title: W4-6_WT_batch_1

description: single cell from heart


title: W4-7_WT_batch_1

status: Public on Sep 12 2018

type: SRA

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

description: single cell from heart

library_source: transcriptomic

data_processing:
Clean reads were mapped to mouse genome (mm10) using Salmon.
TPM (Transcripts Per Kilobase Million) for genes were calculated.
1. We excluded 18 samples with the mapping rates lower than 70%, and we obtained 76 WT single cells and 76 cKO single cells
2. We included GFP and tdTomato sequences in the reference genome for mapping and expression level quantification. Among 76 cKO single cells,  7 low GFP and high tdTomato cells were considered to be WT cells that had not expressed Mesp1-Cre. In 76 WT single cells, 2 low GFP and high tdTomato cells were considered not to be WT cells. These 9 cells with abnormal reporter gene expression were excluded.  Finally we obtained 143 samples for the following data analysis, so we only uploaded gene expression  of 143 samples in the processed file E9.5_Mouse_embryonic_heart_single_cells_143_samples_tpm.txt.   File showing sample filtering: Exclusion_of_27_samples_from_170_total_samples.xlsx
Genome_build: mm10
Supplementary_files_format_and_content: Txt files of gene names and tpm values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: single cell from heart

extract_protocol:
For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette.
Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol.

tag: tissue

value: heart

tag: genotype

value: wild type

tag: strain

tag: age

value: Embryonic day 9.5


title: W4-4_WT_batch_1

description: single cell from heart


title: W5-1_WT_batch_1

description: single cell from heart


title: W5-3_WT_batch_1

description: single cell from heart


title: W4-8_WT_batch_1

description: single cell from heart


title: W5-4_WT_batch_1

description: single cell from heart


title: W5-5_WT_batch_1

description: single cell from heart


title: W5-2_WT_batch_1

description: single cell from heart


title: W5-6_WT_batch_1

description: single cell from heart


title: W6-2_WT_batch_1

description: single cell from heart


title: W6-6_WT_batch_1

description: single cell from heart


title: W6-7_WT_batch_1

description: single cell from heart


title: W6-8_WT_batch_1

description: single cell from heart


title: W7-1_WT_batch_2

description: single cell from heart


title: W5-7_WT_batch_1

description: single cell from heart


title: W5-8_WT_batch_1

description: single cell from heart


title: W7-8_WT_batch_2

description: single cell from heart


title: W7-3_WT_batch_2

description: single cell from heart


title: W8-2_WT_batch_2

description: single cell from heart


title: W7-6_WT_batch_2

description: single cell from heart


title: W8-6_WT_batch_2

description: single cell from heart


title: W8-3_WT_batch_2

description: single cell from heart


title: W8-1_WT_batch_2

description: single cell from heart


title: W8-5_WT_batch_2

description: single cell from heart


title: W4-5_WT_batch_1

description: single cell from heart


title: W8-8_WT_batch_2

description: single cell from heart


title: W9-1_WT_batch_2

description: single cell from heart


title: W9-2_WT_batch_2

description: single cell from heart


title: W8-7_WT_batch_2

description: single cell from heart


title: W9-3_WT_batch_2

description: single cell from heart


title: W9-5_WT_batch_2

description: single cell from heart


title: W9-4_WT_batch_2

description: single cell from heart


title: W9-7_WT_batch_2

description: single cell from heart


title: W9-8_WT_batch_2

description: single cell from heart


title: W7-2_WT_batch_2

description: single cell from heart


title: W7-5_WT_batch_2

description: single cell from heart


title: No_85_pig_1684_BZ

city: Singapore

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine - NTU

description: Old Early BZ

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, adapter sequences are AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to the Sus scrofa 11.1 genome (Ensembl release 91) using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Sus scrofa 11.1 (Ensembl release 91)
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts

molecule: polyA RNA

organism: Sus scrofa

source_name: heart

growth_protocol: Experiments were performed in Yorkshire-landrace swine on days 2 and 14 of age.

extract_protocol:
Cardiac samples (50-80 mg/sample, n= 3 sham and 3 MI animals per condition) from anterior left ventricular wall of sham animals and of infarct zone and border zone of MI animal hearts were collected for RNA studies. Samples were cut into small pieces and immersed in RNAlater solution (Ambion, USA) for 48 hrs at 4°C. Then, tissue samples were homogenized and total RNA was isolated using RNAzol (Sigma-Aldrich, USA) and further purified by Purelink RNA kit (Ambion, USA).
RNA-seq libraries were prepared as previously described (PMID 29160304). Briefly, RNA was quantified using a Qubit RNA High-Sensitivity Assay kit (Life Technologies, USA) and assessed for degradation on the basis of their RNA integrity number using the LabChip GX microfluidics platform and RNA assay reagent kit (Perkin Elmer, USA). TruSeq Stranded mRNA Library Prep kit (Illumina, USA) was used or library preparation and libraries quantified using KAPA library quantification kits (KAPA Biosystems, USA) according to the manufacturer’s protocol. The quality and average fragment size of the final libraries were determined using a LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer, USA). Libraries were sequenced on an Illumina NextSeq sequencer using 76bp Paired End chemistry.

treatment_protocol: Briefly, pigs were anesthetized, intubated, and maintained on a ventilator. A limited left lateral thoracotomy was performed to expose the heart. The branches of the left anterior descending coronary artery and left circumflex coronary arteries were permanently ligated to create an infarction. This consistently gives an infarct size of 15-20% of the left ventricular wall. Then the chest was closed. All animals received analgesia (Ketoprofen: 5 mg/kg/day), and antibiotics (Enrofloxacin: 15mg/kg) after surgery.

tag: individual

tag: breed

value: Yorkshire-landrace

tag: treatment

value: myocardial infarction

value: border zone

tag: rin


title: No_84_pig_1684_IZ

description: Old Early IZ

value: infarct zone


title: No_9_pig_1739_ANTE

description: Young Late Sham

value: SHAM

value: anterior left ventricular wall


title: No_70_pig_1761_IZ

description: Old Late IZ


title: No_74_pig_1631_BZ

description: Old Early BZ


title: No_73_pig_1631_IZ

description: Old Early IZ


title: No_71_pig_1630_IZ

description: Old Early IZ


title: No_72_pig_1630_BZ

description: Old Early BZ


title: No_69_pig_1686_ANTE

description: Old Early Sham


title: No_63_pig_1760_ANTE

description: Old Late Sham


title: No_68_pig_1685_ANTE

description: Old Early Sham


title: No_67_pig_1633_ANTE

description: Old Early Sham


title: No_53_pig_1763_IZ

description: Old Late IZ


title: No_54_pig_1763_BZ

description: Old Late BZ


title: No_52_pig_1762_BZ

description: Old Late BZ


title: No_51_pig_1762_IZ

description: Old Late IZ


title: No_47_pig_1741_IZ

description: Young Late IZ


title: No_48_pig_1741_BZ

description: Young Late BZ


title: No_46_pig_1740_BZ

description: Young Late BZ


title: No_45_pig_1740_IZ

description: Young Late IZ


title: No_44_pig_1734_BZ

description: Young Late BZ


title: No_3_pig_1682_ANTE

description: Young Early Sham


title: No_43_pig_1734_IZ

description: Young Late IZ


title: No_24_pig_1680_BZ

description: Young Early BZ


title: No_62_pig_1759_ANTE

description: Old Late Sham


title: No_22_pig_1623_BZ

description: Young Early BZ


title: No_23_pig_1680_IZ

description: Young Early IZ


title: No_2_pig_1625_ANTE

description: Young Early Sham


title: No_19_pig_1619_IZ

description: Young Early IZ


title: No_20_pig_1619_BZ

description: Young Early BZ


title: No_21_pig_1623_IZ

description: Young Early IZ


title: No_17_pig_1738_ANTE

description: Young Late Sham


title: No_50_pig_1761_BZ

description: Old Late BZ


title: eCLIP.SMI.high_RNase

city: New Haven

first: Yinuo

last: Wang

address: 333 Cedar St C129

department: Molecular Biophysics and Biochemistry

country: USA

institute: Yale University

description: Enhanced PAR-CLIP

data_processing:
For eCLIP, adapters were trimmed using Cutadapt 1.11.
Trimmed reads were mapped using STAR 2.5.1b to a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
PCR duplicates were removed using a custom script (van Nostrand et al., 2016).
CLIPper 0.2.0 with default parameters was used to call peaks on IP samples. The fraction of reads within peaks was normalized to the fraction of reads in corresponding regions of the control samples (SMI and untagged) to identify IP-specific and reproducible clusters.
For high RNase samples, coverage vectors were calculated using fractional assignment of multi-mapping reads.
Mutation analysis of ribosomal RNA-mapping reads was performed as described in Sexton et al., 2017.
For ribosome profiling of recovery samples, FASTX-Toolkit 0.0.14 was used to collapse PCR duplicates.
Adapters and barcodes were trimmed using Cutadapt 1.9.1.
Trimmed reads were mapped using STAR 2.5.3 to a joint reference of GRCh38 (GENCODE release 20) and a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
Uniquely mapped yeast reads were used to determine read 5' ends and raw counts.
Yeast gene RPKMs were scaled using human gene RPKMs, which served as an internal standard in each library.
For ribosome profiling of replete and glucose-starved samples, adapters were trimmed using Cutadapt 1.10.
Trimmed reads were mapped using tophat2 2.0.8b to the Sigma1278b reference downloaded from Saccharomyces Genome Database on June 29, 2014.
Uniquely mapped reads were used to determine read 5′ ends and raw counts.Raw counts were transformed into RPKMs.
Genome_build: GRCh38, Sigma1278b MIT_2009_ACVY01000000, Sigma1278b from SGD on 6/29/2014.
Supplementary_files_format_and_content: fasta: Genome sequence of masked Sigma1278b MIT_2009_ACVY01000000 reference.   GFF3: Annotations of masked Sigma1278b MIT_2009_ACVY01000000 reference.   bed: eCLIP peaks called on IP samples using CLIPper 0.2.0. bedGraph: Read coverage (eCLIP) or read 5' ends (recovery ribosome profiling), no scaling to library size.   wig: Read 5′ ends per million reads (replete and glucose-starved ribosome profiling).  tab-delimited text: Yeast gene raw counts (all ribosome profiling); RPKMs (replete and glucose-starved ribosome profiling); and RPKMs rescaled to internal standard (recovery ribosome profiling).

organism: Saccharomyces cerevisiae

source_name: Budding yeast cells

growth_protocol: Cells were grown in synthetic complete medium with 120 μM uracil to OD600 1.0. 4-thiouracil was added to each culture to a final concentration of 500 μM. Cultures were grown with shaking at 30°C for an additional 3 hours.

