title: 20170912-D10-NA19098


title: 20170912-B10-NA19098

status: Public on Feb 12 2019

type: SRA

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

country: USA

institute: University of Chicago

description:
eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds

library_source: transcriptomic

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT), ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa), and the mCherry and EGFP open reading frames from the FUCCI plasmid.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset-raw.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset-raw.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 20,421 genes (H. sapiens, ERCC, EGFP, mCherry) and 1,536 single cells. The file fucci-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,421 genes for 1,536 single cells. The file fucci-annotation.txt is a tab-delimited plain text file that contains 43 metadata columns for the 1,536 single cells. The file fucci-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 43 metadata columns in fucci-annotation.txt. The file eset-final.rds is a serialized R object of the Bioconductor class ExpressionSet that contains the final data used to produce the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for the 11,093 genes (H. sapiens, ERCC, EGFP, mCherry) and 888 single cells that remained after applying filters for lowly expressed genes and low quality single cells.

molecule: polyA RNA

organism: Homo sapiens

source_name: LCL-derived iPSC

growth_protocol: We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).

tag: cell type

value: LCL-derived iPSC

tag: experiment

tag: well

tag: individual


title: 20170912-B06-NA19098


title: 20170912-B05-NA18870


title: 20170912-B08-NA19098


title: 20170912-B04-NA18870


title: 20170912-B02-NA19098


title: 20170912-A09-NA18870


title: 20170912-A10-NA19098


title: 20170912-A08-NA19098


title: 20170912-C02-NA18870


title: 20170912-A12-NA18870


title: 20170912-A11-NA18870


title: 20170912-B01-NA19098


title: 20170912-A03-NA18870


title: 20170912-A02-NA19098


title: hDC + LPS_donor6

city: Rijswijk

first: Jeffrey

last: Bajramovic

address: Lange Kleiweg 161

department: Alternatives

country: Netherlands

institute: Biomedical Primate Research Centre

data_processing:
The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp, data not shown). Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. 1.6 pM of DNA was loaded and analyzed using NextSeq control software 2.0.2. Image analysis, base calling, and quality verification were performed with Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17. The reads were mapped to reference sequence Homo_sapiens.GCRh37.75 using a short read aligner based on Burrows-Wheeler transform (mismatch rate of max 2%). For the 16 samples the number of reads obtained was between 22537666 – 32979730. The % reads of reads aligned to the reference was between 95.4 – 95.7%. Reads that aligned to multiple locations were between 7.5 – 9.4%. Reads that aligned to genes were between 60.0 – 87.8%. Samtools 0.1.18 was used to sort and index the BAM files. The number of times a read aligned to a gene and normalized read counts in Fragments Per Kilobase Million were determined using in-house developed scripts. The R package DESeq 1.10.1 was used to calculate false discovery rate-corrected p-values for the genes differentially expressed in the tested samples.
Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. 1.6 pM of DNA was loaded and analyzed using NextSeq control software 2.0.2.
Image analysis, base calling, and quality verification were performed with Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
For the 16 samples the number of reads obtained was between 22537666 – 32979730. The % reads of reads aligned to the reference was between 95.4 – 95.7%. Reads that aligned to multiple locations were between 7.5 – 9.4%. Reads that aligned to genes were between 60.0 – 87.8%. Samtools 0.1.18 was used to sort and index the BAM files. The number of times a read aligned to a gene and normalized read counts in Fragments Per Kilobase Million were determined using in-house developed scripts. The R package DESeq 1.10.1 was used to calculate false discovery rate-corrected p-values for the genes differentially expressed in the tested samples.
Genome_build: The reads were mapped to reference sequence Homo_sapiens.GCRh37.75 using a short read aligner based on Burrows-Wheeler transform (mismatch rate of max 2%).

molecule: total RNA

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from human buffy coats obtained from anonymized healthy donors using lymphocyte separation medium gradient centrifugation (Lymphoprep; Axis-Shield, Norway). Monocytes were isolated with anti-CD14 monoclonal antibody-coated Microbeads using MACS single-use separation columns from Miltenyi Biotec (Bergisch Gladbach, Germany) as described by the manufacturer. Purified CD14+ cells were resuspended in RPMI (Gibco - Thermo Fisher, Waltham, MA) containing 10% (v/v) FCS (Gibco) and penicillin 100 U/ml and streptomycin 0.1 mg/mL (Gibco), supplemented with ≥ 4 units recombinant human M-CSF/mL or  ≥ 40 units recombinant human GM-CSF and 200 ng recombinant human IL-4/mL (all Peprotech) to yield macrophages or DC respectively. Half of the medium was replaced by fresh medium containing new growth factors every 3-4 days. After 6-7 days in culture cells were used for functional assays.

extract_protocol:
Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed followed by ligation of sequencing adapters and PCR amplification. The quality and yield after sample preparation was measured with a Fragment Analyzer (Advanced Analytical, Heidelberg, Germany).
The Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) was used to prepare and process the samples.

treatment_protocol: 6 hours exposure to 500 ng/ml LPS in the absence or presence of 5µM adenosine receptor 3 antagonist VUF 8504

tag: donor

value: dendritic cells


title: hDC + LPS + VUF_donor6


title: hDC + VUF_donor6


title: 20170912-A05-NA18870


title: hDC (-)_donor6


title: 20170910-H12-NA19101


title: 20170912-B03-NA19098


title: 20170910-H11-NA19101


title: hDC + LPS_donor5


title: 20170912-B07-NA18870


title: hDC + LPS + VUF_donor5


title: 20170912-A01-NA18870


title: 20170910-H09-NA18855


title: hDC + VUF_donor5


title: 20170912-A06-NA19098


title: hDC (-)_donor5


title: 20170910-H08-NA19101


title: hDC + LPS + VUF_donor4


title: 20170912-A07-NA18870


title: 20170910-H10-NA18855


title: 20170910-H05-NA18855


title: hDC + VUF_donor4


title: hDC + LPS_donor4


title: 20170910-H07-NA19101


title: 20170912-A04-NA18870


title: 20170910-H04-NA18855


title: 20170910-H06-NA18855


title: hDC + LPS + VUF_donor3


title: hDC (-)_donor4


title: hDC + LPS_donor3


title: 20170910-H01-NA19101


title: 20170910-H02-NA19101


title: hDC + VUF_donor3


title: hDC (-)_donor3


title: 20170910-G12-NA19101


title: 20170912-D04-NA19098


title: 952_2__2__2nd tri

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 100 to 300 ng of exosomal RNA was used as input for library construction.

tag: tissue

value: plasma

tag: tissue compartment

value: exosome

tag: full term (normal) vs preterm birth (ptb)

