title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 233

treatment_protocol: 1x106/ml naive T cells were plated in 6 well dishes and incubated for 4 days with (1) IL-12+IL-21+IL-23 (Th1 cell condition) and (2) IL-1b+IL-6+IL-23 (pathogenic Th17 cell condition). Viable CD4+ T cells were sorted with FACS into eGFP+ (i.e. IL-23R+) and eGFP- (i.e. IL-23R-) population as single cells into 96 well plates pre-loaded with 5ul TCL buffer (containing b-mercaptoethanol according to the manufacturer's instructions, Qiagen). cDNA libraries were prepared as outlined in Pawlak M., DeTomaso, D. et al. 2021 and sequenced.


title: H889 hSCLC PROX1 input

status: Public on May 01 2021

type: SRA

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Reads were mapped to hg39 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Bigwig files contain ChIP signal normalized to 10M reads
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq signal in bigwig format

molecule: genomic DNA

organism: Homo sapiens

source_name: H889 hSCLC PROX1

growth_protocol: Cells were maintained in RPMI-1640 media (ThermoFisher Scientific, 11875135) supplemented with 5% heat deactivated fetal bovine serum (Sigma Aldrich) without antibiotics at 37 °C in a humidified atmosphere containing 5% CO2 and 95% air.

extract_protocol:
Cells (~7 x107 cells) in the exponential growth phase were fixed and nuclear extract were prepared. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with 10 μg antibody.
Libraries were constructed by using the NEBNext® ChIP-Seq Library Prep Master Mix (NEB,E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, E7335S, Index Primers Set 2, E7500S) with Agencourt AMPure XP magnetic beads (Beckman coulter, A63881) exactly as per manufacturer’s instructions.

treatment_protocol: no treatment

tag: tissue/cell line

tag: tissue/cell type

value: Small cell lung cancer cell line

tag: passage

tag: antibody


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 241

city: Berkeley

first: David

last: DeTomaso

state: CA

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

library_source: transcriptomic

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_expression_tpm.txt.gz: tab-delimited text table (genes x cells) of TPM-normalized gene expression values.  cell_metadata.txt: tab-delimited table which contains GFP label, genotype, and stimulation for each cell.

molecule: polyA RNA

organism: Mus musculus

source_name: Th17 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

extract_protocol:
Spleen and lymph nodes were extracted and then a single-cell suspension was prepared by homogenization with a syringe plunger and debris was filtered with a 70um filter. Red blood cells were lysed with ACK lysis buffer from Lonza. CD4+ T cells were enriched using a bead protocol from Miltenyi Biotech (cat #. 130-117-043) and then stained with anti-CD44 (clone IM7), anti-CD62L (clone Mel14), anti-CD4 (clone RM4-5) and anti-CD25 (clone PC61) in preparation for FACS. Naive T cells were sorted based on CD44lowCD62LhiCD4+CD25-.
T cells were sorted into 96-well plates containing 5 μl TCL Buffer (QIAGEN) with 1% 2-mercaptoethanol, centrifuged and frozen at −80 °C.  Single-cell sequencing libraries were then created using the Smart-seq2 protocol (Picelli et al., Nature Methods 2014) and carried out as described in Singer et. al, Cell 2016.

tag: differentiation

tag: gfp

tag: genotype

value: IL23R Knockout

tag: cell type

value: CD4 T Cells


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 232


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 229


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 228


title: LNCaP_DHT_AcH3_No.10-3_siCtrl

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: 7_LD_13_AcH3_PSF_inhibitor_AcH3_DHT_R1_merged

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files that summarized significant peak regions (P-value < 1.0xE-4)

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultured in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days. LTAD cells were cultured in phenol red-free RPMI 1640 containing  10% charcoal/dextran treated FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.  Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN).  The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: Cells were treated with vehicle or 10 nM DHT for 24h. Cells were treated with No.10-3 or vehicle for 48 h. Cells were treated with siControl or siPSF (10 nM) for 48 h.

tag: cell line

value: LNCaP cells

value: prostate cancer cells

tag: treatment

value: DHT10 nM + No.10-3 + siControl

tag: chip antibody

value: AcH3 (Millipore06-599)


title: LNCaP_Et_AcH3_siPSF

value: ethanol (Vehicle) treatment + siPSF


title: H889 hSCLC NKX2-1 input

source_name: H889 hSCLC NKX2-1


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 230


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 227


title: H2107 hSCLC PROX1 ChIP

source_name: H2107 hSCLC PROX1

value: H3K27ac (Abcam, Ab4729)


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 237


title: H2107 hSCLC NKX2-PROX1 Input

source_name: H2107 hSCLC NKX2-PROX1


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 226


title: H889 hSCLC NKX2-1 ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 224


title: H128 hSCLC PROX1 Input

source_name: H128 hSCLC PROX1


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 225


title: H2107 hSCLC NKX2-1 ChIP

source_name: H2107 hSCLC NKX2-1


title: H128 hSCLC NKX2-1 Input

source_name: H128 hSCLC NKX2-1


title: H128 hSCLC PROX1 ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 223


title: H128 hSCLC NKX2-1 ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 220


title: LX48 hPDX H3K27ac input

source_name: LX48 hPDX

value: JHU-LX48-SCLC PDX

value: Small cell lung cancer PDX flank


title: LX48 hPDX H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 218


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 217


title: LX22 hPDX H3K27ac input

source_name: LX22 hPDX

value: JHU-LX22-SCLC PDX


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 219


title: LX22 hPDX H3K27ac ChIP


title: LX44 hPDX H3K27ac input

source_name: LX44 hPDX

value: JHU-LX44-SCLC PDX


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 221


title: LX110 hPDX H3K27ac input

source_name: LX110 hPDX

value: JHU-LX110-SCLC PDX


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 214


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 215


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 216


title: LX110 hPDX H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 213


title: LX44 hPDX H3K27ac ChIP


title: H889 hSCLC H3K27ac input

source_name: H889 hSCLC


title: H889 hSCLC H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 222


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 211


title: H69 hSCLC H3K27ac Input

source_name: H69 hSCLC


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 210


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 209


title: H526 SCLC H3K27ac Input

source_name: H526 SCLC


title: H69 hSCLC H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 207


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 206


title: H526 SCLC H3K27ac ChIP


title: H524 hSCLC H3K27ac ChIP

source_name: H524 hSCLC


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 212


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 204


title: H510 hSCLC H3K27ac ChIP

source_name: H510 hSCLC


title: H378 SCLC H3K27ac ChIP

source_name: H378 SCLC


title: H2171 hSCLC H3K27ac Input

source_name: H2171 hSCLC


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 205

source_name: Th17 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 202


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 201


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 203


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 199


title: H82 hSCLC H3K27ac ChIP

source_name: H82 hSCLC


title: H211 SCLC H3K27ac Input

source_name: H211 SCLC


title: H2171 hSCLC H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 208


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 198


title: H211 SCLC H3K27ac ChIP


title: H524 hSCLC H3K27ac Input


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 196


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 197


title: H2107 hSCLC H3K27ac Input

source_name: H2107 hSCLC


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 195


title: H510 hSCLC H3K27ac Input


title: H2107 hSCLC H3K27ac ChIP


title: H378 SCLC H3K27ac Input


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 194


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 193


title: H1092 SCLC H3K27ac Input

source_name: H1092 SCLC


title: Th17 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 200


title: H1092 SCLC H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 96

source_name: Th17 differentiated CD4 T Cell - eGFP_neg_Control

value: Control


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 95


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 94


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 93


title: untreated NK cells, replicate 3

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: LMSCGR

institute: NIAMS/NIH

description:
barcoded 3'adapter: TTCATTCGTATGCCGTCTTCTGCTTG
NK3_wt
small RNA

data_processing:
Base calling was done using CASAVA versions 1.6 - 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA (Farazi et al. 2011, 71:4443) and other non-coding and coding RNA transcriptomes.
Genome_build: GRCh37/hg19
The processed data files contain raw and normalized miRNA counts based on unique miRNA sequences, or based on precursor clusters and sequence families.
Genome_build: hg19
Supplementary_files_format_and_content: raw and normalized read count mapping to small RNA

molecule: total RNA

source_name: NK cells

extract_protocol:
Total RNA from liquid specimen was isolated using TRIzol LS, followed by a 2-propanol precipitation in the presence of glycogen
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (2008, 44:3, 2012, 58:164). Barcoded adapter sequences used for individual samples are indicated.

