title: 0mm_1124

source_name: distance from tumor, patient id

tag: distance from tumor


title: miRNA_LTα/β - MYC, control, replicate 1

status: Public on Sep 19 2018

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

data_processing:
OpenArray Digital PCR Software Software (v1.0, Applied Biosystems) was used to analyze and review the amplification plots and threshold cycle (Ct) values obtained. Default analysis settings were used, except that for baseline estimations data from cycles 2-10 were used, and that for some samples the minimum signal value was set at 100 instead of the default value of 300. Data was then exported, and further analyzed in R using the Bioconductor packages HTqPCR [PMID: 19808880] and limma [PMID: 25605792]. In HTqPCR, the minimum and maximum allowable Ct value were set at 8 and 31, respectively.
The qPCR data was normalized by the ΔCt method, using for each sample as internal reference the mean Ct value of 5 endogenous small non-coding RNA controls (U87, Y1, U6, snoRNA135, snoRNA202).
Next, only those miRNAs that were reliably expressed (i.e. Ct<31) in all samples were included for further analysis. This stringent filtering was applied to limit the screening to a set of robustly expressed miRNAs and to increase statistical power, and resulted in the removal of 620 miRNAs. The remaining 130 miRNAs were included in the statistical analysis.
The non-normalized data file reports the Ct values of 846 miRNAs and controls (non-normalized data). Note that some controls are present multiple times. Ct values of 40 indicates N/A.
The file Feature Category reports the Feature Category (i.e. "OK" and "Undetermined") based on expression (Ct-value) of the target. Features having Ct>31 were considered non-expressed, and were thus labeled "Undetermined".
The file normalized  reports the ΔCt values of 130 robustly expressed miRNAs, obtained after filtering as described above. (ΔCt normalized data).

label: FAMTP

molecule: total RNA

organism: Mus musculus

source_name: control liver tissue sample, obtained from sex- and age-matched transgene negative mouse (LT/MYC experiment)

label_protocol: miRNA expression levels were profiled using the TaqMan OpenArray Rodent MicroRNA Panel (Applied Biosystems; cat.no. 4461105). This platform allows the simultaneous profiling of 750 well-characterized miRNAs (miRBase v15) and 6 controls. Samples were processed according to the manufacturer’s instructions. In brief, for each sample 100ng of total RNA (that included the miRNA fraction) was reverse transcribed using Megaplex RT primers in a set of two pre-defined pools (Pool A and Pool B), each pool contained 381 stem-looped RT primers (375 miRNA targets, 5 positive controls, 1 negative control). The recommended RT thermal cycling conditions were used: i.e. [16°C, 2 min; 42°C, 1 min; 50°C, 1 sec for 40 cycles]; 85°C, 5 min; 4°C hold. The cDNA products (2.5µl) then underwent unbiased PCR preamplification using Megaplex PreAmp Primers in a set of two pools (Pool A and Pool B) of gene-specific forward and reverse primers. Thermal cycling conditions were: 95°C 10 min; 55°C, 2 min; 72°C, 2 min; [95°C, 15 sec, 60°C, 4 min for 12 cycles], 99.9°C, 10 min; 4°C hold. The preamplified cDNA products (4µL) were subsequently 40x diluted in 0.1X TE buffer pH 8.0, and subjected to real-time PCR amplification and analysis using the TaqMan OpenArray Rodent MicroRNA Panel in 3072-well microfluidic (33nL) OpenArray plates that contained dried TaqMan primers and probes for miRNAs and controls.

growth_protocol: Diethylnitrosamine (DEN) driven liver tumors [PMID: 15329734], Lymphotoxin-α/b-(LTa/b) driven tumors [PMID: 15661974] and Myc-driven liver tumors [PMID: 17589519] were generated as described previously. In brief, for generation of DEN-driven tumors, mice were given intraperitoneal injections of DEN (Sigma) at a dose of 10 mg per kg body weight at 15 d of age [PMID: 26502405]. Mice were observed for development of tumors at 9 months of age. For LTα/β driven tumors, tg1223 mice expressing LTα and -β in a liver-specific manner at high level were followed for 12 months for tumor development [PMID: 19800575]. Finally, for Myc-driven liver tumors, TRE-MYC mice were crossed to LAP-tTA (liver-specific promoter) mice. Animals were maintained on doxycycline (200 mg/kg doxy chow) to suppress MYC expression until 8 weeks of age. Doxycycline was then removed, and mice were followed for evidence of tumor formation [PMID: 19061838].

extract_protocol: Total RNA, along with miRNA, was isolated  by Directzol RNA Miniprep (Zymo Research, Irvine, CA). RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for analysis only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free access to chow and water. At the indicated time points, mice were killed and livers were removed. Livers were macroscopically dissected and tumor material, non-tumorous control liver tissue as well as liver tissue from untreated, sex- and age-matched control mice were immediately snap frozen, followed by histopathological confirmation of the tumor tissue.

tag: experiment

value: LT/MYC

tag: mouse id

tag: tissue

value: liver


title: DEN, control, replicate 5

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.40.2).

label: biotin

source_name: control liver tissue sample, obtained from untreated, sex- and age-matched control mouse (DEN experiment)

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

value: DEN


title: miRNA_DEN, tumor, replicate 5

source_name: tumor liver tissue sample, obtained from diethylnitrosamine (DEN)-treated mouse (DEN experiment)


title: DEN, NTL, replicate 2

source_name: non-tumorous liver (NTL) tissue sample, obtained from diethylnitrosamine (DEN)-treated mouse (DEN experiment)


title: set2_invivo_GFP_Plus

type: SRA

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

country: USA

institute: University of Alabama at Birmingham

description: Sorted naïve IL-2.eGFP CD4 T cells were transferred into ActA-LM infected recipients. Total RNA was isolated from ex-vivo sorted CD69+ GFP+ CD4 T cells.

library_source: transcriptomic

data_processing:
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build GRCm38 using Tophat2 (version 2.0.12). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample

source_name: Ex-vivo CD69+ IL-2.eGFP+ CD4 T cells

growth_protocol: All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.

extract_protocol:
Total RNA was isolated with Qiazol and miRNeasy micro kits according to manufacturer’s recommendations (Qiagen 217084 and 79306)
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: For in vitro experiments, sorted naïve IL2.eGFP CD4 or CD8 T cells were stimulated with 5ug/mL anti-CD3, 0.5ug/mL anti-CD28 and irradiated CD4-depleted feeders for 16-20hrs. For ex vivo experiments, sorted naïve IL2.eGFP CD4 T cells were transferred into ActA-LM infected mice and recovered after 18-24hrs. For both experiments, total RNA was isolated from sorted CD69+ IL-2.eGFP+ and CD69+ IL-2.eGFP– CD4 T cells.

tag: strain

value: Splenic CD4 T cells

tag: genotype


title: set3_invivo_GFP_Minus

description: Sorted naïve IL-2.eGFP CD4 T cells were transferred into ActA-LM infected recipients. Total RNA was isolated from ex-vivo sorted CD69+ GFP– CD4 T cells.

source_name: Ex-vivo CD69+ IL-2.eGFP– CD4 T cells


title: DEN, NTL, replicate 1


title: miRNA_LTα/β - MYC, control, replicate 2


title: DEN, control, replicate 4


title: DEN, control, replicate 3


title: 0mm_1122

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

hyb_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

data_processing: Gene-level probeset summary of microarray data were obtained using RMA background correction and quantile normalization provided in Expression Console Software, version 1.4.1 (Affymetrix).  Control probesets and probesets lacking mRNA accession tags were removed from further analysis.  Statistical analysis was performed using the limma R package with paired sample comparison.

organism: Homo sapiens

growth_protocol: 108 samples taken from patients at tumor, 5mm, 10mm, 15mm, 20mm from tumor were subjected to microarray analysis using HG-U133 Plus 2 affymetrix arrays

extract_protocol: RNA was isolated QIAGEN RNeasy MinElute Cleanup Kit. RNA quantity and quality for all samples were determined by bioanalysis (Agilent Technologies), and samples stored in nuclease-free water at −80°C. 10 μg of pooled RNA was used for microarray analysis using HG-U133 Plus 2 (Affymetrix), according to the manufacturer instructions

tag: patient id


title: miRNA_DEN, tumor, replicate 3


title: set2_invivo_GFP_Minus


title: 0mm_1121

scan_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity,  located at NYU Health NY, NY


title: PIM1-overexpressing PC3 + multi-mutant NFACT1 replicate

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

hyb_protocol: The labeled RNA was purified using Quiagen Rneasy mini spin columns and quantified using NanoDrop UV-VIS Spectrophotometer ver. The hybridization was performed in Agilent 2X GE Hybridization Buffer HI-RPM according to Agilent guidelines in Agilent hybridization oven at 65 degrees C 10rpm for 19 hours.

scan_protocol: Scanned on Agilent scanner G2565CA. Images were quantified using Agilent Feature Extraction ver. 11.0.1.1

data_processing: Raw mRNA expression values were imported using limma read.maimages function. Low quality probes were filtered using the distribution of negative control probes as reference.

source_name: PC-3 cells stably transfected with PIM1-overexpressing vector and transiently transfected with multi-mutant NFATC1-overexpessing vector

label_protocol: 100ng of total RNA were labeled using the Agilent Low Input Quick Amp labeling kit according to the manufacturer’s protocol

growth_protocol: The human androgen-independent prostate epithelial adenocarcinoma cell line PC-3 (American Type Culture Collection) was maintained in Roswell Park Memorial Institute (RPMI) -1640 medium, supplemented with 10% fetal bovine serum, L-glutamine and antibiotics. To prepare PC-3-derived cell lines stably overexpressing human PIM family members, PC-3 cells were transfected with pcDNA3.1 based expression vector for Pim-1 or mock-transfected with the empty vector (Thermo Fisher Scientific, Waltham, MA, USA). In addition, all cells were cotransfected with the pCMV-Td-Tomato plasmid (Clontech Laboratories Inc., Mountain View, CA, USA) to be used as a fluorescent follow-up marker. All transfections were performed with Fugene 6 (Promega, Madison, WI) in 3:1 ratio to DNA. After an overnight incubation, positively transfected cells were enriched by antibiotic selection with G418 (Fisher Scientific, Geel, Belgium), first using 300 μg/ml for 48 h and thereafter 500 μg/ml for 14 days. Medium was changed every day during the selection. After selection, maintenance of the transfected plasmids in the stable cell lines generated from pools of cells was ensured by supplementing culture medium with 200 μg/ml of G418.