value: PTB

tag: trimester

tag: patient id


title: 952_3__2__3rd tri


title: 952_1_1st_PTB


title: 20170910-G11-NA18855


title: 20170910-G08-NA18855


title: 20170910-G07-NA18855


title: 952_4__2__Delivery

value: Delivery


title: 20170910-G06-NA18855


title: 20170910-G05-NA18855


title: 20170910-G04-NA18855


title: 20170910-G03-NA18855


title: 854_3__1__3rd tri

value: Normal


title: 854_2_2nd_Normal


title: 880_3__2__3rd tri


title: 20170910-H03-NA18855


title: 854_1__1__1st Tri


title: 20170910-G01-NA19101


title: 787_4__2__Delivery


title: 787_3__2__3rd tri


title: 20170910-F12-NA19101


title: 20170910-G10-NA18855


title: 880_4__2__Delivery


title: 20170910-G09-NA18855


title: 880_2__2__2nd tri


title: 880_1__2__1st Tri


title: 20170910-F10-NA18855


title: 763_2_2nd_Normal


title: 763_3_3rd_Normal


title: 763_4__1__Delivery


title: 20170910-F08-NA18855


title: 787_1__2__1st Tri


title: 20170910-F07-NA19101


title: 763_1__1__1st Tri


title: 20170910-F04-NA19101


title: 759_4_Delivery_Normal


title: 759_1_1st_Normal


title: 20170910-F02-NA19101


title: 20170910-F03-NA18855


title: 735_4__2__Delivery


title: 787_2__2__2nd tri


title: 20170910-E11-NA19101


title: 20170910-E12-NA18855


title: 20170910-F06-NA18855


title: 735_1_1st_PTB


title: 20170910-F09-NA18855


title: 20170910-E10-NA19101


title: 20170910-E09-NA19101


title: 20170910-E07-NA18855


title: 20170910-E06-NA18855


title: 692_2__1__2nd tri


title: 709_1_1st_PTB


title: 759_2_2nd_Normal


title: 20170910-E04-NA18855


title: 709_2__2__2nd tri


title: 20170910-E03-NA18855


title: 20170910-E05-NA19101


title: 709_4__2__Delivery


title: 20170910-F01-NA18855


title: 735_3__2__3rd tri


title: 672_2__1__2nd tri


title: 735_2__2__2nd tri


title: 20170910-E02-NA19101


title: 20170910-E01-NA19101


title: 647_4__1__Delivery


title: 672_1__1__1st Tri


title: 20170910-D11-NA19101


title: 20170910-E08-NA19101


title: 647_2__1__2nd tri


title: 20170910-D12-NA19101


title: 709_3__2__3rd tri


title: 647_1__1__1st Tri


title: 20170910-D08-NA18855


title: 20170910-D10-NA18855


title: 637_3__1__3rd tri


title: 672_3__1__3rd tri


title: 20170910-D07-NA18855


title: 637_4__1__Delivery


title: 20170910-D05-NA18855


title: 20170910-D06-NA18855


title: 20170910-F05-NA18855


title: 637_1_1st_Normal


title: 637_2__1__2nd tri


title: 615_3__1__3rd tri


title: 691_1__1__1st Tri


title: 20170910-D04-NA18855


title: 615_4__1__Delivery


title: 20170910-G02-NA19101


title: 20170910-D03-NA19101


title: 615_2__1__2nd tri


title: 615_1__1__1st Tri


title: 573_2__1__2nd tri


title: 20170910-D02-NA19101


title: 20170910-D01-NA18855


title: 20170910-C11-NA18855


title: 20170910-C12-NA18855


title: 558_3__1__3rd tri


title: 20170910-C10-NA19101


title: 573_1__1__1st Tri


title: 20170910-F11-NA19101


title: 20170910-D09-NA19101


title: 558_2__1__2nd tri


title: 20170910-C07-NA19101


title: 558_1__1__1st Tri


title: 20170910-C06-NA18855


title: 20170910-C09-NA19101


title: 20170910-C05-NA19101


title: 20170910-C08-NA19101


title: 20170910-C03-NA18855


title: 510_1__1__1st Tri


title: 481_2__1__2nd tri


title: 20170910-C01-NA18855


title: 481_3_3rd_Normal


title: 435_4_Delivery_PTB


title: 20170910-C02-NA18855


title: 481_1__1__1st Tri


title: 573_4_Delivery_Normal


title: 20170910-C04-NA19101


title: 20170910-B11-NA18855


title: 435_2__2__2nd tri


title: 20170910-B10-NA18855


title: 414_4__2__Delivery


title: 20170910-B12-NA19101


title: 435_1__2__1st Tri


title: 510_2__1__2nd tri


title: 20170910-B09-NA19101


title: 20170910-B08-NA19101


title: 414_3__2__3rd tri


title: 20170910-B07-NA19101


title: 20170910-B06-NA19101


title: 20170910-B05-NA19101


title: 481_4__1__Delivery


title: 414_2__2__2nd tri


title: 400_4_Delivery_Normal


title: 414_1__2__1st Tri


title: 400_3__1__3rd tri


title: 20170910-B04-NA19101


title: 20170910-B03-NA19101


title: 382_3_3rd_Normal


title: 20170910-B02-NA19101


title: 382_2_2nd_Normal


title: 400_2__1__2nd tri


title: 435_3__2__3rd tri


title: 20170910-B01-NA19101


title: 20170910-A12-NA19101


title: 20170910-A11-NA19101


title: 362_1__1__1st Tri


title: 362_3__1__3rd tri


title: 333_3_3rd_Normal


title: 20170910-A09-NA18855


title: 20170910-A07-NA19101


title: 20170910-A06-NA19101


title: 20170910-A08-NA18855


title: 362_2_2nd_Normal


title: 20170910-A10-NA19101


title: 362_4_Delivery_Normal


title: 382_1__1__1st Tri


title: 400_1__1__1st Tri


title: 20170910-A04-NA18855


title: 20170910-A03-NA18855


title: 20170910-A05-NA18855


title: 333_1__1__1st Tri


title: 323_2__1__2nd tri


title: 323_3__1__3rd tri


title: 323_1_1st_Normal


title: 308_4_Delivery_PTB


title: 20170908-H12-NA18870


title: 308_3__2__3rd tri


title: 308_2__2__2nd tri


title: 20170910-A01-NA19101


title: 20170908-H10-NA18870


title: 20170908-H11-NA18870


title: 20170908-H09-NA18870


title: 20170908-H07-NA19101


title: 20170908-H08-NA19101


title: 333_2__1__2nd tri


title: 308_1__2__1st Tri


title: 20170908-H05-NA18870


title: 20170908-H06-NA19101


title: 291_3__2__3rd tri


title: 291_1__2__1st Tri


title: 20170910-A02-NA19101


title: 274_3__1__3rd tri


title: 291_2__2__2nd tri


title: 20170908-H03-NA18870


title: 20170908-H04-NA18870


title: 20170908-H02-NA19101


title: 20170908-H01-NA19101


title: 274_2__1__2nd tri


title: 274_1__1__1st Tri


title: 222_3__1__3rd tri


title: 217_3__1__3rd tri


title: 20170908-G12-NA18870


title: 20170908-G10-NA19101


title: 222_1__1__1st Tri


title: 20170908-G11-NA18870


title: 20170908-G09-NA19101


title: 20170908-G08-NA19101


title: 217_2_2nd_Normal


title: 164_4_Delivery_PTB


title: 164_3__2__3rd tri


title: 217_1__1__1st Tri


title: 20170908-G05-NA18870


title: 20170908-G07-NA19101


title: 164_2__2__2nd tri


title: 20170908-G01-NA19101


title: 20170908-G03-NA19101


title: 20170908-G02-NA18870


title: 164_1__2__1st Tri


title: 20170908-F12-NA18870


title: 20170908-G06-NA18870


title: 20170908-G04-NA19101


title: H8_EXP7_1

city: Antwerpen

first: Nicolas

last: De Neuter

address: Middelheimlaan 1

country: Belgium

institute: University of Antwerp

data_processing:
trimming of low quality bases. name: Trimmomatic, version: 0.36, parameters: -phred33 HEADCROP:20 SLIDINGWINDOW:4:15 MINLEN:30
removal of polyA tails. custom Perl script, removes polyA tails at the end of reads if the read ends with 7 or more As; also removes reads with length <= 20
read mapping. name: HISAT2, version: 2.0.4, parameters: -x GRCh38_noalt_h2, outputs SAM files
read counting. custom Python script, uses the Python library HTSeq to count how many reads map to each gene. Uses GCF_000001405.31_GRCh38.p5_genomic.gff as an annotation source. (https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.31_GRCh38.p5/GCF_000001405.31_GRCh38.p5_genomic.gff.gz). One output file containing counts is created for each SAM file.
combining read counts. custom Python script, sums up read counts across lanes for a given sample, then combines all samples (columns) into a single count file with genes as rows
Genome_build: GRCh38
Supplementary_files_format_and_content: format: tsv (tab-separated file); content: raw read counts per gene, combined from four sequencing lanes, for each sample (genes as rows and samples as columns). The file genes.txt provides a key to the gene IDs in "combined_lane_counts.txt".

source_name: Whole blood

extract_protocol:
Total RNA was extracted from the Paxgene-blood samples with the Paxgene RNA extraction kit (Qiagen) following the supplier instructions. To concentrate the RNA even more, the clean and concentrator-5 kit (Zymo Research) was used.
Libraries were prepared (following supplier instructions) with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH).

treatment_protocol: Whole blood samples were collected in Paxgene Blood RNA tubes (PreAnalytiX), containing a lysis buffer and RNA stabilizator.

tag: subject id

value: whole blood

tag: sampling day

value: 7 (after vaccination)

tag: repeat


title: H8_EXP7_2


title: H8_EXP3_1

value: 3 (after vaccination)


title: 20170908-F11-NA19101


title: 291_4__2__Delivery


title: H8_EXP3_2


title: 20170908-F10-NA18870


title: H8_EXP0_2

value: 0 (before vaccination)


