title: Tumor T11 WGBS

description: Tumor


title: Day28-LIVER-235_2500ppm_F

status: Public on Apr 30 2020

type: SRA

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

country: USA

institute: Scitovation, LLC.

description:
Day28-Liver 235
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

library_source: transcriptomic

data_processing:
Illumina NextSeq 500 control software v2.1.0 with BCL files uploaded to Illumina BaseSpace for FASTQ file generation.
Sequences trimmed from both based on QC (TRIMMOMATIC, min base QC call of 21, min. retained read length 65bp), and mapped to Illumina iGenomes UCSC mm10 using BOWTIE2.
BAM files from each pair of paired-end files merged by sample with SAMTools, and gene counts extracted with HTSeq.
Genome_build: UCSC mm10 (Illumina iGenomes)
Supplementary_files_format_and_content: *_Male_Female_Counts.txt: Tab-delimited text files of gene counts.

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol: 1.0-2.0 μg total RNA using the manufacturer's standard procedure for the Illumina TruSeq® Stranded mRNA HT Kit.

treatment_protocol: Mice were exposed to 4-Methylimidazole for 2, 5 or 28 days.

tag: strain/background

tag: Sex

value: Female

tag: tissue

value: Liver

tag: treatment

tag: dose

tag: exposure time

value: Day 28

tag: route

value: Feed


title: Tumor T8 WGBS

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

description: Tumor

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Firstly, we trimmed using Trim Galore! (v0.4.1) to remove Illumina adaptors with the options of ' --paired --length 50 --clip_1 6 --clip_2 6 '. After trimming, around 90 Gbp of data remained per sample. Then trimmed reads were aligned to the HG19 reference genome using BSMAP (v2.89) with the option of '-p 8 -R'. Then SAMtools (v. 1.3.1) was used to sort by genomic coordination and make a bam file index. Picard Tools (v.1.92) is used to remove PCR duplicates. After deduplication, ~70Gbp remained per sample. Lastly, we ran MOABS (v. 1.3.4) to compute the methylation ratio per CpG with the option of '--cytosineMinScore 20  --skipRandomChrom 1 -p 4 --keepTemp 0 --processPEOverlapSeq 1 --requiredFlag 2 --excludedFlag 256 --minFragSize 110 --reportCpX G --qualityScoreBase 0 --trimRRBSEndRepairSeq 0  --trimWGBSEndRepairPE1Seq 5 --trimWGBSEndRepairPE2Seq 5'. Around 95% of CpGs are covered by at least five reads.
Given the methylation ratio and coordination computed, we built a data matrix, whose columns are samples and rows are CpGs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation ration (methylated reads/total reads at a given CpG)  for each Sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: Esophageal Squamouse carcinoma

extract_protocol:
Frozen tissues of surgically removed specimens  were used for genomic DNA extraction.  Genomic DNA was extracted with QIAmp DNA Mini kits (Qiagen) from fresh frozen tissue samples. 1μg gDNA was fragmented by sonication with a base pair peak of 300 bp for the resulting fragment, and adaptors were then ligated to both ends of the fragments.  Bisulfite conversion was performed to whole genomes of ten pairs of ESCC and matched normal tissues, where converts cytosine residues of the dinucleotide CpG to uracil but leaves methylated cytosine unaffected. PCR amplification and purification were carried out. The uracil-binding pocket of KAPA HiFi DNA Polymerase has been inactivated, enabling amplification of uracil-containing DNA.
The high quality of the library was estimated by The Qubit® 3.0 Fluorometer. Bisulfite conversion success ratio is 99.18% and 99.49%, respectively in normal and ESCC samples
The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated 400M of paired-end reads (2x125bp)

value: esophageal squamouse carcinoma

tag: tumor pathological stage

value: highly or moderately differentiated

tag: tnm stage


title: Tumor t9 WGBS

description: Tumor

value: highly differentiated


title: normal N2 RNA-Seq

description: normal

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 hg19 genome using STAR_2.4.2a with default parameters.
The expression level of transcript per million (TPM) reads were quantified using RNA-Seq by Expectation-Maximization algorithm (RSEM v1.2.29).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Adjacent normal tissue

extract_protocol:
Frozen tissues of surgically removed specimens or cells from cell culture were used for RNA extraction. RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adjacent normal esophageal tissue


title: Tumor T6 WGBS

description: Tumor

value: moderately differentiated


title: Day28-LIVER-236_2500ppm_F

description:
Day28-Liver 236
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Tumor T2 WGBS

description: Tumor


title: Day28-LIVER-234_2500ppm_F

description:
Day28-Liver 234
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Tumor T7 WGBS

description: Tumor


title: Day28-LIVER-232_2500ppm_M

description:
Day28-Liver 232
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-229_2500ppm_M

description:
Day28-Liver 229
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-230_2500ppm_M

description:
Day28-Liver 230
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-233_2500ppm_F

description:
Day28-Liver 233
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-227_2500ppm_M

description:
Day28-Liver 227
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: normal N15 WGBS

description: normal


title: normal N13 WGBS

description: normal


title: normal N12 WGBS

description: normal


title: Tumor T1 WGBS

description: Tumor


title: Day28-LIVER-225_2500ppm_M

description:
Day28-Liver 225
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: normal N11 WGBS

description: normal


title: normal N8 WGBS

description: normal


title: normal N7 WGBS

description: normal


title: Day28-LIVER-222_1250ppm_F

description:
Day28-Liver 222
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-226_2500ppm_M

description:
Day28-Liver 226
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: normal N6 WGBS

description: normal


title: Day28-LIVER-220_1250ppm_F

description:
Day28-Liver 220
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-223_1250ppm_F

description:
Day28-Liver 223
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: normal N9 WGBS

description: normal


title: Day28-LIVER-219_1250ppm_F

description:
Day28-Liver 219
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: normal N1 WGBS

description: normal


title: normal N2 WGBS

description: normal


title: Day28-LIVER-217_1250ppm_F

description:
Day28-Liver 217
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-218_1250ppm_F

description:
Day28-Liver 218
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-216_1250ppm_M

description:
Day28-Liver 216
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-3_IL10

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
Sequence reads were aligned using STAR aligner with GRCh38 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.
Supplementary_files_format_and_content: normalized and log2 transformed

source_name: EBV-B

growth_protocol: EBV-B cells were generated from B cells of the patients and controls using standard protocols.

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA Library Prep Kit and manufacturer-recommended protocols

treatment_protocol: EBV-B cells from healthy controls (n=3), D427ins17 patients’ (P1, P2, P3),  and AD HIES patients’ (n=3) heterozygous for STAT3 mutations (R382W, V463del, T708N),  were starved by incubation in pure RPMI for two hours, and then stimulated by incubation for  two hours with 100 ng/mL IL-6/IL-6Rα (R&D #8954-SR), 100 ng/mL IL-21 (R&D #8879-  IL), 100 ng/mL IL-23 (R&D #1290-IL), 50 ng/mL IL-10 (R&D #217-IL), or 104 IU/mL IFNα  (IntronA MSD).

tag: disease state

value: AD-HIES Patient


title: Day28-LIVER-214_1250ppm_M

description:
Day28-Liver 214
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-213_1250ppm_M

description:
Day28-Liver 213
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-3_IL23


title: STAT3-3_IL21


title: Day28-LIVER-210_1250ppm_M

description:
Day28-Liver 210
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-3_supIL6


title: STAT3-3_NS

value: NS


title: Day28-LIVER-211_1250ppm_M

description:
Day28-Liver 211
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-209_1250ppm_M

description:
Day28-Liver 209
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-2_IFNa

value: IFNa


title: Day28-LIVER-208_300ppm_F

description:
Day28-Liver 208
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Vehicle

value: Vehicle (0ppm)


title: STAT3-2_IL10


title: STAT3-2_IL23


title: STAT3-2_IL21


title: Day28-LIVER-207_300ppm_F

description:
Day28-Liver 207
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-203_300ppm_F

description:
Day28-Liver 203
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-204_300ppm_F

description:
Day28-Liver 204
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-2_NS


title: Day28-LIVER-205_300ppm_F

description:
Day28-Liver 205
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-2_supIL6


title: Day28-LIVER-198_300ppm_M

description:
Day28-Liver 198
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Male


title: Day28-LIVER-197_300ppm_M

description:
Day28-Liver 197
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-3_IFNa


title: STAT3-1_IFNa


title: Day28-LIVER-196_300ppm_M

description:
Day28-Liver 196
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-1_IL21


title: STAT3-1_IL10


title: Day28-LIVER-195_300ppm_M

description:
Day28-Liver 195
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-1_IL23


title: STAT3-1_supIL6


title: Day28-LIVER-194_300ppm_M

description:
Day28-Liver 194
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: STAT3-1_NS


title: Day28-LIVER-192_150ppm_F

description:
Day28-Liver 192
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-193_300ppm_M

description:
Day28-Liver 193
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P3_IL10

value: Patient 3


title: P3_IFNa


title: P3_IL23


title: P3_IL21


title: Day28-LIVER-206_300ppm_F

description:
Day28-Liver 206
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-190_150ppm_F

description:
Day28-Liver 190
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-189_150ppm_F

description:
Day28-Liver 189
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P3_supIL6


title: Day28-LIVER-188_150ppm_F

description:
Day28-Liver 188
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P3_NS


title: Day28-LIVER-187_150ppm_F

description:
Day28-Liver 187
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P2_IL10

value: Patient 2


title: Day28-LIVER-182_150ppm_M

description:
Day28-Liver 182
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P2_IL23


title: Day28-LIVER-181_150ppm_M

description:
Day28-Liver 181
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P2_IFNa


title: P2_NS


title: Day28-LIVER-180_150ppm_M

description:
Day28-Liver 180
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P2_IL21


title: P1_IFNa

value: Patient 1


title: Day28-LIVER-178_150ppm_M

description:
Day28-Liver 178
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Liver


title: Day28-LIVER-176_VC_F

description:
Day28-Liver 176
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Day 28


title: Day28-LIVER-177_150ppm_M

description:
Day28-Liver 177
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Feed