value: natural killer cells

value: control


title: H1048 SCLC H3K27ac Input

source_name: H1048 SCLC

value: Small cell lung cancer cell line


title: NK cells treated with IL21, replicate 3

description:
barcoded 3'adapter: TTATTTCGTATGCCGTCTTCTGCTTG
NK3_IL21
small RNA

value: IL21 treatment


title: NK cells treated with IL15 and IL21, replicate 3

description:
barcoded 3'adapter: TAGCCTCGTATGCCGTCTTCTGCTTG
NK3_IL15_IL21
small RNA

value: IL15 and IL21 treatment


title: H1048 SCLC H3K27ac ChIP


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 90

value: CD4 T Cells


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 92


title: NK cells treated with IL15, replicate 3

description:
barcoded 3'adapter: TTGGTTCGTATGCCGTCTTCTGCTTG
NK3_IL15
small RNA

value: IL15 treatment


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 91


title: untreated NK cells, replicate 2

description:
barcoded 3'adapter: TTCCGTCGTATGCCGTCTTCTGCTTG
NK2_wt
small RNA


title: NK cells treated with IL21, replicate 2

description:
barcoded 3'adapter: TTACATCGTATGCCGTCTTCTGCTTG
NK2_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 88


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 89


title: NK cells treated with IL15 and IL21, replicate 2

description:
barcoded 3'adapter: TGTGTTCGTATGCCGTCTTCTGCTTG
NK2_IL15_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 86


title: NK cells treated with IL15, replicate 2

description:
barcoded 3'adapter: TGATGTCGTATGCCGTCTTCTGCTTG
NK2_IL15
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 85


title: NK cells treated with IL21, replicate 1

description:
barcoded 3'adapter: TAGGATCGTATGCCGTCTTCTGCTTG
NK1_IL21_92
small RNA


title: NK cells treated with IL15 and IL21, replicate 1

description:
barcoded 3'adapter: TAGAGTCGTATGCCGTCTTCTGCTTG
NK1_IL15_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 84


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 87


title: untreated NK cells, replicate 1

description:
barcoded 3'adapter: TATCATCGTATGCCGTCTTCTGCTTG
NK1_wt
small RNA


title: NK cells treated with IL15, replicate 1

description:
barcoded 3'adapter: TAATATCGTATGCCGTCTTCTGCTTG
NK1_IL15
small RNA


title: exosomes from untreated NK cells, replicate 3

description:
barcoded 3'adapter: TAACGTCGTATGCCGTCTTCTGCTTG
EXO_NK3_wt
small RNA

source_name: exosomes from NK cells


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 82


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 80


title: exosomes from NK cells treated with IL21, replicate 3

description:
barcoded 3'adapter: TTAAGTCGTATGCCGTCTTCTGCTTG
EXO_NK3_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 79


title: exosomes from NK cells treated with IL15 and IL21, replicate 3

description:
barcoded 3'adapter: TCTGATCGTATGCCGTCTTCTGCTTG
EXO_NK3_IL15_IL21
small RNA


title: exosomes from NK cells treated with IL15, replicate 3

description:
barcoded 3'adapter: TCTCCTCGTATGCCGTCTTCTGCTTG
EXO_NK3_IL15_83
small RNA


title: exosomes from untreated NK cells, replicate 2

description:
barcoded 3'adapter: TCTAGTCGTATGCCGTCTTCTGCTTG
EXO_NK2_wt_82
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 78


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 77


title: exosomes from NK cells treated with IL15 and IL21, replicate 2

description:
barcoded 3'adapter: TCGATTCGTATGCCGTCTTCTGCTTG
EXO_NK2_IL15_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 76


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 75


title: exosomes from NK cells treated with IL21, replicate 2

description:
barcoded 3'adapter: TCGCGTCGTATGCCGTCTTCTGCTTG
EXO_NK2_IL21
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 74


title: exosomes from untreated NK cells, replicate 1

description:
barcoded 3'adapter: TCCGTTCGTATGCCGTCTTCTGCTTG
EXO_NK1_wt
small RNA


title: exosomes from NK cells treated with IL15, replicate 2

description:
barcoded 3'adapter: TCCTATCGTATGCCGTCTTCTGCTTG
EXO_NK2_IL15
small RNA


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 73


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 83


title: exosomes from NK cells treated with IL21, replicate 1

description:
barcoded 3'adapter: TCCACTCGTATGCCGTCTTCTGCTTG
EXO_NK1_IL21
small RNA


title: exosomes from NK cells treated with IL15, replicate 1

description:
barcoded 3'adapter: TCACTTCGTATGCCGTCTTCTGCTTG
EXO_NK1_IL15
small RNA


title: Sample_NEUFAM78-05 Medip-Seq

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Medip Sequencing from Sample_NEUFAM78-05

data_processing:
MeDIP: Basecalling using bcl2fastq v2.20.0.422
MeDIP: Quality Check with FASTQC 0.11.5
MeDIP: Trimming adapters and low quality with trimmomatic
MeDIP: Mapping to hg19 human reference with BWA-MEM v0.7.15
MeDIP: Deduplication with Picard Tools
MeDIP: Methylated Regions identified with MACS2
MeDIP: Merging regions with Bedtools
MeDIP: Differential Methyaltion Analysis with edgeR
Supplementary_files_format_and_content: MeDIP: peaks.bed.gz of Methylated regions identified with MACS2 and gzipped
BiSulfite: Basecalling using bcl2fastq v2.20.0.422
BiSulfite: Quality Check with FASTQC 0.11.5
BiSulfite: Trimming adapters and low quality with trimmomatic
BiSulfite: Alignment to hg19 human reference with Bsmap
BiSulfite: Deduplication with Picard Tools
BiSulfite: Filtering for properly paired reads and clipping overlapping regions in pairs
BiSulfite: Methylation analysis with methratio.py (supplied with Bsmap)
BiSulfite: Differential Methyaltion Analysis with methylKit
Genome_build: hg19
Supplementary_files_format_and_content: BiSulfite: Excel files with results coming from methylKit R package including interval region, pvalue, qvalue and methylation difference

source_name: whole blood

extract_protocol:
Whole blood was collected in EDTA tubes and genomic DNA (gDNA) extraction was performed with phenol–chloroform standard method or with the Maxwell 16 blood DNA purification kit (Promega) according to manufacturer’s protocol. Quantity and quality of gDNA were determined by Qubit BR dsDNA assay (ThermoFisher) and 1.5% agarose gel, respectively
MeDIP: One μg of each gDNA sample was mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). Sequencing libraries were prepared with NextFlex Methylseq 1 kit (Bioo Scientific) according to the manufacturer’s protocol
MeDIP: The ligated libraries were pooled and immunoprecipitated in the same reaction using MagMeDIP kit (Diagenode), followed by purification with IPure v2 kit (Diagenode) and PCR amplification. Paired-end sequencing was performed on the Illumina HiSeq 2500 platform with read length of 100 bp.
BiSulfite: A SeqCap Epi custom panel (Roche) was designed by NimbleDesign software (Roche).   Sequencing libraries were prepared with KAPA Hyper Prep kit (Kapa Biosystems) according to the manufacturer’s protocol, starting from 1 μg of gDNA mechanically fragmented on a focused ultrasonicator Covaris E220 (Covaris). After ligation, bisulfite conversion was performed by EZ DNA Methylation-Lighting kit (Zymo Research), followed by enrichment of the regions of interest with custom probes using SeqCap Epi enrichment kit (Roche).

