title: SR-HepG2_shControl-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx

data_processing: Identification of m7G-seq induced mutation. RNA input samples (without reduction or biotinylation, as ‘‘input’’), with reduction and biotinylation samples (before biotin pull-down, as ‘‘before-pulldown’’), and biotin pull-down samples (as ‘‘pulldown’’) were all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 15). Reads were then processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates. The harvested reads were further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.2.1) with at most four mismatches. Identification of sequence variants was carried out by determining the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/ bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. Variants at base “G” were initially collected in before-pulldown or pulldown sample if (1) the sum of G/T or G/C misincorporation count is equal to or larger than 2; (2) the sum of G/T or G/C misincorporation rate is no less than two percent; (3) overall coverage at base “G” was at least 18 reads. Identified guanosine positions (according to the encoding DNA strand) were then filtered to exclude known genomic polymorphism sites (dbSNP). The generated preliminary mutations sites must appear in two replicates of ‘‘before-pulldown’’ or ‘‘pulldown’’ samples. Variants at base ‘G’ in ‘‘input’’ samples serve for removing natural mutations or false positives from both ‘‘before-pulldown’’ and ‘‘pulldown’’ samples. The further analysis to uncover high-confident internal m7G site candidates is based on the comprehensive mutation patterns across input, before-pulldown and pulldown samples.

molecule: other

growth_protocol: Human HeLa, HepG2 and HEK293T cell lines were all purchased from ATCC. HeLa and HepG2 cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco), while HEK293T cell lines were maintained in DMEM (Gibco, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco).

extract_protocol: Around 4 ug human small RNA (< 200 nt) was fragmented into around 50 nt using RNA Fragmentation Reagents (AM8740, Invitrongen) following the manufacturer’s standard protocol. The end repair/3’-dephosphorylation was performed with T4 Polynucleotide Kinase (EK0032, Thermo Fisher Scientific): RNA was mixed with 5 uL 10X T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB) and 5 uL T4 PNK, diluted to a final volume of 50 uL and incubated at 37C for 1 h. Then a further 5’-/3’-dephosphorylation step was conducted at 37C for 1.5 h in 50 uL 1X CutSmart Buffer (NEB) with 5 uL Shrimp Alkaline Phosphatase (rSAP, NEB). Starting with the 3’ -adaptor ligation, repaired and dephosphorylated RNA fragments (20 uL) were incubated with 1.6 uL 100 mM (2 equivalents) 3’ linker (5’rApp-AGATCGGAA GAGCGTCGTG-3SpC3) at 70C for 2 min and transferred to ice immediately. 5 uL 10X T4 RNA Ligase Reaction Buffer, 15 uL 50% PEG8000 and 4 uL T4 RNA ligase 2 truncated KQ (NEB) were added accordingly to the RNA-adaptor mixture, then the reaction was diluted to a final volume of 50 uL and incubated at 25C for 2 h followed by 16C for 8 h or more. The reaction was then diluted to 97 uL, and the excessive adaptors were digested with 3 uL 5’ Deadenylase (NEB) at 30C for 1 h followed by adding 1.5 uL RecJf (NEB) for ssDNA digestion at 37C for another hour. 3’ end ligated RNA was extracted using RNA Clean & Concentrator (Zymo Research). Save 50 ng as ‘‘input’’. To enrich m7G sites, RNA was reduced, biotinylated, and pulled-down in a row. RNA was subjected to reduction by 1 M NaBH4 (freshly prepared in water) as a 5X reaction buffer and incubated at 25C for 45-60 min, with occasional low-speed shaking. RNA was recovered with 7 volumes (to quench the reaction) of RNA Binding Buffer provided by RNA Clean & Concentrator (Zymo Research) and the rest steps remained the same as the protocol. We added 5 uL 1 M MES buffer (pH = 4.5) to the eluted RNA in a volume of 35 uL and mixed it immediately followed by adding 10 uL EZ-Link Hydrazide-Biotin (Thermo Fisher Scientific, 50 mM solution in DMSO). The solution was incubated at 55C for 1 h. RNA was purified quickly (save 50 ng as ‘‘before pulldown’’) and proceeded to pull-down assay with Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific). 20 uL resins was added. Respectively, resins were washed twice with 1X B&W buffer (as the manufacturer’s protocol), resuspended in 2X B&W buffer (with a volume equal to the sample), and incubated with the sample at 4C for 20 min. After pull-down, the resins were washed five times with 1X Wash buffer (50 mM Tris, pH 7.4, 300 mM KCl, 0.05% (v/v) NP-40) and subjected to proteinase K digestion. The digestion reaction was prepared as previously mentioned and incubated at 55C for 30 min. The flow-through was saved and RNA was recovered with RNA Clean & Concentrator (Zymo Research). The 3’ ligated RNA (as ‘‘input’’), the RNA before pull-down assay (as ‘‘before pulldown’’), and final elution after pull-down (as ‘‘pulldown’’) were subjected to reverse transcription. RNAs were first incubated with 1 uL of 2.0 mM RT primer (5’-ACACGACGCTCTTCC GATCT-3’) at 65C for 2 min and cooled on ice immediately. The reactions were then prepared with RNA mixture, 2 uL 10 mM dNTP (Deoxynucleotide (dNTP) Solution Mix, NEB), 2 uL 10X AMV Reverse Transcriptase Reaction Buffer (NEB), 1 uL Recombinant HIV reverse transcriptase (Worthington), and 1 uL RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific) and then incubated the 20 uL reaction mixture at 37C for 1 h. The enzymes were deactivated by incubation at 75C for 5 min and stored on ice. The cDNAs were purified with Oligo Clean and Concentrator (Zymo Research). Purified cDNA was then subject to cDNA 3’-adaptor ligation. The cDNA was first denatured with 1 uL of 50 mM cDNA linker (5’ Phos-NNNNNNNNNNAGATCGGAAG AGCA CACGTCTG-3SpC3) at 75C for 2 min. 2 uL 10X T4 RNA Ligase Reaction Buffer, 10 uL 50% PEG8000, 2 uL 10mM ATP and 1 uL T4 RNA ligase 1 (high concentration, NEB) were added accordingly to the cDNA-adaptor mixture, then the 20 uL reaction was incubated at 25C for 12 h. The library was then amplified with the universal and indexed primers from NEBNext Multiplex Oligos for Illumina (NEB). All libraries were sequenced on Illumina NextSeq 500 with single-end 80 bp read length.

tag: cell line


title: SR-HepG2_shControl-before_pulldown-rep2 (dataset 3)

status: Public on Apr 26 2019

type: SRA

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

country: USA

institute: The University of Chicago

description: 22 sites of internal m7G in tRNAs.xlsx

library_source: transcriptomic

organism: Homo sapiens

treatment_protocol: For the libraries with siRNA knockdown of METTL1: AllStars negative control siRNA (Qiagen, SI03650318) was used as control siRNA in knockdown experiments. METTL1 siRNAs were ordered from Qiagen (siMETTL1-1: SI00076118). Transfection was performed with Lipofectamine RNAi-MAX (Invitrogen) following the manufacturer’s protocols. Generally, 15-cm plates of HeLa cells were prepared for 48 h knockdown. For the libraries with shRNA knockdown: the METTL1 shRNA vector was designed and constructed base on GPP with the construct IP as shRNA TRCN0000304184 and the target sequence as GGTGTATACCATAACCGATGT. Lentiviruses containing the METTL1 shRNAs were then produced in HEK293T cells with packaging plasmids. After 48 h, virus was were collected and used to infect HepG2 cells. Stable METTL1 knockdown cell lines were selected through 5 days of puromycin selection (2 μg/ml).


title: SR-HepG2_shMETTL1-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2_shMETTL1-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2_shMETTL1-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2_shControl-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2_shControl-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siMETTL1-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx

value: HeLa


title: SR-HeLa_siMETTL1-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siMETTL1-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siControl-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: MBL-HEK293T-input-rep2 (dataset 4)

description: processed data file: HEK293T_HighFC.txt

data_processing:
Peak calling is adopted in the analysis of MeRIP data. Adaptors and low-quality reads (length shorter than 15) were trimmed from raw sequencing reads using cutadapt (https://cutadapt.readthedocs.io/en/stable/#).
Reads were then aligned to the relevant genome (human-hg19, mouse-mm10) using Tophat2 (version 2.2.1) without any gaps and allowed for at most two mismatches.
Peaks enriched in immunoprecipitation over input experiments were identified using exomePeak (Meng et al., 2013) and MeTPeak (Cui et al., 2016). For each cell line, only peaks identified (FDR≤0.05) in both replicates were considered as a candidate target. The further annotation of peaks was made use of PAVIS (https://manticore.niehs.nih.gov/pavis2/) and homer software (http://homer.ucsd.edu/homer/ngs/rnaseq/index.html).
All peaks listed in the .xls are with enrichment fold change (FC) larger than 3. These peaks appear consistently in both replicates.
Genome_build: hg19, mm10

molecule: polyA RNA

growth_protocol: Human HeLa, HepG2, and HEK293T cell lines and mouse embryonic stem cells (mESC) and mouse embryonic fibroblasts (MEF) used in this study were all purchased from ATCC. HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco), while HepG2, HEK293T and MEF cell lines were maintained in DMEM (Gibco, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco). mESC cells were grown under a typical feeder-free culture condition: cells were cultured in DMEM (Gibco, 11995), supplemented with 15% FBS, 1% Pen/Strep (Gibco), 1X Glutamax (Gibco), 1X non-essential amino acids (Gibco), 1X 2-Mercaptoethanol (Gibco), and 1000 U/ml leukemia inhibitory factor (Millipore, ESG1107), together with two inhibitors: 3 uM CHIR99021 (Stemgent, dissolved in DMSO) and 1 uM PD0325901 (Stemgent, dissolved in DMSO). mESC cells were distinctively cultured on gelatinized culture plates (0.2% Gelatin). The culture of mESC cells were passaged every 2 days. All cells were cultured at 37 °C under 5.0% CO2.

extract_protocol:
2.0 ug poly(A)+ RNA was decapped and then fragmented into 50-100 nt using RNA fragmentation reagents (Thermo Fisher Scientific) following the manufacturer’s protocol. The fragmented poly(A)-tailed RNA was concentrated with RNA Clean & Concentrator (Zymo Research). The end structures of these RNA fragments were repaired by T4 PNK. The repaired RNA was then incubated with 2 ug MBL anti-m7G antibody (NEB anti-m6A antibody used for negative control in one cell line) in 200 ul IPP buffer (10mM Tris-Cl, pH=7.4; 150 mM NaCl; 0.1% NP-40) with freshly added 5% SUPERase-In RNase inhibitor (Thermo Fisher Scientific) at 4 °C for 2 h. 20 ul Dynabeads Protein G resins (Thermo Fisher Scientific) were washed twice, resuspended in 200 ul IPP buffer and incubated with the antibody-RNA mixture for another 2 h at 4 °C. The resins were then washed with IPP buffer at 4 °C for three times. RNA was finally eluted with proteinase K digestion. 90 ul 1X proteinase K digestion buffer (10X recipe: 10% SDS, 50 mM EDTA, 10 mM Tris-Cl (pH=7.4)) with 10 ul proteinase K was used to resuspend the resins, and the solution was incubated at 55 °C for 30 min. The second round of the digestion was prepared in the same way and incubated at 55 °C for another 30 min. Both flow-throughs were combined, and m7G-containing RNA was recovered with RNA Clean & Concentrator (Zymo Research).
Decapped and fragmented poly(A)+ RNA (as “input”) and immunoprecipitated RNA (as “IP”) were subjected to small RNA library construction following manufacturer’s instructions of NEBNext Small RNA Library Prep Set for Illumina (NEB). All libraries were sequenced on Illumina NextSeq 500 with single-end 80 bp read length.

