title: LNCaP_KD2

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

description: Gene expression in stable cell lines with puromycin selection

hyb_protocol: Labeled, fragmented cRNA was hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K array following manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides at 3um scan resolution.

data_processing: Image data were processed with Agilent Feature Extraction 11.0.1.1. Processed signals were quantile normalized with Agilent GeneSpring 12.0.

source_name: LNCaP, GRB10 knockdown, KD2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Agilent’s One-Colour Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling v6.0 (Agilent Technologies, Santa Clara, CA).

growth_protocol: LNCaP cells were obtained from ATCC, and cultured in RPMI-1640 medium supplemented with 10% FBS .

extract_protocol: Total RNA was isolated using Trizol (Thermo Fisher)

treatment_protocol: Lentiviral particles delivering shRNA were added to the culture media of LNCaP,  puromycin was used at 1 μg/ml to select for infected cells and to maintain stable cell populations.

tag: cell type

value: LNCaP cell

tag: knockdown

value: GRB10  KD


title: SAMPLE 3: DNA methylation in TKO #4-22 mock 10w

status: Public on Sep 30 2020

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

description: Normal cells

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System.

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: 293FT with TET triple KO (TET1, TET2, TET3)

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were maintained in DMEM medium.

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

treatment_protocol: cells were treated with NOC18 (or mock treated) for 10 weeks

tag: cell line


title: D.7 Itk-/- LMN4 rep2

type: SRA

city: Ithaca

first: sabrina

last: solouki

state: NY

address: 530 Campus Rd.

department: Immunology and Infectious Disease

country: USA

institute: Cornell university

description:
D7LMN4_FPKM.txt
d7-WT-LMN4B

library_source: transcriptomic

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts and cuffnorm v2.2.1 was used to generate FPKM values for annotated genes.
Genes with FPKM and annotation were further analyzed in Genespring for PCA, clustering, and differential gene expression. GSEA was also used to analyze biological pathways and enriched genes based on ratios.
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: text file with FPKM

molecule: total RNA

organism: Mus musculus

source_name: CD44lowCD122low CD8+ T cells from Spleen; CD45.1-CD45.2+ post-adoptive transfer

extract_protocol:
CD8+ T cells were sorted from spleens, pelleted, frozen at -80C. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from 50ng total RNA per sample using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation, by the RNA Sequencing Core at Cornell University.

treatment_protocol: Infection with Listeria monocytogenes expressing N4 OVA or T4 OVA peptide variant

value: CD8+ T cells

tag: donor mouse strain

tag: recipient mouse strain

tag: itk genotype

value: Itk-/-

tag: timepoint

value: day 7

tag: listeria treatment


title: HUVEC Endothelial Cells_ 6Gy radiation_rep3

type: RNA

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description:
SG13134300_257236317585_S001_GE1_1105_Oct12_1_2
Gene Expression after 24hrs in 6Gy irradiated endothelial cells

hyb_protocol: The labeled cRNA were fragmented at 60°C and hybridized on to a Agilent Human Gene Expression microarray 8x60k array designed by Genotypic Technology Pvt. Ltd. (AMADID:72363) using Agilent's In Situ Hybridization Kit (Part No.: 5190-0404) according to manufacturer's instructions.

scan_protocol: Scanning was done using Agilent microarray scanner (Agilent Technologies, Part No. G2600D)

data_processing: Raw data was analysed by using GeneSpring GX software (Agilent). The gProcessed signal (dye normalized backgroung substracted signal intensity) was log  base 2 transformed and then for each of the array the 75th percentile value was calculated separately. In each sample the log transformed intensity values for each probe is substracted by the calculated 75th percentile value of the respective array and expression values were obtained.

source_name: Endothelial Cells, 24hrs, 6Gy, replicate 3

label_protocol: cRNA was labeled with Cy3 by using  Agilent Quick Amp labeling kit (p/n5190-0442) following manufacturer's instructions. Labeled cDNA was cleaned using Qiagen Rneasy cloumns (Cat No.: 74106). Dye corporation and cRNA yield was checked by Nanodrop ND-1000

growth_protocol: Human Umbilical Vein endothelial cells (HUVECs) were cultured in Endothelial Cell Growth Medium (ECGM) containing supplements (ECGS, bFGF, EGF, heparin and hydrocortisone) in Endothelial Cell Matrix (ECM) coated flasks with change in media every 2 days. When the cells reached 70-80% confluency, they were trypsinized in 0.25% trypsin-EDTA, pelleted down at 200xg, 5minutes and resuspended in ECGM. The cultures were incubated at 37°C in humidified incubator with 5% CO₂

extract_protocol: RNA was isolated using TRIzol method as per manufacturer's instructions. Concentration and purity of RNA was evaluated by Nanodrop spectrophotometer (Thermo Scientific 1000) and integrity was analyzed by Bioanalyzer (Agilent ; 2100).

treatment_protocol: Endothelial cells were irradiated with 6Gy ionising radiation. Media was replaced with fresh medium in all unirradiated and irradiated  cells. Cells were then incubated for 24hrs at 37°C in humidified incubator with 5% CO₂

tag: tissue

value: Umbilical Cord

tag: passage number

tag: type of cells

value: Endothelial Cells


title: LNCaP_shcontrol_rep1

source_name: LNCaP, shcontrol, replicate1

value: control KD


title: D4ag6917-1: Fibroblast_HGPS affected-3_rep. 1

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina Human HT12v4 Expression Bead Chips (Illumina, San Diego, CA). The arrays were then rinsed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-conjugated Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

source_name: Skin fibroblasts

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Dermal fibroblasts from HGPS patients and clinically unaffected parental controls were obtained from the  Coriell Institute for Medical Research. Fibroblast cells were grown in Dulbecco modified eagle medium (DMEM), supplemented with 15% fetal bovine serum (FBS) (Gibco BRL), 50 µg/ml streptomycin and 50 units/ml penicillin, at 37oC with 5% CO2.  HGPS patient AG03198 (10 yo female) was compared to AG03258 control (36 yo male, father);  HGPS patient AG03513 (13 yo male) was compared to AG03512 control (41 yo female, mother); and HGPS patient AG6917 (3 yo male)  was compared to AG6299 control (34 yo female, mother).

extract_protocol: RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: 2x106 cells were seeded in 10 cm plates and grown overnight, the cells were then rinsed in cold PBS prior to RNA extraction.

tag: gender

value: Male

tag: disease status

value: Hutchinson-Gilford progeria syndrome (HGPS)-affected

tag: age (years)

tag: condition

value: Untransformed

value: Skin fibroblasts


title: D.7 Itk-/- LMN4 rep1

description:
D7LMN4_FPKM.txt
d7-WT-LMN4A


title: LNCaP_shcontrol_rep2

source_name: LNCaP, shcontrol, replicate2


title: D4ag6917-3: Fibroblast_HGPS affected-3_rep. 3


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

tag: Sex

value: male

tag: age

tag: strain


title: Endothelial Cells_ 6Gy radiation_AMF treated_rep3

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_2_3
Gene Expression after 24hrs in 6Gy irradiated amifostine treated endothelial cells

data_processing: Raw data was analysed by using GeneSpring GX software (Agilent). The gProcessed signal (dye normalized backgroung substracted signal intensity) was log base 2 transformed and then for each of the array the 75th percentile value was calculated separately. In each sample the log transformed intensity values for each probe is substracted by the calculated 75th percentile value of the respective array and expression values were obtained.

source_name: Endothelial Cells, 24hrs, 6Gy, amifostine treated, replicate 3

growth_protocol: Bone marrow endothelial cells were cultured in Endothelial Cell Growth Medium (ECGM) in Endothelial Cell Matrix (ECM) coated flasks with change in media every 2 days. When the cells reached 70-80% confluency, they were trypsinized in 0.25% trypsin-EDTA, pelleted down at 100xg, 5minutes and resuspended in ECGM. The cultures were incubated at 37°C in humidified incubator with 5% CO₂

treatment_protocol: Endothelial cells were either treated with 6mM amifostine for 30minutes or irradiated with 6Gy ionising radiation or treated with 6mM amifostine 30minutes prior to 6Gy ionising radiation. Media was replaced with fresh medium in all treated and untreated cells. Cells were then incubated for 24hrs at 37°C in humidified incubator with 5% CO₂

value: Bone Marrow


title: HUVEC Endothelial Cells_ No radiation_rep3

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_1_4
Gene Expression in endothelial cells

source_name: Endothelial Cells replicate 3


title: D4ag6917-2: Fibroblast_HGPS affected-3_rep. 2


title: HUVEC Endothelial Cells_ 6Gy radiation_rep2

description:
SG13134300_257236317585_S001_GE1_1105_Oct12_1_1
Gene Expression after 24hrs in 6Gy irradiated endothelial cells

source_name: Endothelial Cells, 24hrs, 6Gy, replicate 2


title: HUVEC Endothelial Cells_ No radiation_rep2

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_2_4
Gene Expression in endothelial cells

source_name: Endothelial Cells replicate 2


title: HUVEC Endothelial Cells_ 6Gy radiation_rep1

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_2_4
Gene Expression after 24hrs in 6Gy irradiated endothelial cells

