title: 26DBP-1

city: New Brunswick,

first: Jie

last: Liu

state: NJ

address: 76 Lipman Drive

department: Department of Biochemistry and Microbiology

institute: Rutgers University

data_processing:
Raw RNA sequencing reads were trimmed to remove sequencing adapters and low-quality base-pairs using CLC Genomic Workbench 8.5.1 (https://www.qiagenbioinformatics.com/) For quality trimming the quality score parameter was set to 0.01 without allowing any ambiguous nucleotides, for adapter trimming, a partial sequence of the TruSeq adapter (AGATCGGAAGAGC) was searched in the reads and trimmed if found (Parameters: Mismatch cost=2, Gap cost=3, Internal minimum match score=10, End minimum match score=8 ).
CLC Genomic Workbench 8.5.1 was used to align the trimmed reads to the  Desulfoluna spongiiphila AA1 genome assembly (GCF_900101345.1), a read was considered successfully mapped if at least 95% of the read length was at least 95% identical to the target sequence.
The raw read counts matrix for all 6 samples was used as input to the DESeq2 R package for calling differentially expressed genes.
Genome_build: GCF_900101345.1 Desulfoluna spongiiphila AA1
Supplementary_files_format_and_content: The raw read counts are in a tab delimited text file

organism: Desulfoluna spongiiphila

source_name: Bacterial Cell

growth_protocol: D. spongiiphila strain AA1 was pre-grown anaerobically in 3 L medium with 30 mM lactate as electron donor and 20 mM sulfate as electron acceptor for 3 days to a culture density of ~10e7 cells/ml. Then, 300 ml of pre-grown culture was added to 300 ml of fresh sulfate-free medium containing 2 mM lactate.

extract_protocol:
Strain AA1 pellets were resuspended in Trizol reagent (Life Technologies) and lysed on a TissueLyser II (Qiagen) with a 7 mm stainless steel bead by 3 cycles of 2 min 30 s beating and 2 min resting on ice. Chloroform was then added to the suspension and centrifuged at 15,000 g for 15 min at 4°C. The upper aqueous layer  was transferred into new tubes, and an equal volume of 70% ethanol was added. The mixture containing RNA was then purified using RNeasy Mini Kit (Qiagen) by following the manufacturer’s protocol, including the on-column DNase step. RNA quantity and quality was measured on a Nanodrop, Qubit (RNA Broad Range) (Life Technologies) and Agilent Bioanalyzer 2100 with RNA Nano chip.
The quantification of rRNA-depleted samples was measured on Qubit (RNA Broad Range). Libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2, according to the manufacturer's protocol.

treatment_protocol: For the organohalide treatment, 200 µM 2,6-dibromophenol was added as electron acceptor, while an additional 200 µM sulfate was added as electron acceptor in the control treatment.

tag: time


title: 26DBP-3

status: Public on Jan 10 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: treatment


title: Abcg2-ko HPC + Vector, replicate 2

type: RNA

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
myc013
sorted Lin– transduced with MSCV-IRES-YFP vector and cultured in methocult medium

hyb_protocol: Six micrograms (6 ug) of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system

data_processing: Signals were summarized using the Robust Multichip Algorithm (RMA) using Partek Genomics Suite software v6.6 (Partek, Inc)

label: biotin

organism: Mus musculus

source_name: Abcg2-ko HPC + Vector

label_protocol: One hundred nanograms (100 ng) of total RNA were converted into biotinylated cDNA using the Affymetrix 3'IVT Express protocol (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Lineage negative cells (Lin-, HPC) harvested from bone marrow of mice were pre-stimulated for 36 hours in complete bone marrow medium containing 50 ng/ml murine stem cell factor, 20 ng/ml murine interleukin-3 and 30 ng/ml murine interleukin-6

extract_protocol: RNA samples were prepared according to the manufacturer's instructions of Rneasy Mini kit from Qiagen

treatment_protocol: Stimulated cells were then plated on retronectin-coated culture dishes and incubated for 48 hours with retrovirus supernatant, and YFP-positive cells were harvested by flow cytometry then plated in methocult medium. The cells were then harvested for RNA extraction.

tag: genotype/variation

tag: gender

value: female

tag: age

value: 6 - 12 weeks of age

tag: cell type

value: Lin- hematopoietic progenitor cells

value: transduced with MSCV-IRES-YFP vector


title: 11519L-P2-E06: human fallopian tube single cell RNA-seq

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequencing files were trimmed by Trim Galore!, mapped to UCSC hg19 human genome assembly by STAR (Dobin et al., 2012) and counted by FeatureCount (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: read counts in txt format

organism: Homo sapiens

source_name: human fallopian tube

extract_protocol:
The fallopian tube samples were processed in 1 hour, after being collected from the hospital. The tissues were dissociated with Human Tumor Dissociated kit (Miltenyi Biotec) and filtered using 100µm SmarterStrainers (Miltenyi Biotec).
SMART-seq2 for single-cell RNA-seq

value: normal fallopian tube cells

tag: patient id

tag: sample source

value: cryopreserved


title: 11519L-P2-E01: human fallopian tube single cell RNA-seq


title: Sulfate-3

value: Sulfate


title: 11511R-P4-F09: human fallopian tube single cell RNA-seq


title: 11519L-P2-D07: human fallopian tube single cell RNA-seq


title: 11519L-P2-E09: human fallopian tube single cell RNA-seq


title: 11519L-P2-D04: human fallopian tube single cell RNA-seq


title: 11519L-P2-D03: human fallopian tube single cell RNA-seq


title: Sulfate-2


title: 11519L-P2-C03: human fallopian tube single cell RNA-seq


title: 11519L-P2-C10: human fallopian tube single cell RNA-seq


title: WT HPC + MYCN, replicate 2

description:
myc012
sorted Lin– transduced with MSCV-MYCN-IRES-YFP vector and cultured in methocult medium

source_name: WT HPC + MYCN

value: WT


title: 11519L-P2-C06: human fallopian tube single cell RNA-seq


title: 11519L-P2-C07: human fallopian tube single cell RNA-seq


title: 11519L-P2-D12: human fallopian tube single cell RNA-seq


title: 11519L-P1-G11: human fallopian tube single cell RNA-seq


title: 26DBP-2


title: 11519L-P2-C04: human fallopian tube single cell RNA-seq


title: Abcg2-ko HPC + MYCN, replicate 2

description:
myc014
sorted Lin– transduced with MSCV-MYCN-IRES-YFP vector and cultured in methocult medium

source_name: Abcg2-ko HPC + MYCN


title: HCAEC scRNA-seq

city: Buffalo

first: Stylianos

last: Andreadis

state: New York

address: 908 Furnas Hall

department: Department of Chemical and Biological Engineering

institute: University at Buffalo

description: Purchased as Pooled donor cells

data_processing:
Illumina RTA v3.4.4 Basecaller
Cellranger 3.0.1 mkoutput with Bcl2Fastq 2.19.1
Cellranger 3.0.1 Count against GRCh38 genome to produce count matrix
Seurat 3.1.1.9016 used for marker gene analysis and visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV File containing UMI corrected read counts

source_name: Carotid artery endothelial cells

extract_protocol:
Chromimum Single Cell 3' v3 (10x Genomics)
TruSeq Stranded RNA (illumina)

tag: tissue

value: carotid artery

value: Carotid artery endothelial cells

tag: passages

tag: culture conditions

value: Sheared (10dyne/cm2) for 5 days


title: Abcg2-ko HPC + MYCN, replicate 1

description:
myc010
sorted Lin– transduced with MSCV-MYCN-IRES-YFP vector and cultured in methocult medium


title: 11519L-P1-G10: human fallopian tube single cell RNA-seq


title: 11519L-P2-C09: human fallopian tube single cell RNA-seq


title: 11519L-P1-G07: human fallopian tube single cell RNA-seq


title: 11519L-P1-G02: human fallopian tube single cell RNA-seq


title: 11519L-P1-G05: human fallopian tube single cell RNA-seq


title: MC scRNA-seq

description: Pooled cells from 3 donors: No identifying information. Pooling was done immediately before processing for RNAseq.

source_name: Monocytes isolated from Peripheral Blood Mononuclear Cells

value: peripheral blood

value: Freshly isolated

value: 1hr adherence to fibronectin coated dish


title: MCEC scRNA-seq

source_name: Monocyter derived endothelial cells

value: Monocyter derived endothelial cells

value: Differentiated 9days, sheared (10dyne/cm2) for 5 days


title: 11519L-P1-G01: human fallopian tube single cell RNA-seq


title: 11519L-P1-F12: human fallopian tube single cell RNA-seq


title: WT HPC + Vector, replicate 1

description:
myc007
sorted Lin– transduced with MSCV-IRES-YFP vector and cultured in methocult medium

source_name: WT HPC + Vector


title: M-M-41

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the human GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

molecule: polyA RNA

source_name: vastus lateralis muscle

extract_protocol:
Skeletal muscle samples were homogenized in a Bead Ruptor Elite bead mill homogenizer cooled by liquid nitrogen to 10°C for 2 x 20 seconds at 4.2 m/s. Muscle homogenates were processed using the Agencourt RNAdvance Tissue Kit on a BioMek FXP Laboratory Automation Workstation
cDNA libraries were constructed from 250 ng of total RNA using the Universal Plus mRNA-Seq kit from NuGEN

value: Skeletal Muscle

value: Male

tag: group


title: 11519L-P1-F08: human fallopian tube single cell RNA-seq


title: 11519L-P1-F09: human fallopian tube single cell RNA-seq


title: Sulfate-1


title: WT HPC + MYCN, replicate 1

description:
myc008
sorted Lin– transduced with MSCV-MYCN-IRES-YFP vector and cultured in methocult medium

value: female

value: 6 - 12 weeks of age


title: M-M-40


title: 11519L-P1-F07: human fallopian tube single cell RNA-seq


title: 11519L-P1-F03: human fallopian tube single cell RNA-seq


title: 11519L-P1-F06: human fallopian tube single cell RNA-seq


title: M-M-39


title: 11519L-P1-E10: human fallopian tube single cell RNA-seq


title: M-M-38

value: Female


title: 11519L-P1-F02: human fallopian tube single cell RNA-seq

value: normal fallopian tube cells


title: WT HPC + Vector, replicate 2

description:
myc011
sorted Lin– transduced with MSCV-IRES-YFP vector and cultured in methocult medium

value: Lin- hematopoietic progenitor cells

value: transduced with MSCV-IRES-YFP vector


title: M-M-37


title: 11519L-P1-F10: human fallopian tube single cell RNA-seq

value: cryopreserved


title: X1027_3D1_T2

data_processing:
FastQ files were trimmed for adapter sequences and quality. Trimmed reads were then mapped to the human hg19 reference genome using STAR (v2.4.2a) and read counts were obtained using subread FeatureCounts (v1.4.5-p1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: High-grade serou ovarian cancer

extract_protocol:
LCM tumors: Tissue sectioning, H&E staining and the assessment by a gynecological oncology pathologist were performed as previously described (Hellner et al., 2016). Tissue biopsies were frozen down with Fisher Healthcare™ Tissue-Plus O.C.T. Compound (NEG-50, Richard-Allan Scientific) and sectioned by 10µm in CryoStar NX50 Cryostat (Thermo Scientific). The tissue sections were stored at -80°C before proceeding with the staining step.  The pre-chemotherapy tumor biopsies were fresh frozen in OCT and sectioned onto polyethylene naphthalate membrane (PEN) glass slides (MembraneSlide 1.0 PEN, Zeiss) at 6µm and immediately stored at -80°C until the laser capture microdissection (LCM). Prior to LCM, the slides were taken out from -80°C, immediately immerged in 70% ethanol for 2 min, in Cresyl Violet (Sigma Aldrich) for 2 min, rinsed in 95% ethanol five times to remove residual cresyl violet and dried at room temperature for 2min. LCM was conducted on the PALM Laser Microdissection System (Zeiss) and the captured cells were collected onto the adhesive caps of PCR tubes (AdhesiveCap 500 opaque, Zeiss), then immediately resuspended in 10µl lysis buffer (RNAqueous™-Micro Total RNA Isolation Kit, Invitrogen). RNA was extracted according to the manufacturer’s instructions and 3µl of eluate before DNase treatment wass kept for Whole Genome Amplification and stored at -20°C. The remaining RNA was DNase treated, assessed with the Agilent TapeStation 2200 (Agilent) and then stored at -80°C.
The SMARTer Stranded Total RNA-Seq kit v2 - Pico Input (Takara)

tag: patient

value: Tumor

tag: pre/post

value: PRE

value: High-grade serou ovarian cancer


title: X1036_1I3_S2

value: Stroma


title: X1027_3D1_T3


title: M-M-35


title: X1039_2C2_T1


title: M-M-33


title: M-M-34


title: X1027_3D1_T1


title: X1015_1F2_T2


title: M-M-32


title: M-M-31


title: X1019_LPPpreT3


title: M-M-30


title: CT23-replicate3

city: Atlanta

first: Gianluca

last: Tosini

state: GA

address: 720 Westview Dr. SW

department: Pharmacology and Toxicology

institute: Morehouse School of Medicine

data_processing:
Illumina RTA2 was used for basecalling
Alignment was done with bowtie2 (v2.1.0) using default setting
Featured count was done with HTSeq-count (PyCharm Community Edition 2016.3.2) using default settings
Filtering: manually removing identified genes that do not have a featured count of 10 in at least two biological replicates
Normalization was done with RUVseq (3.10) as described in Peixoto et al., 2015, Nucleic Acids Res.
Differential expression was done with edgeR (v3.24.1) with B-H false positive adjustment
Genome_build: mm10
Supplementary_files_format_and_content: excel file contain CPM, log2 fold change, and p-value

source_name: retinal pigment epithelium

extract_protocol:
Anterior portion of the whole eye removed, neural retina peeled off, and posterior portion containing retinal pigment epithelium, choroid, and sclera were placed in RNAlater (Qiagen, 76104) for brief sonication. Isolated retinal pigment epithelium cells were placed in TRIzol (Ambion, 15596018) for total RNA isolation.
RNA library was constructed using QuantSeq™ 3’mRNA-Seq Kit (Lexogen, 015.24) per the manufacturer's protocol.