title: 222_2__1__2nd tri


title: 222_4__1__Delivery


title: 20170908-F09-NA18870


title: H7_EXP7_2


title: 20170908-F08-NA19101


title: H8_EXP0_1


title: 20170908-F07-NA19101


title: 274_4_Delivery_Normal


title: H7_EXP7_1


title: 20170908-F06-NA19101


title: 20170908-F05-NA19101


title: 20170908-F04-NA18870


title: H7_EXP0_2


title: H7_EXP0_1


title: H7_EXP3_2


title: H7_EXP3_1


title: 20170908-F01-NA19101


title: H6_EXP7_1


title: 20170908-E12-NA19101


title: 20170908-F03-NA18870


title: H6_EXP7_2


title: 20170908-F02-NA18870


title: 20170908-E10-NA18870


title: H6_EXP0_2


title: H6_EXP3_2


title: 20170908-E09-NA19101


title: 20170908-E11-NA19101


title: H6_EXP0_1


title: H42_EXP7_2


title: 20170908-E07-NA19101


title: 20170908-E06-NA19101


title: H42_EXP7_1


title: H6_EXP3_1


title: H42_EXP3_2


title: 20170908-E08-NA18870


title: 20170908-E05-NA18870


title: H42_EXP3_1


title: 20170908-E04-NA19101


title: 20170908-E03-NA19101


title: H42_EXP0_2


title: 20170908-E02-NA19101


title: H42_EXP0_1


title: 20170908-E01-NA18870


title: H41_EXP7_1


title: 20170908-D11-NA18870


title: 20170908-D10-NA19101


title: H41_EXP3_2


title: H41_EXP0_2


title: 20170908-D12-NA18870


title: 20170908-D09-NA18870


title: 20170908-D08-NA19101


title: H41_EXP3_1


title: 20170908-D07-NA18870


title: 20170908-D06-NA19101


title: H40_EXP7_2


title: H40_EXP3_1


title: H40_EXP7_1


title: H40_EXP0_1


title: 20170908-D05-NA19101


title: H40_EXP3_2


title: 20170908-D04-NA19101


title: 20170908-D03-NA18870


title: 20170908-D02-NA19101


title: H40_EXP0_2


title: H4_EXP7_2


title: H41_EXP7_2


title: 20170908-D01-NA19101


title: 20170908-C12-NA18870


title: H41_EXP0_1


title: 20170908-C11-NA19101


title: H4_EXP3_1


title: 20170908-C10-NA18870


title: H4_EXP0_2


title: 20170908-C08-NA18870


title: 20170908-C07-NA19101


title: H39_EXP7_1


title: 20170908-C09-NA19101


title: H39_EXP3_2


title: 20170908-C03-NA18870


title: H39_EXP7_2


title: 20170908-C02-NA19101


title: 20170908-C01-NA18870


title: 20170908-C06-NA18870


title: 20170908-C04-NA19101


title: H4_EXP7_1


title: 20170908-B12-NA19101


title: H38_EXP7_1


title: H39_EXP0_2


title: H38_EXP3_2


title: H4_EXP3_2


title: 20170908-B11-NA19101


title: H38_EXP7_2


title: H38_EXP3_1


title: H38_EXP0_2


title: 20170908-B10-NA19101


title: 20170908-C05-NA18870


title: H36_EXP7_2


title: 20170908-B09-NA18870


title: H39_EXP3_1


title: H38_EXP0_1


title: H39_EXP0_1


title: H36_EXP3_2


title: 20170908-B07-NA18870


title: 20170908-B06-NA19101


title: 20170908-B05-NA19101


title: H36_EXP3_1


title: 20170908-B04-NA19101


title: H36_EXP0_2


title: H36_EXP0_1


title: H35_EXP7_2


title: 20170908-B01-NA19101


title: 20170908-A11-NA18870


title: H35_EXP3_2


title: 20170908-B08-NA19101


title: 20170908-B03-NA19101


title: H35_EXP7_1


title: H35_EXP3_1


title: H36_EXP7_1


title: H35_EXP0_2


title: H35_EXP0_1


title: 20170908-A08-NA18870


title: H34_EXP7_1


title: H34_EXP7_2


title: 20170908-A06-NA19101


title: 20170908-A09-NA19101


title: 20170908-A07-NA18870


title: 20170908-B02-NA18870


title: 20170908-A12-NA19101


title: H34_EXP3_1


title: 20170908-A03-NA18870


title: H34_EXP3_2


title: 20170908-A10-NA19101


title: 20170908-A04-NA18870


title: 20170908-A02-NA19101


title: H34_EXP0_2


title: H33_EXP7_2


title: 20170907-H10-NA18855


title: 20170907-H12-NA18855


title: H33_EXP0_2


title: 20170907-H11-NA18855


title: H33_EXP7_1


title: 20170908-A05-NA18870


title: 20170907-H09-NA19098


title: H32_EXP7_1


title: 20170907-H07-NA19098


title: H32_EXP7_2


title: H34_EXP0_1


title: H32_EXP3_1


title: 20170907-H06-NA19098


title: H32_EXP0_2


title: 20170907-H03-NA19098


title: H33_EXP3_1


title: H31_EXP7_2


title: H32_EXP0_1


title: 20170907-H04-NA18855


title: H33_EXP3_2


title: H31_EXP7_1


title: 20170907-H01-NA19098


title: 20170907-H02-NA19098


title: H33_EXP0_1


title: 20170907-G12-NA18855


title: 20170907-H08-NA19098


title: H31_EXP3_2


title: H31_EXP0_1


title: 20170907-G09-NA18855


title: 20170907-G11-NA18855


title: 20170907-H05-NA19098


title: 20170907-G10-NA18855


title: 20170907-G08-NA19098


title: H31_EXP3_1


title: H30_EXP7_1


title: H30_EXP7_2


title: H32_EXP3_2


title: 20170907-G07-NA19098


title: 20170907-G06-NA19098


title: 20170907-G05-NA18855


title: H30_EXP0_2


title: 20170907-G03-NA19098


title: 20170907-G04-NA18855


title: H31_EXP0_2


title: 20170907-G02-NA19098


title: H30_EXP0_1


title: H3_EXP7_2


title: 20170907-G01-NA18855


title: H3_EXP7_1


title: 20170907-F12-NA18855


title: H3_EXP3_1


title: 20170907-F11-NA19098


title: H3_EXP0_1


title: H29_EXP7_2


title: H3_EXP0_2


title: 20170907-F09-NA19098


title: 20170907-F05-NA19098


title: 20170907-F07-NA18855


title: 20170907-F06-NA18855


title: 20170907-F10-NA19098


title: 20170907-F08-NA19098


title: H29_EXP7_1


title: H30_EXP3_1


title: H29_EXP3_2


title: H30_EXP3_2


title: H29_EXP3_1


title: H29_EXP0_2


title: H28_EXP7_2


title: 20170907-F03-NA19098


title: 20170907-F02-NA18855


title: H3_EXP3_2


title: H29_EXP0_1


title: 20170907-E12-NA18855


title: H28_EXP3_2


title: 20170907-F01-NA19098


title: 20170907-E10-NA18855


title: 20170907-E09-NA18855


title: 20170907-E11-NA19098


title: H28_EXP0_1


title: 20170907-E08-NA18855


title: H26_EXP7_1


title: H26_EXP7_2


title: 20170907-E06-NA19098


title: H28_EXP0_2


title: 20170907-E07-NA18855


title: 20170907-E05-NA18855


title: 20170907-E04-NA18855


title: H26_EXP0_2


title: H26_EXP3_1


title: H26_EXP3_2


title: 20170907-F04-NA18855


title: 20170907-E03-NA19098


title: H28_EXP7_1


title: 20170907-E02-NA19098


title: H25_EXP7_1


title: 20170907-E01-NA19098


title: 20170907-D12-NA19098


title: H25_EXP3_2


title: 20170907-D11-NA19098


title: H25_EXP7_2


title: H25_EXP3_1


title: H28_EXP3_1


title: 20170907-D10-NA18855


title: 20170907-D09-NA18855


title: 20170907-D08-NA19098


title: H24_EXP7_2


title: H24_EXP7_1


title: 20170907-D06-NA19098


title: 20170907-D07-NA19098


title: H24_EXP3_1


title: 20170907-D05-NA18855


title: H24_EXP3_2


title: 20170907-D04-NA19098


title: 20170907-D03-NA19098


title: 20170907-D02-NA19098


title: H24_EXP0_1


title: H24_EXP0_2


title: 20170907-D01-NA19098


title: 20170907-C11-NA18855


title: H23_EXP7_1


title: H23_EXP3_2


title: H23_EXP3_1


title: H23_EXP0_2


title: 20170907-C12-NA18855


title: 20170907-C09-NA18855


title: H26_EXP0_1


title: 20170907-C10-NA19098


title: H25_EXP0_1


title: 20170907-C08-NA18855


title: 20170907-C07-NA19098


title: 20170907-C06-NA18855


title: H22_EXP7_1


title: H22_EXP3_2


title: 20170907-C05-NA18855


title: 20170907-C03-NA18855


title: H23_EXP7_2


title: H21_EXP7_2


title: H22_EXP7_2


title: H22_EXP3_1


title: 20170907-C02-NA19098


title: H25_EXP0_2


title: H23_EXP0_1


title: H22_EXP0_1


title: 20170907-C04-NA19098


title: 20170907-C01-NA19098


title: 20170907-B11-NA18855


title: 20170907-B12-NA18855


title: H21_EXP0_1


title: 20170907-B10-NA19098


title: H21_EXP3_2


title: H21_EXP3_1


title: H21_EXP0_2


title: 20170907-B09-NA19098


title: H22_EXP0_2


title: 20170907-B08-NA18855


title: H20_EXP7_2


title: H21_EXP7_1


title: 20170907-B06-NA18855


title: 20170907-B07-NA18855


title: 20170907-B04-NA18855


title: 20170907-B03-NA18855


title: H20_EXP7_1


title: H20_EXP0_2


title: 20170907-B02-NA18855


title: H20_EXP3_2


title: H2_EXP7_2


title: H20_EXP0_1


title: H20_EXP3_1


title: 20170907-B01-NA18855


title: H2_EXP3_2


title: 20170907-A12-NA18855


title: 20170907-B05-NA18855


title: H2_EXP7_1


title: 20170907-A09-NA18855


title: H2_EXP0_1


title: 20170907-A10-NA18855


title: H2_EXP0_2


title: 20170907-A11-NA18855


title: 20170907-A07-NA19098


title: 20170907-A08-NA18855


title: H19_EXP7_2


title: H2_EXP3_1


title: H19_EXP7_1


title: 20170907-A06-NA19098


title: 20170907-A05-NA19098


title: 20170907-A04-NA19098


title: H19_EXP3_2


title: H19_EXP3_1


title: H19_EXP0_2


title: 20170907-A03-NA18855


title: H18_EXP7_2


title: H19_EXP0_1


title: 20170907-A01-NA18855


title: 20170907-A02-NA18855


title: H18_EXP7_1


title: H18_EXP3_2


title: H18_EXP0_2


title: H18_EXP3_1


title: H18_EXP0_1


title: 20170906-H08-NA19098


title: 20170906-H07-NA19098


title: 20170906-H05-NA19098


title: 20170906-H10-NA19098


title: 20170906-H06-NA19101


title: 20170906-H09-NA19101


title: H17_EXP7_1


title: H17_EXP3_2


title: H17_EXP3_1


title: 20170906-H11-NA19098


title: 20170906-H04-NA19101


title: H17_EXP7_2


title: 20170906-H03-NA19101


title: H17_EXP0_2


title: 20170906-H02-NA19098


title: 20170906-H01-NA19098


title: 20170906-G12-NA19098


title: 20170906-H12-NA19101


title: H14_EXP3_2


title: H17_EXP0_1


title: H14_EXP3_1


title: H14_EXP7_2


title: H14_EXP7_1


title: 20170906-G10-NA19098


title: 20170906-G08-NA19098


title: H14_EXP0_2


title: H13_EXP7_2


title: H14_EXP0_1


title: 20170906-G11-NA19098


title: 20170906-G07-NA19098


title: H13_EXP7_1


title: 20170906-G05-NA19098


title: 20170906-G06-NA19101


title: H13_EXP3_2


title: 20170906-G04-NA19101


title: H13_EXP3_1


title: 20170906-G03-NA19101


title: H13_EXP0_1


title: H13_EXP0_2


title: 20170906-G02-NA19098


title: H12_EXP7_1


title: 20170906-F11-NA19101


title: H12_EXP7_2


title: 20170906-F12-NA19098


title: 20170906-F10-NA19098


title: H12_EXP3_2


title: H11_EXP7_2


title: 20170906-G09-NA19101


title: H12_EXP3_1


title: 20170906-F07-NA19098


title: 20170906-F06-NA19098


title: H12_EXP0_1


title: 20170906-F05-NA19098


title: H11_EXP3_1


title: H11_EXP7_1


title: H11_EXP0_2


title: 20170906-F03-NA19098


title: H11_EXP3_2


title: 20170906-F02-NA19098


title: 20170906-G01-NA19098


title: 20170906-F01-NA19101


title: H10_EXP7_1


title: H11_EXP0_1


title: H10_EXP7_2


title: 20170906-E12-NA19098


title: 20170906-F04-NA19098


title: H10_EXP3_2


title: 20170906-E10-NA19101


title: H10_EXP3_1


title: H10_EXP0_2


title: H12_EXP0_2


title: H10_EXP0_1


title: 20170906-E08-NA19101


title: 20170906-F09-NA19098


title: 20170906-E07-NA19098


title: H1_EXP7_1


title: 20170906-F08-NA19101


title: 20170906-E06-NA19101


title: H1_EXP3_2


title: H1_EXP3_1


title: 20170906-E04-NA19098


title: 20170906-E03-NA19098


title: H1_EXP0_1


title: H1_EXP0_2


title: 20170906-E11-NA19098


title: 20170906-E02-NA19098


title: 20170906-E01-NA19101


title: 20170906-E09-NA19098


title: Tal1KO_LMPP_Rag2GFPpos_3

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Reads were aligned to genes using the htseq-count tool from HTSeq V 0.6.1 and gene annotations from Ensembl release 78
The R package EdgeR was used to normalize gene counts and to calculate differential expression statistics for each gene for pairwise comparison of sample groups.
Genes were considered differentially expressed if the the fold change was > 2 and FDR <0.05
Genome_build: mm10
Supplementary_files_format_and_content: txt file with normalized read counts

organism: Mus musculus

source_name: Tal1 KO bone marrow CD135+ LSK

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA).

value: Rag2-GFP positive

value: CD135 positive

tag: genoytpe

value: VaviCre Tal1F/F Rag2GFP


title: 20170906-D11-NA19098


title: 20170906-D12-NA19098


title: 20170906-D10-NA19101


title: H1_EXP7_2


title: 20170906-D09-NA19098


title: Tal1KO_LMPP_Rag2GFPpos_2


title: 20170906-D08-NA19098


title: Tal1KO_LMPP_Rag2GFPpos_1


title: Tal1KOl_LMPP_Rag2GFPneg_1

value: Rag2-GFP negative


title: Tal1KO_HSC_Rag2GFPpos_3

source_name: Tal1 KO bone marrow CD135- LSK

value: CD135 negative


title: 20170906-D06-NA19098


title: 20170906-D07-NA19098


title: Tal1KO_HSC_Rag2GFPpos_2


title: 20170906-E05-NA19098


title: 20170906-D05-NA19101


title: Tal1KO_HSC_Rag2GFPpos_1


title: 20170906-D03-NA19098


title: 20170906-D02-NA19098


title: Tal1KO_LMPP_Rag2GFPneg_2


title: Ctrl_LMPP_Rag2GFPpos_1

source_name: Ctrl bone marrow CD135+LSK

value: wild type (Tal1 F/F) Rag2GFP


title: 20170906-C12-NA19098

value: LCL-derived iPSC


title: Tal1KO_LMPP_Rag2GFPneg_3


title: 20170906-C10-NA19098


title: Ctrl_LMPP_Rag2GFPpos_2


title: 20170906-C09-NA19098


title: Ctrl_LMPP_Rag2GFPneg_3


title: Tal1KO_HSC_Rag2GFPneg_1


title: Ctrl_LMPP_Rag2GFPneg_1


title: Ctrl_HSC_Rag2GFPpos_3

source_name: Ctrl bone marrow CD135- LSK


title: 20170906-C08-NA19098


title: 20170906-D01-NA19101


title: 20170906-C07-NA19098


title: 20170906-D04-NA19098


title: Ctrl_LMPP_Rag2GFPneg_2


title: 20170906-C05-NA19098


title: Ctrl_HSC_Rag2GFPpos_2


title: Tal1KO_HSC_Rag2GFPneg_3


title: 20170906-C06-NA19098


title: Tal1KO_HSC_Rag2GFPneg_2


title: Ctrl_LMPP_Rag2GFPpos_3


title: Ctrl_HSC_Rag2GFPneg_3


title: Ctrl_HSC_Rag2GFPneg_2


title: 20170906-C03-NA19101


title: 20170906-C11-NA19098


title: 20170906-B12-NA19101


title: Y00087: tech. rep. 3

city: Phoenix

first: Wei

last: Lin

state: AZ

address: 445 N. Fifth St.

department: Division of Molecular Medicine

institute: Translational Genomics Research Institute

description: HanSeq_0017_1_PA_Whole_T1_XCSCR_Y00087_H252CAFXY_GAGATGAC

data_processing:
10xGenomics CellRanger
pull out the UMI matrix from the filtered folder
Genome_build: mm10

source_name: large size tumor

growth_protocol: Mice received standard care approved by an IACUC protocol.

