title: TCR95B.BC8

description:
TCR-beta RNA
G08-Brain-TCRB

source_name: patient 8 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: N01-Brain-RNAseq_JJ014

status: Public on May 18 2016

type: SRA

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

description:
poly(A)+ RNA
N01-Brain-RNAseq

library_source: transcriptomic

data_processing:
TCRseq libraries, error correction:  Raw paired-end data (FASTQ output option on MiSeq) was processed for sequencing error correction using a custom software pipeline.  Each mate-pair was first validated using the Burrows-Wheeler Aligner local alignment algorithm, then fully aligned (Smith-Waterman) for site-by-site comparison. Overlapping regions were individually scanned for nucleotide consistency at every position. Mismatches were resolved as follows:  1) If the mismatch occurred at a mapped position, the reference allele was selected. 2) If the location was unmapped or varied from the reference, the nucleotide identity was selected from the mate-paired stands by base quality, if the difference in quality differed by an order of magnitude. 3) If the quality score of the site on both paired reads was similar (<10x difference), the nucleotide identity from R1 was used by default. The output reads were constructed by merging the mate-pair overlapping, corrected regions, and appending the 3’ and 5’ overhangs.
TCRseq libraries, demultiplexing:  Internal 6mer barcode sequences (available through the support documents at [http://media.wix.com/ugd/c9f231_5f7f780864ec41f8a5cc57ffcb2a3277.pdf] were identified within the merged, error-corrected reads using string-search algorithm with linear average search time, whereby a 14-nt sliding window scanned the read from the end proximal to the barcode location (J cassette), the first eight nucleotides corresponding to the end of the conserved constant region of either alpha –chain or beta –chain, and the remaining six nucleotides constituting the manufacturer barcode. Every possible combination of 14-nucleotides was searched for simultaneously using a preprocessed hash table, with a single nucleotide mismatch allowed in each of the constant region and the barcode region, resulting in the assignment of each read to a barcode, or flagging it as “unmatched.”  All reads and their assigned barcode ID proceeded to CDR3 motif filtering.
TCRseq libraries, in silico translation and filtering:  Error corrected output files were in silico translated as previously described, using a custom pipeline writen in Perl, then filtered for sequences encoding an in-frame C/FXFG motif with no intervening stop codons, and thus a productive CDR3.  This output was tabulated by V-J cassette combination, aaCDR3, and combined VJ+aaCDR3 clonotype identifier, totCDR3 (Supplementary Table S2), in which a single count represents an error corrected R1-R2 mate pair of reads.
TCRseq libraries, V and J cassette mapping:  The presence of V or J cassettes was initially identified based on the coordinates to which the read was mapped in a GRCh37.p8 human reference, in which the Beta-chain on Chr. 7 had been masked (location 7q34 91557-667340) and replaced by a patch from Genbank (GRCh37.p9), which offered more up-to-date sequence data on this locus. Our cassette reference contained the entire set of amino acid sequences and CDR3 associated motifs, including pseudogenes, provided by the ImMunoGeneTics (IMGT) information system, for a comprehensive analysis. Sequences were translated into all three reference frames, and the correct CDR3 sequence identified based on the conserved cysteine in the V cassette and the conserved four residue motif in the J cassette.  In order to define the interval on which the TRAV and TRBV cassette family members might be resolved, we used the TCRseq data from all subjects to find the most uptream nucleotide position for each V in the reference sequence included in ≥95% of its mapped reads (for V).  Within this interval and exclusive of the final 5nt, the hamming distances between members of the same family were calculated.  All cases in which two or more validated cassettes were found to have a hamming distance of 0 within the shorter of the two nt intervals were annotated as indistinguishable (e.g. TRBV6-2/3).  Non-validated (pseudogene and ORF) V and J cassettes to which < 100 reads per library were mapped (across all libraries in this study) were considered spurious and discarded, while non-validated but productive, sequence-resolvable cassettes to which > 100 reads per library were mapped were included in the final data set despite their lack of previous validation (TRBV12-2, TRBV26, and TRBV7-1).
RNAseq libraries were mapped to the GRCh37 genome and Illumina iGenomes transcriptome using Tophat 2 and uniquely mapped read counts were computed using HTSeq. The resulting read counts were then normalized using the 'estimateSizeFactors' function in DESeq2.
Genome_build: GRCh37.p8, with TCRb locus (7q34 91557-667340) masked and replaced by a patch from Genbank (GRCh37.p9); V and J cassette sequences for reference mapping imported from IMGT
Supplementary_files_format_and_content: [TCRseq]  text files in tsv format that contain the VJ cassette combination, number of reads, VJ cassette gene names, amino acid CDR3 sequence, nucleotide CDR3 sequence, and insertion length for each observed clone.
Supplementary_files_format_and_content: [RNAseq] Excel spreadhseet containing the number of uniquely mapped reads associated with each gene calculated using HTSeq.

molecule: total RNA

organism: Homo sapiens

source_name: patient 1 (non-glioma), RNA-Seq of brain tissue

extract_protocol:
Total RNA was isolated from cryofrozen human samples using the TissueLyzer system with Qiazol and steel beads (Qiagen).  RNAseq was performed on total RNA through the Columbia Genome Center, and concentration and RIN score obtained by BioAnalyzer.  For TCR library preparation, mRNA was isolated using magnetic oligo-dT Dynabeads (Life Technologies), according to manufacturer protocol, and final concentration determined by Qubit (Life Technologies).  Total RNA was obtained from 2.5x10^6 PBMCs using the Qiagen RNeasy system according to manufacturer instructions.
We utilized the commercially available iRepertoire primer set for nested amplicon rescued multiplex PCR (arm-PCR) of the complementarity-determining region 3 (CDR3) of the human TCR and TCR chains and addition of adaptors for Illumina platform sequencing.  ~400ng of mRNA or total RNA was included for tumor libraries or PBMC libraries respectively.  In our modification of the manufacturer’s protocol, reverse transcription was conducted with a one-step reverse transcription and amplification kit (Qiagen) at 50°C for 40min, 95°C for 15min, seventeen non-exponential thermocycles (94°C/30s, 60°C/2min, 72°C/30s) and ten exponential thermocycles (94°C/30s, 72°C/2min).  PCR1 product was purified using AmpureX-100 magnetic beads (Agencourt).  Secondary amplification of 40% of the resulting product was performed by multiplex PCR (Qiagen), allowing addition of Illumina adapter sequences, with 34 thermocycles (94°C/30s, 55°C/30s, 72°C/30s).  Libraries were purified by agarose gel electrophoresis, cutting between 200-400bp (predicted amplicon size 210-310bp), gel extracted (Qiagen), and sequenced on an Illumina MiSeq, obtaining paired-end reads 220-250nt as described below.

tag: individual

value: patient 1 (non-glioma)

tag: tissue

value: brain


title: TCR94A.BC7

description:
TCR-alpha RNA
G08-Brain-TCRA

data_processing:
Library strategy: TCR-seq
TCRseq libraries, error correction:  Raw paired-end data (FASTQ output option on MiSeq) was processed for sequencing error correction using a custom software pipeline.  Each mate-pair was first validated using the Burrows-Wheeler Aligner local alignment algorithm, then fully aligned (Smith-Waterman) for site-by-site comparison. Overlapping regions were individually scanned for nucleotide consistency at every position. Mismatches were resolved as follows:  1) If the mismatch occurred at a mapped position, the reference allele was selected. 2) If the location was unmapped or varied from the reference, the nucleotide identity was selected from the mate-paired stands by base quality, if the difference in quality differed by an order of magnitude. 3) If the quality score of the site on both paired reads was similar (<10x difference), the nucleotide identity from R1 was used by default. The output reads were constructed by merging the mate-pair overlapping, corrected regions, and appending the 3’ and 5’ overhangs.
TCRseq libraries, demultiplexing:  Internal 6mer barcode sequences (available through the support documents at [http://media.wix.com/ugd/c9f231_5f7f780864ec41f8a5cc57ffcb2a3277.pdf] were identified within the merged, error-corrected reads using string-search algorithm with linear average search time, whereby a 14-nt sliding window scanned the read from the end proximal to the barcode location (J cassette), the first eight nucleotides corresponding to the end of the conserved constant region of either alpha –chain or beta –chain, and the remaining six nucleotides constituting the manufacturer barcode. Every possible combination of 14-nucleotides was searched for simultaneously using a preprocessed hash table, with a single nucleotide mismatch allowed in each of the constant region and the barcode region, resulting in the assignment of each read to a barcode, or flagging it as “unmatched.”  All reads and their assigned barcode ID proceeded to CDR3 motif filtering.
TCRseq libraries, in silico translation and filtering:  Error corrected output files were in silico translated as previously described, using a custom pipeline writen in Perl, then filtered for sequences encoding an in-frame C/FXFG motif with no intervening stop codons, and thus a productive CDR3.  This output was tabulated by V-J cassette combination, aaCDR3, and combined VJ+aaCDR3 clonotype identifier, totCDR3 (Supplementary Table S2), in which a single count represents an error corrected R1-R2 mate pair of reads.
TCRseq libraries, V and J cassette mapping:  The presence of V or J cassettes was initially identified based on the coordinates to which the read was mapped in a GRCh37.p8 human reference, in which the Beta-chain on Chr. 7 had been masked (location 7q34 91557-667340) and replaced by a patch from Genbank (GRCh37.p9), which offered more up-to-date sequence data on this locus. Our cassette reference contained the entire set of amino acid sequences and CDR3 associated motifs, including pseudogenes, provided by the ImMunoGeneTics (IMGT) information system, for a comprehensive analysis. Sequences were translated into all three reference frames, and the correct CDR3 sequence identified based on the conserved cysteine in the V cassette and the conserved four residue motif in the J cassette.  In order to define the interval on which the TRAV and TRBV cassette family members might be resolved, we used the TCRseq data from all subjects to find the most uptream nucleotide position for each V in the reference sequence included in ≥95% of its mapped reads (for V).  Within this interval and exclusive of the final 5nt, the hamming distances between members of the same family were calculated.  All cases in which two or more validated cassettes were found to have a hamming distance of 0 within the shorter of the two nt intervals were annotated as indistinguishable (e.g. TRBV6-2/3).  Non-validated (pseudogene and ORF) V and J cassettes to which < 100 reads per library were mapped (across all libraries in this study) were considered spurious and discarded, while non-validated but productive, sequence-resolvable cassettes to which > 100 reads per library were mapped were included in the final data set despite their lack of previous validation (TRBV12-2, TRBV26, and TRBV7-1).
RNAseq libraries were mapped to the GRCh37 genome and Illumina iGenomes transcriptome using Tophat 2 and uniquely mapped read counts were computed using HTSeq. The resulting read counts were then normalized using the 'estimateSizeFactors' function in DESeq2.
Genome_build: GRCh37.p8, with TCRb locus (7q34 91557-667340) masked and replaced by a patch from Genbank (GRCh37.p9); V and J cassette sequences for reference mapping imported from IMGT
Supplementary_files_format_and_content: [TCRseq]  text files in tsv format that contain the VJ cassette combination, number of reads, VJ cassette gene names, amino acid CDR3 sequence, nucleotide CDR3 sequence, and insertion length for each observed clone.
Supplementary_files_format_and_content: [RNAseq] Excel spreadhseet containing the number of uniquely mapped reads associated with each gene calculated using HTSeq.

