title: scRNAseq_064_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_93

status: Public on Aug 01 2018

type: SRA

city: Basel

first: Alex

middle: Charles

last: Tuck

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT

library_source: transcriptomic

data_processing:
Single-cell RNA-seq data processing: Paired-end reads were preprocessed using Trimmomatic, with the following settings: ILLUMINACLIP:Nextera_PE_adapters.fa:2:30:10:1:true LEADING:28 TRAILING:28 SLIDINGWINDOW:1:28 MINLEN:50. The reads were then aligned to mm10 using gsnap version 2015-09-29 with the following settings: --suboptimal-levels=5 -n 1 -Q –nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data processing for ES to NPC timecourse: reads were mapped to mm10 using tophat version 2.0.14 with the settings --mate-inner-dist -30 --mate-std-dev 80 --library-type fr-firststrand , and providing a --transcriptome-index from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40". Uniquely mapping reads from concordant read pairs were retained by filtering for a quality of 50 and the 0x2 flag (samtools view -b -q 50 -f 0x2).
Bulk RNA-seq data for cell lines with HHRz integrations or deletions: reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data for actinomycin D timecourse (half life calculations): reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
CRAC and NET-seq data:  Sequencing reads were preprocessed for standard analyses as follows:
(i) The 3’ adapter was removed (if present) using fastx_clipper.
(ii) Low quality sequence was removed using the fastx toolkit, specifically fastq_quality_trimmer -t 25, fastq_quality_filter -q 20 -p 90 and fastx_artifacts_filter.
(iii) Reads with identical sequence and 5’ inline unique molecule identifier, UMI, were collapsed, as they are likely to arise from duplication during PCR.
(iv) For CRAC, low complexity regions were trimmed from the 3’ end of reads (regions of 2 nt or more where 80 % or more of the sequence comprises one nucleotide). This is because many Mtr4-bound RNA fragments contain non-genome-encoded oligo(A) tails that can lead to apparently unique mapping of repeat RNAs.
(v) Homopolymers and dinucleotide-rich sequences were removed using prinseq-lite, with settings -min_len 18 -lc_threshold 20 -lc_method dust.
To obtain a set of reads that do not map to repetitive regions of the genome or small non-coding RNAs (e.g. retrotransposons, tRNAs, snoRNAs, rRNA), we then filtered reads as follows. Reads were mapped separately, using novoalign, to three indexes: (i) the mm10 genome, (ii) mm10 protein-coding transcripts (cDNAs), and (iii) pseudochromosomes assembled from RepeatMasker repeats, the ribosomal DNA repeat (Grozdanov et al, 2003) and gencode.vM9 small non-coding RNAs (e.g. miRNA, snoRNA, snRNA, rRNA). “Nonrepeat” reads were then defined as those that mapped better to the mm10 genome or cDNAs, than to any of the repeat RNAs or small non-coding RNAs.
We then mapped reads (either after standard preprocessing, or “nonrepeat” reads filtered as described) using bowtie2 (mode: --sensitive) with mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for single-cell RNA-seq: alignments were converted to bigWig files using picard-tools and bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of the ES to NPC differentiation: IGVtools was used to convert BAM files into bigWig format. The bigWigs are not normalised for library size, and one bigWig file is provided for plus and minus strand mapping reads.
bigWig files for bulk RNA-seq of cell lines with HHRz integrations or deletions were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of cells treated with actinomycin D for RNA half life calculations were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for CRAC and NET-seq data: generally, bigWig files were obtained by taking uniquely mapping reads and converting to bigWig with samtools and bedtools. The "mixed" bigWig files contain data from replicate experiments that has been combined prior to generating the bigWig

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: Cells were cultured on gelatin-coated dishes in 2i medium (NDiff 227 with 0.33 v/v LIF conditioned medium, 1 μM MEK inhibitor PD 0325901 (Tocris) and 3 μM GSK3 inhibitor CHIR99021 (Calbiochem))

extract_protocol: For single cell RNA sequencing, 4000 cells were loaded onto a 10-17 μm Fluidigm C1 Single Cell mRNA Seq IFC, and cells captured according to manufacturer’s instructions. The captured cells were manually annotated under a microscope, to identify capture chambers containing cell debris, dead cells, no cells or multiple cells. Reverse transcription and cDNA preamplification was then performed in the 10-17 μm Fluidigm C1 Single Cell mRNA Seq IFC using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System and Advantage 2 PCR kit. cDNA was harvested and diluted to 0.1-0.3 ng/μl. Sequencing libraries were then prepared using the Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Sample Preparation Index Kit according to the Fluidigm instructions, “Using the C1™ Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing.” The 96 libraries from one IFC were pooled and 150 bp paired-end sequencing performed on the Illumina HiSeq2000.

tag: genetic background

value: CB9 (Cast/EiJ x C57BL/6J)

tag: visual annotation for single cell data

value: multi


title: scRNAseq_063_cell_95

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_94

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_89

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_88

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA

value: double


title: scRNAseq_063_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_83

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC

value: BC8 (C57BL/6J x Cast/EiJ)


title: OK1: OK_seq_aB_72h_NT_rep1

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

library_source: genomic

data_processing:
Library strategy: OK-seq
mouse OK-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done as described previosuly (Petryk et al., 2016)
Analysis done as described previosuly (Petryk et al., 2016)
Genome_build: GRCm38p2/mm10 for mouse
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

molecule: genomic DNA

source_name: Activated primary B cells

extract_protocol:
OK-seq was performed in asynchronous mouse B cells activated for 48 hours, as previously described in a detailed protocol (Petryk et al., 2016).
libraries were prepared and sequenced following standard Illumina protocols

tag: cell type

value: Activated primary B cells

tag: genotype

value: WT

tag: strain


title: scRNAseq_064_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: RNAseq_070_bulk

source_name: neural precursor cell (day 6)

growth_protocol: NPCs were derived from mESCs according to Bibel M. Richter J. Schrenk K. Tucker K.L. Staiger V. Korte M. Goetz M. Barde Y.A. Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nat. Neurosci. 2004;7:1003–1009.

extract_protocol: Bulk RNA-sequencing libraries were prepared and sequenced using the Wellcome Trust Sanger Institute sample preparation pipeline with the Illumina TruSeq Stranded RNA Sample preparation kit. RNA was extracted from 1–2 million cells using the QIAGEN RNA Purification Kit on a QiaCube robot. Sequencing quality control and data quality checks were performed by the Sanger Sequencing facility.


title: RNAseq_072_bulk

source_name: neural precursor cell (day 8)


title: scRNAseq_063_cell_77

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: RS2: Repli_seq_aB_48h_NT_rep1

data_processing:
Library strategy: Repli-seq
mouse Repli-seq reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
Log2 ratio was calculated in 100kb bins. Early and late replicating regions were identified based on the bins having positive and negative values respectively
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Replication timing profiles were determined using TimEX as described (Bartholdy et al., PMID: 25987481) with minor modifications.  Briefly, The S/G1 TimEX ratio, proportional to the replication time during S phase, was measured in mature splenic B cells from wild-type C57BL/6NCr mice.  The G1 population was obtained from mature resting B cells (100% G0/G1 arrested), which were isolated using anti-CD43 MicroBeads (Miltenyi Biotech) for negative selection. To obtain the S-phase population, the resting B cells were activated with LPS (25 mg/ml; Sigma), IL-4 (5 ng/ml; Sigma) and RP105 (0.5 mg/ml; BD) for 48 hours (~70% S-phase).   5 million cells were collected for both populations, and whole genome sequencing was performed using standard Illumina library prep and sequenced on HiSeq 2000.
libraries were prepared and sequenced following standard Illumina protocols


title: RNAseq_069_bulk


title: RNAseq_068_bulk

source_name: neural precursor cell (day 3)


title: scRNAseq_063_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_72

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: RNAseq_067_bulk


title: RNAseq_066_bulk

growth_protocol: Cells were cultured on gelatin-coated dishes in in serum + LIF medium (DMEM, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, 15 % (v/v) fetal bovine serum, 0.1 mM beta-mercaptoethanol, 50 μg/ml penicillin, 80 μg/ml streptomycin and home-made LIF conditioned medium)


title: RNAseq_064_bulk


title: RNAseq_063_bulk


title: scRNAseq_063_cell_82

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_71

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_65

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_66

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_76

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: RNAseq_071_bulk


title: scRNAseq_063_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_60

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_59

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_54

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: RNAseq_065_bulk


title: scRNAseq_063_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT

value: debris


title: scRNAseq_063_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_063_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_53

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_063_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_063_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_063_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT

value: empty


title: scRNAseq_063_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_063_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_063_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_063_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: 3367-HJ-0016