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail III, 0.44U/mL murine RNase inhibitor). Extracts were clarified at 10,000 x g for 5 minutes.
Lysate was digested with 1:2,000,000 RNase I and immunoprecipitated with anti-c-Myc-conjugated beads. A 3′ adapter was ligated and the RNPs separated on a denaturing gel. 35-130 kDa species were size-selected and treated with proteinase K. RNAs were reverse transcribed. A second adapter was ligated to the 3′ end of first-strand cDNA. cDNAs were then amplified by PCR.

treatment_protocol: For UV crosslinking, cultures were poured over ice and pelleted, then resuspended in cold water and transferred to a Petri dish situated on ice. Resuspended cells were crosslinked in a Stratalinker at 365 nm, approximately 5 cm from the UV bulb, for a total of 7.2 J/cm2 (680 s). UV-treated culture was pelleted.

tag: background

value: Sigma1278b Strain F1950

value: MATa ura3 his3 leu2 trp1 lso2{delta}::LSO2-9XHis-2XPrescission-9XMyc-HIS3

tag: antibody

tag: fraction

value: Crosslinked input RNA


title: eCLIP.untagged_1.low_RNase

description: Enhanced PAR-CLIP

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail III, 0.44U/mL murine RNase inhibitor). Extracts were clarified at 10,000 x g for 5 minutes.
Lysate was digested with 1:20,000,000 RNase I and immunoprecipitated with anti-c-Myc-conjugated beads. A 3′ adapter was ligated and the RNPs separated on a denaturing gel. 55-130 kDa species were size-selected and treated with proteinase K. RNAs were reverse transcribed. A second adapter was ligated to the 3′ end of first-strand cDNA. cDNAs were then amplified by PCR.

value: MATa ura3 his3 leu2 trp1

value: anti-c-Myc

value: Crosslinked pulldown RNA


title: eCLIP.untagged.high_RNase

description: Enhanced PAR-CLIP

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail III, 0.44U/mL murine RNase inhibitor). Extracts were clarified at 10,000 x g for 5 minutes.
Lysate was digested with 1:2,000,000 RNase I and immunoprecipitated with anti-c-Myc-conjugated beads. A 3′ adapter was ligated and the RNPs separated on a denaturing gel. 55-130 kDa species were size-selected and treated with proteinase K. RNAs were reverse transcribed. A second adapter was ligated to the 3′ end of first-strand cDNA. cDNAs were then amplified by PCR.


title: eCLIP.CCDC124_IP.high_RNase

description: Enhanced PAR-CLIP

value: MATa ura3 his3 leu2 trp1 lso2{delta}::CCDC124-9XHis-2XPrescission-9XMyc-HIS3


title: No_61_pig_1758_ANTE

description: Old Late Sham


title: eCLIP.untagged_2.low_RNase

description: Enhanced PAR-CLIP


title: eCLIP.Lso2_IP1.high_RNase

description: Enhanced PAR-CLIP

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail III, 0.44U/mL murine RNase inhibitor). Extracts were clarified at 10,000 x g for 5 minutes.
Lysate was digested with 1:2,000,000 RNase I and immunoprecipitated with anti-c-Myc-conjugated beads. A 3′ adapter was ligated and the RNPs separated on a denaturing gel. 35-100 kDa species were size-selected and treated with proteinase K. RNAs were reverse transcribed. A second adapter was ligated to the 3′ end of first-strand cDNA. cDNAs were then amplified by PCR.


title: eCLIP.SMI_2.low_RNase

description: Enhanced PAR-CLIP


title: W6-5_WT_batch_1

description: single cell from heart


title: eCLIP.SMI_1.low_RNase

description: Enhanced PAR-CLIP


title: eCLIP.Lso2_IP1.low_RNase

description: Enhanced PAR-CLIP


title: eCLIP.Lso2_IP2.low_RNase

description: Enhanced PAR-CLIP


title: KO4

city: Dallas

first: Sam

state: TX

address: 5323 Harry Hines Blvd.

department: Surgery

institute: UT Southwestern Medical Center

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and duplicates were removed by SAMtools.
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against GENCODE V20 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package edgeR (v 3.12.1) with FDR <0.05.
The mouse genes were converted into human homologues before Gene Set Enrichment Analysis (GSEA) and GSEA was performed using logCPM expression values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for all samples

extract_protocol:
Total RNA was extracted from bulk pancreas using TRIzol (Invitrogen)  and Qiagen Allprep columns according to the venders’ protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Mouse pancreata

tag: background strain

value: mixed

value: 6-8 weeks old

value: Arid1a knocked out in pancreas

value: pancreas


title: KO2


title: KO1


title: KO3


title: eCLIP.Lso2_IP2.high_RNase

description: Enhanced PAR-CLIP


title: WT3

value: Wild type Arid1a in pancreas


title: No_10_pig_1624_ANTE

description: Young Early Sham

value: Yorkshire-landrace

value: heart


title: LacZ control probe set ChIRP rep 3

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BOWTIE software (V2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: HCC cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: hepatocellular carcinoma (HCC)

tag: chirp probe set

value: LacZ control probe set (Millipore, Massachusetts, USA)


title: LacZ control probe set ChIRP rep 2


title: WT2


title: WT1


title: LacZ control probe set ChIRP rep 1


title: SNHG10 complete probe set ChIRP rep 2

value: SNHG10 complete probe set (RiboBio Biotechnology, Guangzhou, China)


title: SNHG10 complete probe set ChIRP rep 3


title: SNHG10 complete probe set ChIRP rep 1


title: MM89_E3.5_Mettl16_HET

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
Mettl16_salmon_table_E3.5.csv.gz
Mettl16_featureCounts_table_E3.5.csv.gz

data_processing:
The genotype of the mouse embryos giving rise to the individual samples was assessed based on the presence of the reads derived from WT Mettl16 allele (containing CACCAGGATTCGGACAAAACTA or TAGTTTTGTCCGAATCCTGGTG sequence) and from Mettl16 KO allele (containing TCACCAATGTAAATAGATGAGG or CCTCATCTATTTACATTGGTGA sequence). The paired-end reads were sorted into individual libraries based on the barcodes and aligned to NCBI RefSeq transcripts (build mm10) using Salmon v0.7.2 (Patro et al., 2017). The transcript estimates were imported into DESeq2 1.18.1  (Love et al., 2014) and summarized to gene levels using tximport 1.2.0 (Soneson et al., 2015). The DESeq2 was used to obtain lists of differentially expressed genes with statistical significance (adjusted p-value <=0.1). To compare the expression from individual exons and introns, the sequenced reads were aligned to reference mm10 genome using STAR (Dobin et al., 2013) and featureCounts (Liao et al., 2014) was used to obtain the read counts. DESeq2 was applied to search for differences in between genotypes.
For in vitro methylation experiments, the reads were sorted into individual libraries based on the barcodes and the 3′ adaptor sequences were removed using cutadapt 1.9.1 (https://doi.org/10.14806/ej.17.1.200). Only reads of final length of 30 nucleotides with correctly sequenced TACAGAGAA consensus motif at position 12-20 and without any Ns were kept for further analysis using R 3.4.3 (R Core Team, 2017) and Bioconductor (Huber et al., 2015).  For each sequence we obtained the minimum free energy (MFE) secondary structure using RNAfold (Lorenz et al., 2011). We used DESeq2 1.18.1 bioconductor package (Love et al., 2014) to obtain the lists of structures significantly enriched or depleted in m6A-IP libraries when compared to input libraries (adjusted p value < 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: The file for in vitro methylation experiment contains the DESeq2 calculated log2fold changes between m6A IP and input samples for individual RNA structures represented in dot-bracket notation.  The files for mouse testicular samples contain the gene level comparisons obtained by Salmon followed by DESeq2 and comparisons of individual exons/introns obtained by STAR alignment followed by featureCounts and DESeq2 analysis.

source_name: E3.5 mouse embryo

growth_protocol: We targeted the endogenous Mettl16 locus in mouse embryos of the B6D2F1/J hybrid line (also called B6D2; The Jackson Laboratory, stock no. 100006). It is a cross between C57BL/6J (B6) and DBA/2J (D2), and heterozygous for all B6 and D2 alleles. Single-cell mouse embryos were injected with a guide RNA (gRNA) that directs the DNA endonuclease Cas9, and a 170 nt single-stranded DNA (ssDNA) repair template (IDT). The ssDNA carries a triple-stop codon flanked by a 81 nt 5ʹ homology arm and a 75 nt 3ʹ homology arm.  Founder mice were identified by genotyping and crossed with wildtype C57BL/6JRj (Janvier) partners to obtain germline transmission. We obtained two lines: line #2112 where the homology recombination template was inserted, resulting in insertion of a triple-stop codon cassette (sequence: ATGTAAATAGATGA) into exon 3, and line #2175 where a 7 bp deletion led to removal of a splicing donor site in intron 4. It is expected that creation of premature termination codons in both lines should result in removal of the transcripts via nonsense-mediated decay (NMD). Both the generated Mettl16 -/- (KO) lines showed the embryonic lethality phenotype. We used the line #2112 (with the triple-stop codon cassette) for sequence analysis of early embryos.

extract_protocol:
For single-embryo transcriptome sequencing, the isolated E2.5 and E3.5 embryos were visually examined for viability and cell number, and transferred separately into single tubes of 0.2 ml thin-walled 8-tube PCR strips (Thermo, AB-0451). The tubes contained 2 μl of the following mix: 0.4% Triton-X100 (vol/vol) in H2O + 2U/μl SUPERase• In™ RNase Inhibitor (20 U/μL; Thermo, AM2694). Embryos were stored at -80°C prior to processing for Smart-seq2 library preparation.   For in vitro methylation with METTL16 the libraries of randomized 30 nt RNA sequences were chemically synthesized. The sequences had a constant central 9-mer sequence flanked by randomized (represented by N) sequences (MM-RNA-14: N11-UACAGAGAA-N10). In vitro methylation with METTL16 protein was followed by m6A immunoprecipitation using rabbit polyclonal antibody (5 µg; Synaptic Systems, catalog no. 202003).
Polyadenylated transcripts from single embryos (E2.5 or E3.5) were amplified using the Smart-seq2 protocol. The protocol generates libraries that lack strand specificity. Multiple libraries with different barcodes were mixed in equimolar ratios and paired-end sequencing reads were obtained with the NextSeq 500 (EMBL GeneCore facility, Heidelberg). The maximum sequencing length was 80 nt.   Sequencing libraries  for in vitro methylation experiments were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina HiSeq 2000 platform (EMBL Heidelberg Gene core facility).

