title: endometrium OXB treated vs non-treated 3

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

country: Poland

institute: University of Warmia and Mazury

hyb_protocol: Two differentially labelled samples (from OXB treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers's protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with OXB.

organism: Sus scrofa domesticus

source_name: endometrium non-treated

label_protocol: The RNA isolated from the control and OXB treated tissues were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Four mature gilts (Large White x Polish Landrace) were used in the study (n = 4). All individuals were descended from private breeding farm. The gilts were at the age of 7-8 months and the weight of 120 to 130 kg. All animals used in the study were on days 15 to 16 of gestation. The day after coitus was marked as the first day of gestation. Insemination was performed on days 1 to 2 of the oestrous cycle. Pregnancy was confirmed by the presence of conceptuses. 15 to 16 days after coition, gilts were sacrificed. Pigs were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was extracted from tissues using peqGOLD TriFast isolation system according to the manufacturer’s instructions. RNA purity and quantity were measured spectrophotometrically . RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score between 8 and 10 were used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

treatment_protocol: The endometrial explants obtained from the middle of uterine horns were cut into small, irregular slices (3 mm of thickness, 100 mg ± 10%). Tissue explants were washed three times in medium M199. The tissue explants were placed in the separate sterile culture vials with 2 mL medium 199 containing. Cultures were preincubated for 2 h (37°C, 95% O2, 5% CO2). To determine the influence of OXB on the global gene expression in the endometrium, slices were treated with OXB  at the concentration of 10 nM and incubated for another 24 h at the same conditions. Control tissues were incubated without any treatment. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). The endometrial tissue explants were frozen and stored at -80°C for further analyses.

value: non-treated

tag: period of pregnancy

value: days 15 to 16

tag: race

value: Large White x Polish Landrace

tag: gilts age and weight

value: mature/7-8 months/120 to 130 kg

source_name: endometrium OXB-treated

value: endometrium OXB-treated


title: endometrium OXB treated vs non-treated 4

status: Public on Nov 14 2018

type: RNA

molecule: total RNA

tag: treatment


title: SNF053_D0_batch3

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

hyb_protocol: Labelled cRNAs were hybridized to Illumina human HT-12 V4.0 chips for 16 hours at 58°C in batches of 96 samples. The arrays were then washed and stained base on Illumina Wash Protocol.

scan_protocol: The human chips were scanned using BeadArray Scanner 500GX and the images were analyzed using Illumina GenomeStudio Gene Expression v 2011.1.

data_processing: Illumina Genome Studio was used to export the data in raw format. Raw expression data was loaded into R/Bioconductor and normalized using log2 quantile normalization method of the lumi R package.

label: Biotin

organism: Homo sapiens

source_name: PBMC Day 0 pre-vaccination

label_protocol: Biotinylated cRNA was prepared according to the Illumina® Ambion TotalPrep™ 96 RNA Amplification kit (Thermo Fisher Scientific, San Jose, CA, USA) using 300ng of RNA.

growth_protocol: No growth protocol was used. PBMCs isolated from whole blood were directly processed for RNA isolation.

extract_protocol: PBMCs were isolated from whole blood. 1 million PBMCs were washed with 1 mL of PBS and centrifuged. The supernatant was removed. The cell pellet was loosened and lysed in mirVana Lysis/Binding buffer and stored in -80degC before extraction. Total RNA was isolated from PBMCs using mirVana™ miRNA isolation kit (Thermo Fisher Scientific, San Jose, CA, USA). Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: No treatment of PBMCs was performed.

tag: cell type

value: PBMC

tag: time point

value: Day 0

tag: subject id

tag: age (years)

tag: gender

value: Female

tag: ethnicity

value: Chinese

tag: microarray batch


title: SNF054_D0_batch6


title: SNF054_D2_batch6

source_name: PBMC Day 2 post-vaccination

value: Vaxigrip influenza vaccine

value: Day 2


title: endometrium OXB treated vs non-treated 2


title: Sample_3_OCILy3_DMSO_8h_repl3

type: SRA

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: CPM

source_name: OCI-Ly3 cell line

extract_protocol: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

treatment_protocol: Included as additional column of SAMPLES section

value: treated with DMSO for 8h

tag: cell line

value: OCI-Ly3 cell line


title: SNF052_D28_batch8

source_name: PBMC Day 28 post-vaccination

value: Day 28


title: SNF053_D2_batch3


title: endometrium OXB treated vs non-treated 1


title: SNF053_D7_batch3

source_name: PBMC Day 7 post-vaccination

value: Day 7


title: SNF053_D28_batch3


title: OXB treated vs non-treated 4

source_name: myometrium non-treated

treatment_protocol: The myometrial explants obtained from the middle of uterine horns were cut into small, irregular slices (3 mm of thickness, 100 mg ± 10%). Tissue explants were washed three times in medium M199. The tissue explants were placed in the separate sterile culture vials with 2 mL medium 199 containing. Cultures were preincubated for 2 h (37°C, 95% O2, 5% CO2). To determine the influence of OXB on the global gene expression in the myometrium, slices were treated with OXB  at the concentration of 10 nM and incubated for another 24 h at the same conditions. Control tissues were incubated without any treatment. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). The myometrial tissue explants were frozen and stored at -80°C for further analyses.

source_name: myometrium OXB-treated

value: myometrium OXB-treated


title: Sample_2_OCILy3_DMSO_8h_repl2


title: OXB treated vs non-treated 3


title: SNF052_D2_batch8


title: OXB treated vs non-treated 2


title: Sample_1_OCILy3_DMSO_8h_repl1


title: SNF052_D0_batch8


title: SNF051_D7_batch5


title: SNF051_D0_batch5


title: SNF051_D28_batch5


title: 85As2-3

city: Inashiki-gun

first: Kiyoshi

last: Terawaki

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

country: Japan

institute: Tsumura & Co.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >5.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole human Genome Array (4x44K) ver 2.0 (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as feature not positive and significant or feature is not above background were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color MicroArray-Based Gene Expression Analysis (Quick Amp Labeling Kit) . Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was purified with an RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: MKN45cl85 and 85As2 cells were cultured in a 10 cm dish until they were semi-confluent and then removed from the dish by exposure to 0.25% trypsin and 0.2% EDTA for a short time. After centrifugation, total RNA was extracted with an RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s extraction protocol. Three RNA samples from cells cultured on different days were prepared.

value: gastric cancer-derived cell line


title: 85As2-2


title: OXB treated vs non-treated 1

value: non-treated


title: SNF050_D7_batch5


title: SNF051_D2_batch5


title: adiponectin treated vs non-treated 4

hyb_protocol: Two differentially labelled samples (from adiponectin treated and non-treated, control samples) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 60°C. After the hybridization process, the microarrays were washed.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pigs that were and were not treated with adiponectin.

label_protocol: The RNA isolated from the control and adiponectin treated tissues were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader . 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

treatment_protocol: The endometrial explants obtained from the middle of uterine horns were cut into small, irregular slices (3 mm of thickness, 100 mg ± 10%). Tissue explants were washed three times in medium M199. The tissue explants were placed in the separate sterile culture vials with 2 mL medium 199. Cultures were preincubated for 2 h (37°C, 95% O2, 5% CO2). To determine the influence of adiponectin on the global gene expression in the endometrium, slices were treated with adiponectin  at the concentration of 10 µg/ml and incubated for another 24 h at the same conditions. Control tissues were incubated without any treatment. All cultures were prepared in duplicates in four separate experiments for each group (n = 4). The endometrial tissue explants were frozen and stored at -80°C for further analyses.

value: non-treatment

value: days 15 to 16

source_name: endometrium adiponectin-treated

value: adiponectin


title: SNF050_D28_batch5


title: SNF048_D28_batch2

value: Male


title: adiponectin treated vs non-treated 2

value: Large White x Polish Landrace

value: mature/7-8 months/120 to 130 kg


title: MKN45cl85-3


title: SNF050_D2_batch5

value: PBMC

value: Female


title: SNF052_D7_batch8

value: Vaxigrip influenza vaccine

value: Chinese


title: adiponectin treated vs non-treated 3


title: SNF046_D7_batch3


title: SNF048_D2_batch2

value: Day 2


title: adiponectin treated vs non-treated 1


title: SNF049_D28_batch3


title: SNF050_D0_batch5

value: Day 0


title: SNF049_D2_batch3


title: SNF049_D7_batch3


title: 85As2-1


title: SNF049_D0_batch3


title: SNF046_D0_batch3


title: SNF048_D7_batch2


title: SNF046_D2_batch3


title: SNF046_D28_batch3

value: Day 28


title: SNF048_D0_batch2


title: Tcast_2: Tribolium castaneum methylation 2

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

library_source: genomic

data_processing:
Base-calling, Tool: HCS 1.5.15.1
trimming, Tool: trimmomatic v0.32
mapping, Tool: bsseq 2.5
duplicate filtering, Tool: picard
determination of methylation ratio, Tool: python-script from bsseq package
Genome_build: assembly version 3.0 of the T. castaneum genome (https://www.hgsc.bcm.edu)
Supplementary_files_format_and_content: txt file, format: col1: chrom, col2: pos, col3: number of methylated C's in reads at this position, col4: coverage

molecule: genomic DNA

organism: Tribolium castaneum

source_name: eggs

extract_protocol:
Embryos were dechorionated in diluted sodium hypochlorite bleach, washed and then smashed in SDS buffer using an Eppendorf micropestle. After 30 min incubation at 65 °C and RNAse digestion, remaining RNAs were precipitated with LiCl/KAc. After centrifugation, the supernatant was taken and DNA was precipitated with isopropanol, washed in 70% ethanol and then resuspended in TE.
Per sample 5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. The fragmentation (parameters: duty cycle: 10 %; intensity: 5; cycles/burst: 200; cycles: 3) was run for a total fragmentation time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2 % precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95 °C for 15 s, 50 °C for 1 h, both steps repeated 15 times, 4 °C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and PE1.1 and PE2.1 amplification primers (Illumina). PCR thermal profile: 95 °C for 2 min, 95 °C for 30 s, 65 °C for 20 s, 72 °C for 30 s, then repeat from step 2, 11×, 72 °C for 7 min, hold at 4 °C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

tag: tissue

value: eggs


title: healthy_6

city: New Haven

first: Maria

last: Tokuyama

state: CT

address: 300 Cedar Street TAC S640

institute: Yale University

description: 150bp paired-end sequencing

data_processing:
Base-calling: Illumina HiSeq2500 or NextSeq software
Btrim to trim reads; BWA for alignment to hg38 for ERV analysis and TopHat2 for alignment for cellular gene analysis
Aligned reads for filtered based on ERVmap algorithm for ERV analysis
DEseq2 was used to calculate differential gene expression
See detailed methods in Tokuyama M. et al., PNAS 2018.
Genome_build: hg38
Supplementary_files_format_and_content: excel spreadsheet of normalized ERV counts and gene counts

