title: IgG sample

description:
Sample name: MUC2045_IgG
Processed data files:
pheno_data.csv
MUC2045.bw

data_processing:
Basecalling, convesion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: to mm10 using STAR after Cutadapt
Peak-calling: per single m6A-input pair using exomePeak with window_width=100, sliding_step=10, minimal_peak_length=50
Consensus-peaks: Peaks from biological replicates were merged keeping only those ranges supported by a minimum of 2/3 of samples per group (using BEDTools with minimum length 50 nt and merging ranges with less than 50 nt distance, Quinlan and Hall, 2010): see grouppeaks_control.bed and grouppeaks_stress.bed. For quantification with DiffBind (Ross-Innes et al., 2012) a consensus peak set was built with BEDTools including those ranges supported by either 2/3 of samples per group or 1/2 of samples of the entire experiment, furthermore filtered minimum abundancy (dba_score_rpkm_fold =2, dba_score_reads =25 for mouse acute stress): finalpeaks_consensus_all_peaks.bed.
Quantitative analysis: For differential peak analysis m6A-RIP counts extracted from DiffBind (counts_in_peaks.csv) were compared with DESeq2 (Love et al., 2014) (m6A_quantification.csv). Gene expression was analysed using the RNA input samples only employing  DESeq2 (counts used: RNA_counts.csv; analysis: RNA_quantification.csv). p-values were corrected by fdrtool (Strimmer et al., 2008). Significance cutoffs:  absolute fold change > 0.2 (m6A) or > 0.1 (RNA) and Benjamini-Hochberg corrected P-value Q < 0.1. Peaks were annotated using ChIPseeker (Yu et al., 2015) and Biomart (Smedley et al., 2015). Peak bed-files are provided for all consensus peaks used for quantitaive analysis (finalpeaks_consensus_all_peaks.bed), differential methylated peaks (finalpeaks_differential.bed) and putative m6Am peaks (finalpeaks_m6Am.bed).
Visualization: For visualization, bam files were normalised using deepTools (Ramírez et al., 2016) creating a single bigWigfile per sample (MUC2017.bw … MUC2045.bw). Biolgical replicates were merged using UCSC bigWigMerge and UCSC bedGraphTobigWig creating one m6A and one input RNA bigWigfile per condition: average_m6A_control.bw, average_m6A_stress.bw, average_RNA_control.bw, average_RNA_stress.bw.
Genome_build: mm10
Supplementary_files_format_and_content: bed: peak ranges for single biological replicates (singlepeaks_*.bed), merged per group (grouppeaks_*.bed) or further processed see above (finalpeaks_*.bed); bw: normalized bigWig files per sample (MUC20*.bw) or merged per group/fraction (average_*.bw); csv: comma delimited files including raw counts used for DeSeq2 analysis and DeSeq2 (annotated) output.

extract_protocol:
Total RNA was extracted from freshly dissected and flash-frozen cortex with Trizol (Invitrogen) and isopropanol precipitation. After removal of DNA (TurboDNA-free kit, Ambion), PolyA-RNA was enriched with the Genelute mRNA Prep Kit (Sigma), precipiated and diluted to 1ug/ul and fragmeneted using the fragmentation reagents (Life Technologies). 10 ug PolyA RNA fragments per samples were precipitated with 10ug anti-m6A antibody (SySy 202003). 10 ug PolyA RNA fragments mixed equimolar form all samples was precipiated with 10 ug IgG (Cell Signalling Technology 2729) and Protein A/G beads (Thermo Fisher Scientific) and recovered by Proteinase K elution.
Recovered immunoprecipitated fragments per sample or 100 ng of the input PolyA-RNA-fragments per samples were processed with the TruSeq non-stranded mRNA Sample Prep Kit and sequenced on a HiSeq4000 multiplexing all samples(26.7-36.7 Mio. raw reads).

tag: rip antibody

value: Cell Signalling Technology Normal Rabbit IgG Cat 2729 Lot 7

value: IgG RIP


title: m6A sample of stress 6

status: Public on Jul 10 2018

type: SRA

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

country: Germany

institute: Max-Planck-Institute of Psychiatry

description:
Sample name: MUC2043_S6_m6A
Processed data files:
pheno_data.csv
MUC2043.bw
average_m6A_stress.bw
singlepeaks_S6.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: C57BL/6 cortex

treatment_protocol: Animals were treated with 15 min acute restraint stress and returned to their homecage (stress) or left in their homecage (basal) and sacrificed 4 h after.

tag: strain

tag: treatment

value: stress

tag: tissue

value: cortex

value: Synaptic Systems anti-m6A Cat 202003 Lot 56

tag: fraction

value: m6A/m RIP


title: m6A sample of basal 7

description:
Sample name: MUC2044_C7_m6A
Processed data files:
pheno_data.csv
MUC2044.bw
average_m6A_control.bw
singlepeaks_C7.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

value: basal


title: m6A sample of basal 6

description:
Sample name: MUC2042_C6_m6A
Processed data files:
pheno_data.csv
MUC2042.bw
average_m6A_control.bw
singlepeaks_C6.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of stress 5

description:
Sample name: MUC2041_S5_m6A
Processed data files:
pheno_data.csv
MUC2041.bw
average_m6A_stress.bw
singlepeaks_S5.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of stress 4

description:
Sample name: MUC2039_S4_m6A
Processed data files:
pheno_data.csv
MUC2039.bw
average_m6A_stress.bw
singlepeaks_S4.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: Total RNA of Control 3

description:
Sample name: MUC2335_total_C3
Processed data files:
pheno_data.xlsx
cpm_normcounts.csv
quantification.csv

data_processing:
Library strategy: Ribo-Seq
Basecalling, convesion and demultiplexing: Illumina RTA, bcl2fastq2
Alignment: Reads were adapter- and quality-trimming with cutadapt (Martin et al., 2011) keeping only those reads with RA5 adapter present, insert length between 15 and 50 nt and a minimum Phred quality score of 15. After removing rRNA and tRNA sequences remaining sequences were aligned using Tophat/Bowtie1 (Langmead et al., 2009: Trapnell et al., 2009; at default settings to Gencode mm10/VM15).
Quantitative analysis: Translation efficiencies were calculated by dividing ribosome-bound CPM by input CPM after counting reads with HTSeq (Anders et al., 2015, only genes considered with minimum 25 counts per sample). Translation efficiencies were compared using T-tests with significantly regulated genes being defined with an absolute fold change  > 0.5 and a Benjamini-Hochberg corrected P-value=Q < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: cpm_normcounts.csv, quantification.csv

molecule: total RNA

extract_protocol:
Ribosome profiling libraries were prepared using the TruSeq Ribo Profile (Mammalian) Kit (Illumina, San Diego, CA) with the following adjustments: Flash-frozen cortex samples were homogenized in lysis buffer including cycloheximide Keeping 1/5 of the supernatent aside for input libraris, 4/5 of the supernatent were digested with nuclease for ribosome profiling and purified on a sucrose gradient.
Trizol LS purified ribosome protected fragments were processed as described in the TruSeq Ribo Profile Kit with rRNA depletion by RiboZero Gold (mammalian) and remaining fragments size-selected, purified and processed as described. cDNA was purified using a 2.5x AMPure clean-up. PCR was performed on undiluted circularized cDNA with 12 PCR cycles and PCR products on DNA-TBE PAGE. Sequencing was performed on each one lane for ribosome bound fractions and input fractions (indexed each 1-12) of an Illumina HiSeq4000 PE 2x100 (Illumina, San Diego, CA) using only the reverse read (R2).

value: input RNA


title: SRV-0046

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

country: USA

institute: University of Kentucky

description:
RSEM processed, expected count values, found in column 7 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt

data_processing:
De novo assembly of RNA-Seq isotigs was accomplished using Trinity’s three-stage protocol (Inchworm, Chrysalis, and Butterfly).
RSEM was used for count estimation with default parameters
Expected counts were extracted in a matrix file format from the RSEM output.

organism: Ambystoma mexicanum

source_name: mid-zeugopod whole tissue

extract_protocol:
Mid-zeugopod amputations were conducted on all animals. Exactly 1mm distal most tissue was collected immediately after amputation (0hpa) and 24 hpa. Whole RNA tissue was extracted using the TruSeq RNA library prep kit from Illumina.
HudsonAlpha Institute for Biotechnology generated the RNA-Seq data by preparing cDNA libraries and sequencing approximately 50,000,000 100 bp read pairs per sample.

value: mid-zeugopod

tag: time post amputation (hpa)

tag: size of tissue collection


title: m6A sample of basal 5

description:
Sample name: MUC2040_C5_m6A
Processed data files:
pheno_data.csv
MUC2040.bw
average_m6A_control.bw
singlepeaks_C5.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of basal 4

description:
Sample name: MUC2038_C4_m6A
Processed data files:
pheno_data.csv
MUC2038.bw
average_m6A_control.bw
singlepeaks_C4.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: SRV-0045

description:
RSEM processed, expected count values, found in column 6 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt


title: SRV-0043

description:
RSEM processed, expected count values, found in column 4 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt


title: SRV-0042

description:
RSEM processed, expected count values, found in column 3 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt


title: m6A sample of stress 3

description:
Sample name: MUC2037_S3_m6A
Processed data files:
pheno_data.csv
MUC2037.bw
average_m6A_stress.bw
singlepeaks_S3.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of basal 3

description:
Sample name: MUC2035_C3_m6A
Processed data files:
pheno_data.csv
MUC2035.bw
average_m6A_control.bw
singlepeaks_C3.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: SRV-0041

description:
RSEM processed, expected count values, found in column 2 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt


title: KK1 JQ1 - 48 hours - mAdbID:129917

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 129917

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

organism: Homo sapiens

source_name: KK1 JQ1 - 48 hours

label_protocol:
Cy5 Labeling Protocol
Total RNA was labeled with Cy5.

extract_protocol:
Trizol Extraction Protocol
Total RNA was extracted from ATLL cell lines with TRIzol (Life Technologies) and subsequently cleaned up using RNeasy mini-columns (Qiagen).