source_name: patient 8 (glioblastoma), TCR-alpha repertoire of brain tumor tissue

value: patient 8 (glioblastoma)

tag: tcr repertoire

value: TCR-alpha


title: TCR69B.BC6

description:
TCR-beta RNA
G09-Blood-TCRB

source_name: patient 9 (glioblastoma), TCR-beta repertoire of peripheral blood

value: patient 9 (glioblastoma)

value: peripheral blood

value: TCR-beta


title: TCR67A.BC2

description:
TCR-alpha RNA
G07-Blood-TCRA

source_name: patient 7 (glioblastoma), TCR-alpha repertoire of peripheral blood

value: patient 7 (glioblastoma)


title: TCR78B.BC2

description:
TCR-beta RNA
L06-Blood-TCRB

source_name: patient 6 (low-grade glioma), TCR-beta repertoire of peripheral blood

value: patient 6 (low-grade glioma)


title: TCR94B.BC6

description:
TCR-beta RNA
G08-Blood-TCRB

source_name: patient 8 (glioblastoma), TCR-beta repertoire of peripheral blood


title: TCR67B.BC8

description:
TCR-beta RNA
G07-Brain-TCRB

source_name: patient 7 (glioblastoma), TCR-beta repertoire of brain tumor tissue


title: TCR77A.BC1

description:
TCR-alpha RNA
L06-Blood-TCRA

source_name: patient 6 (low-grade glioma), TCR-alpha repertoire of peripheral blood


title: TCR68B.BC8

description:
TCR-beta RNA
G07-Blood-TCRB

source_name: patient 7 (glioblastoma), TCR-beta repertoire of peripheral blood


title: TCR76B.BC2

description:
TCR-beta RNA
L06-Brain-TCRB

source_name: patient 6 (low-grade glioma), TCR-beta repertoire of brain tumor tissue


title: TCR76A.BC1

description:
TCR-alpha RNA
L06-Brain-TCRA

source_name: patient 6 (low-grade glioma), TCR-alpha repertoire of brain tumor tissue


title: TCR29A.BC3

description:
TCR-alpha RNA
L05-Brain-TCRA

source_name: patient 5 (low-grade glioma), TCR-alpha repertoire of brain tumor tissue

value: patient 5 (low-grade glioma)


title: TCR68A.BC2

description:
TCR-alpha RNA
G07-Brain-TCRA

source_name: patient 7 (glioblastoma), TCR-alpha repertoire of brain tumor tissue


title: TCR22A.BC1

description:
TCR-alpha RNA
L04-Blood-TCRA

source_name: patient 4 (low-grade glioma), TCR-alpha repertoire of peripheral blood

value: patient 4 (low-grade glioma)


title: Mtr4_2-HTP

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

data_processing:
Library strategy: CRAC-seq
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Collapsing reads: To remove PCR duplicates, reads mapped to the same start position in the genome and sharing the same 3-nucleotide random barcode sequence were collapsed.
Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence. RPC160-HTP read were additionaly filtered and only 3'linker-containing reads were included to further analyses
Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by novoalign version 2.07.00.
Additional processing: Reads hittables and pilups were created using pyCRAC software, pileups were converted into concat files and final results were obtained using gwide package (https://github.com/tturowski/gwide)
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: Genomic coordinates of mapped reads in gff format

organism: Saccharomyces cerevisiae

source_name: BY4741 Mtr4-HTP

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan. Indicated samples were shifted to synthetic medium with glycerol minus tryptophan and were grown at 37°C for 2h

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: background strain

tag: htp tagged protein

tag: genotype

value: wildtype


title: TCR29B.BC2

description:
TCR-beta RNA
L05-Blood-TCRB

source_name: patient 5 (low-grade glioma), TCR-beta repertoire of peripheral blood


title: Mtr4-HTP


title: Rrp6_2-HTP

source_name: BY4741 Rrp6-HTP


title: TCR23B.BC2

description:
TCR-beta RNA
L04-Blood-TCRB

source_name: patient 4 (low-grade glioma), TCR-beta repertoire of peripheral blood


title: Rrp6-HTP


title: TCR23A.BC3

description:
TCR-alpha RNA
L04-Brain-TCRA

source_name: patient 4 (low-grade glioma), TCR-alpha repertoire of brain tumor tissue


title: TCR109B.BC8

description:
TCR-beta RNA
N03-Blood-TCRB

source_name: patient 3 (non-glioma), TCR-beta repertoire of peripheral blood

value: patient 3 (non-glioma)


title: TCR28A.BC1

description:
TCR-alpha RNA
L05-Blood-TCRA

source_name: patient 5 (low-grade glioma), TCR-alpha repertoire of peripheral blood


title: Rrp44exo-HTP

source_name: BY4741 Rrp44-exo-HTP


title: Rrp44exo_2-HTP


title: TCR111B.BC6

description:
TCR-beta RNA
N03-Brain-TCRB

source_name: patient 3 (non-glioma), TCR-beta repertoire of brain tissue


title: Rrp44_2-HTP

source_name: BY4741 Rrp44-HTP


title: TCR111A.BC4

description:
TCR-alpha RNA
N03-Brain-TCRA

source_name: patient 3 (non-glioma), TCR-alpha repertoire of brain tissue


title: Rrp44-HTP


title: TCR28B.BC4

description:
TCR-beta RNA
L05-Brain-TCRB

source_name: patient 5 (low-grade glioma), TCR-beta repertoire of brain tumor tissue


title: TCR49B.BC2

description:
TCR-beta RNA
N02-Blood-TCRB

source_name: patient 2 (non-glioma), TCR-beta repertoire of peripheral blood

value: patient 2 (non-glioma)


title: Nab2HTP_2

source_name: BY4741 Nab2-HTP


title: C160HTP_maf1_gly_2

source_name: BY4741 Rpc160-HTP_maf1_shifted to glycerol medium


title: TCR48A.BC1

description:
TCR-alpha RNA
N02-Blood-TCRA

source_name: patient 2 (non-glioma), TCR-alpha repertoire of peripheral blood


title: TCR49A.BC3

description:
TCR-alpha RNA
N02-Brain-TCRA

source_name: patient 2 (non-glioma), TCR-alpha repertoire of brain tissue


title: Nab2HTP_1


title: TCR22B.BC4

description:
TCR-beta RNA
L04-Brain-TCRB

source_name: patient 4 (low-grade glioma), TCR-beta repertoire of brain tumor tissue


title: C160HTP_maf1_gly_1


title: wild-type rep2

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing:
3'-adapters were removed by ShortStack 3.3 with options --adapt TGGAATTC. Reads with length shorter than 15 nts after adapter trimming and reads in which adapter sequence was not found were discarded.
Trimmed reads were then aligned to Arabidopsis genome using ShortStack 3.3 with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include non-redundant trimmed reads with raw sequencing count

organism: Arabidopsis thaliana

source_name: immature inflorescence

growth_protocol: Arabidopsis thaliana plants were grown at control condition, with 16 h day / 8h night at 21oC

extract_protocol:
Total RNA from immature Arabidopsis inflorescence was extracted using the miRNeasy Mini kit (Qiagen) per the manufacturer's instructions.
Small RNA libraries were prepared using the TruSeq Small RNA kit (Illumina) per manufacturer's instructions

tag: ecotype

value: wild-type

tag: organ

value: inflorescence


title: TCR44A.BC1

description:
TCR-alpha RNA
N01-Blood-TCRA

source_name: patient 1 (non-glioma), TCR-alpha repertoire of peripheral blood


title: C160HTP_maf1_glu_1

source_name: BY4741 Rpc160-HTP_maf1_glucose medium


title: EndoC ctrl GFP 2

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

description:
RSq55
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

data_processing:
Raw reads were mapped to hg19 transcriptome using STAR version 2.3.0.1.
A custom script was used to count transcripts.
Genome_build: hg19 transcriptome, aggregated from UCSC, RefSeq and GENCODE v12 databases.
Supplementary_files_format_and_content: normalizedCounts_endoC.txt: The processed data file contains 9 tab-delimited columns: the first column is gene symbol, and columns that come after are DESeq normalized counts of the respective samples. We used the DESeq (Huber et al. [PMID: 20979621]) normalization.

source_name: Endo-ßH1C cell line (pancreas), scrambled control, GFP expression

extract_protocol:
ABI picopure RNA extraction kit.
KAPA stranded RNA-Seq kit.

tag: cell line

tag: cell type

value: pancreatic beta-cell line

tag: gain of function

value: GFP

tag: sirna treatment

value: scrambled control


title: C4-4BO: IL1α & PDGF 4

city: Glasgow

first: Rachel

last: Dakin

address: 126 University Place

department: ICAMS

country: United Kingdom

institute: University of Glasgow

description:
molecule: rRNA depleted RNA
IL1α and PDGF treatment together is group3 in edgeR analysis

data_processing:
Adapter sequences trimmed with Flexbar version 2.4
mapping was performed with Tophat version 2.0.9 in conjunction with Bowtie version 1.0.0.
Cufflinks version 2.1.1 was used to detect known and predicted genes and transcripts from the Ensembl gene models for the grch37 release of the human genome. Cuffdiff version 2.1.1 was used to collect FPKM expression values for samples which were run as experimental groups.
For differential expression, the edgeR R Bioconductor 2.12 package was used with the use of the easyRNASeq R Bioconductor package to establish raw read counts from the Tophat2 generated BAM alignment files
Genome_build: GRCh37
Supplementary_files_format_and_content: cpm.csv file contains raw cpm for each gene in each sample. edgeR.csv files contain comparison between groups: logFC, logCPM, p value and FDR

source_name: venous smooth muscle cells

growth_protocol: venous smooth muscle cells were used between passage 4 and 5. Cells (1x105/well) were cultured and plated in uncoated 6 well plates in 15%FBS Smooth Muscle Cell Growth Medium 2 (PromoCell, Heidelberg, Germany) and left to adhere for 24h.

extract_protocol:
Cells were lysed with qiazol and RNA fractation removed following addition of chloroform, further extraction was completed using Qiagen miRNeasy kit according to manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were quiesced in 0.2% serum for 48h followed by addition of 10ng/ml IL1α , 20ng/ml PDGF or both 10ng/ml IL1α and 20ng/ml PDGF together for 72h.