value: retinal pigment epithelium

tag: pooling

value: 2 retinal pigment epithelium samples

value: 8-10 weeks

tag: time point


title: CT23-replicate1


title: CT1-replicate3


title: CT1-replicate1


title: CT23-replicate2


title: X1002_3F7T2


title: CT1-replicate2


title: X1002_3F7ori


title: M-M-29


title: X1022_3A5_T1


title: T_M5_S19: E18.5 trachea RNAseq

city: Boston

first: Randee

last: Young

state: MA

address: 4 Blackfan st

department: Pediatrics

institute: Boston Children's Hospital

data_processing:
Sequences in FASTQ files were aligned to the mouse reference genome using STAR (Dobin et al., 2013).
Reads were counted using featureCounts.
Differential expression analysis was performed using DeSeq2 (Liao et al.,  2014; Love et al., 2014).
Genome_build: GRCm38

source_name: E18.5 trachea RNAseq

extract_protocol:
Control and MyocdCKO E13.5 lungs, E18.5 tracheas, and E18.5 lungs were dissected in PBS and immediately stored in TRIzol Reagent (ThermoFisher Scientific). Tissues were then lysed using a TissueLyser (Qiagen), and total mRNA was extracted using standard TRIzol RNA extraction protocol. mRNA was cleaned using the RNeasy Micro Kit (Qiagen).
cDNA libraries were made for each individual lung or trachea using Illumina TruSeq RNA Library Prep Kit V2 (Illumina) and sequenced on a SR75 run on the HiSeq4000 platform (Illumina).

tag: developmental stage

value: trachea

tag: genotype

value: Tbx4rtTAi/+; tetOcrei/+; MyocdF/F


title: X1039_2C2_T2


title: M-M-28

value: Skeletal Muscle

value: Male


title: T_M6_S20: E18.5 trachea RNAseq


title: X1028_3C4T3


title: X1002_3F8dilC


title: T_M4_S18: E18.5 trachea RNAseq


title: T_M3_S16: E18.5 trachea RNAseq


title: M-M-26


title: M-M-25


title: T_M1_S12: E18.5 trachea RNAseq


title: X1028_3C4T1


title: T_C4_S17: E18.5 trachea RNAseq

value: Tbx4rtTAi/+; tetOcrei/+; MyocdF/+


title: X1038_2A7


title: M-M-23


title: X1015_1F2


title: X1038_2A6


title: T_C3_S15: E18.5 trachea RNAseq


title: M-M-36

value: Female


title: M-M-19


title: T_C1_S11: E18.5 trachea RNAseq


title: M-M-27


title: Abcg2-ko HPC + Vector, replicate 1

description:
myc009
sorted Lin– transduced with MSCV-IRES-YFP vector and cultured in methocult medium

tag: strain

value: female

value: 6 - 12 weeks of age

tag: treatment


title: M-M-18

tag: gender


title: X1006_1B9T3


title: X1006_1B9T2


title: R_M6_S10: E18.5 lung RNAseq

source_name: E18.5 lung RNAseq

value: right lung lobes


title: X1028_3C4T2


title: R_M5_S9: E18.5 lung RNAseq


title: T_M2_S13: E18.5 trachea RNAseq


title: M-M-16

tag: age


title: R_M4_S8: E18.5 lung RNAseq


title: M-M-24


title: M-M-15


title: M-M-22


title: M-M-14


title: T_C2_S14: E18.5 trachea RNAseq


title: M-M-20


title: X1031_3E1T7

tag: cell type


title: X1028_3C4


title: R_M3_S6: E18.5 lung RNAseq


title: X1031_3E1T6


title: R_M1_S2: E18.5 lung RNAseq


title: M-M-11


title: R_M2_S3: E18.5 lung RNAseq


title: X1031_3E1T1


title: X1022_3A5


title: R_C3_S5: E18.5 lung RNAseq


title: R_C4_S7: E18.5 lung RNAseq


title: M-M-08


title: M-M-10


title: M-M-07


title: X1006_1B9T1


title: R_C2_S4: E18.5 lung RNAseq


title: X1008_1C8


title: M-M-06


title: R_C1_S1: E18.5 lung RNAseq


title: X1004_1A8


title: M-M-04


title: M5_S5: E13.5 lung RNAseq

source_name: E13.5 lung RNAseq

value: right and left lung lobes


title: M4_S4: E13.5 lung RNAseq


title: M-M-12


title: M3_S3: E13.5 lung RNAseq


title: X11531_PRET3

value: Tumor


title: X1031_3E1T4

value: PRE


title: M-M-03


title: X11531_PRET1

value: High-grade serou ovarian cancer


title: X11152_G22


title: M-M-01


title: genome DNA sequencing data from T. microellipsoides opaque culture 1

city: Vancouver

first: thomas

last: sierocinski

state: BC

address: 2389 east mall

country: Canada

institute: Renaissance Bioscience

library_source: genomic

data_processing:
de novo assembly using Abyss2.0
RNAseq reads alignement using STAR
transcriptome assembly using cufflink
transcripts annotation using BLAST
differential expression analysis using DESEQ2
Genome_build: assembly
Supplementary_files_format_and_content: bed expression files were created using cufflink, fasta sequence files were obtained using Abyss2.0

molecule: genomic DNA

organism: Torulaspora microellipsoides

source_name: T. microellipsoides opaque cells (log phase)

growth_protocol: Triplicate 25 ml yeast cultures were innoculated at OD600 0.05 and grown to a final OD600 of 1.0 with at room temperature (~23 C) with shaking at 200 r.p.m. Cells were then harvested, and DNA or RNA extracted and processed to generate sequencing libraries.

extract_protocol:
Genomic DNA was purified using a standard phenol-chloroform based extraction. DNA was then treated with RNaseA for 1 hour at 37⁰C, and re-purified with an additional phenol-chroloform extraction. Sequencing libraries were prepared using the Nextera DNA Flex library preparation kit, according to manufacturer’s instructions (Illumina). Total RNA was purified using a standard hot acid-phenol chloroform extraction. RNA was then treated with DNaseI for 1 hour, and re-purified with an additional acid-phenol chloroform extraction.
Sequencing libraries were prepared using the Nextera DNA Flex library preparation kit, according to manufacturer’s instructions (Illumina). Libraries were pooled and loaded onto a NextSeq High Output flow cell, generating paired-end 150 bp reads. RNA was quantified using Qubit fluorometry and 500 ng of each sample used to prepare sequencing libraries were prepared with the TruSeq Stranded mRNA library preparation kit, according to manufacturer’s instructions (Illumina).

tag: growth phase

value: opaque cells (log phase)


title: X1036_1I3T2


title: mRNA sequencing data from T. microellipsoides white culture 2

source_name: T. microellipsoides white cells (log phase)

value: white cells (log phase)


title: genome DNA sequencing data from T. microellipsoides white culture 1


title: X1036_1I3T1


title: C5_S10: E13.5 lung RNAseq


title: M1_S1: E13.5 lung RNAseq


title: X11531_PRET2


title: X1016_1G4


title: C4_S9: E13.5 lung RNAseq


title: mRNA sequencing data from T. microellipsoides white culture 1


title: X1022_3A2


title: mRNA sequencing data from T. microellipsoides opaque culture 3


title: X1G3_new


title: X1016_1G3old


title: C2_S7: E13.5 lung RNAseq


title: mRNA sequencing data from T. microellipsoides opaque culture 1


title: HepG2 cells without esculetin

status: Public on Jan 09 2020

city: Wuhan

first: Songtao

last: Wu

address: Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China

country: China

institute: Hubei University of Chinese Medicine

data_processing:
The expression level of each transcript was calculated by the number of segments per kilobase of exon per million mapped reads (FRKM) method, in order to identify differential expression genes (DEGs) between two different samples.
RSEM (http://deweylab.biostat.wisc.edu/rsem/)(Li and Dewey 2011) was used for quantitative genetic abundances. “The R statistical software package EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html)” (Robinson et al. 2010) was used to assess differences.
Functional enrichment was performed using GO and KEGG compared to the total transcriptome background to determine which DEGs were significantly enriched in GO terms.
“GO functional enrichment and KEGG pathway analysis were performed by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do)”
Genome_build: http://deweylab.biostat.wisc.edu/rsem/
Supplementary_files_format_and_content: tab-delimited text files include FRKM values for each Sample

source_name: HepG2 cells without esculetin

growth_protocol: The HepG2 cells were inoculated into 6-well plates at a concentration of 5 x 105/mL.

extract_protocol:
According to the manufacturer’s instructions (Invitrogen), total RNA was extracted from HepG2 cells with or without TRIzol® Reagent, and genomic DNA was removed with using DNase I (TaKara).
According to the TruSeqTM RNA sample preparation Kit of Illumina, we prepared the RNA-seq transcriptome library by using 5 μg of total RNA. For a short timeperiod of time, we isolated mRNA by oligo(dT) beads and RNA was fragmented through a fragment buffer. The SuperScript double-stranded cDNA synthesis kit was used to synthesize Double-stranded cDNA.
Based on Illumina’s library construction protocol, the synthetic cDNA was then terminal repaired, phosphorylated and added “‘A”’ base. The 200–300 bp cDNA target fragments size on 2% Low Range Ultra Agarose were selected, and 15 PCR cycles were amplified using Phusion DNA polymerase (NEB). Illumina HiSeq X Ten (2 × 150bp read length) was sequenced using the paired-end RNA-seq sequencing library after quantification by TBS380.

treatment_protocol: There are two groups: HepG2 cells without esculetin,  and HepG2 cells containing esculetin

value: tumor stage


title: C1_S6: E13.5 lung RNAseq

value: MyocdF/F


title: Donor Patient 5

city: Baltimore

first: Brandon

last: Peiffer

state: Maryland

address: 720 Rutland ave., Ross 771

department: Surgery

institute: Johns Hopkins

description:
liver homogenate
SAH_Diff_genes.xls

data_processing:
nextseq control 2.2.0.4: illumina control software
Bcl2fastq 2.18.0.12: fastq conversion
RTA 2.4.11: Basecalling
geometric normalization: Cufflinks - Cuffdiff tools
FPKMs and fragment counts are scaled via the median of the geometric means of fragment counts across all libraries, as described in Anders and Huber (Genome Biology, 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Excel file containing relative abundance changes between AH and control (Donor) groups with signficant changes (q<0.05).

source_name: Liver

extract_protocol:
Qiagen RNeasy mini kit
RNA libraries were prepared using TRUseq library prep kit and manufacturers instructions.

tag: Sex

value: F


title: HepG2 cells with esculetin

source_name: HepG2 cells with esculetin


title: M2_S2: E13.5 lung RNAseq

tag: tissue

value: Tbx4rtTAi/+; tetOcrei/+; MyocdF/F


title: Donor Patient 1

description:
liver homogenate
SAH_Diff_genes.xls

value: M


title: Alcoholic Hepatitis Patient 5

description:
liver homogenate
SAH_Diff_genes.xls


title: Alcoholic Hepatitis Patient 4

description:
liver homogenate
SAH_Diff_genes.xls


title: C3_S8: E13.5 lung RNAseq


title: Donor Patient 3

description:
liver homogenate
SAH_Diff_genes.xls


title: Donor Patient 4

description:
liver homogenate
SAH_Diff_genes.xls


title: Alcoholic Hepatitis Patient 1

description:
liver homogenate
SAH_Diff_genes.xls


title: Donor Patient 2

description:
liver homogenate
SAH_Diff_genes.xls


title: Alcoholic Hepatitis Patient 2

description:
liver homogenate
SAH_Diff_genes.xls


title: Alcoholic Hepatitis Patient 3

description:
liver homogenate
SAH_Diff_genes.xls


title: mRNA sequencing data from T. microellipsoides opaque culture 2


title: DCIScom-NS-CTCF

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

data_processing:
FASTQ2: Original unaligned sequence reads produced by the sequencer. Bcl2FastQ converter and barcode splitting version 2.16 were used
Sequencing platform: Illumina NextSeq 500/550, pair-end sequencing (40, 12, 40 cycles)
Peaks are called using the GeneTrack algorithm (PubMed ID: 18388141). Briefly
Significance testing: Briefly, tags are scaled using the NCIS method (PubMed ID: 22883957) and peak significance is calculated comparing the NCIS-scaled sum of tags in a 100 bp window around the peak midpoint of the sample relative to an IgG control. The binomial test is used in conjunction with Benjamini-Hochberg correction at a Q-value of 0.05.
Genome_build: Hg19
Supplementary_files_format_and_content: The (*.gff) output files report the peak-pair left-end (lower coordinate) and the right-end (higher coordinate). The NCIS-normalized tag count associated with the peak-pair is in the score column.

