WNT5A

tag: cell line

value: multiple myeloma cell line MM1.144

tag: genotype

value: ROR2 depletion

tag: agent

value: 8 hours


title: Sham-3.2

description:
RNA-MI-counts.xlsx
S-3.2

value: FVB/N

value: 3 days post-stress


title: H2A.V 10 min control

tag: ChIP

tag: template

tag: assembly

value: DREX assembly on FlyFosmid


title: Sham-3.1

description:
RNA-MI-counts.xlsx
S-3.1


title: input 10 min control

tag: cut

tag: time (min)


title: shRNA#1, stimulation with WNT5A, for 8 hours

description:
MM1.144 cell lines transduced with an shRNA targeting ROR2 (shRNA#1)
MM1.144_Sh3_5a_8h


title: shRNA#1, stimulation with WNT3A, for 45 minutes

description:
MM1.144 cell lines transduced with an shRNA targeting ROR2 (shRNA#1)
MM1.144_Sh3_3a_45

value: 45 minutes


title: shRNA#1, stimulation with WNT5A, for 45 minutes

description:
MM1.144 cell lines transduced with an shRNA targeting ROR2 (shRNA#1)
MM1.144_Sh3_5a_45


title: GCP SL condition 3

city: Chikusa-ku

first: Toshinori

last: Kinoshita

state: Nagoya

address: Furo-cho

department: Graduate School of Science

country: Japan

institute: Nagoya university

description: Gene expression in guard cell protoplast from SL plants

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Arabidopsis thaliana

source_name: Guard cell protoplast, SL condition, replicate 3

label_protocol: standard Agilent protocol

growth_protocol: Arabidopsis thaliana gl1 [Columbia (Col), carrying the homozygous recessive gl1].  Plants were grown on soil in a growth chamber. Short-day (SD) condition; 8-h-white light (100 ｵmol m-2 s-1)/16-h-dark cycle at 22｡C to 24｡C in 50% to 70% relative humidity. Long-day (LD) condition; 16-h-white light (41 ｵmol m-2 s-1)/8-h-dark cycle at 22｡C to 24｡C in 50% to 70% relative humidity.

extract_protocol: none provided by the submitter

treatment_protocol: RNA samples were isolated from GCPs of SS plants at ZT8 and SL plants at ZT16.

value: Guard cell protoplast

tag: ecotype

value: Columbia ecotype (gl)


title: GCP SL condition 2

source_name: Guard cell protoplast, SL condition, replicate 2


title: Scramble, stimulation with WNT5A, for 8 hours

description:
MM1.144 cell lines transduced with a scramble shRNA
MM1.144_Scr_5a_8h

value: control


title: Sham-3.3

description:
RNA-MI-counts.xlsx
S-3.3


title: GCP SL condition 1

source_name: Guard cell protoplast, SL condition, replicate 1


title: GCP SS condition 2

description: Gene expression in guard cell protoplast from SS plants

source_name: Guard cell protoplast, SS condition, replicate 2


title: GCP SS condition 3

source_name: Guard cell protoplast, SS condition, replicate 3


title: Scramble, stimulation with WNT3A, for 8 hours

description:
MM1.144 cell lines transduced with a scramble shRNA
MM1.144_Scr_3a_8h


title: Scramble, no stimulation

description:
MM1.144 cell lines transduced with a scramble shRNA
MM1.144_Scr


title: Sham-7.4

description:
RNA-MI-counts.xlsx
S-7.4

value: 7 days post-stress


title: shRNA#1, no stimulation

description:
MM1.144 cell lines transduced with an shRNA targeting ROR2 (shRNA#1)
MM1.144_Sh3


title: Scramble, stimulation with WNT5A, for 45 minutes

description:
MM1.144 cell lines transduced with a scramble shRNA
MM1.144_Scr_5a_45


title: Scramble, stimulation with WNT3A, for 45 minutes

description:
MM1.144 cell lines transduced with a scramble shRNA
MM1.144_Scr_3a_45


title: VOB2703_Mouse_mm10_pe

status: Public on Jul 21 2019

city: St. Louis

first: Lu

state: Missouri

address: 4905 Children’s Place/305 N. Euclid, 10260 McDonnell Pediatric Research Building

department: Molecular Microbiology

institute: Washington University in St Louis

data_processing:
de-barcode
quality check (picard)
alignment (bbmap_37.10)
gene counts (Salmon_0.8.2)
differential analysis (DESeq2_1.14.0)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts output by Salmon

source_name: Sensitized UTI89 Infected 24 hpi 5

growth_protocol: Mice were purchased from labs denoted above at age of 6 weeks, then husband in cages in group of five in temperature and humidity controlled, well circulated facility with ample food and water supply for 7-8 weeks before initial infection

extract_protocol:
Mouse bladder were removed, flash froze in liquid nitrogen, RNA were extracted with QIAGEN RNeasy Plus kit (74136)
Whole bladder total RNA was fragmented, depleted of genomic DNA, and dephosphorylated before ligating to DNA adaptors carrying 5’-AN8-3’ barcodes with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted for rRNA with the Ribo-Zero rRNA removal kit (Illumina MRZG12324), then synthesized corresponding cDNA libraries.

tag: age

value: 16 weeks

tag: Sex

value: female

value: bladder

value: Envigo International Holdings FKA Harlan

value: Nulliparous

tag: disease

value: UTI

tag: phenotype

value: initial chronic E. coli infection

tag: treatment

value: infected with 1e8 CFU UTI89 WT SpecR


title: VOB2705_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 24 hpi 6

tag: tissue


title: ko 3 control

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

country: Spain

institute: IIB

description: Colonic organoid gene expression after 62 houres of tretament

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 1.65 µg. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours. Further details in One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit manual, Agilent version 6.7.