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
Basecalls performed using CASAVA version 1.8.4
For RNA-seq, all the reads were mapped to the mouse reference genome (GRCm38/mm10) using TopHat (v2.0.13). The alignment was guided using a Gene Transfer File (GTF version GRCm38.85). Low quality mapped reads (MQ<30) were removed from the analysis. Read count tables were generated using HTSeq (v.0.6.0) based on the Ensembl gene annotation file (Ensembl GTF version GRCm38.85) (--mode=union --stranded=no --minaqual=30 --idattr=gene_name –type=exon). All the read count tables were then normalized based on their ERCC RNA Spike-In Mix size factors calculated using the DESeq R package (v.3.0), and Deferential Expression (DE) analyses were performed using DESeq (v3.0). All of the downstream statistical analyses and generating plots were performed in R (v3.1.1). To generate the heat map, upregulated and downregulated genes were clustered separately using R dist function in Euclidian mode and then merged to maintain the clustered order of the genes. The values in the matrix were scaled based on columns and not rows using heatmap.2 R function to make the two different data comparable in a single heat map.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: BigWig and TDF (coverage for mapped reads), count tables (read counts for genomic features)

source_name: Spleen

growth_protocol: P493-6 cells were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were isolated using RNeasy Plus Mini Kit (Qiagen). ERCC RNA Spike-In Mix (Ambion, 4456740) was used following instructions of the product. The amount of spike-in added was calibrated to the RNA yield to ensure the spike-in signal was in the appropriate dynamic range. Specifically, 2μl of a 1:200 diluted ERCC Spike-In Mix 1 was added to one of the samples that had a total RNA of 465ng. Between 1.8μl to 5.4μl of 1:200 diluted ERCC Spike-In Mix 1 were added to other samples (between 240 to 800ng total RNAs) at the same ratio of Spike-in/cell number.
Library preparation and sequencing for RNA and ChIP (and their corresponding input) DNA samples were performed at the Genomic Services Lab at HudsonAlpha Institute for Biotechnology (Huntsville, AL). Briefly, the quality of the total RNA and DNA was assessed using the Agilent 2100 Bioanalyzer. Two rounds of polyA+ selection was performed for RNA samples, followed by conversion to cDNAs. The mRNA library generation kits (Agilent, Santa Clara, CA) and TruSeq ChIP Sample Prep Kit (Illumina) were used generate sequencing libraries per manufacturer’s instructions. The indexed DNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725 K to 825 K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed.

tag: cell types

value: Purified B220+ cells

value: Eu-Myc; Dpy30+/-

tag: treatment


title: 3367-HJ-0013


title: 3367-HJ-0014


title: scRNAseq_063_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: 3367-HJ-0010


title: 3367-HJ-0015

value: Eu-Myc


title: 3367-HJ-0012


title: 3367-HJ-0011


title: 3367-HJ-0009


title: 3367-HJ-0005


title: 3367-HJ-0008


title: scRNAseq_063_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: 3367-HJ-0006


title: 3367-HJ-0004


title: 3367-HJ-0002


title: 3367-HJ-0003


title: scRNAseq_063_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: 3367-HJ-0001


title: scRNAseq_063_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: C_p4

city: La Jolla

first: Edward

last: OBrien

state: CA

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive La Jolla

institute: UCSD

data_processing:
Alignment with Bowtie1.
The obtained reads were mapped to the E. coli MG1655 genome (NC_000913.2) using the short-read aligner Bowtie 25 with two mismatches allowed per read alignment.
To estimate gene expression FPKM values were calculated using cufflinks tool 2.0.2
Genome_build: ASM584v1 (NC_000913.2)
Supplementary_files_format_and_content: tab-delimited .txt files with fpkm values of each condition

organism: Escherichia coli str. K-12 substr. MG1655

source_name: WT strain

growth_protocol: Cultures were grown in batch or chemostat mode, M9 minimal media or LB complex media. Samples for Batch mode were taken from mid-log phase, samples from chemostat were taken once the steady state was achieved

extract_protocol: RNA was extracted by cell lysis followed by column purification and DNAse treatment. RNA-seq was performed following a modified dUTP method (PMID: 23637642). The rRNA was isolated using Epicentre's Ribo-Zero rRNA removal kit for Gram Negative Bacteria.

treatment_protocol: Samples were taken with 2 volumes of RNAprotect reagent (quiagen)

tag: growth mode

value: Chemostat

tag: growth rate (hour^-1)

tag: growth limitation

value: Glucose

tag: media

value: M9 minimal


title: N_p3

value: Ammonium


title: C_p3


title: Ctrl A1b rep33

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Ileal biopsy from Male Non-IBD patient aged 15.8 years at time of biopsy

data_processing:
Sequencing was peformed on the Illumina HiSeq2000
Reads were quantified using kallisto with  Gencode v23 as the reference genome, with transcripts per million as the output.
Genome_build: Gencode v23
Supplementary_files_format_and_content: Tab delimited files with gene symbol and TPM

organism: Homo sapiens

source_name: Ileal biopsy

extract_protocol:
Ileal biopsies were obtained at diagnostic colonoscopies and stored in RNALater at -80.  RNA was isolated using Qiagen AllPrep RNA/DNA MiniKiet.
Poly-A-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, and library preparation were performed using TruSeq RNA Sample preparation (Illumina)

tag: diagnosis

value: Non-IBD

tag: location

tag: Sex

value: Male

tag: age at diagnosis in years

tag: paris age


title: Ctrl A1b rep34


title: Ctrl A1b rep35

description: Ileal biopsy from Female Non-IBD patient aged 16.2 years at time of biopsy

value: Female


title: Ctrl A1b rep36

description: Ileal biopsy from Female Non-IBD patient aged 16.9 years at time of biopsy


title: Ctrl A1b rep25

description: Ileal biopsy from Female Non-IBD patient aged 14.5 years at time of biopsy


title: Ctrl A1b rep32


title: Ctrl A1b rep30

description: Ileal biopsy from Male Non-IBD patient aged 15.3 years at time of biopsy


title: Ctrl A1b rep29

description: Ileal biopsy from Female Non-IBD patient aged 15.3 years at time of biopsy


title: Ctrl A1b rep28

description: Ileal biopsy from Female Non-IBD patient aged 15 years at time of biopsy


title: Ctrl A1b rep26

description: Ileal biopsy from Male Non-IBD patient aged 14.6 years at time of biopsy


title: Ctrl A1b rep24

description: Ileal biopsy from Male Non-IBD patient aged 14.2 years at time of biopsy


title: 3367-HJ-0007


title: Ctrl A1b rep27

description: Ileal biopsy from Female Non-IBD patient aged 14.8 years at time of biopsy


title: Ctrl A1b rep22

description: Ileal biopsy from Female Non-IBD patient aged 13.1 years at time of biopsy


title: N_p4


title: Ctrl A1b rep16

description: Ileal biopsy from Female Non-IBD patient aged 12.3 years at time of biopsy


title: Ctrl A1b rep19

description: Ileal biopsy from Male Non-IBD patient aged 12.8 years at time of biopsy


title: Ctrl A1b rep14

description: Ileal biopsy from Male Non-IBD patient aged 12 years at time of biopsy


title: Ctrl A1b rep15

description: Ileal biopsy from Female Non-IBD patient aged 12 years at time of biopsy


title: Ctrl A1b rep23

description: Ileal biopsy from Male Non-IBD patient aged 13.8 years at time of biopsy


title: Ctrl A1b rep18

description: Ileal biopsy from Female Non-IBD patient aged 12.7 years at time of biopsy


title: Ctrl A1b rep13

description: Ileal biopsy from Female Non-IBD patient aged 11.6 years at time of biopsy


title: Ctrl A1b rep12

description: Ileal biopsy from Male Non-IBD patient aged 11.5 years at time of biopsy


title: Ctrl A1b rep11


title: Ctrl A1b rep10

description: Ileal biopsy from Male Non-IBD patient aged 11.4 years at time of biopsy


title: Ctrl A1b rep21

description: Ileal biopsy from Male Non-IBD patient aged 13 years at time of biopsy


title: Ctrl A1b rep4

description: Ileal biopsy from Male Non-IBD patient aged 10.5 years at time of biopsy


title: Ctrl A1b rep8

description: Ileal biopsy from Female Non-IBD patient aged 11 years at time of biopsy


title: Ctrl A1b rep3


title: Ctrl A1b rep5

description: Ileal biopsy from Female Non-IBD patient aged 10.7 years at time of biopsy


title: Ctrl A1b rep2

description: Ileal biopsy from Female Non-IBD patient aged 10.3 years at time of biopsy


title: Ctrl A1b rep6

description: Ileal biopsy from Male Non-IBD patient aged 10.8 years at time of biopsy


title: Ctrl A1a rep13

description: Ileal biopsy from Female Non-IBD patient aged 9.9 years at time of biopsy


title: Ctrl A1b rep1

description: Ileal biopsy from Male Non-IBD patient aged 10.2 years at time of biopsy


title: Ctrl A1a rep14

description: Ileal biopsy from Female Non-IBD patient aged 10 years at time of biopsy


title: Ctrl A1a rep12

description: Ileal biopsy from Male Non-IBD patient aged 9.7 years at time of biopsy


title: Ctrl A1a rep11

description: Ileal biopsy from Male Non-IBD patient aged 9.3 years at time of biopsy


title: Ctrl A1a rep10

description: Ileal biopsy from Male Non-IBD patient aged 9.2 years at time of biopsy


title: Ctrl A1a rep8

description: Ileal biopsy from Male Non-IBD patient aged 8.7 years at time of biopsy


title: Ctrl A1a rep6

description: Ileal biopsy from Male Non-IBD patient aged 8 years at time of biopsy


title: Ctrl A1a rep4

description: Ileal biopsy from Male Non-IBD patient aged 7.8 years at time of biopsy


title: Ctrl A1a rep5


title: Ctrl A1a rep3


title: Ctrl A1b rep7


title: Ctrl A1a rep1

description: Ileal biopsy from Female Non-IBD patient aged 6.6 years at time of biopsy


title: Ctrl A1a rep9

description: Ileal biopsy from Female Non-IBD patient aged 9 years at time of biopsy


title: Ctrl A1a rep2


title: Ctrl A1b rep17

description: Ileal biopsy from Female Non-IBD patient aged 12.5 years at time of biopsy


title: CD A1b L3 rep88

description: Ileal biopsy from Male CD patient aged 16.0833333333333 years at diagnosis with L3 location and Paris age A1b

value: CD


title: CD A1b L3 rep92

description: Ileal biopsy from Female CD patient aged 16.25 years at diagnosis with L3 location and Paris age A1b


title: Ctrl A1b rep9

description: Ileal biopsy from Male Non-IBD patient aged 11.4 years at time of biopsy


title: CD A1b L1 rep32

description: Ileal biopsy from Male CD patient aged 14.75 years at diagnosis with L1 location and Paris age A1b


title: SiYAP

city: Shanghai

first: jingmin

last: Guan

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biolog

country: China

institute: Shanghai Institutes for Biological Sciences

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removal of rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Clean reads after filtering were aligned to human genome (hg38) by Tophat v2.0.9(1).
The differentially expressed genes were achieved by EBSeq algorithms.
Genes were considered significantly differentially expressed under the following criteria: (1) fold change > 1.5 or < 0.667; (2) FDR < 0.05 (2).
Genome_build: hg38
Supplementary_files_format_and_content: text file includes RPKM values and raw count for each sample.