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 500 nM
Treatment time: 48 hours
In-vitro treatment: KK1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 48 hours.

value: Blood

tag: cell line

tag: disease state

value: Adult T-cell Leukemia/Lymphoma (ATLL)

source_name: KK1 DMSO Treated

label_protocol:
Cy3 Labeling Protocol
Total RNA was labeled with Cy3.

treatment_protocol:
Treatment type: compound
Agent: DMSO Treatment
In-vitro treatment: Cells were treated with DMSO.


title: KK1 JQ1 - 24 hours - mAdbID:129915

description: mAdb experiment ID: 129915

source_name: KK1 JQ1 - 24 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 500 nM
Treatment time: 24 hours
In-vitro treatment: KK1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 24 hours.


title: KK1 sgHBZ_2 - day 7 - mAdbID:129869

description: mAdb experiment ID: 129869

source_name: KK1 sgHBZ_2 - day 7

treatment_protocol:
Treatment type: transduction
In-vitro treatment: Cells were transduced with retroviruses expressing an sgRNA-resistant HBZ isoform and were subsequently transduced with retroviruses co-expressing GFP and sgHBZ #2.

source_name: KK1 sgControl

treatment_protocol:
Treatment type: transduction
In-vitro treatment: Cells were transduced with sgControl vector.


title: ST1 JQ1 - 24 hours - mAdbID:129911

description: mAdb experiment ID: 129911

source_name: ST1 JQ1 - 24 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 24 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 24 hours.

source_name: ST1 DMSO Treated


title: ST1 JQ1 - 12 hours - mAdbID:129910

description: mAdb experiment ID: 129910

source_name: ST1 JQ1 - 12 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 12 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 12 hours.


title: KK1 JQ1 - 36 hours - mAdbID:129916

description: mAdb experiment ID: 129916

source_name: KK1 JQ1 - 36 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 500 nM
Treatment time: 36 hours
In-vitro treatment: KK1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 36 hours.


title: ST1 JQ1 - 36 hours - mAdbID:129912

description: mAdb experiment ID: 129912

source_name: ST1 JQ1 - 36 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 36 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 36 hours.


title: m6A sample of stress 2

description:
Sample name: MUC2034_S2_m6A
Processed data files:
pheno_data.csv
MUC2034.bw
average_m6A_stress.bw
singlepeaks_S2.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: KK1 sgHBZ_1 - day 8 - mAdbID:129866

description: mAdb experiment ID: 129866

source_name: KK1 sgHBZ_1 - day 8

treatment_protocol:
Treatment type: transduction
In-vitro treatment: Cells were transduced with retroviruses expressing an sgRNA-resistant HBZ isoform and were subsequently transduced with retroviruses co-expressing GFP and sgHBZ #1.


title: KK1 sgHBZ_1 - day 9 - mAdbID:129868

description: mAdb experiment ID: 129868

source_name: KK1 sgHBZ_1 - day 9


title: KK1 JQ1 - 12 hours - mAdbID:129914

description: mAdb experiment ID: 129914

source_name: KK1 JQ1 - 12 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 500 nM
Treatment time: 12 hours
In-vitro treatment: KK1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 12 hours.


title: ST1 sgHBZ_2 - day 7 - mAdbID:129863

description: mAdb experiment ID: 129863

source_name: ST1 sgHBZ_2 - day 7

source_name: ST1 sgControl


title: ST1 JQ1 - 48 hours - mAdbID:129913

description: mAdb experiment ID: 129913

source_name: ST1 JQ1 - 48 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 48 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 48 hours.


title: m6A sample of basal 2

description:
Sample name: MUC2033_C2_m6A
Processed data files:
pheno_data.csv
MUC2033.bw
average_m6A_control.bw
singlepeaks_C2.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv

source_name: C57BL/6 cortex


title: ST1 sgHBZ_2 - day 8 - mAdbID:129864

description: mAdb experiment ID: 129864

source_name: ST1 sgHBZ_2 - day 8


title: KK1 sgHBZ_1 - day 7 - mAdbID:129865

description: mAdb experiment ID: 129865

source_name: KK1 sgHBZ_1 - day 7


title: SRV-0044

description:
RSEM processed, expected count values, found in column 5 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt

source_name: mid-zeugopod whole tissue


title: m6A sample of basal 1

description:
Sample name: MUC2031_C1_m6A
Processed data files:
pheno_data.csv
MUC2031.bw
average_m6A_control.bw
singlepeaks_C1.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: m6A sample of stress 1

description:
Sample name: MUC2032_S1_m6A
Processed data files:
pheno_data.csv
MUC2032.bw
average_m6A_stress.bw
singlepeaks_S1.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
m6A_counts_in_peaks.csv
m6A_quantification.csv


title: NCI-H209 siTTF-1

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

hyb_protocol: Hybridization was performed with Hybridization Control Kit (Affymetrix, Inc., cat.# 900454)  and Hybridization, Wash, and Stain Kit (Affymetrix, Inc., cat.# 900720) in GeneChip Hybridization Oven 645 (Affymetrix, Inc.) for 18 hr (60 rpm) at 48 degree celsius. Washing was performed using GeneChip Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Slides were scanned using GeneChip® Scanner 3000 7G

data_processing: Images were digitized with Affymetrix® Expression Console™ Software.

label: biotin

source_name: human small cell lung cancer cell line NCI-H209 electroporated with siRNAs for TTF-1 (siTTF-1)

label_protocol: Biotin-labeled samples were prepared using FlashTagTM Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA Arrays (Affymetrix, Inc., cat.# 901911) .

growth_protocol: NCI-H209 cells were cultured in RPMI1640 + 10% FBS.

extract_protocol: Total RNA was extracted 48 h after siNC or siTTF-1 transfection, using RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA QC was performed by Agilent 2100 Bioanalyzer.

treatment_protocol: NCI-H209 cells (1 × 107) were mixed with 1 μM siRNAs in an electroporation cuvette and electroporated using Gene Pulser II Electroporation Systems (Bio-Rad, Hercules, CA, USA) with voltage 200 V and capacitance 950 μF.

tag: transfection


title: ST1 sgHBZ_1 - day 8 - mAdbID:129862

description: mAdb experiment ID: 129862

source_name: ST1 sgHBZ_1 - day 8


title: NCI-H209 siNTC

source_name: human small cell lung cancer cell line NCI-H209 electroporated with control siRNAs (siNTC)

value: siNC


title: input sample of basal 7

description:
Sample name: MUC2030_C7_input
Processed data files:
pheno_data.csv
MUC2030.bw
average_RNA_control.bw
singlepeaks_C7.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of stress 6

description:
Sample name: MUC2029_S6_input
Processed data files:
pheno_data.csv
MUC2029.bw
average_RNA_stress.bw
singlepeaks_S6.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv

value: acute stress


title: input sample of stress 5

description:
Sample name: MUC2027_S5_input
Processed data files:
pheno_data.csv
MUC2027.bw
average_RNA_stress.bw
singlepeaks_S5.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of basal 6

description:
Sample name: MUC2028_C6_input
Processed data files:
pheno_data.csv
MUC2028.bw
average_RNA_control.bw
singlepeaks_C6.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: ST1 sgHBZ_1 - day 7 - mAdbID:129861

description: mAdb experiment ID: 129861

source_name: ST1 sgHBZ_1 - day 7


title: KK1 shBATF3_A2 - day 2 - repeat 2 - mAdbID:123414

description: mAdb experiment ID: 123414

source_name: KK1 shControl - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 2 days.

source_name: KK1 shBATF3_A2 - day 2

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shBATF3_A2 expression was induced with doxycycline for 2 days.


title: input sample of basal 5

description:
Sample name: MUC2026_C5_input
Processed data files:
pheno_data.csv
MUC2026.bw
average_RNA_control.bw
singlepeaks_C5.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of basal 4

description:
Sample name: MUC2024_C4_input
Processed data files:
pheno_data.csv
MUC2024.bw
average_RNA_control.bw
singlepeaks_C4.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: input sample of stress 4

description:
Sample name: MUC2025_S4_input
Processed data files:
pheno_data.csv
MUC2025.bw
average_RNA_stress.bw
singlepeaks_S4.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: ST1 shBATF3_bp360 - day 1 - mAdbID:123409

description: mAdb experiment ID: 123409

source_name: ST1 shControl - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 1 day.

source_name: ST1 shBATF3_bp360 - day 1

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shBATF3_bp360 expression was induced with doxycycline for 1 day.


title: KK1 shBATF3_A2 - day 2 - repeat 1 - mAdbID:123413

description: mAdb experiment ID: 123413


title: ST1 shBATF3_A2 - day 2 - mAdbID:123408

description: mAdb experiment ID: 123408

source_name: ST1 shControl - day 2

source_name: ST1 shBATF3_A2 - day 2


title: ST1 shIRF4 - day 2 - mAdbID:121928

description: mAdb experiment ID: 121928

source_name: ST1 shIRF4 - day 2

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shIRF4 expression was induced with doxycycline for 2 days.


title: ST1 shBATF3_A2 - day 1 - mAdbID:123407

description: mAdb experiment ID: 123407

source_name: ST1 shBATF3_A2 - day 1

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shBATF3_A2 expression was induced with doxycycline for 1 day.


title: input sample of stress 3

description:
Sample name: MUC2023_S3_input
Processed data files:
pheno_data.csv
MUC2023.bw
average_RNA_stress.bw
singlepeaks_S3.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv

treatment_protocol: Animals were treated with 15 min acute restraint stress and returned to their homecage (stress) or left in their homecage (basal) and sacrificed 4 h after.


title: input sample of basal 3

description:
Sample name: MUC2021_C3_input
Processed data files:
pheno_data.csv
MUC2021.bw
average_RNA_control.bw
singlepeaks_C3.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: genomic DNA from blood buffy coat of subject 46-CaF

type: genomic

city: Buffalo

first: Jie

last: Wang

state: NY

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

description: blood buffy coat sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip (HM450K) using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan Reader using standard recommended Illumina scanner setting.

