title: RF_M_min_rep1


title: ChIP_H2Bub_N_rep1

status: Public on Jun 23 2017

type: SRA

city: New York

first: Lionel

last: Ivashkiv

address: 535 E 70th St

country: USA

institute: Hospital For Special Surgery

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_N_rep1.fastq

library_source: genomic

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using BWA with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

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

treatment_protocol: Cells were treated with or without TNF (10ng/ml) and IFNA (25ng/ml) for 24 hours and LPS (10ng/ml) for 3 hours.

tag: tissue

value: peripheral blood

tag: cell type

value: monocytes


title: RNAseq_M_plus_rep4

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

library_source: transcriptomic

data_processing:
Sequenced reads were first trimmed for adaptor sequences and then aligned against the human transcriptome (each gene represented by its canonical transcript). Only uniquely mapped reads were used in subsequent analyses.
RNA expression levels and ribosome occupancy were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript, taking into account either all reads that map to the transcript (for estimation of RNA levels using RNA-seq data) or only those mapping to its CDS (for estimation of ribosome occupancy).
In estimation of ribosome occupancy in CDS, 5' ends of reads were offset 12 nucleotides to the 3' direction to match the P-site location of ribosome.
Expression estimates were further normalized using quantile normalization.
Only genes with expression level of at least 1.0 RPKM, in either the treated or control conditions, in both the RNA-seq and Ribo-seq datasets were included in subsequent analyses.
Genome_build: The combined dataset includes 10,996 genes.
Supplementary_files_format_and_content: Excel file with RPKM values per sample that were further normalized using quantile normalization. To avoid inflation of FC estimates due to low levels, RPKM levels below 1.0 were set to a floor level of 1.0.

molecule: polyA RNA

source_name: HeLa S3

growth_protocol: HeLa S3 cells or their stable shRNA expressing derivatives were cultured in DMEM supplemented with 10% fetal calf serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin  at 37°C in 5% CO2. Synchronization was done using double-thymidine block.

extract_protocol:
Cells were harvested and lysed in lysis buffer containing 20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1m M DTT, 100 µg/ml Cycloheximide, 1% Triton X-100 and 25 U/ml DNase I. Samples were treated with RNase I to generate ribosome footprints, whereas an undigested portion was used to isolate total mRNA using poly-dT agarose.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Expression of shRNA and thus, induction of hnRNP C knockdown was achieved by treatment with 0.5 ug/ml Doxycyclin for 3 days.

tag: treatment

value: treated with Dox to induce knockdown


title: RNAseq_M_plus_rep3


title: ChIP_H2Bub_IFN_L

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_IFN_L.fastq


title: RNAseq_M_plus_rep1


title: ATAC_SLE_L_rep1

description: ATAC-seq

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 or CASAVA with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol.


title: RNAseq_M_min_rep4

value: untreated


title: ATAC_SLE_N_rep2

description: ATAC-seq


title: RNAseq_M_min_rep2


title: ATAC_SLE_N_rep1

description: ATAC-seq


title: RNAseq_M_min_rep3


title: ATAC_Monocytes_L_rep1

description: ATAC-seq


title: ATAC_Monocytes_L_rep3

description: ATAC-seq


title: RF_M_min_rep2


title: ChIP_H2Bub_N_rep2

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_N_rep2.fastq


title: WT_rep2

city: State College

first: Santhosh

last: Girirajan

state: PA

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Trimmomatic (Bolger et al., 2014) was first used to trim reads as necessary, based on FastQC (bioinformatics.babraham.ac.uk/projects/fastqc) output.
TopHat2 v.2.1.0 (Kim et al., 2013) was used to align the raw sequencing data to the reference fly genome and transcriptome.
HTSeq-Count v.0.6.1 (Anders et al., 2015) was used to calculate raw read counts for each gene.
Genome_build: Dmel 6.08
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts for all transcripts (three technical replicates per biological sample in each file).

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila whole head

growth_protocol: Flies were reared with elav-Gal4>Dicer2 driver at 25°C on conventional cornmeal-sucrose-dextrose-yeast medium.

extract_protocol:
F1 female progeny were collected in groups of 40-50, quickly frozen in liquid nitrogen, and stored at −80°C. For RNA extraction, the heads were separated from their bodies by repetitive cycles of freezing in liquid nitrogen and vortexing. Total RNA was isolated using TRIZOL (Invitrogen, Carlsbad, CA).
We prepared cDNA libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA).

value: whole head

tag: Sex

value: female

tag: tissue-specific knockdown

value: neuronal

tag: RNAi driver

tag: human knockdown gene

value: N/A (wild-type)

tag: fly knockdown gene

tag: fly knockdown vdrc line

value: VDRC WT


title: ATAC_Monocytes_N_rep3

description: ATAC-seq


title: MAPK3_rep3

value: rl


title: ATAC_SLE_L_rep3

description: ATAC-seq


title: WT_rep3


title: ATAC_Monocytes_N_rep2

description: ATAC-seq


title: ATAC_Monocytes_N_rep1

description: ATAC-seq


title: ATAC_IFN_TL_rep3

description: ATAC-seq


title: ATAC_IFN_TL_rep2

description: ATAC-seq


title: KCTD13_rep3


title: ATAC_SLE_N_rep3

description: ATAC-seq


title: WT_rep1


title: MAPK3_rep1


title: ATAC_SLE_L_rep2

description: ATAC-seq


title: KCTD13_rep2


title: ATAC_IFN_T_rep3

description: ATAC-seq


title: RNAseq_M_min_rep1


title: ATAC_IFN_TL_rep1

description: ATAC-seq


title: KCTD13_rep1


title: RNAseq_M_plus_rep2


title: ATAC_IFN_T_rep1

description: ATAC-seq


title: ATAC_Monocytes_L_rep2

description: ATAC-seq


title: ATAC_IFN_L_rep2

description: ATAC-seq


title: DOC2A_rep2

value: rph


title: DOC2A_rep3


title: ATAC_IFN_L_rep1

description: ATAC-seq


title: MAPK3_rep2


title: CORO1A_rep3

value: coro


title: CORO1A_rep1


title: ATAC_IFN_rep2

description: ATAC-seq


title: ATAC_IFN_rep3

description: ATAC-seq


title: ATAC_IFN_L_rep3

description: ATAC-seq


title: CDIPT_rep2

value: CDIPT

value: pis


title: ATAC_TL_rep3

description: ATAC-seq


title: CDIPT_rep1


title: ATAC_TL_rep2

description: ATAC-seq


title: C16orf53_rep3


title: ATAC_IFN_T_rep2

description: ATAC-seq


title: ATAC_TL_rep1

description: ATAC-seq


title: C16orf53_rep1


title: C16orf53_rep2


title: ATAC_T_rep3

description: ATAC-seq


title: DOC2A_rep1


title: ATAC_T_rep2

description: ATAC-seq


title: ATAC_T_rep1

description: ATAC-seq


title: ATAC_L_rep4

description: ATAC-seq


title: CDIPT_rep3


title: ATAC_L_rep3

description: ATAC-seq


title: ATAC_N_rep4

description: ATAC-seq


title: ATAC_L_rep1

description: ATAC-seq


title: ATAC_L_rep5

description: ATAC-seq


title: ATAC_N_rep1

description: ATAC-seq


title: ATAC_L_rep2

description: ATAC-seq


title: ATAC_N_rep3

description: ATAC-seq


title: ATAC_N_rep5

description: ATAC-seq


title: ATAC_N_rep2

description: ATAC-seq


title: Bone_marrow_erythroblast_rep11_RNA-seq

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

country: Canada

institute: Montreal Heart Institute

data_processing:
Sequenced reads were trimmed for the adapter sequence and mapped to the genome (hg19) using Tophat2 (v.2.0.9, with options --library-type fr-firststrand --microexon-search --coverage-search)
We estimated transcript abundance in Fragments Per Kilobase of exon per Megabase of library size (FPKM) with Cufflinks (v.2.2.1, with options --library-type fr-firststrand --max-bundle-frags 50000000)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

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

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

extract_protocol:
Total RNA for RNA sequencing was extracted using the miRNEASY kit (Qiagen).
We performed RNA-sequencing with an Illumina HiSeq2000 sequencer using stranded cDNA library and a paired-ends 100 bp protocol.

tag: developmental stage

value: adult

value: Bone marrow


title: Bone_marrow_erythroblast_rep10_RNA-seq


title: Bone_marrow_erythroblast_rep9_RNA-seq


title: Mettl3 KO_mES_8hr_mRNA half-life quantification

city: Bar Harbor

first: Shengdong

last: Ke

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
We required a minimum quality score of 20 at these index and barcode positions in addition to an average score of 20 for the remaining positions.
The remaining read sequences (actual RNA tags) were mapped to the reference genome (mm10 and hg19) by novoalign program (http://www.novocraft.com) with no more than 2 mismatches (substitutions, insertions or deletions) allowed per read. A minimum of 20nt matches was required and only those reads mapped uniquely to the genome (single hits) were kept. To remove PCR duplicates, we collapsed reads mapped to the same genomic locations (the same start and end) into a single read if they have the same barcode sequence; on the other side, reads mapped to the same location but with distinct barcodes were kept. This step removed PCR duplicates while retaining genuinely unique reads representing independent RNA fragments (the same analysis pipeline for m6A IP, CLIP and its input RNA fragments). To ensure reads unambiguously mapped in the genome, we further mapped the reads by two additional alignment programs (bowtie2 and tophat2). Different from bowtie2 and novoalign, tophat2 allowed mapping across exon-exon junctions. The mapping parameters for bowtie2: -k 4 and for tophat2: --library-type fr-firststrand -p 10, with other parameters in default setting. We kept reads uniquely mapped in the genome by all three programs and the reads which were not mappable by novoalign and bowtie2 but uniquely mapped to exon-exon junctions by tophat2 (requiring at least 4nt overlap on each exon).
Similar to the previous m6A publication (Ke et al., Genes&Development 2015), we searched for the enriched m6A peak regions by scanning the genome using 20nt sliding windows, and evaluating the statistical significance of enrichment by Fisher Exact Test (m6A IP vs. input). Benjamini-Hochberg was implemented to adjust the p value to False Discovery Rate (FDR) for multiple testing. We identified a window as being sigificantly m6A enriched when its FDR was less than 0.05 and the fold of enrichment (m6A IP vs. input) was at least 2 fold in at least 2 out 3 biological replicates. Significantly m6A enriched 20nt windows were concatenated if they were adjacent to each other. Because we did size selection for 20nt~80nt RNA fragments, the resulted m6A peak regions would be mostly 40nt~200nt. We filtered out m6A peak regions less than 40nt. In some cases, m6A peak regions were longer than 200nt, suggesting multiple m6A sites within those peak regions. Thus we split them into multiple m6A peak regions with the minimum number of m6A peaks that could form such a concatenated window.
The splicing completion for a specific internal exon (i.e. “spliced/(spliced+unspliced)(%)” in Figure 1A and “splicing completion index” in Figure 2A) is defined as the number of the spliced RNA molecules (S) divided by the number of total RNA molecules (spliced (S) plus unspliced (US))(Tilgner et al., 2012). S is calculated as the sum of two types of exon-exon junction reads: the exon-exon junction reads that spliced in this internal exon (0.5 x (a+b), a and b are the numbers of exon-exon junctions at each end of this internal exon, Figure 1) and that spliced out it (i.e. exon-exon junctions that connected the adjacent upstream exon to the adjacent downstream exon). US is calculated by enumerating the unspliced exon-intron junction reads (0.5 x (c+d), c and d are the numbers of exon-intron junctions at each end of this internal exon, Figure 1).
To identify pre-mRNA reads that have both intron and m6A containing exon sequences, we focused on precisely mapped m6A sites that are within 80nts of splice sites (the length of our m6A sequencing reads is ~80nt). We required the read length in intronic region to be at least 4nt for these pre-mRNA reads. Furthermore, we also required the number of pre-mRNA reads at each case for CA-RNA be more than 2 as the reliable evidence of existence. In addition, these pre-mRNA reads should not exist in nucleoplasm and cytoplasm RNAs. We identified over 200 internal exons to have m6A-containing exon-intron junction fragments (the full list in Supplemental Table1 and 6 total examples in Figure 3A, 3B and Supplemental Figure 3).
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bed: m6A peak region and precise m6A site; txt: halflife changes in KOvsWT, mRNA expression levels in CA-RNA, nucleoplasmic RNA and cytoplasmic RNA

organism: Mus musculus

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO, 8hr, 3 biological replicates

growth_protocol: Hela cells were grown to 90% confluency in DMEM (Life Technologies) supplemented with 10% Fetal Bovine Serum (Omega), 2mM L-Glutamine (Life Technologies), 1U/mL Penacillin/Streptomycin (Life Technologies), 1x Non-essential Amino Acids (Life Technologies) and 0.1mM Beta-Mercaptoethanol (Sigma). Mouse ES cells were grown according to Geula, S. et al Science 2015.