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

treatment_protocol: PC-3 cells with or without stable PIM1 overexpression were  transiently transfected with wild-type or multi mutant NFATC1 with Fugene HD transfection reagent in 3:1 ratio to DNA.

tag: cell line


title: 0mm_1105

label_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY


title: 0mm_1108


title: 0mm_1120


title: DEN, control, replicate 1


title: 0mm_11205


title: set2_invitro_GFP_Plus

description: Sorted naïve IL-2.eGFP CD4 T cells were stimulated in-vitro. Total RNA was isolated from sorted CD69+ GFP+ T cells.

source_name: In-vitro stimulated CD69+ IL-2.eGFP+ CD4 T cells


title: set2_invitro_GFP_Minus

description: Sorted naïve IL-2.eGFP CD4 T cells were stimulated in-vitro. Total RNA was isolated from sorted CD69+ GFP– T cells.

source_name: In-vitro stimulated CD69+ IL-2.eGFP– CD4 T cells


title: miRNA_DEN, tumor, replicate 1


title: set1_invivo_GFP_Plus


title: set1_invivo_GFP_Minus


title: miRNA_DEN, NTL, replicate 4


title: miRNA_DEN, NTL, replicate 5


title: set1_invitro_GFP_Plus


title: miRNA_DEN, tumor, replicate 2


title: DEN, control, replicate 2


title: PIM1 overexpressing PC3+ wt NFATC1 replicate

source_name: PC-3 cells stably transfected with PIM1-overexpressing vector and transiently transfected with wt NFATC1-overexpressing vector


title: PIM1 overexpressing PC3+ wt NFATC1


title: PIM1-overexpressing PC3 + multi-mutant NFACT1

source_name: PC-3 cells stably transfected with PIM1-overexpressing vector and transiently transfected with multi-mutant NFATC1-overexpressing vector


title: control PC3 + multi-mutant NFATC1 replicate

source_name: PC-3 cells stably transfected with control vector and transiently transfected with multi-mutant NFATC1-overexpressing vector


title: miRNA_DEN, NTL, replicate 3


title: miRNA_DEN, NTL, replicate 1


title: set1_invitro_GFP_Minus


title: control PC3+ wt NFATC1 replicate

source_name: PC-3 cells stably transfected with control vector and transiently transfected with wt NFATC1-overexpressing vector


title: set2 naïve

description: Sorted naïve IL-2.eGFP CD4 T cells

library_source: genomic

data_processing:
fastq QC fastqc
remove adapter trim_galore v0.4.1
mapping Bowtie2 (v2.2.5)
filter/remove duplicates samtools v0.1.19/Picard v2.6.0
peak-calling MACS2 v.2.1.0
normalization/tagcount/bedgraph HOMER v4.9.0
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using HOMER

molecule: genomic DNA

source_name: Sorted naïve IL-2.eGFP CD4 T cells

extract_protocol:
cells sorted from activated CD4 T cells, washed with 1X PBS, and nuclei were isolated. The transposition reaction was carried out using Nextera DNA Sample Preparation Kit
Illumina
Nextera DNA Sample Preparation Kit

treatment_protocol: in vitro activation with 5 ug/ml anti-CD3 and irradiated CD4-depleted feeder cells

value: C57BL/6 Il2eGFP

value: spleen/lymh nodes


title: control PC3 + multi-mutant NFATC1


title: 0mm_1100


title: set2 Il2pos

description: In-vitro stimulated CD69+ IL-2.eGFP+ CD4 T cells


title: control PC3+ wt NFATC1


title: set2 Il2neg

description: In-vitro stimulated CD69+ IL-2.eGFP– CD4 T cells


title: miRNA_DEN, control, replicate 5


title: SK-Hep1 rep 2

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

country: China

institute: West China Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: SK-Hep1 cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: SK-Hep1 cells

tag: screening


title: Xeno-SK-Hep1 rep 1

value: lung metastasis screening


title: Xeno-Hep3B rep 1

source_name: Hep3B cells

value: Hep3B cells


title: Xeno-SK-Hep1 rep 2


title: Xeno-Hep3B rep 2


title: PIM1-overexpressing PC3 replicate

source_name: PC-3 cells stably transfected with PIM1-overexpressing vector


title: miRNA_DEN, control, replicate 4


title: set1 naïve

description: Sorted naïve IL-2.eGFP CD4 T cells


title: miRNA_DEN, control, replicate 3


title: SK-Hep1 rep 1


title: control PC3 replicate

source_name: PC-3 cells stably transfected with control vector


title: miRNA_DEN, NTL, replicate 2


title: control PC3


title: miRNA_DEN, control, replicate 2

source_name: control liver tissue sample, obtained from untreated, sex- and age-matched control mouse (DEN experiment)


title: set1 Il2neg


title: Hep3B rep 1


title: Hep3B rep 2


title: miRNA_DEN, control, replicate 1


title: set1 Il2pos


title: PIM1-overexpressing PC3


title: STM_plus_2

status: Public on Sep 18 2018

city: Hamilton

first: Brian

last: Coombes

state: ON

address: MDCL 2108. 1200 Main St W, McMaster University

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
processed data file: NC_016810_transcripts.txt
processed data file: NC_017718_transcripts.txt
processed data file: NC_017719_transcripts.txt
processed data file: NC_017720_transcripts.txt

data_processing:
Multiple files for each sample were concatenated into a single file. SsrB- and SsrB+ files for each species were loaded on to Rockhopper for alignment to the referene genome and plasmids if applicable.
Genome_build: Reference genome for S. bongori NC_015761. Reference genome for S. Typhimurium NC_016810. Reference for S. Typhimurium plasmids NC_017718 (pCol1B9), NC_017719 (pRSF), NC_017720 (pSLT)
Reads were mapped to the respective genomes with Rockhopper and differential gene expression (SsrB+/SsrB-) was calculated for both species.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial culture

growth_protocol: Overnight bacterial cultures were sub-cultured 1:50 in LB-kanamycin and grown at shaking for 2.5 hours. These were then sub-cultured 1:50 into LPM pH 5.8 and grown to mid log (OD600=0.4-0.5). Bacteria were then pelleted by centrifugation for RNA extraction.

extract_protocol:
RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, resuspended in water for Dnase I treatment for 30 min. Dnase I was inactivated with inactivation beads and RNA was re-precipitated with isopropanol, washed with 75% ethanol, and resuspended in water
RNA was rRNA depleted with RiboZero, and strand specific dUTP sequencing was performed on an Illumina Hi-Seq following standard Illumina protocols

tag: genetic background

value: ∆ssrAB

tag: plasmid

value: pWSK129-PssrA-ssrB D56E


title: STM_minus_1


title: STM_minus_2


title: STM_minus_3


title: STM_plus_3


title: STM_plus_1


title: Dazl GC1 iCLIP 2

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

description: Stable monoclonal cell line with doxycyline inducible Dazl expression

data_processing:
Reads were filtered by quality, collapsed and adapters removed using Galaxy
Reads mapped using Olego (Wu et al., 2013).
Genome_build: mm9
Supplementary_files_format_and_content: BED file contains processed reads from individual samples (color coded:)

source_name: GC1-spg cells (parental line)

growth_protocol: The Dazl open reading frame was PCR amplified using Phusion polymerase (NEB) from WT CD1 mouse cDNA with the following primers: Dazl ORF F: (ACACTCGAGCCACCATGTCTGCCACAACTTCTGAGG), Dazl ORF R: ACAGGATCCTTAGCAGAGATGATCAGATTTAAGC) Dazl ORF was then cloned into pcDNA 4/TO/myc-His C response element (ThermoFisher). Stable monoclonal cell lines were generated from parental GC-1spg cells (ATCC) using the T-Rex System (ThermoFisher) according to manufacturer’s instructions. Monoclonal cell populations were selected with blasticidin and Zeocin (ThermoFisher) antibiotics and tested for Dazl induction by doxycycline induction and western blotting. GC-1spg cells (ATCC) were cultured in DMEM, high glucose medium (ThermoFisher) supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U/mL penicillin, and 100μg/mL streptomycin (all from ThermoFisher) at 37oC, 5% CO2. GC-1spg cell with inducible Dazl expression were maintained in high glucose medium (ThermoFisher) supplemented with 10% (v/v) Tet-system approved FBS (Clontech), 100U/mL penicillin, 100μg/mL streptomycin, 5 μg/mL blasticidin, and 300 μg/mL Zeocin (all from ThermoFisher) at 37oC, 5% CO2.