source_name: HGC-27 cells

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HGC-27 cells were transfected with siRNAs for 48 h

tag: cell line

value: gastric cancer cells

tag: passages

value: YAP siRNA (siYAP)


title: NC

value: control siRNA (n.c.)


title: CD A1b L3 rep57

description: Ileal biopsy from Female CD patient aged 13.6666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep27

description: Ileal biopsy from Female CD patient aged 13.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: KD P493 input

data_processing:
Basecalls performed using CASAVA version 1.8.4
For ChIP-seq, Fastq files were first quality filtered using the FASTX toolkit “fastq_quality_filter” tool, with the following arguments: -q 20 and –p 80, which outputs reads that have a mapq score of at least 20 at least 80% of the bases.  The quality filtered reads were then collapsed to eliminate PCR duplicates using the FASTX toolkit “fastx_collapser”.  The resultant fasta file was aligned using STAR ver. 2.4. The SAM file outputs were converted to BAM using samtools “view” and the BAM converted to BED using BEDtools “bamToBed”. The coverage of H3K4me3 and Myc plus/minus 5kb of all transcription start sites (profiles) were generated using deepTools2.0. The tdf files were generated from bedgraph files using IGVtools “totdf”.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: BigWig and TDF (coverage for mapped reads), count tables (read counts for genomic features)

source_name: P493-6 cells

extract_protocol:
Standard ChIP assays was performed.
Library preparation and sequencing for RNA and ChIP (and their corresponding input) DNA samples were performed at the Genomic Services Lab at HudsonAlpha Institute for Biotechnology (Huntsville, AL). Briefly, the quality of the total RNA and DNA was assessed using the Agilent 2100 Bioanalyzer. Two rounds of polyA+ selection was performed for RNA samples, followed by conversion to cDNAs. The mRNA library generation kits (Agilent, Santa Clara, CA) and TruSeq ChIP Sample Prep Kit (Illumina) were used generate sequencing libraries per manufacturer’s instructions. The indexed DNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725 K to 825 K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed.

treatment_protocol: P493-6 cells were infected with lentiviruses expressing control or Dpy30 shRNAs, followed by puromycin (2 μg/ml) selection for 2–3 days starting from 2 days after infection.

value: B cell

value: Dpy30 shRNA

value: Input


title: CD A1b L3 rep50

description: Ileal biopsy from Male CD patient aged 13.25 years at diagnosis with L3 location and Paris age A1b


title: KD P493 H3K4me3

value: H3K4me3 ChIP


title: Control P493 input

value: scramble shRNA


title: Control P493 H3K4me3


title: KD P493 Myc

value: Myc ChIP


title: CD A1b L1 rep33

description: Ileal biopsy from Male CD patient aged 14.8333333333333 years at diagnosis with L1 location and Paris age A1b


title: Control P493 Myc


title: Ctrl A1a rep7

description: Ileal biopsy from Male Non-IBD patient aged 8.5 years at time of biopsy


title: CD A1b L3 rep47

description: Ileal biopsy from Female CD patient aged 13.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: SiIRF3

value: IRF3 siRNA (siIRF3)


title: P3

city: Madison

first: Mitch

last: Biermann

state: Wisconsin

address: 917 Eagle Heights, Apt D

institute: University of Wisconsin

description:
Processed data file: NvsPvsT_normalgiwiday5CPCsvsPolyICtreatedCPCsvsTGFbetatreatedCPCs_normalizedcounts.txt
Processed data file: NvsP.csv

data_processing:
bcl2fastq-1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR2.4.0j with parameters outFilterScoreMinOverLread 0.5 -- outFilterMatchNminOverLread 0.5; Dobin, A. & Gingeras, T. R. Mapping RNA-seq Reads with STAR. Curr. Protoc. Bioinforma. Ed. Board Andreas Baxevanis Al 51, 11.14.1-11.14.19 (2015).
To annotate RNA-seq data, HTSeq 0.62 was used (Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015)).
Annotated transcript counts were further processed with DeSEq2 for differential gene expression analysis (Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: NvsPvsT_normalgiwiday5CPCsvsPolyICtreatedCPCsvsTGFbetatreatedCPCs_normalizedcounts.txt: Tab-delimited text file includes normalized transcript counts for each sample.
Supplementary_files_format_and_content: NvsT.csv: Comma-separated text file includes significance testing/Fold change calculations for TGFbeta vs. untreated, normal progenitors.
Supplementary_files_format_and_content: NvsP.csv: Comma-separated text file includes significance testing/Fold change calculations for PolyI:C vs. untreated, normal progenitors.

source_name: Human Induced Pluripotent Cell-derived Cardiac Progenitors

extract_protocol:
Cells dissociated and pelleted, flash frozen in liquid nitrogen, and RNA was harvested using Qiagen RNeasy with on-column DNase digestion.
Illumina TruSeq stranded Total RNA kit with rRNA reduction with H/M/R Gold reagents was used with 1 ug of total RNA for the construction of sequencing libraries. Agencourt AMPure XP beads bead purification. 1x100bp single end sequencing was performed.

tag: day3-5 treatment

tag: differentiation day

value: Day 5


title: P1

tag: cell type

value: Induced Pluripotent Cell-derived Cardiac Progenitors


title: P2


title: T2

description:
Processed data file: NvsPvsT_normalgiwiday5CPCsvsPolyICtreatedCPCsvsTGFbetatreatedCPCs_normalizedcounts.txt
Processed data file: NvsT.csv

value: TGFbeta


title: CD A1b L3 rep63

description: Ileal biopsy from Male CD patient aged 14.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep22

description: Ileal biopsy from Female CD patient aged 13.0833333333333 years at diagnosis with L1 location and Paris age A1b


title: T3


title: CD A1b L1 rep21

description: Ileal biopsy from Male CD patient aged 13 years at diagnosis with L1 location and Paris age A1b


title: N3

description:
Processed data file: NvsPvsT_normalgiwiday5CPCsvsPolyICtreatedCPCsvsTGFbetatreatedCPCs_normalizedcounts.txt
Processed data file: NvsT.csv
Processed data file: NvsP.csv

value: untreated


title: CD A1b L3 rep45

description: Ileal biopsy from Female CD patient aged 12.8333333333333 years at diagnosis with L3 location and Paris age A1b


title: N2


title: Sample_MO15

first: Wiebke

last: Arlt

address: Edgbaston

department: Institute of Metabolism and Systems Research  (IMSR)

country: United Kingdom

institute: University of Birmingham

data_processing:
Bcl results files were converted to fastq using bcl2fastq Conversion Software v1.8.4 (Illumina).
RNA-seq reads were mapped onto the human genome (hg19, UCSC annotation) using TopHat software v2.1.0 using default parameters with the following exceptions: --library-type fr-firststrand and using the --GTF parameter provide the UCSC hg19 annotation
BAM files containing the mapping of each read to the genome were sorted using samtools v0.1.19
Counts per gene were calculated using the htseq-count tool from the HTSeq v0.6.1p1 package with the following parameters: --format=bam –minaqual=1 –stranded=reverse --mode=intersection_nonempty
Normalised FPKM values for each gene were calculated using DESeq2 and GenomicFeatures v1.24.4 package from Bioconductor release 3.2. Genes were further standardised via cell transformation. Pathway genes corresponding to adipogenesis, insulin resistance, fatty acid metabolism, lipoprotein and cholesterol metabolism were extracted. Sample types were averaged and genes excluded if there was 0 expression across the compared samples
Genome_build: hg19
Supplementary_files_format_and_content: Tab delineated text files containing counts for each sample

source_name: lipid biopsy

extract_protocol:
RNA was extracted from lipid biopsy samples using the RNeasy Lipid Tissue Mini Kit (cat. no. 74804), with a combination of a Qiagen TissueRuptor (Cat No. 9001273) and QIAShredder columns (Cat No. 79654) used for tissue homogenisation. After homogenisation each sample was split into two tubes, and a further 0.5ml of QIAzol reagent added to each tube. Each tube was then treated as a separate RNA extraction, following the RNeasy Lipid Tissue Mini Kit protocol as written. Once RNA was eluted the aliquots were recombined to give a final volume of 60ul eluted RNA.
All RNA libraries were produced using the Beckman Coulter Biomek FxP (Cat No. A31842) with New England Biolab Ultra Directional RNA Library Prep Kit (Cat No. E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (Cat No. E7600S), using provided protocols. 100ng of total RNA was used for library construction where possible. However in some cases the extracted RNA was at too low a concentration. For these samples 25ng total RNA was used for library construction. 13 cycles of PCR amplification were carried out upon all libraries of 100ng total RNA, and 15 cycles upon libraries with 25ng input total RNA.

