title: CLAma009_05.t3.rep2


title: RHH2305 (scRNA-seq)

status: Public on Nov 22 2018

type: SRA

city: Singapore

first: Yiqun Elaine

last: Cao

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Sensitive

library_source: transcriptomic

data_processing:
Basecalls performed using gis-rpd pipelines/bcl2fastq/ https://github.com/gis-rpd/pipelines/tree/master/bcl2fastq
Single-cell RNA-seq reads were aligned to the hg19 genome assembly
Data were filtered using the RaceID algoritham https://github.com/dgrun/RaceID
Genome_build: hg19
Supplementary_files_format_and_content: good_Data_TPM.txt -- Raw TPM values of 1302 cells for downstream analysis
Supplementary_files_format_and_content: good_Data_cellinfo.txt -- Detailed information of 1302 cells for downstream analysis

molecule: total RNA

organism: Homo sapiens

growth_protocol: Tumors were minced prior to enzymatic dissociation using 4 mg/ml Collagenase type IV (Thermo Fisher, cat. no. 17104019) in DMEM/F12, at 37 °C for 2 hours. Cells were washed using cyclical treatment of pelleting and resuspension in phosphate buffered saline (Thermo Fisher, cat. no 14190235) for 3 cycles. The final cell suspensions were strained through 70 µm cell strainers (Falcon, cat. no. 352350), prior to pelleting and resuspension in RPMI (Thermo Fisher, cat. no 61870036), supplemented with 10% fetal bovine serum (Biowest, cat. no S181B), and 1% penicillin-streptomycin (Thermo Fisher, cat. no. 15140122). Cells were kept in a humidified atmosphere of 5% CO2 at 37°C. Cell line identity was authenticated by comparing the short tandem repeat (STR) profile (Indexx BioResearch) of each cell line to its original tumor.

extract_protocol:
The C1 Single-Cell Auto Prep IFC (Fluidigm) system was employed for single-cell RNA-seq. Single cells were captured, followed by reverse transcription and cDNA pre-amplification in the C1-Chips using the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech).
The mRNA and cDNA was harvested in C1 system followed by barcoding in 96 well plate. We employed Nextra XT Library Prep kit (Illumina) for library tegmentation. The tegmented single-cell libraries were amplified by 12-14 round of PCR cycle.

treatment_protocol: Drug resistant cells were maintained in cisplatin

tag: disease state

value: oral squamous cell carcinoma (OSCC)

tag: cell type

value: Metastatic

tag: passages

tag: response to cisplatin

value: Sensitive


title: CLAma021_05.t7.rep2

type: RNA

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO

description: Gene expression data from deseeded berries pooled from several bunches

hyb_protocol: Affymetrix Fluidics Station 450, Biotin/Streptavidin detection

scan_protocol: The GeneChips were scanned using theGeneChip Scanner 3000

data_processing: Data normalised using the GCRMA R package from Bioconductor

label: biotin

organism: Vitis vinifera

source_name: Grape berry 6 weeks post flowering, machine pruned vines

label_protocol: Affymetrix One Cycle cDNA synthesis kit, Affymetrix GeneChip Sample Cleanup kit, Affymetrix IVT labelling kit

growth_protocol: Berries were collected from bunches on field grown plants

extract_protocol: A modified RNAeasy RNA extraction method (Qiagen)

treatment_protocol: Spur and machine pruning of vines

tag: Cabernet Sauvignon


title: RHH2296 (scRNA-seq)

description: Sensitive


title: RHH2295 (scRNA-seq)

description: Sensitive


title: RHH2294 (scRNA-seq)

description: Sensitive


title: CLAma006_05.t2.rep2

description: Gene expression data from whole berries pooled from several bunches

source_name: Grape berry 1 week post flowering, machine pruned vines


title: RHH2293 (scRNA-seq)

description: Sensitive


title: RHH2292 (scRNA-seq)

description: Sensitive


title: RHH2299 (scRNA-seq)

description: Sensitive


title: RHH2291 (scRNA-seq)

description: Sensitive


title: RHH2289 (scRNA-seq)

description: Sensitive


title: CLAma003_05.t1.rep1

description: Gene expression data from flowers at anthesis

source_name: Anthesis flower sample, machine pruned vines


title: CLAma004_05.t2.rep2


title: RHH2290 (scRNA-seq)

description: Sensitive


title: RHH2286 (scRNA-seq)

description: Sensitive


title: RHH2285 (scRNA-seq)

description: Sensitive


title: RHH2284 (scRNA-seq)

description: Sensitive


title: RHH2277 (scRNA-seq)

description: Sensitive


title: RHH2278 (scRNA-seq)

description: Sensitive


title: CLAsp050_05.t17.rep1

source_name: Grape berry 16 weeks post flowering, spur pruned vines


title: RHH2279 (scRNA-seq)

description: Sensitive


title: RHH2288 (scRNA-seq)

description: Sensitive


title: RHH2276 (scRNA-seq)

description: Sensitive


title: CLAma005_05.t2.rep1


title: RHH2283 (scRNA-seq)

description: Sensitive


title: RHH2287 (scRNA-seq)

description: Sensitive


title: CLAsp051_05.t17.rep2


title: RHH2274 (scRNA-seq)

description: Sensitive


title: RHH2273 (scRNA-seq)

description: Sensitive


title: CLAsp048_05.t16.rep2

source_name: Grape berry 15 weeks post flowering, spur pruned vines


title: RHH2270 (scRNA-seq)

description: Sensitive

value: Primary


title: RHH2282 (scRNA-seq)

description: Sensitive


title: CLAsp047_05.t16.rep1


title: RHH2268 (scRNA-seq)

description: Sensitive


title: CLAsp044_05.t15.rep1

source_name: Grape berry 14 weeks post flowering, spur pruned vines


title: RHH2267 (scRNA-seq)

description: Sensitive


title: RHH2266 (scRNA-seq)

description: Sensitive


title: CLAsp045_05.t15.rep2


title: RHH2265 (scRNA-seq)

description: Sensitive


title: RHH2264 (scRNA-seq)

description: Sensitive


title: RHH2263 (scRNA-seq)

description: Sensitive


title: RHH2280 (scRNA-seq)

description: Sensitive


title: RHH2271 (scRNA-seq)

description: Sensitive


title: RHH2275 (scRNA-seq)

description: Sensitive


title: CLAma038_05.t13.rep1

source_name: Grape berry 12 weeks post flowering, machine pruned vines


title: CLAsp041_05.t14.rep1

source_name: Grape berry 13 weeks post flowering, spur pruned vines


title: RHH2272 (scRNA-seq)

description: Sensitive


title: CLAsp042_05.t14.rep2


title: CLAsp032_05.t11.rep1

source_name: Grape berry 10 weeks post flowering, spur pruned vines


title: CLAsp039_05.t13.rep2

source_name: Grape berry 12 weeks post flowering, spur pruned vines


title: RHH2260 (scRNA-seq)

description: Sensitive


title: RHH2269 (scRNA-seq)

description: Sensitive


title: RHH2259 (scRNA-seq)

description: Sensitive


title: CLAsp036_05.t12.rep2

source_name: Grape berry 11 weeks post flowering, spur pruned vines


title: RHH2281 (scRNA-seq)

description: Sensitive


title: RHH2262 (scRNA-seq)

description: Sensitive


title: CLAsp033_05.t11.rep2


title: RHH2255 (scRNA-seq)

description: Sensitive


title: CLAsp035_05.t12.rep1


title: RHH2261 (scRNA-seq)

description: Sensitive


title: CLAsp023_05.t8.rep1

source_name: Grape berry 7 weeks post flowering, spur pruned vines


title: CLAsp038_05.t13.rep1


title: CLAsp024_05.t8.rep2


title: CLAsp030_05.t10.rep2

source_name: Grape berry 9 weeks post flowering, spur pruned vines


title: CLAsp020_05.t7.rep1

source_name: Grape berry 6 weeks post flowering, spur pruned vines


title: CLAsp021_05.t7.rep2


title: CLAsp029_05.t10.rep1


title: Long term withdrawal LM2-4  2

city: Buffalo

first: John

last: Ebos

state: NY

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

country: USA

institute: Roswell Park Cancer Institute

description:
LTW.2
SAMPLE 11

hyb_protocol: Seven hundred and fifty nanograms of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58oC to the HumanHT-12v4 Expression BeadChip (Illumina; BD-103-0204).

scan_protocol: After Cy3-streptavidin conjugation the BeadChips were imaged using the Illumina iScan Reader.

data_processing: The background corrected gene expression levels were extracted from BeadChip using Illumina's Genome Studio (v2011.1) gene expression module (v1.9.0). Gene expression levels were log2 transformed and quantile normalized using lumi in the R-base Bioconductor package.

source_name: Breast cancer cell line

label_protocol: Five hundred nanograms total RNA was converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer's instructions.

growth_protocol: Cells were maintained in DMEM supplemented with 5% FBS in the presence or absence of 5μM sunitinib. Growth media was refreshed every 3-4 days.

extract_protocol: Total RNA from individual samples was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA was digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.

tag: variant

value: LM2-4 SuR/LT-W

tag: treatment

value: Sunitinib

tag: dose

value: 5 uM

tag: treatment duration

value: > 6 months

tag: withdrawal duration


title: Long term withdrawal LM2-4  3

description:
LTW.3
SAMPLE 12


title: RHH2254 (scRNA-seq)

description: Sensitive


title: RHH2253 (scRNA-seq)

description: Sensitive


title: CLAsp027_05.t9.rep2

source_name: Grape berry 8 weeks post flowering, spur pruned vines


title: Sunitinib resistant LM2-4  2

description:
SuR.2
SAMPLE 8

value: LM2-4 SuR


title: Metastatic LM2-4  3

description:
M.3
SAMPLE 6


title: Long term withdrawal LM2-4  1

description:
LTW.1
SAMPLE 10


title: CLAsp026_05.t9.rep1


title: RHH2258 (scRNA-seq)

description: Sensitive


title: RHH2257 (scRNA-seq)

description: Sensitive


title: Sunitinib resistant LM2-4  3

description:
SuR.3
SAMPLE 9


title: Metastatic LM2-4  1

description:
M.1
SAMPLE 4


title: RHH2256 (scRNA-seq)

description: Sensitive


title: RHH2252 (scRNA-seq)

description: Sensitive


title: CLAsp017_05.t6.rep1

source_name: Grape berry 5 weeks post flowering, spur pruned vines


title: Sunitinib resistant LM2-4  1

description:
SuR.1
SAMPLE 7


title: RHH2251 (scRNA-seq)

description: Sensitive


title: CLAsp015_05.t5.rep2

source_name: Grape berry 4 weeks post flowering, spur pruned vines


title: SW1990

city: Houston

first: Samir

last: Hanash

state: TX

address: 6767 Bertner Ave

institute: UT MD Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA 1.8.2
TopHat alignment used to align sequencing data to hg19 reference genome
Transcript assembly and discovery analyses  performed using Cufflinks
The number of reads was normalized and expressed as fragments per kilobase of exon per million fragments mapped (FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: text files contain FPKM values for each sample

extract_protocol:
mRNA extraction was performed by using Qiagen RNeasy Maxi Kit according to standard protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Pancreatic adenocarcinoma

tag: Sex

value: Male

tag: age at sampling


title: RHH2250 (scRNA-seq)

description: Sensitive


title: CLAsp018_05.t6.rep2


title: CLAsp014_05.t5.rep1


title: RHH2249 (scRNA-seq)