value: HET


title: MM91_E3.5_Mettl16_WT

value: WT


title: MM92_E3.5_Mettl16_HET


title: MM90_E3.5_Mettl16_HET


title: MM82_E3.5_Mettl16_WT


title: MM87_E3.5_Mettl16_KO

value: KO


title: 293 DMSO Pol II

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt v. 1.9.1 with the following parameters: --minimum-length 10 -e 0.05 --times 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 15,10
Alignment was done with Bowtie2 v. 2.2.5 to hg19.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard
BigWig files were generated with deepTools2 v.2.2.4 with bamCoverage tool and the following parameters: -bs 10 --normalizeTo1x 2451960000 -e -p max
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

molecule: genomic DNA

source_name: ChIP-seq

growth_protocol: 293 cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

tag: agent

value: DMSO

tag: chip antibody

value: sc-899X, RNA polymerase II (N-20) X (Santa Cruz Biotechnology)


title: 293 CFIm25 DMSO KO Input

value: 293 CFIm25 KO


title: 293 DRB Pol II

value: DRBI


title: MM81_E3.5_Mettl16_WT


title: WT4

value: Mouse pancreata

value: mixed

tag: tissue


title: MM84_E3.5_Mettl16_WT

tag: genotype


title: 293 CFIm25 DRB KO Input

value: DRB


title: 293 DRB Input


title: 293 CFIm25 DRB KO Pol II


title: 293 DMSO Input


title: MM79_E3.5_Mettl16_KO


title: MM78_E3.5_Mettl16_KO


title: ESPC2 -DOX

city: Cincinnati

first: Sonya

middle: J

last: Ruiz-Torres

state: Ohio

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

data_processing:
Quantification of mRNA expression level was determined based on the ToppHat/Cufflinks pipeline. Reads were aligned to the human hg19/GRCh37 reference genome using ToppHat. The BAM files containing the aligned reads were used to quantify mRNA expression level using Cufflinks with the UCSC known gene reference annotation. RNA expression values were normalized by the fragments per kilobase per megabase calculation (FPKM).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Text files include FPKM values for each sample

source_name: Epidermal stem and progenitor cells

growth_protocol: FA-PSCs were transferred into matrigel-coated plates at low-density and cultured in mTeSR1 supplemented with 100 ng/mL DOX for 1 day. To initiate differentiation (day 0), cells were cultured for 4 days in defined keratinocyte serum-free media (DKSFM, Invitrogen) supplemented with 1% penicillin/streptomycin, 1 μM retinoic acid (RA, Sigma), 25 ng/mL bone morphogenic protein 4 (BMP4, Stemgent), and 100 ng/mL DOX. On day 4, cells were washed with phosphate buffered saline (PBS) and the medium was changed to CnT-07 (CELLnTEC) supplemented with 1% penicillin/streptomycin in the presence or absence of 100 ng/mL DOX. On day 10, CnT-07 medium was also supplemented with 10 μM Y-27632 (Enzo Life Sciences). After 20 days, the cells were transferred to collagen IV-coated plates (Sigma-Aldrich) for expansion in CnT-07 media supplemented with 10 μM Y-27632 in the presence or absence of 100 ng/mL DOX. Media was removed and replaced at 2-day intervals.

extract_protocol:
Total RNA was extracted from FA PSC-derived ESPCs +/-DOX in culture using the Pure RNA Isolation kit (Roche) according to manufacturer protocol. Isolated RNA were quantified (Qubit RNA assay kit) and quality controlled for degradation. RNA sequencing was conducted by the CCHMC DNA sequencing and Genotyping Core. RNA-seq libraries were prepared with the Illumina TruSeq RNA preparation kit.
RNA-seq libraries were prepared with the Illumina TruSeq RNA preparation kit. The libraries were sequenced on an Illumina Hi-Seq 2500 sequencer to obtain 20 million of 75 bp paired-end stranded reads per sample.

treatment_protocol: Cells were washed 3 times with PBS, scrapped in PBS, and collected in tubes.

value: Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)

tag: passage


title: ESPC2 +DOX


title: MM76_E3.5_Mettl16_WT

tag: age


title: MM88_E3.5_Mettl16_WT


title: 293 CFIm25 DMSO KO Pol II


title: MM74_E3.5_Mettl16_WT


title: ESPC1 -DOX


title: MM73_E3.5_Mettl16_WT


title: MM72_E3.5_Mettl16_WT


title: MM70_E3.5_Mettl16_KO


title: Control-5

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

description:
3351-ACP-0022
processed data file: Normalized_Expression_Values.xlsx

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.1. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered based on read quality, alignment quality followed by removing duplicates. Transcript abundance was quantified using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±1.5.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z test using Benjamini Hochberg corrections of 0.05 for false-discovery rate.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized_Expression_Values.xlsx: Excel file with Normalized expression values for each sample.

source_name: cadaveric pancreatic islet tissue

extract_protocol:
RNA was isolated from FACS-sorted β-cells using the RNAqueous®-Micro Total RNA Isolation Kit (Ambion AM1931). Residual genomic DNA was removed with the DNA-free™ system (provided with kit AM1931).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pancreatic beta-cells

tag: donor age

tag: donor sex

value: Male

tag: disease status

value: Non-diabetic


title: Control-4

description:
3351-ACP-0038
processed data file: Normalized_Expression_Values.xlsx


title: Control-2

description:
3351-ACP-0029
processed data file: Normalized_Expression_Values.xlsx

value: Female


title: MM66_E3.5_Mettl16_KO


title: MM67_E3.5_Mettl16_HET


title: MM68_E3.5_Mettl16_WT


title: Control-3

description:
3351-ACP-0016
processed data file: Normalized_Expression_Values.xlsx


title: MM65_E3.5_Mettl16_HET


title: Control-1

description:
3351-ACP-0019
processed data file: Normalized_Expression_Values.xlsx


title: MM71_E3.5_Mettl16_HET


title: Th17-IL-10+ Day 5 2h c-MAF KD shRNA2 RNA-seq Repl_1

city: Bellinzona

first: Samuele

last: Notarbartolo

address: Via Vela 6

institute: Institute for Research in Biomedicine

data_processing:
RNA-seq reads were quality checked and processed with Tuxedo RNA-Seq pipeline (Trapnell, C. et al. 2012) to align reads to human genome assembly GRCh37 and quantify transcripts.
Genome_build: Homo sapiens (GRCh37/hg19)

source_name: primary Th17 lymphocytes

growth_protocol: T cells were cultured in RPMI-1640 medium supplemented with 1% (v/v) glutaMAX™-I, 1% (v/v) non-essential amino acids, 1 mM sodium pyruvate, 50 μM bmercaptoethanol, penicillin (50 U/ml), streptomycin (50 μg/ml), 1% (v/v) kanamycin (all from  Gibco, Life Technologies) and 5% (v/v) human serum (Swiss Blood Center Basel) (hereafter referred as complete medium). 500 U/ml IL-2 (produced in house from IL-2T6 culture supernatants) was added to the culture medium for long term cultures. Single T cell clones were isolated by limiting dilution in 384-well plates (0.65 cells/well) and expanded with allogeneic  irradiated (45 Gy) feeders (2.5 x 104/well) and phytohemagglutinin (PHA, 1 μg/ml; Remel) in IL-2- (500 U/ml) containing complete medium.

extract_protocol:
Total RNA was extracted from at least 106 cells using the E.Z.N.A.® Total RNA Kit I (Omega Bio-tek), including on-column DNAse treatment, according to manufacturer’s instructions.
250 ng for each sample of total RNA isolated from T cell clone pools with the E.Z.N.A.® Total RNA kit I (Omega Bio-tek) was submitted for high coverage (50 million paired-end reads), Tru-Seq standard, strand-specific RNA-sequencing.

treatment_protocol: Resting Th17 cells were left untreated or stimulated with plate-bound antibodies to CD3 (156 ng/cm2, clone: TR66) and CD28 (156 ng/cm2 clone: CD28.2, BD Biosciences) for 2 hours. Recently-activated cells were stimulated in CD3 and CD28 antibody-coated plates for 48 hours, and left in culture in uncoated plates for additional 3 days. On Day 5 they were left untreated or re-stimulated for 2 hours with plate-bound CD3 and CD28 antibodies.

value: primary Th17 lymphocytes

value: Pool of expanded Th17 clones

tag: activation state

value: recently-activated

tag: shRNA

value: c-MAF KD shRNA2


title: Th17-IL-10+ Day 5 2h c-MAF KD shRNA1 RNA-seq Repl_2

value: c-MAF KD shRNA1


title: Th17-IL-10+ Day 5 2h c-MAF KD shRNA1 RNA-seq Repl_1


title: MM64_E3.5_Mettl16_WT

value: WT


title: MM63_E3.5_Mettl16_WT


title: Th17-IL-10+ Day 5 2h c-MAF wt shLuc RNA-seq Repl_2

value: c-MAF wt shLuc


title: Th17-IL-10+ Day 5 2h c-MAF wt shLuc RNA-seq Repl_1


title: MM61_E3.5_Mettl16_KO

value: KO


title: Th17-IL-10- Day 5 ut RNA-seq Repl_2


title: MM59_E3.5_Mettl16_WT


title: ESPC1 +DOX


title: MM60_E3.5_Mettl16_KO


title: Th17-IL-10- Day 5 2h RNA-seq Repl_2


title: Th17-IL-10- Day 0 2h RNA-seq Repl_2

value: resting


title: MM56_E3.5_Mettl16_HET

value: HET


title: Th17-IL-10- Day 0 ut RNA-seq Repl_2


title: Th17-IL-10+ Day 5 ut RNA-seq Repl_2


title: Th17-IL-10+ Day 5 2h RNA-seq Repl_2


title: Th17-IL-10+ Day 0 2h RNA-seq Repl_2


title: MM53_E3.5_Mettl16_WT


title: MM54_E3.5_Mettl16_WT


title: Th17-IL-10- Day 0 2h RNA-seq Repl_1


title: Th17-IL-10+ Day 0 ut RNA-seq Repl_2


title: Th17-IL-10- Day 5 2h RNA-seq Repl_1


title: MM49_E3.5_Mettl16_KO


title: MM48_E3.5_Mettl16_KO


title: Th17-IL-10- Day 0 ut RNA-seq Repl_1


title: Th17-IL-10+ Day 5 2h RNA-seq Repl_1


title: MM47_E3.5_Mettl16_WT


title: Th17-IL-10+ Day 5 ut RNA-seq Repl_1


title: Th17-IL-10+ Day 0 ut RNA-seq Repl_1


title: MM46_E3.5_Mettl16_WT


title: Th17-IL-10+ Day 0 2h RNA-seq Repl_1


title: MM57_E3.5_Mettl16_WT


title: MM44_E2.5_Mettl16_HET

description:
Mettl16_salmon_table_E2.5.csv.gz
Mettl16_featureCounts_table_E2.5.csv.gz