tag: tissue

value: HEK293T cells


title: SR-HeLa_siMETTL1-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siControl-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siControl-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2_shMETTL1-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa-pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-input-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-before_pulldown-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa_siControl-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-before_pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-input-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HEK293T-input-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HepG2-input-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: SR-HeLa-input-rep2 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: mRNA-HeLa-before_pulldown-rep2 (dataset 3)

description: 49_sites_of_internal_m7G_in_mRNA_with_high_estimated_methylation_status.xlsx

data_processing: Identification of m7G-seq induced mutation. RNA input samples (without reduction or biotinylation, as ‘‘input’’), with reduction and biotinylation samples (before biotin pull-down, as ‘‘before-pulldown’’), and biotin pull-down samples (as ‘‘pulldown’’) were all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 15). Reads were then processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates. The harvested reads were further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.2.1) with at most four mismatches. Identification of sequence variants was carried out by determining the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/ bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. Variants at base “G” were initially collected in before-pulldown or pulldown sample if (1) the sum of G/T or G/C misincorporation count is equal to or larger than 2; (2) the sum of G/T or G/C misincorporation rate is no less than two percent; (3) overall coverage at base “G” was at least 18 reads. Identified guanosine positions (according to the encoding DNA strand) were then filtered to exclude known genomic polymorphism sites (dbSNP). The generated preliminary mutations sites must appear in two replicates of ‘‘before-pulldown’’ or ‘‘pulldown’’ samples (mutation sites with a G to T misincorporation rate >40% were removed). 3% misincorporation rate of G/T or G/C (above the background mismatch rate in RNA input samples) was set for ‘‘before-pulldown’’ samples and 8% was set for ‘‘pulldown’’ samples. Variants at base ‘G’ in ‘‘input’’ samples serve for removing natural mutations or false positives from both ‘‘before-pulldown’’ and ‘‘pulldown’’ samples. The further analysis to uncover high-confident internal m7G site candidates is based on the comprehensive mutation patterns across input, before-pulldown and pulldown samples.

extract_protocol: Around 4-6 ug human mRNA (two rounds of polyA+ purification) was fragmented into 50-100 nt using RNA Fragmentation Reagents (AM8740, Invitrongen) following the manufacturer’s standard protocol. The fragmented mRNA was further decapped with the standard decapping procedure (Tobacco Decapping Plus 2, Enzymax) and then concentrated with Oligo Clean and Concentrator (Zymo Research). The end repair/3’-dephosphorylation was performed with T4 Polynucleotide Kinase (EK0032, Thermo Fisher Scientific): RNA was mixed with 5 uL 10X T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB) and 5 uL T4 PNK, diluted to a final volume of 50 uL and incubated at 37C for 1 h. Then a further 5’-/3’-dephosphorylation step was conducted at 37C for 1.5 h in 50 uL 1X CutSmart Buffer (NEB) with 5 uL Shrimp Alkaline Phosphatase (rSAP, NEB). Starting with the 3’ -adaptor ligation, repaired and dephosphorylated RNA fragments (20 uL) were incubated with 1.6 uL 100 mM (2 equivalents) 3’ linker (5’rApp-AGATCGGAA GAGCGTCGTG-3SpC3) at 70C for 2 min and transferred to ice immediately. 5 uL 10X T4 RNA Ligase Reaction Buffer, 15 uL 50% PEG8000 and 4 uL T4 RNA ligase 2 truncated KQ (NEB) were added accordingly to the RNA-adaptor mixture, then the reaction was diluted to a final volume of 50 uL and incubated at 25C for 2 h followed by 16C for 8 h or more. The reaction was then diluted to 97 uL, and the excessive adaptors were digested with 3 uL 5’ Deadenylase (NEB) at 30C for 1 h followed by adding 1.5 uL RecJf (NEB) for ssDNA digestion at 37C for another hour. 3’ end ligated RNA was extracted using RNA Clean & Concentrator (Zymo Research). Save 50 ng as ‘‘input’’. To enrich m7G sites, RNA was reduced, biotinylated, and pulled-down in a row. RNA was subjected to reduction by 1 M NaBH4 (freshly prepared in water) as a 5X reaction buffer and incubated at 25C for 45-60 min, with occasional low-speed shaking. RNA was recovered with 7 volumes (to quench the reaction) of RNA Binding Buffer provided by RNA Clean & Concentrator (Zymo Research) and the rest steps remained the same as the protocol. We added 5 uL 1 M MES buffer (pH = 4.5) to the eluted RNA in a volume of 35 uL and mixed it immediately followed by adding 10 uL EZ-Link Hydrazide-Biotin (Thermo Fisher Scientific, 50 mM solution in DMSO). The solution was incubated at 55C for 1 h. RNA was purified quickly (save 50 ng as ‘‘before pulldown’’) and proceeded to pull-down assay with Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific). 20 uL resins was added. Respectively, resins were washed twice with 1X B&W buffer (as the manufacturer’s protocol), resuspended in 2X B&W buffer (with a volume equal to the sample), and incubated with the sample at 4C for 20 min. After pull-down, the resins were washed five times with 1X Wash buffer (50 mM Tris, pH 7.4, 300 mM KCl, 0.05% (v/v) NP-40) and subjected to proteinase K digestion. The digestion reaction was prepared as previously mentioned and incubated at 55C for 30 min. The flow-through was saved and RNA was recovered with RNA Clean & Concentrator (Zymo Research). The 3’ ligated RNA (as ‘‘input’’), the RNA before pull-down assay (as ‘‘before pulldown’’), and final elution after pull-down (as ‘‘pulldown’’) were subjected to reverse transcription. RNAs were first incubated with 1 uL of 2.0 mM RT primer (5’-ACACGACGCTCTTCC GATCT-3’) at 65C for 2 min and cooled on ice immediately. The reactions were then prepared with RNA mixture, 2 uL 10 mM dNTP (Deoxynucleotide (dNTP) Solution Mix, NEB), 2 uL 10X AMV Reverse Transcriptase Reaction Buffer (NEB), 1 uL Recombinant HIV reverse transcriptase (Worthington), and 1 uL RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific) and then incubated the 20 uL reaction mixture at 37C for 1 h. The enzymes were deactivated by incubation at 75C for 5 min and stored on ice. The cDNAs were purified with Oligo Clean and Concentrator (Zymo Research). Purified cDNA was then subject to cDNA 3’-adaptor ligation. The cDNA was first denatured with 1 uL of 50 mM cDNA linker (5’ Phos-NNNNNNNNNNAGATCGGAAG AGCA CACGTCTG-3SpC3) at 75C for 2 min. 2 uL 10X T4 RNA Ligase Reaction Buffer, 10 uL 50% PEG8000, 2 uL 10mM ATP and 1 uL T4 RNA ligase 1 (high concentration, NEB) were added accordingly to the cDNA-adaptor mixture, then the 20 uL reaction was incubated at 25C for 12 h. The library was then amplified with the universal and indexed primers from NEBNext Multiplex Oligos for Illumina (NEB). All libraries were sequenced on Illumina NextSeq 500 with single-end 80 bp read length.


title: mRNA-HepG2-pulldown-rep1 (dataset 3)

description: 49_sites_of_internal_m7G_in_mRNA_with_high_estimated_methylation_status.xlsx. And Table S3 in Molecular Cell paper titled "Transcriptome-wide Mapping of Internal N-Methylguanosine Methylome in Mammalian mRNA".


title: mRNA-HepG2-before_pulldown-rep1 (dataset 3)


title: SR-HeLa-input-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: mRNA-HeLa-pulldown-rep2 (dataset 3)


title: mRNA-HepG2-before_pulldown-rep2 (dataset 3)


title: SR-HeLa-pulldown-rep1 (dataset 3)

description: 22 sites of internal m7G in tRNAs.xlsx


title: mRNA-HepG2-pulldown-rep2 (dataset 3)


title: mRNA-HeLa-before_pulldown-rep1 (dataset 3)


title: mRNA-HeLa-pulldown-rep1 (dataset 3)


title: mRNA-HeLa-input-rep2 (dataset 3)


title: mRNA-HepG2-input-rep2 (dataset 3)


title: mRNA-HeLa-input-rep1 (dataset 3)


title: Ribo_seq-siControl-riboBound1 (dataset 2)

data_processing:
Adaptors and low-quality bases (length shorter than 18) were trimmed from raw sequencing reads using cutadapt (https://cutadapt.readthedocs.io/en/stable/#)
Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.0.12), with an increased stringency allowing only up to two mismatches per each read pair.
With the sorted BAM file generated in the previous step using Tophat2, RNA-Seq analysis was performed by utilizing cufflinks to produce .fpkm_tracking files.
hg19

molecule: total RNA

source_name: cell

growth_protocol: Human HeLa cells were all purchased from ATCC. HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco), while HEK293T cell lines were maintained in DMEM (Gibco, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco).

