title: mcc.prim.225

description: MCC dataset

source_name: Patient 225

value: C187 COLON SIGMOID


title: mcc.prim.223

status: Public on May 18 2019

type: RNA

city: Tampa

first: Stephanie

middle: L.

last: Schmit

state: FL

address: 12902 USF Magnolia Drive

department: Department of Cancer Epidemiology

country: USA

institute: H. Lee Moffitt Cancer Center

description: MCC dataset

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing:
IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS
Expression tables are log2 expression, IRON normalized signal

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Patient 223

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: tissue

value: primary colorectal cancer

tag: age at diagnosis (years)

tag: Sex

value: FEMALE

tag: anatomical origin

tag: proximal distal tumor classification

value: DISTAL

tag: treatment status classification (see description)

value: PRE

tag: tumor type

value: PRIMARY

tag: site of metastasis


title: mcc.prim.224

description: MCC dataset

source_name: Patient 224

value: MALE

value: C182 COLON ASCENDING

value: PROXIMAL


title: mcc.prim.243

description: MCC dataset

source_name: Patient 243

value: C209 RECTUM

value: RECTUM

value: POST-CHEM-RAD


title: mcc.prim.220

description: MCC dataset

source_name: Patient 220


title: mcc.prim.222

description: MCC dataset

source_name: Patient 222


title: mcc.prim.217

description: MCC dataset

source_name: Patient 217

value: C199 RECTOSIGMOID JUNCTION


title: mcc.prim.219

description: MCC dataset

source_name: Patient 219


title: mcc.prim.218

description: MCC dataset

source_name: Patient 218


title: mcc.prim.215

description: MCC dataset

source_name: Patient 215

value: C184 COLON TRANSVERSE


title: mcc.prim.216

description: MCC dataset

source_name: Patient 216

value: C180 COLON CECUM


title: mcc.prim.213

description: MCC dataset

source_name: Patient 213


title: mcc.prim.214

description: MCC dataset

source_name: Patient 214


title: mcc.prim.211

description: MCC dataset

source_name: Patient 211


title: mcc.prim.209

description: MCC dataset

source_name: Patient 209


title: mcc.prim.207

description: MCC dataset

source_name: Patient 207

value: C185 COLON SPLENIC FLEXURE


title: mcc.prim.204

description: MCC dataset

source_name: Patient 204


title: mcc.prim.206

description: MCC dataset

source_name: Patient 206

value: POST-CHEM


title: mcc.prim.205

description: MCC dataset

source_name: Patient 205


title: mcc.prim.200

description: MCC dataset

source_name: Patient 200


title: mcc.prim.202

description: MCC dataset

source_name: Patient 202


title: mcc.prim.201

description: MCC dataset

source_name: Patient 201


title: mcc.prim.199

description: MCC dataset

source_name: Patient 199


title: mcc.prim.203

description: MCC dataset

source_name: Patient 203


title: mcc.prim.221

description: MCC dataset

source_name: Patient 221


title: mcc.prim.198

description: MCC dataset

source_name: Patient 198


title: mcc.prim.197

description: MCC dataset

source_name: Patient 197


title: mcc.prim.196

description: MCC dataset

source_name: Patient 196


title: mcc.prim.191

description: MCC dataset

source_name: Patient 191

value: C187 COLON SIGMOID

value: POST-RAD


title: mcc.prim.193

description: MCC dataset

source_name: Patient 193

value: primary colorectal cancer

value: FEMALE


title: mcc.prim.195

description: MCC dataset

source_name: Patient 195

value: PRE


title: mcc.prim.194

description: MCC dataset

source_name: Patient 194

value: PRIMARY


title: mcc.prim.192

description: MCC dataset

source_name: Patient 192

value: MALE


title: mcc.prim.188

description: MCC dataset

source_name: Patient 188


title: mcc.prim.189

description: MCC dataset

source_name: Patient 189


title: mcc.prim.187

description: MCC dataset

source_name: Patient 187

value: DISTAL


title: mcc.prim.190

description: MCC dataset

source_name: Patient 190


title: mcc.prim.186

description: MCC dataset

source_name: Patient 186


title: mcc.prim.210

description: MCC dataset

source_name: Patient 210

value: C186 COLON DESCENDING


title: mcc.prim.208

description: MCC dataset

source_name: Patient 208

value: PROXIMAL


title: mcc.prim.184

description: MCC dataset

source_name: Patient 184

value: C182 COLON ASCENDING


title: mcc.prim.185

description: MCC dataset

source_name: Patient 185

value: C209 RECTUM

value: RECTUM

value: POST-CHEM-RAD


title: mcc.prim.212

description: MCC dataset

source_name: Patient 212

value: C199 RECTOSIGMOID JUNCTION


title: mcc.prim.183

description: MCC dataset

source_name: Patient 183


title: mcc.prim.181

description: MCC dataset

source_name: Patient 181


title: mcc.prim.178

description: MCC dataset

source_name: Patient 178

value: C184 COLON TRANSVERSE


title: mcc.prim.180

description: MCC dataset

source_name: Patient 180


title: mcc.prim.179

description: MCC dataset

source_name: Patient 179

value: C180 COLON CECUM


title: mcc.prim.176

description: MCC dataset

source_name: Patient 176


title: mcc.prim.177

description: MCC dataset

source_name: Patient 177

value: C187 COLON SIGMOID


title: mcc.prim.175

description: MCC dataset

source_name: Patient 175


title: mcc.prim.174

description: MCC dataset

source_name: Patient 174


title: mcc.prim.173

description: MCC dataset

source_name: Patient 173


title: mcc.prim.171

description: MCC dataset

source_name: Patient 171


title: mcc.prim.172

description: MCC dataset

source_name: Patient 172

value: POST-CHEM


title: mcc.prim.170

description: MCC dataset

source_name: Patient 170

value: primary colorectal cancer


title: mcc.prim.169

description: MCC dataset

source_name: Patient 169

value: FEMALE


title: mcc.prim.167

description: MCC dataset

source_name: Patient 167

value: PRE


title: mcc.prim.168

description: MCC dataset

source_name: Patient 168

value: PRIMARY


title: mcc.prim.165

description: MCC dataset

source_name: Patient 165


title: mcc.prim.166

description: MCC dataset

source_name: Patient 166

value: MALE


title: mcc.prim.164

description: MCC dataset

source_name: Patient 164


title: mcc.prim.159

description: MCC dataset

source_name: Patient 159


title: mcc.prim.162

description: MCC dataset

source_name: Patient 162

value: DISTAL


title: mcc.prim.160

description: MCC dataset

source_name: Patient 160


title: mcc.prim.158

description: MCC dataset

source_name: Patient 158


title: mcc.prim.161

description: MCC dataset

source_name: Patient 161


title: mcc.prim.163

description: MCC dataset

source_name: Patient 163


title: mcc.prim.157

description: MCC dataset

source_name: Patient 157


title: mcc.prim.155

description: MCC dataset

source_name: Patient 155


title: mcc.prim.154

description: MCC dataset

source_name: Patient 154


title: mcc.prim.156

description: MCC dataset

source_name: Patient 156


title: mcc.prim.152

description: MCC dataset

source_name: Patient 152


title: mcc.prim.182

description: MCC dataset

source_name: Patient 182


title: mcc.prim.153

description: MCC dataset

source_name: Patient 153


title: mcc.prim.150

description: MCC dataset

source_name: Patient 150


title: mcc.prim.151

description: MCC dataset

source_name: Patient 151


title: mcc.prim.148

description: MCC dataset

source_name: Patient 148


title: mcc.prim.149

description: MCC dataset

source_name: Patient 149


title: mcc.prim.147

description: MCC dataset

source_name: Patient 147

value: POST-RAD


title: mcc.prim.145

description: MCC dataset

source_name: Patient 145

value: PROXIMAL


title: mcc.prim.143

description: MCC dataset

source_name: Patient 143


title: mcc.prim.141

description: MCC dataset

source_name: Patient 141


title: mcc.prim.142

description: MCC dataset

source_name: Patient 142


title: mcc.prim.140

description: MCC dataset

source_name: Patient 140


title: mcc.prim.139

description: MCC dataset

source_name: Patient 139


title: mcc.prim.136

description: MCC dataset

source_name: Patient 136

value: C186 COLON DESCENDING


title: mcc.prim.137

description: MCC dataset

source_name: Patient 137


title: mcc.prim.138

description: MCC dataset

source_name: Patient 138

value: C182 COLON ASCENDING


title: mcc.prim.133

description: MCC dataset

source_name: Patient 133

value: RECTUM


title: mcc.prim.132

description: MCC dataset

source_name: Patient 132

value: C209 RECTUM

value: POST-CHEM-RAD


title: mcc.prim.134

description: MCC dataset

source_name: Patient 134


title: mcc.prim.131

description: MCC dataset

source_name: Patient 131


title: mcc.prim.130

description: MCC dataset

source_name: Patient 130


title: mcc.prim.127

description: MCC dataset

source_name: Patient 127

value: C184 COLON TRANSVERSE


title: mcc.prim.126

description: MCC dataset

source_name: Patient 126


title: mcc.prim.128

description: MCC dataset

source_name: Patient 128


title: mcc.prim.124

description: MCC dataset

source_name: Patient 124


title: mcc.prim.125

description: MCC dataset

source_name: Patient 125


title: mcc.prim.146

description: MCC dataset

source_name: Patient 146


title: mcc.prim.123

description: MCC dataset

source_name: Patient 123


title: mcc.prim.144

description: MCC dataset

source_name: Patient 144


title: mcc.prim.122

description: MCC dataset

source_name: Patient 122


title: mcc.prim.120

description: MCC dataset

source_name: Patient 120

value: C199 RECTOSIGMOID JUNCTION


title: mcc.prim.119

description: MCC dataset

source_name: Patient 119

value: C180 COLON CECUM


title: mcc.prim.118

description: MCC dataset

source_name: Patient 118


title: mcc.prim.116

description: MCC dataset

source_name: Patient 116

value: C187 COLON SIGMOID


title: mcc.prim.117

description: MCC dataset

source_name: Patient 117

value: primary colorectal cancer


title: mcc.prim.115

description: MCC dataset

source_name: Patient 115


title: mcc.prim.114

description: MCC dataset

source_name: Patient 114

value: POST-CHEM


title: mcc.prim.113

description: MCC dataset

source_name: Patient 113

value: PRE


title: mcc.prim.112

description: MCC dataset

source_name: Patient 112

value: PRIMARY


title: mcc.prim.135

description: MCC dataset

source_name: Patient 135

value: MALE


title: mcc.prim.111

description: MCC dataset

source_name: Patient 111


title: mcc.prim.110

description: MCC dataset

source_name: Patient 110

value: DISTAL


title: mcc.prim.108

description: MCC dataset

source_name: Patient 108

value: FEMALE


title: mcc.prim.109

description: MCC dataset

source_name: Patient 109

value: PROXIMAL


title: mcc.prim.129

description: MCC dataset

source_name: Patient 129


title: mcc.prim.107

description: MCC dataset

source_name: Patient 107


title: mcc.prim.104

description: MCC dataset

source_name: Patient 104


title: mcc.prim.101

description: MCC dataset

source_name: Patient 101


title: mcc.prim.121

description: MCC dataset

source_name: Patient 121


title: mcc.prim.100

description: MCC dataset

source_name: Patient 100


title: mcc.prim.105

description: MCC dataset

source_name: Patient 105


title: mcc.prim.103

description: MCC dataset

source_name: Patient 103


title: mcc.prim.98

description: MCC dataset

source_name: Patient 98


title: mcc.prim.95

description: MCC dataset

source_name: Patient 95


title: mcc.prim.97

description: MCC dataset

source_name: Patient 97


title: mcc.prim.96

description: MCC dataset

source_name: Patient 96


title: mcc.prim.93

description: MCC dataset

