title: Wildtype NF54 Mature Activated Gametocytes

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: Mature gametocyte RNA

growth_protocol: P. falicparum parasites were cultivated in vitro in human blood group A+ erythrocytes. All parasite stages were maintained in RPMI1640/HEPES medium (Gibco) supplemented with 10% v/v heat inactivated human A+ serum, 50 µg/ml hypoxanthine, and 10 µg/ml gentamicin.

extract_protocol: Total RNA isolation was performed using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: P. falciparum gametocytes were enriched via Percoll gradient. Gametogenesis was induced by adding xanthurenic acid in a final concentration of 100 µM dissolved in 1% v/v 0.5 M NH4OH/ddH2O and incubation for 30 min at room temperature (RT).

tag: strain

tag: drug

source_name: Mixed gametocyte and asexual blood stage reference pool

value: NF54 and 3D7


title: V43DNA_R218_2weeks_post1stALVAC

status: Public on Feb 23 2018

type: RNA

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

country: USA

institute: Northwestern University

description: transcriptional profilling of blood taken 2 weeks after the 1st ALVAC boost  (week 14)

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R (version 3.4.3) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.50.1). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.32.10).

label: biotin

molecule: total RNA

organism: Macaca mulatta

source_name: blood sample from donor R218 taken 2 weeks after the 1st ALVAC boost

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Blood Kit. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

tag: donor

tag: immunization

tag: time after immunization

value: 2 weeks

tag: prime

value: DNA

tag: number of siv challenge to infection

tag: tissue

value: blood


title: V43DNA_R218_24hours_post2ndALVAC

description: transcriptional profilling of blood taken 24 hours after the 2nd ALVAC boost  (week 24)

source_name: blood sample from donor R218 taken 24 hours after the 2nd ALVAC boost

value: 24 hours


title: PIP4K_48h_siRNA2_BJ_normal_rep3

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

description:
SAMPLE 23
replicate 3

hyb_protocol: cRNA yields were quantified with a Agilent Bioanalyzer, and 750 ng of biotin-labeled cRNA was hybridized to the Illumina HT-12 v4.0 Expression Beadchip according to manufacturer’s instructions (Illumina, Inc.)

scan_protocol: Dried bead chips were scanned on the Illumina BeadArray Reader confocal scanner (Illumina, Inc.)

data_processing:
Illumina GenomeStudio Gene Expression Analysis Module generated raw intensity.
Gene expression signals obtained after chip scanning were quantile normalized in Partek Genomics Suite v6.6 (Partek Inc.). Genes with a normalized maximum average signal <100 in all groups were considered similar to background and removed from further analysis. Sample outliers were detected via principal component analysis in Partek. Differentially expressed genes were identified via 1-way ANOVA with post-hoc contrasts specifying the desired pair-wise comparisons. The magnitude of differential gene expression between 2 groups was expressed as the logarithm of the fold-change (base 2), and the statistical significance of differences in gene expression were ascertained by the false discovery rate (FDR). For most analyses, genes with an absolute log fold-change >0.58 and FDR <5% were considered significantly differentially expressed.

organism: Homo sapiens

label_protocol: Biotin-labeled cRNA was prepared from 250-500 ng of total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion Inc.)

growth_protocol: Isogenic BJ human foreskin fibroblast cell lines, including non-transformed (normal) and transformed BJ cells were gown in DMEM with 10% FBS

extract_protocol: RNA was extracted with Trizol reagent,. RNeasy Mini Kit (Qiagen) was used to fast purification of high-quality RNA from cells

treatment_protocol: where indicated cells were treated with DMSO, compounds a131 or a166, or siRNAs against PIP4Ks

tag: cell type

value: BJ normal cells

tag: treatment

value: PIP4K siRNA2


title: PIP4K_48h_siRNA2_BJ_normal_rep2

description:
SAMPLE 22
replicate 2


title: PIP4K_48h_siRNA1_BJ_normal_rep1

description:
SAMPLE 18
replicate 1

value: PIP4K siRNA1


title: Control_48h_siRNA_BJ_normal_rep2

description:
SAMPLE 16
replicate 2

value: Control siRNA


title: V43DNA_R218_prevax

description: transcriptional profilling of blood taken pre-vaccination (week -1)

source_name: blood sample from donor R218 taken pre-vaccination

value: prevax


title: PIP4K_48h_siRNA1_BJ_normal_rep2

description:
SAMPLE 19
replicate 2


title: Control_48h_siRNA_BJ_normal_rep3

description:
SAMPLE 17
replicate 3


title: PIP4K_48h_siRNA2_BJ_normal_rep1

description:
SAMPLE 21
replicate 1


title: 7-Helix-1 Knockout 2E6 Mature Activated Gametocytes

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

value: Blasticidin, 5.4 µM


title: a166_24h_BJ_normal_rep2

description:
SAMPLE 10
replicate 2


title: Control_48h_siRNA_BJ_normal_rep1

description:
SAMPLE 15
replicate 1


title: MLS_402-91_untreated

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization of 3.75µg fragmented and labelled ssDNA, including hybridization controls, were performed using the GeneChip Human Gene 2.0 ST Array (Affymetrix) in 45°C for 16h with 60rpm rotation. Wash and staining was performed using the GeneChip Hybridization Wash and Stain Kit on a GeneChip Fluidics Station 450 (AFFymetrix).

scan_protocol: Scanning was performed using the GeneChip Scanner 3000 7G with GeneChip Command Console Software (Affymetrix)

data_processing: RMA normalization was performed using Expression console version 1.3.0.187 (Affymetrix)

source_name: MLS cell line 402-91

label_protocol: 300ng total RNA was processed with the WT Expression Kit (Ambion) and 10µg cRNA was converted to ssDNA. 5.5µg ssDNA was labelled and fragmented using the GenChip WT Terminal Labeling and Controls Kit (Affymetrix)

extract_protocol: Total RNA was extracted using Rneasy micro kit (Qiagen), including DNase treatment, according to the manufacturer's recommendations

treatment_protocol: Cells were treated with 45nM doxorubicin (Sigma-Aldrich) every second day and harvested after 5 days. Untreated control cells were included.

tag: cell line

value: Myxoid Liposarcoma cells (MLS)

tag: treated with

value: none (untreated control)


title: a131_24h_BJ_Transformed_rep3

description:
SAMPLE 14
replicate 3

value: BJ transformed cells


title: a131_24h_BJ_Transformed_rep2

description:
SAMPLE 13
replicate 2


title: MLS_1765-92_doxorubicin

source_name: MLS cell line 1765-92

value: 45nM doxorubicin


title: a166_24h_BJ_normal_rep1

description:
SAMPLE 9
replicate 1


title: MLS_402-91_doxorubicin


title: MLS_1765-92_untreated


title: RMS28901-5

type: SRA

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

library_source: transcriptomic

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-5.sort.readcount.txt
Genome_build: hg19

source_name: CD19+CD11chi IgD+ B cells

growth_protocol: Peripheral blood B cells from SLE patients, healthy subjects or RA patients were isolated using human B cell enrichment kit (StemCell Technologies) and stained for indicated markers. The purity of the sorted populations was routinely >90%.

extract_protocol:
RNA was isolated using PicoPure RNA isolation kit (Thermo Fisher Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Subject with Systemic lupus erythematosus (SLE)

tag: collection

tag: cell surface marker

value: CD19+ CD11chi CD27- IgD+

value: CD19+ CD11chi CD27- IgD+ B cells


title: a166_24h_BJ_normal_rep3

description:
SAMPLE 11
replicate 3


title: a131_24h_BJ_normal_rep3

description:
SAMPLE 7
replicate 3


title: RMS28901-2

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-2.sort.readcount.txt
Genome_build: hg19

source_name: CD19+CD11chi IgD- B cells

value: CD19+ CD11chi CD27- IgD-

value: CD19+ CD11chi CD27- IgD-  B cells


title: PIP4K_48h_siRNA1_BJ_normal_rep3

description:
SAMPLE 20
replicate 3


title: Heterozygous_RNA-seq_52ph

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
The first 8 bp sequences of the 5’ end of the sequencing reads were trimmed using Trimmomatic, as recommended by the Ovation® Single Cell RNA-seq System (NuGEN) protocol.
Trimmed high quality reads were then mapped to the mouse genome (mm10) using STAR v2.4.2a
Mapped read counts were obtained using Htseq
Differential expression analysis was performed using DESeq2 using default settings except "cooksCutoff=FALSE"
Genome_build: mm10
Supplementary_files_format_and_content: Differential_Expression_Normalized_Counts.txt file was generated using DESeq2 and contains normalized counts in addition to adjusted Pvalues and log fold change. The *.counts.txt files are the raw counts generated from Htseq which served as the input for Deseq2.

organism: Mus musculus

source_name: E9.5 Placental Endothelial Cells_Heterozygous_RNA-seq

extract_protocol:
Endothelial cell RNA was isolated from GFP positive cells sorted from individual dissected placental labyrinth of control Ctcf fl/+;Tie2-cre;RosamT/mG and mutant Ctcf fl/fl;Tie2- cre;RosamT/mG embryos using Direct-zol TM RNA MiniPrep Plus Kit (Zymo Research) and treated with DNase according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using the Ovation® Single Cell RNA-seq System (NuGEN) and sequenced in single-end sequence reads (50 bp in length) on the Illumina HiSeq 2500 platform

tag: developmental stage

tag: genotype

value: Ctcf fl/+;Tie2-cre;Rosa mT/mG/+

value: Placenta

tag: cells

value: GFP +ve endothelial cells FACS from placnetal tissue


title: Mutant_RNA-seq_25pm

source_name: E9.5 Placental Endothelial Cells_Mutant_RNA-seq

value: Ctcf fl/fl;Tie2-cre;Rosa mT/mG/+


title: Mutant_RNA-seq_2pm


title: Heterozygous_RNA-seq_50ph


title: Mutant_RNA-seq_6pm


title: Heterozygous_RNA-seq_7ph


title: a131_24h_BJ_normal_rep2

description:
SAMPLE 6
replicate 2

value: BJ normal cells


title: a131_24h_BJ_normal_rep4

description:
SAMPLE 8
replicate 4


title: V43DNA_R224_24hours_post1stALVAC

description: transcriptional profilling of blood taken 24 hours after the 1st ALVAC boost  (week 12)

source_name: blood sample from donor R224 taken 24 hours after the 1st ALVAC boost

value: 24 hours

value: blood


title: MLS_2645-94_doxorubicin

source_name: MLS cell line 2645-94


title: MLS_2645-94_untreated


title: a131_0h_BJ_normal_rep3

description:
SAMPLE 3
replicate 3

value: DMSO


title: HeLa_siCCAR2+H2O2_rep2

city: Seoul

first: Ja-Eun

last: Kim

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description:
replicate 2
8_siCCAR2+H2O2

hyb_protocol: Following fragmentation, cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