extract_protocol:
Twelve 15-cm plates of HeLa cells were prepared for 48 h knockdown (siControl, siMETTL1, six plates each). Cycloheximide (CHX) was added to the media at 100 mg ml–1 for 7 min. After removing the media,  the cells were collected by cell lifter with 5 ml cold PBS with CHX (100 mg ml–1). The cell suspension was spun at 500g for 5 min to obtain the cell pellet. 1 ml lysis buffer (10 mM Tris, pH 7.4, about 150mM KCl, 5 mM MgCl2, 100 mg ml–1 CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U ml–1 SUPERasin) was added to suspend the cells and then kept on ice for 15 min. After centrifugation at 13,000g for 15 min, the supernatant was collected and absorbance tested at 260 nm (150–200 A260 nm ml–1 ). To the lysate, 8 ul DNase Turbo was added. The lysate was then split by the ratio of 1:4 (Portion I/Portion II). 4 ul Super RNasin was added to Portion I. 40 ul MNase buffer and 3 ul MNase (6,000 gel units, NEB) was added to Portion II. Both portions were kept at room temperature for 15 min, and then 8 ul SUPERasin was added to Portion II to stop the reaction. Portion I was saved and mixed with 1 ml TRIzol to purify input mRNA.   Ribosome-bound RNA: A 10/50% w/v sucrose gradient was prepared in a lysis buffer without Triton-X-100. Portion II was loaded onto the sucrose gradient and centrifuged at 4 C for 3 h at 28,000 r.p.m. (Beckman, rotor SW28). The sample was then fractioned and analysed by Gradient Station (BioCamp) equipped with ECONO UV monitor (BioRad) and fraction collector (FC203B, Gilson). The fractions corresponding to 80S monosome (not 40S or 60S) were collected, combined, and mixed with an equal volume of TRIzol to purify the RNA. The RNA pellet was dissolved in 30 ul water, mixed with 30 ul 2X TBE-urea loading buffer (Invitrogen), and separated on a 10% TBE-urea gel. A 21-nt and a 42-nt ssRNA oligo were used as size markers, and the gel band between 21 and 42 nt was cut. 600 ul extraction buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml–1 RNasin) was added to the gel. The gel slurry was heated at 65 C for 10 min with shaking, and then filtered through 1 ml Qiagen filter. RNA was concentrated by ethanol precipitation and finally dissolved in 10 ul of RNase-free water.   mRNA input: the input RNA was first purified by TRIzol and the input mRNA was then separated by PolyATract. The resulting mRNA was concentrated by ethanol precipitation and dissolved in 10 ul of RNase-free water. The mRNA was fragmented by RNA fragmentation kit (Ambion). The reaction was diluted to 20 ul and cleaned up by micro Bio-Spin 30 column (cut-off: 20 bp; exchange buffer to Tris).
mRNA input and ribosome-bound RNA were subjected to small RNA library construction following manufacturer’s instructions of NEBNext Small RNA Library Prep Set for Illumina (NEB). All libraries were sequenced on Illumina HiSeq 4000 with single-end 50 bp read length.

treatment_protocol: AllStars negative control siRNA (Qiagen, SI03650318) was used as control siRNA in knockdown experiments. METTL1 siRNAs was ordered from Qiagen (siMETTL1: SI00076118). Transfection was performed with Lipofectamine RNAi-MAX (Invitrogen) following the manufacturer’s protocols.

tag: sample type

value: cell culture


title: Ribo_seq-siMETTL1-riboBound2 (dataset 2)


title: HeLa-WDR4-PARCLIP1 (dataset 1)

data_processing:
Adaptors and low-quality bases (length shorter than 18) were trimmed from raw sequencing reads using cutadapt (https://cutadapt.readthedocs.io/en/stable/#)
Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.0.12), with an increased stringency allowing only up to three mismatches per each read pair.
Reliable T to C mutations were characterized by PIPE-CLIP package, which will generate a .bed file named reliableMutations.pipeclip.bed to show potential mutation sites.
hg19

growth_protocol: Human HeLa and HEK293T cell lines were all purchased from ATCC. HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco), while HEK293T cell lines were maintained in DMEM (Gibco, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco).

extract_protocol:
We followed the previously reported PAR-CLIP protocol (https://www.jove.com/video/2034/par-clip-method-to-identify-transcriptome-wide-binding-sites-rna) with the following modifications. Sample preparation: twelve 15-cm plates of HEK 293T cells were seeded for each replicate and grown to 80% confluency before the addition of 4 ul 1 M 4SU to each plate. After 18 hours incubation, the media was aspirated; the cells were washed once with 5 ml ice-cold PBS for each plate and crosslinked by 0.15 J cm-2 365 nm UV light twice when on ice. The crosslinked cells were collected with cell lifters. The mouse anti-eIF4E antibody was applied to perform the immunoprecipitation.   Mild enzyme digestion: The first round of T1 digest was carried out with 0.2 U ml-1 for 15 min instead of 1 U ml-1 for 15 min. The second round of T1 digest was conducted with 10 U ml-1 for 8 min instead of 50 U ml-1 for 15 min.
The final recovered RNA sample was further extracted by RNA Clean & Concentrator (Zymo Research) before library construction by NEBNext Small RNA Library Prep Set for Illumina (NEB). All libraries were sequenced on Illumina HiSeq 4000 with single-end 50 bp read length.


title: Ribo_seq-siMETTL1-input2 (dataset 2)


title: Ribo_seq-siMETTL1-input1 (dataset 2)


title: Ribo_seq-siControl-input2 (dataset 2)


title: Ribo_seq-siControl-riboBound2 (dataset 2)


title: HeLa-METTL1-PARCLIP2 (dataset 1)


title: Ribo_seq-siControl-input1 (dataset 2)


title: HeLa-METTL1-PARCLIP1 (dataset 1)


title: HEK293T-WDR4-PARCLIP2 (dataset 1)


title: mRNA-HepG2-input-rep1 (dataset 3)


title: HEK293T-WDR4-PARCLIP1 (dataset 1)


title: HEK293T-METTL1-PARCLIP2 (dataset 1)


title: HEK293T-METTL1-PARCLIP1 (dataset 1)


title: HEK293T-eIF4E-PARCLIP1 (dataset 1)


title: Ribo_seq-siMETTL1-riboBound1 (dataset 2)


title: HEK293T-RNMT-PARCLIP1 (dataset 1)


title: HEK293T-RNMT-PARCLIP2 (dataset 1)


title: sgC_5mC

status: Public on Mar 05 2019

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

library_source: genomic

data_processing:
Files were uploaded to usegalaxy.org server. After passing FASTQC analysis, raw FASTQ sequence quality files were converted with FASTQ Groomer and aligned to human genome (hg19) with BWA for Illumina with default parameters. Aligned SAM files were converted to BAM and sorted by chromosome position. Alignment statisitics was calculated using FlagStat. Peak Calling was performed using MACS2 peakcalling with the following parameters: Effective genome size=2451960000, Band width for picking regions to compute fragment size=300, Set lower mfold bound=5, Set upper mfold bound=50, Peak detection based on=q-value, Minimum FDR (q-value) cutoff for peak detection=0.01, Build Model=create_model, When set, scale the small sample up to the bigger sample=False, Use fixed background lambda as local lambda for every peak region=False, When set use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling=1.0, The small nearby region in basepairs to calculate dynamic lambda=1000, The large nearby region in basepairs to calculate dynamic lambda=10000, Composite broad regions=nobroad, How many duplicate tags at the exact same location are allowed=1. Bedgraph files from MACS2 output were converted to BigWig for Peak visualization. DMR were calculated using MACS2 bdgdiff using 5mC outputs and inputs for each sample with correction for sequencing depth and –g 60. Genomic Regions were annotated using EpiExplorer and NextBio using PileUp values as peak scores. Analysis of Overlap between bed files was performed using the function Intersect at The Genomic Hyperbrowser as described in EpiExplorer documentation (epiexplorer.mpi-inf.mpg.de).
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 tabular file output for peaks identified in sample sgC_5mC relative to sgC_input and sgPKCi_5mC  relative to sgPKCi_input

molecule: genomic DNA

source_name: C42B cells

growth_protocol: C42B cells were cultured in Rosewell Park Memorial Instiute 1640 (RPMI 1640, GIBCO), supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, and 100 U/ml penicillin and 100 µg/ml streptomycin, in an atmosphere of 95% air and 5% CO2

extract_protocol:
Total genomic DNA from samples was extracted using QIAamp DNA mini kit (QIAGEN) and eluted in DDW. 20 mg of total genomic DNA was diluted in 50 ml TE and sonicated using Covaris S2 with the following parameters (Duty 5%, Cycles/burst = 200, time=60s, 4 cycles using a microTUBE AFA Fiber Snap-Cap). Sonicated DNA was cleaned with Qiagen PCR clean UP (QIAGEN) and eluted in 30 ml of EB
2 mg of sonicated genomic DNA was used to prepare libraries using NEBNext Ultra II DNA Library Prep kit (Illumina) following manufacturer’s instructions. Size-selected, end-repaired and adapter-ligated fragments (libraries) were denatured 10 min at 95C and immediately transferred to ice. 500 ng of library DNA were diluted in 500 ml of ice-cold IP buffer (20mM Tris-Cl, pH 8, 2mM EDTA, 1% Triton-X, 150 mM NaCl) with the addition of 1 mg of anti-5mC antibody (33D3, Diagenode) and incubated at 4C overnight. Same amount of library was kept aside for input sequencing and incorporated later to the Elution steps

treatment_protocol: No treatment was applied. Cells were harvested at ~70% confluency 48h after plating.

tag: cell type

value: Prostate Cancer tumor

tag: genotype/variation

value: sgC (WT)


title: sgPKCi-R_2

data_processing:
FASTq files were processed using RNAseq Alignment module in BaseSpace (Illumina), using default parameters. Reads were aligned to human (hg19) genome using STAR. Differentially expressed genes were calculated using DeSeq2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM gene expression values for all human genes (hg19) for all samples

extract_protocol:
RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X76) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: PKCl/i KO rescued with WT-PKCi (sgPKCl/i-R)


title: sgPKCi_3

value: PKCl/i KO (sgPKCl/i)


title: sgPKCi_Input


title: sgPKCi_5mC


title: HeLa-WDR4-PARCLIP2 (dataset 1)


title: sgPKCi_2


title: sgPKCi-R_1


title: sgC_2


title: sgC_Input


title: NPY-GFP 1 hr refeed ZT2 collection 4

status: Public on Mar 04 2019

first: Nathan

last: Waldeck

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

data_processing:
Reads were aligned to mm10 genome assembly using STAR 2.5.1
raw count tables were constructed using featureCounts from the subread command line tools
DESeq was used to normalize counts and perform differential gene expression
Plots were created using ggplot2, pheatmap, heatmap.2, and default plotting packages in R 3.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: All normalized counts were calculated using variance stabilization within DESeq2 and are listed by gene name in the tab-delimited text file "agrp-counts.txt"

organism: Mus musculus

source_name: AgRP+ ARH neurons

extract_protocol:
Cell suspensions were dissociated from Vibratome slices of the ARH nucleus from NPY-GFP mice and FACS Sorted for GFP expression. RiboTag samples were immunoprecipitated using an established protocol (Sanz et al., 2009) and purified using Qiagen Rneasy Micro Kit. All samples were amplified using Takara Clontech SMART-seq v4 Ultra Low Input RNA Kit for sequencing.
Amplified samples were constructed into sequenicng libraries using Illumina Nextera XT prep kit with manual normalization. Samples were quantified using BioAnalyzer and Qubit.