extract_protocol: Libraries were processed similarly to HITS-CLIP libraries (Hannigan et al., 2017) with the following changes -  No 5’linker ligation step was performed.  The RT primer contained iSp18 spacers and phosphorylated 5’ end permitting circularization of first strand cDNA (after gel purification) to generate a PCR template without linearization (as described by (Ingolia, 2010))

treatment_protocol: Iinducible GC1-spg cells were treated with 10 ng/mL doxycycline and harvested after 24 hours.

tag: agent

value: Doxycycline

value: Type B Spermatogonial Cells


title: Dazl GC1 iCLIP 3


title: GC1-spg +dox 1 RNA-Seq

data_processing:
Libraries were sequenced at the CWRU Sequencing Core. Identical reads within each library were collapsed and rRNA sequences removed. Read mapping, gene expression quantification, and differential gene expression analysis was performed using Olego and Quantas (Wu et al., 2013)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

growth_protocol: The Dazl open reading frame was PCR amplified using Phusion polymerase (NEB) from WT CD1 mouse cDNA with the following primers: Dazl ORF F: (ACACTCGAGCCACCATGTCTGCCACAACTTCTGAGG), Dazl ORF R: ACAGGATCCTTAGCAGAGATGATCAGATTTAAGC) Dazl ORF was then cloned into pcDNA 4/TO/myc-His C response element (ThermoFisher). Stable monoclonal cell lines were generated from parental GC-1spg cells using the T-Rex System (ThermoFisher) according to manufacturer?s instructions. Monoclonal cell populations were selected with blasticidin and Zeocin (ThermoFisher) antibiotics and tested for Dazl induction by doxycycline induction and western blotting. GC-1spg cells (ATCC) were cultured in DMEM, high glucose medium (ThermoFisher) supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U/mL penicillin, and 100?g/mL streptomycin (all from ThermoFisher) at 37oC, 5% CO2. GC-1spg cell with inducible Dazl expression were maintained in high glucose medium (ThermoFisher) supplemented with 10% (v/v) Tet-system approved FBS (Clontech), 100U/mL penicillin, 100?g/mL streptomycin, 5 ?g/mL blasticidin, and 300 ?g/mL Zeocin (all from ThermoFisher) at 37oC, 5% CO2.

extract_protocol: Following induction, cells were immediately scraped into lysis buffer containing the translation elongation inhibitor emetine. (10mM Tris-HCl(7.4), 5mM MgCl2, 100mM KCl, 1% TritonX-100, 0.1mg/mL emetine, 2mM DTT, cOmplete Mini EDTA-free protease inhibitor). 50% of the lysate was treated with 0.2U/uL RNaseI (ThermoFisher) for 30 minutes at room temperature. The remaining lysate (gradient input) was reserved for RNA-Seq library preparation. Ribosome protected footprints were run on a 10-45% sucrose gradient and monosome associated RNA was purified using ethanol precipitation followed by miRNeasy Kit (Qiagen). In parallel, RNA from the gradient inputs was purified using the RNeasy Mini Kit (Qiagen), fragmented by partial alkaline hydrolysis and size selected. Purified RNA fragments from monosome fractions and gradient inputs were RQ1 DNase treated (Promega), rRNA depleted (RiboZero rRNA Removal kit ? human/ mouse/ rat, Illumina) and processed concurrently. Libraries were processed similarly to HITS-CLIP libraries (Hannigan et al., 2017) with the following changes - No 5' linker ligation step was used. A preadenylated 3? linker was used in place of the traditional 3? RNA linker (as described in Ingolia et al., 2012).   The RT primer contained a iSp18 spacers and phosphorylated 5? end permitting circularization of first strand cDNA (after gel purification) to generate a PCR template without linearization (as described by (Ingolia, 2010))

treatment_protocol: Three 10 cm plates in triplicate of inducible GC1-spg cells were treated with 10 ng/mL doxycycline (GC1-spg +dox 1, 2, and 3 (lysates were later split to become samples 4, 5, 6, 10, 11, and 12)). Three 10 cm plates in triplicate were left untreated (GC1-spg -dox 1, 2, and 3 (lysate were later split to become samples 1, 2, 3, 7, 8, and 9)). Cell were harvested after 24 hours.


title: GC1-spg -dox 3 RNA-Seq


title: GC1-spg -dox 2 RNA-Seq


title: GC1-spg +dox 3 RNA-Seq


title: GC1-spg -dox 1 RNA-Seq


title: GC1-spg +dox 3 Ribsome Profiling

data_processing:
Library strategy: Ribo-Seq
Libraries were sequenced at the CWRU Sequencing Core. Identical reads within each library were collapsed and rRNA sequences removed. Read mapping, gene expression quantification, and differential gene expression analysis was performed using Olego and Quantas (Wu et al., 2013)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph


title: Dazl GC1 iCLIP 1


title: GC1-spg +dox 1 Ribsome Profiling


title: GC1-spg -dox 3 Ribsome Profiling


title: GC1-spg +dox 2 Ribsome Profiling


title: GC1-spg -dox 1 Ribsome Profiling


title: RNA-seq-WT2-L10

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was applied to calculate raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw read counts from RNA-seq samples.

source_name: Mammary gland

growth_protocol: Mouse mammary tissues were harvested at day one and ten of lactation (L1 and L10).

extract_protocol:
Total RNA was extracted from frozen mammary tissue from wild type mice at day one and ten of lactation and purified with RNeasy Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen).
Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 2500 instrument (Illumina).

tag: strain/background

tag: genotype/variation

value: wild-type

tag: Stage

value: Lactation day 10

value: Mammary gland


title: RNA-seq-WT4-L1

value: Lactation day 1


title: RNA-seq-WT3-L10


title: RNA-seq-WT1-L10


title: ChIP-seq-Kidney-E12-Ramp3-STAT3_rep2

data_processing:
The ChIP-seq analysis workflow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012) with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied for the generation of bedGraph files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bedGraph: bedGraph of ChIP-seq.

source_name: Kidney

growth_protocol: Mouse mammary and kidney tissues were harvested at day one and ten of lactation (L1 and L10).

extract_protocol: Libraries for sequencing were prepared using standard Illumina protocols.

value: Kidney

tag: chip antibody

value: STAT3 (Santa Cruz, sc-482)


title: RNA-seq-WT1-L1


title: ChIP-seq-Kidney-E12-Ramp3-Pol2_rep2

value: RNA polymerase II (Abcam, ab5408)


title: RNA-seq-WT2-L1


title: RNA-seq-WT4-L10


title: ChIP-seq-Kidney-E12-Ramp3-Pol2_rep1


title: ChIP-seq-Kidney-E12-Ramp3-GR_rep2

value: GR (Thermo Scientific, PA1-511A)


title: ChIP-seq-Kidney-E12-Ramp3-H3K27ac_rep2

value: H3K27ac (Abcam, ab4729)


title: GC1-spg +dox 2 RNA-Seq


title: ChIP-seq-Kidney-E12-Ramp3-GR_rep1


title: ChIP-seq-Kidney-E12-Ramp3-H3K27ac_rep1


title: GC1-spg -dox 2 Ribsome Profiling


title: ChIP-seq-Kidney-WT-Pol2_rep2


title: ChIP-seq-Kidney-WT-Pol2_rep1


title: ChIP-seq-Kidney-WT-GR_rep2


title: ChIP-seq-Kidney-WT-H3K27ac_rep1


title: ChIP-seq-Kidney-WT-STAT3_rep2


title: ChIP-seq-Kidney-WT-GR_rep1


title: ChIP-seq-Kidney-WT-STAT3_rep1


title: ChIP-seq-E2-Ramp3-L10-H3K27ac_rep2


title: ChIP-seq-E2-Ramp3-L10-Pol2_rep2


title: ChIP-seq-E2-Ramp3-L10-Pol2_rep1


title: ChIP-seq-E2-Ramp3-L10-H3K27ac_rep1


title: ChIP-seq-E2-Ramp3-L10-STAT5A_rep1

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: ChIP-seq-E12-Ramp3-L10-Pol2_rep2


