title: input-MDA231

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

institute: Shantou University Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2.1.0 with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using ballgown:2.10.0 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: MDA-MB-231 cells were purchased from ATCC and cultured under the conditions according to ATCC recommendation.

extract_protocol:
MDA-MB-231 cells were harvested when they reached 90%, then, 2×107 cells were washed in ice cold PBS and resuspended in 100 μl of RIP Lysis Buffer combined with a protease inhibitor cocktail and RNase inhibitors. 100μl cell lysates were incubated with beads coated with 5 μg of control mouse IgG or antibody against CASC3 (Santa cruz, USA) and antibody against MTDH (Abcam, USA) or against Flag with rotation at 4 °C overnight. After the lysates were treated with proteinase K buffer, immune-precipitated RNA was sequenced on a Illumina NovaSeq 6000 system.
KAPA Stranded RNA-Seq Library Prep Kit (Illumina, USA).

treatment_protocol: Cells were seeded in 6-well plates and cultured to 60%-70% confluence before transfection. pEZ-93-CASC3 or pEZ-93-MTDH plasmids were transiently transfected using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer's protocol.

tag: cell type

value: breast cancer cell

tag: rip antibody


title: RIP-MTDH

status: Public on Jun 25 2020

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: anti-Flag


title: RIP-CASC3


title: Lp1_1_7.9 (L001)

city: Philadelphia

first: Amanda

last: Glazier

state: PA

department: Biology

country: USA

institute: Temple University

data_processing:
Quality check with Fastqc
Cutadapt v1.15 with an overlap of 10and a minimum length of 60 and Trimmomatic v0.36 with a Phred threshold of 30, leading and trailing score threshold of 3, and length minimum of 50 were used to trim adapters and quality filter
Bowtie2v2.3.4 was used to align reads to the transcriptome
DESeq2 was used for analyses, including abundance normalization

organism: Desmophyllum pertusum

source_name: Polyp from experimental tissue

growth_protocol: Fragments were maintained at the respective pH regimes and sampled at 2, 4.5, and 8.5 weeks

extract_protocol:
Qiagen RNAeasy kit
single-end Illumina HiSeq 2500

tag: colony

value: Colony 1

tag: time point

value: time point 1

tag: ph treatment

tag: tissue

value: polyp


title: eiF2S1 selective 40S Ribosome FPs, 250 ng/mlHela Cells [3_40S_eiF2_TM250]

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

description:
40S_eIF2S1_TM_1
processed data file: Master_Data_Table.xlsx

data_processing:
Library strategy: Ribo-seq
Adapter sequences and randomized nucleotides (Nextflex) or polyA stretches (Clonentech) were trimmed from raw reads using cutadapt.
Nuclear and mitochondrial ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
The remaining reads were separately aligned to the human transcriptome (Ensembl transcript assembly 94) and human genome using BBmap. Multiple mappings were allowed.
Genome_build: GRCh38; Ensembl transcript assembly 94
Supplementary_files_format_and_content: Master_Data_Table1.xlsx: Excel file includes values that are normalized to sequencing depth (divided by number of mappings and multiplied by a scaling factor).

source_name: HeLa Cells

growth_protocol: HeLa cells were cultured in DMEM +10% fetal bovine serum +100 U/ml Penicillin/Streptomycin (Gibco 15140122).

extract_protocol:
For cell harvest, growth medium was poured off and cells were quickly washed with ice-cold  washing solution (1x PBS 10 mM MgCl2 800 µM Cycloheximide). Washing solution was immediately poured off and freshly prepared crosslinking solution (1x PBS, 10 mM MgCl2, 200 µM Cycloheximide, 0.025% PFA, 0.5 mM DSP) was added to the cells. Cells were incubated with crosslinking solution for 15 minutes at room temperature while slowly rocking. Crosslinking solution was then poured off and remaining crosslinker was inactivated for 5 minutes with ice-cold quenching solution (1x PBS, 10 mM MgCl2, 200 µM Cycloheximide, 300 mM Glycine). Quenching solution was poured off and 150 µl of lysis buffer (0,25 M HEPES pH 7.5, 50 mM MgCl2, 1 M KCl, 5% NP40, 1000 μM CHX) was added to each 15 cm dish, resulting in 750µL of lysate. Lysis was carried out at 4°C.
After RNA extraction from total and IP-purified fractions, RNA quality and integrity were determined on an Agilent Bioanalyzer using the total RNA Nano 6000 Chip. For size selection, RNA was run on 15% Urea-Polyacrylamide gels (Invitrogen) and fragments of size 20-60 nt (80S libraries) and 20-80 nt (40S libraries) were excised using the Agilent small RNA ladder as a reference. RNA was extracted from the gel pieces by smashing the gels into small pieces with gel smasher tubes and extracting the RNA in 0.5 ml of 10 mM Tris pH 7 at 70°C for 10 minutes. Gel pieces were removed and RNA was precipitated using Isopropanol.  Footprints were then dephosphorylated using T4 PNK (NEB) for 2 hours at 37°C in PNK buffer without ATP. Footprints were then again precipitated and purified using isopropanol. For 40S footprints, contaminating 18S rRNA fragments were depleted as follows. Prevalent 18S rRNA fragments from the first round of 40S footprinting were used to design complementary Biotin-TEG-DNA oligonucleotides (sequences listed in Supplemental Table 4, ordered from Sigma-Aldrich). 100ng of RNA footprints were then hybridized to a mixture (proportional to occurrence of the fragment, listed in Suppl. Table 4) of these DNA oligos (in 40x molar excess) in (0.5M NaCl, 20mM Tris pH7.0, 1mM EDTA, 0.05% Tween20) by denaturing for 90 sec at 95C and then annealing by reducing the temperature by -0.1C/sec down to 37°C, then incubating 15min at 37°C. Hybridized species were pulled out using Streptavidin magnetic beads (NEB) by incubating at room temperature for 15 minutes, and the remaining RNA was purified by isopropanol precipitation. Footprints were then assayed using an Agilent Bioanalyzer small RNA chip and Qubit smRNA kit. 25 ng or less of footprint RNA was used as input for library preparation with SMARTer smRNA-SeqKit for Illumina from Takara / Clontech Laboratories according to the manufacturer’s instructions. Deep-sequencing libraries were sequenced on the Illumina Next-Seq 550 system.

treatment_protocol: Cellular stress conditions were induced by treatment with Tunicamycin at 1 µg / ml or 250 ng / ml for 16 hours.

value: HeLa

tag: rrna depletion

value: Custom rRNA Depletion

tag: library preparation kit

value: Takara

tag: index name

tag: index sequence

value: GAGATTCC


title: eiF2S1 selective 80S Ribosome FPs, 250 ng/mlHela Cells [3_80S_eiF2_TM250]

description:
80S_eIF2S1_TM_1
processed data file: Master_Data_Table.xlsx

value: Ribo Zero Gold

value: TAATGCGC


title: eiF2S1 selective 40S Ribosome FPs, Untreated Hela Cells [3_40S_eiF2_UT]

description:
40S_eIF2S1_1
processed data file: Master_Data_Table.xlsx

value: CGCTCATT


title: S2-DSRC AdMTase-seq (2 U Hia5) - rep1

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

library_source: genomic

data_processing:
Library strategy: AdMTase-seq
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: dm6
Supplementary_files_format_and_content: 5% FDR peak calls as .bed file

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2-DSRC cells

growth_protocol: S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL; Hela cells were grown at room temerature to 90% confluency

extract_protocol: Short DNA fragments were subjected to standard Illumina library construction

treatment_protocol: Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above.

value: S2-DSRC cells

tag: m6a-mtase conditions

value: 2 U Hia5 for 20min at 37C

tag: antibody

value: Millipore Sigma ABE572


title: Frot2_tRH

city: Woods Hole

first: Elena

last: Lopez Peredo

state: MA

address: 7 MBL St

institute: Marine Biological Laboratory

description: Gene expression during desiccation in Flechtneria rotunda

data_processing:
Basecalls performed using CASAVA version 1.4
Trimmomatic 0.35
assembly was subjected to a three-step refinement by removal of contigs (a) with <10 accumulated aligned reads across all time points and replicates, (b) corresponding to rRNA and (c) encoding bacterial transcripts. Non-algal transcripts were identified using blastx as implemented in BLAST+ against nr NCBI database with a cut-off e-value of 10-5. Taxonomical information for filtering bacterial transcripts was obtained using the flag -outfmt “6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sskingdoms sscinames sblastnames stitle”
Libraries were individually aligned to their respective reference transcriptomes using Bowtie 2 v.2.2 . Transcript abundance was estimated using RSEM v.1.2.28 . Expression matrices including read counts matrix, normalized ‘transcripts per million transcripts’ (TPM), and standardized ‘trimmed mean of M-values’ (TMM) were generated using Trinity script abundance_estimates_to_matrix.pl.
Differential expression analysis was performed on count data generated with RSEM using DESeq2. A gene was classified as a DEG if the change in its expression exceeded 4-fold (Log2 2-FC) in pairwise comparisons with a significance level <0.001 (adjusted p-value after Benjamini-Hochberg (BH) correction for multiple testing.
Assembly file has been submitted to the TSA.  TSA submission number: SUB5854707.
Genome_build: Trinity v2.1, jaccard clip option
Supplementary_files_format_and_content: Srot_plant_DE_genes.counts.matrix (Read counts from expression analysis)
Srot_plant_DE_genes.TMM.EXPR.matrix (Normalized expression data from DESeq2)

organism: Flechtneria rotunda

source_name: algal cells in culture

growth_protocol: grown for six weeks in 250 mL Erlenmeyer flasks containing 150 mL of autoclaved BBM+WH medium

extract_protocol:
ZR Plant RNA MiniPrep™ (Zymo, Irvine, USA) followed by RNA Clean & Concentrator™-5 (Zymo, Irvine, USA)
Ovation Arabidopsis RNA-seq Systems (NuGEN, San Carlos, CA, USA). Nuclear, chloroplast, mitochondrial and bacterial ribosomic RNA (rRNA) was removed during the InDA-C adaptor cleavage step using a combination of commercially available oligos targeting prokaryote and green plant rRNA genes (Arabidopsis kit; NuGEN S02070, S02076, R01758, F01278) supplemented with 105 custom-made oligos

treatment_protocol: “Hydrated” stage were collected immediately after transferring 40 µL of algal cultures to a round cover glass. “Early” and “Late” desiccation stages corresponded to a volume-loss of 25% and 60% respectively and were collected 2.5 h and 7.5 h into the desiccation time course. The “Dry” stage corresponded to fully flattened dots (Fig. S1E). Dry algal dots remained in the drying chamber 11 additional hours until collection (circa 24 h after the beginning of the experiment). Finally, the “Rehydrated” stage corresponded to algal dots collected one hour after rehydration.