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were obtained from whole blood using Ficoll-Paque and RNA was extracted using an RNeasy Mini Kit (Qiagen).
Illumina library preparation kit for polyA RNA

tag: disease

value: healthy


title: SLE_15

description: 150bp paired-end sequencing

value: Peripheral blood mononuclear cells (PBMCs)

value: systemic lupus erythematosus


title: healthy_4

description: 150bp paired-end sequencing


title: SLE_16

description: 150bp paired-end sequencing


title: Tcast_1: Tribolium castaneum methylation 1


title: healthy_5

description: 150bp paired-end sequencing


title: SLE_14

description: 150bp paired-end sequencing


title: healthy_3

description: 150bp paired-end sequencing


title: SLE_13

description: 150bp paired-end sequencing


title: healthy_2

description: 150bp paired-end sequencing


title: SNF045_D2_batch4


title: SNF045_D7_batch4

value: Day 7


title: SNF044_D7_batch2


title: Cultured dermal fibroblasts from young specimen (1227 2018)

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

organism: Mus musculus

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: RNA was isolated using magnetic beads from 5000 cells. Library preparation and cDNA amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 23 cycles.

tag: strain

tag: age

value: Young specimen

value: dermal fibroblasts

tag: sample type

value: Cultured


title: MKN45cl85-1

value: gastric cancer-derived cell line


title: SNF045_D0_batch4


title: Cultured dermal fibroblasts from old specimen (1228 2018)

value: Old specimen


title: MKN45cl85-2


title: SNF042_D7_batch5

value: PBMC


title: SLE_12

description: 150bp paired-end sequencing


title: Cultured dermal fibroblasts from young specimen (1229 2018)

value: Female


title: SNF044_D28_batch2

value: Vaxigrip influenza vaccine

value: Male


title: SNF045_D28_batch4

value: Chinese


title: Cultured dermal fibroblasts from old specimen (1225 2018)


title: Cultured dermal fibroblasts from old specimen (1226 2018)


title: healthy_1

description: 150bp paired-end sequencing


title: SNF042_D2_batch5

value: Day 2


title: SNF044_D2_batch2


title: SLE_11

description: 150bp paired-end sequencing


title: SNF044_D0_batch2

value: Day 0


title: SNF042_D28_batch5

value: Day 28


title: SLE_20

description: 150bp paired-end sequencing


title: SLE_10

description: 150bp paired-end sequencing


title: SLE_19

description: 150bp paired-end sequencing


title: SLE_18

description: 150bp paired-end sequencing


title: SLE_9

description: 150bp paired-end sequencing


title: SLE_8

description: 150bp paired-end sequencing


title: SLE_17

description: 150bp paired-end sequencing


title: SLE_7

description: 150bp paired-end sequencing


title: - ligase replicate 3

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

data_processing:
library strategy: RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem)
The files are processed as described in the github repository ChimeraTie
The source code of all scripts are provided in the github repository at https://github.com/dekkerlab/chimera-tie.
Transcriptome was created by mapping non-rRNA/snRNA mapping reads from a - ligase library to the GRCh37 genome using RSEM (bowtie2 and default parameters) (Li and Dewey, 2011); the highest abundance isoform was chosen as the single reference transcript for each gene.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab separated text files with pair-wise interactions

source_name: HEK293 - ligase

growth_protocol: Flp-In TRex-HEK293 cells containing a stable copy of FLAG-tagged Magoh routinely were grown in Dulbecco's modified eagle medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin. For generating each EJC (exon junction complex) RIPPLiT library, cells were grown in six 15-cm plates for immunoprecipitation.

extract_protocol:
Total cell extracts generated by sonication in a buffer containing 300 mM NaCl were used for EJC immunoprecipition.
SMARTer smRNASeq Kit (Clontech, 635030)

treatment_protocol: Expression of the FLAG-tagged protein was induced with tetracycline for ~16 hr. One hour prior to cell harvesting, Haringtonine was added to 2 ng/mL.

tag: cell line background

tag: genotype/variation

value: No ligase

tag: 1st ip

value: anti-FLAG (Sigma A2220)

tag: 2nd ip

value: anti-eIF4AAIII (Bethyl A302-980A)


title: SLE_6

description: 150bp paired-end sequencing

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)

value: systemic lupus erythematosus


title: SLE_5

description: 150bp paired-end sequencing


title: - ligase replicate 2

value: Flp-In TRex-HEK293 cells containing a stable copy of FLAG-tagged Magoh

tag: treatment


title: - ligase replicate 1


title: SLE_4

description: 150bp paired-end sequencing


title: + ligase replicate 3

source_name: HEK293 + ligase

value: + ligase (T4 Rnl 1, NEB M0204S)


title: Cultured dermal fibroblasts from old specimen (1223 2018)

value: dermal fibroblasts

value: Cultured


title: Cultured dermal fibroblasts from young specimen (1224 2018)

value: Young specimen


title: SLE_3

description: 150bp paired-end sequencing


title: SNF042_D0_batch5

value: PBMC

tag: time point

tag: subject id

value: Female


title: SNF040_D7_batch3

value: Vaxigrip influenza vaccine

value: Day 7

tag: age (years)

tag: gender


title: In vivo dermal fibroblasts from old specimen (1221 2018)

value: Old specimen

value: In vivo


title: Cultured dermal fibroblasts from young specimen (1222 2018)


title: + ligase replicate 2


title: SNF040_D28_batch3

value: Day 28

tag: ethnicity

value: Chinese

tag: microarray batch


title: In vivo dermal fibroblasts from young specimen (1220 2018)


title: SLE_2

description: 150bp paired-end sequencing


title: In vivo dermal fibroblasts from old specimen (1219 2018)


title: SNF040_D0_batch3

value: Day 0


title: In vivo dermal fibroblasts from young specimen (1216 2018)


title: In vivo dermal fibroblasts from young specimen (1218 2018)


title: In vivo dermal fibroblasts from old specimen (1217 2018)


title: SLE_1

description: 150bp paired-end sequencing


title: + ligase replicate 1

value: anti-FLAG (Sigma A2220)

value: anti-eIF4AAIII (Bethyl A302-980A)


title: SNF039_D7_batch2


title: SNF040_D2_batch3

value: Day 2


title: SNF039_D0_batch2


title: ICM64

city: Aurora

first: Mary

middle: E

last: Sweet

state: CO

department: Medicine

institute: University of Colorado Anschutz

data_processing:
Reads were filtered for quality and aligned to the GRchr37/hg19 version of the reference human genome using gSNAP with parameters: --max-mismatches=0.06 -i2 -n2 --force-xs-dir and tolerance to SNPs in dbSNP build 138
Expression in terms of RPKM (reads per kilobase of transcript per million reads mapped) was derived using Cufflinks and Ensembl’s GRch37.82 GTF.
Due to the high proportion of cardiac mRNA reads known to map to the mitochondria, mitochondrial genes were removed from the GTF file for a final set of 57,974 annotations.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene and sample

molecule: polyA RNA

source_name: left ventricle

extract_protocol:
Frozen tissue was placed in liquid nitrogen and broken up using mortar and pestle to obtain a piece approximately 2 x 2 x 2 mm in size, macroscopically free of fatty infiltration, fibrosis, and blood. Tissue was placed immediately in TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) and mechanically homogenized using an IKA T25 Ultra-Turaxx homogenizer. Tissue was homogenized for approximately 60 seconds, or until no visible chunks of tissue remained. RNA was extracted using the mirVana miRNA isolation kit (Thermo Fisher Scientific) enriched for total RNA isolation according to manufacturer’s instructions with the exception of replacing the Lysis/Binding Buffer with TRIzol. All samples were DNase treated using TURBO DNA-free Kit (Thermo Fisher Scientific). RNA was quantified at 260nm using a NanoDrop1000 (Thermo Fisher Scientific), and RNA integrity (RIN) was measured using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Assay (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN ≥ 7.0, and ranged from 7.0-9.3.
PolyA transcripts were isolated from 1µg total RNA using oligo-dT beads and the cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

treatment_protocol: Explanted failing hearts were collected from adult patients undergoing heart cardiac transplantation at the University of Colorado Hospital as part of the Division of Cardiology Cardiac Tissue Biobank. Non-failing samples were obtained from organ donors whose hearts could not be placed for transplantation due to size, ABO mismatch or other factors. Immediately on explantation, left ventricular free wall aliquots of approximately 1 gram and remote from tissue scarring or infarcted segments were immersed in liquid nitrogen, transported to the laboratory, and stored at -80°C.

tag: tissue

value: left ventricle

value: ischemic cardiomyopathy

tag: Sex

value: Male


title: ICM63

tag: disease


title: SNF039_D2_batch2


title: In vivo dermal fibroblasts from old specimen (1215 2018)

tag: strain

tag: age

value: dermal fibroblasts


title: ICM61


title: SNF039_D28_batch2


title: ICM59


title: dermal fibroblasts from young specimen (1335 2018)

source_name: dermal fibroblasts from young specimen

extract_protocol: The skin was dissected, the subdermis removed, the remaining tissue chopped and digested with Collagenase 1. Dermal fibroblasts that were negative for the lineage markers CD45, CD117, CD24, CD31 and EpCam and positive for the fibroblast marker Pdgfra and CD34 were FACS isolated. RNA was purified using magnetic beads from 5000 cells. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 21 cycles.