tag: tissue

value: Adipose

tag: gender

tag: age

value: PCOS

value: DHEA


title: MO22-33077060

value: Female

tag: treatment


title: CD A1b L3 rep48

value: CD


title: MO22-32975022


title: MO21-32994972


title: MO19-33079062


title: MO19-32990980


title: MO18-33074053


title: MO18-32967035


title: CD A1b L3 rep37

description: Ileal biopsy from Male CD patient aged 12.4166666666667 years at diagnosis with L3 location and Paris age A1b

value: Male


title: MO16-33081057


title: CD A1b L3 rep36

description: Ileal biopsy from Female CD patient aged 12.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: T1


title: MO14-33077056


title: Sample_MO24


title: Sample_MO9


title: MO15-32982010


title: Sample_MO23


title: CD A1b L3 rep32

description: Ileal biopsy from Male CD patient aged 12.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: Sample_MO13


title: Sample_MO12


title: MO21-33079063


title: Sample_MO11


title: Sample_MO10


title: MO9-32971006


title: MO9-33077063


title: CD A1b L1 rep14

description: Ileal biopsy from Female CD patient aged 11.5833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep26

description: Ileal biopsy from Female CD patient aged 11.75 years at diagnosis with L3 location and Paris age A1b


title: MO16-32993971


title: MO24-33059134


title: MO24-32977011


title: MO13-32989980


title: MO23-32974008


title: MO15-33078059


title: MO13-33079060


title: CD A1b L3 rep25

description: Ileal biopsy from Female CD patient aged 11.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: Sample_MO38

value: Normal


title: MO14-32994966


title: Sample_MO36


title: Sample_MO35


title: Sample_MO34


title: MO38-33067080


title: Sample_MO31


title: Sample_MO32


title: MO36-32971996


title: MO37-33080070


title: MO37-32994975


title: MO36-33060139


title: MO35-33074054


title: MO23-33064107


title: MO34-33075057


title: MO34-32973013


title: MO33-33076063


title: MO33-32975028


title: MO31-33065122


title: MO35-32990984


title: MO32-33081063


title: CD A1b L1 rep4

description: Ileal biopsy from Female CD patient aged 10.6666666666667 years at diagnosis with L1 location and Paris age A1b


title: Col_d

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: sRNA library from Arabidopsis wildtype Col-0 unopened flower bud

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043)
Genome_build: None
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts

organism: Arabidopsis thaliana

source_name: A. thaliana - unopened bud

growth_protocol: Plants were grown in growth chamber under 16hr-day condition at 23oC. Six-Eight week old plants were harvested.

extract_protocol:
Samples were immediately frozen in liquid nitrogen until total RNA isolation was performed. Total RNA was isolated using Trizol reagents or plant RNA reagent, both from Invitrogen.
Small RNAs libraries were constructed as previously described (C Lu et al. 2007). Small RNA libraries were sequenced on an Illumina GAIIx or Illumina HiSeq 2000 instrument at the Delaware Biotechnology Institute.
small RNA sequencing using Illumina single-end reads.

value: unopened bud

tag: ecotype


title: Sample_MO33


title: CD A1b L3 rep1

description: Ileal biopsy from Female CD patient aged 10 years at diagnosis with L3 location and Paris age A1b


title: CD A1a L3 rep36

description: Ileal biopsy from Male CD patient aged 9.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep35


title: CD A1a L3 rep32

description: Ileal biopsy from Female CD patient aged 9.25 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep22

description: Ileal biopsy from Male CD patient aged 8.83333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep29

description: Ileal biopsy from Male CD patient aged 9.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep40

description: Ileal biopsy from Female CD patient aged 9.75 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L3 rep8

description: Ileal biopsy from Male CD patient aged 10.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1a L3 rep21

description: Ileal biopsy from Female CD patient aged 8.83333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L1 rep1

description: Ileal biopsy from Female CD patient aged 6.91666666666667 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L1 rep3

description: Ileal biopsy from Male CD patient aged 8.16666666666667 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L3 rep16

description: Ileal biopsy from Female CD patient aged 8.66666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep3

description: Ileal biopsy from Male CD patient aged 6.5 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep42

description: Ileal biopsy from Male CD patient aged 16.75 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep41

description: Ileal biopsy from Female CD patient aged 16.5833333333333 years at diagnosis with L2 location and Paris age A1b


title: MO32-32975027


title: CD A1b L2 rep37

description: Ileal biopsy from Male CD patient aged 15.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep36

description: Ileal biopsy from Female CD patient aged 15.75 years at diagnosis with L2 location and Paris age A1b


title: MO31-32982014


title: MO38-32971997


title: CD A1b L2 rep31

description: Ileal biopsy from Male CD patient aged 15.0833333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep23

description: Ileal biopsy from Female CD patient aged 13.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep24

description: Ileal biopsy from Female CD patient aged 14.0833333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep33

description: Ileal biopsy from Male CD patient aged 15.25 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep22

description: Ileal biopsy from Male CD patient aged 13.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Ctrl A1b rep31

description: Ileal biopsy from Male Non-IBD patient aged 15.6 years at time of biopsy

value: Non-IBD


title: CD A1b L2 rep20

description: Ileal biopsy from Male CD patient aged 13.75 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep18

description: Ileal biopsy from Male CD patient aged 13.3333333333333 years at diagnosis with L2 location and Paris age A1b


title: ES1: END_seq_aB_28h_HU_28h_10mM_rep1

description: Control: END_seq_aB_28h_NT_rep1

data_processing:
Library strategy: END-seq
mouse and human reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), HCT116 (7.5 million per agarose plug)were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols

value: Activated primary B cells

tag: genotype

value: WT

tag: strain


title: ES4: END_seq_aB_28h_NT_rep1

description: Control: N/A


title: CD A1b L2 rep16

description: Ileal biopsy from Male CD patient aged 12.75 years at diagnosis with L2 location and Paris age A1b

tag: diagnosis


title: CD A1b L2 rep40

description: Ileal biopsy from Male CD patient aged 16.3333333333333 years at diagnosis with L2 location and Paris age A1b

tag: location


title: CD A1b L2 rep13

description: Ileal biopsy from Female CD patient aged 12.5833333333333 years at diagnosis with L2 location and Paris age A1b

tag: Sex


title: Holly Mare

city: Ithaca

first: Wojciech

last: Pawlowski

state: NY

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

data_processing:
FASTQC software used for quality check
Sequenced reads were trimmed for adaptor sequence, filter low-quality sequence
Trimmed reads were aligned to the equine genome sequence (NCBI reference assembly EquCab2.0) with TopHat version 2.1.1
Cuffdiff version 2.2.1 was used to get raw read count at gene level
edgeR was for normalization and statistical analysis for identifying differentially expressed genes
Genome_build: NCBI reference assembly EquCab2.0
Supplementary_files_format_and_content: abundance measurements

organism: Equus caballus

source_name: peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from blood samples and stored at -80C. RNA was isolated with the RNeasy kit including on-column DNase I digestion, as directed (Qiagen, Valencia CA).
RNA libraries were prepared as directed by the Illumina TruSeq Stranded mRNA Library Prep Kit. Samples were barcoded for multiplexing with the following adapters: day 1 Inga foal index 2; day 1 Konstance foal index 4; day 1 Wild Rose foal index 5; day 1 Neinke 2014 foal index 6; day 42 Inga foal index 7; day 42 Konstance foal index 12; day 42 Wild Rose foal index 13; day 42 Neinke 2014 foal index 14; Inga mare index 15; Holly mare index 16; Wild Rose mare index 18; Neinke mare index 19

value: adult

value: female

tag: breed

value: Quarter Horse


title: Neinke 2014 mare

value: KWPN Royal Dutch Sport Horse


title: Day 42 Neinke 2014 foal

value: day 42

value: male

value: Warmblood


title: Inga mare


title: CD A1b L2 rep12

description: Ileal biopsy from Female CD patient aged 12.3333333333333 years at diagnosis with L2 location and Paris age A1b

tag: age at diagnosis in years

tag: paris age


title: CD A1b L2 rep15

description: Ileal biopsy from Male CD patient aged 12.6666666666667 years at diagnosis with L2 location and Paris age A1b


title: Wild Rose mare

value: Hanoverian


title: Day 42 Wild Rose foal


title: Day 42 Inga foal


title: CD A1b L2 rep30


title: CD A1b L2 rep9

description: Ileal biopsy from Male CD patient aged 11.4166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep11

description: Ileal biopsy from Female CD patient aged 11.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep32

description: Ileal biopsy from Male CD patient aged 15.1666666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep8

description: Ileal biopsy from Female CD patient aged 11.0833333333333 years at diagnosis with L2 location and Paris age A1b


title: Day 1 Wild Rose foal

value: day 1


title: Day 1 Konstance foal


title: CD A1b L2 rep6

description: Ileal biopsy from Male CD patient aged 10.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Day 1 Inga foal


title: CD A1b L2 rep3

description: Ileal biopsy from Female CD patient aged 10.5833333333333 years at diagnosis with L2 location and Paris age A1b

value: Female


title: CD A1a L2 rep13

description: Ileal biopsy from Female CD patient aged 9.75 years at diagnosis with L2 location and Paris age A1a

value: CD


title: CD A1a L2 rep12

description: Ileal biopsy from Female CD patient aged 9.58333333333333 years at diagnosis with L2 location and Paris age A1a


title: Day 42 Konstance foal


title: CD A1a L2 rep8

description: Ileal biopsy from Female CD patient aged 8.83333333333333 years at diagnosis with L2 location and Paris age A1a


title: bulk ChIP seq (SOX30_input)