data_processing: R package minfi was used to processed the raw data, All the data is normalized using stratified quantile normalization(preprocessQuantile). Several probe filtering criteria are applied, 1. Detection P-value bigger than 0.01 in at least one sample. 2. located in the sex chromosomes (X and Y) , 3. SNPs at the CpG sites. 4. non-specific probes detected by Chen et al. (PMCID: PMC3592906). The remaining probes were used to adjust the batch effect by ComBat.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: blood buffy coat of subject 46-CaF

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from blood buffy coat using FlexiGene DNA Kit (Qiagen, CA) following the manufacturer’s protocol.

tag: gender

value: female

tag: arsenic exposure

value: Yes

tag: disease status

value: skin leisons


title: genomic DNA from blood buffy coat of subject 43-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 43-CaM

value: male


title: ST1 shBATF3_bp360 - day 2 - mAdbID:123410

description: mAdb experiment ID: 123410

source_name: ST1 shBATF3_bp360 - day 2

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shBATF3_bp360 expression was induced with doxycycline for 2 days.


title: ST1 shIRF4 - day 1 - mAdbID:121927

description: mAdb experiment ID: 121927

source_name: ST1 shIRF4 - day 1

treatment_protocol:
Treatment type: coding sequence transduction
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shIRF4 expression was induced with doxycycline for 1 day.


title: input sample of stress 2

description:
Sample name: MUC2020_S2_input
Processed data files:
pheno_data.csv
MUC2020.bw
average_RNA_stress.bw
singlepeaks_S2.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv

source_name: C57BL/6 cortex


title: KK1 shIRF4 - day 1 - repeat 2 - mAdbID:119930

description: mAdb experiment ID: 119930

source_name: KK1 shIRF4 - day 1

source_name: KK1 shControl - day 1


title: input sample of basal 2

description:
Sample name: MUC2019_C2_input
Processed data files:
pheno_data.csv
MUC2019.bw
average_RNA_control.bw
singlepeaks_C2.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: KK1 shIRF4 - day 2 - repeat 2 - mAdbID:119931

description: mAdb experiment ID: 119931

source_name: KK1 shIRF4 - day 2


title: genomic DNA from blood buffy coat of subject 48-CaF

description: blood buffy coat sample

source_name: blood buffy coat of subject 48-CaF


title: genomic DNA from blood buffy coat of subject 50-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 50-CaM


title: genomic DNA from blood buffy coat of subject 35-CaF

description: blood buffy coat sample

source_name: blood buffy coat of subject 35-CaF


title: KK1 shIRF4 - day 1 - repeat 1 - mAdbID:118871

description: mAdb experiment ID: 118871


title: genomic DNA from blood buffy coat of subject 28-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 28-CaM


title: genomic DNA from blood buffy coat of subject 39-CaF

description: blood buffy coat sample

source_name: blood buffy coat of subject 39-CaF


title: genomic DNA from blood buffy coat of subject 44-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 44-CaM


title: input sample of stress 1

description:
Sample name: MUC2018_S1_input
Processed data files:
pheno_data.csv
MUC2018.bw
average_RNA_stress.bw
singlepeaks_S1.bed
grouppeaks_stress.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv


title: genomic DNA from blood buffy coat of subject 40-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 40-CaM


title: genomic DNA from blood buffy coat of subject 31-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 31-CaM


title: genomic DNA from blood buffy coat of subject 33-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 33-CaM


title: genomic DNA from blood buffy coat of subject 36-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 36-CaM


title: KK1 shIRF4 - day 2 - repeat 1 - mAdbID:118872

description: mAdb experiment ID: 118872

source_name: KK1 shControl - day 2


title: genomic DNA from blood buffy coat of subject 45-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 45-CaM


title: Ex3_CD138pos_GFPneg

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed and cDNA was used to generate biotinylated cRNA by in vitro transcription, which was finally fragmented, and 15 µg cRNA was hybridized to mouse genome 430 2.0 GeneChip arrays at 45 °C rotating for 16 h in a hybridization oven 645 (Affymetrix). Finally, arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix hybridization, wash and stain Kit and GeneChip Fluidics Workstation FS450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner GCS3000 7G, using the GCOS software from Affymetrix.

data_processing: CHP and CEL files were generated at the DRFZ with GeneChip Operating System (GCOS, Affymetrix). CEL files were analyzed at INRA, France (Luc Jouneau and Pierre Boudinot). Only chips, which fulfilled all chip and hybridization quality criteria, were selected for analysis. Normalization has been performed using R package GCRMA. To detect which probe sets were expressed in a given sample and to get Present/Marginal/Absent calls mas5calls function of affy R package was used. Differential expression was detected using limma R package.

source_name: IL-10(neg) plasmocytes from Salmonella infected mice

growth_protocol: IL-10eGFP mice (C57BL/6 background, female) were challenged intravenously with Salmonella typhymurium (strain SL7207, 10e7 CFU). Mice were sacrificed on the next day, and spleens were harvested.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including on-column DNase I digestion to remove remaining genomic DNA (Qiagen). The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Single cell suspensions were prepared, and cells were stained with antibody against CD138 conjugated to PE (1/400; from BD Pharmingen) followed by incubation with anti-PE microbeads (Miltenyi Biotech). CD138+ were then enriched on Automacs using the program possel_d2. Cells were then stained with anti-CD19-PerCP, anti-CD138-PE, and antibodies against CD11b, CD11c, and TCRb conjugated to APC as a bin channel to eliminate possible contaminants. DAPI was added to exclude dead cells. IL-10eGFP+CD138hi and IL-10eGFP-CD138hi cells were subsequently isolated on a cell sorter. The purity of the samples was always above 98-99%.

tag: strain background

tag: genotype/variation

tag: challenged with

value: S. typhymurium SL7207

value: spleen

tag: cell type

value: CD138hi plasmocytes

tag: sorted fraction


title: input sample of basal 1

description:
Sample name: MUC2017_C1_input
Processed data files:
pheno_data.csv
MUC2017.bw
average_RNA_control.bw
singlepeaks_C1.bed
grouppeaks_control.bed
finalpeaks_consensus_all_peaks.bed
finalpeaks_differential.bed
finalpeaks_m6Am.bed
RNA_counts.csv
RNA_quantification.csv

source_name: C57BL/6 cortex

tag: strain

value: cortex

tag: rip antibody


title: genomic DNA from blood buffy coat of subject 37-CaF

description: blood buffy coat sample

source_name: blood buffy coat of subject 37-CaF


title: genomic DNA from blood buffy coat of subject 200-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 200-F

value: normal


title: Ex2_CD138pos_GFPneg

label_protocol: GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction

tag: tissue


title: genomic DNA from blood buffy coat of subject 29-CaF

description: blood buffy coat sample

source_name: blood buffy coat of subject 29-CaF


title: genomic DNA from blood buffy coat of subject 34-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 34-CaM


title: F1_Testis_chlordecone_H3K4me3_ChIPseq_R2

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

institute: Université de Rennes 1

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10/Ensembl using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2. The H3K4me3 mark peaks were identified using MACS 2.1.1.20160309 (Feng et al. 2012) with two biological replicate samples, including input from F1, shift-size window 73 bp, no model, with p-value threshold <10E−5. The number of mapped reads was multiplied by a scale factor to normalize the total number of reads in different samples. To compare the H3K4me3 CHIP datasets of CD-treated and control samples, differential peak calling was performed using several steps. First, we kept only peaks with average values above the 50th quantile; second, we selected the peaks with fold changes above 1.5 or 2 and FDR <10 %. Statistical significance was calculated using a Limma test (Ritchie et al. 2015). The results were visualized in the Integrative genomics viewer IGV version 2.4.2 (Thorvaldsdottir et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files

source_name: testes

extract_protocol: The testes from F1 generations were taken for anti-H3K4me3 ChIP-seq as previously described (Gely-Pernot et al, 2015).  Two biological replicates used for each condition. We hypothesize that chlordecone cause changes in H3K4me3 due to transgenerational effect of pesticides (Skinner et al, Science 2005).

treatment_protocol: We treated adult female mice with chlordecone with doses 0 (control) and 100 µg/kg/day during gestation period E6.5- E15.5. Male born from Chlordecone-treated mice were crossed for three generations. The testes from F1 generations were taken for anti-H3K4me3 ChIP-seq

tag: chip antibody

value: Rabbit anti-H3K4me3 (Millipore 07-473)

value: testes

tag: agent

value: chlordecone


title: genomic DNA from blood buffy coat of subject 108-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 108-GM

value: No


title: genomic DNA from blood buffy coat of subject 42-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 42-CaM


title: genomic DNA from blood buffy coat of subject 200-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 200-GM


title: F1_Testis_chlordecone_H3K4me3_ChIPseq_R1


title: F1_Testis_Control_H3K4me3_ChIPseq_R2


title: genomic DNA from blood buffy coat of subject 200-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 200-GF


title: Ex3_CD138pos_GFPpos

source_name: IL-10(pos) plasmocytes from Salmonella infected mice


title: F1_Testis_Control_H3K4me3_ChIPseq_R1


title: Ex1_CD138pos_GFPneg


title: genomic DNA from blood buffy coat of subject 108-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 108-D


title: genomic DNA from blood buffy coat of subject 27-CaM

description: blood buffy coat sample

source_name: blood buffy coat of subject 27-CaM


title: ZFP521 KO LSK2

city: Denver

first: James

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

data_processing:
Adapters were trimmed, low quality bases, and reads <30bp were removed using ea-utils v1.05.
Reads were mapped to the genome using Tophat2 v2.1.1 using reference genome UCSC mm10.
Mapped reads with MAPQ<10 were removed using samtools v1.5, and coordinates were sorted using Picard Tools v2.9.4.
Genes were quantified using htseq v0.8.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text (gzipped); counts per sample and gene (output of htseq-count)

source_name: Bone marrow hematopoietic stem cells

growth_protocol: BM was harvested from Zfp521-/- mice and Ctrl littermates and Linneg cKit+ Sca1+ “LSK” cells were FACS purified.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit. Total RNA was isolated using RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
Libraries were constructed from 20 ng total RNA using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Carlos, CA). Libraries were subsequently subjected to 76 cycles of NextSeq 500 sequencing (Illumina, San Diego, CA).