source_name: DCIScom-NS

growth_protocol: Control (NS) and BCL9 KD DCIS.com cells were cultured in 4x 15 cm plates in biological replicates each. Culture media is DMEM/F12 supplemented with 5% horse serum and 1% antibiotic

extract_protocol:
Lysates were clarified from sonicated nuclei and BCL9 and pSTAT3 were pulled down with 2ug antibody uisng ChIP-exo protocol.
Details of the method can be found in a publication by H.S. Rhee and B.F. Pugh in Cell 2011, 147(6):1408-1419 titled “Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution"

treatment_protocol: 50-60 million cells for each replicate was collected for cross linking

tag: cell line

value: breast cancer cell line

value: Non-scrambled control

tag: chip antibody

value: CTCF (Miilipore 7729)

tag: biological replicate

value: Positive control


title: DCIScom-BCL9KD-BCL9-2

source_name: DCIScom-BCL9 KD

value: BCL9-knock down

value: BCL9 (Protein Tech 22947-I-AP)


title: DCIScom-NS-IgG

value: IgG

value: Negative control


title: liver_maternal high fat diet_rep2

type: genomic

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: maternal high fat diet

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

source_name: MeDIP DNA from maternal high fat diet

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from fat samples using Dneasy Blood & Tissue Kit.

value: liver

value: 3 week

tag: condition

value: maternal high fat diet

tag: sample type

value: MeDIP

label: Cy 3

source_name: input DNA from maternal high fat diet

value: input


title: liver_maternal inulin early intervention_rep2

description: maternal inulin early intervention

source_name: MeDIP DNA from maternal inulin early intervention

value: maternal inulin early intervention

source_name: input DNA from maternal inulin early intervention


title: liver_maternal high fat diet_rep3

description: maternal high fat diet


title: liver_maternal high fat diet_rep1

description: maternal high fat diet


title: DCIScom-BCL9KD-BCL9-1


title: liver_maternal inulin early intervention_rep1

description: maternal inulin early intervention


title: DCIScom-NS-BCL9-2


title: DCIScom-NS-BCL9-1


title: WT3prime_Testis rep4

city: Seika-cho, Soraku-gun

first: Thomas

middle: N.

last: Sato

state: Kyoto

address: 2-2-2 Hikaridai

country: Japan

institute: Karydo TherapeutiX, Inc.

data_processing:
Illumina bcl2fastq ver 2.17 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using tophat2 ver 2.1.1 with parameter -p 8
Count data were caclulated using htseq-count ver 0.9.1 with parameters -f bam -r pos -s no
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count for each tissue

source_name: Testis

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent followed by Kozawa et al., 2018. iScience(doi: 10.1016/j.isci.2018.03.014.).
RNA libraries were prepared for sequencing using QuatSeq 3'mRNA-Seq Library Prep Kit for illumina

value: Testis

tag: drug treatment

value: WT(No treated)


title: DCIScom-NS-pS727STAT3-1

value: Phospho S727 STAT3 (Cell signaling 9134S)


title: DCIScom-BCL9KD-pS727STAT3-2

value: breast cancer cell line


title: DCIScom-NS-pS727STAT3-2

value: Non-scrambled control


title: WT3prime_Testis rep2


title: DCIScom-NS-pS727STAT3-3


title: WT3prime_WAT rep4

source_name: WAT

value: WAT


title: ANT_2

city: Seattle

middle: A

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structures

institute: University of Washington

data_processing:
Base calling and sample demultiplexing performed by Cell Ranger (3.0.2) mkfastq.
Sequences were aligned to genome and UMI counts were created using Cell Ranger (3.0.2) count.
Downstream analysis was performed in R.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger filtered output files, containing gene names, cell barcodes, and expression matrices.

source_name: Retinal microglia

extract_protocol:
Cells were dissociated with papain and processed for 10x single-cell RNA-seq analysis according to manufacturer's instructions.
10x libraries were prepared according to manufacturer's instructions.

value: Retinal microglia

value: ANT treated early timepoint


title: WT3prime_Stomach rep4

source_name: Stomach

value: Stomach


title: DCIScom-BCL9KD-pS727STAT3-1

value: BCL9-knock down


title: WT3prime_Stomach rep2


title: ANTsi_2

value: ANT treated with stat inhibitor early timepoint


title: WT3prime_WAT rep2


title: WT3prime_Skin rep4

source_name: Skin

value: Skin


title: DCIScom-NS-BCL9-3

value: BCL9 (Protein Tech 22947-I-AP)


title: WT3prime_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: WT3prime_SkMuscle rep2


title: WT3prime_Skin rep2


title: WT3prime_Eye rep1

source_name: Eye

value: Eye


title: WT3prime_Colon rep4

source_name: Colon

value: Colon


title: WT3prime_Jejunum rep4

source_name: Jejunum

value: Jejunum


title: WT3prime_Jejunum rep2


title: WT3prime_Ileum rep2

source_name: Ileum

value: Ileum


title: WT3prime_Ileum rep4

value: WT(No treated)


title: WT3prime_Eye rep3


title: WT3prime_Colon rep2


title: WT3prime_ThyroidG rep3

source_name: ThyroidG

value: ThyroidG


title: WT3prime_BM rep4

source_name: BM

value: BM


title: WT3prime_Thymus rep2

source_name: Thymus

value: Thymus


title: WT3prime_BM rep2


title: WT3prime_Spleen rep4

source_name: Spleen

value: Spleen


title: WT3prime_Skull rep1

source_name: Skull

value: Skull


title: WT3prime_ParotidG rep4

source_name: ParotidG

value: ParotidG


title: WT3prime_Thymus rep4


title: WT3prime_Skull rep3


title: WT3prime_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: WT3prime_ThyroidG rep1


title: WT3prime_Spleen rep2


title: WT3prime_ParotidG rep2


title: WT3prime_PituitaryG rep1


title: WT3prime_Pancreas rep4

source_name: Pancreas

value: Pancreas


title: M-M-02

source_name: vastus lateralis muscle

value: Skeletal Muscle

value: Male

tag: group


title: WT3prime_Pancreas rep2


title: WT3prime_Lung rep2

source_name: Lung

value: Lung


title: WT3prime_Lung rep4


title: WT3prime_Heart rep2

source_name: Heart

value: Heart


title: WT3prime_Liver rep4

source_name: Liver

value: Liver


title: WT3prime_Kidney rep4

source_name: Kidney

value: Kidney


title: WT3prime_Heart rep4


title: WT3prime_Brain rep4

source_name: Brain

value: Brain


title: WT3prime_Kidney rep2


title: WT3prime_Liver rep2


title: WT3prime_Brain rep2


title: WT3prime_Aorta rep1

source_name: Aorta

value: Aorta


title: WT3prime_AdrenalG rep3

source_name: AdrenalG

value: AdrenalG

value: WT(No treated)


title: WT3prime_Aorta rep3


title: WT3prime_AdrenalG rep1


title: Teriparatide_WAT rep1

source_name: WAT

value: WAT

value: Teriparatide


title: Teriparatide_WAT rep2


title: Teriparatide_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: Teriparatide_ThyroidG rep4


title: Teriparatide_Stomach rep1

source_name: Stomach

value: Stomach


title: Teriparatide_Thymus rep2

source_name: Thymus

value: Thymus


title: Teriparatide_Stomach rep2


title: Teriparatide_Spleen rep1

source_name: Spleen

value: Spleen


title: Teriparatide_Thymus rep1


title: Teriparatide_Skull rep2

source_name: Skull

value: Skull


title: Teriparatide_Spleen rep2


title: Teriparatide_Testis rep2

source_name: Testis

value: Testis


title: Teriparatide_Skin rep2

source_name: Skin

value: Skin


title: Teriparatide_Skull rep1


title: Teriparatide_Skin rep1


title: Teriparatide_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Teriparatide_SkMuscle rep1

source_name: SkMuscle

value: SkMuscle


title: Teriparatide_ParotidG rep1

source_name: ParotidG

value: ParotidG


title: Teriparatide_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Teriparatide_SkMuscle rep2


title: Teriparatide_PituitaryG rep2


title: Teriparatide_Pancreas rep1


title: Teriparatide_Lung rep2

source_name: Lung

value: Lung


title: Teriparatide_Testis rep1


title: Teriparatide_Liver rep1

source_name: Liver

value: Liver


title: Teriparatide_Lung rep1


title: Teriparatide_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: Teriparatide_Ileum rep2

source_name: Ileum

value: Ileum


title: Teriparatide_Ileum rep1


title: Teriparatide_Kidney rep1

source_name: Kidney

value: Kidney


title: Teriparatide_Heart rep2

source_name: Heart

value: Heart

value: Teriparatide


title: Teriparatide_Liver rep2


title: Teriparatide_Heart rep1


title: Teriparatide_Eye rep1

source_name: Eye

value: Eye


title: Teriparatide_Colon rep2

source_name: Colon

value: Colon


title: Teriparatide_Kidney rep2


title: Teriparatide_Eye rep2


title: Teriparatide_Jejunum rep1


title: Teriparatide_Colon rep1


title: Teriparatide_Brain rep1

source_name: Brain

value: Brain


title: Teriparatide_BM rep2

source_name: BM

value: BM


title: Teriparatide_BM rep1


title: Teriparatide_Aorta rep4

source_name: Aorta

value: Aorta


title: Teriparatide_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: Teriparatide_AdrenalG rep1


title: Sofosbuvir_WAT rep2

source_name: WAT

value: WAT

value: Sofosbuvir


title: Teriparatide_Aorta rep1


title: Teriparatide_ParotidG rep2

value: ParotidG


title: Sofosbuvir_WAT rep1


title: Sofosbuvir_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: Sofosbuvir_Thymus rep2

source_name: Thymus

value: Thymus


title: Sofosbuvir_Thymus rep1


title: Sofosbuvir_Testis rep1

source_name: Testis

value: Testis


title: Sofosbuvir_Spleen rep1

source_name: Spleen

value: Spleen


title: Sofosbuvir_Testis rep2


title: Teriparatide_Brain rep2


title: Sofosbuvir_Spleen rep2


title: Sofosbuvir_Skull rep1

source_name: Skull

value: Skull


title: Sofosbuvir_Skull rep2


title: mRNA sequencing data from T. microellipsoides white culture 3

source_name: T. microellipsoides white cells (log phase)

value: white cells (log phase)


title: Sofosbuvir_Skin rep1

source_name: Skin

value: Skin


title: Sofosbuvir_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: Sofosbuvir_Skin rep2


title: liver_maternal inulin early intervention_rep3

description: maternal inulin early intervention

source_name: MeDIP DNA from maternal inulin early intervention

value: maternal inulin early intervention

value: MeDIP

value: liver

value: 3 week

source_name: input DNA from maternal inulin early intervention

value: input


title: Sofosbuvir_SkMuscle rep1


title: Sofosbuvir_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: Sofosbuvir_PituitaryG rep1


title: Sofosbuvir_ParotidG rep1

source_name: ParotidG


title: Sofosbuvir_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Sofosbuvir_ParotidG rep2

value: Sofosbuvir


title: Sofosbuvir_Lung rep1

source_name: Lung

value: Lung


title: Sofosbuvir_Lung rep2


title: Sofosbuvir_Liver rep1

source_name: Liver

value: Liver


title: Sofosbuvir_Liver rep2


title: Sofosbuvir_Pancreas rep1


title: Sofosbuvir_Stomach rep2

source_name: Stomach

value: Stomach


title: Sofosbuvir_Stomach rep1


title: Sofosbuvir_Kidney rep2

source_name: Kidney

value: Kidney


title: Sofosbuvir_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Sofosbuvir_Ileum rep1