description: Sensitive


title: Metastatic LM2-4  2

description:
M.2
SAMPLE 5


title: Parental LM2-4  1

description:
P.1
SAMPLE 1


title: Parental LM2-4  2

description:
P.2
SAMPLE 2


title: Parental LM2-4  3

description:
P.3
SAMPLE 3


title: PANC-1

value: Pancreatic ductal adenocarcinoma


title: RHH2248 (scRNA-seq)

description: Sensitive


title: RHH2247 (scRNA-seq)

description: Sensitive


title: Panc 03.27

value: Female


title: Hs 766T

source_name: Hs 766T

value: Hs 766T

tag: disease

value: Derived from metastatic site:Lymph node


title: MIA PaCa-2

source_name: MIA PaCa-2

value: MIA PaCa-2


title: RHH2245 (scRNA-seq)

description: Sensitive


title: RHH2244 (scRNA-seq)

description: Sensitive


title: HPAF-II

source_name: HPAF-II

value: HPAF-II


title: RHH2243 (scRNA-seq)

description: Sensitive

value: oral squamous cell carcinoma (OSCC)


title: SU.86.86

value: Derived from metastatic site:Liver


title: RHH2242 (scRNA-seq)

description: Sensitive

value: Sensitive


title: Capan-2


title: AsPC-1

value: Derived from metastatic site:Ascites


title: RHH2241 (scRNA-seq)

description: Sensitive

value: Primary


title: CLAsp005_05.t2.rep1

source_name: Grape berry 1 week post flowering, spur pruned vines


title: CLAsp009_05.t3.rep2

source_name: Grape berry 2 weeks post flowering, spur pruned vines


title: CLAsp004_05.t2.rep2

source_name: Anthesis flower sample, spur pruned vines


title: CLAsp008_05.t3.rep1


title: CLAsp003_05.t1.rep1


title: CLAsp006_05.t2.rep2


title: CLAsp012_05.t4.rep2

source_name: Grape berry 3 weeks post flowering, spur pruned vines


title: RHH2239 (scRNA-seq)

description: Sensitive


title: 3N

city: Shanghai

first: Jie

last: Chen

address: Dongan Road

country: China

institute: Fudan University Shanghai Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using TopHat v2.1.0 with default parameters.
Gene expression levels were calculated by featurecount
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes and expression levels

source_name: Normal tissue adjacent to gastric cancer

extract_protocol:
Tissues RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of ribosome depleted sequencing libraries.
Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.

tag: tissue


title: 3T

source_name: Gastric cancer

value: Gastric cancer


title: CFPAC-1


title: RHH2238 (scRNA-seq)

description: Sensitive


title: WINpd034_05.t16.rep2

source_name: Grape berries 15 weeks post flowering, prolonged deficit irrigation

extract_protocol: The modified RNAeasy RNA extraction method (Qiagen)

treatment_protocol: Standard irrigation and prolonged deficit irrigation of vines


title: WINpd036_05.t17.rep2

source_name: Grape berries 16 weeks post flowering, prolonged deficit irrigation


title: 2T


title: WINpd033_05.t16.rep1


title: WINpd032_05.t15.rep2

source_name: Grape berries 14 weeks post flowering, prolonged deficit irrigation


title: WINpd035_05.t17.rep1


title: 2N

value: Normal tissue adjacent to gastric cancer


title: RHH2246 (scRNA-seq)

description: Sensitive


title: RHH2237 (scRNA-seq)

description: Sensitive


title: 1T


title: RHH2240 (scRNA-seq)

description: Sensitive


title: RHH2235 (scRNA-seq)

description: Sensitive


title: 1N


title: WINpd030_05.t14.rep2

source_name: Grape berries 13 weeks post flowering, prolonged deficit irrigation


title: RHH2234 (scRNA-seq)

description: Sensitive


title: WINpd031_05.t15.rep1


title: RHH2233 (scRNA-seq)

description: Sensitive


title: RHH2232 (scRNA-seq)

description: Sensitive


title: FT293-HuR-rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Base calling:  Illumina v 1.9
Alignment: Short reads were aligned wit TopHat2 against human genome GRCh38 (default parameters)
Gene counts: Reads were assigned to GRCh38.82 genes with htseq-count function from HTSeq package (parameters adjusted for strand-specific, paired-ends reads)
Exon-bin counts: Reads were assigned to individual exon-bins (as defined in DEXSeq) using dexseq_count.py included in DEXSeq package (default options)
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Tab-delimited text files including read count values for each gene (or exon-bins as defined by DEXSeq package) in each sample. Last 5 rows contain summaries of ambiguous and low-quality reads

source_name: FT293 cells overexpressing GFP-HuR

growth_protocol: GFP-, GFP-TIA1b-, GFP-TIARb-, and GFP-HuR-expressing FT293 cell lines were generated using the Flp-In T-Rex System (Invitrogen)

extract_protocol:
Total RNA was isolated with the RNeasy kit (Qiagen) and RNA quality was assessed using Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FT293 cell line

tag: expression construct

value: GFP-HuR


title: FT293-HuR-rep3


title: RHH2236 (scRNA-seq)

description: Sensitive


title: RHH2231 (scRNA-seq)

description: Sensitive


title: FT293-TIAR-rep3

source_name: FT293 cells overexpressing GFP-TIARb

value: GFP-TIARb


title: FT293-TIAR-rep2


title: RHH2228 (scRNA-seq)

description: Sensitive


title: FT293-TIA1-rep3

source_name: FT293 cells overexpressing GFP-TIA1b


title: RHH2227 (scRNA-seq)

description: Sensitive


title: WINpd025_05.t12.rep1

source_name: Grape berries 11 weeks post flowering, prolonged deficit irrigation


title: WINpd028_05.t13.rep2

source_name: Grape berries 12 weeks post flowering, prolonged deficit irrigation


title: WINpd024_05.t11.rep2

source_name: Grape berries 10 weeks post flowering, prolonged deficit irrigation


title: RHH2230 (scRNA-seq)

description: Sensitive


title: WINpd027_05.t13.rep1


title: FT293-TIA1-rep1


title: RHH2226 (scRNA-seq)

description: Sensitive


title: FT293-TAI1-rep2


title: WINpd029_05.t14.rep1


title: RHH2225 (scRNA-seq)

description: Sensitive


title: WINpd023_05.t11.rep1


title: FT293-HuR-rep1


title: CLAsp011_05.t4.rep1


title: WINpd026_05.t12.rep2


title: WINpd022_05.t10.rep2

source_name: Grape berries 9 weeks post flowering, prolonged deficit irrigation


title: WINpd021_05.t10.rep1


title: FT293-TIAR-rep1


title: FT293-GFP-rep2

source_name: FT293 cells overexpressing GFP (control)

value: GFP (control)


title: WINpd019_05.t9.rep1

source_name: Grape berries 8 weeks post flowering, prolonged deficit irrigation


title: RHH2223 (scRNA-seq)

description: Sensitive


title: RHH2224 (scRNA-seq)

description: Sensitive


title: WINpd020_05.t9.rep2


title: FT293-GFP-rep1


title: WINpd018_05.t8.rep2

source_name: Grape berries 7 weeks post flowering, prolonged deficit irrigation


title: WINpd017_05.t8.rep1


title: RHH2222 (scRNA-seq)

description: Sensitive


title: RHH2221 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest,cardiomyocyte diff [Sample 67]

city: New York

first: Julie

middle: Anne

last: Eggenberger

address: 1 Gustave L. Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
DNase-treated
TableS9_CMdiff_allsamples_RPKM.xlsx
TableS9_read_counts.xlsx

data_processing:
Illumina software was used for basecalling
RNA-Seq reads were trimmed for adaptor sequences and mapped to the whole human (h19) or murine (mm10) genome using STAR aligner
Merged read counts were obtained using the Illumina software RNA Express
Genome_build: UCSC h19 or UCSC mm10
Supplementary_files_format_and_content: All processed files were downloaded as tab-delimited text files and saved as .xlsx files

source_name: Induced Pluripotent Stem Cells

growth_protocol: iPS cells were cultured in E8 and StemFlex media,FFs and 293Ts were cultured in DMEM/10%FBS,mES cells were cultured in 2i media

extract_protocol:
RNA was harvested using Trizol reagent.
Libraries were prepared using the TruSeq RNA Library Preparation Kit version 2 (Illumina) according to the manufacturer’s instructions.  In brief, 1ug of total mRNA was purified using oligo-dT RNA purification beads.  Eluted RNA was fragmented and reverse transcribed, followed by a second strand synthesis, end repair, A-tailing, adaptor ligation and PCR amplification.  Libraries were quantified using a universal complete KAPA Library Quantification Kit (KAPA Biosystems).  Pooled libraries were sequenced on an Illumina MiSeq or an Illumina NextSeq platform.

value: iPSC 2607 clone 4

value: low passage

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,cardiomyocyte diff


title: RHH2219 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest,cardiomyocyte diff [Sample 68]


title: RHH2220 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h plus 5d rest,cardiomyocyte diff [Sample 66]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,cardiomyocyte diff


title: iPSC-GFP dox 48h plus 5d rest,cardiomyocyte diff [Sample 65]


title: RHH2218 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest,ectoderm diff [Sample 64]

description:
DNase-treated
TableS8_allsamples_RPKM.xlsx
TableS8_read_counts.xlsx

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,ectoderm diff


title: RHH2217 (scRNA-seq)

description: Sensitive


title: WINpd016_05.t7.rep2

source_name: Grape berries 6 weeks post flowering, prolonged deficit irrigation


title: WINpd014_05.t6.rep2

source_name: Grape berries 5 weeks post flowering, prolonged deficit irrigation


title: WINpd015_05.t7.rep1


title: iPSC-GFP dox 48h plus 5d rest,ectoderm diff [Sample 62]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,ectoderm diff


title: RHH2215 (scRNA-seq)

description: Sensitive

value: oral squamous cell carcinoma (OSCC)


title: RHH2216 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest,ectoderm diff [Sample 63]


title: iPSC-GFP dox 48h plus 5d rest,ectoderm diff [Sample 61]


title: WINpd011_05.t5.rep1

source_name: Grape berries 4 weeks post flowering, prolonged deficit irrigation


title: WINpd012_05.t5.rep2


title: iPSC-IRF7del dox 48h plus 5d rest,endoderm diff [Sample 60]

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,endoderm diff


title: RHH2214 (scRNA-seq)

description: Sensitive

value: Sensitive


title: WINpd013_05.t6.rep1


title: iPSC-IRF7del dox 48h plus 5d rest,endoderm diff [Sample 59]


title: RHH2213 (scRNA-seq)

description: Sensitive


title: WINpd010_05.t4.rep2

source_name: Grape berries 3 weeks post flowering, prolonged deficit irrigation


title: RHH2212 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h plus 5d rest,endoderm diff [Sample 58]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,endoderm diff


title: iPSC-GFP dox 48h plus 5d rest,endoderm diff [Sample 57]


title: RHH2210 (scRNA-seq)

description: Sensitive

value: Primary


title: WINpd008_05.t3.rep2

source_name: Grape berries 2 weeks post flowering, prolonged deficit irrigation


title: WINpd007_05.t3.rep1


title: iPSC-IRF7del dox 48h plus 5d rest,mesoderm diff [Sample 56]