value: Lin-neg, Sca1-pos, cKit-pos bone marrow progenitors

tag: genotype

value: Zfp521 knockout


title: ZFP521 KO LSK1


title: genomic DNA from blood buffy coat of subject 200-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 200-D


title: F3_Testis_Input_DNA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
About 200 millions tags were derived from anti-H3K4me3 ChIP and input. The resulting sequences were mapped back to the mouse mm10/ Ensembl genome using Bowtie 2. Only tags that passed the quality filter and mapped uniquely to the genome were used.  The H3K4me3 mark peaks were identified using MACS 2.1.0 (Feng et al. 2012) with two biological replicate samples, including corresponding input, shift-size window 73 bp, no model, with p-value threshold <10E−5. The number of mapped reads was multiplied by a scale factor to normalize the total number of reads in different samples. To compare the H3K4me3 CHIP datasets of Chlordecone-treated and control samples, differential peak calling was performed using several steps. First,  we kept only peaks with average values above the 50th quantile; second, we selected the peaks with fold changes above 1.5 or 2 and FDR <10 %. Statistical significance was calculated using a Limma test (Ritchie et al. 2015). The results were visualized in the Integrative genomics viewer IGV version 2.3.36 (Thorvaldsdottir et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files

growth_protocol: We treated adult female mice with chlordecone with doses 0 (control),  100 µg/kg/day and 1 mg/kg/day during gestation period E6- E15. Male born from Chlordecone- treated mice were crossed for a three generations. The testes from F3 generations were taken for mRNA extraction. For mRNA extraction we used column. Three biological replicates used for each condition . We hypothesize that chlordecone cause changes in mRNA due to transgenerational effect of pesticides (Skinner et al, Science 2005).


title: Ex2_CD138pos_GFPpos


title: Ex1_CD138pos_GFPpos


title: F3_Testis_chlordecone_H3K4me3_ChIPseq_R2


title: Ctrl LSK2

value: Wild type


title: F3_Testis_chlordecone_H3K4me3_ChIPseq_R1


title: genomic DNA from blood buffy coat of subject 108-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 108-GF


title: Ctrl LSK1


title: F3_Testis_Control_H3K4me3_ChIPseq_R2


title: Hamster_GV_oocyte_br2_reanalyzed

city: Zagreb

first: Vedran

last: Franke

address: Horvatovac 102a

department: Department of biology

country: Croatia

institute: University of Zagreb

data_processing:
Reads were Mapped to the mm10/mesAur1 genome versions using the STAR aligner. Coverage tracks were constructed using UCSC tools
Genome_build: mm10, mesAur1
Supplementary_files_format_and_content: bigWig files were generated in a non stranded mode using UCSC tools. The tracks are not normalized for library size

growth_protocol: Oocytes and early embryos were obtained from superovulated mice as described previously (Nagy, 2003).   Resumption of meiosis during culture of GV oocytes was prevented with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX, Sigma). Animal experiments were approved by the Institutional Animal Use and Care Committees and were carried out in accordance with the European Union regulations.

extract_protocol:
Total RNA was extracted from triplicates of 25 wild type or knock-out GV oocytes, MII eggs or 1-cell zygotes   using a PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instructions (Thermo Fisher Scientific, Philadelphia, PA). Each sample was spiked in with 0.2 pg of synthesized Renilla luciferase mRNA before extraction as a normalization control.
Non-stranded RNAseq libraries were constructed using the Ovation RNA-seq system V2 (NuGEN, San Carlos, CA) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN, San Carlos, CA). RNAseq libraries were pooled and sequenced by 125 bp paired-end reading using the Illumina HiSeq at the High Throughput Genomics Core Facility at University of Utah, Salt Lake City, UT.

value: WT

value: oocyte

tag: developmental stage

value: GV


title: genomic DNA from blood buffy coat of subject 108-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 108-F


title: F3_Testis_Control_H3K4me3_ChIPseq_R1


title: genomic DNA from blood buffy coat of subject 106-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 106-GF


title: genomic DNA from blood buffy coat of subject 106-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 106-F


title: Hamster_GV_oocyte_br1_reanalyzed


title: genomic DNA from blood buffy coat of subject 106-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 106-S


title: Mouse_1cell_embryo_br3_reanalyzed

value: zygote


title: genomic DNA from blood buffy coat of subject 064-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 064-GM

value: female

value: Yes


title: Mouse_1cell_embryo_br2_reanalyzed


title: Mouse_1cell_embryo_br1_reanalyzed


title: genomic DNA from blood buffy coat of subject 066-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 066-GM


title: genomic DNA from blood buffy coat of subject 106-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 106-GM


title: genomic DNA from blood buffy coat of subject 066-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 066-F

value: male


title: genomic DNA from blood buffy coat of subject 066-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 066-D


title: Mouse_MII_oocyte_br3_reanalyzed

value: MII


title: genomic DNA from blood buffy coat of subject 064-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 064-F


title: genomic DNA from blood buffy coat of subject 063-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 063-GF


title: genomic DNA from blood buffy coat of subject 064-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 064-GF


title: genomic DNA from blood buffy coat of subject 066-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 066-GF


title: Mouse_MII_oocyte_br1_reanalyzed


title: genomic DNA from blood buffy coat of subject 059-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 059-S


title: genomic DNA from blood buffy coat of subject 061-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 061-F


title: genomic DNA from blood buffy coat of subject 063-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 063-F


title: genomic DNA from blood buffy coat of subject 063-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 063-GM


title: genomic DNA from blood buffy coat of subject 064-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 064-D


title: genomic DNA from blood buffy coat of subject 061-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 061-D


title: Mouse_MII_oocyte_br2_reanalyzed


title: genomic DNA from blood buffy coat of subject 063-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 063-S


title: Mouse_GV_oocyte_br1_reanalyzed


title: Mouse_GV_oocyte_br2_reanalyzed


title: Mouse_1cell_embryo_KO_br3


title: NS-SV-DCmiRNA

city: Tokushima

first: noriko

last: mizusawa

address: 3-18-15 Kuramoto-cho

department: Department of Medical Pharmacology

country: Japan

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

hyb_protocol: Samples were resuspended in 18µl of RNAse free water and prepared for hybridization by adding 4.5µl of 10X GE Blocking agent and 22.5µl of 2X Hi-RPM Hybridization Buffer. After heat denature (100˚C, 5min), immediately on ice, and the hybridization was performed at 55˚C for 20h and at a constant speed rotation.

scan_protocol: Agilent DNA Microarray Scanner (G2505C),(Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.5.1.1 (Agilent).

source_name: NS-SV-DC

label_protocol: 100µg of total RNA were dephosphorylated using Calf Instestine Alkaline Phosphatase(37˚C 30 min). Single molecules of Cyanine 3-pCp provided were ligated to the 3' end of the dephosphorylated RNA molecules (16˚C 2 h). Labeled RNAs were dried down using a speed-vacuum concentrator.

extract_protocol: Total RNA was extracted from NS-SV-AC and NS-SV-DC cells using a mirVana PARIS kit (Ambion, Austin, TX, USA).  Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: NS-SV-AC and NS-SV-DC cells were cultured at 37°C in SFKM (Gibco BRL, Grand Island, NY, USA) in an incubator with an atmosphere containing 5% CO2.

value: submandibular gland (duct-like) cell line

tag: cell line

value: NS-SV-DC


title: genomic DNA from blood buffy coat of subject 057-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 057-S

value: normal


title: genomic DNA from blood buffy coat of subject 058-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 058-GF


title: genomic DNA from blood buffy coat of subject 058-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 058-GM


title: genomic DNA from blood buffy coat of subject 058B-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 058B-F


title: Mouse_1cell_embryo_KO_br2


title: genomic DNA from blood buffy coat of subject 058B-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 058B-GF


title: 7C: JEKO1-IB-6H

city: Cambridge

first: Sabah

last: Kadri

state: Massachusetts

address: 7 Cambridge Center

department: Computational Biology

institute: Broad institute

data_processing:
Quality (QC) of the sequencing data was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the transcriptome using STAR
Transcript abundance was estimated using Cufflinks
Differentially expressed genes between DMSO and drug-treated conditions were identified using DESeq2
Gene Set Enrichment Analysis (GSEA, Version 2.2.2) was used to identify significant pathways associated with the differentially expressed genes
Gene sets enriched in B-cell malignancies were derived from the gene expression database of the Staudt laboratory  (http://lymphochip.nih.gov/signaturedb/index.html)
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance counts

source_name: B cell lymphoma cell line

growth_protocol: All lines were cultured in PRMI 1640 medium supplemented with 10% Fetal Bovine Serum and 100 µg/mL penicillin/streptomycin. Cells were maintained in a humidified 37oC/5% CO2 incubator.

extract_protocol:
Total RNA was isolated using RNA mini kit (QIAGEN, Maryland, US) following manufacturer’s instructions. All samples were quantified with QubitTM RNA assay (Life technology, Carlsbad, CA) and quality was assessed using Agilent Bioanalyzer (Santa Clara, CA).
Library preparations were performed using TruSeq Stranded RNA Sample Preparation kit (Illumina, San Diego, CA). The quality of the library was assessed using D1K ScreenTapes on Agilent TapeStation (Santa Clara, CA) and quantity was assessed by Taqman® qPCR assay directed to the adaptors. Each library was single-end sequenced with read length of 50 bp on Illumina Hi-Seq 2500 at a depth of 30 million reads.  QC metrics were calculated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the transcriptome using STAR and transcript abundance was estimated using Cufflinks. Differentially expressed genes between DMSO and drug-treated conditions were identified using DESeq2.