source_name: Endothelial Cells, 24hrs, 6Gy, replicate 1


title: C4ag6299-3: Fibroblast_Ctr for HGPS affected-3_rep.3

value: Female

value: Clinically unaffected


title: D.7 WT LMN4 rep3

description:
D7LMN4_FPKM.txt
d7-Itk-LMN4C

tag: cell type

value: WT


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad001


title: HUVEC Endothelial Cells_ No radiation_rep1

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_1_4
Gene Expression in endothelial cells

source_name: Endothelial Cells replicate 1


title: D.7 WT LMN4 rep1

description:
D7LMN4_FPKM.txt
d7-Itk-LMN4A

tag: donor mouse strain


title: D.7 WT LMN4 rep2

description:
D7LMN4_FPKM.txt
d7-Itk-LMN4B

tag: recipient mouse strain


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad004


title: SAMPLE 5: DNA methylation in WT #4-4 mock 10w

description: Normal cells

tag: cell line

value: 293FT wild type


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad004


title: Endothelial Cells_ 6Gy radiation_AMF treated_rep1

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_2_1
Gene Expression after 24hrs in 6Gy irradiated amifostine treated endothelial cells

source_name: Endothelial Cells, 24hrs, 6Gy, amifostine treated, replicate 1


title: Endothelial Cells_ 6Gy radiation_rep2

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_1_2
Gene Expression after 24hrs in 6Gy irradiated endothelial cells


title: D.7 Itk-/- LMT4 rep3

description:
D0&D7LMT4_FPKM.txt
d7-WT-LMT4C

value: CD8+ T cells

tag: itk genotype

tag: timepoint


title: D.7 Itk-/- LMT4 rep2

description:
D0&D7LMT4_FPKM.txt
d7-WT-LMT4B

value: Itk-/-

tag: listeria treatment


title: D3ag3513-3: Fibroblast_HGPS affected-2_rep. 3

tag: tissue


title: D3ag3513-2: Fibroblast_HGPS affected-2_rep. 2


title: C4ag6299-2: Fibroblast_Ctr for HGPS affected-3_rep.2


title: Endothelial Cells_ 6Gy radiation_rep3

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_1_3
Gene Expression after 24hrs in 6Gy irradiated endothelial cells

tag: passage number

tag: type of cells


title: D.7 WT LMT4 rep3

description:
D0&D7LMT4_FPKM.txt
d7-Itk-LMT4C

value: day 7


title: C4ag6299-1: Fibroblast_Ctr for HGPS affected-3_rep.1

tag: gender

tag: disease status


title: LNCaP_KD1

source_name: LNCaP, GRB10 knockdown, KD1

value: LNCaP cell

tag: knockdown

value: GRB10  KD


title: D.7 WT LMT4 rep2

description:
D0&D7LMT4_FPKM.txt
d7-Itk-LMT4B


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad002

tag: brain region


title: Endothelial Cells_ 6Gy radiation_AMF treated_rep2

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_2_2
Gene Expression after 24hrs in 6Gy irradiated amifostine treated endothelial cells

source_name: Endothelial Cells, 24hrs, 6Gy, amifostine treated, replicate 2

value: Endothelial Cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B11_ad001

tag: Sex


title: Endothelial Cells_ 6Gy radiation_rep1

description:
SG13134300_257236317584_S001_GE1_1105_Oct12_1_1
Gene Expression after 24hrs in 6Gy irradiated endothelial cells


title: Endothelial Cells_ No radiation_AMF treated_rep3

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_2_3
Gene Expression after 24hrs in amifostine treated endothelial cells

source_name: Endothelial Cells, 24hrs, amifostine treated, replicate 3


title: D3ag3513-1: Fibroblast_HGPS affected-2_rep. 1

value: Male

tag: age (years)

tag: condition


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad012

tag: age

tag: strain


title: D.7 Itk-/- LMT4 rep1

description:
D0&D7LMT4_FPKM.txt
d7-WT-LMT4A

tag: cell type

tag: donor mouse strain

tag: recipient mouse strain


title: C3ag3512-3: Fibroblast_Ctr for HGPS affected-2_rep.3


title: D.0 Itk-/- rep3

description:
D0&D7LMT4_FPKM.txt
d0-WT-R3

source_name: CD44lowCD122low CD8+ T cells from Spleen

tag: itk genotype

tag: timepoint

value: day 0


title: C3ag3512-2: Fibroblast_Ctr for HGPS affected-2_rep.2

value: Untransformed

tag: tissue


title: Endothelial Cells_ No radiation_AMF treated_rep2

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_2_2
Gene Expression after 24hrs in amifostine treated endothelial cells

source_name: Endothelial Cells, 24hrs, amifostine treated, replicate 2

tag: passage number


title: D.0 Itk-/- rep2

description:
D0&D7LMT4_FPKM.txt
d0-WT-R2

tag: listeria treatment


title: Endothelial Cells_ No radiation_rep3

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_1_3
Gene Expression in endothelial cells

tag: type of cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad008


title: D.0 Itk-/- rep1

description:
D0&D7LMT4_FPKM.txt
d0-WT-R1


title: D1ag3199-3: Fibroblast_HGPS affected-1_rep. 3

tag: gender

tag: disease status

value: Hutchinson-Gilford progeria syndrome (HGPS)-affected

value: Skin fibroblasts


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad006

tag: brain region

value: SSs

value: male


title: Endothelial Cells_ No radiation_AMF treated_rep1

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_2_1
Gene Expression after 24hrs in amifostine treated endothelial cells

source_name: Endothelial Cells, 24hrs, amifostine treated, replicate 1

value: Bone Marrow


title: D1ag3199-2: Fibroblast_HGPS affected-1_rep. 2

value: Female


title: D.0 WT rep3

description:
D0&D7LMT4_FPKM.txt
d0-Itk-R3

value: WT


title: Endothelial Cells_ No radiation_rep2

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_1_2
Gene Expression in endothelial cells


title: D.0 WT rep2

description:
D0&D7LMT4_FPKM.txt
d0-Itk-R2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad004

tag: Sex


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B10_ad002


title: D1ag3199-1: Fibroblast_HGPS affected-1_rep. 1

tag: age (years)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad012


title: Mouse_ICMa: Mouse ICM rep 1

city: Atherton

first: Morteza

last: Roodgar

address: 26 Selby Ln

department: Genetics

institute: Stanford University

description: RNA sequencing_low input_50 cells

data_processing: The RNAseq analysis was conducted using STAR RNA-seq aligner and RSEM transcript quantification software and the pipeline currently used for the ENCODE project (Consortium, 2004; Dobin et al., 2013; Li and Dewey, 2011). For the downstream analysis DeSEQ2 was used for differential expression analysis (Love et al., 2014). The commonly expressed genes among species were used for quantitative cross-species expression comparisons. The gene-gene interaction networks are based on known interactions on string database(Szklarczyk et al., 2016).

source_name: blastocyst inner cell mass_ICM

extract_protocol: The rhesus macaque blastocysts on day 5 post IVF was used for immunosurgery to remove zonae pellucidae and trophectoderm as explained elsewhere(Mitalipov et al., 2006). In summary, the zonae pellucidae of rhesus blastocysts will be removed by exposure to 0.5% pronase in TH3 medium for 45 seconds. For immunosurgical isolation of rhesus ICM to remove trophectoderm, zona pellucidae-free rhesus blastocysts were exposed to rabbit anti-rhesus spleen serum for 30 minutes at 37°C from VandeVoort laboratory at UC Davis. Subsequently, the blastocysts were washed in TH3 medium for 3 times and were incubated in guinea pig complement reconstituted with HECM-9 (1:2 vol/vol) at 37°C for 30 minutes(Mitalipov et al., 2006). After the incubation, the trophectoderm was removed mechanically using a small-bore pipette (125μM inner diameter) and the clumps of ICM cells from each blastocyst were washed in PBS and placed in a separate PCR tube containing 5μL of RNAse-free water with 5% RNAse inhibitor. The ICMs were quickly frozen on dry ice and were stored at -80°C for cDNA synthesis and RNA-seq library preparation. The cDNA synthesis and RNA-seq were conducted directly from ICM cells using SMART-Seq V4 Ultra Low input cDNA synthesis kit (Clonetech Inc.). The cDNA concentration was measured using Quibit kit and Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.). The cDNA from each ICM were used for library preparation following Illumina Nextera XT kit protocol (Illumina Inc.). The quality and the quantity of the final library were evaluated using Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.),Kappa kit, and the Agilent 2100 Bioanalyzer instrument. Dual index RNA-seq library from ICMs were pooled together with dual index RNAseq libraries of approximately 50 iPSCs for sequencing with dual index Illumia platform on a HiSeq 4000 sequencing machine. The low input cDNA synthesis and RNA-seq library preparation for ICMs and iPSCs were performed simultaneously on similar number of cells and pooled together to be sequenced in the same batch to minimize the potential batch effects. The sequencing coverage approximately 50 million reads per RNA-seq sample.

value: ICM isolated from mouse blatocyst

tag: treatment

value: Immunosurgery removing trophectoderm to isolate ICM


title: D.0 WT rep1

description:
D0&D7LMT4_FPKM.txt
d0-Itk-R1

value: CD8+ T cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad001

tag: age


title: C1ag3257-3: Fibroblast_Ctr for HGPS affected-1_rep.3

source_name: Skin fibroblasts

value: Clinically unaffected

tag: condition

value: PDL 12


title: C1ag3257-1: Fibroblast_Ctr for HGPS affected-1_rep.1


title: Mouse_ICMb: Mouse ICM rep 2

description: RNA sequencing_low input_50 cells

tag: cell type


title: Mouse_ICMc: Mouse ICM rep 3

description: RNA sequencing_low input_50 cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad007

tag: strain


title: Thyroid_carcinoma_3 [miRNA]

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C)

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the limma package. Spot-level raw intensities were background-corrected using the normexp method and normalized with quantile normalization.