value: primary venous smooth muscle cells

tag: passage

tag: treatment

value: 0.2% serum + 10ng/ml IL1α + 20ng/ml PDGF


title: TCR109A.BC7

description:
TCR-alpha RNA
N03-Blood-TCRA

source_name: patient 3 (non-glioma), TCR-alpha repertoire of peripheral blood

value: TCR-alpha


title: TCR44B.BC4

description:
TCR-beta RNA
N01-Brain-TCRB

source_name: patient 1 (non-glioma), TCR-beta repertoire of brain tissue

value: patient 1 (non-glioma)

value: brain


title: EndoC ctrl GFP 1

description:
RSq54
PolyA RNA
Processed data file: normalizedCounts_endoC.txt


title: C10-1BO: IL1α & PDGF 1


title: C6-3BO: IL1α & PDGF 3


title: TCR45A.BC3

description:
TCR-alpha RNA
N01-Brain-TCRA

source_name: patient 1 (non-glioma), TCR-alpha repertoire of brain tissue


title: C160HTP_wt_gly_1

source_name: BY4741 Rpc160-HTP_wildtype_shifted to glycerol medium


title: EndoC T-Ag 2046 SIX3

description:
RSq53
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 2046, SIX3 expression

value: T-Antigen siRNA 2046


title: C160HTP_wt_gly_2


title: E4-4PD: PDGF 4

description:
molecule: rRNA depleted RNA
PDGF treatment is group1 in edgeR analysis

value: 0.2% serum + 20ng/ml PDGF


title: TCR48B.BC4

description:
TCR-beta RNA
N02-Brain-TCRB

source_name: patient 2 (non-glioma), TCR-beta repertoire of brain tissue

value: TCR-beta


title: C160HTP_wt_glu_2


title: EndoC T-Ag 2046 SIX2

description:
RSq52
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 2046, SIX2 expression


title: wild-type rep3


title: C160HTP_maf1_glu_2


title: EndoC T-Ag 460 SIX3

description:
RSq50
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 460, SIX3 expression

value: T-Antigen siRNA 460


title: wild-type rep1


title: EndoC T-Ag 2046 GFP

description:
RSq51
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 2046, GFP expression


title: E8-2PD: PDGF 2


title: TCR45B.BC2

description:
TCR-beta RNA
N01-Blood-TCRB

source_name: patient 1 (non-glioma), TCR-beta repertoire of peripheral blood

value: peripheral blood


title: E6-3PD: PDGF 3


title: C160HTP_wt_glu_1

value: wildtype


title: BY4741


title: D4-1IL: IL1α 4

description:
molecule: rRNA depleted RNA
IL1α treatment is group2 in edgeR analysis

value: 0.2% serum + 10ng/ml IL1α


title: C8-2BO: IL1α & PDGF 2


title: FOLFIRI 2

city: Aurora

first: Andrea

last: Bonetto

state: Colorado

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description:
AB14.18
Library27_27

data_processing:
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file includes row counts, log2 fold change values, p-values and FDR.

organism: Mus musculus

source_name: Skeletal muscle (Quadriceps)

extract_protocol:
Quadriceps muscle was excised, flash frozen in liquid nitrogen, and total RNA was extracted using the Qiagen miRNeasy Mini Kit. The Life Technologies SOLiD RNA-Seq kit (#4445374) was used with 1 ug of total RNA for the construction of sequencing libraries.
SOLiD Total RNA-seq Kit

treatment_protocol: CD2F1 male mice (8 week-old) were treated with Folfiri (30mg/kg 5-FU, 90mg/kg Leucovorin, 24mg/kg CPT-11, i.p., twice/week) for up to 5 weeks.

tag: strain

tag: Sex

value: male


title: EndoC T-Ag 460 GFP

description:
RSq48
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 460, GFP expression


title: FOLFIRI 3

description:
AB14.19
Library28_28


title: D6-1IL: IL1α 3


title: FOLFIRI 4

description:
AB14.20
Library29_29


title: Acetate 6

city: Basel

first: Christoph

last: Hess

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University Basel

data_processing:
The prepared libraries were sequenced on the Illumina NextSeq 500 using a v2 kit with 75 cycles and high output.
The resulting reads were mapped to the mm10 reference genome using the STAR software version 2.4.0h (GitHub, Inc.).
Resulting mapping files in bam format were analyzed using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) from the HTSeq framework (version 0.6.0) for read count numbers to specific genomic features (whole genes).
Finally, the raw count files were inputted to the statistical analysis software DESeq2 (version 1.6.3) from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: mapped raw read counts

source_name: OT-I T cells

growth_protocol: OVA-specific OT-I memory T cells were activated with 10^–9 M OVA peptide in the presence of splenocytes for 3 d, followed by 3-4 d culture in IL-15 (10 ng/mL) in absence of OVA peptide.

extract_protocol: The total RNA input material was used to make barcoded and ready to sequence libraries using the Illumina TruSeq Stranded mRNA Sample Preparation Kits.

treatment_protocol: 5 mM acetate was added during the last 3 days of culture

value: Lymph node


title: FOLFIRI 1

description:
AB14.17
Library26_26


title: Control 5


title: EndoC T-Ag 460 SIX2

description:
RSq49
PolyA RNA
Processed data file: normalizedCounts_endoC.txt

source_name: Endo-ßH1C cell line (pancreas), T-Ag siRNA 460, SIX2 expression

value: pancreatic beta-cell line


title: Vehicle 4

description:
AB14.4
Library21_21


title: D8-1IL: IL1α 2


title: F4-4CON: control 4

description: molecule: rRNA depleted RNA

value: 0.2% serum


title: F6-3CON: control 3

description: molecule: rRNA depleted RNA


title: E10-1PD: PDGF 1


title: Vehicle 2

description:
AB14.2
Library19_19


title: Control 3


title: Acetate 2


title: Vehicle 3

description:
AB14.3
Library20_20


title: F8-2CON: control 2

description: molecule: rRNA depleted RNA


title: Vehicle 1

description:
AB14.1
Library18_18


title: WT1_liver_5hmC_input [hmeDIP-seq]

status: Public on May 17 2016

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

library_source: genomic

data_processing:
Reads mapped to mm10 mouse build
Data binned into 200bp windows across the genome
Data converted into mm9 build and into a wiggle (.wig) file
data normalised by read count
enriched (5hmC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: mm9
Supplementary_files_format_and_content: .wig file

molecule: genomic DNA

source_name: WT Liver Tissue

extract_protocol:
Sheared gDNA was enriched using Anti 5hmc - Active Motif prior to enrichment through magnetic IgG beads. Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 15 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue type

value: liver


title: Tet1-/-_liver_5hmC_input [hmeDIP-seq]

source_name: Tet1-/-  Liver Tissue

value: Tet1 null


title: Tet1-/-_liver_5hmC [hmeDIP-seq]

tag: antibody

value: 5-hmC - Active Motif (cat# 39769)


title: WT1_liver_5hmC [hmeDIP-seq]


title: F10-1CON: Control 1

description: molecule: rRNA depleted RNA

source_name: venous smooth muscle cells

value: primary venous smooth muscle cells


title: 2190.WM

city: Gainesville

first: Thomas

middle: C

last: Foster

state: Florida

address: 1149 Newell Drive Bldg 59

department: Neuroscience

institute: University of Florida-McKnight Brain Institute

data_processing:
Low quality reads were removed from fastq files and  the data was aligned to the rn5 genome using the two step alignment method for Ion Proton transcriptome data with TopHat2 and Bowtie2 in the Partek Flow servers (Partek Inc.).
Two step alignment parameters included tophat --b2-sensitive -p 8 -N 4 -a 8 -m 0 -i 50. Bowtie 2 parameters: --very-sensitive-local
Gene level counts were generated using the featureCounts function in the R package, Rsubread. The Rnor_5.0.78.gtf file was used for annotation and count normalization was performed with the DESeq package in R.
Genome_build: rn5
Supplementary_files_format_and_content: comma separated values files which contain the normalized counts for each sample.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Rats were anesthetized with isoflurane, decapitated and the brain was rapidly removed. The prelimbic and infralimbic mPFC, white matter and hippocampal region CA1 were collected. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC. RNA was isolated with the RNeasy Lipid Tissue Mini kit (Qiagen, cat#: 74804) and DNase digestion was performed with the RNase-Free DNase Set (Qiagen, cat#: 79254).
250ng of RNA was used for polyA selection with the Dynabeads mRNA DIRECT Micro kit (Thermo Fisher, cat #: 61021). Transcriptome libraries were made with the Ion Total RNA-seq Kit v2 (Thermo Fisher, cat#: 4475936) with the addition of the Ion Xpress barcodes for multiplex sequencing (Thermo Fisher, cat#: 4475485).

tag: brain tissue

value: White matter

tag: age

value: Aged

tag: age impairment


title: 2191.WM


title: 2185.WM


title: D10-1IL: IL1α 1


title: 2184.WM


title: 2182.WM


title: 2181.WM


title: 2175.WM

value: Young


title: 2180.WM


title: 121448.WM


title: 2172.WM


title: 2176.WM


title: Acetate 4

tag: tissue


title: 121413.WM


title: 121412.WM


title: 2190.CA1

value: Unimpaired


title: 121445.WM


title: 121437.WM


title: 2191.CA1

value: Impaired


title: 2189.CA1


title: Control 1


title: 2184.CA1


title: 2189.WM


title: 2175.CA1


title: 2180.CA1


title: 2173.CA1


title: 2181.CA1


title: 2173WM


title: 121448.CA1


title: 121445.CA1


title: 2185.CA1


title: 121437.CA1


title: HFM_D6_Rep6

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
Base Calling: Real-time analysis and base calling were performed using the Hi-seq Control Software, version 2.2.38 (Illumina) to generate sequence reads with associated base quality scores.
Removal of low quality reads: RNA-seq reads, flagged as low quality by CASAVA 1.8 (Illumina), or with an average PHRED read quality score below 15, or in which ≥5 of the last 10 bases had a quality score below 2, were removed.
Sequence alignment: Reads were aligned to the pig reference genome sequence assembly (Sscrofa10.2) using TopHat 1.4.0 with default parameters. The number of reads uniquely mapped to each gene was determined using Ht-seq count (v0.5.3.p3).
Differential gene expression analysis: Differentially expressed genes (DEG) were identified using the Bioconductor package ‘edgeR’. Raw expression counts were converted to counts per million (CPM). Genes with very low expression levels were filtered out of the dataset by setting an expression threshold of CPM>1 in at least 8 samples. Compositional differences between libraries due to difference in library size were normalized using the ‘Trimmed mean of M values’ (TMM) method. A negative binomial model was fitted to the data and gene and tag-wise dispersions were estimated using the quantile-adjusted conditional maximum likelihood (qCML) method. Differential expression was determined using an exact test for the following two time-point contrasts: D2vD0 and D6vD2, and the following three group contrasts: LFMvHFM at D0, D2, and D6. For the time-point contrasts, genes were classified as differentially expressed if they had an absolute fold change >1.5 and a False Discovery Rate (FDR) <0.05. For the group contrasts, less stringent criteria were adopted: an absolute fold-change of >1.2 and a P value of <0.05. Additional Gene Set Enrichment Analyses (GSEA) were carried out on the data to identify more statistically robust differences between LFM and HFM groups.
Gene function analyses: For the time-point contrasts, gene function analyses were carried out on lists of upregulated and downregulated genes using the Canonical Pathway analysis feature of Ingenuity Pathway Analysis software. Analyses used a right-tailed Fisher’s Exact Test to identify pathways that were enriched in the gene set compared to the reference set (all genes in the human genome). An FDR≤0.05 cutoff was used for statistical significance. For the group contrasts, gene set enrichment analysis (GSEA; Subramanian et al., 2005; PNAS 102(43): 15545-50) was run on pre-ranked lists of all genes from the edgeR analyses. Ranking was by statistical significance and direction of expression with the trait of interest (i.e. positive log2 fold change values at the top of the list and negative values at the bottom). Gene sets that were significantly associated with fetal mortality groups were identified from the H (Hallmark), C2 (Curated), C5 (Gene Ontology), and C7 (Immunologic) collections of gene sets in the Molecular Signatures Database (MSigDB). Gene set enrichment scores were calculated using the ‘classic’ method. The null distributions used to calculate the statistical significance of the enrichment scores were generated by permutation of gene sets for each contrast. Adjustment for multiple hypothesis testing was performed by determination of FDR. Enrichment scores with an FDR <0.25 were considered to be significant.
Genome_build: Sscrofa 10.2