source_name: Patient 93


title: mcc.prim.94

description: MCC dataset

source_name: Patient 94


title: mcc.prim.91

description: MCC dataset

source_name: Patient 91


title: mcc.prim.90

description: MCC dataset

source_name: Patient 90


title: mcc.prim.88

description: MCC dataset

source_name: Patient 88


title: mcc.prim.86

description: MCC dataset

source_name: Patient 86


title: mcc.prim.87

description: MCC dataset

source_name: Patient 87


title: mcc.prim.89

description: MCC dataset

source_name: Patient 89


title: mcc.prim.83

description: MCC dataset

source_name: Patient 83


title: mcc.prim.82

description: MCC dataset

source_name: Patient 82


title: mcc.prim.84

description: MCC dataset

source_name: Patient 84

value: C185 COLON SPLENIC FLEXURE


title: mcc.prim.80

description: MCC dataset

source_name: Patient 80


title: mcc.prim.85

description: MCC dataset

source_name: Patient 85

value: C182 COLON ASCENDING


title: mcc.prim.79

description: MCC dataset

source_name: Patient 79


title: mcc.prim.106

description: MCC dataset

source_name: Patient 106


title: mcc.prim.102

description: MCC dataset

source_name: Patient 102


title: mcc.prim.99

description: MCC dataset

source_name: Patient 99

value: RECTUM


title: mcc.prim.76

description: MCC dataset

source_name: Patient 76

value: C183 COLON HEPATIC FLEXURE


title: mcc.prim.77

description: MCC dataset

source_name: Patient 77

value: C209 RECTUM

value: POST-CHEM-RAD


title: mcc.prim.75

description: MCC dataset

source_name: Patient 75

value: C186 COLON DESCENDING


title: mcc.prim.73

description: MCC dataset

source_name: Patient 73


title: mcc.prim.74

description: MCC dataset

source_name: Patient 74


title: mcc.prim.72

description: MCC dataset

source_name: Patient 72


title: mcc.prim.69

description: MCC dataset

source_name: Patient 69


title: mcc.prim.71

description: MCC dataset

source_name: Patient 71

value: C199 RECTOSIGMOID JUNCTION


title: mcc.prim.70

description: MCC dataset

source_name: Patient 70

value: C180 COLON CECUM


title: mcc.prim.68

description: MCC dataset

source_name: Patient 68

value: primary colorectal cancer


title: mcc.prim.61

description: MCC dataset

source_name: Patient 61


title: mcc.prim.66

description: MCC dataset

source_name: Patient 66


title: mcc.prim.62

description: MCC dataset

source_name: Patient 62


title: mcc.prim.64

description: MCC dataset

source_name: Patient 64

value: C184 COLON TRANSVERSE


title: mcc.prim.63

description: MCC dataset

source_name: Patient 63

value: PRE


title: mcc.prim.81

description: MCC dataset

source_name: Patient 81

value: PRIMARY


title: mcc.prim.65

description: MCC dataset

source_name: Patient 65


title: mcc.prim.92

description: MCC dataset

source_name: Patient 92


title: mcc.prim.60

description: MCC dataset

source_name: Patient 60


title: mcc.prim.58

description: MCC dataset

source_name: Patient 58

value: MALE


title: mcc.prim.57

description: MCC dataset

source_name: Patient 57


title: mcc.prim.55

description: MCC dataset

source_name: Patient 55


title: mcc.prim.78

description: MCC dataset

source_name: Patient 78


title: mcc.prim.59

description: MCC dataset

source_name: Patient 59

value: POST-CHEM


title: mcc.prim.52

description: MCC dataset

source_name: Patient 52


title: mcc.prim.51

description: MCC dataset

source_name: Patient 51


title: mcc.prim.49

description: MCC dataset

source_name: Patient 49

value: FEMALE


title: mcc.prim.50

description: MCC dataset

source_name: Patient 50

value: PROXIMAL


title: mcc.prim.48

description: MCC dataset

source_name: Patient 48


title: mcc.prim.46

description: MCC dataset

source_name: Patient 46

value: C187 COLON SIGMOID

value: DISTAL


title: mcc.prim.43

description: MCC dataset

source_name: Patient 43


title: mcc.prim.67

description: MCC dataset

source_name: Patient 67


title: mcc.prim.44

description: MCC dataset

source_name: Patient 44


title: mcc.prim.42

description: MCC dataset

source_name: Patient 42


title: mcc.prim.41

description: MCC dataset

source_name: Patient 41

value: RECTUM


title: mcc.prim.37

description: MCC dataset

source_name: Patient 37


title: mcc.prim.36

description: MCC dataset

source_name: Patient 36


title: mcc.prim.39

description: MCC dataset

source_name: Patient 39


title: mcc.prim.56

description: MCC dataset

source_name: Patient 56


title: mcc.prim.38

description: MCC dataset

source_name: Patient 38


title: mcc.prim.34

description: MCC dataset

source_name: Patient 34

value: C211 ANAL CANAL


title: mcc.prim.35

description: MCC dataset

source_name: Patient 35


title: mcc.prim.53

description: MCC dataset

source_name: Patient 53


title: mcc.prim.54

description: MCC dataset

source_name: Patient 54

value: C182 COLON ASCENDING


title: mcc.prim.33

description: MCC dataset

source_name: Patient 33

value: C209 RECTUM


title: mcc.prim.32

description: MCC dataset

source_name: Patient 32


title: mcc.prim.30

description: MCC dataset

source_name: Patient 30


title: mcc.prim.47

description: MCC dataset

source_name: Patient 47

value: POST-CHEM-RAD


title: mcc.prim.28

description: MCC dataset

source_name: Patient 28


title: mcc.prim.24

description: MCC dataset

source_name: Patient 24


title: mcc.prim.27

description: MCC dataset

source_name: Patient 27


title: mcc.prim.25

description: MCC dataset

source_name: Patient 25


title: mcc.prim.22

description: MCC dataset

source_name: Patient 22


title: mcc.prim.45

description: MCC dataset

source_name: Patient 45


title: mcc.prim.26

description: MCC dataset

source_name: Patient 26

value: C186 COLON DESCENDING


title: mcc.prim.21

description: MCC dataset

source_name: Patient 21

value: C199 RECTOSIGMOID JUNCTION


title: mcc.prim.23

description: MCC dataset

source_name: Patient 23

value: primary colorectal cancer


title: mcc.prim.17

description: MCC dataset

source_name: Patient 17

value: C180 COLON CECUM


title: mcc.prim.18

description: MCC dataset

source_name: Patient 18

value: PRE


title: mcc.prim.19

description: MCC dataset

source_name: Patient 19

value: PRIMARY


title: mcc.prim.16

description: MCC dataset

source_name: Patient 16


title: mcc.prim.15

description: MCC dataset

source_name: Patient 15


title: mcc.prim.13

description: MCC dataset

source_name: Patient 13


title: mcc.prim.31

description: MCC dataset

source_name: Patient 31

value: MALE


title: mcc.prim.29

description: MCC dataset

source_name: Patient 29


title: Pdx1+Ngn3-rMSC

type: SRA

city: Shenyang

first: hongtu

last: li

state: Liaoning

address: No.10, Puhe street, Huanggu District

country: China

institute: Liaoning Province Research Institute of Family Planning

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using SOAP2.0 with parameters -m 0 -x 10000 -s 40 -l 32 -v 5 -r 2 -p 6
Reads Reads Per Kilobase per Million of library size (RPKM) were calculated using a protocol from Mortazavi, B. A. Williams, et al, Nature Methods. (2008). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: mesenchymal stem cells_transfected with Pdx1 and Ngn3

extract_protocol:
RNA was extracted with trizol-based techniques.
The quantity of RNA was determined with an ultraviolet spectrometer and electrophoresis in a denaturing formaldehyde agarose gel. Subsequently we used oligo(dT) beads to isolate mRNA, and added the fragmentation buffer to disrupt the mRNA. The first-strand cDNA were synthesized using the random hexamer primer. The second-strand cDNA were synthesized using the first-strand cDNA as the template. The templates were amplified with PCR, purified with the QiaQuick PCR extraction kit after the addition of a poly(A) tail connected with sequencing adapters. The sizes of the fragments were confirmed with an agarose gel electrophoresis and the sequences were determined with 1G Illumina GA platform.

value: bone marrow

tag: cell type

value: mesenchymal stem cells

tag: passage

tag: strain

value: Sprague-Dawley


title: mcc.prim.11

description: MCC dataset

source_name: Patient 11

value: PROXIMAL

value: POST-RAD


title: NC-rMSC

source_name: mesenchymal stem cells_untransfected


title: mcc.prim.10

description: MCC dataset

source_name: Patient 10

value: FEMALE

value: C183 COLON HEPATIC FLEXURE


title: mcc.prim.9

description: MCC dataset

source_name: Patient 9

value: C182 COLON ASCENDING


title: mcc.prim.8

description: MCC dataset

source_name: Patient 8

value: C184 COLON TRANSVERSE


title: mcc.prim.6

description: MCC dataset

source_name: Patient 6

value: DISTAL


title: AdiposeTissue3

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

library_source: genomic

data_processing:
Mate-pair fastq files were merged and samples were processed as single-end
Reads containing sequencing adapters were removed using TagDust version 1.12 with parameters -f 0.001
Reads with low base quality were removed with fastq_quality_filter (FASTX Toolkit version 0.0.13.2) with parameters -Q 33 -q 20 -p 90
Filtered reads were aligned to the hg19 human genome using bowtie2 version 2.3.4.1 in single-end mode with parameters --np 6 -S <sam_file>
Nuclear chromosome alignments with high mapping uniqueness were selected using samtools version 1.6 with parameters -q 20 and each nuclear chromosome
Alignments overlapping Duke excluded and Dac blacklisted regions were removed using bedtools version 2.25.0
Alignments were shifted by +4 on the + strand and -5 on the - strand using awk
Peaks were called with MACS2 version 2.1.0.20140616 with parameters callpeak -q 0.05 --nomodel --shift -100 --extsize 200 --bdg --keep-dup 1
For adipose tissue samples, representative peaks were constructed by taking the union of peaks across the three individuals. For SGBS preadipocytes and adipocytes, representative peaks were determined by: (1) Peaks were called on individual replicates (replicate peaks) and on reads merged across replicates (merged peaks). (2) Merged peaks that shared at least one base with a replicate peak in 2 or more replicates were considered representative peaks.
Fimo version 4.11.2 was used to scan the hg19 genome for JASPAR core 2016 vertebrate motifs with parameters --max-stored-scores 100000000 --parse-genomic-coord
Footprints were identified for 17 transcription factors using centipede. Please see the accompanying manuscript for detailed footprinting methods. Note that footprints were only reported for the SGBS sample with 400k cells due to excessive duplication in the SGBS sample with 800k cells.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 and contain ATAC-seq peak genomic coordinates, fold change over background, p-value, q-value, and peak summit position. Enrichment bigWig files represent ATAC-seq signal fold change over background and were calculated by dividing ATAC-seq signal calculated by MACS2 by the background estimated by MACS2. The bed file containing representative peaks for adipose tissue is not a traditional bed file and may need modification to work with programs expecting typical bed6 or bed12 files. The modified bed files contain 6 columns. The first 3 columns are in traditional bed format. If a bed record corresponds to a peak found only in one sample, then the 4th, 5th, and 6th columns represent the MACS2-calculated peak p-value, q-value, and the rank of the peak p-value (1 being strongest peak) for that sample. If a bed record represents peaks merged across samples, then the 4th, 5th, and 6th columns are the mean of peak p-value, q-value, and p-value rank across the respective samples.