tag: strain

tag: Stage

value: Rehydrated


title: S2-DSRC AdMTase-seq (6 U Hia5) - rep1

value: 6 U Hia5 for 20min at 37C


title: Total 40S Ribosome FPs 250 ng/ml Hela Cells [3_40S_Total_TM250]

description:
40S_Total_TM_1
processed data file: Master_Data_Table.xlsx

value: TCCGGAGA


title: Ades2_tON

description: Gene expression during desiccation in Acutodesmus deserticola

data_processing:
Basecalls performed using CASAVA version 1.4
Trimmomatic 0.35
assembly was subjected to a three-step refinement by removal of contigs (a) with <10 accumulated aligned reads across all time points and replicates, (b) corresponding to rRNA and (c) encoding bacterial transcripts. Non-algal transcripts were identified using blastx as implemented in BLAST+ against nr NCBI database with a cut-off e-value of 10-5. Taxonomical information for filtering bacterial transcripts was obtained using the flag -outfmt “6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sskingdoms sscinames sblastnames stitle”
Libraries were individually aligned to their respective reference transcriptomes using Bowtie 2 v.2.2 . Transcript abundance was estimated using RSEM v.1.2.28 . Expression matrices including read counts matrix, normalized ‘transcripts per million transcripts’ (TPM), and standardized ‘trimmed mean of M-values’ (TMM) were generated using Trinity script abundance_estimates_to_matrix.pl.
Differential expression analysis was performed on count data generated with RSEM using DESeq2. A gene was classified as a DEG if the change in its expression exceeded 4-fold (Log2 2-FC) in pairwise comparisons with a significance level <0.001 (adjusted p-value after Benjamini-Hochberg (BH) correction for multiple testing.
Assembly file has been submitted to the TSA.  TSA submission number: SUB5854543.
Genome_build: Trinity v2.1, jaccard clip option
Supplementary_files_format_and_content: Sdes_RSEM_plant_genes.counts.matrix (Read counts from expression analysis)
Sdes_RSEM_plant_genes.TMM.EXPR.matrix (Normalized expression data from DESeq2)

organism: Tetradesmus deserticola

value: Dry


title: Ades1_tON


title: Frot1_tRH


title: Frot2_tON


title: Ades2_t75

value: Late desesiccation


title: Total 40S Ribosome FPs Untreated Hela cells [3_40S_Total_UT]

description:
40S_Total_3
processed data file: Master_Data_Table.xlsx

value: ATTACTCG


title: S2-DSRC AdMTase-seq (20 U Hia5) - rep1

value: 20 U Hia5 for 20min at 37C


title: Ades1_t75


title: Frot1_tON


title: S2-DSRC AdMTase-seq (60 U Hia5) - rep1

value: 60 U Hia5 for 20min at 37C


title: S2-DSRC AdMTase-seq (200 U Hia5) - rep1

value: 200 U Hia5 for 20min at 37C


title: Frot2_t75

value: Late desiccation


title: eiF3B Selective 80S Ribosome FPs Hela Cells [2_80S_eIF3B]

description:
80S_eIF3B_2
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Takara

value: GAGATTCC


title: Ades1_t25

value: Early desiccation


title: Total 80S Ribosome FPs Hela cells [2_80S_Total]

description:
2_80S_Total
processed data file: Master_Data_Table.xlsx

value: Ribo Zero Gold


title: eiF4G1 Selective 40S Ribosome FPs Hela Cells [2_40S_eIF4G1]

description:
40S_eIF4G1_1
processed data file: Master_Data_Table.xlsx

value: TCCGCGAA


title: Frot1_t75


title: Ades2_t0

value: Hydrated


title: S2-DSRC m6A-IP-seq

value: S2-DSRC cells

value: Untreated

value: Millipore Sigma ABE572


title: Ades1_t0


title: Frot2_t25


title: post-status epilepticus P2X7-/- 2

type: RNA

city: Dublin

first: Giorgia

last: Conte

address: 123 St stephen's green

department: Physiology and medical physics

country: Ireland

institute: Royal College of surgeons in Ireland

description: P2X7-KO post-SE 2

scan_protocol: The mix of Pre-Amp product and Master-Mix was loaded onto a 384-well OpenArray plate. OpenArray panels were automatically loaded by the OpenArray AccuFill System (Thermo Fisher Scientific, Waltham, Massachusetts) and run on a QuantStudio 12 K Flex Real-Time PCR system.

data_processing:
754 murine miRNAs were amplified from each sample together with 16 replicates of four internal controls (ath-miR159a (negative control), RNU48, RNU44 and U6 rRNA). OpenArray Ct values were normalised to the global mean (GMN).
processed data file includes the global mean

organism: Mus musculus

source_name: hippocampus

label_protocol: MiRNA profiling was performed using the OpenArray platform (ThermoFisher Scientific, Waltham, Massachusetts) (Jimenez-Mateos et al., 2015). OpenArray reverse transcription reaction was performed according to the manufacturer’s protocol using 1 µg of total RNA from each sample (each sample was a pool of 2 hippocampi from different mice). Before loading samples onto the OpenArray, cDNA was pre-amplified following the manufacturer’s recommendation. The pre-amplified product was then diluted with 0.1X TE (1/40). Subsequently, 22.5 µl of the diluted pre-amplified product was added to the same volume of 2X Taqman OpenArray Real time PCR Master Mix (Cat No. 4462164, AB).

extract_protocol: Total RNA was extracted from the ipsilateral hippocampus from wt and P2rx7-/- mice 8 h post intraamygdala vehicle or KA using the Trizol method (Engel et al., 2013). RNA quantity was measured using a Nanodrop Spectrophotometer (Thermo Scientific, Waltham, Massachusetts). Only samples with an absorbance ratio at 260/280 between 1.8–2.2 were considered acceptable. RNA degradation was not assessed. RNA dilutions were made up in nuclease-free water.

treatment_protocol: control vehicle or kainic acid intra-amygdala injection

value: hippocampus

tag: age

value: 8 weeks

tag: genotype


title: post-status epilepticus P2X7-/- 3

description: P2X7-KO post-SE 3


title: eiF3B Selective 40S Ribosome FPs Hela Cells [2_40S_eIF3B]

description:
40S_eIF3B_2
processed data file: Master_Data_Table.xlsx

value: CGGCTATG


title: Frot1_t25


title: Total 40S Ribosome FPs Hela cells [2_40S_Total]

description:
40S_Total_2
processed data file: Master_Data_Table.xlsx

value: CTGAAGCT


title: post-status epilepticus P2X7-/- 1

description: P2X7-KO post-SE 1


title: Frot2_t0


title: post-status epilepticus WT 3

description: WT post-SE 3

value: wild type


title: Ecos2_tRH

description: Gene expression during desiccation in Enallax costatus

data_processing:
Basecalls performed using CASAVA version 1.4
Trimmomatic 0.35
assembly was subjected to a three-step refinement by removal of contigs (a) with <10 accumulated aligned reads across all time points and replicates, (b) corresponding to rRNA and (c) encoding bacterial transcripts. Non-algal transcripts were identified using blastx as implemented in BLAST+ against nr NCBI database with a cut-off e-value of 10-5. Taxonomical information for filtering bacterial transcripts was obtained using the flag -outfmt “6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sskingdoms sscinames sblastnames stitle”
Libraries were individually aligned to their respective reference transcriptomes using Bowtie 2 v.2.2 . Transcript abundance was estimated using RSEM v.1.2.28 . Expression matrices including read counts matrix, normalized ‘transcripts per million transcripts’ (TPM), and standardized ‘trimmed mean of M-values’ (TMM) were generated using Trinity script abundance_estimates_to_matrix.pl.
Differential expression analysis was performed on count data generated with RSEM using DESeq2. A gene was classified as a DEG if the change in its expression exceeded 4-fold (Log2 2-FC) in pairwise comparisons with a significance level <0.001 (adjusted p-value after Benjamini-Hochberg (BH) correction for multiple testing.
Assembly file has been submitted to the TSA.  TSA submission number: SUB5854930.
Genome_build: Trinity v2.1, jaccard clip option
Supplementary_files_format_and_content: Scos_RSEM_plant_genes.counts.matrix (Read counts from expression analysis)
Scos_RSEM_plant_genes_ordered.TMM.EXPR.matrix (Normalized expression data from DESeq2)

organism: Enallax costatus

value: Rehydrated


title: RNA-seq Hela Cells [1_RNS_Total]

description:
RNA_seq_1
processed data file: Master_Data_Table.xlsx

value: Nextflex

value: GCTGTA


title: post-status epilepticus WT 2

description: WT post-SE 2


title: Ecos1_tRH


title: Frot1_t0


title: eiF4G1 Selective 80S Ribosome FPs Hela Cells [2_80S_eIF4G1]

description:
80S_eIF4G1_1
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Takara

value: ATTCAGAA


title: Ades2_t25

value: Early desiccation


title: eiF3B Selective 80S Ribosome FPs  Hela Cells [1_80S_eiF3B]

description:
80S_eIF3B_1
processed data file: Master_Data_Table.xlsx

value: Ribo Zero Gold

value: GTATAG


title: Ecos2_tON

value: Dry


title: Total 80S Ribosome FPs Hela cells [1_80S_Total]

description:
1_80S_Total
processed data file: Master_Data_Table.xlsx

value: CGTGAT


title: post-status epilepticus WT 1

description: WT post-SE 1


title: Ecos1_tON


title: Ecos2_t75

value: Late desiccation


title: control P2X7-/- 3

description: P2X7-KO 3

value: hippocampus


title: control P2X7-/- 2

description: P2X7-KO 2

value: 8 weeks


title: Total 40S Ribosome FPs Hela cells [1_40S_Total]

description:
40S_Total_1
processed data file: Master_Data_Table.xlsx

value: ATTACTCG


title: Ecos1_t75


title: control P2X7-/- 1

description: P2X7-KO 1


title: control WT 3

description: WT 3


title: K562 Fiber-seq (20 U Hia5) rep3

data_processing:
Library strategy: DNA-seq
Pacbio software pbalign, bamSieve, ipdSummary from smrtlink-release_8.0.0.79519
Subreads were aligned using pbalign --concordant --hitPolicy=randombest --minAccuracy 70 --minLength 50
bamSieve was used to extract single-molecule-coverage subsets of the aligned data for analysis with ipdSummary --pvalue 0.001 --identify m6A
Genome_build: hg38
Supplementary_files_format_and_content: bed formatted mapped molecule locations with ZMW ID in column 4

source_name: K562 cells

growth_protocol: S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL.

extract_protocol:
PCR-free PacBio libraries were constructed using standard protocol.
Long-read PacBio HiFi/CCS sequencing

treatment_protocol: Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above and genomic DNA was extracted then subjected to shearing and then PacBio library construction.