tag: tissue

value: whole blood

tag: condition

value: healthy

tag: Sex

value: male

tag: family

tag: age


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 72


title: exosomes from NK cells treated with IL15 and IL21, replicate 1

description:
barcoded 3'adapter: TCATCTCGTATGCCGTCTTCTGCTTG
EXO_NK1_IL15_IL21
small RNA


title: Sample_NEUFAM78-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM78-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 68


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 81


title: Sample_NEUFAM78-03 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM78-03

value: MS

value: female


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 66


title: Sample_NEUFAM78-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM78-02


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 64


title: Sample_NEUFAM77-07 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-07


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 69


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 65


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 71


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 67


title: Sample_NEUFAM78-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM78-01


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 62


title: Sample_NEUFAM77-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 60


title: Sample_NEUFAM77-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-05


title: Sample_NEUFAM77-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-04


title: Sample_NEUFAM77-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-02


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 59


title: Sample_NEUFAM77-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM77-01


title: Sample_NEUFAM78-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM78-04


title: Sample_NEUFAM76-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 58


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 57


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 56


title: Sample_NEUFAM76-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-04


title: Sample_NEUFAM76-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-05


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 63


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 54


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 55


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 53


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 50


title: Sample_NEUFAM76-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-01


title: Sample_NEUFAM76-03 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-03


title: Sample_NEUFAM76-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM76-02


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 52


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 51


title: Sample_NEUFAM41-11 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-11


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 49


title: Sample_NEUFAM41-09 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-09


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 61


title: Sample_NEUFAM41-08 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-08


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 47


title: Sample_NEUFAM41-10 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-10


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 48


title: Sample_NEUFAM41-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-05


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 46


title: Sample_NEUFAM41-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 45


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 43


title: Sample_NEUFAM41-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-01


title: Sample_NEUFAM34-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 44


title: Sample_NEUFAM34-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-05


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 41


title: Sample_NEUFAM34-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-04


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 40


title: Sample_NEUFAM34-03 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-03


title: Sample_NEUFAM34-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-01


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 36


title: Sample_NEUFAM34-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-02


title: Sample_NEUFAM41-07 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM41-07


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 37


title: Sample_NEUFAM07-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM07-04


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 38


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 35


title: Sample_NEUFAM07-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM07-02


title: Sample_NEUFAM07-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM07-05


title: Sample_NEUFAM07-03 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM07-03


title: Sample_NEUFAM34-08 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM34-08


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 33


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 42


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 39


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 32


title: Sample_NEUFAM07-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM07-01


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 70


title: Sample_NEUFAM05-13 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-13


title: Sample_NEUFAM05-14 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-14


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 31


title: Sample_NEUFAM05-06 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 34


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 29


title: Sample_NEUFAM05-05 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-05


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 30


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 28


title: Sample_NEUFAM05-02 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-02


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 26


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 25


title: Sample_NEUFAM05-01 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-01


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 23


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 22


title: Sample_MSFAM02_07 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_07


title: Sample_NEUFAM05-03 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-03


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 21


title: Sample_MSFAM02_04 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_04


title: Sample_MSFAM02_03 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_03


title: Sample_MSFAM02_02 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_02


title: Sample_MSFAM02_06 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_06


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 20


title: Sample_MSFAM02_01 Medip-Seq

description: Medip Sequencing from Sample_MSFAM02_01


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 19


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 16


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 17


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 18


title: DU145_riba_NRF1

description:
ChIP by NRF1 antibody (Abcam ab55744)
Sample 32

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files that summarized significant peak regions (P-value < 10xE-4)

source_name: prostate cancer cells

growth_protocol: LNCaP, DU145 and 22Rv1 cells were cultured in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

treatment_protocol: 22Rv1 and LNCaP cells were treated with vehicle or dihydrotestosterone (DHT) 10 nM for 24 h. 22Rv1 and DU145 cells were treated with 10　μM riba (ribavirin) fpr 48 h. For AR knockdown, cells were transfected with siControl or siAR (10 nM) 72 h before fixation.