extract_protocol:
Mitlenyi Mouse Tumor Dissociation Kit
10x Genomics Chromium Single Cell 3’ Library Kit (v2 chemistry)
Pair ended library with 16bp 10X barcode and i7 sample index

treatment_protocol: These were untreated control mice and did not receive any treatment

value: pancreatic ductal adenocarcinoma (PDAC) tumor

tag: strain

value: KPC


title: Y00087: tech. rep. 4

description: HanSeq_0017_1_PA_Whole_T1_XCSCR_Y00087_H252CAFXY_TGCCGTGG


title: 20170906-C01-NA19098


title: 20170906-C02-NA19098


title: Ctrl_HSC_Rag2GFPpos_1


title: Y00029: tech. rep. 3

description: HanSeq_0004_1_PA_SCS_T1_XCSCR_Y00029_H5HVVBGX5_GGACACGT

source_name: medium size tumor


title: Y00029: tech. rep. 4

description: HanSeq_0004_1_PA_SCS_T1_XCSCR_Y00029_H5HVVBGX5_TACTCTTC


title: 20170906-B09-NA19101


title: 20170906-B10-NA19098


title: Y00087: tech. rep. 1

description: HanSeq_0017_1_PA_Whole_T1_XCSCR_Y00087_H252CAFXY_ACTTCATA


title: 20170906-C04-NA19098


title: 20170906-B08-NA19098


title: Y00029: tech. rep. 2

description: HanSeq_0004_1_PA_SCS_T1_XCSCR_Y00029_H5HVVBGX5_CCTGTGCG


title: 20170906-B07-NA19101


title: Y00029: tech. rep. 1

description: HanSeq_0004_1_PA_SCS_T1_XCSCR_Y00029_H5HVVBGX5_ATGAGAAA


title: 20170906-B04-NA19101


title: 20170906-B06-NA19098


title: Male 20 min digestion SSP

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

description:
ML_20
Male F123 mESCs from Cast/129 backgrond

library_source: genomic

data_processing:
library strategy: Mnase-SSP
Reads were mapped to a combined Burrows-Wheeler reference of mm10 using bowtie2. They were then filtered using custom Python scripts to generate deduplicated, sorted, indexed BAM files
Genome_build: mm10
Supplementary_files_format_and_content: processed data are aligned, deduplicated, sorted, and indexed BAM files that all scripts in the associated GitHub account

molecule: genomic DNA

source_name: Male F123 mESCs from Cast/129 backgrond

growth_protocol: Cells are grown under standard mESC culture conditions (15% FBS, serum + LIF, 1X Pen/Strep) on 0.1% gelatin (following two passages on mitotically inactivated MEF feeders)

extract_protocol:
Cells are lysed using a standard phenol-choloroform-isoamyl alcohol purification
Mnase-SSP is performed using the single-stranded library prep of Gansauge and Meyer (Nature Prot. 2013)
Libraries are sequenced with a custom read 1 primer on Illumina MiSeq or NextSeq instruments

treatment_protocol: Nuclei are isolated and treated with a limited amount of micrococcal nuclease for a specific amount of time

tag: strain background

tag: Sex

value: Male

tag: cell line

value: mES cells


title: 20170906-B05-NA19098

tag: cell type

tag: experiment


title: 20170906-B03-NA19098

tag: well

tag: individual


title: 20170906-B02-NA19101


title: Male 5 min digestion SSP

description:
ML_5
Male F123 mESCs from Cast/129 backgrond


title: Male 2.5 min digestion SSP

description:
ML_2.5
Male F123 mESCs from Cast/129 backgrond


title: 20170906-B11-NA19098


title: Y00087: tech. rep. 2

description: HanSeq_0017_1_PA_Whole_T1_XCSCR_Y00087_H252CAFXY_CTAGACCT

tag: tissue


title: Male 10 min digestion SSP

description:
ML_10
Male F123 mESCs from Cast/129 backgrond


title: 20170906-B01-NA19101


title: 20170906-A12-NA19098


title: Female mESC SSP rep1

description:
FL_R1_SSP
Female F121 mESCs from Cast/129 backgrond

value: Female


title: 20170906-A11-NA19098


title: Ctrl_HSC_Rag2GFPneg_1


title: Male mESC SSP rep 1

description:
ML_R1_SSP
Male F123 mESCs from Cast/129 backgrond


title: Male mESC SSP rep 2

description:
ML_R2_SSP
Male F123 mESCs from Cast/129 backgrond


title: 20170906-A09-NA19098


title: 20170906-A08-NA19098


title: 20170906-A10-NA19098


title: 20170906-A07-NA19101


title: Stat1-/- T Post-transfer rep 3

city: Boston

first: Scott

last: Snapper

state: MA

address: 300 Longwood Avenue, Enders 670

department: GI/Nutrition

institute: Boston Children's Hospital

description:
KO3
Spleen and Lymph Node

data_processing:
Data was analyzed using the VIPER pipeline (https://bitbucket.org/cfce/viper/ ).
Reads were aligned using STAR.
Transcripts were assembled using Cufflinks.
Differential analysis was performed with DESeq2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Raw counts are provided as STAR_Gene_Counts.csv.
Supplementary_files_format_and_content: Normalized values are provided as Cuff_Gene_Counts.csv.
Supplementary_files_format_and_content: Differential expression analysis of KO vs. WT are shown, with 2_vs_1.deseq.csv representing the pre-transfer setting and KO_v_WT.deseq.csv representing the post-transfer setting.

source_name: CD4+ T cells

extract_protocol:
T cells were either sorted by MACS negative selection and lysed with RLT lysis buffer (Pre-transfer) or FACS-sorted from spleen and lymph nodes of Rag1-/- mice directly into RLT lysis buffer (post transfer). RNA was extracted using the Qiagen RNeasy Micro Kit.
Clontech SMARTer v4 kit.

tag: genotype/variation

value: CD4+ T cells

tag: time point

value: Post-transfer


title: Stat1-/- T Post-transfer rep 2

description:
KO2
Spleen and Lymph Node


title: Ctrl_NIH3T3_1_3READS

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
For 3'READs data, reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq reads were aligned to mm9 using STAR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/gene

source_name: Fibroblast

extract_protocol:
TRIzol
See the "extraction protocol" column in the SAMPLES section.
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).                                                            RNA-seq: Poly(A)+ RNA in 5 µg of total RNA was purified twice using 10 µl of oligo(dT)25 magnetic beads (NEB) following the manufacturer’s protocol. RNA was then fragmented by partial alkaline hydrolysis (94 °C for 2 min), 3’ dephosphorylated with shrimp alkaline phosphatase, and 5’ phosphorylated with T4 PNK. The RNA fragments were sequentially ligated to a 5’ adenylated 3' blocked 3' adapter (5’-Aden/NNNNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC, where N is a random nucleotide) with RNA ligase 2 truncated, KQ (200 U/µl) and to a 5′ adaptor (5’-CCUUGGCACCCGAGAAUUCCA) with T4 RNA ligase I. Reverse transcription of ligation product, cDNA amplification by PCR, and library purification were performed as described above for the 3’READS procedure.

treatment_protocol: See the "protocol" column in the SAMPLES section. Untreated: cells were cultured in normal medium; Sodium Arsenite treatment: 250 µM, 1 h; Recovery: After 1 h sodium arsenite treatment, cells were washed and cultured in normal medium again; 4sU labeling: 1 h (before harvest) culture in medium containing 50  µM of 4-sU.

tag: treatment

value: Untreated

tag: protocol

tag: purpose

value: Analysis of siPcf11-induced APA


title: siPcf11_NIH3T3_2_3READS


title: 20170906-A05-NA19101


title: Stat1-/- T Post-transfer rep 1

description:
KO1
Spleen and Lymph Node


title: WT T Post-transfer rep 3

description:
WT3
Spleen and Lymph Node

value: WT


title: 20170906-A03-NA19098


title: WT T Post-transfer rep 2

description:
WT2
Spleen and Lymph Node


title: 20170906-A06-NA19098


title: siPcf11_NIH3T3_1_3READS


title: 20170906-A02-NA19098


title: 20170906-A01-NA19098


title: 20170905-H12-NA18870


title: Stat1-/- T Pre-transfer rep 3

description:
YK2-3
Spleen and Lymph Node

value: Pre-transfer


title: WT T Post-transfer rep 1

description:
WT1
Spleen and Lymph Node


title: Stat1-/- T Pre-transfer rep 2

description:
YK2-2
Spleen and Lymph Node


title: 20170905-H10-NA18870


title: 20170905-H08-NA18870


title: Stat1-/- T Pre-transfer rep 1

description:
YK2-1
Spleen and Lymph Node


title: Ctrl_NIH3T3_2_3READS


title: WT T Pre-transfer rep 3

description:
YK1-3
Spleen and Lymph Node


title: WT T Pre-transfer rep 2

description:
YK1-2
Spleen and Lymph Node


title: WT T Pre-transfer rep 1

description:
YK1-1
Spleen and Lymph Node


title: 20170905-H07-NA18870


title: 20170905-H09-NA18870


title: 20170906-A04-NA19098


title: 20170905-H06-NA18870


title: 20170905-H05-NA18870


title: C2C12_diff_1_3READS

description:
3'READS
Analysis of APA during C2C12 differentiation

data_processing:
Adapter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
For 3'READs data, reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq reads were aligned to mm9 using STAR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/gene

source_name: Myoblast

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).                                                            RNA-seq: Poly(A)+ RNA in 5 µg of total RNA was purified twice using 10 µl of oligo(dT)25 magnetic beads (NEB) following the manufacturer’s protocol. RNA was then fragmented by partial alkaline hydrolysis (94 °C for 2 min), 3’ dephosphorylated with shrimp alkaline phosphatase, and 5’ phosphorylated with T4 PNK. The RNA fragments were sequentially ligated to a 5’ adenylated 3' blocked 3' adapter (5’-Aden/NNNNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC, where N is a random nucleotide) with RNA ligase 2 truncated, KQ (200 U/µl) and to a 5′ adaptor (5’-CCUUGGCACCCGAGAAUUCCA) with T4 RNA ligase I. Reverse transcription of ligation product, cDNA amplification by PCR, and library purification were performed as described above for the 3’READS procedure.

treatment_protocol: Untreated: cells were cultured in normal medium; Sodium Arsenite treatment: 250 µM, 1 h; Recovery: After 1 h sodium arsenite treatment, cells were washed and cultured in normal medium again; 4sU labeling: 1 h (before harvest) culture in medium containing 50  µM of 4-sU.

tag: treatment or genotype


title: C2C12_diff_2_3READS


title: C2C12_pro_2_3READS


title: C2C12_pro_1_3READS


title: 20170905-H11-NA18870

description:
eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds


title: 20170905-H04-NA18870


title: 20170905-H02-NA18855


title: 20170905-H01-NA18855


title: 20170905-H03-NA18855


title: 20170905-G11-NA18855


title: Pcf11_IPAKO_4T1_2_3READS

description:
3'READS
Analysis of Pcf11-IPAKO-induced APA


title: 20170905-G12-NA18855


title: siPcf11_C2C12_input_2_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: siPcf11_C2C12_4sU_1_3READS

description:
3'READS
Analysis of differential decay of APA isoforms

value: siPcf11, with 4sU labeling

tag: molecule subtype

value: 4sU-labeled RNA


title: siPcf11_C2C12_input_1_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: Ctrl_4T1_1_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: 20170905-G10-NA18855


title: siPcf11_C2C12_4sU_2_3READS


title: Ctrl_4T1_2_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: Pcf11_IPAKO_4T1_1_3READS


title: 20170905-G06-NA18855


title: Ctrl_C2C12_input_2_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: 20170905-G09-NA18870


title: 20170905-G05-NA18870


title: 20170905-G03-NA18870


title: 20170905-G02-NA18855


title: 20170905-G07-NA18870


title: 20170905-G04-NA18870


title: Ctrl_C2C12_input_1_3READS

description:
3'READS
Analysis of siPcf11-induced APA


title: Ctrl_C2C12_4sU_1_3READS

value: Untreated, with 4sU labeling


title: Female mESC SSP rep1 No Melt

description:
FL_R1_SSP_nomelt
Female F121 mESCs from Cast/129 backgrond


title: 20170905-G01-NA18870


title: 20170905-G08-NA18855


title: 20170905-F12-NA18855


title: Male mESC SSP rep 1 No Melt

description:
ML_R1_SSP_nomelt
Male F123 mESCs from Cast/129 backgrond


title: Female mESC DSP rep 2

description:
FL_R2_DSP
Female F121 mESCs from Cast/129 backgrond


title: BCRF8CBGJ

city: Augusta

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

data_processing:
Illumina Casava1.8.2 software used for basecalling, bcl2fastq2_v2 software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBIM37 whole genome using tophat-2.0.12 with parameters --library-type fr-firststrand
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Combined FPKMs of all samples into one combinedfpkm table
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values combined for all Samples ...