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations

extract_protocol: Total RNA was extracted from snap-frozen tissues with Trizol reagent.

tag: disease

tag: histology

value: PTC

value: F


title: CCS_5

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

country: China

institute: China Agricutural University

description: 13966X47(column header in raw counts file)

data_processing:
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to mm10 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Genome_build: mm10
Supplementary_files_format_and_content: txt, raw counts

source_name: tumor

growth_protocol: genetically induced tumor

extract_protocol:
harvested and snap frozen at primary tumor morbidity
Illumina RiboZero
RNA-Seq(ribosomal RNA depletion)

treatment_protocol: no pharmacological treatments

tag: genotype

value: HprtCre; Ewsr1-loxP; Atf1-loxP


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad006


title: Thyroid_carcinoma_14 [miRNA]


title: C1ag3257-2: Fibroblast_Ctr for HGPS affected-1_rep.2

value: Male

tag: tissue


title: Non-neoplasticthyroid_6 [miRNA]

value: M


title: CCS_4a

description: 13966X45(column header in raw counts file)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad004


title: CCS_6

description: 13966X48(column header in raw counts file)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad002


title: CCS_3

description: 13966X44(column header in raw counts file)


title: C3ag3512-1: Fibroblast_Ctr for HGPS affected-2_rep.1

value: Untransformed


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B1_ad008


title: FR_Mock _30hpi_rep4

city: Utrecht

first: Sarah

last: Courbier

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

data_processing:
Basecalls were performed using Illumina's bcl2fastq v1.8.4.
RNA-seq reads quality was controlled with FastQC v0.10.1.
Reads were aligned to the tomato reference genome version SL3.0 with ITAG3.20 annotations using STAR v2.4.2a (Dobin et al., 2013).
RNA-seq were counted using HTSeq-Count 0.6.1p1 (Anders et al., 2015).
Reads were normalized by their size factor via quantile normalization using the R package DESeq v1.18.0.
Genome_build: SL3.0

organism: Solanum lycopersicum

source_name: Leaf discs originating from the third oldest leaf

growth_protocol: Tomato (Solanum lycopersicum cv. Moneymaker) seeds were sown in wet vermiculite. After 10 days, seedlings were transferred into 9 x 9 cm pots with regular potting soil (Primasta® soil, the Netherlands). Tomato plants were grown for three weeks after transplanting in climate chambers (MD1400 ; Snijders, The Netherlands) in long day photoperiod (8 h dark / 16 h light) at 150 µmol m-2 s-1 photosynthetically active radiation (PAR) using the Philips GreenPower LED research modules (Signify B.V) white.

extract_protocol:
Total mRNA was isolated by using mRNA pull down method with magnetic streptavidin beads (Townsley et al., 2015)
Non-strand specific library according to Townsley et al. (2015) with minor modifications. Total mRNA was isolated from ground tomato leaf tissue using biotin oligo primers and magnetic streptavidin beads. mRNA pellets were washed and fragmentated. cDNAs were synthesized by using reverse transcriptase, PolI, RNAseH and T4 polymerase. cDNAs were washed and ligated to non-strand specific adapters and enriched by PCR. Libraries were size-selected (350bp) and eluted in Tris-HCl buffer. Libraries were sequenced using 1 x 75 pb high output Illumina NEXTseq500.

treatment_protocol: Plants were exposed to either control white light or white light supplemented with Philips GreenPower LED research modules far-red (FR) far-red-enriched light for five days (starting at ZT = 3 on the first day) prior to inoculation with Botrytis cinerea spores or a mock solution.

tag: barcode sequence

value: AAGAGCAT

tag: barcode id

tag: light pretreatment

value: Far-red enriched light

tag: infection

value: Mock

tag: timepoint

value: 30 hr

tag: replicate


title: CT_Mock _30hpi_rep4

value: CGCGATTA

value: White light


title: FR_B.c._24hpi_rep4

value: GCCGAATG

value: 24 hr


title: FR_B.c._30hpi_rep4

value: TCTCTCCG


title: CT_B.c._24hpi_rep4

value: CGCTCCAC


title: CT_B.c._30hpi_rep4

value: TCTGCCGC


title: CCS_2R

description: 13966X43(column header in raw counts file)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad012

tag: brain region

value: SSs

tag: Sex

value: male


title: FR_Mock _24hpi_rep4

value: ACTATCAC


title: Non-neoplasticthyroid_2 [miRNA]


title: Thyroid_carcinoma_8 [miRNA]

value: PTC

value: F


title: Thyroid_carcinoma_12 [miRNA]


title: CCS_4b

description: 13966X46(column header in raw counts file)

value: HprtCre; Ewsr1-loxP; Atf1-loxP


title: CCS_2L

description: 13966X42(column header in raw counts file)


title: CT_Mock _24hpi_rep4

value: GGTTCGCT


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad007


title: CCS_1

description: 13966X41(column header in raw counts file)


title: FR_B.c._30hpi_rep3

value: TAGTAAGG

value: Far-red enriched light


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad010


title: CT_B.c._30hpi_rep3

value: TCACCTAC

value: 30 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad004


title: FR_Mock _30hpi_rep3

value: ATTCATAG

value: Mock


title: CT_B.c._24hpi_rep3

value: TGCCGTCC

value: White light

value: 24 hr


title: FR_B.c._24hpi_rep3

value: CACACGTA


title: CT_Mock _30hpi_rep3

value: TAGACACC


title: Non-neoplasticthyroid_3 [miRNA]


title: Thyroid_carcinoma_30 [miRNA]

value: PTC+PDTC


title: Thyroid_carcinoma_15 [miRNA]

value: M


title: Non-neoplasticthyroid_5 [miRNA]


title: Thyroid_carcinoma_20 [miRNA]

value: PTC


title: Thyroid_carcinoma_7 [miRNA]

value: F


title: Thyroid_carcinoma_18 [miRNA]


title: Thyroid_carcinoma_10 [miRNA]


title: H3K4me3 ChIP shctrl 2

city: GOETTINGEN

first: SHILPA

last: PATIL

state: No further selection needed

address: ROBERT KOCH STRASSE 40

country: Germany

institute: UNIVERSITY MEDICAL CENTER GOETTINGEN

description: H3K4me3 ChIP shctrl 2

data_processing:
Raw reads were quality-checked using FastQC
Alignment against mm9 mouse reference genome was done by using BOWTIE2 version 0.4
Peak calling was performed by MACS2 version 2.1.0
Diffbind (Bioconductor R package) was utilized for differential binding analysis
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: NKC cells were cultured in DMEM supplemented with 10% FCS and 1% NEAA.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: NKC

tag: treatment

value: shRNA control


title: H3K4me3 ChIP shctrl 3

description: H3K4me3 ChIP shctrl 3


title: H3K4me3 ChIP shEZH2 2

description: H3K4me3 ChIP shEZH2 2

value: shRNA EZH2


title: H3K4me3 ChIP shEZH2 1

description: H3K4me3 ChIP shEZH2 1


title: H3K4me3 ChIP shEZH2 3

description: H3K4me3 ChIP shEZH2 3


title: H3K4me3 ChIP shctrl 1

description: H3K4me3 ChIP shctrl 1


title: H3K27me3 ChIP shEZH2 3

description: H3K27me3 ChIP shEZH2 3


title: Thyroid_carcinoma_6 [miRNA]

tag: age


title: Thyroid_carcinoma_4 [miRNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A9_ad008

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad010


title: CT_Mock _24hpi_rep3

value: CATCTTCA


title: FR_Mock _24hpi_rep3

value: GTGACATG

value: Far-red enriched light


title: FR_B.c._30hpi_rep2

value: GGCTAGGC

value: 30 hr


title: H3K27me3 ChIP shEZH2 2

description: H3K27me3 ChIP shEZH2 2


title: H3K27me3 ChIP shEZH2 1

description: H3K27me3 ChIP shEZH2 1


title: Thyroid_carcinoma_28 [miRNA]


title: H3K27me3 ChIP shctrl 3

description: H3K27me3 ChIP shctrl 3


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad004


title: H3K27me3 ChIP shctrl 2

description: H3K27me3 ChIP shctrl 2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad007


title: EZH2 ChIP shctrl 3

description: EZH2 ChIP shctrl 3


title: CT_Mock _30hpi_rep2

value: GTCAACAA

value: White light

value: Mock


title: CT_B.c._24hpi_rep2

value: GATGACAA

value: 24 hr


title: FR_B.c._24hpi_rep2

value: TAACGGTC


title: H3K27me3 ChIP shctrl 1

description: H3K27me3 ChIP shctrl 1


title: EZH2 ChIP shctrl 2

description: EZH2 ChIP shctrl 2


title: FR_Mock _24hpi_rep2

value: TTAGGTCT


title: Thyroid_carcinoma_17 [miRNA]

value: PTC

value: F


title: Thyroid_carcinoma_16 [miRNA]