value: DU145 cells

value: riba

tag: antibody manufacturer and catalog number

value: Abcam ab55744


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 15


title: DU145_NRF2

description:
ChIP by NRF2 antibody (Active motif 61659)
Sample 31

value: Active motif 61659


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 27

value: Control


title: DU145_NRF1

description:
ChIP by NRF1 antibody (Abcam ab55744)
Sample 30


title: Sample_NEUFAM05-04 Medip-Seq

description: Medip Sequencing from Sample_NEUFAM05-04


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 24


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 13


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 14


title: DU145_riba_Input_2

description:
Input for Sample 32, 33
Sample 29

value: input


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 11


title: DU145_riba_input

description:
Input for Sample 27
Sample 26


title: DU145_Input_3

description:
Input for Sample 30, 31
Sample 28


title: DU145_riba_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 27

value: Abcam ab19857


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 9


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 10


title: DU145_OCT4_rep2

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 25


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 7


title: DU145_Input_2

description:
Input for Sample 25
Sample 24


title: DU145_pol II

description:
ChIP by RNA pol II (millipore 05-623)
Sample 23

value: RNA pol II

value: millipore 05-623


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 6


title: DU145_riba_NRF2

description:
ChIP by NRF2 antibody (Active motif 61659)
Sample 33


title: DU145_AcH3K27

description:
ChIP by AcH3K27 (Abcam ab177178)
Sample 22

value: Abcam ab177178


title: DU145_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 21


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 5

value: CD4 T Cells


title: DU145_input

description:
Input for Sample 21, 22, 23
Sample 20


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 4


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 3


title: 22Rv1_Input_siAR

description:
Input for Sample 11, 8
Sample 18

value: 22Rv1 cells

value: DHT10 nM + siAR


title: 22Rv1_Input_Cont

description:
Input for Sample 16, 13, 12, 9
Sample 19

value: DHT10 nM + siControl


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 2


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 12


title: 22Rv1_Input_riba

description:
Input for Sample 14, 15, 10, 7
Sample 17

value: DHT10 nM + riba


title: 22Rv1_Oct4_Cont_rep2

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 16

value: DHT10 nM


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 384

source_name: Th1 differentiated CD4 T Cell - eGFP_pos_IL23R Knockout

value: IL23R Knockout


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 1


title: 22Rv1_Oct4_riba

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 15


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 383


title: 22Rv1_Oct4_riba_rep2

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 14


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 382


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 379


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 380


title: 22Rv1_pol II_siAR

description:
ChIP by RNA pol II (millipore 05-623)
Sample 11


title: Th17 differentiated CD4 T Cell - eGFP_neg, Control, cell 8


title: 22Rv1_pol II_Cont

description:
ChIP by RNA pol II (millipore 05-623)
Sample 12


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 378


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 377


title: 22Rv1_pol II_riba_

description:
ChIP by RNA pol II (millipore 05-623)
Sample 10


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 376


title: 22Rv1_AcH3K27_riba

description:
ChIP by AcH3K27 (Abcam ab177178)
Sample 7


title: 22Rv1_AcH3K27_Cont

description:
ChIP by AcH3K27 (Abcam ab177178)
Sample 9


title: 22Rv1_AcH3K27_siAR

description:
ChIP by AcH3K27 (Abcam ab177178)
Sample 8


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 375


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 374


title: 22Rv1_DHT_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 6


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 373


title: LNCaP_DHT_input

description:
Input for Sample 3
Sample 4

value: LNCaP cells


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 372


title: 22Rv1_Vehicle_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 5

value: ethanol (Vehicle) treatment


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 371


title: LNCaP_Vehicle_input

description:
Input for Sample 1
Sample 2


title: LNCaP_Vehicle_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 1


title: 22Rv1_FOXM1_Cont

description:
ChIP by FOXM1 (diagenode C15410232)
Sample 13

value: diagenode C15410232


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 370


title: LNCaP_DHT_OCT4

description:
ChIP by OCT4 antibody (Abcam ab19857)
Sample 3


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 381


title: PD58

city: Auckland

first: Xi

middle: Hua

last: Wu

state: Auckland

address: 85 Park Road, Grafton

department: Centre for Brain Research

country: New Zealand

institute: University of Auckland

data_processing:
Overview: Analysis of paired end reads followed the pipeline developed by Trapnell and colleagues, Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7:562-578.
Raw paired-end reads were first trimmed for adapters using Trimmomatic v0.33. Surviving reads longer than 36 bases were used for downstream analysis
The paired-end reads were then aligned to reference human genome, UCSC build hg19, using Tophat2 (v2.1.0) and Bowtie2 (v2.2.6). All samples achieved mapping of reads above 90% to the reference.
Aligned reads were then pooled, assembled and analysed for differential gene expression using the Cufflnks (v2.2.1) package
Cuffdiff outputs were then analysed using R package cummerbund to extract FPKM (fragments per kilobase of transcript per million mapped reads) expression values
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: tab-delimited text file containing FPKM values for all significant differentially expressed genes detected for each sample

source_name: fresh-frozen brain tissue

extract_protocol:
The human STN from fresh-frozen human brain blocks were carefully dissected, protected for quality using RNA-later Ice and total RNA extracted using RNeasy Lipid Tissue Mini kit (Qiagen) and QIAzol Lysis buffer (Qiagen)
RNA-seq libraries were constructed using Truseq RNA Access Kit (Illumina)

tag: disease state

value: Parkinson's Disease

value: Brain, subthalamic nucleus

value: F


title: PD8


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 367


title: PD33

value: M


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 366


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 365


title: PD15


title: PD16


title: PD54


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 363


title: PD50


title: H168

value: control


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 362


title: H121


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 360


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 369


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 359


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 368


title: H122


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 356


title: H109


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 357


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 355


title: H131


title: H123


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 354


title: H204


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 364


title: H137


title: rat sperm_Sample R23

city: Providence

first: Susan

last: Hall

state: RI

address: Box G-E5

institute: Brown University

data_processing:
The sequencing configuration used was 2 x 150 bp, single index, per lane with estimated data output of 350M raw paired-end reads per lane.
RNA-sequencing data from each species was aligned to the genome of the corresponding species (human; hg19 version, mouse; mm10 version, rat; rn6 version) using Bowtie
Raw counts of comparable transcripts from all three species were combined and normalized using the upper quartile method  to compare abundance across species. The average normalized counts to the nearest integer were calculated for each transcript for each species, and the number of transcripts that had each abundance was plotted to find the distribution of counts. The linear fit curve (lm function in R) was calculated on the natural log of the variables to find the goodness of fit of the exponential curve and start values for the non-linear fit curve (nls function in R). The exponential equation y = ae(-bx) was used to determine p = 0.05 and p= 0.01, where a and b constants were derived from the non-linear fit curve.
Genome_build: human; hg19 version, mouse; mm10 version, rat; rn6 version
Supplementary_files_format_and_content: normalized expression

organism: Rattus norvegicus

source_name: rat sperm

growth_protocol: Semen specimens were collected from men aged 18 to 55 years with proven fertility. Rat and mouse semen specimens were collected via needle punctures of the cauda epididymides.

extract_protocol:
RNA was collected from human ejaculated sperm, rat and mouse (cauda) epididymal sperm using the method previously described by E. Bianchi et al, 2018.
PolyA-purified mRNA-sequencing: Poly A selection libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment involved

tag: strain

value: Fischer rats

value: sperm


title: rat sperm_Sample R24


title: rat sperm_Sample R22


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 350

value: CD4 T Cells


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 361


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 351


title: rat sperm_Sample R21


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 353


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 352


title: rat sperm_Sample R20


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 349


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 348


title: H120


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 358


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 347


title: rat sperm_Sample R15


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 346


title: SK4: chronic knockdown 4

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

description: Rcho-1 TS cells were maintained in Stem State Medium for 10 days after transduced with control shRNA.

data_processing:
Following generation of sequencing images, the pixel-level raw darta collection, image analysis, and base-calling were performed by Real Time Analysis software (Illumina)
Base call files were converted to qseq files by BCL converter (Illumina), and qseq files were converted to fastq files for downstream analysis.
Reads from fastq files were mapped to the rat reference genome (Rnor_5.0.7) using CLC Bio Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark)
Genome_build: Rnor5
Supplementary_files_format_and_content: excel file containing reads per kilobase per million reads (RPKM).

source_name: Rcho1 TS cells

extract_protocol:
RNA was extracted from cultured cells using TriReagent according to the manufacturer's recommendations.
Libraries were prepared from poly-A containing RNAs according to protocols provided by the TruSeq RNA sample preparation kits (Illumina).

value: Trophoblast stem (TS) cell

value: SATB1 knockdown

tag: Stage

value: chronic


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 345


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 344


title: SK1: chronic knockdown 1


title: SK3: chronic knockdown 3


title: SK2: chronic knockdown 2


title: SS4: chronic contol 4


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 343


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 342


title: SS3: chronic contol 3


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 341


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 339


title: AK4: acute knockdown 4

description: Rcho-1 TS cells were maintained in Stem State Medium for 4 days after transduced with control shRNA.

value: acute


title: SS2: chronic contol 2


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 340


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 338


title: rat sperm_Sample R19


title: AK3: acute knockdown 3


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 337


title: AS4: acute control 4


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 335


title: AK2: acute knockdown 2


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 334


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 333


title: AS3: acute control 3


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 332


title: AS2: acute control 2


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 331


title: AS1: acute control 1


title: SS1: chronic contol 1


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 328


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 326


title: AK1: acute knockdown 1


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 325


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 324


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 323


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 336


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 327


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 320


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 321


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 319


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 329


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 330


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 318


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 317


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038401

type: RNA

city: West Point

first: Keith

last: Tanis

address: 770 Sumnetown Pike

institute: Merck & Co, Inc

hyb_protocol: Purified Cy3 or Cy5 complementary RNA was hybridized to two microarrays with fluor reversal for 24 hr in a hybridization chamber, washed, and scanned. Sample studies utilized GPL15569 and others GPL3631 as indicated in the sample annotations. Each GEO sample represents the mean of the 2 fluor-reversed hybridizations.