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

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: HeLa, siCCAR2-transfected, H2O2-treated, 2 hr

label_protocol: Biotinylated cRNA were prepared from total RNA using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G sodium, 100 microg/ml streptomycin sulfate, and 0.25 microg/ml amphotericin B. Cells were incubated at 37 degrees in 5% CO2 incubator.

extract_protocol: RNA was extracted using Qiagen RNeasy Plus Micro kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: HeLa cells were transfected with siCCAR2. Forty-eight hours after transfection, the cells were treated with 0.5 mM H2O2 treatment for 2 hr.

tag: sirna

tag: agent

tag: time point

value: 2 hr


title: HeLa_Con+H2O2_rep2

description:
replicate 2
7_CON+H2O2

source_name: HeLa, control, H2O2-treated, 2 hr

value: control


title: a131_0h_BJ_normal_rep1

description:
SAMPLE 1
replicate 1


title: a131_24h_BJ_normal_rep1

description:
SAMPLE 5
replicate 1


title: HeLa_siCCAR2_rep2

description:
replicate 2
6_siCCAR2

source_name: HeLa, siCCAR2-transfected, non-treated, 0 hr

value: non-treated

value: 0 hr


title: HeLa_siCCAR2+H2O2_rep3

description:
replicate 3
12_siCCAR2+H2O2


title: HeLa_siCCAR2_rep3

description:
replicate 3
10_siCCAR2


title: HeLa_Con+H2O2_rep3

description:
replicate 3
11_CON+H2O2


title: HeLa_siCCAR2+H2O2_rep1

description:
replicate 1
4_siCCAR2+H2O2


title: HeLa_Con_rep3

description:
replicate 3
9_CON

source_name: HeLa, control, non-treated, 0 hr


title: HeLa_Con+H2O2_rep1

description:
replicate 1
3_CON+H2O2


title: HeLa_Con_rep2

description:
replicate 2
5_CON


title: a131_0h_BJ_normal_rep4

description:
SAMPLE 4
replicate 4


title: a131_0h_BJ_normal_rep2

description:
SAMPLE 2
replicate 2


title: HeLa_siCCAR2_rep1

description:
replicate 1
2_siCCAR2


title: HeLa_Con_rep1

description:
replicate 1
1_CON


title: V43DNA_R222_24hours_post1stALVAC

source_name: blood sample from donor R222 taken 24 hours after the 1st ALVAC boost

tag: donor

tag: immunization

tag: time after immunization

value: DNA


title: HaCaT cell lines T2 HPV18E6 infection, biological rep1

status: Public on Feb 22 2018

city: Cape Town

first: Lamech

last: Mwapagha

address: Anzio Road Observatory

department: Medical Biochemistry

country: South Africa

institute: University of Cape Town/ICGEB

description: Gene expression data from HaCaT cell lines infected with HPV18E6

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human gene ST 2.0 arrays were used for gene expression on an affymetrix platform. 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:
Data analysis was done using the Partek® Genomics Suite™ 6.6 software.The raw data was first normalized using Robust Multi-array Average (RMA). After normalization a preliminary data analysis on the samples was done using Principal Components Analysis (PCA) to explore whether differences or similarities existed between the samples.
A list of the most significantly differentially expressed genes was then generated using volcano plots set at a fixed fold-change cut-off of between –2.0 and 2.0 with a significance FDR of ≤ 0.05

source_name: HPV 18-A_14032013.CPGR.rma-gene-full

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: HaCaT Cells were cultured at 37°C in  a humidified atmosphere of 5 % CO2 in Dulbecco’s modified eagle’s medium (DMEM) supplemented with 10 % heat inactivated foetal calf serum (FCS), 2mM L-glutamine, 100U/ml penicillin and 100μg/ml streptomycin (complete DMEM). The medium was changed every 2 days, and the cells were sub-cultured when 90% confluent, by dislodging the cells with 0.05% trypsin-EDTA. Once detached, the trypsin-EDTA was inactivated by the addition of 5 ml of complete DMEM. Cells were collected by centrifugation at 4000 rpm for 5 minutes, re-suspended in complete DMEM and re-plated at a ratio of 1:3.  Cells were regularly checked for mycoplasma contamination.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells were washed once with PBS and infected at a multiplicity of infection (MOI) of 100 using a polycation (DEAE-Dextran). For infection, 1ml of complete DMEM was mixed with the recombinant adenovirus and 1µl of DEAE-dextran (7.5µg/ml) was added drop-wise onto each well. Control cells were left uninfected. The plates were incubated at 37°C in a humidified atmosphere containing 5% CO2 for 1 hour and centrifuged for 1 hour at 2000rpm at 37°C. A fresh aliquot of DMEM/E6/DEAE Dextran was added and the above step repeated. The cells were infected with the Adeno-HPVE6 for 48 hours after which DNA, RNA and protein were extracted and analysed to confirm the expression of HPV11E6 and HPV18E6 by qRT-PCR, western blotting and confocal microscopy

value: HaCaT cell lines infected with HPV18E6 for 48 h


title: HaCaT cell lines T1 HPV11E6 infection, biological rep3

description: Gene expression data from HaCaT cell lines infected with HPV11E6

source_name: HPV 11-C_14032013.CPGR.rma-gene-full

value: HaCaT cell lines infected with HPV11E6 for 48 h


title: HaCaT cell lines T1 HPV11E6 infection, biological rep2

source_name: HPV 11-B_14032013.CPGR.rma-gene-full


title: HaCaT cell lines T2 HPV18E6 infection, biological rep2

source_name: HPV 18-C_14032013.CPGR.rma-gene-full


title: HaCaT cell lines T2 HPV18E6 infection, biological rep3


title: HaCaT cell lines T0, biological rep1

description: Gene expression data from HaCaT cell lines uninfected

value: HaCaT cell lines uninfected


title: HaCaT cell lines T1 HPV11E6 infection, biological rep1

source_name: HPV 11-A_14032013.CPGR.rma-gene-full


title: HaCaT cell lines T0, biological rep2


title: HaCaT cell lines T0, biological rep3


title: Bone_marrow_erythroblast_rep11_miRNA

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

institute: Montreal Heart Institute

description: small RNA

data_processing:
We removed adapter sequences using the fastxclipper tool (v.0.0.14). We removed reads that mapped to ribosomal genes using bowtie (v.1.0.0, with options -n 0 -S –best --chunkmbs 200). We mapped reads to both mature and precursor miRNA sequences from miRBASE release 21 using mirDeep2 (v.0.0.5)
We tested differential expression of miRNAs using the R package DESeq2 (v.1.12.4)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Erythroblast differentiated from human bone marrow CD34+ hematopoietic stem cells

growth_protocol: Fetal and adult erythroblasts were generated from CD34+ hematopoietic stem cells using a two-phase serum-free culture as described previously (Sankaran VG et al. Science 2008).

extract_protocol:
Total RNA for RNA sequencing was extracted using the miRNEASY kit (Qiagen).
Illumina TruSeq Small RNA

value: adult

tag: tissue


title: Bone_marrow_erythroblast_rep3_miRNA

description: small RNA

value: Erythroblast differentiated from human bone marrow CD34+ hematopoietic stem cells


title: Bone_marrow_erythroblast_rep10_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep9_miRNA

description: small RNA

source_name: Erythroblast differentiated from human fetal liver CD34+ hematopoietic stem cells

value: fetal


title: Fetal_liver_erythroblast_rep11_miRNA

description: small RNA

value: Erythroblast differentiated from human fetal liver CD34+ hematopoietic stem cells


title: Bone_marrow_erythroblast_rep7_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep5_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep4_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep2_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep8_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep6_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep1_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep0_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep8_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep10_miRNA

description: small RNA


title: Bone_marrow_erythroblast_rep9_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep6_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep7_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep5_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep4_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep3_miRNA

description: small RNA


title: Fetal_liver_erythroblast_rep2_miRNA

description: small RNA


title: sncRNA_7_3

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
miRNA.csv
piRNA.csv
rRNA.csv
rmskGenome.csv
tRNA.csv

data_processing:
Reads were aligned to the hg19 genome using the subread aligner, keeping only uniquely assigned reads
Unmapped reads were extracted and mapped to a genome consisting only of ribosomal RNA sequences where all rRNA genes with identical sequences were removed leaving only one copy, allowing for up to 10 alignments per read.
Reads that were unmapped to rRNA were extracted and aligned to a genome consisting only of miRNA sequences where all miRNA genes with identical sequences were removed leaving only one copy. Only unique alignments were allowed.
Unmapped reads were extracted and the procedure above was repeated, mapping to piRNAs, tRNAs and repeatmasker sequences. Each time keeping only unique alignments.
Reads aligning to the genome were counted using featureCounts, reads mapping to rRNA were reported by the aligner, reads mapping to miRNA, piRNA, tRNA and repeatmasker were counted by samtools.
The R statistical environment was used to combine the reads aligning to the genome with the reads aligning to rRNA, miRNA, piRNA, tRNA and repeatmasker genomes, to get the final counts reported here.
Genome_build: hg19
Supplementary_files_format_and_content: comma-seperated text files with the raw counts of miRNA, piRNA, rRNA and repeatMasker reads. Total number of reads that mapped to rRNA.

source_name: motile semen

extract_protocol:
Total RNA was isolated by the TRIzol® method (Life Technologies) from the sperm cells of 6 men before and after the 6-week exercise intervention, and after 3 months of detraining
The sRNA libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer's instructions. Molecules of 20-50 nucleotides were separated by acrylamide gel electrophoresis, extracted, and sequenced

tag: participant

tag: training status

value: Detrained

tag: body type

value: lean


title: sncRNA_7_2

value: Trained


title: sncRNA_7_1

value: Untrained


title: Fetal_liver_erythroblast_rep1_miRNA

description: small RNA


title: sncRNA_24_2


title: sncRNA_20_3


title: sncRNA_24_1


title: sncRNA_25_1


title: sncRNA_27_2


title: sncRNA_27_3


title: sncRNA_25_3


title: sncRNA_17_1


title: sncRNA_11_1


title: sncRNA_11_3


title: sncRNA_18_2


title: sncRNA_20_1


title: sncRNA_15_2


title: sncRNA_25_2


title: sncRNA_11_2


title: sncRNA_20_2


title: sncRNA_27_1


title: sncRNA_18_1


title: a131_24h_BJ_Transformed_rep1

description:
SAMPLE 12
replicate 1

tag: cell type

value: BJ transformed cells

tag: treatment


title: sncRNA_15_1


title: sncRNA_17_2


title: RRBS_9_3

description:
methReads.csv
predictedMeth.csv
totalReads.csv

library_source: genomic

data_processing:
reads were preprocessed with trim_galore with the --rrbs flag set
preprocessed reads were aligned agains hg19 using Bismark using the --bowtie2 flag
methylation levels were extracted using bismark_methylation_extractor with the --gzip, -s and --comprehensive flags set
bismark2bedGraph was run on the CpG_context files
coverage files were read by BiSeq, and clustered by the clusterSites function, with the parameters perc.samples = 0.5, min.sites = 5 and max.dist = 100
Sites with more then 90th percentile reads were excluded and smoothed methylation levels were predicted by the predictMeth function
Genome_build: hg19
Supplementary_files_format_and_content: Csv files with CpG level information on the total number of reads covering a CpG, the number of methylated reads covering a CpG and the smoothed estimate of methylation level.