title: ChIP-seq-E12-Ramp3-L10-Pol2_rep1


title: ChIP-seq-Kidney-E12-Ramp3-STAT3_rep1


title: ChIP-seq-E12-Ramp3-L10-H3K27ac_rep1


title: ChIP-seq-E12-Ramp3-L10-H3K27ac_rep2


title: ChIP-seq-E12-Ramp3-L10-STAT5A_rep1


title: ChIP-seq-E12-Ramp3-L10-STAT5A_rep2


title: ChIP-seq-delE3-L10-Pol2_rep1


title: ChIP-seq-delE1-delE3-L10-Pol2_rep1


title: ChIP-seq-delE3-L10-H3K27ac_rep2


title: ChIP-seq-delE3-L10-STAT5A_rep2


title: ChIP-seq-delE1-delE2-delE3-L10-GR_rep2


title: ChIP-seq-delE1-delE2-delE3-L10-GR_rep3


title: ChIP-seq-delE1-delE2-delE3-L10-GR_rep1


title: ChIP-seq-Kidney-WT-H3K27ac_rep2


title: ChIP-seq-delE1-delE2-delE3-L10-H3K27ac_rep1


title: ChIP-seq-delE1-delE2-delE3-L10-STAT5A_rep2


title: ChIP-seq-delE1-delE2-delE3-L10-STAT5A_rep1


title: ChIP-seq-delE1-delE2-delE3-L1-GR_rep1


title: ChIP-seq-E2-Ramp3-L10-STAT5A_rep2


title: ChIP-seq-delE1-delE3-L10-GR_rep1


title: ChIP-seq-delE1-delE2-delE3-L1-STAT5A_rep1


title: ChIP-seq-delE1-delE3-L10-GR_rep2


title: ChIP-seq-delE1-delE3-L10-STAT5A_rep2


title: ChIP-seq-delE1-delE3-L10-H3K27ac_rep2


title: ChIP-seq-delE1-delE3-L10-H3K27ac_rep1


title: ChIP-seq-delE3-L10-H3K27ac_rep1


title: ChIP-seq-delE3-L10-STAT5A_rep1


title: ChIP-seq-delE1-delE3-L1-GR_rep2


title: ChIP-seq-delE1-delE3-L10-STAT5A_rep1


title: ChIP-seq-delE1-delE3-L1-GR_rep1


title: ChIP-seq-delE1-delE3-L1-H3K27ac_rep2


title: ChIP-seq-delE1-delE3-L1-H3K27ac_rep1


title: ChIP-seq-delE1-delE3-L1-STAT5A_rep2


title: ChIP-seq-delE1-L10-GR_rep1


title: ChIP-seq-delE1-delE3-L1-STAT5A_rep1


title: ChIP-seq-delE1-L10-GR_rep2


title: ChIP-seq-delE1-L10-H3K27ac_rep2


title: ChIP-seq-delE1-L10-H3K27ac_rep1


title: ChIP-seq-delE1-delE2-delE3-L10-H3K27ac_rep2


title: ChIP-seq-delE1-L1-GR_rep1


title: ChIP-seq-delE1-L10-STAT5A_rep2


title: ChIP-seq-delE1-L1-H3K27ac_rep1


title: ChIP-seq-delE1-L10-STAT5A_rep1


title: ChIP-seq-WT-L10-MED1_rep2

value: MED1 (Bethyl Laboratory, A300-793A)


title: ChIP-seq-WT-L10-MED1_rep1


title: ChIP-seq-WT-L10-GR-rep1


title: ChIP-seq-WT-L10-GR-rep2


title: ChIP-seq-WT-L10-H3K27ac-rep2


title: ChIP-seq-WT-L10-STAT5A-rep2


title: ChIP-seq-WT-L10-STAT5A-rep1


title: ChIP-seq-WT-L10-H3K27ac-rep1


title: ChIP-seq-WT-L1-GR-rep2


title: ChIP-seq-WT-L1-GR-rep1


title: ChIP-seq-WT-L1-STAT5A-rep2


title: ChIP-seq-WT-L1-STAT5A-rep1


title: ChIP-seq-delE1-L1-STAT5A_rep1


title: CD7: CK1750 DMSO treated replicate 4

city: Boston

first: Samuel

last: Rowbotham

state: MA

address: 300 Longwood Avenue

department: Stem Cell Hem/Onc

institute: Boston Children's Hospital

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg19 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: comma separated value (csv) files for all samples

source_name: Kras; p53 lung adenocarcinoma cell line CK1750

growth_protocol: cells were cultured in DMEM+10%FBS 4mM L-glutamine and penicillin/streptomycin at 37°C, 5% CO2.

extract_protocol:
RNA was extracted using the Agilent Absolute RNA microprep kit following the manufacturer's instructions
RNA libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

treatment_protocol: Cells were grown in the presence of 1 µM UNC0638 in 0.01% DMSO or 0.01% DMSO as a vehicle control for 96 hours. Media was refreshed after 48hrs with new drug.

value: Kras; p53 lung adenocarcinoma

tag: tumor grade

value: High grade mouse lung adenocarcinoma


title: TD7: TnM2 DMSO treated replicate 4

source_name: Kras; p53 lung adenocarcinoma cell line TnM2


title: TD5: TnM2 DMSO treated replicate 2


title: CU7: CK1750 UNC0638 treated replicate 4


title: TU4: TnM2 UNC0638 treated replicate 1


title: TD6: TnM2 DMSO treated replicate 3


title: TU6: TnM2 UNC0638 treated replicate 3


title: TD4: TnM2 DMSO treated replicate 1


title: CD5: CK1750 DMSO treated replicate 2


title: TU5: TnM2 UNC0638 treated replicate 2


title: CU5: CK1750 UNC0638 treated replicate 2


title: CD6: CK1750 DMSO treated replicate 3


title: CU4: CK1750 UNC0638 treated replicate 1


title: miRNA_DEN, tumor, replicate 4

source_name: tumor liver tissue sample, obtained from diethylnitrosamine (DEN)-treated mouse (DEN experiment)

tag: experiment

value: DEN

value: liver


title: TU7: TnM2 UNC0638 treated replicate 4


title: CU6: CK1750 UNC0638 treated replicate 3


title: CD4: CK1750 DMSO treated replicate 1


title: WT1

city: Houston

first: Jongchan

last: Kim

address: 6565 MD Anderson Blvd

institute: UT MD Anderson

data_processing:
raw reads were mapped to mm9 using tophat2 with default parameters
read count was calculated using htseq-count
normalized gene expression and differentical expressed genes were calcualted using edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalzed gene expression values. Each column represent a sample.

source_name: Mouse mammary tumor

growth_protocol: Mice were housed in the conventional animal colony at MD Anderson Cancer Center

extract_protocol:
Mammary tumors were collected from three groups of female mice (PyMT;Malat1 wild-type (WT), PyMT;Malat1 knockout (KO) and PyMT;Malat1 knockout;Malat1 transgenic animals (TG)) and snap-froze in the liquid nitrogen. Total RNA was extracted from the biological duplicate samples (n = 2 each group) using the RNeasy Mini Kit (Qiagen, 74104), according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mammary tumor

value: MMTV-PyMT

value: Malat1 wild-type


title: WT2


title: TG1

value: Malat1 knockout;Malat1 transgenic


title: TG2


title: KO1

value: Malat1 knockout


title: KO2


title: MDA-FVII, replicate1

city: Leiden

first: Henri

middle: H

last: Versteeg

address: Albinusdreef 2

department: Einthoven Lab for Experimental Vascular Medicine

institute: Leiden University Medical Center

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised by using loess normalisation via a Lumi library

source_name: MDA-FVII

label_protocol: RNA was amplified and labeled using Illumina TotalprepTM -96 RNA Amplification Kit (Ambion, #4393543)

growth_protocol: Cells were seeded in 6-wells plates and grown for three days

extract_protocol: RNA was extracted using Nucleospin II (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol.

treatment_protocol: cells were left untreated


title: Achilles_Running R1R

city: Ghent

first: Isabelle

last: Cambré

address: De Pintelaan 185

country: Belgium

institute: Ugent

description: Gene expression from Achilles tendon voluntary running condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The normalized expression values of the different conditions were compared with the limma package of Bioconductor (Smyth [2004], Smyth [2005]). For each of the contrasts, we test whether it is signiﬁcantly deviating from 0 with a moderated t-statistic (implemented in limma). The resulting p-values are corrected for multiple testing with Benjamini-Hochberg (Benjamini and Hochberg [1995]) to control the false discovery rate.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction followed by RNA extraction with Qiagen Rneasy microkit.

treatment_protocol: Adult C57BL/6 mice are placed in either control condition (regular cage) or voluntary running (cage with running wheel available) condition during 14 days

tag: condition

value: voluntary running condition

tag: tissue

value: Achilles tendon inclusive enthesis

tag: age

value: 11 - 12 weeks


title: MDA-pcDNA, replicate3

description: replicate 3

source_name: MDA-pcDNA


title: MDA-FVII, replicate4

description: replicate 4


title: MDA-FVII, replicate2

description: replicate 2


title: Achilles_Running R3L1

source_name: Achilles tendon voluntary running condition

tag: strain


title: Achilles_Running R4L


title: Achilles_Running R2L


title: Achilles_Control C2L

description: Gene expression from Achilles tendon control condition

source_name: Achilles tendon control condition

value: control


title: Achilles_Control_C1R


title: MDA-pcDNA, replicate2

description: replicate 2

tag: cell line


title: MDA-pcDNA, replicate4

description: replicate 4


title: MDA-FVII, replicate3

description: replicate 3


title: WT_IL22_L013013

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: WT_IL22_(L013013_S012587_E08027-S1_FT124 Orga #1294IL22 10ng/ml_1)

data_processing:
cutadapt (Martin, 2011): removing adapter and low quality sequences
TopHat2 (Trapnell et al, 2012): align RNA-Seq reads to mm10/Ensemble (GrCm38)
HTSeq (Anders et al, 2015): generate gene expressio nvalues
DESeq2 (Love et al, 2014): analze and visualize differential gene expression
Genome_build: mm10/Ensemble (GrCm38)
Supplementary_files_format_and_content: textfile, tab delimited, DESeq2 output summarized

source_name: intesitnal organoids

growth_protocol: Mouse intestinal organoids were cultivated as described before (Sato et al., 2009). In brief, small intestine was removed and cleared of intestinal content by flushing the intestine with HBSS. After removal of residual fat and Peyer’s patches the intestine was cut longitudinally and then laterally in pieces of 0.5cm. Intestinal pieces were incubated in ice cold PBS + 10 nM EDTA for 10min for 4 times, intermitted by vigorous shaking and replacement with fresh PBS + 10 nM EDTA after every shaking process. The crypt suspension was then strained through a 100µm strainer, followed by a spin with 1200rpm at 4°C. Pure epithelial crypts were suspended in BD Matrigel® (BD Bioscience/Heidelberg, Germany) to a concentration of 5-10 crypts/1 µl Matrigel, embedded in 24-well plates and cultivated in intestinal stem cell medium (IntestiCult™ Organoid Growth Medium (Mouse), Stemcell Technologies, Vancouver, Canada) based on previously described organoid medium containing murine EGF, murine Noggin and human R-Spondin 1 (Sato et al., 2009). Medium was changed every other day and organoids were stimulated after 3-6 days of cultivation after passage.