source_name: Ileum

value: Ileum


title: Sofosbuvir_Kidney rep1


title: Sofosbuvir_Heart rep1

source_name: Heart

value: Heart


title: Sofosbuvir_Jejunum rep2


title: Sofosbuvir_Ileum rep2


title: Sofosbuvir_Eye rep2

source_name: Eye

value: Eye


title: Sofosbuvir_Heart rep2


title: Sofosbuvir_BM rep2

source_name: BM

value: BM


title: Sofosbuvir_Colon rep1

source_name: Colon

value: Colon


title: Sofosbuvir_Eye rep1


title: Sofosbuvir_Brain rep1

source_name: Brain

value: Brain


title: Sofosbuvir_Brain rep2


title: Sofosbuvir_Colon rep2


title: Sofosbuvir_BM rep1


title: Risedronate_WAT rep2

source_name: WAT

value: WAT

value: Risedronate


title: Sofosbuvir_Aorta rep2

source_name: Aorta

value: Aorta


title: Sofosbuvir_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: Sofosbuvir_Aorta rep1


title: Risedronate_WAT rep1


title: Sofosbuvir_AdrenalG rep1


title: Risedronate_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: Risedronate_Thymus rep2

source_name: Thymus

value: Thymus


title: Sofosbuvir_Jejunum rep4

value: Sofosbuvir


title: Sofosbuvir_ThyroidG rep2


title: Risedronate_Thymus rep1


title: Risedronate_ThyroidG rep2


title: Risedronate_Testis rep2

source_name: Testis

value: Testis


title: Sofosbuvir_Jejunum rep1


title: Risedronate_Spleen rep2

source_name: Spleen

value: Spleen


title: Risedronate_Stomach rep1

value: Stomach


title: Risedronate_Spleen rep1


title: Risedronate_Testis rep1


title: Risedronate_Skull rep1

source_name: Skull

value: Skull


title: Risedronate_Skull rep2


title: Risedronate_Skin rep2

source_name: Skin

value: Skin


title: Risedronate_Skin rep1


title: Risedronate_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Risedronate_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: Risedronate_ParotidG rep1


title: Risedronate_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: Risedronate_PituitaryG rep1


title: Risedronate_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: Risedronate_Pancreas rep1


title: Risedronate_Liver rep1

source_name: Liver

value: Liver


title: Risedronate_Kidney rep2

source_name: Kidney

value: Kidney


title: Risedronate_SkMuscle rep1

value: Risedronate


title: Risedronate_Liver rep2


title: Risedronate_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: Risedronate_Ileum rep1

source_name: Ileum

value: Ileum


title: Risedronate_Stomach rep2

source_name: Stomach


title: Risedronate_Lung rep2

source_name: Lung

value: Lung


title: Risedronate_Jejunum rep1


title: Risedronate_Eye rep2

source_name: Eye

value: Eye


title: Risedronate_Lung rep1


title: Risedronate_Heart rep1

source_name: Heart

value: Heart


title: Risedronate_Heart rep2


title: Risedronate_Kidney rep1


title: Risedronate_Ileum rep2


title: Risedronate_Eye rep1


title: Risedronate_Colon rep1

source_name: Colon

value: Colon


title: Risedronate_Colon rep2


title: Risedronate_BM rep2

source_name: BM

value: BM


title: Risedronate_Brain rep1

source_name: Brain

value: Brain


title: Risedronate_Aorta rep2

source_name: Aorta

value: Aorta


title: Risedronate_Aorta rep1


title: Risedronate_AdrenalG rep1

source_name: AdrenalG

value: AdrenalG


title: Repatha_WAT rep1

source_name: WAT

value: WAT

value: Repatha


title: Repatha_WAT rep3


title: Repatha_Thymus rep3

source_name: Thymus

value: Thymus


title: Repatha_ThyroidG rep4

source_name: ThyroidG

value: ThyroidG


title: Repatha_Thymus rep1


title: Repatha_Stomach rep3

value: Stomach


title: Repatha_Testis rep1

source_name: Testis

value: Testis


title: Risedronate_Brain rep2

value: Risedronate


title: Repatha_Spleen rep1

source_name: Spleen

value: Spleen


title: Repatha_Skull rep3

source_name: Skull

value: Skull


title: Repatha_Spleen rep3


title: Repatha_Stomach rep1


title: Repatha_SkMuscle rep3

source_name: SkMuscle

value: SkMuscle


title: Repatha_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Repatha_Skull rep1


title: Repatha_Skin rep1

source_name: Skin

value: Skin


title: Repatha_Skin rep3


title: Repatha_ParotidG rep1

source_name: ParotidG

value: ParotidG


title: Repatha_ParotidG rep3


title: Repatha_PituitaryG rep2


title: Risedronate_BM rep1

value: BM


title: Repatha_Pancreas rep3

source_name: Pancreas

value: Pancreas


title: Risedronate_AdrenalG rep2


title: Repatha_Lung rep3

source_name: Lung

value: Lung


title: Repatha_ThyroidG rep2


title: Repatha_Lung rep1


title: Repatha_Testis rep3


title: Repatha_Kidney rep3

source_name: Kidney

value: Kidney


title: Repatha_Liver rep1

source_name: Liver

value: Liver


title: Repatha_Jejunum rep1

source_name: Jejunum

value: Jejunum

value: Repatha


title: Repatha_SkMuscle rep1


title: Repatha_Eye rep3

source_name: Eye

value: Eye


title: Repatha_Heart rep1

source_name: Heart

value: Heart


title: Repatha_Colon rep3

source_name: Colon

value: Colon


title: Repatha_Colon rep1


title: Repatha_Heart rep3


title: Repatha_BM rep3

source_name: BM


title: Repatha_Eye rep1


title: Repatha_Brain rep1

source_name: Brain

value: Brain


title: Repatha_Brain rep3


title: Repatha_BM rep1


title: Repatha_Pancreas rep1


title: Repatha_AdrenalG rep1

source_name: AdrenalG

value: AdrenalG


title: Repatha_Aorta rep2

source_name: Aorta

value: Aorta


title: Repatha_AdrenalG rep3


title: Repatha_Aorta rep3


title: Olanzapine_WAT rep2

source_name: WAT

value: WAT

value: Olanzapine


title: Olanzapine_ThyroidG rep2

source_name: ThyroidG

value: ThyroidG


title: Olanzapine_WAT rep1


title: Repatha_Liver rep3


title: Olanzapine_ThyroidG rep1


title: Repatha_Jejunum rep3


title: Olanzapine_Thymus rep2

source_name: Thymus

value: Thymus


title: Olanzapine_Thymus rep1


title: Repatha_Kidney rep1


title: Olanzapine_Testis rep2

source_name: Testis

value: Testis


title: Olanzapine_Testis rep1


title: Repatha_Ileum rep1

source_name: Ileum

value: Ileum


title: Repatha_Ileum rep3


title: Olanzapine_Stomach rep1

source_name: Stomach

value: Stomach


title: Olanzapine_Skull rep2

source_name: Skull

value: Skull


title: Olanzapine_Spleen rep1

source_name: Spleen

value: Spleen


title: Olanzapine_Skin rep2

source_name: Skin

value: Skin


title: Olanzapine_Skin rep1


title: Olanzapine_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: Olanzapine_Pancreas rep1

source_name: Pancreas

value: Pancreas


title: Olanzapine_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: Olanzapine_ParotidG rep1


title: Olanzapine_Skull rep1


title: Olanzapine_PituitaryG rep1

source_name: PituitaryG

value: PituitaryG


title: Olanzapine_PituitaryG rep2


title: Olanzapine_Lung rep2

source_name: Lung

value: Lung


title: Olanzapine_Liver rep1

source_name: Liver

value: Liver


title: Olanzapine_Lung rep1


title: Olanzapine_Ileum rep2


title: Olanzapine_Kidney rep1

source_name: Kidney

value: Kidney


title: Olanzapine_Jejunum rep1

source_name: Jejunum

value: Jejunum


title: Olanzapine_Ileum rep1

value: Olanzapine


title: Olanzapine_Spleen rep2


title: Olanzapine_Stomach rep2


title: Olanzapine_Jejunum rep2


title: Olanzapine_Eye rep1

source_name: Eye

value: Eye


title: Olanzapine_Eye rep2


title: Olanzapine_Heart rep2

source_name: Heart

value: Heart


title: Olanzapine_Kidney rep2


title: Olanzapine_Colon rep1

source_name: Colon

value: Colon


title: Olanzapine_Brain rep2

source_name: Brain

value: Brain


title: Olanzapine_Brain rep1


title: Olanzapine_BM rep2

source_name: BM

value: BM


title: Olanzapine_Colon rep2


title: Olanzapine_BM rep1


title: Olanzapine_SkMuscle rep1


title: Olanzapine_Pancreas rep2


title: Olanzapine_Aorta rep1

source_name: Aorta

value: Aorta


title: Olanzapine_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: Olanzapine_Aorta rep2


title: Lurasidone_WAT rep1

source_name: WAT

value: WAT

value: Lurasidone


title: Lurasidone_ThyroidG rep2

source_name: ThyroidG

value: ThyroidG


title: Olanzapine_Liver rep2


title: Lurasidone_ThyroidG rep1


title: Lurasidone_Testis rep2

source_name: Testis

value: Testis


title: Lurasidone_Thymus rep1

source_name: Thymus

value: Thymus


title: Olanzapine_Heart rep1


title: Lurasidone_Stomach rep1

source_name: Stomach

value: Stomach


title: Lurasidone_Spleen rep2

source_name: Spleen

value: Spleen


title: Lurasidone_Stomach rep2


title: Lurasidone_Spleen rep1


title: Lurasidone_Skull rep2

source_name: Skull

value: Skull


title: Lurasidone_Skull rep1


title: Lurasidone_Skin rep2

source_name: Skin

value: Skin


title: Lurasidone_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: Lurasidone_Skin rep1


title: Lurasidone_PituitaryG rep1

source_name: PituitaryG

value: PituitaryG


title: Lurasidone_PituitaryG rep2


title: Olanzapine_AdrenalG rep1

value: Olanzapine


title: Lurasidone_WAT rep2


title: Lurasidone_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: Lurasidone_Lung rep1

source_name: Lung

value: Lung


title: Lurasidone_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Lurasidone_Liver rep2

source_name: Liver

value: Liver


title: Lurasidone_Thymus rep2


title: Lurasidone_Lung rep2


title: Lurasidone_ParotidG rep1


title: Lurasidone_Kidney rep2

source_name: Kidney

value: Kidney


title: Lurasidone_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: Lurasidone_Kidney rep1

value: Lurasidone


title: Lurasidone_Testis rep1


title: Lurasidone_Ileum rep1

source_name: Ileum

value: Ileum


title: Lurasidone_Ileum rep2


title: Lurasidone_Jejunum rep1


title: Lurasidone_Liver rep1


title: Lurasidone_Heart rep2

source_name: Heart

value: Heart


title: Lurasidone_Eye rep2

source_name: Eye

value: Eye


title: Lurasidone_Heart rep1


title: Lurasidone_SkMuscle rep1


title: Lurasidone_Colon rep1

source_name: Colon

value: Colon


title: Lurasidone_Colon rep2


title: Lurasidone_Brain rep1

source_name: Brain

value: Brain


title: Lurasidone_BM rep2

source_name: BM

value: BM


title: Lurasidone_Eye rep1


title: Lurasidone_Aorta rep2

source_name: Aorta

value: Aorta


title: Lurasidone_BM rep1


title: Lurasidone_Pancreas rep1


title: Lurasidone_AdrenalG rep1

source_name: AdrenalG

value: AdrenalG


title: Lenalidomide_WAT rep4

source_name: WAT

value: WAT

value: Lenalidomide


title: Lenalidomide_WAT rep3


title: Lurasidone_AdrenalG rep2


title: Lenalidomide_ThyroidG rep4

source_name: ThyroidG

value: ThyroidG


title: Lenalidomide_ThyroidG rep3


title: Lenalidomide_Testis rep4

source_name: Testis

value: Testis


title: Lenalidomide_Thymus rep4

source_name: Thymus

value: Thymus


title: Lenalidomide_Stomach rep3

source_name: Stomach

value: Stomach


title: Lurasidone_Aorta rep1


title: Lenalidomide_Thymus rep3


title: Lenalidomide_Spleen rep4

source_name: Spleen

value: Spleen


title: Lenalidomide_Testis rep3


title: Lenalidomide_Spleen rep3


title: Lenalidomide_Stomach rep4


title: Lenalidomide_Skull rep3

source_name: Skull

value: Skull


title: Lenalidomide_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: Lenalidomide_Skull rep4


title: Lurasidone_Brain rep2

value: Lurasidone


title: Lenalidomide_SkMuscle rep3


title: Lenalidomide_PituitaryG rep4

source_name: PituitaryG

value: PituitaryG


title: Lenalidomide_Skin rep4

source_name: Skin

value: Skin


title: Lenalidomide_ParotidG rep3

source_name: ParotidG

value: ParotidG


title: Lenalidomide_PituitaryG rep3


title: Lenalidomide_Skin rep3


title: Lenalidomide_Pancreas rep4

source_name: Pancreas

value: Pancreas


title: Lenalidomide_ParotidG rep4


title: Lenalidomide_Pancreas rep3


title: Lenalidomide_Lung rep4

source_name: Lung

value: Lung


title: Lenalidomide_Lung rep3


title: Lenalidomide_Liver rep4

source_name: Liver

value: Liver


title: Lenalidomide_Liver rep3


title: Lenalidomide_Kidney rep3

source_name: Kidney

value: Kidney


title: Lenalidomide_Kidney rep4


title: Lenalidomide_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Lenalidomide_Ileum rep4