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome mm10) using TopHat (v 2.0.12) -pass mapping steps.
For ChIP-seq data, trimmed clean reads were aligned to mouse reference genome mm10) using bowtie2 (v 2.2.3) -pass mapping steps.
Genome_build: mm10
Supplementary_files_format_and_content: UMIcount.txt files include the UMI count values of RefSeq genes
Supplementary_files_format_and_content: INCLUSION_LEVELS_FULL.tab files include RNA-seq alternative splicing result, in which '_R1' column represents estimated percent of sequence inclusion (PSI/PSU/PIR, PSI: percent spliced in (for EX), PSU: percent splice site usage (for ALTD and ALTA), PIR: percent intron retention (for INT))  and '_R1-Q' column represents quality scores and number of corrected inclusion and exclusion reads
Supplementary_files_format_and_content: bedgraph files include of signal density of ChIP-seq

source_name: Germ cells

extract_protocol:
For RNA-seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L).
For ChIP-seq data, we constructed the sequencing libraries using Next Gen DNA Library Kit and Next Gen Indexing Kit(ACTIVE MOTIF #53216&53264).

value: Testis

value: germ cells

value: Wild type

tag: developmental stage

value: round spermatids

tag: chip antibody

value: none (Input)


title: bulk ChIP seq (SOX30_cKO)

value: Sox30 knock out

value: Sox30 (Abclonal, A11715)


title: bulk ChIP seq (SOX30_wildtype)


title: CD A1a L2 rep7

description: Ileal biopsy from Female CD patient aged 8.5 years at diagnosis with L2 location and Paris age A1a


title: Day 1 Neinke 2014 foal


title: CD A1a L2 rep4

description: Ileal biopsy from Female CD patient aged 7.83333333333333 years at diagnosis with L2 location and Paris age A1a


title: CD A1a L2 rep6


title: single cell RNA seq (SpAS21_4_RS7o8)

molecule: polyA RNA


title: CD A1a L2 rep2

description: Ileal biopsy from Female CD patient aged 6.75 years at diagnosis with L2 location and Paris age A1a


title: single cell RNA seq (SpAS21_5_RS7o8)


title: CD A1b L2 rep4

description: Ileal biopsy from Male CD patient aged 10.6666666666667 years at diagnosis with L2 location and Paris age A1b

value: Male


title: Ctrl A1b rep20

description: Ileal biopsy from Male Non-IBD patient aged 12.9 years at time of biopsy

value: Non-IBD


title: single cell RNA seq (SpAS21_2_RS7o8)


title: LNCaP_Cas_Sec_4374R

city: Buffalo

first: Xin

last: Chen

address: Elm & Carlton Streets

department: Pharmacology & Therapeutics

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg38) by TopHat (version 2.0.10) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from GENCODE Release 21 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Number of fragments in each gene

source_name: LNCaP secondary CRPC

extract_protocol:
Total RNA was extracted by Rneasy mini kit (Qiagen)
Libraries were generated using the Illumina TruSeq Stranded Total RNA LT Sample Prep kit according to the manufacturer's guidelines.

tag: cell line

value: LNCaP

tag: passages

value: surgical castration+MDV3100 treatment in male NOD/SCID-γ mice


title: LNCaP_Cas_Sec_4368R


title: LNCaP_Cas_Pri_4372R

source_name: LNCaP primary CRPC

value: surgical castration in male NOD/SCID-γ mice


title: CD A1b L2 rep2

description: Ileal biopsy from Male CD patient aged 10.5 years at diagnosis with L2 location and Paris age A1b


title: single cell RNA seq (SpAS20_5_lP)

tag: tissue

tag: cell type

value: spermatocytes


title: single cell RNA seq (SpAS21_1_RS7o8)


title: LNCaP_Cas_Pri_4370R


title: CD A1b L2 rep7

description: Ileal biopsy from Male CD patient aged 11 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L2 rep9


title: LNCaP_Cas_Sec_4365R


title: LNCaP_Cas_Pri_4373R


title: single cell RNA seq (SpAS20_3_lP)


title: single cell RNA seq (SpAS20_4_lP)


title: LNCaP_AD_2744L

source_name: LNCaP androgen dependent (AD) tumors

value: testosterone pellets implated in male NOD/SCID-γ mice


title: LNCaP_AD_2666


title: CD A1a L2 rep3

description: Ileal biopsy from Female CD patient aged 7.25 years at diagnosis with L2 location and Paris age A1a


title: single cell RNA seq (SpAS20_2_lP)


title: LNCaP_Cas_Pri_4370L


title: bulk ChIP seq (SOX30_FRT_FRT)


title: single cell RNA seq (SpAS19_5_eP)


title: LNCaP_AD_4530R


title: single cell RNA seq (SpAS19_4_eP)


title: LAPC9_AI14_4794

source_name: LAPC9 castration resistant tumors (CRPC)

value: surgical castration in male NOD/SCID mice


title: single cell RNA seq (SpAS19_3_eP)


title: LAPC9_AI14_4791


title: single cell RNA seq (SpAS21_3_RS7o8)


title: LAPC9_AD3_4753

source_name: LAPC9 androgen dependent (AD) tumors

value: testosterone pellets implated in male NOD/SCID mice


title: LAPC9_AD1_4247


title: LAPC9_AI11_4251R


title: single cell RNA seq (SpAS18_4_lPL)


title: LAPC9_AD4_3800


title: single cell RNA seq (SpAS18_5_lPL)


title: single cell RNA seq (SpAS18_1_lPL)


title: single cell RNA seq (SpAS18_3_lPL)


title: LAPC9_AI11_4374L


title: single cell RNA seq (SpAS20_1_lP)


title: LAPC9_AD1_4246


title: single cell RNA seq (SpAS17_4_RS1o2)


title: LAPC9_AD1_4245


title: LAPC9_AI11_4248


title: single cell RNA seq (SpAS19_1_eP)


title: single cell RNA seq (SpAS16_4_D)


title: single cell RNA seq (SpAS16_5_D)


title: single cell RNA seq (SpAS17_5_RS1o2)


title: single cell RNA seq (SpAS19_2_eP)


title: LNCaP_AD_1283R


title: ΔcspA2 ΔcspA4_Free_2

city: Pullman

first: Jason

last: Price

address: 100 Dairy Rd

institute: Washington State University

data_processing:
Reads were aligned to Sm2011 genome with the program tophat
Cuffdiff program was used to estimate read abundance by gene feature and to perform differential expression analysis
Genome_build: Sinorhizobium meliloti 2011 genome acc=GMI11495-Rm2011G
Supplementary_files_format_and_content: cuffdiff output files organized in a .txt file are provided for free-living and nodule comparisons

organism: Sinorhizobium meliloti

source_name: ΔcspA2 ΔcspA4_Free

extract_protocol:
Trizol extraction followed by modified Rneasy RNA clean-up protocol
Truseq stranded total RNA (Illumina)

tag: genotype/variation

value: {delta}cspA2 {delta}cspA4

tag: growth condition

value: free-living culture


title: single cell RNA seq (SpAS17_2_RS1o2)

value: Testis

value: germ cells


title: ΔcspA2 ΔcspA4_Free_3


title: single cell RNA seq (SpAS16_3_D)

value: Wild type


title: single cell RNA seq (SpAS16_2_D)


title: single cell RNA seq (SpAS18_2_lPL)


title: single cell RNA seq (SpAS15_5_mP)


title: ΔcspA2 ΔcspA4_Free_1


title: WT_Free_3

value: WT


title: single cell RNA seq (SpAS15_4_mP)


title: WT_Free_1


title: WT_Free_2


title: single cell RNA seq (SpAS15_3_mP)


title: single cell RNA seq (SpAS15_1_mP)


title: ΔcspA2 ΔcspA4_Nod_1

source_name: ΔcspA2 ΔcspA4_Nod

value: symbiotic nodule tissue 28 dpi


title: ΔcspA2 ΔcspA4_Nod_2


title: single cell RNA seq (SpAS15_2_mP)


title: single cell RNA seq (SpAS14_5_Z)


title: single cell RNA seq (SpAS14_3_Z)


title: single cell RNA seq (SpAS14_4_Z)


title: WT_Nod_3


title: WT_Nod_2


title: WT_Nod_1


title: single cell RNA seq (SpAS14_2_Z)


title: single cell RNA seq (SpAS17_3_RS1o2)

value: round spermatids


title: cspa5_bound_2

data_processing:
Reads were aligned to Sm2011 genome with the program tophat
The bedcov command of the samtools program was used to estimate read abundance by gene feature
Gene features with less than 2 estimated reads in any of the "input" samples were discarded from the data set
Read abundance values were normalized by total mapped reads for each sample and the "bound" read sample values were normalized by "input" read abundance values in Microsoft excel
RobiNA software was used to perform EdgeR statistical analysis between control and experimental samples
Genome_build: Sinorhizobium meliloti 2011 genome acc=GMI11495-Rm2011G
Supplementary_files_format_and_content: gene_countstable.txt contains normalized read coverage by gene feature for all samples

extract_protocol:
Immunoprecipitiation followed by Trizol extraction and modified RNeasy RNA cleanup protocol
Truseq stranded total RNA (Illumina)

tag: ip antibody

value: GFP-Trap®_A agarose beads (Chromotek Cat # gta-20)

tag: growth stage

value: mid-log phase (free-living)


title: cspa5_bound_1

tag: strain

tag: genotype


title: single cell RNA seq (SpAS14_1_Z)


title: single cell RNA seq (SpAS17_1_RS1o2)


title: MitoRNA rep1

city: Strasbourg

first: Anne-Marie

last: Duchêne

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

description: Mitochondrial RNA

data_processing:
First two libraries (ADE01 & ADE02) were sequenced with Illumina Hiseq2000 and base calling was performed with CASAVA 1.8.2, the rest of the libraries (ADE03 to ADE06) were sequenced with Illumina Hiseq 2500 and image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Mapping was performed using Tophat2 version 2.0.8b and Bowtie2 version 2.1.0
The 6 libraries were first mapped on the mitochondrial and plastidial genomes. These mapped reads were eliminated
The remaining reads were then mapped on the potato transcriptome and nuclear genome with 2 allowed mismatches
Counting and differential analysis between the mitochondrial and the total extracts were performed with HTSeq-count version 0.5.4p3 and DESeq2 (package R3.0.1) version 1.6.3.
transcriptome build: PGSC_DM_v3.4_transcript-update_representative.fasta , from http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml
Genome_build: PGSC_DM_v4.03_pseudomolecules.fasta , from http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml
Supplementary_files_format_and_content: raw counts of sequencing reads against genes (one file per library) and normaliszed abundance measurment (one file in total)
Supplementary_files_format_and_content: DESeq2_output.txt: normalized abundance measurements (DESeq2 output)