source_name: E2.5 mouse embryo


title: MM45_E2.5_Mettl16_WT


title: MM55_E3.5_Mettl16_KO


title: MM43_E2.5_Mettl16_HET


title: Th17-IL-10- Day 5 H3K27ac ChIP Repl_2

data_processing:
Data processing was run on the Fish the ChIPs automated pipline (Barozzi, I., Termanini, A., Minucci, S. & Natoli, G. Fish the ChIPs: a pipeline for  automated genomic annotation of ChIP-Seq data. Biol Direct 6, 51 2011).
Alignment: Bowtie
Peak calling: MACS 1.4
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: Processed data included in the submission are: Excel files (.merge.xlsx) containing peaks genomic coordinates, MACS p-value, FDR and fold enrichmnt; tiled data files (.tdf) files for ChIP-seq data graphical visualization in the Integrative Genome Viewer software

growth_protocol: T cells were cultured in RPMI-1640 medium supplemented with 1% (v/v) glutaMAX™-I, 1% (v/v) non-essential amino acids, 1 mM sodium pyruvate, 50 μM bmercaptoethanol, penicillin (50 U/ml), streptomycin (50 μg/ml), 1% (v/v) kanamycin (all from  Gibco, Life Technologies) and 5% (v/v) human serum (Swiss Blood Center Basel) (hereafter referred as complete medium). 500 U/ml IL-2 (produced in house from IL-2T6 culture supernatants) was added to the culture medium for long term cultures. Single T cell clones were isolated by limiting dilution in 384-well plates (0.65 cells/well) and expanded with allogeneic  irradiated (45 Gy) feeders (2.5 x 10^4/well) and phytohemagglutinin (PHA, 1 μg/ml; Remel) in IL-2- (500 U/ml) containing complete medium.

extract_protocol:
ChIP was performed as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013). Briefly, 20-50 x 106 cells were fixed in 1% formaldehyde (Sigma-Aldrich) for exactly 10 min at RT under rotation. Crosslinking reaction was quenched by the addition of 125 mM Tris-HCl pH 7.6 for 5 min at  RT. Cells were washed 3 times with ice-cold PBS. The cell pellet was then resuspended in RIPA buffer (without Triton X-100) supplemented with protease inhibitors (Halt™ Protease Inhibitor Cocktail, Thermo Scientific) and frozen at -80°C. Chromatin was sheared with a Bioruptor® Plus bath sonicator (Diagenode) applying the following settings: 5 x 10 cycles 30 sec ON and 60 sec OFF, high intensity, at 4°C. Every 10 cycles samples were mixed and briefly spun down. The shearing of DNA into 200-300 bp fragments was evaluated by electrophoresis on a 1.5% agarose gel. Prior to IP, 1% Triton X-100 was added to the sample and an aliquot was stored at -20°C as input control. Antibody-bound Protein G dynabeads™ (Life Technologies) were added to each sample (10 μg c-MAF antibody per sample) and immunoprecipitation was performed overnight at 4°C on a rotating wheel. The day after, dynabeads were thoroughly washed: 6 times with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), then twice with RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), twice with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-Deoxycholate), and once with TE buffer. ChIP DNA was eluted with direct elution buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS) and subjected to RNAse A and proteinase K treatment before overnight de-crosslinking at 65°C. Finally, de-crosslinked DNA was purified with SPRI magnetic beads and eluted in 10 mM Tris-Cl pH 8.0. ChIP DNA was quantified by picogreen on a Qubit 2.0 device.
ChIP-seq libraries were prepared as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013).

treatment_protocol: Resting Th17 cells were stimulated with plate-bound antibodies to CD3 (156 ng/cm2, clone: TR66) and CD28 (156 ng/cm2 clone: CD28.2, BD Biosciences). Recently-activated cells were stimulated in CD3 and CD28 antibody-coated plates for 48 hours, and left in culture in uncoated plates for additional 3 days. On Day 5 they were re-stimulated for 2 hours with plate-bound CD3 and CD28 antibodies.

value: Rabbit polyclonal to histone H3 (acetyl K27); ChIP Grade antibody - Abcam, Cat# ab4729, Lot# GR312658-1.


title: MM42_E2.5_Mettl16_WT


title: MM41_E2.5_Mettl16_KO


title: MM51_E3.5_Mettl16_HET


title: MM52_E3.5_Mettl16_KO


title: MM50_E3.5_Mettl16_KO


title: Th17-IL-10+ Day 0 H3K27ac ChIP Repl_2


title: Th17-IL-10- Day 0 H3K27ac ChIP Repl_2


title: Th17-IL-10+ Day 5 H3K27ac ChIP Repl_2


title: MM40_E2.5_Mettl16_KO


title: Th17-IL-10- Day 5 H3K27ac ChIP Repl_1


title: Th17-IL-10- Day 5 ut RNA-seq Repl_1


title: MM39_E2.5_Mettl16_HET


title: MM38_E2.5_Mettl16_KO


title: Th17-IL-10+ Day 5 H3K27ac ChIP Repl_1


title: Th17-IL-10- Day 0 H3K27ac ChIP Repl_1


title: MM37_E2.5_Mettl16_HET


title: MM35_E2.5_Mettl16_KO


title: MM34_E2.5_Mettl16_KO


title: MM32_E2.5_Mettl16_WT


title: MM33_E2.5_Mettl16_HET


title: MM29_E2.5_Mettl16_KO


title: MM31_E2.5_Mettl16_HET


title: MM28_E2.5_Mettl16_HET


title: Th17-IL-10+ Day 0 H3K27ac ChIP Repl_1


title: MM27_E2.5_Mettl16_WT


title: MM25_E2.5_Mettl16_WT


title: MM24_E2.5_Mettl16_KO


title: MM36_E2.5_Mettl16_KO


title: MM26_E2.5_Mettl16_HET


title: MM23_E2.5_Mettl16_KO


title: MM22_E2.5_Mettl16_HET


title: MM20_E2.5_Mettl16_KO


title: MM21_E2.5_Mettl16_HET


title: MM17_E2.5_Mettl16_KO


title: MM18_E2.5_Mettl16_HET


title: MM62_E3.5_Mettl16_HET


title: CPC10

city: San Diego

first: Taeyong

last: Kim

state: California

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

data_processing:
The raw data was processed with the STAR aligner (version 2.5.2b). Reads were aligned to the Mus musculus genome.
Sequenced reads were aligned to the mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab separated values of expression matrix; rows are genes; columns are cells

source_name: c-Kit+ cardiac progenitor cells

extract_protocol:
Adult c-Kit+ CPCs were isolated and expanded as previously described. Twelve-week-old FVB female mice were heparinized and anesthetized by ketamine-xylazine solution. Hearts were removed from the chest cavity and perfused on a Langendorff system at 1mL/min flow rate at 37ºC with perfusion buffer (NaCl, KCl, KH2PO4, Na2HPO4, MgSO4•7H2O, NaHCO3, KHCO3 HEPES, Taurine, Glucose, and BDM) for blood removal, and tissue was subsequently digested for 10-15 minutes with Liberase DH digestion buffer (Roche 05401089001, 5 mg/mL in perfusion buffer). Heart was collected in STOP buffer (10% Bovine calf serum, 12.5 µM CaCl2), minced into 1 mm3 and dissociated through pipetting. The non-myocyte population was separated through serial cell straining (100µm, 40µm, and 30µm pore size), followed by centrifugation at ~300 rfc for 10 minutes. Lin-cKit+ CPCs were obtained by immunomagnetic sorting with Lineage depletion kit and CD117-conjugated Microbeads (Miltenyi Biotech 130-048-102). Isolated CPCs were cultured in growth medium ((Dulbecco's modified Eagle's medium, 10% embryonic stem cells FBS, 1% insulin-transferrin-selenium, leukemia inhibitory factor [10 ng/ml], basic fibroblast growth factor [10 ng/ml], epidermal growth factor [20 ng/ml], L-glutamine [0.07mg/mL], 1% penicillin-streptomycin-glutamine, 0.1% gentamicin, 2% B27 supplement, 1% N2 supplement). Cells were plated on a pre-coated (0.1% porcine gelatin) cell culture-grade dish. Adherent cultures were expanded and passaged five times when 40% confluency was reached and used for single-cell RNA-seq.
Transcriptome of 12 single cells were processed by Clontech Smart-Seq v4 kit and Illummina Nextera XT kit according to the manufacturers instructions.

value: c-Kit+ cardiac progenitor cells

tag: environment

value: cultured


title: CPC11


title: CPC9


title: CPC8


title: CPC7


title: MM14_E2.5_Mettl16_HET


title: CPC6


title: TAZN3

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

description: TAZKo cells in normoxia

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
Reads were counted using FeaturesCount.
Genome_build: mm10
Supplementary_files_format_and_content: Count files.

source_name: Embryonic fibroblasts

growth_protocol: Cell were cultured in DMEM, supplemented with 10% [v/v] fetal bovine serum (FBS) (GIBCO, Invitrogen) at 37°C under a 5% CO2 humidified atmosphere

extract_protocol:
RNA was isolated using Trizol (Thermo Scientific) with vendors protocol and further purified with RNA clean and concentrator (ZymoResearch).
Libraries were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

treatment_protocol: Cells were subjected to 24 hours of hypoxia using in vivo hypoxia workstation (manufacturer: Baker Ruskinn, UK)

value: MEFs

tag: strain

tag: genotype/variation

value: TAZKo

tag: condition

value: normoxia


title: WTN2

description: WT cells in normoxia

tag: cell type


title: WTN1

description: WT cells in normoxia


title: WTH3

description: WT cells subjected to hypoxia

value: hypoxia


title: CPC5


title: MM19_E2.5_Mettl16_HET


title: CPC4


title: WTH2

description: WT cells subjected to hypoxia


title: TAZN2

description: TAZKo cells in normoxia


title: TAZN1

description: TAZKo cells in normoxia


title: CPC3


title: WTN3

description: WT cells in normoxia


title: MM15_E2.5_Mettl16_HET


title: CPC12


title: MM16_E2.5_Mettl16_KO


title: CPC2


title: CPC1


title: TAZH2

description: TAZKo cells subjected to hypoxia


title: TAZH1

description: TAZKo cells subjected to hypoxia


title: 9_Input

data_processing:
The raw reads were aligned to the mouse reference genome (GRCh38/mm10) using default parameters in BWA v0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2 and SPP version 1.4 (Kharchenko et al., 2008) with an IDR = 0.01 for each replicate and pseudoreplicates.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: ChIP-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ChIP-seq fold change over control

growth_protocol: Cells were maintained in keratinocyte-SFM media supplemented with bovine pituitary extract and epidermal growth factor per manufacturer instruction (Thermo Fisher Scientific, 17005042).