title: Thyroid_carcinoma_1 [miRNA]


title: Thyroid_carcinoma_26 [miRNA]

value: M


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad010

value: SSs


title: Non-neoplasticthyroid_4 [miRNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad006

value: male


title: EZH2 ChIP shctrl 1

description: EZH2 ChIP shctrl 1

value: NKC

value: shRNA control


title: CT_B.c._30hpi_rep2

value: CTATTCTT


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A8_ad002


title: FR_Mock _30hpi_rep2

value: CAAGATAT

value: Far-red enriched light


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad001


title: Thyroid_carcinoma_2 [miRNA]


title: FR_B.c._30hpi_rep1

value: GTAGAGAT

value: 30 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad006


title: RNA-seq cas9EZH2 3

data_processing:
Raw reads were quality-checked using FastQC
Alignment against mm9 mouse reference genome was done by using TopHat2 (version 2.1.0)
Fragment per kilobase (FPKM) values were obtained by cuffnorm (version 2.2.1)
Differential gene expression was dervived by cuffdiff (version 2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: Differential gene expression

source_name: NKC_CRISPR/Cas9 EZH2

extract_protocol:
RNA was harvested using Trizol reagent
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: PDAC (pancreatic ductal adenocarcinoma) cell line carrying pancreas specific-Kras mutation (KrasG12D)

tag: transfected with

value: CRISPR/Cas9 EZH2


title: Thyroid_carcinoma_11 [miRNA]

tag: disease


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad004

tag: strain


title: RNA-seq cas9EZH2 2


title: CT_B.c._30hpi_rep1

value: AATTGCGG

value: White light


title: FR_Mock _30hpi_rep1

value: AGGTATTC

value: Mock


title: Thyroid_carcinoma_23 [miRNA]

tag: histology

value: PDTC+PTC

value: F


title: Thyroid_carcinoma_25 [miRNA]

value: PDTC

value: M


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad008

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad012


title: D.7 WT LMT4 rep1

description:
D0&D7LMT4_FPKM.txt
d7-Itk-LMT4A

source_name: CD44lowCD122low CD8+ T cells from Spleen; CD45.1-CD45.2+ post-adoptive transfer

value: CD8+ T cells

tag: donor mouse strain

tag: recipient mouse strain

tag: itk genotype

value: WT

value: day 7

tag: listeria treatment


title: RNA-seq cas9ctrl 1

source_name: NKC_CRISPR/Cas9 control

value: NKC

value: CRISPR/Cas9 control


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad001


title: Thyroid_carcinoma_9 [miRNA]


title: Non-neoplasticthyroid_1 [miRNA]


title: CT_B.c._24hpi_rep1

tag: barcode sequence

value: ACTCAGGT

tag: barcode id

tag: light pretreatment

tag: infection

value: 24 hr


title: CT_Mock _24hpi_rep2

value: GGTCGTAT

tag: timepoint

tag: replicate


title: CT_Mock _30hpi_rep1

value: GTCAGGTT

value: White light

value: 30 hr


title: RNA-seq cas9ctrl 3

tag: cell line

value: PDAC (pancreatic ductal adenocarcinoma) cell line carrying pancreas specific-Kras mutation (KrasG12D)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A7_ad002

tag: brain region

tag: Sex

tag: age


title: Thyroid_carcinoma_13 [miRNA]

tag: disease

value: PTC

value: F


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad010

tag: strain


title: Thyroid_carcinoma_5 [miRNA]

tag: histology


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad007


title: FR_B.c._24hpi_rep1

value: CAGAACGC

value: Far-red enriched light


title: RNA-seq cas9ctrl 2

tag: cell type

tag: transfected with


title: Thyroid_carcinoma_19 [miRNA]


title: RNA-seq shEZH2 3

source_name: NKC_shRNA EZH2

value: shRNA EZH2


title: RNA-seq shEZH2 1


title: RNA-seq shctrl 3

source_name: NKC_shRNA control

value: shRNA control


title: RNA-seq shEZH2 2


title: RNA-seq cas9EZH2 1

value: CRISPR/Cas9 EZH2


title: FR_Mock _24hpi_rep1

value: TCAACGTG

value: Mock


title: Thyroid_carcinoma_24 [miRNA]


title: FR_B.c._18hpi_rep4

value: CCACCTCT

value: 18 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad006

value: SSs

value: male


title: CT_Mock _24hpi_rep1

value: AGTATACT

value: 24 hr


title: FR_Mock _18hpi_rep4

value: TGTTATCA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad008


title: Endothelial Cells_ No radiation_rep1

description:
SG13134300_257236317583_S001_GE1_1105_Oct12_1_1
Gene Expression in endothelial cells

source_name: Endothelial Cells replicate 1

tag: tissue

value: Bone Marrow

tag: passage number

tag: type of cells

value: Endothelial Cells


title: WholeTissuePLA_T1_PLA_L3

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

data_processing:
Illumina RTA software v1.18.66.3.
Fastq files extracted with bcl2fastq2 Conversion Software
Reads were pre-processed with Cutadapt to remove Illumina adaptors.
Resulting reads were mapped and quantified on the sheep  transcriptome (Ensembl gene-build Oar3.1 version ) using RSEM
Data were normalized using TMM method from limma Bioconductor package
Genome_build: Oar3.1 v75
Supplementary_files_format_and_content: tab-delimited text files include normalized RSEM expected counts values for each sample

organism: Ovis aries

source_name: PLA – Posterior Left Atria

extract_protocol:
RNA was isolated following standard procedures
RNAseq libraries were constructed using the Illumina NEBNext Ultra™ RNA Library Prep Kit and established protocols.

treatment_protocol: Atrial fibrillation was induced using a tachypacing device implanted in the right atrium of the sheep heart.

tag: sheep id

tag: condition

value: Transition

tag: atria

value: Left

tag: technical replicate


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A5_ad002


title: CT_B.c._12hpi_rep4

tag: barcode sequence

value: ACCAGCGC

tag: barcode id

tag: light pretreatment

value: White light

tag: infection

tag: timepoint

value: 12 hr

tag: replicate


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A5_ad010

tag: brain region

tag: Sex

tag: age

tag: strain


title: WholeTissuePLA_Saline4_L7


title: FR_B.c._12hpi_rep4

value: GATCCTTG

value: Far-red enriched light


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A5_ad008


title: WholeTissuePLA_T2_PLA_L5


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad004


title: WholeTissuePLA_Saline4_L8


title: RNA-seq shctrl 2

tag: cell line

value: NKC

tag: cell type

value: PDAC (pancreatic ductal adenocarcinoma) cell line carrying pancreas specific-Kras mutation (KrasG12D)

tag: transfected with

value: shRNA control


title: CT_Mock _18hpi_rep4

value: CTACGGCG

value: Mock

value: 18 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A6_ad002

value: SSs

value: male


title: RNA-seq shctrl 1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A5_ad004


title: CT_Mock _12hpi_rep4

value: GCAAGGCA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A5_ad012


title: FR_Mock _12hpi_rep4

value: CATAGATT


title: WholeTissuePLA_Saline3_L8

tag: sheep id

value: Transition


title: Thyroid_carcinoma_29 [miRNA]

tag: disease

tag: histology

value: PDTC

value: M


title: FR_B.c._18hpi_rep3

value: AGTGCATC


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad001


title: WholeTissuePLA_Saline3_L7

tag: condition

tag: atria

value: Left

tag: technical replicate


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad007


title: WholeTissuePLA_Saline1_L8


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad010


title: CT_Mock _18hpi_rep3

tag: barcode sequence

value: GAGAAGGT

tag: barcode id

tag: light pretreatment

value: White light


title: FR_Mock _18hpi_rep3

value: TTACACTA

value: Far-red enriched light

tag: infection

tag: timepoint

tag: replicate


title: CT_B.c._18hpi_rep3

value: TCTAACTT


title: CT_B.c._12hpi_rep3

value: TGACTAGT

value: 12 hr


title: WholeTissuePLA_Saline2_L8


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad012

tag: brain region

tag: Sex

tag: age


title: FR_B.c._12hpi_rep3

value: CACGGCTG


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad012

value: SSs

tag: strain


title: FR_B.c._18hpi_rep2

value: TGTCCGGA

value: 18 hr


title: CT_Mock _12hpi_rep3

value: TTCTGACG

value: Mock


title: WholeTissuePLA_Saline1_L7

value: Transition


title: CT_B.c._18hpi_rep4

value: GACGGTAG


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad007

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad002


title: WholeTissuePLA_Control3_L8

value: Sham

value: Left


title: FR_Mock _12hpi_rep3

value: AGACACGG


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad006


title: WholeTissuePLA_S1_PLA_L3


title: WholeTissuePLA_S2_PLA_L5


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad006


title: CT_B.c._18hpi_rep2

value: ACTTAACC

value: White light


title: WholeTissuePLA_S3_PLA_L6

value: Control


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A4_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad004


title: WholeTissuePLA_Control3_L7


title: FR_Mock _18hpi_rep2

value: GTTGTCGG

value: Far-red enriched light


title: Thyroid_carcinoma_22 [miRNA]

value: PDTC

value: M


title: WholeTissuePLA_Control2_L8


title: WholeTissuePLA_Control1_L8


title: WholeTissuePLA_Control2_L7


title: WholeTissuePLA_Saline2_L7


title: CMs_RAA_S4_Sham_L7

source_name: Isolated Cardiomyocytes – Right atrial appendage

value: Right


title: CT_Mock _18hpi_rep2

value: CCGGTGCT

value: 18 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A3_ad008

value: SSs


title: FR_B.c._12hpi_rep2

value: GTTGGATA

value: 12 hr


title: CMs_RAA_S4_Sham_L8


title: CMs_RAA_D24_Transition_L8

value: Transition


title: CMs_RAA_D27_Transition_L7


title: FR_B.c._18hpi_rep1

value: ATAAGAAC


title: CT_B.c._18hpi_rep1

value: GCGCATTC


title: FR_Mock _12hpi_rep2

value: TCGAATCG

value: Mock


title: CMs_RAA_S3_Sham_L8

value: Sham


title: CT_Mock _12hpi_rep2

value: TACCATTG

value: White light


title: CMs_RAA_D24_Transition_L7


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad004

value: male


title: rtTA_d2_2

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: d2 and d7-gene counts

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Genome_build: mm10
Supplementary_files_format_and_content: read counts for each genes were given in the processed data files

source_name: MEF

growth_protocol: MEFs were cultured in DMEM+10% FBS, at 37℃ in incubator.