molecule: genomic DNA

source_name: whole adipose tissue

growth_protocol: SGBS preadipocytes were maintained at 37º with 5% CO2 in DMEM:F12 supplemented with 10% FBS and 5% 3.3 mM biotin/1.7 mM panthotenate solution

extract_protocol:
SGBS cells were rinsed with DPBS, and lysed in nuclei isolation buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin as detergent.
Omni ATAC-seq was performed with 50k cells and 25 ul 2x TD buffer, 2.5 ul transposase, 16.5 ul PBS, 0.5 ul 1% digitonin, 5.5 ul H2O per reaction
Adipose tissue was pulverized in liquid nitrogen and lysed in nuclei isolation buffer containing 20 mM Tris-Hcl, 50 mM EDTA, 60 mM KCL, 40% glycerol, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 1% NP-40
ATAC-seq was performed on 12 or 36 mg of flash frozen human adipose tissue biopsies 2.5 ul transposase

treatment_protocol: SGBS adipocytes were differentiated from preadipocytes in DMEM:F12 supplemented with 5% 3.3 mM biotin/1.7 mM panthotenate solution, 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine, 50 nM dexamethasone, 500 uM IBMX, and 2 uM rosiglitazone. After four days, differentiated SGBS cells were maintained a further 10 days in DMEM:F12 supplemented with 5% 3.3 mM biotin/1.7 mM panthotenate solution, 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine.

tag: subject

value: individuals in Metabolic Syndrome in Men (METSIM) study

value: subcutaneous adipose tissue

tag: number cells

value: 36mg tissue


title: AdiposeTissue1


title: mcc.prim.5

description: MCC dataset

source_name: Patient 5

value: primary colorectal cancer


title: sNPFR_s_10

city: Boston

first: Benjamin

last: Okaty

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
alekseyenko_2019_counts.txt
alekseyenko_2019_normalized_cpms.txt

data_processing:
Base calls performed using 2.2.0.4 - RTA 2.4.11 or 2.2.68 - RTA 1.18.66.3
RNA-seq reads were mapped to the Drosophila genome BDGP6.94, downloaded from Ensembl using the STAR aligner, which was also used for feature quantification
Raw counts were converted to normalized counts per million (CPM) values using edgeR
Genome_build: Drosophila genome BDGP6.94, downloaded from Ensembl
Supplementary_files_format_and_content: tab delimited text files containing raw counts and CPM values

organism: Drosophila melanogaster

source_name: brain_single cell

extract_protocol:
Small pools (15-60 neurons) and single GFP-labeled neurons were manually sorted by mouth aspiration using a glass micropipette from protease digested, acutely dissociated (TRH-Gal4) or pinned (sNPFR-Gal4) fly brains
RNA was harvested from collected cells using the Picopure RNA Isolation kit, and cDNA libraries were generated from purified RNA using the SMART-Seq v4 Ultra Low Input kit (Clontech). 12 or 17 cycles of PCR amplification were used for cell pools or single cells, respectively. Next generation sequencing libraries were then prepared using the Nextera XT kit (Illumina)

value: sNPFR-Gal4 GFP labeled neuron

value: brain


title: sNPFR_s_7


title: AdiposeTissue2

value: 12mg tissue


title: SBM5

city: West Lafayette

first: Theresa

middle: M

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

institute: Purdue University

data_processing:
FastQC (v 0.10.1) was used to assess sequence quality, and quality trimming was done using FASTX toolkit (v 0.0.13).
Bases with less than Phred33 score of 30 were removed and resulted in reads of at least 50 bases.
Reads were mapped against the bowtie2-indexed Bos taurus genome using Tophat (v 2.0.9) with default parameters, and the genome annotation file (.gtf) from Ensembl was used to associate the genome with annotated features.
Raw read counts of each sample for each gene feature were generated with HTSeq (v 0.5.3p7) using Tophat output and Bos taurus annotations.
Counts were merged using custom perl scripts and used for downstream differential gene expression (DE) analysis.
Genome_build: Bos_taurus.UMD3.1.73.dna.toplevel.fa (Downloaded from Ensembl version 73)
Supplementary_files_format_and_content: Tab delimited file containing read counts for genes from each sample

organism: Bos taurus

source_name: longissimus muscle

extract_protocol:
Longissimus muscle samples were pulverized under liquid nitrogen and total RNA was extracted using a NucleoSpin RNA II kit (Macherey-Nagel, Bethlehem, PA, USA).  Samples were continually frozen at -80o C or colder until they were placed in the guanidinium based lysis solution provided in the RNA extraction kit.
The TruSeq Stranded Total RNA Library Prep Kit was used to generate library

tag: breed

value: Angus x Simmental

value: male

tag: age


title: mcc.prim.7

description: MCC dataset

source_name: Patient 7

value: C180 COLON CECUM

value: PRE

value: PRIMARY


title: mcc.prim.20

description: MCC dataset

source_name: Patient 20

value: FEMALE

value: PROXIMAL


title: mcc.prim.4

description: MCC dataset

source_name: Patient 4

value: MALE

value: C187 COLON SIGMOID


title: sNPFR_p_16

source_name: brain_pooled sample

value: sNPFR-Gal4 GFP labeled neurons


title: TRH_p_57

value: TRH-Gal4 GFP labeled neurons


title: SBM4


title: SBM3


title: mcc.prim.3

description: MCC dataset

source_name: Patient 3

value: C209 RECTUM

value: RECTUM

value: POST-CHEM-RAD


title: mcc.prim.2

description: MCC dataset

source_name: Patient 2

value: primary colorectal cancer


title: mcc.prim.14

description: MCC dataset

source_name: Patient 14

value: C182 COLON ASCENDING


title: mcc.prim.12

description: MCC dataset

source_name: Patient 12

value: DISTAL


title: mcc.prim.1

description:
MCC dataset
Treatment status classification (PRE=not exposed to chemotherapy and or radiation Prior To Surgical Resection (PTSR); POST=exposed to chemotherapy and or radiation PTSR; POST-CHEM-RAD=exposed to both chemotherapy and radiation PTSR; POST-RAD=exposed to radiation only PTSR; POST-CHEM=exposed to chemotherapy only PTSR

source_name: Patient 1

value: C183 COLON HEPATIC FLEXURE


title: SBM2

value: Angus x Simmental

value: male


title: SBM1


title: DDGS5


title: DDGS4


title: DDGS3


title: DDGS2


title: DDGS1


title: Col0_3

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: Wild type mock treatment

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1  with cutoff 20
The sequences were aligned using Erne-meth 2.1.1 with default options and set the output as a bismark coverage file
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated> fields

organism: Arabidopsis thaliana

source_name: Wild type mock treatment

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany). Genomic DNA from three individual plants for both WT and msh1 memory line were used for subsequent Bisulfite methylome sequencing experiment.
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: The 5-azacytidine treatment protocol was adopted from Griffin et al  and Yang et al . Col-0 wild type and msh1 memory line seeds were surface-sterilized in 10% (v/v) sodium hypochlorite, rinsed thoroughly with sterile water, and sown in 8-oz clear cups (Fabri-Kal, USA) containing 30 mL 0.5 M Murashige and Skoog medium (Sigma, USA) supplemented with 1% (w/v) agar and 0 (control) or 100 μM 5-azacytidine (Sigma, USA). 10 days old plant were collected for RNAseq

tag: replicate type

value: biological rep 3

value: whole plant with root

tag: background ecotype

tag: genotype

value: wildtype


title: Col0_2

description: Wild type mock treatment

growth_protocol: Col-0 wild type and msh1 memory line seeds were surface-sterilized in 10% (v/v) sodium hypochlorite, rinsed thoroughly with sterile water, and sown in 8-oz clear cups (Fabri-Kal, USA) containing 30 mL 0.5 M Murashige and Skoog medium (Sigma, USA) supplemented with 1% (w/v) agar and 0 (control) or 100 μM 5-azacytidine (Sigma, USA).

value: biological rep 2

tag: tissue


title: Sm2B3001: sample

city: Giessen

first: Matthew

last: McIntosh

address: Heinrich-Buff-Ring 26-32

department: Microbiology and Molecular Biology

country: Germany

institute: University of Giessen

data_processing:
Raw sequence reads were trimmed for adaptor sequences and leading/trailing low quality (or N) bases using trimmomatic version 0.39 with the following parameters: PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
The paired sequences were mapped to the reference genome using bowtie2 version 2.2.6. Each set of paired-end reads was mapped by bowtie2 -x bowtie_index_smeliloti -1 sample_R1.fq -2 sample_R2.fq -sam sample
Mapped sequences in SAM file format were converted to BAM and sorted using samtools 1.9: samtools view -bS sample.sam > sample.bam
Reads Per Kilobase Million (RPKM) normalization was performed for every file using the function bamCoverage from deeptools version 3.2.1: bamCoverage --normalizeUsing RPKM --binSize 10 -b sample.sorted.bam -o sample.bw
Genome_build: GCF_000006965.1_ASM696v1 (S. meliloti 1021)
Supplementary_files_format_and_content: bigwig

organism: Sinorhizobium meliloti

growth_protocol: Cells were grown in LB/mc medium, in well aerated, well shaken cultures at 32 degrees.

extract_protocol:
Lysates were clarified and F-DnaA-DNA complexes were isolated with magnetic beads coated with Flag antibody.
Quality of the DNA samples were checked with the Agilent High Sensitivity DNA Kit using the Agilent 2100 Bioanalyzer (Agilent) before sequencing using MiSeq (Illumina) in accordance with the manufacturer's instructions. The barcoded ChIP-Seq libraries yielded approximately 800 000 reads per sample of 75 bp length. Sequence reads were mapped onto the reference genome (S. meliloti 1021; GCF_000006965.1_ASM696v1)

treatment_protocol: Cells were harvested during exponential growth, and passed three times through the French Press.