value: 20 U Hia5 for 10min at 37C


title: K562 Fiber-seq (500 U Hia5) rep2

value: 500 U Hia5 for 10min at 37C


title: Ecos2_t25


title: control WT 2

description: WT 2

value: wild type


title: Ecos2_t0

value: Hydrated


title: control WT 1

description: WT 1


title: K562 Fiber-seq (500 U Hia5) rep1 run1


title: K562 Fiber-seq (500 U Hia5) rep1 run2


title: Ecos1_t25


title: Ecos1_t0


title: eiF3B Selective 40S Ribosome FPs Hela Cells [1_40S_eiF3B]

description:
40S_eIF3B_1
processed data file: Master_Data_Table.xlsx

value: GAGATTCC


title: T1DM_2

city: Shanghai

first: Caiyan

last: Zhang

address: 399, Wanyuan Road

institute: Children's Hospital of Fudan University

description: ceRNA expression in PBMCs from T1DM patient

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R

source_name: PBMCs, T1DM, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Freshly drawn peripheral blood from healthy volunteers and T1DM patients was sent to suffer from microarray analysis.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease state

value: type 1 diabetes mellitus

value: peripheral blood mononuclear cells (PBMCs)

tag: gender

value: female

value: 9 y


title: T1DM_4

source_name: PBMCs, T1DM, replicate 4

value: 4 y


title: Normal_4

description: ceRNA expression in PBMCs from healthy volunteer

source_name: PBMCs, healthy volunteer, replicate 4

value: healthy


title: T1DM_1

source_name: PBMCs, T1DM, replicate 1

value: male


title: T1DM_3

source_name: PBMCs, T1DM, replicate 3


title: Normal_2

source_name: PBMCs, healthy volunteer, replicate 2


title: 4T1 cells co-cultured with AI macrophages, biological rep1

status: Public on Jun 24 2020

city: London

first: Valentí

last: Gómez

address: UCL Cancer Institute, 72 Huntley Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

description:
AI_Macrophage_Rep1
Gene expression data from 4T1 cells after co-cultured with anti-inflammatory macrophages.

hyb_protocol: 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Gene 2.0 ST Array.

scan_protocol: GeneChips were scanned using the Affymetrix platform GCS3000 Scanner.

data_processing: CEL files were normalised together in the Expression Console software package (Affymetrix), using the Robust Multi-array Average (RMA) sketch algorithm (gene-level). Data was quality control assessed by using standard metrics and guidelines for the Affymetrix microarray system.

label: biotin

source_name: 4T1 cell line

label_protocol: Biotinylated cDNA were prepared from 0.5 ug total RNA using Encore® Biotin Module (NuGen).

growth_protocol: 4T1 breast cancer cells and polarised macrophages were co-cultured for 24hrs in DMEM +10% FBS.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy Mini Kit according to the manufacturer instructions.

treatment_protocol: Macrophage population was labelled with CD11b antibody-microbeads and negatively depleted from the co-culture using a LD Depletion Column MACS System (Miltenyi Biotech) according to the manufacturer instructions. The flow-through tumour population was washed with PBS and place on ice prior to RNA extraction.

tag: cell line

tag: cell type

value: Breast cancer, triple negative:HER- PR- ER-

tag: co-culture

value: Anti-inflammatory macrophages


title: 4T1 cells co-cultured with AI macrophages, biological rep2

description:
AI_Macrophage_Rep2
Gene expression data from 4T1 cells after co-cultured with anti-inflammatory macrophages.


title: Normal_3

source_name: PBMCs, healthy volunteer, replicate 3


title: 4T1 cells co-cultured with AI macrophages, biological rep3

description:
AI_Macrophage_Rep3
Gene expression data from 4T1 cells after co-cultured with anti-inflammatory macrophages.


title: 4T1 cells co-cultured with PI macrophages, biological rep3

description:
PI_Macrophage_Rep3
Gene expression data from 4T1 cells after co-cultured with pro-inflammatory macrophages.

value: Pro-inflammatory macrophages


title: 4T1 cells co-cultured with PI macrophages, biological rep1

description:
PI_Macrophage_Rep1
Gene expression data from 4T1 cells after co-cultured with pro-inflammatory macrophages.


title: Normal_1

source_name: PBMCs, healthy volunteer, replicate 1


title: Untreated_P260_BiolRep_5

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira street

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

description:
5th untreated P260 biological replicate
raw_table.txt
normalized_table.txt

data_processing:
Base-calling and adapter & index removal was performed by Illumina Basespace
Quality assessment and pre-processing operations were performed on the raw reads using PRINSEQ version 0.20.4 with the arguments ‘-min_qual_mean 20 -trim_qual_right 20 -trim_qual_left 20 -min_len 60’
The pre-processed FASTQ files were mapped on the UCSC mm10 reference genome using HISAT2 version 2.1.0 with the argument '--score-min L,0.0,-0.5'
The resulting BAM files were analyzed with the Bioconductor package metaseqR. Briefly, the BAM files were first summarized to a 3'UTR read counts table and the final gene counts table for each gene model was calculated from the corresponding 3’ UTR regions. The counts table was normalized using the DESeq normalization and filtered for possible artifacts. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500bp,  ii) genes with read counts below the median read counts of the total normalized count distribution, iii) genes whose biotype matched the following: rRNA, IG_V_pseudogene and TR_V_pseudogene, iv) genes where 25% of samples were not above 10 counts across all samples and v) genes with mean RPGM normalized values below 0.01 (i.e. the ratio of normalized reads per gene model).
The resulting gene counts table was subjected to differential expression analysis using the PANDORA weighted p-value method, implemented in metaseqR. Genes presenting a Benjamini-Hochberg false discovery rate (FDR) less than 0.05 and fold change (for each contrast) greater than 0.58 or less than -0.58 in log2 scale (corresponding to 1.5 times up and down in natural scale respectively) were considered differentially expressed.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: raw_table.txt: Tab-delimited files containing raw counts for each Ensembl gene
normalized_table.txt: Tab-delimited file containing DESeq normalized counts for each Ensembl gene

source_name: liver

growth_protocol: C57Bl6 mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12 hr light/dark cycle and fed a standard chow diet containing 19% protein and 5% fat (Altromin 1324) and water ad libitum.

extract_protocol:
Total RNA was prepared by homogenizing liver pieces in 10 volumes of Nucleozol reagent followed by the addition of 2 volumes of chlorophorm and centrifugation at 12.000 g for 15 minutes. The aqueous phases were precipitated with isopropanol and subjected to a second extraction as above, but with Trizol reagent. The RNA samples were digested with 10 units of DNase I for 10 min at 37 0C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation.
RNA-seq libraries were generated using QuantSeq 3’ mRNA-Seq FWD kit from Lexogen and sequenced in an Illumina NextSeq 500 system.
RNA-seq, 3'Quant-seq

treatment_protocol: Single intraperitoneal injection of 25 mg/kg diethylnitrosamine (DEN, N0756; Sigma) at postnatal day 14. Control-ASO or Smyd3-ASOs were injected twice a week intraperitonelly after day 133 until day 260.

value: liver

tag: treatment

value: No treatment

value: Normal liver

value: liver cells


title: Untreated_P260_BiolRep_4

description:
4th untreated P260 biological replicate
raw_table.txt
normalized_table.txt

tag: tissue


title: SK3-C7

city: Albany

first: Sneha

last: Damal Villivalam

state: CA

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

data_processing:
Library strategy: 5hmC Seal-seq
5hmC-seq analysis: Sequencing reads was trimmed adapter using cutadapt
5hmC-seq analysis : reads were  aligned to  mouse genome mm10 using BWA with default parameters http://bio-bwa.sourceforge.net/.  MethylQA was used to processed the aligned BAM files. Concordantly aligned read-pairs were  selected and deduplicated using Picard tool (https://broadinstitute.github.io/picard/).
Aligned reads were deduplicated usind Picard tool. BigWig files were generated using Homer and bedGraphToBigWIg in RPM scale.
Genome_build: mm10
Supplementary_files_format_and_content: RPM-normalized bigwig file

source_name: Inguinal white adipose tissue

growth_protocol: c57bl/6 mice were maintained in chow diet

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen. For 5hmc Seal seq, genomic DNA was extracted phenol/choloroform method. 250ng genomic DNA was used. Libraries were prepared using standard Illumina protocol
Libraries were prepared by the genome sequencing facility following manufacturers instructions for the standard illumina protocol for 5hmC Seal seq.

treatment_protocol: For 5hmc Seal seq Mice were kept at room temperture or exposed to cold temparate 4 C for 7 days.

value: Inguinal white adipose tissue

tag: exposure condition

value: Cold 7 days


title: SK4-C7


title: SK1-RT

value: Room temperature


title: P3_bulk_3

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: RNA was fragmented and hybridized to an Affymetrix Mouse 430 2.0 array (Applied Biosystems™, Cat#900495).

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running the GCOS 1.1.1 software.

data_processing:
For mSSCs profiled from P3, Ad, and Ad/MF joints, the corresponding CEL files were normalized by MAS5 using the affy v1.66.0 R package, mapped to NCBI Entrez gene identifiers using a custom chip definition file for Mouse Genome 430 2.0 microarrays (‘mouse4302mmentrezgcdf’), and converted to Mouse Genome Informatics (MGI) gene symbols using the org.Mm.eg.db v3.11.1 R package. Gene expression values were log2-normalized prior to downstream analysis.
For bulk tissues and mSSCs from Ad/MF joints treated with control (PBS), BMP2, and VEGFR1, the corresponding CEL files were normalized using the Gene Expression Commons platform (https://gexc.riken.jp) and. Briefly, gene expression profiles were normalized against a common reference of >11,939 Affymetrix Mouse Genome 430 2.0 microarrays. Each gene’s expression was then transformed to percentile ranks (range: –100% to +100%) based on its relative value to the reference.
Two matrices consisting of (1) percentile ranks or relative gene expression activity from GEXC for bulk tissues and mSSCs from Ad/MF joints treated with control (PBS), BMP2, and VEGFR1 and (2) custom-cdf- and MAS5-normalized expression for mSSCs profiled from P3, Ad, and Ad/MF joints.

label: streptavidin

label_protocol: RNA was streptavidin-labeled as recommended by Affymetrix protocol.

extract_protocol: For RNA extraction of mSSCs, 500 to 1,000 cells were FAC-sorted directly into 1 mL TRIzol LS (Invitrogen, Cat#10296028). For bulk tissues, bones were flash frozen in liquid nitrogen, crushed into powder, and added directly into 1 mL TRIzol. RNA was isolated with the RNeasy Micro Kit (Qiagen, Cat#74004) and twice amplified with an Arcturus™ RiboAmp™ PLUS Kit (Applied Biosystems™, Cat#KIT0521).