extract_protocol:
Cells were fixed with fresh 1% formaldehyde for 10 min at room temperature and 125 mM glycine was added to inactivate the fixation. Cells were washed by cold PBS 3 times and collected. Cross-linked chromatin was sonicated into fragments of a size range between 250 and 500 nucleotides (Covaris). H3K27Ac antibody (Abcam, ab4729) was incubated with the solubilized DNA fragments at 4°C overnight. Antibody–chromatin complexes were captured by protein A/G Agarose beads (Pierce #20423) and eluted with 1% SDS after extensive washing. The cross-link between DNA and chromatin proteins was reversed by incubation overnight at 65°C. DNA was purified by QIAquick PCR Purification Kit (Qiagen 28104) and dissolved into 30 μL TE buffer per immunoprecipitation.
ChIP-seq libraries were generated using KAPA LTP library preparation kit(KK8230) following the manufacturer’s protocol (Kapa Biosystems).

treatment_protocol: We used lentiviral delivery of Crispr/Cas9 to generate Arid1a knockout cells. The cells that underwent editing but retained Arid1a expression on Western were used as controls.

tag: clone

value: pancreatic duct

value: pancreatic epithelial cells (HPDE)

tag: source

value: derived from single cell clone

value: ARID1A Knockout


title: 71_H3K27Ac

value: ARID1A Wildtype

tag: chip antibody

value: H3K27ac (Abcam, catalog# ab4729, lot# GR3216173-1)


title: 71_Input

tag: tissue


title: WTH1

description: WT cells subjected to hypoxia

value: WT


title: P3: Pre-Eclampsia Sample 3

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description: miRNA

data_processing:
Instrumentiation: Illumina NextSeq 500
Sequencing kit: TruSeq Rapid SBS Kits (#FC-402-4002, lllumina)
Clean Reads: Raw sequences were generated as clean reads from Illumina Nextseq by real-time base calling and quality filtering. The clean reads were recorded in FASTQ format, containing the read information, sequences and quality encoding. The clean reads were located in a FASTQ format file.
Trimmed Reads: Subsequently, the 3’ adapter sequence was trimmed from the clean reads and the reads with lengths shorter than 15 nt were discarded. As the 5’-adaptor was also used as the sequencing primer site, the 5’-adaptor sequence is not present in the sequencing reads. The trimmed reads were recorded in FASTA format.
Aligned Reads: The trimmed reads (length³15nt) were aligned to the human pre-miRNA in miRBase 21, using NovoAlign software (NovoCraft, Selangor, Malaysia). For miRNA alignment, the maximum mismatch was 1. Reads with counts less than 2 were discarded when calculating the miRNA expression. The alignment results were saved in text files.
Normalization: The miRNA expression levels were measured and normalized as transcripts per million of total aligned miRNA reads (TPM).
miRNA Expression Profiles: The miRNA read counts are used to estimate the expression level of each miRNA. The sequence counts for all the miRNAs in the samples are compiled in an Excel file
Genome_build: miRBase 21 Release
Supplementary_files_format_and_content: C*_Homo_sapiens_hsa_novoalign_premiRNA.txt: Pre-miRNA alignment result for the trimmed reads of each sample
Supplementary_files_format_and_content: premiRNA_alignment_raw.txt: Annotations and read counts of all mature miRNA variants (isomiRs) in each sample (Raw Data)
Supplementary_files_format_and_content: premiRNA_alignment_normalization.txt: Annotations and read counts of all mature miRNA variants (isomiRs) in each sample (Normalized Data)
Supplementary_files_format_and_content: miRNA_Expression_Analysis.xls: The miRNA read counts are used to estimate the expression level of each miRNA. The sequence counts for all the miRNAs in the samples are compiled in this file (Sheet "Raw":Raw miRNA expression)
Supplementary_files_format_and_content: miRNA_Expression_Analysis.xls: The miRNA read counts are used to estimate the expression level of each miRNA. The sequence counts for all the miRNAs in the samples are compiled in this file (Sheet "Normalized": Normalized miRNA expression)
Supplementary_files_format_and_content: PreEclampsia_vs_Controls_Comparison.xls: miRNA expression for Pre-Eclampsia (P) vs Controls (C) (based on TagCount_ALL_Isoform data). This file contains also the p-values as well as the FDR tests for comparing each miRNA.

source_name: Woman with pre-eclampsia

extract_protocol:
Phlebotomy was performed by a trained health professional. In brief, 2ml of whole blood were taken from each subject and remained in an EDTA tube for 30min. Tubes were immediately thereafter centrifuged for 10min at 2000rpm. Plasma was removed and stored in 2ml Eppendorf tubes. Plasma samples were kept immediately thereafter at a -80oC storage until further processing. For total RNA extraction, 100ul of plasma were added to 1ml TRIzol (Life Technologies, Foster City, CA), treated with DNase I (Ambion, Austin, USA) and enriched for small RNAs (siRNAs, miRNAs) using the mirVana microRNA Isolation kit (Ambion, Austin, USA). RNA quantity and purity were measured using a Nanodrop spectrophotometer (ND-1000, NanoDrop Technologies, Houston, TX, USA).
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~130-150 bp PCR amplified fragments (corresponding to ~15-35nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina Nextseq per the manufacturer’s instructions.

tag: blood subcomponent

value: Plasma

value: Blood

tag: gender

value: female

tag: diagnosis

value: late onset preeclampsia (LOPE)


title: P4: Pre-Eclampsia Sample 4

description: miRNA


title: P5: Pre-Eclampsia Sample 5

description: miRNA


title: P2: Pre-Eclampsia Sample 2

description: miRNA


title: TAZH3

description: TAZKo cells subjected to hypoxia


title: C5: Uncomplicated Pregnancy Control 5

description: miRNA

source_name: Woman with uncomplicated pregnancy

value: uncomplicated pregnancy


title: OPM2-NT-2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description: Control

data_processing:
Sequence reads were aligned to the GRCh38/hg38 build of the human genome using the Subread aligner. Only uniquely mapped reads were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Fragment counts from some samples were merged together. OPM2-NT-1 was merged with OPM2-NT-2, OPM2-Empty_vector-1 was merged with OPM2-Empty_vector-2, MM1S-Empty_vector-1 was merged with MM1S-Empty_vector-2, and H929-Empty_vector-1 was merged with H929-Empty_vector-2. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in any library.
The counts were then converted to log2 CPM values, quantile normalized and precision weighted with the ‘voom’ function of the limma package. After normalization, the expression levels were converted into log2 fragments per kilobase per per million(FPKM), and a linear model was fitted to each gene. Empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.15 or less. The differentially expressed genes were further filtered out if they do not have at lease 1 RPKM in any of the two conditions in the comparison, or if it failed to achieve at least 1.5 fold change between the two comparisons.
Genome_build: hg38
Supplementary_files_format_and_content: A tab-delimited text file include normalized log2-FPKM values for all samples after merging and normalisation. The supplementary file 'raw_counts.txt' includes raw read counts for genes in each library.

source_name: OPM2 Human multiple myeloma cell line

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Human multiple myeloma cell lines were treated with doxycycline 1μg/mL to induce gRNA expression or lenalidomide 10μM and cultured for 72hrs before flow cytrometry sorting for live cells (based on FCS-SSC characteristics) and RNA extraction.

tag: cell line

value: OPM2 Human multiple myeloma cell line

value: Control

value: Human multiple myeloma cell

tag: agent


title: OPM2-Len-72B

description: Lenalidomide 10μM treatment

value: Lenalidomide 10uM treatment

value: Lenalidomide 10uM


title: OPM2-NT-1

description: Control


title: OPM2-Empty vector-2

description: Empty vector control - doxycycline (1μg/mL) treated

value: Empty vector control


title: OPM2-IKZF1-20-1

description: CRISPR-Cas9 inducible IKZF1 knockout

value: CRISPR-Cas9 inducible IKZF1 knockout


title: OPM2-IKZF1-20-2

description: CRISPR-Cas9 inducible IKZF1 knockout


title: P1: Pre-Eclampsia Sample 1

description: miRNA


title: C4: Uncomplicated Pregnancy Control 4

description: miRNA


title: OPM2-Len-72A

description: Lenalidomide 10μM treatment


title: OPM2-IKZF3-35-2

description: CRISPR-Cas9 inducible IKZF3 knockout

value: CRISPR-Cas9 inducible IKZF3 knockout


title: C1: Uncomplicated Pregnancy Control 1

description: miRNA


title: OPM2-Empty vector-1


title: C2: Uncomplicated Pregnancy Control 2

description: miRNA


title: OPM2-IKZF3-35-1

description: CRISPR-Cas9 inducible IKZF3 knockout


title: MM1S-Empty vector-1

source_name: MM1S Human multiple myeloma cell line

value: MM1S Human multiple myeloma cell line


title: MM1S-Empty vector-2


title: MM1S-IKZF1-20-1

description: CRISPR-Cas9 inducible IKZF1 knockout


title: 9_H3K27Ac

value: pancreatic duct

value: pancreatic epithelial cells (HPDE)

value: derived from single cell clone

tag: genotype

value: ARID1A Knockout


title: H929-IKZF1-20-2

description: CRISPR-Cas9 inducible IKZF1 knockout

source_name: H929 Human multiple myeloma cell line

value: H929 Human multiple myeloma cell line


title: H929-IKZF1-20-1

description: CRISPR-Cas9 inducible IKZF1 knockout


title: H929-Empty vector-2


title: C3: Uncomplicated Pregnancy Control 3

description: miRNA

value: Plasma

value: Blood

value: female


title: H929-Empty vector-1


title: fresh_CPC

description: 98 bp Read1, 8 bp i7 Index, and 26 bp Read2

data_processing:
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 2.0). Reads were aligned to the Mus musculus genome.
1615 and 850 cells were recovered from freshly isolated and cultured CPC samples, respectively. Cells with less than 1000 genes or more than 10% of mitochondrial gene UMI count were filtered out and genes detected less than in three cells were filtered out. Altogether, 2383 cells and 15786 genes were kept for downstream analysis using Seurat R Package (v2.3.0).
Sequenced reads were aligned to the mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