tag: genotype/variation


title: Sm2B3001: control

value: no tag


title: Col0_1

description: Wild type mock treatment

value: biological rep 1


title: Col0AZA_3

description: Wild type treated with 5-azacytidine

source_name: Wild type treated with 5-azacytidine


title: Prb2_line36o_repB

city: Toronto

first: James

last: Ellis

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description: Prb2 36o b

hyb_protocol: Standard Affymetrix GeneChip Expression Wash, Stain, and Scan For Cartridge Arrays (performed by The Centre for Applied Genetics, tcag.ca)

data_processing:
Data was processed using the multiple BioConductor packages in R. Probe-level data was summarized at transcript level using the RMA algorithm (Gautier et al., 2004). Before differential expression analysis, the 2995 control probesets which were not annotated to a chromosome were removed. Differential expression of transcript clusters was determined using limma (Ritchie et al., 2015). Transcript clusters were defined as differentially expressed if the Benjamini-Hochberg adjusted p-value was lower than 0.05 and log2(Fold Change) was greater than 1.25. For gene set enrichment analysis, transcript clusters were collapsed such that an individual gene was represented by the transcript cluster with the maximum average expression value (Subramanian et al., 2005) and all transcript clusters not mapping to HUGO gene names were removed. The results of continuous gene set enrichment analysis were visualized as an enrichment map, showing only those gene sets that met the cut-off false discover rate of 0.1% (Merico et al., 2010).
probe group file contained in pd.hta.2.0 R package
meta-probeset file contained in hta20sttranscriptcluster.db R package

label: streptavidin-phycoerythrin

growth_protocol: All differentiations began with sub-confluent iPS cell lines growing as colonies in feeder-free conditions. The embryoid body (EB) stage was initiated by gently detaching iPS cells with 2 mg/ml collagenase IV. EBs were maintained in N2 media (DMEM:F12 supplemented with 1x N2, 1x non-essential amino acids, 2 μg/ml heparin (Sigma) and 10 ng/ml human recombinant FGF-2 (Peprotech)). Dual SMAD inhibitors were also added during the EB stage: 2 μM dorsomorphin (Sigma) and 10 μM SB431542 (Stemgent). EBs were seeded on plates coated with 0.1 mg/ml poly-L-ornithine (PLO) (Sigma) and 20 μg/ml laminin (Roche) and 1 week later neural rosettes were isolated manually. Neural rosettes were re-seeded for a secondary rosette step. Secondary rosettes were manually isolated and then dissociated with accutase (Innovative Cell Technologies) to obtain neuronal precursor cells (NPCs). NPCs were grown at high density (~1.5-6.5 x 105 per cm2) on PLO/laminin-coated plates in NPC medium (DMEM:F12 supplemented with 1x N2, 1x B27 (without retinoic acid), 1x non-essential amino acids, 1μg/ml laminin, 2 μg/ml heparin (Sigma) and 10 ng/ml human recombinant FGF-2 (Peprotech)). NPCs were dissociated with accutase and either cryopreserved in 10% DMSO NPC medium or passaged every 5-7 days for up to ~8 passages. To promote neuronal differentiation NPCs were seeded at low density (2.5 x 104 per cm2) in complete neuronal differentiation medium (Neurobasal medium supplemented with 1x N2 and 1x B27 (without retinoic acid), 1x Glutamax, 1x penicillin/streptomycin, 1 mg/ml laminin (Roche), 200ng/ml ascorbic acid (Sigma), 1 mM dibutyryl cAMP (Sigma), BDNF, GDNF, and IGF-I (each 10 ng/ml; PeproTech)). NPCs were seeded on matrigel for short term (<4 weeks) culturing or on PLO/laminin-coated plates for long-term culturing. Neuronal medium was changed every other day.

extract_protocol: Unless otherwise indicated, all reagents were acquired Thermo-Fisher Scientific. Total RNA was harvested with TRIzol reagent following the manufacturer’s instructions. After TRIzol extraction the aqueous phase (~0.45 ml) was collected and extracted once or twice with equal volumes of chloroform. RNA was precipitated by adding 0.7 volumes of isopropanol and 1 μl of 20 mg/ml glycogen. RNA pellets were washed twice with 75% ethanol and transferred to new 1.5 ml tubes. RNA was suspended in 20-50 μl of nuclease free water (Wisent). Genomic DNA contamination was removed by treating with Amplification Grade RNase- free DNase.

treatment_protocol: NPCs were seeded on 10 cm plates (3-8 x 106 cells per plate) and on days 2-12 were treated with 2.5 μM DAPT (Sigma) to promote differentiation. On days 12-14 the cells were treated with 10 μM cytosine-D-arabinofuranoside (AraC; Sigma) to kill proliferating cells. On day 21 the cells were dissociated with accutase and processed for magnetic cell sorting. After accutase treatment cell clumps were removed with two sequential filtration steps: first with a 100 μm cell strainer (Corning) and then a 40 μm pre-separation filter (Miltenyi Biotec). MACS reagents and equipment were acquired from Miltenyi, and MACS was performed following the manufacturer’s instructions. Primary antibodies used to label and deplete NPCs and astrocytes were previously described (Yuan et al., 2011). After MACS-enrichment the neurons were suspended in cND medium and re- seeded on Matrigel-coated plates (Corning). Neurons to be used for gene expression were seeded on 12 well plates (5x105 neurons per well), and total RNA was harvested 7 days following MACS.

tag: subject status

value: autism spectrum disorder (ASD) subject with PTCHD1 locus microdeletions

tag: gender

value: PTCHD1AS NULL

tag: cell type source

value: Neural precursor cells from iPSC line

value: neurons

tag: neuron age

value: 4 wks; MACS-purified at 3 weeks and grown for additional 1 week


title: Control vs. SP Treated BM Stroma Replicate 2

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Paired biological replicate 2 of 3. Control BM stromal cells vs. Substance P treated BM stromal cells. Stromal cells were harvested from the same donor.

hyb_protocol: Equal amounts of cDNA from control and stimulated BM stroma were added together and dried down. Samples were resuspended and heated to 90 °C for two minutes. Following addition of hybridization buffer, samples were added to cDNA arrays, coverslips were applied, and incubated overnight at 65 °C. Hybrids were detected with the NEN Life Science Tyramide Signal Amplification system.

scan_protocol: Scanned on GSI Lumonics ScanArray 3000. Images were quantified using NEN data analysis, version 2.0.

data_processing: log2 transformed, background subtracted signal intensity

source_name: Vehicle treated BM stroma

label_protocol: Total RNA was used to prepare cDNA probes. cDNA probes were labeled with biotin and DNP for control and stimulated stroma respectively. Total RNA, control RNA, and biotin or DNP reaction mix were mixed and incubated at 65 °C for 10 minutes, cooled to 25 °C for 5 minutes, and warmed to 42 °C. After addition of 10X RT reaction buffer and AMV RT/RNase inhibitor mix, the samples were reverse transcribed at 42 °C for 1 h, denatured at 95 °C for 5 minutes, and snap cooled on ice. 1N NaOH was added, followed by incubation at 37 °C for 10 minutes. 1N HCl was added, followed by 3M Na Acetate, 100% ethanol. Following precipitation, samples were washed with 70% and 95% ethanol, dried, and resuspended in 1X TE (10 mM Tris, 1 mM EDTA, pH 7.5).

growth_protocol: Stroma was prepared from BM aspirates of healthy donors, 18 to 25 years of age. Unfractionated cells from BM aspirates were cultured at 37°C in α-MEM with 12.5% FCS, 12.5% horse serum, 0.1 μM hydrocortisone, 0.1 mM 2-ME, and 1.6 mM glutamine. At day 3, red blood cells and granulocytes were eliminated by Ficoll-Hypaque density gradient and the mononuclear fraction replaced into the tissue culture flask. Cultures were reincubated with weekly replacement of 50% medium until confluence.

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

value: BM stroma prepared from BM aspirate of healthy donor

tag: treatment

value: Vehicle

source_name: Substance P treated BM stroma

value: 10 nM Substance P


title: Prb1_line2.27a_repB

description: Prb1 2.27 b

scan_protocol: Standard Affymetrix GeneChip Expression Wash, Stain, and Scan For Cartridge Arrays (performed by The Centre for Applied Genetics, tcag.ca)

value: PTCHD1/PTCHD1AS NULL

tag: cell type


title: Col0AZA_1

description: Wild type treated with 5-azacytidine


title: Prb2_line5_repB

description: Prb2 5 b

label_protocol: Standard Affymetrix GeneChip Expression Wash, Stain, and Scan For Cartridge Arrays (performed by The Centre for Applied Genetics, tcag.ca)


title: Control vs. SP Treated BM Stroma Replicate 1

description: Paired biological replicate 1 of 3. Control BM stromal cells vs. Substance P treated BM stromal cells. Stromal cells were harvested from the same donor.


title: Ctrl2_line93_repB

description: Ctl2 93 b

value: control

value: female

value: WT


title: Control vs. SP Treated BM Stroma Replicate 3

description: Paired biological replicate 3 of 3. Control BM stromal cells vs. Substance P treated BM stromal cells. Stromal cells were harvested from the same donor.