extract_protocol:
Total RNAs were isolated from cells and mouse tissues according to manufacturer’s instructions using TRIzol reagent (Cat.# 15596, Life Technologies), then was resuspended in RNA-free water, digested with RQ1 RNase-Free DNase (Cat. # M6101, Promega) for 20 min at 37°C and then subject to phenol/chloroform extraction and ethanol precipitation. The resulted total RNA pallet was resuspended in RNA-free water. PolyA+ RNAs were selected using Dynabeads® mRNA Purification Kit (Cat.# 61006, Invitrogen) according to the manufacturer’s protocol.
The PolyA+ RNA was fragmented to 20~80nt nucleotide fragments by alkaline hydrolysis (1mM EDTA, 6mM Na2CO3, 44mM NaHCO3, pH~9.3) at 95°C for 18 minutes, then the RNA fragments precipitated following standard ethanol precipitation. Dynabeads Protein A beads (250ul, Cat. # 10008D, Life Technologies) was pretreated with BSA (Cat. # B9000S, NEB) for 45 minutes at room temperature to reduce background. Anti-m6A rabbit polyclonal antibody (25ug, Cat. # 202003, Synaptic Systems) was then conjugated to Dynabeads Protein at room temperature for 1 hour. The fragmented polyA+ RNAs (3ug) were subject to PAGE selection for 20nt~80nt size and then incubated with the antibody in 1x PXL buffer (1x PBS, 0.1% SDS, 0.5% Sodium Deoxycholate and 0.5% NP-40) supplemented with 2% RNasin® Plus RNase Inhibitor (Cat. # N2615, Promega) for 2 hours at 4°C.  After incubation, the bead and antibody was washed 5 times by 4 different wash buffers: first twice by ice cold Nelson Low Salt Buffer (15mM Tris pH7.5 and 5mM EDTA), once by ice cold Nelson High Salt Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS and 1M NaCl), once by ice cold Nelson Stringent Wash Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS, 120mM NaCl and 25mM KCl) and last wash by ice cold NT-2 Buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2 and 0.05% NP-40). After the stringent wash series, the bead and antibody was split into two halves: one half performed m6A-CLIP leg, and the other half had its bounded RNA eluted with 0.5mg/mL N6-methyladenosine sodium salt (Cat. # M2780, Sigma-Aldrich) at 4°C for 1 hour (m6A-IP leg).  The eluted RNA was ethanol precipitated and re-suspended in RNase-free water for downstream cDNA library preparation. The eluted RNA from m6A-IP step and the input RNA fragments were first treated with T4 PNK to remove its 3’phospho group and then ligated to 68 pmol pre-adenylated DNA linker (L32N from IDT) with T4 RNA ligase2, truncated KQ (Cat. # M0373L, NEB) overnight at 16°C. This ligation mixture was subject to 8% PAGE purification to harvest the ligated product. The purified RNAs from m6A-IP, m6A-CLIP and their input RNA fragments were all subject to the same BrdU-CLIP cDNA library preparation. The detailed BrdU-CLIP cDNA library protocol was described previously (Weyn-Vanhentenryck et al., 2014).

tag: strain background

tag: genotype/variation

value: Mettl3 KO

value: embryonic stem (ES) cells

tag: rna type

value: PolyA+ RNA


title: Bone_marrow_erythroblast_rep8_RNA-seq


title: Mettl3 KO_mES_2hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO, 2hr, 3 biological replicates


title: Mettl3 KO_mES_4hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO, 4hr, 3 biological replicates


title: Mettl3 KO_mES_1hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO, 1hr, 3 biological replicates


title: Mettl3 KO_mES_0hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO, 0hr, 3 biological replicates


title: Bone_marrow_erythroblast_rep7_RNA-seq


title: Bone_marrow_erythroblast_rep6_RNA-seq


title: Bone_marrow_erythroblast_rep5_RNA-seq


title: WT_mES_2hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Wild Type, 2hr, 3 biological replicates

value: Wild Type


title: WT_mES_8hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Wild Type, 8hr, 3 biological replicates


title: WT_mES_1hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Wild Type, 1hr, 3 biological replicates


title: WT_mES_4hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Wild Type, 4hr, 3 biological replicates


title: Bone_marrow_erythroblast_rep4_RNA-seq


title: Bone_marrow_erythroblast_rep3_RNA-seq


title: Bone_marrow_erythroblast_rep2_RNA-seq


title: WT_mES_0hr_mRNA half-life quantification

source_name: PolyA+ RNA, mouse ES cells, Wild Type, 0hr, 3 biological replicates


title: Bone_marrow_erythroblast_rep1_RNA-seq


title: Mettl3 KO_mES_m6A-CLIP

data_processing:
library strategy: m6A-CLIP-seq
We required a minimum quality score of 20 at these index and barcode positions in addition to an average score of 20 for the remaining positions.
The remaining read sequences (actual RNA tags) were mapped to the reference genome (mm10 and hg19) by novoalign program (http://www.novocraft.com) with no more than 2 mismatches (substitutions, insertions or deletions) allowed per read. A minimum of 20nt matches was required and only those reads mapped uniquely to the genome (single hits) were kept. To remove PCR duplicates, we collapsed reads mapped to the same genomic locations (the same start and end) into a single read if they have the same barcode sequence; on the other side, reads mapped to the same location but with distinct barcodes were kept. This step removed PCR duplicates while retaining genuinely unique reads representing independent RNA fragments (the same analysis pipeline for m6A IP, CLIP and its input RNA fragments). To ensure reads unambiguously mapped in the genome, we further mapped the reads by two additional alignment programs (bowtie2 and tophat2). Different from bowtie2 and novoalign, tophat2 allowed mapping across exon-exon junctions. The mapping parameters for bowtie2: -k 4 and for tophat2: --library-type fr-firststrand -p 10, with other parameters in default setting. We kept reads uniquely mapped in the genome by all three programs and the reads which were not mappable by novoalign and bowtie2 but uniquely mapped to exon-exon junctions by tophat2 (requiring at least 4nt overlap on each exon).
Similar to the previous m6A publication (Ke et al., Genes&Development 2015), we searched for the enriched m6A peak regions by scanning the genome using 20nt sliding windows, and evaluating the statistical significance of enrichment by Fisher Exact Test (m6A IP vs. input). Benjamini-Hochberg was implemented to adjust the p value to False Discovery Rate (FDR) for multiple testing. We identified a window as being sigificantly m6A enriched when its FDR was less than 0.05 and the fold of enrichment (m6A IP vs. input) was at least 2 fold in at least 2 out 3 biological replicates. Significantly m6A enriched 20nt windows were concatenated if they were adjacent to each other. Because we did size selection for 20nt~80nt RNA fragments, the resulted m6A peak regions would be mostly 40nt~200nt. We filtered out m6A peak regions less than 40nt. In some cases, m6A peak regions were longer than 200nt, suggesting multiple m6A sites within those peak regions. Thus we split them into multiple m6A peak regions with the minimum number of m6A peaks that could form such a concatenated window.
The splicing completion for a specific internal exon (i.e. “spliced/(spliced+unspliced)(%)” in Figure 1A and “splicing completion index” in Figure 2A) is defined as the number of the spliced RNA molecules (S) divided by the number of total RNA molecules (spliced (S) plus unspliced (US))(Tilgner et al., 2012). S is calculated as the sum of two types of exon-exon junction reads: the exon-exon junction reads that spliced in this internal exon (0.5 x (a+b), a and b are the numbers of exon-exon junctions at each end of this internal exon, Figure 1) and that spliced out it (i.e. exon-exon junctions that connected the adjacent upstream exon to the adjacent downstream exon). US is calculated by enumerating the unspliced exon-intron junction reads (0.5 x (c+d), c and d are the numbers of exon-intron junctions at each end of this internal exon, Figure 1).
To identify pre-mRNA reads that have both intron and m6A containing exon sequences, we focused on precisely mapped m6A sites that are within 80nts of splice sites (the length of our m6A sequencing reads is ~80nt). We required the read length in intronic region to be at least 4nt for these pre-mRNA reads. Furthermore, we also required the number of pre-mRNA reads at each case for CA-RNA be more than 2 as the reliable evidence of existence. In addition, these pre-mRNA reads should not exist in nucleoplasm and cytoplasm RNAs. We identified over 200 internal exons to have m6A-containing exon-intron junction fragments (the full list in Supplemental Table1 and 6 total examples in Figure 3A, 3B and Supplemental Figure 3).
Genome_build: mm10, hg19
Supplementary_files_format_and_content: bed: m6A peak region and precise m6A site; txt: halflife changes in KOvsWT, mRNA expression levels in CA-RNA, nucleoplasmic RNA and cytoplasmic RNA

source_name: PolyA+ RNA, mouse ES cells, Mettl3 KO

tag: antibody

value: m6A antibody (Synaptic Systems, 202003)


title: Fetal_liver_erythroblast_rep11_RNA-seq

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

value: fetal

value: Fetal liver


title: Bone_marrow_erythroblast_rep0_RNA-seq


title: RNA_L_rep2

description:
mRNA-seq
RNA_L_rep2.fastq

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed(http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
Cufflinks version 2.2.1 (Trapnell et al., 2012 Nat Protoc) was used to estimate the abundance of transcripts.
Genome_build: hg19

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood

value: monocytes


title: WT_mES_m6A-CLIP

source_name: PolyA+ RNA, mouse ES cells, Wild Type


title: Fetal_liver_erythroblast_rep10_RNA-seq


title: SL33600_CDKO

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base. Filtered reads were assessed for quality using FastQC (1). 1. Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010.
Reads were splice-aware aligned to the reference genome using STAR (2), and reads overlapping gene regions were counted using featureCounts (3). 2. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; doi:10.1093/bioinformatics/bts635. 3. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923-30. doi:10.1093/bioinformatics/btt656
The DESeq2 Bioconductor package (4) in the R statistical computing environment (5) was used for normalizing count data, performing exploratory data analysis, estimating dispersion, and fitting a negative binomial model for each gene comparing the expression from Tgif mutants versus wild type samples. 4. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi:10.1186/PREACCEPT-8897612761307401. 5. R Core Development Team. R: A Language and Environment for Statistical Computing. ISBN 3-900051-07-0, URL http://www.R-project.org/. Vienna, Austria; 2010.
After obtaining a list of differentially expressed genes, log fold changes, and p-values, Benjamini-Hochberg False Discovery Rate procedure was used to correct p-values for multiple testing.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated file, including raw read counts for each sample

source_name: Tgif1;Tgif2 null_9 dpc embryo

extract_protocol:
RNA was isolated using an Absolutely RNA Miniprep Kit (Agilent) according to the manufacturer's instructions.
Poly-A RNA-seq libraries were generated at HudsonAlpha with Illumina barcodes and sequenced (Illumina HiSeq) to a target depth of ~ 25M paired end 50bp reads per sample
RNA-seq, poly A selection, 50bp paired end reads.