value: Young specimen


title: SNF038_D7_batch4

value: PBMC


title: ICM56


title: SNF038_D0_batch4

value: Female


title: dermal fibroblasts from young specimen (1333 2018)


title: SNF036_D28_batch1

value: Vaxigrip influenza vaccine


title: FB_RNA_rep4

city: Baltimore

first: Andy

last: McCallion

state: MD

address: 733 N Broadway, MRB 446

department: Institute of Genetic Medicine

institute: Johns Hopkins School of Medicine

data_processing:
Libraries were pooled and sequenced on Illumina’s HiSeq 2500 in Rapid Run mode with 2x100bp reads to an average depth of >90 million reads per library. Quality of sequencing was evaluated using FastQC. FASTQ files were aligned to mm9 using HISAT2 (v2.0.1-beta) with --dta specified. Aligned reads from individual samples were quantified against a reference transcriptome using the Rsubread package (v1.22.3) function “featureCounts” with the following options: isPairedEnd = TRUE, requireBothEndsMapped = TRUE, isGTFAnnotationFile = TRUE, useMetaFeature = TRUE. The GENCODE vM9 GTF was downloaded (date: March 30, 2016) and lifted over from the mm10 to the mm9 genome using CrossMap (v0.2.2) with default parameters. This was used for quantification, in which gene-level raw counts were converted to RPKM values and means for each region were calculated.
Supplementary_files_format_and_content: tab-delimited text file containing a matrix of FPKM expression estimates for each gene in each sample
Genome_build: mm9

source_name: E15.5 forebrain dopaminergic neurons

growth_protocol: Tg(Th-EGFP)DJ76Gsat mice (Th-EGFP) were generated by the GENSAT Project and purchased through the Mutant Mouse Resource and Research Centers Repository. Colony maintenance matings were between hemizygous male Th-EGFP mice and female Swiss Webster (SW) mice, obtained from Charles River Laboratories. This same mating scheme was used to establish timed matings, generating litters for assay; day on which vaginal plug is observed, E0.5.

extract_protocol:
Pooled brain regions were dissociated using the Papain Dissociation System (Worthington Biochemical Corporation). The tissue was dissociated in the papain solution for 30 minutes at 37°C, with gentle trituration every 10 minutes using a sterile Pasteur pipette. Following dissociation, cells were passed through a 40µm cell strainer into a 50mL conical, centrifuged for 5 minutes at 300g, resuspended in albumin-inhibitor solution containing DNase, applied to a discontinuous density gradient, and centrifuged for 6 minutes at 70g. The resulting cell pellet was resuspended in HBSS with Mg2+ and Ca2+ and submitted to FACS. Aliquots of 50,000 EGFP+ cells were sorted directly into 300µL HBSS with Mg2+ and Ca2+ with 10% FBS for ATAC-seq. Aliquots containing ≥50,000 EGFP+ cells were sorted into kit-provided lysis buffer for RNA-seq.
Total RNA was extracted using the Purelink RNA Micro Kit (Invitrogen). Following FACS isolation into kit-provided lysis buffer, samples were homogenized and RNA extraction proceeded using manufacturer’s recommendations. Total RNA integrity was determined using the RNA Pico Kit (Agilent). RNA samples were sent to the Sidney Kimmel Comprehensive Cancer Center Next Generation Sequencing Core at Johns Hopkins for library preparation, using the Ovation RNA-Seq System V2 (Nugen), and sequencing.

treatment_protocol: Pregnant SW mice were euthanized at E15.5 and the embryos were removed and immediately placed in chilled Eagle’s Minimum Essential Media (EMEM) on ice. Embryos were decapitated and brains were removed into Hank’s Balanced Salt Solution without Mg2+ and Ca2+ (HBSS w/o) on ice. Under a fluorescent microscope, EGFP+ brains were identified and microdissected to yield the desired forebrain (FB) and midbrain (MB) regions desired. Microdissected regions were placed in fresh HBSS w/o on ice, and pooled per litter for dissociation.

value: Tg(Th-EGFP)DJ76Gsat x Swiss Webster

value: Forebrain

value: Th-EGFP+ sorted dopaminergic neurons


title: ICM55


title: FB_RNA_rep3


title: dermal fibroblasts from old specimen (1336 2018)

source_name: dermal fibroblasts from old specimen

value: Old specimen


title: SNF038_D28_batch4

value: Day 28

value: Chinese


title: ICM54


title: dermal fibroblasts from old specimen (1334 2018)


title: SNF038_D2_batch4


title: FB_RNA_rep2


title: In vivo dermal fibroblasts from young specimen (1214 2018)

tag: sample type

value: In vivo


title: ICM58


title: SNF036_D7_batch1

value: Day 7


title: ICM53


title: SNF036_D2_batch1

value: Day 2


title: dermal fibroblasts from young specimen (1330 2018)


title: dermal fibroblasts from old specimen (1329 2018)


title: SNF035_D7_batch2


title: FB_RNA_rep1


title: ICM52

value: left ventricle


title: SNF035_D2_batch2


title: MB_RNA_rep4

source_name: E15.5 midbrain dopaminergic neurons

value: Midbrain


title: ICM50

value: ischemic cardiomyopathy

value: Male


title: dermal fibroblasts from ND - Young specimen [2082 2016]

extract_protocol: The skin was dissected, the subdermis removed, the remaining tissue chopped and digested with Collagenase 1. Dermal fibroblasts that were negative for the lineage markers CD45, CD117, CD24, CD31 and EpCam and positive for the fibroblast marker Pdgfra and CD34 were FACS isolated. RNA was purified using magnetic beads from 10,000 cells. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 20 cycles.

treatment_protocol: 9-months-old female mice were either fed a normal diet ad libitum for 9 months (ND group), a normal diet for 2 months followed by 30% caloric restriction for 7 months of (CR group), or a 30% caloric restriction for 7 months followed by a normal diet for 2 months (CR-ND group). Old mice were sacrificed at 18 months of age. Young mice (4-weeks-old) were fed ND ad libitum for 4 weeks. n=5 (biological replicates)

value: female

value: dermal fibroblasts

value: Young specimen

tag: diet

value: Normal Diet (ND)

tag: group

value: ND - Young


title: MB_RNA_rep3

value: Tg(Th-EGFP)DJ76Gsat x Swiss Webster


title: ICM49


title: ICM47


title: MB_RNA_rep2

value: Th-EGFP+ sorted dopaminergic neurons


title: MB_RNA_rep1


title: dermal fibroblasts from CR/ND - Old specimen [2080 2016]

value: Old specimen

value: Caloric Restricted diet followed by Normal Diet (CR/ND)

value: CR/ND - Old


title: dermal fibroblasts from young specimen (1328 2018)


title: dermal fibroblasts from ND - Old specimen [2079 2016]

value: ND - Old


title: SNF036_D0_batch1

source_name: PBMC Day 0 pre-vaccination

value: PBMC

value: Day 0

value: Female

value: Chinese


title: SNF035_D28_batch2

value: Vaxigrip influenza vaccine

value: Day 28


title: SNF035_D0_batch2


title: DCM78

value: left ventricle

value: dilated cardiomyopathy


title: MB_ATAC_rep2 (DeepSeq)

data_processing:
Individual ATAC-seq libraries were sequenced on the Illumina MiSeq to a minimum depth of 20 million, 2x75bp reads per library. A single MB ATAC-seq library was sequenced on the Illumina HiSeq in Rapid Run mode with 2x100bp reads, to a depth of ≥350 million paired-end reads. Quality of sequencing was evaluated using FastQC (v0.11.2; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to mm9 using Bowtie2 (v2.2.5), under --local mode. Reads aligning to the mitochondrial genome, unknown and random chromosomes, and PCR duplicates were removed prior to peak calling (SAMtools). Peaks were called on individual libraries and on a concatenated file combining all MB and all FB libraries (“Joint”) using MACS2 (v2.1.1.20160309) “callpeak” with options: --nomodel --nolambda -B -f BAMPE --gsize mm --keep-dup all.
Supplementary_files_format_and_content: tab-delimited text file containing the peak calls from MACS2
Genome_build: mm9

extract_protocol:
Pooled brain regions were dissociated using the Papain Dissociation System (Worthington Biochemical Corporation). The tissue was dissociated in the papain solution for 30 minutes at 37°C, with gentle trituration every 10 minutes using a sterile Pasteur pipette. Following dissociation, cells were passed through a 40µm cell strainer into a 50mL conical, centrifuged for 5 minutes at 300g, resuspended in albumin-inhibitor solution containing DNase, applied to a discontinuous density gradient, and centrifuged for 6 minutes at 70g. The resulting cell pellet was resuspended in HBSS with Mg2+ and Ca2+ and submitted to FACS. Aliquots of 50,000 EGFP+ cells were sorted directly into 300µL HBSS with Mg2+ and Ca2+ with 10% FBS for ATAC-seq. Aliquots containing ≥50,000 EGFP+ cells were sorted into kit-provided lysis buffer for RNA-seq.
ATAC-seq library preparation generally follows the steps as set out in the original ATAC-seq paper with minor modifications. Aliquots of 50,000 EGFP+ cells were centrifuged for 5 minutes at 4°C and 500g, washed with 50µL of chilled PBS and centrifuged again for 5 minutes at 4°C and 500g. The cell pellet was resuspended in lysis buffer, as set out in the protocol, and cells were left to lyse for 5 minutes at 4°C before being centrifuged for 10 minutes at 4°C at 500g. The resulting nuclei pellet was transposed, as written, using the transposase from the Nextera DNA Library Preparation Kit. Following transposition, DNA was purified with the MinElute Reaction Clean-up Kit (Qiagen) and eluted in 10µL elution buffer. Libraries were amplified according to the original ATAC-seq protocol. The qPCR surveillance steps were modified such that the additional number of cycles of amplification were calculated as ¼ maximum intensity, so as to limit PCR duplication rates in the final libraries. Amplified libraries were purified with Ampure XP beads (Beckman Coulter) following the Nextera DNA Library Prep Protocol Guide. Libraries were quantified using the Qubit dsDNA High Sensitivity Assay (Invitrogen) in combination with the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Assay (Agilent).