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,mesoderm diff


title: RHH2209 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest,mesoderm diff [Sample 55]


title: RHH2211 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h plus 5d rest,mesoderm diff [Sample 53]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest,mesoderm diff


title: iPSC-GFP dox 48h plus 5d rest,mesoderm diff [Sample 54]


title: WINpd005_05.t2.rep1

source_name: Grape berries 1 week post flowering, prolonged deficit irrigation


title: WINpd009_05.t4.rep1


title: WINpd006_05.t2.rep2


title: RHH2208 (scRNA-seq)

description: Sensitive


title: RHH2206 (scRNA-seq)

description: Sensitive


title: RHH2207 (scRNA-seq)

description: Sensitive


title: WINpd004_05.t1.rep2

source_name: Anthesis flower sample,  prolonged deficit irrigation


title: WINpd003_05.t1.rep1


title: iPSC-IRF7del dox 48h plus 5d rest [Sample 51]

description:
DNase-treated
TableS8_allsamples_RPKM.xlsx
TableS8_read_counts.xlsx
TableS9_CMdiff_allsamples_RPKM.xlsx
TableS9_read_counts.xlsx

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest


title: WINco036_05.t17.rep2

source_name: Grape berries 16 weeks post flowering, normal irrigation


title: iPSC-IRF7del dox 48h plus 5d rest [Sample 52]


title: RHH2204 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h plus 5d rest [Sample 50]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment and 5 days rest


title: RHH2205 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h plus 5d rest [Sample 49]


title: WINco034_05.t16.rep2

source_name: Grape berries 15 weeks post flowering, normal irrigation


title: WINco035_05.t17.rep1


title: iPSC-IRF7del [Sample 48]

value: transduced with pTRE3G-IRF7del and treated with puromycin for 16h


title: RHH2201 (scRNA-seq)

description: Sensitive


title: RHH2203 (scRNA-seq)

description: Sensitive


title: WINco033_05.t16.rep1


title: WINco032_05.t15.rep2

source_name: Grape berries 14 weeks post flowering, normal irrigation


title: WINco031_05.t15.rep1


title: iPSC-IRF7del [Sample 47]


title: RHH2200 (scRNA-seq)

description: Sensitive


title: iPSC-GFP [Sample 46]

value: transduced with pTRE3G-GFP and treated with puromycin for 16h


title: WINco030_05.t14.rep2

source_name: Grape berries 13 weeks post flowering, normal irrigation


title: iPSC-GFP [Sample 45]

value: iPSC 2607 clone 4


title: RHH2198 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest [Sample 44]

description:
DNase-treated
TableS6_Differential_iPSC_IRF7vGFP_rest.xlsx
TableS6_iPSC_IRF7vGFP_rest_STRING.xlsx
TableS6_read_counts.xlsx

value: low passage


title: RHH2197 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h plus 5d rest [Sample 43]


title: iPSC-GFP dox 48h plus 5d rest [Sample 42]


title: WINco028_05.t13.rep2

source_name: Grape berries 12 weeks post flowering, normal irrigation


title: RHH2196 (scRNA-seq)

description: Sensitive


title: RHH2194 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h [Sample 40]

description:
DNase-treated
TableS5_Differential_iPSC_IRF7vGFP_48h.xlsx
TableS5_iPSC_IRF7vGFP_48h_STRING.xlsx
TableS5_read_counts.xlsx

value: transduced with pTRE3G-IRF7del,treated with puromycin for 16h followed by 48h doxycycline treatment


title: WINco026_05.t12.rep2

source_name: Grape berries 11 weeks post flowering, normal irrigation


title: WINco027_05.t13.rep1


title: iPSC-GFP dox 48h plus 5d rest [Sample 41]


title: WINco024_05.t11.rep2

source_name: Grape berries 10 weeks post flowering, normal irrigation


title: WINco025_05.t12.rep1


title: RHH2199 (scRNA-seq)

description: Sensitive


title: iPSC-IRF7del dox 48h [Sample 39]


title: iPSC-GFP dox 48h [Sample 38]

value: transduced with pTRE3G-GFP,treated with puromycin for 16h followed by 48h doxycycline treatment


title: WINco029_05.t14.rep1


title: RHH2192 (scRNA-seq)

description: Sensitive


title: iPSC-GFP dox 48h [Sample 37]


title: WINco020_05.t9.rep2

source_name: Grape berries 8 weeks post flowering, normal irrigation


title: RHH2195 (scRNA-seq)

description: Sensitive


title: WINco019_05.t9.rep1


title: RHH2190 (scRNA-seq)

description: Sensitive


title: 293T IRF7del [Sample 36]

description:
DNase-treated
TableS4_Differential_IRF7_to_GFP.xlsx
TableS4_read_counts_II.xlsx

source_name: Fibroblasts

value: transfected using Lipofectamine 2000 with pCAGGS-IRF7del


title: RHH2191 (scRNA-seq)

description: Sensitive


title: RHH2202 (scRNA-seq)

description: Sensitive


title: RHH2189 (scRNA-seq)

description: Sensitive


title: WINco021_05.t10.rep1

source_name: Grape berries 9 weeks post flowering, normal irrigation


title: WINco023_05.t11.rep1


title: RHH2188 (scRNA-seq)

description: Sensitive


title: 293T GFP [Sample 34]

value: transfected using Lipofectamine 2000 with pCAGGS-EGFP


title: RHH2187 (scRNA-seq)

description: Sensitive

value: oral squamous cell carcinoma (OSCC)


title: RHH2193 (scRNA-seq)

description: Sensitive


title: 293T GFP [Sample 33]


title: 293T KLF4/IRF7del [Sample 32]

description:
DNase-treated
TableS4_DEseq_GFP_vs_IRF7_KLF4.xlsx
TableS4_DEseq_GFP_vs_IRF7.xlsx
TableS4_DEseq_GFP_vs_KLF4.xlsx
TableS4_read_counts_I.xlsx

value: transfected using Lipofectamine 2000 with pCAGGS-KLF4 and pCAGGS-IRF7del


title: 293T IRF7del [Sample 35]


title: 293T KLF4/IRF7del [Sample 31]


title: WINco017_05.t8.rep1

source_name: Grape berries 7 weeks post flowering, normal irrigation


title: RHH2185 (scRNA-seq)

description: Sensitive

value: Sensitive


title: RHH2229 (scRNA-seq)

description: Sensitive


title: WINco022_05.t10.rep2


title: RHH2186 (scRNA-seq)

description: Sensitive


title: 293T IRF7del [Sample 30]


title: WINco015_05.t7.rep1

source_name: Grape berries 6 weeks post flowering, normal irrigation


title: RHH2184 (scRNA-seq)

description: Sensitive


title: WINco013_05.t6.rep1

source_name: Grape berries 5 weeks post flowering, normal irrigation


title: WINco018_05.t8.rep2


title: WINco012_05.t5.rep2

source_name: Grape berries 4 weeks post flowering, normal irrigation


title: RHH2183 (scRNA-seq)

description: Sensitive


title: 293T KLF4 [Sample 28]

value: transfected using Lipofectamine 2000 with pCAGGS-KLF4


title: RHH2182 (scRNA-seq)

description: Sensitive

value: Primary


title: FT293-GFP-rep3

source_name: FT293 cells overexpressing GFP (control)

value: FT293 cell line

value: GFP (control)


title: RHH2181 (scRNA-seq)

description: Sensitive


title: 293T KLF4 [Sample 27]


title: RHH2180 (scRNA-seq)

description: Sensitive


title: 293T GFP [Sample 26]


title: RHH2179 (scRNA-seq)

description: Sensitive


title: WINco011_05.t5.rep1


title: WINco014_05.t6.rep2


title: WINco016_05.t7.rep2


title: 293T IRF7del [Sample 29]


title: WINco010_05.t4.rep2

source_name: Grape berries 3 weeks post flowering, normal irrigation


title: 293T GFP [Sample 25]


title: RHH2178 (scRNA-seq)

description: Sensitive


title: WINco009_05.t4.rep1


title: RHH2177 (scRNA-seq)

description: Sensitive


title: Myr1_1

city: Stanford

first: Adit

last: Naor

state: CA

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

institute: Stanford

description: Infected with RH∆myr1 parasites

data_processing:
Illumina Nextseq 500 model instrument was used for sequencing, Sequenced reads were trimmed for adaptor sequence.
Raw reads were uploaded onto the CLC Genomics Workbench 8.0 (Qiagen) platform for independent alignments against the human genomes (Ensembl.org/ hg19) and Toxoplasma Type I GT1 strain (ToxoDB-24, GT1 genome)
Supplementary_files_format_and_content: tab-delimited text files include number of reads value for each Sample

source_name: Human foreskin fibroblast - tissue culture

growth_protocol: HFFs were serum-starved for 24 hours before infection by growth in DMEM containing 0.5% serum. They were then infected with the indicated line of tachyzoites at an MOI of 5, for  6hours. Multiplex sequencing libraries were generated with RNA Sample Prep Kit (Illumina) according to manufacturer’s instructions and pooled for a single high-throughput sequencing run using the Illumina NextSeq platform (Illumina Nextseq 500 model instrument)at thethe Stanford University Functional Genomic Facility (SFGF).

extract_protocol:
1 ml TRIzol reagent (Invitrogen) was added to each T25 and the cells were scraped. Lysates were collected into RNAse/DNAse-free Eppendorf tubes and frozen at −20 °C. Total RNA was extracted following the manufacturer’s instructions, with some modifications. Briefly: frozen samples were thawed on ice and 0.2 ml chloroform was added to TRIzol suspensions, which were then mixed by inverting 10 times, and incubated for 5 minute. Tubes were then spun at 12,000 rpm for 15 min at 4 °C. RNA in the aqueous phase was transferred into a fresh tube and 0.5 ml absolute isopropyl alcohol was added. Each tube was inverted three times and incubated at 4°C for 10 min. They were then spun at 12,000 rpm for 20 min at 4 °C. After decanting the supernatants, RNA pellets were washed with 1 ml 75% ethanol. Tubes were mixed by inverting 10 times and then spun at 12,000 rpm for 20 min at 4°C. Supernatants were removed and the RNA pellets were air-dried in open tubes for approximately 10 min. The RNA pellets were resuspended in 30 μl RNase-free DEPC-water.
Multiplex sequencing libraries were generated with RNA Sample Prep Kit (Illumina) according to manufacturer’s instructions and pooled for a single high-throughput sequencing run using the Illumina NextSeq platform (Illumina Nextseq 500 model instrument) at thethe Stanford University Functional Genomic Facility (SFGF).

tag: time point

value: 6 hours post infection

tag: agent

value: Infected with RH∆myr1 parasites

value: Toxoplasma gondii


title: Myr1_2

description: Infected with RH∆myr1 parasites


title: RHH2176 (scRNA-seq)

description: Sensitive

tag: disease state

tag: cell type


title: 1618-NK-H47

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: blood

extract_protocol: RNA Libraries are prepared using the Illumina TruSeq RNA Exome protocol and kit reagents.