molecule: genomic DNA

extract_protocol:
genomic DNA was extracted from the sperm cells of 12 men before and after the exercise intervention, as well as after the detraining period, with the Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare, Life Sciences). The protocol was modified for processing of sperm, according to the manufacturer's recommendations.
200ng of genomic DNA was digested with 40U of MspI enzymes (New England Biolabs) and ligated to TruSeq (Illumina) sequencing adaptors. Bisulfite conversion was conducted once with the EpiTect bisulfite kit (Qiagen) in accordance with the manufacturer's instructions, and the converted DNA was amplified by PCR and sequenced


title: Fetal_liver_erythroblast_rep0_miRNA

description: small RNA


title: RRBS_9_1


title: RRBS_9_2


title: RRBS_8_1


title: RRBS_8_3


title: sncRNA_15_3


title: RRBS_8_2


title: RRBS_7_1


title: RRBS_7_3


title: RRBS_27_2


title: RRBS_18_3


title: RRBS_5_3


title: RRBS_27_1


title: RRBS_27_3


title: RRBS_24_3


title: RRBS_24_2


title: RRBS_15_3


title: RRBS_16_1


title: RRBS_17_2


title: RRBS_17_1


title: RRBS_17_3


title: RRBS_18_2


title: RRBS_15_2


title: RRBS_16_2


title: RRBS_24_1


title: RRBS_16_3


title: RRBS_15_1


title: RRBS_5_1


title: RRBS_14_3


title: RRBS_14_2


title: RRBS_7_2


title: RRBS_5_2


title: RRBS_11_3


title: RRBS_14_1


title: RRBS_11_1


title: RRBS_11_2


title: RRBS_18_1


title: LPS + PC, DCs, Donor 2

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

institute: University of Copenhagen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: human blood

label_protocol: Standard Illumina labelling protocol

growth_protocol: DCs were cultured from human monocytes for 4 days

extract_protocol: Total RNA was extracted using Qiagen RNAeasy minikit

treatment_protocol: DCs were treated with either LPS (10 ng/mL), LPS + PC (10 ug/mL) or LPS + ABF (10 ug/mL) for 6 hours

tag: individual

value: Donor 2

value: blood

value: dendritic cell (DC)

value: LPS + PC


title: LPS + ABF, DCs, Donor2

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: LPS + ABF, DCs

treatment_protocol: DCs were treated with either LPS (10 ng/mL) or LPS + ABF (10 ug/mL) for 6 hours

value: LPS + ABF


title: LPS, DCs, Donor2

source_name: LPS, DCs

value: LPS


title: Kidney Tissue from WT Mice Replicate 12

city: Stanford

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

institute: Stanford University

description:
Biological replicate 12 of 18. Kidney tissue, harvested from WT mice.
WT-rep12

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent Hybridization Chamber Kit. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent p/n G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (A. 7.0.1) was used for background subtraction and LOWESS normalization.

source_name: Kidney Tissue from WT Mice

label_protocol: 5 µg of total RNA were primed with T7 Promoter Primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV-RT, and 10 mM dNTP, Cy3- or Cy5-label

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

treatment_protocol: Kidenys were collected from ko or wt mice at age 0, 1day, 2 days, 3 days, 7 days or 14 days.

tag: genotype/variation

value: WT

tag: age

value: day 3

value: Kidney

tag: strain

source_name: Mouse Universal Reference RNA

tag: cell line

value: Cell Line Mixture


title: LPS + PC, DCs, Donor 1

value: Donor 1


title: Kidney Tissue from WT Mice Replicate 6

description:
Biological replicate 6 of 18. Kidney tissue, harvested from WT mice.
WT-rep6

value: day 2


title: Kidney Tissue from WT Mice Replicate 17

description:
Biological replicate 17 of 18. Kidney tissue, harvested from WT mice.
WT-rep17

value: day 14


title: Kidney Tissue from WT Mice Replicate 4

description:
Biological replicate 4 of 18. Kidney tissue, harvested from WT mice.
WT-rep4

value: day 1


title: Kidney Tissue from WT Mice Replicate 8

description:
Biological replicate 8 of 18. Kidney tissue, harvested from WT mice.
WT-rep8


title: Kidney Tissue from WT Mice Replicate 18

description:
Biological replicate 18 of 18. Kidney tissue, harvested from WT mice.
WT-rep18


title: Kidney Tissue from WT Mice Replicate 3

description:
Biological replicate 3 of 18. Kidney tissue, harvested from WT mice.
WT-rep3


title: Kidney Tissue from WT Mice Replicate 15

description:
Biological replicate 15 of 18. Kidney tissue, harvested from WT mice.
WT-rep15

value: day 7


title: LPS, DCs, Donor1


title: Kidney Tissue from WT Mice Replicate 16

description:
Biological replicate 16 of 18. Kidney tissue, harvested from WT mice.
WT-rep16


title: Kidney Tissue from WT Mice Replicate 11

description:
Biological replicate 11 of 18. Kidney tissue, harvested from WT mice.
WT-rep11


title: Kidney Tissue from WT Mice Replicate 10

description:
Biological replicate 10 of 18. Kidney tissue, harvested from WT mice.
WT-rep10


title: Kidney Tissue from WT Mice Replicate 7

description:
Biological replicate 7 of 18. Kidney tissue, harvested from WT mice.
WT-rep7


title: LPS + ABF, DCs, Donor3

value: Donor 3


title: Kidney Tissue from WT Mice Replicate 14

description:
Biological replicate 14 of 18. Kidney tissue, harvested from WT mice.
WT-rep14


title: LPS, DCs, Donor3


title: Kidney Tissue from WT Mice Replicate 13

description:
Biological replicate 13 of 18. Kidney tissue, harvested from WT mice.
WT-rep13


title: LPS + PC, DCs, Donor 3


title: Kidney Tissue from KO Mice Replicate 18

description:
Biological replicate 18 of 18. Kidney tissue, harvested from KO mice.
KO-rep18

source_name: Kidney Tissue from KO Mice

value: KO


title: Kidney Tissue from KO Mice Replicate 16

description:
Biological replicate 16 of 18. Kidney tissue, harvested from KO mice.
KO-rep16


title: Kidney Tissue from WT Mice Replicate 5

description:
Biological replicate 5 of 18. Kidney tissue, harvested from WT mice.
WT-rep5


title: Kidney Tissue from WT Mice Replicate 9

description:
Biological replicate 9 of 18. Kidney tissue, harvested from WT mice.
WT-rep9


title: LPS + ABF, DCs, Donor1


title: Kidney Tissue from WT Mice Replicate 1

description:
Biological replicate 1 of 18. Kidney tissue, harvested from WT mice.
WT-rep1

value: day 0


title: Kidney Tissue from WT Mice Replicate 2

description:
Biological replicate 2 of 18. Kidney tissue, harvested from WT mice.
WT-rep2


title: Control pig 3

description: gene expression data from jejunum  mucosa

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard Affymetrix normalization

organism: Sus scrofa

source_name: Pig (Uninfected control)

label_protocol: Standard Affymetrix protocol

growth_protocol: Pigs were housed indoors

extract_protocol: Pigs were euthanised and  a piece of tissue from the mid-point of the jejunum was disscted out, washed and frozen

treatment_protocol: Pigs were aged approx. 4 weeks at the start of trickle infection of A. suum, consisting of 25 eggs/kg/day

value: Uninfected

value: jejunum mucosa tissue


title: Control pig 2


title: Kidney Tissue from KO Mice Replicate 12

description:
Biological replicate 12 of 18. Kidney tissue, harvested from KO mice.
KO-rep12


title: Control pig 9


title: Control pig 7


title: Control pig 8


title: Control pig 1


title: Control pig 5


title: Kidney Tissue from KO Mice Replicate 10

description:
Biological replicate 10 of 18. Kidney tissue, harvested from KO mice.
KO-rep10


title: Control pig 6


title: Kidney Tissue from KO Mice Replicate 5

description:
Biological replicate 5 of 18. Kidney tissue, harvested from KO mice.
KO-rep5


title: Kidney Tissue from KO Mice Replicate 13

description:
Biological replicate 13 of 18. Kidney tissue, harvested from KO mice.
KO-rep13


title: Kidney Tissue from KO Mice Replicate 6

description:
Biological replicate 6 of 18. Kidney tissue, harvested from KO mice.
KO-rep6


title: Kidney Tissue from KO Mice Replicate 14

description:
Biological replicate 14 of 18. Kidney tissue, harvested from KO mice.
KO-rep14


title: Kidney Tissue from KO Mice Replicate 8

description:
Biological replicate 8 of 18. Kidney tissue, harvested from KO mice.
KO-rep8


title: Infected pig 10

source_name: Pig (A. suum infected)

value: Ascaris suum


title: Kidney Tissue from KO Mice Replicate 4

description:
Biological replicate 4 of 18. Kidney tissue, harvested from KO mice.
KO-rep4


title: Kidney Tissue from KO Mice Replicate 15

description:
Biological replicate 15 of 18. Kidney tissue, harvested from KO mice.
KO-rep15


title: Control pig 4


title: Kidney Tissue from KO Mice Replicate 11

description:
Biological replicate 11 of 18. Kidney tissue, harvested from KO mice.
KO-rep11


title: Infected pig 9


title: Infected pig 8


title: Kidney Tissue from KO Mice Replicate 17

description:
Biological replicate 17 of 18. Kidney tissue, harvested from KO mice.
KO-rep17


title: Kidney Tissue from KO Mice Replicate 9

description:
Biological replicate 9 of 18. Kidney tissue, harvested from KO mice.
KO-rep9


title: Kidney Tissue from KO Mice Replicate 3

description:
Biological replicate 3 of 18. Kidney tissue, harvested from KO mice.
KO-rep3


title: Kidney Tissue from KO Mice Replicate 7

description:
Biological replicate 7 of 18. Kidney tissue, harvested from KO mice.
KO-rep7


title: Infected pig 5


title: Infected pig 6


title: Infected pig 2


title: Infected pig 4


title: Infected pig 3


title: Infected pig 1


title: 10d-4

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

country: China

institute: Shanghai University

description: Cardiomyocytes isolated from P10 rat displayed reduced proliferation rate versus P0.

hyb_protocol: The labeled RNA were hybridized for 20 hr at 55°C on Agilent-038112 Array. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis.
Differentially expressed miRNAs were identified through fold change as well as P value calculated using t-test.