extract_protocol:
mRNA isolation of PBS washed cells, snap frozen tissue and PBS washed Matrigel containing organoids was performed using RNEasy Kit (Qiagen, Hilden, Germany). cDNA synthesis was performed using RevertAid Premium cDNA Synthesis Kit (Fermentas) according to manufacturer’s protocol
Illumina TrueSeq RNA v2, prepared according to the manufacturer's guidelines, resulting in an average of 28 million reads per sample
RNA-Seq, paired end

treatment_protocol: control and IL22 (10ng/ml)

value: intestinal epithelia

tag: genotype

value: WT (Atg16l1 fl/fl)

tag: stimulation

value: IL22 10ng/ml


title: Hearts, B6 mice, 8-month-old, rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Cardiac gene expression data of 8-month-old non-transgenic B6 mice

hyb_protocol: For hybridization, 15 µg of fragmented, biotin-labeled cRNA were incubated with the chip (Affymetrix Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: Hearts isolated from 8-month-old non-transgenic B6 mice

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

growth_protocol: The study was performed with 8-month-old male Tg-RKIP mice, Tg-GRK2K220R mice, Tg-SCD1 mice, Tg-UCP1 mice, and age-matched non-transgenic B6 control mice. Mice had free access to food and water, and were fed a standard rodent chow. At an age of 8 months, hearts were isolated from the different groups of transgenic mice and non-transgenic B6 control mice.

extract_protocol: Total cardiac RNA was isolated with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study was performed with hearts isolated from five groups of male mice, i.e. (i) 8-month-old Tg-RKIP mice with myocardium-specific expression of PEBP1 (RKIP), (ii) 8-month-old Tg-GRK2K220R mice with myocardium-specific expression of the dominant-negative GRK2-K220R mutant (ADRBK1-K220R), (iii) 8-month-old Tg-SCD1 mice with myocardium-speciific expression of SCD1, (iv) 8-month-old Tg-UCP1 mice with myocardium-speciific expression of UCP1, and (v) 8-month-old, non-transgenic B6 control mice. All transgenic mice had B6 background.

value: Heart

tag: Sex

value: male

value: non-transgenic B6


title: WT_ctrl_L013010

description: WT_ctrl_(L013010_S012584_E08024-S1_FT124 Orga #1294Ctrl_2)


title: WT_ctrl_L013009

description: WT_ctrl_(L013009_S012583_E08023-S1_FT124 Orga #1294Ctrl_1)


title: WT_IL22_L013014

description: WT_IL22_(L013014_S012588_E08028-S1_FT124 Orga #1294IL22 10ng/ml_2)


title: Achilles_Control C2R


title: WT_IL22_L013008

description: WT_IL22_(L013008_S012582_E08022-S1_FT124 Orga #1293IL22 10ng/ml 2)


title: MDA-pcDNA, replicate1

description: replicate 1


title: Achilles_Running R4R


title: Hearts, Tg-UCP1 mice, 8-month-old, rep2

description: Cardiac gene expression data of 8-month-old Tg-UCP1 mice

source_name: Hearts isolated from 8-month-old Tg-UCP1 mice


title: Achilles_Running R2R


title: Hearts, Tg-SCD1 mice, 8-month-old, rep2

description: Cardiac gene expression data of 8-month-old Tg-SCD1 mice

source_name: Hearts isolated from 8-month-old Tg-SCD1 mice


title: Hearts, Tg-UCP1 mice, 8-month-old, rep1


title: WT_IL22_L013007

description: WT_IL22_(L013007_S012581_E08021-S1_FT124 Orga #1293IL22 10ng/ml 1)


title: Hearts, B6 mice, 8-month-old, rep1


title: Hearts, Tg-SCD1 mice, 8-month-old, rep1


title: WT_ctrl_L013004

description: WT_ctrl_(L013004_S012578_E08018-S1_FT124 Orga #1293Ctrl 2)


title: KO_IL22_L013002

description: KO_IL22_(L013002_S012576_E08016-S1_FT124 Orga #1292IL22 10ng/ml 2)

value: KO (Atg16l1dIEC)


title: KO_IL22_L013001

description: KO_IL22_(L013001_S012575_E08015-S1_FT124 Orga #1292IL22 10ng/ml 1)


title: KO_ctrl_L012997

description: KO_ctrl_(L012997_S012571_E08011-S1_FT124 Orga #1292Ctrl_1)


title: KO_ctrl_L012998

description: KO_ctrl_(L012998_S012572_E08012-S1_FT124 Orga #1292Ctrl_2)


title: WT_ctrl_L013003

description: WT_ctrl_(L013003_S012577_E08017-S1_FT124 Orga #1293Ctrl 1)


title: KO_IL22_L012996

description: KO_IL22_(L012996_S012570_E08010-S1_FT124 Orga #1290IL22 10ng/ml_2)


title: KO_ctrl_L012992

description: KO_ctrl_(L012992_S012566_E08006-S1_FT124 Orga #1290Ctrl_2)


title: Hearts, Tg-RKIP mice, 8-month-old, rep1

description: Cardiac gene expression data of 8-month-old Tg-RKIP mice

source_name: Hearts isolated from 8-month-old Tg-RKIP mice

value: Tg-RKIP


title: 10-cell random sample 14

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

hyb_protocol: 1 µg of labeled cDNA in 5 µl was mixed with 10 µl GEX hybridization buffer, denatured at 94ºC for 4 min and then added directly to the BeadChip prewarmed to 58ºC.  Slides were incubated at 58ºC for 20 hr and washed according to the manufacturer's recommendations.

scan_protocol: Direct hybridization 1

data_processing: The data were batch processed using the lumi R package (PMID: 18467348) using a detection threshold of 0.05 and simple scaling normalization (ssn).

label: Alexa Fluor 555

molecule: polyA RNA

source_name: ECM-attached MCF10A-5E cells grown in 3D culture for 10 days

label_protocol: Direct aminoallyl labeling to Alexa Fluor 555

growth_protocol: Cells were grown as a matrigel overlay culture in DMEM/F12 containing 2% matrigel, 2% horse serum, 5 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, and 1x penicillin-streptomycin for 10 days, with refeeding at days 4 and 8.

extract_protocol: 3D cultures were cryoembedded and sectioned.  Cells were isolate by laser-capture microdissection, and RNA was isolated by proteinase K digestion of the microdissected cells.

tag: culture day


title: Hearts, Tg-GRK2K220R mice, 8-month-old, rep1

description: Cardiac gene expression data of 8-month-old Tg-GRK2K220R mice

source_name: Hearts isolated from 8-month-old Tg-GRK2K220R mice


title: N309-50_2DK_rep-1

city: Camden

first: Kwangwon

last: Lee

state: New Jersey

address: 200 Federal St.