scan_protocol: Arrays were scanned using a laser confocal scanner.

data_processing:
Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels using the Rosetta Resolver error model as described in PMID: 16522673.
The submitted raw data files include the mean intensity values from the Cy3,Cy5 fluor-reversed hybridizations.

source_name: Soleus; Day 15; Cerivastatin Control Pool

label_protocol: Total RNA was reverse transcribed using an oligo-dT primer containing a T7 RNA polymerase promoter site, followed by complementary strand synthesis using random hexamers. In vitro transcription (IVT) was then performed using RNA polymerase and the RNA was then labeled with one of two fluorescent dyes, Cy3 and Cy5.

extract_protocol: Trizol reagent (1 ml per 100 mg of tissue) was added to the tissue, and samples homogenized immediately. An aliquot of the homogenate was then transferred to a separate vial and chloroform extracted to remove proteins. The remaining tissue homogenate was stored at –70C for future use. The supernatant was then transferred to a separate vial, and RNA isolated using Qiagen RNeasy columns or 96-well plates as described by the manufacturer. Following RNA isolation, samples were treated with DNase to remove contaminating DNA, and quantified.

treatment_protocol: The compounds, vehicles, frequency of administration, dose levels and time points collected are presented in the sample annotations. In general, the study details were consistent between protocols and were as follows: male and/or female Sprague-Dawley CD (SD) or rats were obtained from Charles River Laboratories, Inc. (Raleigh, North Carolina). The rats were approximately seven to eight weeks of age and weighed from 125 to 325 grams at the start of the study. The animals were acclimated for approximately one week and randomized into the treatment and control groups. In general, five rats were included in each treatment group. Doses were calculated based on animal body weight, and the last dose was given 24 hours prior to necropsy in studies with daily dosing. All animals were fasted overnight prior to necropsy. Tissue samples (liver, kidney, heart, and skeletal muscle) were collected from each animal at necropsy. Tissue sections were removed and processed for histopathology assessment, and an additional adjacent tissue section removed and placed immediately on dry ice for genomic analyses, allowing for direct comparison of the gene expression response to histopathology outcome. For the skeletal muscle, the quadriceps muscle group was selected as a representative muscle, consisting of 3 muscles (vastus lateralis, vastus medialis, and rectus femoris) comprised of predominantly Type II (glycolytic) muscle fibers, and 1 muscle (vastus intermedius) comprised of predominantly Type I (oxidative) muscle fibers. Tissue samples were stored at –70C until RNA extraction.

tag: sample type

value: Study Compound Control Pool

tag: study

source_name: Skeletal Muscle (Soleus)

value: Skeletal Muscle (Soleus)

tag: compound

value: (PPARα) MSDA

tag: necropsy day

tag: dose

tag: dose unit

value: mkd

tag: animal number


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 322

tag: differentiation

tag: gfp

tag: genotype

value: IL23R Knockout

tag: cell type


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038399

tag: tissue


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 150mkd; #038403


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 316


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 314


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 315


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 150mkd; #038419


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 150mkd; #038415


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038387


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 150mkd; #038417


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038377


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038397


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 150mkd; #038421


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038393


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038371


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 312


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038373


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 311


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 310


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 313


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 025mkd; #038391


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 309


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038369


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038541

value: Cerivastatin+MSDA


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038363


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038523


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 308


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 306


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038533


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 307


title: US-1046071 vs. Soleus; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038529


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 301


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 304


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 303


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 305


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 302


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 298


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 299


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 300


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 015mkd 1126-005:1121

source_name: Quad Day 08 Vehicle Control Pool

source_name: Skeletal Muscle (Quad)

value: Skeletal Muscle (Quad)


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 000mkd 1126-005:1011


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 015mkd 1126-005:1124


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 015mkd 1126-005:1123


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 000mkd 1126-005:1009


title: Quad Day 08 Vehicle Control Pool vs. Quad; Day 08; MSDJ; 000mkd 1126-005:1010


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 297


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038541

source_name: Quad; Day 15; Cerivastatin Control Pool


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038535


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 296


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038523


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038539


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 295


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 294


title: Quad; Day 08; MSDJ; 000mkd 1126-005:1012 vs. Quad Day 08 Vehicle Control Pool


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 293


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 291


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 292


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 290


title: Th1 differentiated CD4 T Cell - eGFP_pos, IL23R Knockout, cell 289


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038371


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038369


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.5mkd; MSDA 150mkd; #038533


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038365


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038367


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 190

source_name: Th1 differentiated CD4 T Cell - eGFP_pos_Control

value: Control


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 189


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 188


title: US-1046072 vs. Quad; Day 15; Cerivastatin 0.0mkd; MSDA 000mkd; #038363


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 187


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 186


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 200 mkd #06-60216

source_name: Liver

value: Liver

value: Thioacetamide


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 100 mkd #06-60192


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 100 mkd #06-60198


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 200 mkd #06-60212


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 000 mkd #06-60156


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 185


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 184


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 192


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 191


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 000 mkd #06-60154


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 200 mkd #06-60208


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 183


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 182


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 000 mkd #06-60152


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 200 mkd #06-60210


title: Liver; Thioacetamide; Day 3 Control Pool vs. Liver; Thioacetamide; Day 3; 200 mkd #06-60214


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 181


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 200 mkd #06-60206


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 180


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 200 mkd #06-60202


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 179


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 200 mkd #06-60204


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 178


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 100 mkd #06-60188


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 100 mkd #06-60186


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 176


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 177


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 173


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 174


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 172


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 171


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 100 mkd #06-60182


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 168


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 169


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 175


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 000 mkd #06-60142


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 100 mkd #06-60184


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 166


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 167


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 000 mkd #06-60146


title: C1 (ip) Liver Day 3 Vehicle Control Pool (2) vs. Liver Day 3 Lithocholic Acid 16mkd # 1145

value: Lithocholic Acid


title: C1 (ip) Liver Day 3 Vehicle Control Pool (2) vs. Liver Day 3 Lithocholic Acid 16mkd # 1147


title: Liver; Thioacetamide; Day 2 Control Pool vs. Liver; Thioacetamide; Day 2; 000 mkd #06-60144


title: C1 (ip) Liver Day 3 Vehicle Control Pool (2) vs. Liver Day 3 Lithocholic Acid 16mkd # 1148


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 000 mkd #06-60038

source_name: Liver; Genipin; Day 3 Control Pool

value: Genipin


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 165

value: CD4 T Cells


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 075 mkd #06-60064


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 164


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 075 mkd #06-60062


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 163


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 170


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 075 mkd #06-60060


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 162


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 160


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 000 mkd #06-60034


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 161


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 000 mkd #06-60036


title: Liver; Genipin; Day 3 Control Pool vs. Liver; Genipin; Day 3; 075 mkd #06-60058


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 150 mkd #06-60088

source_name: Liver; Genipin; Day 2 Control Pool


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 150 mkd #06-60086


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 159


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 150 mkd #06-60084


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 000 mkd #06-60026


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 000 mkd #06-60024


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 150 mkd #06-60078


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 150 mkd #06-60072


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 158


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 157


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 156


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 154


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 155


title: Liver; Genipin; Day 2 Control Pool vs. Liver; Genipin; Day 2; 000 mkd #06-60022