extract_protocol:
Adult c-Kit+ CPCs were isolated and expanded as previously described. Twelve-week-old FVB female mice were heparinized and anesthetized by ketamine-xylazine solution. Hearts were removed from the chest cavity and perfused on a Langendorff system at 1mL/min flow rate at 37ºC with perfusion buffer (NaCl, KCl, KH2PO4, Na2HPO4, MgSO4•7H2O, NaHCO3, KHCO3 HEPES, Taurine, Glucose, and BDM) for blood removal, and tissue was subsequently digested for 10-15 minutes with Liberase DH digestion buffer (Roche 05401089001, 5 mg/mL in perfusion buffer). Heart was collected in STOP buffer (10% Bovine calf serum, 12.5 µM CaCl2), minced into 1 mm3 and dissociated through pipetting. The non-myocyte population was separated through serial cell straining (100µm, 40µm, and 30µm pore size), followed by centrifugation at ~300 rfc for 10 minutes. Lin-cKit+ CPCs were obtained by immunomagnetic sorting with Lineage depletion kit and CD117-conjugated Microbeads (Miltenyi Biotech 130-048-102). Fresh isolated CPCs were separated for immediate single-cell RNA-Seq analysis or cultured in growth medium ((Dulbecco's modified Eagle's medium, 10% embryonic stem cells FBS, 1% insulin-transferrin-selenium, leukemia inhibitory factor [10 ng/ml], basic fibroblast growth factor [10 ng/ml], epidermal growth factor [20 ng/ml], L-glutamine [0.07mg/mL], 1% penicillin-streptomycin-glutamine, 0.1% gentamicin, 2% B27 supplement, 1% N2 supplement). Cells were plated on a pre-coated (0.1% porcine gelatin) cell culture-grade dish. Adherent cultures were expanded and passaged five times when 40% confluency was reached and used for single-cell RNA-seq.
The Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3' Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V2 User Guide.

value: c-Kit+ cardiac progenitor cells

value: fresh


title: hop1 red1 rec8 input 4h

city: New York

first: Hajime

last: Murakami

state: NY

address: 1275 york ave

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description:
source of  scaled coverage
hop1red1rec8_ChIP_scaled.txt
hop1red1rec8_input.txt

data_processing:
Base calls perfomed using HiSeq Control Software for samples sequenced on Illumina HiSeq 2500
Reads trimmed with cutadapt
Mapped with BWA MEM
Sort by Queryname with PICARD
Compute coverage using a custom script of bedtools and custom python code
Coverage maps were scaled by qPCR as described (Murakami and Keeney 2014)
Genome_build: For S. cerevisiae strains, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for strains with translocations, reads were mapped to custom genome assembly genetated from sacCer2; for S. mikatae IFO1815, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: Tab delimited text files include 10 bp-binned coverage maps of scaled ChIP efficiency (ChIP/input), ChIP or input for the each time point. Pos indicates the first coordinate within each bin.

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142.

extract_protocol: ChIP was performed as described (Aparicio et al., 2004; Mendoza et al., 2009; Metivier et al., 2003; Panizza et al., 2011) with modifications. Rec114-Myc diploids were sporulated and 50 mL of meiotic culture (2 x 10^9 cells) was collected at different times and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 μg/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 μL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking at 6.5 m/s for 1 min x 10 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with “M” intensity, 30 sec ON/ 30 sec OFF for 15 min x 3 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 3–5 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.

tag: developmental stage

value: meiotic prophase

value: REC114-Myc hop1 red1 rec8

tag: time in meiosis (h)


title: hop1 red1 input 6h

description:
source of  scaled coverage
hop1red1_ChIP_scaled.txt
hop1red1_input.txt

value: REC114-Myc hop1 red1


title: hop1 red1 rec8 input 2h


title: cultured_CPC

tag: environment

value: cultured


title: hop1 red1 rec8 input 6h


title: hop1 red1 input 4h


title: hop1 red1 input 2h


title: Pancreas_WT_Caer_rep 5

type: RNA

city: Stockholm

first: Rainer

middle: Lothar

last: Heuchel

address: Karolinska Institutet, Novum, KFC, Plan 6A, PaCaRes Lab

department: Clinical Science, Intervention and Technology (CLINTEC)

country: Sweden

institute: Karolinska Institutet

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Packages from Bioconductor were used for analysis. Robust Multichip Average expression using oligo package was used for normalization and calculation of gene expression. A non-specific filter was applied before further analysis, to include genes with an expression signal of >50 in at least 20% of all samples. To identify differentially expressed genes (p value < 0.01), Limma package was used.

label: biotin

source_name: pancreas

label_protocol: standard Affymetrix protocol

extract_protocol: Pancreas samples were grinded in liquid nitrogen and total RNA was extracted. The RNA was treated with DNAse. Agilent 2100 bioanalyzer was used to assess RNA integrity and degraded RNA samples were excluded from further processing.

tag: strain


title: No_83_pig_1737_ANTE

description: Young Late Sham

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, adapter sequences are AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to the Sus scrofa 11.1 genome (Ensembl release 91) using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Sus scrofa 11.1 (Ensembl release 91)
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts

source_name: heart

extract_protocol:
Cardiac samples (50-80 mg/sample, n= 3 sham and 3 MI animals per condition) from anterior left ventricular wall of sham animals and of infarct zone and border zone of MI animal hearts were collected for RNA studies. Samples were cut into small pieces and immersed in RNAlater solution (Ambion, USA) for 48 hrs at 4°C. Then, tissue samples were homogenized and total RNA was isolated using RNAzol (Sigma-Aldrich, USA) and further purified by Purelink RNA kit (Ambion, USA).
RNA-seq libraries were prepared as previously described (PMID 29160304). Briefly, RNA was quantified using a Qubit RNA High-Sensitivity Assay kit (Life Technologies, USA) and assessed for degradation on the basis of their RNA integrity number using the LabChip GX microfluidics platform and RNA assay reagent kit (Perkin Elmer, USA). TruSeq Stranded mRNA Library Prep kit (Illumina, USA) was used or library preparation and libraries quantified using KAPA library quantification kits (KAPA Biosystems, USA) according to the manufacturer’s protocol. The quality and average fragment size of the final libraries were determined using a LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer, USA). Libraries were sequenced on an Illumina NextSeq sequencer using 76bp Paired End chemistry.

tag: individual

tag: breed

value: Yorkshire-landrace

tag: treatment

value: SHAM

value: anterior left ventricular wall

tag: rin

value: heart


title: Pancreas_WT_Caer_rep 3


title: Pancreas_WT_NaCl_rep 2


title: Pancreas_WT_NaCl_rep 1


title: rec8 input 6h

description:
source of  scaled coverage
rec8_ChIP_scaled.txt
rec8_input.txt

value: REC114-Myc rec8


title: ControlCy3_vs_ADOCy5_Rep3

city: Quebec

first: Francois

last: Richard

state: Quebec

address: 2425 rue de l'agriculture

department: Sciences animales

country: Canada

institute: Université Laval

description: Biological replicate 3 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Please note that the left-most column of the raw data files does not contain the feature number for Agilent arrays.

organism: Bos indicus

source_name: ADO

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Ovaries from slaughterhouse were transported to the laboratory in a thermos containing saline solution (0.9 % NaCl) supplemented with antibiotic and antimycotic agents at 30°C. Time between ovaries collection and treatments never exceed 4h. Follicles between 3 to 6 mm were aspirated and their fluid was harvested. Cumulus-oocyte complexes containing several layers of cumulus cells and homogeneous cytoplasm were selected under stereomicroscope.

extract_protocol:
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
amp protocol: This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: The culture medium was HEPES-buffered tyrode lactate medium supplemented with 10% fetal bovine serum, 0.2 mM pyruvic acid, 50 µg/ml gentamicin, 1 µg/ml 17ß-oestradiol, recombinant human FSH (0.5 µg/ml) and +/- adenosine (3 mM).

value: ovary

tag: cell type

value: cumulus cells

tag: number per pool

value: ADO-treated cumulus cells

source_name: Ct

value: Control cumulus cells


title: Pancreas_WT_NaCl_rep 5


title: Pancreas_WT_NaCl_rep 4


title: Pancreas_WT_Caer_rep 1


title: rec8 input 4h


title: Pancreas_WT_Caer_rep 2


title: ControlCy3_vs_ADOCy5_Rep4

description: Biological replicate 4 of 4

tag: tissue


title: ADOCy3_vs_ControlCy5_Rep2

description: Biological replicate 2 of 4


title: rec8 input 2h


title: red1 input 6h

description:
source of  scaled coverage
red1_ChIP_scaled.txt
red1_input.txt

value: REC114-Myc red1


title: ADOCy3_vs_ControlCy5_Rep4

description: Biological replicate 4 of 4


title: Lame306 Area3

description: Biological replicate 2 of 4

treatment_protocol: The culture medium was HEPES-buffered tyrode lactate medium supplemented with 10% fetal bovine serum, 0.2 mM pyruvic acid, 50 µg/ml gentamicin, 1 µg/ml 17ß-oestradiol, adenosine (3 mM), and +/- recombinant human FSH (0.5 µg/ml).