organism: Sus scrofa

source_name: Whole blood

growth_protocol: 133 Landrace gilts were obtained from a high-health nucleus herd that was free of PRRSV according to clinical signs and serologic testing. Groups of gilts were selected over 12 bi-weekly replicates, estrus-synchronized, and bred homosperimcally to Yorkshire boars. Pregnant gilts were housed in gestation stalls until gestation day 80±1, and then transferred to a biosafety level 2 facility at the University of Saskatchewan. After a period of acclimation, 114 gilts were inoculated on gestation day 85±1 (Experiment day 0) with 1x105 TCID50 PRRSV isolate NVSL 97-7895: 2 mL intramuscularly and 1 mL into each nostril. Nineteen control gilts were mock inoculated in a similar manner with Minimal Essential Medium (MEM). Blood samples for transcriptomic analysis were collected into Tempus blood RNA tubes (Thermo Fisher Scientific, Waltham, MA, USA) on 0 (prior to inoculation), 2, and 6 dpi. Heparinized blood samples for flow cytometry and serum samples for PRRSV quantification and cytokine analysis were also collected. Gilts were humanely euthanized and necropsied on 21 dpi (gestation day 106±1). The preservation status of each fetus in the gilt uterus was recorded, and the percentage of dead fetuses was calculated for each litter. Two groups of gilts exhibiting low or high fetal mortality (LFM or HFM; n=8) were selected. LFM gilts had a low % fetal death (<25%) and low mean PRRSV RNA concentration in fetal thymus (Mean PRRS virus score of <1.5 out of 3). HFM gilts had high % fetal death (>75%) and high mean PRRSV RNA concentration in fetal thymus (PRRSV score of >1.5 out of 3)

extract_protocol:
Total RNA was isolated from each of the 0, 2, and 6 dpi samples from each LFM and HFM gilt using the Preserved Blood RNA Purification kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer’s instructions. The highly abundant HBA1, HBA2, and HBB globin transcripts were then selectively depleted from each RNA sample according to a previously published method (Choi et al., 2014. BMC Genomics 15:952) in order to increase the sensitivity of RNA-sequencing for detection of lowly expressed transcripts. RNA was quantified by spectrophotometry using a Nanodrop ND 2000 (Thermo Fisher Scientific) and quality was assessed by digital electrophoresis using a 2200 Tapestation (Agilent Technologies, Santa Clara, USA). The mean sample RNA Integrity Number (RIN) was 7.9 (range 7.1-9.3).
A total of 48 cDNA libraries were constructed for RNA-sequencing (RNA-seq) from thymus and endometrium samples of individual fetuses. Libraries were constructed from 1 μg of input total RNA using the TruSeq RNA sample preparation kit v2 (Illumina, San Diego, USA) according to the manufacturer’s instructions. DNA libraries were sequenced at the Genome Quebec Innovation Centre (McGill University, Montreal, Canada). Library insert size distribution was assessed on a LabChip GX instrument (Perkin Elmer, Waltham, USA) using a high sensitivity chip. Library concentration was determined using a KAPA Library Quantification Kit (KAPA Biosystems) on a Lightcycler 480 II instrument (Roche Life Science, Indianapolis, USA). Cluster formation was performed on the cBot instrument (Illumina) with eight libraries per lane (7 pM per library) using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Paired-end 100 bp cycle sequencing was performed on a HiSeq 2000 (Illumina) using the TruSeq SBS kit v3-HS (Illumina).

treatment_protocol: Blood samples for transcriptomic analysis were collected into Tempus blood RNA stabilization tubes (Thermo Fisher Scientific, Waltham, MA, USA), shaken vigorously for 5 seconds, and stored at -20C.

tag: group

value: HFM

tag: time point


title: HFM_D6_Rep7


title: HFM_D6_Rep8


title: HFM_D6_Rep5


title: HFM_D6_Rep4


title: 121412.CA1


title: HFM_D6_Rep3


title: 1932.CA1


title: 1936.CA1


title: 1931.CA1


title: HFM_D2_Rep8


title: HFM_D6_Rep1


title: 121413.CA1


title: HFM_D6_Rep2


title: 1935.CA1


title: 2182.CA1


title: 2172.CA1


title: 1929.CA1


title: HFM_D2_Rep6


title: 1930.CA1


title: HFM_D2_Rep4


title: HFM_D2_Rep5


title: HFM_D2_Rep7


title: HFM_D2_Rep3


title: 1928.CA1


title: HFM_D2_Rep2


title: 1926.CA1


title: 1925.CA1


title: 1924.CA1


title: 1920.CA1


title: HFM_D0_Rep8


title: HFM_D2_Rep1


title: HFM_D0_Rep7


title: HFM_D0_Rep6


title: 1919.CA1


title: 2191.mPFC

value: medial prefrontal cortex


title: 1918.CA1


title: 2190.mPFC


title: HFM_D0_Rep3


title: HFM_D0_Rep4


title: 2189.mPFC


title: HFM_D0_Rep2


title: 2185.mPFC


title: 1927.CA1


title: HFM_D0_Rep5


title: 2184.mPFC


title: HFM_D0_Rep1


title: 2182.mPFC


title: LFM_D6_Rep7

value: LFM


title: 2181.mPFC


title: LFM_D6_Rep6


title: LFM_D6_Rep8


title: 2180.mPFC


title: 2176.mPFC


title: LFM_D6_Rep5


title: LFM_D6_Rep3


title: 2173.mPFC


title: 2172.mPFC


title: LFM_D6_Rep1


title: 121448.mPFC


title: LFM_D2_Rep8


title: 121445.mPFC


title: 121437.mPFC


title: LFM_D2_Rep6


title: 121413.mPFC


title: LFM_D2_Rep5


title: 121412.mPFC


title: 1935.mPFC


title: LFM_D2_Rep3


title: LFM_D2_Rep2


title: LFM_D0_Rep8


title: LFM_D2_Rep1


title: LFM_D6_Rep2


title: LFM_D0_Rep7


title: 1932.mPFC


title: 1930.mPFC


title: LFM_D2_Rep4


title: 2175.mPFC


title: 1928.mPFC


title: LFM_D2_Rep7


title: LFM_D0_Rep5


title: 1927.mPFC


title: LFM_D6_Rep4


title: 1936.mPFC


title: 1926.mPFC


title: LFM_D0_Rep2


title: LFM_D0_Rep4


title: 1925.mPFC


title: 1931.mPFC


title: 1924.mPFC


title: LFM_D0_Rep1


title: MEC_ENDO_Rep12

data_processing:
Base calling: Real-time analysis and base calling were performed using the Hi-seq Control Software, version 2.2.38 (Illumina) to generate sequence reads with associated base quality scores.
Removal of low quality reads: RNA-seq reads, flagged as low quality by CASAVA 1.8 (Illumina), or with an average PHRED read quality score below 15, or in which ≥5 of the last 10 bases had a quality score below 2, were removed.
Sequence alignment: Reads were aligned to the pig reference genome sequence assembly (Sscrofa10.2) using TopHat 1.4.0 with default parameters. The number of reads uniquely mapped to each gene was determined using Ht-seq count (v0.5.3.p3).
Differential gene expression analysis: Differentially expressed genes (DEG) were identified using the Bioconductor package ‘edgeR’. Raw expression counts were converted to counts per million (CPM). Genes with very low expression levels were filtered out of the dataset by setting an expression threshold of CPM>1 in at least 12 samples. Compositional differences between libraries due to difference in library size were normalized using the ‘Trimmed mean of M values’ (TMM) method. A negative binomial model was fitted to the data and gene and tag-wise dispersions were estimated using the quantile-adjusted conditional maximum likelihood (qCML) method. Differential expression was determined using an exact test for the following three contrasts for both tissues: UNINF v CON, INF v UNINF, and MEC v INF. Genes were classified as differentially expressed if they had an absolute fold change >1.5 and a False Discovery Rate (FDR) <0.05.
Weighted Gene Network Correlation Analysis: Gene co-expression network analysis was performed using the software package ‘WGCNA’ for each of the three contrasts in two tissues described above.  The normalized CPM expression data generated by ‘edgeR’ were transformed using the function log2 (x+1) to stabilize variance prior to use in WGCNA. To construct the network, a matrix of co-expression similarity, pairwise correlations, for all genes across all samples in each contrast was made. Next, a weighted network adjacency matrix was obtained by raising the co-expression similarity to a power β whose value was determined by application of the approximate scale-free topology criterion [29]. After network construction, average linkage hierarchical clustering was used to identify clusters of highly interconnected gene ‘modules’ using the topological overlap measure of network interconnectedness as the input. A dynamic hybrid tree cutter was used to identify the branches of the hierarchical clustering dendogram corresponding to modules. Network construction and module detection were performed using the function ‘blockwiseModules’, with the following parameter values: a maximum block size of 15000 (sufficiently large to analyze all genes in a single block), a minimum module size of 30, a medium sensitivity to cluster splitting of 2, and a cut height for module merging of 0.25. The value of β ranged from 6-10. The gene expression profile of a module can be summarized by the module ‘eigengene’, defined as the first principal component of the expression matrix. Correlations between the module eigengene and the two categorical traits in each contrast were determined. Correlations between the eigengene and viral RNA titers were also calculated for the appropriate contrasts. The threshold for association significance was set at an absolute correlation of >0.3 and a P value of <0.1.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier) produced by the program Ht-seq count.