value: Tgif1;Tgif2 null

tag: age

value: 9.0 dpc embryo

value: whole embryo


title: SL33598_CDKO


title: Fetal_liver_erythroblast_rep9_RNA-seq


title: SL33596_CDKO


title: SL33597_CDKO


title: Fetal_liver_erythroblast_rep8_RNA-seq


title: SL33595_CDKO


title: Fetal_liver_erythroblast_rep7_RNA-seq


title: SL33594_CDKO


title: Fetal_liver_erythroblast_rep6_RNA-seq


title: SL33593_CDKO


title: SL33599_CDKO


title: Fetal_liver_erythroblast_rep5_RNA-seq


title: SL33592_WT

source_name: WT_9 dpc embryo

value: wild type


title: SL33591_WT


title: SL33589_WT


title: Fetal_liver_erythroblast_rep2_RNA-seq


title: Fetal_liver_erythroblast_rep0_RNA-seq


title: Fetal_liver_erythroblast_rep1_RNA-seq


title: SL33590_WT


title: STlo_4

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

description: wild type

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
We trimmed all reads to 44 bases and aligned to mm9 with Bowtie version 1.0.0 (Allowed up to 3 mismatches, but required unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate RPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with tag counts and RPKM values for each RefSeq gene model.

source_name: Mouse liver ducts

extract_protocol:
FACS(BD, Influx) sorted cells were directly put into TRIzol for RNA preparation.
Libraries were made with illumina TruSeq kit V2.0 under manufacture's protocol.Four samples for each population were processed to ensure detecting comparable genes.

value: Mouse liver ducts

tag: strain

value: liver

tag: sorted cell


title: STlo_3

description: wild type

tag: tissue


title: HeLa_Cytoplasmic RNA_Ribo 0_RNA-seq

source_name: Cytoplasmic RNA, Ribo 0, human HeLa cells

value: Cytoplasmic RNA, Ribo 0


title: HeLa_Cytoplasmic RNA_PolyA_RNA-seq

source_name: Cytoplasmic RNA, PolyA+, human HeLa cells

value: Cytoplasmic RNA, PolyA+


title: HeLa_Nucleoplasmic RNA_Ribo 0_RNA-seq

source_name: Nucleoplasmic RNA, Ribo 0, human HeLa cells

value: Nucleoplasmic RNA, Ribo 0


title: STlo_1

description: wild type

tag: cell type


title: STlo_2

description: wild type


title: SThi_4

description: wild type


title: SThi_3

description: wild type


title: HeLa_Cytoplasmic RNA_Ribo 0_m6A-CLIP

tag: cell line

value: HeLa


title: SThi_1

description: wild type


title: HeLa_Cytoplasmic RNA_PolyA_m6A-CLIP


title: Fetal_liver_erythroblast_rep3_RNA-seq


title: Fetal_liver_erythroblast_rep4_RNA-seq


title: HeLa_CA-RNA_Ribo 0_m6A-CLIP

source_name: CA-RNA,Ribo 0, human HeLa cells

value: CA-RNA,Ribo 0


title: HeLa_Nucleoplasmic RNA,_Ribo 0_m6A-CLIP


title: HeLa_CA-RNA,Ribo 0_RNA-seq


title: SC-WGBS 9

city: Bronx

first: Bo

last: Yu

state: NY

address: 1300 Morris Park Ave, Block 621

institute: Albert Einstein College of Medicine

description:
Bisulfite treated DNA
MII

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality reads using Trim_Galore.
Bismark21 was used for read mapping, deduplication, and methylation calling.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with methylation calling for each covered chromosomal position, including CpG and non-CpG methylations

source_name: oocyte

extract_protocol:
Zona pellucida was removed. Each oocyte was washed in PBS and frozen in 2ul PBS and stored in -80oC.
single cell WGBS using Zymos pico MethylSeq kit
Single cell whole genome bisulfite sequencing

value: oocyte

tag: maturation stage

value: MII


title: SC-WGBS 11

description:
Bisulfite treated DNA
MI

value: MI


title: SC-WGBS 5

description:
Bisulfite treated DNA
MII


title: SC-WGBS 4

description:
Bisulfite treated DNA
GV

value: GV


title: SC-WGBS 8

description:
Bisulfite treated DNA
MII


title: SC-WGBS 2

description:
Bisulfite treated DNA
MI


title: SC-WGBS 6

description:
Bisulfite treated DNA
MII


title: SC-WGBS 3

description:
Bisulfite treated DNA
MI


title: SC-WGBS 1

description:
Bisulfite treated DNA
GV


title: hNEC-Sox2

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads were aligned to genome using Bowtie-1.0.0 with default parameters.
Only the uniquely mapped reads were retained,and removing duplicated reads.
The peak-calling tool GeneTrack was used to predicted nucleosomes,while MACS-1.4.2 was used to predicted Sox2 binding sites with the following setting: p-value(1e-4), enrichment fold (10).
Genome_build: hg19
Supplementary_files_format_and_content: bed files provides the enrichment regions of histone modifications and Sox2 on the genome.

source_name: neuroectoderm cells

growth_protocol: Culture and neural differentiation of hESC were performed according to the standard protocol which can be found at http://www.wicell.org.Briefly,hESC colonies were detached from MEFs and form aggregates to initiate the neural differentiation procedure by withdrawing bFGF. We changed medium with NIM(contained modified N2 and 1 mg/ml of heparin) after 4 days of suspension culture to guide neuroectodermal specification.Then We plated cells on Day6 and get hNECs on Day10.

extract_protocol:
Chromatin were sheared to fragements by using different strategy for histone modifications(MNase-digested) and Sox2(Sonication),then histone-DNA or Sox2-DNA complexes were isolated with corresponding antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

value: hESC-derived neuroectoderm cells

tag: passages


title: hESC-Sox2

source_name: human embryonic stem cells

value: hESC


title: hESC-H3K36me3


title: hNEC-H3K36me3


title: hNEC-nucleosome

data_processing:
Sequencing reads were aligned to genome using Bowtie-1.0.0 with default parameters.
Only the uniquely mapped reads were retained,and removing duplicated reads.
The resulting reads were used to predict nucleosome positions by using the peak-calling tool GeneTrack.
Genome_build: hg19
Supplementary_files_format_and_content: bed files lists nucleosome positions that were generated by GeneTrack

extract_protocol:
~2*10^7 cells were cross-linked,then were digested with 2.5μl MNase(NEB# M0247S; 2,000 gel units/μl) at 37℃ for 20 min to generate a majority of mononucleosomal fragments (>=80%) with some smaller and di-nucleosome-sized fragments.Only mononucleosomal DNA fragments (~150 bp) were gel purified, pooled and prepared for sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.


title: hNEC-H3K9ac


title: SC-WGBS 10

description:
Bisulfite treated DNA
MII


title: hESC-H3K9ac


title: ATAC_IFN_rep1

description: ATAC-seq

source_name: Primary human monocyte-derived macrophages

value: peripheral blood

value: monocytes


title: SThi_2

description: wild type


title: hNEC-H3K4me3


title: hESC-H3K4me3


title: SC-WGBS 7

description:
Bisulfite treated DNA
MII


title: SC-WGBS: BY29

description: Bisulfite treated DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality reads using Trim_Galore.
Bismark21 was used for read mapping, deduplication, and methylation calling.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph generated from Bismark

extract_protocol:
Zona pellucida was removed. Each oocyte was washed in PBS and frozen in 2ul PBS and stored in -80oC.
Single cell whole genome bisulfite sequencing using Zymos pico MethylSeq kit

tag: gender

value: female


title: SC-WGBS: BY27

description: Bisulfite treated DNA


title: hESC-H3K27me3


title: SC-WGBS: BY23

description: Bisulfite treated DNA


title: hESC-nucleosome


title: SC-WGBS: BY13

description: Bisulfite treated DNA


title: SC-WGBS: BY18

description: Bisulfite treated DNA


title: SC-WGBS: BY19

description: Bisulfite treated DNA


title: SC-WGBS: BY14

description: Bisulfite treated DNA


title: SC-WGBS: BY16

description: Bisulfite treated DNA


title: SC-WGBS: BY20

description: Bisulfite treated DNA


title: SC-WGBS: BY17

description: Bisulfite treated DNA


title: SC-WGBS: BY21

description: Bisulfite treated DNA


title: SC-WGBS: BY11

description: Bisulfite treated DNA


title: hNEC-H3K27me3


title: SC-WGBS: BY8

description: Bisulfite treated DNA


title: SC-WGBS: BY6

description: Bisulfite treated DNA


title: SC-WGBS: BY5

description: Bisulfite treated DNA


title: SC-WGBS: BY2

description: Bisulfite treated DNA


title: SC-WGBS: BY7

description: Bisulfite treated DNA


title: Y+S3

city: Nanjing

first: Qingping

last: Ma

state: Jiangsu

address: Weigang No. 1

institute: Nanjing Agricultural University

data_processing:
Illumina HiSeq 4000 platform was used for sequencing
The raw data were filtered by removing the adapter sequences, low-quality reads (the rate of reads which quality value ≤ 10 is more than 20%) and the reads with unknown nucleotides larger than 5%
The fragments per kb per million fragments (FPKM) method was used to calculate the expression of unigenes
Supplementary_files_format_and_content: excel type file including FPKM values for each sample,

organism: Camellia sinensis

source_name: leaves

growth_protocol: Two-year-old tea plants growing well (Camellia sinensis cv. Huangjinya) in the experimental field of the Tea Institute of Shandong Academy of Agricultural Sciences in Tai’an, China (N36°11′, E117°10′, 153 m above sea level) were used in this experiment

extract_protocol:
Tea leaves at the third position from the top of both groups were harvested and frozen quickly in liquid nitrogen and the RNA was extracted by Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One group of tea plants was shaded by a single layer shade net which reduced light intensity by about 45%, and another group of tea plants grown in the same field without the shade net was used as the control.

tag: cultivar

value: Hunagjinya

tag: leaf colour

value: green

value: two-year old


title: SC-WGBS: BY3

description: Bisulfite treated DNA


title: Y2

value: yellow


title: Y3


title: Y1


title: X4404_nAcc_S_SL7857

status: Public on Jun 22 2017

city: Huntsville

first: Kevin

last: Bowling

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 using Tophat and Cufflinks
Read counts for each transcript were compiled across all post-mortem tissues samples
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts for all genes across all post-mortem human brain tissues (using GENCODE v9 for transcript/gene models)

extract_protocol:
Homogenates of post-mortem brain tissues were made using the MPBio FastPrep instrument, while RNAs were extracted using the Norgen Animal RNA isolation kit
RNA-seq was performed as previously described (Gertz et al. 2012)