value: AgRP+ ARH neurons

tag: time point

tag: genotype

tag: treatment

value: Effective 24-hr Fast, 1-hr refeed


title: sgC_3


title: NPY-GFP 1 hr refeed ZT2 collection 5


title: NPY-GFP 1 hr refeed ZT2 collection 2


title: HEK293T-eIF4E-PARCLIP2 (dataset 1)


title: NPY-GFP 1 hr refeed ZT2 collection 1


title: sgPKCi-R_3


title: NPY-GFP 1 hr refeed ZT14 collection 3


title: sgPKCi_1


title: WT-BMAL1fx  no Leptin Admin ZT2 Collection 4

value: PBS Administration (Ctrl)


title: NPY-GFP 1 hr refeed ZT14 collection 4


title: NPY-GFP 1 hr refeed ZT14 collection 1


title: WT-BMAL1fx  w/Leptin Admin ZT2 Collection 3

value: Leptin Administration


title: NPY-GFP 1 hr refeed ZT14 collection 2


title: WT-BMAL1fx  no Leptin Admin ZT2 Collection 2


title: NPY-GFP 1 hr refeed ZT2 collection 3


title: WT-BMAL1fx  no Leptin Admin ZT2 Collection 1


title: WT-BMAL1fx  w/Leptin Admin ZT2 Collection 2


title: sgC_1


title: WT-BMAL1fx  no Leptin Admin ZT2 Collection 3


title: WT-BMAL1fx  w/Leptin Admin ZT2 Collection 1


title: WT-BMAL1fx  no Leptin Admin ZT14 Collection 2


title: WT-BMAL1fx  no Leptin Admin ZT14 Collection 3


title: WT-BMAL1fx  no Leptin Admin ZT14 Collection 1


title: WT-BMAL1fx  w/Leptin Admin ZT14 Collection 3


title: shNT-1

type: RNA

hyb_protocol: We followed manufacturer's protocol

scan_protocol: We followed manufacturer's protocol

data_processing: CEL files were processed using ExpressionFileCreator Software at https://genepattern.broadinstitute.org with the RMA method and default parameters.

label: biotin

source_name: Immortalized normal prostate epithelial cell line

label_protocol: We followed manufacturer's protocol

growth_protocol: PrEC were cultured using the media Clonetics™ PrEGM™ Bulletkit™ in an atmosphere of 95% air and 5% CO2.

extract_protocol: RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit.

treatment_protocol: shNT and shPKCl/i cells were collected under basal conditions, 48 hours after plating

value: Prostate

value: shNT


title: WT-BMAL1fx  w/Leptin Admin ZT14 Collection 2


title: shPKCi-3

value: shPKCl/i


title: shNT-3


title: shPKCi-2


title: shPKCi-1


title: AgRP-BMAL1-KO no Leptin Admin ZT2 Collection 4


title: AgRP-BMAL1-KO no Leptin Admin ZT2 Collection 3


title: WT-BMAL1fx  w/Leptin Admin ZT14 Collection 1


title: AgRP-BMAL1-KO w/Leptin Admin ZT2 Collection 3


title: shNT-2


title: AgRP-BMAL1-KO w/Leptin Admin ZT2 Collection 2


title: AgRP-BMAL1-KO no Leptin Admin ZT14 Collection 3


title: AgRP-BMAL1-KO no Leptin Admin ZT2 Collection 2


title: AgRP-BMAL1-KO w/Leptin Admin ZT2 Collection 1


title: AgRP-BMAL1-KO no Leptin Admin ZT14 Collection 1


title: AgRP-BMAL1-KO no Leptin Admin ZT14 Collection 2


title: NPY-GFP Fasted ZT2 Collection 6

value: Effective 24-hr Fast


title: AgRP-BMAL1-KO w/Leptin Admin ZT14 Collection 1


title: NPY-GFP Fasted ZT2 Collection 5


title: AgRP-BMAL1-KO w/Leptin Admin ZT14 Collection 2


title: NPY-GFP Fasted ZT2 Collection 3


title: NPY-GFP Fasted ZT2 Collection 7


title: NPY-GFP Fasted ZT2 Collection 4


title: NPY-GFP Fasted ZT2 Collection 1


title: NPY-GFP Fasted ZT14 Collection 8


title: NPY-GFP Fasted ZT14 Collection 7


title: NPY-GFP Fasted ZT14 Collection 6


title: NPY-GFP Fasted ZT14 Collection 5


title: NPY-GFP Fasted ZT14 Collection 3


title: AgRP-BMAL1-KO w/Leptin Admin ZT14 Collection 3


title: NPY-GFP Fasted ZT14 Collection 2


title: NPY-GFP Ad Lib Fed ZT2 Collection 6

value: Ad Lib Diet


title: NPY-GFP Fasted ZT2 Collection 2


title: NPY-GFP Ad Lib Fed ZT2 Collection 4


title: NPY-GFP Ad Lib Fed ZT2 Collection 3


title: NPY-GFP Ad Lib Fed ZT2 Collection 1


title: NPY-GFP Ad Lib Fed ZT14 Collection 1


title: NPY-GFP Ad Lib Fed ZT14 Collection 3


title: NPY-GFP Fasted ZT14 Collection 4


title: AGRP RiboTag Fasted ZT2 Collection 4

value: AGRP-Cre;RiboTag


title: AGRP RiboTag Fasted ZT2 Collection 5


title: NPY-GFP Ad Lib Fed ZT14 Collection 2


title: NPY-GFP Ad Lib Fed ZT2 Collection 2


title: AGRP RiboTag Fasted ZT2 Collection 2


title: AGRP RiboTag Fasted ZT14 Collection 2


title: AGRP RiboTag Fasted ZT2 Collection 1


title: AGRP RiboTag Ad Lib Fed ZT2 Collection 3


title: AGRP RiboTag Fasted ZT14 Collection 4


title: AGRP RiboTag Fasted ZT14 Collection 1


title: AGRP RiboTag Fasted ZT14 Collection 5


title: NPY-GFP Fasted ZT14 Collection 1


title: AGRP RiboTag Ad Lib Fed ZT2 Collection 1


title: AGRP RiboTag Ad Lib Fed ZT14 Collection 4


title: AGRP RiboTag Ad Lib Fed ZT14 Collection 2


title: AGRP RiboTag Fasted ZT14 Collection 3


title: AGRP RiboTag Ad Lib Fed ZT2 Collection 2


title: NPY-GFP Ad Lib Fed ZT2 Collection 5


title: AGRP RiboTag Ad Lib Fed ZT14 Collection 1


title: AGRP BMAL1 KO 3


title: AGRP RiboTag Fasted ZT2 Collection 3


title: AGRP BMAL1 KO 1


title: WT-BMAL1 FX Ctrl 1


title: WT-BMAL1 FX Ctrl 2


title: AGRP RiboTag Ad Lib Fed ZT14 Collection 3


title: CD8 control Replicate 1

status: Public on Jan 08 2019

first: Thomas

last: Ciucci

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: FPM normalization was performed with the FPM function of the DEseq2 package

source_name: Spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina)
Libraries were pooled and  sequenced with paired-end reads of 126bp on a HiSeq2500 sequencer (Illumina) to reach 50 million read pairs per sample

tag: infection

value: LCMV Arm d30 pi

tag: population


title: CD4 ThpokAD Replicate 2

value: Ox40-Cre+ Thpokfl/fl


title: CD8 control Replicate 3


title: CD8 control Replicate 2


title: CD4 ThpokAD Replicate 3


title: CD4 control Replicate 2


title: CD4 control Replicate 1


title: siblings replicate 3

status: Public on Jan 21 2019

city: Lausanne

first: Benjamin

middle: D

last: Weger

state: VD

address: Station 15

department: SV

country: Germany

institute: EPFL

description: counts.txt

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i
A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene, all exons of the respective annotated protein-coding transcripts were considered.
Genome_build: Zv10
Supplementary_files_format_and_content: raw counts

organism: Danio rerio

source_name: whole larvae

extract_protocol:
20 larvae were sampled and homogenized with micropestles (Eppendorf, #Z317314-1PAK) in 900 µl Quizol reagent before being stored overnight at -80°C. Samples were passed several times through a syringe (BD Microlance, 0.5 x 25 mm, #3086982), and RNA was extracted using the RNeasy Plus  Universal Kit (Qiagen, #73442) according to the manufacturer’s instructions. The integrity of the total RNA was checked on an agarose gel and with a NanoDrop spectrometer (Thermo Scientific). Only RNA with A260/280 values ≥2 and A260/230 values ≥1 were used for the subsequent analysis.
Library prep for total RNA Ribozero

value: siblings

tag: age

value: 5 dpf

tag: circadian time


title: fdx1b mutant replicate 3

description: counts.txt

value: fdx1b mutants


title: CD4 control Replicate 3


title: siblings replicate 1

description: counts.txt


title: fdx1b mutant replicate 2

description: counts.txt


title: siblings replicate 2

description: counts.txt


title: CD4 ThpokAD Replicate 1


title: AGRP BMAL1 KO 2


title: Thpok_Input1

data_processing:
Illumina RTA 2.4.11 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence (phred < 32) on the Partek Flow server
Filtered reads were mapped to mm10 whole genome using bowtie v1.0.0 with defauft parameters on the Partek Flow server
Peaks were called using MACS2 callpeak
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated with the bamCoverage function of the deeptools package

source_name: CD4 T cells

growth_protocol: Splenic CD4+ T cells from ThpokBio/+ Rosa26BirA or Rosa26BirA animals were enriched using Dynabeads Untouched Mouse CD4 cells kit (Invitrogen) and stimulated with anti-CD3 (1mg/ml), anti-CD28 (3mg/ml) and IL-12 (10ng/ml) for 3 days and then with IL-2 (100ng/ml) for another day

extract_protocol:
DNA was  treated with proteinase K and RNase (both at 0.2mg/ml) before purification using the QIAquick PCR purification kit (Qiagen)
Accel-NGS 2S DNA reagent (Swift)
Libraries were sequenced (75bp single-ended reads) on a NextSeq sequencer (Illumina)

treatment_protocol: Live cells were sorted, washed in PBS and fixed in 1% formaldehyde-containing PBS for 5 min at 37 degrees. Following quenching with 0.125M glycine, cells pellets were snap-frozen on dry ice and stored at -80 degrees. Frozen fixed cells were then lysed in 1% SDS RIPA buffer (20 mM Tris-HCl pH 7.6, 2 mM EDTA, 150 mM NaCl, 0.1% sodium deoxycholate, 1% TritonX100) for 30 minutes at 4°C, spun down and sonicated in 0.1% SDS RIPA buffer using a Qsonica Q800R sonicator (30s on, 59s off, 85% amplitude) to obtain a sheared chromatin with an average size of 200bp. Sheared chromatin was pre-cleared with protein-A magnetic beads (Invitrogen 10001D) followed by immunoprecipitation with M280 Streptavidin beads (Invitrogen 11205D). After washing, immunoprecipitated chromatin was reverse-crosslinked by overnight incubation at 70°C in 50nM 50mM Tris-HCl pH 8., 10mM EDTA , 1% SDS buffer

tag: strain

value: ThpokBio BirA

tag: immunoprecipitation


title: d7_WT

description: CD44high GP66:I-Ab+ RosaYFP+ T cells were sorted and capture

data_processing:
Basecalling was performed using RTA 1.12.4.2
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger software to produce the fastqfiles
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: barcode file, gene file and gene expression matrix

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads of 26x98bp or 26x57bp  on a NextSeq500 sequencer (Illumina).