organism: Rattus norvegicus

source_name: Cardiomyocytes isolated from postnatal day 10 (P10) rat

label_protocol: Total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Total RNA were isolated from cardiomyocytes using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

value: cardiomyocyte

tag: gender

value: male or female

value: postnatal day 10 (P10)


title: 10d-1


title: 10d-3


title: 0d-1

source_name: Cardiomyocytes isolated from postnatal day 0 (P0) rat

value: postnatal day 0 (P0)


title: 0d-3


title: Infected pig 7

tag: agent


title: Kidney Tissue from Sham Mice Replicate_38

description:
Biological replicate 38 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep38
5 day Sham_28d

source_name: Kidney Tissue from Sham Mice

treatment_protocol: Mice were anesthetized and subjected to unilateral obstruction. The left ureter was clipped with a microvascular clamp to generate an obstructed kidney for either 1 day or 5 days. Kidney was collected at 0, 10 days and 28 days after clamp was removed. For each time point additional mice underwent dissection of the left ureter without ligation to serve as sham controls.

tag: stress (obstruction)

value: Sham

tag: stress (obstruction) duration

value: 5 day

tag: collection time after end of stress (obstruction)

value: Kidney


title: 10d-2


title: 0d-4


title: Kidney Tissue from Sham Mice Replicate_34

description:
Biological replicate 34 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep34
5 day Sham_28d

value: Cell Line Mixture


title: Kidney Tissue from Sham Mice Replicate_29

description:
Biological replicate 29 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep29
5 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_30

description:
Biological replicate 30 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep30
5 day Sham_10d


title: Kidney Tissue from KO Mice Replicate 1

description:
Biological replicate 1 of 18. Kidney tissue, harvested from KO mice.
KO-rep1


title: Kidney Tissue from Sham Mice Replicate_35

description:
Biological replicate 35 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep35
5 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_37

description:
Biological replicate 37 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep37
5 day Sham_28d


title: 0d-2


title: miRNA_stroke_18

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

description:
Sample#18
LH_58_TGACCA_L002

data_processing:
Basecalling was performed using Casava software version1.8.2 (Illumina).
Bioinformatic analyses were performed according to Stokowy et al (Stokowy T, Eszlinger M, Swierniak M, Fujarewicz K, Jarzab B, Paschke R, Krohn K. Analysis options for high-throughput sequencing in miRNA expression profiling. BMC research notes. 2014;7:144).
Adapter trimming and quality filtering was done using Cutadapt software, quality conrol was done using FastQC program (Bioinformatics Group at the Babraham Institute, UK).
Mapping was performed using bowtie2 alignment to the sequence of the human genome (hg19) allowing one mismatch and alignments to multiple reference targets. miRNA sequences were identified by intersecting human genomic miRNA coordinates from miRbase 20 using BEDTools.
Differential expression of miRNAs was calculated using DESeq2 and EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: CSV (comma-separated values) file created by DESeq2 and EdgeR

extract_protocol:
RNA samples with length < 1000 nucleotides were isolated from two plasma aliquots of 200 µl using the miRCURY RNA Isolation Kit – Biofluids (Exiqon).
Reverse transcription was performed with the miScript Reverse Transcription kit (Qiagen) according to the manufacturer’s protocols in a 10 μL reaction. 500 ng of RNA prepared from the plasma samples was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) following the instructions of the manufacturer. The barcoded libraries were size restricted between 140 and 165 base pairs for additional enrichment of miRNAs, purified and quantified using the Library Quantification Kit-Illumina/Universal (KAPA Biosystems, Woburn, MA, USA) according to the instructions of the manufacturer. Libraries were pooled at a concentration of 10 nM for cluster generation using an Illumina cBot. Sequencing of 50 base pairs was performed with an Illumina HighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell following the instructions of the manufacturer.

tag: subject group

value: Ischemic Stroke (IS) patients

value: Platelet-poor-plasma

tag: molecule subtype

value: miRNA


title: miRNA_stroke_20

description:
Sample#20
LH_60_GCCAAT_L002

tag: tissue


title: Kidney Tissue from Sham Mice Replicate_36

description:
Biological replicate 36 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep36
5 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_31

description:
Biological replicate 31 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep31
5 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_28

description:
Biological replicate 28 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep28
5 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_33

description:
Biological replicate 33 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep33
5 day Sham_10d


title: miRNA_stroke_16

description:
Sample#16
LH_56_CGATGT_L002


title: Kidney Tissue from Sham Mice Replicate_27

description:
Biological replicate 27 of 39. Kidney tissue, harvested at 0 day after 5 day  sham.
Sham-rep27
5 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_32

description:
Biological replicate 32 of 39. Kidney tissue, harvested at 10 day after 5 day  sham.
Sham-rep32
5 day Sham_10d


title: miRNA_stroke_12

description:
Sample#12
LH_52_CTTGTA_L002


title: miRNA_stroke_14

description:
Sample#14
LH_54_AGTTCC_L002


title: miRNA_stroke_15

description:
Sample#15
LH_55_ATCACG_L002


title: miRNA_stroke_13

description:
Sample#13
LH_53_AGTCAA_L002


title: miRNA_stroke_11

description:
Sample#11
LH_51_GGCTAC_L001


title: miRNA_stroke_19

description:
Sample#19
LH_59_ACAGTG_L002


title: miRNA_stroke_10

description:
Sample#10
LH_50_TAGCTT_L001


title: miRNA_stroke_17

description:
Sample#17
LH_57_TTAGGC_L002


title: miRNA_stroke_09

description:
Sample#09
LH_49_GATCAG_L001


title: miRNA_stroke_06

description:
Sample#06
LH_46_GCCAAT_L001


title: miRNA_stroke_07

description:
Sample#07
LH_47_CAGATC_L001


title: miRNA_stroke_08

description:
Sample#08
LH_48_ACTTGA_L001


title: miRNA_stroke_05

description:
Sample#05
LH_45_ACAGTG_L001


title: miRNA_stroke_04

description:
Sample#04
LH_44_TGACCA_L001


title: Kidney Tissue from Sham Mice Replicate_24

description:
Biological replicate 24 of 39. Kidney tissue, harvested at 0 day after 5 day  sham.
Sham-rep24
5 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_25

description:
Biological replicate 25 of 39. Kidney tissue, harvested at 0 day after 5 day  sham.
Sham-rep25
5 day Sham_0d


title: miRNA_stroke_03

description:
Sample#03
LH_43_TTAGGC_L001


title: Kidney Tissue from KO Mice Replicate 2

description:
Biological replicate 2 of 18. Kidney tissue, harvested from KO mice.
KO-rep2

value: day 1


title: miRNA_stroke_02

description:
Sample#02
LH_42_CGATGT_L001


title: Kidney Tissue from Sham Mice Replicate_39

description:
Biological replicate 39 of 39. Kidney tissue, harvested at 28 day after 5 day  sham.
Sham-rep39
5 day Sham_28d


title: miRNA_stroke_01

description:
Sample#01
LH_41_ATCACG_L001


title: Kidney Tissue from Sham Mice Replicate_23

description:
Biological replicate 23 of 39. Kidney tissue, harvested at 0 day after 5 day  sham.
Sham-rep23
5 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_26

description:
Biological replicate 26 of 39. Kidney tissue, harvested at 0 day after 5 day  sham.
Sham-rep26
5 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_22

description:
Biological replicate 22 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep22
1 day Sham_28d

value: 1 day


title: Kidney Tissue from Sham Mice Replicate_21

description:
Biological replicate 21 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep21
1 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_19

description:
Biological replicate 19 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep19
1 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_17

description:
Biological replicate 17 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep17
1 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_20

description:
Biological replicate 20 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep20
1 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_16

description:
Biological replicate 16 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep16
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_15

description:
Biological replicate 15 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep15
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_14

description:
Biological replicate 14 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep14
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_18

description:
Biological replicate 18 of 39. Kidney tissue, harvested at 28 day after 1 day  sham.
Sham-rep18
1 day Sham_28d


title: Kidney Tissue from Sham Mice Replicate_13

description:
Biological replicate 13 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep13
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_12

description:
Biological replicate 12 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep12
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_11

description:
Biological replicate 11 of 39. Kidney tissue, harvested at 10 day after 1 day  sham.
Sham-rep11
1 day Sham_10d


title: Kidney Tissue from Sham Mice Replicate_9

description:
Biological replicate 9 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep9
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_10

description:
Biological replicate 10 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep10
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_7

description:
Biological replicate 7 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep7
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_8

description:
Biological replicate 8 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep8
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_5

description:
Biological replicate 5 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep5
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_6

description:
Biological replicate 6 of 39. Kidney tissue, harvested at 0 day after 1 day  sham.
Sham-rep6
1 day Sham_0d


title: Kidney Tissue from Sham Mice Replicate_4

description:
Biological replicate 4 of 39. Kidney tissue, harvested from normal mouse.
Sham-rep4
Normal control

value: Normal control


title: TCellStg1-6

type: genomic

first: Moshe

last: Szyf

address: 3655 Sir William Osler Promenade

institute: McGill University

hyb_protocol: Perfromed at Genome Quebec Innovation Centre

data_processing: We normalized and analyzed the data using GenomeStudio® Methylation Module v1.8.  Infinum HD methylation assay was utilized, with Illumina Custom statistics, background subtraction, normalization and a Benjamini Hochberg false discovery rate <0.05  (adjusted P value <0.001).  Differentially methylated CGs were filtered by using a DiffScore of ± 33 (Illumina custom) and delta beta value of ± 0.20.  Two rounds of data cleanup were performed to remove sex bias.  First, average beta values for male controls were compared to average beta values of female controls in GenomeStudio®.  This generated a list of CGs that were determined to be significantly different in male and female controls (Diffscore ± 15, adjusted P value <0.05).  This CG list was then used to remove all corresponding CGs from differential methylation analysis downstream.  Second, once differential methylation analysis was performed for each group relative to control, each dataset was split by sex and average beta values in males and females were compared. Values that were significantly different (Student’s t-test, P<0.05) between males and females were removed to avoid sex-bias.

label: Cy3 and Cy5

source_name: genomic DNA from T cell

label_protocol: Bisulfite conversion and Illumina HumanMethyaltion450k BeadChip sequencing were performed at Genome Quebec Innovation Centre

extract_protocol: Blood was collected in EDTA purple top tubes. PBMC were isolated from whole blood by Ficoll-Paque PLUS (GE Healthcare) gradient according to standard procedures. T cells were isolated using antiCD3 immuno-magnetic beads (Dynabead Life technologies) following the manufacturer recommended protocol. DNA was extracted using the Wizard genomic DNA extraction kit (Promega) following manufacturer recommended protocol.