title: Day28-LIVER-175_VC_F

description:
Day28-Liver 175
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-191_150ppm_F

description:
Day28-Liver 191
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P1_IL21


title: Day28-LIVER-174_VC_F

description:
Day28-Liver 174
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P1_IL23


title: Day28-LIVER-173_VC_F

description:
Day28-Liver 173
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P1_supIL6


title: Day28-LIVER-172_VC_F

description:
Day28-Liver 172
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-170_VC_F

description:
Day28-Liver 170
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P1_NS


title: C3_IFNa

value: control


title: Day28-LIVER-168_VC_M

description:
Day28-Liver 168
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-166_VC_M

description:
Day28-Liver 166
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: C3_IL21


title: P2_supIL6


title: Day28-LIVER-164_VC_M

description:
Day28-Liver 164
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Day28-LIVER-162_VC_M

description:
Day28-Liver 162
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: P1_IL10


title: Day28-LIVER-161_VC_M

description:
Day28-Liver 161
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Lung_159_2500ppm_F

description:
LUNG_159
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt

source_name: Lung

value: Female

value: Lung

value: Day 5


title: C2_IFNa


title: C2_IL21


title: Lung_153_2500ppm_F

description:
LUNG_153
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C2_NS


title: Lung_141_1250ppm_F

description:
LUNG_141
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C3_IL10


title: C1_IL10


title: Lung_142_1250ppm_F

description:
LUNG_142
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Day28-LIVER-167_VC_M

description:
Day28-Liver 167
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: C3_supIL6


title: Lung_139_1250ppm_F

description:
LUNG_139
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C1_IL21


title: Lung_138_1250ppm_F

description:
LUNG_138
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C3_IL23


title: C3_NS


title: Lung_137_1250ppm_F

description:
LUNG_137
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C1_NS


title: Lung_127_300ppm_F

description:
LUNG_127
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: C2_IL23


title: C2_IL10


title: Lung_158_2500ppm_F

description:
LUNG_158
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_155_2500ppm_F

description:
LUNG_155
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP137683

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

data_processing:
High- throughput RNA sequencing of prepared libraries was performed on the Illumina HiSeq 4000 platform to 75bp PE at the Wellcome Center for Human Genetics (Oxford, UK)
Reads were trimmed for Nextera, Smart-seq2 and Illumina adapter sequences using skewer-v0.1.125
Trimmed read pairs were mapped to human genome GRCh37 using HISAT2 version 2.0.0-beta
Uniquely mapped read pairs were counted using featureCounts43, subread- 1.5.044, using exons annotated in ENSEMBL annotations, release 75
Mapping QC metrics were obtained using picard-tools-1.92 CollectRnaSeqMetrics.jar
Genome_build: human genome GRCh37
Supplementary_files_format_and_content: Raw count data after mapping in tab seperated format. Each row is a gene and each column is a sample. Ensemble gene IDs are used.

extract_protocol:
Liver biopsy samples were available for 198 patients. Total RNA was extracted from patient liver biopsies at baseline (pre-treatment) using RNeasy mini kits (Qiagen). Briefly, liver biopsy samples were mechanically disrupted in the presence of lysis buffer and homogenized using a QIAshredder. Tissue lysates were then centrifuged and clarified supernatants were transferred into new microcentrifuge tubes (pellets were discarded). Next, 1 volume of 70% ethanol was added to the lysates and samples were mixed by gentle vortexing . 700uL of sample was then transferred into RNeasy spin columns (with 2mL collection tubes) and centrifuged at 10000 rpm for 15 seconds. Column flow-through was discarded. DNase digestion was subsequently performed to eliminate any contamination from genomic DNA. 80uL of DNase I solution (10uL DNase I stock + 70uL Buffer RDD) was added directly to RNeasy spin columns and incubated at room temperature for 15 minutes. Following DNase incubation, the columns were washed with 350uL of Buffer RW1 and centrifuged at 10000 rpm for 15 seconds. Flow-through was discarded and 500uL of Buffer RPE was added to the spin columns. Columns were then centrifuged again at 10000 rpm for 15 seconds and flow-through was discarded. An additional 500uL of Buffer RPE was added to the spin columns and columns were centrifuged at 10000 rpm for 2 minutes. Finally, spin columns were transferred into new microcentrifuge tubes and 30uL of RNase-free water was added directly to the column membrane. Columns were then centrifuged at 10000 rpm for 1 minute to elute the RNA.
RNA yield was quantified using a NanoDrop spectrophotometer. Selected samples were also run on an Agilent TapeStation system to assess RNA quality and purity. Library preparation from purified RNA samples was performed using the Smart-Seq2 protocol.

value: liver

tag: diagnosis

value: HCV-infected patient

tag: age

tag: cirrhosis present

value: No

value: White


title: C2_supIL6


title: Lung_126_300ppm_F

description:
LUNG_126
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP136496


title: C1_IFNa

value: IFNa


title: Day28-LIVER-183_150ppm_M

description:
Day28-Liver 183
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt


title: Lung_125_300ppm_F

description:
LUNG_125
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_140_1250ppm_F

description:
LUNG_140
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP170576

value: Yes


title: Lung_124_300ppm_F

description:
LUNG_124
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP168744

value: Male


title: Lung_123_300ppm_F

description:
LUNG_123
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP190204


title: C1_IL23


title: sP183749


title: C1_supIL6


title: Lung_121_300ppm_F

description:
LUNG_121
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP106397


title: Lung_111_150ppm_F

description:
LUNG_111
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP177110


title: Lung_112_150ppm_F

description:
LUNG_112
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_110_150ppm_F

description:
LUNG_110
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_107_150ppm_F

description:
LUNG_107
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_106_150ppm_F

description:
LUNG_106
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_105_150ppm_F

description:
LUNG_105
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_093_VC_F

description:
LUNG_93
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt

value: Vehicle

value: Vehicle (0ppm)


title: sP115443


title: sP178363


title: sP188444


title: Lung_092_VC_F

description:
LUNG_92
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_160_2500ppm_F

description:
LUNG_160
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_096_VC_F

description:
LUNG_96
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP146375

value: Asian


title: sP128168


title: sP158841


title: Lung_090_VC_F

description:
LUNG_90
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_089_VC_F

description:
LUNG_89
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP181490


title: sP181156


title: Lung_151_2500ppm_M

description:
LUNG_151
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP177216


title: Lung_150_2500ppm_M

description:
LUNG_150
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP192709


title: sP100267


title: Lung_149_2500ppm_M

description:
LUNG_149
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP123089


title: sP155550


title: Lung_148_2500ppm_M

description:
LUNG_148
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP151383


title: sP148217


title: Lung_147_2500ppm_M

description:
LUNG_147
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_135_1250ppm_M

description:
LUNG_135
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_146_2500ppm_M

description:
LUNG_146
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP181504


title: Lung_091_VC_F

description:
LUNG_91
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_133_1250ppm_M

description:
LUNG_133
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP185855


title: Lung_134_1250ppm_M

description:
LUNG_134
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP150457


title: sP159504


title: Lung_130_1250ppm_M

description:
LUNG_130
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_129_1250ppm_M

description:
LUNG_129
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_131_1250ppm_M

description:
LUNG_131
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_120_300ppm_M

description:
LUNG_120
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP198579


title: Lung_119_300ppm_M

description:
LUNG_119
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP114378


title: sP182357


title: Lung_118_300ppm_M

description:
LUNG_118
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP177915


title: sP165902


title: Lung_116_300ppm_M

description:
LUNG_116
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_114_300ppm_M

description:
LUNG_114
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_117_300ppm_M

description:
LUNG_117
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP176778


title: Lung_104_150ppm_M

description:
LUNG_104
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP109004


title: Lung_100_150ppm_M

description:
LUNG_100
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP156377


title: sP171043


title: sP183236


title: sP103391


title: Lung_098_150ppm_M

description:
LUNG_098
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_099_150ppm_M

description:
LUNG_099
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP197710


title: sP103228


title: Lung_097_150ppm_M

description:
LUNG_097
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP170074


title: sP182144


title: Lung_088_VC_M

description:
LUNG_088
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_086_VC_M

description:
LUNG_086
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP144302


title: Lung_084_VC_M

description:
LUNG_084
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP195991


title: sP176316


title: sP188146


title: Lung_083_VC_M

description:
LUNG_083
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Lung_081_VC_M

description:
LUNG_081
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP136748


title: Lung_082_VC_M

description:
LUNG_082
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: sP172479


title: sP156938


title: Lung_101_150ppm_M

description:
LUNG_101
processed data: 4MEI_Day5_LUNG_Male_Female_Counts.txt


title: Day5_LIVER_160_2500ppm_F

description:
Day5-LIVER_160
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt

value: Liver


title: Day5_LIVER_159_2500ppm_F

description:
Day5-LIVER_159
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP161993


title: Day5_LIVER_157_2500ppm_F

description:
Day5-LIVER_157
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP141234


title: sP119818


title: Day5_LIVER_156_2500ppm_F

description:
Day5-LIVER_156
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_155_2500ppm_F

description:
Day5-LIVER_155
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP179638


title: Day5_LIVER_154_2500ppm_F

description:
Day5-LIVER_154
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP170049


title: Day5_LIVER_143_1250ppm_F

description:
Day5-LIVER_143
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_144_1250ppm_F

description:
Day5-LIVER_144
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP164104


title: sP115906


title: sP187542


title: sP192858


title: Day5_LIVER_137_1250ppm_F

description:
Day5-LIVER_137
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_138_1250ppm_F

description:
Day5-LIVER_138
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_128_300ppm_F

description:
Day5-LIVER_128
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP118785


title: Day5_LIVER_127_300ppm_F

description:
Day5-LIVER_127
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP188415


title: sP109428


title: Day5_LIVER_123_300ppm_F

description:
Day5-LIVER_123
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_122_300ppm_F

description:
Day5-LIVER_122
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_126_300ppm_F

description:
Day5-LIVER_126
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_121_300ppm_F

description:
Day5-LIVER_121
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP109287


title: sP115698


title: sP191590


title: Day5_LIVER_112_150ppm_F

description:
Day5-LIVER_112
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP118115