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 153


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 151


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 152


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 60mg/kg #2035

source_name: Kidney Day 14 Vehicle Control Pool

source_name: Kidney

value: Kidney

value: Tobramycin


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 150


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 148


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 149


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 60mg/kg #2034


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 30mg/kg #2017


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 30mg/kg #2018


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 146


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 145


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 60mg/kg #2036


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 147


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 30mg/kg #2019


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 144


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 30mg/kg #2020


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Puromycin 20mg/kg #1970

value: Puromycin


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 142


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 141


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Tobramycin 60mg/kg #2033


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Puromycin 20mg/kg #1971


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Puromycin 20mg/kg #1969


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mg/kg #1938

value: Puromycin/Tobramycin


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Puromycin 20mg/kg #1972

value: Study Compound Control Pool


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 143


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 140


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mg/kg #1940


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 138


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Puromycin 75mg/kg #1981

source_name: Kidney Day 7 Vehicle Control Pool


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Puromycin 75mg/kg #1982


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Puromycin 75mg/kg #1984


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mg/kg #1936


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 135


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 136


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 137


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 133


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 134


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 139


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 132


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 131


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mg/kg #1937


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 129


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 130


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Puromycin 75mg/kg #1983


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mg/kg #1933


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 128


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mg/kg #1934


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mg/kg #1935


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 HCB 40mkd #2084

value: Hexachloro 1,3 butadiene


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 HCB 40mkd #2083


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 127


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 126


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 124


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 125


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 HCB 40mkd #2082


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mkd #2051


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 123


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mkd #2050


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mkd #2052


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 HCB 40mkd #2081


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 121


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 120


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) HCB 100mkd #2085


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) HCB 100mkd #2086


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mkd #2049


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) HCB 100mkd #2088


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 122


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 118


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 119


title: LTAD_siPSF_vehicle

description: Gene expression data from LTAD cells treated with vehicle (ethanol) after transfected with siPSF

hyb_protocol: The samples were hybridized to Human Gene-1.0 ST arrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-1_0-st-v1
program-name = Expression Console
program-version = 1.2.1.20

label: biotin

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

tag: cell line

value: LTAD

value: prostate cancer cells

tag: sirna

value: siPSF

tag: ligand

value: Vehicle


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) Vehicle 0mkd #2039

value: mkd


title: LTAD_siControl_No.10-3

description: Gene expression data from LTAD cells treated with No.10-3 after trasfected with siControl

value: siControl + No.10-3


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 117

value: Control


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 116


title: H889 hSCLC FOXA2 Input

source_name: H889 hSCLC FOXA2

tag: tissue/cell line

tag: tissue/cell type

value: Small cell lung cancer cell line

tag: passage

tag: antibody


title: LTAD_siControl_vehicle

description: Gene expression data from LTAD cells treated with vehicle (ethanol) after transfected with siControl

value: siControl


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) Vehicle 0mkd #2037

tag: sample type

tag: study

tag: compound


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 114


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) Vehicle 0mkd #2038

tag: necropsy day

tag: dose

tag: dose unit


title: LNCaP_DHT_No.10-3

description: Gene expression data from LNCaP cells  treated with DHT 10 nM and No.10-3

value: LNCaP

value: DHT 10 nM


title: H889 hSCLC FOXA2 ChIP

value: H3K27ac (Abcam, Ab4729)


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 D-Serine 750 mkd #2444

source_name: Kidney Day 3 Vehicle Control Pool

value: Kidney

value: D-serine

tag: animal number


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 D-Serine 750 mkd #2442


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 D-Serine 750 mkd #2443


title: LNCaP_DHT_control

description: Gene expression data from LNCaP cells treated with DHT 10 nM


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 Vehicle 0 mkd #2408


title: LNCaP_vehicle_No.10-3

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) and No.10-3


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 115

tag: differentiation

tag: gfp

tag: genotype

value: CD4 T Cells


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 112

tag: cell type


title: Sample_28

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method  Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

tag: cell line

tag: treatment

value: YK-S

tag: time point


title: Sample_26

value: YK-R


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 111


title: Sample_29


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 Vehicle 0 mkd #2406

value: Study Compound Control Pool

tag: tissue


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 D-Serine 750 mkd #2441


title: Sample_25


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 Vehicle 0 mkd #2405


title: Kidney Day 14 Vehicle Control Pool vs. Kidney Male Day 14 Vehicle 0mg/kg #1939

value: Puromycin/Tobramycin


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) Vehicle 0mkd #2040

value: Hexachloro 1,3 butadiene


title: Sample_30


title: Kidney Day 3 (6-9 hrs) Vehicle Control Pool vs. Kidney Male Day 3 (6-9 hrs) HCB 100mkd #2087


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 110


title: LNCaP_vehicle_control

description: Gene expression data from LNCaP cells treated with vehicle (ethanol)

value: prostate cancer cells

tag: sirna

tag: ligand

value: Vehicle


title: Sample_27


title: Kidney Day 3 Vehicle Control Pool vs. Kidney Male Day 3 Vehicle 0 mkd #2407

tag: sample type

value: mkd


title: Sample_24

value: DMSO


title: Sample_22


title: Sample_20


title: Sample_21


title: Sample_23


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 113

value: Control


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 109


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 108


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 106


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 107


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Allopurinol 100mkd #2144

tag: study

value: Allopurinol


title: Sample_19


title: Sample_17


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 105


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Allopurinol 100mkd #2142

tag: compound


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Allopurinol 100mkd #2143

tag: necropsy day


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 103


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Allopurinol 100mkd #2141

tag: dose


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 104


title: Sample_14


title: Sample_16


title: Sample_18


title: Sample_12


title: Sample_15


title: Sample_13


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 102


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mkd #2046

tag: dose unit


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mkd #2047

tag: animal number


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mkd #2045


title: Kidney Day 7 Vehicle Control Pool vs. Kidney Male Day 7 Vehicle 0mkd #2048


title: Sample_11


title: Sample_7


title: Sample_9


title: Sample_10


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 101

tag: differentiation


title: Sample_6


title: Sample_4


title: mouse sperm_Sample M4

source_name: mouse sperm

tag: strain

value: sperm


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 100

tag: gfp

tag: genotype


title: Sample_8

tag: cell line


title: mouse sperm_Sample M2


title: mouse sperm_Sample M3


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 99

tag: cell type


title: miR-206 Pulldown (PD) Rep 2 (AAGCCT)

city: El Cerrito

first: Christapher

middle: S

last: Morrissey

address: 7447 seaview Pl

institute: DNAnexus

description: PD-RNA Targets

data_processing:
Library strategy: miRNA pulldown
Raw sequencing reads were first analyzed with FastQC from the Babraham Institute
RNA-seq data meeting the FastQC quality standards were then quantified (counts and TPM) using Kallisto
Values for genes with an average TPM of <1 for replicates were designated as 0 TPMs
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: Tranfected FAPs

growth_protocol: Growth was in 20%FBS, 10%HS, 5ng/ml FGF, 1XPS, DMEM (GM), until cells were ~80% confluent

extract_protocol:
A miRNA pulldown procedure was used as described by Wani and Cloonan (2014)
Libraries were prepared using the CloneTech SMARTer and Nugen Oviation V2 kits per the manufacturer's protocol. ERCCs were included but not used for normalization.