title: Prb1_line2.27a_repA

description: Prb1 2.27 a

value: male


title: Prb2_line5_repA

description: Prb2 5 a


title: Ctrl2_line93_repA

description: Ctl2 93 a


title: Ctrl2_line14_repB

description: Ctl2 14 b


title: Prb2_line36o_repA

description: Prb2 36o a


title: Ctrl2_line14_repA

description: Ctl2 14 a


title: PC2

city: Jerusalem

first: Yiska

last: Weisblum

address: Kiryat Hadassah

country: Israel

institute: Hadassah Hebrew University Medical Center

description:
processed data file: DESeq2_normc_pla.csv
PC2_S12

data_processing:
The NextSeq basecalls files were converted to fastq files using bcl2fastq version 2.15.0.4 with default parameters.
Raw reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32.
Adapter sequences were removed using cutadapt version 1.7.1 with parameters -O 1 --match-read-wildcards -m 15
The remaining reads were further filtered using the fastq_quality_filter program of the FASTX package (version 0.0.14) with a quality threshold of 20 in at least 90% of the read's positions.
The processed fastq files were mapped to the human genome GRCh38 using TopHat version 2.0.14 with Ensembl release 78 annotations. The following configuration was used: -N 3 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 3
Quantification of raw counts per gene was done using cuffquant (cufflinks version 2.2.1) with parameters -b -u -M (masking for genes of type IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA, lincRNA and misc_RNA).
Raw counts were obtained by running cuffnorm on the cuffquant output.
Normalization and differential expression were done with DESeq2 version 1.6.3, for each tissue separately, while filtering out genes with a total of less than 2 counts in all samples, and using default parameters. The significance threshold was set to padj<0.1
Differential expression results were combined with gene details taken from BioMart (Ensembl, release 78).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values

source_name: Placenta

extract_protocol:
Tissues were washed extensively, frozen and RNA was purified using M&N Nucleospin RNA purification kit according to the protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols for the Nextseq library construction

value: Placenta

tag: pool number

tag: time post infection

tag: infection

value: HCMV


title: ML_1

description: memory line mock treatment

source_name: memory line mock treatment

value: whole plant with root

value: msh1 memory line


title: Col0AZA_2

description: Wild type treated with 5-azacytidine

value: biological rep 2

value: wildtype


title: Ctrl1_line2_repB

description: Ctl1 2 b

value: Neural precursor cells from iPSC line


title: ML_2

description: memory line mock treatment


title: Prb2_line15_repA

description: Prb2 15 a

value: autism spectrum disorder (ASD) subject with PTCHD1 locus microdeletions

value: PTCHD1AS NULL

value: neurons


title: PZ2

description:
processed data file: DESeq2_normc_pla.csv
PZ2_S11

value: ZIKV


title: Prb1_line2.22iii_repB

description: Prb1 2.22iii b

value: 4 wks; MACS-purified at 3 weeks and grown for additional 1 week


title: PM2

description:
processed data file: DESeq2_normc_pla.csv
PM2_S10

value: Mock


title: ML_3

description: memory line mock treatment

value: biological rep 3


title: Ctrl2_line6_repB

description: Ctl2 6 b

value: control

value: female


title: MLAZA_2

description: memory line treated with 5-azacytidine

source_name: memory line treated with 5-azacytidine


title: MLAZA_1

description: memory line treated with 5-azacytidine

value: biological rep 1


title: Prb1_line2.22iii_repA

description: Prb1 2.22iii a

value: male

value: PTCHD1/PTCHD1AS NULL


title: ML_decrossed_pool

description:
pool of 3 memory line decrossed plants
Only used for initial technical control. Samples were not proceeded further.

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1  with cutoff 20
bowtie2 with default parameter was used for read alignment
F-seq with -f 400 (fragment size) (Boyle er al. 2008) was used for peak calling
Genes withing 2kb up and down stream of the significant peaks where extracted.
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separated values ; <gene_id>,<Name>,<description>. CSV files contain list of genes within 2 kb up and downstream of the significant peaks.
C2_vs_C4_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_2 vs ML_crosslinked_1
C3_vs_C4_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_3 vs ML_crosslinked_1
C2_vs_C5_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_2 vs ML_crosslinked_2
C3_vs_C5_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_3 vs ML_crosslinked_2
C2_vs_C6_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_2 vs ML_crosslinked_3
C3_vs_C6_peaks_AtML.AssociatedGenes.2kbupdown.csv: Col0_crosslinked_3 vs ML_crosslinked_3

growth_protocol: Plants were germinated in MS media at 24°C, 12 hr light and 12 hr dark cycle for 14 days and crosslinked with formaldehyde.

extract_protocol:
Col-0 wild type and msh1 memory line were grown, crosslinked and chromatin isolated as described in (Omidbakhshfard et al., 2014).
Libraries were prepared and sequenced by BGI-Tech (Shenzhen, China)

value: pool of 3 biological rep

value: whole rosette


title: Ctrl2_line6_repA

description: Ctl2 6 a

value: WT


title: DC2

description:
processed data file: DESeq2_normc_dec.csv
DC2_S9

source_name: Decidua

value: Decidua

value: HCMV


title: Ctrl1_line2_repA

description: Ctl1 2 a

value: Neural precursor cells from iPSC line


title: DM2

description:
processed data file: DESeq2_normc_dec.csv
DM2_S7


title: MLAZA_3

description: memory line treated with 5-azacytidine

value: whole plant with root

value: msh1 memory line


title: Col0_decrossed_pool

description:
pool of 3 wild type decrossed plants
Only used for initial technical control. Samples were not proceeded further.

value: wild type


title: ML_crosslinked_3

description:
memory line crosslinked
C2_vs_C6_peaks_AtML.AssociatedGenes.2kbupdown.csv
C3_vs_C6_peaks_AtML.AssociatedGenes.2kbupdown.csv


title: PM1

description:
processed data file: DESeq2_normc_pla.csv
PM1_S4

value: Placenta


title: PZ1

description:
processed data file: DESeq2_normc_pla.csv
PZ1_S5

value: ZIKV


title: DC1

description:
processed data file: DESeq2_normc_dec.csv
DC1_S3


title: DZ2

description:
processed data file: DESeq2_normc_dec.csv
DZ2_S8


title: DZ1

description:
processed data file: DESeq2_normc_dec.csv
DZ1_S2


title: ML_crosslinked_2

description:
memory line crosslinked
C2_vs_C5_peaks_AtML.AssociatedGenes.2kbupdown.csv
C3_vs_C5_peaks_AtML.AssociatedGenes.2kbupdown.csv

value: biological rep 2


title: DM1

description:
processed data file: DESeq2_normc_dec.csv
DM1_S1

value: Mock


title: ML_crosslinked_1

description:
memory line crosslinked
C2_vs_C4_peaks_AtML.AssociatedGenes.2kbupdown.csv
C3_vs_C4_peaks_AtML.AssociatedGenes.2kbupdown.csv


title: PI518671_treatment_control_5d_R3

city: Brookings

first: Madhav

middle: P.

last: Nepal

state: South Dakota

address: Northern Plains Biostress 249D

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
Quality control of reads was accessed using FastQC program (version 0.11.3) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The results from FastQC were visualized using MultiQC v1.3. Trimming was done using Btrim64 (version 0.2.0) 24 to remove low quality bases (QC value > 20; 5-bp window size). High-quality single-end reads were mapped against the primary coding sequences of G. max (Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz) obtained from the Phytozome database using Salmon ver.0.9.1 accessed from Bioconda channel.
Genome_build: Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz
Supplementary_files_format_and_content: tab-delimited matrix text file include transcript abundance values for each sample

organism: Glycine max

extract_protocol:
Frozen root samples from each treatment were grounded in liquid nitrogen with pestle and mortar to a fine powder followed by their processing for total RNA extraction using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination using manual’s instructions.
The cDNA libraries were constructed using NEBNext Ultra II RNA library 96 single index kit prep kit and sequenced using Illumina HiSeq 3000 (single read end utilizing a 100 –bp read length) at Iowa State University Sequencing Facilities.

value: 5 day post aphid infestation

value: Whole roots


title: PI518671_treatment_control_5d_R1


title: Col0_crosslinked_3

description:
wild type crosslinked
This sample was used as control. Final processed file is listed under corresponding comparison with Memory lines. See Data Processing section

value: biological rep 3


title: Col0_crosslinked_2


title: PI518671_treatment_control_5d_R2


title: MN1806CN_treatment_control_5d_R3


title: mcc.prim.40

description: MCC dataset

source_name: Patient 40

value: primary colorectal cancer

tag: age at diagnosis (years)

tag: Sex

value: FEMALE

tag: anatomical origin

value: C180 COLON CECUM

tag: proximal distal tumor classification

value: PROXIMAL

tag: treatment status classification (see description)

value: PRE

tag: tumor type

value: PRIMARY

tag: site of metastasis


title: MN1806CN_treatment_control_5d_R2

tag: genotype

tag: age

tag: tissue


title: MN1806CN_treatment_control_5d_R1


title: MN1806CN_treatment_SCNAphid_5d_R3


title: MN1806CN_treatment_SCNAphid_5d_R2


title: 81C_APP_Water

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: sample extracted from cortex

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: cortex

label_protocol: According to manufacturer's instructions

growth_protocol: Mice were housed in a pathogen-free facility, 5 to 6 per cage, maintained on a 12h/12h light-dark cycle (light on at 8am; off at 8 pm) with ad libitum access to food and water.

extract_protocol: Total RNA were extracted from hippocampi and cortex for each mouse, and purified using the RNeasy Lipid Tissue Mini Kit (Qiagen, France).

treatment_protocol: H2O or MSX-3 a water-soluble prodrug of the potent and highly selective A2AR antagonist MSX-2 that crosses the blood-brain barrier, was given to the mice in the drinking water at a 0.3 g/L dose. Animals were randomized according to their body weight in four following experimental groups: WT/H2O, WT/MSX-3, APP/PS1/H2O and APP/PS1/MSX-3.  Treatment started at 3 months of age and continued until 9-10 months of age.

value: APP

tag: agent

value: Water

value: cortex


title: 81H_APP_Water

description: sample extracted from hippocampus

source_name: hippocampus

value: hippocampus


title: MN1806CN_treatment_Aphid_5d_R1


title: MN1806CN_treatment_Aphid_5d_R3


title: MN1806CN_treatment_Aphid_5d_R2


title: 71H_WT_Water

description: sample extracted from hippocampus

value: WT


title: MN1806CN_treatment_SCN_5d_R3


title: 77H_WT_MSX3

description: sample extracted from hippocampus


title: 71C_WT_Water

description: sample extracted from cortex


title: 56H_WT_Water

description: sample extracted from hippocampus


title: MN1806CN_treatment_SCN_5d_R2


title: 49H_WT_MSX3

description: sample extracted from hippocampus


title: 77C_WT_MSX3

description: sample extracted from cortex


title: 56C_WT_Water

description: sample extracted from cortex


title: 49C_WT_MSX3

description: sample extracted from cortex


title: PI518671_treatment_SCNAphid_5d_R3


title: 325H_APP_Water

description: sample extracted from hippocampus


title: PI518671_treatment_SCNAphid_5d_R1


title: MN1806CN_treatment_SCN_5d_R1


title: 325C_APP_Water

description: sample extracted from cortex


title: 323H_APP_Water

description: sample extracted from hippocampus


title: 323C_APP_Water

description: sample extracted from cortex


title: PI518671_treatment_SCNAphid_5d_R2


title: RNP_AAV6_BG_HPRT rep3

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

state: CA

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
cpm.txt
RNP_AAV6_BG_HPRT.3

data_processing:
RNA sequencing reads were aligned to the reference mouse genome (hg38) using STAR (Dobin et al., 2013).
Raw expression levels were quantified for all annotated genes (Ensembl 92).
Raw expression levels were normalized to CPM values (counts-per-million) using edgeR (Robinson et al., 2010)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include CPM values for all samples

source_name: RNP with DNA donor template, AAV6 based vector, version 2

extract_protocol:
Cells were resuspended in RLT buffer+ β-ME following manufacture protocol (RNEasy Micro kit, Qiagen, Venlo, Netherlands), and snap frozen in LN2 to be stored at -80ºC until RNA extraction (RNEasy Micro kit, Qiagen, Venlo, Netherlands)
RNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGEN Technologies Redwood City, CA)

value: blood

value: CD34+ PBSCs

value: RNP + AAV6_BG_HPRT


title: PI518671_treatment_Aphid_5d_R2

value: 5 day post aphid infestation


title: PI518671_treatment_Aphid_5d_R1

value: Whole roots


title: pkac_LL_C_1

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description: one of two biological replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: delta-pkac1 grown on cellulose in constant light