title: Day5_LIVER_111_150ppm_F

description:
Day5-LIVER_111
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP156807


title: Day5_LIVER_110_150ppm_F

description:
Day5-LIVER_110
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP117277


title: sP125680


title: Day5_LIVER_109_150ppm_F

description:
Day5-LIVER_109
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_142_1250ppm_F

description:
Day5-LIVER_142
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_140_1250ppm_F

description:
Day5-LIVER_140
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_108_150ppm_F

description:
Day5-LIVER_108
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP164852


title: sP147062


title: sP128208


title: sP147765


title: Day5_LIVER_095_VC_F

description:
Day5-LIVER_095
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_106_150ppm_F

description:
Day5-LIVER_106
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP189317


title: Day5_LIVER_094_VC_F

description:
Day5-LIVER_094
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_093_VC_F

description:
Day5-LIVER_093
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP123807


title: Day5_LIVER_091_VC_F

description:
Day5-LIVER_091
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_090_VC_F

description:
Day5-LIVER_090
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP175046


title: sP128058


title: sP135791


title: sP115799


title: Day5_LIVER_152_2500ppm_M

description:
Day5-LIVER_152
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_089_VC_F

description:
Day5-LIVER_089
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_151_2500ppm_M

description:
Day5-LIVER_151
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP136145


title: sP190486


title: sP170623


title: Day5_LIVER_150_2500ppm_M

description:
Day5-LIVER_150
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_148_2500ppm_M

description:
Day5-LIVER_148
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP133542


title: Day5_LIVER_146_2500ppm_M

description:
Day5-LIVER_146
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP159072


title: sP105113


title: Day5_LIVER_147_2500ppm_M

description:
Day5-LIVER_147
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_134_1250ppm_M

description:
Day5-LIVER_134
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP107442


title: sP124139


title: sP178898


title: Day5_LIVER_133_1250ppm_M

description:
Day5-LIVER_133
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_131_1250ppm_M

description:
Day5-LIVER_131
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP135364


title: sP134901


title: Day5_LIVER_132_1250ppm_M

description:
Day5-LIVER_132
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_130_1250ppm_M

description:
Day5-LIVER_130
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_129_1250ppm_M

description:
Day5-LIVER_129
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP137489


title: Day5_LIVER_119_300ppm_M

description:
Day5-LIVER_119
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP192758


title: sP107292


title: Day5_LIVER_117_300ppm_M

description:
Day5-LIVER_117
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_116_300ppm_M

description:
Day5-LIVER_116
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_115_300ppm_M

description:
Day5-LIVER_115
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP182829


title: Day5_LIVER_114_300ppm_M

description:
Day5-LIVER_114
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP130086


title: Day5_LIVER_104_150ppm_M

description:
Day5-LIVER_104
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_113_300ppm_M

description:
Day5-LIVER_113
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP173117


title: sP172223


title: sP120855


title: sP155883


title: Day5_LIVER_102_150ppm_M

description:
Day5-LIVER_102
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_101_150ppm_M

description:
Day5-LIVER_101
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_100_150ppm_M

description:
Day5-LIVER_100
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP138504


title: sP140521


title: Day5_LIVER_103_150ppm_M

description:
Day5-LIVER_103
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_088_VC_M

description:
Day5-LIVER_088
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP169235


title: Day5_LIVER_085_VC_M

description:
Day5-LIVER_085
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP130312


title: sP186220


title: Day5_LIVER_084_VC_M

description:
Day5-LIVER_084
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day5_LIVER_097_150ppm_M

description:
Day5-LIVER_097
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP166876


title: sP199150


title: Day5_LIVER_082_VC_M

description:
Day5-LIVER_082
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: sP129388

value: Not Permitted


title: Day5_LIVER_083_VC_M

description:
Day5-LIVER_083
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt

value: Feed


title: sP117607


title: Day2-LUNG-79_300mg-kg_F

description:
Day2-LUNG_79
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

value: Day 2

value: Gavage


title: sP160318


title: Day5_LIVER_081_VC_M

description:
Day5-LIVER_081
processed data: 4MEI_Day5_LIVER_Male_Female_Counts.txt


title: Day2-LUNG-78_300mg-kg_F

description:
Day2-LUNG_78
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

value: Female

value: Lung


title: sP161117

value: liver


title: sP149431

value: HCV-infected patient


title: Day2-LUNG-76_300mg-kg_F

description:
Day2-LUNG_76
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-75_300mg-kg_F

description:
Day2-LUNG_75
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP187273


title: sP151129

value: No


title: Day2-LUNG-74_300mg-kg_F

description:
Day2-LUNG_74
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-73_300mg-kg_F

description:
Day2-LUNG_73
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP167177

value: White


title: Day2-LUNG-64_200mg-kg_F

description:
Day2-LUNG_64
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP173143


title: Day2-LUNG-61_200mg-kg_F

description:
Day2-LUNG_61
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP162258


title: sP123592


title: sP171101


title: Day2-LUNG-60_200mg-kg_F

description:
Day2-LUNG_60
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-59_200mg-kg_F

description:
Day2-LUNG_59
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-58_200mg-kg_F

description:
Day2-LUNG_58
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP155261


title: Day2-LUNG-48_100mg-kg_F

description:
Day2-LUNG_48
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP146881


title: Day2-LUNG-47_100mg-kg_F

description:
Day2-LUNG_47
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-57_200mg-kg_F

description:
Day2-LUNG_57
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP101167


title: sP107232


title: sP132310


title: Day2-LUNG-45_100mg-kg_F

description:
Day2-LUNG_45
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP105523

value: Other


title: sP151376


title: Day2-LUNG-43_100mg-kg_F

description:
Day2-LUNG_43
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP127376


title: Day2-LUNG-46_100mg-kg_F

description:
Day2-LUNG_46
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP127579


title: Day2-LUNG-32_50mg-kg_F

description:
Day2-LUNG_32
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-31_50mg-kg_F

description:
Day2-LUNG_31
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP149918


title: sP125624


title: Day2-LUNG-30_50mg-kg_F

description:
Day2-LUNG_30
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP174224


title: Day2-LUNG-28_50mg-kg_F

description:
Day2-LUNG_28
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP105067


title: Day2-LUNG-27_50mg-kg_F

description:
Day2-LUNG_27
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP123372


title: Day2-LUNG-26_50mg-kg_F

description:
Day2-LUNG_26
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP127478


title: sP144485


title: sP151412

value: Yes


title: Day2-LUNG-15_VC_F

description:
Day2-LUNG_15
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

value: Vehicle (0mg/kg-d)


title: Day2-LUNG-16_VC_F

description:
Day2-LUNG_16
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

value: Vehicle


title: Day2-LUNG-13_VC_F

description:
Day2-LUNG_13
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP180267


title: Day2-LUNG-42_100mg-kg_F

description:
Day2-LUNG_42
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-12_VC_F

description:
Day2-LUNG_12
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP116892


title: Day2-LUNG-10_VC_F

description:
Day2-LUNG_10
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-72_300mg-kg_M

description:
Day2-LUNG_72
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

value: Male


title: sP162131


title: sP174322


title: Day2-LUNG-69_300mg-kg_M

description:
Day2-LUNG_69
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP169868


title: sP171006


title: Day2-LUNG-66_300mg-kg_M

description:
Day2-LUNG_66
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-68_300mg-kg_M

description:
Day2-LUNG_68
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-67_300mg-kg_M

description:
Day2-LUNG_67
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP145389


title: Day2-LUNG-65_300mg-kg_M

description:
Day2-LUNG_65
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-56_200mg-kg_M

description:
Day2-LUNG_56
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP106019


title: Day2-LUNG-54_200mg-kg_M

description:
Day2-LUNG_54
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-53_200mg-kg_M

description:
Day2-LUNG_53
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP159294


title: Day2-LUNG-51_200mg-kg_M

description:
Day2-LUNG_51
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP193474


title: sP126889


title: Day2-LUNG-09_VC_F

description:
Day2-LUNG_09
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP170078


title: sP127903

value: Asian


title: Day2-LUNG-49_200mg-kg_M

description:
Day2-LUNG_49
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-40_100mg-kg_M

description:
Day2-LUNG_40
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP136130


title: sP178318


title: Day2-LUNG-39_100mg-kg_M

description:
Day2-LUNG_39
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-35_100mg-kg_M

description:
Day2-LUNG_35
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP111529


title: sP154801


title: sP116149


title: sP107295


title: Day2-LUNG-52_200mg-kg_M

description:
Day2-LUNG_52
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-23_50mg-kg_M

description:
Day2-LUNG_23
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-22_50mg-kg_M

description:
Day2-LUNG_22
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-08_VC_M

description:
Day2-LUNG_08
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-21_50mg-kg_M

description:
Day2-LUNG_21
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP165046


title: Day2-LUNG-17_50mg-kg_M

description:
Day2-LUNG_17
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP127419


title: sP102963


title: sP182421


title: Day2-LUNG-06_VC_M

description:
Day2-LUNG_06
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-38_100mg-kg_M

description:
Day2-LUNG_38
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: Day2-LUNG-36_100mg-kg_M

description:
Day2-LUNG_36
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP111499

value: Native Hawaiian or Pacific Islander


title: Day2-LUNG-05_VC_M

description:
Day2-LUNG_05
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP199191


title: sP155173


title: sP153686


title: sP114175


title: Day2-LUNG-33_100mg-kg_M

description:
Day2-LUNG_33
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: sP113570