extract_protocol:
TRIzol following manufacturer's protocol
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

treatment_protocol: MEFs were infected with Ascl1/Brn3b/Isl1 overexpressing lentiviruses, doxycycline was added on day 0 to induce Ascl1/Brn3b/Isl1 expression, cells were switched to neuronal medium (DMEM/F12+GlutaMAX+N2+B27+Forskolin+FGF2) on day 2 of reprogramming; medium was half-changed every other day.

tag: treatment

value: infected with rtTA-lentiviruses

tag: collecting day

value: day 7


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad001


title: CMs_RAA_D27_Transition_L8

tag: sheep id

value: Right


title: CMs_RAA_S3_Sham_L7


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad002


title: rtTA_d2_1

description: d2 and d7-gene counts


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad012


title: CT_B.c._12hpi_rep1

value: CTACATGC


title: CT_Mock _18hpi_rep1

value: GAATCAAT

value: 18 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad008

value: SSs


title: WholeTissuePLA_Control1_L7

value: Left


title: FR_Mock _18hpi_rep1

value: TCCTCGGT

value: Far-red enriched light


title: ABI-_d7 w. FGF2_2

description: d2 and d7-gene counts

value: MEFs negative for ABI


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad010


title: FR_B.c._12hpi_rep1

value: TTGAGGAG

value: 12 hr


title: CT_B.c._12hpi_rep2

value: TCCGCTCA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A2_ad006


title: CMs_RAA_D23_Transition_L8

value: Transition


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad008


title: FR_Mock _12hpi_rep1

value: GCGTACAT

value: Mock


title: CMs_RAA_D23_Transition_L7


title: CT_Mock _12hpi_rep1

value: GGTCAATT

value: White light


title: CT_B.c._6hpi_rep4

value: ACGCCGAG

value: 6 hr


title: ABI-_d7 w. FGF2_1

description: d2 and d7-gene counts

value: day 7


title: ABI-_d7_1

description: d2 and d7-gene counts


title: ABI-_d7_2

description: d2 and d7-gene counts


title: CMs_RAA_D20_Chronic_L8

value: Chronic

value: Right


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad007

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad006


title: ABI+_d7 w. FGF2_1

description: d2 and d7-gene counts


title: CMs_RAA_D16_Chronic_L8


title: CMs_RAA_D16_Chronic_L7


title: FR_Mock _6hpi_rep4

value: CGCAACCG

value: Far-red enriched light


title: FR_B.c._6hpi_rep4

value: CGGTTACC


title: CMs_RAA_D19_Chronic_L8


title: ABI+_d7_2

description: d2 and d7-gene counts


title: ABI+_d7 w. FGF2_2

description: d2 and d7-gene counts


title: CT_Mock _6hpi_rep4

value: AACAGGCG

value: 0 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A11_ad010


title: CMs_RAA_C1_Control_L8

value: Control


title: CMs_RAA_C1_Control_L7


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A11_ad012


title: CT_B.c._0hpi_rep4

value: GTGGCTGA


title: CMs_RAA_D20_Chronic_L7


title: FR_B.c._0hpi_rep4

value: TTGCTTAT


title: FR_Mock _0hpi_rep4

value: ACATCTTA

value: Mock


title: ABI+_d7_1

description: d2 and d7-gene counts


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A11_ad008


title: CMs_LAA_S4_Sham_L8

source_name: Isolated Cardiomyocytes – Left atrial appendage

value: Sham

value: Left


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A12_ad002


title: CT_Mock _0hpi_rep4

value: GCCTGAAC

value: White light

value: 6 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A11_ad006

value: SSs


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A10_ad012

value: male


title: CMs_RAA_D19_Chronic_L7

value: Chronic

value: Right


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A11_ad007


title: ABI_d2_1

description: d2 and d7-gene counts

value: day 2


title: I_d2_1

description: d2 and d7-gene counts

value: infected with Isl1-lentiviruses


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A10_ad008


title: CMs_LAA_S3_Sham_L8


title: B_d2_2

description: d2 and d7-gene counts

value: infected with Brn3b-lentiviruses


title: I_d2_2

description: d2 and d7-gene counts


title: B_d2_1

description: d2 and d7-gene counts


title: CT_Mock _6hpi_rep3

value: CGGCAGAT


title: A_d2_2

description: d2 and d7-gene counts

value: infected with Ascl1-lentiviruses


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A10_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A10_ad006


title: CMs_LAA_S4_Sham_L7


title: CT_B.c._6hpi_rep3

value: TCATGCTG


title: A_d2_1

description: d2 and d7-gene counts


title: CT_B.c._0hpi_rep3

value: CCTGGAAG

value: 0 hr


title: FR_Mock _6hpi_rep3

value: TCGATATC

value: Far-red enriched light

value: Mock


title: ABI_2

description: d13-iRGC-gene counts

source_name: ABI-iRGC

value: day 13


title: CMs_LAA_S3_Sham_L7

value: Sham

value: Left


title: CMs_LAA_D27_Transition_L8

value: Transition


title: CMs_LAA_D24_Transition_L8


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad012

value: SSs

value: male


title: CMs_LAA_D24_Transition_L7


title: ABI_1

description: d13-iRGC-gene counts


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A10_ad002


title: BAM_2

description: d13-iRGC-gene counts

source_name: BAM-iN


title: CT_Mock _0hpi_rep3

value: TGCTCATG

value: White light


title: CMs_LAA_D23_Transition L7


title: BAM_1

description: d13-iRGC-gene counts


title: FR_Mock _0hpi_rep3

value: TTAGCCAG


title: CT_B.c._6hpi_rep2

value: CGGCGATG

value: 6 hr


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad006


title: rtTA_2

description: d13-iRGC-gene counts

source_name: MEFs

value: infected with rtTA-lentiviruses


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad004


title: rtTA_1

description: d13-iRGC-gene counts


title: CMs_LAA_D20_Chronic_L7

value: Chronic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad008


title: CMs_LAA_D23_Transition_L8


title: FR_B.c._6hpi_rep2

value: GATGTGCC


title: CMs_LAA_D20_Chronic_L8


title: CMs_LAA_D19_Chronic_L8


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_A1_ad010


title: FR_B.c._0hpi_rep3

value: CCATCAGG

value: 0 hr


title: CMs_LAA_D27_Transition_L7


title: Sperm, F2-NHS-2 (sRNA-seq)

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with F2_NHS_2 in the column of processed data file

data_processing:
The 50nt sequence tags from HiSeq sequencing went through the data cleaning first,
which included getting rid of the low quality tags and several kinds of contaminants from the
50nt tags. Length distribution of clean tags was then summarized. Afterwards, the standard
bioinformatics analysis was used to annotate the clean tags into different categories and to take
those which cannot be annotated to any category to predict the novel miRNA and base edit of potential known miRNA
Genome_build: mm10
Supplementary_files_format_and_content: SpermsRNATPM.txt

extract_protocol:
Mouse sperm samples were isolated for RNA. Then small RNA samples were sequenced.
Smalll RNA was used for the library.