tag: strain background

value: Ox40-Cre+ Thpokwt/wt RosaYFP+

value: LCMV Arm d7 pi

value: Spleen


title: TotalCD44_2

description: Total CD44high CD4+ and CD8+ T cells were sorted separetly and mixed 50/50 before capture

value: wild type

value: CD44high T cells


title: Thpok_Input3


title: d7_KO

value: Ox40-Cre+ Thpokfl/fl RosaYFP+


title: d7_GP66

description: CD44high CD4+ GP66:I-Ab+ T cells were sorted and capture


title: fdx1b mutant replicate 1

description: counts.txt


title: d30_WT


title: TotalCD44_1


title: Thpok_Input2


title: d30_KO


title: Thpok_ChIP3

value: Streptavidin


title: Control_ChIP2

value: BirA


title: Thpok_ChIP2


title: Thpok_ChIP1


title: WT1

status: Public on Dec 20 2018

description: Small intestinal tissue from wild type mouse

data_processing:
FASTq files were processed using RNAseq Alignment module in BaseSpace (Illumina), using default parameters. Reads were aligned to mouse (mm10) genome using STAR. Differentially expressed genes were calculated using DeSeq2.
Genome_build: mm10
Supplementary_files_format_and_content: processed data file consist of an excel file matrix with gene symbols and FPKM counts for all samples

source_name: Small intestine

extract_protocol:
A piece of small intestines were collected, frozen on dry ice, and RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit. PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small intestine

value: 12 weeks old

value: Villincre-negative, PKClambda f/f, PKCzeta f/f


title: WT2


title: DKO_240

description: Small intestinal tissue from intestinal epithelial cell-specific aPKC-DKO mouse

source_name: Small intestinal epithelial cell

extract_protocol:
Small intestines were isolated using EDTA, frozen on dry ice, and RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit. PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small intestinal epithelial cell

value: 8 weeks old

value: Villincre-positive, PKClambda f/f, PKCzeta f/f


title: DKO-TUMOR3

description: Small intestinal tumor tissue from intestinal epithelial cell-specific aPKC-DKO mouse

source_name: Small intestinal tumor

value: Small intestinal tumor


title: DKO_260


title: LKO_256

value: Villincre-positive, PKClambda f/f


title: DKO_223


title: LKO_250


title: DKO-TUMOR2


title: WT3


title: DKO_231


title: LKO_251


title: DKO-TUMOR1


title: Control_ChIP1


title: LKO_224


title: ZKO_22

value: Villincre-positive, PKCzeta f/f


title: ZKO_20


title: WT_259


title: WT_254


title: ZKO_19


title: WT_216


title: Crushed_3

status: Public on Oct 08 2018

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

data_processing:
Preprocessing with Trimmomatic (options SLIDINGWINDOW:4:10 AVGQUAL:20 MINLEN:20) and Flexbar (-u 20 --pre-trim-left 4 --pre-trim-right 4).
Read mapping and quantification performed with RSEM
Genome_build: GRCm38
Supplementary_files_format_and_content: Count files based on RSEM providing raw counts (column transcript count) and normalized counts (TPM, FPKM)

source_name: Sciatic nerve

extract_protocol:
Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian Total RNA
Clontech, built-in rRNA removal

tag: background strain

value: Crush injured sciatic nerve

value: wild-type

value: 3 days post crush injury


title: Crushed_2


title: Crushed_4


title: Uncrushed_3

value: Sciatic nerve

value: uncrushed surgery control


title: Uncrushed_1


title: Contralat_4

value: Contralateral sciatic nerve


title: Crushed_1


title: Contralat_3


title: iDgcr8_mutant_3

extract_protocol:
Illumina TruSeq RNA stranded
Ribosomal Depletion with Ribo Zero

value: P0-CreERT2 -/+ Dgcr8 flox/flox

value: 3 months post tamoxifen induction


title: iDicer_mutant_1

value: P0-CreERT2 -/+ Dicer1 flox/flox


title: Uncrushed_2


title: iDgcr8_control_1

value: P0-CreERT2 -/- Dgcr8 flox/flox


title: iDgcr8_mutant_2


title: iDgcr8_control_3


title: iDgcr8_mutant_1


title: iDicer_mutant_2


title: iDgcr8_control_2


title: iDicer_control_1

value: P0-CreERT2 -/- Dicer1 flox/flox


title: Contralat_1


title: iDicer_mutant_3


title: iDicer_control_3


title: P1-Drosha_Mutant_3

extract_protocol:
Illumina TruSeq RNA stranded
Ribosomal Depletion with Ribo Zero
Illumina TruSeq RNA stranded or Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian Total RNA

value: Dhh-Cre +/- Drosha flox/flox

tag: developmental stage

value: post natal day 1


title: P1-Drosha_Control_1

value: Dhh-Cre -/- control


title: iDicer_control_2


title: P1-Drosha_Mutant_1


title: P1-DGCR8KO2

value: Dhh-Cre +/- Dgcr8 flox/flox


title: P1-Drosha_Control_3


title: P1-Drosha_Control_2


title: P1-Drosha_Mutant_2


title: Contralat_2


title: P1-DicerKO2

value: Dhh-Cre +/- Dicer1 flox/flox


title: P1-DGCR8KO1


title: P1-Dicer-ctr2


title: P1-DicerKO1


title: P1-Dicer-ctr1


title: P1-DicerKO3


title: P1-Dicer-ctr3


title: P1-DGCR8KO3


title: JeKo-1

status: Public on Aug 09 2018

last: Albero

address: 1130 St Nicholas Ave

institute: Columbia University

description: Established cell lines from a patient diagnosed with mantle cell lymphoma

data_processing:
Illumina Miseq software used for basecalling.
Reads were aligned using Bowtie, v4.3.4 against the human GRCh37/Hhg19 reference genome.
Expression for each gene we quantified using TopHat v2.0.9 with default parameters and the human GRCh37/Hhg19 as a reference genome.
Gene expression values (quantified as reads per kilobase of transcript per million reads, RPKMs) were calculated using edgeR Bioconductor package.
Genome_build: GRCh37/Hhg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Mantle cell lymphoma cell line

growth_protocol: We used four well-characterized MCL cell lines (Z-138, Granta-519, JeKo-1 and UPN-1 ) and a lymphoblastoid leukemic cell line JVM-13 cell line. All cells were routinely cultured at 37ºC and 5% CO2 in RPMI (Gibco) except GRANTA-519 that was grown in DMEM (Gibco) Media was supplemented with 10% fetal bovine serum, 500 µg/ml of streptomycin and 500 units/mL of penicillin (Gibco). Cells were passed every 2-3 days.

extract_protocol:
Total RNA was isolated using Trizol (Zymo Research), under manufacturer's guidelines.
Preparation of RNA-seq libraries was carried out using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's standard protocol

tag: cell line

tag: passages

tag: disease

value: Mantle cell lymphoma


title: Z-138


title: UPN1


title: JVM13-Cyclin D1

description: Established cell lines from a patient diagnosed with B pro-lymphocytic leukemia

source_name: Lymphoblastic cell line

value: B pro-lymphocytic leukemia

tag: transduction

value: retroviral vector to express a empty vector with the puromycin resistance gene and the cyclin D1 gene with the mutation T286A


title: Granta-519


title: 21_p62ffFSP1cre_187

status: Public on Feb 14 2018

description: p62FSP1KO (p62Ko in the stroma)

data_processing:
FASTq files were processed using RNAseq Alignment module in BaseSpace (Illumina), using default parameters. Reads were aligned to mouse mm10 genome using STAR. Differentially expressed genes were calculated using DeSeq2.
Genome_build: mm10
Supplementary_files_format_and_content: processed data file consist of an excel file matrix with gene symbols and FPKM counts for all samples

source_name: Prostate

extract_protocol:
Prostates were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit. PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Prostate

value: 52 weeks old


title: 17_p62ffFSP1cre_155

description: p62FSP1KO (p62Ko in the stroma)


title: 14_p62ff_134

description: p62f/f (wild type)

value: wild type


title: sgp62NoGln_17

description: Processed data file RNASeq WPMY

data_processing:
FASTq files were processed using RNAseq Alignment module in BaseSpace (Illumina), using default parameters. Reads were aligned to human hg19 genome using STAR. Differentially expressed genes were calculated using DeSeq2.
Genome_build: hg19
Supplementary_files_format_and_content: processed data file consist of an excel file matrix with gene symbols and FPKM counts for all samples

source_name: Human Prostate Fibroblast

growth_protocol: DMEM 10% dyalized FBS,

extract_protocol:
Cells were culture in the specified conditions, and RNA was harvested using Trizol reagent and purified using Omnigen RNA extraction kit. PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No glutamine 24h

value: sgp62 (p62 KO)

tag: treatment conditions

value: DMEM 10% dyalized FBS, No Gln 24h


title: sgp62NoGln_18

description: Processed data file RNASeq WPMY

tag: genotype


title: sgCNoGln_6

description: Processed data file RNASeq WPMY

value: sgC (wild type)


title: sgCNoGln_4

description: Processed data file RNASeq WPMY


title: sgCNoGln_5

description: Processed data file RNASeq WPMY


title: sgp62NoGln_16

description: Processed data file RNASeq WPMY


title: 13_p62ff_135

description: p62f/f (wild type)


title: 15_p62ff_203

description: p62f/f (wild type)


title: 19_p62ffFSP1cre_213

description: p62FSP1KO (p62Ko in the stroma)


title: JVM-13-Empty

value: retroviral vector to express an empty vector with the puromycin resistance gene to be used as a control.


title: Enriched astrocyte mRNA CETP_3

status: Public on Mar 01 2018

city: Montreal

first: Lisa

middle: Marie

last: Munter

state: Quebec

address: 3649 Prom. Sir-William-Osler

department: Pharmacology

country: Canada

institute: McGill University

hyb_protocol: 4 µg of ds cDNA were hybridized for 16hr at 45°C on a Mouse Clariom S array. Chip was washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chip was scanned using the Affymetrix GeneChip® scanner 3000

data_processing: The data were analyzed with  using Affymetrix default analysis settings and global scaling as normalization method. Further analysis was performed using Ingenuity pathways analysis

label: Biotin

source_name: astrocyte, CETP, 1%chol. diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Pico protocol from 10 ng total RNA.

growth_protocol: CETP transgenic animals(B6.CBA-Tg(CETP)5203Tall/J) were fed for 2 months (2-4 month) with a diet containing 1% cholesterol, WT animals were fed a standard diet

extract_protocol: GLAST positive astrocytes were purified from whole mouse brains using magnetic ACSA-2 affinity kit (Miltenyi biotech) according to manufacteurs instructions. Astrocyte purity was determined to be more than 70% using flow cytometry (GFAP). total RNA was extracted using the macherey & nagel RNA isolation kit according to manufacteurs instructions.