source_name: cell line

growth_protocol: The BBC2, ZNF112 and BCRF8C cells were cultured in RPMI 1640 medium containing 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The BBC2, ZNF112 and BCRF8C cells were treated with 30nM, 3nM and 1.5nM BGJ398 or DMSO for 24h, then the cells were harvested for analysis.

value: Balb/c

value: SCLL cell line derived from BM of disease mice

tag: agent


title: Ctrl_C2C12_4sU_2_3READS

tag: strain


title: 20170905-F10-NA18870

value: LCL-derived iPSC


title: 20170905-F09-NA18870


title: Female mESC DSP rep 1

description:
FL_R1_DSP
Female F121 mESCs from Cast/129 backgrond

tag: strain background


title: 20170905-F08-NA18870


title: Female mESC SSP rep 2

description:
FL_R2_SSP
Female F121 mESCs from Cast/129 backgrond

tag: Sex


title: Male mESC DSP rep 1

description:
ML_R1_DSP
Male F123 mESCs from Cast/129 backgrond

tag: cell line


title: 20170905-F07-NA18855

tag: cell type


title: 20170905-F05-NA18855

tag: experiment


title: 20170905-F06-NA18855

tag: well


title: 20170905-F11-NA18855

tag: individual


title: 20170905-F03-NA18855


title: 20170905-F04-NA18855


title: 20170905-F02-NA18870


title: 20170905-E12-NA18870


title: FVB/129P2 backcross 3 IgG ChIPseq, 2

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Reads were mapped to GRCm38 using bowtie2 with default settings.
Peak calling was performed using MACS2 (v2.1.1) (Feng et al., 2012) using IgG as control.
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeak

source_name: FVB/129P2 backcross 3

extract_protocol:
Cells were fixed in 1% formaldehyde; 50mM Hepes-KOH; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA. Cell lysis was performed in LB1 buffer with final pH 7,5 (50 mM Hepes-KOH; 140mM NaCl; 1mM EDTA, 10% Glycerol, 0.5% NP-40; 0,25% Triton X-100; Proteinase inhibitor) for 20 minutes at 4°C. Subsequently, nuclei were lysed using LB2, pH 8,0 (10mM Tris-HCl; 200 mM NaCl; 1mM EDTA; 0,5mM EGTA; Proteinase inhibitor) for 10 minutes at 4°C. Pellets were resuspended in LB3 pH8,0 (10mM Tris-HCl; 100mM NaCl; 1 mM EDTA; 0,5mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; Proteinase inhibitor). Crosslinked chromatin was sheared (400-800 bp) using a Covaris S2 with Tube and Caps (Covaris, 520048), using the following settings: duty cycle: 10%, intensity: 4, cycles per burst: 200 time 40 seconds with 20 cycles. Chromatin precipitation was performed overnight using antibody-bound (CTCF 5 l, SMC1 10 l, Igg 10 per IP) proteinA coupled DynaBeads (Invitrogen). Elution and decrosslinking was performed overnight at 65°C in EB pH 8,0 (50mM Tris-HCl; 10mM EDTA; 1% SDS). Samples were treated with Proteinase K and RNAseA for 2 hours. DNA was isolated using phenol extraction and ethanol precipitation.
Library preparation was done using a KAPA Library preparation kit using the manufacturer’s protocol.

value: FVB/129P2 backcross

tag: antibody

value: IgG


title: FVB/129P2 backcross 3 IgG ChIPseq, 1

tag: genotype/variation


title: 20170905-F01-NA18870


title: DM_TR_4

city: Bar Harbor

first: Jarod

middle: Alton

last: Rollins

state: ME

address: 159 Old Bar Harbor Rd

institute: MDI Biological Laboratory

data_processing:
Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software. The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute. Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq v2.20. The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.
w
Aligned reads were counted per gene using the python script HTseq  version 0.6.1 with the parameters: --stranded=no -a 0
Calculation of normalized counts per million (cpm) was performed using edgeR version 3.0. The dataset was normalized using the trimmed mean of M-values method with the calcNormFactors() command and tagwise dispersion was estimated using the estimateGLMTagwiseDisp() command. CPM values were exported using the command cpm() with the parameters: count=y,log=F,prior.count=0.03,normalized.lib.sizes=T.
Genome_build: Ensemble version 66
Supplementary_files_format_and_content: A single tab delimited file, CPM.txt contains the CPM for each gene.id for each sample submitted

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were raised at 20°C on nematode growth media with OP50 as the food source

extract_protocol:
After lysis total RNA was isolated using Trizol as recommended by the manufacturer, polysomal bound RNA was collected using polysomal profiling with 10-50% sucrose gradients.
TruSeq RNA kit, unstranded

treatment_protocol: Starting at day one of adults hood, worms were fed OP50 at 10^11 CFU for well fed treatment or at 10^9 CFU for dietary restriction.

tag: tissue

value: whole worm

value: Ad Libitum

tag: fraction

value: polysome bound RNA

tag: strain/genotype


title: DM_TR_3

tag: treatment


title: FVB/129P2 backcross 1 IgG ChIPseq

source_name: FVB/129P2 backcross 1


title: FVB/129P2 backcross 2 H3K27ac ChIPseq

source_name: FVB/129P2 backcross 2


title: Male mESC DSP rep 2

description:
ML_R2_DSP
Male F123 mESCs from Cast/129 backgrond

value: Male

value: mES cells


title: SAM24342227 Macrophage ctrl

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

description: RNA isolated from macrophages and monocytes sorted from MC38 tumors

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment. Files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: cells sorted from MC38 tumors

extract_protocol: RNA was extracted and quantified with RNA Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol. Concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). 0.1ug of total RNA was used as an input material for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina).

value: Macrophage

tag: treatment name

value: ctrl


title: DM_TR_1


title: DM_TO_4

value: total RNA


title: FVB/129P2 backcross 3 H3K27ac ChIPseq, 2


title: 20170905-E11-NA18870

source_name: LCL-derived iPSC


title: DM_TR_2


title: DM_TO_3


title: DM_TO_2


title: 20170905-E09-NA18855


title: SAM24342235 Macrophage aPDL1


title: 20170905-E08-NA18855


title: BCRF8CD

value: DMSO


title: DR_TR_4

value: Dietary Restriction


title: SAM24342224 Monocyte ctrl

value: Monocyte


title: DM_TO_1


title: SAM24342233 Macrophage aPDL1


title: DR_TR_3


title: FVB/129P2 backcross 3 H3K27ac ChIPseq, 1


title: FVB/129P2 backcross 1 H3K27ac ChIPseq


title: SAM24342234 Monocyte aPDL1


title: DR_TR_1


title: SAM24342239 Macrophage aPDL1


title: DR_TO_4


title: DR_TO_3


title: DR_TR_2


title: 20170905-E05-NA18855


title: 20170905-E06-NA18870


title: DR_TO_1


title: AL_TR_3


title: AL_TR_4


title: 20170905-E04-NA18855


title: 20170905-E07-NA18855


title: SAM24342232 Monocyte aPDL1


title: DR_TO_2


title: SAM24342238 Monocyte aPDL1


title: 20170905-E02-NA18855


title: 20170905-E03-NA18870


title: AL_TO_4


title: SAM24342226 Monocyte ctrl


title: AL_TO_3


title: AL_TR_1


title: 20170905-E01-NA18870


title: AL_TO_2


title: SAM24342236 Monocyte aPDL1


title: AL_TO_1


title: SAM24342223 Macrophage ctrl


title: 20170905-D12-NA18855


title: siPcf11_3T3L1_RNAseq_1

description:
RNAseq
Gene expression analysis

tag: treatment or genotype


title: Ctrl_3T3L1_RNAseq_1

description:
RNAseq
Gene expression analysis

value: Untreated


title: SAM24342228 Monocyte ctrl


title: 20170905-D11-NA18855


title: Adult_Sox17iECKO_3

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: 6-week-old mice, were intraperitoneally treated with four  injections of 1.5 mg tamoxifen once every other day, followed by 1 week prior to harvesting.

data_processing:
Iontorrent BaseCaller was used for basecalling
samtools (v1.5) was used for extracting sequencing data in fastq format from bam files.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim Galore (v0.4.1) with parameters trim_galore --fastqc --clip_R1 5 --three_prime_clip_R1 5
Trimmed reads were mapped to mm10 whole genome using STAR v 2.5.3a
transcripts per million (TPM) were calculated based on simple formula from Pachter L,arXiv.org. 2011.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: freshly isolated brain endothelial cells

extract_protocol:
Brains were enzymatically digested in combination with gentleMACS Octo Dissociator (Miltenyi Biotech),  using Neural Tissue Dissociation kits (P) (130-092-628; Miltenyi Biotech) for embryos at E15.5 and pups at P5,  and Adult Brain Dissociation kits (130-107-677; Miltenyi Biotech) for pups at P9 and adults. After dissociation,  myelin cell debris and erythrocytes were removed according to the manufacturer protocol. ECs were enriched by  depletion of CD45-positive cells with CD45 MicroBeads (30-052-301; Miltenyi Biotech), followed by positive  selection using CD31 MicroBeads (30-097-418; Miltenyi Biotech). The final cell pellets were washed with PBS  and processed for total RNA extraction. Total RNA was isolated using Maxwell RSC simplyRNA cells and  tissue kits (AS1390, Promega), according to the manufacturer protocol.
For each timepoint, the RNA-Seq was performed on three indipendent biological replicates.  Libraries for RNA sequencing were prepared following the manufacturer protocols for transcriptome sequencing  with an Ion Proton sequencer (ThermoFisher Scientific). Briefly, 1 μg total RNA was poly-A selected using  Dynabeads mRNA Direct Micro Purification kits (61021; ThermoFisher Scientific), according to manufacturer  protocol. About 50 ng poly-A RNA were used to prepare strand-specific barcoded RNA libraries, with Ion Total  RNA-Seq kits v2.0 (4475936; ThermoFisher Scientific). Briefly poly-A RNAs were fragmented with RNAse III  and purified with Nucleic Acid Binding Beads. After purification, the fragmented poly-A RNAs were hybridized  and ligated with Ion Adaptor, and subsequently reverse transcribed for cDNA preparation. The cDNAs were  amplified with Ion Torrent barcode primer and purified with Nucleic Acid Binding Beads. The final libraries  were quantified on a fluorimeter (Qubit) with HS DNA (ThermoFisher Scientific), and checked for size on an  Agilent Bioanalyzer with HS DNA kits (Agilent).  Four barcoded libraries were pooled together on an equimolar basis to the final concentration of 11 pM,  and clonally amplified using Ion Proton Hi-QTemplate kits (ThermoFisher Scientific). With an IonOneTouch 2  instrument (ThermoFisher Scientific). After emulsion PCR, DNA positive Ion Sphere Particles (ISPs) were  recovered and enriched according to standard protocols, using an IonOneTouch ES instrument (ThermoFisher  Scientific). A sequencing primer was annealed to DNA-positive ISPs and the sequencing polymerase bound,  prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was carried out according to  the Ion Proton Hi-Q Sequencing kit protocol on and Ion Proton instrument.