value: ICR

tag: tissue

value: Sperm

tag: generation


title: CMs_LAA_D16_Chronic_L8

tag: condition

tag: atria


title: FR_Mock _6hpi_rep2

tag: barcode sequence

value: AATCACCT

value: Far-red enriched light

value: Mock


title: CMs_LAA_D19_Chronic_L7

value: Left

tag: technical replicate


title: Sperm, F2-NHS-3 (sRNA-seq)

description: The group information is prefixed with F2_NHS_3 in the column of processed data file


title: FR_B.c._0hpi_rep2

value: GTATCTCG

tag: barcode id

tag: light pretreatment


title: FR_Mock _0hpi_rep2

value: ATGTTGCG

tag: infection

tag: timepoint


title: Sperm, F2-con-2 (sRNA-seq)

description: The group information is prefixed with  F2_Con_2 in the column of processed data file


title: FR_B.c._6hpi_rep1

value: ATAGTATG

tag: replicate


title: CMs_LAA_C1_Control_L7

value: Control


title: CMs_LAA_D16_Chronic_L7


title: CT_Mock _6hpi_rep2

value: CTTGAACT

value: White light


title: CT_Mock _0hpi_rep2

value: TCGGTTGG


title: WholeTissue_RAA_D30_Transition_L6

source_name: WholeTissue – Right atrial appendage

value: Transition

value: Right


title: FR_Mock _6hpi_rep1

value: CGTGGTGC

value: 6 hr


title: Sperm, F2-con-3 (sRNA-seq)

description: The group information is prefixed with  F2_Con_3 in the column of processed data file

value: ICR


title: Sperm, F2-con-1 (sRNA-seq)

description: The group information is prefixed with  F2_Con_1 in the column of processed data file

value: Sperm


title: CMs_LAA_C1_Control_L8


title: WholeTissue_RAA_D27_Transition_L5


title: WholeTissue_RAA_D27_Transition_L6


title: Sperm, F2-NHS-1 (sRNA-seq)

description: The group information is prefixed with  F2_NHS_1 in the column of processed data file


title: WholeTissue_RAA_D24_Transition_L6


title: CT_B.c._6hpi_rep1

value: AACGAGTC


title: FR_B.c._0hpi_rep1

value: AGCGTTAC

value: Far-red enriched light

value: 0 hr


title: FR_Mock _0hpi_rep1

value: GACTGCCT

value: Mock


title: Sperm, F1-con-1 (sRNA-seq)

description: The group information is prefixed with  F1_Con_1 in the column of processed data file


title: WholeTissue_RAA_C1_Sham_L6


title: CT_Mock _0hpi_rep1

value: ATGATTGA


title: WholeTissue_RAA_D24_Transition_L5


title: Sperm, F1-NHS-1 (sRNA-seq)

description: The group information is prefixed with  F1_NHS_1 in the column of processed data file


title: Sperm, F1-con-2 (sRNA-seq)

description: The group information is prefixed with  F1_Con_2 in the column of processed data file


title: WholeTissue_RAA_S4_Sham_L6

value: Sham


title: Sperm, F0-con-3 (sRNA-seq)

description: The group information is prefixed with  F0_Con_3 in the column of processed data file


title: Sperm, F1-con-3 (sRNA-seq)

description: The group information is prefixed with  F1_Con_3 in the column of processed data file


title: WholeTissue_RAA_C1_Sham_L5

value: Control


title: Sperm, F0-NHS-2 (sRNA-seq)

description: The group information is prefixed with F0_NHS_2 in the column of processed data file


title: Sperm, F0-con-1 (sRNA-seq)

description: The group information is prefixed with F0_Con_1 in the column of processed data file


title: Sperm, F0-NHS-3 (sRNA-seq)

description: The group information is prefixed with F0_NHS_3 in the column of processed data file


title: W5BA10-2_intestine

description: The group information is prefixed with W5BA10_2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: gene_expression.txt (RPKMs, readcounts)

extract_protocol:
Mouse small intestine samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: Intestine


title: CT_B.c._0hpi_rep1

value: GCTATTCT

value: White light


title: W5BA10-3_intestine

description: The group information is prefixed with W5BA10_3 in the column of processed data file


title: WholeTissue_RAA_D15_Chronic_L6

value: Chronic

value: Right


title: WholeTissue_RAA_D16_Chronic_L5


title: CT_B.c._0hpi_rep2

value: CGTGTGTT


title: W5BA0-2_intestine

description: The group information is prefixed with  W5BA0_2 in the column of processed data file

value: ICR


title: WholeTissue_RAA_D16_Chronic_L6


title: WholeTissue_RAA_D19_Chronic_L6


title: WholeTissue_RAA_D19_Chronic_L5


title: WholeTissue_RAA_S3_Sham_L6


title: WholeTissue_LAA_D30_Transition_L6

source_name: WholeTissue – Left atrial appendage

value: Transition

value: Left


title: Sperm, F1-NHS-3 (sRNA-seq)

description: The group information is prefixed with F1_NHS_3 in the column of processed data file

value: Sperm


title: WholeTissue_RAA_D30_Transition_L5


title: W5BA0-1_intestine

description: The group information is prefixed with W5BA0_1 in the column of processed data file


title: Sperm, F1-NHS-2 (sRNA-seq)

description: The group information is prefixed with F1_NHS_2 in the column of processed data file


title: CT_Mock _6hpi_rep1

source_name: Leaf discs originating from the third oldest leaf

value: GTGCTACA

value: 6 hr


title: WholeTissue_RAA_S3_Sham_L5


title: WholeTissue_RAA_S4_Sham_L5


title: W5BA0-3_intestine

description: The group information is prefixed with  W5BA0_3 in the column of processed data file


title: WholeTissue_RAA_D15_Chronic_L5


title: W5BA10-1_intestine

description: The group information is prefixed with  W5BA10_1 in the column of processed data file


title: WholeTissue_LAA_D27_Transition_L6


title: WholeTissue_LAA_D27_Transition_L5


title: WholeTissue_LAA_D30_Transition_L5


title: Sperm, F0-con-2 (sRNA-seq)

description: The group information is prefixed with  F0_Con_2 in the column of processed data file


title: W5A0-2_intestine

description: The group information is prefixed with W5A0_2 in the column of processed data file


title: W5A10-2_intestine

description: The group information is prefixed with W5A10_2 in the column of processed data file


title: W5A10-1_intestine

description: The group information is prefixed with W5A10_1 in the column of processed data file


title: WholeTissue_LAA_D24_Transition_L6


title: WholeTissue_LAA_C1_Control_L5


title: W5A0-1_intestine

description: The group information is prefixed with W5A0_1 in the column of processed data file


title: WholeTissue_LAA_S4_Sham_L6


title: Sperm, F2_NHS_1 (RNA-seq)

description: The group information is prefixed with  F2_NHS_1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: All FPKM.txt

extract_protocol:
Mouse sperm samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: cell type


title: W5A0-3_intestine

description: The group information is prefixed with W5A0_3 in the column of processed data file


title: WholeTissue_LAA_S4_Sham_L5


title: Sperm, F2_Con_2 (RNA-seq)

description: The group information is prefixed with  F2_Con_2 in the column of processed data file


title: WholeTissue_LAA_D15_Chronic_L6


title: WholeTissue_LAA_C1_ControlL6


title: W5A10-3_intestine

description: The group information is prefixed with W5A10_3 in the column of processed data file


title: WholeTissue_LAA_D24_Transition_L5


title: Sperm, F2_Con_3 (RNA-seq)

description: The group information is prefixed with  F2_Con_3 in the column of processed data file


title: WholeTissue_LAA_S3_Sham_L5


title: Sperm, F2_Con_1 (RNA-seq)

description: The group information is prefixed with  F2_Con_1 in the column of processed data file


title: Sperm, F1_Con_3 (RNA-seq)

description: The group information is prefixed with  F1_Con_3 in the column of processed data file


title: Sperm, F2_NHS_2 (RNA-seq)

description: The group information is prefixed with F2_NHS_2 in the column of processed data file


title: Sperm, F1_NHS_2 (RNA-seq)


title: WholeTissue_LAA_D19_Chronic_L5


title: WholeTissue_LAA_D19_Chronic_L6


title: Sperm, F1_NHS_3 (RNA-seq)

description: The group information is prefixed with F1_NHS_3 in the column of processed data file


title: Sperm, F1_Con_2 (RNA-seq)

description: The group information is prefixed with  F1_Con_2 in the column of processed data file


title: 21_2

city: Taian

first: chuansong

last: quan

state: - Select -

address: yingsheng road 2

department: School of Basic Medical Sciences

institute: shandong first medical university

description: BCRseq data

data_processing:
Reads with low quality or adaptor contamination were filtered out, and the clean reads were aligned to Genome Reference Consortium Human genome build 38 using HISAT2.The featureCounts package was used to count reads aligned to each gene in order to quantify gene expression levels.
The filtered reads were aligned to BCR germline sequences using MiXCR. VDJtools52 was used for downstream analysis including clonotype filtering, diversity analysis, and repertoire overlap.
Genome_build: human GRCh38
Genome_build: IMGT Repertoire
Supplementary_files_format_and_content: featruecounts

source_name: PBMC

extract_protocol:
RNA was purified from PBMCs using the RNeasy Plus Mini Kit (Qiagen, Germany). RNA concentration and integrity number were determined with the RNA Bioanalyzer (Agilent).As for BCR sequencing, the third complementary determining region (CDR3) of BCR H chain was amplified in a multiplex PCR.
Libraries were generated according to the manufacturer’s instructions.