scan_protocol: Scanned on a G2505C DNA microarray scanner (Agilent) with Protocol GE1_1105_Oct12 and Grid 028005_D_F_20140728.

data_processing: Images were analyzed by Feature Extraction Software (Agilent v11.5), which performed feature quantitation and background subtraction by spatial detrending algorithms. Subsequent processing was performed with GeneSpring 13 software (Agilent), 1) values below 1 were thresholded to 1, and on-chip probe replicates summarized by computing their geometric mean; 2) values were Logbase2 transformed; 3) a global normalization step adjusted then all the probe intensities within an array, by subtracting the 75th percentile of each array from the log transformed signal value of each entity; and 4) in order to visualize relative differences between samples, independently of the abundance level, a Per-gene Baseline Transformation was done by subtracting for each probe signal the median of its intensities among all samples.

source_name: Colon organoids derived from VDR KO mouse_biological replicate 3_EtOH treated

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit, version 6.7,  by following manufacturer instructions. Agilent manual G4140-90040 of Sep2014. Amplification: by RNA polymerases.

growth_protocol: Mouse colonic crypts were isolated and embebbed on Matrigel to establish a 3D stem cell enriched culture as previously decribed in Sato et al 2007

extract_protocol: Total RNA was extracted using TRIZOL and NucleoSpin miRNA extraction kit (Macherey-Nagel)

treatment_protocol: 1,25(OH)2D3 was added to culture media to a final concntration of 100nM. The treatment was repeated every 48 hours (coincident with culture media change).

tag: strain

tag: genotype/variation

value: VDR KO

value: EtOH

tag: gender

value: Female

value: 2 months


title: VOB3291_Mouse_mm10_pe_rerun

source_name: Sensitized UTI89 Infected 24 hpi 3


title: VOB3275_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 24 hpi 2


title: ko 3 tratamiento

source_name: Colon organoids derived from VDR KO mouse_biological replicate 3_1,25(OH)2D3 treated


title: VOB3274_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 24 hpi 1


title: wt 3 control

source_name: Colon organoids derived from wt mouse_biological replicate 3_EtOH treated

value: wild type


title: wt 2 tratamiento

source_name: Colon organoids derived from wt mouse_biological replicate 2_1,25(OH)2D3 treated

value: 3 months


title: wt 3 tratamiento

source_name: Colon organoids derived from wt mouse_biological replicate 3_1,25(OH)2D3 treated


title: ko 2 tratamiento

source_name: Colon organoids derived from VDR KO mouse_biological replicate 2_1,25(OH)2D3 treated


title: ko 2 control

source_name: Colon organoids derived from VDR KO mouse_biological replicate 2_EtOH treated


title: VOB4401_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 24 hpi 5

value: spontaneously resolved initial E. coli infection


title: VOB4395_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 24 hpi 4


title: wt 1 tratamiento

source_name: Colon organoids derived from wt mouse_biological replicate 1_1,25(OH)2D3 treated

value: Male


title: ko 1 control

source_name: Colon organoids derived from VDR KO mouse_biological replicate 1_EtOH treated


title: VOB4393_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 24 hpi 3


title: GCP SS condition 1

source_name: Guard cell protoplast, SS condition, replicate 1

value: Guard cell protoplast

value: Columbia ecotype (gl)


title: VOB4414_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 24 hpi 4

value: 16 weeks

value: female

value: initial PBS mock infection, no disease


title: VOB2662_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 24 hpi 3

value: bladder

value: Envigo International Holdings FKA Harlan

value: Nulliparous


title: VOB2672_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 24 hpi 1

value: UTI

value: infected with 1e8 CFU UTI89 WT SpecR


title: VOB2964_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 24 hpi 1


title: VOB2965_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 24 hpi 2


title: VOB3303_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 6 hpi 3

value: initial chronic E. coli infection


title: VOB3723_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 6 hpi 2


title: VOB2702_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 24 hpi 4


title: VOB3722_Mouse_mm10_pe

source_name: Sensitized UTI89 Infected 6 hpi 1


title: VOB3065_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 6 hpi 3


title: wt 2 control

source_name: Colon organoids derived from wt mouse_biological replicate 2_EtOH treated

value: EtOH

value: Female


title: VOB3063_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 6 hpi 2


title: VOB3062_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 6 hpi 1


title: ko 1 tratamiento

source_name: Colon organoids derived from VDR KO mouse_biological replicate 1_1,25(OH)2D3 treated

value: VDR KO

value: 2 months


title: VOB2962_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 6 hpi 2


title: VOB2963_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 6 hpi 3


title: VOB2961_Mouse_mm10_pe

source_name: Adult Naïve UTI89 Infected 6 hpi 1


title: 3his4wk_sensitized_uti_8

source_name: Sensitized UTI89 Infected 3.5 hpi 8


title: VOB2701_Mouse_mm10_pe

source_name: Resolved UTI89 Infected 24 hpi 2

value: spontaneously resolved initial E. coli infection


title: 3his4wk_sensitized_uti_7

source_name: Sensitized UTI89 Infected 3.5 hpi 7


title: 3his4wk_sensitized_uti_6

source_name: Sensitized UTI89 Infected 3.5 hpi 6


title: 3his4wk_sensitized_uti_4

source_name: Sensitized UTI89 Infected 3.5 hpi 4


title: 3his4wk_sensitized_uti_3

source_name: Sensitized UTI89 Infected 3.5 hpi 3


title: wt 1 control

source_name: Colon organoids derived from wt mouse_biological replicate 1_EtOH treated