source_name: uterine endometrium

growth_protocol: 133 Landrace gilts were obtained from a high-health nucleus herd that was free of PRRSV according to clinical signs and serologic testing. Groups of gilts were selected over 12 bi-weekly replicates, estrus-synchronized, and bred homosperimcally to Yorkshire boars. Pregnant gilts were housed in gestation stalls until gestation day 80±1, and then transferred to a biosafety level 2 facility at the University of Saskatchewan. After a period of acclimation, 114 gilts were inoculated on gestation day 85±1 (Experiment day 0) with 1x105 TCID50 PRRSV isolate NVSL 97-7895: 2 mL intramuscularly and 1 mL into each nostril. Nineteen control gilts were mock inoculated in a similar manner with Minimal Essential Medium (MEM). Gilts were humanely euthanized on Experiment day 21. The gravid uterus of each gilt tract was removed intact, placed in a trough, and orientated from left oviduct to right oviduct. The uterine horns were opened and fetuses numbered sequentially according to their position within the horn. The preservation status of each fetus was recorded in situ as: viable (live at the time of gilt necropsy, normal pink appearance), meconium-stained (live at time of gilt necropsy, stained with meconium), decomposed (dead prior to gilt necropsy, with primarily white skin), autolysed (dead prior to gilt necropsy, with over 50% brown-colored skin), or mummified (dead, <20 cm in length and considered dead prior to PRRSV-inoculation). Mummified fetuses were counted, but excluded from sampling and further analyses. After clamping the umbilical cord, each fetus (starting with live fetuses i.e. those classified as viable or meconium-stained) was removed from the uterus together with its umbilical cord, and a portion of allantochorion and uterus adjacent to the umbilical stump.

extract_protocol:
Total RNA was isolated from 10-20 mg of endometrium and thymus of each fetus using an ‘All Prep RNA/DNA isolation Mini kit’ (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified by spectrophotometry using a Nanodrop ND 2000 (Thermo Fisher Scientific, Waltham, USA). RNA quality was assessed by digital electrophoresis using a ‘2200 Tapestation’ (Agilent Technologies, Santa Clara, USA). The mean RNA Integrity Number (RIN) sample value was 9.0 for thymus (range 8.0-9.8) and 8.3 for endometrium (range 7.5-8.8).
A total of 96 cDNA libraries were constructed for RNA-sequencing (RNA-seq) from thymus and endometrium samples of individual fetuses. Libraries were constructed from 1 μg of input total RNA using the TruSeq RNA sample preparation kit v2 (Illumina, San Diego, USA) according to the manufacturer’s instructions. DNA libraries were sequenced at the Genome Quebec Innovation Centre (McGill University, Montreal, Canada). Library insert size distribution was assessed on a LabChip GX instrument (Perkin Elmer, Waltham, USA) using a high sensitivity chip. Library concentration was determined using a KAPA Library Quantification Kit (KAPA Biosystems) on a Lightcycler 480 II instrument (Roche Life Science, Indianapolis, USA). Cluster formation was performed on the cBot instrument (Illumina) with eight libraries per lane (7 pM per library) using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Paired-end 100 bp cycle sequencing was performed on a HiSeq 2000 (Illumina) using the TruSeq SBS kit v3-HS (Illumina).

treatment_protocol: Samples of endometrium (including adherent placental layers) adjacent to the umbilical attachment site and fetal thymus were snap-frozen in liquid nitrogen and immediately stored at -80°C.

tag: infection status

value: MEC

value: uterine endometrium


title: MEC_ENDO_Rep11


title: 1920.mPFC


title: 1918.mPFC


title: 1929.mPFC


title: LFM_D0_Rep6


title: MEC_ENDO_Rep10


title: 1919.mPFC


title: MEC_ENDO_Rep7


title: LFM_D0_Rep3


title: MEC_ENDO_Rep8


title: MEC_ENDO_Rep5


title: MEC_ENDO_Rep4


title: MEC_ENDO_Rep1


title: MEC_ENDO_Rep3


title: MEC_ENDO_Rep6


title: wild type fq

city: Shanghai

first: Xinze

last: Chen

address: 333 Nanchen Road

country: China

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl plants release-19 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays subsp. mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endosperm

value: 18 DAP

tag: genotype


title: H5

city: San Francisco

first: Charlie

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

description: Samples are essentially "identical" (FACS purified cells, then run on a C1 for single cell RNAseq), and defined by the flow cytometry gating strategy provided.

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC
Gene expression modeled using RSEM version 1.2.21 with Bowtie2 2.2.3 for read alignment. Default parameters were used.
Genome_build: Release GRCm38 of the mouse genome
Supplementary_files_format_and_content: Tab delimited text files showing TPM for all genes

source_name: Monocyte derived macrophages isolated from ipsilateral hemisphere of mouse brains 1 day after TBI

extract_protocol:
Monocyte-derived macrophages isolated from ipsilateral brain tissues were isolated by FACS on an AriaII.  Total RNA was isolated, converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: cell type

value: monocyte-derived macrophage

tag: cell surface markers

tag: sample type

value: single cell


title: INF_ENDO_Rep12

value: INF


title: dek35 mutant fq


title: MEC_ENDO_Rep2


title: INF_ENDO_Rep11


title: MEC_ENDO_Rep9


title: H3

tag: strain


title: H2


title: H1


title: G5


title: H3K27ac ChIP-seq

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

data_processing:
Illumina Casava1.9 software used for basecalling.
reads were aligned with Bowtie2
peaks were called using MACS2.0
Genome_build: hg19
Supplementary_files_format_and_content: text file with MACS2.0 output

source_name: LOUCY cell line_H3K27ac_ChIP

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
library preparation was performed using the standard Illumina protocol. Sequenced with an unstranded single end sequencing protocol.

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 100*10^6 cells were cross-linked with 1,1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 ul of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 10 μg of H3K27ac-specific antibody (Abcam, ab4729). The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.

tag: cell line

value: LOUCY

value: T-ALL


title: G4


title: INF_ENDO_Rep8


title: H3K4me3_ctrl-T

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using CASAVA.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 with the default configuration.
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed files were generated using Macs14.

source_name: brain tumor, control, H3K4me3 ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Tumor tissues were cross-linked in 1% formaldehyde at room temperature for 15 min and then quenched with 125 mM glycine for 5 min. Then the samples were rinsed, resuspended in lysis buffer (50 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.25% Triton X-100 and 0.5% NP-40 and protease inhibitor cocktail) and incubated on ice for 10 min. Lysates were centrifuged and pellets were resuspended in nuclei washing buffer (200 mM NaCl, 1 mM EDTA, 1 mM EGTA, 10 mM Tris pH 8.0, and protease inhibitor cocktail) with gentle rocking at 4°C. Nuclei were pelleted and resuspended in 1 ml of sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Nuclear suspensions were sonicated with a Covaris S220 sonicator (total time 8 min). Antibody (chromatin: antibody = 4:1) was added to chromatin and incubated at 4°C overnight. Chromatin-protein complex was immunoprecipitated with protein A/G plus agarose beads and washed sequentially, twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), twice with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 500 mM NaCl) and twice with LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris [pH 8.0]) and once with 1xTE buffer. Immunoprecipitates were then eluted in elution buffer at 65°C for 1 h. Eluted chromatin was subjected to reverse-crosslink and chromatin fragment purification with QIAGEN PCR purification columns.
ChIP-Seq libraries were prepared using NEBNext ChIP-Seq Library Prep Kit according to manufacturer's instructions.

tag: strain/background

value: mixed C57Bl/6;129Sv;CD-1

value: Ptenf/fP53f/f (control)

value: brain tumor (glioma)

tag: Stage

value: 25 days post virus injection

tag: chip antibody


title: G3


title: INF_ENDO_Rep9


title: INF_ENDO_Rep7


title: H3K27Ac_Olig2cKO

source_name: brain tumor, Olig2cKO, H3K27Ac ChIP

tag: genotype/variation

value: Ptenf/fP53f/fOlig2f/f (Olig2cKO)

value: H3K27Ac (Active Motif, cat# 39133, lot# 1613007)


title: H3K4me3_Olig2cKO

source_name: brain tumor, Olig2cKO, H3K4me3 ChIP


title: F5


title: F4


title: INF_ENDO_Rep10


title: INF_ENDO_Rep5


title: input DNA

source_name: LOUCY cell line_input


title: E8


title: INF_ENDO_Rep6


title: H3K27Ac_ctrl-T

source_name: brain tumor, control, H3K27Ac ChIP


title: E6


title: F3


title: F1


title: F8


title: Olig2

source_name: brain tumor, control, Olig2 ChIP

value: Olig2 (Millipore, cat# AB9610)


title: E4


title: Ctx_3

data_processing:
RNA-seq reads were mapped using TopHat with default settings (http://ccb.jhu.edu/software/tophat/index.shtml).
TopHat output data were then analyzed by Cufflinks to calculate FPKM values for known transcripts in mouse genome reference mm9.
Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: normal brain cortex

extract_protocol:
RNAs were isolated from the tumor cells, OPCs, astrocytes and normal cortex with Trizol as recommended by the manufacturer.
RNA libraries were prepared for sequencing using the Illumina RNA-seq preparation Kit (Illumina).

value: wild type

value: brain cortex


title: G2


title: E3


title: 2176.CA1

tag: brain tissue

value: Young


title: Ctx_2


title: E2


title: INF_ENDO_Rep2

value: uterine endometrium


title: E1


title: Ctx_1


title: D8


title: INF_ENDO_Rep1


title: mAstrocyte

source_name: normal brain astrocytes

value: astrocytes


title: D6

value: monocyte-derived macrophage


title: INF_ENDO_Rep4


title: D5

value: single cell


title: UNINF_ENDO_Rep12

value: UNINF


title: mOPC

source_name: normal brain OPCs

value: oligodendrocyte progenitor cells (OPCs)


title: INF_ENDO_Rep3

value: INF


title: D3


title: D2


title: Olig2cKO tumor cell_5

source_name: brain tumor cells, Olig2cKO

value: mixed C57Bl/6;129Sv;CD-1


title: D1


title: UNINF_ENDO_Rep10


title: C8


title: UNINF_ENDO_Rep11


title: D4


title: Olig2cKO tumor cell_4


title: C3


title: C2


title: UNINF_ENDO_Rep9


title: Olig2cKO tumor cell_2


title: C4


title: UNINF_ENDO_Rep8


title: C1


title: B6


title: UNINF_ENDO_Rep7


title: Olig2cKO tumor cell_1


title: B5


title: Ctrl tumor cell_5

source_name: brain tumor cells, control


title: UNINF_ENDO_Rep6


title: B3


title: B4


title: B2


title: A7


title: A6


title: Olig2cKO tumor cell_3


title: UNINF_ENDO_Rep4


title: A5


title: C5


title: Ctrl tumor cell_2


title: UNINF_ENDO_Rep3


title: A3


title: A4


title: UNINF_ENDO_Rep5


title: A2


title: UNINF_ENDO_Rep2


title: Ctrl tumor cell_1


title: UNINF_ENDO_Rep1


title: Ctrl tumor cell_4


title: Ctrl tumor cell_3


title: CON_ENDO_Rep12

value: CON


title: mES_GFP-Ring1b

city: Nijmegen

first: Susan

middle: L

last: Kloet

address: Geert Grooteplein 26, Route 274

department: Proteomics and Chromatin Biology

country: Netherlands

institute: RIMLS-Radboud Universiteit

data_processing:
Mapping was performed with an in-house Ruby script using BWA alignment to the mm9 genome allowing one mismatch.
Data were filtered on quality and duplicates were removed using samtools.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file contains filtered, aligned reads.