value: mouse astrocytes

value: CETP transgenic, #634

tag: diet

value: 1percent cholesterol diet

value: 1% cholesterol enriched


title: Enriched astrocyte mRNA WT_2

source_name: astrocyte, WT, std diet

value: wild type,  #533

value: standard diet

value: standard


title: Enriched astrocyte mRNA CETP_5

source_name: astrocyte, CETP, std diet

value: CETP transgenic, #131


title: Enriched astrocyte mRNA WT_3

value: wild type,  #635


title: Enriched astrocyte mRNA CETP_1

value: CETP transgenic, #531


title: Tc17 WT, technical rep2

status: Public on Nov 27 2017

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were processed using Partek software using RMA Background Correction and  Quantile Normalization

label_protocol: standard Affymetrix protocol

growth_protocol: Naïve CD8+ T cells were sorted and activated with anti-CD3 (1ug/ml) and anti-CD28 (3ug/ml) for 4 days

extract_protocol: Total RNA extraction using MiniRNeasy column (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Activated CD8+ T cells were culture in presence of IL-12 (Tc1) or IL-6 and TGFb (Tc17) for 3 days and culture for an additional day with IL-2

tag: cell type

value: WT


title: Enriched astrocyte mRNA CETP_4

value: CETP transgenic, #751


title: Tc17 WT, biological rep1


title: Enriched astrocyte mRNA CETP_2

value: CETP transgenic, #631


title: Tc17 KO, technical rep2


title: Tc1, biological rep1


title: Tc1 KO, biological rep2


title: Tc17, biological rep2


title: Tc17 WT, biological rep2


title: Tc17 KO, biological rep2


title: Tc1 KO, technical rep2


title: Tc17, biological rep1


title: Tc1 KO, biological rep1


title: Tc1 WT, technical rep2


title: Tc17 KO, biological rep1


title: Tc17, technical rep2


title: Tc1, technical rep2


title: Tc1 WT, biological rep1


title: Tc1, biological rep2


title: Tc1 WT, biological rep2


title: 424007T2Trt Rep 4

status: Public on Jul 21 2017

description: Processed data file: gene_exp.diff

data_processing:
Fast-X Toolkit was used to trim off adapters and remove low-quality reads (PHRED <= 33).
Aligned to soybean reference genome and supplied annotations Gmax_275_Wm82.a2.v1 using TopHat 2.0.13.
Transcript Assembly completed using Cufflinks 2.2.1.
Differential expression tested using cuffdiff 2.2.1 with parameters --max-bundle-frags 500000 -b -u
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: gene_exp.diff: Tab-delimited differential expression file using FPKM values.

organism: Glycine soja

source_name: leaf tissue, second trifoliate, sensitive, 75 ppb ozone

growth_protocol: Plants were germinated in a charcoal-filtered greenhouse and moved to continuously stirred tank reactors (CSTRs) at 2 weeks in Raleigh, NC.

extract_protocol:
Total RNA was isolated using Qiagen Plant RNeasy Mini Kit (Cat No./ID: 74904) with on-column DNase I digest.
Standard Illumina Protocol.

treatment_protocol: Plants were exposed to a 75 ppb ozone treatment for 7 hours alongside a charcoal-filtered control at < 10 ppb ozone.

value: leaf

tag: leaf position

value: Second trifoliate

tag: treatment

value: 75 ppb ozone


title: 507656T3Trt Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, third trifoliate, resistant, 75 ppb ozone

value: Third trifoliate


title: 507656T3CF Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, third trifoliate, resistant, charcoal filtered

value: Charcoal filtered


title: 424007T3Trt Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, third trifoliate, sensitive, 75 ppb ozone


title: 507656T2Trt Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, second trifoliate, resistant, 75 ppb ozone


title: 424007T1Trt Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, first trifoliate, sensitive, 75 ppb ozone

value: First trifoliate


title: Prkci-fl/fl-VilCre-D

status: Public on Aug 23 2017

description: replicate 1

data_processing: The data were normalised using quantile normalisation with IlluminaGenomeStudio and analysed in ArrayTrack. Comparison analysis was performed using Moderated T-test with asymptotic p-value computation with corrected p-value cutoff of 0.05 and fold change cutoff of 1.0.

source_name: Intestinal crypt

growth_protocol: Mice were fed regular diet and housed as established in the IACUC-approved protocol

extract_protocol: Crypt isolation and intestinal epithelial cell (IEC) isolation were performed as described previously (Llado et al., 2015). Isolated crypts or IECs were pelleted and then lysed for RNA extraction. Total RNA from mouse tissues was extracted using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instruction.

treatment_protocol: No special protocol was followed prior to organ harvest.

value: Intestinal crypts

tag: genotype/variation

value: Prkci-fl/fl-VilCre


title: Prkci-fl/fl-C

description: replicate 3

value: Prkci-fl/fl


title: Prkci-fl/fl-VilCre-E

description: replicate 2


title: Prkci-fl/fl-VilCre-F

description: replicate 3


title: Prkci-fl/fl-B

description: replicate 2


title: Prkci-fl/fl-A

description: replicate 1


title: 424007T3CF Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, third trifoliate, sensitive, charcoal filtered


title: 424007T2CF Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, second trifoliate, sensitive, charcoal filtered


title: 507656T1CF Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, first trifoliate, resistant, charcoal filtered


title: 507656T1Trt Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, first trifoliate, resistant, 75 ppb ozone


title: 507656T3Trt Rep 3

description: Processed data file: gene_exp.diff


title: 507656T2Trt Rep 3

description: Processed data file: gene_exp.diff


title: 507656T1Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424007T3Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424007T2Trt Rep 3

description: Processed data file: gene_exp.diff


title: 507656T3CF Rep 3

description: Processed data file: gene_exp.diff


title: 507656T2CF Rep 3

description: Processed data file: gene_exp.diff

source_name: leaf tissue, second trifoliate, resistant, charcoal filtered


title: 424007T3CF Rep 3

description: Processed data file: gene_exp.diff


title: 424007T1Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424007T2CF Rep 3

description: Processed data file: gene_exp.diff


title: 507656T2CF Rep 4

description: Processed data file: gene_exp.diff


title: 407179T2Trt Rep 4

description: Processed data file: gene_exp.diff


title: 407179T1Trt Rep 4

description: Processed data file: gene_exp.diff


title: 407179T3Trt Rep 4

description: Processed data file: gene_exp.diff


title: 424123T3CF Rep 4

description: Processed data file: gene_exp.diff


title: 424123T1Trt Rep 4

description: Processed data file: gene_exp.diff


title: 424007T1CF Rep 4

description: Processed data file: gene_exp.diff

source_name: leaf tissue, first trifoliate, sensitive, charcoal filtered


title: 407179T2CF Rep 4

description: Processed data file: gene_exp.diff


title: 424007T1CF Rep 3

description: Processed data file: gene_exp.diff


title: 424123T3Trt Rep 4

description: Processed data file: gene_exp.diff


title: 407179T3Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424123T2CF Rep 4

description: Processed data file: gene_exp.diff


title: 407179T2Trt Rep 3

description: Processed data file: gene_exp.diff


title: 407179T3CF Rep 4

description: Processed data file: gene_exp.diff


title: 424123T2Trt Rep 3

description: Processed data file: gene_exp.diff


title: 407179T1CF Rep 4

description: Processed data file: gene_exp.diff


title: 507656T1CF Rep 3

description: Processed data file: gene_exp.diff


title: 407179T2CF Rep 3

description: Processed data file: gene_exp.diff


title: 407179T3CF Rep 3

description: Processed data file: gene_exp.diff


title: 424123T3Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424123T1Trt Rep 3

description: Processed data file: gene_exp.diff


title: 407179T1CF Rep 3

description: Processed data file: gene_exp.diff


title: 424123T3CF Rep 3

description: Processed data file: gene_exp.diff


title: 424123T1CF Rep 3

description: Processed data file: gene_exp.diff


title: 424123T2Trt Rep 4

description: Processed data file: gene_exp.diff


title: 424123T2CF Rep 3

description: Processed data file: gene_exp.diff


title: 507656T2Trt Rep 2

description: Processed data file: gene_exp.diff


title: 507656T1Trt Rep 2

description: Processed data file: gene_exp.diff


title: 407179T1Trt Rep 3

description: Processed data file: gene_exp.diff


title: 424007T3Trt Rep 2

description: Processed data file: gene_exp.diff


title: 507656T3CF Rep 2

description: Processed data file: gene_exp.diff


title: 424007T3CF Rep 2

description: Processed data file: gene_exp.diff


title: 507656T2CF Rep 2

description: Processed data file: gene_exp.diff


title: 424007T2Trt Rep 2

description: Processed data file: gene_exp.diff


title: 507656T3Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424007T1CF Rep 2

description: Processed data file: gene_exp.diff


title: 424007T2CF Rep 2

description: Processed data file: gene_exp.diff


title: 424007T2Trt Rep 1

description: Processed data file: gene_exp.diff


title: 507656T2Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424007T3CF Rep 1

description: Processed data file: gene_exp.diff


title: 424007T1Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424007T3Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424007T1CF Rep 1

description: Processed data file: gene_exp.diff


title: 507656T1CF Rep 1

description: Processed data file: gene_exp.diff


title: 507656T3Trt Rep 2

description: Processed data file: gene_exp.diff


title: 507656T1Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424007T2CF Rep 1

description: Processed data file: gene_exp.diff


title: 507656T1CF Rep 2

description: Processed data file: gene_exp.diff


title: 507656T2CF Rep 1

description: Processed data file: gene_exp.diff


title: 424123T1Trt Rep 2

description: Processed data file: gene_exp.diff


title: 507656T3CF Rep 1

description: Processed data file: gene_exp.diff


title: 424123T3Trt Rep 2

description: Processed data file: gene_exp.diff


title: 407179T1CF Rep 2

description: Processed data file: gene_exp.diff


title: 424123T2Trt Rep 2

description: Processed data file: gene_exp.diff


title: 424007T1Trt Rep 2

description: Processed data file: gene_exp.diff


title: 407179T1Trt Rep 1

description: Processed data file: gene_exp.diff


title: 407179T3CF Rep 2

description: Processed data file: gene_exp.diff


title: 424123T1Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424123T3CF Rep 2

description: Processed data file: gene_exp.diff


title: 407179T2CF Rep 2

description: Processed data file: gene_exp.diff


title: 407179T1Trt Rep 2

description: Processed data file: gene_exp.diff


title: 424123T3Trt Rep 1

description: Processed data file: gene_exp.diff


title: 407179T1CF Rep 1

description: Processed data file: gene_exp.diff


title: 424123T2CF Rep 2

description: Processed data file: gene_exp.diff


title: 424123T1CF Rep 1

description: Processed data file: gene_exp.diff


title: 407179T2Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424123T2CF Rep 1

description: Processed data file: gene_exp.diff


title: 424123T2Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424123T3CF Rep 1

description: Processed data file: gene_exp.diff


title: 407179T2CF Rep 1

description: Processed data file: gene_exp.diff


title: 407179T3CF Rep 1

description: Processed data file: gene_exp.diff


title: 407179T2Trt Rep 2

description: Processed data file: gene_exp.diff


title: 407179T3Trt Rep 1

description: Processed data file: gene_exp.diff


title: 424123T1CF Rep 2

description: Processed data file: gene_exp.diff


title: HSC-p62KO-Veh-2

status: Public on Nov 23 2016

data_processing:
Fastq files containing passed-QC reads were uploaded to BaseSpace. Filtering, mapping and abundance measurements (FPKM) were performed with the app RNAexpress (Illumina) within BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include FPKM raw counts from RNAexpress app.