value: Distal Femur

tag: cell

value: bulk tissue


title: P3_bulk_1


title: Untreated_P260_BiolRep_3

description:
3rd untreated P260 biological replicate
raw_table.txt
normalized_table.txt


title: Adult_MF_bulk_1


title: Adult_uninjured_bulk_5


title: P3_bulk_2


title: SK2-RT


title: Untreated_P260_BiolRep_1

description:
1st untreated P260 biological replicate
raw_table.txt
normalized_table.txt


title: 4T1 cells co-cultured with PI macrophages, biological rep2

description:
PI_Macrophage_Rep2
Gene expression data from 4T1 cells after co-cultured with pro-inflammatory macrophages.


title: Smyd3_ASO_BiolRep_4_TechRep3

description:
3rd technical replicate of the 4th Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt

value: DEN treatment / Smyd3 ASO treatment after P133

value: DEN induced tumors

value: hepatocellular carcinoma


title: Adult_uninjured_bulk_4


title: Adult_MF_bulk_3


title: Adult_MF_mSSC_control

value: mSSC

value: PBS

tag: gating strategy


title: Adult_uninjured_bulk_3


title: Adult_MF_bulk_2


title: Adult_MF_mSSC_VEGFr1


title: Smyd3_ASO_BiolRep_2_TechRep3

description:
3rd technical replicate of the 2nd Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Adult_uninjured_bulk_1


title: Control_ASO_BiolRep_6_TechRep2

description:
raw_table.txt
normalized_table.txt

value: DEN treatment / Control ASO treatment after P133


title: Control_ASO_BiolRep_5_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_5_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Untreated_P260_BiolRep_2

description:
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_2_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_3_TechRep2

description:
raw_table.txt
normalized_table.txt


title: DEN_treated_P133_BiolRep_2

description:
raw_table.txt
normalized_table.txt

value: DEN treatment / No ASO treatment


title: DEN_treated_P133_BiolRep_3

description:
3rd DEN-treated P133 biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_1_TechRep2

description:
raw_table.txt
normalized_table.txt


title: DEN_treated_P133_BiolRep_4

description:
4th DEN-treated P133 biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_4_TechRep2

description:
raw_table.txt
normalized_table.txt


title: DEN_treated_P133_BiolRep_1

description:
1st DEN-treated P133 biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_3_TechRep3

description:
3rd technical replicate of the 3rd Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_1_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_6_TechRep1

description:
1st technical replicate of the 6th Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_6

description:
6th Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Adult_uninjured_bulk_2


title: Control_ASO_BiolRep_3_TechRep1

description:
1st technical replicate of the 3rd Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_5_TechRep1

description:
1st technical replicate of the 5th Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_4_TechRep1

description:
1st technical replicate of the 4th Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_3_TechRep1

description:
1st technical replicate of the 3rd Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_2_TechRep1

description:
1st technical replicate of the 2nd Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_1_TechRep1

description:
1st technical replicate of the 1st Control-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Control_ASO_BiolRep_4_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_2_TechRep1

description:
1st technical replicate of the 2nd Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_1_TechRep1

description:
1st technical replicate of the 1st Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_3_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_2_TechRep2

description:
raw_table.txt
normalized_table.txt


title: Smyd3_ASO_BiolRep_5_TechRep1

description:
1st technical replicate of the 5th Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt


title: Status epilepticus Wild-type rep4

city: Dublin 2

first: David

last: Henshall

address: 123 Saint Stephen Green

institute: FutureNeuro centre, Royal College of Surgeons in Ireland

data_processing:
performed by a service provider (Exiqon A/S, Vedbaek, Denmark) using the Tuxedo software package, which is a  combination of open-source software (Bowtie2 v. 2.2.2, Tophat v2.0.11 and  Cufflinks v2.2.1), and implements peer-reviewed statistical methods
Genome_build: GRCm38, Ensembl_70
Supplementary_files_format_and_content: Fpkm_tracking files contain the normalized gene expression levels for all genes expressed in each sample

source_name: ipsilateral hippocampus

growth_protocol: Mice were mated in trios (one male and two females). For breeding, either a single heterozygous male was mated with two homozygous mutant female mice or a single homozygous male mated with two heterozygous females. Wild type mice were also mated in trios.Animals were used at either three or nine months old. Mice were housed in a climate-controlled biomedical facility on a 12-hour light/dark cycle with food and water provided ad libitum.

extract_protocol:
Total RNA was extracted and library preparation was performed using an Illumina TruSeq Stranded mRNA Sample Prep Kit (poly-A enrichment)
Poly-A enriched total RNA-Seq

treatment_protocol: Status epilepticus was induced by unilateral intraamygdala microinjection of kainic acid. Briefly, animals were anesthetized with isoflurane (5% induction and 1-2% for maintenance), placed in a stereotaxic frame and maintained normothermic by means of a feedback-controlled heat blanket. A craniotomy was performed and a 26-gauge steel guide cannula was positioned over the surface of the dura.

value: C57BL/6JOlaHsd and 129P2/OlaHsd

value: Wild-type

value: hippocampus

tag: injected coumpounds

value: Kainic acid

tag: days after injection

value: 1 day


title: Status epilepticus MiR-22 Knockout rep2

value: Mir22tm1.1Arod, Stock No:018155 (Jackson Lab)

value: MiR-22 Knockout


title: Status epilepticus MiR-22 Knockout rep3


title: Status epilepticus MiR-22 Knockout rep1


title: Status epilepticus Wild-type rep3


title: Smyd3_ASO_BiolRep_4_TechRep1

description:
1st technical replicate of the 4th Smyd3-ASO biological replicate
raw_table.txt
normalized_table.txt

value: liver


title: Status epilepticus Wild-type rep2


title: Status epilepticus MiR-22 Knockout rep4


title: Control intestine rep2

city: Boston

first: Priscilla

last: Cheung

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

data_processing:
The fastq to counts conversion was performed using the indropIndex and the indropCounts functions, which are part of the rCASC framework (Alessandri et al., Gigascience 2019). The indropCounts function, which invokes the inDrop pipeline v20170126 (https://github.com/indrops/indrops), was used with the following options: M=10, U=2, D=400, and low.complexity.mask="False" and the following packages: Bowtie v1.1.1.1, Samtools v 1.3.1, RSEM v1.3.0, and Java v1.8.0.
Genome_build: mm10
Supplementary_files_format_and_content: Genes-versus-cells UMI-filtered count matrix

molecule: polyA RNA

source_name: intestinal epithelial cells

extract_protocol:
A piece of intestine was extracted from mice and incubated in 4 mM EDTA in PBS with gentle rocking for 40 min at 4°C. The small intestine was then shaken to dissociate epithelial cells. After removal of the smooth muscle layer, the remaining supernatant was centrifuged and incubated in 3 mg/mL collagenase/dispase in PBS for 6 min at 37’C with repeated up and down pipetting. The single cells were then placed on ice, centrifuged, filtered through 70 µm strainers, and stained in 2% FBS/PBS with fluorescent conjugated EpCAM, CD45, and TER119 antibodies diluted 1:100 for 30 min at 4°C. For each condition, 5000 EpCAM+CD45-TER119-DAPI- cells were sorted on a BD FACSAria II, using a 100 µm nozzle, and encapsulated using inDrop v2 (1CellBio) following manufacturer's instructions.
Whole transcriptome libraries were prepared as described in Zilionis et al., Nature Protocols 2017.

treatment_protocol: Mice were injected intraperitoneally with 2 mg of tamoxifen and harvested 7 days post injection.

value: small intestine

value: adult

value: Lats1fl/fl Lats2fl/fl

value: tam


title: Control intestine rep1


title: Lats intestine rep2

value: Lrig1-CreERT2 Lats1fl/fl Lats2fl/fl


title: DSS colon

source_name: colonic epithelial cells

extract_protocol:
A piece of intestine was extracted from mice and incubated in 4 mM EDTA in PBS with gentle rocking for 40 min at 4°C. The colon was then cut open and scraped with a coverslip to dissociate the crypts. After removal of the smooth muscle layer, the remaining supernatant was centrifuged and incubated in 3 mg/mL collagenase/dispase in PBS for 6 min at 37’C with repeated up and down pipetting. The single cells were then placed on ice, centrifuged, filtered through 70 µm strainers, and stained in 2% FBS/PBS with fluorescent conjugated EpCAM, CD45, and TER119 antibodies diluted 1:100 for 30 min at 4°C. For each condition, 5000 EpCAM+CD45-TER119-DAPI- cells were sorted on a BD FACSAria II, using a 100 µm nozzle, and encapsulated using inDrop v2 (1CellBio) following manufacturer's instructions.
Whole transcriptome libraries were prepared as described in Zilionis et al., Nature Protocols 2017.

treatment_protocol: Mice were treated with or without 3.5% DSS in drinking water for 5 days followed by normal water for 3 days.

value: colon

value: 2 months

value: female

value: DSS


title: Control colon

value: untreated


title: combinenPM-M16

city: San Diego

first: Amin

last: Haghani

address: 5510 Morehouse Dr

institute: Altos labs

description: RNAseq B6 exposure 2017.txt

data_processing:
Reads were aligned to the mouse reference genome RefSeq mm10 with Tophat2 (v2.0.8b)
restricted to uniquely mapping reads with 3 possible mismatches
Quantification of reads per RefSeq gene in Partek (E/M)
Normalization: Add: 1.0, Upper Quartile
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: tab-delimited text files include gene annotations and count values for each gene

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) and RNAeasy Mini Kit (Qiagen) with DNase digestion.
Libraries were made with the TRUseq Stranded mRNA Kit (Illumina) with 1 mg of RNA.