value: brain

tag: brain region

value: nAcc

tag: age at death

tag: clinical diagnosis

value: Schizophrenia

value: M

tag: ethnicity

value: Caucasian

tag: post-mortem interval

tag: brain ph


title: X4357_nAcc_S_SL7856


title: X4296_nAcc_S_SL7855


title: X4413_nAcc_S_SL7858


title: SC-WGBS: BY9

description: Bisulfite treated DNA

value: oocyte


title: X4087_AnCg_B_SL7853

source_name: AnCg_Bipolar Disorder

value: AnCg

value: Bipolar Disorder

value: F


title: X3085_DLPFC_B_SL7847

source_name: DLPFC_Bipolar Disorder

value: DLPFC


title: CORO1A_rep2

source_name: Drosophila whole head

value: whole head

tag: Sex

tag: tissue-specific knockdown

value: neuronal

tag: RNAi driver

tag: human knockdown gene

tag: fly knockdown gene

value: coro

tag: fly knockdown vdrc line


title: X2976_AnCg_S_SL7846

tag: tissue


title: X3410_DLPFC_S_SL7848


title: X2664_AnCg_C_SL7845

value: Control

value: Asian


title: X3927_AnCg_B_SL7851


title: X3588_nAcc_C_SL7849


title: Y+S2

value: Hunagjinya

value: green

tag: age

value: two-year old


title: Y+S1


title: X4405_AnCg_B_SL7808

value: brain

tag: gender


title: X2384_nAcc_S_SL7843

value: nAcc

value: Schizophrenia


title: X2311_AnCg_B_SL7842

value: M

value: Caucasian


title: X3634_DLPFC_M_SL7806

source_name: DLPFC_Major Depression

value: Major Depression


title: X3433_DLPFC_C_SL7807


title: X3525_DLPFC_S_SL7803


title: X2976_DLPFC_S_SL7805


title: X2248_AnCg_C_SL7809

value: AnCg


title: X4242_nAcc_B_SL7854

source_name: nAcc_Bipolar Disorder

value: Bipolar Disorder

value: F


title: X2505_DLPFC_S_SL7844

value: DLPFC


title: X3618_DLPFC_B_SL8435


title: X3667_DLPFC_M_SL7801


title: X3228_DLPFC_C_SL7804

value: Pacific Islander


title: X4463_DLPFC_S_SL7802


title: X4345_AnCg_B_SL7799


title: X3004_AnCg_M_SL7798

source_name: AnCg_Major Depression


title: X3523_AnCg_C_SL7800


title: X3982_nAcc_M_SL7852

source_name: nAcc_Major Depression


title: X4419_AnCg_B_SL7703


title: X4404_DLPFC_S_SL7704


title: X4639_AnCg_B_SL7702


title: X4262_nAcc_B_SL7700


title: X3772_AnCg_B_SL7699


title: X3452_DLPFC_B_SL7701


title: X4357_AnCg_S_SL7695


title: X4242_AnCg_B_SL7696


title: X3365_DLPFC_M_SL7698


title: X4639_DLPFC_B_SL7697


title: X2619_AnCg_C_SL7631


title: X3481_nAcc_M_SL7694


title: X3651_AnCg_S_SL7633


title: X3281_DLPFC_C_SL7632


title: X3993_DLPFC_S_SL7628


title: X2619_nAcc_C_SL7627


title: X3686_AnCg_C_SL7630


title: X2316_AnCg_C_SL7620


title: X3774_DLPFC_C_SL7625


title: X3755_AnCg_M_SL7619


title: X4404_AnCg_S_SL7624


title: X2566_nAcc_B_SL7622


title: X4345_DLPFC_B_SL7617


title: X3965_AnCg_C_SL7615


title: X3774_AnCg_C_SL7629


title: X4242_DLPFC_B_SL7616


title: X4284_DLPFC_S_SL7626

value: African American


title: X3711_DLPFC_B_SL7618


title: X3993_nAcc_S_SL7613


title: X2292_DLPFC_C_SL7614

value: Control


title: X3706_AnCg_C_SL7621


title: X4001_nAcc_M_SL7611


title: X2208_AnCg_M_SL7409


title: X3525_nAcc_S_SL7612


title: X3038_AnCg_B_SL7408


title: X2316_nAcc_C_SL7623


title: X3651_DLPFC_S_SL7405


title: X3071_AnCg_M_SL7406


title: X3994_AnCg_M_SL7407


title: X3709_DLPFC_M_SL7404


title: X4383_nAcc_B_SL7402


title: X3836_nAcc_M_SL7401


title: X3836_DLPFC_M_SL7403


title: X4413_AnCg_S_SL7398


title: X2353_AnCg_S_SL7399


title: X3684_AnCg_S_SL7400


title: X4385_DLPFC_S_SL7394


title: X4114_DLPFC_S_SL7396


title: X2566_DLPFC_B_SL7395


title: X3079_nAcc_B_SL7392


title: X4463_nAcc_S_SL7390


title: X2315_nAcc_M_SL7391


title: X2941_nAcc_S_SL7389

value: Other


title: X3410_AnCg_S_SL7387


title: X3709_AnCg_M_SL7386


title: X2267_AnCg_M_SL7388


title: X2248_DLPFC_C_SL7393


title: X3965_DLPFC_C_SL7383


title: X2950_AnCg_S_SL7385


title: X3071_DLPFC_M_SL7384


title: X3706_DLPFC_C_SL7381


title: X4087_DLPFC_B_SL7382


title: X4063_nAcc_C_SL7377


title: X3706_nAcc_C_SL7378


title: X3275_AnCg_C_SL7397


title: X3426_AnCg_M_SL7157


title: X3774_nAcc_C_SL7380


title: X3451_AnCg_B_SL7159


title: X3974_AnCg_M_SL7158


title: X3228_AnCg_C_SL7156


title: X3241_nAcc_B_SL7151


title: X2267_DLPFC_M_SL7154


title: X2664_DLPFC_C_SL7152

value: Asian


title: X3031_DLPFC_M_SL7155


title: X3965_nAcc_C_SL7150


title: X2950_nAcc_S_SL7149


title: X2956_AnCg_S_SL7147


title: X1881_AnCg_B_SL7146


title: X3085_AnCg_B_SL7144


title: X4656_DLPFC_S_SL7143


title: X2311_nAcc_B_SL7379


title: X3038_DLPFC_B_SL7142


title: X3684_DLPFC_S_SL7140


title: X3228_nAcc_C_SL7138


title: X4213_nAcc_S_SL7139


title: X3018_DLPFC_C_SL7141


title: X3755_nAcc_M_SL7137


title: X4656_AnCg_S_SL6673


title: X3018_AnCg_C_SL6671


title: X2315_DLPFC_M_SL6668


title: X3772_DLPFC_B_SL7153


title: X2208_DLPFC_M_SL6669


title: X3281_nAcc_C_SL6670


title: X3196_nAcc_C_SL7148


title: X2384_AnCg_S_SL6672


title: X2956_DLPFC_S_SL6667


title: X3085_nAcc_B_SL6665


title: X3618_nAcc_B_SL6663


title: X3451_nAcc_B_SL6664


title: X4046_AnCg_M_SL7145


title: X2292_AnCg_C_SL6660


title: X2944_AnCg_M_SL6661


title: X3836_AnCg_M_SL6658


title: X4619_DLPFC_S_SL6657


title: X3651_nAcc_S_SL6653


title: X2384_DLPFC_S_SL6654


title: X3410_nAcc_S_SL6650


title: X2466_AnCg_B_SL6647


title: X3365_nAcc_M_SL7136


title: X3711_AnCg_B_SL6648


title: X3572_AnCg_C_SL6649


title: X4262_AnCg_B_SL6646


title: X3994_DLPFC_M_SL6666


title: X4046_DLPFC_M_SL6645


title: X2208_nAcc_M_SL6641


title: X4419_DLPFC_B_SL6644


title: X3709_nAcc_M_SL6662


title: X2466_DLPFC_B_SL6642


title: X3031_nAcc_M_SL6639


title: X4405_nAcc_B_SL6640


title: X2505_AnCg_S_SL6659


title: X4619_AnCg_S_SL6614


title: X3667_AnCg_M_SL6615


title: X4001_DLPFC_M_SL6612


title: X3241_DLPFC_B_SL6611


title: X2353_DLPFC_S_SL6655


title: X2941_DLPFC_S_SL6610


title: X4385_nAcc_S_SL6652


title: X4656_nAcc_S_SL6608


title: X1834_DLPFC_C_SL6609


title: X2292_nAcc_C_SL6606


title: X4359_nAcc_B_SL6607


title: X1834_nAcc_C_SL6605


title: X3481_AnCg_M_SL6416


title: X3452_AnCg_B_SL6414


title: X3516_DLPFC_C_SL6413


title: X3523_DLPFC_C_SL6643


title: X4114_AnCg_S_SL6415


title: X2466_nAcc_B_SL6638


title: X3572_DLPFC_C_SL6412


title: X4463_AnCg_S_SL6616


title: X2941_AnCg_S_SL6613


title: X4366_DLPFC_B_SL6411


title: X4301_DLPFC_S_SL6410


title: X3667_nAcc_M_SL6408


title: X4345_nAcc_B_SL6409


title: X3038_nAcc_B_SL6406


title: X3452_nAcc_B_SL6407


title: X3186_AnCg_C_SL6345


title: X4385_AnCg_S_SL6346


title: X4405_DLPFC_B_SL6342


title: X3241_AnCg_B_SL6344


title: X3064_AnCg_M_SL6343


title: X3426_DLPFC_M_SL6341


title: X2805_DLPFC_C_SL6340


title: X3426_nAcc_M_SL6337


title: X4296_DLPFC_S_SL6339


title: X4087_nAcc_B_SL6338


title: X4001_AnCg_M_SL6417


title: X3772_nAcc_B_SL6336


title: X3071_nAcc_M_SL6335


title: X3710_AnCg_M_SL6133


title: X3974_DLPFC_M_SL6130


title: X3365_AnCg_M_SL6135


title: X3588_DLPFC_C_SL6129


title: X3451_DLPFC_B_SL6131


title: X3168_nAcc_M_SL6127


title: X3004_nAcc_M_SL6126


title: X3686_DLPFC_C_SL6128


title: X3974_nAcc_M_SL6125


title: X4063_AnCg_C_SL6003


title: X4359_AnCg_B_SL6002


title: X2805_AnCg_C_SL6134


title: X3993_AnCg_S_SL6001


title: X3525_AnCg_S_SL6004


title: X2619_DLPFC_C_SL6000


title: X3433_AnCg_C_SL6132


title: X3168_DLPFC_M_SL5997


title: X2944_DLPFC_M_SL5998


title: X3686_nAcc_C_SL5993


title: X3572_nAcc_C_SL5995


title: X4284_nAcc_S_SL5996


title: X3079_AnCg_B_SL5892


title: X2316_DLPFC_C_SL5999


title: X3168_AnCg_M_SL5890


title: X2950_DLPFC_S_SL5888


title: X4383_DLPFC_B_SL5887


title: X3671_AnCg_M_SL5891


title: X2311_DLPFC_B_SL5885


title: X3519_DLPFC_C_SL5886


title: X2956_nAcc_S_SL5884


title: X3281_AnCg_C_SL5883


title: X3711_nAcc_B_SL5882


title: X3186_nAcc_C_SL5881


title: X3671_nAcc_M_SL6124


title: X4639_nAcc_B_SL32273


title: X4619_nAcc_S_SL32272


title: X4419_nAcc_B_SL32271


title: X4114_nAcc_S_SL32268


title: X4366_nAcc_B_SL32270


title: X3994_nAcc_M_SL32266


title: X4046_nAcc_M_SL32267


title: X4301_nAcc_S_SL32269


title: X3927_nAcc_B_SL32265


title: X3684_nAcc_S_SL32263


title: X3710_nAcc_M_SL32264


title: X2267_nAcc_M_SL32262


title: X1881_nAcc_B_SL32261


title: X4413_DLPFC_S_SL32260


title: X3519_nAcc_C_SL32255


title: X4359_DLPFC_B_SL32259


title: X4262_DLPFC_B_SL32257


title: X3634_nAcc_M_SL32256


title: X4357_DLPFC_S_SL32258


title: X3018_nAcc_C_SL32251


title: X4063_DLPFC_C_SL32249


title: X3433_nAcc_C_SL32253


title: X3275_nAcc_C_SL32252


title: X3982_DLPFC_M_SL32248


title: X3516_nAcc_C_SL32254


title: X3710_DLPFC_M_SL32247


title: X3671_DLPFC_M_SL32246


title: X3186_DLPFC_C_SL32242


title: X3275_DLPFC_C_SL32244


title: X4213_DLPFC_S_SL32250


title: X4383_AnCg_B_SL32241


title: X4296_AnCg_S_SL32238


title: X4366_AnCg_B_SL32240


title: X3196_DLPFC_C_SL32243


title: X4301_AnCg_S_SL32239


title: X3982_AnCg_M_SL32235


title: X4284_AnCg_S_SL32237


title: X4213_AnCg_S_SL32236


title: X3634_AnCg_M_SL32234


title: X3064_DLPFC_M_SL32231


title: X3004_DLPFC_M_SL32230


title: X3519_AnCg_C_SL32227


title: X1881_DLPFC_B_SL32229


title: X3196_AnCg_C_SL32225


title: X3481_DLPFC_M_SL32245


title: X2976_nAcc_S_SL31508


title: X3516_AnCg_C_SL32226


title: X2805_nAcc_C_SL31507


title: X2353_nAcc_S_SL31505


title: X3031_AnCg_M_SL31504


title: X1834_AnCg_C_SL31501


title: X2315_AnCg_M_SL31502


title: X2664_nAcc_C_SL31506


title: X2566_AnCg_B_SL31503


title: Exp102_d7_EPCRLow_5

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for sequencing adapters and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