department: Department of Biology

institute: Rutgers University

description: Progeny of North American and African Parents (Low RI Phenotype)

data_processing:
Illumina reads were demultiplexed and quality controlled using FastQC v0.11.4
Adaptor sequences and reads shorter than 36 bp with a quality score lower than 15 were removed using Cutadapt v1.3
The processed reads were mapped to the reference genome from JGI using TopHat2 V2.1.1
Aligned reads were counted with HTSeq framework v0.9.1
Samtools mpileup package was used to retrieve SNPs and Insertion or deletion of bases (Indels)
SNPs were annotated using Useq v8.6.2
EdgeR and DEseq applied to calculate differential gene expression
Supplementary_files_format_and_content: tab delimited text files contain differential gene expression between high RI and Low RI phenotypes

organism: Neurospora discreta

source_name: Mycelia and conidia

growth_protocol: For RNA sequencing, mycelial pads of respective strains were entrained in 12h:12h light-dark cycle with constant 25C in low glucose media

extract_protocol:
Trizol based RNA extraction was done from mycelial pads and verified the concentration and integrity of RNA using Fragment analyzer with high sensitivity RNA analysis kit
Standard Illumina protocols were used for library preperation and sequencing

value: Fungi

tag: growth conditions

value: Light-Dark cycles (12:12)

tag: sample type

tag: phenotype

value: low RI


title: N309-50_2DK_rep-3

value: Progeny of North American and African Parents


title: N309-50_2DK_rep-2


title: KO_ctrl_L012991

description: KO_ctrl_(L012991_S012565_E08005-S1_FT124 Orga #1290Ctrl_1)


title: N309-50_2h_rep-3


title: 10-cell random sample 8


title: 10-cell random sample 13


title: 10-cell random sample 15


title: KO_IL22_L012995

description: KO_IL22_(L012995_S012569_E08009-S1_FT124 Orga #1290IL22 10ng/ml_1)


title: 10-cell random sample 12


title: Hearts, Tg-RKIP mice, 8-month-old, rep2

tag: genotype/variation


title: N309-50_2h_rep-1


title: N309-50_2h_rep-2


title: 10-cell random sample 9


title: 10-cell random sample 11


title: N309-50_1h_rep-3


title: N309-50_1h_rep-2


title: N309-50_1h_rep-1


title: 10-cell random sample 5


title: N309-50_15M_rep-3


title: 10-cell random sample 4


title: 10-cell random sample 10


title: N309-89_2DK_rep-3

description: Progeny of North American and African Parents (High RI Phenotype)

value: high RI


title: N309-50_15M_rep-1


title: 10-cell pool-and-split control replicate 16


title: Hearts, Tg-GRK2K220R mice, 8 month-old, rep2


title: 10-cell random sample 7


title: 10-cell random sample 6


title: 10-cell random sample 3


title: N309-89_2DK_rep-2


title: 10-cell random sample 1


title: 10-cell random sample 16


title: N309-50_15M_rep-2


title: N309-89_2DK_rep-1


title: N309-89_2h_rep-3


title: N309-89_2h_rep-1


title: N309-89_1h_rep-3


title: 10-cell pool-and-split control replicate 14


title: 10-cell pool-and-split control replicate 13


title: 10-cell random sample 2


title: 10-cell pool-and-split control replicate 15


title: 10-cell pool-and-split control replicate 11


title: 10-cell pool-and-split control replicate 8


title: 10-cell pool-and-split control replicate 10


title: 10-cell pool-and-split control replicate 5


title: 10-cell pool-and-split control replicate 12


title: 10-cell pool-and-split control replicate 9


title: N309-89_1h_rep-1


title: N309-89_15M_rep2


title: N309-89_2h_rep-2


title: 10-cell pool-and-split control replicate 7


title: N309-89_1h_rep-2


title: N309-89_15M_rep3


title: FGSC8578_2DK_rep1

description: North American Parent (Low RI Phenotype)

value: North American Parent


title: N309-89_15M_rep1


title: FGSC8578_2DK_rep2


title: OB: Osteoblast RNA-seq

city: Suwon

first: Jinyoung

last: Park

address: Seobu-ro 2066, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore v0.4.0, then mapped to mm9 whole genome using bowtie2 v2.2.6 with default parameters
"Fragments per kilobase of transcript per million fragments mapped" (FPKM) were calculated using a protocol from cufflinks v2.2.0. The FPKM value is a measure of the expression of a transcript, normalized by transcript length and the total number of fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Sequenced reads fastq files were performed quality control using FastQC (v0.11.3) for improving reads quality before mapped to mouse reference genome (NCBI37/mm9). Then reads were mapped to reference using TopHat (v2.0.11) with default parameters. Generated BAM files were changed into wig files.

source_name: Osteoblast

growth_protocol: Mouse myoblst cell line C2C12 was maintained in growth state in the growth media (10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin (P/S) in DMEM). Myoblast was differentiated into myotubes by incubation in differentiation media (2% Horse serum, 1% P/S in DMEM) for 3 days. C2C12 myoblast was also trans-differentiated into osteoblast by incubation in the Bone Morphogenic Protein 2 (BMP2) contatining differentiation media (5% FBS, 1% P/S, 200ug/ml BMP2 in DMEM) for 3 days.

extract_protocol:
Total RNA was extracted from myoblast, myotube and osteoblast by QIAGEN RNeasy® mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Osteoblast


title: FGSC8578_2h_rep1


title: 10-cell pool-and-split control replicate 4


title: MT: Myotube RNA-seq

source_name: Myotube

value: Myotube


title: 10-cell pool-and-split control replicate 6


title: FGSC8578_1h_rep3


title: FGSC8578_1h_rep2


title: FGSC8578_2DK_rep3


title: 10-cell pool-and-split control replicate 2


title: MB: Myoblast RNA-seq

source_name: Myoblast

value: Myoblast


title: 10-cell pool-and-split control replicate 3


title: FGSC8578_15M_rep2


title: FGSC8578_1h_rep1


title: FGSC8578_15M_rep1


title: 10-cell pool-and-split control replicate 1


title: FGSC8831_2DK_rep2

description: African Parent (High RI Phenotpe)

value: African Parent


title: FGSC8831_2DK_rep1

description: African Parent (High RI Phenotpe)


title: FGSC8831_2DK_rep3

description: African Parent (High RI Phenotpe)


title: FGSC8831_2h_rep3

description: African Parent (High RI Phenotpe)


title: FGSC8831_2h_rep2

description: African Parent (High RI Phenotpe)


title: FGSC8831_2h_rep1

description: African Parent (High RI Phenotpe)


title: BG546 #3

city: New York

first: David

last: Bechhofer

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Department of Pharmacology and Systems Therapeutics

institute: Icahn School of Medicine at Mount Sinai

description: Total RNA with rRNA removed

data_processing:
Base-calling was performed by Illumina CASAVA software.
Reads from fastq files were aligned to Bacillus subtilis genome by Bowtie 2 with --local option
SAMtools and BEDtools were used to count reads mapped to specific genes. Gene annoatation reference was obtained from NCBI databse.
Homemade Python script was used to normalize and compare the read abundance (reads/base) and 5'/3' ratio of each transcripts as described in the published article (Liu, B., Deikus, G., Bree, A., Durand, S., Kearns, D. B. and Bechhofer, D. H. (2014), Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains. Molecular Microbiology, 94: 41–55. doi:10.1111/mmi.12748)
Genome_build: NC_000964.3
Supplementary_files_format_and_content: xlsx file containing read abundance and 5'/3' ratio of all genes in both strains.

organism: Bacillus subtilis

source_name: PNPase mutant; ΔpnpA::neo

growth_protocol: The cells were cultured in LB medium at 37°C until mid-log phase.

extract_protocol:
Total RNA was extracted with hot phenol method, and ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit for bacteria
Libraries were constructed according to the standard Illumina RNA-seq protocol

tag: genotype on ribonucleases

tag: growth condition

value: 37°C LB medium to mid-log phase


title: FGSC8578_2h_rep3


title: FGSC8831_1h_rep3

description: African Parent (High RI Phenotpe)


title: FGSC8831_1h_rep1

description: African Parent (High RI Phenotpe)


title: FGSC8831_1h_rep2

description: African Parent (High RI Phenotpe)


title: BG546 #2

description: Total RNA with rRNA removed


title: FGSC8578_2h_rep2


title: BG546 #1

description: Total RNA with rRNA removed


title: FGSC8831_15M_rep3

description: African Parent (High RI Phenotpe)


title: SBG_plus_2

description: processed data file: NC_015761_transcripts.txt

organism: Salmonella bongori

source_name: bacterial culture

tag: genetic background

value: wild-type

tag: plasmid

value: pWSK129-PssrA-ssrB D56E


title: SBG_plus_3


title: SBG_plus_1


title: FGSC8578_15M_rep3

tag: tissue


title: BG1 #3

description: Total RNA with rRNA removed

source_name: wild type

value: wild type


title: FGSC8831_15M_rep2

description: African Parent (High RI Phenotpe)


title: FGSC8831_15M_rep1

description: African Parent (High RI Phenotpe)


title: BG1 #1

description: Total RNA with rRNA removed


title: BG1 #2

description: Total RNA with rRNA removed


title: I60-1000

city: Beijing

first: Baoyang

last: Hu

state: Select State/Province

address: Beichenxilu

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology

description: FOXG1s/s hESC line

data_processing:
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.
The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study.
The BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: hESC-derived cortical GABA interneuron

growth_protocol: hPSCs were cultured until reach ~80 confluences. Induction of neural progenitors was adapted from previous article. On day 0, cells were dissociated with Dispase (1 U ml−1), then hPSCs aggregates were harvested by centrifugation and plated in ultra-low-attachment 10 cm dishes (Corning, 430591) to form embryoid bodies. From day 1, the telencephalic induction was started by changing the medium to NIM medium with dual SMAD inhibition consisting of DMEM-F12, 1x N2 supplement (A1370701), 1x B27 supplement, minus vitamin A (12587010), 1x GlutaMAX Supplement (35050061), 0.5X MEM Non-Essential Amino Acids Solution (11140050), 110 μM 2-mercaptoethanol (Sigma-Aldrich, M6250), 0.05% (v/v) Bovine Albumin Fraction V Solution (Sigma-Aldrich, B2064), 1x Penicillin-Streptomycin (10378016), 100 nM LDN193189 (Selleck, S2618), 10 μM SB431542 (Slleck, S1067), 2 μM XAV939 (Selleck, S1180). Media was replenished daily until day 8. Then, EBs were plated on Matrigel (BD, 356234) pre-coated 6-well plates and neuronal rosettes could be observed within a few days. From day 9, medium was changed to NPC medium consisting of DMEM-F12, 0.15% (w/v) Detrose (Sigma-Aldrich, G6152), 110 μM 2-mercaptoethanol (Sigma-Aldrich, M6250), 1x N2 supplement, 1x B27 supplement without vitamin A, 20 ng/ml FGF2 (Peprotech). NPC medium was changed daily for 4 days until day 13.