source_name: mouse embryonic stem cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepped using 5ng of ChIP material and the Kapa Hyper Prep Kit for Illumina Sequencing (Kapa Biosystems) according to manufacturer's protocol.

value: ES

tag: chip-antibody

value: abcam ab290


title: A1


title: dM2_6_90

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: Research Center for Molecular Medicine

description:
DE_analysis.xls, Decay_analysis.xls
26255

data_processing:
mapping: GSNAP
differential expression: DESeq2
Decay of mRNA was quantified assuming a model of exponential decay (Ross, 1995). For each gene, a linear model was fitted with log2-transformed FPKM as target variables and time after Actinomycin D addition as explanatory variable. Therefore the slope of the linear model estimates the rate of mRNA decay for each gene. Half-life may be calculated as the inverse of the rate.
Genome_build: mm10
Supplementary_files_format_and_content: DE_analysis.xls (Differential expression analysis), Decay_analysis.xls (mRNA decay analysis)

extract_protocol:
BMDMs were stimulated with LPS (10 ng/ml) for 3, 6 h or left untreated. Medium was then replaced by a fresh medium containing actinomycin D (5 µg/ml). Total RNA was isolated using TRIzol Reagent 0, 45, 90 min after addition of actinomycin D.
SENSE mRNA-Seq Library Prep Kit (Lexogen)

value: BMDM

value: TTP-/-

tag: stimulation

value: LPS

tag: time

value: 6 h

tag: protocol to block transcription

value: ActD,  90 min


title: dM3_6_90

description:
DE_analysis.xls, Decay_analysis.xls
26256


title: dM3_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26253

value: ActD,  45 min


title: dM1_6_90

description:
DE_analysis.xls, Decay_analysis.xls
26254


title: CON_ENDO_Rep11

tag: tissue

value: uterine endometrium


title: NPC_H3K4me1

source_name: neural progenitor cells

value: NPC

value: H3K4me1 abcam 8895


title: dM2_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26252


title: CON_ENDO_Rep10

source_name: uterine endometrium

tag: infection status


title: dM3_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26250

value: ActD,  0 min


title: CON_ENDO_Rep9


title: dM1_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26248


title: NPC_Pcgf2

data_processing:
Mapping was performed with an in-house Ruby script using BWA alignment to the mm9 genome allowing one mismatch.
Data were filtered on quality and duplicates were removed using samtools.
Peaks were called using MACS 2.0 with a q-value of 0.001.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain filitered, aligned reads and called peaks.

value: ES-derived neural progenitor cells

value: Pcgf2 sc-10744x Santa Cruz


title: NPC_Ring1b

value: Ring1b D22F2 Cell Signaling


title: NPC_input


title: CON_ENDO_Rep8


title: NPC_Ezh2

value: Ezh2 Diagenode pAB-039-050


title: W1_6_90

description:
DE_analysis.xls, Decay_analysis.xls
26245

value: WT


title: W2_6_90

description:
DE_analysis.xls, Decay_analysis.xls
26246


title: W3_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26244


title: W2_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26243


title: CON_ENDO_Rep7

value: CON


title: CON_ENDO_Rep6


title: W1_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26242


title: W3_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26241


title: dM1_6_45

description:
DE_analysis.xls, Decay_analysis.xls
26251


title: W2_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26240


title: mES_Pcgf2

value: ES


title: mES_Ring1b


title: dM2_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26249

value: BMDM


title: dM3_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26231

value: TTP-/-

value: 3 h


title: W3_6_90

description:
DE_analysis.xls, Decay_analysis.xls
26247

value: LPS

value: 6 h


title: dM2_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26230

value: ActD,  90 min


title: W1_6_0

description:
DE_analysis.xls, Decay_analysis.xls
26239


title: dM3_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26228

value: ActD,  45 min


title: mES_Ezh2


title: dM1_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26229


title: CON_ENDO_Rep3

value: uterine endometrium


title: CON_ENDO_Rep2


title: NPC_Suz12

value: Suz12 Abcam ab12073


title: mES_Suz12


title: dM3_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26225

value: ActD,  0 min


title: mES_input


title: dM2_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26224


title: dM1_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26226


title: MEC_THY_Rep12

source_name: fetal thymus

value: MEC

value: fetal thymus


title: CON_ENDO_Rep1


title: CON_ENDO_Rep5


title: CON_ENDO_Rep4


title: MEC_THY_Rep11


title: olig2cKOtumor_6

data_processing:
RNA-seq reads were mapped using TopHat with default settings.(http://tophat.cbcb.umd.edu)
TopHat output data were then analyzed by Cufflinks to (1) calculate FPKM values for known transcripts in mouse genome reference mm9; (2) test the changes of gene expression between Olig2cKO and control tumors..
Genome_build: All sequencing data were mapped to mm9
Supplementary_files_format_and_content: txt files of gene expression FPKM values

source_name: brain tumor

extract_protocol:
RNAs were isolated from the brain tumor tissue of the control tumor mice and Olig2cKO tumor mice  with trizol as recommended by the manufacturer.RNA-seq libraries were prepared using Illumina RNA-seq preparation Kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: mixed C57Bl/6;129Sv;CD-1

value: brain tumor

tag: genotype

value: Pten lox/lox :P53lox/lox :Olig2lox/lox


title: W3_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26222

tag: cell type

value: WT


title: olig2cKOtumor_5


title: olig2cKOtumor_4


title: CG3

city: Guangzhou

first: Huifeng

last: Peng

address: Wushan Road No.381, Tianhe District

institute: South China University of Technology

data_processing:
Illumina Casava1.8+ software used for basecalling.
Clean reads were mapped to the transcripts sequence of C-169 available on Phytozome V10 (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10#) by Bowtie software.Only 1 bp mismatch was allowed
Accession ids represents JGI gene ID in Coccomyxa subellipsoidea C-169.
Supplementary_files_format_and_content: Microsoft office excel file with reads counts, RPKM, fold change and false dicovery rate (FDR).

organism: Coccomyxa subellipsoidea C-169

source_name: Coccomyxa subellipsoidea 2% CO2

growth_protocol: Coccomyxa subellipsoidea C-169 was incubated in 250-mL Erlenmeyer flasks containing 100 mL Bold’s Basal Medium (BBM) with continuous illumination provided by fluorescent light of ~60 μmol m-2 s-1 at 25 ℃ on an orbital shaker (130 rpm).

extract_protocol:
Total RNA was extracted from AG and CG cells using TRIzol (Invitrogen, Carlsbad, CA, USA) and incubated with DNase I (Takara, Dalian, China) for 30 min at 37℃.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

tag: culture condition

tag: culture duration

value: 4 days


title: CG2


title: olig2cKOtumor_3


title: W1_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26220

tag: strain

value: BMDM


title: MEC_THY_Rep10


title: MEC_THY_Rep9


title: CG1


title: dM2_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26227

value: TTP-/-


title: W3_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26219

value: 3 h


title: AG3

source_name: Coccomyxa subellipsoidea 0.04% CO2


title: W2_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26218

value: LPS


title: MEC_THY_Rep8


title: olig2cKOtumor_2


title: AG2


title: dM1_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26223


title: ctrltumor_4

value: Pten lox/lox :P53lox/lox


title: W1_3_45

description:
DE_analysis.xls, Decay_analysis.xls
26217


title: ctrltumor_3


title: MEC_THY_Rep6


title: W3_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26216


title: W2_3_90

description:
DE_analysis.xls, Decay_analysis.xls
26221

value: ActD,  90 min


title: olig2cKOtumor_1


title: ctrltumor_2


title: W1_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26214


title: ctrltumor_1


title: MEC_THY_Rep4


title: W2_3_0

description:
DE_analysis.xls, Decay_analysis.xls
26215


title: MEC_THY_Rep3


title: MEC_THY_Rep5


title: dM3_0

description:
DE_analysis.xls, Decay_analysis.xls
26207

value: 0 h


title: dM2_0

description:
DE_analysis.xls, Decay_analysis.xls
26206


title: MEC_THY_Rep2


title: dM_LPS7

description: rRNA depleted RNA

data_processing:
Reads were mapped to mouse genome (mm9 assembly) with Segemehl v0.1.3-349M
RNA abundance was quantified using Cufflinks
Genome_build: mm9

growth_protocol: Murine bone marrow derived macrophages were produced from the bone marrow isolated from femur and tibia of 7- to 9-week-old TTPΔM or WT littermates’ mice. Macrophages were cultivated in DMEM (Sigma) supplemented with 10% FBS (Sigma), 100 U/ml penicillin (SIgma), 100 μg/ml streptomycin (Sigma) and CSF-1 derived from L929-cells as previously described (Kovarik et al. 1998).

extract_protocol:
Total RNA  from BMDMs was isolated with TRIzol reagent (Life Technologies) according to the manufacturer protocol. Ribosomal RNA was depleted using Ribo-Zero rRNA removal kit (Epicenter).
RNA was fragmented using RNA fragmentation reagent (Ambion). Enzymatically 5’-pre-adenylated RNA adaptor was ligated to RNA 3’-end. cDNA was produced using primer specific to 3’-adaptor sequence. cDNA was size selected (200-300 nt) using non-denaturing gel, recovered and circularized using Circligase II (Epicenter). DNA oligo complementary to BamHI site was annealed and digested with BamHI (ThermoScientific) in order to linearize cDNA. cDNA was the PCR-amplified with primers specific for linker regions.

treatment_protocol: BMDMs were cultured  on 15 cm cell-culture treated dishes in medium supplemented with 100 µM 4-thiouridine (Sigma) for 16 hours prior to experiment. The cells were then stimulated with LPS (10 ng/ml, Sigma) for 6 hours.

value: C57BL/6 TTP fl/fl LysMCre

value: Primary bone marrow derived macrophages


title: MEC_THY_Rep1


title: INF_THY_Rep12

value: INF


title: dM1_0

description:
DE_analysis.xls, Decay_analysis.xls
26205


title: MEC_THY_Rep7

value: MEC


title: W3_0

description:
DE_analysis.xls, Decay_analysis.xls
26204


title: DMSO

city: xi'an

first: Zhiying

last: Ai

state: shannxi

address: No.3 Taicheng Road, Yangling

institute: Northwest A&F University (NWAFU)

data_processing:
Basecalls performed using Perl package developed by BGI
We will get rid of some contaminant reads from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: mm9
Supplementary_files_format_and_content: The .txt files report clean reads: ength, abundance, sequence.

growth_protocol: The J1 mESCs were gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol:
Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The J1 mESCs were treated with a final concentration of  PD0325901 (1 μM), DMSO (1μL) for 24 h.