tag: patient group

value: moderate

tag: time period

value: recovered

tag: disease

value: Hemorrhagic fever with renal syndrome


title: WholeTissue_LAA_S3_Sham_L6

value: Sham


title: 37_1

description: BCRseq data

value: severe

value: acute


title: WholeTissue_LAA_D15_Chronic_L5


title: WholeTissue_LAA_D16_Chronic_L6


title: 18_2

description: BCRseq data


title: 21_1

description: BCRseq data


title: Sperm, F1_NHS_1 (RNA-seq)

description: The group information is prefixed with  F1_NHS_1 in the column of processed data file

tag: strain

tag: treatment


title: Sperm, F2_NHS_3 (RNA-seq)

description: The group information is prefixed with F2_NHS_3 in the column of processed data file


title: 37_3

description: BCRseq data


title: Sperm, F0_Con_1 (RNA-seq)

description: The group information is prefixed with F0_Con_1 in the column of processed data file


title: Sperm, F0_NHS_3 (RNA-seq)

description: The group information is prefixed with F0_NHS_3 in the column of processed data file


title: Sperm, F0_NHS_2 (RNA-seq)

description: The group information is prefixed with F0_NHS_2 in the column of processed data file


title: Sperm, F1_Con_1 (RNA-seq)

description: The group information is prefixed with  F1_Con_1 in the column of processed data file


title: Sperm, F0_Con_2 (RNA-seq)

description: The group information is prefixed with  F0_Con_2 in the column of processed data file


title: Testis, MNC-3

description: The group information is prefixed with  MNC-3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: All_geneFPKM.csv

tag: tissue

value: Testis

value: MNC (vector control of M receptor lentivirus)

tag: genotype

value: control


title: Testis, MNC-2

description: The group information is prefixed with  MNC-2 in the column of processed data file


title: WholeTissue_LAA_D16_Chronic_L5

tag: sheep id

tag: condition

value: Chronic


title: 14_3

description: BCRseq data


title: Sperm, F0_Con_3 (RNA-seq)

description: The group information is prefixed with  F0_Con_3 in the column of processed data file

tag: generation


title: Sperm, F0_NHS_1 (RNA-seq)

description: The group information is prefixed with  F0_NHS_1 in the column of processed data file


title: 9_2

description: BCRseq data


title: 18_1

description: BCRseq data


title: 7_2

description: BCRseq data


title: Plasma, healthy_30

first: Yumin

last: Zhu

address: Tsinghua University

department: Life Science

institute: Tsinghua University

data_processing:
We used Cutadapt to remove adapters and read pairs with average quality score below 30 in either read of the pair.
Paired reads were first mapped to rRNA database (from NCBI RefSeq database). The unmapped reads were then mapped to the human genome sequences (UCSC genome build hg38).
A genome index was generated using STAR with splicing junction annotations from GENCODE V27. Remaining reads after the first two steps were mapped to the circular RNAs from circBase.
We removed duplicated read pairs using picard MarkDuplicates because the dataset contained a large proportion of duplicated reads due to PCR amplification in library construction.
Finally, a gene count matrix was generated using featureCounts with options “-M -p -s 1 -t exon -g gene_id”.
Genome_build: hg38
Supplementary_files_format_and_content: tab-limited text file for raw counts

source_name: healthy donor's plasma

extract_protocol:
QIAzol was used to lyse plasma to extract all RNA
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Cat.Nos. 634414 ), SMARTer Stranded Total RNAseq-Pico Input Mammalian kit (Clontech). First, total RNA is converted to cDNA, and then adapters for Illumina sequencing (with specific barcodes) are added through PCR using only a limited number of cycles. The PCR products are purified, and then ribosomal cDNA is depleted. The cDNA fragments from Protocol D are further amplified with primers universal to all libraries. Lastly, the PCR products are purified once more to yield the final cDNA library.

tag: disease state

value: healthy donor

tag: gender

value: M

tag: age

tag: Stage

value: plasma


title: Testis, MNC-1

description: The group information is prefixed with  MNC-1 in the column of processed data file

value: ICR


title: 14_1

description: BCRseq data


title: 7_1

description: BCRseq data


title: Testis, M5-1

description: The group information is prefixed with  M5-1 in the column of processed data file

value: M5 knockdown


title: Testis, M5-3

description: The group information is prefixed with M5-3 in the column of processed data file


title: Testis, M3-2

description: The group information is prefixed with  M3-2 in the column of processed data file

value: M3 knockdown


title: 9_1

description: BCRseq data


title: Testis, M1-3

description: The group information is prefixed with M1-3 in the column of processed data file

value: M1 knockdown


title: Plasma, healthy_27

value: F


title: Testis, M5-2

description: The group information is prefixed with M5-1 in the column of processed data file


title: Testis, M1-2

description: The group information is prefixed with M1-2 in the column of processed data file


title: Testis, M1-1

description: The group information is prefixed with M1-1 in the column of processed data file


title: Plasma, healthy_25


title: Plasma, healthy_29


title: Plasma, healthy_23


title: Testis, Con-1

description: The group information is prefixed with Con-1 in the column of processed data file

value: Con


title: Testis, M3-1

description: The group information is prefixed with M3-1 in the column of processed data file


title: Plasma, healthy_28


title: Plasma, healthy_26


title: Testis, M3-3

description: The group information is prefixed with  M3-3 in the column of processed data file


title: Plasma, healthy_22


title: 6RARA71_RV_S21

city: Indianapolis

first: Robert

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

description:
total RNA (>17 nucleotides)
RNA-Seq bam files after alignment to rat Rn6 genome

data_processing:
FastQC/MultiQC v0.11.5
STAR v2.5
NGSUtils/bamutils v0.5.9
subread/featureCounts v1.5.1
edgeR ROBUST option on v3.22.5
Genome_build: Rn6
Supplementary_files_format_and_content: Excel summarized output file includes gene level fold change as log2 (HH/RA-RA), uncorrected p-values, and FDR corrected q-values. At the sample level, there is log2(FPKM) and raw count data.

organism: Rattus norvegicus

source_name: Heart Right Ventricle (RV)

growth_protocol: The females delivered naturally at term. Pups were weaned at 21 days and physiologic experiments and animal sacrifice with tissue harvest occurred at 6 weeks of age.

extract_protocol:
Fresh frozen tissue (~25-50mg) from rat lung or heart RV was ground with a mortar and pestle kept on dry ice. The pulverized tissue was homogenized in 1ml Trizol using the Polytron homogenizer at 20krpm for 1 minute on ice. Total RNA was isolated from the Trizol homogenate after high speed centrifugation (20 minutes, 4C) using Zymo Direct-zol column procedure and included on-column DNase digestion. RNA quality and integrity was determined by UV spectrum ratios and Agilent BioAnalyzer Tapestation.
Libraries were prepared using the KAPA mRNA Hyperprep Dual Index Kit, and both tissues’ libraries were mixed and run on the Illumina HiSeq4000 in one flowcell across five lanes.

treatment_protocol: Room air versus a hypobaric hypoxia chamber, depressurized to an equivalent of an inspired oxygen fraction of 15%, was used to simulate a 9,000 feet environment.

value: Sprague Dawley

value: Heart Right Ventricle (RV)

tag: Sex

value: male

tag: litter

value: RARA

tag: rna rin


title: 6RARA72_RV_S32


title: Plasma, healthy_24


title: 6RARA67_RV_S20

value: female


title: Testis, Con-2

description: The group information is prefixed with Con-2 in the column of processed data file

value: Testis


title: Testis, Con-3

description: The group information is prefixed with Con-3 in the column of processed data file

value: control


title: Plasma, healthy_17


title: Plasma, healthy_21


title: Plasma, healthy_18


title: Plasma, healthy_20


title: Plasma, healthy_19


title: Plasma, healthy_15


title: 4RARA44_RV_S51


title: 4RARA42_RV_S7


title: Plasma, healthy_13


title: 4RARA40_RV_S18


title: 4RARA43_RV_S19


title: Plasma, healthy_12


title: Sperm, F0-NHS-1 (sRNA-seq)

value: Sperm


title: Plasma, healthy_11

value: healthy donor


title: 6RARA65_RV_S29


title: DPAn-6 rep1

city: Los Angeles

first: Qiu-Lan

last: Ma

address: 11301 Wilshire Boulevard Los Angeles, CA

institute: University Of California Los Angeles

data_processing:
Sequenced reads were mapped to mouse (mm10)  genome using STAR version 2.5.3a.  Read counts per gene were quantified by STAR with parameter --quantMode GeneCounts  using ensembl GRCm38.88.gtf.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file with raw read counts per gene for all samples

source_name: brain cortex

extract_protocol:
Total RNA was isolated from mouse brain cortex tissue using Ambion RNAqueous® phenol-free total RNA isolation kit with DNase treatment according to the manufacturer’s instructions (Ambion Inc. Austin, Texas, USA).Total RNA was qualified using an Agilent BioAnalyzer of High Sensitivity RNA ScreenTapeÒ for Eukaryotic RNA Analysis, and 1 µg was used for poly(A) mRNA selection and library construction with IlluminaÒ Platforms KAPA mRNA HyperPrep kit (KK8580 08098115702) according to the manufacturer's instructions (KR1352 – v4.17).
DNA libraries were prepared using KAPA mRNA (Roche) according to the manufacturer’s instructions

value: brain cortex

value: 14 month


title: CTRL rep7

value: 12 month


title: DPAn-6 rep2


title: 4RARA41_RV_S42


title: DPAn-6 rep4


title: DPAn-6 rep5


title: DPAn-6 rep3


title: CTRL rep6


title: Plasma, healthy_8

value: plasma


title: 4HH40_RV_S48

value: HH


title: 4RARA38_RV_S39


title: CTRL rep5


title: CTRL rep4


title: Plasma, healthy_16

value: M


title: 4RARA39_RV_S17


title: 4HH37_RV_S3


title: Plasma, healthy_10


title: Plasma, healthy_14


title: CTRL rep1


title: 4HH39_RV_S26


title: 4HH33_RV_S25


title: 4HH36_RV_S47


title: Plasma, healthy_7


title: CTRL rep2


title: 3HH28_RV_S23


title: Plasma, healthy_3

value: F


title: Plasma, healthy_4


title: Plasma, healthy_6


title: 4HH38_RV_S16


title: Plasma, liver_cancer_35

source_name: liver cancer patient's plasma

value: liver cancer patient

value: C


title: CTRL rep3


title: Plasma, healthy_9


title: 3HH29_RV_S2

value: Sprague Dawley

value: Heart Right Ventricle (RV)