treatment_protocol: JeKo-1 and MAVER-1 were treated with ibrutinib and selienxor for 6 hr.

value: B cell lymphoma cell line


title: genomic DNA from blood buffy coat of subject 058B-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 058B-S


title: genomic DNA from blood buffy coat of subject 057-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 057-GF


title: genomic DNA from blood buffy coat of subject 057-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 057-GM


title: Mouse_GV_oocyte_br3_reanalyzed


title: Mouse_1cell_embryo_KO_br1


title: 7B: JEKO1-IB-6H


title: genomic DNA from blood buffy coat of subject 061-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 061-GF


title: genomic DNA from blood buffy coat of subject 059-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 059-F


title: genomic DNA from blood buffy coat of subject 057-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 057-F


title: genomic DNA from blood buffy coat of subject 058-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 058-F


title: genomic DNA from blood buffy coat of subject 049-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 049-GM


title: genomic DNA from blood buffy coat of subject 049-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 049-F


title: Mouse_MII_oocyte_KO_br2


title: 6C: MAVER-PU-6H

value: MAVER


title: genomic DNA from blood buffy coat of subject 058-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 058-S

value: No


title: genomic DNA from blood buffy coat of subject 059-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 059-GM


title: ZDF + Vehicle - Sample 6

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

data_processing:
All reads ≥16nts in length were aligned to the rat genome (Rnor5.0) by Bowtie1(v1.1.2)[30] allowing one mismatch. DEseq2 (v1.18.1)[31] was used to  identify significant (p<0.05) differentially (absolute fold change >1.5) expressed liver miRNAs.
miRNAs that were detected in the sequencing experiment are reported in the processed data file (401 miRNAs). miRNA were considered "detectable" and included in the analysis is 50% of sample had > 5 reads (median 5 reads).
Genome_build: Rnor5.0
Supplementary_files_format_and_content: .csv file includes RPKM values for each Sample

organism: Rattus norvegicus

source_name: ZDF + Vehicle, liver

extract_protocol:
livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Norgen Total RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ZDF-Leprfa/Crl

value: Liver

tag: age

tag: phenotype

value: Obese

value: Vehicle


title: ZDF + Vehicle - Sample 5


title: genomic DNA from blood buffy coat of subject 056-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 056-D

tag: gender

tag: arsenic exposure


title: 7-A: JEKO1-IB-6H


title: Mouse_MII_oocyte_KO_br1

value: oocyte


title: genomic DNA from blood buffy coat of subject 056-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 056-GF

tag: disease status


title: Mouse_MII_oocyte_KO_br3


title: NS-SV-ACmiRNA

source_name: NS-SV-AC

value: submandibular gland (acinar-like) cell line

value: NS-SV-AC


title: genomic DNA from blood buffy coat of subject 049-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 049-GF


title: genomic DNA from blood buffy coat of subject 026-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 026-S


title: genomic DNA from blood buffy coat of subject 026-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 026-GM

value: female


title: genomic DNA from blood buffy coat of subject 049-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 049-D

value: Yes


title: 6B: MAVER-PU-6H

source_name: B cell lymphoma cell line


title: Mouse_GV_oocyte_KO_br3

value: GV


title: genomic DNA from blood buffy coat of subject 056-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 056-F

value: male


title: 6A: MAVER-PU-6H


title: genomic DNA from blood buffy coat of subject 056-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 056-GM


title: Mouse_GV_oocyte_KO_br1


title: 5C: MAVER-KPT-6H


title: 5B: MAVER-KPT-6H


title: genomic DNA from blood buffy coat of subject 026-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 026-GF


title: genomic DNA from blood buffy coat of subject 026-M

description: blood buffy coat sample

source_name: blood buffy coat of subject 026-M


title: ko3

city: Cincinnati

first: Jose

last: Cancelas

state: OH

address: 3333 Burnet Ave, ML 7013

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and using TopHat/Cufflinks pipeline to align, and Cufflinks as Expression Counter, FPKM-per gene as final output
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include FPKM values for each Sample ...

source_name: p190-BCR-ABL+ leukemic B-cell precursors

extract_protocol:
Total RNA from sorted purified p190-BCR-ABL+ B cell  precursors of leukemic WT (n = 3 samples) mice  or Klf5Δ/Δ (n = 3 samples) mice was isolated (RNeasy  Micro Kit, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ZDF + Vehicle - Sample 1


title: genomic DNA from blood buffy coat of subject 025-M

description: blood buffy coat sample

source_name: blood buffy coat of subject 025-M


title: 5A: MAVER-KPT-6H


title: Mouse_GV_oocyte_KO_br2


title: Lean - Sample 6

source_name: Lean, liver

value: Lean


title: ko2

value: p190-BCR-ABL+ leukemic B-cell precursors


title: ZDF + Vehicle - Sample 3


title: 4C: MAVER-IB-6H


title: Lean - Sample 5


title: ko1


title: genomic DNA from blood buffy coat of subject 025-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 025-S

value: normal


title: ZDF + Vehicle - Sample 2

source_name: ZDF + Vehicle, liver


title: genomic DNA from blood buffy coat of subject 025-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 025-GM


title: Lean - Sample 4


title: 4B: MAVER-IB-6H

value: B cell lymphoma cell line


title: genomic DNA from blood buffy coat of subject 025-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 025-GF


title: 4A: MAVER-IB-6H

value: MAVER


title: Lean - Sample 3


title: Lean - Sample 2


title: 3C: MAVER-DMSO-6H


title: wt3

value: WT


title: wt2


title: wt1


title: genomic DNA from blood buffy coat of subject 024-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 024-GF


title: 3B: MAVER-DMSO-6H


title: Lean - Sample 1

value: ZDF-Leprfa/Crl


title: 3A: MAVER-DMSO-6H


title: ZDF + Colesevelam - Sample 6

source_name: ZDF + Colesevelam, liver

value: Liver

value: Colesevelam


title: 2C: JEKO1-DMSO-6H


title: ZDF + Colesevelam - Sample 5

value: Obese


title: ZDF + Colesevelam - Sample 4


title: genomic DNA from blood buffy coat of subject 024-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 024-F


title: 2B: JEKO1-DMSO-6H


title: genomic DNA from blood buffy coat of subject 024-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 024-GM


title: 2A: JEKO1-DMSO-6H


title: ZDF + Colesevelam - Sample 3


title: ZDF + Colesevelam - Sample 2


title: UCLA4 Naïve t2iLGoY

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Preprocessing: 10bp were trimmed from the beginning of each read to remove possible adapter contamination
Alignment: Reads were aligned using Bsmap with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent*1000

source_name: UCLA4 Naïve t2iLGoY

growth_protocol: Conventional human primed ESCs (WIBR3 cell line, DPE-OCT4GFP, UCLA1, UCLA3, UCLA4, UCLA5, UCLA9 and UCLA17 cell lines) were maintained on Matrigel (Corning) coated dishes in E8-medium (Stem Cell Technologies) and passaged using Versene solution (Life Technologies). For maintenance, cells were passaged every 4-5 days. Established naïve hESC lines were cultured on irradiated CF-1 MEFs (2.5x106 cells per 9.5 cm2) in 4i/LA medium with the indicated concentration of PD0325901 and passaged every 6-7 days. Cells were feeded daily with fresh medium. 5i/LAF medium contained a 50:50 mixture of DMEM/F-12 (Life Technologies) and Neurobasal medium (Life Technologies) containing 1x N2 supplement (Life Technologies), 1x B27 supplement (Life Technologies), 10 ng/mL bFGF (Peprotech), 1% nonessential amino acids (Life Technologies), 1mM GlutaMAX (Life Technologies), penicillin-streptomycin (Life Technologies), 0.1 mM beta-mercaptoethanol (Life Technologies), 50 μg/mL BSA (Life Technologies), 0.5 μM IM-12 (Axon Medchem), 0.5 μM SB590885 (Axon Medchem), 1 μM WH-4-023 (Axon Medchem), 10 μM Y-27632 (Axon Medchem), 20 ng/mL Activin A (Peprotech), 20 ng/mL rhLIF (Peprotech), 0.5% KSR (Life Technologies) and 0.5 or 1 μM PD0325901 (Axon Medchem)

extract_protocol:
DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) and quantified using the Qubit dsDNA High Sensitivity Kit (Life Technologies).
Libraries were created using the Nugen Ovation bisulfite kit.

treatment_protocol: Cells were harvested following acutase treatment and processed for DNA extraction

value: human embryonic stem cells

value: naive hESCs


title: T0_S1

city: Montpellier

last: Blondin

address: 2 place Pierre Viala

description:
T0_S1
Gene expression in sample from EC1118 strain, biological rep 1, at 0 min time point.