growth_protocol: CD34+CD45RA- cord blood derived cells were cultured for 7 days in serum free media with cytokines (100ng/ml SCF, 100ng/mlFLT3, 50ng/ml TPO) supplemented with UM171 (38nM)

extract_protocol:
RNA extraction using trizol was performed on the sorted population: EPCR+, EPCRlow, EPCR-  using RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)

tag: cell type

value: CD34+CD45RA- cord blood cells

tag: protocol

value: 7 day expansion in UM171

tag: sorted cell population

value: EPCRlow


title: Exp102_d7_EPCRLow_4


title: Exp102_d7_EPCR+_3

value: EPCR+


title: Exp100_d7_EPCRLow_1


title: Exp100_d7_EPCRLow_3


title: Exp100_d7_EPCR-_2

value: EPCR-


title: X3618_AnCg_B_SL32233

value: brain

tag: brain region

tag: age at death


title: Exp100_d7_EPCR-_1


title: Exp100_d7_EPCR-_3


title: X3079_DLPFC_B_SL32232

tag: clinical diagnosis

value: M

tag: ethnicity

value: Caucasian


title: Exp100_d7_EPCRLow_2


title: Exp100_d7_EPCR+_2


title: Exp100_d7_EPCR+_1


title: X3588_AnCg_C_SL32228

value: AnCg

tag: post-mortem interval

tag: brain ph


title: 183L

city: Torrance

first: Tsai-Der

last: Chuang

state: California

address: 1124 WEST CARSON STREET

department: OB-GYN

institute: LA Biomed at UCLA medical center

description:
processed data file:
mRNA: X190_FC1.5_pVal0.05_470_genes.txt
miRNA: X190_FC1.5_pVal0.05_12_genes.txt
lncRNA: X190_FC1.5_pVal0.05_414_genes.txt

data_processing:
Demultiplexing performed by bcl2fastq v2.17
LncRNA reads were aligned onto the LNCpedia High-confidence database version 4 and read counts were generated with the RSEM pipeline. miRNA alignment and read count was performed using the CAP-miRSeq pipeline and the latest miRBase human dataset (miRBase: http://www.mirbase.org). mRNA reads were aligned onto the UCSC Human Genome hg19 using the Bowtie2 aligner and read counts were generated with the RSEM pipeline.  Differentially expressed lncRNA, miRNA and mRNA (coding genes) were identified using the EdgeR package and further sorted based on 1.5 fold change cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing read counts, expression levels (CPM), expression change (logFC), etc.

source_name: Leiomyoma #183

extract_protocol:
Total RNA was isolated from leiomyoma and matched myometrium using miRNeasy Mini Kit (Qiagen, Germantown, MD) and RNA concentration and integrity were determined using a Nanodrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) according to manufacturer’s protocols.
Samples with RNA integrity numbers (RIN) greater than or equal to 9 were used for library preparation. Briefly, one microgram of total RNA from each tissue was used to produce strand-specific cDNA libraries using the Truseq (Illumina, San Diego, CA) according to manufacturer's instructions. Individual libraries were then sequenced using 12 lanes of 76-bp paired-end reads on an Illumina Genome Analyzer IIx to an average depth of 50 M reads per library. For the production of miRNA sequencing libraries 500 ng of total RNA from the tissues was used and libraries were prepared according to the specifications of the Truseq small-RNA kit (Illumina). Each library was then pooled and sequenced on a MiSeq single-ended 35-bp run (Illumina) to >1 M reads per library.

tag: ethinity

value: Hispanic

value: uterus

tag: tissue subtype

value: Leiomyoma


title: 183M

source_name: Myometrium #183

value: Myometrium


title: 190M

description:
processed data file:
mRNA: X189_FC1.5_pVal0.05_1128_genes.txt
miRNA: X189_FC1.5_pVal0.05_42_genes.txt
lncRNA: X189_FC1.5_pVal0.05_792_genes.txt

source_name: Myometrium #190


title: 189L

description:
processed data file:
mRNA: X183_FC1.5_pVal0.05_913_genes.txt
miRNA: X183_FC1.5_pVal0.05_15_genes.txt
lncRNA: X183_FC1.5_pVal0.05_520_genes.txt

source_name: Leiomyoma #189


title: 189M

source_name: Myometrium #189


title: Bloodlinc_ChIRP-seq_Rnase_CTL

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Library strategy: ChiRP-seq
Reads were mapped to mm9 using bowtie2 (Langmead and Salzberg 2012). Peak calling was performed on uniquely-mapped reads relative to input control using MACS (Zhang et al. 2008) with default parameters and “--bw=300 --mfold 10 30”. High-confidence peaks were identified based on several criteria. First, peak coverage was quantified using BEDTools (Quinlan and Hall 2010), and only peaks with an average per-base coverage greater than 10 reads were considered. Then only peaks with a relative read density >10-fold over the background model and an absolute read pileup >100 for the complete probe set or >50 for the split probe sets were retained. Finally, peaks in treated samples overlapping peaks in the input, RNase, or untreated controls were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Uniquely-mapped reads in bigwig format. Peaks in text format.

source_name: MEL

growth_protocol: 40 million MEL cells were harvested after 5 days of 2% DMSO-induced differentiation

extract_protocol:
ChIRP-seq was conducted as described (Chu et al. 2011; Chu et al. 2012).
Non-strand-specific cDNA libraries were sequenced on an Illumina HiSeq2000 platform.

value: 2% DMSO day 5

value: MEL


title: Bloodlinc_ChIRP-seq_noProbes_CTL


title: Bloodlinc_ChIRP-seq_oddProbes


title: Exp102_d7_EPCR-_4


title: 60-T

city: Albuquerque

first: Kristina

middle: Antonia

last: Trujillo

state: New Mexico

address: 915 Camino de Salud NE

department: Cell Biology and Physiology

institute: University of New Mexico

data_processing:
BaseCalling with IonTorrent BaseCaller version 5.0.13
Aligned with IonTorrent tmap version 5.0.13
Aligned with STAR version 2.5.1b
Feature Counts generated with htseq-count 0.61p1, options -f bam --stranded=no -m union
Normalization and pairwise differential expression analysis using R 3.2.2, edgeR 3.12.0 and DESeq 1.22.0
Genome_build: Human GRCh37 PII d5
Supplementary_files_format_and_content: csv table of feature counts per gene per sample

source_name: breast fibroblasts_tumor

growth_protocol: Primary culture according to Stampfer, 1985 PMID: 3857588. Grown in DMEM 10%FBS. Passage 2 cells

extract_protocol:
Qiagen RNAEasy kit
DNaseI treatment, Thermo Fisher Ribo Minus, Ion Total RNASeq Library Kit v2

value: fibroblasts

value: breast

tag: culture protocol

value: primary culture Passage 2

tag: tumor status

value: tumor tissue

tag: patient id


title: 60-5cm

source_name: breast fibroblasts_adjacent normal 5 cm

tag: tissue

value: adjacent normal tissue


title: 60-1cm

source_name: breast fibroblasts_adjacent normal 1 cm


title: DXS//PS-37 rep1

city: St. Louis

first: Malia

last: Gehan

state: Missouri

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
BBTools (v36.20)   using parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo ktrim=l k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=20 minlen=20 (Bushnell, 2016). Any parameters not specified were run as default.
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to index the transcripts with the default parameters and the Manihot esculenta genome (Mesculenta_305_v6.1.transcript.fa.gz) from Phytozome (Goodstein et al., 2012).
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to quantify reads with parameters:-t 40 -b 100. Any parameters not specified were run as default.
Genome_build: Manihot esculenta genome (Mesculenta_305_v6.1.transcript.fa.gz) from Phytozome (Goodstein et al., 2012)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Manihot esculenta

source_name: DXS//PS-37_storage root

growth_protocol: The transgenic 60444 lines co-expressing crtB and DXS genes, and the non-transgenic control cultivar 60444 were field tested at the Isabela Agriculture Research Station of the University of Puerto Rico, Mayaguez, Puerto Rico. Four consecutive trials were conducted, the first established from invtro plants, while the three subsequent trials were established from stake cuttings. All trials were conducted under permit conforming to all rules and regulation of the United State Department of Agriculture and the Puerto Rican Department of Agriculture. For RNA-sequencing samples were obtained from the third-generation stake-derived plants harvested at 12 months after planting. This third generation trial was established in a randomized complete block design with 6 reps with 10 plants/line/rep. Only samples obtained from the first three reps were used for sequencing. At harvest, storage roots were dugout (1 root per plant per rep) and peeled, chopped and immediately flash frozen in liquid Nitrogen and shipped on dry ice to the University Nebraska Lincoln for processing.

extract_protocol:
Total RNA was extracted from 200 mg of freezdried storage root tissue following protocol (Kumar et al. 2007)
For library preparation, Illumina TruSeq sample preparation kit with polyA mRNA selection was used with one microgram of total RNA per sample, following manufacturer’s instructions (Illumina). Nine libraries were pooled and sequenced using an Illumina HiSeq 2000 with paired-end reads of 101 bp at MOgene LC, St. Louis, MO.

tag: cultivar/line

tag: genotype/variation

value: Transgenic co-expressing DXS and crtB genes

tag: timepoint

value: 12 months after planting from confined field trial

value: storage root


title: 55-T

tag: cell type


title: DXS//PS-37 rep2


title: Bloodlinc_ChIRP-seq_evenProbes

tag: protocol


title: DXS//PS-37 rep3


title: 55-5cm


title: DXS//PS-20 rep2

source_name: DXS//PS-20_storage root


title: 55-1cm


title: -vitC allo-iTregs 2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; htseqcounts*.rpkm files: CSV format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: -vitC allo-iTregs

extract_protocol:
Total RNA was isolated from purified APCs with RNAeasy Plus mini kit (Qiagen).
Purification of poly‑A containing mRNA was done using poly‑T oligo attached magnetic beads (Illumina). Following the purification, the mRNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).

tag: strain background

value: Foxp3 RFP reporter

tag: age

value: 6-10 weeks

value: secondary lymphoid organs (spleen and peripherla LNs)

value: in vitro induced alloantigen specific regulatory T cells

tag: cell subtype

value: FACS sorted allo-iTregs (CD4+CD90.2+Foxp3RFP+)

tag: treated with

value: none (untreated)


title: 53-T


title: DXS//PS-20 rep1


title: +vitC allo-iTregs 3

source_name: +vitC allo-iTregs

value: vitamin C


title: 190L

source_name: Leiomyoma #190

value: Hispanic

value: uterus

value: Leiomyoma


title: Wild-type 60444 rep3

source_name: Wild-type 60444_storage root

value: non-transgenic control harvested at 12 months


title: -vitC allo-iTregs 3


title: +vitC allo-iTregs 1


title: 53-1cm

value: fibroblasts

value: breast

value: primary culture Passage 2


title: 53-5cm

value: adjacent normal tissue


title: +vitC allo-iTregs 2


title: Wild-type 60444 rep2

value: 12 months after planting from confined field trial


title: Wild-type 60444 rep1

value: storage root


title: MCF7_ChIP_LowCell_Input

city: Stanford

first: Mark

middle: A

last: Zarnegar

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: Input for low cell Native chromatin ChIP-seq

data_processing:
Sequence reads were generated by Illumina's NextSeq500 platform.
MCF7 reads were aligned to the hg19 genome using Bowtie 1.1.2 with the following parameters: (-5 = 15; -e = 40; -v = 2; -m = 1). Neurosphere reads were aligned to the mm9 genome using Bowtie 2.2.6.2 using -very-fast-local.
Samtools was used to convert and/or filter alignements to BAM files containing all reads with MAPQ > 1
BAM files were then used with Deeptools bamCoverage to produce normalized (RPKM) BigWig signal tracks using 100 bp bins.  Reads were extended to 500 bp.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: BigWig files contain RPKM nnormalized genome-wide signals generated with bamCoverage verison 2.3.6.0.  Scores were calculated using 100 bp bins after extending reads to 500 bp.