value: NK

value: Hypoxia

tag: subject


title: 1618-NK-N37

value: Normoxia


title: 1616-NK-H5


title: 1616-NK-N1


title: 239010_2

description: Infected with RH∆239010 parasites

value: Infected with RHdelta239010 parasites


title: 239010_1

description: Infected with RH∆239010 parasites


title: 1614-NK-H7


title: RH_1

description: Infected with RH parasites

value: Infected with RH parasites


title: Mock_2

description: Mock infected

value: Mock infected


title: RH_2

description: Infected with RH parasites


title: 1614-NK-N1


title: epi71

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Library strategy: DNA-Seq
The raw reads were trimmed using Trimmomatic to remove adapter sequences. Reads with an averaged value of at least 15 in a 4 nucleotide window were trimmed from both ends. After trimming, reads pairs with at least one mate shorter that 36 bp were discarded.
The remaining reads were aligned with bowtie2 (Langmead and Salzberg, 2012) with the –no mixed and –non deterministic option, against the reference TAIR10 Arabidopsis genome (www.arabidopsis.org).
Genome coverage was calculated for each genome position using genomecov (bedtools v2.26.0) and normalized to Arabidopsis genome and library size. Arabidopsis genomic regions with a coverage of more than 2.5 fold or less than 0.2 fold of the average genome coverage in the Col-0 wild type control were masked, to avoid to call peaks in regions with high copy number or not enough covered (e.g. plastids DNA insertion, ribosomal repeats, microsatellites).
Peak call was done for each epiRILs mapped bam file in comparison to the Col-0 control condition with macs2 (https://github.com/taoliu/MACS/), setting the fragment size to 75 and extended size to 400 bp, and the options –B, -SPMR and –no model, and using a Columbia-0 sample as control.
The Log based background subtraction was performed with macs2 bdgcmp with “logLR” as model and a p-value threshold of 0.00001.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files contain list of peaks from macs2 output, in xls format

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis epiRIL seeds were sown on ½ x MS (Plant) medium plates and grown for 14 days under Long day light conditions (16h of light).

extract_protocol:
Approximately 10 seedlings were harvested per epiRIL for ~100mg tissue from which DNA was extracted using the Qiagen DNeasy Plant Mini Kit, following the manufacturer’s instructions (Qiagen N.V., Hilden, Germany).
Before library preparation, DNA was fragmented to an average insert size of 350bp using 24 cycles of 30 seconds each on a Bioruptor® Diagenode sonication device. The genomic DNA sequencing libraries for the Arabidopsis epiRILs were prepared using the TruSeq DNA PCR-Free LT Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA), starting from  1.1µg of sonicated DNA. Libraries were validated using the High Sensitivity D1000 screentape on the 2200 Tapestation instrument (Agilent technologies, Santa Clara, CA) and the LightCycler® 480 Instrument II using the LightCycler® 480 SYBR Green I Master mix (Roche, Basel, Switzerland).

tag: ecotype

value: seedling

tag: age

value: 2 weeks

tag: line

value: met1-3 derived epiRIL epi71 F9


title: epi70

value: met1-3 derived epiRIL epi70 F9


title: Col-0 rep2

value: Col-0 wild type replicate 2


title: Col-0 rep1

value: Col-0 wild type replicate 1


title: met1-3 mutant

value: met1-3 mutant


title: epi69

value: met1-3 derived epiRIL epi69 F9


title: CTRL-10597

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description: rRNA depleted

data_processing:
Sequencing reads were trimmed using Trimmomatic (v0.32), removing adaptor and other Illumina-specific sequences as well as the first four bases from the start of each read, and low-quality bases at the end of each read, using a 4 bp sliding window to trim where average window quality fell below 30 (phred33 < 30). Trimmed reads < 30 bp were discarded.
Reads were aligned using STAR (v2.3.0e) with default parameter
Gene expression levels were estimated by quantifying uniquely mapped reads to exonic regions using featureCounts (v1.4.4) and the Ensembl gene annotation set
Normalization of the counts and differential expression analysis was performed with DESeq2 v1.14.1
For splicing analysis, we used rMATS v3.2.5 with default parameters. We performed the analysis on untrimmed reads, using the Mus musculus GRCm38 release 87 Ensembl gtf as exon annotation file. A non-redundant list of genes displaying significant AS events was generated by selecting the most statistically significant AS event per gene with more than 10% inclusion level difference. Benjamini-Hochberg correction was applied to this non-redundant set of events. The final list of AS affected genes contains events with FDR < 0.05 in genes that pass a minimum expression threshold (normalized mean expression > 50).
Genome_build: mm10
Supplementary_files_format_and_content: Ensembl.ensGene.exon.norm.tsv: normalized exon counts from DEseq2 of the 8 samples
Supplementary_files_format_and_content: rMATS tsv files, 5 alternative splicing event types; only events with a basemean expression > 50, absolute inclusion level difference > 0.1, FDRadj < 0.05 and the most significant event if multiple events were present in the same gene were kept. SAMPLE1 correspond to the controls and SAMPLE2 correspond to the PRMT5 FF Cg1cre

organism: Mus musculus

source_name: activated splenic primary B-cells

growth_protocol: Cγ1-cre and Prmt5F/F Cγ1-cre splenic B cells were plated on 40LB feeder cells, that express CD40L, BAFF and supplemented with IL-4 (1ng/mL). B cells were separated from the feeder cells by elutriation at day 4 after plating.

extract_protocol:
Total RNA was extracted from 4 independent biological samples per genotype, using RNeasy plus Mini kit (Quiagen) and quality controlled using RNA Pico chip on Bioanalyzer (Agilent).
Samples were depleted of rRNA using Ribo-zero Gold rRNA removal kit H/M/R (Illumina Hu Mm Rt). Libraries were constructed using the KAPA stranded RNA-Seq kit (Roche), which included fragmentation, cDNA, dsDNA, ER, ATL, Ligation and PCR enrichment and purified by KAPA magnetic beads (Roche). The mean fragment size obtained was 308bp. QC validation was performed on HSdna chip on Bioanalyzer and Q-PCR titration with NEBnext Library quant Kit for Illumina (NEB). Sequencing PE125 on HiSeq2500 with v4 chemistry (Illumina) at the Genome Center (Quebec)

tag: strain

tag: genotype

tag: excision

value: Control


title: bead-free DNA

first: Peter

last: Sims

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

description: synthetic DNA molecules that falls off from mRNA capturing beads (the dropseq beads) after sonication

data_processing:
For RNA-Seq:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 and GRCm38 using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.
For bead-free DNA Sample:
Read 1 file was generated on basespace.
12-nt cell barcodes (CBs) and 8-nt sample index were extracted from each read.
For each cell barcode that has an associated RNA-Seq profile from Sample 1 and each of the 128 sample index sequences on a white list, we counted the number of reads that contains both the cell barcode and a sample index that is within 1 hamming distance from the sample index on the white list. The counts were then organized in a table format where each row contains the counts of a cell barcodes across all 128 samples and each column contains the counts of different cell barcodes in one of the 128 samples.
Supplementary_files_format_and_content: Tab-delimited text files that contain the counts of cell barcodes in each of the 128 bead-free libraries.

organism: synthetic construct

source_name: synthetic DNA

extract_protocol:
Drop-Seq beads were vortexed for 1 minute, sonicated for 5 minutes, and incubated at 4°C for 12 hours. The resulting supernatent was used for downstream library construction.
The bead-free single-stranded DNAs were hybridized to a primer, and then converted to double-stranded DNA molecules which were then PCR amplified, purified by Ampure XP beads and gel electrophoresis.

tag: cell line


title: CTRL-10596

description: rRNA depleted


title: Mock_1

description: Mock infected

value: 6 hours post infection


title: WINco005_05.t2.rep1

source_name: Grape berries 1 week post flowering, normal irrigation

tag: Cabernet Sauvignon


title: WINco004_05.t1.rep2

source_name: Anthesis flower sample,  normal irrigation


title: WINco006_05.t2.rep2


title: WINco003_05.t1.rep1


title: epi67

value: met1-3 derived epiRIL epi67 F9


title: U87_3T3_scRNAseq [PJ061-709]

description: U87 cells and 3T3 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplimented with 10% (v/v) Fetal Bovine Serum (FBS).

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Brain and embyro

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: U87 cells and 3T3 cells


title: U87_3T3_scRNAseq [PJ061-710]


title: Ripe Red berry at veraison (SIB_B2_RR_4.t10.rep1)

description: gene expression data from a deseeded ripe red berry taken from a bunch at veraison

source_name: ripe red berry at veraison

label_protocol: Affymetrix Two Cycle cDNA synthesis kit, Affymetrix GeneChip Sample Cleanup kit, Affymetrix IVT labelling kit


title: CTRL-10370

description: rRNA depleted


title: CTRL-10650

description: rRNA depleted


title: epi66

value: met1-3 derived epiRIL epi66 F9


title: WINco007_05.t3.rep1

source_name: Grape berries 2 weeks post flowering, normal irrigation


title: WINco008_05.t3.rep2


title: Ripe Red berry at veraison (SIB_B2_RR_5.t10.rep2)


title: Red berry at veraison (SIB_B2_RE_5.t10.rep2)

description: gene expression data from a deseeded red single berry taken from a bunch at veraison

source_name: red berry at veraison


title: epi68

value: met1-3 derived epiRIL epi68 F9


title: Red berry at veraison (SIB_B2_RE_4.t10.rep1)


title: Blush grape berry at veraison (SIB_B2_BL_5.t10.rep2)

description: gene expression data from a deseeded blush single berry taken from a bunch at veraison

source_name: blush grape berry at veraison


title: U87_3T3_scRNAseq [PJ061-708]


title: U87_3T3_scRNAseq [PJ061-707]


title: Blush grape berry at veraison (SIB_B2_BL_3.t10.rep1)


title: epi65

value: met1-3 derived epiRIL epi65 F9


title: PRMT5-10770

description: rRNA depleted

value: PRMT5 FF Cgamma1-cre

value: Prmt5 excised in activated B cells


title: Soft green grape berry at veraison (SIB_B2_SG_1.t10.rep1)

description: gene expression data from a deseeded soft green single berry taken from a bunch at veraison

source_name: soft green grape berry at veraison


title: Hard green grape berry at veraison (SIB_B2_HG_1.t10.rep2)

description: gene expression data from a deseeded hard green single berry taken from a bunch at veraison

source_name: hard green grape berry at veraison


title: Soft green grape berry at veraison (SIB_B2_SG_2.t10.rep2)


title: epi64

value: seedling

value: met1-3 derived epiRIL epi64 F9


title: epi63

value: 2 weeks

value: met1-3 derived epiRIL epi63 F9


title: PRMT5-10618

description: rRNA depleted


title: epi61

value: met1-3 derived epiRIL epi61 F9


title: U87_3T3_scRNAseq [PJ061-705]


title: PRMT5-10771

description: rRNA depleted


title: U87_3T3_scRNAseq [PJ061-706]


title: epi60

value: met1-3 derived epiRIL epi60 F9


title: PRMT5-10617

description: rRNA depleted


title: U87_3T3_scRNAseq [PJ061-703]


title: U87_3T3_scRNAseq [PJ061-704]


title: U87_3T3_scRNAseq [PJ061-702]


title: epi58

value: met1-3 derived epiRIL epi58 F9


title: U87_3T3_scRNAseq [PJ061-701]


title: Hard green grape berry at veraison (SIB_B2_HG_3.t10.rep1)


title: epi57

value: met1-3 derived epiRIL epi57 F9


title: epi55

value: met1-3 derived epiRIL epi55 F9


title: epi52

value: met1-3 derived epiRIL epi52 F9


title: epi51

value: met1-3 derived epiRIL epi51 F9


title: epi53

value: met1-3 derived epiRIL epi53 F9


title: epi50

value: met1-3 derived epiRIL epi50 F9


title: epi49

value: met1-3 derived epiRIL epi49 F9


title: 29Q-3

first: Xin

last: Yang

address: 1130 Saint Nicholas Ave, ICRC building

department: Institute for Cancer Genetics

data_processing:
Normal sequence Hiseq 4000 PE150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x  -1  -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: GRCH38
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...