value: T cell

tag: disease state

value: liver cancer stage 4


title: TCellStg1-3

scan_protocol: Perfromed at Genome Quebec Innovation Centre


title: TCellStg2-4


title: TCellStg4-9


title: Stg4-9

source_name: genomic DNA from PBMC

value: PBMC


title: Kidney Tissue from Sham Mice Replicate_3

description:
Biological replicate 3 of 39. Kidney tissue, harvested from normal mouse.
Sham-rep3
Normal control


title: Stg4-8


title: Stg4-7


title: Stg4-3


title: TCellStg3-6


title: TCellStg4-3


title: TCellStg2-3


title: Kidney Tissue from Sham Mice Replicate_1

description:
Biological replicate 1 of 39. Kidney tissue, harvested from normal mouse.
Sham-rep1
Normal control


title: Stg4-5


title: Stg4-4


title: TCellStg4-2


title: Stg4-2


title: Stg4-1


title: Stg3-10

value: liver cancer stage 3


title: Stg3-9


title: Stg4-6


title: TCellStg1-1


title: Kidney Tissue from RUUO Mice Replicate_36

description:
Biological replicate 36 of 36. Kidney tissue, harvested after 28 days of RUUO.
RUUO-rep36
5 day Ob_28d

source_name: Kidney Tissue from RUUO Mice

value: RUUO


title: Kidney Tissue from RUUO Mice Replicate_35

description:
Biological replicate 35 of 36. Kidney tissue, harvested after 28 days of RUUO.
RUUO-rep35
5 day Ob_28d


title: Stg3-8


title: Kidney Tissue from Sham Mice Replicate_2

description:
Biological replicate 2 of 39. Kidney tissue, harvested from normal mouse.
Sham-rep2
Normal control


title: Kidney Tissue from RUUO Mice Replicate_33

description:
Biological replicate 33 of 36. Kidney tissue, harvested after 28 days of RUUO.
RUUO-rep33
5 day Ob_28d


title: Stg3-4


title: TCellStg2-2


title: Stg3-5


title: Stg3-6


title: Kidney Tissue from RUUO Mice Replicate_31

description:
Biological replicate 31 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep31
5 day Ob_10d


title: Stg3-3


title: Stg3-7


title: Kidney Tissue from RUUO Mice Replicate_34

description:
Biological replicate 34 of 36. Kidney tissue, harvested after 28 days of RUUO.
RUUO-rep34
5 day Ob_28d


title: Stg2-6

value: liver cancer stage 2


title: Stg3-2


title: Stg3-1


title: SB2 KD-ADAR1 Edited Replicate 2

city: Houston

first: Enrique

last: Fuentes-Mattei

state: Texas

address: 1901 East Rd., Unit Number: 1950

department: Experimental Therapeutics

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto an Affymetrix Human Genome U133 Plus 2.0 Array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Nexus Expression 3 software v14.0 (BioDiscovery) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

source_name: SB2 transfected cells edited

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: SB2 KD-ADAR1 were transfected overnight, using RNA iMAX, with WT or edited miR-378a-3p, in triplicates.

extract_protocol: 24 hours after cell transfection RNA was purified. Quality control was performed for each RNA sample to check the integrity of the samples.

treatment_protocol: Micro-RNA for miR-378a-3p WT or edited was transfected using RNA iMAX.

value: SB2 KD-ADAR1

value: non-metastatic melanoma cancer cells


title: SB2 KD-ADAR1 Edited Replicate 3


title: Stg2-8


title: Stg2-10


title: Stg2-9


title: Stg2-7


title: Stg2-5


title: Kidney Tissue from RUUO Mice Replicate_29

description:
Biological replicate 29 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep29
5 day Ob_10d

value: 5 day


title: Kidney Tissue from RUUO Mice Replicate_30

description:
Biological replicate 30 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep30
5 day Ob_10d

value: Kidney


title: Kidney Tissue from RUUO Mice Replicate_32

description:
Biological replicate 32 of 36. Kidney tissue, harvested after 28 days of RUUO.
RUUO-rep32
5 day Ob_28d

value: Cell Line Mixture


title: Stg2-3


title: Stg2-1


title: Kidney Tissue from RUUO Mice Replicate_28

description:
Biological replicate 28 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep28
5 day Ob_10d


title: Kidney Tissue from RUUO Mice Replicate_27

description:
Biological replicate 27 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep27
5 day Ob_10d


title: Stg2-2


title: Stg2-4


title: V2a interneuron

city: La Jolla

first: Samuel

middle: L

last: Pfaff

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: 3’ scRNA-Seq is sequenced as paired-end however only the second read is used to align while the first read contains the cell and UMI barcodes. Individual samples are provided as four separate pairs of files but are processed as a single sample.

data_processing:
Raw sequencing data was demultiplexed using bcl2fastq v2.18.0.12.
FASTQ files were processed with 10x “cellranger” software to acquire control UMI counts
“cellranger” alignments were further parsed into individual cell files
UMI counts were generated from transcriptome based alignments of the individual cell files to find expression of additional genes not included in the cellranger reference. These UMI were compared to the cellranger UMI counts for consistency before downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The include processed file includes gene-level UMI counts for all cells detected by the cellranger pipeline in CSV format. NOTE: only genes detected in at least 2 cells are included. This is the final UMI matrix all analysis was performed on. The included BAM file was generated with cellranger.

molecule: polyA RNA

source_name: Cervical and lumbar spinal cord

extract_protocol:
Cervical and lumbar segments were dissected from 2 neonates at P0 in aCSF, and cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical) with 5% Trehalose, 50uM APV, and 800uM KA added during the dissociation process (Saxena et al., 2012). Via FACS (FACSDIVA, BD), 2800 cervical cells and 2800 lumbar cells were collected into 500ul of FACS buffer (Sternfeld et al., 201). Cell suspension was centrifuged and resuspended in 60ul of FACS buffer, 33.4ul of which was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 12 cycles used for cDNA amplification and 11 cycles for library amplification.

tag: animals

value: mix of C57BL/6J and CB6F1/J


title: Stg1-10

tag: cell type


title: Kidney Tissue from RUUO Mice Replicate_26

description:
Biological replicate 26 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep26
5 day Ob_10d


title: SB2 KD-ADAR1 Mimic Replicate 3

source_name: SB2 transfected cells mimic


title: SB2 KD-ADAR1 Mimic Replicate 1


title: SB2 KD-ADAR1 Mimic Replicate 2


title: Control_MEF_RNAseq 3

city: Oxford

first: Amy

last: Royall

state: Oxfordshire

address: Radcliffe Observatory Quarter

department: Zoology

country: United Kingdom

institute: University of Oxford

description:
Poly-A-tailed enriched RNA
Control rep 3

data_processing:
Raw reads generated using FeatureCounts software
Genome_build: mm10
Supplementary_files_format_and_content: Excel document showing raw reads for all geneIDs for each replicate of all 5 experimental conditions gathered from default FeatureCount output

growth_protocol: Primary MEFs were cultured in DMEM containing 10% Feotal Bovine Serum and 1% Penstrep on plasticware coated in 0.001% poly-L-Lysine

extract_protocol:
Cells were FACs sorted and GFP positive cells collected. Total RNA was extracted using Qiagen micro Rneasy kit.
Libraries were processed by the Wellcome Trust Centre for Human Genetics for HiSeq4000 sequencing

treatment_protocol: Cells were electroporated using NEPA21 electroporation system using constructs with a co-expressed GFP gene

tag: passage

value: Mouse Embryonic Fibroblasts

tag: ectopically expressed gene

value: Empty Vector


title: Stg1-9

value: liver cancer stage 1


title: Kidney Tissue from RUUO Mice Replicate_25

description:
Biological replicate 25 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep25
5 day Ob_10d


title: Control_MEF_RNAseq 1

description:
Poly-A-tailed enriched RNA
Control rep 1


title: Control_MEF_RNAseq 2

description:
Poly-A-tailed enriched RNA
Control rep 2


title: Stg1-6


title: Stg1-8


title: Stg1-1


title: Kidney Tissue from RUUO Mice Replicate_24

description:
Biological replicate 24 of 36. Kidney tissue, harvested after 10 days of RUUO.
RUUO-rep24
5 day Ob_10d


title: Stg1-3


title: SB2 KD-ADAR1 Edited Replicate 1


title: Stg1-7


title: OboxA7_MEF_RNAseq 3

description:
Poly-A-tailed enriched RNA
OboxA7 rep 3


title: Stg1-5


title: Kidney Tissue from RUUO Mice Replicate_22

description:
Biological replicate 22 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep22
5 day Ob_0d


title: Stg1-2


title: Kidney Tissue from RUUO Mice Replicate_21

description:
Biological replicate 21 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep21
5 day Ob_0d


title: OboxA7_MEF_RNAseq 2

description:
Poly-A-tailed enriched RNA
OboxA7 rep 2


title: Kidney Tissue from RUUO Mice Replicate_20

description:
Biological replicate 20 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep20
5 day Ob_0d


title: OboxA7_MEF_RNAseq 1

description:
Poly-A-tailed enriched RNA
OboxA7 rep 1


title: HepC7

value: hepatitis


title: OboxA4_MEF_RNAseq 3

description:
Poly-A-tailed enriched RNA
OboxA4 rep 3


title: OboxA4_MEF_RNAseq 2

description:
Poly-A-tailed enriched RNA
OboxA4 rep 2


title: Stg1-4


title: HepC4


title: HepC10


title: OboxA4_MEF_RNAseq 1

description:
Poly-A-tailed enriched RNA
OboxA4 rep 1


title: HepC9


title: OboxA1_MEF_RNAseq 3

description:
Poly-A-tailed enriched RNA
OboxA1 Replicate 3


title: HepC8


title: HepC6


title: OboxA1_MEF_RNAseq 2

description:
Poly-A-tailed enriched RNA
OboxA1 Replicate 2


title: HepB10


title: HepC2


title: HepC3


title: HepC5


title: HepC1


title: Kidney Tissue from RUUO Mice Replicate_19

description:
Biological replicate 19 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep19
5 day Ob_0d


title: HepB9


title: HepB8


title: OboxA1_MEF_RNAseq 1

description:
Poly-A-tailed enriched RNA
OboxA1 Replicate 1


title: Kidney Tissue from RUUO Mice Replicate_15

description:
Biological replicate 15 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep15
1 day Ob_28d

value: 1 day


title: CrxOS_MEF_RNAseq 3

description:
Poly-A-tailed enriched RNA
CrxOS rep 3

value: CrxOS


title: Kidney Tissue from RUUO Mice Replicate_17

description:
Biological replicate 17 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep17
1 day Ob_28d


title: Kidney Tissue from RUUO Mice Replicate_14

description:
Biological replicate 14 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep14
1 day Ob_28d


title: Kidney Tissue from RUUO Mice Replicate_18

description:
Biological replicate 18 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep18
5 day Ob_0d


title: Kidney Tissue from RUUO Mice Replicate_16

description:
Biological replicate 16 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep16
1 day Ob_28d


title: CrxOS_MEF_RNAseq 2

description:
Poly-A-tailed enriched RNA
CrxOS rep 2


title: CrxOS_MEF_RNAseq 1

description:
Poly-A-tailed enriched RNA
CrxOS rep 1


title: HepB5


title: Kidney Tissue from RUUO Mice Replicate_13

description:
Biological replicate 13 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep13
1 day Ob_28d