value: Midbrain


title: SNF033_D28_batch2

value: Male


title: SNF033_D7_batch2

value: Day 7


title: DCM76


title: Six3;Six6 DKO Retina Rep2

city: BRONX

first: Wei

last: Liu

address: 1300 Morris Park Avenue

department: Ophthalmology

institute: Albert Einstein College of Medicine

data_processing:
After trimming adapters with Trim Galore (v. 0.3.7), RNA-Seq reads were aligned back to mouse genome mm10 using Tophat (v. 2.0.13).
The number of reads mapped back to each gene was calculated with HTseq (v.0.6.1)  using Refseq gene annotation (downloaded from the UCSC genome browser in 03/17).
The Cuffdiff in Cufflinks package (v. 2.2.1) was used to generate FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Embryonic Retina

extract_protocol:
Six3F/F; Six6+/– dams crossed with Six3F/F; CAGGCre-ERTM; Six6+/– male mice were intraperitoneally injected with Tamoxifen (0.15 mL of 20 mg/mL stock solution in corn oil per mice) at E10.5 (approximately 2pm) and E11.5 (approximately 9 am). Retinas from E13.5 embryos (noon) were dissected out in ice-cold PBS, rinsed, and stored overnight at 4 °C. After RNAlater was removed, the samples were stored at -80 °C until purification.   The retinas with the following genotypes were used for RNA isolation using the RNeasy Micro Kit (Qiagen) after genotyping: 1) WT (Six3F/F; Six6+/+), 2) Six3 KO (Six3F/F; CAGGCre-ERTM; Six6+/+), 3) Six6 KO (Six3F/F; Six6–/–), 4) DKO (Six3F/F; CAGGCre-ERTM; Six6–/–). The retinas were homogenized with an electric pellet pestle motor in 500uL of Qiazol and treated with RNase-free DNase set (Qiagen). Total RNA was eluted in 14uL of RNase-free water. The quantity and quality of RNA were verified using Qubit fluorometer (Thermo Fisher Scientific) and Bioanalyzer (Agilent Genomics), respectively.
RNA libraries were prepared for sequencing using KAPA RNA HyperPrep Kit with RiboErase

tag: developmental stage

value: Retina

value: NMRI

tag: genotype/variation


title: DCM74


title: dermal fibroblasts from CR/ND - Old specimen [2078 2016]

value: female

value: dermal fibroblasts

value: Old specimen


title: DCM77


title: Six3;Six6 DKO Retina Rep3


title: SNF033_D2_batch2

source_name: PBMC Day 2 post-vaccination

tag: cell type

tag: treatment

value: Day 2


title: Six6KO Retina Rep2


title: dermal fibroblasts from ND/CR - Old specimen [2076 2016]

value: Normal Diet followed by Caloric Restricted diet (ND/CR)

value: ND/CR - Old


title: Six6KO Retina Rep1


title: DCM73


title: SNF033_D0_batch2

value: PBMC

tag: time point

value: Day 0

tag: subject id


title: SNF032_D7_batch2

value: Vaxigrip influenza vaccine

tag: age (years)

tag: gender

value: Chinese


title: dermal fibroblasts from ND - Old specimen [2077 2016]

value: Normal Diet (ND)

value: ND - Old


title: SNF032_D2_batch2

tag: ethnicity

tag: microarray batch


title: DCM72

tag: tissue

value: left ventricle

value: dilated cardiomyopathy

tag: Sex


title: dermal fibroblasts from ND - Young specimen [2075 2016]

value: Young specimen

value: ND - Young


title: DCM75

tag: disease

value: Female


title: dermal fibroblasts from ND/CR - Old specimen [1996 2016]

value: female

tag: age


title: dermal fibroblasts from ND - Old specimen [1995 2016]

value: dermal fibroblasts


title: Six3;Six6 DKO Retina Rep1

value: Retina

tag: strain

value: NMRI


title: Six3KO Retina Rep3


title: dermal fibroblasts from ND - Young specimen [1993 2016]

tag: diet


title: SNF032_D0_batch2

value: Male


title: dermal fibroblasts from CR/ND - Old specimen [1999 2016]

value: Old specimen

value: Caloric Restricted diet followed by Normal Diet (CR/ND)

tag: group

value: CR/ND - Old


title: dermal fibroblasts from CR/ND - Old specimen [1994 2016]


title: SNF032_D28_batch2

source_name: PBMC Day 28 post-vaccination

value: PBMC

value: Vaxigrip influenza vaccine

value: Day 28


title: SNF031_D7_batch5

source_name: PBMC Day 7 post-vaccination

value: Day 7

value: Chinese


title: DCM46

value: left ventricle

value: dilated cardiomyopathy


title: dermal fibroblasts from ND - Old specimen [1992 2016]

value: Normal Diet (ND)

value: ND - Old


title: Six3KO Retina Rep2

tag: developmental stage


title: DCM43


title: WT Retina Rep3

tag: genotype/variation

value: wild type


title: DCM39


title: dermal fibroblasts from old specimen (1331 2018)

tag: cell type

value: dermal fibroblasts


title: DCM38


title: dermal fibroblasts from ND/CR - Old specimen [1991 2016]

value: female

value: Normal Diet followed by Caloric Restricted diet (ND/CR)

value: ND/CR - Old


title: SNF031_D28_batch5

tag: treatment

value: Female


title: WT Retina Rep1

value: Retina

value: NMRI


title: SNF031_D2_batch5

value: PBMC

tag: time point

value: Day 2


title: DCM44

value: Male


title: dermal fibroblasts from ND/CR - Old specimen [1989 2016]

value: Old specimen


title: dermal fibroblasts from ND - Young specimen [1990 2016]

value: Young specimen

value: ND - Young


title: Six3KO Retina Rep1


title: SNF031_D0_batch5

value: Day 0

tag: subject id

value: Chinese


title: dermal fibroblasts from CR/ND - Old specimen [1988 2016]

value: Caloric Restricted diet followed by Normal Diet (CR/ND)

value: CR/ND - Old


title: DCM35

value: left ventricle

value: dilated cardiomyopathy


title: SNF030_D7_batch1

value: Vaxigrip influenza vaccine

value: Day 7

tag: age (years)


title: DKO-AI [GC010336]

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

description: DKO-AI    (DKO_HPC_M_ACE-I_P)

data_processing:
Raw read data was aligned to the mouse reference genome to with tophat 2.0.13
Gene count was performed with HT-Seq count 0.5.3p3, options -s no -a 10 -i gene_name
Differential expression analysis was performed with DESeq and edgeR
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: text file with raw counts

source_name: Heart _DKO_ACE-I

growth_protocol: DKO mice were backcrossed for at least 10 generations into the C57BL/6J background, resulting in mice having a 98.4% C57BL/6J background. Homozygous DKO (LDLR-/-;ob/ob) mice were generated using classical intercrossing strategies, for which heterozygous ob/+ and C57BL/6 (WT) mice were purchased from Harlan Laboratory. The mice were genotyped by PCR for LDLR and ob genotype as described before7.

extract_protocol:
Hearts were collected at the age of 24 weeks. Three hearts per group were snap-frozen in liquid nitrogen. Total RNA was extracted using the TRIzol reagent protocol (Invitrogen), purified on an RNeasy spin column (Qiagen), and DNase treated. RNA sample quality was assessed by Nanodrop.
Illumina True Seq Stranded

treatment_protocol: The effect of 12-week ACE-I treatment on gene expression in the heart was investigated. In the ACE-I treated groups (DKO-AI and WT-AI) mice were injected with ACE-inhibitor captopril (10 mg/kg/day IP) between 12 and 24 weeks of age. In the control groups (DKO-CO and WT-CO), animals received an equal volume of physiological saline NaCl 0.9%.

value: LDLR-/- and ob/ob (backcrossed into C57BL/6J)

value: whole heart

value: post natal 24 weeks

tag: genotype

value: DKO


title: SNF030_D2_batch1

value: PBMC

value: Day 2

tag: gender

tag: ethnicity


title: SNF030_D28_batch1

value: Day 28

value: Male

tag: microarray batch


title: DKO-AI [GC010335]

description: DKO-AI    (DKO_HPC_M_ACE-I_P)

tag: tissue


title: DCM34

tag: disease

tag: Sex


title: SNF030_D0_batch1


title: DCM33

tag: age


title: WT Retina Rep2

value: Retina

tag: strain

value: NMRI

value: wild type


title: dermal fibroblasts from ND - Young specimen [1987 2016]

value: female

value: dermal fibroblasts

value: Young specimen

tag: diet

value: Normal Diet (ND)

tag: group

value: ND - Young


title: DKO-AI [GC010334]

description: DKO-AI    (DKO_HPC_M_ACE-I_P)


title: dermal fibroblasts from ND - Old specimen [1986 2016]

value: Old specimen

value: ND - Old


title: SNF029_D28_batch2

value: Vaxigrip influenza vaccine

value: Chinese


title: SNF029_D7_batch2

value: Day 7


title: dermal fibroblasts from High Fat Diet (HFD) specimen 4

treatment_protocol: 2-months-old female mice were fed for 6 months with a high fat diet or control diet.

value: High Fat Diet (HFD)

tag: quality control status

value: Included


title: dermal fibroblasts from ND/CR - Old specimen [1985 2016]

value: Normal Diet followed by Caloric Restricted diet (ND/CR)

value: ND/CR - Old


title: DCM31

value: left ventricle

value: dilated cardiomyopathy

value: Male


title: DKO-CO [GC010339]

description: DKO-CO  (DKO_M_ACE-I_M)

value: LDLR-/- and ob/ob (backcrossed into C57BL/6J)

value: whole heart

value: post natal 24 weeks

value: DKO


title: DKO-CO [GC010330]

description: DKO-CO  (DKO_M_ACE-I_M)


title: DCM32


title: DKO-CO [GC010329]

description: DKO-CO  (DKO_M_ACE-I_M)


title: CKO [SAM24333408]

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
Single-cell RNA-seq data were processed with an in-house analysis pipeline.  Reads were demultiplexed based on perfect matches to known 10x cell barcode  sequences. These sequences were downloaded from the 10x genomics website  (Chromium Single Cell 3' v2 kit).
Transcript reads were aligned to the mouse reference genome (GRCm38)  using GSNAP (2013-10-10). Only uniquely mapping reads were considered for  downstream analysis. Transcript counts for a given gene were based on the  number of unique UMIs for reads overlapping exons in sense orientation. To  account for sequencing or PCR errors we allowed for one mismatch when  collapsing UMI sequences.
Cell barcodes were filtered by requiring a minimum number of detected  transcripts. Sample-specific cutoffs were set to 0.1 times the total transcript  count for the cell barcode at rank 30 (corresponding to the 99th percentile for  3,000 cells).
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Cortical cells

extract_protocol:
For single cell RNA sequencing, E16.5 cortex was dissociated into single cells at 37°C for 30 min with a Worthington Biochemical Papain Dissociation Kit (Cat# LK003150).  A Vi-CELL XR cell counter (Beckman Coulter) was used to determine the cell density and viability.  All samples had >90% viable cells.  Samples were processed using a Chromium Single Cell 3’ Library and Gel bead kit v2 (10x Genomics) according to manufacturer instructions.
cDNAs and libraries were prepared according to manufacturer instructions (10x Genomics).  Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using a Kapa Library Quantification Kit (Kapa Biosystems).  Each library was sequenced in one lane of a HiSeq4000 (Illumina) per manufacturer recommendations (10x Genomics).