source_name: Ileum

value: Ileum

value: Lenalidomide


title: Lenalidomide_Ileum rep3


title: Lenalidomide_Eye rep3

source_name: Eye

value: Eye


title: Lenalidomide_Heart rep3

source_name: Heart

value: Heart


title: Lenalidomide_Heart rep4


title: Lenalidomide_Eye rep4


title: Lenalidomide_Colon rep4

source_name: Colon

value: Colon


title: Lenalidomide_Brain rep4

source_name: Brain

value: Brain


title: Lenalidomide_Brain rep3


title: Lenalidomide_BM rep4

source_name: BM

value: BM


title: Lenalidomide_Colon rep3


title: Lenalidomide_BM rep3


title: Lenalidomide_Aorta rep3

source_name: Aorta

value: Aorta


title: Lenalidomide_AdrenalG rep4

source_name: AdrenalG

value: AdrenalG


title: Lenalidomide_Aorta rep4


title: Lenalidomide_AdrenalG rep3


title: FivePercentSucrose_WAT rep1

source_name: WAT

value: WAT

value: FivePercentSucrose


title: FivePercentSucrose_WAT rep2


title: FivePercentSucrose_Thymus rep2

source_name: Thymus

value: Thymus


title: FivePercentSucrose_Thymus rep1


title: FivePercentSucrose_ThyroidG rep2

source_name: ThyroidG

value: ThyroidG


title: FivePercentSucrose_Testis rep1

source_name: Testis

value: Testis


title: FivePercentSucrose_Stomach rep2

source_name: Stomach

value: Stomach


title: FivePercentSucrose_Testis rep2


title: FivePercentSucrose_ThyroidG rep1


title: Lenalidomide_Jejunum rep4


title: FivePercentSucrose_Skull rep2

source_name: Skull

value: Skull


title: FivePercentSucrose_Spleen rep2

source_name: Spleen

value: Spleen


title: FivePercentSucrose_Stomach rep1


title: FivePercentSucrose_Skin rep1

source_name: Skin

value: Skin


title: FivePercentSucrose_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: FivePercentSucrose_Skin rep2


title: FivePercentSucrose_Spleen rep1


title: FivePercentSucrose_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: FivePercentSucrose_SkMuscle rep1


title: FivePercentSucrose_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: FivePercentSucrose_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: FivePercentSucrose_PituitaryG rep1


title: FivePercentSucrose_ParotidG rep1


title: FivePercentSucrose_Pancreas rep1


title: FivePercentSucrose_Liver rep2

source_name: Liver

value: Liver


title: FivePercentSucrose_Lung rep2

source_name: Lung

value: Lung


title: FivePercentSucrose_Lung rep1


title: FivePercentSucrose_Liver rep1


title: FivePercentSucrose_Kidney rep2

source_name: Kidney

value: Kidney


title: FivePercentSucrose_Kidney rep1


title: FivePercentSucrose_Ileum rep2

source_name: Ileum

value: Ileum


title: FivePercentSucrose_Ileum rep1


title: FivePercentSucrose_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: FivePercentSucrose_Heart rep2

source_name: Heart

value: Heart

value: FivePercentSucrose


title: FivePercentSucrose_Heart rep1


title: FivePercentSucrose_Eye rep1

source_name: Eye

value: Eye


title: FivePercentSucrose_Skull rep1


title: FivePercentSucrose_Colon rep2

source_name: Colon

value: Colon


title: FivePercentSucrose_Colon rep1


title: FivePercentSucrose_Brain rep2

source_name: Brain

value: Brain


title: FivePercentSucrose_Brain rep1


title: FivePercentSucrose_BM rep1

source_name: BM

value: BM


title: FivePercentSucrose_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: FivePercentSucrose_Aorta rep2

source_name: Aorta

value: Aorta


title: FivePercentSucrose_Aorta rep1


title: FivePercentSucrose_BM rep2


title: FivePercentSucrose_AdrenalG rep1


title: EMPAOral2wks_ThyroidG rep2

source_name: ThyroidG

value: ThyroidG

value: EMPA


title: EMPAOral2wks_WAT rep1

source_name: WAT

value: WAT


title: EMPAOral2wks_ThyroidG rep1


title: EMPAOral2wks_WAT rep2


title: EMPAOral2wks_Stomach rep2

source_name: Stomach

value: Stomach


title: FivePercentSucrose_Jejunum rep1


title: FivePercentSucrose_Eye rep2


title: EMPAOral2wks_Spleen rep2

source_name: Spleen

value: Spleen


title: EMPAOral2wks_Thymus rep1

source_name: Thymus

value: Thymus


title: EMPAOral2wks_Testis rep2

source_name: Testis

value: Testis


title: EMPAOral2wks_Stomach rep1


title: EMPAOral2wks_Thymus rep2


title: EMPAOral2wks_Spleen rep1


title: EMPAOral2wks_Skull rep4

source_name: Skull

value: Skull


title: EMPAOral2wks_Skin rep1

source_name: Skin

value: Skin


title: EMPAOral2wks_Testis rep1


title: EMPAOral2wks_Skin rep2


title: EMPAOral2wks_Skull rep3


title: EMPAOral2wks_SkMuscle rep1

source_name: SkMuscle

value: SkMuscle


title: EMPAOral2wks_SkMuscle rep2


title: EMPAOral2wks_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: EMPAOral2wks_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: EMPAOral2wks_Lung rep1

source_name: Lung

value: Lung


title: EMPAOral2wks_Lung rep2


title: EMPAOral2wks_Liver rep2

source_name: Liver

value: Liver


title: EMPAOral2wks_ParotidG rep1


title: EMPAOral2wks_Pancreas rep1

source_name: Pancreas

value: Pancreas


title: EMPAOral2wks_Pancreas rep2


title: EMPAOral2wks_PituitaryG rep1


title: EMPAOral2wks_Liver rep1


title: EMPAOral2wks_Kidney rep2

source_name: Kidney

value: Kidney


title: EMPAOral2wks_Kidney rep1


title: EMPAOral2wks_Ileum rep1

source_name: Ileum

value: Ileum


title: EMPAOral2wks_Jejunum rep1

source_name: Jejunum

value: Jejunum


title: EMPAOral2wks_Ileum rep2

value: EMPA


title: EMPAOral2wks_Heart rep2

source_name: Heart

value: Heart


title: EMPAOral2wks_Eye rep2

source_name: Eye

value: Eye


title: EMPAOral2wks_Brain rep2

source_name: Brain

value: Brain


title: EMPAOral2wks_Brain rep1


title: EMPAOral2wks_Aorta rep4

source_name: Aorta

value: Aorta


title: EMPAOral2wks_Colon rep1

source_name: Colon

value: Colon


title: EMPAOral2wks_Heart rep1


title: EMPAOral2wks_BM rep2

source_name: BM

value: BM


title: EMPAOral2wks_BM rep1


title: EMPAOral2wks_Eye rep1


title: EMPAOral2wks_Aorta rep3


title: EMPAOral2wks_AdrenalG rep1

source_name: AdrenalG

value: AdrenalG


title: EMPAOral2wks_AdrenalG rep2


title: Dox2mgmL_WAT rep4

source_name: WAT

value: WAT

value: Dox


title: Dox2mgmL_WAT rep3


title: Dox2mgmL_Thymus rep3

source_name: Thymus

value: Thymus


title: EMPAOral2wks_Jejunum rep2


title: Dox2mgmL_Thymus rep4


title: Dox2mgmL_Testis rep4

source_name: Testis

value: Testis


title: Dox2mgmL_Testis rep3


title: Dox2mgmL_Stomach rep3

source_name: Stomach

value: Stomach


title: Dox2mgmL_Spleen rep4

source_name: Spleen

value: Spleen


title: Dox2mgmL_Spleen rep3


title: Dox2mgmL_Stomach rep4


title: Dox2mgmL_Skull rep4

source_name: Skull

value: Skull


title: EMPAOral2wks_Colon rep2


title: Dox2mgmL_Skull rep3


title: Dox2mgmL_Skin rep3

source_name: Skin

value: Skin


title: Dox2mgmL_Skin rep4


title: Dox2mgmL_Pancreas rep3

source_name: Pancreas

value: Pancreas


title: Dox2mgmL_ParotidG rep4

source_name: ParotidG

value: ParotidG


title: Dox2mgmL_ParotidG rep3


title: Dox2mgmL_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: Dox2mgmL_Pancreas rep4


title: Dox2mgmL_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Dox2mgmL_PituitaryG rep4


title: Dox2mgmL_Lung rep3

source_name: Lung

value: Lung


title: Dox2mgmL_ThyroidG rep3

source_name: ThyroidG

value: ThyroidG


title: Dox2mgmL_Lung rep4


title: Dox2mgmL_Liver rep4

source_name: Liver

value: Liver


title: Dox2mgmL_Kidney rep4

source_name: Kidney

value: Kidney


title: Dox2mgmL_Liver rep3


title: Dox2mgmL_Kidney rep3


title: Dox2mgmL_ThyroidG rep4


title: Dox2mgmL_Ileum rep4

source_name: Ileum

value: Ileum


title: Dox2mgmL_Heart rep3

source_name: Heart

value: Heart


title: Dox2mgmL_Ileum rep3

value: Dox


title: Dox2mgmL_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Dox2mgmL_Heart rep4


title: Dox2mgmL_SkMuscle rep3


title: Dox2mgmL_Colon rep4

source_name: Colon

value: Colon


title: Dox2mgmL_Brain rep4

source_name: Brain

value: Brain


title: Dox2mgmL_Eye rep3

source_name: Eye

value: Eye


title: Dox2mgmL_BM rep4

source_name: BM

value: BM


title: Dox2mgmL_Brain rep3


title: Dox2mgmL_BM rep3


title: Dox2mgmL_Colon rep3


title: Dox2mgmL_Aorta rep4

source_name: Aorta

value: Aorta


title: Clozapine_ThyroidG rep4

value: Clozapine


title: Dox2mgmL_AdrenalG rep4

source_name: AdrenalG

value: AdrenalG


title: Clozapine_Thymus rep4

source_name: Thymus

value: Thymus


title: Dox2mgmL_AdrenalG rep3


title: Clozapine_ThyroidG rep3


title: Clozapine_Testis rep4

source_name: Testis

value: Testis


title: Clozapine_Testis rep3


title: Clozapine_Stomach rep3

source_name: Stomach

value: Stomach


title: Clozapine_WAT rep3

source_name: WAT

value: WAT


title: Dox2mgmL_Jejunum rep4


title: Clozapine_Stomach rep4


title: Dox2mgmL_Eye rep4


title: Clozapine_Spleen rep3

source_name: Spleen

value: Spleen


title: Clozapine_Skull rep4

source_name: Skull

value: Skull


title: Clozapine_Spleen rep4


title: Clozapine_Skin rep4

source_name: Skin

value: Skin


title: Clozapine_Skin rep3


title: Clozapine_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: Clozapine_SkMuscle rep3


title: Clozapine_PituitaryG rep4

source_name: PituitaryG

value: PituitaryG


title: Clozapine_ParotidG rep4

source_name: ParotidG

value: ParotidG


title: Clozapine_ParotidG rep3


title: Dox2mgmL_Aorta rep3

value: Dox


title: Clozapine_Pancreas rep4

source_name: Pancreas

value: Pancreas


title: Clozapine_Thymus rep3


title: Clozapine_Lung rep4

source_name: Lung

value: Lung


title: Clozapine_WAT rep4


title: Clozapine_Liver rep3

source_name: Liver

value: Liver


title: Clozapine_PituitaryG rep3


title: Clozapine_Pancreas rep3


title: Clozapine_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Clozapine_Ileum rep4

source_name: Ileum

value: Ileum

value: Clozapine


title: Clozapine_Ileum rep3


title: Clozapine_Heart rep3

source_name: Heart

value: Heart


title: Clozapine_Skull rep3


title: Clozapine_Heart rep4


title: Clozapine_Eye rep4

source_name: Eye

value: Eye


title: Clozapine_Colon rep3

source_name: Colon

value: Colon


title: Clozapine_Brain rep4

source_name: Brain

value: Brain


title: Clozapine_Brain rep3


title: Clozapine_Eye rep3


title: Clozapine_Colon rep4


title: Clozapine_BM rep3

source_name: BM

value: BM


title: Clozapine_BM rep4


title: Clozapine_Aorta rep4

source_name: Aorta

value: Aorta


title: Clozapine_AdrenalG rep4

source_name: AdrenalG

value: AdrenalG


title: Clozapine_Liver rep4


title: Clozapine_Aorta rep3


title: Clozapine_Lung rep3


title: Clozapine_AdrenalG rep3


title: Clozapine_Kidney rep4

source_name: Kidney

value: Kidney


title: Clozapine_Kidney rep3


title: Cisplatin_WAT rep3

source_name: WAT

value: WAT

value: Cisplatin


title: Clozapine_Jejunum rep4


title: Cisplatin_WAT rep1


title: Cisplatin_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: Cisplatin_ThyroidG rep3