tag: developmental stage

value: Adult

value: Freshly isolated brain endothelial cells


title: 20170905-D10-NA18855

value: LCL-derived iPSC


title: SAM24342222 Monocyte ctrl


title: Adult_Sox17iECKO_2

tag: strain


title: Adult_wt_3

value: Sox17flox/flox/Cdh5(PAC)-Cre-ERT2- (wt)


title: SAM24342229 Macrophage ctrl


title: Adult_wt_2


title: 20170905-D08-NA18855


title: SAM24342240 Monocyte aPDL1


title: 20170905-D09-NA18870


title: Adult_wt_1


title: 20170908-A01-NA18870


title: 20170905-D07-NA18855


title: P9_Sox17iECKO_3

description: Pups were treated subcutaneously with 100 μg tamoxifen in the neck skin for  every pup of the litter on postnatal day 1 (P1);

value: Pups, P9


title: AL_TR_2

value: whole worm


title: 20170905-D06-NA18870


title: SAM24342221 Macrophage ctrl


title: SAM24342225 Macrophage ctrl


title: 20170905-D05-NA18870


title: Adult_Sox17iECKO_1


title: P9_wt_3


title: P9_wt_2


title: P9_wt_1


title: SAM24342230 Monocyte ctrl


title: P5_Sox17iECKO_1

value: Pups, P5


title: SAM24342237 Macrophage aPDL1


title: P9_Sox17iECKO_2


title: 20170905-D04-NA18870


title: 20170905-D03-NA18855


title: P5_Sox17iECKO_3


title: P9_Sox17iECKO_1


title: P5_wt_3


title: 20170905-D02-NA18855


title: P5_wt_2


title: H4_EXP0_1

source_name: Whole blood

tag: subject id

value: whole blood

tag: sampling day

value: 0 (before vaccination)

tag: repeat


title: SAM24342231 Macrophage aPDL1

tag: cell type


title: E15.5_Sox17iECKO_2

description: Pregnant females were defined following overnight mating, where they were examined the following  morning for the presence of a vaginal plug; if present, this was counted as day 0.5 pc. Pregnant females were intraperitoneally treated with two injections of 1 mg  tamoxifen on days 11.5 and 13.5 post-coitum (pc).

value: Embryo, E15.5


title: 20170905-D01-NA18855

tag: experiment


title: E15.5_wt_3


title: E15.5_Sox17iECKO_1


title: E15.5_wt_2


title: E15.5_wt_1


title: 20170905-C12-NA18855

tag: well


title: 20170905-C11-NA18855

tag: individual


title: RNA-seq of ConvD [Sample 4-7]

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with abundance data

source_name: CD44- T cells

extract_protocol:
Cells enriched by flow cytometry were directly collected in RNA extraction buffer (RLT-buffer supplemented with beta-Mercaptoethanol)
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 22 ng (Sample 1 and 2) or 1ng (Sample 3 and 4) total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Sample 1 and 2) or NEBnext Low Input kit for Illumina (Sample 3 and 4) according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: FACS sorted T cells

tag: diet

value: conventional diet

value: CD44- T cells

value: Peyer's patch


title: RNA-seq of ConvD [Sample 4-5]


title: RNA-seq of ConvD [Sample 4-4]


title: P5_wt_1


title: BAH14_S4_L001_R1_001

city: Budapest

first: Abel

last: Decmann

address: Korányi str. 2a

department: Department of Internal Medicine and Oncology

country: Hungary

institute: Semmelweis University

data_processing:
trimming of adapters using cutadapt (http://cutadapt.readthedocs.io/en/stable/guide.html).
Reads with less than 16 bp insert sequences or with less than 10 bp Unique Molecular Index (UMI) were discarded.
Alignment of reads was performed using bowtie (http://bowtie-bio.sourceforge.net/index.shtml),
miRbase V21 was used for miRNAs.
Genome_build: miRbase V21
Supplementary_files_format_and_content: .xls file was generated by Qiagen online primary data analysing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).

source_name: bilateral adrenal hyperplasia

extract_protocol:
EDTA-anticoagulated plasma samples were isolated by QIAGEN miRNeasy Serum/Plasma Kit
Library was made by QIAseq microRNA Library Kit (by Qiagen)

value: plasma

tag: method

value: EDTA-anticoagulated plasma


title: BAH13_S3_L001_R1_001

tag: tissue


title: BAH12_S2_L001_R1_001


title: RNA-seq of ConvD [Sample 4-2]


title: bah10_S5_L001_R1_001


title: 20170905-C08-NA18855

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT), ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa), and the mCherry and EGFP open reading frames from the FUCCI plasmid.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset-raw.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset-raw.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 20,421 genes (H. sapiens, ERCC, EGFP, mCherry) and 1,536 single cells. The file fucci-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,421 genes for 1,536 single cells. The file fucci-annotation.txt is a tab-delimited plain text file that contains 43 metadata columns for the 1,536 single cells. The file fucci-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 43 metadata columns in fucci-annotation.txt. The file eset-final.rds is a serialized R object of the Bioconductor class ExpressionSet that contains the final data used to produce the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for the 11,093 genes (H. sapiens, ERCC, EGFP, mCherry) and 888 single cells that remained after applying filters for lowly expressed genes and low quality single cells.

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).


title: RNA-seq of ConvD [Sample 4-1]


title: 20170905-C09-NA18855


title: bah8_S3_L001_R1_001


title: E15.5_Sox17iECKO_3


title: bah9_S4_L001_R1_001


title: RNA-seq of ConvD [Sample 4-6]


title: RNA-seq of ConvD [Sample 3-8]

source_name: CD44+ T cells

value: CD44+ T cells


title: 20170905-C07-NA18855


title: RNA-seq of ConvD [Sample 3-7]


title: 20170905-C06-NA18855


title: BAH4_S4_L001_R1_001


title: BAH5_S5_L001_R1_001


title: RNA-seq of ConvD [Sample 3-6]


title: BAH3_S3_L001_R1_001


title: 20170905-C10-NA18855


title: RNA-seq of ConvD [Sample 4-8]


title: 20170905-C05-NA18855


title: BAH11_S1_L001_R1_001


title: RNA-seq of ConvD [Sample 3-5]


title: 20170905-C04-NA18870


title: 20170905-C03-NA18870


title: APA14_S8_L001_R1_001

source_name: aldosterone-producing adenoma


title: bah7_S2_L001_R1_001


title: BAH2_S2_L001_R1_001


title: APA12_S6_L001_R1_001


title: RNA-seq of ConvD [Sample 3-4]


title: RNA-seq of ConvD [Sample 3-1]


title: APA13_S7_L001_R1_001


title: APA16_S10_L001_R1_001


title: APA11_S5_L001_R1_001


title: APA15_S9_L001_R1_001


title: bah6_S1_L001_R1_001


title: RNA-seq of ConvD [Sample 3-2]


title: 20170905-C02-NA18870


title: 20170905-C01-NA18855


title: BAH1_S1_L001_R1_001


title: 20170905-B12-NA18855


title: apa7_S7_L001_R1_001


title: RNA-seq of ED [Sample 2-5]

value: elemental diet

value: CD4+ T cells


title: 20170905-B11-NA18855


title: apa8_S8_L001_R1_001


title: RNA-seq of ED [Sample 2-6]


title: apa6_S6_L001_R1_001


title: RNA-seq of ED [Sample 2-4]


title: APA5_S10_L001_R1_001


title: APA3_S8_L001_R1_001


title: APA1_S6_L001_R1_001


title: apa10_S10_L001_R1_001


title: 20170905-B08-NA18870


title: 20170905-B07-NA18855


title: apa9_S9_L001_R1_001


title: APA2_S7_L001_R1_001


title: RNA-seq of ED [Sample 2-1]


title: Exo-CPCcomm _20171005_Lei ON 244643_1_12

type: RNA

first: Wanling

last: Xuan

state: Georgia

address: 1460 laney walker blvd, CB-3712

department: Vascular Biology Center

description: Commercial human CPCs derived from human iPS cells (Catalog: R1093, Cellular Dynamics International)

hyb_protocol: The tagged microRNA product was diluted 1 to 5, and 5 μl was combined with 20 μl of Reporter probes in hybridization buffer and 5 μl of Capture probes overnight (17 hours) at 65°C to permit hybridization of probes with specific target sequences. Excess probes were removed using two-step magnetic bead-based purification on an automated fluidic handling system (nCounter Prep Station) and target/probe complexes were immobilized on the cartridge for data collection.

scan_protocol: The nCounter Digital Analyzer took images of immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. For each cartridge, a high-density scan encompassing 325 fields of view was performed.

data_processing:
NanoString raw data was analyzed with nSolver™ software, provided by NanoString Technologies. The mean plus 2 times the standard deviation of Negative Control Probes was used to perform background subtraction; positives were used to perform technical normalization to adjust lane by lane variability due to differences in hybridization, purification or binding.
Data was then normalized by calculating the geometric mean of the spikes present in each sample, as recommended by NanoString.

label: multiplexed DNA tags (miR-tag)

source_name: commerical cardiac progenitor cells

label_protocol: The assay allows measurement of 800 different microRNAs at the same time in each sample. 3.5 μl of suspension RNA was annealed with multiplexed DNA tags (miR-tag) and bridges target specifics. Mature microRNAs were bonded to specific miR-tags using a Ligase enzyme, and excess tags were removed by enzyme clean-up step.

extract_protocol: Conditioned medium was collected and exosomes were isolated by centrifugation at 3000 rpm for 30 min to remove cells and debris, followed by filtration through a 0.22 μm filter to remove the remaining debris. Then the medium was further concentrated to 500 μl using Amicon Ultra-15 100 kDa centrifugal filter units (Millipore). Isolation of exosomes in the concentrated medium was carried out through qEV size exclusion columns (Izon Science). Exosome fractions were collected and concentrated by Amicon Ultra-4 10 KDa centrifugal filter units to a final volume of <100 μl.

treatment_protocol: Human iPSC cell line ACS-1021 (ATCC, USA), and CPCs induced by ISX-9 were cultured. In some cases, EB and commercial human CPCs were also cultured.

value: exosomes


title: Exo-CPCcomm _20171005_Lei ON 244643_1_11


title: Exo-EB_20171005_Lei ON 244643_1_09

description: embryoid bodies from human iPSC ACS-1021 (ATCC, USA)

source_name: embryoid bodies from human iPSC


title: Exo-CPCcomm _20171005_Lei ON 244643_1_10


title: Exo-EB_20171005_Lei ON 244643_1_08


title: RNA-seq of ConvD [Sample 1-6]

source_name: CD4+ T cells


title: Exo-EB_20171005_Lei ON 244643_1_07


title: 20170905-E10-NA18855

last: Blischak

value: LCL-derived iPSC


title: Exo-CPCISX-9_20171005_Lei ON 244643_1_06

description: cardiac progenitor cells induced by ISX-9 (20μM)


title: 20170905-B06-NA18870

description:
eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds


title: RNA-seq of ConvD [Sample 1-4]


title: RNA-seq of ConvD [Sample 1-5]


title: 20170905-B05-NA18855


title: Exo-CPCISX-9_20171005_Lei ON 244643_1_05

source_name: cardiac progenitor cells induced by ISX-9


title: 20170905-B09-NA18855


title: 20170905-B10-NA18870


title: APA4_S9_L001_R1_001


title: RNA-seq of ED [Sample 2-3]


title: RNA-seq of ED [Sample 2-2]


title: 20170905-B04-NA18855


title: RNA-seq of ConvD [Sample 1-3]


title: 20170905-B03-NA18870


title: Exo-iPS_20171005_Lei ON 244643_1_03

description: Human iPSC cell line ACS-1021 (ATCC, USA)

source_name: human iPSC


title: Exo-iPS_20171005_Lei ON 244643_1_01


title: RNA-seq of ConvD [Sample 1-2]


title: 20170905-B02-NA18855


title: RNA-seq of ConvD [Sample 1-1]


title: Exo-iPS_20171005_Lei ON 244643_1_02


title: muscle_WIK_vehicle-exposed_female_vs_Casper_3

type: genomic

city: Portland

first: Kim

middle: H

last: Brown

state: OR

address: 1719 SW 10th Ave

department: Department of Biology

institute: Portland State University

description:
WIK vehicle-exposed female vs Casper, replicate 3
WIK_veh_K

hyb_protocol: Samples with specific activity between 20-60 (where [dye pmol/uL]/[DNA ng/uL]*1000 = specific activity) were fragmented, hybridized to array slides at 65°C for 40 hours, washed briefly, and scanned on an Agilent SureScan array scanner.