tag: background strain

value: COP1 KO


title: DCM29


title: DCM28


title: DCM26


title: dermal fibroblasts from High Fat Diet (HFD) specimen 2

value: female

value: dermal fibroblasts


title: DCM24


title: CKO [SAM24333407]


title: SNF029_D2_batch2

tag: cell type

value: PBMC

tag: treatment

value: Vaxigrip influenza vaccine

value: Day 2


title: dermal fibroblasts from High Fat Diet (HFD) specimen 3

value: High Fat Diet (HFD)


title: DCM22


title: DCM21


title: HET [SAM24333405]

value: HET


title: COP1.cJun DKO SAM3461519

data_processing: Reads were aligned to the NCBIM37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from E18.5 brains

extract_protocol:
Total RNA was extracted from E18.5 brains with the olfactory bulbs removed using the MirVana miRNA isolation kit (Invitrogen).
Libraries were prepared from 1 μg of total RNA with TruSeq RNA Sample Preparation Kit v2 (Illumina).  Library size was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent) and concentration was determined by Library quantification kit (KAPA). Libraries were multiplexed five per lane and then sequenced in a HiSeq2500 (Illumina) to generate 50 million paired end 75 bp reads.

value: brain

tag: developmental stage

tag: genotype/variation

value: COP1.cJun DKO


title: DCM20

value: left ventricle


title: SNF029_D0_batch2

tag: time point

value: Day 0

tag: subject id

tag: age (years)

value: Chinese


title: SNF028_D28_batch4

value: Day 28

tag: gender

value: Female

tag: ethnicity

tag: microarray batch


title: dermal fibroblasts from Normal Diet (ND) specimen 2

tag: Sex

tag: tissue

value: Normal Diet (ND)

value: Included


title: COP1.cJun.ETV1.ETV5 QKO SAM3461513

value: COP1.cJun.ETV1.ETV5 QKO


title: dermal fibroblasts from Normal Diet (ND) specimen 3

value: female


title: HET [SAM24333406]

tag: age

tag: genotype


title: dermal fibroblasts from Normal Diet (ND) specimen 4

value: dermal fibroblasts

tag: group

value: Excluded


title: dermal fibroblasts from High Fat Diet (HFD) specimen 1

tag: quality control status


title: SNF028_D0_batch4

value: PBMC


title: DCM19

tag: disease

value: dilated cardiomyopathy

value: Male


title: SNF027_D28_batch1

tag: cell type

value: Vaxigrip influenza vaccine


title: SNF028_D2_batch4

tag: treatment

value: Day 2


title: SNF028_D7_batch4

value: Day 7


title: dermal fibroblasts from Normal Diet (ND) specimen 1


title: COP1.cJun DKO SAM3461518

value: brain

tag: developmental stage

value: COP1.cJun DKO


title: dermal fibroblasts from specimen treated with vehicle (control) 4

label_protocol: 7.8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

treatment_protocol: The backskin of 12-months-old mice was treated topically 3 times per week with 300ul Acetone containing 150nmoles GW9662 or with 300ul Acetone alone (as a control) for a period of 6 months.

value: vehicle (control)


title: SNF027_D7_batch1

value: Chinese


title: DCM18

value: left ventricle


title: DCM17


title: SNF027_D2_batch1

value: Female


title: SNF027_D0_batch1

value: Day 0


title: COP1.cJun.ETV1 TKO SAM3461512

tag: genotype/variation

value: COP1.cJun.ETV1 TKO


title: DCM16


title: COP1 KO SAM3461516

value: COP1 KO


title: COP1 het control SAM3461514

value: COP1 het control


title: dermal fibroblasts from specimen treated with PPARGamma inhibitor 3

value: dermal fibroblasts

value: PPARGamma inhibitor


title: SNF024_D7_batch1

value: PBMC

tag: time point


title: dermal fibroblasts from specimen treated with PPARGamma inhibitor 4


title: dermal fibroblasts from specimen treated with PPARGamma inhibitor 2


title: COP1.cJun.ETV1 TKO SAM3461511


title: DCM13

value: dilated cardiomyopathy

value: Male


title: DCM12


title: COP1 KO SAM3461517


title: DCM11


title: SNF024_D28_batch1

value: Vaxigrip influenza vaccine

value: Day 28

tag: subject id


title: dermal fibroblasts from specimen treated with vehicle (control) 2


title: dermal fibroblasts from specimen treated with vehicle (control) 3


title: DCM8


title: dermal fibroblasts from specimen treated with PPARGamma inhibitor 1


title: dermal fibroblasts from specimen treated with vehicle (control) 1


title: SNF024_D2_batch1

value: Day 2

tag: age (years)


title: SNF024_D0_batch1

tag: gender


title: SNF023_D7_batch8

value: Day 7

tag: ethnicity


title: SNF023_D28_batch8

tag: microarray batch


title: Dlk1+ Sca1+ pre-adipogenic fibroblasts from biological replicate NB3

extract_protocol: The skin was dissected, the subdermis removed, the remaining tissue chopped and digested with Collagenase 1. Dermal fibroblasts that were negative for the lineage markers CD45, CD117, CD31 and EpCam and positive for the fibroblast marker Pdgfra and CD34 were further subdivided into papillary fibroblasts (CD26+/Dlk1-/Sca1-), reticular fibroblasts (CD26-/Dlk1+/Sca1-) and two pre-adipogenic subtypes defined as CD26-/Dlk1+/Sca1+ and CD26-/Dlk1-/Sca1+ using FACS. RNA was isolated using magnetic beads from 4,500 cells. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 21 cycles.

value: isolated dermal fibroblasts cells from 2-days-old newborn mice

tag: biological replicate

tag: cell population

value: Dlk1+ Sca1+ pre-adipogenic fibroblasts


title: DCM14

tag: tissue

value: left ventricle

tag: age

tag: Sex


title: SNF023_D0_batch8

extract_protocol: PBMCs were isolated from whole blood. 1 million PBMCs were washed with 1 mL of PBS and centrifuged. The supernatant was removed. The cell pellet was loosened and lysed in mirVana Lysis/Binding buffer and stored in -80degC before extraction. Total RNA was isolated from PBMCs using mirVana™ miRNA isolation kit (Thermo Fisher Scientific, San Jose, CA, USA). Total RNA integrity was assessed by Agilent Bioanalyzer.

value: Female

value: Chinese


title: COP1.cJun.ETV1.ETV5 QKO SAM3461510

value: brain

value: COP1.cJun.ETV1.ETV5 QKO


title: LowPi_Rhizobia_Rep2

city: Tlalnepantla

first: Oswaldo

last: Valdés-López

state: Mexico

address: Av. De los Barrios 1. Los Reyes Iztacala

department: Biology

country: Mexico

institute: FES Iztacala, UNAM

data_processing:
Basecall using the P. vulgaris genome (v2.1)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to P. vulgaris  whole genome using bowtie v0.12.2. The trimmed RNAseq reads were then aligned to this index reference genome using TopHat, which also reports splice junction sites
Expression level of each transcript/gene was assessed by measuring the level of RNA-seq alignments using the tool Cufflinks tool from the Tuxedo pipeline protocol from Trapnell, Cole et al., Nature Protocols 7.3 (2012). The quantified expression level was represented by Fragments per Kilobase of transcript per Million mapped reads (FPKM) values. The differential expression levels of quantified genes were then calculated using the tool Cuffdiff.
Genome_build: PVul2.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Phaseolus vulgaris

source_name: zone of the roots susceptible to rhizobium

growth_protocol: Seedlings were grown on Fharraeus/Agar medium with no nitrogen

extract_protocol:
total RNA was purifing by using Trizol and Zymo purification columns
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: seedlings were grown under optipal phosphate (1mM) or deficient Pi conditions (5 uM)

value: Rhizobia inoculated root

tag: cultivar

value: Negro Jamapa

tag: rhizobia strain

value: Rhizobium tropici CIAT899

value: Low Pi


title: SNF023_D2_batch8

tag: cell type

value: PBMC


title: LowPi_Rhizobia_Rep3

tag: treatment

value: zone of the roots susceptible to rhizobium


title: DCM4

tag: disease

value: dilated cardiomyopathy

value: Male


title: COP1 het control SAM3461515

tag: developmental stage

tag: genotype/variation

value: COP1 het control


title: DCM3


title: LowPi_Rhizobia_Rep1


title: DCM6


title: LowPi_Mock_Rep3

value: Mock inoculated root


title: DCM2


title: LowPi_Mock_Rep2


title: SNF020_D7_batch1

value: Vaxigrip influenza vaccine

tag: time point

value: Day 7

tag: subject id


title: LowPi_Mock_Rep1


title: Dlk1- Sca1+ pre-adipogenic fibroblasts from biological replicate NB3

value: isolated dermal fibroblasts cells from 2-days-old newborn mice

value: Dlk1- Sca1+ pre-adipogenic fibroblasts


title: Dlk1- Sca1+ pre-adipogenic fibroblasts from biological replicate NB2


title: SNF020_D28_batch1

value: Day 28

tag: age (years)

tag: gender

value: Female

value: Chinese


title: NF7

value: left ventricle

value: non-failing


title: OptimalPi_Rhizobia_Rep3

value: Rhizobia inoculated root

value: Negro Jamapa

value: Rhizobium tropici CIAT899

value: optimal Pi


title: Dlk1+ reticular fibroblasts from biological replicate NB3

value: Dlk1+ reticular fibroblasts


title: Dlk1+ Sca1+ pre-adipogenic fibroblasts from biological replicate NB2

value: Dlk1+ Sca1+ pre-adipogenic fibroblasts


title: NF6

value: Male


title: SNF020_D2_batch1

value: PBMC

value: Day 2

tag: ethnicity

tag: microarray batch


title: OptimalPi_Rhizobia_Rep2

value: zone of the roots susceptible to rhizobium


title: NF5


title: CD26+ upper papillary fibroblasts from biological replicate NB3

value: isolated dermal fibroblasts cells from 2-days-old newborn mice

tag: biological replicate

tag: cell population

value: CD26+ upper papillary fibroblasts


title: SNF019_D28_batch7

value: Vaxigrip influenza vaccine

value: Day 28


title: Dlk1- Sca1+ pre-adipogenic fibroblasts from biological replicate NB1

tag: tissue

value: Dlk1- Sca1+ pre-adipogenic fibroblasts


title: NF8

value: left ventricle

tag: age

tag: Sex


title: SNF019_D7_batch7

value: Day 7

value: Chinese


title: CD26+ upper papillary fibroblasts from biological replicate NB2


title: NF4

value: non-failing


title: OptimalPi_Mock_Rep2

value: Mock inoculated root

tag: cultivar

value: Negro Jamapa

tag: rhizobia strain

value: Rhizobium tropici CIAT899


title: NF3


title: NF15


title: OptimalPi_Rhizobia_Rep1

tag: treatment

value: Rhizobia inoculated root

value: optimal Pi


title: NF2

tag: disease

value: Male


title: OptimalPi_Mock_Rep1


title: Dlk1+ reticular fibroblasts from biological replicate NB2

value: Dlk1+ reticular fibroblasts


title: SNF020_D0_batch1

tag: cell type

value: PBMC

value: Day 0

value: Female


title: NF14


title: SNF015_D7_batch7

value: Vaxigrip influenza vaccine


title: SNF019_D0_batch7


title: NF13


title: SNF019_D2_batch7

value: Day 2


title: dermal fibroblasts from old specimen 2

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

label_protocol: 6 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: The skin was dissected, the subdermis removed, the remaining tissue chopped and digested with Collagenase 1. Dermal fibroblasts that were negative for the lineage markers CD45, CD117, CD24, CD31 and EpCam and positive for the fibroblast marker Pdgfra and CD34 were FACS isolated. RNA was isolated using TRIzol and further purified with QIAGEN RNeasy Mini Columns. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 18 cycles.