treatment_protocol:
ApoE-TR mouse: nPM exposure for 5 h/day, 3 days/week, for 15 weeks
ApoE-TR mouse: Filtered air exposure for 5 h/day, 3 days/week, for 15 weeks
C57BL/6J mouse: nPM exposure for 5 h/day, 3 days/week, for 8 weeks
C57BL/6J mouse: Filtered air exposure for 5 h/day, 3 days/week, for 8 weeks

tag: Sex

value: Male

value: Wt

value: nPM

value: Cerebral Cortex

tag: age (month)

tag: srtain


title: combinenPM-M11

description: RNAseq B6 exposure 2017.txt


title: Lats intestine rep1

tag: strain

tag: age


title: combinenPM-M12

description: RNAseq B6 exposure 2017.txt

tag: genotype


title: combinenPM-F52

description: RNAseq B6 exposure 2017.txt

value: Female


title: combinenPM-F51

description: RNAseq B6 exposure 2017.txt


title: combinenPM-M10

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-M6

description: RNAseq B6 exposure 2017.txt

value: Ct


title: Status epilepticus Wild-type rep1

value: C57BL/6JOlaHsd and 129P2/OlaHsd

value: Wild-type

value: hippocampus

value: Kainic acid

value: 1 day


title: combineCTRL-M2

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-M3

description: RNAseq B6 exposure 2017.txt


title: Adult_MF_mSSC_BMP2

value: Distal Femur

value: mSSC


title: combineCTRL-M0

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-F43

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-F42

description: RNAseq B6 exposure 2017.txt


title: combinenPM-F53

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-F40

description: RNAseq B6 exposure 2017.txt


title: combineCTRL-F41

description: RNAseq B6 exposure 2017.txt


title: E4 F39nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F39nPM

value: ApoE-TR


title: E4 F08 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F08 nPM


title: E3 F67 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F67 nPM


title: E3 F59 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F59 nPM


title: E3 F70 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F70 nPM


title: E3 F55 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F55 nPM


title: E4 M23nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M23nPM


title: combinenPM-F50

description: RNAseq B6 exposure 2017.txt


title: E4 F23 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F23 nPM


title: E3 F66 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F66 ctrl


title: E3 M58 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M58 nPM


title: E4 M33nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M33nPM


title: E4 M93 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M93 nPM


title: E3 F61 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F61 ctrl


title: E4 F21 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F21 ctrl


title: E3 M56 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M56 nPM


title: E3 F63 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F63 ctrl


title: E4 M65 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M65 nPM


title: E3 F52 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 F52 ctrl


title: E4 F7 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F7 ctrl


title: E4 M91 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M91 ctrl


title: E4 F38 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F38 ctrl


title: E4 F27 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F27 nPM


title: E4 M 21 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M 21 ctrl


title: E4 M32 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M32 ctrl


title: E3 M53 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M53 nPM


title: E3 M76 nPM

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M76 nPM


title: E3 M55 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M55 ctrl


title: E3 M73 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M73 ctrl


title: E3 M63 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M63 ctrl


title: E3 M 51 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E3 M 51 ctrl


title: E4 F26 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 F26 ctrl


title: P1129ESCP6.129.Male.ESC

city: College Station

middle: William

last: Threadgill

state: TX

address: Reynolds Medical Building 428

department: Department of Veterinary Pathobiology and Department of Molecular and Cellular Medicine

institute: Texas A&M University

description:
P1129ESCP6_S1
P1129ESCP6-35650635

data_processing:
A total of 453 million reads were checked for any adaper seqeunces and to trim any low-quality bases using Trimmomatic resulting in approximately 285 million filtered reads (63%) out of which a total of 229 million filtered reads (approximately 80%) mapped to the GRcm38/mm10 assembly.
Read mapping was perfromed using Tophat version 2.1.1
HTSeq was used to generate raw read counts per gene using intersection-nonempty parameter to account for ambiguous read mappings
Differential gene expression tests were then performed used DESeq2 following recommended guidelines by the authors
Genome_build: GRcm38/mm10
Supplementary_files_format_and_content: counts

source_name: NOD iPSC Colony # 52 Female 2iS

growth_protocol: EpiSCs were maintained in standared EpiSC conditions. 129S1 iPSCs were maintained in standared ESC conditions unless specifically stated. All ESCs and iPSCs from non-permissive strains were meaintained in 2iS media. 2iS media is described in publication.

extract_protocol:
RNA extractions were performed using the Promega maxwell LEV SimplyRNA extraction kit
RNA integrity was confirmed using an Agilent Bioanalyzer. cDNA libraries were created using the TruSeq Stranded mRNA library prep kit (Illumina). Samples were pooled and run on a 150 x 150 high output NextSeq500, generating 800 million paired end reads (approximately 32 million reads/sample)
TruSeq Stranded mRNA library prep kit (Illumina)

treatment_protocol: iPSCs from non-permissive mouse strains were derived using the 2iS reprogramming appraoch, which involved adding 2iS Media three days into reprogramming. Derived iPSC conlied from non-permissive mouse strains were maintained in 2iS media.

value: NOD

value: female

value: Induced Plruipotent Stem Cells

tag: colony #


title: P1129Well1P21.129.Male.iPSC

description:
P1129Well1P21_S5
P1129Well1P21-35640733

source_name: NOD iPSC Colony # 7 Female 2iS


title: P1129Well17P302iS.129.Male.iPSC.2iS

description:
P1129Well17P302iS_S4
P1129Well17P302iS-35634753

source_name: WSB iSPC Colony # 28 Female 2iS

value: WSB


title: P1129Well17P20.129.Male.iPSC

description:
P1129Well17P20_S3
P1129Well17P20-35654624

source_name: WSB iPSC Colony # 25 Male 2iS

value: male


title: P1129Well8P17.129.Female.iPSC

description:
P1129Well8P17_S8
P1129Well8P17-35635732

source_name: WSB iPSC Colony # 23 Female 2iS


title: P1129Well1P312iS.129.Male.iPSC.2iS

description:
P1129Well1P312iS_S6
P1129Well1P312iS-35652628

source_name: WSB ESC Male

value: Embryonic Stem Cells


title: P1129Well5P19.129.Female.iPSC

description:
P1129Well5P19_S7
P1129Well5P19-35648633

source_name: WSB iPSC Colony # 12 Male 2iS


title: P1129EpiSCP16.129.Male.EpiSC

description:
P1129EpiSCP16_S2
P1129EpiSCP16-35649631

source_name: NOD iPSC Colony # 3 Male 2iS


title: P1WSBS25P16.WSB.Male.iPSC.2iS

description:
P1WSBS25P16_S18
P1WSBS25P16-35654627

source_name: NOD ESC Male


title: P1WSBS28P20.WSB.Female.iPSC.2iS

description:
P1WSBS28P20_S19
P1WSBS28P20-35636727

source_name: NOD iPSC Colony # 35 Male 2iS


title: P1WSBS23P16.WSB.Female.iPSC.2iS

description:
P1WSBS23P16_S17
P1WSBS23P16-35654626

source_name: NOD EpiSC Male

value: Epiblast Stem Cells


title: P1WSBS12P16.WSB.Male.iPSC.2iS

description:
P1WSBS12P16_S16
P1WSBS12P16-35640736

source_name: 129 iPSC Colony # 8 Female


title: P1WSBESCP6.WSB.Male.ESC

description:
P1WSBESCP6_S15
P1WSBESCP6-35646632

source_name: 129 iPSC Colony # 5 Female


title: E4 M3 ctrl

description: RNAseq TR-APOE exposure 2012.txt

source_name: E4 M3 ctrl

value: Male

value: Cerebral Cortex


title: P1NODS35P16.NOD.Male.iPSC.2iS

description:
P1NODS35P16_S11
P1NODS35P16-35637731

source_name: 129 iPSC Colony # 1 Male


title: P1NODS52P18.NOD.Female.iPSC.2iS

description:
P1NODS52P18_S13
P1NODS52P18-35647631

source_name: 129 iPSC Colony # 1 Male 2iS


title: P1NODEpiSCP38.NOD.Male.EpiSC

description:
P1NODEpiSCP38_S10
P1NODEpiSCP38-35636725

source_name: 129 EpiSC Male


title: P1NODESCP6.NOD.Male.ESC

description:
P1NODESCP6_S9
P1NODESCP6-35633753

source_name: 129 ESC Male


title: P1NODS3P26.NOD.Male.iPSC.2iS

description:
P1NODS3P26_S12
P1NODS3P26-35647630

source_name: 129 iPSC Colony # 17 Male


title: P1NODS7P17.NOD.Female.iPSC.2iS

description:
P1NODS7P17_S14
P1NODS7P17-35640735

source_name: 129 iPSC Colony # 17 Male 2iS


title: TGF-beta-treated fibroblasts cultured on tissue culture plastic

city: Southampton

first: Sara

last: Waise

state: Hampshire

address: Somers Building MP284, Southampton General Hospital, Tremona Road

department: Cancer Sciences

institute: University of Southampton

description: TCP.TGF

data_processing:
Base calls performed with bcl2fastq 2.18
All read pairs with a quality score of <10 were filtered
Reads were aligned to the human genome using STAR v2.5
Aligned exonic reads were tagged with a gene name
Digital expression matrices were created by counting the number of unique UMIs per gene per cell. Samples from three individual patients were merged together into a single matrix
Genome_build: hg19
Supplementary_files_format_and_content: Digital expression matrices in tab-delinated text file

source_name: Lung

growth_protocol: Primary fiboblasts were cultured in DMEM supplemented with L-glutamine (1% v/v; Sigma), penicillin-streptomycin (1% v/v; Sigma) and foetal calf serum (FCS; 10% v/v for routine maintenance and 1% v/v for experimentation; Biosera). Cells were cultured either on tissue culture plastic (TCP) or low elastic modulus plates (2 kPa).

extract_protocol:
Cells were washed with phosphate-buffered saline before detachment using trypsin-EDTA (Sigma-Aldrich) and collection in fresh growth medium. Following centrifugation at 1500 rpm for 5 minutes, the resulting cell pellet was suspended in cell suspension buffer (90% ddH20, 9% Optiprep (Sigma), 1% PBS with 0.1% BSA)
Libraries were prepared for sequencing as per the Drop-seq and standard Illumina protocols

treatment_protocol: Human Recombinant TGF-β1 (R&D Systems) was reconstituted in 4mM HCl, 0.1% (w/v) BSA and administered to cells at a dose of 2 ng/ml. Human recombinant IL-1β (ThermoFisher) was reconstituted in deionised water and administered at 10 ng/ml.

value: Lung

value: fibroblasts

tag: cultured on

value: tissue culture plastic

value: TGF-beta-treated


title: Untreated fibroblasts cultured on tissue culture plastic

description: TCP.CTR

tag: cell type

value: Untreated


title: Untreated fibroblasts cultured on low elastic modulus plates

value: low elastic modulus plates


title: IL-1 beta-treated fibroblasts cultured on low elastic modulus plates

value: IL-1 beta-treated


title: TGF-beta-treated fibroblasts cultured on low elastic modulus plates


title: DistA_pos_28327

city: Ithaca

first: Ian

middle: Michael

last: Rose

address: Ithaca, NY 14850

institute: Cornell University

data_processing:
use fastp (https://github.com/OpenGene/fastp) to trim adapter sequences and move UMI sequences
align with STAR (version 2.7) 2-pass method
remove duplicate reads based on UMI
Apply GATK3 to correct sequencing bias
use featureCounts function provided by the Rsubread R package to create a count matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix of normalized counts. Each row is a gene identified by ENTREZID, each column is a sample.