source_name: Mouse Hepatic Stellate Cells

extract_protocol: PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: Mouse Hepatic Stellate Cells

tag: source

value: cell-line

tag: growth protocol

value: DMEM 10% FBS 5mM HEPES

tag: extract protocol

value: Total RNA from cultured cells was isolated using the TRIzol reagent (Life  Techbologies) and the RNeasy Mini Kit (QIAGEN), followed by DNase treatment.


title: HSC-p62KO-Cal-2


title: HSC-p62KO-Veh-1


title: HSC-WT-Cal-1


title: HSC-p62KO-Cal-1


title: 407179T3Trt Rep 2

description: Processed data file: gene_exp.diff


title: TSC1f/f Cre positive-1 Specific deletion of TSC1 in hepatocytes

data_processing:
Fastq files containing passed-QC reads were uploaded to BaseSpace. Filtering, mapping and abundance measurements (FPKM) were performed with the app RNAexpress (Illumina) within BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files include FPKM raw counts from RNAexpress app.

source_name: Liver

growth_protocol: p62F/F and Tsc1 F/F mice (Mori et al., 2009; Muller et al., 2013) were backcrossed to C57BL/6  mice for at least 7 generations, and then bred with Alb-Cre transgenic mice (also on C57BL/6  background) to generate p62F/F; Alb-Cre (p62Δhep) and Tsc1F/F; Alb-Cre (Tsc1Δhep)mice, respectively.  p62Δhep mice were crossed to Tsc1Δhep and MUP-uPA mice to generate p62F/F; Tsc1F/F; Alb-Cre  (Tsc1/p62Δhep) mice and p62Δhep/MUP-uPA transgenic mice, respectively. Genotyping was performed as  described (Muller et al., 2013)

extract_protocol:
Dissected liver sections were removed, flash frozen on dry ice, and RNA was harvested using Trizol RNA extraction.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 or paired-end sequenced on Illumina HiSeq 2000 using the High output V2 kit (Illumina Inc., San Diego CA).

tag: background strain

value: Liver

value: TSC1f/f Cre positive Specific deletion of TSC1 in hepatocytes


title: TSC1f/f / p62f/f mice AlbCre positive - Specific deletion of TSC1 and p62 in hepatocytes 3


title: TSC1f/f Cre positive-3 Specific deletion of TSC1 in hepatocytes


title: TSC1f/f / p62f/f mice AlbCre positive - Specific deletion of TSC1 and p62 in hepatocytes 1


title: TSC1f/f / p62f/f mice AlbCre positive - Specific deletion of TSC1 and p62 in hepatocytes 2


title: TSC1f/f Cre positive-2 Specific deletion of TSC1 in hepatocytes


title: WT TR MEFs in in vitro culture condition-1

status: Public on May 06 2017

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University

description: Gene expression under in vitro culture condition

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539A.

data_processing: The data were analyzed using GeneSpring GX software (Agilent).

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from dish-cultured MEFs and tumors allografted to nu/nu mice using Isogen (Nippon Gene). The total RNA was additionally purified with an RNeasy mini kit (Qiagen).

value: MEF

value: WT

tag: growth condition

value: dish


title: Keap1–/– TR MEFs in allograft condition-1

description: Gene expression under allograft condition

source_name: Keap1–/– TR MEFs in allograft condition

value: tumor


title: WT TR MEFs in allograft condition-1

source_name: WT TR MEFs in allograft condition


title: WT TR MEFs in in vitro culture condition-2


title: p62KO-3

value: tissue

value: DEN injection and High Fat Diet (HFD)

value: Dissected liver sections were removed, flash frozen on dry ice, and RNA was harvested using Trizol RNA extraction.


title: WT TR MEFs in allograft condition-2


title: WT-2


title: p62KO-2


title: p62KO-1


title: HSC-WT-Cal-2


title: HSC-WT-Veh-1


title: Keap1–/– TR MEFs in in vitro culture condition-1


title: WT-3


title: HSC-WT-Veh-2


title: Keap1–/– TR MEFs in in vitro culture condition-2


title: p62f/f mice AlbCre positive - Specific deletion of p62 in hepatocytes 3


title: Keap1–/– TR MEFs in allograft condition-2


title: p62f/f mice AlbCre positive - Specific deletion of p62 in hepatocytes 1


title: p62f/f mice AlbCre positive - Specific deletion of p62 in hepatocytes 2


title: p62f/f mice Cre negative - WT 1

value: p62f/f mice Cre negative - WT


title: WT-1


title: p62f/f mice Cre negative - WT 2


title: RCC162 VHLmut

status: Public on Jun 01 2016

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Aligned to hg19 using tophat v2.0.13 and Gencode V19 transcript models
Expression estimates (FPKM) derived using cufflinks v2.0.2, including Gencode V19 transcript models
Read counts generated using GenomicFeatures package in Bioconductor with UCSC hg19 "knownGene" transcript models
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks gene.fpkm_tracking files

source_name: Renal cell carcinoma

extract_protocol:
RNA was extracted from frozen tumor tissue and cultured cells using the QiagenRNeasy Kit
Illumina TruSeq RNA Sample Preparation Kit v2

value: Cell line

value: VHL mutant

tag: disease state

value: renal cell carcinoma


title: RCC222 VHLmut


title: RCC162 Tumor

value: Tumor


title: RCC407 Tumor


title: RCC222 Tumor


title: RCC162 VHLwt

value: VHL wild type


title: p62f/f mice Cre negative - WT 3


title: RCC022 Tumor


title: RCC323 Tumor


title: RCC323 VHLwt


title: RCC407 VHLwt


title: RCC222 VHLwt


title: RCC323 VHLmut


title: RCC243 VHLwt


title: RCC234 Tumor


title: RCC407 VHLmut


title: RCC022 VHLwt


title: RCC022 VHLmut


title: RCC243 VHLmut


title: N17rrp6Rep3

status: Public on May 23 2016

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

description:
transcriptome analysis
processed data file: N17.CUTs.txt

data_processing:
Using Bowtie v0.12.7 reads were first mapped to a single repeat of the rDNA locus allowing two mismatches to remove rRNA reads.
Remaining reads were mapped uniquely allowing up to two mismatches.
Per nucleotide read coverage was obtained using BEDTools v2.16.2 genomeCoverageBed
Raw coverage values were modified to correct for A bias in first nt of read and normalized by the tens of millions of reads mapped.
Corrected per nucleotide coverage was averaged across replicates.
Genome_build: S288c: Saccharomyces Genome Database assembly version 64 (aka SacCer3); Sigma: reference Genotype to Phenotype: A Complex Problem, Dowell et al. Science 328(5977):469 (2010); JAY291: reference Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production, Argueso et al. Genome Research 19:2258-2270 (2009), also available from Saccharomyces Genome Database; N17: from the Saccharomyces Genome Sequencing project, downloaded from the Sanger Welcome Trust FTP site
Supplementary_files_format_and_content: tab-delimited; CUT annotations and abundance measurements

organism: Saccharomyces paradoxus

source_name: yeast, mid-log phase_N17

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 0.6-0.69

extract_protocol:
Poly(A) RNA was isolated using two rounds of Dyna bead mRNA isolation kit
Strand specific RNA-seq libraries were constructed from 500ng of poly(A) RNA using the Illumina RNA ligation library protocol from Levin et al. Nat. Meth. 2010.  All samples were barcoded using Illumina TruSeq small RNA-seq indexed PCR primers.

tag: strain

value: HO::lox-Kan-lox, rrp6::NatMX

tag: growth phase

value: mid-log phase


title: N17WTRep3


title: N17rrp6Rep4


title: Sigma1278brrp6Rep2

description:
transcriptome analysis
processed data file: Sigma1278b.CUTs.txt

organism: Saccharomyces cerevisiae

source_name: yeast, mid-log phase_Sigma1278b

value: rrp6::KanMX, his3delta1,  leu2delta0, ura3delta0


title: rhombomere1_gata2cko_rep2

status: Public on Nov 01 2016

city: Heidelberg

first: Kaia

last: Achim

address: Meyerhofstr. 1

department: Developmental Biology Unit

institute: EMBL

description: Pool of 6 samples

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A

scan_protocol: Illumina BeadArray Reader, BeadScan software version 3.5

data_processing: The intensity values were extracted with Illumina’s GenomeStudio software v 1.0 . These values were further quantile-normalized.

source_name: embryonic rhombomere 1, gata2cko

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Mouse husbandry was maintained according to the guidelines of the Laboratory Animal Center, University of Helsinki, and in agreement with the  the National Animal Experiment Board in Finland.

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: no treatment

value: ICR (CD-1)

tag: developmental stage


title: rhombomere1_gata2cko_rep1

description: Pool of 6 samples


title: rhombomere1_wildtype_rep3

description: Pool of 6 samples

source_name: embryonic rhombomere 1, wildtype


title: rhombomere1_gata2cko_rep3

description: Pool of 6 samples


title: Sigma1278bWTRep2

value: ura3-52, leu2::hisG, his3::hisG


title: JAY291WTRep1

description:
transcriptome analysis
processed data file: JAY291.CUTs.txt

source_name: yeast, mid-log phase_JAY291

extract_protocol:
Poly(A) RNA was isolated using a single round of Qiagen oligotex mRNA isolation kit.
Strand specific RNA-seq libraries were constructed from 500ng of poly(A) RNA using the Illumina RNA ligation library protocol from Levin et al. Nat. Meth. 2010.  All samples were barcoded using Illumina TruSeq small RNA-seq indexed PCR primers.