treatment_protocol: Cells were  maintained for 48 hours in 10%HS, 1xPS, DMEM (BM) following transfection and then processed with the extraction protocol

tag: organ source

value: Skeletal Muscle

tag: cell source

value: Sorted Sca1+ FAPs

tag: molecule subtype

value: miR-206-biotin-PD RNA


title: mouse sperm_Sample M1

tag: tissue


title: Sample_3

tag: treatment

tag: time point


title: Sample_5


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 1mkd # 057802

source_name: Day 8, Control Pool

tag: sample type

tag: study

source_name: Heart

value: Heart

tag: compound

value: Isoproterenol


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 1mkd # 057796

tag: necropsy day

tag: dose

tag: dose unit


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 1mkd # 057804

tag: animal number


title: Sample_1

value: YK-S


title: Sample_2

value: YK-R


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 1mkd # 057810

value: Study Compound Control Pool


title: miR-Control Rep 2 (ACCTCA)

description: PD-RNA Targets

tag: strain

value: Control-biotin-PD RNA


title: miR-206 Pulldown (PD) Rep1 (AGTGAG)

description: PD-RNA Targets


title: miR-Control Rep1 (AACCAG)

description: PD-RNA Targets


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 97

tag: differentiation

tag: gfp

tag: genotype

value: CD4 T Cells


title: Th1 differentiated CD4 T Cell - eGFP_pos, Control, cell 98

tag: cell type


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 0mkd # 057590


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 287

source_name: Th1 differentiated CD4 T Cell - eGFP_neg_IL23R Knockout

value: IL23R Knockout


title: mouse sperm_Sample M5


title: H3K27me3_Tunicamycin_ChIPSeq

city: Shanghai

first: Xu

last: Wang

address: No. 639, Zhizaoju Road

country: China

institute: Shanghai Jiao Tong university, School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: bw

growth_protocol: MEFs were isolated from mice on postcoital day 12.5-13.5. Briefly, embryos were dissected into 10 ml of sterile PBS, voided of internal organs, and sheared through 18-gauge syringes in the presence of 0.25% trypsin/1 mM EDTA. After a 15 min incubation with gentle shaking at 37°C, DMEM with 10% fetal bovine serum (FBS) was added to inactivate trypsin. The cells were plated onto 100-mm cell culture dishes and incubated for 24 h at 37°C. Adherent cells were used as MEFs. All MEFs in this study were used within five passages.

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

treatment_protocol: Cells were treated with Vehicle (0.1% DMSO)or Tunicamycin (2μg/ml) for 6h.

tag: strain background

value: mouse embryonic fibroblasts

tag: passage

value: Tunicamycin (2μg/ml) for 6h

tag: chip antibody


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 286


title: H3K27me3_Vehicle_ChIPSeq

tag: treatment

value: Vehicle (0.1% DMSO) for 6h


title: input_Tunicamycin_DNA


title: H3K4me3_Vehicle_ChIPSeq


title: H3K4me3_Tunicamycin_ChIPSeq


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 0mkd # 057586

tag: tissue

value: mkd


title: Kidney, Wildtype_replicate_4 (ALc1-8)

city: Charlestown

first: Alexander

last: Marneros

state: MA

address: 13th Street

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: whole kidney

extract_protocol:
RNA was isolated from kidneys or cells with Trizol reagent (Life technologies) and further purified with the Directzol RNA MiniPrep kit from Zymo (R2050).
200ng of total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Ilumina (E7420L) was used. 15 cycles of PCR were done. Quality control of libraries was done via Bioanalyzer High Sensitivity DNA and Tape Station High Sensitivity D5000 Screen Tape. Quantification of the samples was done via qPCR using the BioRad CFX96. The reagent kit for qPCR was the Kapa Library Quantification Kit for Illumina (KK4824).

value: WT

value: whole kidney


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 0mkd # 057584

tag: sample type


title: Day 8, Control Pool vs. heart; Day 8; Isoproterenol 0mkd # 057582

tag: study


title: Kidney, Wildtype_replicate_3 (ALc1-6)


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 288


title: Kidney, Knockout_replicate_4 (ALc1-7)

value: KO Six2Cre+TFAP2Afl/flTFAP2Bfl/WT mice


title: Kidney, Wildtype_replicate_2 (ALc1-4)


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 284


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 283


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057826

source_name: Day 3 Control Pool

tag: compound


title: Kidney, Knockout_replicate_3 (ALc1-5)


title: Kidney, Knockout_replicate_1 (ALc1-1)


title: input_Vehicle_DNA


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 282


title: Kidney, Knockout_replicate_2 (ALc1-2)


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057824

tag: necropsy day


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 285


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 281


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 280


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057822

tag: dose


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057818

tag: dose unit


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057820

tag: animal number


title: Kidney, Wildtype_replicate_1 (ALc1-3)


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057816


title: GCEPB+_Replicate2

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

description:
gender: Female-Male
fpkm_RNAseq and counts_RNAseq

data_processing:
The reads were quality-trimmed to remove ambigious bases at read ends and adapter sequences using cutadapt and only uniquely mapped concordant mate pairs were used in the downstream analysis. The trimmed reads were aligned to the mouse reference genome sequence (mm10) using Tophat v2.1. Transcripts were assembled using Cufflinks, and the expression level estimation for each gene was calculated. These values are reported in fragments per kilobase of transcript per million fragments mapped (FPKM). Total read counts for each gene were calculated using HTseq.
genome build: mm10
processed data files format and content: fpkm_RNAseq.xls and counts_RNAseq.xls contain the gene expression levels in 15 samples.

source_name: Ventricular-Subventricular Zone

extract_protocol:
Cell populations were directly FACS-sorted into PicoPure RNA isolation kit (Arcturus) and immediately frozen on dry ice to increase RNA yield. All RNA preparations were treated with DNAse(Qiagen).
Whole transcriptome amplification was performed using the SMARTer Ultra Low Input RNA Sequencing-HV Kit (Clontech), which utilizes modified oligo(dT) primers. cDNA libraries were generated with Nextera transposase (Illumina) according to the manufacturer’s protocol. The samples were analyzed on an Agilent Bioanalyzer. High quality libraries were sequenced as paired-end 100bp reads on a HiSeq2000/2500 (Illumina) at Columbia Genome Center.

tag: gender

value: pooled male and female

tag: strain


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057814


title: GCEPB-_Replicate1


title: GCEPB-_Replicate2


title: GCEPB+_Replicate1


title: GCPB+_Replicate2


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 279

tag: differentiation

tag: gfp


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 1mkd # 057812


title: GCPB+_Replicate1


title: GPB+_Replicate2


title: GPB+_Replicate1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 278

tag: genotype

tag: cell type


title: CTX-RNAseq-Replicate2

source_name: Cortex


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 277


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 276


title: CTX-RNAseq-Replicate1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 275


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 274


title: CGP37157 treated C.elegans rep2 [CGP_rep2_04_12]

city: Valladolid.

first: Javier

last: Alvarez

address: Calle Sanz y Forés, 3

country: Spain

institute: IBGM, CSIC / Univerity of Valladolid

data_processing:
Mapping vs reference genome (HISAT2)
Analysis of differential expression (multi QC)
Reads count (FeatureCounts)
Sttistical analysis (DESeq2, EdgeR, SARTools)
Supplementary_files_format_and_content: DESeq/EdgeR expression analysis

organism: Caenorhabditis elegans

source_name: CGP37157 treated C.elegans

growth_protocol: For worm synchronization, eggs were placed overnight in NGM plates without OP50 to cause L1 larvae arrest. After 12 hours, L1 larvae were transferred to NGM plates seeded with OP50 and let develop at 20ºC. As soon as they reach the young adult stage, worms were transferred to control and treatment (50µM CGP37157) seeded plates, incubated at 20ºC and transferred every day to new plates. At day 5 of treatment, total RNA extraction was performed.