source_name: Fallopian tube fragment

extract_protocol:
Trizol-LS
Lexogen Quant-Seq

tag: fallopian tube region

value: distal

tag: aldh activity

value: positive


title: DistA_pos_28407


title: DistA_neg_31060

value: negative


title: DistA_pos_25072


title: ProxA_pos_23227

value: proximal


title: DistA_neg_31043


title: DistA_pos_31043


title: DistA_pos_31060


title: DistA_pos_23379


title: DistA_neg_28327


title: HTO data from enriched CD4+ Memory T cells

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

description: cell hashing data from CD4+ Memory T cells enriched from human peripheral blood

data_processing:
Standard 10X Genomics CellRanger pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, the raw UMI count matrix is stored in a csv file with features as row names and cell barcodes as column names.

source_name: Blood

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

tag: tissue

value: blood

value: CD4+ Memory T cells

tag: sample type

value: single cell HTO


title: HTO data from human PBMC

description: cell hashing data from human PBMC

value: PBMC


title: RNA data from enriched CD4+ Memory T cells

description: scRNA data from CD4+ Memory T cells enriched from human peripheral blood, this sample not used in the publication.

value: single cell RNA


title: ADT data from human PBMC

description: single cell protein data from human PBMC

value: single cell surface protein


title: RNA data from human PBMC

description: scRNA data from human PBMC


title: DistA_neg_28407


title: DistA_neg_23379


title: DistA_neg_25072


title: DistA_neg_23360


title: DistA_neg_23174


title: ProxA_pos_28407


title: ProxA_pos_28327


title: ProxA_pos_31043


title: ProxA_pos_25072


title: ProxA_neg_31060


title: ProxA_pos_26782


title: DistA_neg_23227


title: ProxA_pos_23429


title: DistA_pos_23181


title: ProxA_pos_23174


title: DistA_pos_23227


title: DistA_neg_23429


title: ProxA_neg_26782


title: ProxA_neg_25072


title: OCT7+SGC0946_input_rep2

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
Read quality was screened using FastQC (http://www.bioinformatics.bbsrc.ac.us/projects/fastqc). Sequencing reads were aligned to GRCh38 reference genome using bowtie2 (v 2.2.5). Samtools 1.2 (Li et al., 2009) was used to filter the alignments with MAPQ smaller that 7 (-q 7), and to retain only the proper pairs (-f99, -f147, -f83, -f163). The downstream analysis was performed within R environment.
Input DNA from each sample was used as controls. The peak calling was performed using MACS2 (v 2.1.1) with ’--BAMPE’ option.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: Peaks from MACS2 callpeak in narrowPeak format

source_name: iPSC intermediate cells

growth_protocol: Fibroblasts were infected with retroviruses containing each tested combination and cultured in hESC medium with or without SGC0946.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using the NEBNext Ultra II DNA library prep kit (NEB).

treatment_protocol: The cells were grown with or without SGC0946 treatment.

value: OCT7-transduced iPSC intermediate cells that were cultured with SGC0946

tag: tagged protein

tag: day of reprogramming

value: day 8

tag: chip antibody

value: none (input)


title: OCT7+SGC0946_rep2

value: FLAG (F1804; Sigma)


title: OCT7+SGC0946_input_rep1


title: ProxA_pos_31060


title: OCT4_input_rep1

value: OCT4-transduced iPSC intermediate cells

value: day 2


title: ProxA_neg_23174


title: ProxA_neg_28327


title: ProxA_neg_23227


title: OCT7_rep1

value: OCT7-transduced iPSC intermediate cells


title: ProxA_neg_28407


title: Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) rep2

city: Hamilton

first: Ish

last: Jain

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

data_processing:
Illumina HiSeq platform by Genome Quebec
Sequenced reads were trimmed for illumina adaptor sequence using TrimGalore-master, and the quality was controlled by masking for low-complexity or low-quality sequence using FastQC
The sequence reads that passed quality filters were then used for further analysis
Alignment method STAR was used to align sequence reads to the reference genome
Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq package in R.
Genome_build: UCSC (cb4)
Supplementary_files_format_and_content: raw counts for all genes

organism: Caenorhabditis briggsae

source_name: Whole animal

growth_protocol: The worms were grown on standard NGM growth media and maintained at 20 degrees

extract_protocol:
RNA was extracted from synchronized L3 animals using standard TRIZOL methods (Invitrogen). Animals were staged prior to harvest by mounting a sample and observing them under the Nomarski microscope. RNA was extracted just prior to the stage when vulval precursors (Pn.p cells) initiate division
Three independent biological replicates were prepared from AF16, Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) strains for RNAseq, and the samples were processed, kapa depleted for rRNA and sequenced using Illumina HiSeq 2000 SR platform by Genome Quebec.

treatment_protocol: The worms were bleached and synchronized twice before collecting the RNA

tag: developental stage


title: OCT7+SGC0946_rep1


title: OCT7_rep2


title: OCT7_input_rep2


title: OCT4_input_rep2


title: OCT4_rep1


title: Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) rep3


title: Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) rep1


title: Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) rep3


title: Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) rep2


title: 06_3990Michigan_DIPG-007_IDH1shRNA

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

data_processing:
Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina). Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Supplementary_files_format_and_content: csv file with called peaks

source_name: DIPG cell line

growth_protocol: Cells were cultured in Neurobasal A supplemented with N2, B27, L-glutamine (2 mM), Pen/strep (1X), heparin (2 μg/mL), human-EGF (20 ng/mL), human-bFGF (20 ng/mL), and BSA (45 ng/ml)

extract_protocol: For ATAC-Seq 100,000 cells were collected by centrifugation at 500g for 5min. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).

treatment_protocol: To knockdown genes using shRNA, 1,500,000 HEK293T cells were plated on 100mm dishes 24 hrs before transfection. Next day, media was changed to 5ml of HEK293T media. 2.5ug transfer DNA, 2.5ug Packaging DNA Premix, and 15ul TransIT-Lenti Reagent were mixed in 500ul Opti-MEM media using pipet and incubated at room temperature for 10 min. The mixture was added dropwise to the HEK293T cell dish and swirled gently to distribute. The transfected cells were incubated at 37°C and 5% CO2 to produce virus for 72 hrs. Lentivirus particles were harvested by centrifugation at 300g for 5min and filtered using 0.45um PVDF filter. Lentivirus particles were plated onto dissociated target cells. After 18 hrs, lentiviral-particle-containing media was removed and target cell media was added. After 3 days, infected cells were treated with a proper antibiotic for selection. To knockdown genes using siRNA, 3,000,000 cells were plated on T25. 15ul of TransIT-X2 and 13ul of 10uM siRNA were mixed in 500ul Neurobasal A media and incubated for 30 min. The mixture was added dropwise to the cell and swirled gently to distribute. The transfected cells were incubated at 37°C and 5% CO2 for 72 hrs.

tag: cell line

value: H3.3K27M HSJD-DIPG007

value: DIPG cell line


title: Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) rep1


title: 05_3990Michigan_DIPG-007_IDH1shRNA


title: OCT7_input_rep1


title: AF16 wild-type isolate rep3

value: AF16 wild-type isolate


title: 04_3990Michigan_DIPG-007_HK2shRNA


title: OCT4_rep2


title: AF16 wild-type isolate rep2


title: 03_3990Michigan_DIPG-007_HK2shRNA


title: 02_3990Michigan_DIPG-007_GLUD1shRNA


title: 1_3694Michigan_DIPG-007_Nontargeted

value: Non targeted scrambled shRNA


title: 01_3990Michigan_DIPG-007_GLUD1shRNA


title: 2_3694Michigan_DIPG-007_Nontargeted


title: NEU_P149

city: Cusano Milanino

first: Luciano

last: Calzari

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

data_processing:
fastq files were checked for quality using FastQC tool (v0.11.5)
fastq files were aligned to reference genome (GRCh38) using STAR (version 2.5.2b)
Aligned BAM files were used for allocation to genes with featureCounts (version 1.6.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: TAB-delimited text file containing counts values for each Sample (obtained from featureCounts tool).

source_name: Cortical neuron (70 d) differentiated from Blood Derived Induced Pluripotent Stem Cells (iPSCs)

extract_protocol:
Total RNA was extracted with Quick-RNA MiniPrep Kit (Zymo Research – catalog number R1054). RNA quality was assessed through the RNA 6000 Nano Kit (Agilent) on an Agilent Bioanalyzer. RNA Integrity Number (RIN) was determined for every sample. Only samples with RIN >7.5 were processed.
Sequencing libraries were prepared in two batches using TruSeq Stranded mRNA Library Prep (Illumina). 800 nanograms of total RNA were used as input. Oligo-attached magnetic beads were used for removing ribosomal RNA and globin mRNA from RNA samples. After a purification step, samples RNA were fragmented at 94°C for 8 minutes. RNA fragments were retro-transcribed to cDNA using Random Hexamer Primers. All cDNAs were indexed and amplified with 11 PCR cycles. Final libraries were validated with the Agilent DNA 1000 kit (Agilent) and sequenced on a NextSeq 500 platform (Illumina), producing 75 × 2 bp paired-end reads.

tag: individual

tag: disease state

value: RSTS

value: Cortical neuron differentiated from blood-derived iPSCs

tag: time

tag: Sex

value: M

tag: age(years) at withdrawal

tag: gene(nm accession)

tag: coding mutation

tag: protein substitution


title: NEU_P158

tag: cell type

value: F


title: NEU_C1

value: control

value: no mutation


title: PRO_C3

source_name: Neural progenitor (35 d) differentiated from Blood Derived Induced Pluripotent Stem Cells (iPSCs)

value: Neural progenitor differentiated from blood-derived iPSCs


title: FC113 fin clipped at 20 weeks during normal aging

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4. Then, they were quality-trimmed and filtered for low complexity using preprocess from the SGA assembler 0.10.13 (-q 30 -m 50 --dust). The passed reads were mapped to the repeat-masked N. furzeri reference genome (assembly version Nfu_20150522, "hardmasked"; gene annotation version 150922) with TopHat2 2.1.0 under conservative settings (--b2-sensitive --no-coverage-search --no-novel-juncs --no-novel-indels --transcriptome-max-hits=1). For each gene, reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 (multi-mapping or multi-overlapping reads were not counted).
Genome_build: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de/).
Supplementary_files_format_and_content: csv (comma-separated values) file containing the gene id in the 1st column and the number of assigned reads (=counts) in the remaining 228 columns.

organism: Nothobranchius furzeri

source_name: fin clip

growth_protocol: Animal maintenance was performed as described in Baumgart et al. 2012. (PMID:22487494)

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA v2 sample preparation kit following the manufacturer's instructions.