source_name: Human colon cancer cells

growth_protocol: HCT116 cells were obtained from ATCC and maintained at 37℃ and 5% CO2 in DMEM supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA is used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PHF5A K29Q


title: WT-1

value: WT


title: 29Q-1


title: 29Q-2


title: WT-2


title: epi48

value: met1-3 derived epiRIL epi48 F9


title: epi47

value: seedling

value: met1-3 derived epiRIL epi47 F9


title: mES IRF9-VPR 12h plus 5d rest [Sample 76]

description:
DNase-treated
TableS7_DE_mES_IRF9VPRvGFP_rest.xlsx
TableS7_read_counts_II.xlsx

source_name: Murine Embryonic Stem Cells

value: mES clone 39

tag: passages

value: low passage

tag: treatment

value: transfected using Lipofectamine 2000 with in vitro transcribed IRF9-VPR mRNA for 12h followed by 5 days rest


title: mES IRF9-VPR 12h plus 5d rest [Sample 75]


title: epi59

tag: tissue

value: 2 weeks

value: met1-3 derived epiRIL epi59 F9


title: mES GFP 12h plus 5d rest [Sample 74]

value: transfected using Lipofectamine 2000 with in vitro transcribed GFP mRNA for 12h followed by 5 days rest


title: epi46

value: met1-3 derived epiRIL epi46 F9


title: mES IRF9-VPR 12h [Sample 72]

description:
DNase-treated
TableS7_DE_mES_IRF9VPRvGFP_12h.xlsx
TableS7_read_counts_I.xlsx

value: transfected using Lipofectamine 2000 with in vitro transcribed IRF9-VPR mRNA for 12h


title: epi45

value: met1-3 derived epiRIL epi45 F9


title: epi43

value: met1-3 derived epiRIL epi43 F9


title: WT-3


title: epi54

value: met1-3 derived epiRIL epi54 F9


title: epi42

value: met1-3 derived epiRIL epi42 F9


title: mES GFP 12h [Sample 70]

value: transfected using Lipofectamine 2000 with in vitro transcribed GFP mRNA for 12h


title: mES IRF9-VPR 12h [Sample 71]


title: mES GFP 12h [Sample 69]


title: epi41

value: met1-3 derived epiRIL epi41 F9


title: epi38

value: met1-3 derived epiRIL epi38 F9


title: epi39

value: seedling

value: met1-3 derived epiRIL epi39 F9


title: epi40

value: met1-3 derived epiRIL epi40 F9


title: epi36

value: met1-3 derived epiRIL epi36 F9


title: epi34

value: met1-3 derived epiRIL epi34 F9


title: epi32

value: 2 weeks

value: met1-3 derived epiRIL epi32 F9


title: epi33

value: met1-3 derived epiRIL epi33 F9


title: epi35

value: met1-3 derived epiRIL epi35 F9


title: mES GFP 12h plus 5d rest [Sample 73]

value: mES clone 39

value: low passage

value: transfected using Lipofectamine 2000 with in vitro transcribed GFP mRNA for 12h followed by 5 days rest


title: epi30

value: met1-3 derived epiRIL epi30 F9


title: epi27

value: met1-3 derived epiRIL epi27 F9


title: epi31

value: met1-3 derived epiRIL epi31 F9


title: epi25

value: met1-3 derived epiRIL epi25 F9


title: epi44

value: met1-3 derived epiRIL epi44 F9


title: epi28

value: seedling

value: met1-3 derived epiRIL epi28 F9


title: epi23

value: met1-3 derived epiRIL epi23 F9


title: epi22

value: met1-3 derived epiRIL epi22 F9


title: epi21

value: met1-3 derived epiRIL epi21 F9


title: epi37

value: 2 weeks

value: met1-3 derived epiRIL epi37 F9


title: Long term withdrawal RENCA  3

description:
LTW.3
SAMPLE 12

hyb_protocol: Seven hundred and fifty nanograms of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58oC to the MouseWG-6v2 Expression BeadChip (Illumina; BD-201-0202).

source_name: Kidney cancer cells

growth_protocol: Cells were maintained in RPMI supplemented with 5% FBS in the presence or absence of 5μM sunitinib. Growth media was refreshed every 3-4 days.

tag: variant

value: RENCA SuR/LT-W

value: Sunitinib

tag: dose

value: 5 uM

tag: treatment duration

value: > 2 months

tag: withdrawal duration


title: Short term withdrawal RENCA  2

description:
STW.2
SAMPLE 8

value: RENCA SuR/ST-W

value: 48 hours


title: epi26

value: met1-3 derived epiRIL epi26 F9


title: Short term withdrawal RENCA  1

description:
STW.1
SAMPLE 7


title: epi19

value: met1-3 derived epiRIL epi19 F9


title: epi20

value: met1-3 derived epiRIL epi20 F9


title: Long term withdrawal RENCA  1

description:
LTW.1
SAMPLE 10


title: Long term withdrawal RENCA  2

description:
LTW.2
SAMPLE 11


title: epi17

value: met1-3 derived epiRIL epi17 F9


title: epi24

value: seedling

value: met1-3 derived epiRIL epi24 F9


title: epi16

value: met1-3 derived epiRIL epi16 F9


title: epi18

value: met1-3 derived epiRIL epi18 F9


title: epi15

value: met1-3 derived epiRIL epi15 F9


title: epi14

value: 2 weeks

value: met1-3 derived epiRIL epi14 F9


title: Short term withdrawal RENCA  3

description:
STW.3
SAMPLE 9


title: Sunitinib resistant RENCA  1

description:
SuR.1
SAMPLE 4

value: RENCA SuR


title: Sunitinib resistant RENCA  2

description:
SuR.2
SAMPLE 5

value: Sunitinib


title: A375 NRASQ61R cells induced without dox for 5days, biological rep1

city: Boston

first: Raj

last: Kumar

state: MA

address: 50 Blossom St

department: Dermatology

institute: MGH

hyb_protocol: Following fragmentation, 50ng/µl of cRNA were hybridized at 45°C for 16 hours at 60 RPM on GeneChip Human PrimeView Gene Expression Arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450, according to the manufacturer’s instructions

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000.

data_processing: Images were extracted with Affymetrix GeneChip Command Console (AGCC) and the data were analyzed using GeneChip Expression Console.

source_name: Human melanoma cell culture, collected at 5th day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA @ 33ng/ul (Affymetrix 3’ IVT Plus Kit).

growth_protocol: One million melanoma cells were seaded into 10 cm petriplates and grown over night

extract_protocol: Total RNA was isolated using Qiagen RNeasy extraction kit.

treatment_protocol: Induced with/ without doxycycline to express second oncogene for 5 days .

value: Skin cancer

tag: genotype/variation

value: endogenous BRAFV600E mutation

tag: disease state

value: Melanoma

value: stably infected with doxycycline inducible hNRASQ61R pLVX-TRE3G-ZsGreen1 vector


title: Sunitinib resistant RENCA  3

description:
SuR.3
SAMPLE 6

value: 5 uM

value: > 2 months


title: A375 VECTOR cells with dox for 5days, biological rep2

value: stably infected with doxycycline inducible empty pLVX-TRE3G-ZsGreen1 vector


title: Parental RENCA  1

description:
P.1
SAMPLE 1

value: RENCA


title: Parental RENCA  3

description:
P.3
SAMPLE 3


title: epi12

tag: ecotype

value: seedling

value: met1-3 derived epiRIL epi12 F9


title: epi13

tag: age

value: met1-3 derived epiRIL epi13 F9


title: A375 VECTOR cells without dox for 5days, biological rep1


title: GMEL VECTOR cells with dox for 5days, biological rep2


title: epi09

tag: line

value: met1-3 derived epiRIL epi09 F9


title: A375 NRASQ61R cells induced with dox for 5days, biological rep2


title: SKMEL119 BRAFV600E cells induced with dox for 5days, biological rep2

value: endogenous NRASQ61R mutation

value: stably infected with doxycycline inducible hBRAFV600E pLVX-TRE3G-ZsGreen1 vector


title: epi10

value: 2 weeks

value: met1-3 derived epiRIL epi10 F9


title: GMEL NRASQ61R cells induced without dox for 5days, biological rep1


title: GMEL VECTOR cells without dox for 5days, biological rep1


title: GMEL NRASQ61R sells induced with dox for 5days, biological rep2


title: epi08

value: met1-3 derived epiRIL epi08 F9


title: iPSC-IRF7del dox 48h plus 5d rest, 5d FBS diff,2

description:
test
SAMPLE 8

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.thermofisher.com/us/en/home/life-science/stem-cell-research/taqman-hpsc-scorecard-panel/scorecard-software.html
Rn values (normalized reporter value) is the fluorescent signal normalized to the signal of the passive reference dye. Delta Rn value is the Rn value of the experimental reaction minus the Rn value of the baseline signal generated by the instrument.
For the normalization this program uses a panel of housekeeping genes: ACTB (x4), CTCF, EP300 and SMAD1
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data
Fold Change worksheet reports test/average of reference ratios

label: FAM

label_protocol: PCR assays were performed using the hPSC Scorecard panel (Applied Biosystems, catalog A15872) following the Manufacturer’s instructions. Reverse transcription was performed from 1 ug total RNA using the High Capacity RNA-to-cDNA reverse transcription kit (Applied Biosystems, catalog 4387406). Quantitative real-time PCR were performed (Applied Biosystems ViiA 7 System) with (protocol).

growth_protocol: iPS cultured in StemFlex and differentiatied in StemFlex minus supplement plus 10%FBS

extract_protocol: Total RNA was extracted with Trizol followed by DNase I treatment

treatment_protocol: iPS cultured in StemFlex with 1ug/ml doxycycline

tag: cell type

value: iPSC 2607 clone 4 transduced with IRF7del

value: 48h doxycycline plus 5d rest

tag: differentiation time

value: 5d FBS differentiation


title: Long term withdrawal 3T3 3

description:
LTW.3
SAMPLE 12

source_name: Fibroblasts

value: 3T3 SuR/LT-W

value: Sunitinib


title: Parental RENCA  2

description:
P.2
SAMPLE 2


title: iPSC-IRF7del dox 48h plus 5d rest, 5d FBS diff,1

description:
test
SAMPLE 7


title: SKMEL119 BRAFV600E cells induced without dox for 5days, biological rep1

value: Skin cancer

value: Melanoma


title: epi07

source_name: whole seedling

value: met1-3 derived epiRIL epi07 F9


title: Short term withdrawal 3T3 3

description:
STW.3
SAMPLE 9

value: 3T3 SuR/ST-W

value: 5 uM

value: > 2 months

value: 48 hours


title: Short term withdrawal 3T3 2

description:
STW.2
SAMPLE 8


title: Long term withdrawal 3T3 2

description:
LTW.2
SAMPLE 11


title: Long term withdrawal 3T3 1

description:
LTW.1
SAMPLE 10


title: SKMEL119 VECTOR cells with dox for 5 days, biological rep2

value: endogenous NRASQ61R mutation

value: stably infected with doxycycline inducible empty pLVX-TRE3G-ZsGreen1 vector


title: epi05

value: seedling

value: 2 weeks

value: met1-3 derived epiRIL epi05 F9


title: Short term withdrawal 3T3 1

description:
STW.1
SAMPLE 7


title: iPSC-IRF7del dox 48h plus 5d rest,2

description:
test
SAMPLE 4

value: iPSC 2607 clone 4 transduced with IRF7del


title: epi04

value: met1-3 derived epiRIL epi04 F9


title: iPSC-IRF7del dox 48h plus 5d rest,1

description:
test
SAMPLE 3

value: 48h doxycycline plus 5d rest


title: iPSC-GFP dox 48h plus 5d rest, 5d FBS diff,2

description:
test
SAMPLE 6

source_name: iPSC-GFP

value: iPSC 2607 clone 4 transduced with GFP

value: 5d FBS differentiation


title: SKMEL119 VECTOR cells without dox for 5 days, biological rep1

value: Skin cancer


title: epi03

value: met1-3 derived epiRIL epi03 F9


title: iPSC-GFP dox 48h plus 5d rest, 5d FBS diff,1

description:
test
SAMPLE 5


title: Sunitinib resistant 3T3 2

description:
SuR.2
SAMPLE 5

value: 3T3 SuR

value: Sunitinib


title: Sunitinib resistant 3T3 3

description:
SuR.3
SAMPLE 6

value: 5 uM


title: iPSC-GFP dox 48h plus 5d rest,2

description:
test
SAMPLE 2


title: epi01

value: met1-3 derived epiRIL epi01 F9


title: Sunitinib resistant 3T3 1

description:
SuR.1
SAMPLE 4

value: > 2 months


title: iPSC-GFP dox 48h plus 5d rest,1

description:
test
SAMPLE 1


title: epi06

value: met1-3 derived epiRIL epi06 F9


title: Parental 3T3 2

description:
P.2
SAMPLE 2


title: Parental 3T3 1

description:
P.1
SAMPLE 1


title: Sae2 S input

status: Public on Nov 21 2018

city: Austin

first: Tanya

middle: T.