title: sP161327


title: Day2-LUNG-04_VC_M

description:
Day2-LUNG_04
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt


title: PB_GM12878_long-TUC-seq_Rep2

city: irvine

first: Sorena

last: Rahmanian

state: ca

address: 2134 verano pl

department: Center for Complex Biological Systems

institute: University of California Irvine

description: 8 hrs 1mM 4SU treated GM12878 + 3hrs osmium- replicate 2

data_processing:
we used Minimap2 v2.17 with iso-seq settings for mapping the PacBio data
TranscriptClean v2.0.2 was used on mapped PacBio data without mismatch correction. The splice junction file was obtained using GENCODE v29 using one of the accesory scripts
TALON v4.4.2 was used for annotation and quantification of PacBio data. The database was initialized with GENCODE v29
We used STAR 2.6 to map Illumina TUC-seq reads to Hg38 build
We created sub-categories of the illumina TUC-seq data based on the number of T to C substitutions in the reads to 4 groups: all reads, reads with > 2 , > 4 and > 6 T to C
For each categories in illumina data we counted the abundance for each transcript in gencode v29 annotation file using express v1.5.1
Genome_build: hg38
Supplementary_files_format_and_content: TXT table format, Pacbio abundance files generated by TALON and Illumina abundances generated by eXpress for each category of reads

growth_protocol: ENCODE protocol for GM12878 cell line specific

extract_protocol:
The RNeasy Plus Mini Kit was used for RNA extraction following the manufacturer instructions
The extracted RNA was treated with exonuclease for 1 hour and the SIV control set 3 was added at 0.03%, then we made cDNA following smart-seq II protocol
For PacBio samples we used "Preparing SMRTbell®  Libraries Using Express Template Prep Kit 2.0 With  Low DNA Input" and for illumina samples, we used "Nextra DNA library prep"

tag: 4su treatment

value: 8 hrs of  1mM 4SU

tag: osmium treatment

value: 3 hrs of osmium tetroxide

tag: library protocol

value: PacBio SMRTbell protocol

tag: cell line


title: Day2-LUNG-24_50mg-kg_M

description:
Day2-LUNG_24
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

tag: strain/background

value: Day 2

value: Gavage


title: sP117541

tag: Sex


title: PB_GM12878_Osmium_ctrl

description: Osmium-treated GM12878 cells without any 4SU incorporation

value: no 4SU


title: Day2-LUNG-03_VC_M

description:
Day2-LUNG_03
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

tag: tissue

value: Lung


title: sP101838

value: liver

value: HCV-infected patient


title: PB_GM12878_long-TUC-seq_Rep1

description: 8 hrs 1mM 4SU treated GM12878 + 3hrs osmium- replicate 1


title: sP145136

value: White


title: Day2-LUNG-18_50mg-kg_M

description:
Day2-LUNG_18
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

tag: treatment


title: sP126203


title: Day2-LUNG-01_VC_M

description:
Day2-LUNG_01
processed data: 4MEI_Day2_LUNG_Male_Female_Counts.txt

tag: dose


title: Day2-LIVER-80_300mg-kg_F

description:
Day2-LIVER_80
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Female

value: Liver

tag: exposure time


title: Day2-LIVER-77_300mg-kg_F

description:
Day2-LIVER_77
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

tag: route


title: sP180254

value: No


title: Day2-LIVER-76_300mg-kg_F

description:
Day2-LIVER_76
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP194674


title: Day2-LIVER-75_300mg-kg_F

description:
Day2-LIVER_75
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP100960


title: y0-3

city: St. Louis

first: Indira

middle: U

last: Mysorekar

state: MO

address: 425 S. Euclid Ave, OB/GYN, BJCIH 10th Floor, Attn: Mysorekar Lab

department: OB/GYN

institute: Washington University in St. Louis School of Medicine

description: Young 3

data_processing:
Reads were aligned to the Ensembl GRCm38.76 top-level assembly with STAR version 2.0.4b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount version 1.4.5
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: tab-delimited txt file with samples, raw gene counts for all samples by gene

source_name: whole bladder

extract_protocol:
RNeasy Mini kit (74101, Qiagen) and RNase-free DNase digestion kit (79254, Qiagen)
Ribo-Zero rRNA depletion kit (Illumina)

value: whole bladder

tag: strain

tag: source

value: NIA

tag: age in months


title: y0-1

description: Young 1


title: a0-5

description: Aged 4


title: a0-2

description: Aged 1


title: a0-4

description: Aged 3


title: a0-3

description: Aged 2


title: y0-2

description: Young 2


title: Day2-LIVER-74_300mg-kg_F

description:
Day2-LIVER_74
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP157819

tag: diagnosis


title: Day2-LIVER-73_300mg-kg_F

description:
Day2-LIVER_73
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP193748

tag: age

value: Male


title: Day2-LIVER-64_200mg-kg_F

description:
Day2-LIVER_64
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP168993

tag: cirrhosis present


title: sP139564


title: Day2-LIVER-61_200mg-kg_F

description:
Day2-LIVER_61
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: y0-4

description: Young 4


title: sP168290


title: Day2-LIVER-60_200mg-kg_F

description:
Day2-LIVER_60
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: iBlasts_IgG_rep1

city: New York

first: Josephine

last: Wesely

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The DNA sequencing reads were aligned to the hg19 using Bowtie2 (version 2.2.6) with default parameters. MACS2 (version 2.1.1) was used to identify the enriched regions for RUNX1 binding relative to the IgG control with the shifting model and q-value 0.01 followed by the subtraction of known dark regions
Genome_build: UCSC hg19
Supplementary_files_format_and_content: xlsx, showing RUNX1 peaks and reads for each duplicate

source_name: human iPSCs

extract_protocol:
Formaldehyde fixed cell pellets were suspended into 0.5ml of sonication buffer (0.1% SDS, 1% Triton, 1 mM EDTA, 16.7 mM Tris pH 8, 167 mM NaCl) with 1x proteasome inhibitor cocktail (Millipore, #535140). The samples were sonicated with Bioruptor Pico (Diagenode) for 12 cycle with 30s on/off. ChIP was performed at 4°C O/N with 1 mg of chromatin DNA sample, 1.5 mg of antibody to RUNX1 (Abcam, ab23980) or normal Rabbit IgG (Santa Cruz Biotech, sc-2027), 20 mL of magnetic Protein A/G beads (NEB). The beads were washed twice with each following buffer: high salt buffer (0.1% SDS, 1 % Triton, 2 mM EDTA, 20 mM Tris pH 8, 500 mM NaCl); Li buffer (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris pH 8); Tris (pH 8). The beads were suspended in 13 ml of H2O, 15 ml of TD and 2 ml of TDE1 (Illumina, 15028212) and incubated at 37°C with constant shaking for 1 h. The beads were washed twice with TE (pH 8), resupsended in 20 ml buffer (100 mM Tris pH 8, 1mM EDTA, 0.1% SDS, 250 mM NaCl) with 1 ml of Proteinase K (Invitrogen, AM2546) and incubated at 65°C for 4 h. The DNA in the supernatant was purified with 2x Ampure beads (Beckman).
The purified DNA was used for PCR for 12 cycles with a pair of P7 and P5 index primers

value: day 18

tag: chip antibody

value: IgG


title: Day2-LIVER-59_200mg-kg_F

description:
Day2-LIVER_59
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: iLSCs_igG_rep2


title: iBlasts_igG_rep2


title: sP133073


title: sP190359

value: Asian


title: iBlasts_RUNX1_rep2


title: Day2-LIVER-48_100mg-kg_F

description:
Day2-LIVER_48
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: iBlasts_RUNX1_rep1


title: sP141051

value: Yes


title: sP170396


title: Day2-LIVER-58_200mg-kg_F

description:
Day2-LIVER_58
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Day 2


title: iLSCs_igG_rep1


title: iLSCs_RUNX1_rep1


title: iLSCs_RUNX1_rep2


title: Day2-LIVER-47_100mg-kg_F

description:
Day2-LIVER_47
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Gavage


title: C.elegans L4_control rep2

type: RNA

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Raised on NGM for 48 hours (L1 to L4 stage)

hyb_protocol: 5 μg of Biotin labeled cDNA was fragmented and hybridized to the Affymetrix C. elegans Gene 1.0 ST arrays as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing: To summarize the probe level data in the Affymetrix GeneChip® arrays, CEL files of C.elegans pOPC7 control condition was imported into the Affymetrix Expression ConsoleTM software for the quality control, data normalization and fold change algorithm. RMA normalization was carried out in Expression COnsole. Exported excel file with all genes and their exposure/control fold changes are listed.

label: Biotin

organism: Caenorhabditis elegans

source_name: C.elegans L4_control

label_protocol: 200 ng of total RNA was subjected to cDNA conversion and amplification using NuGEN Ovation Pico WTA V2 kit, to produce biotin-labelled cDNA.

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L4 stage in the presence of 1 mg/mL sodium perchlorate.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

treatment_protocol: L1 stage animals were exposed 48 hours at 20 ºC to 1 mg/mL sodium perchlorate supplemented to both the agar medium and the food source (E. coli OP50).

tag: Stage

value: staged L4 hermaphrodite

value: control


title: C.elegans L4_control rep3


title: C.elegans L4_Perchlorate rep1

description: Raised on NGM for 48 hours (L1 to L4 stage) in the presence of 1 mg/mL sodium perchlorate

source_name: C.elegans L4_Perchlorate

value: perchlorate


title: sP169995

value: liver

value: HCV-infected patient


title: C.elegans L4_control rep1


title: C.elegans L4_Perchlorate rep2


title: sP103917

value: Female


title: Day2-LIVER-46_100mg-kg_F

description:
Day2-LIVER_46
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Liver


title: sP199426

value: White


title: C.elegans L4_Perchlorate rep3


title: sP137018

value: No


title: sP188972


title: Day2-LIVER-43_100mg-kg_F

description:
Day2-LIVER_43
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-45_100mg-kg_F

description:
Day2-LIVER_45
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-42_100mg-kg_F

description:
Day2-LIVER_42
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP150610


title: sP151380


title: Day2-LIVER-57_200mg-kg_F

description:
Day2-LIVER_57
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP197619


title: sP151949


title: Day2-LIVER-28_50mg-kg_F

description:
Day2-LIVER_28
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP150411


title: Day2-LIVER-29_50mg-kg_F

description:
Day2-LIVER_29
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-27_50mg-kg_F

description:
Day2-LIVER_27
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-25_50mg-kg_F

description:
Day2-LIVER_25
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-15_VC_F

description:
Day2-LIVER_15
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Vehicle

value: Vehicle (0mg/kg-d)