source_name: Breast cancer cells

growth_protocol: MCF7 were grown according to ATCC instructions. To produce neurospheres, mice (Black6 from a mixed C57Bl6 and B6C3 background) were euthanized by CO2, decapitated, and their brains immediately removed. The subventricular zone (SVZ) was micro-dissected and stored in ice-cold PBS for further processing. The tissue was digested using Liberase DH (Roche) and DNase I (250 U ml−1) at 37 °C for 20 min followed by trituration. Digested tissue was washed in ice-cold HBSS without calcium and magnesium, filtered through a 40-μm filter and FACS-sorted as Lineage−CD24− cells into neurosphere growth media that is, Neurobasal-A (Invitrogen) supplemented with Glutamax (Life Technologies), 2% B27-A (Invitrogen), mouse recombinant epidermal growth factor (EGF; 20 ng ml−1) and basic fibroblast growth factor (bFGF; 20 ng ml−1) (Shenandoah Biotechnology). Lineage cells were depleted using mouse CD45, CD31, and Ter119 (Biolegend).

extract_protocol:
For ChIP samples,unfixed cells were clarified after enzymmatically digesting and lysing cells, then histone-DNA complexes were isolated with antibody. For TCL samples, cells were permeablized and treated with restriction enzymes to fragment chromatin, then diluted with lysis buffer.  Antibody-adapter complexes were added to chromatin fragment solution, then a ligation mix was added to facilitate proximity ligation of the antibody bound adapter.  DNA was puried and ligated DNA was amplified prior to library construction.
Libraries were prepared with Illumina's NEXTERA DNA prep kit (FC-121-1031)

tag: chip antibody


title: P1-2

city: Guangzhou

first: Endashaw

middle: Jebessa

last: Bekele

state: Guangduong

address: Wushan street,Tianhe district

department: Animal Genetics, Breeding and Reproduction

institute: South China Agricultural University

description: RNase R treated and ribo- RNAs

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences and low quality reads were filtered with the Fastx-Toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/) and Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Sequenced reads were assembled by Cufflinks, and mapped to chicken genome using Bowtie software (http://bowtie-bio.sourceforge.net /index.shtml) and Tophat (Trapnell et al., Bioinformatics, 2009).
Annotating high confidence miRNA using deep sequencing data (Kozomara A, Nucleic Acids Res 2014)
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: Excel file with abundance measurements. A fasta file with the novel miRNA sequences is available on the series record.

organism: Gallus gallus

source_name: leg muscle

extract_protocol:
Total RNA was extracted from two embryonic and one post hatch chick leg muscle using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: leg muscle

value: 1 day post hatch

tag: breed

value: Xinghua chicken

tag: Sex

value: female


title: P1-1

description: RNase R treated and ribo- RNAs


title: brl1K242R mutant, mst2D cells_small RNA-seq

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: size selected small RNA from whole cell lysate

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 instrument.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
for mRNA: Illumina 3' adaptors were trimmed using the preprocessingReads function from QuasR by trimming the 3'end with GATCGGAAGAGCACACGTCTGAACTCCAGTCAC. for smallRNA TGGAATTCTCGGGTGCCAAGG
Fastq files were aligned to the S. pombe genome using qAlign. Paramters for RNA and smallRNA: Bowtie 1.4.0 with parameters -m 100 --best --strata
Bowtie sam out put was converted to wig files using qExportWig from the QuasR package. For smallRNA: window size of 1bp and strand-specificity. Output was log2(x+1) transformed. For mRNA: window size of 10bp and strand-specificity.
Genome_build: sPombe160708
Supplementary_files_format_and_content: wig files containing normalized genome mapping read counts for visualization in UCSC or IGV.

organism: Schizosaccharomyces pombe

source_name: sRNA-seq from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and brl1 mutated to K242R and mst2 deleted

growth_protocol: Cells were grown in YES to OD=0.5 and harvested

extract_protocol:
Total RNA was isolated from exponentially growing cells using hot phenol. For sRNA-Seq, the RNA was fractionated using RNeasy Midi columns (Qiagen). The flow-through fraction was precipitated and aliquots of 25 ug were separated by 17.5% PAGE to isolate the 18–28-nucleotide fraction.
Libraries were prepared using either the TruSeq Stranded mRNA library Prep Kit (for RNA) or the Illumina TruSeq small RNA kit according to manufacturers instructions. For barcodes, see sample characteristics.

tag: strain

tag: genotype

value: h+ leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+ shade6-250/natMX mst2D::kanR brl1-K242R

tag: illumina barcode

value: CTTGTA


title: MCF7_H3K27me3_Rep2_TCLSeq

description: Native chromatin TCL-seq using 2000 cells

value: H3K27me3 (Active Motif #39155)


title: brl1K242R mutant cells_small RNA-seq

source_name: sRNA-seq from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and brl1 mutated to K242R

value: h- leu1-32 ura4-D18 ade6-704 trp1+::ade6+ shade6-250/natMX brl1-K242R

value: CGATGT


title: DXS//PS-20 rep3

value: Transgenic co-expressing DXS and crtB genes


title: E16-2

description: RNase R treated and ribo- RNAs

value: E16 embryo age


title: MCF7_H3K27me3_2K_Rep2_ChIPSeq

description: Native chromatin ChIP-seq using 2000 cells


title: MCF7_H3K27me3_2K_Rep1_ChIPSeq


title: MCF7_H3K27ac_200_Rep2_ChIPSeq

description: Native chromatin ChIP-seq using 200 cells

value: H3K27ac (Active Motif #39133)


title: MCF7_H3K27ac_200_Rep1_ChIPSeq

value: breast


title: E11-1

description: RNase R treated and ribo- RNAs

value: E11 embryo age


title: E11-2

description: RNase R treated and ribo- RNAs


title: MCF7_H3K27ac_400_Rep2_ChIPSeq

description: Native chromatin ChIP-seq using 400 cells


title: -vitC allo-iTregs 1

value: Foxp3 RFP reporter

value: 6-10 weeks

value: secondary lymphoid organs (spleen and peripherla LNs)

value: in vitro induced alloantigen specific regulatory T cells

value: FACS sorted allo-iTregs (CD4+CD90.2+Foxp3RFP+)

value: none (untreated)


title: MCF7_H3K27ac_2K_Rep2_ChIPSeq


title: MCF7_H3K27ac_400_Rep1_ChIPSeq


title: MCF7_H3K27ac_2K_Rep1_ChIPSeq


title: wild type RNA-seq

description: stranded poly(A)-selected mRNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene

source_name: poly(A) selected RNA from whole cell lysate

value: h- leu1-32 ura4-D18 ade6-704 trp1+::ade6+ shade6-250/natMX


title: mst2D RNA-seq

description: stranded poly(A)-selected mRNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and mst2 deleted

value: h+ leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ shade6-250/natMX mst2D::kanR

value: GCCAAT


title: paf1-Q264Stop, mst2D sRNA-seq

description: small RNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and paf1 mutated to Q264Stop (paf1sms8) and mst2 deleted

source_name: size selected small RNA from whole cell lysate

value: h- leu1-32 ura4-D18 ade6-704 trp1+::ade6+ shade6-250/natMX paf1-sms8::LEU2 mst2D::kan

value: CAGATC


title: paf1-Q264Stop, mst2D RNA-seq

description: stranded poly(A)-selected mRNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and paf1 mutated (paf1sms8, paf1-Q264Stop) and mst2 deleted

value: ATCACG


title: paf1-Q264Stop sRNA-seq

description: small RNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and paf1 mutated to Q264Stop (paf1sms8)

value: h- leu1-32 ura4-D18 ade6-704 trp1+::ade6+ shade6-250/natMX paf1-sms8::LEU2

value: ACTTGA


title: paf1-Q264Stop RNA-seq

description: stranded poly(A)-selected mRNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and paf1 mutated (paf1sms8, paf1-Q264Stop)

value: GATCAG


title: wild type sRNA-seq

description: small RNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene


title: pdp3D RNA-seq

description: stranded poly(A)-selected mRNA sequencing from strain expressing siRNAs targeting an inserted cox4 intron in the ade6 gene and pdp3 deleted

value: h+ leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ shade6-250/natMX pdp3D::kan

value: CTGAAGCT-GGCTCTGA


title: MCF7_H3K36me3_2K_Rep2_ChIPSeq

value: breast

value: H3K36me3 (Abcam ab9050)


title: MCF7_H3K27ac_10K_Rep2_ChIPSeq

description: Native chromatin ChIP-seq using 10,000 cells

value: H3K27ac (Active Motif #39133)


title: MCF7_H3K27ac_10K_Rep1_ChIPSeq


title: MCF7_H3K36me3_2K_Rep1_ChIPSeq


title: E16-1

description: RNase R treated and ribo- RNAs

value: leg muscle

value: E16 embryo age

value: Xinghua chicken

value: female


title: Sin3a-Mut2

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

description:
mRNA
Sin3a deletion in E12.5 mouse lung endoderm.
Processed data file: Sin3a_mutant-vs_het_control_fpkm.txt

data_processing:
Alignment was done by using Tophat (Bowtie2).
Differentiation expression and FPKM were generated by Cufflink.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Sin3a_mutant-vs_het_control_fpkm.txt: Tab-delimited gene count table generated from pipeline tophat->cufflinks includes normalized FPKMs.

source_name: embryonic lung, Sin3a-Mut

extract_protocol:
RNA extracted from dissected embryonic lungs using Qiagen miRNeasy microkit.
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with paired-end 75bp sequencing chemistry.

tag: strain/background

value: Shh-Cre;Sin3a flox/flox

tag: developmental stage

value: lung


title: Sin3a-Mut1

tag: tissue


title: Sin3a-Mut3

tag: genotype/variation


title: D3.75 Bry+ cells 48h-Dox ChIPSeq

city: Boston

first: avinash

last: waghray

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

description: Mesodermal-derivatives from mESCs

data_processing:
ChIPSeq: Fastq files were mapped to the genome using Bowtie (v1.0): bowtie -p 4 -n 2 -l 100 --best -m 1
ChIPSeq: The mapped output file was processed through MACS analysis (v1.4) software to determine peaks: macs14 -t  -c -g mm -w -S -n
ChIPSeq: Homer software was used for annotation of the peaks: annotatePeaks.pl mm9
ChIPSeq: Wig files: generated by the MACS program
Genome_build: mm9

source_name: D3.75 Bry+ cells 48h-Dox

growth_protocol: Bry-GFP+ cells sorted from embryoid bodies at day 3.75 of in vitro differentiation and cultured in StemPro-34 media

extract_protocol:
For ChIPSeq, 10 million cells were trypsinized and fixed with 11% formaldehyde in media for 20 minutes with rotation. The fixation reaction was stopped by adding 125 mM Glycine solution and rotating the mixture for 5 minutes at room temperature. Cells were then quick frozen and stored at -80ºC. Cells were thawed and lysed first in 200 μl of lysis Buffer I, followed by 200 μl of lysis buffer II. The resulting nuclear pellets were suspended in 135 μl of lysis buffer III. Sonication was performed using the Covaris sonication instrument using the following settings: Time: 10 minutes, Duty cycle: 5%, Intensity: 4, Cycles per burst: 200, Temperature: 4ºC. Finally, 65 μl of the sonicated solution was used to perform the ChIP pull down using Protein G Dynabeads conjugated to anti-Flag antibody, overnight at 4ºC. Cells without Dox were used as negative control.
For ChIPSeq, DNA library preparation was done using the NEB ChIP-Seq sample preparation kit. The libraries were run on HiSeq 2000 machines at the genomics shared resource facility (SRF) at Icahn School of Medicine at Mount Sinai, NY. The concentration of the libraries was assayed using Agilent Bioanalyzer and sequenced using 1*100bp on a HiSeq 2000 platform