organism: Solanum tuberosum

source_name: from purified mitochondria

extract_protocol:
Mitochondrial and total RNA were extracted using Tri Reagent® (Molecular Research Center) according to the manufacter’s instructions. For total RNA, the protocol was slightly modified to eliminate starch. RNA were then DNAse-treated with DNAse RQ1 (Promega). Cytosolic mRNAs were purified from RNA extracts using oligo-dT magnetic beads. The use of oligo-dT allowed the elimination of many mitochondrial mRNAs, because stable mitochondrial mRNAs lack polyA tails.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: TotRNA rep1

description: Total RNA

source_name: Total RNA


title: single cell RNA seq (SpAS13_5_L)


title: single cell RNA seq (SpAS16_1_D)


title: ΔcspA2 ΔcspA4_Nod_3


title: cspa4_bound_2


title: single cell RNA seq (SpAS13_4_L)


title: cspa2_bound_1


title: cspa2_bound_2


title: single cell RNA seq (SpAS13_2_L)


title: single cell RNA seq (SpAS13_1_L)


title: cspa4_bound_1


title: single cell RNA seq (SpAS12_5_mPL)


title: control_bound_1

value: wild type


title: single cell RNA seq (SpAS12_3_mPL)


title: cspa5_input_1

value: none (input)


title: cspa5_input_2


title: single cell RNA seq (SpAS12_4_mPL)


title: single cell RNA seq (SpAS13_3_L)


title: single cell RNA seq (SpAS12_2_mPL)


title: single cell RNA seq (SpAS12_1_mPL)


title: cspa4_input_1


title: cspa2_input_2


title: single cell RNA seq (SpAS11_6_lG1)


title: cspa2_input_1


title: single cell RNA seq (SpAS11_5_lG1)


title: cspa4_input_2


title: control_input_2


title: single cell RNA seq (SpAS11_4_mG1)


title: N1

description:
Processed data file: NvsPvsT_normalgiwiday5CPCsvsPolyICtreatedCPCsvsTGFbetatreatedCPCs_normalizedcounts.txt
Processed data file: NvsT.csv
Processed data file: NvsP.csv

value: Induced Pluripotent Cell-derived Cardiac Progenitors

tag: day3-5 treatment

value: untreated

tag: differentiation day

value: Day 5


title: control_input_1


title: single cell RNA seq (SpAS11_3_mG1)

value: spermatocytes


title: control_bound_2


title: single cell RNA seq (SpAS11_2_eG1)


title: single cell RNA seq (SpAS11_1_eG1)


title: Wt_d

description: sRNA library constructed from Arabidopsis Col-0 unopened flower buds

value: unopened bud

tag: ecotype


title: single cell RNA seq (SpAS10_5_TypeBS)

value: spermatogonia


title: AtCM

description: mixed stage inflorescence of Arabidopsis ecotype Col-0

source_name: A. thaliana - mixed stage inflorescence

value: mixed stage inflorescence


title: QS-PH8-2

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM method (Reads Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: FPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida tropicalis genome
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candida tropicalis

growth_protocol: Lee's GlcNAc medium and cultured at 30 oC for 12h.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ph condition


title: QS-PH8-1


title: QS-PH7-2


title: single cell RNA seq (SpAS10_3_TypeBS)

value: Testis


title: QS-PH7-1


title: QS-PH5-2


title: single cell RNA seq (SpAS10_2_TypeBS)

value: germ cells


title: GVHD-1 [SD4]

first: Stella

last: Davies

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: GVHD_mucosal biopsy

extract_protocol:
Total RNA was extracted from GI mucosal tissue using Rneasy Mini Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: children

tag: subject status

value: Gastrointestinal (GI) graft versus host disease (GVHD)

value: GI mucosal tissue


title: QS-PH5-1


title: single cell RNA seq (SpAS10_4_TypeBS)

value: Wild type

tag: developmental stage


title: GVHD-2 [SD7]


title: single cell RNA seq (SpAS9_5_A1)


title: No GVHD-2 [SD8]

source_name: No GVHD_mucosal biopsy

value: no Gastrointestinal (GI) graft versus host disease (GVHD)


title: No GVHD-1 [SD5]


title: single cell RNA seq (SpAS10_1_TypeBS)


title: single cell RNA seq (SpAS9_1_A1)


title: single cell RNA seq (SpSC34)


title: single cell RNA seq (SpSC35)


title: TotRNA rep3

description: Total RNA

value: WT


title: single cell RNA seq (SpSC33)


title: single cell RNA seq (SpAS9_2_A1)


title: MitoRNA rep2

description: Mitochondrial RNA


title: TotRNA rep2

description: Total RNA


title: single cell RNA seq (SpSC32)

value: round spermatids


title: single cell RNA seq (SpSC37)


title: single cell RNA seq (SpSC27)


title: single cell RNA seq (SpSC28)


title: single cell RNA seq (SpAS9_4_A1)


title: single cell RNA seq (SpAS9_3_A1)


title: single cell RNA seq (SpSC31)


title: single cell RNA seq (SpSC36)


title: single cell RNA seq (SpSC29)


title: single cell RNA seq (SpSC19)


title: single cell RNA seq (SpSC22)


title: single cell RNA seq (SpSC24)


title: single cell RNA seq (SpSC21)


title: single cell RNA seq (SpSC20)


title: MitoRNA rep3

description: Mitochondrial RNA


title: single cell RNA seq (SpSC18)


title: single cell RNA seq (SpSC25)


title: single cell RNA seq (SpSC15)


title: single cell RNA seq (SpSC17)


title: single cell RNA seq (SpSC16)


title: single cell RNA seq (SpSC14)


title: single cell RNA seq (SpSC13)


title: single cell RNA seq (SpSC12)


title: single cell RNA seq (SpSC10)


title: single cell RNA seq (SpSC26)


title: single cell RNA seq (SpSC30)


title: single cell RNA seq (SpSC8)


title: single cell RNA seq (SpSC9)

value: spermatocytes and round spermatids


title: single cell RNA seq (SpSC7)

value: spermatogonia and spermatocytes


title: single cell RNA seq (SpSC6)


title: RNA sequencing of Mycobacterium dioxanotrophicus PH-06 treated with glucose

city: Houston

first: Ya

last: He

state: Texas

department: Department of Civil and Environmental Engineering

institute: Rice University

description: Extracted from PH-06 cells after grown on glucose

data_processing:
Raw reads were mapped to the whole genome sequencing of PH-06
The relative gene expression levels were estimated using EDGE-pro v 1.3.1 (http://ccb.jhu.edu/software/EDGE-pro/)
Genome_build: CP020809-CP020813
Supplementary_files_format_and_content: Excel file; gene expression fold and raw read count

organism: Mycobacterium dioxanotrophicus

source_name: PH-06 cells grown on glucose

growth_protocol: Mycobacterium dioxanotrophicus PH-06 was grown in ammonium mineral salts (AMS) medium amended with 500 mg/L of dioxane as the carbon source.

extract_protocol:
The RNA extraction was performed according to the protocol of RNase Mini Kit (Qiagen, Hilden, Germany).
mRNA libraries were prepared following Illumina mRNA-Seq Sample Prep Kit.

treatment_protocol: PH-06 cells in exponential phase (when half of the added substrates were consumed) were centrifuged and washed with AMS medium three times before total RNA extraction.

tag: phenotype

value: Dioxane degrader


title: single cell RNA seq (SpSC4)


title: LNCaP_Cas_Sec_4369R

tag: cell line

value: LNCaP

tag: passages

tag: treatment

value: surgical castration+MDV3100 treatment in male NOD/SCID-γ mice


title: single cell RNA seq (SpSC2)

tag: tissue

tag: cell type


title: single cell RNA seq (SpSC3)

value: spermatocytes


title: single cell RNA seq (SpSC01)

value: spermatogonia


title: iPS.NG_2

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using TopHat v2.0.10; reads in genes were counted with htseq-count (HTSeq version 0.6.1p1) ; differential expression analysis was performed with DESeq2 (v 1.10.1)
TPM estimation was performed with RSEM (v1.2.25)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (standard output RSEM)

source_name: control vascular organoids

extract_protocol:
cDNA synthesis and amplification were performed from total RNA using SMARTer RNA Kit (Clontech) according to the manufacturers instructions.
Library construction protocol not provided.

value: iPSC line NC8

value: endothelial cell

value: vascular organoids

tag: medium

value: control

tag: gender

value: male


title: iPS.DI_1

source_name: diabetic vascular organoids

value: diabetic


title: iPS.DI_2


title: single cell RNA seq (SpSC11)

value: Testis

value: germ cells

value: Wild type


title: iPS.NG_1


title: NB1

city: Ulsan

first: Robert

middle: J.