title: sP184911


title: sP149872

value: Male


title: sP134204


title: Day2-LIVER-14_VC_F

description:
Day2-LIVER_14
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-11_VC_F

description:
Day2-LIVER_11
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-12_VC_F

description:
Day2-LIVER_12
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: sP196399


title: 0201hAstroA

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

data_processing:
Reference index was created based on the human transcriptome GRCh38 ensembl release 91 available through ensembl ftp (Homo_sapiens.GRCh38.cdna.all.fa.gz, Homo_sapiens.GRCh38.ncrna.fa.gz). Sequences in scafold chromosomes were removed before creating the reference index (keeping only chromosomes 1, 2, …, 22, X and Y). Transcript index was created with kallisto (version kallisto_linux-v0.43.1)
Kallisto was used by to estimate transcript abundances (counts per transcript). Version: kallisto_linux-v0.43.1
Gene annotations were obtained from the headers of the corresponding fasta files used to create the reference index.
Transcript abundances were summarized at the gene level using tximport R library
Genome_build: GRCh38 ensembl release 91
Supplementary_files_format_and_content: TAB delimited files contain ensembl transcript ID (target_id), transcript lenght (length), effective transcript length (eff_length) and estimated counts (est_counts) from kallisto

molecule: polyA RNA

source_name: iPSC astrocytes

extract_protocol:
RNA samples were prepared using standard poly-A isolation protocol (HiSeq 3000/4000 SBS Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: iPSC-derived astrocytes

tag: disease status

value: Ctrl


title: Day2-LIVER-32_50mg-kg_F

description:
Day2-LIVER_32
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

tag: strain/background


title: 042hAstroC

tag: cell line


title: Day2-LIVER-72_300mg-kg_M

description:
Day2-LIVER_72
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

tag: Sex

tag: tissue


title: sP167557

value: Yes


title: 042hAstroB


title: Day2-LIVER-69_300mg-kg_M

description:
Day2-LIVER_69
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

tag: treatment

tag: dose

value: Day 2


title: Day2-LIVER-68_300mg-kg_M

description:
Day2-LIVER_68
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

tag: exposure time

tag: route

value: Gavage


title: Day2-LIVER-26_50mg-kg_F

description:
Day2-LIVER_26
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-67_300mg-kg_M

description:
Day2-LIVER_67
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 0301hAstroC


title: Day2-LIVER-66_300mg-kg_M

description:
Day2-LIVER_66
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 0301hAstroA


title: Day2-LIVER-10_VC_F

description:
Day2-LIVER_10
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 0301hAstroB


title: Day2-LIVER-56_200mg-kg_M

description:
Day2-LIVER_56
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-65_300mg-kg_M

description:
Day2-LIVER_65
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-54_200mg-kg_M

description:
Day2-LIVER_54
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-09_VC_F

description:
Day2-LIVER_09
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 0201hAstroC


title: Day2-LIVER-53_200mg-kg_M

description:
Day2-LIVER_53
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-52_200mg-kg_M

description:
Day2-LIVER_52
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 48 hrs treated

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
Drop-seq
muc4209

data_processing:
For preprocessing of the single cell data of human mesenchymal cells, the Dropseq computational pipeline was used (version 2.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.2a) was used for mapping. Reads were aligned to the hg19 reference genome (GSE63269). For barcode filtering, we excluded barcodes with less than 200 genes detected. A high proportion (> 10%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed these unqualified cells from the downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Raw count matrix (MesothelialCells_rawcounts.mtx) from Drop-seq experiments with 20027 genes and 16899 cells in market matrix format and corresponding column (MesothelialCells_barcodes.txt) and row (MesothelialCells_genes.txt) labels. Cell-level metadata (MesothelialCells_meta_data.txt).

source_name: Lung tissue

growth_protocol: Met-5A cells were grown in culture and stressed for 15 min by desiccation.

extract_protocol:
Single cells were diluted in PBS, supplemented with 0.04% bovine serum albumin up to a final concentration of 100 cells/µl. Using a microfluidic PDMS device (Nanoshift), single cells were co-encapsulated in droplets with barcoded beads (Chemgenes Corporation, Wilmington, MA) at a final concentration of 120 beads/uL. Droplets were collected for 15 min/sample. After droplet breakage, beads were harvested, washed, and prepared for on bead mRNA reverse transcription (Maxima RT, Thermo Fisher). Following an exonuclease I (New England Biolabs) treatment for the removal of unused primers, beads were counted, aliquoted (2000 beads/reaction, equals ~100 cells/reaction), and pre-amplified by 13 PCR cycles (primers, chemistry, and cycle conditions identical to those previously described in Macosko et al., 2015).
PCR products were pooled and purified twice using 0.6x clean-up beads (CleanNA). Prior to tagmentation, cDNA samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB was used (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

treatment_protocol: At the  time points 8h, 24h, 48h and 72 h samples were incubated for 5 minutes in Trypsin-EDTA solution at 37°C. Trypsin was inactivated with ice cold assay medium and cells were washed twice with ice cold PBS.

value: Mesothelial cell line

tag: number of cells


title: 72 hrs treated

description:
Drop-seq
muc4210


title: 24 hrs treated

description:
Drop-seq
muc4208


title: Day2-LIVER-50_200mg-kg_M

description:
Day2-LIVER_50
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 8 hrs treated

description:
Drop-seq
muc4207


title: 042hAstroA


title: Day2-LIVER-40_100mg-kg_M

description:
Day2-LIVER_40
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-39_100mg-kg_M

description:
Day2-LIVER_39
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-38_100mg-kg_M

description:
Day2-LIVER_38
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 0 hrs untreated

description:
Drop-seq
muc4206


title: Day2-LIVER-34_100mg-kg_M

description:
Day2-LIVER_34
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-24_50mg-kg_M

description:
Day2-LIVER_24
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-22_50mg-kg_M

description:
Day2-LIVER_22
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-21_50mg-kg_M

description:
Day2-LIVER_21
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-20_50mg-kg_M

description:
Day2-LIVER_20
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-08_VC_M

description:
Day2-LIVER_08
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-07_VC_M

description:
Day2-LIVER_07
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-36_100mg-kg_M

description:
Day2-LIVER_36
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-18_50mg-kg_M

description:
Day2-LIVER_18
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-05_VC_M

description:
Day2-LIVER_05
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: 2_hESC_Wt_D0 Rep2

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Raw reads were aligned to the human genome (hg19), and splice junctions were mapped using TopHat v2.1.0 with default parameters
Gene based read counts were obtained using featureCount v1.5.0-p1
To perform normalization and statistical evaluation with negative binomial model between conditions on the count data, we used DESeq2 v1.10.1 Biconductor package
Genes were considered differentially expressed when showing an absolute log2 fold change (treatment/control) ≥ 1.5 with adjusted p-value (padj) ≤0.05.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain gene counts that can be used as input of DESEQ2

source_name: human Embryonic Stem cells

growth_protocol: Day 11 NPC (NPC D11) were differentiated from human embryonic stem cells in N2/B27 media supplemented with dual SMAD inhibitors. NPC D21 are obtained with further differentiation of NPC D11 for 10 more days in N2/B27 media supplemented with dual SMAD inhibitors.

extract_protocol:
Cells are lysed with Trizol reagent (Qiagen) and RNA is extracted with chloroform. Extracted RNA was further cleaned with RNAeasy kit (Qiagen) and on-column DNA digestion according to the manufacturer’s instructions.
Strand-specific Tru-Seq RNA-Seq library preparation

treatment_protocol: Until appearance of neural rosettes dual SMAD inhibitors were added everyday of differentiation protocol. When neural rosettes appear, dual SMAD inhibitors were withdrawn and N2/B27 media is supplemented with basic FGF for 3-4 days.

value: human Embryonic Stem cells

tag: differentiation time

value: 0 days

tag: genotype

value: Wild Type


title: Day2-LIVER-01_VC_M

description:
Day2-LIVER_01
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Day2-LIVER-49_200mg-kg_M

description:
Day2-LIVER_49
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: LJA96

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trimmomatics
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using Hisat2
We used Ensembl genes as the gene annotation file, including 24,616 genes, and the gene expression levels were then determined by FPKM values for accounting for differences in sequence depth and gene length. The FPKM of genes were quantified using StringTie
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: FPKM value matrix for all genes annotated in ensembl database

organism: Bos taurus

source_name: Diencephalon

extract_protocol: total RNA was extracted from snap frozen tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The quantity and purity of RNA were measured using a NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA)

tag: breed

value: Hereford

tag: age

value: adult

value: Diencephalon


title: Day2-LIVER-23_50mg-kg_M

description:
Day2-LIVER_23
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Liver


title: Day2-LIVER-03_VC_M

description:
Day2-LIVER_03
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt


title: Volinanserin 4

city: Exeter

first: Yasaman

last: Malekizadeh

address: Barrack Road

department: Biomedical and Clinical Science

institute: University of Exeter

data_processing:
Star aligner (version 2.6.1a) was used to align the RNA reads to the reference genome
Samtools (version 0.1.16) was used to convert the fastq data to sam and then bam files followed by sorting the bam files
featureCounts (version 1.6.1) was used to generate bam files
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 (version 1.16.1) was used to generate differentially expressed genes in samples based on negative binomial distribution. Statistical filtering  based on calculated log2 of 1.5-fold change and a false discovery rate adjusted P-value ≤0.05 was used to generate the gene lists used in subsequent analysis

source_name: Human Neuroblastoma cells

growth_protocol: SH-SY5Y neuroblastoma cells were grown in T175 flasks in media (DMEM/F-12, GlutaMAX™ supplement) containing 10% filtered fetal bovine serum (Gibco™ Fetal Bovine Serum, heat inactivated). The day before experimentarion, cells were seeded in 6 well plates at density of 7x104 cells per well and kept in the same media.

extract_protocol:
To extract the RNA, the media containing the vehicle or compound was removed and 500μl of Trizol (Invitrogen Trizol reagent) was applied to each well. Cells were mixed thoroughly with the reagent and collected for RNA extraction. RNA was purified using an RNA kit (Direct-zol™ RNA MiniPrep  w/ Zymo-Spin™ IIC Columns, capped) as shown in the instruction manual and stored at -80°C.
Illumina HiSeq 2500 standard mode sequencing system was used to sequence RNA samples (poly-A tail library preparation, 125bp paired end, 20 million reads per sample).