extract_protocol:
Total RNA was extracted from approximately 10^6 cells using the miRNeasy Mini Kit (QIAGEN, 217004).
mRNA were purified using poly-T oligo-attached magnetic beads. Then, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The first strand cDNA were produced from cleaved RNA fragments using reverse transcriptase and random primers and then second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were purified and enriched with PCR amplification. Finally, we quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: ASV treatment started from day4.

value: hESC-derived cortical GABA interneuron

tag: foxg1 dosage

tag: differentiation stage

value: day 60

tag: asv concentration


title: I60-100

description: FOXG1s/s hESC line


title: I60-50

description: FOXG1s/s hESC line

value: 50 nM


title: SBG_minus_1

data_processing:
Multiple files for each sample were concatenated into a single file. SsrB- and SsrB+ files for each species were loaded on to Rockhopper for alignment to the referene genome and plasmids if applicable.
Genome_build: Reference genome for S. bongori NC_015761. Reference genome for S. Typhimurium NC_016810. Reference for S. Typhimurium plasmids NC_017718 (pCol1B9), NC_017719 (pRSF), NC_017720 (pSLT)
Reads were mapped to the respective genomes with Rockhopper and differential gene expression (SsrB+/SsrB-) was calculated for both species.


title: SBG_minus_2


title: TY1-PA3898 rep1

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

data_processing:
Aligned to PAO1 genome using NGS mapping Bowtie2 on usegalaxy.org
Peaks called using MACS2 callpeak on usegalaxy.org
Genome_build: ASM676v1

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa PAO1-PA3898::Tn/pUCP20TQ-lacIq strain and wildtype strain was grown in 2 ml of LB overnight. Cells were diluted 100x into 3 ml of fresh LB medium with appropriate concentration of IPTG for induction and grown at 30°C for 48 h without shaking.

extract_protocol:
One ml aliquots were harvested and cell pellets were resuspended and cross-linked by the addition of PFA to a final concentration of 4% and incubation at room temperature for 15 min with gentle mixing. Cross-linking was quenched by addition of glycine to a final concentration of 125 mM (0.75 M stock). Cells are harvested and washed twice with Tris-buffered saline (20 mM Tris-Cl pH 7.5, 150 mM NaCl), and resuspended in 50 μl Immunoprecipitation (IP) buffer (20 mM Tris-Cl pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, mini-protease inhibitor cocktail (Roche)). Lysozyme was added to final concentration of 1 mg/ml, sufficient lysis was achieved by freezing and thawing 2-3 times. Samples were spun down and supernatants were diluted in nebulization buffer (TE buffer pH8.0 with 10% glycerol). DNA was sheared to an average size of 100–500 bp (majority 200-400 ideally) in a Roche nebulizer. Fragmented DNA complex containing the TY-1 tagged regulator protein was enriched using TY1 mouse monoclonal antibody and DiaMag protein A-coated magnetic beads (Diagenode). Enriched DNA-regulator complex was reverse crosslinked overnight at 65 °C and purified through phenol/chloroform extraction and sodium acetate/isopropanol precipitation.
Purified DNA fragments were used as template for library construction according to Illumina ChIP-seq sample preparation protocol and sequenced at TUCF Genomics core facility.

treatment_protocol: Induced with IPTG for expression of TY1-PA3898.

tag: chip-seq antibody


title: I60-0

description: FOXG1s/s hESC line


title: TRIM21_KO_virus_+_rh9C12-H433A_replicate_3 [sample_31]

status: Public on Sep 17 2018

city: Cambridge

first: Leo

middle: C

last: James

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Sequencing as well as sequence demultiplexing of samples according to barcodes was performed at the CRUK Genomics Core, Cambridge. Transcript-level abundances were quantified using kallisto (with the parameters: --single -l 515 -s 60) against GRCm38.p6 Ensembl cDNA.
Transcript-level abundances were then imported into R using the tximport package and converted into gene-level abundances. Three non-coding transcripts Trim21-203, (ENSMUST00000209679.1), Trim21-204 (ENSMUST00000209907.1) and Trim21-205 (ENSMUST00000210261.1) were omitted during this stage.
Differential expression analysis was performed using the DESeq2 package separately for each two conditions to be compared (using the DESeqDataSetFromTximport function), and all lists were filtered to contain exclusively protein coding genes.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: kallisto gene-level effective lengts. estimated counts and TPM values

extract_protocol:
6-week old animals were culled by cervical dislocation, livers were removed and flash frozen. Total RNA was extracted from three individual pieces of liver using Quizol reagent. Libraries were constructed using Illumina TruSeq® Stranded mRNA Library Prep Kit with 1µg total RNA input.
According to Illumina TruSeq® Stranded mRNA Library Prep Kit

tag: strain background

value: male

tag: age

value: 6 weeks

value: TRIM21 KO

tag: treatmet

value: whole liver


title: Input DNA


title: TRIM21_KO_virus_+_rh9C12-H433A_replicate_1 [sample_29]

tag: Sex

value: female


title: TRIM21_KO_virus_+_rh9C12-WT_replicate_4 [sample_28]

source_name: TRIM21_KO_virus_+_rh9C12-WT_whole liver


title: TRIM21_KO_virus_+_rh9C12-H433A_replicate_2 [sample_30]


title: TRIM21_KO_virus_+_rh9C12-H433A_replicate_4 [sample_32]


title: SBG_minus_3

extract_protocol:
RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, resuspended in water for Dnase I treatment for 30 min. Dnase I was inactivated with inactivation beads and RNA was re-precipitated with isopropanol, washed with 75% ethanol, and resuspended in water
RNA was rRNA depleted with RiboZero, and strand specific dUTP sequencing was performed on an Illumina Hi-Seq following standard Illumina protocols


title: TRIM21_KO_virus_+_rh9C12-WT_replicate_2 [sample_26]


title: TRIM21_KO_virus_+_rh9C12-WT_replicate_3 [sample_27]


title: AC9 overexpression #1

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
393P-AC9-1
Mice 9393P cells with AC9 overexpression, sample 1.

hyb_protocol: According to the manufacturer’s instructions.

data_processing: Expression arrays were processed and RMA normalized using BioConductor.

source_name: mice 9393P cells, AC9 overexpression

label_protocol: RNA fluorescent labeling reaction and hybridization were performed using the Affymetrix (Clariom S WT Plus) according to the manufacturer’s instructions.

growth_protocol: All cell lines were maintained in RPMI supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated from cell lines by the RNeasy Mini Kit (Qiagen). RNA quality and quantity were evaluated on a NanoDrop spectrophotometer.

treatment_protocol: Cells were transfected using jetPRIME® Versatile DNA/siRNA transfection reagent (Polyplus). Stable cell transfectants were selected with puromycin (InvivoGene) or G418 (Corning).

tag: cell line

tag: stable transfection


title: AC9 overexpression #2

description:
393P-AC9-2
Mice 9393P cells with AC9 overexpression, sample 2.

scan_protocol: According to the manufacturer’s instructions.


title: AC9 overexpression #3

description:
393P-AC9-3
Mice 9393P cells with AC9 overexpression, sample 3.


title: Empty VECTOR #2

description:
393P-VEC-2
Mice 9393P cells with VECTOR, sample 2.

source_name: mice 9393P cells, empty VECTOR

value: VECTOR


title: TRIM21_KO_virus only_replicate_1 [sample_21]

source_name: TRIM21_KO_virus only_whole liver

tag: genotype/variation

value: virus only


title: TRIM21_KO_virus only_replicate_2 [sample_22]


title: TRIM21_KO_virus only_replicate_4 [sample_24]


title: TRIM21_KO_virus only_replicate_3 [sample_23]


title: Empty VECTOR #3

description:
393P-VEC-3
Mice 9393P cells with VECTOR, sample 3.


title: TRIM21_KO_uninfected_replicate_2 [sample_18]

source_name: TRIM21_KO_uninfected_whole liver

value: uninfected


title: TRIM21_KO_uninfected_replicate_4 [sample_20]


title: TRIM21_KO_uninfected_replicate_3 [sample_19]


title: TRIM21_KO_uninfected_replicate_1 [sample_17]


title: WT_virus_+_rh9C12-H433A_replicate_2 [sample_14]

source_name: WT_virus_+_rh9C12-H433A_whole liver

value: WT


title: Empty VECTOR #1

description:
393P-VEC-1
Mice 9393P cells with VECTOR, sample 1.