last: Mitchell

address: 50 UNIST-gil

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

data_processing:
The B. bacteriovorus HD100 reference genome was downloaded from NCBI database, and the quality filtered reads were aligned to the genome using Bowtie 2.
Analyses and visualization of the RNA sequencing reads were performed using the CLRNASeqTM program (ChunLab, South Korea).The RNA sequencing reads in each sample were normalized using RPKM (Reads Per Kilobase Million) method.
Genome_build: BX842601.2
Supplementary_files_format_and_content: Excel file contains the total reads as well as the RPKM values for the genes in each sample

organism: Bdellovibrio bacteriovorus HD100

source_name: AP B. bacteriovorus incubated in Nutrient broth (replicate 1)

growth_protocol: The predatory bacterium B. bacteriovorus was always cultured and maintained in HEPES buffer with CaCl2 and MgCl2 salts added to it at concentrations of 4 mM and 2 mM, respectively using Escherichia coli MG1655 as a prey. The prey was routinely suspended at an OD of 1.0 and the predator was added and incubated at 30◦C in a shaking incubator. The culture is usually cleared within 24 hours. B. bacteriovorus was then separated from the remaining E. coli cells by filtering through 0.45 µm filters before transfering portion of it to the subsequent culture

extract_protocol:
RNA was extracted using Trizol / chloroform extraction method. RNA purification was done using RNeasy Mini kit (Qiagen, USA). The RNA concentration was then measured using a NanoDrop spectrophotometer. The RNA quality was assessed in Agilent 2100 bioanalyzer using RNA Nano-Chips (Agilent, USA).
Ribosomal RNA depletion was performed using the Ribo-zero rRNA removal kit (Epicentre, USA). Libraries for sequencing were made using the Truseq Standard mRNA sample preparation kit (Illumina, USA). The sequencing was done using single-end 50 bp sequencing on the Illumina Hiseq 2500 platform.

treatment_protocol: B. bacteriovorus, from 24 h predatory cultures prepared in HEPES buffer, was filtered (0.45 µM), concentrated and then re-suspended in HEPES buffer, or 1x NB (20 ml each). All the media were supplemented with CaCl2 and MgCl2 as usual.  After a 4 h  incubation in a 30ºC shaking incubator, B. bacteriovorus cells from all the tubes were collected by centrifugation (16,000xg, 10 min), and the RNA was extracted

tag: strain


title: Mix1-T2

city: Oldenburg

first: Hanna

last: Koch

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: Institute for Chemistry and Biology of the Marine Environment

description:
PRO1512_S10_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv

data_processing:
HiSeq Control v3.3.52 as well as RTA v2.7.3 software used for sequencing.
Sequenced reads were quality-checked (FastQC v0.11.2) and  trimmed  (trim_galore v0.4.1). Trimmed paired-end reads were pseudoaligned to all genes of A. macleodii 83-1 using kallisto v0.43.0 (Indexing: k-mer length of 31). Kallisto quant was run using 100 bootstraps to obtain transcript abundance counts.
Differential expression was analyzed using the DESeq2 (v1.14.0) R package.
Genome_build: Alteromonas_83-1_IMG_genes.fasta
Supplementary_files_format_and_content:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv: DESeq2 output comparing Glucose-T1 (G1) with  Glucose-T2 (G2)
DeSeq2_Mix-T1_vs_Mix-T2.csv: DESeq2 output comparing Mix-T1 (M1) with  Mix-T2 (M2)
DeSeq2_Glucose-T1_vs_Mix-T1.csv: DESeq2 output comparing Glucose-T1 (G1) with  Mix-T1 (M1)
DeSeq2_Glucose-T2_vs_Mix-T2.csv: DESeq2 output comparing Glucose-T2 (G2) with  Mix-T2 (M2)

organism: Alteromonas macleodii

source_name: Mix_T2_bacterial culture

extract_protocol:
Total nucleic acids were extracted from all biomass samples using the MasterPure RNA purification kit (Epicentre, Madison, WI). DNA was depleted using Turbo DNA-free Kit (Thermo Fisher) and rRNA was removed by using the Ribo-Zero kit (Illumina, San Diego, CA).
After chemical fragmentation, transcriptome libraries (average size of 362bp) were prepared using the TruSeq RNA protocol (Illumina).

treatment_protocol: Polysaccharide-mix samples: each 0.02% laminarin/alginate/pectin were added to seawater minimal medium. Glucose samples: 0.06% glucose was added to seawater minimal medium. Cultures were inoculated and incubated 2L Erlenmeyer flasks containing each 400 mL medium. Biomass samples were taken at T1 (13h) and T2 (21h) of incubations for transcriptomic analysis.

tag: growth condition

value: polysaccharide mix

tag: time point

value: T2 (21h of incubation)


title: NB2

source_name: AP B. bacteriovorus incubated in Nutrient broth (replicate 2)


title: Mix3-T2

description:
PRO1512_S12_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv


title: NB3

source_name: AP B. bacteriovorus incubated in Nutrient broth (replicate 3)


title: H2

source_name: AP B. bacteriovorus incubated in HEPES buffer (replicate 2)


title: Mix2-T2

description:
PRO1512_S11_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv


title: Mix3-T1

description:
PRO1512_S9_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv

source_name: Mix_T1_bacterial culture

value: T1 (13h of incubation)


title: H1

source_name: AP B. bacteriovorus incubated in HEPES buffer (replicate 1)


title: Mix1-T1

description:
PRO1512_S7_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv


title: single cell RNA seq (SpSC5)

source_name: Germ cells


title: Mix2-T1

description:
PRO1512_S8_tRNA
processed data file:
DeSeq2_Mix-T1_vs_Mix-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv


title: Glucose3-T2

description:
PRO1512_S6_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv

source_name: Glc_T2_bacterial culture

value: 0.06% glucose


title: 14d_sample_3

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: ERCC spikes added

data_processing:
Torrent Suite version 4.4 or 5.0.4 used for basecalling.
The sequenced reads were trimmed for adaptor sequence, and length (Trimmomatic).
The sequenced reads were mapped using Bowtie2 (-q -p 15 -x bsub_168 -U $i"_*.fastq" -S $i"_*.sam"') or Tmap, and counted using Htseq (-a 10 -t gene -i Name $i"_*.sam" *.gff > *_$i.txt).
The following genes had the same sequences as the ERCC spikes, and were therefore excluded from futher analyses: BSU01370 (adk), BSU01380 (mapA), BSU05930 (rimI), BSU05940 (tsaD), BSU17430 (hflX), BSU01430 (rpoA), BSU22470 (bshBA), BSU22480 (mgsA), BSU22490 (dapB), BSU22500 (ypjD), BSU27900 (pheA), BSU27910 (yszB), BSU23380 (lysA).
Genome_build: NC_000964.3
Supplementary_files_format_and_content: tab-delimited text files containing read counts per gene for each sample.

organism: Bacillus subtilis

source_name: batch culture

growth_protocol: B. subtilis (ΔspoIIE) were set up in accordance with the starvation assay, however, a 1 l volume of SMM was used for culturing and 1 l of starvation buffer. On the 14th day of starvation 1 L cultures underwent suction filtration using 90 mm filter membrane with 0.45 µm pores (Millipore). For transcriptomic comparison stationary phase and exponential phase cells were also collected through filtration. For stationary phase, 1 l ΔspoIIE cultures were grown overnight (16-18 hours) at 37ºC with continuous aeration. For exponential phase, 1 L ΔspoIIE cultures were grown to an OD600 of ~0.2 at 37ºC with continuous aeration. Cells were collected into a pellet and instantly frozen in liquid nitrogen and stored at -80ºC

extract_protocol:
To isolate RNA, cell pellets were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified using the RNeasy kit (Qiagen), including an on-column treatment with the RNase-free DNase set (Qiagen). The concentration was measured on a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined using the 2200 TapeStation System with Agilent RNA ScreenTapes (Agilent Technologies).
A ribosomal RNA depletion was performed using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Illumnia). Bar-coded RNA libraries were generated according to the manufacturers’ protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress RNA-Seq barcoding kit (Thermo Fisher Scientific). The size distribution and yield of the barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). Sequencing was performed on the Ion Proton system using the Ion PI Chips (Thermo Fisher Scientific) according to the manufacturers’ protocols.

tag: genotype

tag: growth

value: 14 days

tag: experiment

tag: replicate


title: log_phase_1

description: ERCC spikes added

value: log phase


title: log_phase_2

description: ERCC spikes added


title: Glucose3-T1

description:
PRO1512_S3_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv

source_name: Glc_T1_bacterial culture


title: RNA sequencing of Mycobacterium dioxanotrophicus PH-06 treated with 1,4-dioxane

description: Extracted from PH-06 cells after grown on 1,4-dioxane

source_name: PH-06 cells grown on 1,4-dioxane

value: Dioxane degrader


title: Glucose1-T2

description:
PRO1512_S4_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv


title: Glucose2-T1

description:
PRO1512_S2_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv


title: H3

source_name: AP B. bacteriovorus incubated in HEPES buffer (replicate 3)


title: on_sample_2

description: ERCC spikes added

value: overnight


title: Glucose1-T1

description:
PRO1512_S1_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T1_vs_Mix-T1.csv


title: on_sample_1

description: ERCC spikes added


title: MTF2 shRNA clone 7 replicate 2

status: Public on Jul 31 2018

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Replicate data was analyzed using TopHat v1.4.1 and Cuffdiff 1.3.0
DAVID analysis of signficantly
Cytoscape Enrichment Map  visualization
Genome_build: hg19, Ensembl 67
Supplementary_files_format_and_content: gene_exp.diff

source_name: cord blood

extract_protocol:
RNA was isolated (Arcturus PicoPure Kit, LifeTech) and Dnase treated (Qiagen).
Iillumina TruSeq Library Prep Kit

treatment_protocol: HSPCs (Lin - CD34 + ) were transduced either with the GFP-tagged MTF2 shRNA clone or a scrambled shRNA control. The transduced GFP + cells were sorted 72 hours post transduction using a MoFlo sorter. RNA was extracted from 150,000 cells per condition for RNA-seq analysis.