treatment_protocol: Each 4 wells of each 6 well plate were treated with the vehicle (DMSO) or the compound (Amisulpride, Risperidone or Volinanserin) for 24 hours

value: SH-SY5Y Human Neuroblastoma cells

tag: passage

value: Volinanserin


title: LJA81

source_name: Hippocampus

value: Hippocampus


title: Volinanserin 3


title: 12-OPAhNPCd21-3_Rep3

source_name: Neural progenitor cells

value: ES cell derived neural progenitor cells

value: 3 weeks


title: Day2-LIVER-06_VC_M

description:
Day2-LIVER_06
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Male

value: Vehicle

value: Vehicle (0mg/kg-d)


title: Volinanserin 2


title: Day2-LIVER-37_100mg-kg_M

description:
Day2-LIVER_37
processed data: 4MEI_Day2_LIVER_Male_Female_Counts.txt

value: Day 2

value: Gavage


title: Volinanserin 1


title: LJA48

source_name: Thyroid

value: Thyroid


title: 14-OPA1hetNPd22_S86_Rep1


title: LJA38


title: 9-OPAhNPCd21-2_Rep2


title: 0201hAstroB

value: iPSC-derived astrocytes

value: Ctrl


title: Risperidone 4

value: Risperidone


title: 14-ctrlNPCd21-4_Rep4


title: Risperidone 3


title: LJA296

source_name: follicle

value: Hereford

value: adult

value: follicle


title: 11-ctrlNPCd21-3_Rep3


title: LJA32


title: Risperidone 2

value: SH-SY5Y Human Neuroblastoma cells


title: 8-ctrlNPCd21-2_Rep2


title: 1_hESC_Wt_D0 Rep1

value: human Embryonic Stem cells

value: 0 days

value: Wild Type


title: LJA295


title: 15-OPAhNPCd21-4_Rep4

value: ES cell derived neural progenitor cells

value: 3 weeks


title: Risperidone 1


title: LJA293


title: 13-CTRL-NPd22_S84_Rep1


title: Amisulpride 3

value: Amisulpride


title: Amisulpride 4


title: 2-OPAhNPCd11-3_Rep3

value: 11 days


title: Amisulpride 2


title: LJA294


title: 9-OPA1hetNSCd11-2_S39_Rep2


title: 6-OPAhNPCd11-4_Rep4


title: LJA291


title: Amisulpride 1


title: LJA292a


title: LJA290


title: 5-ctrlNPCd11-4_Rep4


title: 7-OPA1hetNSCd11-1_S42_Rep1


title: DMSO 4

value: DMSO


title: LJA289


title: Sample_1-ctrlNPCd11-3_Rep3


title: DMSO 3


title: DMSO 1


title: 6-ConNSCd11-1_S38_Rep1


title: 8-ConNSCd11-2_S43_Rep2


title: LJA287


title: LJA288


title: DMSO 2


title: LJA286

source_name: Reticulum

value: Reticulum


title: 11-OPA1hetneuron7w_S41_Rep1

source_name: neurons

value: ES cell derived neurons

value: 7 weeks


title: LJA285

source_name: Rumen

value: Rumen


title: 10-Con-neuron7w_S40_Rep1


title: LJA282

source_name: Omasum

value: Omasum


title: LJA283

source_name: Jejunum

value: Hereford

value: Jejunum


title: PANC-1-high-Lovastatin-3

city: Kunming

first: Hongjin

state: China / Yunnan

address: Xichang Road#295

country: China

institute: The NHC Key Laboratory of Drug Addiction Medicine

data_processing:
We aligned the sequencing reads to a human genome reference (hg19) using TopHat version 2.0.13.
The resulting read alignments were assembled through Cufflinks version 1.1, and it created a novel transcript using Cufflinks reference annotation-based transcript (RABT) algorithm.
The transcripts combined with Cuffcompare were used to calculate relative abundances of each transcript through Cuffdiff.
Gene expression levels were determined by measuring the sum of fragments per kilobase of exon model per million mapped reads (FPKM) values of its exons.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression with FPKM

source_name: pancreatic cancer cells

growth_protocol: Human pancreatic cancer cell lines MiaPaCa-2 and PANC-1 (ATCC, Manassas, VA, USA) were maintained in DMEM medium supplemented with 2 mM glutamine, 1 mM Na-pyruvate, 100 units/mL penicillin, and 100 μg/mL streptomycin and 10% fetal bovine serum (FBS) at 37 ̊C in a humidified atmosphere containing 10% CO2.

extract_protocol:
~4×10^6 cells were havested and total RNA were extracted with RNeasy Mini Kit (Qiagen, Valencia, CA).
The mRNA was purified and fragmented from total RNA (2 μg) using poly-T oligo-attached magnetic beads with two rounds of purification. Cleaved RNA fragments primed with random hexamers were reverse transcribed into first-strand cDNA using reverse transcriptase and random primers. The RNA template was removed and synthesized a replacement strand to generate double-strand cDNA. End repair, A-tailing, adaptor ligation, cDNA template purification and enrichment of the purified cDNA templates using PCR were then performed.
Constructed libraries were 150 bp paired-end sequenced by an Illumina X10 sequencer, following manufacturer’s instructions.

value: pancreatic cancer cells

tag: passages

value: treat with 20μM Lovastatin


title: LJA284

source_name: RumenPapillae

value: adult

value: RumenPapillae


title: PANC-1-high-Simvastatin-2

value: treat with 20μM Simvastatin


title: PANC-1-high-Lovastatin-2


title: PANC-1-high-Simvastatin-3


title: LJA281

source_name: Ileum

value: Ileum


title: PANC-1-high-Simvastatin-1


title: PANC-1-high-Fluvastatin-3

value: treat with 20μM Fluvastatin


title: LJA28

source_name: Midbrain

value: Midbrain


title: LJA279

source_name: Spleen

value: Spleen


title: LJA280

source_name: Duodenum

value: Duodenum


title: PANC-1-high-Fluvastatin-2


title: PANC-1-high-Lovastatin-1


title: LJA278

source_name: Caecum

value: Caecum


title: mouse hearts with coronary artery ligation and FOXO3-GE-MPCs implantation_1

city: BeiJing

first: Wang

last: Kang

address: Building 104, yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of genome research, Chinese Academy of Sciences

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 Mouse refference genome using histat2 software.
Genome_build: mm10 for Mouse.
Supplementary_files_format_and_content: read count

source_name: RNA sequencing of the infarct border zone of the mouse hearts with coronary artery ligation and FOXO3-GE-MPCs implantation

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol (Thermo Fisher Scientific).
For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: strain

value: NOD-SCID

value: heart


title: LJA277


title: mouse hearts with coronary artery ligation and FOXO3-GE-MPCs implantation_2

source_name: RNA sequencing of the infarct border zone of the mouse hearts with coronary artery ligation and FOXO4-GE-MPCs implantation


title: PANC-1-low-Simvastatin-3

value: treat with 2μM Simvastatin


title: PANC-1-high-Fluvastatin-1


title: mouse hearts with coronary artery ligation_3

source_name: RNA sequencing of the infarct border zone of the mouse hearts with coronary artery ligation

value: coronary artery ligation


title: mouse hearts with coronary artery ligation_2


title: PANC-1-low-Simvastatin-2


title: PANC-1-low-Simvastatin-1


title: LJA274

source_name: Abomasum

value: Hereford

value: Abomasum


title: LJA276


title: mouse hearts with coronary artery ligation_1


title: mouse hearts with coronary artery ligation and FOXO3-GE-MPCs implantation_3

source_name: RNA sequencing of the infarct border zone of the mouse hearts with coronary artery ligation and FOXO5-GE-MPCs implantation


title: PANC-1-low-Lovastatin-3

value: pancreatic cancer cells

value: treat with 2μM Lovastatin


title: LJA273

source_name: Supraspinatus

value: adult

value: Supraspinatus


title: mouse hearts with sham surgery_3

source_name: RNA sequencing of the infarct border zone of the mouse hearts with sham surgery

value: sham


title: PANC-1-low-Lovastatin-2


title: LJA272


title: mouse hearts with sham surgery_2


title: LJA271


title: mouse hearts with sham surgery_1


title: LJA270

source_name: Semimembranosus

value: Semimembranosus


title: PANC-1-low-Fluvastatin-3

value: treat with 2μM Fluvastatin


title: PANC-1-low-Fluvastatin-2


title: PANC-1-low-Lovastatin-1


title: LJA268


title: PANC-1-low-Fluvastatin-1


title: LJA267a

source_name: Infraspinatus

value: Infraspinatus


title: PANC-1-Control-3

value: Control


title: LJA266


title: PANC-1-Control-2


title: CD8TexStem_p45Tg_TCF1cutrun_r2

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

data_processing:
Library strategy: CUT&RUN
Cut&run reads were trimmed to 51bp and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 unique reads) using macs14 (with -p 1e-5, --nomodel and --shiftize 73 parameters)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized signal track (in bigwig format) for each cut&run sample.

source_name: exhausted CD8+ T cells

growth_protocol: CD45.2+  p45Tg P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by LCMV-clone 13 infection. On day 30 postinfection, the splenocytes were harvested, CD45.1+ cells were depleted, followed by cell sorting to collect CD45.2+Tex-stem cells for downstream analysis.

extract_protocol:
p45 Tg Tex-stem cells  were sort-purified from the spleen, and nuclei extracted, treated with anti-Tcf1 antibody followed by protein-A-micrococcal nuclease, and DNA fragments collected.
The Tcf1 antibody-directed, Mnase-generated DNA fragments were collected, PCR-amplified to generate sequencing libraries.