value: dermal fibroblasts

tag: group

value: old specimen


title: SNF015_D28_batch7

tag: time point

value: Day 28


title: Dlk1+ reticular fibroblasts from biological replicate NB1

value: isolated dermal fibroblasts cells from 2-days-old newborn mice


title: OptimalPi_Mock_Rep3

value: zone of the roots susceptible to rhizobium


title: T.DP.Th.Rorc(γt)GFP/GFP#1

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Trimming for adapter sequences and low quality reads (original script and sickle1.2)
Mapping of reads to the mouse reference genome (mm10) with bowtie aligner version 2.2.4
Filtering out non-uniquely mapped reads by samtools view -q 30 (samtools 0.1.19)
Removing chrM mapped reads (0.1~20%, median=4.1%) and duplicated reads (7~69%, median=22%) by Picard Tools (picard-1.138) to prepare bam files for each sample
Removing mapped fragments which are spanning more than 120bp to improve resolutions and decrease technical sample-to-sample deviations in pile-up tarces
Merging replicates for a population and computing piling-up traces with macs2 (2.1.1)
Normalization of pile-up traces by quantile normalization taking every 25bp bin to make bigwig files for each population
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Thymus

extract_protocol:
Immunocytes were isolated to high purity by flow cytometry according to ImmGen SOP using the antibodies and gates manifested in ImmGen website (www.immgen.org). After the 2nd rounds of sorting, 10,000 cells (except very rare cell populations including LTHSC.34-.BM, LTHSC.34+.BM and STHSC.150-.BM which were sorted 677, 2483 and 3660 cells respectively) were collected in 100uL of BAMBANKER (serum-free cell freezing medium, No.302-14681, Wako, Osaka, Japan) pre-chilled on ice. Tubes were kept on ice at most 30min until frozen in a cell freezing container with isopropyl alcohol (-1°C/min rate, 4C to -80C) and stored at -80C until preparing ATAC-seq libraries.
Frozen cells were thawed, washed with 1mL of PBS containing protease inhibitors (cOmplete EDTA-free protease inhibitor cocktail, Roche Diagnostics, Basel, Switzerland) and cell pellets were resuspended in 10uL of Tn5transposase mixture: 1xTagment DNA Buffer, 0.5uL Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, illumine, CA, USA) and 0.2mg/ml digitonin (#G9441, Promega, WI, USA) on ice. Then, the cells were incubated at 37C for 30min with agitation followed by DNA isolation using MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction. To construct libraries, the 1st round of PCR was performed in 50uL using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with a set of primers (0.5uM each) and following thermal cycles: 5min at 72°C, 30 sec at 98°C, followed by 7 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec] and a final extension at 72°C for 5mn. The PCR products were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter, CA, USA) (0.65x and 1.8x volume to remove long and short fragments respectively) and eluted in 18uL of EB (Qiagen). For avoiding an over amplification which can produce more GC bias, 2uL of the eluted DNA were subjected to qPCR (StepOnePlus Real-Time PCR System, Life Technologies, CA, USA) in 20uL employing SYBR GreenI (final 0.6x SYBR GreenI, Life Technologies) and the same set of primers (1.25uM each) as in the 1st round of PCR. After running qPCR (30sec at 98°C, followed by 30 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec]), amplification curves were examined and the optimal number of PCR cycles were estimated as the cycles where amplifications reach 1/4 of maximum. 12.5uL of the eluted DNA were subjected to the 2nd round of PCR in 50uL with NEBNext High-fidelity 2x PCR master mix, a set of primers (1.25uM each) and following thermal cycles: 30 sec hot-start at 98°C, followed by 7~13 cycles [98°C for 10 sec, 63°C for 30 sec and 72°C for 60 sec] and a final extension at 72°C for 5mn. The libraries were purified by Agencourt AMPure XP beads (x1.8 vol.), quantified by qPCR employing Power SYBR Green PCR Master mix (ThermoFisher scientific, MA, USA) and a common set of primers (P5_FW and P7_RV, 0.2uM each) and pooled, which were sequenced for paired-end (38+37bp) on an Illumina Next-seq 500 instrument in a high-output mode.

tag: strain

tag: genotype

value: Rorc(gammat)GFP/GFP

value: DP Thymocytes


title: T.DP.Th.Rorc(γt)GFP/GFP#2


title: dermal fibroblasts from old specimen 4


title: T.DP.Th.Rorc(γt)+/GFP#2

value: Rorc(gammat)+/GFP


title: CD26+ upper papillary fibroblasts from biological replicate NB1

value: CD26+ upper papillary fibroblasts


title: NF12

value: left ventricle

value: non-failing


title: Dlk1+ Sca1+ pre-adipogenic fibroblasts from biological replicate NB1

value: Dlk1+ Sca1+ pre-adipogenic fibroblasts


title: T.DP.Th.Rorc(γt)+/GFP#1


title: dermal fibroblasts from old specimen 3


title: SNF015_D2_batch7

data_processing: Illumina Genome Studio was used to export the data in raw format. Raw expression data was loaded into R/Bioconductor and normalized using log2 quantile normalization method of the lumi R package.

value: PBMC

tag: subject id

tag: age (years)

tag: gender

value: Chinese


title: NF11

value: Female


title: dermal fibroblasts from young specimen 4

value: young specimen


title: dermal fibroblasts from old specimen 1


title: SNF014_D7_batch7

value: Vaxigrip influenza vaccine

value: Day 7

value: Male

tag: ethnicity

tag: microarray batch


title: SNF015_D0_batch7

value: Day 0


title: SNF014_D28_batch7

value: Day 28


title: Ngn3 null endocrine progenitors

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Sequenced reads were trimmed using Trimgalore (https://github.com/FelixKrueger/TrimGalore) and mapped to the mouse genome mm10 assembly using the WALT aligner.
We achieved ∼9-10x coverage of symmetric CpG sites and subsequently processed mapped reads using MethPipe methylation analysis pipeline in order to identify hypomethylated and differentially methylated regions
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: pancreas

growth_protocol: primary cells

extract_protocol:
Endocrine cells were  were enriched by flow sorting for Ngn3eGFP expressing cells. Cells were > 95% viable. Cells were directly lysed for DNA preparation.
Genomic DNA was prepared using a Qiagen genomic DNA isolation kit. Transposomes were assembled with Tn5 enzyme purified in house using a plasmid construct kindly provided by the Sandberg lab and according to protocols previously described (Picelli et al., 2014). Tagmentation, oligonucleotide replacement and gap repair were carried out on 75ng of genomic DNA. Bisulfite conversion of DNA was performed using the EZ DNA Methylation Lightning kit (Zymo cat # D5030) according to the manufacturers recommendations. After desulphonation and purification of sodium bisulfite treated libraries, samples were amplified for 12 cycles with the Kapa HiFi HotStart Uracil+ Ready Mix according to the manufacturers instructions.
WGBS libraries were sequenced on the Illumina Novaseq (paired end 150bp read lengths), obtaining approximately 400 million reads per library.

tag: genotype/variation

value: Ngn3 null endocrine progenitors

value: endocrine enrichment

value: Mixed genetic background, >95percent ICR, <2.5%C57Bl/6, <2.5percent 129svev


title: Ngn3 heterozygous islet progenitors

value: Ngn3 heterozygous islet progenitors


title: Sirt2KO-Cerulein rep1

city: Chicago

first: Nobuo

last: Horikoshi

state: IL

address: 303 E Superior St

department: Radiation Oncology

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC.
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.
The cleaned reads were aligned to the Mus musculus genome (mm10) using STAR.
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from UCSC (University of California Santa Cruz).
Normalization and differential expression were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample.

source_name: Pancreas

extract_protocol:
Pancreas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent (PureLink RNA Mini Kit). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acute pancreatitis (AP) was induced by three times, eight hourly intraperitoneal injection of cerulein (100 ug/kg) (Sigma, St. Louis, MO) in 3-4 month-old mice. Age-matched control mice were administered comparable injection of PBS.

value: Mix (C57BL x B129)

tag: tissue

value: pancreas

tag: age

value: 2 days post last injection


title: Sirt2KO-Cerulein rep2


title: Sirt2KO-Cerulein rep3


title: NF10

source_name: left ventricle

value: left ventricle

value: non-failing

tag: Sex


title: GA treatment rep1

city: Tai'an

first: Shuxin

last: Zhang

address: DaiZong Street NO.61

country: China

institute: Shandong Agricultural University

data_processing:
Cutadapt (version 1.2.1) was used to filter out low-quality sequences, and to find and remove 5’- and 3’-adapter sequences from the raw tags
Tags with the size range of 18-28 nt were retained for subsequent analysis
The clean sequencing tags in fastq format were firstly transformed into fasta format and collapsed to make each sequence entry unique using fastq2fastq and collapse_reads_md scripts in mirdeep2 package, respectively
collapsed tags in fasta format were aligned to the maize B73 reference (v2)using Bowtie (version 0.12.8)
Only tags that matched perfectly to less than 20 genomic regions with 0 mismatch in the Z. mays genome were used for MIRNA annotation
Genome_build: maize B73 reference (v2)
Supplementary_files_format_and_content: tab-delimited text files include count values for each mature miRNA and its precusor

organism: Zea mays

source_name: embryo

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA, and then small RNAs were enriched using polyethylene glycol (PEG8000). For small RNA library construction, enriched small RNAs were ligated with 3’ RNA adapter, and fractionated through 15% denaturing polyacrylamide gel electrophoresis (PAGE). Products with a length of 36 to 44 nucleotides (nt) were ligated with 5’ RNA adapter, and used to perform RT-PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment time