title: WT_virus_+_rh9C12-WT_replicate_4 [sample_12]

source_name: WT_virus_+_rh9C12-WT_whole liver


title: WT_virus_+_rh9C12-WT_replicate_2 [sample_10]


title: WT_virus_+_rh9C12-WT_replicate_3 [sample_11]


title: WT_virus_only_replicate_4 [sample_08]

source_name: WT_virus_only_whole liver


title: WT_virus_+_rh9C12-H433A_replicate_3 [sample_15]


title: TRIM21_KO_virus_+_rh9C12-WT_replicate_1 [sample_25]


title: WT_virus_+_rh9C12-H433A_replicate_4 [sample_16]


title: WT_virus_+_rh9C12-H433A_replicate_1 [sample_13]


title: WT_virus_only_replicate_1 [sample_05]


title: WT_uninfected_replicate_3 [sample_03]

source_name: WT_uninfected_whole liver


title: WT_uninfected_replicate_4 [sample_04]


title: WT_uninfected_replicate_2 [sample_02]


title: WT_uninfected_replicate_1 [sample_01]


title: WT_virus_only_replicate_3 [sample_07]


title: WT_virus_+_rh9C12-WT_replicate_1 [sample_09]


title: WT_virus_only_replicate_2 [sample_06]


title: Rec27-FLAG_interacting

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

data_processing:
Base calling: Illumina Real Time Analysis software, v1.12.4 or v1.17.21.3
De-multiplexing: Illumina CASAVA software, v1.8.0 or 1.8.2
Read alignment: Burrows-Wheeler Aligner, v 0.7.9a
Terminal base (bp 50) removed from each read; only first 49 used for alignment.  One mismatch was permitted in the 49 bp.  Each paired-end read was mapped separately and only analyzed further if both ends successfully mapped to single chromosomal position.
Uniquely mapping paired-reads were compiled and analyzed in R
Genome_build: Sanger Center S. pombe genome, August 2010 version
Supplementary_files_format_and_content: Unique ligation list

organism: Schizosaccharomyces pombe

source_name: Meiotic culture

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize the cells. Nitrogen was added and the temperature shifted to 34°C, marking the start of meiosis, and cells harvested at 3.5hr.

extract_protocol:
Formaldehyde was added to a final concentration of 1% in 500 mL of culture. Chromatin was prepared and sonicated as in Fowler et al. 2013 Mol. Cell 49:983-996.  DNA was sheared to ~1000 bp and the epitope tagged protein of interest was immunoprecipitated.  For conformation capture samples ("interacting"), the immunoprecipitate was ligated while immobilized on magnetic beads and subsequently eluted.  Crosslinks were removed with high temperature incubation and protein digested using proteinase K.  For "de-crosslinked" samples, immunoprecipitated chromatin was eluted, crosslinks removed, and protein digested prior to DNA ligation.  In both cases, the ligated DNA was finally ethanol precipitated and amplified using one of two different kits (Sequenase Version 2.0 DNA Sequencing Kit, Affymetrix; or REPLI-g Single Cell Kit, Qiagen).
DNA from all samples was amplified using either a Sequenase Version 2.0 DNA Sequencing Kit (for anti-GFP) or a Qiagen REPLI-g Single Cell Kit (for anti-FLAG).  DNA was quantified using a Bioanalyzer (Invitrogen).  Sequencing libraries were each prepared from 1 µg of DNA.  DNA was initially fragmented with a Covaris LE220 Focused-ultrasonicator (Covaris, Woburn, MA) using factory settings for an average size of 300 bp.  Library DNA was prepared using the KAPA DNA Library Preparation and HiFi PCR Kits (Kapa Biosystems, Wilmington, MA) on a PerkinElmer Sciclone NGSx Workstation (PerkinElmer, Waltham, MA) for Rec25-FLAG and Rec27-FLAG IPs, or the Epicentre Nextera DNA Sample Prep kit (Illumina, Inc., San Diego, CA) manually for Rec27-GFP IPs.

tag: epitope tag

tag: relevant genotype

value: pat1-114 rec12D

tag: material ligated

value: Crosslinked DNA complexes


title: Rec25-FLAG_de-crosslinked

value: Purified IP (de-crosslinked) DNA


title: Rec25-FLAG_interacting


title: Rec27-FLAG_de-crosslinked


title: Skin NL Week 0 Placebo MSSM-17

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

description: Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Hybridization conditions: 4.4um ssDNA, 45C, 18h, 55-60rpm.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Quality control of Affymetrix chips was done using standard QC metrics and R packages. Microarray quality control images were scrutinized for spatial artifacts using Harshlight. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date and chip lot number were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies from lesional and non-lesional skin at baseline, week 4 and week 12 were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

tag: patient id

tag: lot

value: NL

tag: week

value: Wk 0

tag: treatment

value: Placebo


title: Skin NL Week 12 Drug MSSM-16

description: Gene expression data from skin biopsy

tag: tissue

value: Wk 12

value: Drug


title: Skin NL Week 12 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-16

description: Gene expression data from skin biopsy

value: Wk 4


title: Skin NL Week 4 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-17

description: Gene expression data from skin biopsy

value: LS


title: Skin LS Week 0 Placebo MSSM-17

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-17

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-19

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-17

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-16

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-16

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-15

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-16

description: Gene expression data from skin biopsy


title: 254706910144_b2 - trip1-1_rep1 vs WT1-1_rep1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Are cell wall genes affected in a triple WD40 mutant (LWD1xLWD2xTTG1)?

hyb_protocol: WT1-1_rep1 Cy5 / trip1-1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: stem - Greenhouse Hygrometry: 60% temperature: 21°C

extract_protocol: WT1-1_rep1:3ng. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: wild type

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: trip1-1_rep1:3ng. (Qiagen_RNeasy.pdf)

value: triple WD40 mutant (LWD1xLWD2xTTG1)


title: 254706910144_b3 - WT3-1_rep2 vs trip3-1_rep2

hyb_protocol: trip3-1_rep2 Cy5 / WT3-1_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: trip3-1_rep2:3ng. (Qiagen_RNeasy.pdf)

extract_protocol: WT3-1_rep2:3ng. (Qiagen_RNeasy.pdf)


title: Skin LS Week 12 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-16

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-19

description: Gene expression data from skin biopsy


title: 254706910144_b1 - WT1-1_rep1 vs trip1-1_rep1

hyb_protocol: trip1-1_rep1 Cy5 / WT1-1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Skin NL Week 0 Drug MSSM-03

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-18

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-15

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-19

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: 254706910144_b4 - trip3-1_rep2 vs WT3-1_rep2

hyb_protocol: WT3-1_rep2 Cy5 / trip3-1_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Skin LS Week 12 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-12

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-11

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-14

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-09

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-020

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug MSSM-09

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-020

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-020

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-13

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo RU-019

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-020

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo MSSM-02

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-08

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-020

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-07

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-019

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-09

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-018

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-017

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-017

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-017

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-017

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-016

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-015

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-10

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-012

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-012

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-012

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-012

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-014

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-012

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug MSSM-06

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-013

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo RU-013

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo RU-011

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo MSSM-05

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Placebo MSSM-05

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-010

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-009

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo RU-008

description: Gene expression data from skin biopsy


title: Skin NL Week 12 Drug RU-007

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-008

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Drug RU-007

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-007

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-007

description: Gene expression data from skin biopsy


title: HCT116 sh p53 exosome

city: Suita

first: Shunsuke

last: Yoshii

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

country: Japan

institute: Osaka University Graduate School of Medicine

description: Exosomes were collected from the conditioned medium of each cell line using sequential centrifugation method. Expression profiling of human mature miRNA in exosomes derived from HCT116sh control and HCT116sh p53 cells was performed using a 3D-Gene® miRNA oligo chip (Toray Industries Inc., Tokyo, Japan).

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: colon cancer cell line

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Prior to collection of the culture medium, the cancer cells were washed with phosphate-buffered saline, and the medium was switched to fresh serum-free DMEM. Then, each line were incubated for 48 hours.

extract_protocol: RNA samples were extracted from exosome using 3D-Gene RNA extraction reagent from liquid sample and miRNesy mini kit (QIAGEN).

treatment_protocol: The medium was first centrifuged at 300 ×g for 10 minutes and then at 2,000 ×g for 10 minutes to precipitate the cells. The supernatant was then centrifuged at 10,000 ×g for 30 minutes and then ultracentrifuged at 100,000 ×g for 70 minutes to pellet extracellular vesicles, which were then washed by suspension in PBS. These vesicles were then ultracentrifuged at 100,000 ×g for 70 minutes. The final pellet was resuspended in 100 μl of PBS.

value: primary colon cancer

tag: cell compartment

value: exosome

value: sh p53


title: Skin LS Week 12 Drug RU-004

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo RU-006

description: Gene expression data from skin biopsy


title: HCT116 sh control exosome

value: sh control


title: Skin NL Week 0 Placebo RU-008

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-007

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Placebo RU-006

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Placebo MSSM-05

description: Gene expression data from skin biopsy


title: Skin NL Week 0 Drug RU-007

description: Gene expression data from skin biopsy


title: Skin LS Week 4 Drug RU-005

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Drug RU-005

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo RU-006

description: Gene expression data from skin biopsy


title: Skin NL Week 4 Placebo MSSM-05

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Drug RU-005

description: Gene expression data from skin biopsy


title: Skin LS Week 0 Placebo RU-006

description: Gene expression data from skin biopsy


title: Skin LS Week 12 Placebo RU-006

description: Gene expression data from skin biopsy