title: Cisplatin_Thymus rep3

source_name: Thymus

value: Thymus


title: Cisplatin_Testis rep3

source_name: Testis

value: Testis


title: Cisplatin_Stomach rep3

source_name: Stomach

value: Stomach


title: Cisplatin_Stomach rep1


title: Cisplatin_Testis rep1


title: Cisplatin_Spleen rep1

source_name: Spleen

value: Spleen


title: Cisplatin_Skull rep3

source_name: Skull

value: Skull


title: Cisplatin_Skull rep2


title: Cisplatin_Skin rep1

source_name: Skin

value: Skin


title: Cisplatin_Skin rep3


title: Cisplatin_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Cisplatin_Spleen rep3


title: Cisplatin_SkMuscle rep3

source_name: SkMuscle

value: SkMuscle


title: Cisplatin_ParotidG rep3

source_name: ParotidG

value: ParotidG


title: Cisplatin_PituitaryG rep2


title: Cisplatin_ParotidG rep1


title: Cisplatin_Lung rep3

source_name: Lung

value: Lung


title: Cisplatin_Pancreas rep1

source_name: Pancreas

value: Pancreas


title: Cisplatin_Lung rep1


title: Cisplatin_Liver rep3

source_name: Liver

value: Liver


title: Cisplatin_Liver rep1


title: Cisplatin_Kidney rep1


title: Cisplatin_Kidney rep3


title: Cisplatin_Thymus rep2


title: Cisplatin_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Cisplatin_Ileum rep3

source_name: Ileum

value: Ileum


title: Cisplatin_Eye rep3

source_name: Eye

value: Eye


title: Cisplatin_Ileum rep1

value: Cisplatin


title: Cisplatin_Jejunum rep1


title: Cisplatin_Heart rep1

source_name: Heart

value: Heart


title: Cisplatin_Eye rep1


title: Cisplatin_Heart rep3


title: Cisplatin_Brain rep3

source_name: Brain

value: Brain


title: Cisplatin_Colon rep1

source_name: Colon

value: Colon


title: Cisplatin_Brain rep1


title: Cisplatin_SkMuscle rep1


title: Cisplatin_BM rep1

source_name: BM

value: BM


title: Cisplatin_BM rep3


title: Cisplatin_Aorta rep1

source_name: Aorta

value: Aorta


title: Cisplatin_Pancreas rep3


title: Cisplatin_AdrenalG rep1

source_name: AdrenalG

value: AdrenalG


title: Asenapine_WAT rep3

source_name: WAT

value: WAT

value: Asenapine


title: Asenapine_Thymus rep4

source_name: Thymus

value: Thymus


title: Asenapine_ThyroidG rep4

source_name: ThyroidG

value: ThyroidG


title: Asenapine_ThyroidG rep3


title: Asenapine_Thymus rep3


title: Asenapine_Testis rep4

source_name: Testis

value: Testis


title: Cisplatin_Colon rep3


title: Asenapine_Testis rep3


title: Asenapine_Stomach rep3

source_name: Stomach

value: Stomach


title: Asenapine_Stomach rep4


title: Asenapine_Skull rep4

source_name: Skull

value: Skull


title: Asenapine_Spleen rep4

source_name: Spleen

value: Spleen


title: Asenapine_Skin rep4

source_name: Skin

value: Skin


title: Asenapine_Spleen rep3


title: Asenapine_Skin rep3


title: Asenapine_SkMuscle rep3

source_name: SkMuscle

value: SkMuscle


title: Cisplatin_Aorta rep3

value: Cisplatin


title: Asenapine_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Asenapine_WAT rep4


title: Asenapine_PituitaryG rep1


title: Asenapine_ParotidG rep3

source_name: ParotidG

value: ParotidG


title: Asenapine_ParotidG rep4


title: Cisplatin_AdrenalG rep3


title: Asenapine_Pancreas rep4

source_name: Pancreas

value: Pancreas


title: Asenapine_Pancreas rep3


title: Asenapine_Lung rep3

source_name: Lung

value: Lung


title: Asenapine_Lung rep4


title: Asenapine_Liver rep3

source_name: Liver

value: Liver


title: Asenapine_Kidney rep3

source_name: Kidney

value: Kidney


title: Asenapine_Kidney rep4


title: Asenapine_Jejunum rep4

source_name: Jejunum

value: Jejunum


title: Asenapine_Ileum rep4

source_name: Ileum

value: Ileum

value: Asenapine


title: Asenapine_Liver rep4


title: Asenapine_Skull rep3


title: Asenapine_SkMuscle rep4


title: Asenapine_Jejunum rep3


title: Asenapine_Eye rep4

source_name: Eye

value: Eye


title: Asenapine_Ileum rep3


title: Asenapine_Colon rep4

source_name: Colon

value: Colon


title: Asenapine_Brain rep4

source_name: Brain

value: Brain


title: Asenapine_Heart rep3

source_name: Heart

value: Heart


title: Asenapine_Eye rep3


title: Asenapine_Brain rep3


title: Asenapine_Colon rep3


title: Asenapine_Aorta rep4

source_name: Aorta

value: Aorta


title: Asenapine_Brain rep1


title: Asenapine_Brain rep2


title: Asenapine_BM rep4

source_name: BM

value: BM


title: Aripiprazole_WAT rep4

source_name: WAT

value: WAT

value: Aripiprazole


title: Asenapine_AdrenalG rep3

source_name: AdrenalG

value: AdrenalG


title: Asenapine_BM rep3


title: Asenapine_Aorta rep3


title: Aripiprazole_ThyroidG rep4

source_name: ThyroidG

value: ThyroidG


title: Aripiprazole_ThyroidG rep2


title: Asenapine_AdrenalG rep4


title: Aripiprazole_WAT rep2


title: Aripiprazole_Thymus rep4

source_name: Thymus

value: Thymus


title: Aripiprazole_Stomach rep4

source_name: Stomach

value: Stomach


title: Aripiprazole_Testis rep4

source_name: Testis

value: Testis


title: Asenapine_Heart rep4


title: Aripiprazole_Stomach rep2


title: Aripiprazole_Thymus rep2


title: Aripiprazole_Testis rep2


title: Aripiprazole_Spleen rep4

source_name: Spleen

value: Spleen


title: Aripiprazole_Spleen rep2


title: Aripiprazole_Skull rep2

source_name: Skull

value: Skull


title: Aripiprazole_Skin rep4

source_name: Skin

value: Skin


title: Aripiprazole_Skin rep2


title: Aripiprazole_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: Aripiprazole_SkMuscle rep2


title: Aripiprazole_Skull rep4


title: Aripiprazole_ParotidG rep4

source_name: ParotidG

value: ParotidG


title: Aripiprazole_PituitaryG rep3

source_name: PituitaryG

value: PituitaryG


title: Aripiprazole_ParotidG rep2


title: Aripiprazole_Lung rep4

source_name: Lung

value: Lung


title: Aripiprazole_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Aripiprazole_Pancreas rep4


title: Aripiprazole_Lung rep2


title: Aripiprazole_Liver rep4

source_name: Liver

value: Liver


title: Aripiprazole_Liver rep2


title: Aripiprazole_Kidney rep4

source_name: Kidney

value: Kidney


title: Aripiprazole_Kidney rep2


title: Aripiprazole_Ileum rep4

source_name: Ileum

value: Ileum


title: Aripiprazole_Jejunum rep2

source_name: Jejunum

value: Jejunum

value: Aripiprazole


title: Aripiprazole_Heart rep2

source_name: Heart

value: Heart


title: Aripiprazole_Heart rep4


title: Aripiprazole_Ileum rep2


title: Aripiprazole_Colon rep4

source_name: Colon

value: Colon


title: Aripiprazole_Colon rep2


title: Aripiprazole_Eye rep2

source_name: Eye

value: Eye


title: Aripiprazole_Eye rep4


title: Aripiprazole_Brain rep4

source_name: Brain

value: Brain


title: Aripiprazole_PituitaryG rep4


title: Aripiprazole_Brain rep2


title: Aripiprazole_BM rep2

source_name: BM

value: BM


title: Aripiprazole_BM rep4


title: Aripiprazole_Aorta rep3

source_name: Aorta

value: Aorta


title: Aripiprazole_AdrenalG rep4

source_name: AdrenalG

value: AdrenalG


title: Aripiprazole_Aorta rep2


title: Aripiprazole_AdrenalG rep2


title: Alendronate_WAT rep1

source_name: WAT

value: WAT

value: Alendronate


title: Alendronate_WAT rep2


title: Alendronate_Thymus rep2

source_name: Thymus

value: Thymus


title: Alendronate_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: Alendronate_ThyroidG rep2


title: Alendronate_Thymus rep1


title: Alendronate_Testis rep2

source_name: Testis

value: Testis


title: Alendronate_Testis rep1


title: Alendronate_Stomach rep2

source_name: Stomach

value: Stomach


title: Alendronate_Stomach rep1


title: Alendronate_Spleen rep2

source_name: Spleen

value: Spleen


title: Alendronate_Skull rep2

source_name: Skull

value: Skull


title: Alendronate_Spleen rep1


title: Alendronate_Skin rep2

source_name: Skin

value: Skin


title: Alendronate_SkMuscle rep1

source_name: SkMuscle

value: SkMuscle


title: Alendronate_Skull rep1


title: Alendronate_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: Alendronate_PituitaryG rep1


title: Alendronate_ParotidG rep1

source_name: ParotidG

value: ParotidG


title: Alendronate_Skin rep1


title: Alendronate_Pancreas rep2

source_name: Pancreas

value: Pancreas


title: Alendronate_Lung rep1

source_name: Lung

value: Lung


title: Alendronate_Lung rep2


title: Alendronate_Pancreas rep1


title: Alendronate_Liver rep1

source_name: Liver

value: Liver


title: Alendronate_Kidney rep2

source_name: Kidney

value: Kidney


title: Alendronate_ParotidG rep2


title: Alendronate_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: Alendronate_Jejunum rep1


title: Alendronate_Liver rep2


title: Alendronate_Ileum rep1

source_name: Ileum

value: Ileum


title: Alendronate_Heart rep2

source_name: Heart

value: Heart

value: Alendronate


title: Alendronate_Heart rep1


title: Alendronate_Eye rep2

source_name: Eye

value: Eye


title: Alendronate_Ileum rep2


title: Alendronate_Eye rep1


title: Aripiprazole_Jejunum rep4

value: Aripiprazole


title: Alendronate_SkMuscle rep2


title: Alendronate_Colon rep2

source_name: Colon

value: Colon


title: Alendronate_Colon rep1


title: Alendronate_Brain rep2

source_name: Brain

value: Brain


title: Alendronate_Brain rep1


title: Alendronate_BM rep2

source_name: BM

value: BM


title: Alendronate_Aorta rep1

source_name: Aorta

value: Aorta


title: Alendronate_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: Alendronate_Aorta rep2