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% microcrystalline cellulose as carbon source in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: strain


title: pkac_LL_C_2

description: one of two biological replicates


title: 319H_APP_MSX3

description: sample extracted from hippocampus


title: RNP_AAV6_BG rep2

description:
cpm.txt
RNP_AAV6_BG.2

source_name: RNP with DNA donor template, AAV6 based vector, version 1

tag: treatment

value: RNP + AAV6_BG


title: 319C_APP_MSX3

description: sample extracted from cortex


title: RNP_AAV6_BG rep1

description:
cpm.txt
RNP_AAV6_BG.1

tag: cell type


title: RNP_ssODN rep3

description:
cpm.txt
RNP_ssODN.3

source_name: RNP with DNA donor template, single-stranded oligodeoxynucleotides

value: RNP + ssODN


title: 318C_WT_Water

description: sample extracted from cortex


title: PI518671_treatment_SCN_5d_R2


title: 318H_WT_Water

description: sample extracted from hippocampus


title: PI518671_treatment_SCN_5d_R1


title: pkac_DD_C_2

description: one of two biological replicates

source_name: delta-pkac1 grown on cellulose in constant darkness


title: RNP_ssODN rep2

description:
cpm.txt
RNP_ssODN.2


title: RNP_AAV6_BG_HPRT rep1

description:
cpm.txt
RNP_AAV6_BG_HPRT.1


title: RNP_AAV6_BG_HPRT rep2

description:
cpm.txt
RNP_AAV6_BG_HPRT.2


title: RNP_AAV6_BG rep3

description:
cpm.txt
RNP_AAV6_BG.3


title: 308H_WT_Water

description: sample extracted from hippocampus


title: pkac_DD_C_1

description: one of two biological replicates


title: 310H_WT_Water

description: sample extracted from hippocampus


title: 310C_WT_Water

description: sample extracted from cortex


title: RNP_ssODN rep1

description:
cpm.txt
RNP_ssODN.1


title: 308C_WT_Water

description: sample extracted from cortex


title: MN1806CN_treatment_SCNAphid_5d_R1


title: PC1

description:
processed data file: DESeq2_normc_pla.csv
PC1_S6

value: Placenta

tag: pool number

value: HCMV


title: AAV6_BG_HPRT rep3

description:
cpm.txt
AAV6_BG_HPRT.3

source_name: DNA donor template, AAV6 based vector, version 2


title: AAV6_BG_HPRT rep2

description:
cpm.txt
AAV6_BG_HPRT.2


title: 304H_WT_MSX3

description: sample extracted from hippocampus


title: PI518671_treatment_control_30d_R3

value: 30 day post aphid infestation


title: PI518671_treatment_control_30d_R2


title: PI518671_treatment_Aphid_5d_R3


title: PI518671_treatment_control_30d_R1


title: AAV6_BG rep2

description:
cpm.txt
AAV6_BG.2

source_name: DNA donor template, AAV6 based vector, version 1


title: ssODN rep3

description:
cpm.txt
ssODN.3

source_name: DNA donor template, single-stranded oligodeoxynucleotides

value: ssODN


title: AAV6_BG rep1

description:
cpm.txt
AAV6_BG.1


title: 304C_WT_MSX3

description: sample extracted from cortex


title: MN1806CN_treatment_control_30d_R1


title: ssODN rep1

description:
cpm.txt
ssODN.1


title: ssODN rep2

description:
cpm.txt
ssODN.2


title: RNP rep1

description:
cpm.txt
RNP.1

source_name: RNP - ribonucleoprotein, Cas9 + sgRNA

value: RNP


title: RNP rep3

description:
cpm.txt
RNP.3


title: MN1806CN_treatment_control_30d_R2


title: MN1806CN_treatment_SCNAphid_30d_R3


title: AAV6_BG_HPRT rep1

description:
cpm.txt
AAV6_BG_HPRT.1


title: RNP rep2

description:
cpm.txt
RNP.2


title: AAV6_BG rep3

description:
cpm.txt
AAV6_BG.3


title: Mock rep3

description:
cpm.txt
Mock.3

source_name: Mock control

value: Mock


title: 303H_WT_MSX3

description: sample extracted from hippocampus


title: 303C_WT_MSX3

description: sample extracted from cortex


title: MN1806CN_treatment_SCNAphid_30d_R2


title: Mock rep1

description:
cpm.txt
Mock.1


title: Mock rep2

description:
cpm.txt
Mock.2


title: 298H_WT_MSX3

description: sample extracted from hippocampus


title: 298C_WT_MSX3

description: sample extracted from cortex


title: 293H_APP_MSX3

description: sample extracted from hippocampus

value: APP


title: MN1806CN_treatment_SCNAphid_30d_R1


title: 293C_APP_MSX3

description: sample extracted from cortex

value: cortex


title: MN1806CN_treatment_Aphid_30d_R3


title: 283H_APP_MSX3

description: sample extracted from hippocampus

value: hippocampus


title: T6h_1: Treated-6h-1_S4

first: Xiaojiang

last: Cui

address: 3884 Fredonia  Dr#F

department: Surgery Dept

institute: Cedars Sinai Medical Center

data_processing:
Tophat2 (2.0.7) [1] was applied to align sequencing reads to the reference mouse genome (GRCm38/mm10).
The relative gene expression RPKM and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Mus Musculus.GRCm38.82).
Protein coding genes with at least 2 RPKM on average in either condition were used to perform the differential gene expression analysis ( fibroblast ctrl vs fibroblast chemo ) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample ...

source_name: epithelial cells

extract_protocol:
RNA was isolated from the  using RNeasy Mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human breast cancer cell

tag: passages


title: T6h_2: Treated-6h-2_S5


title: Cntl3: Control-1_S3


title: MN1806CN_treatment_SCN_30d_R3


title: THP-1_R1881_2_H3

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

country: Italy

institute: Istituto Nazionale Tumori

description: ChIP-seq

data_processing:
Alignment of the sequences was performed on Human Reference Genome (assembly hg19, February 2009)
Reads were filtered based on MAPQ quality (>20)
Peaks called by both DFilter (bs=100, ks=50, nonzero) and MACS peak caller (P=10-7 ) were used for the analysis
For peaks and motif analysis the Cistrome platform was used (cistrome.org)
Cis-regulatory element annotation system (CEAS) was used for analysis of the genomic distributions of binding sites. Integrative Genomic View (IGV) and SeqMINER were used for peaks visualization andI ingenuity Pathway Analysis (IPA) (QUIAGEN 2015) was used for analysis of predicted AR-target genes
Genome_build: hg19
Supplementary_files_format_and_content: tdf files, interesct of Dfilter and MACS peaks

source_name: THP-1 LPS+IFNɣ

growth_protocol: Asherent THP-1 cells were routinely cultured in T75 flask in RPMI mediumd supplemented with 10% FBS and 1% Pen-strep. Cells were split 1:3 once per week

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: THP-1 cells were  stimulated with 20ng/ml of PMA in hormone-deprived medium and for 2 days, followed by stimulation with 10ng/m of LPS and 10ng/ml of IFNɣ for 24 hrs. Cells were then stimulated for 4 hours with R118 (synthetic testosterone) or DMSO control

value: Monocytc cell line

tag: antibody concentration

tag: chip antibody

value: Anti-H3K27ac (Active Motif, 39133)


title: Cntl1: Control-1_S1


title: sNPFR_s_6

description:
alekseyenko_2019_counts.txt
alekseyenko_2019_normalized_cpms.txt

source_name: brain_single cell

value: sNPFR-Gal4 GFP labeled neuron

value: brain


title: THP-1_R1881_1_H3

description: ChIP-seq


title: MN1806CN_treatment_SCN_30d_R2

value: Whole roots


title: sNPFR_s_4


title: sNPFR_s_3


title: THP-1_DMSO_2_H3

description: ChIP-seq


title: 281H_APP_MSX3

description: sample extracted from hippocampus


title: 282C_WT_MSX3

description: sample extracted from cortex

value: WT


title: sNPFR_s_2


title: MN1806CN_treatment_Aphid_30d_R1


title: 281C_APP_MSX3

description: sample extracted from cortex


title: 267C_APP_MSX3

description: sample extracted from cortex


title: 267H_APP_MSX3

description: sample extracted from hippocampus


title: PI518671_treatment_SCNAphid_30d_R2


title: THP-1_R1881_2_AR

description: ChIP-seq

value: Anti-AR (Millipore, 06-680)


title: sNPFR_s_1


title: MN1806CN_treatment_SCN_30d_R1


title: THP-1_R1881_1_AR

description: ChIP-seq


title: THP-1_DMSO_2_AR

description: ChIP-seq


title: 266H_APP_MSX3

description: sample extracted from hippocampus


title: PI518671_treatment_SCNAphid_30d_R1


title: THP-1_DMSO_1_H3

description: ChIP-seq


title: TRH_p_60

source_name: brain_pooled sample

value: TRH-Gal4 GFP labeled neurons


title: TRH_p_45


title: PI518671_treatment_Aphid_30d_R3


title: PI518671_treatment_SCN_5d_R3

value: 5 day post aphid infestation


title: PI518671_treatment_Aphid_30d_R2

value: 30 day post aphid infestation


title: TRH_p_40


title: THP-1_DMSO_1_AR

description: ChIP-seq


title: PI518671_treatment_Aphid_30d_R1


title: PI518671_treatment_SCN_30d_R3


title: RNA_BW35773-T

city: Columbia

first: Youwen

last: Zhang

state: South Carolina

address: 715 Sumter Street CLS109

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina (Columbia)

data_processing:
Sequences were aligned to the Pman_1.0 genome using STAR version 2.6.1 and output as sam files
The sam files were then converted to bam files with Samtools version 1.6 with parameters -bh -F 3840 -q 255
Reads were counted using the featureCounts function of the Subreads package (Liao et al., 2013) in R using Gencode M6 GTF and summarized at exon, transcript, or gene level
Genome_build: Pman_1.0
Supplementary_files_format_and_content: comma-separated values file with counts for each sample

organism: Peromyscus maniculatus

source_name: Ear punch

growth_protocol: Fresh ear punches were collected from deer mice. Ear punches were washed for 2 minutes in 70% EtOH and moved to RPMI-1640 medium (HyClone) supplemented with 10% FBS (Gibco), 500 u/mL Penicillin and 500 uL/mL L-Glutamine (complete RPMI). Ear punches were minced into small pieces and then digested by collagenase I (5 mg/ml in RPMI-1640) for 1 hour. Tissue debris from digested ear punches was removed once cells were visible. Cells were cultivated in complete RPMI at 37°C in a humidified incubator containing 5% CO2, and passaged when cells were at 90% confluency or above.