title: Kidney Tissue from RUUO Mice Replicate_11

description:
Biological replicate 11 of 36. Kidney tissue, harvested at 10 days after 1 day  RUUO.
RUUO-rep11
1 day Ob_10d


title: HepB1


title: Kidney Tissue from RUUO Mice Replicate_10

description:
Biological replicate 10 of 36. Kidney tissue, harvested at 10 days after 1 day  RUUO.
RUUO-rep10
1 day Ob_10d


title: HepB2


title: HepB4


title: HepB7


title: Ctrl7

value: control


title: Kidney Tissue from RUUO Mice Replicate_9

description:
Biological replicate 9 of 36. Kidney tissue, harvested at 10 days after 1 day  RUUO.
RUUO-rep9
1 day Ob_10d


title: Kidney Tissue from RUUO Mice Replicate_23

description:
Biological replicate 23 of 36. Kidney tissue, harvested at 0min after 5 day  RUUO.
RUUO-rep23
5 day Ob_0d


title: Ctrl10

value: PBMC


title: Ctrl6


title: HepB6


title: Kidney Tissue from RUUO Mice Replicate_8

description:
Biological replicate 8 of 36. Kidney tissue, harvested at 10 days after 1 day  RUUO.
RUUO-rep8
1 day Ob_10d


title: Ctrl5


title: Ctrl9


title: Ctrl3


title: Ctrl8


title: Kidney Tissue from RUUO Mice Replicate_6

description:
Biological replicate 6 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep6
1 day Ob_0d


title: HepB3


title: Kidney Tissue from RUUO Mice Replicate_7

description:
Biological replicate 7 of 36. Kidney tissue, harvested at 10 days after 1 day  RUUO.
RUUO-rep7
1 day Ob_10d


title: Tcell-ctrl10

value: T cell


title: Ctrl4


title: Kidney Tissue from Sham Mice Replicate 59

description:
Biological replicate 59 of 60.
Sham-rep59

treatment_protocol: Mice were anesthetized and subjected to unilateral obstruction for 0, 0.5h, 1h, 3h, 5h, 7h, 12h, 1 day, 3 days, 5 days or 7 days. The left ureter was ligated to generate an obstructed kidney. For each time point additional mice underwent dissection of the left ureter without ligation to serve as sham controls.

value: Sham

tag: time after stress (obstruction)


title: Kidney Tissue from RUUO Mice Replicate_4

description:
Biological replicate 4 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep4
1 day Ob_0d

value: RUUO


title: Kidney Tissue from Sham Mice Replicate 57

description:
Biological replicate 57 of 60.
Sham-rep57


title: Kidney Tissue from Sham Mice Replicate 60

description:
Biological replicate 60 of 60.
Sham-rep60


title: Kidney Tissue from RUUO Mice Replicate_5

description:
Biological replicate 5 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep5
1 day Ob_0d


title: Tcell-ctrl6


title: Kidney Tissue from Sham Mice Replicate 58

description:
Biological replicate 58 of 60.
Sham-rep58


title: Tcell-ctrl4


title: Mamary Tumor 3720-EA

city: East Lansing

first: Daniel

middle: Patrick

last: Hollern

state: MI

address: 2194 Biomedical Physical Sciences

institute: Michigan State University

description: Gene expression data from mouse mammary tumor tissue.

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse430A_2 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara,

data_processing: The data were analyzed using Stratagene's ArrayAssist Enterprise using Affymetrix default analysis settings.

source_name: Mamary Tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animal use and husbandry was in accordance with institutional and federal guidelines.

extract_protocol: Total RNA from mouse mammary tumors was extracted using the Qiagen RNeasy Midi kit.

tag: sample type

value: WT|squamous


title: Kidney Tissue from RUUO Mice Replicate_2

description:
Biological replicate 2 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep2
1 day Ob_0d

tag: strain


title: Mamary Tumor 3716-EA


title: Tcell-ctrl5


title: Ctrl1


title: Kidney Tissue from Sham Mice Replicate 56

description:
Biological replicate 56 of 60.
Sham-rep56

tag: cell line


title: Kidney Tissue from RUUO Mice Replicate_1

description:
Biological replicate 1 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep1
1 day Ob_0d


title: Mamary Tumor 3746-EA


title: Tcell-ctrl9


title: Tcell-ctrl3


title: Mamary Tumor 3723-EA


title: Mamary Tumor 3766-EA

value: WT|microacinar


title: Tcell-ctrl8


title: Kidney Tissue from Sham Mice Replicate 53

description:
Biological replicate 53 of 60.
Sham-rep53


title: Mamary Tumor 3755-EA

value: WT|papillary


title: Kidney Tissue from Sham Mice Replicate 55

description:
Biological replicate 55 of 60.
Sham-rep55

value: Kidney


title: Mamary Tumor 3765-EA


title: Mamary Tumor 3759-EA


title: Kidney Tissue from Sham Mice Replicate 52

description:
Biological replicate 52 of 60.
Sham-rep52

value: Cell Line Mixture


title: Kidney Tissue from Sham Mice Replicate 54

description:
Biological replicate 54 of 60.
Sham-rep54


title: Kidney Tissue from RUUO Mice Replicate_3

description:
Biological replicate 3 of 36. Kidney tissue, harvested at 0min after 1 day  RUUO.
RUUO-rep3
1 day Ob_0d


title: Tcell-ctrl2


title: Mamary Tumor 3744-EA


title: Kidney Tissue from Sham Mice Replicate 48

description:
Biological replicate 48 of 60.
Sham-rep48


title: Tcell-ctrl1


title: Mamary Tumor 3740-EA


title: Mamary Tumor 3749-EA


title: Mamary Tumor 3739-EA


title: Tcell-ctrl7


title: Kidney Tissue from Sham Mice Replicate 49

description:
Biological replicate 49 of 60.
Sham-rep49


title: Mamary Tumor 3741-EA


title: Kidney Tissue from Sham Mice Replicate 50

description:
Biological replicate 50 of 60.
Sham-rep50


title: Kidney Tissue from Sham Mice Replicate 47

description:
Biological replicate 47 of 60.
Sham-rep47


title: Mamary Tumor 3737-EA


title: Infected macrophages 24h of CD300E activation replicate 4

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Labelled RNA was hybridized onto microarray slides using a rotational oven at 65° C for 17 h.

scan_protocol: Mycroarrays were scanned in an Agilent microarray scanner (model G2565CA). Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Raw microarray data were purified for the presence of long non-coding RNAs and quantile normalized. Probe expression values that did not pass filter (positive and significant) were set as NA (not available). Probes with more than 1 NA for condition were excluded from the analysis

source_name: Healthy male blood donor

label_protocol: 200 ng of total RNA were used for Cy3 labelling according to Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Monocytes derived from buffy coats obtained from healthy blood donors were prepared as described previously (Amedei A et al., J Clin Invest 2006). For macrophage differentiation, 5 × 10^5 monocytes, seeded in 24-well plates, were cultured in RPMI 20% FBS in the presence of 100 ng/ml M-CSF (Miltenyi Biotec. Bergisch Gladbach, Germany) for a 6-d differentiation.

extract_protocol: Total RNA from macrophages was isolated with TRIzol reagent (ThermoFisher) according to manufacturer protocol. RNA quantification was performed using the NanoDrop 1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). Total RNA integrity in each sample was assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano and the Small RNA Nano LabChips, respectively (Agilent Technologies, Palo Alto, CA, USA). Only total RNA samples with an RNA integrity number > 7 were used for mRNA gene expression analysis.

treatment_protocol: Monocyte-derived macrophages were cultured for 1 d in culture medium without M-CSF, before stimuli application. 48h of Hp stimulation were performed to enhance the expresion of CD300E. Helicobacter pylori strain N6 was maintained in 5% CO2 at 37°C on Columbia agar plates supplemented with 5% horse blood (ThermoFisher, Waltham, MA, USA). Colonies were taken directly from plates and suspended in RPMI 20% FBS without any antibiotic. Number of bacteria cells was determined by spectroscopic optical density measurement at 600 nm (1 O.D.= 109 Colony Forming Units –CFU- /ml). Before proceeding with the infection experiments, bacteria motility was verified at the optical microscope. After macrophages infection cells were detached with 5 mM Na-EDTA, pelleted and seeded at the density of 250,000 per well onto a 24-well plate coated with anti CD300E (Abcam, clone UP-H2) or with isotype control for 3, 6 and 24 h. Samples were collected and stored for RNA extraction and analysis.

value: monocyte-derived macrophages

tag: gender

value: male

value: healthy


title: Kidney Tissue from Sham Mice Replicate 51

description:
Biological replicate 51 of 60.
Sham-rep51


title: Kidney Tissue from Sham Mice Replicate 46

description:
Biological replicate 46 of 60.
Sham-rep46


title: Mamary Tumor 3733-EA


title: Infected macrophages 24h of CD300E activation replicate 3


title: Mamary Tumor 3754-EA


title: Ctrl2


title: Kidney Tissue from Sham Mice Replicate 44

description:
Biological replicate 44 of 60.
Sham-rep44


title: Kidney Tissue from Sham Mice Replicate 45

description:
Biological replicate 45 of 60.
Sham-rep45


title: Mamary Tumor 3730-EA

description: Gene expression data from mouse mammary tumor tissue.