value: wild type

value: Male


title: 3his4wk_sensitized_pbs_4

source_name: Sensitized Mock Infected 24 hpi 4

value: mock infection (PBS)


title: 3his4wk_sensitized_pbs_6

source_name: Sensitized Mock Infected 24 hpi 6

value: 16 weeks


title: 3his4wk_sensitized_pbs_8

source_name: Sensitized Mock Infected 24 hpi 8

value: female


title: 3his4wk_sensitized_uti_2

source_name: Sensitized UTI89 Infected 3.5 hpi 2


title: 3his4wk_sensitized_pbs_1

source_name: Sensitized Mock Infected 24 hpi 1


title: 3his4wk_sensitized_pbs_2

source_name: Sensitized Mock Infected 24 hpi 2


title: 3his4wk_resolved_uti_8

source_name: Resolved UTI89 Infected 3.5 hpi 8


title: 3his4wk_resolved_uti_7

source_name: Resolved UTI89 Infected 3.5 hpi 7


title: 3his4wk_resolved_uti_5

source_name: Resolved UTI89 Infected 3.5 hpi 5


title: 3his4wk_resolved_uti_6

source_name: Resolved UTI89 Infected 3.5 hpi 6


title: 3his4wk_sensitized_pbs_5

source_name: Sensitized Mock Infected 24 hpi 5


title: 3his4wk_resolved_uti_4

source_name: Resolved UTI89 Infected 3.5 hpi 4


title: 3his4wk_resolved_uti_2

source_name: Resolved UTI89 Infected 3.5 hpi 2


title: 3his4wk_resolved_uti_1

source_name: Resolved UTI89 Infected 3.5 hpi 1


title: 3his4wk_resolved_pbs_8

source_name: Resolved Mock Infected 24 hpi 8


title: 3his4wk_resolved_pbs_7

source_name: Resolved Mock Infected 24 hpi 7


title: 3his4wk_sensitized_uti_1

source_name: Sensitized UTI89 Infected 3.5 hpi 1


title: 3his4wk_sensitized_uti_5

source_name: Sensitized UTI89 Infected 3.5 hpi 5


title: 3his4wk_resolved_pbs_5

source_name: Resolved Mock Infected 24 hpi 5


title: 3his4wk_resolved_pbs_6

source_name: Resolved Mock Infected 24 hpi 6


title: 3his4wk_resolved_pbs_2

source_name: Resolved Mock Infected 24 hpi 2


title: 3his4wk_resolved_pbs_3

source_name: Resolved Mock Infected 24 hpi 3


title: 3his4wk_naive_uti_8

source_name: Adult Naïve UTI89 Infected 3.5 hpi 8

value: initial PBS mock infection, no disease


title: 3his4wk_naive_uti_7

source_name: Adult Naïve UTI89 Infected 3.5 hpi 7

value: bladder


title: 3his4wk_sensitized_pbs_7

source_name: Sensitized Mock Infected 24 hpi 7

value: Envigo International Holdings FKA Harlan


title: 3his4wk_sensitized_pbs_3

source_name: Sensitized Mock Infected 24 hpi 3

value: Nulliparous


title: 3his4wk_resolved_uti_3

source_name: Resolved UTI89 Infected 3.5 hpi 3

value: UTI


title: 3his4wk_naive_pbs_5

source_name: Adult Naïve Mock Infected 24 hpi 5


title: 3his4wk_naive_uti_4

source_name: Adult Naïve UTI89 Infected 3.5 hpi 4

value: infected with 1e8 CFU UTI89 WT SpecR


title: 3his4wk_naive_uti_6

source_name: Adult Naïve UTI89 Infected 3.5 hpi 6


title: 3his4wk_naive_pbs_6

source_name: Adult Naïve Mock Infected 24 hpi 6


title: 3his4wk_naive_uti_2

source_name: Adult Naïve UTI89 Infected 3.5 hpi 2


title: 3his4wk_naive_uti_1

source_name: Adult Naïve UTI89 Infected 3.5 hpi 1


title: 3his4wk_naive_uti_3

source_name: Adult Naïve UTI89 Infected 3.5 hpi 3


title: 3his4wk_naive_uti_5

source_name: Adult Naïve UTI89 Infected 3.5 hpi 5


title: 3his4wk_naive_pbs_7

source_name: Adult Naïve Mock Infected 24 hpi 7


title: 3his4wk_resolved_pbs_4

source_name: Resolved Mock Infected 24 hpi 4


title: 3his4wk_naive_pbs_4

source_name: Adult Naïve Mock Infected 24 hpi 4


title: 3his4wk_naive_pbs_3

source_name: Adult Naïve Mock Infected 24 hpi 3


title: 3his4wk_naive_pbs_8

source_name: Adult Naïve Mock Infected 24 hpi 8


title: 3his4wk_resolved_pbs_1

source_name: Resolved Mock Infected 24 hpi 1


title: 3his4wk_naive_pbs_2

source_name: Adult Naïve Mock Infected 24 hpi 2


title: 3his4wk_naive_pbs_1

source_name: Adult Naïve Mock Infected 24 hpi 1


title: c3hhen_24h_11

source_name: C3H/HeN UTI89 Infected 24 hpi 4

value: 8 weeks

value: infected with 1e8 CFU UTI89 WT KanR


title: c3hhen_24h_10

source_name: C3H/HeN UTI89 Infected 24 hpi 3


title: c3hhen_24h_9

source_name: C3H/HeN UTI89 Infected 24 hpi 2


title: Suspension HeLa-Cas9 cells, N4_7b_83

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7b_83-N4_7b_83

data_processing:
Library strategy: CRISPR screen
The fastq files were combined based on PCR replicates and were processed using MaGECK to generate sgRNA counts. Brunello sgRNA library was used as the reference for counting
Supplementary_files_format_and_content: Count data table and the reference Brunello sgRNA Library provided in MS Excel format