title: Alendronate_BM rep1


title: Alendronate_AdrenalG rep1


title: APAP2hrs_WAT rep1

source_name: WAT

value: WAT

value: APAP


title: APAP2hrs_ThyroidG rep1

source_name: ThyroidG

value: ThyroidG


title: APAP2hrs_Thymus rep1

source_name: Thymus

value: Thymus


title: APAP2hrs_Testis rep2

source_name: Testis

value: Testis


title: APAP2hrs_Testis rep1


title: APAP2hrs_WAT rep2


title: APAP2hrs_ThyroidG rep2


title: Alendronate_Kidney rep1

value: Kidney


title: APAP2hrs_Thymus rep2


title: APAP2hrs_Stomach rep1

source_name: Stomach

value: Stomach


title: APAP2hrs_Spleen rep2

source_name: Spleen

value: Spleen


title: APAP2hrs_Skull rep1

source_name: Skull

value: Skull


title: APAP2hrs_Skull rep2


title: APAP2hrs_Skin rep2

source_name: Skin

value: Skin


title: APAP2hrs_Stomach rep2


title: APAP2hrs_Spleen rep1


title: APAP2hrs_Skin rep1


title: APAP2hrs_SkMuscle rep2

source_name: SkMuscle

value: SkMuscle


title: APAP2hrs_PituitaryG rep2

source_name: PituitaryG

value: PituitaryG


title: APAP2hrs_ParotidG rep2

source_name: ParotidG

value: ParotidG


title: APAP2hrs_PituitaryG rep1


title: APAP2hrs_ParotidG rep1


title: APAP2hrs_Lung rep2

source_name: Lung

value: Lung


title: APAP2hrs_Kidney rep2

source_name: Kidney


title: APAP2hrs_Lung rep1


title: APAP2hrs_Liver rep1

source_name: Liver

value: Liver


title: APAP2hrs_Kidney rep1


title: APAP2hrs_Liver rep2


title: APAP2hrs_Jejunum rep2

source_name: Jejunum

value: Jejunum


title: APAP2hrs_Ileum rep2

source_name: Ileum

value: Ileum


title: APAP2hrs_Pancreas rep1

source_name: Pancreas

value: Pancreas


title: APAP2hrs_Eye rep2

source_name: Eye

value: Eye

value: APAP


title: APAP2hrs_Ileum rep1


title: APAP2hrs_Eye rep1


title: APAP2hrs_Heart rep1

source_name: Heart

value: Heart


title: APAP2hrs_Jejunum rep1


title: APAP2hrs_Brain rep1

source_name: Brain

value: Brain


title: APAP2hrs_BM rep2

source_name: BM

value: BM


title: APAP2hrs_SkMuscle rep1


title: APAP2hrs_BM rep1


title: APAP2hrs_Aorta rep2

source_name: Aorta

value: Aorta


title: APAP2hrs_Aorta rep1


title: APAP2hrs_AdrenalG rep2

source_name: AdrenalG

value: AdrenalG


title: APAP2hrs_Colon rep1

source_name: Colon

value: Colon


title: APAP2hrs_Pancreas rep2


title: 0.5percentCMC0.25percentTween80_WAT rep4

source_name: WAT

value: WAT


title: 0.5percentCMC0.25percentTween80_WAT rep3


title: APAP2hrs_AdrenalG rep1


title: ChIP_seq_input_H3K27ac_sorted_hPGCLCs_UCLA2_rep1

city: Cambridge

last: Sun

address: 455 Main St

department: EECS

institute: Whitehead Institute

data_processing:
FastQC were used to check the quality of the sequencing reads. Then reads were mapped to the reference hg19 genome using bowtie by allowing maximal two mismatches per reads and take one best hit when the reads can be mapped to multiple places. PCR duplciates were removed using SAMtools and ChIPseq tracks were generated with deeptools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks

source_name: UCLA2 sorted hPGCLCs

growth_protocol: hESCs were cultured on mitomycin C-inactivated mouse embryonic fibroblasts (MEFs) in hESC media, which is composed of 20% knockout serum replacement (KSR) (GIBCO, 10828-028), 100mM L-Glutamine (GIBCO, 25030-081), 1x MEM Non-Essential Amino Acids (NEAA) (GIBCO, 11140-050), 55mM 2-Mercaptoethanol (GIBCO, 21985-023), 10ng/mL recombinant human FGF basic (R&D systems, 233-FB), 1x Penicillin-Streptomycin (GIBCO, 15140-122), and 50ng/mL primocin (InvivoGen, ant-pm-2) in DMEM/F12 media (GIBCO, 11330-032). The hESCs were split every 7 days using Collagenase type IV (GIBCO, 17104-019). All hESC lines used in this study are registered with the National Institute of Health Human Embryonic Stem Cell Registry and are available for research use with NIH funds. Mycoplasma test (Lonza, LT07-418) was performed every month. All experiments were approved by the UCLA Embryonic Stem Cell Research Oversight Committee.

extract_protocol: ChIP-seq of hESCs, iMeLCs, day 4 aggregates was performed using anti-TFAP2C antibodies and libraries were constructed with Ovation Ultralow Systems V2 (NuGEN, 0344). ChIP-seq of sorted day4 hPGCLCs using anti-H3K27ac antibodies was performed using Low Cell ChIP-Seq Kit (ACTIVE MOTIF, 53804).

treatment_protocol: hESCs were dissociated into single cells with 0.05% Trypsin-EDTA (GIBCO, 25300-054) and plated onto Human Plasma Fibronectin (Invitrogen, 33016-015)-coated 12-well-plates at the density of 200,000 cells/well in 2mL/well of iMeLC media, which is composed of 15% KSR (GIBCO, 10828-028), 1x NEAA (GIBCO, 11140-050), 0.1mM 2-Mercaptoethanol (GIBCO, 21985-023), 1x Penicillin-Streptomycin-Glutamine (GIBCO, 10378-016), 1mM sodium pyruvate (GIBCO, 11360-070), 50ng/mL Activin A (Peprotech, AF-120-14E), 3mM CHIR99021 (Stemgent,04-0004), 10mM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow’s MEM (GMEM) (GIBCO, 11710-035). After 24 hr, iMeLCs were dissociated into single cells with 0.05% Trypsin-EDTA and plated into ultra-low cell attachment U-bottom 96-well plates (Corning, 7007) at the density of 3,000 cells/well in 200ml/well of hPGCLC media, which is composed of 15% KSR (GIBCO, 10828-028), 1x NEAA (GIBCO, 11140-050), 0.1mM 2-Mercaptoethanol (GIBCO, 21985-023), 1x Penicillin-Streptomycin-Glutamine (GIBCO, 10378-016), 1mM sodium pyruvate (GIBCO, 11360-070), 10ng/mL human LIF (Millipore, LIF1005), 200ng/mL hu- man BMP4 (R&D systems, 314-BP), 50ng/mL human EGF (R&D systems, 236-EG), 10mM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow’s MEM (GMEM) (GIBCO, 11710-035).

value: hPGCLCs

value: none (input)


title: 0.5percentCMC0.25percentTween80_ThyroidG rep3

source_name: ThyroidG

value: ThyroidG


title: 0.5percentCMC0.25percentTween80_Thymus rep4

source_name: Thymus

value: Thymus


title: ChIP_seq_input_TFAP2C_day4_aggregate_UCLA2_rep1

value: aggregates


title: APAP2hrs_Heart rep2


title: ChIP_seq_H3K27ac_sorted_hPGCLCs_UCLA2_rep3

tag: antibody source

value: Abcam, catalog number:ab4729, lot number GR3231937-1


title: APAP2hrs_Colon rep2


title: 0.5percentCMC0.25percentTween80_Testis rep4

source_name: Testis

value: Testis


title: ChIP_seq_H3K27ac_sorted_hPGCLCs_UCLA2_rep1


title: ChIP_seq_TFAP2C_day4_aggregate_UCLA2_rep2

source_name: UCLA2 hPGCLC aggregates

value: Santa Cruz, catalog number:sc-8977, lot G1112


title: 0.5percentCMC0.25percentTween80_Testis rep3


title: ChIP_seq_TFAP2C_day4_aggregate_UCLA2_rep1


title: 0.5percentCMC0.25percentTween80_Thymus rep3


title: 0.5percentCMC0.25percentTween80_Stomach rep3

source_name: Stomach

value: Stomach


title: 0.5percentCMC0.25percentTween80_Stomach rep4


title: ChIP_seq_TFAP2C_iMeLC_UCLA1_rep1

source_name: UCLA1 iMeLC

value: iMeLC


title: ChIP_seq_TFAP2C_iMeLC_UCLA1_rep2


title: APAP2hrs_Brain rep2

value: APAP


title: ChIP_seq_TFAP2C_hESC_UCLA1_rep2

source_name: UCLA1 hESC

value: hESC


title: 0.5percentCMC0.25percentTween80_Spleen rep4

source_name: Spleen

value: Spleen


title: ChIP_seq_TFAP2C_hESC_UCLA1_rep1


title: 0.5percentCMC0.25percentTween80_Skull rep3

source_name: Skull

value: Skull


title: 0.5percentCMC0.25percentTween80_Skull rep4


title: Midostaurin_6

city: COLUMBUS

first: Lindsey

last: Brinton

state: Oh

address: 410 W 12TH AVE

department: Internal Medicine

institute: The Ohio State University

description:
Midostaurin_6_RRA.gene_summary.txt
Midostaurin_6_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt

data_processing:
trim the 3p end with skewer, -r 0.2
trim the 5p end with skewer, -r 0.2
count reads with mageck
robust rank algorithm (RRA) with mageck
Supplementary_files_format_and_content: two .txt files, sgrna_summary with read counts of all sgrnas, and also a file collapsed at the gene level. Statistics based on their algorithm are provided (p-value and FDR), a score from their algorithm, and basic log fold change.

source_name: CRISPR KO HiSeq

growth_protocol: MOLM-13 cells were grown in RPMI media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin/L-glutamine

extract_protocol:
Cells were harvested, DNA extracted via Qiagen Blood & Cell Culture DNA Midi Kit per manufacturer’s instructions, and the sgRNA cassette retrieved via PCR as described by Broad sequencing protocol on Addgene.
The P5 mix and P7 primers design from this protocol were used with the following New England Biolabs NEBNext Indexes: 17, 24, 26, 28, 29, 31, 33, 34, 35, 36, 42.

treatment_protocol: 2.5×106 cells/well were plated in each well of 12-well plates with total cells equal to 400 cells/sgRNA × 76,441 sgRNAs × 100/infection efficiency(%). Media containing lentiviral particles was added at2ug/mL polybrene and spinoculated at 450×g for 90 min. After six hours, cells were centrifuged 300×g for 10 min. and resuspended in complete media. Puromycin selection with 10ug/mL was started after 48 hours and continued for seven days of selection to remove essential and non-transduced cells. Cultures were then exposed to drug for five days or three days if viability fell below 20%.

tag: passage

tag: crispr library

value: Brunello

value: 30nM midostaurin


title: ChIP_seq_input_TFAP2C_day4_aggregate_UCLA2_rep2


title: 0.5percentCMC0.25percentTween80_Skin rep4

source_name: Skin

tag: strain

value: Skin


title: Day0_6

description:
DMSO_6_RRA.gene_summary.txt
DMSO_6_RRA.sgrna_summary.txt
Midostaurin_6_RRA.gene_summary.txt
Midostaurin_6_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt

value: baseline


title: 0.5percentCMC0.25percentTween80_ThyroidG rep4


title: 0.5percentCMC0.25percentTween80_SkMuscle rep4

source_name: SkMuscle

value: SkMuscle


title: Midostaurin_5

description:
Midostaurin_5_RRA.gene_summary.txt
Midostaurin_5_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_SkMuscle rep3


title: 0.5percentCMC0.25percentTween80_Skin rep3


title: DMSO_5

description:
DMSO_5_RRA.gene_summary.txt
DMSO_5_RRA.sgrna_summary.txt

value: DMSO control


title: Day0_5

description:
DMSO_5_RRA.gene_summary.txt
DMSO_5_RRA.sgrna_summary.txt
Midostaurin_5_RRA.gene_summary.txt
Midostaurin_5_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_PituitaryG rep4

source_name: PituitaryG

value: PituitaryG


title: Midostaurin_4

description:
Midostaurin_4_RRA.gene_summary.txt
Midostaurin_4_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Spleen rep3


title: Gilteritinib_4

description:
Gilteritinib_4_RRA.gene_summary.txt
Gilteritinib_4_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt

value: 2nM gilteritinib


title: 0.5percentCMC0.25percentTween80_PituitaryG rep3


title: 0.5percentCMC0.25percentTween80_ParotidG rep4

source_name: ParotidG

value: ParotidG


title: 0.5percentCMC0.25percentTween80_ParotidG rep3


title: 0.5percentCMC0.25percentTween80_Pancreas rep4

source_name: Pancreas

value: Pancreas


title: Midostaurin_3

description:
Midostaurin_3_RRA.gene_summary.txt
Midostaurin_3_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Liver rep4

source_name: Liver

value: Liver


title: 0.5percentCMC0.25percentTween80_Pancreas rep3


title: DMSO_6

description:
DMSO_6_RRA.gene_summary.txt
DMSO_6_RRA.sgrna_summary.txt


title: DMSO_3

description:
DMSO_3_RRA.gene_summary.txt
DMSO_3_RRA.sgrna_summary.txt


title: Day0_3

description:
DMSO_3_RRA.gene_summary.txt
DMSO_3_RRA.sgrna_summary.txt
Gilteritinib_3_RRA.gene_summary.txt
Gilteritinib_3_RRA.sgrna_summary.txt
Midostaurin_3_RRA.gene_summary.txt
Midostaurin_3_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Lung rep3

source_name: Lung

value: Lung


title: Gilteritinib_2

description:
Gilteritinib_2_RRA.gene_summary.txt
Gilteritinib_2_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Liver rep3


title: DMSO_2

description:
DMSO_2_RRA.gene_summary.txt
DMSO_2_RRA.sgrna_summary.txt


title: 0.5percentCMC0.25percentTween80_Kidney rep4

source_name: Kidney

value: Kidney


title: Day0_2

description:
DMSO_2_RRA.gene_summary.txt
DMSO_2_RRA.sgrna_summary.txt
Gilteritinib_2_RRA.gene_summary.txt
Gilteritinib_2_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: Gilteritinib_1

description:
Gilteritinib_1_RRA.gene_summary.txt
Gilteritinib_1_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: DMSO_1

description:
DMSO_1_RRA.gene_summary.txt
DMSO_1_RRA.sgrna_summary.txt


title: 0.5percentCMC0.25percentTween80_Jejunum rep3

source_name: Jejunum

value: Jejunum


title: Day0_1

description:
DMSO_1_RRA.gene_summary.txt
DMSO_1_RRA.sgrna_summary.txt
Gilteritinib_1_RRA.gene_summary.txt
Gilteritinib_1_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: DMSO_4

description:
DMSO_4_RRA.gene_summary.txt
DMSO_4_RRA.sgrna_summary.txt


title: Gilteritinib_3

description:
Gilteritinib_3_RRA.gene_summary.txt
Gilteritinib_3_RRA.sgrna_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Ileum rep3

source_name: Ileum

value: Ileum


title: Day0_4

description:
DMSO_4_RRA.gene_summary.txt
DMSO_4_RRA.sgrna_summary.txt
Gilteritinib_4_RRA.gene_summary.txt
Gilteritinib_4_RRA.sgrna_summary.txt
Midostaurin_4_RRA.gene_summary.txt
Midostaurin_4_RRA.sgrna_summary.txt
Mido_all_RRA_Controls.gene_summary.txt
Gilt_all_RRA_Controls.gene_summary.txt


title: 0.5percentCMC0.25percentTween80_Lung rep4


title: ChIP_seq_H3K27ac_sorted_hPGCLCs_UCLA2_rep2

source_name: UCLA2 sorted hPGCLCs

value: hPGCLCs

value: Abcam, catalog number:ab4729, lot number GR3231937-1


title: 0.5percentCMC0.25percentTween80_Heart rep3

source_name: Heart

value: Heart


title: RBM2627_rep3

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT2 against hg38.
Uniquely mapped and properly paired reads were used for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from bam files using genomecov tools from bedtools, tpm-normalized and then converted using bedGraphtoBigWig. The score represents strand specific tpm per base.