title: Mamary Tumor 3717-EA


title: Infected macrophages 24h of CD300E activation replicate 1


title: Mamary Tumor 3732-EA


title: Kidney Tissue from Sham Mice Replicate 42

description:
Biological replicate 42 of 60.
Sham-rep42


title: Infected macrophages no CD300E activation 24h control replicate 4


title: Infected macrophages 24h of CD300E activation replicate 2


title: Kidney Tissue from Sham Mice Replicate 43

description:
Biological replicate 43 of 60.
Sham-rep43


title: Kidney Tissue from Sham Mice Replicate 41

description:
Biological replicate 41 of 60.
Sham-rep41


title: Mamary Tumor 3712-EA


title: Infected macrophages no CD300E activation 24h control replicate 3


title: Infected macrophages no CD300E activation 24h control replicate 2


title: Mamary Tumor 3706-EA


title: Kidney Tissue from Sham Mice Replicate 40

description:
Biological replicate 40 of 60.
Sham-rep40


title: Kidney Tissue from Sham Mice Replicate 39

description:
Biological replicate 39 of 60.
Sham-rep39


title: Mamary Tumor 3703-EA


title: Infected macrophages 6h of CD300E activation replicate 2


title: Kidney Tissue from Sham Mice Replicate 38

description:
Biological replicate 38 of 60.
Sham-rep38


title: Infected macrophages 6h of CD300E activation replicate 3


title: Mamary Tumor 3719-EA


title: Mamary Tumor 3699-EA


title: Kidney Tissue from Sham Mice Replicate 37

description:
Biological replicate 37 of 60.
Sham-rep37


title: Infected macrophages 6h of CD300E activation replicate 1


title: Mamary Tumor 3696-EA


title: Mamary Tumor 3701-EA


title: Infected macrophages no CD300E activation 24h control replicate 1


title: Infected macrophages 6h of CD300E activation replicate 4


title: Kidney Tissue from Sham Mice Replicate 35

description:
Biological replicate 35 of 60.
Sham-rep35


title: Infected macrophages no CD300E activation 6h control replicate 4


title: Kidney Tissue from Sham Mice Replicate 36

description:
Biological replicate 36 of 60.
Sham-rep36


title: Infected macrophages no CD300E activation 6h control replicate 2


title: Mamary Tumor 3691-EA


title: Infected macrophages no CD300E activation 6h control replicate 3


title: Mamary Tumor 3694-EA


title: Kidney Tissue from Sham Mice Replicate 34

description:
Biological replicate 34 of 60.
Sham-rep34


title: Kidney Tissue from Sham Mice Replicate 33

description:
Biological replicate 33 of 60.
Sham-rep33


title: Infected macrophages 3h of CD300E activation replicate 3


title: Mamary Tumor 3761-EA


title: Mamary Tumor 3731-EA


title: Kidney Tissue from Sham Mice Replicate 32

description:
Biological replicate 32 of 60.
Sham-rep32


title: Mamary Tumor 3729-EA


title: Mamary Tumor 3763-EA


title: Infected macrophages no CD300E activation 3h control replicate 4


title: Mamary Tumor 3762-EA


title: Kidney Tissue from Sham Mice Replicate 29

description:
Biological replicate 29 of 60.
Sham-rep29


title: Infected macrophages no CD300E activation 6h control replicate 1


title: Infected macrophages 3h of CD300E activation replicate 1


title: Kidney Tissue from Sham Mice Replicate 30

description:
Biological replicate 30 of 60.
Sham-rep30


title: Mamary Tumor 3722-EA


title: Mamary Tumor 3738-EA


title: Kidney Tissue from Sham Mice Replicate 27

description:
Biological replicate 27 of 60.
Sham-rep27


title: Kidney Tissue from Sham Mice Replicate 25

description:
Biological replicate 25 of 60.
Sham-rep25


title: Kidney Tissue from Sham Mice Replicate 28

description:
Biological replicate 28 of 60.
Sham-rep28


title: Mamary Tumor 3714-EA

description: Gene expression data from mouse mammary tumor tissue.


title: Mamary Tumor 3752-EA


title: Kidney Tissue from Sham Mice Replicate 24

description:
Biological replicate 24 of 60.
Sham-rep24


title: Infected macrophages no CD300E activation 3h control replicate 1


title: Infected macrophages no CD300E activation 3h control replicate 2


title: Mamary Tumor 3726-EA


title: Infected macrophages 3h of CD300E activation replicate 2


title: Kidney Tissue from Sham Mice Replicate 26

description:
Biological replicate 26 of 60.
Sham-rep26


title: Mamary Tumor 3704-EA


title: Kidney Tissue from RUUO Mice Replicate_12

description:
Biological replicate 12 of 36. Kidney tissue, harvested at 28 days after 1 day  RUUO.
RUUO-rep12
1 day Ob_28d


title: Infected macrophages no CD300E activation 3h control replicate 3


title: Mamary Tumor 3751-EA


title: Mamary Tumor 3728-EA


title: Kidney Tissue from Sham Mice Replicate 22

description:
Biological replicate 22 of 60.
Sham-rep22


title: Mamary Tumor 3724-EA


title: Kidney Tissue from Sham Mice Replicate 31

description:
Biological replicate 31 of 60.
Sham-rep31


title: Kidney Tissue from Sham Mice Replicate 23

description:
Biological replicate 23 of 60.
Sham-rep23


title: Mamary Tumor 3747-EA


title: Kidney Tissue from Sham Mice Replicate 21

description:
Biological replicate 21 of 60.
Sham-rep21


title: Mamary Tumor 3705-EA


title: Kidney Tissue from Sham Mice Replicate 18

description:
Biological replicate 18 of 60.
Sham-rep18


title: Mamary Tumor 3689-EA


title: Kidney Tissue from Sham Mice Replicate 20

description:
Biological replicate 20 of 60.
Sham-rep20


title: Kidney Tissue from Sham Mice Replicate 19

description:
Biological replicate 19 of 60.
Sham-rep19


title: Mamary Tumor 3697-EA


title: Mamary Tumor 3756-EA


title: Kidney Tissue from Sham Mice Replicate 17

description:
Biological replicate 17 of 60.
Sham-rep17


title: Mamary Tumor 3750-EA


title: Kidney Tissue from Sham Mice Replicate 16

description:
Biological replicate 16 of 60.
Sham-rep16


title: Mamary Tumor 3708-EA


title: Kidney Tissue from Sham Mice Replicate 14

description:
Biological replicate 14 of 60.
Sham-rep14


title: Kidney Tissue from Sham Mice Replicate 15

description:
Biological replicate 15 of 60.
Sham-rep15


title: Kidney Tissue from Sham Mice Replicate 13

description:
Biological replicate 13 of 60.
Sham-rep13


title: Mamary Tumor 3748-EA


title: Kidney Tissue from Sham Mice Replicate 10

description:
Biological replicate 10 of 60.
Sham-rep10


title: Mamary Tumor 3727-EA

description: Gene expression data from mouse mammary tumor tissue.


title: Kidney Tissue from Sham Mice Replicate 12

description:
Biological replicate 12 of 60.
Sham-rep12


title: Mamary Tumor 3725-EA


title: Mamary Tumor 3718-EA


title: Kidney Tissue from Sham Mice Replicate 9

description:
Biological replicate 9 of 60.
Sham-rep9


title: Kidney Tissue from Sham Mice Replicate 8

description:
Biological replicate 8 of 60.
Sham-rep8


title: Mamary Tumor 3715-EA


title: Kidney Tissue from Sham Mice Replicate 7

description:
Biological replicate 7 of 60.
Sham-rep7


title: Mamary Tumor 3710-EA


title: Kidney Tissue from Sham Mice Replicate 6

description:
Biological replicate 6 of 60.
Sham-rep6


title: AU565 Cells treated with DAC rep2

city: Lyon

first: Robert

last: Dante

address: 28, rue Laennec

department: Department of Tumoral Escape

country: France

institute: Cancer Research Center – Lyon

description:
AU565 _DAC
AU-DAC-2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Signal_A and Signal_B intensities in idat files

label: Cy5 and Cy3

source_name: AU565 _DAC

growth_protocol: SKBR3 and AU565 cell lines were cultivated as the manufacturer’s instructions (ATCC).

extract_protocol: Genomic DNA was extracted from cell lines using the QIAmp DNA Mini Kit (Qiagen)

treatment_protocol: SKBR3 and AU565 were treated by CAF-CMs or DAC as specified in the methods section

tag: treated with

value: DAC


title: Kidney Tissue from Sham Mice Replicate 11

description:
Biological replicate 11 of 60.
Sham-rep11

tag: stress (obstruction)


title: Kidney Tissue from Sham Mice Replicate 5

description:
Biological replicate 5 of 60.
Sham-rep5


title: AU565 Cells treated with CAF15-CM rep2

description:
AU565 _CAF15-CM
AU-CAF15-2

source_name: AU565 _CAF15-CM


title: Mamary Tumor 3721-EA


title: AU565 Cells treated with CAF11-CM rep1

description:
AU565 _CAF11-CM
AU-CAF11-1

source_name: AU565 _CAF11-CM


title: Mamary Tumor 3742-EA

value: E2F2 KO|microacinar


title: Kidney Tissue from Sham Mice Replicate 1

description:
Biological replicate 1 of 60.
Sham-rep1

source_name: Mouse Universal Reference RNA


title: Kidney Tissue from Sham Mice Replicate 3

description:
Biological replicate 3 of 60.
Sham-rep3


title: Mamary Tumor 3702-EA


title: Mamary Tumor 3735-EA


title: Mamary Tumor 3734-EA


title: Mamary Tumor 3736-EA


title: Kidney Tissue from UUO Mice Replicate 60

description:
Biological replicate 60 of 60.
UUO-rep60

source_name: Kidney Tissue from UUO Mice

value: UUO


title: Mamary Tumor 3698-EA


title: AU565 Cells none treated rep2

description:
AU565 _none
AU-1_-2

source_name: AU565 _none


title: AU565 Cells treated with CAF15-CM rep1

description:
AU565 _CAF15-CM
AU-CAF15-1


title: Mamary Tumor 3713-EA


title: AU565 Cells none treated rep1

description:
AU565 _none
AU-1_-1


title: Kidney Tissue from Sham Mice Replicate 4

description:
Biological replicate 4 of 60.
Sham-rep4


title: Kidney Tissue from UUO Mice Replicate 59

description:
Biological replicate 59 of 60.
UUO-rep59


title: Mamary Tumor 3760-EA


title: Mamary Tumor 3758-EA


title: Kidney Tissue from UUO Mice Replicate 57

description:
Biological replicate 57 of 60.
UUO-rep57


title: SKBR3 Cells treated with CAF15-CM rep1

description:
SKBR3_CAF15-CM
SK-CAF15-1


title: Mamary Tumor 3753-EA


title: AU565 Cells treated with CAF11-CM rep2

description:
AU565 _CAF11-CM
AU-CAF11-2


title: SKBR3 Cells treated with DAC rep2

description:
SKBR3_DAC
SK-DAC-2


title: Mamary Tumor 3745-EA


title: SKBR3 Cells treated with DAC rep1

description:
SKBR3_DAC
SK-DAC-1


title: SKBR3 Cells treated with CAF15-CM rep2

description:
SKBR3_CAF15-CM
SK-CAF15-2


title: Mamary Tumor 3711-EA


title: AU565 Cells treated with DAC rep1

description:
AU565 _DAC
AU-DAC-1


title: SKBR3 Cells treated with CAF11-CM rep2

description:
SKBR3_CAF11-CM
SK-CAF11-2


title: Kidney Tissue from UUO Mice Replicate 51

description:
Biological replicate 51 of 60.
UUO-rep51


title: Kidney Tissue from UUO Mice Replicate 55

description:
Biological replicate 55 of 60.
UUO-rep55


title: Mamary Tumor 3757-EA


title: Mamary Tumor 3743-EA


title: Mamary Tumor 3764-EA


title: SKBR3 Cells none treated rep2

description:
SKBR3_none
SK-1_-2


title: Kidney Tissue from UUO Mice Replicate 53

description:
Biological replicate 53 of 60.
UUO-rep53


title: SKBR3 Cells treated with CAF11-CM rep1

description:
SKBR3_CAF11-CM
SK-CAF11-1


title: Mamary Tumor 3695-EA


title: Kidney Tissue from UUO Mice Replicate 52

description:
Biological replicate 52 of 60.
UUO-rep52


title: Mamary Tumor 3692-EA


title: Kidney Tissue from UUO Mice Replicate 58

description:
Biological replicate 58 of 60.
UUO-rep58


title: SKBR3 Cells none treated rep1

description:
SKBR3_none
SK-1_-1


title: Mamary Tumor 3709-EA


title: Kidney Tissue from UUO Mice Replicate 46

description:
Biological replicate 46 of 60.
UUO-rep46


title: Mamary Tumor 3690-EA


title: Mamary Tumor 3700-EA


title: Kidney Tissue from Sham Mice Replicate 2

description:
Biological replicate 2 of 60.
Sham-rep2


title: Kidney Tissue from UUO Mice Replicate 45

description:
Biological replicate 45 of 60.
UUO-rep45


title: Kidney Tissue from UUO Mice Replicate 50

description:
Biological replicate 50 of 60.
UUO-rep50


title: Kidney Tissue from UUO Mice Replicate 48

description:
Biological replicate 48 of 60.
UUO-rep48


title: Kidney Tissue from UUO Mice Replicate 47

description:
Biological replicate 47 of 60.
UUO-rep47


title: Mamary Tumor 3707-EA


title: 95 plus 7.75hr

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
processed data column: 95plus7.75 rpkm
processed data file: mRNA Ndt80 induction experiment.txt