extract_protocol:
DNA purification using Gentra Puregene cell kit, 1-2 x 10^7 protocol
Crispr Screening via PCR of sgRNAs according to protocol by Doench et al., DOI: 10.1038/nbt.3437
Crispr Library DNA Sequencing

treatment_protocol: Hela-Cas9 cells were transfected with Brunello library

tag: sort id

value: Sort 4, negative

tag: library description

value: Galectin-3 negative population after sort 4 (gated around population peak), sample c

tag: library

tag: time

value: 7 days post sort

tag: collection replicate

tag: pcr replicate


title: Suspension HeLa-Cas9 cells, N4_7b_71

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7b_71-N4_7b_71


title: Suspension HeLa-Cas9 cells, N4_7b_59

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7b_59-N4_7b_59


title: Suspension HeLa-Cas9 cells, N4_7a_47

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7a_47-N4_7a_47

value: Galectin-3 negative population after sort 4 (gated around population peak), sample b


title: Suspension HeLa-Cas9 cells, N4_7b_95

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7b_95-N4_7b_95


title: Suspension HeLa-Cas9 cells, N4_7a_35

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7a_35-N4_7a_35


title: Human epimermal keratinocytes, vehicle treated control, biological rep 2

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

institute: Seoul National University

description: Control batch2

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: primary HEKS cell culture_vehicle for 24 hrs

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

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

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

treatment_protocol: At passge 2, when NHKs were confluent in culture,10 microM of hydroquinone was treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell type

value: human epidermal keratinocytes (HEKs)

tag: passage

value: passage 2

value: vehicle for 24 hrs


title: Suspension HeLa-Cas9 cells, N4_4a_94

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_4a_94-N4_4a_94

value: Galectin-3 negative population after sort 4 (gated around population peak), sample a

value: 4 days post sort


title: Suspension HeLa-Cas9 cells, N4_4a_82

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_4a_82-N4_4a_82


title: Human epimermal keratinocytes, vehicle treated control, biological rep 1

description: Control batch1


title: Suspension HeLa-Cas9 cells, N4_7a_11

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7a_11-N4_7a_11


title: Suspension HeLa-Cas9 cells, N4_7a_23

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_7a_23-N4_7a_23


title: c3hhen_24h_8

source_name: C3H/HeN UTI89 Infected 24 hpi 1

tag: age

value: female


title: c3hhen_6h_4

source_name: C3H/HeN UTI89 Infected 6 hpi 1

tag: Sex

value: bladder


title: c3hhen_6h_7

source_name: C3H/HeN UTI89 Infected 6 hpi 4

value: Envigo International Holdings FKA Harlan

tag: disease


title: c3hhen_6h_6

source_name: C3H/HeN UTI89 Infected 6 hpi 3

value: Nulliparous

tag: phenotype


title: Human epimermal keratinocytes, hydroquinone 10 microM treated, biological rep 2

description: Hydroquinone batch2

source_name: primary HEKS cell culture_10 uM hydroquinone for 24 hrs

tag: treatment

value: 10 microM hydroquinone for 24 hrs


title: Suspension HeLa-Cas9 cells, M4_7b_46

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7b_46-M4_7b_46

value: Sort 4, mid-negative

value: Galectin-3 mid-negative population after sort 4 (gated around population peak), sample c


title: Suspension HeLa-Cas9 cells, M4_7b_34

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7b_34-M4_7b_34


title: c3hhen_6h_5

source_name: C3H/HeN UTI89 Infected 6 hpi 2

value: 8 weeks

tag: tissue

value: UTI

value: infected with 1e8 CFU UTI89 WT KanR


title: Suspension HeLa-Cas9 cells, N4_4a_70

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_4a_70-N4_4a_70

value: Sort 4, negative


title: c3hhen_3.5h_3

source_name: C3H/HeN UTI89 Infected 3.5 hpi 3

tag: strain

value: mock infection (PBS)


title: Suspension HeLa-Cas9 cells, N4_4a_58

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N4_4a_58-N4_4a_58


title: c3hhen_3.5h_1

source_name: C3H/HeN UTI89 Infected 3.5 hpi 1


title: Human epimermal keratinocytes, hydroquinone 10 microM treated, biological rep 1

description: Hydroquinone batch1

value: human epidermal keratinocytes (HEKs)