value: gibberellin acid

value: embryo


title: GA treatment rep2

tag: treatment


title: ABA treatment rep2

value: abscisic acid


title: ABA treatment rep1


title: WT-Cerulein rep3

value: wild type


title: NF1

extract_protocol:
Frozen tissue was placed in liquid nitrogen and broken up using mortar and pestle to obtain a piece approximately 2 x 2 x 2 mm in size, macroscopically free of fatty infiltration, fibrosis, and blood. Tissue was placed immediately in TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) and mechanically homogenized using an IKA T25 Ultra-Turaxx homogenizer. Tissue was homogenized for approximately 60 seconds, or until no visible chunks of tissue remained. RNA was extracted using the mirVana miRNA isolation kit (Thermo Fisher Scientific) enriched for total RNA isolation according to manufacturer’s instructions with the exception of replacing the Lysis/Binding Buffer with TRIzol. All samples were DNase treated using TURBO DNA-free Kit (Thermo Fisher Scientific). RNA was quantified at 260nm using a NanoDrop1000 (Thermo Fisher Scientific), and RNA integrity (RIN) was measured using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Assay (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN ≥ 7.0, and ranged from 7.0-9.3.
PolyA transcripts were isolated from 1µg total RNA using oligo-dT beads and the cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

tag: disease


title: CK rep2


title: SNF014_D0_batch7

city: Singapore

first: Vipin

last: Narang

institute: Singapore Immunology Network (SIgN)

tag: cell type

value: PBMC

value: Chinese


title: dermal fibroblasts from young specimen 3

source_name: dermal fibroblasts from young specimen

value: dermal fibroblasts

tag: group

value: young specimen


title: dermal fibroblasts from young specimen 2


title: dermal fibroblasts from young specimen 1


title: SNF014_D2_batch7

value: Vaxigrip influenza vaccine

tag: time point

value: Day 2

value: Male


title: SNF013_D2_batch4

value: Female


title: SNF013_D28_batch4

value: Day 28


title: WT-Cerulein rep2

tag: strain

value: Mix (C57BL x B129)

value: pancreas


title: SNF012_D7_batch7

value: Day 7


title: SNF012_D28_batch7


title: SNF013_D7_batch4


title: SNF013_D0_batch4

value: Day 0


title: WT-Cerulein rep1

value: 2 days post last injection

tag: genotype


title: CK rep1

value: embryo


title: WT-PBS rep3


title: WT-PBS rep2


title: CD4low T cells rep1

city: ShangHai

first: Chao

last: Wang

address: 1954HuaShan road

institute: Shanghai Jiao Tong University

description:
processed data file:
CD4low_vs_murine_N_CD4.xls
CD4low_vs_murine_N_CD4_diff.xls

data_processing:
Raw fastq was analyzed using FastQC and Trimmomatic to remove adapters and low quality reads.
Clean reads were mapped to hg19 or mm9 using STAR.
Raw read counts were calculated by HTseq-count.
DEseq2 was applied to calculated the normalized gene counts and differential expressed genes.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: normalized gene counts and differential expressed genes.

source_name: CD4low T cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA LT V2 Sample Prep Kit(Illumina, Sandiego) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: castrated TRAMP; PCa mouse model

value: peripheral blood

value: CD4low T cells


title: CD4low T cells rep2


title: murine naïve CD4 rep2

source_name: murine naïve CD4 cells

value: wild type

value: murine naive CD4 cells


title: WT-PBS rep1


title: murine naïve CD4 rep1


title: D8

city: Nanjing

first: Xin

state: Jiangsu

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

description: the eighth day of subcutaneous preadipocyte differentiation

data_processing:
Raw sequencing data was evaluated by FAST-QC
Raw reads after quality control testing were mapped to the reference pig genome version 11.1 (Sscrofa 11.1) using HiSAT2 program (V2.0.5) for mRNAs and lncRNAs, and BWA-MEM for circRNAs
The normalized expression level of each gene was measured by fragments per kilobase of transcript per million reads mapped (FPKM) for mRNAs and lncRNAs, and spliced reads per billion mapping (SRPBM) for circRNAs
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM (for mRNAs and lncRNAs) or SRPBM (for circRNAs) values for each gene

organism: Sus scrofa

extract_protocol:
Adipocytes at different differentiation stages were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from D0, D2, D4, and D8 (3 individuals/group) was pooled in equal amounts to generate mixed sample respectively. Sequencing libraries were prepared using NEB Next Ultra Directional RNA LibraryPrep Kit (NEB, Ispawich, MA, USA).
Libraries were prepared for sequencing using Illumina Solexa transcriptome sequencing protocol after removing ribosomal RNA

treatment_protocol: The different differentiation stages (D0, D2, D4, and D8) of subcutaneous preadipocyte

tag: breed

value: Chinese Erhualian pigs

tag: differentiation stage

value: male


title: D4

description: the forth day of subcutaneous preadipocyte differentiation


title: D272Mut4

first: You-Qiang

last: Su

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: oocyte

extract_protocol:
The cell was lysised and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later, they were euthanized, and their ovariaies were collected and lysed in 350ul RLT buffer for RNA extraction.

value: 3 week

value: oocyte


title: HD_TSP_5

city: Paris

first: Emmanuel

last: Clave

state: Paris

address: INSERM

country: France

institute: UMRS 1160

hyb_protocol: Hybridation on GeneChip Human U133 plus 2.0 Arrays (Affymetrix) with 10 ng of labeled cRNA following manufacturer's protocols. Staining and washing has been realised on fluidics (FS 450, Affymetrix)

scan_protocol: Arrays scanning  has been realised using the GeneChip Scanner 3000 7G (Affymetrix) with AGCC software

data_processing: Probe set summarization and data  normalisation are realised from.CEL files  using algorithm Maximum Rank Sum (MAXRS) and normalized with global normalization (MAS 5) methods

label_protocol: Total RNA were amplified using the ExpressArt mRNA amplification Pico kit (AmpTec GmbH, Hambourg, Germany) and labeled with the BioArray HighYield RNA transcript labeling kit (Enzo Life Sciences, Villeurbanne, France),

growth_protocol: No

extract_protocol: micro Rneasy kit (Qiagen) with DNAase

treatment_protocol: After ficoll gradient separation mononuclear cell were sorted using a FACS ARIA III, 500 cells for each population were directly collected into Qiagen RLT buffer

tag: individual

value: healthy control (1204)

tag: disease state

value: control

tag: cell population

value: TSP


title: HD_TSP_6

value: healthy control (91879)


title: SNF011_D28_batch8

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

treatment_protocol: No treatment of PBMCs was performed.

value: PBMC

value: Vaxigrip influenza vaccine

value: Day 28

tag: subject id

tag: age (years)

tag: gender

value: Female

tag: ethnicity

value: Chinese

tag: microarray batch


title: HD_CD10_5


title: SNF011_D2_batch8

tag: treatment

value: Day 2


title: SNF012_D2_batch7

tag: cell type


title: HD_TSP_7

value: healthy control (2518)


title: GVHD_CD10_5

value: allo-HSCT patient (CATJ)

value: GVHD grade 2


title: HD_CD10_6


title: SNF012_D0_batch7

source_name: PBMC Day 0 pre-vaccination

value: Day 0


title: SNF011_D7_batch8

value: Day 7


title: HD_CD10_7


title: D272Mut3

tag: age

value: 3 week

tag: tissue


title: HD_CD10_4

value: healthy control (9181)


title: SNF011_D0_batch8

tag: time point


title: GVHD_TSP_5


title: SNF010_D7_batch2


title: D272Mut2

tag: strain

tag: genotype

value: oocyte


title: D2

description: the second day of subcutaneous preadipocyte differentiation

tag: breed

value: Chinese Erhualian pigs

tag: Sex

value: male


title: D0

description: subcutaneous preadipocyte

source_name: subcutaneous preadipocyte

tag: differentiation stage


title: METTL3_6hpi_IP_rep3

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_M3ko_rep3_S12_001
processed data file: 6hpi_m6A_IP.txt

data_processing:
Prior to alignment, polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Then, reads that were not aligned to the genome were aligned to the transcriptome.
Genome_build: hg19 + NCBI EF999921.1
Supplementary_files_format_and_content: *.txt: Tab-separated text files with numbers of aligned reads for each gene.

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Primary fibroblasts

extract_protocol:
Total RNA was extracted using TRI reagent.
mRNA was isolated using polyA selection kit (Ambion) and then fragmented. Fragments were then dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified. m6A-immunoprecipitation was done as previously described (Schwartz et al., Cell Reports, 2014).

value: Primary fibroblasts

tag: infection

value: HCMV for 6 hr

tag: ip antibody

value: anti-m6A antibody (Synaptic Systems)


title: WT4

value: WT


title: METTL3_6hpi_IP_rep1

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_M3ko_rep1_S8_001
processed data file: 6hpi_m6A_IP.txt


title: WT3


title: HD_CD10_3

tag: individual

value: healthy control (91705)

tag: disease state

value: control

tag: cell population


title: METTL3_6hpi_IP_rep2

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_M3ko_rep2_S10_001
processed data file: 6hpi_m6A_IP.txt


title: D272Mut1


title: METTL3_6hpi_input_rep3

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_M3ko_rep3_S6_001
processed data file: 6hpi_m6A_IP.txt


title: WT2


title: METTL3_6hpi_input_rep2

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_M3ko_rep2_S4_001
processed data file: 6hpi_m6A_IP.txt


title: HD_TSP_4

value: TSP


title: METTL3_6hpi_input_rep1

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_M3ko_rep1_S2_001
processed data file: 6hpi_m6A_IP.txt


title: WT1


title: GTMut4

value: GTMut


title: Control_6hpi_IP_rep3

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_I8ctrl_rep3_S11_001
processed data file: 6hpi_m6A_IP.txt


title: HD_TSP_3


title: SNF010_D2_batch2

source_name: PBMC Day 2 post-vaccination

value: PBMC

value: Vaxigrip influenza vaccine

value: Day 2

tag: subject id

tag: age (years)

tag: gender

value: Female

tag: ethnicity

value: Chinese


title: GTMut3

tag: age

value: 3 week


title: HD_TSP_2

value: healthy control (31785)


title: SNF010_D0_batch2

tag: cell type

tag: treatment

value: Day 0

tag: microarray batch


title: SNF010_D28_batch2

source_name: PBMC Day 28 post-vaccination

tag: time point

value: Day 28


title: HD_CD10_2


title: GTMut1

tag: strain

tag: genotype

tag: tissue

value: oocyte


title: SNF008_D7_batch2

source_name: PBMC Day 7 post-vaccination

value: Day 7


title: SNF006_D7_batch1

value: Male


title: GTWT4

value: GTWT


title: HD_CD10_1

value: healthy control (31515)


title: SNF008_D2_batch2


title: Control_6hpi_input_rep3

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_I8ctrl_rep3_S5_001
processed data file: 6hpi_m6A_IP.txt