value: Lin(-)CD34+ sorted


title: MTF2 shRNA clone 3 replicate 2


title: scramble control replicate 2


title: 14d_sample_1

description: ERCC spikes added


title: MTF2 shRNA clone 7 replicate 1


title: Glucose2-T2

description:
PRO1512_S5_tRNA
processed data file:
DeSeq2_Glucose-T1_vs_Glucose-T2.csv; DeSeq2_Glucose-T2_vs_Mix-T2.csv


title: scramble control replicate 1


title: 14d_sample_2

description: ERCC spikes added


title: RNA_Seq_25C_CT51

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

institute: University of Geneva

description:
Sample 10
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt

data_processing:
Tag mapping with TopHat2
Quantification with Cufflinks software suite
Genome_build: dm3
Supplementary_files_format_and_content: Cufflinks output files

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were grown Schneider medium using standard cell culture methods.

extract_protocol:
Standard RNA extraction with Zymo Direct-zol™ RNA kits
Illumina TrueSeq platform compatible dual-indexed multiplex library protocol was followed.

treatment_protocol: Cells were entrained by temperature cycles and after a medium change were transferred to constant temperature (25 degrees Celsius). RNA was extracted at the indicated time points after the last medium change.

value: S2 cells

tag: time

tag: temperature


title: RNA_Seq_25C_CT72

description:
Sample 17
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT81

description:
Sample 20
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT69

description:
Sample 16
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT63

description:
Sample 14
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT75

description:
Sample 18
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT54

description:
Sample 11
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT57

description:
Sample 12
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT60

description:
Sample 13
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT78

description:
Sample 19
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT27

description:
Sample 2
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT45

description:
Sample 8
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT30

description:
Sample 3
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT48

description:
Sample 9
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT33

description:
Sample 4
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT39

description:
Sample 6
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: RNA_Seq_25C_CT42

description:
Sample 7
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: H3K27me3 MTF2 knockdown shRNA 7 healthy sample 1

data_processing:
Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6. Reads were mapped separately to the reference human (hg19) and Drosophila melanogaster (BDGP6.0) genome assemblies using Bowtie 2.2.6
Genome_build: hg19, Ensembl 67
Supplementary_files_format_and_content: peak, bigwig

source_name: bone marrow

extract_protocol:
Samples were sheared using a Covaris sonicator until DNA reached a final size of 100-300bp. 750ng of drosophila spike in chromatin (Active Motif) was added to each sonicated sample. 4ug of anti-H3K27me3 antibody (Cell Signaling, c36B11) or H3 (Abcam, ab1791) was bound to pre-blocked Protein A7 magnetic beads (Millipore) in combination with 2ug of Spike-in antibody (Active Motif) for 12 hours. The beads were then combined with sonicated sample containing Drosophila spike in chromatin and incubated overnight. After incubation, beads were collected and DNA-antibody complexes were eluted at 65 o C. Crosslinks were reversedovernight at 65 o C. Samples were treated with Proteinase K (Fisher Scientific) and RNaseA (Fisher Scientific) and DNA was purified using phenol-chloroform. All ChIP-seq experiments were cell number normalized and 150,000 cells per biological sample were used for each H3 and H3K27me3 ChIP experiment.
For sequencing total ChIP DNA was used for library preparation (NextFlex Illumina Chip-seq kit).

tag: antibody

tag: type

value: MTF2 knockdown

tag: cell sorting

tag: status

value: Healthy


title: H3K27me3 MTF2 knockdown shRNA 7 healthy sample 2


title: H3K27me3 refractory AML sample 4

value: refractory

value: Diagnostic AML


title: H3K27me3 MTF2 knockdown shRNA 3 healthy sample 2


title: RNA_Seq_25C_CT66

description:
Sample 15
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: H3K27me3 MTF2 knockdown shRNA 3 healthy sample 1


title: H3K27me3 refractory AML sample 2


title: MTF2 shRNA clone 3 replicate 1


title: RNA_Seq_25C_CT36

description:
Sample 5
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: H3K27me3 refractory AML sample 1


title: RNA_Seq_25C_CT24

description:
Sample 1
S2_genes_25C.fpkm_table.txt
S2_genes_25C.attr_table.txt


title: H3K27me3 refractory AML sample 3


title: H3K27me3 healthy sample 2

value: healthy


title: H3K27me3 healthy sample 1


title: H3 MTF2 knockdown shRNA 3 healthy sample 2


title: H3 refractory AML sample 4


title: H3 refractory AML sample 3


title: H3 MTF2 knockdown shRNA 7 healthy sample 1


title: H3K27me3 responsive AML sample 2

value: responsive


title: H3 refractory AML sample 1


title: H3K27me3 responsive AML sample 1


title: H3 responsive AML sample 1


title: H3 MTF2 knockdown shRNA 7 healthy sample 2


title: H3 responsive AML sample 2


title: ChIP-seq clf-28 anti-H2A.Z replicate 1

city: Bethesda

first: Benjamin

last: Carter

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

data_processing:
Strand-specific sequencing was performed using the Illumina HiSeq platform according to the manufacturer's instructions.
Short reads were trimmed of adapter sequences and low-quality bases using Trimmomatic.
Reads were mapped to the TAIR10 genome using NCBI Magic-BLAST (RNA-seq) or Bowtie2 in very-sensitive-end-to-end mode (ChIP-seq).
Differential expression of RNAs was determined using edgeR and the Araport11 gene annotations. Regions of enrichment and differential enrichment of epigenetic marks was determined using SICER and SICER-df. Differentially enriched genes were identified by cross-referencing regions of enrichment from SICER-df with the Araport11 gene annotations using the closestBed function of BEDtools.
ChIP-seq alignments were converted to normalized bigwig files using the bamCoverage utility of deepTools2 with the RPKM normalization method.
Genome_build: TAIR10
Supplementary_files_format_and_content: The untrimmed counts matrix and final output from the edgeR analysis are provided as tab-delimited text and contain the gene expression data and differential expression scores. The raw SICER-df outputs are provided as tab-delimited text and were analyzed relative to WT and relative to H3 and contain the p-value calculations for regions of differential enrichment. Bigwig tracks of the ChIP-seq data were generated using deepTools2 with RPKM normalization.
H3 files used in this study were for normalization of the other samples (i.e. no processed files for individual H3 samples)

source_name: 3-week-old shoots

growth_protocol: Seeds were sown in soil pots, stratified for 3d at 4°C, and grown under 16h light for three weeks prior to sample collection.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Plant Mini Kit and DNAse-treated with a Zymo RNA Clean and Concentrator kit. Chromatin extraction and IP was performed as described in doi: 10.1074/jbc.M802129200.
cDNA libraries were prepared using the Rubicon Genomics ThruPLEX DNA-seq kit. ChIP DNA libraries were prepared using the NEB Ultra II DNA Library prep kit. Libraries were prepared according to manufacturer's instructions.

tag: tissue

value: 3-week-old shoots

tag: chip antibody

value: Anti-H2A.Z (rabbit polyclonal)


title: ChIP-seq pie1-5 anti-H2A.Z replicate 2


title: ChIP-seq pie1-5 anti-H2A.Z replicate 1


title: H3 healthy sample 2


title: ChIP-seq WT anti-H2A.Z replicate 2

value: WT


title: ChIP-seq pie1-5 anti-H3K27me3 replicate 2

value: Anti-H3K27me3 Millipore 07-449


title: ChIP-seq pkl-1 anti-H2A.Z replicate 2


title: ChIP-seq clf-28 anti-H2A.Z replicate 2


title: ChIP-seq pie1-5 anti-H3K27me3 replicate 1


title: H3 healthy sample 1


title: ChIP-seq clf-28 anti-H3K27me3 replicate 1


title: ChIP-seq clf-28 anti-H3K27me3 replicate 2


title: ChIP-seq pkl-1 anti-H3K27me3 replicate 2


title: ChIP-seq pkl-1 anti-H2A.Z replicate 1


title: H3 MTF2 knockdown shRNA 3 healthy sample 1


title: H3 refractory AML sample 2


title: ChIP-seq pkl-1 anti-H3 replicate 1

value: Anti-H3 abcam ab1791


title: ChIP-seq WT anti-H3K27me3 replicate 2


title: ChIP-seq clf-28 anti-H3 replicate 1


title: ChIP-seq pie1-5 anti-H3 replicate 1


title: ChIP-seq clf-28 anti-H3 replicate 2


title: ChIP-seq pkl-1 anti-H3 replicate 2


title: ChIP-seq pkl-1 anti-H3K27me3 replicate 1


title: ChIP-seq WT anti-H3K27me3 replicate 1


title: ChIP-seq pkl-1 input DNA replicate 1

value: No IP (input)


title: ChIP-seq pie1-5 anti-H3 replicate 2


title: ChIP-seq WT input DNA replicate 2


title: ChIP-seq pkl-1 input DNA replicate 2


title: ChIP-seq clf-28 input DNA replicate 1


title: RNA-seq pie1-5 replicate 3


title: ChIP-seq WT anti-H3 replicate 2


title: ChIP-seq clf-28 input DNA replicate 2


title: RNA-seq pie1-5 replicate 1


title: RNA-seq clf-28 replicate 2


title: RNA-seq clf-28 replicate 3


title: ChIP-seq WT anti-H2A.Z replicate 1


title: ChIP-seq pie1-5 input DNA replicate 2


title: RNA-seq clf-28 replicate 1


title: RNA-seq pkl-1 replicate 3


title: ChIP-seq WT input DNA replicate 1


title: RNA-seq pkl-1 replicate 2


title: RNA-seq pkl-1 replicate 1


title: ChIP-seq WT anti-H3 replicate 1


title: RNA-seq pie1-5 replicate 2


title: RNA-seq WT replicate 1


title: RNA-seq WT replicate 2


title: RNA-seq WT replicate 3