title: c3hhen_pbs_2

source_name: C3H/HeN Mock Infected 24 hpi 2


title: c3hheouj_24h_2

source_name: C3H/HeOuJ UTI89 Infected 24 hpi 2

value: The Jackson Laboratory


title: c3hheouj_6h_5

source_name: C3H/HeOuJ UTI89 Infected 6 hpi 5


title: c3hheouj_24h_5

source_name: C3H/HeOuJ UTI89 Infected 24 hpi 5


title: c3hhen_pbs_1

source_name: C3H/HeN Mock Infected 24 hpi 1


title: c3hhen_3.5h_2

source_name: C3H/HeN UTI89 Infected 3.5 hpi 2


title: c3hheouj_24h_3

source_name: C3H/HeOuJ UTI89 Infected 24 hpi 3


title: c3hheouj_6h_4

source_name: C3H/HeOuJ UTI89 Infected 6 hpi 4


title: Suspension HeLa-Cas9 cells, M4_7a_93

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7a_93-M4_7a_93

value: Galectin-3 mid-negative population after sort 4 (gated around population peak), sample b

value: 7 days post sort


title: Suspension HeLa-Cas9 cells, M4_4a_45

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_4a_45-M4_4a_45

value: Galectin-3 mid-negative population after sort 4 (gated around population peak), sample a

value: 4 days post sort


title: Suspension HeLa-Cas9 cells, M4_7a_81

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7a_81-M4_7a_81


title: c3hheouj_24h_4

source_name: C3H/HeOuJ UTI89 Infected 24 hpi 4

value: female

value: bladder


title: Suspension HeLa-Cas9 cells, M4_7a_57

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7a_57-M4_7a_57


title: Suspension HeLa-Cas9 cells, M4_7b_10

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7b_10-M4_7b_10


title: c3hheouj_6h_3

source_name: C3H/HeOuJ UTI89 Infected 6 hpi 3

value: Nulliparous


title: c3hhen_pbs_3

source_name: C3H/HeN Mock Infected 24 hpi 3

value: Envigo International Holdings FKA Harlan


title: c3hheouj_24h_1

source_name: C3H/HeOuJ UTI89 Infected 24 hpi 1


title: Suspension HeLa-Cas9 cells, M4_7b_22

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7b_22-M4_7b_22

value: Sort 4, mid-negative


title: Suspension HeLa-Cas9 cells, M4_4a_21

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_4a_21-M4_4a_21


title: Suspension HeLa-Cas9 cells, U3_10a_53

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U3_10a_53-U3_10a_53

value: Sort 3, unsorted control

value: Unsorted population, collected after sort 3

value: 10 days post sort


title: Suspension HeLa-Cas9 cells, M4_4a_09

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_4a_09-M4_4a_09


title: Suspension HeLa-Cas9 cells, M4_4a_33

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_4a_33-M4_4a_33


title: Suspension HeLa-Cas9 cells, U3_10a_89

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U3_10a_89-U3_10a_89


title: c3hheouj_3.5h_10

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 10

value: 8 weeks

value: UTI

value: infected with 1e8 CFU UTI89 WT KanR


title: c3hheouj_6h_2

source_name: C3H/HeOuJ UTI89 Infected 6 hpi 2


title: Suspension HeLa-Cas9 cells, U3_10a_77

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U3_10a_77-U3_10a_77


title: c3hheouj_6h_1

source_name: C3H/HeOuJ UTI89 Infected 6 hpi 1


title: Suspension HeLa-Cas9 cells, N3_13b_92

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13b_92-N3_13b_92

value: Sort 3, negative

value: Galectin-3 negative population after sort 3 (lowest 1 %), sample c

value: 13 days post sort


title: c3hheouj_3.5h_9

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 9

value: The Jackson Laboratory


title: Suspension HeLa-Cas9 cells, M4_7a_69

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library M4_7a_69-M4_7a_69

value: Galectin-3 mid-negative population after sort 4 (gated around population peak), sample b

value: 7 days post sort


title: Suspension HeLa-Cas9 cells, U3_10a_65

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U3_10a_65-U3_10a_65


title: Suspension HeLa-Cas9 cells, N3_13b_80

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13b_80-N3_13b_80


title: c3hheouj_3.5h_8

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 8

value: female


title: c3hheouj_3.5h_6

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 6

value: bladder


title: Suspension HeLa-Cas9 cells, N3_13b_68

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13b_68-N3_13b_68


title: Suspension HeLa-Cas9 cells, N3_13a_44

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13a_44-N3_13a_44

value: Galectin-3 negative population after sort 3 (lowest 1 %), sample b


title: Suspension HeLa-Cas9 cells, N3_13b_56

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13b_56-N3_13b_56


title: Suspension HeLa-Cas9 cells, N3_13a_32

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13a_32-N3_13a_32


title: Suspension HeLa-Cas9 cells, N3_13a_08

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13a_08-N3_13a_08


title: Suspension HeLa-Cas9 cells, U2_8a_40

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U2_8a_40-U2_8a_40

value: Sort 2, unsorted control

value: Unsorted population, collected after sort 2

value: 8 days post sort


title: Suspension HeLa-Cas9 cells, N3_10a_91

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_10a_91-N3_10a_91

value: Galectin-3 negative population after sort 3 (lowest 1 %), sample a


title: Suspension HeLa-Cas9 cells, N3_10a_67

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_10a_67-N3_10a_67

value: 10 days post sort


title: c3hheouj_3.5h_1

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 1

value: 8 weeks

value: Nulliparous


title: c3hheouj_3.5h_4

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 4

value: UTI

value: infected with 1e8 CFU UTI89 WT KanR


title: c3hheouj_pbs_7

source_name: C3H/HeOuJ Mock Infected 24 hpi 7

value: mock infection (PBS)