value: splenocytes

value: p45 Tcf1 transgenic

tag: cell phenotype

value: CD8+, CXCR5+, Tim3–


title: CD8TexStem_p45Tg_TCF1cutrun_r1


title: LJA265


title: LJA264


title: PANC-1-Control-1

source_name: pancreatic cancer cells


title: MiaPaCa-2-high-Simvastatin-3

value: treat with 20μM Simvastatin


title: MiaPaCa-2-high-Simvastatin-2


title: LJA263


title: CD8TexStem_WT_ATAC_r2

data_processing:
ATAC-seq reads were trimmed to 36bp from 3'end and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 reads) using macs2 PE mode (with -q 0.01 and --keep-dup 1 parameters).
Genome_build: mm10
Supplementary_files_format_and_content: Normalized signal track (in bigwig format) for each ATAC-seq sample.

growth_protocol: CD45.2+ WT or p45Tg P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by LCMV-clone 13 infection. On day 30 postinfection, the splenocytes were harvested, CD45.1+ cells were depleted, followed by cell sorting to collect CD45.2+Tex-stem or Tex-term cells for downstream analysis.

extract_protocol:
WT or p45 Tg Tex-stem cells, along with WT Tex-term cells were sort-purified from the spleen, treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

value: wild type


title: LJA262

source_name: Urethra

value: Urethra


title: CD8TexTerm_WT_ATAC_r1

value: CD8+, CXCR5–, Tim3+


title: MiaPaCa-2-high-Simvastatin-1


title: MiaPaCa-2-high-Lovastatin-3

value: treat with 20μM Lovastatin


title: CD8TexStem_WT_ATAC_r1


title: LJA261

source_name: bladder

value: Hereford

value: bladder


title: CD8TexStem_p45Tg_ATAC_r2


title: LJA259

value: adult


title: MiaPaCa-2-high-Lovastatin-1

value: pancreatic cancer cells


title: MiaPaCa-2-high-Lovastatin-2


title: LJA260

source_name: Ureter

value: Ureter


title: MiaPaCa-2-high-Fluvastatin-3

value: treat with 20μM Fluvastatin


title: LJA257


title: tabula-muris-senis-facs

first: Angela

last: Oliveira Pisco

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description:
tabula_muris_senis_facs_raw_counts
SmartSeq2 single-cell raw counts

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned using to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data is available as h5ad and loom. Metadata is available from the h5ad or as separate csv.

extract_protocol:
RNAeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
10X genomics and Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT
Nextera tagmentation according to the standard protocol for single cell RNA-seq


title: CD8TexStem_p45Tg_ATAC_r1


title: LJA258


title: MiaPaCa-2-high-Fluvastatin-2


title: tabula-muris-senis-droplet

description:
tabula_muris_senis_droplet_raw_counts
10X genomics single-cell raw counts


title: CD8TexTerm_WT_ATAC_r2


title: MiaPaCa-2-high-Fluvastatin-1


title: LJA256


title: LJA255


title: KO_WT_IL4_4_M2 [invitro_IL4]

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
#genome alignment single read: STAR --genomeDir ~/STAR_mm10_GENOME_DIR  --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
#genome alignment paired-end read: STAR --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --runThreadN 20 --sjdbGTFfile ~/mm10/mm10_genes.gtf  --genomeDir ~/STAR_mm10_GENOME_DIR_150 --readFilesIn $f1 $f2 --outFileNamePrefix $out --outSAMstrandField intronMotif
#counting reads: featureCounts -t exon -g gene_id -a ~/mm10/mm10_genes.gtf -T 20
#DGE with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts read counts for all samples

source_name: bone marrow-derived macrophages

growth_protocol: Control and MHD3KO mice were euthanized, and bone marrow were extracted for hindlimb femurs. Bone marrow cells were cultured for 7 days in DMEM supplemented with 10% FBS and 30% L929 media for 7 days on petri dishes to allow macrophage differentiation.

extract_protocol:
After treatment, cells were immediately lysed in trizol and RNA purified with RNeasy RNA isolation kit according to the manufacturers instructions.  Illumina Truseq Stranded RNA Total RNA library prep kit was used with 1ug RNA of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 7 days of differeniation, BMDM were replated, rested overnight before treated with BSA control, LPS(5ng/ml for 4 hours), IL4 (100ng/ml for 24hours). For rescue macrophages, retrovirus expressing Y298F or WT HDAC3 were added to BMDM 4 days post harvest from femurs. For siRNA experiments, siRNA were addded 24 hours after replating of the macrophages on the 7th day post harvest.

value: 8 weeks

value: MHD3KO +WT HDAC3

tag: agent


title: MiaPaCa-2-low-Simvastatin-3

tag: cell line

value: treat with 2μM Simvastatin


title: young_1

description: single cell

data_processing:
cellranger v3.0.1
Genome_build: mm10
Supplementary_files_format_and_content: count matrix, gene name, and cell barcode files for each sample from cellranger processing

source_name: bladder CD45 enriched

extract_protocol:
Chromium Single Cell 5′ Library and Gel Bead Kit
scRNA-seq

treatment_protocol: Bladders were digested with Multi-tissue dissociation kit (130-110- 201, Miltenyi) for 30 min at 37°. Bladder cells were filtered, washed, and incubated with magnetic CD45 microbeads (130-052-301, Miltenyi) and purified by two sequential positive selections. Cells were washed and resuspended at appropriate concentrations for loading into 10X Chromium Controller.

value: bladder CD45 enriched

tag: cell type

value: immune cells

tag: source

value: NIA

value: 3 months


title: aged_1

description: single cell

tag: tissue

value: 18 months


title: LJA254


title: MiaPaCa-2-low-Simvastatin-2

tag: treatment


title: MHD3KO_LPS_3 [invivo]

description:
invivo_counts.txt
WT C57Bl6, MHD3KO, NS-DAD mice and their control littermates of 8-week-old were intraperitoneally injected with either phosphate-buffered saline (PBS, Sigma) or 10 mg/kg of purified LPS (Sigma E. Coli O111:B4) at 4PM. Without thioglycolate stimulation, peritoneal cells were harvested 6h after LPS or PBS injection at 10PM and passed through pre-separation filters (Miltenyi Biotec, 130-041-407) to obtain a single-cell suspension. Peritoneal macrophages were then isolated by MACS (Magnetic-Activated Cell Sorting) as previously described40, following the manufacturer instructions (Miltenyi Biotec, 130-110-434) and using MiniMACS columns (Miltenyi Biotec, 130-042-201). RNA were isolated from purified cells using TRIzol (Invitrogen) with the RNeasy micro kit (Qiagen)

source_name: peritoneal macrophages

value: LPS


title: MHD3KO_LPS_4 [invivo]


title: KO_WT_IL4_3_M2 [invitro_IL4]


title: KO_WT_IL4_2_M2 [invitro_IL4]


title: MiaPaCa-2-low-Simvastatin-1


title: KO_WT_IL4_1_M2 [invitro_IL4]


title: MiaPaCa-2-low-Lovastatin-3

value: treat with 2μM Lovastatin


title: LJA252a


title: MHD3KO_LPS_2 [invivo]


title: MHD3KO_LPS_1 [invivo]


title: LJA251


title: MiaPaCa-2-low-Lovastatin-2


title: KO_WT_3_M2 [invitro_IL4]


title: LJA250a


title: KO_WT_4_M2 [invitro_IL4]


title: LJA249


title: MHD3KO_PBS_2 [invivo]

value: PBS


title: MiaPaCa-2-low-Fluvastatin-3

value: treat with 2μM Fluvastatin


title: KO_WT_2_M2 [invitro_IL4]


title: LJA248

value: Hereford


title: Control_LPS_4 [invivo]

value: control


title: MiaPaCa-2-low-Fluvastatin-2

value: pancreatic cancer cells


title: LJA253

value: adult


title: Y298F_IL4_4_M2 [invitro_IL4]

value: MHD3KO +Y298F


title: LJA243

source_name: Diaphragm

value: Diaphragm


title: MiaPaCa-2-Control-2

value: Control


title: Control_LPS_2 [invivo]

value: 8 weeks


title: MHD3KO_PBS_3 [invivo]


title: Y298F_IL4_1_M2 [invitro_IL4]


title: LJA239

source_name: Esophagus

value: Esophagus


title: Control_PBS_4 [invivo]


title: LJA240

source_name: Liver

value: Liver


title: Control_PBS_3 [invivo]


title: MHD3KO_PBS_1 [invivo]


title: LJA244

source_name: CorpusLuteum

value: CorpusLuteum


title: Y298F_3_M2 [invitro_IL4]


title: KO_WT_1_M2 [invitro_IL4]

value: MHD3KO +WT HDAC3


title: Y298F_4_M2 [invitro_IL4]


title: Control_PBS_2 [invivo]


title: MiaPaCa-2-low-Fluvastatin-1


title: LJA236

source_name: Atrium

value: Atrium


title: Y298F_2_M2 [invitro_IL4]


title: LJA235

source_name: Ventricle

value: Ventricle


title: Control_PBS_1 [invivo]


title: Control_LPS_3 [invivo]

value: LPS


title: Y298F_1_M2 [invitro_IL4]


title: Y298F_IL4_3_M2 [invitro_IL4]


title: MiaPaCa-2-Control-3


title: LJA234b


title: LJA241


title: Control_LPS_1 [invivo]


title: Y298F_IL4_2_M2 [invitro_IL4]


title: MiaPaCa-2-Control-1


title: KO_IL4_4_M2 [invitro_IL4]

value: MHD3KO+empty vector


title: a_400nM_2_SAHA_LPS [SAHA]


title: LJA233


title: LJA237

source_name: Aorta

value: Aorta


title: KO_IL4_3_M2 [invitro_IL4]


title: LJA232a

value: Hereford


title: a_400nM_1_SAHA_LPS [SAHA]

value: control


title: KO_IL4_2_M2 [invitro_IL4]


title: a_400nM_3_SAHA [SAHA]


title: KO_IL4_1_M2 [invitro_IL4]


title: LJA230

source_name: Adrenal

value: Adrenal


title: LJA229

value: adult


title: LJA228


title: a_400nM_1_SAHA [SAHA]


title: KO_4_M2 [invitro_IL4]


title: a_100nM_3_SAHA_LPS [SAHA]