tag: strain

tag: animal id

value: male

value: fin clip

tag: age at fin clip (weeks)

tag: age at death (days)

tag: condition

value: normal aging


title: FC115 fin clipped at 20 weeks during normal aging

tag: tissue


title: FC114 fin clipped at 10 weeks during normal aging


title: FC113 fin clipped at 10 weeks during normal aging


title: FC114 fin clipped at 20 weeks during normal aging


title: FC115 fin clipped at 10 weeks during normal aging


title: FC116 fin clipped at 10 weeks during normal aging


title: FC112 fin clipped at 10 weeks during normal aging


title: NEU_C3


title: NEU_P46


title: FC111 fin clipped at 20 weeks during normal aging


title: FC112 fin clipped at 20 weeks during normal aging


title: NEU_C4


title: FC111 fin clipped at 10 weeks during normal aging


title: AF16 wild-type isolate rep1

tag: developental stage


title: FC110 fin clipped at 20 weeks during normal aging


title: FC116 fin clipped at 20 weeks during normal aging


title: PRO_P149


title: NEU_P34


title: PRO_C2


title: FC109 fin clipped at 20 weeks during normal aging


title: FC109 fin clipped at 10 weeks during normal aging


title: PRO_P158


title: NEU_C2


title: FC108 fin clipped at 20 weeks during normal aging


title: PRO_P207


title: PRO_P46


title: PRO_P34


title: FC108 fin clipped at 10 weeks during normal aging


title: FC106 fin clipped at 10 weeks during normal aging


title: FC106 fin clipped at 20 weeks during normal aging


title: FC107 fin clipped at 20 weeks during normal aging


title: PRO_C4


title: Clone 9-Week 4

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: Amplified sgRNA pools

data_processing:
Library strategy: CRISPR Screen
The adaptor sequences were trimmed using cutadapt (v1.18) and the untrimmed reads were removed
gRNAs were mapped to the annotation file and read count table were made
MAGeCK (0.5.8) [3] was used to normalize the count table based on median normalization and fold changes and the significance of the changes in the conditions were calculated for genes and sgRNAs.
Supplementary_files_format_and_content: read count

source_name: KP cell pools

growth_protocol: KP-Cas9 cells were transfected with lentivirus pool (MOI=0.2), and selected by using 5ug/ml Blasticidin, and the cultured for 2 weeks for expanding. At week 2, harvested part of the cell pool as input ctrl, and subcutaneously injected cell pool to into the B6 Rag1-/- mice and B6 WT mice to form tumors. Then performed 3 weeks' treatment and harvest tumors.

extract_protocol:
For Library, just used plasmid pool as PCR template; For input cell pool, extracted genomic DNA was used as PCR template; For tumor samples, homogenated tumor and extracted genomic DNA, and then used as PCR template.
For Library, just amplied sgRNA pool from the plasmid pool; For Input cell pool, amplied sgRNA pool from genomic DNA; For samples from treatment groups, amplied sgRNA pool from genomic DNAs.

treatment_protocol: ID-IgG group has 12 tumors, which were treated with IgG control; ID-PD1 group has 12 tumors, which were treated with anti-PD1; IC-IgG group has 12 tumors, which were treated with IgG control; IC-PD1 group has 12 tumors, which were treated with anti-PD1. Here ID means immunodeficient mice (B6 Rag1-/-), and IC means immunocompetent mice (B6 WT).

value: In vitro cultured cells


title: Clone 7-Week 4

description: Amplified sgRNA pools


title: PRO_C1


title: Clone 9-Week 2

description: Amplified sgRNA pools


title: FC105 fin clipped at 20 weeks during normal aging


title: FC105 fin clipped at 10 weeks during normal aging


title: FC110 fin clipped at 10 weeks during normal aging


title: Clone 7-Week 2

description: Amplified sgRNA pools


title: NEU_P207


title: FC104 fin clipped at 10 weeks during normal aging


title: FC103 fin clipped at 20 weeks during normal aging


title: FC104 fin clipped at 20 weeks during normal aging


title: FC103 fin clipped at 10 weeks during normal aging


title: FC102 fin clipped at 20 weeks during normal aging


title: FVB Healthy liver RNA (Sample_3_FVBxPyMT_F1_Liver_10484)

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: RNA-seq data from snap frozen tissue or cultured cells

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: Healthy liver

growth_protocol: cells were grown in tissue culture or isolated from mice and snap frozen

extract_protocol:
RNA was isolated from flash-frozen tissue. First the tissue was mechanically dissociated using a tissue grinder while submerged in 1 ml of TriPure (Roche). 200 µl of chloroform (Sigma-Aldrich) was then added and the soluble fraction was isolated by centrifugation at 12,000 rpm for 15 minutes at 4°C. RNA was then precipitated with the addition of 500 µl isopropanol and incubation of the sample at -20°C for 2 hours. Pure RNA was then extracted using the RNA: DNA mini-prep kit (Zymogen) and finally samples were eluted in 100 µl (PT) or 50 µl (metastases) of DEPC water (Quality Biological). RNA was isolated from cell lines using TriPure as described above but following isopropanol precipitated RNA was washed with 75% ethanol (Sigma-Aldrich), and then again with 95% ethanol before being resuspended in 100 µl DEPC water.
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: all samples are untreated

tag: mouse strain

value: FVB

tag: oncogenic driver

tag: cell line name

tag: model

value: WT mouse


title: FVB Healthy liver RNA (Sample_6_FVBxPyMT_F1_Liver_10274)


title: FVB Healthy liver RNA (Sample_4_FVBxPyMT_F1_Liver_10272)


title: FVB Healthy liver RNA (Sample_5_FVBxPyMT_F1_Liver_10273)


title: FC107 fin clipped at 10 weeks during normal aging

tag: Sex


title: FC102 fin clipped at 10 weeks during normal aging


title: FC101 fin clipped at 20 weeks during normal aging


title: C3Tag GEMM FVB primary tumor RNA (Sample_1_C3Tag_2_PT-ax)

source_name: Primary Mammary Tumor

value: GEMM


title: M6 Allograft intracardiac injection tumor adj liver RNA (Sample_7_M6_IC_1266_Liver)

source_name: tumor adjacent liver

value: Allograft intracardiac injection


title: FC100 fin clipped at 20 weeks during normal aging


title: 6DT1 Allograft intracardiac injection tumor adj liverRNA (Sample_34_6DT1_6_Liver)

value: cMYC


title: M6 Allograft intracardiac injection brain met RNA (Sample_6_M6_IC_1266_BrainMet)

source_name: Brain metastasis


title: Met1 Allograft intracardiac injection tumor adj liver RNA (Sample_32_Met_1_8_Liver)

value: PyMT


title: FC100 fin clipped at 10 weeks during normal aging


title: FC99 fin clipped at 20 weeks during normal aging


title: Met1 Allograft intracardiac injection tumor adj pleen RNA (Sample_30_Mer1_IC_6_Spleen)

source_name: tumor adjacent spleen


title: FC99 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection tumor adj liver RNA (Sample_2_M6_IC_1278_Liver)


title: FC98 fin clipped at 20 weeks during normal aging


title: Met1 Allograft intracardiac injection liver met RNA (Sample_28_Mer1_IC_6_LiverMetA)

source_name: Liver Metastasis


title: FC97 fin clipped at 20 weeks during normal aging


title: Met1 Allograft intracardiac injection tumor adj liver RNA (Sample_27_Mer1_IC_6_Liver)


title: FC98 fin clipped at 10 weeks during normal aging


title: FC97 fin clipped at 10 weeks during normal aging


title: Met1 Allograft intracardiac injection liver met RNA (Sample_29_Mer1_IC_6_LiverMetB)


title: Met1 Allograft intracardiac injection brain met RNA (Sample_26_Met1_IC_1_BrainMet)


title: C3Tag GEMM FVB primary tumor RNA (Sample_2_C3Tag_93_PT-ax)

value: FVG


title: Met1 Allograft intracardiac injection tumor adj spleen RNA (Sample_23_Met1_IC_1_Spleen)


title: M6 Allograft intracardiac injection tumor adj liver RNA (Sample_19_M6_IC_1274_Liver)


title: FC96 fin clipped at 10 weeks during normal aging


title: FC101 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection tumor adj liver RNA (Sample_14_M6_IC_1297_Liver)


title: M6 Allograft intracardiac injection tumor adj liver RNA (Sample_11_M6_IC_1294_Liver)


title: FC95 fin clipped at 20 weeks during normal aging


title: FC96 fin clipped at 20 weeks during normal aging


title: Mvt1 tissue culture RNA (Mvt1-cells_isolation3_sample1011-11)

source_name: tissue culture

value: cMYC / VEGF

value: tissue culture


title: FC94 fin clipped at 20 weeks during normal aging


title: FC94 fin clipped at 10 weeks during normal aging


title: FC95 fin clipped at 10 weeks during normal aging


title: FC93 fin clipped at 20 weeks during normal aging


title: Met1 tissue culture RNA (Met1-cells_isolation3_sample1011-12)


title: M6 tissue culture RNA (M6-cells_isolation3_sample1011-15)

value: BALB


title: M6 tissue culture RNA (M6-cells_isolation2_sample1011-14)


title: FC93 fin clipped at 10 weeks during normal aging


title: FC92 fin clipped at 20 weeks during normal aging


title: FC92 fin clipped at 10 weeks during normal aging


title: M6 tissue culture RNA (M6-cells_isolation1_sample1011-13)


title: 67NR tissue culture RNA (67NR-cells_isolation2_sample1011-19)

value: unknown


title: 67NR tissue culture RNA (67NR-cells_isolation1_sample1011-18)


title: FC91 fin clipped at 10 weeks during normal aging


title: 4T07 tissue culture RNA (4T07-cells_isolation2_sample1011-17)


title: FC91 fin clipped at 20 weeks during normal aging


title: FC90 fin clipped at 20 weeks during normal aging


title: FC90 fin clipped at 10 weeks during normal aging


title: 4T07 tissue culture RNA (4T07-cells_isolation1_sample1011-16)


title: FC89 fin clipped at 20 weeks during normal aging


title: Mvt1 tissue culture RNA (Mvt1-cells_isolation1_KS60)


title: Mvt1 tissue culture RNA (Mvt1-cells_isolation2_KS61)


title: FC89 fin clipped at 10 weeks during normal aging


title: FC88 fin clipped at 20 weeks during normal aging


title: Met1 tissue culture RNA (Met1-cells_isolation2_KS63)


title: FC88 fin clipped at 10 weeks during normal aging


title: FVB healthy lung RNA (LungUncond_mousePF3_KS57)

source_name: healthy lung


title: FC87 fin clipped at 10 weeks during normal aging


title: FVB healthy lung RNA (LungUncond_mousePF2_KS34)


title: FVB healthy lung RNA (LungUncond_mousePF1_KS33)


title: 6DT1 tissue culture RNA (6DT1-cells_isolation3_sample1011-20)


title: FC86 fin clipped at 10 weeks during normal aging


title: FVB healthy lung RNA (LungUncond_mouse9591_KS35)