title: c3hheouj_3.5h_7

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 7


title: Suspension HeLa-Cas9 cells, N3_13a_20

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_13a_20-N3_13a_20

value: Sort 3, negative

value: 13 days post sort


title: Suspension HeLa-Cas9 cells, U2_8a_16

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U2_8a_16-U2_8a_16


title: c3hheouj_3.5h_2

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 2

value: The Jackson Laboratory


title: c3hheouj_3.5h_5

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 5


title: Suspension HeLa-Cas9 cells, N3_10a_79

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_10a_79-N3_10a_79


title: c3hheouj_pbs_6

source_name: C3H/HeOuJ Mock Infected 24 hpi 6


title: c3hheouj_pbs_5

source_name: C3H/HeOuJ Mock Infected 24 hpi 5


title: c3hheouj_pbs_9

source_name: C3H/HeOuJ Mock Infected 24 hpi 9


title: Suspension HeLa-Cas9 cells, U2_8a_04

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U2_8a_04-U2_8a_04


title: Suspension HeLa-Cas9 cells, N3_10a_55

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N3_10a_55-N3_10a_55


title: Suspension HeLa-Cas9 cells, U2_8a_28

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U2_8a_28-U2_8a_28


title: c3hheouj_3.5h_3

source_name: C3H/HeOuJ UTI89 Infected 3.5 hpi 3


title: c3hheouj_pbs_4

source_name: C3H/HeOuJ Mock Infected 24 hpi 4


title: Suspension HeLa-Cas9 cells, N2_8a_41

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N2_8a_41-N2_8a_41

value: Sort 2, negative

value: Galectin-3 negative population after sort 2 (lowest 2 %)


title: c3hheouj_pbs_10

source_name: C3H/HeOuJ Mock Infected 24 hpi 10

value: female

value: bladder


title: c3hheouj_pbs_8

source_name: C3H/HeOuJ Mock Infected 24 hpi 8


title: c3hheouj_pbs_2

source_name: C3H/HeOuJ Mock Infected 24 hpi 2


title: c3hheouj_pbs_1

source_name: C3H/HeOuJ Mock Infected 24 hpi 1


title: c57bl6j_24h_4

source_name: C57BL/6J UTI89 Infected 24 hpi 4


title: Suspension HeLa-Cas9 cells, U1_8a_85

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U1_8a_85-U1_8a_85

value: Sort 1, unsorted control

value: Unsorted population, collected after sort 1


title: Suspension HeLa-Cas9 cells, N2_8a_29

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N2_8a_29-N2_8a_29

value: 8 days post sort


title: Suspension HeLa-Cas9 cells, N2_8a_05

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N2_8a_05-N2_8a_05


title: c57bl6j_24h_5

source_name: C57BL/6J UTI89 Infected 24 hpi 5


title: Suspension HeLa-Cas9 cells, N2_8a_17

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N2_8a_17-N2_8a_17


title: c57bl6j_24h_3

source_name: C57BL/6J UTI89 Infected 24 hpi 3


title: c57bl6j_24h_1

source_name: C57BL/6J UTI89 Infected 24 hpi 1


title: Suspension HeLa-Cas9 cells, N1_8a_75

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_8a_75-N1_8a_75

value: Sort 1, negative

value: Galectin-3 negative population after sort 1 (lowest 10 %), sample b


title: c57bl6j_6h_5

source_name: C57BL/6J UTI89 Infected 6 hpi 5

value: 8 weeks


title: Suspension HeLa-Cas9 cells, U1_8a_73

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U1_8a_73-U1_8a_73


title: Suspension HeLa-Cas9 cells, U1_8a_49

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U1_8a_49-U1_8a_49


title: Suspension HeLa-Cas9 cells, U1_8a_61

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library U1_8a_61-U1_8a_61


title: c57bl6j_6h_4

source_name: C57BL/6J UTI89 Infected 6 hpi 4

value: Nulliparous


title: Suspension HeLa-Cas9 cells, N1_8a_87

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_8a_87-N1_8a_87


title: c57bl6j_6h_3

source_name: C57BL/6J UTI89 Infected 6 hpi 3

value: UTI


title: Suspension HeLa-Cas9 cells, N1_8a_51

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_8a_51-N1_8a_51


title: c57bl6j_6h_2

source_name: C57BL/6J UTI89 Infected 6 hpi 2

value: infected with 1e8 CFU UTI89 WT KanR


title: c57bl6j_24h_2

source_name: C57BL/6J UTI89 Infected 24 hpi 2


title: Suspension HeLa-Cas9 cells, N1_0a_39

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_0a_39-N1_0a_39

value: Galectin-3 negative population after sort 1 (lowest 10 %), sample a

value: 0 days post sort


title: Suspension HeLa-Cas9 cells, N1_8a_63

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_8a_63-N1_8a_63


title: c57bl6j_3.5h_10

source_name: C57BL/6J UTI89 Infected 3.5 hpi 10


title: c57bl6j_6h_1

source_name: C57BL/6J UTI89 Infected 6 hpi 1


title: Suspension HeLa-Cas9 cells, N1_0a_03

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_0a_03-N1_0a_03


title: c3hheouj_pbs_3

source_name: C3H/HeOuJ Mock Infected 24 hpi 3

value: mock infection (PBS)


title: c57bl6j_3.5h_9

source_name: C57BL/6J UTI89 Infected 3.5 hpi 9

value: The Jackson Laboratory


title: c57bl6j_3.5h_8

source_name: C57BL/6J UTI89 Infected 3.5 hpi 8


title: CNE2-KO41b

city: Changsha

first: zhenqi

last: qin

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

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,Bowtie/Bowtie2 was used for building the genome index,  and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM(Fragments Per Kilobase Per Million Mapped Fragments) was then calculated to estimate the expression level of genes in each sample
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: nasopharyngeal carcinoma cell line

growth_protocol: Human WT CNE2 and KO  cell lines were cultured and maintained in Dulbecco's modified RPMI-1640 medium containing 10% (v/v) fetal bovine serum (FBS) (Life Technologies) at 37℃.