value: Control

source_name: FSH

value: FSH


title: ADOCy3_vs_ControlCy5_Rep3

description: Biological replicate 3 of 4


title: Pancreas_WT_Caer_rep 4


title: ControlCy3_vs_ADOCy5_Rep2

description: Biological replicate 2 of 4


title: Lame306 Area4

description: Biological replicate 1 of 4


title: ControlCy3_vs_ADOCy5_Rep1

description: Biological replicate 1 of 4


title: ADOCy3_vs_ControlCy5_Rep1

description: Biological replicate 1 of 4


title: Lame306 Area2

description: Biological replicate 3 of 4


title: Pancreas_WT_NaCl_rep 3


title: red1 input 2h


title: red1 input 4h


title: MM1S-IKZF1-20-2

description: CRISPR-Cas9 inducible IKZF1 knockout

value: MM1S Human multiple myeloma cell line

tag: genotype/variation

value: CRISPR-Cas9 inducible IKZF1 knockout

value: Human multiple myeloma cell


title: hop1 input 6h

description:
source of  scaled coverage
hop1_ChIP_scaled.txt
hop1_input.txt

value: meiotic prophase

value: REC114-Myc hop1


title: hop1 input 4h


title: Pancreas_WT_Caer_rep 6


title: TL89 input 4h

description:
source of  scaled coverage
TL89_ChIP_scaled.txt
TL89_input.txt

value: REC114-Myc reciprocal translocation between chr8 and chr9


title: TL89 input 2h


title: TL14 input 6h

description:
source of  scaled coverage
TL14_ChIP_scaled.txt
TL14_input.txt

value: REC114-Myc reciprocal translocation between chr1 and chr4


title: TL14 input 2h


title: zip3 input 2h

description:
source of  scaled coverage
zip3_ChIP_scaled.txt
zip3_input.txt

value: REC114-Myc zip3


title: TL14 input 4h


title: wild type input 6h

description:
source of  scaled coverage
wt_ChIP_scaled.txt
wt_input.txt


title: zip3 input 4h


title: wild type input 2h


title: zip3 input 6h


title: wild type input 4h


title: hop1 red1 rec8 ChIP 6h

description:
source of  scaled coverage
hop1red1rec8_ChIP_scaled.txt
hop1red1rec8_ChIP.txt

tag: antibody

value: anti-Myc antibody (9E10); BioXcell (catalog number:BE0238)

value: REC114-Myc hop1 red1 rec8


title: hop1 red1 rec8 ChIP 4h


title: TL89 input 6h


title: hop1 red1 rec8 ChIP 2h


title: hop1 red1 ChIP 6h

description:
source of  scaled coverage
hop1red1_ChIP_scaled.txt
hop1red1_ChIP.txt

value: REC114-Myc hop1 red1


title: hop1 input 2h


title: rec8 ChIP 6h

description:
source of  scaled coverage
rec8_ChIP_scaled.txt
rec8_ChIP.txt

value: REC114-Myc rec8


title: Lame306 Area1

description: Biological replicate 4 of 4

value: ovary

value: cumulus cells


title: WGC027967_microRNA

city: Shenzhen

first: Yan

last: Zhang

state: Guangdong

address: No.3688，Nanhai Avenue

department: College of Life Sciences and Oceanography

institute: Shenzhen University

data_processing:
The original reads were mapped to human genome (hg19, UCSC) using TopHat2 tool (version 2.0.
The raw counts of genes were obtained using htseq-count package (version 0.6.1) in Python (version 2.7) with default settings
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: PC

extract_protocol:
Fresh samples were collected after the surgery, frozen in RNAlater solution (Invitrogen, Carlsbad, CA) immediately, and then stored at -80°C. Total RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA). The Illumina TruSeq Small RNA Sample Preparation protocol was used to prepare small RNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreas tumor

tag: subject id

tag: patient diagnosis

value: pancreatic cancer


title: WGC027969_microRNA


title: retina_ko_rep1

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Gene expression data from a mouse retina lacking Trim9

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the University of Iowa DNA facility.

scan_protocol: Amplified RNA was scanned from Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the University of Iowa DNA Facility.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: adult retina

label_protocol: Total RNA was amplified, biotinylated, and fragmented using the Ambion MessageAmp III RNA amplification kit according to manufacturer's instructions.

growth_protocol: Trim9 deficient mice were obtained from Dr. Stephanie Gupton and are described in detail in (Winkle et al. 2014).  The mice lack exon 1 of Trim9 due to a cre-mediated excision event through crossing with CMV-cre mice. Littermates were allowed to develop normally until maturity when retinas were isolated.

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

treatment_protocol: Embryos were removed from the dam, retinas were isolated and then washed in 1X PBS.

value: adult retina

value: Trim9 KO


title: hop1 red1 ChIP 2h


title: Lame305 Area3

description: Biological replicate 2 of 4

value: FSH

value: Control


title: retina_wt_rep1

description: Gene expression data from a wildtype mouse retina

value: wild type


title: WGC027959_microRNA


title: Lame305 Area2

description: Biological replicate 3 of 4


title: red1 ChIP 6h

description:
source of  scaled coverage
red1_ChIP_scaled.txt
red1_ChIP.txt

value: meiotic prophase

value: REC114-Myc red1


title: rec8 ChIP 2h


title: red1 ChIP 2h


title: red1 ChIP 4h


title: Lame305 Area4

description: Biological replicate 1 of 4


title: retina_wt_rep2


title: retina_ko_rep2


title: hop1 red1 ChIP 4h


title: retina_wt_rep3


title: Lame305 Area1

description: Biological replicate 4 of 4


title: WGC027961_microRNA


title: hop1 ChIP 4h

description:
source of  scaled coverage
hop1_ChIP_scaled.txt
hop1_ChIP.txt

value: REC114-Myc hop1


title: retina_ko_rep3


title: hop1 ChIP 6h


title: WGC026147_microRNA


title: WGC026145_microRNA


title: hop1 ChIP 2h


title: TL89 ChIP 6h

description:
source of  scaled coverage
TL89_ChIP_scaled.txt
TL89_ChIP.txt

value: REC114-Myc reciprocal translocation between chr8 and chr9


title: WGC026141_microRNA


title: WGC024538_microRNA


title: rec8 ChIP 4h

value: anti-Myc antibody (9E10); BioXcell (catalog number:BE0238)


title: WGC024528_microRNA


title: TL89 ChIP 2h


title: TL14 ChIP 6h

description:
source of  scaled coverage
TL14_ChIP_scaled.txt
TL14_ChIP.txt

value: REC114-Myc reciprocal translocation between chr1 and chr4


title: WGC027968_microRNA

source_name: Normal

value: normal pancreas


title: TL14 ChIP 2h


title: TL14 ChIP 4h


title: WGC027966_microRNA


title: control_D1_ATAC-Seq

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

data_processing:
FASTQ files of ATAC-Seq data were aligned to the mouse mm10 reference using Bowtie2
Low quality mapped reads were removed using samtools (view –q 35) and only unique reads mapping to a single genomic location and strand were kept
Resulting SAM files were converted to BAM format using SAM tools. Peak calling was performed using MACS2 with parameters call peak -f BAMPE -n NAME -g <int> --keep-dup all
Peak sets called in individual replicates were combined and individual peaks merged if overlapping within 300 bp to form a union peak set.
Only one tag from each unique position was considered to avoid clonal artifacts from sequencing. The threshold for the number of tags that determined a valid peak was selected at a false discovery rate of 0.001 determined by peak finding using randomized tag positions in a genome with an effective size of 2×109 bp. We also required peaks to have at least 4-fold more tags (normalized to total count) than input control samples. In addition, we required 4-fold more tags relative to the local background region (10 kb) to avoid identifying regions with genomic duplications or nonlocalized binding. Annotated positions for promoters, exons, introns and other features were based on Refseq transcripts and repeat annotations from the University of California, Santa Cruz.
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: Oligodendrocyte

growth_protocol: Mouse OPCs were obtained from cortices of mouse brains as described7. Briefly, dissociated P4-P7 mouse cortices cells were sequentially immunopanned on anti-GalC, and then anti-O4 antibody coated plates to harvest OPCs. Purified OPCs were trypsinized and plated onto poly-D-lysine-coated plates. Cells were grown in DMEM/F-12 (GIBCO) with addition of 2% B-27 (GIBCO), 1% N2 (GIBCO), 20 ng/ml PDGF-AA (Peprotech, 100-13A), 10 ng/ml CNTF (Peprotech, 450-02), 20 ng/ml bFGF (Sino Biological, 10014-HNAE), and 1 ng/ml NT3 (Peprotech, 450-03). For OPCs differentiation, triiodothyronine (T3) (60 nM) added to the media and PDGF-AA, bFGF and NT3 were removed.

extract_protocol:
50,000 mouse OPCs were washed once with 50 L of cold PBS resuspended in 50 μl lysis buffer
According to the protocol of TruePrepTM DNA Library Prep Kit V2 for Illumina’s instructions (TD501, Vazyme)

value: forebrain-derived Oligodendrocyte

tag: age

value: post natal day 4-7


title: Seh1cKO_D1_ATAC-Seq

tag: genotype


title: smik input 4h

description:
source of  scaled coverage
smik_ChIP_scaled.txt
smik_input.txt

organism: Saccharomyces mikatae

tag: developmental stage


title: smik input 6h

tag: time in meiosis (h)


title: zip3 ChIP 4h

description:
source of  scaled coverage
zip3_ChIP_scaled.txt
zip3_ChIP.txt

value: REC114-Myc zip3


title: smik input 2h


title: WGC027958_microRNA


title: wild type ChIP 6h

description:
source of  scaled coverage
wt_ChIP_scaled.txt
wt_ChIP.txt


title: WGC026146_microRNA


title: WGC027960_microRNA


title: WGC026144_microRNA


title: WGC026140_microRNA


title: control_DO_ATAC-Seq


title: TL89 ChIP 4h


title: wild type ChIP 4h


title: smik ChIP 4h

description:
source of  scaled coverage
smik_ChIP_scaled.txt
smik_ChIP.txt


title: wild type ChIP 2h


title: WGC024539_microRNA


title: smik ChIP 2h


title: WT_a-_input12

description:
source of  scaled coverage
Mer2_ChIP_scaled.txt
Mer2_input.txt

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Reads trimmed with cutadapt
Mapped with BWA MEM
Sort by Queryname with PICARD
Compute coverage using a custom script of bedtools and custom python code
Coverage maps were scaled by qPCR as described (Murakami and Keeney 2014)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: (scaled Mer2 ChIP coverage map: Me2_ChIP_scaled.txt) tab delimited text files include each scaled ChIP efficiency (ChIP/input) for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (Me2 ChIP coverage map: Mer2_ChIP.txt) tab delimited text files include ChIP coverage for the each time point at each nucleotide position in the genome
Supplementary_files_format_and_content: (Me2 input coverage map: Mer2_input.txt) tab delimited text files include input coverage for the each time point at each nucleotide position in the genome

extract_protocol: ChIP was performed as described (Aparicio et al., 2004; Mendoza et al., 2009; Metivier et al., 2003; Panizza et al., 2011) with modifications. Mer2-Myc diploids were sporulated and 50 mL of meiotic culture (2 x 10^9 cells) was collected at different times and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 μg/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 μL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking at 6.5 m/s for 1 min x 10 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with “M” intensity, 30 sec ON/ 30 sec OFF for 15 min x 3 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 3–5 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.