treatment_protocol: Culture for 48 hours in the presence or absence of doxycycline (Dox)

value: Mesodermal derivatives from mESCs

tag: cell line

value: AinV/Bry-GFP ESC line

tag: expression

value: control


title: D3.75 Bry+ cells 48h+Dox ChIPSeq

description: Mesodermal-derivatives from mESCs expressing Flag-Hes5

source_name: D3.75 Bry+ cells 48h+Dox

tag: cell type


title: Sin3a-hetCont3

description:
mRNA
Processed data file: Sin3a_mutant-vs_het_control_fpkm.txt

source_name: embryonic lung, Sin3a-hetCont

value: Shh-Cre;Sin3a flox/+


title: Sin3a-hetCont2


title: Sin3a-hetCont1


title: 148B-CA3-4

status: Public on Jun 21 2017

city: Davis

first: Rayna

middle: Michelle

last: Harris

address: 1 Shields Ave

institute: University of California Davis

data_processing:
Raw reads were downloaded from the Amazon cloud server to the Stampede Cluster at the Texas Advanced Computing Facility for processing and analysis.
RNA quality was checked using the bioinformatic program FASTQC.
Low quality reads and adapter sequences were removed using the program Cutadapt.
To explore gross patterns at the whole transcriptome level, we used a Kallisto for read counting and mapping.
We used DESeq2 for gene expression normalization and quantification
We used the a rank-based gene ontology analysis of gene expression data using the R package GO MWU
Statistics on the principal component analyses were conduct in R
Genome_build: Gencode MV11 mouse transcriptome
Supplementary_files_format_and_content: kallisto count files

source_name: 15148B CA3 control

extract_protocol:
RNA from CA1, CA3, and from DG was isolated using the Maxwell 16 LEV RNA Isolation Kit (Promega).
NA libraries were prepared by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin using the Illumina HiSeq platform.

treatment_protocol: Mice were either collected from their home cage or subjected to one of three behavioral manipulations: control, consistent cognitive training or conflict cognitive training.

value: hippocampus

tag: rnaseqid

tag: mouse

tag: year

value: WT

tag: region

tag: jobnumber

tag: group


title: 148B-CA1-4

source_name: 15148B CA1 control


title: 148A-DG-3

source_name: 15148A DG conflict

value: DG

value: conflict


title: 148A-CA3-3

source_name: 15148A CA3 conflict


title: 148A-CA1-3

source_name: 15148A CA1 conflict


title: 148-DG-2

source_name: 15148 DG homecage

value: homecage


title: 148-CA3-2

source_name: 15148 CA3 homecage


title: 147D-CA3-1

source_name: 15147D CA3 control


title: 148-CA1-2

source_name: 15148 CA1 homecage


title: 147C-CA1-3

source_name: 15147C CA1 consistent

value: consistent


title: 147-CA3-4

source_name: 15147 CA3 homecage


title: 147-DG-4

source_name: 15147 DG homecage


title: 147D-DG-1

source_name: 15147D DG control


title: 147C-DG-3

source_name: 15147C DG consistent


title: 147C-CA3-3

source_name: 15147C CA3 consistent


title: 146C-DG-4

source_name: 15146C DG consistent


title: 146D-CA3-3

source_name: 15146D CA3 control


title: 146C-CA1-4

source_name: 15146C CA1 consistent


title: 146D-DG-3

source_name: 15146D DG control


title: 146D-CA1-3

source_name: 15146D CA1 control


title: 147-CA1-4

source_name: 15147 CA1 homecage


title: 146B-CA3-2

source_name: 15146B CA3 control


title: 146B-CA1-2

source_name: 15146B CA1 control


title: 146B-DG-2

source_name: 15146B DG control


title: 148B-DG-4

source_name: 15148B DG control


title: 146A-CA1-2

source_name: 15146A CA1 conflict


title: 146A-DG-2

source_name: 15146A DG conflict


title: 145B-DG-1

source_name: 15145B DG control


title: 145B-CA1-1

source_name: 15145B CA1 control


title: 146A-CA3-2

source_name: 15146A CA3 conflict


title: 144D-DG-2

source_name: 15144D DG control


title: 145A-CA3-2

source_name: 15145A CA3 conflict


title: 145A-CA1-2

source_name: 15145A CA1 conflict


title: 144D-CA3-2

source_name: 15144D CA3 control


title: 144C-DG-2

source_name: 15144C DG consistent


title: 145A-DG-2

source_name: 15145A DG conflict


title: 143D-DG-3

source_name: 15143D DG control


title: 144A-CA3-2

source_name: 15144A CA3 conflict


title: 144B-CA1-1

source_name: 15144B CA1 control


title: 144A-DG-2

source_name: 15144A DG conflict


title: 144C-CA3-2

source_name: 15144C CA3 consistent


title: 144A-CA1-2

source_name: 15144A CA1 conflict


title: 144C-CA1-2

source_name: 15144C CA1 consistent


title: 143D-CA1-3

source_name: 15143D CA1 control


title: 143C-CA1-1

source_name: 15143C CA1 consistent


title: 143B-CA1-1

source_name: 15143B CA1 control


title: 143B-DG-1

source_name: 15143B DG control


title: 143A-DG-1

source_name: 15143A DG conflict


title: 143A-CA3-1

source_name: 15143A CA3 conflict


title: 142C-DG-S

source_name: 15142C DG consistent


title: 142C-CA1-S

source_name: 15142C CA1 consistent


title: RNA-seq_WT.P56.adult

first: Alex

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

description:
Wild-type Adult
Gompers_logRPKM_Matrix.txt

data_processing:
Base calls were performed with bcl2fastq2.
RNA-seq: FASTQ files were aligned to the mouse genome (mm9) using STAR (2.4.2a).
ChIP-seq: Reads were filtered and mapped to the mouse genome mm9 via BWA (v0.7.13) and peak-calling was performed using MACS (v2.10) with a p-value cutoff of 1E-4.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files containing coverage, and txt containing MACS2 peak-calls.

source_name: Bulk forebrain

extract_protocol:
Bulk forebrain was microdissected from Chd8+/del5 and matched WT littermates at e12.5,e14.5, e17.5, P0, and from adults (>P56). Total RNA was isolated using Ambion RNAqueous and assayed using an AgilentBioAnalyzer instrument.
Stranded mRNA sequencing libraries were prepared using TruSeqStranded mRNA kits and 6-12 samples per lane were pooled and sequenced on the IlluminaHiSeq platform using a single end 50 bp (e14.5, e17.5, P0, adult) or paired end 100 bp (e12.5) strategy.

tag: Stage


title: Chd8_Input_merged

description: Chd8 Input merged

extract_protocol:
ChIP-seq was performed on cross-linked adult mouse forebrain following established protocols using Chd8 antibody (ab114126; Abcam). Two biological replicates were generated with matched input control libraries generated and sequenced alongside IP libraries.
Libraries were prepped using the NuGen Ovation Ultralow Library System V2, and pooled and single end 50 sequenced on one lane of a HiSeq 4000.

tag: chip antibody

tag: strain


title: RNA-seq_Het.P56.adult

description:
Het Adult
Gompers_logRPKM_Matrix.txt

tag: genotype

value: Het


title: RNA-seq_Het.P0.Chd8

description:
Het P0
Gompers_logRPKM_Matrix.txt


title: RNA-seq_WT.P0.Chd8

description:
Wild-type P0
Gompers_logRPKM_Matrix.txt


title: Chd8_ChIP_merged

description: Chd8 ChIP merged

value: Chd8 (Abcam ab114126)


title: RNA-seq_WT.e14.5

description:
Wild-type e14.5
Gompers_logRPKM_Matrix.txt


title: RNA-seq_Het.e14.5

description:
Het e14.5
Gompers_logRPKM_Matrix.txt


title: RNA-seq_WT.e17.5

description:
Wild-type e17.5
Gompers_logRPKM_Matrix.txt


title: RNA-seq_WT.e12.5

description:
Wild-type e12.5
Gompers_logRPKM_Matrix.txt


title: 144B-CA3-1

source_name: 15144B CA3 control


title: prp8-N1869D_TechRep_2

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Trimming of adapters using Trimmomatic with parameters: 3:30:10 and MINLEN:18.
Trimmed reads were aligned to the S. cerevisiae genome (Ensembl R64‐1‐1) using Bowtie2 end-to-end alignment. Parameters of alignment were ‘score‐min L,‐0.4,‐0.4 –very‐sensitive’.
For identification of lariat reads spanning the lariat branch, each read that failed to align to the genome in end‐to‐end fashion was considered a candidate lariat branch read. These reads were split into mate paired reads at every GT nucleotide in the forward and reverse complement strands. The subset of mate pairs where each read in the mate pair is at least 10 nucleotides were candidates for alignment. These reads were then assessed for alignment using Bowtie2 in paired‐end mode with the fragment containing the GT as mate 1 and the other as mate 2, using parameters ‘–ff ‐I 0 ‐X 5000 –no‐mixed –no‐discordant’.. Since a single read split in this fashion can yield several possible alignments, the possible GT split gnments were collapsed into a single best available paired‐end alignment defined as the alignment that minimizes the number of mismatches.
5’SS, Br locations and strandedness were obtained from each lariat read using the position of GT on the lariat read alignment.
Genome_build: S.cerevisiae-Ensembl R64-1-1
Supplementary_files_format_and_content: Excel file which includes splice site locations and counts

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: 30C; rich media

extract_protocol:
Cells were harvested by filtration, flash frozen in liquid Nitrogen and RNA was extracted using hot acid-phenol, chloroform extraction. 5ug total RNA was used as input for Illumina Ribo-Zero Gold kit (Yeast) followed by treatment with RNaseR (Epicentre).
RNA libraries were prepared for sequencing using altered double strand cDNA synthesis conditions followed by standard Illumina TruSeq RNA-seq protocol with modified cleanup strategy between steps.

tag: strain info.

value: mat a prp8D::LYS2 his3 leu2 ura3 lys2 dbr1::Kan pRS313-prp8-N1869D


title: prp8-V1860D

value: mat a prp8D::LYS2 his3 leu2 ura3 lys2 dbr1::Kan pRS313-prp8-V1860D


title: prp8-N1869D


title: prp8-N1869D_TechRep_1


title: 143C-DG-S

source_name: 15143C DG consistent


title: 192_oocyte

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description: other, cell lysate

data_processing:
The libraries were aligned against the Bos taurus genome UMD3.1 downloaded from Ensembl using the STAR (v2.5.2) aligner. Only reads with a unique match to the genome and less than five mismatches were further filtered to eliminate duplicates with picard (v2.5, http://broadinstitute.github.io/picard/).
The bam files containing non-duplicated reads were used as input for Cufflinks (v.2.2.1) together with Ensembl gene annotation UMD3.1.87 to obtain fragments per kilogram per million reads (FPKM) data. Genes were subjected to analytical procedures if FPKM>0.5 in eight or more cells of each group (oocytes, innerCC, outerCC).
The non-duplicated reads were submited to counting according to the Ensembl gene annotation UMD3.1.87 using HTSeq (v. 0.6.1) software.
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

organism: Bos taurus

source_name: oocyte

extract_protocol:
We extracted RNA from cumulus cells using the guanidinium thiocyanate-phenol chloroform procedure (Trizol reagent, Thermofisher), with the addition of 0.5ul GlycoBlue Coprecipitant (Thermofisher) as a RNA carrier.  For the oocytes, we added 2l of the lysis buffer (20 IU/l RNase inhibitor (Amresco), 0.2% Triton X-100 (Amresco)) to the tube.
We eluted the RNA from CCs in 4ml of a solution containing dNTPs and oligo-dT30VN and proceeded with the polyA+ whole transcriptome amplification with the Smart-seq2 protocol for cDNA amplification. For the oocytes, we added 2l of the lysis buffer (20 IU/l RNase inhibitor (Amresco), 0.2% Triton X-100 (Amresco)) to the tube and proceeded with the polyA+ whole transcriptome amplification with the Smart-seq2 protocol for cDNA amplification. The samples were subjected to 16 cycles of PCR amplification. For all samples, we used one ng of amplified cDNA for library preparation using the Nextera XT DNA library preg Kit (Illumina, Inc), as and followed the procedures described in the Smart-seq2 protocol.