last: Paull

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

description: Lib 43

data_processing:
alignment with BWA-MEM
duplicatemarking:PicardMarkDuplicates
QC:samtoolsflagstat,idxstats
Peakcalling:macs2
Genome_build: saccer3
Supplementary_files_format_and_content: bam files

organism: Saccharomyces cerevisiae

source_name: TP3352 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 sae2::KMX

growth_protocol: alpha factor synchronization then either held in G1 or released into growth for 50 min., with or without camptothecin (100 uM)

extract_protocol:
see BioRxiv https://doi.org/10.1101/394924
NEBNext DNA Library prep kit for Illumina (E6040S)

treatment_protocol: see growth protocol

tag: immunoprecipitation

value: input

tag: phase

value: S

value: TP3352 MATa his3delta1 leu2delta0 met15delta0 ura3delta0 sae2::KMX


title: Sae2 S IP

description: Lib 45

value: Flag-tagged Sae2


title: Parental 3T3 3

description:
P.3
SAMPLE 3


title: Sae2 S + CPT IP

description: Lib 48

value: camptothecin (100 uM)


title: Sae2 S + CPT bead control

description: Lib 47

value: bead control


title: Sae2 S + CPT input

description: Lib 46


title: Sae2 G1 + CPT IP

description: Lib 42


title: Sae2 G1 + CPT input

description: Lib 40


title: Sae2 G1 IP

description: Lib 39


title: epi02

value: seedling

value: 2 weeks

value: met1-3 derived epiRIL epi02 F9


title: Sae2 G1 input

description: Lib 37


title: red1-pG162A 30% spike-in anti-red1 ChIP

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

department: Biology

institute: New York University

description: ah9048_30-70_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg

data_processing:
ChIP-seq reads trimmed for low-quality sequence and mapped to a custom hybrid S288C/SK1 genome using bowtie v1.2.0 with parameters -q -m 1 -v 0 -p 8 -S
Peaks called using macs2 v2.1.1 command “callpeak” with parameters --keep-dup="auto" -B --nomodel --extsize 200 --SPMR -g 1.2e7
Normalized signal track produced by comparing ChIP treatment against input control using macs2 v2.1.1 command “bdgcmp” with parameter -m FE
Genome_build: Custom hybrid S288C/SK1 genome built by concatenating recently published S288C and SK1 genome assemblies (Yue et al. Nat. Genet. 2017)
Supplementary_files_format_and_content: bedGraph files: Fold enrichment of ChIP signal track compared to input sample at each base position

source_name: Cell suspension in synchronous meiosis

growth_protocol: Synchronous meiosis cultures were prepared by inoculating BYTA medium at OD600 = 0.3 and growing for 16.5 hours at 30°C. Cells were washed twice with water, resuspended in SPO medium at OD600 = 2.0 and incubated at 30°C.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using Illumina TruSeq DNA Sample Prep Kits v1, with adaptors used at 1:20 dilution. Amplified ChIP DNA between 300 and 500 bp was gel purified on 1.8% agarose and quantified using the Qubit assay HS kit as well as an Agilent 2200 TapeStation System. Fragments were sequenced on an Illumina NextSeq 500 instrument using a 100-bp single-end sequencing protocol.

tag: chip antibody

value: Anti-Red1 (Lot#16440; kind gift of N. Hollingsworth)

tag: meiotic time-point

value: 3 hours

tag: strain


title: red1-pG162A 30% spike-in Input


title: Sae2 G1 bead control

description: Lib 38

tag: treatment


title: red1-pG162A 25% spike-in Input

description: ah9048_25-75_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A 20% spike-in anti-red1 ChIP

description: ah9048_20-80_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A 15% spike-in anti-red1 ChIP

description: ah9048_15-85_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A 20% spike-in Input


title: red1-pG162A 10% spike-in anti-red1 ChIP

description: ah9048_10-90_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A 25% spike-in anti-red1 ChIP


title: red1-pG162A 15% spike-in Input


title: red1-pG162A 10% spike-in Input


title: red1-pG162A 5% spike-in anti-red1 ChIP

description: ah9048_5-95_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: Sae2 G1 + CPT bead control

description: Lib 41


title: WT 30% spike-in anti-red1 ChIP

description: ah119_30-70_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A 5% spike-in Input


title: WT 30% spike-in Input


title: WT 25% spike-in anti-red1 ChIP

description: ah119_25-75_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 20% spike-in anti-red1 ChIP

description: ah119_20-80_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 15% spike-in anti-red1 ChIP

description: ah119_15-85_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 5% spike-in anti-red1 ChIP

description: ah119_5-95_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 10% spike-in Input

description: ah119_10-90_spike-in_06032018_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 20% spike-in Input


title: WT 5% spike-in Input


title: WT 15% spike-in Input


title: spo11-Y135F anti-gH2AX ChIP

description: AH4206spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg

value: Anti-Histone H2A phospho S129 (gamma-H2AX; abcam Ref. # ab15083)


title: WT 10% spike-in anti-red1 ChIP


title: ycs4S/ycs4S anti-gH2AX ChIP

description: AH7011spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/red1 Input rep3

description: AH8219spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/ycs4S Input rep3


title: ycs4S/red1 anti-gH2AX ChIP


title: spo11-Y135F Input


title: red1/RED1 anti-gH2AX ChIP

description: AH8220spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT anti-gH2AX ChIP

description: AH119spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1/RED1 Input rep3


title: WT Input rep4


title: ycs4S/RED1 Input rep3

description: AH8218spike-gh2ax-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/red1 anti-Red1 ChIP rep2

description: AH8219spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/red1 Input rep1

description: AH8219spike-chip_122017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/red1 anti-Red1 ChIP rep1


title: ycs4S/RED1 anti-gH2AX ChIP


title: ycs4S/red1 Input rep2


title: ycs4S/ycs4S Input rep2

description: AH7011spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT 25% spike-in Input


title: ycs4S/ycs4S anti-Red1 ChIP rep2


title: ycs4S/ycs4S anti-Red1 ChIP rep1

description: AH7011spike-chip_122017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/ycs4S Input rep1


title: red1/RED1 anti-Red1 ChIP rep2

description: AH8220spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1/RED1 anti-Red1 ChIP rep1

description: AH8220spike-chip_122017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1/RED1 Input rep2


title: ycs4S/RED1 Input rep2

description: AH8218spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1/RED1 Input rep1


title: ycs4S/RED1 anti-Red1 ChIP rep1

description: AH8218spike-chip_122017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: ycs4S/RED1 Input rep1


title: hop1Δ anti-Red1 ChIP rep2

description: ah9120spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: Sae2 S bead control

description: Lib 44


title: hop1Δ Input rep1

description: AH9120spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: rec8Δ anti-Red1 ChIP rep2

description: AH8151spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: rec8Δ Input rep2


title: hop1Δ Input rep2


title: set1Δ Input rep2

description: ah8584spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: hop1Δ anti-Red1 ChIP rep1


title: set1Δ anti-Red1 ChIP rep2


title: dot1Δ rec8Δ Input rep2

description: AH8115spike-Red1-ChIP_011618_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: dot1Δ rec8Δ Input rep1

description: ah8115spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: set1Δ Input rep1

description: AH8584spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: set1Δ anti-Red1 ChIP rep1


title: dot1Δ set1Δ anti-Red1 ChIP rep2

description: ah8583spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: dot1Δ set1Δ anti-Red1 ChIP rep1

description: AH8583spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: rec8Δ anti-Red1 ChIP rep1

description: ah8151spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: dot1Δ set1Δ Input rep2


title: dot1Δ set1Δ Input rep1


title: ycs4S/RED1 anti-Red1 ChIP rep2


title: dot1Δ Input rep2

description: ah8104spikein_11082017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A anti-Red1 ChIP rep1

description: AH9048spikein-060717_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: dot1Δ anti-Red1 ChIP rep1

description: AH8104spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A Input rep2

description: AH9048spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: red1-pG162A Input rep1


title: dot1Δ Input rep1


title: red1-pG162A anti-Red1 ChIP rep2


title: WT anti-Red1 ChIP rep3

description: AH119spike-ChIP_122017_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: rec8Δ Input rep1


title: WT anti-Red1 ChIP rep2

description: AH119spikein-100917_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT Input rep3


title: dot1Δ rec8Δ anti-Red1 ChIP rep2


title: dot1Δ rec8Δ anti-Red1 ChIP rep1


title: WT Input rep2


title: WT anti-Red1 ChIP rep1

description: AH119spikein-060717_trimmed_S288c_SK1_Yue_PM_FE.bdg


title: WT Input rep1


title: dot1Δ anti-Red1 ChIP rep2


title: SU-DHL6 Y-803 500nM 8h-exp2 (Agilent)

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Standard Agilent miRNA microarray system hybridization protocol

scan_protocol: Microarrays were scanned following the Agilent microarray scanner protocol, and the image analysis and quantitation were performed by the Agilent Feature Extraction software

data_processing: Data analysis by GeneSpring 7.3.1 . R-LIMMA package, normalization method: Quantile, the probe with the highest p value (i.e. least significant) was chosen to represent the gene.  We filtered out control probes and low expressed probes. We computed the 95% percentile of the negative control probes on each array. We kept probes that were at least 10% brighter than the negative controls on at least two arrays.