tag: treatment

value: DMSO

tag: cell line

value: J1 mESC


title: PD03


title: AG1


title: W2_0

description:
DE_analysis.xls, Decay_analysis.xls
26203

tag: genotype/variation


title: INF_THY_Rep10

value: fetal thymus


title: INF_THY_Rep11


title: HuR PAR-iCLIP rep2

description: HuR bound RNA

data_processing:
Reads were mapped to mouse genome (mm9 assembly) with Segemehl v0.1.3-349M
Peak finding was performed using Pyicos ModFDR method for peak finding, together with a modified filtering algorithm for the use with PAR-iCLIP crosslink sites, which can be seen as reads of length one.
Peak filtering: Our custom filtering method splits peak regions surrounding the highest peak signal, henceforth named summit in accordance with Pyicos, once certain height-thresholds are reached. Cutoffs were defined based on signals detected in known TTP targets. Peaks with a summit signal below 100 pileups are considered background and discarded. With a sliding window approach, starting from the summit, a peak is first split when its height falls below 30% of the summit signal. Emerging subpeaks with a summit above this cutoff and 100 pileups are then recursively split when their signal falls below 10% of their summit. Final split-peaks contain a high amount of crosslink signal and allow us to analyze protein binding sites with high resolution. Replicates of each experimental setup were analyzed separately. Width and position of peaks vary slightly between experiments. For the ranked lists of TTP and HuR target genes, we collect peaks from all replicates and filter out peaks that do not have an overlap with peaks in all other replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tables include annotation of filtered peaks in the following format chromosome:start-end(strand), peak score, genomic feature (5' UTR, CDS, 3' UTR, intron)

source_name: HuR PAR-iCLIP

extract_protocol: As described at Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. 2010. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17(7): 909-915; Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jr., Jungkamp AC, Munschauer M et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1): 129-141.

tag: clip antibody

value: anti-HuR


title: HuR PAR-iCLIP rep1

description: HuR bound RNA


title: TTP PAR-iCLIP rep3

description: TTP bound RNA

source_name: TTP PAR-iCLIP

value: anti-TTP


title: G8

description: Samples are essentially "identical" (FACS purified cells, then run on a C1 for single cell RNAseq), and defined by the flow cytometry gating strategy provided.

source_name: Monocyte derived macrophages isolated from ipsilateral hemisphere of mouse brains 1 day after TBI

value: monocyte-derived macrophage

tag: cell surface markers

tag: sample type

value: single cell


title: INF_THY_Rep8


title: INF_THY_Rep9


title: PB_Liver_tumour_2_Expression [RNA-seq]

data_processing:
Paired ends aligned using FASTQ paired-end parser
Quality control and Tophat 1.20 Alignment
General sequence statistics calculated
Quantitated Gene expression patterns
DESeq analysis to determine differentially expressed transcripts
Genome_build: mm9
Supplementary_files_format_and_content: .wig file

source_name: Mouse Liver Tumour

extract_protocol:
Total RNA was extracted by Trizol prior to preparing for genome wide sequencing by commercial partner (BaseCear, Netherlands)
Strand-specific, paired end RNA-Seq libraries generated by commercial partner (BaseCear, Netherlands) following standardised PolyA enrichement mehtods developped by Illumina

tag: strain background

value: wild type

tag: gender

value: male

tag: treated with

value: 35 weeks phenobarbital

tag: tissue type

value: liver tumour


title: INF_THY_Rep7

tag: infection status

tag: tissue


title: TTP PAR-iCLIP rep1

description: TTP bound RNA

tag: cell type


title: PB_Liver_tumour_1_Expression [RNA-seq]


title: INF_THY_Rep6


title: PB2_liver_Expression [RNA-seq]

source_name: Mouse Liver Tissue

value: 12 weeks phenobarbital

value: Liver


title: Knockdown control 4

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: processed data file: A2B1A1_isoform_exp.diff

data_processing:
adaptor trimming with cutadapt version 1.8.3; cutadapt -m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards  -o <output_trimmed.fastq.gz> <input.fastq.gz> > <output_log.out>
remove unwanted rRNA reads with bowtie 2 version 2.2.2
map to transcriptome/genome with tophat 2.0.13; tophat -o <tophat_output_dir> --transcriptome-index=<tophat_transc_files>/<ref_genes> --library-type=fr-firststrand --no-novel-juncs </path-to-Bowtie2Index/genome> <input_trimmed.fastq.gz>
quantify gene expression with cuffquant v 2.2.1; cuffquant -p <processors> -o <cuffquant_output_dir> --library-type=fr-firststrand <ref_genes.gff>
analyze gene expression with cuffdiff version 2.2.1; cuffdiff -p <processors> -o <output_dir> --use-sample-sheet --library-type fr-firststrand <ref_genes.gff> output_file
Genome_build: hg19
Supplementary_files_format_and_content: isoform.diff tab delimited text file with rows for normalized refseq transcript abundance

source_name: A549 cells

extract_protocol:
trizol extraction, DNAse digestion, and second phenol chloroform extraction
Ribosomal RNA was subtracted from total RNA samples using the RiboZero Magnetic Gold H/M/R Kit (Illumina); NEBNext Ultra Directional RNA Library Prep Kit
TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs)

tag: knockdown

value: control


title: Knockdown hnRNP A2/B1+A1 1

value: hnRNP A2/B1+A1


title: PB_Liver_tumour_3_Expression [RNA-seq]


title: INF_THY_Rep5

value: INF


title: PB1_liver_Expression [RNA-seq]


title: WT2_liver_Expression [RNA-seq]


title: INF_THY_Rep4


title: W1_0

description:
DE_analysis.xls, Decay_analysis.xls
26202

value: BMDM

value: WT

tag: stimulation

value: LPS

tag: time

value: 0 h


title: Knockdown control 3


title: WT1_liver_Expression [RNA-seq]


title: liver_INPUT.fastq

data_processing:
Reads mapped to mm10 mouse build
Data binned into 200bp windows across the genome
Data converted into mm9 build and into a wiggle (.wig) file
data normalised by read count
enriched (5mC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: mm9
Supplementary_files_format_and_content: .wig file

extract_protocol:
Chromatin extraction, H3K27me3 enrichemnt and sequencing performed by Active Motif. Chromatin was extracted from relevant tissue sample and sheared to produce mono-, di- and tri-mer length fragments of chromatin. Crosslinked, sheared gDNA was enriched using Anti H3K27me3 (active motif). Following decrosslinking, DNA libraries were prepared for sequencing on Illumina Hiseq.
Libraries were constructed following Illumina protocols and run by Active Motif

treatment_protocol: 8 week old Male C3H/HeJ mice taken and either kept as a control set (+12 weeks normal diet) or exposed to short term (12 week) or long term (35 week) Phenobarbital in drinking water in order to determine effects of PB on tumourigenesis.


title: Knockdown hnRNP A1 2

description: processed data file: A1_isoform_exp.diff

value: hnRNP A1


title: Knockdown control 2

description:
processed data file: A1_isoform_exp.diff
processed data file: A2B1_isoform_exp.diff


title: Knockdown hnRNP A2/B1 2

description: processed data file: A2B1_isoform_exp.diff

value: hnRNP A2/B1


title: Knockdown hnRNP A2/B1+A1 2


title: INF_THY_Rep2

data_processing:
Base calling: Real-time analysis and base calling were performed using the Hi-seq Control Software, version 2.2.38 (Illumina) to generate sequence reads with associated base quality scores.
Removal of low quality reads: RNA-seq reads, flagged as low quality by CASAVA 1.8 (Illumina), or with an average PHRED read quality score below 15, or in which ≥5 of the last 10 bases had a quality score below 2, were removed.
Sequence alignment: Reads were aligned to the pig reference genome sequence assembly (Sscrofa10.2) using TopHat 1.4.0 with default parameters. The number of reads uniquely mapped to each gene was determined using Ht-seq count (v0.5.3.p3).
Differential gene expression analysis: Differentially expressed genes (DEG) were identified using the Bioconductor package ‘edgeR’. Raw expression counts were converted to counts per million (CPM). Genes with very low expression levels were filtered out of the dataset by setting an expression threshold of CPM>1 in at least 12 samples. Compositional differences between libraries due to difference in library size were normalized using the ‘Trimmed mean of M values’ (TMM) method. A negative binomial model was fitted to the data and gene and tag-wise dispersions were estimated using the quantile-adjusted conditional maximum likelihood (qCML) method. Differential expression was determined using an exact test for the following three contrasts for both tissues: UNINF v CON, INF v UNINF, and MEC v INF. Genes were classified as differentially expressed if they had an absolute fold change >1.5 and a False Discovery Rate (FDR) <0.05.
Weighted Gene Network Correlation Analysis: Gene co-expression network analysis was performed using the software package ‘WGCNA’ for each of the three contrasts in two tissues described above.  The normalized CPM expression data generated by ‘edgeR’ were transformed using the function log2 (x+1) to stabilize variance prior to use in WGCNA. To construct the network, a matrix of co-expression similarity, pairwise correlations, for all genes across all samples in each contrast was made. Next, a weighted network adjacency matrix was obtained by raising the co-expression similarity to a power β whose value was determined by application of the approximate scale-free topology criterion [29]. After network construction, average linkage hierarchical clustering was used to identify clusters of highly interconnected gene ‘modules’ using the topological overlap measure of network interconnectedness as the input. A dynamic hybrid tree cutter was used to identify the branches of the hierarchical clustering dendogram corresponding to modules. Network construction and module detection were performed using the function ‘blockwiseModules’, with the following parameter values: a maximum block size of 15000 (sufficiently large to analyze all genes in a single block), a minimum module size of 30, a medium sensitivity to cluster splitting of 2, and a cut height for module merging of 0.25. The value of β ranged from 6-10. The gene expression profile of a module can be summarized by the module ‘eigengene’, defined as the first principal component of the expression matrix. Correlations between the module eigengene and the two categorical traits in each contrast were determined. Correlations between the eigengene and viral RNA titers were also calculated for the appropriate contrasts. The threshold for association significance was set at an absolute correlation of >0.3 and a P value of <0.1.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier) produced by the program Ht-seq count.