extract_protocol:
RNAs were extracted with Qiagen RNeasy Plus Mini kit (Qiagen, Valencia, CA, USA). RNA integrity was assessed using the Agilent Bioanalyzer and samples had a quality score >8.0.
RNA libraries were prepared using established protocol with NEBNExt Ultra II Directional Library Prep Kit for Illumina, (NEB, Lynn, MA). Each library was made with one of the TruSeq barcode index sequences and samples were sequenced across three lanes. The pools were clustered at 6.5 pM on a pair end read flow cell and sequenced for 300 cycles on an Illumina Hiseq 4000.

treatment_protocol: Cells were split into 6-well plates, 300,000 cells/well, and cultivated for 24 hours. Then cells were treated with tunicamycin (5 mg/mL) for 5 hours, immediately followed by RNA extraction.

tag: stock

value: BW

value: fibroblasts

tag: developmental stage

value: 4-weeks old postnatal

value: tunicamycin


title: 266C_APP_MSX3

description: sample extracted from cortex

source_name: cortex

value: APP

value: cortex


title: RNA_BW35772-T


title: 261H_APP_Water

description: sample extracted from hippocampus

source_name: hippocampus

value: Water

value: hippocampus


title: RNA_BW35773-C

value: control


title: PI518671_treatment_SCN_30d_R1


title: RNA_BW35772-C


title: PI518671_treatment_SCN_30d_R2


title: RNA_BW35770-T


title: 261C_APP_Water

description: sample extracted from cortex


title: 259C_APP_Water

description: sample extracted from cortex


title: PI518671_treatment_SCNAphid_30d_R3


title: 259H_APP_Water

description: sample extracted from hippocampus


title: 258H_WT_Water

description: sample extracted from hippocampus


title: RNA_BW35770-C


title: tRNAseq differentiating rep4

status: Public on May 17 2019

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Trim_galore! (v0.4.0) with "--paired --stringency 6 -a TGGAATTCTCGG -a2 GATCGTCGGACT" was used to trim small RNA adapters and to remove reads shorter than 20 nucleotides.
Bowtie (v1.1.2) with "-n 2 -y -k 1 --nomaqround --allow-contain" was used to align the reads to high-confidence tRNAs in GtRNAdb.
Samtools (v0.1.19) mpilup with "-BQ 0 -t AD -vuf" was used to report base coverage per positions. A-to-G substitutions at the anticodon wobble position were interpreted as inosine.
Genome_build: hg38
Supplementary_files_format_and_content: A vcf file with coverage and substitutions per tRNA base.

growth_protocol: hESC were maintained in Essential 8 media (Thermo Fisher Scientific) on hESC-Qualified Matrigel (Corning) coated plates at 37°C, 5 % CO2. Cultures were dissociated in clumps using 0.5mM EDTA every 4 days and media was renewed daily.

extract_protocol:
Total RNA was extracted using Trizol. After DNAse treatment and de-aminoacylation, tRNAs were size excised from a TBE-UREA polyacrylamide gel. Fragments ends were repaired used T4 PNK.
Libraries from the tRNAs were prepared using the TruSeq Small RNA library preparation Kit from Illumina.

treatment_protocol: Differentiating hESC were cultured in MEF-conditioned KSR media plus 1uM retinoic acid in DMSO, while the control hESC population was maintained in MEF-conditioned KSR media completed with 4 ng/mL FGF2. Self-renewing cells were collected at Day 0, while differentiating cells at day 5 of treatment.

value: human embryonic stem cells

tag: cell line

tag: condition

value: differentiating


title: untreated

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

data_processing:
Raw sequence reads were quality checked using quality control tool FastQC.
Read mapping was performed by bowtie2 (https://bioinformatics.readthedocs.io/en/latest/bowtie2/) using the raw fastq data files. Option ‘--very-sensitive-local’ was set to carry out soft trimming and highest sensitivity.
Expression values for coding genes were calculated from read count data using the Transcript Per Million (TPM) method (doi:10.1007/s12064-012-0162-3). A cutoff of at least 10 TPM was used to determine genes that were assumed as expressed. TPM values below the cutoff were adjusted to 10 for calculation of the corresponding fold changes.
Genome_build: CP000243
Supplementary_files_format_and_content: Excel files including TPM values for each sample

organism: Escherichia coli UTI89

source_name: RNA-seq

growth_protocol: 1 CFU of agar grown UPEC strain UTI89 was inoculated into 5 mL of pooled human urine and incubated overnight (~15 h) without shaking. 1 mL of the urine grown bacterial suspension was transferred to 200 mL of pooled human urine with and without OWE and incubated at 37 °C for 2 h to reach the mid-logarithmic phase.

extract_protocol:
The suspension was centrifuged (5 min, 4 °C) and the bacterial pellet was resuspended in 35 µL lysis buffer (lysozyme in TE buffer, 85 mg/mL). After 10 min incubation at RT and gentle vortexing every 10 sec, 1 mL TRizol ® (Thermo Fisher Scientific) was added and the isolation process was continued according to the manufacturer's protocol. 10 µg of isolated total RNA were used for DNA digestion, using the Turbo DNase (Turbo-DNA-free™ Kit, Thermo Fisher Scientific) according to the manufacturer's instructions.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified (11 PCR cycles) to about 10-20 ng/µl using a high fidelity DNA polymerase. The TruSeq barcode sequences AGGATAGG or TCAGAGCC, which are part of the 5' TruSeq sequencing adapter were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: 1 mL of the bacterial culture with an OD600 of 1 was mixed with 0.125 mL of stop solution (95 % ethanol, 5 % phenol).

value: strain UTI89


title: tRNAseq differentiating rep3


title: MN1806CN_treatment_Aphid_30d_R2

value: Whole roots


title: tRNAseq differentiating rep2


title: tRNAseq self-renewing rep4

value: self-renewing


title: tRNAseq differentiating rep1


title: tRNAseq self-renewing rep3


title: Cntl2: Control-1_S2

value: human breast cancer cell


title: 258C_WT_Water

description: sample extracted from cortex

value: WT


title: 255H_APP_Water

description: sample extracted from hippocampus


title: 255C_APP_Water

description: sample extracted from cortex


title: tRNAseq self-renewing rep2


title: 283C_APP_MSX3

description: sample extracted from cortex


title: CFPAC-1_shBACH1/shControl

city: Guangzhou

first: Xudong

last: Huang

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: differentially expressed genes of shBACH1 VS. shControl in CFPAC-1 cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: shBACH1 and shControl CFPAC-1 cells were cultured in IMDM medium supplemented with 10% FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from shBACH1 and shControl CFPAC-1 cells using TRIzol reagent following the manufacturer's recommendation. RNA was quantified using a NanoDrop-2000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: CFPAC-1 cells were infected with lentiviral shRNA vector, shBACH1 and shControl, respectively. The supernatant was replaced with complete culture media after 24 h, followed by selection with puromycin. After selection, shBACH1 and shControl CFPAC-1 cells were used to performed gene expression profile analysis.

value: Pancreatic cancer cell line

tag: genotype/variation

value: shControl


title: OWE treated

value: Orthosiphon stamineus


title: bv2

city: Aurora

first: Rajeev

last: Vibhakar

state: CO

department: Pediatrics/Hematology/Oncology

institute: University of Colorado Anschutz Medical Campus

data_processing:
The reads were trimmed and clipped for quality control in Trimmomatic (v0.36).
Read quality was checked for each sample using FastQC v0.10.1.
High quality reads were then imported into STAR (v2.4.0.1) for alignment into BAM files.
The function summarizeOverlaps from the GenomicAlignments package (v1.16.0) was used to count the reads from BAM files.
DESeq (v1.32.0) was then used to get differential expression genes on the raw counts.
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: xcel file includes raw read counts.

source_name: medulloblastoma cell line D458

growth_protocol: D458 cell lines were cultured in DMEM (Gibco, Carlsbad, CA) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and 1× L-glutamine (Cellgro). Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated from two separate D458 shSETD8 and shNull clones using RNeasy Mini kit (Qiagen).
illumina TruSeq stranded mRNA

treatment_protocol: Stable cell lines were established using gene specific mission shRNAs (Cat# 359304, 130139, 148268) or non-targeting control (Sigma-Aldrich, St. Louis, MO).  Cells were plated at 5x105 in a 6-well dish in growth medium containing 8µg/mL polybrene. Viral particles were added with 8µg/mL polybrene and incubated for 7 hrs.  Transduced cells were disaggregated, grown, and selected with 1µg/mL puromycin for 14 days.  Transformants were confirmed by qPCR and western blot.

value: SETD8 wild type

tag: cell source

value: brain


title: bv5

value: SETD8 80% knockdown


title: T6h_3: Treated-6h-3_S6


title: Hi-Myc, I3C treatment Rep 3

city: Boston

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
FASTQ files from an Illumina HiSeq 4000 with 75 cycles were obtained from the Molecular Biology Core Facilities at Dana Farber Cancer Institute.
TrimGalore v0.4.0 was implemented to remove potential adapter sequences with option "--fastqc"
Trimmed reads were aligned with STAR (v2.5.2b), using mm10 as the reference genome
Aligned reads were sorted with samtools (v1.3) (with parameter "-n")and mapped to ensembl (v89) gene features using featureCounts with the parameter "-s 2" from the subread package (v1.5.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files (txt) were generated from featureCounts output.

source_name: Hi-Myc, I3C treatment

extract_protocol:
RNAs were extracted from dorsolateral prostates (DLPs) of Genetically Engineered Mouse Models (GEMMs, 5 months of age) by using the the pureLink RNA Kit (Invitrogen). Ribosomal RNA removal was carried out using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) according to the manufacturer’s protocol.
RNAs derived from GEMM DLPs were subjected to next-generation sequencing (NGS) to generate deep coverage RNA-Seq data. RNA-seq libraries were prepared using Illumina TruSeq RNA Sample Prep Kit V2 and subjected to deep sequencing with Illumina HiSeq 4000 at the Molecular Biology Core Facilities at Dana Farber Cancer Institute. To achieve comprehensive coverage for each sample, we generated ~32-39 million single end reads.