extract_protocol:
total RNA was harvested using Trizol reagent from NPC cells ,Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: nasopharyngeal carcinoma cell line

tag: genoytpe

value: knockout tp53  in CNE2 by  using the CRISPR-Cas9 gene editing system


title: CNE2-KO41a


title: c57bl6j_3.5h_5

source_name: C57BL/6J UTI89 Infected 3.5 hpi 5

value: female


title: c57bl6j_3.5h_7

source_name: C57BL/6J UTI89 Infected 3.5 hpi 7

value: bladder


title: c57bl6j_3.5h_6

source_name: C57BL/6J UTI89 Infected 3.5 hpi 6


title: c57bl6j_3.5h_4

source_name: C57BL/6J UTI89 Infected 3.5 hpi 4


title: c57bl6j_3.5h_2

source_name: C57BL/6J UTI89 Infected 3.5 hpi 2


title: c57bl6j_3.5h_1

source_name: C57BL/6J UTI89 Infected 3.5 hpi 1


title: c57bl6j_3.5h_3

source_name: C57BL/6J UTI89 Infected 3.5 hpi 3


title: c57bl6j_pbs_10

source_name: C57BL/6J Mock Infected 24 hpi 10


title: c57bl6j_pbs_9

source_name: C57BL/6J Mock Infected 24 hpi 9


title: Suspension HeLa-Cas9 cells, N1_0a_15

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_0a_15-N1_0a_15

tag: sort id


title: Suspension HeLa-Cas9 cells, N1_0a_27

description: DNA from Suspension HeLa-Cas9 cells transfected with Brunello library N1_0a_27-N1_0a_27

tag: library description


title: c57bl6j_pbs_7

source_name: C57BL/6J Mock Infected 24 hpi 7


title: CNE2(WTc)

value: wildtype


title: CNE2-KO41c


title: CNE2(WTb)


title: c57bl6j_pbs_6

source_name: C57BL/6J Mock Infected 24 hpi 6


title: iPS-1(p31)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500/3000 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: Fibroblast-derived induced pluripotent stem cells at passage 31

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: iPS cells

tag: gender

value: male


title: iPS-2(p51)

source_name: Fibroblast-derived induced pluripotent stem cells at passage 51


title: iPS-2(p32)

source_name: Fibroblast-derived induced pluripotent stem cells at passage 32


title: iPS-1(p53)

source_name: Fibroblast-derived induced pluripotent stem cells at passage 53


title: c57bl6j_pbs_5

source_name: C57BL/6J Mock Infected 24 hpi 5


title: c57bl6j_pbs_4

source_name: C57BL/6J Mock Infected 24 hpi 4


title: CNE2(WTa)

source_name: nasopharyngeal carcinoma cell line


title: D6_SK_L_P_III_2D

city: Leiden

first: Vera

middle: van der

last: Noord

state: South Holland

address: Einsteinweg 55

department: Drug Discovery and Safety

institute: Leiden University

data_processing:
Marking duplicates, sorting and indexing were performed using sambamba software.
Gene expression was quantified using the FeatureCounts software (version 1.4.6) based on the ENSEMBL gene annotation for GRCH38 (release 84).
RNA-Seq data was normalized by trimmed mean of M-values (TMM) using EdgeR’s normalization-factor (Bioconductor software) followed by quantile normalization and presented in Log2 fold change (Log2 FC) scales.
Log2 FC of 0.5 used as cut-off for differentially expressed genes.
Data normalized to control (DMSO) and monotherapies (lapatinib; PHA-767491)
Genome_build: hg38
Supplementary_files_format_and_content: normalized abundances measurements

source_name: SKBR7 triple-negative breast cancer cell line

growth_protocol: All cell lines were maintained in RPMI-1640 medium (Gibco, ThermoFisher Scientific,  Breda, The Netherlands)supplemented with 10% FBS (Thermo Fisher Scientific; 10270106) and 25 IU/ml Penicillin and 25 μg/ml Streptomycin (ThermoFisher  Scientific; 15070-063). Cells were cultured in a humidified incubator at 37oC, 5% CO2.

extract_protocol:
RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (RNA-Seq) was performed using Illumina high-throughput RNA sequencing.
DNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit. The DNA libraries were sequenced according to the Illumina TruSeq v3 protocol on an Illumina HiSeq2500 sequencer. Paired-end reads were generated of 100 base-pairs in length. Alignment was performed using the HiSat2 aligner (version 2.2.0.4) against the human GRCh38 reference genome. Gene expression was quantified using the FeatureCounts software (version 1.4.6) based on the ENSEMBL gene annotation for GRCH38 (release 84).

treatment_protocol: Cells were seeded overnight in 6-well plates and treated in triplicate for 6 hours with individual or combined kinase inhibitors (PHA-767491, lapatinib)  or vehicle (DMSO).