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: yeast cells were either grown in YEPD for exponential growth or sporulation medium

extract_protocol:
For ribosome profiling, cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009. For mRNA, cells were flash frozen and lysed using hot acid phenol and SDS as described in Ingolia et al., Science, 2009
As described in Ingolia et al, Science 2009

tag: strain background

tag: cellular state

value: meiotic cells (strain brun95) with Ndt80 induction

value: mRNA


title: 95 plus 7hr

description:
processed data column: 95plus7 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: snR19_uu Rep2

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: WT vs. snR19_uu

hyb_protocol: Labelled cDNA was hybridized according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806)

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePic Pro 6.1 software

data_processing: Background subtraction and lowess normalization was applied according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806)

source_name: WT snR19

label_protocol: Total RNA was reverse transcribed and labelled according to Inada, M & Pleiss, JA. Methods in Enzymology, 2010 (PMID 20946806)

growth_protocol: Cells were innoculated at an OD~0.05 in 25mL YPD media and collected by vacuum filtration at mid-log-phase growth (OD~0.5).

extract_protocol: Total RNA was isolated by Acid-phenol extraction followed by ethanol precipitation and resuspension in 50uL TE buffer

tag: genotype

value: wild type

source_name: Mutant snR19_uu

value: U1 snRNA (snR19) variant


title: Mamary Tumor 3688-EA

description: Gene expression data from mouse mammary tumor tissue.


title: 95 plus 6.5hr

description:
processed data column: 95plus6.5 rpkm
processed data file: mRNA Ndt80 induction experiment.txt

tag: molecule subtype


title: Kidney Tissue from UUO Mice Replicate 42

description:
Biological replicate 42 of 60.
UUO-rep42

tag: tissue


title: 95 plus 6hr

description:
processed data column: 95plus6 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: Foxc1cKOFP Replicate 3

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

description: Biological replicate 3 of 2, Cy3 is mouse RNA and Cy5 is mouse reference

hyb_protocol: not provided

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 8 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
The result Yi is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol: The dome-shaped footpads were colllected with 1mm punch biopsies under disection microscope and were frozen in dry ice imediately, and were kept in -80C until use. The frozen fooptads were dissolved in 1ml of TRIzol reagent by homogenization. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 10 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for 10 minutes at room temperature. The sample was centrifuged again at 4C for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry and ddH2O was then added in the appropriate volume and then transferred to -80C for storage.

value: foot pad

value: Foxc1 KO

tag: background strain

tag: mouse identifier

source_name: Universal Mouse Reference

value: Reference


title: Kidney Tissue from UUO Mice Replicate 40

description:
Biological replicate 40 of 60.
UUO-rep40


title: Kidney Tissue from UUO Mice Replicate 49

description:
Biological replicate 49 of 60.
UUO-rep49


title: 95 plus 5.75hr

description:
processed data column: 95plus5.75 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: Kidney Tissue from UUO Mice Replicate 41

description:
Biological replicate 41 of 60.
UUO-rep41


title: Kidney Tissue from UUO Mice Replicate 56

description:
Biological replicate 56 of 60.
UUO-rep56


title: Foxc1cKOFP Replicate 4

description: Biological replicate 4 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: Mamary Tumor 3693-EA

value: E2F1 KO|microacinar


title: Kidney Tissue from UUO Mice Replicate 36

description:
Biological replicate 36 of 60.
UUO-rep36


title: snR19_uu Rep1

description: snR19_uu vs. WT


title: Kidney Tissue from UUO Mice Replicate 43

description:
Biological replicate 43 of 60.
UUO-rep43


title: Kidney Tissue from UUO Mice Replicate 37

description:
Biological replicate 37 of 60.
UUO-rep37


title: Kidney Tissue from UUO Mice Replicate 38

description:
Biological replicate 38 of 60.
UUO-rep38


title: Kidney Tissue from UUO Mice Replicate 39

description:
Biological replicate 39 of 60.
UUO-rep39


title: 95 minus 7.75hr

description:
processed data column: 95minus7.75 rpkm
processed data file: mRNA Ndt80 induction experiment.txt

value: meiotic cells (strain brun95) without Ndt80 induction


title: Mamary Tumor 3687-EA

description: Gene expression data from mouse mammary tumor tissue.


title: Foxc1WTFP Replicate 4

value: wildtype


title: Foxc1cKOFP Replicate 1

description: Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: Foxc1cKOFP Replicate 2

description: Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: 95 minus 6hr

description:
processed data column: 95minus6 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: Foxc1WTFP Replicate 2


title: Kidney Tissue from UUO Mice Replicate 35

description:
Biological replicate 35 of 60.
UUO-rep35

value: Kidney

value: Cell Line Mixture


title: Foxc1WTFP Replicate 3

description: Biological replicate 3 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: 95 minus 5.5hr

description:
processed data column: 95minus5.5 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: Kidney Tissue from UUO Mice Replicate 34

description:
Biological replicate 34 of 60.
UUO-rep34


title: 1.5hr mRNA prepped in parallel for replicate2

description:
processed data column: 1.5 mrnaRPKM REP2
processed data file: timecourse parallel replicates.txt

value: meiotic cells in sporulation medium


title: 6hr mRNA prepped in parallel for replicate1

description:
processed data column: 6hr mrna RPKM REP1
processed data file: timecourse parallel replicates.txt


title: 1.5hr mRNA prepped in parallel for replicate1

description:
processed data column: 1.5 mrna RPKM REP1
processed data file: timecourse parallel replicates.txt

data_processing:
library strategy: ribosome profiling
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations


title: 95 minus 4hr

description:
processed data column: 95minus4 rpkm
processed data file: mRNA Ndt80 induction experiment.txt


title: 3hr mRNA prepped in parallel for replicate2

description:
processed data column: 3hr mrna RPKM REP2
processed data file: timecourse parallel replicates.txt


title: 6hr fps prepped in parallel for replicate1

description:
processed data column: 6hr fp RPKM REP1
processed data file: timecourse parallel replicates.txt

value: ribosome footprints


title: 0hr mRNA prepped in parallel in parallel to the main timecourse samples for replicate 1

description:
processed data column: 0hr mrna rpkm repl 2
processed data file: timecourse parallel replicates.txt


title: 3hr mRNA prepped in parallel for replicate1


title: 6hr mRNA prepped in parallel for replicate2

description:
processed data column: 6hr mrna RPKM REP2
processed data file: timecourse parallel replicates.txt


title: Kidney Tissue from UUO Mice Replicate 32

description:
Biological replicate 32 of 60.
UUO-rep32


title: Kidney Tissue from UUO Mice Replicate 33

description:
Biological replicate 33 of 60.
UUO-rep33


title: Kidney Tissue from UUO Mice Replicate 31

description:
Biological replicate 31 of 60.
UUO-rep31


title: Foxc1WTFP Replicate 1

description: Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: 6hr fps prepped in parallel for replicate2

description:
processed data column: 6hr fpRPKM REP2
processed data file: timecourse parallel replicates.txt


title: Kidney Tissue from UUO Mice Replicate 29

description:
Biological replicate 29 of 60.
UUO-rep29


title: 3hr fps prepped in parallel for replicate1

description:
processed data column: 3hr fp RPKM REP1
processed data file: timecourse parallel replicates.txt


title: 3hr fps prepped in parallel for replicate2

description:
processed data column: 3hr fp RPKM REP2
processed data file: timecourse parallel replicates.txt


title: 1.5hr fps prepped in parallel for replicate2

description:
processed data column: 1.5 fp rpkm REPL2
processed data file: timecourse parallel replicates.txt


title: Kidney Tissue from UUO Mice Replicate 27

description:
Biological replicate 27 of 60.
UUO-rep27


title: Kidney Tissue from UUO Mice Replicate 28

description:
Biological replicate 28 of 60.
UUO-rep28


title: Kidney Tissue from UUO Mice Replicate 24

description:
Biological replicate 24 of 60.
UUO-rep24


title: Kidney Tissue from UUO Mice Replicate 23

description:
Biological replicate 23 of 60.
UUO-rep23


title: Kidney Tissue from UUO Mice Replicate 20

description:
Biological replicate 20 of 60.
UUO-rep20


title: Kidney Tissue from UUO Mice Replicate 30

description:
Biological replicate 30 of 60.
UUO-rep30


title: Kidney Tissue from UUO Mice Replicate 19

description:
Biological replicate 19 of 60.
UUO-rep19


title: Kidney Tissue from UUO Mice Replicate 25

description:
Biological replicate 25 of 60.
UUO-rep25


title: Kidney Tissue from UUO Mice Replicate 26

description:
Biological replicate 26 of 60.
UUO-rep26


title: Kidney Tissue from UUO Mice Replicate 22

description:
Biological replicate 22 of 60.
UUO-rep22


title: Kidney Tissue from UUO Mice Replicate 54

description:
Biological replicate 54 of 60.
UUO-rep54


title: Kidney Tissue from UUO Mice Replicate 21

description:
Biological replicate 21 of 60.
UUO-rep21


title: 1.5hr fps prepped in parallel for replicate1

description:
processed data column: 1.5 fp RPKM REPL1
processed data file: timecourse parallel replicates.txt


title: 0hr fps prepped in parallel  in parallel to the main timecourse samples for replicate 1

description:
processed data column: 0hr fp-repl1-rpkm
processed data file: timecourse parallel replicates.txt


title: vegetative exponential fps prepped in parallel to the main timecourse samples for replicate 1

description:
processed data column: veg exp fp rpkm repl 1
processed data file: timecourse parallel replicates.txt

value: vegetative exponential OD600=0.6


title: Kidney Tissue from UUO Mice Replicate 16

description:
Biological replicate 16 of 60.
UUO-rep16


title: MATa/a 4.5hr mrna from totRNA-seq

description:
processed data column: MATa/a totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt

value: non-meiotic cells in sporulation medium