value: MER2-Myc ars_delta

tag: time in meiosis

value: time = 6 hr  in meiosis

tag: chip antibody


title: WT_a-_input11

value: time = 5 hr  in meiosis


title: zip3 ChIP 6h


title: WGC022997_microRNA

value: pancreatic cancer


title: WT_a-_input10

value: time = 4.5 hr  in meiosis


title: Riboseq.minus_glu.lso2_2

city: New Haven

first: Yinuo

last: Wang

address: 333 Cedar St C129

institute: Yale University

description: Ribosome-protected mRNA

data_processing:
Library strategy: ribosome footprint profiling
For eCLIP, adapters were trimmed using Cutadapt 1.11.
Trimmed reads were mapped using STAR 2.5.1b to a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
PCR duplicates were removed using a custom script (van Nostrand et al., 2016).
CLIPper 0.2.0 with default parameters was used to call peaks on IP samples. The fraction of reads within peaks was normalized to the fraction of reads in corresponding regions of the control samples (SMI and untagged) to identify IP-specific and reproducible clusters.
For high RNase samples, coverage vectors were calculated using fractional assignment of multi-mapping reads.
Mutation analysis of ribosomal RNA-mapping reads was performed as described in Sexton et al., 2017.
For ribosome profiling of recovery samples, FASTX-Toolkit 0.0.14 was used to collapse PCR duplicates.
Adapters and barcodes were trimmed using Cutadapt 1.9.1.
Trimmed reads were mapped using STAR 2.5.3 to a joint reference of GRCh38 (GENCODE release 20) and a masked version of Sigma1278b MIT_2009_ACVY01000000 containing single copies of tRNA and rRNA genes on an artificial chromosome.
Uniquely mapped yeast reads were used to determine read 5' ends and raw counts.
Yeast gene RPKMs were scaled using human gene RPKMs, which served as an internal standard in each library.
For ribosome profiling of replete and glucose-starved samples, adapters were trimmed using Cutadapt 1.10.
Trimmed reads were mapped using tophat2 2.0.8b to the Sigma1278b reference downloaded from Saccharomyces Genome Database on June 29, 2014.
Uniquely mapped reads were used to determine read 5′ ends and raw counts.Raw counts were transformed into RPKMs.
Genome_build: GRCh38, Sigma1278b MIT_2009_ACVY01000000, Sigma1278b from SGD on 6/29/2014.
Supplementary_files_format_and_content: fasta: Genome sequence of masked Sigma1278b MIT_2009_ACVY01000000 reference.   GFF3: Annotations of masked Sigma1278b MIT_2009_ACVY01000000 reference.   bed: eCLIP peaks called on IP samples using CLIPper 0.2.0. bedGraph: Read coverage (eCLIP) or read 5' ends (recovery ribosome profiling), no scaling to library size.   wig: Read 5′ ends per million reads (replete and glucose-starved ribosome profiling).  tab-delimited text: Yeast gene raw counts (all ribosome profiling); RPKMs (replete and glucose-starved ribosome profiling); and RPKMs rescaled to internal standard (recovery ribosome profiling).

source_name: Budding yeast cells

growth_protocol: Cells were grown in YPAD to OD600 1.0, then spun down and transferred to YPA (lacking glucose) for 3 hours. Cycloheximide was added to culture to a final concentration of 0.1 mg/mL and shaken for 2 minutes.

extract_protocol:
Cells were lysed by vortexing with glass beads in polysome lysis buffer (20 mM HEPES-KOH pH 7.4, 2 mM MgAc, 0.1 M KAc, 0.1 mg/mL cycloheximide, 1% TritonX-100). Extracts were clarified at 21,000 × g for 20 minutes.
Lysate was digested with 15U/A260 RNase I. 80S footprints were isolated from a sucrose gradient, enriched for small RNAs, and size-selected from 26-31 nucleotides. A 3′ adapter was ligated and samples treated with subtractive hybridization oligos to deplete ribosomal RNA. The RNA was reverse transcribed, circularized, and PCR amplified.

treatment_protocol: Cycloheximide-treated cells were poured over ice, spun down, and washed twice with polysome lysis buffer (20 mM HEPES-KOH pH 7.4, 2 mM MgAc, 0.1 M KAc, 0.1 mg/mL cycloheximide, 1% TritonX-100).

tag: background

value: Sigma1278b Strain F1950

value: MATa ura3 his3 leu2 trp1 lso2{delta}::kan


title: zip3 ChIP 2h

value: meiotic prophase


title: WGC022998_microRNA

value: pancreas tumor


title: Riboseq.minus_glu.lso2_1

description: Ribosome-protected mRNA


title: smik ChIP 6h


title: WGC027967_mRNA


title: Riboseq.minus_glu.WT_2

description: Ribosome-protected mRNA

value: MATa ura3 his3 leu2 trp1


title: Riboseq.minus_glu.WT_1

description: Ribosome-protected mRNA


title: WT_a-_input9

value: time = 4 hr  in meiosis


title: Riboseq.replete.lso2_3

description: Ribosome-protected mRNA

growth_protocol: Cells were grown in YPAD to OD600 0.6-0.7 (early log phase). Cycloheximide was added to culture to a final concentration of 0.1 mg/mL and shaken for 2 minutes.


title: WGC027961_mRNA


title: WT_a-_input8

value: time = 3.5 hr  in meiosis


title: WT_a-_input7

value: time =3 hr  in meiosis


title: WT_a-_input6

value: time = 2.5 hr  in meiosis


title: WGC027959_mRNA


title: Riboseq.replete.lso2_2

description: Ribosome-protected mRNA


title: Riboseq.replete.lso2_1

description: Ribosome-protected mRNA


title: WGC026145_mRNA


title: WT_a-_input5

value: time = 2 hr  in meiosis


title: Riboseq.replete.WT_3

description: Ribosome-protected mRNA


title: WT_a-_input4

value: time =1.5 hr  in meiosis


title: WGC026147_mRNA


title: WGC024529_microRNA

value: normal pancreas


title: Riboseq.replete.WT_2

description: Ribosome-protected mRNA


title: Riboseq.replete.WT_1

description: Ribosome-protected mRNA


title: WGC024528_mRNA


title: WT_a-_input2

value: MER2-Myc ars_delta

value: time = 0.5 hr  in meiosis


title: WT_a-_input3

value: time =1 hr  in meiosis


title: WGC024538_mRNA

value: pancreatic cancer


title: WT_a-_ChIP12

description:
source of  scaled coverage
Mer2_ChIP_scaled.txt
Mer2_ChIP.txt

value: time = 6 hr  in meiosis

value: anti-Myc antibody (9E10); BioXcell (catalog number:BE0238)


title: WGC027969_mRNA


title: WT_a-_input1

value: time = 0 hr  in meiosis


title: WGC027968_mRNA


title: WGC022998_mRNA


title: WT_a-_ChIP11

value: meiotic prophase

value: time = 5 hr  in meiosis


title: WGC027966_mRNA


title: WT_a-_ChIP10

value: time = 4.5 hr  in meiosis


title: WGC027960_mRNA


title: WGC026141_mRNA

value: pancreas tumor


title: WT_a-_ChIP9

value: time = 4 hr  in meiosis


title: WGC027958_mRNA


title: WT_a-_ChIP8

value: time = 3.5 hr  in meiosis


title: WGC026146_mRNA


title: WT_a-_ChIP7

value: time =3 hr  in meiosis


title: WGC026144_mRNA


title: WT_a-_ChIP6

value: time = 2.5 hr  in meiosis


title: WGC026140_mRNA


title: WT_a-_ChIP5

value: time = 2 hr  in meiosis


title: WGC024539_mRNA

value: normal pancreas


title: WT_a-_ChIP4

value: MER2-Myc ars_delta

value: time =1.5 hr  in meiosis


title: Donor3_control

city: Isehara

first: Tomoko

last: Nakai

state: Kanagawa

department: Orthopaedic Surgery, Surgical Science

country: Japan

institute: Tokai University School of Medicine

hyb_protocol: Hybridized on a SurePrint G3 Human GE 860K v2 Microarray (Agilent Technology) using a Gene Expression Hybridization Kit (Agilent Technology).

scan_protocol: Analyzed using an Agilent DNA Microarray Scanner (G2600D SG13164306) with the AgilentG3_HiSen_GX_1Color protocol (Agilent Technology).

data_processing:
Probe level data were converted to expression values using the Agilent Feature Extraction 11.5.1.1 (Agilent Technology).
Gene Spring ver.13 (Agilent Technology) was used for 75-percentile normalization, detection of genes with an average two-fold or higher change in expression, and for graphing.

source_name: cultured 1week,control,replicate 3

label_protocol: Cy3-labeled cRNA was prepared from 100ng RNA using a Low Input Quick Amp Labeling Kit (Agilent Technology, Santa Clara CA).

growth_protocol: Nucleus pulposus (NP) cells were enzymatically isolated from lumber IVD herniation that were harvested from four donor patients. Cells were cultured in alpha MEM supplemented with 10% fetal bovine serum.

extract_protocol: RNA was prepared using SV Total RNA Isolation System (Promega, Madison, WI)  following the manufacturer's recommendations. The protocol includes an on-column DNase digestion.

treatment_protocol: The biological activity of NTP was expressed in NTP Units (NU).The cells were treated with 1.0 mNU/ml NTP with 0.17 mM ascorbic acid 2 phosphate every second day.

value: control


title: Donor4_control

source_name: cultured 1week,control,replicate 4


title: WGC024529_mRNA

value: pancreatic cancer


title: 256449110010_b2 - 8_D20_F1 vs 6_D15_F1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Delineation of the metabolic pathways involved in maize endosperm vitreousness.

hyb_protocol: 6_D15_F1 Cy5 / 8_D20_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Zea mays

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

growth_protocol: seed - outdoor

extract_protocol: 6_D15_F1:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: days after pollination

value: floury endosperm

tag: line

value: dent maize

tag: harvest date

extract_protocol: 8_D20_F1:100mg. (Qiagen_RNeasy.pdf)


title: 256449110009_b4 - 15_D20_V2 vs 13_D15_V2

hyb_protocol: 13_D15_V2 Cy5 / 15_D20_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 13_D15_V2:100mg. (Qiagen_RNeasy.pdf)

value: vitreous endosperm

extract_protocol: 15_D20_V2:100mg. (Qiagen_RNeasy.pdf)


title: Donor4_treatment

source_name: cultured 1week,NTP,replicate 4

tag: treatment

value: NTP