label_protocol: Agilent's miRNA microarray system V2.2 miRNA with Complete Labeling and Hyb Kit according to the manufacture’s protocol

extract_protocol: Trizol according to manufacture's instructions

tag: cell line

tag: time


title: SU-DHL6 Y-803 500nM 4h-exp1 (Agilent)


title: SU-DHL6 Y-803 500nM 4h-exp2 (Agilent)


title: SU-DHL6 nt-exp2 (Agilent)

source_name: SU-DHL6 nt

value: Untreated


title: SU-DHL6 DMSO 4h-exp1 (Agilent)

source_name: SU-DHL6 DMSO 4h

value: DMSO


title: SU-DHL2 Y-803 500nM 8h-exp2_rep (Agilent)


title: SU-DHL6 DMSO 4h-exp2 (Agilent)


title: SU-DHL6 DMSO 8h-exp1 (Agilent)

source_name: SU-DHL6 DMSO 8h


title: SU-DHL2 Y-803 500nM 8h-exp2 (Agilent)


title: SU-DHL2 Y-803 500nM 8h-exp1 (Agilent)


title: SU-DHL2 Y-803 500nM 4h-exp2 (Agilent)


title: SU-DHL2 DMSO 8h-exp2_rep (Agilent)

source_name: SU-DHL2 DMSO 8h


title: SU-DHL2 Y-803 500nM 4h-exp1 (Agilent)


title: SU-DHL2 DMSO 8h-exp2 (Agilent)


title: SU-DHL2 DMSO 4h-exp2 (Agilent)

source_name: SU-DHL2 DMSO 4h


title: SU-DHL2 DMSO 8h-exp1 (Agilent)


title: SU-DHL2 DMSO 4h-exp1 (Agilent)


title: Dohh2 nt-exp2 (Agilent)

source_name: Dohh2 nt


title: SU-DHL6 Y-803 500nM 8h-exp1 (Agilent)


title: Dohh2 Y-803 500nM 4h-exp2 (Agilent)


title: SU-DHL6 nt-exp1 (Agilent)


title: Dohh2 Y-803 500nM 8h-exp1 (Agilent)


title: SU-DHL6 DMSO 8h-exp2 (Agilent)


title: Dohh2 Y-803 500nM 8h-exp2 (Agilent)


title: Dohh2 nt-exp1 (Agilent)


title: Dohh2 Y-803 500nM 4h-exp1 (Agilent)


title: Dohh2 DMSO 8h-exp1 (Agilent)

source_name: Dohh2 DMSO 8h


title: Dohh2 DMSO 4h-exp2 (Agilent)

source_name: Dohh2 DMSO 4h


title: HMC1.2_AQ1_1uM_4

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
Illumina Sequencing by HiSeq4000
Sequenced reads were trimmed for adaptor sequence, then mapped to either GRCh38 or CanFam3.1 reference genome using HISAT2 v.2.0.5
Uniquely-mapped reads aligned to exons were counted with HTSeq v.0.6.1, then tested for the presence of DEGs by the DESeq2 R package v.1.14.1
Genome_build: GRCh38 or CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each Sample

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% penicillin/streptomycin (Gibco, Thermo Scientific, Waltham, USA). The C2 culture medium was supplemented with 1 mM sodium pyruvate.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (Qiagen Italia, Milano, Italy).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded in 6-well plates (9x105 cells/well) and treated with two doses of AQ1 (1 µM and 2 µM) for 12 hours. For each experiment, we included also untreated and DMSO-treated cells. Five different experiments were conducted for each cell line.

value: Adult

value: Human-derived mast cell leukemia

tag: passages

value: 1uM G-quadruplex-biding ligand AQ1


title: HMC1.2_AQ1_2uM_2

value: 2uM G-quadruplex-biding ligand AQ1


title: HMC1.2_AQ1_2uM_3


title: HMC1.2_AQ1_2uM_1


title: HMC1.2_AQ1_1uM_3


title: HMC1.2_AQ1_2uM_4


title: HMC1.2_AQ1_1uM_1


title: SU-DHL2 nt-exp1 (Agilent)

source_name: SU-DHL2 nt


title: SU-DHL2 nt-exp2 (Agilent)


title: HMC1.2_DMSO_4


title: HMC1.2_AQ1_1uM_2


title: Dohh2 DMSO 8h-exp2 (Agilent)


title: HMC1.2_DMSO_3


title: HMC1.2_DMSO_2


title: HMC1.2_CTRL_4


title: HMC1.2_DMSO_1


title: HMC1.2_CTRL_3


title: 292In

city: St Paul

first: Fernando

last: Leite

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

description:
PolyA RNA
Sample 31
processed data file: rawreadLeite.txt

data_processing:
Trimmed via trimmomatic.
Mapping performed with TopHAT (v2.0.13) using bowtie (v2.2.4.0).
Raw read counts were quantified via Subreads using Feature counts.
Genome_build: Sus scrofa 3.0 (susScr3) (Sscrofa10.2)
Supplementary_files_format_and_content: rawreadLeite.txt: Tab-delimited text file includes raw read counts.

organism: Sus scrofa

source_name: terminal ileum

extract_protocol:
Immediately following necropsy, a section of ileum 2-3 cm immediately proximal to the ileocecal junction and adjacent to Peyer's patch was opened longitudinally and scraped using the edge of a microscope slide. The sample was immediately placed in RNAlater (ThermoFisher) and total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen). RNA quantity and quality were assessed using RiboGreen RNA and Agilent Analysis system, respectively.
Illumina Library Creation.

tag: tissue

value: Terminal ileum

value: Non-infected

tag: time point

value: 28 days

tag: animal id


title: 86In

description:
PolyA RNA
Sample 35
processed data file: rawreadLeite.txt


title: 1385In

description:
PolyA RNA
Sample 28
processed data file: rawreadLeite.txt

value: Infected with Lawsonia intracellularis


title: 76In

description:
PolyA RNA
Sample 34
processed data file: rawreadLeite.txt


title: 300In

description:
PolyA RNA
Sample 30
processed data file: rawreadLeite.txt


title: 149In

description:
PolyA RNA
Sample 33
processed data file: rawreadLeite.txt


title: 189In

description:
PolyA RNA
Sample 27
processed data file: rawreadLeite.txt


title: HMC1.2_CTRL_1


title: 197In

description:
PolyA RNA
Sample 29
processed data file: rawreadLeite.txt


title: 175In

description:
PolyA RNA
Sample 32
processed data file: rawreadLeite.txt


title: HMC1.2_CTRL_2


title: 295In

description:
PolyA RNA
Sample 23
processed data file: rawreadLeite.txt

value: 21 days


title: 1386In

description:
PolyA RNA
Sample 24
processed data file: rawreadLeite.txt


title: 147I

description:
PolyA RNA
Sample 22
processed data file: rawreadLeite.txt


title: 94In

description:
PolyA RNA
Sample 25
processed data file: rawreadLeite.txt


title: 190In

description:
PolyA RNA
Sample 20
processed data file: rawreadLeite.txt


title: 142In

description:
PolyA RNA
Sample 21
processed data file: rawreadLeite.txt


title: 96In

description:
PolyA RNA
Sample 18
processed data file: rawreadLeite.txt


title: 145I

description:
PolyA RNA
Sample 19
processed data file: rawreadLeite.txt


title: 192I

description:
PolyA RNA
Sample 17
processed data file: rawreadLeite.txt


title: 97I

description:
PolyA RNA
Sample 16
processed data file: rawreadLeite.txt


title: 144In

description:
PolyA RNA
Sample 15
processed data file: rawreadLeite.txt


title: 173In

description:
PolyA RNA
Sample 14
processed data file: rawreadLeite.txt


title: 194In

description:
PolyA RNA
Sample 26
processed data file: rawreadLeite.txt


title: 1381In

description:
PolyA RNA
Sample 13
processed data file: rawreadLeite.txt


title: 92In

description:
PolyA RNA
Sample 9
processed data file: rawreadLeite.txt

value: 14 days


title: 98In

description:
PolyA RNA
Sample 11
processed data file: rawreadLeite.txt


title: 193In

description:
PolyA RNA
Sample 10
processed data file: rawreadLeite.txt


title: 90In

description:
PolyA RNA
Sample 7
processed data file: rawreadLeite.txt


title: 188In

description:
PolyA RNA
Sample 5
processed data file: rawreadLeite.txt


title: 148In

description:
PolyA RNA
Sample 3
processed data file: rawreadLeite.txt


title: 87In

description:
PolyA RNA
Sample 6
processed data file: rawreadLeite.txt


title: 99In

description:
PolyA RNA
Sample 2
processed data file: rawreadLeite.txt


title: 294In

description:
PolyA RNA
Sample 8
processed data file: rawreadLeite.txt


title: 139In

description:
PolyA RNA
Sample 1
processed data file: rawreadLeite.txt


title: 140In

description:
PolyA RNA
Sample 12
processed data file: rawreadLeite.txt


title: Dohh2 DMSO 4h-exp1 (Agilent)


title: AS_CD452_nt_6_atac

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description: merged_annotated_ATAC_20171119B_AS_NT_peaks_raw.txt

data_processing:
bcl2fastq/2.17.1.14
alignment using bowtie2 using default parameters
PCR duplication were removed using picard-tools (v1.108).
findPeaks <input tag directory> -o <out file> -style factor -size 300
FDR in Homer peak creation (http://homer.ucsd.edu/homer/)
annotatePeaks.pl <merged peaks.bed> mm9 -d <list of tag directory> > merged_annotated_ATAC_<<samples specific>>_peaks_counts.txt
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9
Supplementary_files_format_and_content: Normalized read counts of merged peaks across all conditions

extract_protocol:
Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Brains were dissected, crudely chopped and incubated for 20 min at 37°C in a 1 ml HBSS solution containing 2% BSA, 1 mg/ml Collagenase D (Sigma) and 50µg/ml DNase1 (Sigma). Next, the homogenates were filtered through a 150μm mesh, washed with cold FACS buffer (2% FCS, 1mM EDTA in PBS-/-) and centrifuged at 2200 RPM, at 4°C, for 5 min. For the enrichment of microglia, the cell pellet was re-suspended with 3ml of 40% percoll solution and centrifuged at 2200 RPM, no acceleration and breaks, at RT for 15 min. Next, the cell pellet was resuspended, passed through 80µm mesh, washed with 5ml FACS buffer and centrifuged at 1400 RPM at 4°C for 5 min, followed by antibody (Ab) labeling and flow cytometry analysis.
30,000-50,000 microglia cells were sorted into 100μl of MACS buffer. Libraries were prepared according to Lara-Astiaso et al. 2014.

treatment_protocol: Mice were irradiated (950 cGy) and transffered with a donor BM. After either 3.5 or 9 months, mice were injected with 2.5 mg/kg LPS or not injected, and were scrificed after 12 hours.

tag: genotype

value: WT

tag: organ

value: Brain


title: AS_CD452_nt_4_atac


title: AS_CD452_LPS_3_atac

description: merged_annotated_ATAC_20171119B_AS_LPS_peaks_raw.txt


title: AS_CD451_nt_5_atac


title: AS_CD451_nt_4_atac


title: AS_CD452_nt_5_atac


title: 77In

description:
PolyA RNA
Sample 4
processed data file: rawreadLeite.txt


title: Ring1AB-2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Raw reads were trimmed with cutadapt (1.12) using the Trim Galore! (0.4.4) wrapper and subsequently aligned to the complete human ribosomal RNA sequence with bowtie (1.2).
Reads that did not align to rRNA were then mapped to the human reference genome (GRCh37/hg19) and read counts per gene were generated with with STAR (2.5.2b) --quantMode GeneCounts.
Raw reads were trimmed as part of bcl2fastq for Illumina adapters and aligned with RSEM (1.2.25) and Bowtie2 (2.2.6) to GRCh37/hg19 using default parameters.
The GTF file was obtained from genocdegenes.org (comprehensive gene annotation Release 19/GRCh37.p13)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene count files in txt format

source_name: cell line

growth_protocol: HAP1 cells were cultured in IMDM media supplemented with 10% FBS and 1% L-Glutamine.

extract_protocol:
Total RNA was extracted using Trizol reageant following manufacturer's instructions
Libraries were prepaired using Illumina TruSeq Stranded mRNA Library Prep.