title: KO_2_M2 [invitro_IL4]


title: KO_1_M2 [invitro_IL4]


title: a_100nM_2_SAHA_LPS [SAHA]


title: LJA220


title: MiaPaCa-2-low-Lovastatin-1

value: pancreatic cancer cells

value: treat with 2μM Lovastatin


title: LJA222

source_name: Thalamus

value: Thalamus


title: a_400nM_3_SAHA_LPS [SAHA]

value: 8 weeks


title: WT_IL4_4_M2 [invitro_IL4]

value: control+empty vector


title: a_100nM_1_SAHA_LPS [SAHA]


title: LJA219


title: a_100nM_3_SAHA [SAHA]


title: WT_IL4_2_M2 [invitro_IL4]


title: WT_IL4_3_M2 [invitro_IL4]


title: LJA218


title: a_100nM_2_SAHA [SAHA]


title: a_100nM_1_SAHA [SAHA]


title: WT_IL4_1_M2 [invitro_IL4]


title: a_25nM_3_SAHA_LPS [SAHA]


title: a_400nM_2_SAHA [SAHA]


title: KO_3_M2 [invitro_IL4]


title: LJA212


title: WT_4_M2 [invitro_IL4]


title: WT_3_M2 [invitro_IL4]


title: LJA224

source_name: Pons

value: Pons


title: LJA209a

source_name: SalivaryGland

value: SalivaryGland


title: a_25nM_2_SAHA_LPS [SAHA]


title: LJA207


title: WT_2_M2 [invitro_IL4]


title: LJA206


title: LJA205


title: a_25nM_2_SAHA [SAHA]


title: a_25nM_3_SAHA [SAHA]


title: WT_1_M2 [invitro_IL4]


title: LJA204b

source_name: Trachea

value: Trachea


title: a_25nM_1_SAHA [SAHA]


title: LJA204a


title: a_0nM_3_SAHA_LPS [SAHA]


title: LJA215


title: a_0nM_2_SAHA_LPS [SAHA]


title: LJA203


title: a_25nM_1_SAHA_LPS [SAHA]


title: a_0nM_1_SAHA_LPS [SAHA]


title: a_0nM_3_SAHA [SAHA]


title: LJA201


title: LJA168


title: a_0nM_2_SAHA [SAHA]


title: LJA167


title: a_0nM_1_SAHA [SAHA]


title: LJA163


title: sip65_3_LPS [siRNA]


title: sip65_2_LPS [siRNA]


title: LJA162


title: LJA161

source_name: Follicle

value: Follicle


title: sip65_1_LPS [siRNA]


title: Parasite RNA rep2

city: Chengdu

first: Jing-wen

last: Lin

address: No. 17, Section 3, People's South Road

institute: West China Second Hospital

description:
Parasite RNA
P. c. chabaudi AS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: This dataset was generated to confirm that Plasmodium RNA (malaria parasite) does not hybridise well on Illumina mouse bead array.  And as expected, the normalisation step cannot be performed due to the low number of probes detected in parasite samples.  This was the reason that we left out normalised value.

label: biotin

organism: Plasmodium chabaudi

source_name: Parasite pellet

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol:
mouse RNA was isolated using PerfectPure RNA Blood Kit (5 PRIME) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Caliper LabChip GX (Caliper Life Sciences)
Parasite RNA was extracted using RiboPure RNA Purification Kit (Ambion) according to the manufacturer’s protocols.

treatment_protocol: Female C57BL/6 mice aged between 6–8 weeks were injected intraperitoneally with 105 infected red blood cells of P. chabaudi AS.

tag: gender

value: Female

value: 6-8 weeks

value: Blood

tag: experiment

tag: infection

value: infected

tag: day

value: day 8

tag: mouse selection

value: random


title: LJA160

tag: breed

value: Hereford


title: LJA202

tag: age

value: adult


title: LJA159


title: sip65_2_veh [siRNA]

source_name: bone marrow-derived macrophages

tag: genotype

value: control


title: sip65_3_veh [siRNA]


title: naïve blood rep3

description: naïve blood

source_name: Mouse Blood

value: naïve

value: day 0


title: Infected D8 rep5

description: Infected D8


title: Parasite RNA rep1

description:
Parasite RNA
P. c. chabaudi AS


title: LJA158


title: Infected D8 rep4

description: Infected D8


title: G_CCE_MMTR_N_d3

city: Seoul

first: Chul Geun

last: Kim

address: wangsimni-ro 222

department: Life Science

country: South Korea

institute: Hanyang University

description: d3 MMTR N-term OE.Signal

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse WG-6 expression v.2 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing:
Array data export processing and analysis was performed using Illumina BeadStudio v3.2 (Illumina).
Background correction was performed using the Affymetrix Robust Multi-array Analysis background correction model, variance stabilization was performed using log2 scaling, and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: G-CCE cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: G-CCE lines were maintained in DMEM supplemented with 15% heat-inactivated fetal bovine serum (FBS; Gibco, 16141079), 1X MEM Non-Essential Amino Acids Solution (Sigma-Aldrich, M7145), 300 μM monothioglycerol (Sigma-Aldrich, M6145), 1X penicillin/streptomycin, and 1000 U/ml Leukemia inhibitory factor (LIF, Sigma-Aldrich, ESG1107) in 0.1% gelatin coated cell culture dishes.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: G-CCE lines overexpressing MMTR/Dmap1 and N- and C-terminal fragments of MMTR were obtained by transfection of pcDNA-Flag-MMTR/Dmap1 into G-CCE cells using Lipofectamine 2000 reagent. MMTR/Dmap1 shRNA and mshRNA G-CCE lines were established by transduction of lentiviruses of each group into G-CCE cells in the presence of 8 μg/ml polybrene. To induce differentiation of G-CCE cells, Leukemia inhibitory factor (LIF) was eliminated from the culture media for 3 days.

value: mouse embryonic stem cells

value: G-CCE

tag: leukemia inhibitory factor status

value: (-) for 3 days from media

tag: transfection


title: Infected D8 rep3

description: Infected D8

tag: strain


title: naïve blood rep2

description: naïve blood


title: Infected D8 rep1

description: Infected D8


title: naïve blood rep1

description: naïve blood


title: sip65_1_veh [siRNA]

value: 8 weeks

tag: agent


title: Infected D8 rep2

description: Infected D8


title: siATF3_3_LPS [siRNA]


title: LJA156


title: LJA157

source_name: prostrate

value: prostrate


title: siATF3_2_LPS [siRNA]


title: siATF3_1_LPS [siRNA]


title: AE9

city: Cincinnati

first: Latha

last: Satish

state: OH

address: 3229 Burnet Avenue

department: Research

institute: Shriners Hospitals for Children

description: countsTable.xls

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Burn Skin (Eschar Tissue)

extract_protocol:
Total RNA was extracted from normal skin and burn eschar tissues using RNeasy Mini Kit from Qiagen Inc,. RNA quality was determined by Capillary electrophoresis using an Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

value: discarded burn tissue


title: siATF3_3_veh [siRNA]


title: LJA143

source_name: Mammary

value: Mammary


title: siATF3_2_veh [siRNA]


title: G_CCE_MMTR_F_d3

description: d3 MMTR full length OE.Signal

tag: cell line


title: AE6

description: countsTable.xls


title: AE7

description: countsTable.xls


title: G_CCE_MMTR_N_d0

description: d0 MMTR N-term OE.Signal

tag: cell type


title: siATF3_1_veh [siRNA]


title: G_CCE_MMTR_F_d0

description: d0 MMTR full length OE.Signal


title: G_CCE_MMTR_C_d3

description: d3 MMTR C-term OE.Signal


title: G_CCE_MMTR_C_d0

description: d0 MMTR C-term OE.Signal


title: G_CCE_MMTRi_d3

description: d3 MMTRi.Signal


title: siATF2_3_LPS [siRNA]


title: siATF2_2_LPS [siRNA]


title: AE5

description: countsTable.xls

source_name: Normal Skin

value: discarded normal skin


title: AE4

description: countsTable.xls


title: siATF2_1_LPS [siRNA]


title: G_CCE_MMTRi_d0

description: d0 MMTRi.Signal


title: 071317_CD14p16p_mock_33F

city: Charlestown

first: Pritha

last: Sen

state: Massachusetts

address: 149 13th street

institute: Massachusetts General Hospital

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071317_CD14p16p_mock_33F

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Single-cell libraries were aligned to hg19 reference genome and UMI count files were generated using the Illumina BaseSpace SureCell application
Genome_build: hg19

extract_protocol:
Desired monocyte populations for sorted by flow cytometry and RNA was harvested using Qiagen RNeasy micro kit and on column Dnase digestion was performed. RNA quantity and quality was analyzed on Agilent Bioanalyzer.
Lexogen QuantSeq Kit was used for the construction of bulk sequencing libraries. SureCell WTA 3' Library Prep Kit was used for the construction of single-cell sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells were stimulated with PMA at 100 ng/ml for 48 hours prior to infection with TB40/E-5. Human peripheral blood mononuclear cells (PBMC) were isolated from CMV IgG negative immunocompetent donors and cultured ex vivo in donor autologous serum and infected with TB40/E-5.

value: mock

value: F

tag: immune status

value: immunocompetent

tag: virus strain


title: 071317_CD14p16p_TB40_33F

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071317_CD14p16p_TB40_33F

tag: treatment

value: CMV


title: G_CCE_WT_d3

description: d3 WT.Signal


title: AE3

description: countsTable.xls

tag: tissue


title: G_CCE_WT_d0

description: d0 WT.Signal


title: AE2

description: countsTable.xls


title: siATF2_2_veh [siRNA]


title: AE8

description: countsTable.xls


title: 071717_CD14p16p_mock_27F

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071717_CD14p16p_mock_27F

tag: gender


title: siATF2_3_veh [siRNA]


title: 070517_CD14p16p_TB40_50M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
070517_CD14p16p_TB40_50M


title: AE1

description: countsTable.xls


title: 070517_CD14p16p_mock_50M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
070517_CD14p16p_mock_50M

value: M


title: siATF2_1_veh [siRNA]