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the microarray hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using R 3.1.1 software and the limma package. Normalization was done by the quantile method considering all arrays.

organism: Saccharomyces cerevisiae EC1118

source_name: T0 repetition 1

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: The cells were grown in a medium containing 200 g/l glucose, 100 mg/l of assimilable nitrogen (amino acids and ammonium) at 24°C.

extract_protocol: Total RNA extraction was performed with Trizol reagent, and purified with RNeasy kit (Qiagen).

treatment_protocol: 10^9 cells were harvested by filtration and frozen at -80°C.

tag: growth condition

value: nitrogen starvation

tag: treatment

tag: time point (min)

tag: array

tag: block


title: T15_S2

description:
T15_S2
Gene expression in sample from EC1118 strain, biological rep 2, at 15 min time point.

source_name: T15 repetition 2

value: diammonium phosphate (DAP) addition


title: UCLA4 Naïve Cobimetinib 0.5mM

source_name: UCLA4 Naïve Cobimetinib 0.5mM

tag: cell type


title: ZDF + Colesevelam - Sample 1

tag: strain

tag: tissue


title: UCLA4 Naïve Refametinib 0.5mM

source_name: UCLA4 Naïve Refametinib 0.5mM


title: ZDF + Vehicle - Sample 4

tag: agent

value: Vehicle


title: Long-library_GFP+ rep2

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

data_processing:
library strategy: tAD-seq
Sequence were trimmed: Y-linker and UMI sequences was removed from the second (reverse) read
Reads were mapped using bowtie version 0.12.9 (options -v 3 -m 1 --best –strata –X 2000)
Mapped reads were collapsed by coordinates and by UMI, and then separated into six different reading frames
Mapped reads from two replicates were merged for downstream analysis
Coverage in each reading frame was calculated by using bedtools genomeCoverageBed
For each fragment were calculated enrichment between GFP- and GFP+ cells to detect tADs (for more details see methods in the paper)
Genome_build: Selected 180TF together with flanking backbone sequences (2100nt at each side) were used to create custom bowtie index (TFbb_list180_linear)
Supplementary_files_format_and_content:
custom genome file in twoBit format (TFbb_list180_linear.2bit), submitted as TFbb_list180_linear.fa.
TF coordinate in bigBed format  (TFbb_list180_linear_anno.bigbed)
coverage files for each sample and each frame in bigWig format

organism: Drosophila melanogaster

source_name: Fragmented cDNA from TF CDS

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Medium (Gibco; cat. no. 21720-024) supplemented with 10% heat inactivated FBS (Sigma; cat. no. F7524)

extract_protocol:
GFP+ cells were mixed with 3x10^6 un-transfected S2 cells to increase the mRNA recovery of GFP+ cells. Total RNA was isolated using Qiagen RNeasy Maxi or Mini prep kits for GFP-and positive cells, respectively. PolyA+ RNA purification was performed using Invitrogen Dynabeads Oligo-dT25 (cat. no. 610-05) followed by Ambion TurboDNase (cat. no. AM2239) treatment according to manufacturers’ protocols, also described previously in Arnold et al. Science 2013. TurboDNAse treated RNA was cleaned up using Qiagen RNeasy MinElute reaction clean up kit (cat. no. 74204) according to the manufacture’s protocol. First strand cDNA synthesis was performed with 1µl of Invitrogen’s SuperscriptIII (50°C for 60 min, 70°C for 15min; cat. no. 18080085) using a reporter-RNA specific primer (agttccttggcacccgagaattccaNNNNNNNNNNCGTGTGCTCTTCCGATCT) for 1-5µg of polyA+ RNA in 20µl total volume.
We amplified the total amount of Gal4-DBD-candidate cDNA obtained from reverse transcription for Illumina sequencing by a 2-step nested PCR strategy using the KAPA Hifi Hot Start Ready Mix (KAPA Biosystems; cat. no. KK2602). In the first PCR (98°C for 45s; followed by 15 cycles of 98°C for 15s, 65°C for 30s, 72°C for 70s), cDNA was amplified using 2 Gal4-candidate-specific primers (AAGCCACCATGGAAAAG*G*C*C*A*T & AGTTCCTTGGCACCCGAGAA*T*T*C), one of which spans the splice junction of the mhc16 intron (5 and 3 nucleotides at the 3’ends are protected by phosphorothioate bonds, respectively), in a total of 10 reactions. This specifically amplifies the Gal4-DBD-candidate cDNAs and suppresses residual plasmid background. PCR products were purified by Agencourt AMPureXP DNA beads (ratio beads/PCR 0.9) and eluted in 20µl EB. The entire purified PCR product from each reaction served as template for the second PCR (98°C for 45s; followed by 8-12 cycles of 98°C for 15s, 65°C for 30s, 72°C for 15s) with the KAPA Hifi Hot Start Ready Mix using the following primers: aatgatacggcgaccaccgagatctacacXXXXXXXXacactctttccctacacgacgctcttccgatct (XXXXXXXX indicates the position of the index sequence for NGS)  and caagcagaagacggcatacgagatGTCGTGATgtgactggagttccttggcacccgagaattcca, which adds the overhangs that are required for flow cell hybridization and cluster generation prior to Illumina sequencing. PCR products were purified by Agencourt AMPureXP DNA beads (ratio beads/PCR 1.4), pooled and subjected to NGS (Illumina MiSeq platform).

value: Scheider's S2 cells


title: T15_S3

description:
T15_S3
Gene expression in sample from EC1118 strain, biological rep 3, at 15 min time point.

source_name: T15 repetition 3


title: UCLA4 Naïve TAK-733 0.5mM

source_name: UCLA4 Naïve TAK-733 0.5mM


title: T15_S1

description:
T15_S1
Gene expression in sample from EC1118 strain, biological rep 1, at 15 min time point.

source_name: T15 repetition 1


title: Long-library_GFP+ rep1


title: genomic DNA from blood buffy coat of subject 024-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 024-S

value: male

value: Yes


title: genomic DNA from blood buffy coat of subject 020-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 020-F

value: No


title: genomic DNA from blood buffy coat of subject 022-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 022-D

value: female

value: normal


title: genomic DNA from blood buffy coat of subject 019-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 019-GM


title: UCLA5 Naïve PD03 0.5mM

source_name: UCLA5 Naïve PD03 0.5mM


title: UCLA9 Naïve PD03 1mM

source_name: UCLA9 Naïve PD03 1mM


title: T45_S2

description:
T45_S2
Gene expression in sample from EC1118 strain, biological rep 2, at 45 min time point.

source_name: T45 repetition 2


title: T60_S3

description:
T60_S3
Gene expression in sample from EC1118 strain, biological rep 3, at 60 min time point.

source_name: T60 repetition 3


title: Short-library_GFP+ rep2


title: T0_S3

description:
T0_S3
Gene expression in sample from EC1118 strain, biological rep 3, at 0 min time point.

source_name: T0 repetition 3


title: UCLA9 Naïve PD03 0.5mM

source_name: UCLA9 Naïve PD03 0.5mM


title: genomic DNA from blood buffy coat of subject 020-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 020-D


title: Long-library_GFP- rep1


title: genomic DNA from blood buffy coat of subject 020-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 020-GM


title: T45_S3

description:
T45_S3
Gene expression in sample from EC1118 strain, biological rep 3, at 45 min time point.

source_name: T45 repetition 3


title: UCLA5 Naïve PD03 1mM

source_name: UCLA5 Naïve PD03 1mM


title: genomic DNA from blood buffy coat of subject 019-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 019-D


title: genomic DNA from blood buffy coat of subject 017-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 017-GM


title: genomic DNA from blood buffy coat of subject 019-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 019-GF


title: Short-library_GFP+ rep1

source_name: Fragmented cDNA from TF CDS


title: Short-library_GFP- rep2


title: UCLA4 Naïve PD03 0.5mM

source_name: UCLA4 Naïve PD03 0.5mM


title: UCLA4 Naïve PD03 1mM

source_name: UCLA4 Naïve PD03 1mM


title: genomic DNA from blood buffy coat of subject 017B-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 017B-S


title: genomic DNA from blood buffy coat of subject 017B-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 017B-GM


title: T60_S2

description:
T60_S2
Gene expression in sample from EC1118 strain, biological rep 2, at 60 min time point.

source_name: T60 repetition 2


title: Short-library_GFP- rep1


title: UCLA1 Naïve PD03 0.5mM

source_name: UCLA1 Naïve PD03 0.5mM


title: genomic DNA from blood buffy coat of subject 019-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 019-F


title: genomic DNA from blood buffy coat of subject 017-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 017-D


title: T30_S1

description:
T30_S1
Gene expression in sample from EC1118 strain, biological rep 1, at 30 min time point.

source_name: T30 repetition 1


title: genomic DNA from blood buffy coat of subject 017-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 017-GF


title: T45_S1

description:
T45_S1
Gene expression in sample from EC1118 strain, biological rep 1, at 45 min time point.

source_name: T45 repetition 1


title: genomic DNA from blood buffy coat of subject 017-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 017-F


title: UCLA1 Naïve PD03 1mM

source_name: UCLA1 Naïve PD03 1mM


title: miR994

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

description: mRNA

data_processing:
A genome index was built for the latest build of the D. melanogaster genome (dm6) using STAR v. 2.4 (options --runMode genomeGenerate --genomeFastaFiles dm6.fa --sjdbGTFfile dmel-all-r6.07.gff --sjdbOverhang 40 --sjdbGTFtagExonParentTranscript Parent) (Dobin et al. 2013), with “dmel-all-r6.07.gff” referring to fly transcript models annotated in FlyBase release 6.07, processed to have a single “Parent ID/exon” combination per line.
Raw reads were aligned to this genome index with STAR (options --outFilterType BySJout --outFilterMultimapScoreRange 0 --readMatesLengthsIn Equal --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --outSAMstrandField intronMotif --outStd SAM).
For each sample, expression level data (measured in Fragments Per Kilobase Million, or FPKM) was computed using cufflinks v. 2.1.1 (options --library-type fr-secondstrand -b dm6.fa -u --max-bundle-frags 100000000 --compatible-hits-norm) (Trapnell et al., 2010), using fly transcript models of protein-coding genes annotated in FlyBase v 6.07.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression measurements (FPKM) with lower and upper FPKM confidence intervals, one for each RNA-seq sample. Report was generated by cufflinks.

source_name: S2 cells

growth_protocol: Drosophila Schneider 2 (S2) cells were grown in Express Five serum-free media (GIBCO) supplemented with glutamine to 16 mM. Upon reaching confluency (every ~3-5 days), cells were passaged at a dilution of at least 1:15 following mechanical resuspension with a scraper. Prior to resuspension, the conditioned media containing suspended cells was aspirated off and replaced with an equal volume of fresh media in order to select for attached cells.