scan_protocol: Data were extracted from raw TIFF files using Agilent FeatureExtraction software with grid file 049635_D_F_20130524 and scan protcol CGH_1100_Jul11.

data_processing: Normalized, background subtracted log10 ratios of processed Red signal/processed Green signal (strain/Casper) via Agilent FeatureExtraction software.  Processed data files contain Log10 ratios of processed Red signal/processed Green signal (test/reference = strain/Casper)

organism: Danio rerio

source_name: white muscle from adult WIK female

label_protocol: Custom designed 1x1M zebrafish whole genome CGH arrays, BioPrime array CGH labeling kit (Invitrogen), and Cyanine-3/5 labeled dCTP (Perkin Elmer) were used following manufacturer’s protocols. AB, Tuebingen, and WIK were labeled with Cy-5 and Caseper was labeled with Cy-3. Labeled DNA was purified on Amicon Ultra (Millipore) columns with 0.1X SSC per the manufacturer’s protocol and quantified on a NanoDrop spectrophotometer.

extract_protocol: Muscle tissue was collected from adult zebrafish housed within the Brown lab zebrafish facility for 2 generations. AB, Tuebingen, and WIK zebrafish were originally sourced from ZIRC (Eugene, OR) as batches of 100 embryos. Individuals were sexed via visual identification of eggs or testes at the time of dissection. Pooled Casper samples were collected from 30 homogenized whole fish. Total DNA was extracted on Qiagen DNeasy columns per the manufacturer's protocol. Nucleic acid concentrations were determined on a Nanodrop Spectrophotometer 2000.

tag: age

value: adult

value: white muscle

value: WIK

value: 20 ppm (v/v) acetone vehicle

tag: Sex

value: female

source_name: whole body homogenate from pooled Casper adults

value: Casper

value: whole body homogenate


title: muscle_WIK_vehicle-exposed_male_vs_Casper_3

description:
WIK vehicle-exposed male vs Casper, replicate 3
WIK_veh_L

source_name: white muscle from adult WIK male

tag: treatment

value: male


title: muscle_WIK_vehicle-exposed_male_vs_Casper_1

description:
WIK vehicle-exposed male vs Casper, replicate 1
WIK_veh_G


title: muscle_WIK_vehicle-exposed_male_vs_Casper_2

description:
WIK vehicle-exposed male vs Casper, replicate 2
WIK_veh_H


title: muscle_WIK_vehicle-exposed_female_vs_Casper_2

description:
WIK vehicle-exposed female vs Casper, replicate 2
WIK_veh_J


title: 20170905-B01-NA18855

first: John

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago


title: muscle_WIK_PCB-exposed_female_vs_Casper_3

description:
WIK PCB-exposed female vs Casper, replicate 3
WIK_PCB_L


title: muscle_WIK_PCB-exposed_male_vs_Casper_2

description:
WIK PCB-exposed male vs Casper, replicate 2
WIK_PCB_K


title: muscle_WIK_vehicle-exposed_female_vs_Casper_1

description:
WIK vehicle-exposed female vs Casper, replicate 1
WIK_veh_F


title: 20170905-A12-NA18855


title: Exo-CPCISX-9_20171005_Lei ON 244643_1_04


title: 20170905-A10-NA18870


title: muscle_WIK_PCB-exposed_male_vs_Casper_1

description:
WIK PCB-exposed male vs Casper, replicate 1
WIK_PCB_J


title: 20170905-A08-NA18870


title: muscle_WIK_PCB-exposed_female_vs_Casper_1

description:
WIK PCB-exposed female vs Casper, replicate 1
WIK_PCB_H


title: muscle_WIK_PCB-exposed_female_vs_Casper_2

description:
WIK PCB-exposed female vs Casper, replicate 2
WIK_PCB_I


title: muscle_WIK_naïve_male_vs_Casper_2

description:
WIK naïve male vs Casper, replicate 2
WIK_cont_M

value: naive


title: muscle_WIK_PCB-exposed_male_vs_Casper_3

description:
WIK PCB-exposed male vs Casper, replicate 3
WIK_PCB_N


title: 20170905-A09-NA18855


title: muscle_WIK_naïve_male_vs_Casper_3

description:
WIK naïve male vs Casper, replicate 3
WIK_cont_P


title: 20170905-A07-NA18855


title: muscle_WIK_naïve_male_vs_Casper_1

description:
WIK naïve male vs Casper, replicate 1
WIK_cont_L


title: 20170905-A06-NA18870

description:
eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds


title: ZNFDMSO

source_name: cell line

value: Balb/c

tag: cell line

value: SCLL cell line derived from BM of disease mice

tag: agent

value: DMSO


title: muscle_WIK_naïve_female_vs_Casper_3

description:
WIK naïve female vs Casper, replicate 3
WIK_cont_J


title: 20170905-A11-NA18855


title: muscle_WIK_naïve_female_vs_Casper_1

description:
WIK naïve female vs Casper, replicate 1
WIK_cont_G


title: 20170905-A05-NA18870


title: muscle_Tuebingen_vehicle-exposed_male_vs_Casper_3

description:
Tuebingen vehicle-exposed male vs Casper, replicate 3
TU_veh_N

source_name: white muscle from adult Tuebingen male

value: Tuebingen


title: BBCDMSO


title: muscle_Tuebingen_vehicle-exposed_male_vs_Casper_2

description:
Tuebingen vehicle-exposed male vs Casper, replicate 2
TU_veh_M


title: ZNFBGJ


title: muscle_Tuebingen_vehicle-exposed_female_vs_Casper_1

description:
Tuebingen vehicle-exposed female vs Casper, replicate 1
TU_veh_H

source_name: white muscle from adult Tuebingen female


title: 20170905-A03-NA18855

source_name: LCL-derived iPSC


title: BBCBGJ


title: 20170905-A02-NA18870


title: muscle_Tuebingen_vehicle-exposed_male_vs_Casper_1

description:
Tuebingen vehicle-exposed male vs Casper, replicate 1
TU_veh_G


title: 20170905-A04-NA18870


title: muscle_Tuebingen_PCB-exposed_male_vs_Casper_3

description:
Tuebingen PCB-exposed male vs Casper, replicate 3
TU_PCB_N


title: muscle_Tuebingen_PCB-exposed_female_vs_Casper_3

description:
Tuebingen PCB-exposed female vs Casper, replicate 3
TU_PCB_L


title: P5_Sox17iECKO_2

description: Pups were treated subcutaneously with 100 μg tamoxifen in the neck skin for  every pup of the litter on postnatal day 1 (P1);

source_name: freshly isolated brain endothelial cells

tag: developmental stage

value: Pups, P5

value: Freshly isolated brain endothelial cells


title: muscle_Tuebingen_PCB-exposed_male_vs_Casper_2

description:
Tuebingen PCB-exposed male vs Casper, replicate 2
TU_PCB_M

tag: strain


title: muscle_WIK_naïve_female_vs_Casper_2

description:
WIK naïve female vs Casper, replicate 2
WIK_cont_H


title: muscle_Tuebingen_PCB-exposed_female_vs_Casper_2

description:
Tuebingen PCB-exposed female vs Casper, replicate 2
TU_PCB_J


title: muscle_Tuebingen_PCB-exposed_male_vs_Casper_1

description:
Tuebingen PCB-exposed male vs Casper, replicate 1
TU_PCB_I


title: muscle_Tuebingen_PCB-exposed_female_vs_Casper_1

description:
Tuebingen PCB-exposed female vs Casper, replicate 1
TU_PCB_F


title: 20170905-A01-NA18870


title: muscle_Tuebingen_naïve_male_vs_Casper_3

description:
Tuebingen naïve male vs Casper, replicate 3
TU_cont_K


title: muscle_Tuebingen_vehicle-exposed_female_vs_Casper_3

description:
Tuebingen vehicle-exposed female vs Casper, replicate 3
TU_veh_K


title: muscle_Tuebingen_vehicle-exposed_female_vs_Casper_2

description:
Tuebingen vehicle-exposed female vs Casper, replicate 2
TU_veh_I


title: muscle_Tuebingen_naïve_female_vs_Casper_3

description:
Tuebingen naïve female vs Casper, replicate 3
TU_cont_N


title: muscle_Tuebingen_naïve_female_vs_Casper_2

description:
Tuebingen naïve female vs Casper, replicate 2
TU_cont_H


title: muscle_Tuebingen_naïve_male_vs_Casper_2

description:
Tuebingen naïve male vs Casper, replicate 2
TU_cont_J


title: liver_vehicle_WIK_male_3

description: mRNA expression of WIK male following acetone vehicle exposure

hyb_protocol: Samples with total cRNA yields greater than 1.65 µg and specific activity greater than 6 pmol Cy3/µg were fragmented, hybridized to array slides at 65°C for 17 hours, washed briefly, and scanned on an Agilent SureScan array scanner.

scan_protocol: Data were extracted from raw TIFF files using Agilent FeatureExtraction software with grid file 026437_D_F_20140627 and scan protcol AgilentHD_GX_1Color.

data_processing: The cyclic loess method was used for inter-array normalization and replicate probes were averaged within arrays using the limma R package (Ritchie et al. 2015).

source_name: vehicle-exposed liver, WIK, male, individual 3

label_protocol: Commercially available 4x44K zebrafish mRNA expression arrays, RNA spike-in kit, and Low Input Quick Amp one-color labeling kit (Agilent) were used following manufacturer’s protocols. In brief, cDNA was synthesized from RNA and transcribed into cRNA using Cyanine-3 fluorescent dCTP. Labeled cRNA was purified using a Qiagen RNeasy mini kit per the manufacturer’s protocol and quantified on a NanoDrop spectrophotometer.

extract_protocol: Liver tissue was disrupted with a mortar and pestle prior to homogenization by passing the samples through a nuclease-free syringe and needle in beta-mercaptoethanol lysis buffer. Total RNA was extracted on Qiagen RNeasy columns per the manufacturer's protocol. Nucleic acid concentrations were determined on a Nanodrop Spectrophotometer 2000 and exhibited high 260/280 ratios of 2.09 ± 0.02, respectively (average ± SD).

treatment_protocol: All samples were collected from adult zebrafish housed within the Brown lab zebrafish facility for 2 generations. AB, Tuebingen, and WIK zebrafish were originally sourced from ZIRC (Eugene, OR) as batches of 100 embryos. Livers were extracted from adults aged 12-18 months within 30 minutes of ice water euthanasia and immediately frozen in liquid nitrogen. Individuals were sexed via visual identification of eggs or testes at the time of dissection.