value: HAP1 cells

value: RING1A, RING1B KO


title: Ring1AB_BAP1-1

value: RING1A, RING1B, BAP1 KO


title: Ring1AB-1


title: Ring1AB_BAP1-2


title: AS_CD451_nt_6_atac


title: CREBBP-KO.1

description:
CREBBP-KO.1
Raw files were generated by a co-author on the manuscript.

data_processing:
Raw reads were trimmed with cutadapt (1.12) using the Trim Galore! (0.4.4) wrapper and subsequently aligned to the complete human ribosomal RNA sequence with bowtie (1.2).
Reads that did not align to rRNA were then mapped to the human reference genome (GRCh37/hg19) and read counts per gene were generated with with STAR (2.5.2b) --quantMode GeneCounts.
BAM files for the CREBBP-KO and HAP1-WT samples were obtained from the Institut de Cancérologie Gustave Roussy and counts for these samples were generated using featureCounts (1.5.1) with the following parameters: -C -p -s 2 -T 8 -F GTF -t exon
Raw reads were trimmed as part of bcl2fastq for Illumina adapters and aligned with RSEM (1.2.25) and Bowtie2 (2.2.6) to GRCh37/hg19 using default parameters.
FASTQ files for these samples were generated with Picard Tools SamToFastq (2.6.0).
The GTF file was obtained from genocdegenes.org (comprehensive gene annotation Release 19/GRCh37.p13)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Read counts per gene are output from featureCounts for CREBBP-KO and HAP1-WT samples and STAR for all others.

source_name: HAP1 cells

value: CREBBP KO


title: HAP1-WT.2

description:
HAP1-WT.2
Raw files were generated by a co-author on the manuscript.


title: B_EC2dKORA24h_2

value: BAP1 EZH2 KO

value: retinoic acid


title: AS_CD452_LPS_1_atac


title: AS_CD452_LPS_2_atac


title: AS_CD451_LPS_2_atac


title: AS_CD451_LPS_1_atac


title: AS_BM_microglia_12h_control_8_CD452

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
For example: the UMI GTACTGGT will appear in the following format: @NB501465:106:HFFKNBGX2:1:11101:5035:1075:AGGCTAAGTACTGGT:A6/A/E//EE////E:0
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) located in fastq header.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Brains were dissected, crudely chopped and incubated for 20 min at 37°C in a 1 ml HBSS solution containing 2% BSA, 1 mg/ml Collagenase D (Sigma) and 50µg/ml DNase1 (Sigma). Next, the homogenates were filtered through a 150μm mesh, washed with cold FACS buffer (2% FCS, 1mM EDTA in PBS-/-) and centrifuged at 2200 RPM, at 4°C, for 5 min. For the enrichment of microglia, the cell pellet was re-suspended with 3ml of 40% percoll solution and centrifuged at 2200 RPM, no acceleration and breaks, at RT for 15 min. Next, the cell pellet was resuspended, passed through 80µm mesh, washed with 5ml FACS buffer and centrifuged at 1400 RPM at 4°C for 5 min, followed by antibody (Ab) labeling and flow cytometry analysis.
10,000 microglia cells were sorted into 40μl of Lysis Buffer (Life Technologies) and stored at -80°C. mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to manufacturer’s guidelines. for library construction we used a derivation of MARS-seq as described (Jaitin et al., 2014).


title: AS_CD451_LPS_3_atac


title: HAP1-WT.1

description:
HAP1-WT.1
Raw files were generated by a co-author on the manuscript.


title: BAP1KORA24h_2

value: BAP1 KO


title: B_EC2dKOcontrol_2


title: CREBBP-KO.2

description:
CREBBP-KO.2
Raw files were generated by a co-author on the manuscript.


title: AS_BM_microglia_12h_control_8_CD451


title: AS_BM_microglia_12h_control_7_CD451


title: BAP1KOcontrol_2


title: AS_BM_microglia_12h_control_7_CD452


title: WTcontrol_2


title: WTRA24h_2


title: B_EC2dKOcontrol_1


title: AS_BM_microglia_12h_control_5_CD452


title: AS_BM_microglia_12h_control_5_CD451


title: AS_BM_microglia_12h_control_6_CD451


title: AS_BM_microglia_12h_LPS_4_CD451


title: AS_BM_microglia_12h_LPS_2_CD452


title: AS_BM_microglia_12h_LPS_3_CD452


title: AS_BM_microglia_12h_LPS_3_CD451


title: WTcontrol_1


title: B_EC2dKORA24h_1


title: WTRA24h_1


title: Colon

city: Suita

first: Ryosuke

last: Negoro

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Colon

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: Before the initiation of enterocyte differentiation, human iPS cells were dissociated into clumps by using dispase (Roche) and plated onto growth factor reduced BD Matrigel Basement Membrane Matrix (BD Biosciences). These cells were cultured in the MEF-conditioned medium for 2-3 days. The differentiation protocol for the induction of definitive endoderm cells was described previously (Takayama et al., 2014). Briefly, for the definitive endoderm differentiation, human iPS cells were cultured for 4 days in Wnt3A-expressing cell-conditioned RPMI1640 medium (Sigma-Aldrich) containing 100 ng/ml Activin A (R&D Systems), 1×GlutaMAX, 0.2% fetal bovine serum (FBS), and 1×B27 Supplement Minus Vitamin A (Thermo Fisher Scientific). For the induction of intestinal progenitor cells, the definitive endoderm cells were cultured for 4 days in an intestinal differentiation medium, DMEM-High Glucose medium (FUJIFILM Wako) containing 10% knockout serum replacement (KSR, Thermo Fisher Scientific), 1% non-essential amino acid Solution (NEAA; Thermo Fisher Scientific), penicillin-streptomycin (P/S) and 1×GlutaMAX supplemented with 20 nM LY2090314 (MedChem Express). Then, for the induction of small intestinal epithelial-like cells, the intestinal progenitor cells were cultured for 20 days in Wnt3A-, R-spondin- and Noggin-expressing cell-conditioned intestinal differentiation medium containing 10 μM SB202190, 1 μM dexamethasone (DEX; FUJIFILM Wako), 50 ng/ml epidermal growth factor (EGF; R&D Systems), and 20 ng/ml insulin-like growth factor-1 (IGF-1; R&D Systems).

tag: tissue/cell type

value: human adult colon


title: iPSCs

source_name: iPSCs

value: undifferentiated human iPS cells


title: BAP1_EZH2_KO_2


title: BAP1KOcontrol_1


title: BAP1_EZH2_KO_1


title: EZH2_BAP1_KO_1

value: EZH2 BAP1 KO


title: BAP1KORA24h_1


title: EZH2_KO_2

value: EZH2 KO


title: AS_BM_microglia_12h_LPS_2_CD451


title: Small Intestine

source_name: Small Intestine

value: human adult small intestine


title: hiPS-SIECs

source_name: hiPS-SIECs

value: human iPS cells derived-Small Intestinal Epithelial cells


title: AS_BM_microglia_12h_LPS_1_CD452


title: AS_BM_microglia_12h_control_6_CD452


title: AS_BM_microglia_12h_LPS_1_CD451


title: BAP1_KO_2


title: BAP1_KO_1


title: Transit amplifying rep4

city: Woolloongabba

first: Jatin

last: Patel

address: 37 Kent Street

institute: The University of Queensland

description:
EVP_TA_D_DESeq2-normalized-counts-genes.GRCm38.p5.E91.tsv
differential_exp_EVP_TA.tsv
differential_exp_TA_D.tsv

data_processing:
After sequencing, fastq files were generated using bcl2fastq2 (v2.17).
The RNA-seq reads were mapped to the Mus musculus mm10 genome with STAR version 2.5.3a (Dobin et al 2013) using Ensembl annotation (GRCm38, release 91).
Reads were quantified with HTSeqcount version 0.6.1 (Anders et al, 2015) using the attribute gene_id from the Ensembl GTF file GRCm38 release 91 as feature ID.
Read count normalisation and differential gene expression analysis was performed using DESeq2 version 1.10.1 (Love et al 2014).
Genome_build: mm10 (NCBI build GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample and differential expression results from DESeq2

source_name: endothelial hierarchy

extract_protocol:
RNA was extracted from sorted EVP, TA and D cells using a QIAGEN mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA quality and concentration was assessed using A260nm/A280nm spectroscopy on the Nanodrop ND-1000 (Thermo-scientific, Langenselbold, Germany). 5-100ng of RNA was used for cDNA synthesis using the Superscript III Reverse Transcription Kit (Invitrogen, Mount Waverley, Australia).
RNA-Seq libraries were prepared from purified total RNA using a modified Smart-Seq2 protocol developed by Picelli et al. 2 ng of purified total RNA (0.4 ng/µL) was combined with 1 µL of 10 µM oligo-dT primer (/5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies) and 1 µL of dNTP mix (10 mM each; Invitrogen, y02256), then the protocol was continued as described. Briefly, the RNA was reverse transcribed with the Smart-Seq2 TSO (/5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, Integrated DNA Technologies), followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol, except for the PCR preamplification where the Smart-Seq2 ISPCR primer (/5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies) was added to a final concentration of 0.25 µM. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA sample preparation kit (Illumina, FC-131-1096), with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Agilent Bioanalyzer with the High Sensitivity DNA kit (Agilent Technologies,  4067-4626). Libraries were pooled in equimolar ratios, and the pool was quantified by qPCR using the KAPA Library Quantification Kit - Illumina/Universal (KAPA Biosystems, KK4824) in combination with the Life Technologies Viia 7 real time PCR instrument. Sequencing was performed using the Illumina NextSeq500 (NextSeq control software v2.0.2/ Real Time Analysis v2.4.11). The library pool was diluted and denatured according to the standard NextSeq protocol (Document # 15048776 v02), and sequenced to generate paired-end 76 bp reads using a 150 cycle NextSeq500/550 High Output reagent Kit v2 (Catalog # FC-404-2002).

tag: cell type

value: Transit amplifying


title: AS_BM_microglia_12h_LPS_4_CD452


title: BAP1_rescue_3


title: WT_2


title: Transit amplifying rep1


title: BAP1_KO_4


title: BAP1_KO_3


title: Transit amplifying rep3


title: BAP1_rescue_2


title: Transit amplifying rep2


title: Endovascular progenitor rep5

description:
EVP_TA_D_DESeq2-normalized-counts-genes.GRCm38.p5.E91.tsv
differential_exp_EVP_TA.tsv
differential_exp_EVP_D.tsv

value: Endovascular progenitor


title: Endovascular progenitor rep4


title: ASXL1_2_KO_2

value: ASXL1 ASXL2 KO


title: Definitive differentiated rep5

description:
EVP_TA_D_DESeq2-normalized-counts-genes.GRCm38.p5.E91.tsv
differential_exp_EVP_D.tsv
differential_exp_TA_D.tsv

value: Definitive differentiated


title: Endovascular progenitor rep2


title: Endovascular progenitor rep1


title: Endovascular progenitor rep3


title: EZH2_BAP1_KO_2


title: WT_1

value: WT


title: A2_2

value: ASXL2 KO


title: EZH2_KO_1


title: A2_1


title: ASXL1_2_KO_1


title: Transit amplifying rep5


title: Definitive differentiated rep4


title: Definitive differentiated rep3


title: Definitive differentiated rep2


title: E_1


title: Definitive differentiated rep1


title: A1_2

value: ASXL1 KO


title: B_2


title: A1_1


title: B_1


title: W_1


title: R_1

value: RING1B KO


title: W_2


title: E_2


title: R_2