extract_protocol:
Cells were lysed in 1 ml TRI Reagent (Ambion). Following extraction from the lysate, total RNA was cleaned up using the RNeasy Mini kit (Qiagen) and subjected to polyA selection using oligo(dT) Dynabeads (Invitrogen) to isolate mRNA.
Strand-specific mRNA-Seq libraries for Illumina sequencing were prepared as described (Guo et al. 2010), with differences noted below. Briefly, polyA-selected RNA was hydrolyzed in alkaline buffer, resulting in fragments bearing 5'-hydroxyl and 3'-phosphate groups. Fragments between 36-55 nt were size selected and end-specific adapters were sequentially ligated onto each terminus; prior to each ligation step, the appropriate 3' or 5' end chemistry was generated through dephosphorylation or phosphorylation, respectively. Adapter-flanked fragments were reverse transcribed and the resulting cDNA PCR-amplified for 19 cycles using primers complementary to each adapter. The PCR products were purified on a denaturing formamide gel and submitted for deep sequencing.

treatment_protocol: Twenty-four hours prior to transfection, cells were seeded into 6-well plates at 2.5 x 10^6 per well (in 2 ml media). Each well was co-transfected with 2.5 µg plasmid (25% p2032-GFP, 75% pUC19) plus 25 nM miRNA duplex (or for mock transfections, with plasmid only) using 5 µl DharmaFECT Duo (Dharmacon). Equal volumes of nucleic acid and DharmaFECT Duo diluted in 1X PBS were combined and incubated at room temperature for 20 minutes to form transfection complexes that were then added dropwise to the cells (500 µl/well). Twenty-four hours after transfection, cells were harvested, resuspended in 1X PBS, passed through a 70 µm filter, and stained with 5 µg/ml propidium iodide (PI). For each transfection, 3-5 x 10^6 GFP-positive and PI-negative cells were isolated by FACS.

tag: transfection


title: S2 cell 3p-seq

description:
3P-seq of mRNA
Poly(A)-Position Profiling by Sequencing (3P-Seq)

data_processing:
Reads were mapped to the Drosophila genome using bowtie, filtering for those that contain at least 2 terminal Adenosines
Genome_build: dm6
Supplementary_files_format_and_content: BED file containing the read counts corresponding to the uniquely mapped positions of 3' tags.

source_name: S2 cell 3p-seq

extract_protocol:
3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html
3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html

value: Schneider 2 (S2) cells


title: T0_S2

description:
T0_S2
Gene expression in sample from EC1118 strain, biological rep 2, at 0 min time point.

source_name: T0 repetition 2


title: genomic DNA from blood buffy coat of subject 017B-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 017B-F


title: WIBR3 Naïve PD03 0.5mM

source_name: WIBR3 Naïve PD03 0.5mM


title: miR263a

description: mRNA


title: T30_S3

description:
T30_S3
Gene expression in sample from EC1118 strain, biological rep 3, at 30 min time point.

source_name: T30 repetition 3


title: WIBR3 Naïve PD03 1mM

source_name: WIBR3 Naïve PD03 1mM


title: miR124

description: mRNA


title: genomic DNA from blood buffy coat of subject 017B-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 017B-GF


title: T30_S2

description:
T30_S2
Gene expression in sample from EC1118 strain, biological rep 2, at 30 min time point.

source_name: T30 repetition 2


title: UCLA9 Primed

source_name: UCLA9 Primed

value: primed hESCs


title: miR92a

description: mRNA


title: genomic DNA from blood buffy coat of subject 016-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 016-GF


title: genomic DNA from blood buffy coat of subject 016-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 016-GM


title: miR4

description: mRNA


title: UCLA5 Primed

source_name: UCLA5 Primed


title: UCLA4 Primed

source_name: UCLA4 Primed


title: T60_S1

description:
T60_S1
Gene expression in sample from EC1118 strain, biological rep 1, at 60 min time point.

source_name: T60 repetition 1


title: mock transfection, rep 3

description: mRNA

value: mock


title: miR1

description: mRNA


title: Long-library_GFP- rep2

source_name: Fragmented cDNA from TF CDS


title: mock transfection, rep 2

description: mRNA


title: genomic DNA from blood buffy coat of subject 016-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 016-D


title: genomic DNA from blood buffy coat of subject 013-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 013-GM


title: WIBR3 Primed

source_name: WIBR3 Primed


title: UCLA1 Primed

source_name: UCLA1 Primed


title: mock transfection, rep 1

description: mRNA

source_name: S2 cells


title: genomic DNA from blood buffy coat of subject 013-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 013-F


title: genomic DNA from blood buffy coat of subject 013-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 013-D


title: Eff_IV_Kpos_rep3_A9431

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan-SQ

data_processing: Raw data filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio, cutoff is 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

source_name: CD4+Foxp3-CD44hi cells sorted from lung

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

growth_protocol: Six to twelve week old male and female C57BL/6[TgH]EGFP:Foxp3 mice were obtained through a supply contract between the NIAID/NIH and Taconic Farms

extract_protocol: The RNA was isolated using the Direct-zol RNA kit (Zymoresearch, Irvine, CA) following manufacturer’s instructions

treatment_protocol: For mouse Mtb infections, animals were exposed to ~100 CFU of Mtb H37Rv strain using an aerosol inhalation exposure system (Glas-Col, LLC, Terre Haute, IN).  Dose calculations were measured by serial dilutions of lung homogenates on 7H11 agar plates supplemented with oleic acid-albumin-dextrose-catalase (Difco, Detroit, MI) immediately post exposure. Effector CD4 T cells were isolated from the lungs of Mtb infected Foxp3-EGFP mice on day 28 post-infection after administration of anti-CD45 at 2μg per mouse by intravenous injection 3 minutes prior to euthanasia.  The lungs were harvested, minced, placed into RPMI containing 1 mg/ml Collagenase D (Roche-Diagnostics, Indianapolis, IN), 1 mg/ml hyaluronidase, 50 U/ml DNase I and 1 mM aminoguanidine (all from Sigma-Aldrich, St. Louis, MO), and incubated at 37°C for 45 minutes with shaking.  The lungs were passed through a 100μm cell strainer, and washed with PBS containing 20% fetal bovine serum (FBS).  The lymphocytes were isolated by centrifugation through a density gradient of 37% Percoll from GE Healthcare Bio-Sciences (Uppsala, Sweden).  The red blood cells were lysed with ACK lysis buffer (KD Medical, Columbia MD), and the cells were counted.  The cells were stained with anti-CD4 (1:100), CD44 (1:100), and KLRG1 (1:100) for 30 minutes at 4°C, and then washed twice with PBS + 1% FBS. The cells were stained with a viability dye Fixable Viability Dye eFluor 780 from eBioscience Inc. (San Diego, CA) for 20 minutes at 4°C, and then washed twice with PBS + 1% FBS.  The cells were gated on live CD4+Foxp3-CD44hi cells were sorted into four populations: KLRG1-ivCD45dim, KLRG1-ivCD45+, KLRG1+ivCD45dim, and KLRG1+ivCD45+ on a BD Aria sorter (double check the sorter in 1E08).   The cells were collected in PBS + 1% FBS, and centrifuged.  The cell pellets were lysed in Trizol, and stored at -80°C until RNA isolation.  This was repeated for five independent experiments, pooling the lungs of 15 to 25 mice for each sort.

tag: sort fraction

value: effector

tag: pulmonary compartment

value: intravascular

tag: klrg1 marker

tag: experimental replicate


title: Nve_PA_Kneg_rep4_A9439

value: naive

value: parchyma


title: Eff_PA_Kneg_rep3_A9432


title: Eff_IV_Kneg_rep3_A9433


title: Eff_IV_Kneg_rep4_A9438


title: Eff_PA_Kpos_rep4_A9435


title: Eff_PA_Kneg_rep2_A9427


title: genomic DNA from blood buffy coat of subject 016-M

description: blood buffy coat sample

source_name: blood buffy coat of subject 016-M

tag: gender


title: genomic DNA from blood buffy coat of subject 008-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 008-GM

tag: arsenic exposure


title: CLP-24h-8 (exosomal RNA)

city: Baltimore

first: Lin

last: Zou

address: 20 Penn Street, HSF II-GS003C

department: Anesthesiology

institute: University of Maryland School Of Medicine

hyb_protocol: For each sample, FirePlex Particles (35 μl) are added to a well of 96-well flitler plate and fitlered. Three additional wells for no-sample controls are also prepared. Next, 25  μl of Hybridization Buffer is added to each well followed by 25  μl sample. The plate is incubated at 37oC for 60 minutes while shaking at 750 rpm

scan_protocol: Particles are scanned on an EMD Milipore Guava 8HT or 6HT flow cytometter

data_processing:
The flow cytometer output was analyzed with the FirePlexTM Analysis Wrokbench software, avaialble on the Abcam website at www.abcam.com/FireflyAnalysisSoftware, and R.
[normalization method applied to the signal intensity data]:
A geNorm-like algorithm is applied to the data in order to select the three most appropriate miRNAs for normalization in the experiment. To improve the likelihood of identifying three appropriate normalization candidates, several miRNA targets identified by others [Chen et al] and by Abcam in an independent analysis are automatically included in the fixed panels. The miRNAs selected for normalization of the current samples are: hsa-let-7i-5p, hsa-mir-20a-5p, hsa-miR-29a-3p.
Chen X., Liang H., Guan D., Wang C., Hu X., et al. (2013) A Combination of Let-7d, Let-7g and Let-7i Serves as a Stable Reference for Normalization of Serum microRNAs. PLoS ONE 8(11): e79652.

label: Fireplex

source_name: plasma exosome

label_protocol: Oligonucleotide adapters are ligated to each end of the hybridized miRNA to serve as PCR priming sites. Labelled miRNAs are dehybridized from particles and undergo one-step RT-PCR with a biotinlyated primer.