value: 20 ppm (v/v) acetone vehicle for 24 hours


title: liver_vehicle_WIK_male_2

source_name: vehicle-exposed liver, WIK, male, individual 2


title: muscle_AB_vehicle-exposed__vs_Casper_3

description:
AB vehicle-exposed  vs Casper, replicate 3
AB_veh_N

source_name: white muscle from adult AB

value: AB


title: liver_PCB_WIK_male_2

description: mRNA expression of WIK male following PCB exposure

source_name: PCB-exposed liver, WIK, male, individual 2

value: 130 ng/L PCB-126 for 24 hours

value: adult


title: liver_vehicle_WIK_female_3

description: mRNA expression of WIK female following acetone vehicle exposure

source_name: vehicle-exposed liver, WIK, female, individual 3

value: WIK


title: muscle_Tuebingen_naïve_female_vs_Casper_1

description:
Tuebingen naïve female vs Casper, replicate 1
TU_cont_F

value: white muscle


title: liver_PCB_WIK_male_1

source_name: PCB-exposed liver, WIK, male, individual 1


title: liver_vehicle_WIK_female_2

source_name: vehicle-exposed liver, WIK, female, individual 2

value: female


title: muscle_AB_vehicle-exposed_male_vs_Casper_2

description:
AB vehicle-exposed male vs Casper, replicate 2
AB_veh_M

source_name: white muscle from adult AB male

value: 20 ppm (v/v) acetone vehicle

value: Casper


title: liver_vehicle_WIK_male_1

source_name: vehicle-exposed liver, WIK, male, individual 1

value: male


title: liver_PCB_WIK_male_3

source_name: PCB-exposed liver, WIK, male, individual 3


title: muscle_Tuebingen_naïve_male_vs_Casper_1

description:
Tuebingen naïve male vs Casper, replicate 1
TU_cont_G

value: naive

source_name: whole body homogenate from pooled Casper adults

value: whole body homogenate


title: muscle_AB_vehicle-exposed_female_vs_Casper_3

description:
AB vehicle-exposed female vs Casper, replicate 3
AB_veh_J

source_name: white muscle from adult AB female


title: liver_PCB_WIK_female_2

description: mRNA expression of WIK female following PCB exposure

source_name: PCB-exposed liver, WIK, female, individual 2


title: liver_PCB_WIK_female_3

source_name: PCB-exposed liver, WIK, female, individual 3


title: muscle_AB_vehicle-exposed_male_vs_Casper_1

description:
AB vehicle-exposed male vs Casper, replicate 1
AB_veh_I


title: root_24h_20C_rep1

city: Halle

first: Carolin

last: Delker

address: Betty-Heimann-Str. 5

department: Crop Physiology

institute: Martin Luther University Halle

hyb_protocol: Labeled samples were hybridized to the Genechip ATH1 Genome Array (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/)

scan_protocol: The GeneArrays were scanned using the Affymetrix GeneChip Scanner (Affymetrix) using standard NASC protocols.

data_processing: Raw data was processed with the simpleaffy R package to obtain robust multi-chip average (RMA)- normalized log2 expression levels using default settings. The eBayes function of the limma R package was used to compute log fold changes (LFCs), t-values, P values and to correct P values for multiple testing.

label: Biotin

organism: Arabidopsis thaliana

source_name: roots control_20°C_24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5d 20°C, long day (16hL/8hD), 120 µmol/m2/sec PAR from white light LEDs

extract_protocol: Qiagen RNeasy Plant Mini Kit + on-column DNase treatment

treatment_protocol: seedlings were shifted at ZT7 on day 5 and harvested at ZT10 for 3h temperature treatments or at ZT7 on day 6 for 24h treatments. Control plants remained at 20°C but were harvested at the same time.

tag: germplasm/accession

tag: temperature

tag: timepoint

value: roots


title: root_24h_20C_rep3


title: liver_vehicle_WIK_female_1

source_name: vehicle-exposed liver, WIK, female, individual 1


title: root_3h_20C_rep3

source_name: roots control_20°C_3h


title: root_24h_28C_rep3

source_name: roots treatment_28°C_24h


title: root_3h_20C_rep2


title: muscle_AB_vehicle-exposed_female_vs_Casper_1

description:
AB vehicle-exposed female vs Casper, replicate 1
AB_veh_F


title: root_24h_28C_rep2


title: root_24h_20C_rep2


title: liver_vehicle_Tuebingen_male_3

description: mRNA expression of Tuebingen male following acetone vehicle exposure

source_name: vehicle-exposed liver, Tuebingen, male, individual 3


title: Myotonic Dystrophy Type 2 Line 1 [DM2-1]

city: Chicago

first: Anthony

middle: Martin

last: Gacita

address: 303 E Superior St. Lurie 7-240

department: Center for Genetic Medicine

institute: Northwestern Univeristy Feinberg School of Medicine

description:
DM_E01
RNA-Seq from DM2 Patient-Derived IPSC Cardiomyocyte

data_processing:
Differential Expression Analysis:
Reads were aligned to hg38 using STAR 2.5.2.
HT-seq was used to assign reads to transcripts
EdgeR was used to normalize counts calculate differential expression. Counts per million file (CPM) is included.
Differentially expressed genes were filtered for an FDR p-value < 0.05, absolute fold change > 2, and > 2 average CPM.
Overrepresented Pathways and Gene Ontologies were identified using InnateDB using an FDR < 0.05.
Differential Splicing Analysis:
RNA-sequencing reads were uniformly trimmed to 75bp using trimmomatic.
Reads were aligned to hg19 using STAR 2.5.2.
Bam files were merged and used as inputs to MISO to generate percent spliced in (PSI) values for event annotations including skipped exons (SE), retained introns (RI), mutually-exclusive exons (MXE), alternative 5’ splice sites (A5SS), alternative 3’ splice sites (A3SS), and full isoforms.
MISO was used to make pairwise comparisons to identify differentailly expressed isoforms
Differential events were filted for > 20 counts supporting the alternative isoform, a bayes factor > 10, and change in PSI > 0.20.
Genome_build: hg38 or hg19
Supplementary_files_format_and_content: CPM_levels.txt includes the counts per million for for all genes in each samples outputted by EdgeR.
Supplementary_files_format_and_content: splicing_comparisons.xlsx includes the unfiltered results from comparing the merged files for each event type.

source_name: Myotonic Dystrophy Type 2_IPSC-Cardiomyocyte

extract_protocol:
RNA was extracted from cells using TRIzol and the Aurum Total RNA Mini Kit (Bio-Rad, Hercules, CA; 7326820).
TruSeq Sranded mRNA-Seq Library Prep (Illumina)

tag: phenotype

value: Myotonic Dystrophy Type 2

tag: study code

tag: cell type

value: IPSC-Cardiomyocyte

tag: molecule subtype

value: cytoplasmic RNA


title: root_3h_20C_rep1


title: root_24h_28C_rep1


title: muscle_AB_vehicle-exposed_female_vs_Casper_2

description:
AB vehicle-exposed female vs Casper, replicate 2
AB_veh_G


title: liver_PCB_WIK_female_1

source_name: PCB-exposed liver, WIK, female, individual 1


title: Myotonic Dystrophy Type 2 Line 2 [DM2-2]

description:
DM_E02
RNA-Seq from DM2 Patient-Derived IPSC Cardiomyocyte


title: Myotonic Dystrophy Type 1 Line 2 [DM1-2]

description:
DM_F01
RNA-Seq from DM1 Patient-Derived IPSC Cardiomyocyte

source_name: Myotonic Dystrophy Type 1_IPSC-Cardiomyocyte

value: Myotonic Dystrophy Type 1


title: muscle_AB_PCB-exposed_male_vs_Casper_3

description:
AB PCB-exposed male vs Casper, replicate 3
AB_PCB_K


title: root_3h_28C_rep1

source_name: roots treatment_28°C_3h


title: muscle_AB_PCB-exposed_female_vs_Casper_3

description:
AB PCB-exposed female vs Casper, replicate 3
AB_PCB_L


title: Myotonic Dystrophy Type 1 Line 1 [DM1-1]

description:
DM_D01
RNA-Seq from DM1 Patient-Derived IPSC Cardiomyocyte


title: root_3h_28C_rep2


title: liver_vehicle_Tuebingen_male_2

source_name: vehicle-exposed liver, Tuebingen, male, individual 2

value: Tuebingen

value: 20 ppm (v/v) acetone vehicle for 24 hours


title: Control shRNA

city: Guangzhou

first: Shuqiang

last: Liu

state: Guangdong

address: Outer ring road No. 232

country: China

institute: Guangzhou University of Chinese Medicine

description:
shN_NS
Perform human gene expression microarray after transfection with shRNA for 7 days

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.
Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2, T-test p-value < 0.05

source_name: Control shRNA

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: transfection with shRNA for 7 days

value: Hepatocellular carcinoma cell line MHCC-97H

tag: genotype/variation

value: control


title: liver_PCB_Tuebingen_male_3

description: mRNA expression of Tuebingen male following PCB exposure

source_name: PCB-exposed liver, Tuebingen, male, individual 3

value: 130 ng/L PCB-126 for 24 hours

value: adult


title: UGT2B15 shRNA1

description:
SH1_NS
Perform human gene expression microarray after transfection with shRNA for 7 days

source_name: UGT2B15 shRNA

value: UGT2B15 deficiency


title: muscle_AB_PCB-exposed_male_vs_Casper_2

description:
AB PCB-exposed male vs Casper, replicate 2
AB_PCB_I

source_name: white muscle from adult AB male

value: white muscle

value: AB

source_name: whole body homogenate from pooled Casper adults


title: Healthy Control 2 [WT-2]

description:
CTRL_U19
RNA-seq from Healhty IPSC-Cardiomyocyte

source_name: Healthy Control_IPSC-Cardiomyocyte

value: Healthy 2


title: liver_PCB_Tuebingen_male_2

source_name: PCB-exposed liver, Tuebingen, male, individual 2

value: male


title: cotyledon_24h_28C_rep2

source_name: cotyledons treatment_28°C_24h

value: cotyledons


title: Healthy Control 1 [WT-1]

description:
CTRL_U11
RNA-seq from Healhty IPSC-Cardiomyocyte

value: Healthy 1


title: muscle_AB_PCB-exposed_female_vs_Casper_1

description:
AB PCB-exposed female vs Casper, replicate 1
AB_PCB_G

source_name: white muscle from adult AB female

value: female

value: Casper

value: whole body homogenate


title: cotyledon_24h_28C_rep3


title: UGT2B15 shRNA2

description:
SH2_NS
Perform human gene expression microarray after transfection with shRNA for 7 days


title: cotyledon_3h_28C_rep3

source_name: cotyledons treatment_28°C_3h


title: liver_vehicle_Tuebingen_male_1

source_name: vehicle-exposed liver, Tuebingen, male, individual 1


title: liver_vehicle_Tuebingen_female_3

description: mRNA expression of Tuebingen female following acetone vehicle exposure

source_name: vehicle-exposed liver, Tuebingen, female, individual 3


title: muscle_AB_PCB-exposed_male_vs_Casper_1

description:
AB PCB-exposed male vs Casper, replicate 1
AB_PCB_F


title: muscle_AB_PCB-exposed_female_vs_Casper_2

description:
AB PCB-exposed female vs Casper, replicate 2
AB_PCB_J


title: liver_PCB_Tuebingen_male_1

source_name: PCB-exposed liver, Tuebingen, male, individual 1


title: muscle_AB_naïve_female_vs_Casper_3

description:
AB naïve female vs Casper, replicate 3
AB_cont_N

value: naive