value: Primary fibroblasts

tag: infection

value: HCMV for 6 hr


title: GVHD_CD10_3

value: allo-HSCT patient (MERT)

value: GVHD grade 2


title: GVHD_TSP_4

value: allo-HSCT patient (MESV)

value: TSP


title: GTMut2

value: GTMut


title: SNF008_D28_batch2

value: PBMC

value: Vaxigrip influenza vaccine

value: Female

value: Chinese


title: GTWT3

value: 3 week


title: HD_TSP_1

value: control


title: GVHD_CD10_4


title: Control_6hpi_IP_rep1

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_I8ctrl_rep1_S7_001
processed data file: 6hpi_m6A_IP.txt

tag: ip antibody

value: anti-m6A antibody (Synaptic Systems)


title: GTWT2

value: oocyte


title: SNF008_D0_batch2

value: Day 0


title: Control_6hpi_IP_rep2

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
IP_I8ctrl_rep2_S9_001
processed data file: 6hpi_m6A_IP.txt


title: GTWT1

value: GTWT


title: GTD2724


title: Control_6hpi_input_rep2

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_I8ctrl_rep2_S3_001
processed data file: 6hpi_m6A_IP.txt

value: Primary fibroblasts


title: GVHD_TSP_3

tag: individual


title: SNF006_D28_batch1

value: Day 28

value: Male


title: SNF006_D0_batch1


title: NoGVHD_CD10_6

value: allo-HSCT patient (TCHW)

tag: disease state

value: GVHD grade 0


title: SNF005_D7_batch6R

value: Day 7


title: SNF005_D2_batch6R

value: Day 2


title: NoGVHD_TSP_5

value: allo-HSCT patient (MALA)

value: GVHD grade 1

tag: cell population

value: TSP


title: Control_6hpi_input_rep1

description:
Cells were infected with HCMV for 6 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
Input_I8ctrl_rep1_S1_001
processed data file: 6hpi_m6A_IP.txt

value: HCMV for 6 hr


title: SNF005_D28_batch6R

value: PBMC

value: Vaxigrip influenza vaccine

tag: subject id

value: Chinese


title: GVHD_CD10_2

value: allo-HSCT patient (RAMR)

value: GVHD grade 2


title: GTD2723

value: 3 week

value: oocyte


title: SNF006_D2_batch1

tag: age (years)


title: NoGVHD_CD10_5


title: METTL3_input_rep3

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_input_rep3
processed data file: 72hpi_m6A_IP.txt

value: Primary fibroblasts

value: HCMV for 72 hr


title: METTL3_IP_rep3

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_IP_rep3
processed data file: 72hpi_m6A_IP.txt

value: anti-m6A antibody (Synaptic Systems)


title: GVHD_TSP_2


title: GTD2722


title: SNF004_D7_batch3

tag: gender

value: Male


title: GTD2721


title: METTL3_input_rep2

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_input_rep2
processed data file: 72hpi_m6A_IP.txt


title: METTL3_IP_rep1

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_IP_rep1
processed data file: 72hpi_m6A_IP.txt


title: SNF004_D28_batch3

value: Day 28

tag: ethnicity


title: GVHD_TSP_1

value: allo-HSCT patient (JARM)

value: GVHD grade 3


title: GVHD_CD10_1


title: SNF004_D0_batch3

value: Day 0


title: GT4

tag: age

value: GT


title: NoGVHD_TSP_6

value: allo-HSCT patient (TCHW)

value: GVHD grade 0

value: TSP


title: METTL3_input_rep1

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
M3_input_rep1
processed data file: 72hpi_m6A_IP.txt

tag: cell type


title: GT3


title: Control_IP_rep2

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_IP_rep2
processed data file: 72hpi_m6A_IP.txt


title: GT2


title: Control_input_rep3

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_input_rep3
processed data file: 72hpi_m6A_IP.txt


title: Control_IP_rep1

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_IP_rep1
processed data file: 72hpi_m6A_IP.txt


title: Control_input_rep2

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_input_rep2
processed data file: 72hpi_m6A_IP.txt


title: SNF004_D2_batch3

value: PBMC

tag: treatment

value: Vaxigrip influenza vaccine

value: Day 2

value: Chinese


title: Control_IP_rep3

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_IP_rep3
processed data file: 72hpi_m6A_IP.txt


title: SNF002_D7_batch2

value: Day 7

value: Female

tag: microarray batch


title: NoGVHD_CD10_4

value: allo-HSCT patient (ADIJ)


title: NoGVHD_TSP_3

value: allo-HSCT patient (SAIA)


title: NoGVHD_TSP_4


title: SGR-100-2

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

data_processing:
The raw reads were first cleaned to remove low quality reads by using a software, Sickle (Joshi and Fass, 2011). For Sickle analysis, following parameters were used: minimum length >= 30 bp and quality score >=30.
All trimmed reads from the same species were de novo assembled to reference transcriptome contigs by using Trinity (Grabherr et al., 2011, Haas et al., 2013).
The trimmed reads were aligned to reference transcriptome contigs by using Tophat2 (Langmead et al., 2009, Trapnell et al., 2009, Kim and Salzberg, 2011, Kim et al., 2013).
The normalized expression values (FPKM) were measured by using Cufflink (Trapnell et al., 2010).
The differentially expressed (DE) contigs were then identified by using Cuffdiff 2 (Trapnell et al., 2013)
Genome_build: de novo Transcriptome assembly was performed. The FASTA files of assembled transcripts are available on the series record. UG_ASR_Trininity.fasta =  Phakopsora pachyrhizi; UG_SGR_Trininity.fasta = Puccinia emaculata.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Puccinia emaculata

source_name: Germinating urediniospore_100mM Phi

growth_protocol: Urediniospores of Pe and Pp were dusted on 1× germination solution [500× stock: 0.0036% nonanol (v/v), 0.025% Tween 20 (v/v), 50% ethanol (v/v), in autoclaved distilled water] supplemented with 10 or 100 mM Phi on a Petri plate. Urediniospores were allowed to germinate for 24 h in the dark. After 24 h, germinated urediniospores were collected by skimming them from the surface of the solution with the help of a cover slip.

extract_protocol:
total RNA from Phi‐treated Pe and Pp was isolated using an RNeasy plant mini kit (Qiagen). Two biological replicates were used for each treatment. Illumina TruSeq sequencing‐by‐synthesis chemistry was used on a HiSeq 2000 platform (Illumina, https://www.illumina.com/) to generate paired‐end reads (2 × 100 bp).
As per Illumina library preparation guide

treatment_protocol: Treatments: 0 mM Phi, 10 mM Phi, and 100 mM Phi

value: Germinating urediniospore


title: NoGVHD_CD10_3


title: Control_input_rep1

description:
Cells were infected with HCMV for 72 hours. Following extraction, RNA was either immuno-precipitated with anti-m6A antibody (synaptic systems) (IP) or left untreated (Input).
I8_input_rep1
processed data file: 72hpi_m6A_IP.txt

value: Primary fibroblasts

value: HCMV for 72 hr


title: SGR-100-1


title: SNF002_D28_batch2

tag: time point

value: Day 28


title: GT1

tag: strain

value: 3 week

value: oocyte


title: METTL3_5hpi_rep2

description:
Cells were infected with HCMV for 5 hours.
M3_5hpi_rep2
processed data file: 5hpi.txt

value: HCMV for 5 hr


title: SO-4014-Repl4-LTB-ve120731166_S3(Healthy Control Replicate3)

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: C V Raman Road

department: Biochemistry

country: India

institute: IISC

data_processing:
Trimming and adapter removal using trimmomatic
differential expression analysis using the TUXEDO protocol
Tophat2 (v2.0.9)→cufflinks(v2.2.1)-→cuffdiff (v2.2.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated fpkm_tracking files

source_name: whole Blood sample

extract_protocol:
RNA isolation kit (Applied Biosystems)
NEXTflexRapid Directional RNA-Seqlibrary; NEXTflex™ RNA-Seq Barcode Adapters were added

treatment_protocol: Tuberculosis DOTS treatment

value: whole blood

tag: Sex

tag: patient diagnosis

value: healthy

tag: disease status


title: SO-4014-Repl4-LTB-ve12073100_S2(Healthy Control Replicate2)

tag: tissue

value: Male


title: SGR-10-2

source_name: Germinating urediniospore_10mM Phi


title: Brain telencephalon rep2

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the illumina HiSeq 4000 sequencing platform were cleaned up with the Cutadapt program to trim off sequencing adaptors and low quality bases with a quality phred-like score<20.  Reads <40 bases were excluded from RNA-seq analysis.
ICBR scripts along with SAMtools and the DESeq, EdgeR, and Bayseq (DEB) computational applications were applied to generate the gene expression data, including fold changes and p-values, to remove duplicates or artifacts from PCR, and choose uniquely mapped reads for gene expression analysis. Digital gene expression was assessed by counting the number of transcripts that mapped to a gene sequence
Genome_build: FHM_All_PTA_Assem.fasta
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Pimephales promelas

source_name: tissue

extract_protocol:
Tissue extractions followed procedures previously described (Garcia-Reyero et al., 2009; Bisesi et al., 2017).  Briefly, tissues were homogenized in RNA Stat-60 (TelTest) using a handheld rotary homogenizer followed by organic separation with chloroform.
RNA was then subjected to a second round of RNA Stat-60/Chloroform extraction, followed by precipitation in isopropanol overnight at -20°C.  RNA was washed twice with 75% ethanol, dried, and reconstituted in RNAsecure (ThermoFisher Scientific). Reconstituted RNA was DNase-treated to remove possible genomic DNA contamination using Turbo DNase (ThermoFisher Scientific). The quality of the RNA was assessed using an Agilent Bioanalyzer 2100.  Only samples with RNA integrity numbers (RINs) exceeding 8 were used for sequencing.  Samples were then quantified using a ThermoFisher Scientific Qubit 3.0 fluorimeter.

treatment_protocol: Fish were sacrificed at different times for three different experiments by submersion in buffered 250 mg/L MS-222 (Western Chemical).

value: telencephalon

tag: location

value: the Aquatic Toxicology Core Laboratory at the University of Florida

value: Adult male


title: NoGVHD_TSP_2

tag: individual

value: allo-HSCT patient (AUGD)

tag: disease state

value: GVHD grade 1

value: TSP


title: METTL3_5hpi_rep1

description:
Cells were infected with HCMV for 5 hours.
M3_5hpi_rep1
processed data file: 5hpi.txt

tag: infection


title: SO-4014-120731114_S1(Healthy Control Replicate1)