value: fetal thymus


title: WT_LPS7

description: rRNA depleted RNA

tag: strain

value: Primary bone marrow derived macrophages


title: INF_THY_Rep1


title: TTP PAR-iCLIP rep2

description: TTP bound RNA

value: anti-TTP


title: Ctnnb1_Tumour1_H3K27me3 [ChIP-seq]

source_name: Mouse Liver tumour tissue

value: wild type

value: 1 initial dose of DEN followed by 35 weeks phenobarbital

value: Liver tumour tissue

tag: chip antibody

value: Anti H3K27me3 - Millipore (cat # 07-449)


title: Knockdown hnRNP A1 1

tag: cell line


title: 12_week_PB_1_liver_H3K27me3 [ChIP-seq]

tag: genotype/variation

value: 12 week phenobarbital

value: liver


title: UNINF_THY_Rep11

value: UNINF


title: WT1_liver_H3K27me3 [ChIP-seq]


title: Knockdown control 1

value: control


title: UNINF_THY_Rep10


title: INF_THY_Rep3

value: INF


title: UNINF_THY_Rep8


title: UNINF_THY_Rep7


title: UNINF_THY_Rep4


title: UNINF_THY_Rep5


title: UNINF_THY_Rep2


title: UNINF_THY_Rep1


title: UNINF_THY_Rep3


title: UNINF_THY_Rep6


title: UNINF_THY_Rep9


title: CON_THY_Rep12

value: CON


title: CON_THY_Rep10


title: dsRNA-seq_rep1

city: Philadelphia,

first: Nathan

middle: Daniel

last: Berkowitz

state: Pennsylvania

address: 433 S University Ave.

institute: University of Pennsylvania

description:
dsRNA
HEK293T_unstranded_structScore.plus.bw

data_processing:
Raw reads were processed using Cutadapt  to remove 3' adapter sequences when detected
Reads under 12nt in length after trimming were discarded
The remaining reads were collapsed to nonredundant sequence tags
Processed reads were mapped to the Human genome using TopHat (v2.0.12)
Alignments for technical sequencing library replicates were merged using the merge tool in the samtools suite (0.1.18)
Base-wise read coverage was calculated for the ssRNA-seq and dsRNA-seq alignments separately using the genome coverage tool of the bedtools suite (v2.20.1)
The structure score was calculated as the generalized log ratio of dsRNA-seq to ssRNA-seq reads at each nucleotide position, with positive and negative scores indicating ds- and ssRNA, respectively
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file of structure scores

source_name: HEK293T Cells

growth_protocol: HEK293T cells were seeded in 15-cm standard Corning tissue culture treated culture dishes (Sigma, St Louis, MO), grown to 90% confluence (approximately 18 million cells) in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-glucose, 10% fetal bovine serum (FBS (Atlanta Biologics, Atlanta, GA)) and Pen/Strep (Fisher Scientific, Waltham, MA).

extract_protocol:
RNA was isolated using the Qiagen miRNeasy RNA isolation kit following the manufacturer’s protocol (Qiagen, Valencia, CA).
Libraries were produced using the Illumina smRNA-seq library preparation kit.

treatment_protocol: A 37% formaldehyde solution (Sigma, St. Louis, MO) was added drop-wise with mixing directly to cell culture dishes containing 90% confluent cells to a final concentration of 1% and incubated at RT for 10 minutes. The cross-linking reaction was quenched with 1 M glycine (Sigma, St Louis, MO) at a final concentration of 125 mM for 5 minutes with mixing. Then, cells were washed twice with ice-cold PBS and collected. The resulting cell lysate was treated with RNase-free DNase (Qiagen, Valencia, CA). The proteins were then denatured and digested by treatment with 1% SDS and 0.1 mg/mL proteinase K (Roche, Basel, Switzerland) for 15 minutes at RT. Subsequently, these DNA- and protein-depleted lysates were ethanol precipitated and resuspended in 850 μl of RIP buffer. The dsRNA-seq samples were treated with 5 L (50-100 Units) of RNaseOne in 1X RNaseOne buffer and 200 μg of BSA at 37°C for 1 hour.  The ssRNA-seq samples were treated with 25 L (0.0025 Units) of RNase V1 in 1X RNA structure buffer for 1 hour at RT.  Any remaining cross-links were reversed following RNase digestion by incubating at 65°C for 2 hours.

tag: treatment

value: ssRNase-treated (RNaseOne)


title: CON_THY_Rep11

extract_protocol:
Total RNA was isolated from 10-20 mg of endometrium and thymus of each fetus using an ‘All Prep RNA/DNA isolation Mini kit’ (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified by spectrophotometry using a Nanodrop ND 2000 (Thermo Fisher Scientific, Waltham, USA). RNA quality was assessed by digital electrophoresis using a ‘2200 Tapestation’ (Agilent Technologies, Santa Clara, USA). The mean RNA Integrity Number (RIN) sample value was 9.0 for thymus (range 8.0-9.8) and 8.3 for endometrium (range 7.5-8.8).
A total of 96 cDNA libraries were constructed for RNA-sequencing (RNA-seq) from thymus and endometrium samples of individual fetuses. Libraries were constructed from 1 μg of input total RNA using the TruSeq RNA sample preparation kit v2 (Illumina, San Diego, USA) according to the manufacturer’s instructions. DNA libraries were sequenced at the Genome Quebec Innovation Centre (McGill University, Montreal, Canada). Library insert size distribution was assessed on a LabChip GX instrument (Perkin Elmer, Waltham, USA) using a high sensitivity chip. Library concentration was determined using a KAPA Library Quantification Kit (KAPA Biosystems) on a Lightcycler 480 II instrument (Roche Life Science, Indianapolis, USA). Cluster formation was performed on the cBot instrument (Illumina) with eight libraries per lane (7 pM per library) using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Paired-end 100 bp cycle sequencing was performed on a HiSeq 2000 (Illumina) using the TruSeq SBS kit v3-HS (Illumina).


title: CON_THY_Rep8


title: dsRNA-seq_rep2

value: ssRNase-treated (Rnase One)


title: ssRNA-seq_rep1

description:
ssRNA
HEK293T_unstranded_structScore.plus.bw

value: dsRNase-treated (RNase V1)


title: ssRNA-seq_rep2


title: CON_THY_Rep5


title: Knockdown hnRNP A2/B1 1

value: hnRNP A2/B1


title: CON_THY_Rep6

value: fetal thymus


title: CON_THY_Rep4


title: CON_THY_Rep3


title: CON_THY_Rep7


title: CON_THY_Rep2


title: CON_THY_Rep1


title: WT CC 3 [RRBS]

status: Public on May 16 2016

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

source_name: WT CC

extract_protocol:
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. After lysed for 3h at 50°C, naked genomic DNA were relesed.
The released naked DNA was digested by MspI(Fermentas,ER0541),The digested DNA was then end-repaired and tailed with an extra A to the 3'blunted ends.Illumina standard premethylated indexed adaptors were ligated with the dA-tailed DNA fragments. Bisulfite conversion was then performed using the MethyCode bisulfite conversion kit (Invitrogen,MECOV-50) followed by two rounds of PCR enrichment.After PCR enrichment, DNA fragments between 200 and 500bp were size-selected by a 12% native polyacrylamide TBE gel.

treatment_protocol: We separated the blastomeres of lived 2- or 4-cell stage embryos. One blastomere was harvested for single-cell sequencing, and the rest were further cultured in an aggregation plate to record the final development fate

tag: development stage

value: 6-8 weeks post natal

value: cumulus cell


title: WT 4-cell 3 [RRBS]

source_name: WT 4-cell

value: normal embryo


title: WT 4-cell 2 [RRBS]


title: WT 2-cell 2 [RRBS]

source_name: WT 2-cell


title: WT 4-cell 1 [RRBS]


title: CON_THY_Rep9


title: WT 2-cell 3 [RRBS]


title: WA09-INM mononucleosomes

city: Athens

first: wenjuan

last: zhang

state: GA

address: 120 Green street, Life Science Building, Room B304B

institute: University of Georgia

description: Human ISL1+ nascent mesoderm cells derived from WA09-hESC

data_processing:
All read pairs were mapped to the human genome (hg18) using the Burrows-Wheeler Aligner (BWA) tool (Li and Durbin 2009) with the default parameters documented in the bwa-0.5.9 version.
The nucleosome occupancy at a given DNA base pair was calculated by log2(normalized mononucleosomal fragment counts/normalized randomly cut genomic DNA fragment counts).
Supplementary files format and content: Uniquely mapped fragments are in tab separated text files with three columns: (1) Chromosome, (2) fragment start site, (3) fragment end site
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include coordinates for perfectly mapped read pairs of each sample

source_name: WA09-INM mononucleosomes

extract_protocol: WA09-hESCs were maintained in StemPro defined media (Invitrogen). Differentiation to INM and SMCs was achieved by supplementation of defined media with Wnt3a (25 ng/ml) and BMP4 (50 ng/ml) for 4 and 21 days, respectively. Chromatin was processed by optimizing a previously published protocol (Ozsolak et al. 2007; Schones et al. 2008; Spetman et al. 2011) with 200 units of MNase (Worthington Biochemical Corp.) and incubation at 25°C for 5 min, which typically yielded 80-90% mononucleosomal DNA. All DNA samples were required to have a 260/280 absorbance ratio around 1.8 for downstream applications. The about 150bp DNA fragments were gel purified (Spetman et al. 2011), and sequenced from both ends to yield 90bp end sequence pairs using Illumina Genome Analyzer at the BGI. As a control, genomic DNA was extracted following the same protocol but without MNase-digestion, randomly cut to 100-200bp fragment s, and sequenced from both ends.

value: Human ISL1+ nascent mesoderm cells


title: WA09-hESC mononucleosomes

description: Human embryonic cells WA09

source_name: WA09-hESC mononucleosomes

value: Human embryonic cells WA09


title: WA09-gDNA control

description: Human embryonic cells WA09

source_name: WA09-gDNA control


title: NT 4-cell to blastocyst 6 [RRBS]

source_name: NT 4-cell to blastocyst

value: nuclear transfer embryo


title: WA09-SMC mononucleosomes

description: Human smooth muscle cells derived from WA09-hESC

source_name: WA09-SMC mononucleosomes

value: Human smooth muscle cells


title: NT 4-cell to blastocyst 5 [RRBS]


title: NT 4-cell to blastocyst 7 [RRBS]


title: NT 4-cell to blastocyst 3 [RRBS]


title: NT 4-cell to blastocyst 4 [RRBS]


title: NT 2-cell to blastocyst 4 [RRBS]

source_name: NT 2-cell to blastocyst


title: NT 2-cell to blastocyst 8 [RRBS]


title: WT 2-cell 1 [RRBS]


title: NT 4-cell to blastocyst 1 [RRBS]


title: NT 2-cell to blastocyst 6 [RRBS]


title: NT 2-cell to blastocyst 3 [RRBS]


title: NT 2-cell to blastocyst 7 [RRBS]


title: NT 2-cell to blastocyst 2 [RRBS]


title: WT CC 2 [RRBS]


title: WT CC 1 [RRBS]


title: NT 2-cell to blastocyst 5 [RRBS]


title: NT 2-cell arrest 8 [RRBS]

source_name: NT 2-cell arrest


title: NT 4-cell arrest 2 [RRBS]

source_name: NT 4-cell arrest


title: NT 4-cell arrest 1 [RRBS]


title: NT 4-cell to blastocyst 2 [RRBS]


title: NT 2-cell to blastocyst 1 [RRBS]


title: NT 4-cell arrest 4 [RRBS]


title: NT 2-cell arrest 1 [RRBS]


title: NT 2-cell arrest 7 [RRBS]


title: NT 2-cell arrest 2 [RRBS]