value: oocyte


title: 192_innerCC

description: RNA

source_name: cumulus cells

value: cumulus cells


title: 191_oocyte

description: other, cell lysate


title: 191_outerCC

description: RNA


title: 191_innerCC

description: RNA


title: 190_outerCC

description: RNA


title: RNA-seq_Het.e17.5

description:
Het e17.5
Gompers_logRPKM_Matrix.txt


title: 189_oocyte

description: other, cell lysate


title: 189_innerCC

description: RNA


title: 189_outerCC

description: RNA


title: 188_outerCC

description: RNA


title: 188_oocyte

description: other, cell lysate


title: 188_innerCC

description: RNA


title: 187_oocyte

description: other, cell lysate


title: 186_outerCC

description: RNA


title: 187_innerCC

description: RNA


title: prp8-V1870N

value: mat a prp8D::LYS2 his3 leu2 ura3 lys2 dbr1::Kan pRS313-prp8-V1870N


title: 186_oocyte

description: other, cell lysate


title: 187_outerCC

description: RNA


title: 186_innerCC

description: RNA


title: PRP8-WT

value: mat a prp8D::LYS2 his3 leu2 ura3 lys2 dbr1::Kan pRS313-PRP8


title: prp8-V1860N

value: mat a prp8D::LYS2 his3 leu2 ura3 lys2 dbr1::Kan pRS313-prp8-V1860N


title: 185_outerCC

description: RNA


title: 185_oocyte

description: other, cell lysate


title: 190_oocyte

description: other, cell lysate


title: 190_innerCC

description: RNA


title: 184_outerCC

description: RNA


title: 181_outerCC

description: RNA


title: 183_innerCC

description: RNA


title: 180_outerCC

description: RNA


title: 183_oocyte

description: other, cell lysate


title: 181_oocyte

description: other, cell lysate


title: 181_innerCC

description: RNA


title: 180_oocyte

description: other, cell lysate


title: 179_outerCC

description: RNA


title: 143C-CA1-S


title: 177_outerCC

description: RNA


title: 178_innerCC

description: RNA


title: 178_outerCC

description: RNA


title: 177_innerCC

description: RNA


title: 176_outerCC

description: RNA


title: 180_innerCC

description: RNA


title: 176_oocyte

description: other, cell lysate


title: 184_oocyte

description: other, cell lysate


title: 176_innerCC

description: RNA


title: 185_innerCC

description: RNA


title: 177_oocyte

description: other, cell lysate


title: H8A_S92_L003_001_Transplant

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell transcriptome from transplanted liver bud
data.lb.transplant.csv

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) or mouse genome (mm10 from UCSC) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38, mm10
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

source_name: iPSC line TkDA3-4

growth_protocol: see information for each individual sample

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.
mRNA-seq


title: 183_outerCC

description: RNA


title: H4B_S184_L006_001_Transplant

treatment_protocol: see information for each individual sample

value: Single cell transcriptome from transplanted liver bud


title: H5B_S185_L006_001_Transplant


title: H6B_S186_L005_001_Transplant


title: H4B_S184_L005_001_Transplant


title: 179_innerCC

description: RNA


title: 178_oocyte

description: other, cell lysate


title: G9B_S177_L001_001_Transplant


title: H1B_S181_L005_001_Transplant


title: G8A_S80_L003_001_Transplant


title: H11B_S191_L006_001_Transplant


title: 179_oocyte

description: other, cell lysate


title: H3B_S183_L006_001_Transplant


title: H12B_S192_L001_001_Transplant


title: H10B_S190_L006_001_Transplant


title: G7A_S79_L005_001_Transplant


title: G2B_S170_L001_001_Transplant


title: G3B_S171_L005_001_Transplant


title: G2B_S170_L006_001_Transplant


title: G1B_S169_L005_001_Transplant


title: F7B_S163_L001_001_Transplant


title: F8B_S164_L005_001_Transplant


title: F7A_S67_L003_001_Transplant


title: F9A_S69_L006_001_Transplant


title: G10B_S178_L006_001_Transplant


title: F6A_S66_L006_001_Transplant


title: F5A_S65_L006_001_Transplant


title: F6B_S162_L006_001_Transplant


title: F5A_S65_L003_001_Transplant


title: F7B_S163_L006_001_Transplant


title: 184_innerCC

description: RNA


title: F3B_S159_L001_001_Transplant


title: F3A_S63_L003_001_Transplant


title: F2B_S158_L006_001_Transplant


title: G1B_S169_L006_001_Transplant


title: F1B_S157_L006_001_Transplant


title: F12A_S72_L005_001_Transplant


title: F10B_S166_L006_001_Transplant


title: F4B_S160_L001_001_Transplant


title: F3A_S63_L005_001_Transplant


title: G6B_S174_L001_001_Transplant


title: G3B_S171_L006_001_Transplant


title: F2A_S62_L006_001_Transplant


title: F10B_S166_L005_001_Transplant


title: F4B_S160_L006_001_Transplant


title: F12B_S168_L006_001_Transplant


title: E7B_S151_L006_001_Transplant


title: E8B_S152_L001_001_Transplant


title: E6B_S150_L001_001_Transplant


title: F11B_S167_L006_001_Transplant


title: F10A_S70_L006_001_Transplant


title: E6B_S150_L006_001_Transplant


title: F4A_S64_L003_001_Transplant


title: E6A_S54_L006_001_Transplant


title: E9B_S153_L006_001_Transplant


title: E5A_S53_L006_001_Transplant


title: E4A_S52_L006_001_Transplant


title: E6A_S54_L005_001_Transplant


title: E8A_S56_L006_001_Transplant


title: E3A_S51_L006_001_Transplant


title: E3B_S147_L006_001_Transplant


title: E2A_S50_L003_001_Transplant


title: E9A_S57_L006_001_Transplant


title: E1B_S145_L006_001_Transplant


title: E4B_S148_L001_001_Transplant


title: E7A_S55_L006_001_Transplant


title: E5B_S149_L001_001_Transplant


title: E12A_S60_L003_001_Transplant


title: E1A_S49_L003_001_Transplant


title: D9B_S141_L006_001_Transplant


title: E10A_S58_L003_001_Transplant


title: E11A_S59_L003_001_Transplant


title: E12B_S156_L006_001_Transplant


title: E1A_S49_L006_001_Transplant


title: E10B_S154_L001_001_Transplant


title: D9A_S45_L005_001_Transplant


title: D8B_S140_L005_001_Transplant


title: D7B_S139_L001_001_Transplant


title: D8B_S140_L006_001_Transplant


title: D5B_S137_L006_001_Transplant


title: D5A_S41_L006_001_Transplant


title: D4B_S136_L006_001_Transplant


title: D4A_S40_L006_001_Transplant


title: D2B_S134_L006_001_Transplant


title: D3A_S39_L006_001_Transplant


title: D2A_S38_L005_001_Transplant


title: D2A_S38_L006_001_Transplant


title: D1B_S133_L006_001_Transplant


title: D1A_S37_L005_001_Transplant


title: D3B_S135_L001_001_Transplant


title: D11B_S143_L001_001_Transplant


title: D1B_S133_L001_001_Transplant


title: D10A_S46_L006_001_Transplant


title: C9B_S129_L006_001_Transplant


title: C7B_S127_L006_001_Transplant


title: C8B_S128_L006_001_Transplant


title: C6B_S126_L001_001_Transplant


title: C7A_S31_L003_001_Transplant


title: C5A_S29_L006_001_Transplant


title: C7B_S127_L001_001_Transplant


title: C5A_S29_L005_001_Transplant


title: C4B_S124_L006_001_Transplant


title: D11B_S143_L006_001_Transplant


title: C4B_S124_L005_001_Transplant


title: C6A_S30_L003_001_Transplant


title: C4B_S124_L001_001_Transplant


title: C3B_S123_L006_001_Transplant


title: C4A_S28_L006_001_Transplant


title: D3B_S135_L006_001_Transplant


title: C2B_S122_L006_001_Transplant


title: C3A_S27_L005_001_Transplant


title: C1A_S25_L003_001_Transplant


title: C3B_S123_L001_001_Transplant


title: D12B_S144_L005_001_Transplant


title: B9A_S21_L006_001_Transplant


title: C11B_S131_L006_001_Transplant


title: B9A_S21_L003_001_Transplant


title: C5B_S125_L006_001_Transplant


title: B9B_S117_L006_001_Transplant


title: B6B_S114_L006_001_Transplant


title: B7A_S19_L006_001_Transplant


title: B6B_S114_L001_001_Transplant


title: B8A_S20_L006_001_Transplant


title: B4A_S16_L006_001_Transplant


title: B3B_S111_L001_001_Transplant


title: B7B_S115_L006_001_Transplant


title: B3B_S111_L006_001_Transplant


title: B2B_S110_L006_001_Transplant


title: B2B_S110_L001_001_Transplant


title: B3A_S15_L003_001_Transplant


title: B11B_S119_L001_001_Transplant


title: B12B_S120_L006_001_Transplant


title: C1A_S25_L006_001_Transplant


title: 192_outerCC

description: RNA


title: B10A_S22_L006_001_Transplant


title: B1B_S109_L006_001_Transplant


title: B4B_S112_L005_001_Transplant


title: B1A_S13_L005_001_Transplant


title: B10B_S118_L001_001_Transplant


title: B10B_S118_L005_001_Transplant


title: B10A_S22_L005_001_Transplant


title: A8B_S104_L006_001_Transplant


title: A8B_S104_L001_001_Transplant


title: A7A_S7_L006_001_Transplant


title: A6B_S102_L006_001_Transplant


title: A9B_S105_L001_001_Transplant


title: A5B_S101_L001_001_Transplant


title: A5A_S5_L006_001_Transplant


title: A4B_S100_L006_001_Transplant


title: A2B_S98_L001_001_Transplant


title: A3A_S3_L003_001_Transplant


title: A2A_S2_L006_001_Transplant


title: A4A_S4_L006_001_Transplant


title: A1B_S97_L006_001_Transplant


title: A1B_S97_L005_001_Transplant


title: A12B_S108_L006_001_Transplant


title: A1A_S1_L006_001_Transplant


title: A11B_S107_L006_001_Transplant


title: A9B_S105_L006_001_Transplant


title: A9B_S105_L005_001_Transplant


title: A11B_S107_L001_001_Transplant


title: A10A_S10_L005_001_Transplant


title: F2_LTLB2

description:
Single cell transcriptome from late time point liver buds
data.lb.late.csv


title: F3_LTLB2

value: Single cell transcriptome from late time point liver buds


title: G7_LTLB2


title: H6_LTLB2


title: E8_LTLB2


title: G2_LTLB2


title: G4_LTLB2


title: E4_LTLB2


title: H7_LTLB2


title: H2_LTLB2


title: E6_LTLB2


title: E5_LTLB2


title: G9_LTLB2


title: H1_LTLB2


title: E7_LTLB2


title: E2_LTLB2


title: E1_LTLB2


title: D6_LTLB2


title: D8_LTLB2


title: D5_LTLB2


title: D3_LTLB2


title: D1_LTLB2


title: C9_LTLB2


title: G1_LTLB2


title: C7_LTLB2


title: C5_LTLB2


title: D4_LTLB2


title: F5_LTLB2


title: E3_LTLB2


title: D9_LTLB2


title: C2_LTLB2


title: B6_LTLB2


title: C4_LTLB2


title: C12_LTLB2


title: B9_LTLB2


title: B3_LTLB2


title: C1_LTLB2


title: B10_LTLB2


title: A8_LTLB2


title: C3_LTLB2


title: A9_LTLB2


title: B8_LTLB2


title: B11_LTLB2


title: B12_LTLB2