title: FC85 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB tumor adjacent Lung RNA (LungPrecond_mouseBL5Rf_RNALT5)

source_name: tumor adjacent Lung


title: FC86 fin clipped at 20 weeks during normal aging


title: FC84 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM FVB tumor adjacent Lung RNA (LungPrecond_mouse9469f_RNALT4)


title: MMTV-PyMT GEMM FVB tumor adjacent Lung RNA (LungPrecond_mouse9462f_RNALT3)


title: FC85 fin clipped at 10 weeks during normal aging


title: FC84 fin clipped at 10 weeks during normal aging


title: FC83 fin clipped at 20 weeks during normal aging


title: FC83 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB tumor adjacent Lung RNA (LungPrecond_mouse9201m_RNALT2)


title: MMTV-PyMT GEMM FVB tumor adjacent Lung RNA (LungPrecond_mouse9200m_RNALT1)


title: 6DT1 tissue culture RNA (6DT1-cells_isolation2_KS32)


title: Met1 tissue culture RNA (Met1-cells_isolation1_KS62)


title: 6DT1 tissue culture RNA (6DT1-cells_isolation1_KS31)


title: FC87 fin clipped at 20 weeks during normal aging


title: 67NR tissue culture RNA (67NR-cells_AS2)


title: 67NR tissue culture RNA (67NR-cells_AS1)


title: FC81 fin clipped at 20 weeks during normal aging


title: 4T1 tissue culture RNA (4T1-cells_isolation2_KS59)


title: FC81 fin clipped at 10 weeks during normal aging


title: 4T1 tissue culture RNA (4T1-cells_isolation1_KS58)


title: FC80 fin clipped at 20 weeks during normal aging


title: FC80 fin clipped at 10 weeks during normal aging


title: FC79 fin clipped at 20 weeks during normal aging


title: FC79 fin clipped at 10 weeks during normal aging


title: FC78 fin clipped at 20 weeks during normal aging


title: 4T07 tissue culture RNA (4T07-cells_AS1)


title: FC78 fin clipped at 10 weeks during normal aging


title: FC77 fin clipped at 20 weeks during normal aging


title: FC82 fin clipped at 20 weeks during normal aging


title: FC77 fin clipped at 10 weeks during normal aging


title: 6DT1 Allograft tail vein injection liver met RNA (Sample_35_6DT1_6_LiverMetA)

value: Allograft tail vein injection


title: FC76 fin clipped at 20 weeks during normal aging


title: Met1 Allograft intracardiac injection liver met RNA (Sample_33_Met_1_8_LiverMet)


title: FC82 fin clipped at 10 weeks during normal aging


title: Met1 Allograft intracardiac injection spleen met RNA (Sample_31_Mer1_IC_6_SpleenMet)

source_name: spleen metastasis


title: Met1 Allograft intracardiac injection spleen met RNA (Sample_25_Met1_IC_1_SpleenMetB)


title: FC76 fin clipped at 10 weeks during normal aging


title: FC75 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection spleen met RNA (Sample_22_M6_IC_1274_SpleenMet)


title: Met1 Allograft intracardiac injection spleen met RNA (Sample_24_Met1_IC_1_SpleenMetA)


title: FC74 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_21_M6_IC_1274_LiverMetB)


title: FC74 fin clipped at 10 weeks during normal aging


title: FC75 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_20_M6_IC_1274_LiverMetA)


title: FC73 fin clipped at 10 weeks during normal aging


title: 4T1 tissue culture RNA (4T1-cells_AS2)


title: 4T1 tissue culture RNA (4T1-cells_AS1)


title: 4T07 tissue culture RNA (4T07-cells_AS2)


title: FC73 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection lung met RNA (Sample_17_M6_IC_1274_LungMetA)

source_name: lung metastasis


title: 6DT1 Allograft tail vein injection liver met RNA (Sample_36_6DT1_6_LiverMetB)


title: M6 Allograft intracardiac injection liver met RNA (Sample_16_M6_IC_1297_LiverMetB)


title: FC72 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_15_M6_IC_1297_LiverMetA)


title: FC71 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_12_M6_IC_1294_LiverMetA)


title: FC70 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_9_M6_IC_1266__LiverMetB)


title: FC71 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_10_M6_IC_KH01_MetB)


title: M6 Allograft intracardiac injection spleen met RNA (Sample_5_M6_IC_1266_SpleenMet)


title: FC69 fin clipped at 20 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_13_M6_IC_1294_LiverMetB)


title: M6 Allograft intracardiac injection liver met RNA (Sample_8_M6_IC_1266_LiverMetA)


title: M6 Allograft intracardiac injection liver met RNA (Sample_4_M6_IC_1278_LiverMetB)


title: M6 Allograft intracardiac injection liver met RNA (Sample_1_M6_IC_1_LiverMetB)


title: FC69 fin clipped at 10 weeks during normal aging


title: M6 Allograft intracardiac injection liver met RNA (Sample_3_M6_IC_1278_LiverMetA)


title: Mutant_2

city: Portland

first: Supender

last: Kaur

state: Oregon

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology and Immuno

institute: Oregon health and science university

description: Mutant animals on PA14-24HOURS

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Caenorhabditis elegans genome WS220
The  htseq-count were further analyesd for the  differentially expressed features from count tables using DESeq2
Genome_build: Caenorhabditis elegans genome WS220
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample ...

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to young adult stage at 20oC

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and added to the P.aeruginosa PA14 seeded plates at 25oC for 24 hours . After that worms were washed with M9  thrice to get rid of bacteris and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: Whole organism

tag: age

value: Young adults

tag: genotype


title: FC70 fin clipped at 10 weeks during normal aging

value: male

value: fin clip


title: Mutant_3

description: Mutant animals on PA14-24HOURS


title: M6 Allograft intracardiac injection lung met RNA (Sample_18_M6_IC_1274_LungMetB)


title: FC68 fin clipped at 20 weeks during normal aging

value: normal aging


title: FC72 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_10062_PT)

value: MOLF


title: Mutant_1

description: Mutant animals on PA14-24HOURS


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10062_Met_C)


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10062_Met_B)


title: FC68 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10062_Met_A)


title: FC67 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10048_Met_B)


title: Control_1

description: Control animals on PA14-24HOURS


title: Sample_H3

city: New York

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data was analyzed by following the procedure described here. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in ≥90% bases, the good quality reads were aligned to the University of California Santa Cruz’s Mus musculus reference genome and transcriptome (build mm10) using the Burrows-Wheeler Aligner.43 The reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were combined to calculate as expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads44 in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log2 base scale. Principal component analysis was first performed to assess the sample correlations using the expression data of all the genes. The DEGs in diabetic mice versus control mice were identified by the R package DEGseq for sorted GECs, and we selected the genes based on DEGseq adjusted P < 0.05 and 1.5-fold change. The limma test45 was applied for analysis of data in isolated glomeruli with a cutoff of P < 0.05 and 1.5-fold change. The Gene Ontology and pathway analysis for the differentially expressed genes were then performed using INGENUITY IPA (http://www.ingenuity.com/products/ipa) and online tool Enrichr.19 The read coverage of gene functional elements was also visualized by IGV tool (Integrative Genome Viewer; http://www.broadinstitute.org/igv/) from the genome alignment file. Heat map analysis was performed for the top 50 fold-changed DEGs with DEGseq test after median center transformed using Multiple Experiment Viewer (Web MEV) software (mev.tm4.org).46
Genome_build: mm10

source_name: Mouse kidney cortices

extract_protocol:
Kidney were removed, flash frozen on dry ice, and RNA was harvested using RNeasy mini kit. TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse kidney cortices

value: Mrl/Mpj wild type

tag: treatment

value: Vehicle


title: FC67 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10048_Met_A)

value: GEMM


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10047_Met_C)

value: PyMT


title: FC66 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_10047_PT)


title: Sample_H2


title: Control_3

description: Control animals on PA14-24HOURS


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10043_Met_C)


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_10043_PT)


title: Vehicle_2_7

value: Mrl/lpr


title: FC66 fin clipped at 10 weeks during normal aging


title: Control_2

description: Control animals on PA14-24HOURS


title: FC65 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_10000PT)


title: Sample_H1


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10047_Met_B)


title: Multi_2_6

value: Multi-target


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_10048_PT)


title: FC65 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10000_Met_C)


title: Multi_2_39


title: FC64 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10000_Met_B)


title: MMTV-PyMT GEMM MOLF primary tumor RNA (PyMT_MOLF_9878_PT)


title: Vehicle_2_36


title: FC64 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT_CAST_10131_PT)

value: CAST


title: Predisone_2_35

value: Prednisone


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_10043_Met_B)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10131_Met_B)


title: FC63 fin clipped at 10 weeks during normal aging


title: FK506_2_3


title: FC62 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT_CAST_10077_PT)


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT_CAST_10075_PT)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10077_Met_A)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10077_Met_B)


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_9878_Met_B)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10131_Met_A)


title: FC63 fin clipped at 20 weeks during normal aging


title: FC62 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10075_Met_A)


title: MMF_2_27

value: MMF


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT_MOLF_9878_Met_A)


title: FK506_2_24


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10075_Met_C)


title: FC61 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT_CAST_10073_PT)


title: FC61 fin clipped at 20 weeks during normal aging


title: Predisone_2_23


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10073_Met_C)


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10073_Met_A)


title: MMTV-PyMT GEMM CAST primary tumor RNA (PyMT_CAST_10055_PT)


title: Multi_2_18


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10055_Met_B)


title: FC60 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10055_Met_C)


title: Vehicle_2_17


title: MMTV-PyMT GEMM CAST lung met RNA (PyMT_CAST_10055_Met_A)


title: Predisone_2_29


title: FC60 fin clipped at 10 weeks during normal aging


title: MMF_2_14


title: MMTV-neu GEMM FVB primary tumor RNA (PyMT-Neu_PT-ING_mouse472CH_sample1011-34)

value: FVB

value: Neu


title: FC59 fin clipped at 10 weeks during normal aging


title: MMTV-neu GEMM FVB lung met RNA (PyMT-Neu_LuMet2_mouse472CH_sample1011-35)


title: FC59 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT-MOLFJ_PT_9944_KS136)


title: FK506_2_12


title: MMF_2_1


title: FC58 fin clipped at 20 weeks during normal aging


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT-MOLFJ_LM1_9884_KS135)


title: MMTV-PyMT GEMM MOLF lung met RNA (PyMT-MOLFJ_PT_9884_KS134)


title: FC58 fin clipped at 10 weeks during normal aging


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9470_RNAPT11)


title: MMTV-PyMT GEMM FVB primary tumor RNA (PyMT-FVB_PT_mouse9336_RNAPT09)