extract_protocol:
control and treated worms were collected with distilled H2O, transferred to a Falcon tube and washed three times to eliminate eggs or larvae left in the plates. Then they were transferred to an eppendorf tube, the rest of the supernatant was carefully removed and three freezing-unfreezing cycles in liquid nitrogen were performed.  Then, 10-20 silica beads and 500 µl of TRizolTM were added to each frozen sample, samples were homogenized using a beads homogenizer for 1 minute and incubated in ice for 5 more minutes. Then 100µl of chloroform were added to each sample, incubated for 3 minutes and centrifuged at 4ºC, 15 minutes at 15.000 rpm. The upper phase was then transferred to another eppendorf tube and finally, a solution 1:1 (v/v) of the sample and Ethanol 70% was prepared. For RNA purification, the QIAGEN RNEasy Mini Kit was used.
1 microgram RNA was prepared using TruSeq Stranded mRNA kit, following Illumina instructions. RNA quality and quantity was assesed using  a Fragment Analyzer (AATI) and Qubit (ThermoFisher). Libraries run on a HiSeq1500 Illumina in 100 cicles paired-end reads.

treatment_protocol: 50µM CGP37157 seeded plates, incubated at 20ºC

tag: strain background

tag: age

value: 5 days old nematodes


title: CGP37157 treated C.elegans rep1 [CGP_rep1_02_12]

tag: treatment


title: CGP37157 treated C.elegans rep3 [CGP_rep3_17_12]


title: WT C. elegans control rep.3 [Control_rep3_17_12]

source_name: WT C. elegans control

value: none (control)


title: WT C. elegans control rep.2 [Control_rep2_04_12]


title: WT C. elegans control rep.1 [Control_rep1_02_12]


title: NCF003 - neonatal cardiac fibroblast

city: Medford

first: Lauren

middle: D

last: Black III

address: 4 Colby Street

department: Biomedical Engineering

institute: Tufts University

data_processing:
sequencing and base-calling performed on the Illumina HiSeq 2500 and software installed on system via the Tufts University Core Facility genomics division (TUCF Genomics)
sequenced reads were quality-checked with FASTQC and adapter-trimmed with trimmomatic-0.39, and mapped to the Rn6 rat whole genome using STAR v 2.5.2b using settings --runThreadN 16 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Read counting was performed in the featureCounts by importing Aligned.sortedByCoord.out.bam files from STAR into subread/1.6.3.
featureCounts read counts output was loaded into the DESeq2 environment in R for normalization of gene counts and downstream analysis
Genome_build: Rn6
Supplementary_files_format_and_content: Raw gene counts for all mapped genes and all samples
Supplementary_files_format_and_content: DESeq2-normalized gene counts

source_name: Cardiac fibroblast - heart

growth_protocol: P0 isolated fetal, neonatal, and adult Sprague Dawley rat cardiac fibroblasts were cultured to confluency in T75 flasks, in DMEM supplemented with 1% Penicillin/Streptomycin, 10% fetal bovine serum, and 0.1mM ascorbic acid.

extract_protocol:
Cells were lysed with 1mL of ice-cold TRIzol reagent and RNA was isolated via manufacturer protocol - 200uL of cholorform were mixed into the 1mL of trizol/lysate, and aqueous upper layer of RNA was isolated and purified of chemical contaminants and gDNA via a SurePrep RNA cleanup and concentration kit, and ThermoScientific RapidOut DNA removal kit. RNA was quantified on a Nanodrop 2000 UV-vis spectrophotometer and stored at -80C until further use.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Cardiac fibroblast - heart

value: Sprague Dawley

value: P1 - postnatal day 1


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 273

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_expression_tpm.txt.gz: tab-delimited text table (genes x cells) of TPM-normalized gene expression values.  cell_metadata.txt: tab-delimited table which contains GFP label, genotype, and stimulation for each cell.


title: NCF002 - neonatal cardiac fibroblast


title: NCF001 - neonatal cardiac fibroblast


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 272


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 0mkd # 057602

tag: sample type

value: Study Compound Control Pool

value: Heart

value: Isoproterenol


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 0mkd # 057598

tag: study


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 1mkd # 057838

source_name: Day 2 Control Pool

tag: compound


title: ACF003 - adult cardiac fibroblast

value: 7-week old


title: ACF002 - adult cardiac fibroblast


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 1mkd # 057836

tag: necropsy day


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 0mkd # 057596

tag: dose


title: ACF001 - adult cardiac fibroblast


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 1mkd # 057830

tag: dose unit


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 271

value: IL23R Knockout

value: CD4 T Cells


title: Day 3 Control Pool vs. heart; Day 3; Isoproterenol 0mkd # 057600

tag: animal number


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 268


title: FCF001 - fetal cardiac fibroblast

value: E18 - embryonic day 18


title: IR-7 rep4

city: Seoul

first: Yunhyeong

last: Kim

address: kyunghee daero 23

country: South Korea

institute: KYH

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Tooth and periodontal ligament

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Tooth and periodontal ligament

value: post natal day 21

value: IR

tag: time

value: 7 days


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 1mkd # 057832

value: mkd


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 270

extract_protocol:
Spleen and lymph nodes were extracted and then a single-cell suspension was prepared by homogenization with a syringe plunger and debris was filtered with a 70um filter. Red blood cells were lysed with ACK lysis buffer from Lonza. CD4+ T cells were enriched using a bead protocol from Miltenyi Biotech (cat #. 130-117-043) and then stained with anti-CD44 (clone IM7), anti-CD62L (clone Mel14), anti-CD4 (clone RM4-5) and anti-CD25 (clone PC61) in preparation for FACS. Naive T cells were sorted based on CD44lowCD62LhiCD4+CD25-.
T cells were sorted into 96-well plates containing 5 μl TCL Buffer (QIAGEN) with 1% 2-mercaptoethanol, centrifuged and frozen at −80 °C.  Single-cell sequencing libraries were then created using the Smart-seq2 protocol (Picelli et al., Nature Methods 2014) and carried out as described in Singer et. al, Cell 2016.


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 267


title: IR-7 rep1


title: FCF002 - fetal cardiac fibroblast

tag: strain


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 269

tag: differentiation


title: IR-7 rep5


title: IR-3 rep5

value: 3 days


title: IR-3 rep4


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0.25mkd # 057786


title: IR-7 rep3


title: FCF003 - fetal cardiac fibroblast


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0.25mkd # 057780


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0mkd # 057618


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 265

tag: gfp


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 264

tag: genotype


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0.25mkd # 057782


title: IR-3 rep1


title: IR-7 rep2


title: IR-3 rep3


title: IR-3 rep2


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0mkd # 057612


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 266

tag: cell type


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 263


title: DR-7 rep6

value: DR


title: DR-7 rep4


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 261


title: IR-3 rep6


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 262


title: IR-7 rep6


title: DR-7 rep3


title: DR-7 rep2


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0mkd # 057614


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 260


title: DR-3 rep6


title: Day 2 Control Pool vs. heart; Day 2; Isoproterenol 0mkd # 057616


title: US-1098243 vs. Heart; Day 14; Angiotensin II; 984mkd # 053376

source_name: Heart Day 14 Angiotensin II Control pool

value: Angiotensin II


title: DR-3 rep5


title: DR-3 rep4


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 258


title: DR-3 rep3


title: DR-7 rep1


title: DR-3 rep1


title: DR-3 rep2


title: Th1 differentiated CD4 T Cell - eGFP_neg, IL23R Knockout, cell 257