title: A6_SK_DMSO_III_2D

value: SKBR7 triple-negative breast cancer cell line


title: c57bl6j_pbs_3

source_name: C57BL/6J Mock Infected 24 hpi 3


title: c57bl6j_pbs_2

source_name: C57BL/6J Mock Infected 24 hpi 2


title: B6_SK_Lap_III_2D

value: Lapatinib (3.16 µM)


title: A5_SK_DMSO_II_2D


title: D5_SK_L_P_II_2D


title: c57bl6j_pbs_1

source_name: C57BL/6J Mock Infected 24 hpi 1

value: 8 weeks


title: c57bl6j_pbs_8

source_name: C57BL/6J Mock Infected 24 hpi 8


title: A2_Hs_DMSO_II_2D

source_name: Hs578T triple-negative breast cancer cell line


title: fibroblast-2

description: Fibroblast cells

source_name: Fibroblast cells

value: fibroblast cells


title: C3_Hs_PHA_III_2D

value: Hs578T triple-negative breast cancer cell line


title: A3_Hs_DMSO_III_2D


title: C4_SK_PHA_I_2D


title: A4_SK_DMSO_I_2D


title: B4_SK_Lap_I_2D


title: B1_Hs_Lap_I_2D


title: B2_Hs_LAP_II_2D


title: D3_Hs_L_P_III_2D


title: C2_Hs_PHA_II_2D


title: C1_Hs_PHA_I_2D


title: D2_Hs_L_P_II_2D


title: D1_Hs_L_P_I_2D


title: C5_SK_PHA_II_2D


title: C6_SK_PHA_III_2D


title: B5_SK_Lap_II_2D


title: A1_Hs_DMSO_I_2D


title: D4_SK_L_P_I_2D


title: ChIP6-control

data_processing:
Sequencing reads were aligned to the GRCh37/hg19 genome assembly with Bowtie2 (Langmead and Salzberg 2012).
peaks were called using MACS2 with the following setting: --qvalue=0.15, --nomodel and --extsize 200 using as control concatenated same-patient alignment files from input treated (calcitriol) and untreated (vehicle)
MACS2 bdgdiff function was used to obtain statistically enriched DNA regions using the pileup data obtained from the peak calling.
Genome_build: Hg19
Supplementary_files_format_and_content: Pileups for the input corrected files on .bdg format and enreached VDR binding genomic sites upon calcitriol treatment (*Dpeaks_*) compared to EtOH treatment (*Cpeaks_*) in .bed format

source_name: Colonic Stem cell enriched culture

growth_protocol: Human colon organoids from two patients in each starting sample were cultured on 6-well dishes in the presence of 100 nM calcitriol or vehicle for 2 h. The 3D culture media was changed every other day and it was composed of 50% Advanced DMEM/F12, 50% Wnt3a-conditioned medium, 10 mM HEPES, 10 mM Glutamax, 10 mM nicotinamide (Sigma-Aldrich), 1x N2 (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 1:100 Primocin, 0.1 μg/mL Noggin (Peprotech, NJ, USA), 1 μg/mL Gastrin (Tocris, Bristol, UK), 1 μg/mL RSPO1 (Sino Biological, Beijing, China), 50 ng/mL EGF (Peprotech), 0.02 μM PGE2 (Sigma-Aldrich), 1 μM LY-2157299 (Axon Medchem, VA, USA), 10 μM SB-202190 (Sigma-Aldrich) and 10 μM Y-27632 (Tocris).

extract_protocol:
DNA-protein crosslinking was done by incubation with 1% formaldehyde (Thermo Fisher Scientific) for 8 min in rotation at 4ºC. Crosslinking was quenched with 1.25 mM glycine (Bio-Rad) in PBS for 5 min. We transferred the organoid solution to a 50 mL conical tube for centrifugation at 2500 rpm for 5 min at 4ºC. Supernatant was removed and the pellet was washed twice in cold PBS, transferred to a 1.5 mL eppendorf tube and lysed in 1 mL ChIP-lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1 and 1x protease cocktail inhibitors (cOmplete, EDTA-free (Roche, Basel, Switzerland)) for 1 h. We used a 21G syringe to homogenize the solution and force the lysis. Samples were sonicated for 20 min at maximum intensity at 4ºC in a S220 Focused-ultrasonicator (Covaris, MA, USA).
Both ChIP'ed and input DNA samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB, MA, USA). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a single double-sided SPRI size selection. Cluster generation was performed on an Illumina flow cell and sequenced in the 50 base single-read format on an Illumina HiSeq2500 instrument by following manufacturer's protocols.

treatment_protocol: 1,25(OH)2D3 was added to culture media to a final concntration of 10uM and the treatment lasted 2h.

value: colonic organoids

tag: passages

value: primary culture

tag: chip antibody

value: rabbit-monoclonal VDR antibody (Cell Signalling, custom made 2 mg/mL, MA, USA)

value: EtOH


title: ChIP6-Input-Pool

value: calcitriol


title: ChIP8.Vit.D


title: ChIP6.Vit.D


title: B3_Hs_Lap_III_2D


title: zr7530-CDK12-3

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

institute: College of Medicine, Hanyang University

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.6.0c
Raw counts were calculated using featureCounts from Subread package v1.6.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted using TRIzol reagents. The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 1 ug total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2500. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer.

value: mammary gland/breast

value: epithelial

value: adenocarcinoma

tag: lentivirus

value: CDK12 (pLVX-CDK12)


title: ChIP8.Input

tag: cell type


title: zr7530-CDK12-2


title: zr7530-CDK12-1


title: ChIP8.Cont


title: ChIP5-control


title: ChIP8.Input.Vit.D


title: zr7530-con-rep3

value: control (pLVX)


title: fibroblast-1

description: Fibroblast cells


title: ChIP5-vitD-Input


title: zr7530-con-rep1


title: ChIP5-control-Input