tag: strain background

value: FVB

value: Hi-Myc

value: I3C treatment

value: dorsolateral prostates (DLPs)


title: Hi-Myc, I3C treatment Rep 2


title: Hi-Myc, BKM120 treatment Rep 3

source_name: Hi-Myc, BKM120 treatment

value: BKM120 treatment


title: Hi-Myc, BKM120 treatment Rep 1


title: Hi-Myc, Vehicle treatment Rep 3

source_name: Hi-Myc, Vehicle treatment

value: Vehicle treatment


title: Hi-Myc, GDC002 treatment Rep 2

source_name: Hi-Myc, GDC002 treatment

value: GDC002 treatment


title: Hi-Myc, BYL719 treatment Rep 2

source_name: Hi-Myc, BYL719 treatment

value: BYL719 treatment


title: Hi-Myc, GDC002 treatment Rep 1


title: Hi-Myc, Vehicle treatment Rep 2


title: Hi-Myc, BYL719 treatment Rep 3


title: Hi-Myc, Vehicle treatment Rep 1


title: Hi-Myc, BYL719 treatment Rep 1


title: tRNAseq self-renewing rep1

value: human embryonic stem cells

value: self-renewing


title: sNPFR_s_5

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Base calls performed using 2.2.0.4 - RTA 2.4.11 or 2.2.68 - RTA 1.18.66.3
RNA-seq reads were mapped to the Drosophila genome BDGP6.94, downloaded from Ensembl using the STAR aligner, which was also used for feature quantification
Raw counts were converted to normalized counts per million (CPM) values using edgeR
Genome_build: Drosophila genome BDGP6.94, downloaded from Ensembl
Supplementary_files_format_and_content: tab delimited text files containing raw counts and CPM values

extract_protocol:
Small pools (15-60 neurons) and single GFP-labeled neurons were manually sorted by mouth aspiration using a glass micropipette from protease digested, acutely dissociated (TRH-Gal4) or pinned (sNPFR-Gal4) fly brains
RNA was harvested from collected cells using the Picopure RNA Isolation kit, and cDNA libraries were generated from purified RNA using the SMART-Seq v4 Ultra Low Input kit (Clontech). 12 or 17 cycles of PCR amplification were used for cell pools or single cells, respectively. Next generation sequencing libraries were then prepared using the Nextera XT kit (Illumina)

value: sNPFR-Gal4 GFP labeled neuron


title: Hi-Myc; Wwp1+/+ Rep 3

source_name: Hi-Myc; Wwp1+/+

value: Mixed (C57/BJ6, FVB)

value: Hi-Myc; Wwp1+/+


title: Hi-Myc, BKM120 treatment Rep 2


title: Hi-Myc; Wwp1+/+ Rep 2


title: Hi-Myc; Wwp1-/- Rep 2

source_name: Hi-Myc; Wwp1-/-

value: Hi-Myc; Wwp1-/-


title: bv6


title: bv1

value: SETD8 wild type


title: Hi-Myc; Wwp1+/+ Rep 1


title: Hi-Myc; Wwp1-/- Rep 3


title: Hi-Myc, I3C treatment Rep 1


title: P3_rep2

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description: scRNA-seq data from isolated male germ cells at P3

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
A total of 8 transcriptomes (n=3 for E16.5, n=2 for P0, n=2 for P3, and n=1 for P6) were merged in R using the Seurat package 1 (v2.3.2).
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: >1,300 genes for E16.5 #1; >1,900 genes and <80,000 UMI counts for E16.5 #2; >1,200 genes for P0 #1; >1,000 genes and <30,000 UMI counts for P0 #2; >1,500 genes and <70,000 UMI counts for P3 #1; <35,000 UMI counts for P3 #2; <40,000 UMI counts for P6. Filtering based on percent mitochondrial genes detected was conservatively set at <25% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type, proliferation status, and developmental state.
Germ cells were isolated from a small number of contaminating cells in the dataset based on Dazl and Ddx4 transcript abundance before the entire dataset was normalized, scaled (“vars.to.regress” included number of genes, number of UMIs, percent mitochondrial transcripts, and age replicate), and dimensionally reduced using Seurat.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: testicular germ cells

extract_protocol:
Single cell suspensions of E16.5, P0, P3, or P6 quadruple-transgenic testes were prepared and germ cells isolated using FACS with an SH800 machine (Sony Biotechnology) gating for tdTomato+ cells. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

value: Mixed C57/B6 and 129

value: male germ cells


title: P6_rep1

description: scRNA-seq data from isolated male germ cells at P6


title: P0_rep2

description: scRNA-seq data from isolated male germ cells at P0


title: Hi-Myc; Wwp1-/- Rep 1


title: P3_rep1


title: Be-g2.rep2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
Female, Code: 18-06-A014
Be0.ATACseq.Peak.Data.rpm.txt

data_processing:
Raw sequencing reads were mapped to the hg38 version of the human genome using Bowtie-1.1.1 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files are normalized to reads per million (rpm) using R/Bioconductor
Supplementary_files_format_and_content: tab delimited text file containing rpm normalized data for all peaks and all samples.

source_name: B cells

growth_protocol:
Purified naive B cells were co-cultured (1x106 cells/ml) for 3 days with 5microg/ml anti-Ig (Jackson ImmunoResearch), 5microg/ml R848 (Invivogen), 50U/ml IL-2 (Peprotech) and IFNg (R&D).
Purified naïve B cells were culture for 3 days with anti-Ig and R848 alone (Be-0) or in combination with IFNg (Be-IFNg), IL-2 (Be-IL2) or IL-2 plus IFNg (Be.g2).

extract_protocol: 10,000 cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

tag: Sex

value: Female

tag: sorting markers

value: No Sorting/Total Cells

tag: be type


title: Be-IFNg.rep2

growth_protocol:
Purified naive B cells were co-cultured (1x106 cells/ml) for 3 days with 5microg/ml anti-Ig (Jackson ImmunoResearch), 5microg/ml R848 (Invivogen), and IFNg (R&D).
Purified naïve B cells were culture for 3 days with anti-Ig and R848 alone (Be-0) or in combination with IFNg (Be-IFNg), IL-2 (Be-IL2) or IL-2 plus IFNg (Be.g2).


title: Be-IFNg.rep1

description:
Female, Code: 18-05-A063
Be0.ATACseq.Peak.Data.rpm.txt


title: Be-IL2.rep2

growth_protocol:
Purified naive B cells were co-cultured (1x106 cells/ml) for 3 days with 5microg/ml anti-Ig (Jackson ImmunoResearch), 5microg/ml R848 (Invivogen) and 50U/ml IL-2 (Peprotech)
Purified naïve B cells were culture for 3 days with anti-Ig and R848 alone (Be-0) or in combination with IFNg (Be-IFNg), IL-2 (Be-IL2) or IL-2 plus IFNg (Be.g2).


title: Be-0.rep2

growth_protocol:
Purified naive B cells were co-cultured (1x106 cells/ml) for 3 days with 5microg/ml anti-Ig (Jackson ImmunoResearch), and 5microg/ml R848 (Invivogen).
Purified naïve B cells were culture for 3 days with anti-Ig and R848 alone (Be-0) or in combination with IFNg (Be-IFNg), IL-2 (Be-IL2) or IL-2 plus IFNg (Be.g2).


title: Be-0.rep1


title: P0_rep1

tag: strain


title: Be-g2.rep1


title: Be-IL2.rep1


title: 282H_WT_MSX3

description: sample extracted from hippocampus

tag: genotype

value: WT

tag: agent

tag: tissue

value: hippocampus


title: MDA-MB-231 cells_Combination repeat 1

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: [Gene_Exp_17_AAG.diff]  normalized expression values for single drug 17-AAG
Supplementary_files_format_and_content: [Gene_Exp_Belinostat.diff]  normalized expression values for single drug Belinostat
Supplementary_files_format_and_content: [Gene_Exp_Combination.diff]  normalized expression values for the Combination of 17-AAG and Belinostat

source_name: MDA-MB-231 cells_Combination

growth_protocol: density 1e7 MDA-MB-231 cells in 15cm dish, 24 hours, to 70% confluentence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with compounds or DMSO, after 24 hours

tag: disease state

value: breast cancer

value: MDA-MB-231 cells

value: Combination


title: MDA-MB-231 cells_Combination repeat 2


title: MDA-MB-231 cells_Belinostat repeat 2

source_name: MDA-MB-231 cells_Belinostat

value: Belinostat


title: MDA-MB-231 cells_Belinostat repeat 1


title: MDA-MB-231 cells_17-AAG repeat 2

source_name: MDA-MB-231 cells_17-AAG


title: MDA-MB-231 cells_17-AAG repeat 1


title: MDA-MB-231 cells_DMSO repeat 1

source_name: MDA-MB-231 cells_DMSO

value: DMSO


title: MDA-MB-231 cells_DMSO repeat 2


title: A1847 DMSO 48h 2

city: Philadelphia

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description:
WT A1847 treated with DMSO.
DMSO Replicate 2.
mRNA enriched

data_processing:
Illumina basespace for RNA alignment.
Cufflink and Cuffdiff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DMSO-GSK_gene.txt: Tab-delimited text file with log2 fold change, p and q values, gene_id.

source_name: Ovarian cancer cell line

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS, 1x Penicillin/Streptomycin, 2mM L-Glutamine, and 5 ug/mL Insulin in a 37C incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using a GeneJet RNA Purification Kit (Thermo Scientific) according to manufacturer's instructions.
TruSeq stranded mRNA library kit (Cat# 20020595).

treatment_protocol: Cells were treated with DMSO or 10 nM trametinib (GSK212) for 48 hours. Media was changed and fresh drug was added 4 hours prior to collection.

tag: cell type

value: Ovarian cancer cell line

tag: treatment


title: Keratinocyte_rep2 [ATAC-seq]

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

description:
Transposed chromatin
processed data file: ATAC_count_annotated.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Kundajelab pipeline for ATAC-seq (https://github.com/kundajelab/atac_dnase_pipelines) was used for read processing, peak calling, and quality control.
A reference peak file was created by merging all pooled peaks from all four conditions and then merging peaks closer than 100 bp.
Raw reads falls in the reference peak regions were counted individually for each sample by using bedtools multicov.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ATAC_count_annotated.txt contains read counts for reference peaks.

source_name: Primary keratinocyte

growth_protocol: Primary fibroblasts were grown in αMEM medium and primary keratinocytes were grown in KGM medium.

extract_protocol:
After defreezing, viability and cell number were quantified with Countes (Invitrogen), and nuclei were extracted from approximately 25,000 live cells with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100) on ice for 5 min. Transposase reaction was then carried out.
Illumina adaptors were introduced by 9 to 12 total cycles PCR reaction. Amplified DNA fragments were then purified with QIAGEN MinElute PCR Purification Kit and size selected twice with Agencourt AMPure XP (1:1.5 and 1: 0.5 sample to beads; Beckman Coulter, Fullerton, CA, USA).

treatment_protocol: After infection and selection with Puromycin, DOX treatment (500ng/mL) was started at day0 for 5 days (until day5). At day2, medium was changed to KGM medium. Cells were collected at day7 and stored at -80 degree in cell banker solution before usage.

value: Fibroblast

tag: transgene

value: TP63, KLF4, OVOL2

tag: passages


title: Keratinocyte_rep1 [ATAC-seq]


title: TK_MCS_rep2 [ATAC-seq]

source_name: Dermal fibroblast

value: TP63, KLF4


title: TK_MCS_rep1 [ATAC-seq]


title: TK_OVOL2_rep1 [ATAC-seq]


title: TK_OVOL2_rep2 [ATAC-seq]


title: MCS_OVOL2_rep2 [ATAC-seq]


title: A1847 10 nM Trametinib 48h 1

description:
WT A1847 treated with 10 nM GSK212.
Treatment Replicate 1.
mRNA enriched

tag: cell line

value: Trametinib (GSK212)


title: MCS_MCS_rep2 [ATAC-seq]

value: empty vector


title: A1847 10 nM Trametinib 48h 2

description:
WT A1847 treated with 10 nM GSK212.
Treatment Replicate 2.
mRNA enriched