value: WT


title: rhombomere1_wildtype_rep2

description: Pool of 6 samples


title: rhombomere1_wildtype_rep1

description: Pool of 6 samples


title: S288crrp6Rep1

description:
transcriptome analysis
processed data file: S288c.CUTs.txt

source_name: yeast, mid-log phase_S288c

value: rrp6::KanMX, his3delta1,  leu2delta0, ura3delta0, met15delta0


title: S288cWTRep2

value: his3delta1, lys2delta0, leu2delta0, ura3delta0


title: Sigma1278bWTRep1


title: JAY291rrp6Rep2


title: JAY291WTRep2


title: S288cWTRep1


title: P4_DicerKO_n1

status: Public on Oct 12 2015

data_processing:
CASAVA pipeline v.1.8 was used for the base-calling of this run.
The ncPRO pipeline was used to map the reads against the mouse genome (version mm9) and the rat genome (version rn4). We used Bowtie with default options (but -m 5000 and -e 50).
The miRNA quantities were normalized by the number of mapped reads from the corresponding library and then multiplied by 1000000 to obtain the unit in reads per million (RPM).
The R software package DESeq R (Version 1.14.0) was used to assess the statistical significance of differences in gene expression.
Genes showing altered expression with adjusted p-value < 0.05 (Benjamini and Hochberg method) were considered as differentially expressed.
Genome_build: mm9 (rn4 for primary SC)
Supplementary_files_format_and_content: Tab delimited read count

source_name: sciatic nerves

extract_protocol:
Sciatic nerves were freed from perineurial fibroblast layer and homogenized with a chilled pestle. Total RNA was subsequently extracted using Qiazol according to manufacturers description.
After RNA quality assessment with a Bioanalyzer 2100 (Agilent), the fraction of 15-35 nt was purified using gel electrophoresis and linked to Illumina TruSeq adapters. For multiplexing, barcodes were introduced during PCR amplification. Sequencing was performed using the Illumina HiSeq 2000 platform with a read length of 50 bp

value: dhhCre+/- Dicerfl/fl

tag: age

value: postnatal day 4


title: N17WTRep4


title: P4_DicerKO_n2


title: P60_n2

value: wild-type

value: postnatal day 60


title: P30_n1

value: postnatal day 30


title: P30_n2


title: P10_n2

value: postnatal day 10


title: P10_n1


title: P4_n2


title: Sigma1278brrp6Rep1


title: P1_n2

value: postnatal day 1


title: S288crrp6Rep2


title: P4_n1


title: P1_n1


title: E17_5_n2

value: embryonal day 17.5


title: P1_Lin28_tg_mut_n2

data_processing:
the obtained raw reads were first cleaned by removing adapter sequences and trimming low quality ends. Sequence alignment of the resulting high-quality reads to the mouse reference genome (build mm10) and quantification of gene level expression was carried out using RSEM (Version 1.2.12).
The R software package from Bioconductor, DESeq2 (Version 1.4.5)33, was used to assess the statistical significance of differences in gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet include RPKM values, log2 fold changes and adjusted p-values

extract_protocol:
Sciatic nerves were freed from perineurial fibroblast layer and homogenized with a chilled pestle. Total RNA was subsequently extracted using Qiazol according to manufacturers description.
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were depleted of ribosomal RNA using Ribo Zero Gold (Epicentre¨) and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit¨ (1.0) Fluorometer and the Caliper GX LabChip¨ GX (Caliper Life Sciences, Inc.). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-HCl 10 mM (pH 8.5) with 0.1% Tween 20. The TruSeq PE Cluster Kit v3-cBot-HS or TruSeq SR Cluster Kit v3-cBot-HS (Illumina, Inc.) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing were performed on the Illumina HiSeq 2000 paired end at 2 X101 bp or single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc.)

value: mixed

value: dhhCre+/- Lin28tg-/-


title: P1_Lin28_tg_mut_n3


title: P1_Lin28_tg_mut_n1


title: P1_Lin28_tg_ctr_n3

value: dhhCre-/- Lin28tg+/-


title: P1_Lin28_tg_ctr_n2


title: P1_Lin28_tg_ctr_n1


title: P1_Dicer_mut_n2

description: Re-accessioned as GSM1581955


title: P1_Dicer_mut_n3

description: Re-accessioned as GSM1581956


title: P1_Dicer_ctr_n3

description: Re-accessioned as GSM1581953

value: dhhCre-/- Dicerfl/wt


title: P1_Dicer_mut_n1

description: Re-accessioned as GSM1581954


title: P1_Dicer_ctr_n2

description: Re-accessioned as GSM1581952


title: primarySC

organism: Rattus norvegicus


title: P1_Dicer_ctr_n1

description: Re-accessioned as GSM1581951


title: E17_5_n1


title: JAY291crrp6Rep1

value: mid-log phase


title: P60_n1


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 4

status: Public on Jul 23 2014

hyb_protocol: Total RNA was extracted from six independent orthotopic tumors from WT and p62 KO mice and hybridized on Affymetrics mouse ST 1.0 microarrays.

scan_protocol: Scanning of the images and the first pass processing of probe-level fluorescence intensities was performed using the Microarray Suite 5.0 software (MAS 5.0; Affymterix, Santa Clara, CA).

data_processing: The data was normalized, and the calculation of the gene-specific summary measures was performed by the robust multi-array average (RMA) procedure (Irizarry et al., 2003) based on the Entrez gene-centric probeset definitions provided by the University of Michigan “brainarray” group (Dai et al., 2005).

source_name: prostate orthotopic tumors_WT C57BL6

label_protocol: Biotin. Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer's instructions

growth_protocol: Murine TRAMP-C2Re3 prostate carcinoma cells (5×10^4) were injected orthotopically into the prostates of WT, p62 KO, and p62/IL-6 DKO mice and harvested after 60 days, as previously described (Olson et al., 2006)

extract_protocol: Total RNA was extracted using Tri-Zol according to the manufacturer's instructions.

tag: strain background

tag: recipient strain genotype

value: wild type

tag: injected with

value: TRAMP-C2Re3 prostate carcinoma cells

tag: tissue harvested

value: TRAMP-C2Re3 prostate orthotopic tumors


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 2


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 5


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 5

source_name: prostate orthotopic tumors_p62 KO C57BL6

value: p62 KO


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 6


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 2


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 4


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 3


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 1


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 3


title: TRAMP-C2Re3 prostate orthotopic tumors in p62 KO C57BL6 mouse 6


title: hiPS-12 c.III p.30 XIST-

status: Public on Dec 03 2013

city: Boston

first: Ruslan

last: Sadreyev

state: MA

address: 185 Cambridge St

institute: Harvard Medical School/ Mass General Hospital

description: Gene expression data from hiPS-12 c.III

hyb_protocol: Biotinylated & fragmented cDNA is added to a hybridization solution containing several control oligos, then hybridized to a human U133 Plus 2.0 microarray chip overnight at 45C.

scan_protocol: Human U133 Plus 2.0 microarray chips were scanned using Affymetrix GCS3000

data_processing: The data were analyzed using R Bioconductor Affy package, with RMA applied as summarization and normalization method.

source_name: hiPS-12 c.III p.30 (HO); XIST-

label_protocol: The purified cDNA (starting with 300ng total RNA) is first fragmented using a chemical & enzymatic process, then the fragmented product is biotin-labeled to the 3'-hydroxyl end of the cDNA (NuGen Ovation V2 protocol).

growth_protocol: All hiPSCs were cultured with MEFs using hESC cell medium (Anguera et al Cell Stem Cell 2012)

extract_protocol: Total RNA was isolated with TriZOL according to their protocol.

treatment_protocol: All hiPSCs were treated & cultured using the same cell medium.

tag: line

value: hiPS-12 c.III

tag: parental cell line

value: IMR-90 fibroblasts

tag: cell type

value: XIST-


title: hiPS-3 p.14 XIST+

description: Gene expression data from hiPS-3

source_name: hiPS-3 p.14 (HO); XIST+

value: XIST+


title: hiPS-11 p.16 XIST+ rep2

description: Gene expression data from hiPS-11 grown at high oxygen

source_name: hiPS-11 p.16 (HO); XIST+


title: TRAMP-C2Re3 prostate orthotopic tumors in WT C57BL6 mouse 1


title: hiPS-12 p.23 XIST+

description: Gene expression data from hiPS-12

source_name: hiPS-12 p.23 (LO); XIST+


title: hiPS-9 c.III p.19 XIST-

description: Gene expression data from hiPS-9 c.III

source_name: hiPS-9 c.III p.19 (HO); XIST-

value: hiPS-9 c.III


title: hiPS-11 p.16 XIST+ rep1

description: Gene expression data from hiPS-11 grown at low oxygen

source_name: hiPS-11 p.16 (LO); XIST+


title: hiPS-1 p.31 XIST+

description: Gene expression data from hiPS-1

source_name: hiPS-1 p.31 (HO); XIST+


title: hiPS-10 p.24 XIST+

description: Gene expression data from hiPS-10

source_name: hiPS-10 p.24 (HO); XIST+


title: hiPS-9 p.7 XIST+

description: Gene expression data from hiPS-9

source_name: hiPS-9 p.7 (HO); XIST+


title: hiPS-2 p.9 XIST+

description: Gene expression data from hiPS-2

source_name: hiPS-2 p.9 (HO); XIST+


title: hiPS-2 c.III p.50 XIST-

description: Gene expression data from hiPS-2 c.III grown at low oxygen

source_name: hiPS-2 c.III p.50 (LO); XIST-

value: hiPS-2 c.III


title: hiPS 12D-1 c.III p.30 XIST-

description: Gene expression data from hiPS 12D-1

source_name: hiPS 12D-1 c.III p.30 (HO); XIST-

tag: source

value: Huntington's Disease patient


title: Erythroid cells from 2 mo old female Xist heterozygous (2lox/-) mutant

status: Public on Feb 20 2013

description:
Gene expression data from Erythroid cells from 2 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

hyb_protocol: Following fragmentation, 5ug of cDNA were hybridized for 16 hrs at 45C on Affymetrix Mouse Gene 1.0ST microarrays. GeneChps were washed and stained in the Affymetric Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000 7G. The data was collected using the Command Console Version 3.2.

data_processing: The data were analyzed using R Bioconductor Affy package, with RMA applied as summarization and normalization method (Irizarry et al., 2003).

source_name: FACS sorted Ter119+ erythroid cells

label_protocol: RNA was labeled using NuGen Ovation Pico WTA v2 System paired with the Encore Biotin Module (NuGEN).

extract_protocol: Total RNA from cells was isolated using Trizol reagent (Invitrogen).

tag: genotype

value: Xist heterozgous (2lox/-) mutant mouse

value: 2 months old

tag: gender

value: female

tag: genetic background

value: 129Sv/Jae x B6.Cg-Tg (Vav1-cre)A2Kio/J

value: Ter119+ erythroid cells


title: Myeloid cells from 12 mo old female Xist homozygous (-/-) mutant

description:
Gene expression data from myeloid cells from 12 months old female Xist homozygous (-/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted CD11b+ myeloid cells

value: Xist homozygous (-/-) mutant mouse

value: 12 months old

value: CD11b+ myeloid cells


title: B cells from 12 mo old female Xist homozygous (-/-) mutant

description:
Gene expression data from B cells from 12 months old female Xist homozygous (-/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted B220+ B-lymphocytes

value: B220+ B-lymphocytes


title: Myeloid cells from 2 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from myeloid cells from 2 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: LSK+CD34- HSCs from 2 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from LSK+CD34- HSCs from 2 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted LKS+CD34- hematopoietic stem cells (HSC)

value: Xist wild-type (2lox/+) mouse


title: LSK+CD34- HSCs from 12 mo old female Xist homozygous (-/-) mutant

description:
Gene expression data from LSK+CD34- HSCs from 12 months old female Xist homozygous (-/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

value: LKS+CD34- hematopoietic stem cells (HSC)


title: Erythroid cells from 12 mo old female Xist homozygous (-/-) mutant

description:
Gene expression data from erythroid cells from 12 months old female Xist homozygous (-/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: Erythroid cells from 2 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from erythroid cells from 2 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: LSK+CD34- HSCs from 6 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from LSK+CD34- HSCs from 6 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

value: 6 months old