source_name: siRBM26+siRBM27 total RNA replicate 3

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual.
Libraries were prepared at BGI using BGI Long Non-coding RNA Sequencing service (ribo-depletion followed by total RNA sequencing).

treatment_protocol: siRNA transfections were performed targeting EGFP(control), ZC3H3 or RBM26+RBM27

value: HeLa

tag: genotype

tag: batch

value: batch RBM2


title: RBM2627_rep1

source_name: siRBM26+siRBM27 total RNA replicate 1

value: batch RBM


title: EGFP_rep3 batch RBM

source_name: EGFP(control) total RNA replicate 3

value: siEGFP


title: RBM2627_rep2

source_name: siRBM26+siRBM27 total RNA replicate 2


title: 0.5percentCMC0.25percentTween80_Eye rep3

source_name: Eye

value: Eye


title: 0.5percentCMC0.25percentTween80_Eye rep4


title: EGFP_rep2 batch RBM

source_name: EGFP(control) total RNA replicate 2


title: ZC3H3_rep3

source_name: siZC3H3 total RNA replicate 3

value: batch ZC3H3


title: EGFP_rep1 batch RBM

source_name: EGFP(control) total RNA replicate 1


title: 0.5percentCMC0.25percentTween80_Kidney rep3


title: 0.5percentCMC0.25percentTween80_Colon rep4

source_name: Colon

value: Colon


title: 0.5percentCMC0.25percentTween80_Jejunum rep4


title: 0.5percentCMC0.25percentTween80_Brain rep4

source_name: Brain

value: Brain


title: ZC3H3_rep2

source_name: siZC3H3 total RNA replicate 2


title: 0.5percentCMC0.25percentTween80_Colon rep3


title: 0.5percentCMC0.25percentTween80_Brain rep3


title: EGFP_rep3 batch ZC3H3

source_name: siEGFP(control) total RNA replicate 3


title: ZC3H3_rep1

source_name: siZC3H3 total RNA replicate 1


title: 0.5percentCMC0.25percentTween80_BM rep4

source_name: BM

value: BM


title: EGFP_rep2 batch ZC3H3

source_name: siEGFP(control) total RNA replicate 2


title: 0.5percentCMC0.25percentTween80_Ileum rep4

source_name: Ileum


title: 0.5percentCMC0.25percentTween80_BM rep3


title: EGFP_rep1 batch ZC3H3

source_name: siEGFP(control) total RNA replicate 1


title: 0.5percentCMC0.25percentTween80_Heart rep4

source_name: Heart


title: 0.5percentCMC0.25percentTween80_Aorta rep3

source_name: Aorta

value: Aorta


title: K562_PMA_1nM_AP_rep1

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Amplification of virus inserts
K562_PMA_FDR_0.01.bed

data_processing:
Sequence reads were aligned using bowtie.
A GFF file was made from aligned reads pooled from all experiments. Then read counts were calculated using HTSeq.
Final enrichment was calculated by MAGeCK.

growth_protocol: K562 cells were cultured in RPMI 1640 with Lglutamine, 10% FBS and Pen-Strep.

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Blood Maxi Kit.
Genome DNA was amplified using Illumina PCR primer 1.0 and 2.0 using PCR. PCR products were then size-selected and purified. Final products were sequenced by Illumina HiSeq 4000 platform. Sequence reads were aligned using bowtie.

treatment_protocol: K562 cells were infected with the virus library at MOI 0.5 by spin infection. Two days after infection, cells were selected by 2mg/ml puromycin for another 5 days. Cells were then differentiated with 10nM PMA (phorbol 12-myristate 13-acetate) for 2 days. Cells were divided into differentiated non-treated control cells and the other half of cells were treated with 1nM AP20187 for 18hr to induce apoptosis.

tag: cell type

value: chronic myelogenous leukemia

tag: treatment


title: 0.5percentCMC0.25percentTween80_Aorta rep4


title: K562_PMA_1nM_AP_rep2


title: 0.5percentCMC0.25percentTween80_AdrenalG rep4

source_name: AdrenalG

value: AdrenalG


title: 0.5percentCMC0.25percentTween80_AdrenalG rep3


title: K562_PMA_rep2

value: control


title: K562_PMA_rep1


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 5

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
Differential expression testing using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM)  for each gene (rows) in each sample (columns)

source_name: Gfi1b-eGFP mouse intestinal epithelial cells

extract_protocol:
Full length RNAseq (SMART-Seq2)
3' polyA RNA seq
10X Genomics Chromium Prep


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 6


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 4


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 3


title: MM4855_Lung

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A225

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Lung

extract_protocol:
Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Thermo Fisher Scientific)
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

treatment_protocol: Blood and whole lung samples obtained from C57Bl/6 and C3HeB/FeJ mice infected with low and high doses of Mycobacterium tuberculosis

value: Uninfected

tag: dose

tag: day

tag: gender

value: Female


title: MM4854_Lung

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A224


title: MM4853_Lung

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A223


title: BAL_Pre_InVitro_38_RNA_Prenegin_Vitro_BAL_01_16_19

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the GenomicRanges package in R/Bioconductor and the UCSC mm9 KnownGene table. Reads overlapping exons were normalized to reads per kilobase per million (RPKM)
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes for each sample.

source_name: Airway CD8 memory T cells FACS sorted for RNA before in vitro culture

extract_protocol:
1000 cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 200 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: sorting markers

value: Live/Dead- CD8+ CD44hi FluNP366-374Db+ CD45.2+

tag: organ

value: Lung Airway

tag: stimulation

value: 35 days post Influenza X31 infection, 2 days post-transfer

tag: pre-transfer matched sample


title: SPL_Pre_InVitro_35_RNA_Pre_In_Vitro_Spl_02_12_19


title: SPL_PreTransfer_33_RNA_Pre_IT_Spl_2_2_26_19

source_name: Spleen CD8 memory T cells FACS sorted for RNA before in vitro cuture

value: Spleen


title: MM4851_Lung

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A221


title: SPL_PreTransfer_32_RNA_Pre_IT_Spl_1_2_26_19


title: SPL_PreTransfer_37_RNA_Preneg_IT_IP_Spl_Tem_sample_01_22_19


title: SPL_InVitro_31_RNA_Post_In_Vitro_Spl_02_14_19

source_name: Spleen CD8 memory T cells cultured in vitro in complete media for 48 hours


title: BAL_Pre_InVitro_rep3_34_RNA_Pre_In_Vitro_BAL_02_12_19


title: BAL_Pre_InVitro_39_RNA_Prenegin_Vitro_BAL_01_22_19


title: SPL_InVitro_30_RNA_Post_In_Vitro_Spl_01_24_19


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 2


title: Ileal tuft cells from C57BL/6J mice, Mouse Rep 1


title: ventral_rep3

city: Tsukuba-shi

first: Yu

last: Hayashi

address: Tennodai 1-1-1

institute: University of Tsukuba

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Following tissue lysis using QIAzol Lysis Reagent (Qiagen), total RNA was extracted and purified using miRNeasy Micro Kit (Qiagen) according to the manufacturer's instructions

tag: Sex

value: male

tag: age

value: 8 weeks

tag: tissue

value: Brainstem; ventral


title: ventral_rep1


title: dorsal_rep1

value: Brainstem; dorsal


title: target_rep3

value: Brainstem; target


title: target_rep2


title: ventral_rep2


title: dorsal_rep2


title: dorsal_rep3


title: target_rep1


title: SPL_InVitro_29_RNA_Post_In_Vitro_Spl_01_18_19


title: MM4852_Lung

description:
HN878_D_Uninfected_C3HeBFeJ
GRA502A222


title: SPL_PreTransfer_36_RNA_Preneg_IT_IP_Spl_Tem_sample_01_16_19


title: BAL_InVitro_27_RNA_Post_In_Vitro_BAL_2_01_24_19

source_name: Airway CD8 memory T cells cultured in vitro in complete media for 48 hours


title: BAL_InVitro_28_RNA_Post_In_Vitro_BAL_2neg1_02_14_19


title: MM4850_Lung

description:
HN878_D_High_C3HeBFeJ
GRA502A220

value: High


title: MM4849_Lung

description:
HN878_D_High_C3HeBFeJ
GRA502A219


title: MM4845_Lung

description:
HN878_D_Low_C3HeBFeJ
GRA502A215

value: Low


title: MM4844_Lung

description:
HN878_D_Low_C3HeBFeJ
GRA502A214


title: MM4846_Lung

description:
HN878_D_High_C3HeBFeJ
GRA502A216


title: MM4847_Lung

description:
HN878_D_High_C3HeBFeJ
GRA502A217


title: BAL_InVitro_24_RNA_Post_In_Vitro_BAL_1_01_24_19


title: MM4842_Lung

description:
HN878_D_Low_C3HeBFeJ
GRA502A212


title: BAL_InVitro_25_RNA_Post_In_Vitro_BAL_1neg1_02_14_19


title: MM4843_Lung

description:
HN878_D_Low_C3HeBFeJ
GRA502A213


title: BAL_InVitro_26_RNA_Post_In_Vitro_BAL_2_01_18_19


title: BAL_Post_IT_22_RNA_Post_IT_BAL_2neg3_2_28_19

source_name: Spleen CD8 memory T cells transferred into the airways of congenic mice during acute Sendai infection


title: BAL_Post_IT_21_RNA_Post_IT_BAL_2neg2_2_28_19


title: MM4840_Lung

description:
HN878_A_Uninfected_C57Bl6
GRA502A210


title: MM4841_Lung

description:
HN878_D_Low_C3HeBFeJ
GRA502A211


title: MM4836_Lung

description:
HN878_A_Uninfected_C57Bl6
GRA502A206


title: BAL_Post_IT_18_RNA_Post_IT_BAL_1neg1_2_28_19


title: MM4838_Lung

description:
HN878_A_Uninfected_C57Bl6
GRA502A208


title: BAL_Post_IT_20_RNA_Post_IT_BAL_1neg3_2_28_19


title: MM4848_Lung

description:
HN878_D_High_C3HeBFeJ
GRA502A218


title: MM4839_Lung

description:
HN878_A_Uninfected_C57Bl6
GRA502A209


title: BAL_Post_IT_19_RNA_Post_IT_BAL_1neg2_2_28_19


title: BAL_Post_IT_17_RNA_Post_IT_2_01_22_19

source_name: Spleen CD8 memory T cells transferred into the airways of congenic mice


title: BAL_Post_IT_16_RNA_Post_IT_2_01_18_19


title: MM4837_Lung

description:
HN878_A_Uninfected_C57Bl6
GRA502A207


title: MM4835_Lung

description:
HN878_A_High_C57Bl6
GRA502A205


title: BAL_Post_IT_15_RNA_Post_IT_1_01_22_19


title: BAL_InVitro_23_RNA_Post_In_Vitro_BAL_1_01_18_19


title: MM4834_Lung

description:
HN878_A_High_C57Bl6
GRA502A204


title: BAL_Post_IT_14_RNA_Post_IT_1_01_18_19


title: MM4833_Lung

description:
HN878_A_High_C57Bl6
GRA502A203


title: BAL_Post_IP_13_RNA_Post_IP_2_01_22_19

source_name: Spleen CD8 memory T cells transferred into the peritoneum of congenic mice

value: Peritoneum


title: BAL_Post_IP_12_RNA_Post_IP_2_01_18_19