extract_protocol: Exosome was purfied from plasam via ultracentrifuge. RNA was extracted for plasma exosome using miRNeasy Micro Kit (Qiagen)

tag: genotype

value: WT

tag: disease state

value: cecal ligation and puncture (CLP) model of sepsis

tag: rna source

value: plasma exosome

value: Male

tag: time

value: 24 hours post-surgery


title: Eff_IV_Kpos_rep2_A9426


title: genomic DNA from blood buffy coat of subject 008-GF

description: blood buffy coat sample

data_processing: R package minfi was used to processed the raw data, All the data is normalized using stratified quantile normalization(preprocessQuantile). Several probe filtering criteria are applied, 1. Detection P-value bigger than 0.01 in at least one sample. 2. located in the sex chromosomes (X and Y) , 3. SNPs at the CpG sites. 4. non-specific probes detected by Chen et al. (PMCID: PMC3592906). The remaining probes were used to adjust the batch effect by ComBat.

source_name: blood buffy coat of subject 008-GF

value: male

tag: disease status


title: genomic DNA from blood buffy coat of subject 013-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 013-GF


title: CLP-24h-5 (exosomal RNA)


title: Solvent + TNFa

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description:
Test
Female+male (50%-50%)
SAMPLE 2

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For normalization, the average of five housekeeping genes (Gusb, Hprt, Hsp90ab1, Gapdh, Actb) were used.
Target gene signals normalized to housekeeping genes; 2^-delta CT, where delta CT = (Ct Target − Ct HKG)]
The web-based software package automatically performs all delta delta Ct based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change data file reports test/control (i.e., Solvent/OGG1 inhibitor/TNFa challenge) ratios.

label: SYBR Green

source_name: Lung lysate

label_protocol: PCR assays were performed using the Mouse Inflammatory Cytokines & Receptors PCR array PAMM-011Z (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the Superscript® III First Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Solvent, OGG1 inhibitor (30 mg per kg) was administered intra-peritoneally, challenge of lungs was performed by administration of TNFa via  intranasal route.

value: Balbc J

value: lung

tag: age

value: 8 weeks

tag: Sex

value: pooled male and female


title: CLP-24h-7 (exosomal RNA)

tag: strain


title: genomic DNA from blood buffy coat of subject 008-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 008-F

extract_protocol: Genomic DNA was extracted from blood buffy coat using FlexiGene DNA Kit (Qiagen, CA) following the manufacturer’s protocol.

value: Yes

value: normal


title: Eff_IV_Kneg_rep1_A9423

city: Bethesda


title: Eff_PA_Kneg_rep1_A9422


title: SRV-0010

city: Lexington

first: Varun

last: Dwaraka

address: 741 South Limestone St.

institute: University of Kentucky

description:
RSEM processed, expected count values, found in column 7 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt

data_processing:
De novo assembly of RNA-Seq isotigs was accomplished using Trinity’s three-stage protocol (Inchworm, Chrysalis, and Butterfly).
RSEM was used for count estimation with default parameters
Expected counts were extracted in a matrix file format from the RSEM output.

organism: Ambystoma maculatum

source_name: mid-zeugopod whole tissue

extract_protocol:
Mid-zeugopod amputations were conducted on all animals. Exactly 1mm distal most tissue was collected immediately after amputation (0hpa) and 24 hpa. Whole RNA tissue was extracted using the TruSeq RNA library prep kit from Illumina.
HudsonAlpha Institute for Biotechnology generated the RNA-Seq data by preparing cDNA libraries and sequencing approximately 50,000,000 100 bp read pairs per sample.

tag: tissue

value: mid-zeugopod

tag: time post amputation (hpa)

tag: size of tissue collection


title: genomic DNA from blood buffy coat of subject 008-D

city: Buffalo

last: Wang

address: Elm and Carlton Streets

description: blood buffy coat sample

source_name: blood buffy coat of subject 008-D

value: female


title: CLP-24h-4 (exosomal RNA)


title: CLP-24h-6 (exosomal RNA)


title: genomic DNA from blood buffy coat of subject 006-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 006-GF


title: Eff_PA_Kpos_rep3_A9430

tag: sort fraction

value: effector


title: genomic DNA from blood buffy coat of subject 006-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 006-GM


title: Eff_IV_Kneg_rep5_A9443

tag: pulmonary compartment

value: intravascular


title: CLP-24h-3 (exosomal RNA)


title: Nve_IV_Kneg_pool A_A9445

value: naive

tag: klrg1 marker

value: pool A


title: genomic DNA from blood buffy coat of subject 003-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 003-S


title: Nve_IV_Kneg_pool B_A9446

tag: experimental replicate

value: pool B


title: genomic DNA from blood buffy coat of subject 003-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 003-F

tag: gender


title: genomic DNA from blood buffy coat of subject 005-S

description: blood buffy coat sample

source_name: blood buffy coat of subject 005-S

tag: arsenic exposure


title: SRV-0008

description:
RSEM processed, expected count values, found in column 5 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt


title: genomic DNA from blood buffy coat of subject 005-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 005-GF


title: CLP-24h-2 (exosomal RNA)

tag: genotype

value: WT

value: cecal ligation and puncture (CLP) model of sepsis

value: plasma exosome


title: SRV-0006

description:
RSEM processed, expected count values, found in column 3 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt


title: genomic DNA from blood buffy coat of subject 005-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 005-GM


title: SRV-0009

description:
RSEM processed, expected count values, found in column 6 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt


title: Nve_PA_Kneg_rep5_A9444

source_name: CD4+Foxp3-CD44hi cells sorted from lung

value: parchyma


title: genomic DNA from blood buffy coat of subject 006-D

description: blood buffy coat sample

source_name: blood buffy coat of subject 006-D


title: CLP-24h-1 (exosomal RNA)

tag: disease state

value: Male

value: 24 hours post-surgery


title: sham-24h-5 (exosomal RNA)

value: control

tag: rna source


title: Nve_PA_Kneg_rep1_A9424


title: genomic DNA from blood buffy coat of subject 003-GF

description: blood buffy coat sample

source_name: blood buffy coat of subject 003-GF

value: male


title: sham-24h-4 (exosomal RNA)

source_name: plasma exosome

tag: time


title: SRV-0005

description:
RSEM processed, expected count values, found in column 2 of processed data file
AMAC_RNASEQ_EXPCOUNT.txt


title: Eff_PA_Kneg_rep5_A9442


title: genomic DNA from blood buffy coat of subject 006-F

description: blood buffy coat sample

source_name: blood buffy coat of subject 006-F

value: Yes

tag: disease status


title: genomic DNA from blood buffy coat of subject 003-GM

description: blood buffy coat sample

source_name: blood buffy coat of subject 003-GM

value: normal


title: sham-24h-2 (exosomal RNA)


title: sham-24h-3 (exosomal RNA)

data_processing:
The flow cytometer output was analyzed with the FirePlexTM Analysis Wrokbench software, avaialble on the Abcam website at www.abcam.com/FireflyAnalysisSoftware, and R.
[normalization method applied to the signal intensity data]:
A geNorm-like algorithm is applied to the data in order to select the three most appropriate miRNAs for normalization in the experiment. To improve the likelihood of identifying three appropriate normalization candidates, several miRNA targets identified by others [Chen et al] and by Abcam in an independent analysis are automatically included in the fixed panels. The miRNAs selected for normalization of the current samples are: hsa-let-7i-5p, hsa-mir-20a-5p, hsa-miR-29a-3p.


title: Eff_PA_Kpos_rep5_A9440


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 206 F2]

city: Athens

first: Mandi

last: Murph

state: GA

address: 250 West Green Street, Room 312

department: Pharmaceutical & Biomedical Sciences

institute: University of Georgia

description:
Tumor 206 F2
Experimental Group 2

data_processing:
Normalization of raw Ct values from qRT-PCR was performed using Exiqon's recommended software, GenEx, according to instructions provided: http://www.biomcc.com/genex-download.html
Both plates (total of ~750 microRNAs and spike in microRNA controls) were calibrated to each other. Experimental groups with greater than 50% missing data were removed from analysis, as were any microRNAs that were considered outliers within their experimental groups, resulting in 373 microRNAs for further analysis.
All data was normalized to miR-16-5p, a microRNA widely regarded as a control microRNA, and also to the Wildtype group which was considered the control group.
Data was automatically calculated by software to result in relative ratios of experimental groups with respect to the control groups and all data was graphed using GraphPad Prism for publication purposes.

source_name: Transgenic AT-ATX mouse (with tumor) serum

label_protocol: cDNA was used to perform quantitative real-time PCR using SYBR Green and Exiqon's ExiLENT SYBR Green Master Mix and Exiqon's Ready-to-use Serum microRNA PCR Panels I and II plates. PCR was run for 40 cycles.

extract_protocol:
Blood was collected from mice upon necropsy and centrifuged at 4000rpm for 3 minutes prior to serum collection.
50uL serum was used to extract total RNA using Exiqon's RNA Isolation Kit, and cDNA was subsequently made with total RNA using the Exiqon Universal cDNA Synthesis Kit II.

value: Serum

tag: genotype/variation

value: Transgenic AT-ATX

value: Spontaneous tumor(s)


title: Eff_IV_Kpos_rep5_A9441

value: effector

value: intravascular


title: Eff_PA_Kneg_rep4_A9437


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 99 F4]

description:
Tumor 99 F4
Experimental Group 2


title: genomic DNA from blood buffy coat of subject 005-F

first: Jie

institute: Roswell Park Comprehensive Cancer Center

description: blood buffy coat sample

source_name: blood buffy coat of subject 005-F


title: Vehicle (solvent)

description:
Control
Female+male (50%-50%)
SAMPLE 1

source_name: Lung lysate

value: Balbc J

value: lung

tag: age

value: 8 weeks

tag: Sex

value: pooled male and female


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 88F?]

description:
Tumor 88F?
Experimental Group 2

tag: tissue


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 77 F2]

description:
Tumor 77 F2
Experimental Group 2


title: Transgenic AT-ATX mouse; spontaneous tumor(s) [Tumor 85 F1]

description:
Tumor 85 F1
Experimental Group 2