title: Plasma, healthy_1


title: Plasma, healthy_2


title: 3HH23_RV_S1

value: male


title: 3HH25_RV_S44

value: female


title: Plasma, liver_cancer_33

value: B


title: Plasma, liver_cancer_32


title: 3HH21_RV_S34


title: Plasma, healthy_5


title: 3HH27_RV_S45


title: Plasma, liver_cancer_34


title: 6RARA71_Lung_S54

source_name: Lung

value: Lung

value: RARA


title: Plasma, liver_cancer_29

value: A


title: 3HH30_RV_S36


title: 6RARA72_Lung_S10


title: 6RARA70_Lung_S31


title: Plasma, liver_cancer_30


title: 6RARA65_Lung_S53


title: 6RARA67_Lung_S9


title: 4RARA45_Lung_S52


title: Plasma, liver_cancer_25


title: 3HH20_RV_S33


title: Plasma, liver_cancer_31


title: 4RARA43_Lung_S50


title: Plasma, liver_cancer_22


title: 4RARA41_Lung_S28


title: 4RARA42_Lung_S49


title: Plasma, liver_cancer_24


title: Plasma, liver_cancer_27


title: Plasma, liver_cancer_26


title: 6RARA66_Lung_S8


title: Plasma, liver_cancer_23


title: Plasma, liver_cancer_19


title: MSPB1b_replicate: Human iPSCs rep 4 (tech rep)

description: RNA sequencing_low input_50 cells

organism: Macaca mulatta

source_name: induced pluripotent stem cells_iPSCs

tag: cell type

value: iPSCs derived from blood peripheral mononuclear cells

value: untreated


title: Plasma, liver_cancer_17


title: Plasma, liver_cancer_20


title: Plasma, liver_cancer_18


title: 6RARA68_Lung_S30


title: Plasma, liver_cancer_16


title: Rh_ICMb_replicate: Rhesus macaque ICM rep 2 (tech rep)

description: RNA sequencing_low input_50 cells

source_name: blastocyst inner cell mass_ICM

value: ICM isolated from rhesus blatocyst

value: Immunosurgery removing trophectoderm to isolate ICM


title: Plasma, liver_cancer_21

value: plasma


title: Plasma, liver_cancer_15

value: M


title: 4RARA40_Lung_S41


title: 4HH38_Lung_S4

value: HH


title: Plasma, liver_cancer_28

value: liver cancer patient


title: 4RARA44_Lung_S43


title: 4RARA38_Lung_S6


title: cKO input

city: Wuhan

first: Lichao

last: Xu

address: luojiashan

institute: Wuhan University

data_processing:
Cutadapt (version 1.16, http:// cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were aligned to the mouse reference genome (mm10) using BWA (version 0.7.15, http://bio-bwa.sourceforge.net) with the default settings
Peaks calling was finished by MACS2 (version 2.1.1, https://github.com/taoliu/MACS) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cut- off 1E-10 --extsize 147
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: cortex

extract_protocol:
For each experiment, single-cell suspensions from E13.5 dorsal cortices were collected as described above. Cells were cross-linked for 10 min at room temperature with 1% formaldehyde and then quenched with 0.125 M of glycine for 5 min. Cross-linked samples were then rinsed in PBS twice, and harvested in ice-cold IP buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.1, 5 mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 1× Roche protease inhibitor cocktail, and 1 mM PMSF), followed by sonication in a Bioruptor Pico (Diagenode) at a setting of ‘30s on/ 30s off, 30 cycles’ at 4°C. 20 μl aliquot were taken for checking the efficiency of sonication. After de-crosslinked in de-crosslink buffer (1% SDS, 250mM NaCl in TE buffer) for 3 h, the sample was purified with DNA purification kit (QIAGEN), followed by DNA electrophoresis with 2% agarose gel. 30 μl lysate (3%) was kept to quantify DNA before immunoprecipitation (input). Immunoprecipitation was further performed with sheared chromatin and 3 μg anti-H3K36me3 antibody (abcam, ab9050) overnight at 4°C on a rotating wheel. Next day, immunocomplexes were incubated with 50 μl Protein G sepharose beads for 4 h at 4°C, followed by washing 3 times with wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) and once with wash buffer II (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS). Protein-DNA complexes were de-crosslinked in 120 μl de-crossed buffer (TE buffer) and shaked at 65℃ for 3 h. DNA extraction, precipitation, and resuspension were performed using DNA purification kit (QIAGEN).
ChIP-seq libraries were constructed by StepWise DNA Lib Prep Kit for Illumina (Abclonal RK20202). For each sample, 40 μl purified ChIP DNA (about 300 pg) was end-repaired for dA tailing, followed by adaptor ligation with Full DNA Adapter Kit for Illumina Set_A (Abclonal RK20282). Each adaptor was marked with an index of 6 bp, which can be recognized after mixing different samples together. Adaptor-ligated ChIP DNA was purified by AMPure XP beads (1:1) and then used as template for 16 cycles of PCR amplification. Amplified ChIP DNA was purified again using AMPure XP beads (1:1) in 22 μl low-EDTA TE buffer. For multiplex sequencing, libraries with different index were mixed together with equal molar quantities by considering appropriate sequencing depth (20 million reads per library). Libraries were sequenced by Illumina Hi-seq X Ten platform with pair-end reads of 150 bp.

value: cortex

value: Embryo 13.5

value: Emx1-Cre;Setd2 f f (cKO)

tag: chip antibody


title: 4HH40_Lung_S27

value: Sprague Dawley


title: Plasma, liver_cancer_13


title: 4RARA39_Lung_S40

value: female


title: Plasma, liver_cancer_11

value: F


title: Rh_ICMc: Rhesus macaque ICM rep 3

description: RNA sequencing_low input_50 cells

data_processing: The RNAseq analysis was conducted using STAR RNA-seq aligner and RSEM transcript quantification software and the pipeline currently used for the ENCODE project (Consortium, 2004; Dobin et al., 2013; Li and Dewey, 2011). For the downstream analysis DeSEQ2 was used for differential expression analysis (Love et al., 2014). The commonly expressed genes among species were used for quantitative cross-species expression comparisons. The gene-gene interaction networks are based on known interactions on string database(Szklarczyk et al., 2016).


title: Rh_ESCa: Rhesus ESC rep 1

description: RNA sequencing_low input_50 cells

source_name: Embryonic stem cells_ESCs

value: ESC deived from rhesus blastocyst


title: Rh_iPSCb: Rhesus macaque iPSCs rep 2

description: RNA sequencing_low input_50 cells


title: Rh_ESCb: Rhesus ESC rep 2

description: RNA sequencing_low input_50 cells


title: Rh_iPSCa: Rhesus macaque iPSCs rep 1

description: RNA sequencing_low input_50 cells


title: 4HH39_Lung_S5

value: Lung


title: Plasma, liver_cancer_10

value: A


title: control input

value: control


title: Plasma, liver_cancer_12


title: 4HH37_Lung_S38

value: male


title: 4HH36_Lung_S15


title: Plasma, liver_cancer_9


title: 4HH33_Lung_S37


title: Plasma, liver_cancer_14


title: Rh_ICMb: Rhesus macaque ICM rep 2

description: RNA sequencing_low input_50 cells

value: ICM isolated from rhesus blatocyst


title: Rh_ICMa: Rhesus macaque ICM rep 1

description: RNA sequencing_low input_50 cells

value: Immunosurgery removing trophectoderm to isolate ICM


title: 3HH30_Lung_S24


title: 3HH28_Lung_S46


title: Plasma, liver_cancer_8

value: plasma


title: 3D Hi-C rep1

city: Shanghai

first: Xin

last: Liu

state: Shanghai

address: 800 Dong Chuan Rd.

department: School of Biomedical Engineering

institute: Shanghai Jiaotong University

data_processing:
Library strategy: Hi-C
We mapped all Hi-C reads to the mm10 mouse reference genome using Bowtie 2 (v2.2.9) iteratively as described. For each end of the Hi-C reads, we first mapped an outermost length of 30 bp, and if this length of region failed to map uniquely, we then included an additional 20 bp in the next round of mapping. This procedure was continued until the mapping length reached the full read length, which is 150 bp. Read pairs with mapping quality (MAPQ) larger than 30 for each end were kept, followed by removing the reads mapped to the same restriction fragment and dangling reads which have a separating genomic distance shorter than 500 bp.
We generated Hi-C contact matrices at 1 Mb, 100 kb or 40 kb resolutions for each chromosome and normalized using ICE. And we annotated domains using the software Armatus v1.0 with the gamma parameter set to 0.8.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files were generated using software Armatus (v 1.0), there are three columes in the txt file, representing chromosome names, start positions and end positions repectively.

source_name: AML12 (alpha mouse liver 12) cell line

growth_protocol: AML12 (alpha mouse liver 12) cells were cultured in a mix of Dulbecco`s modified Eagle’s medium and Ham’s F12 medium (1:1) containing 10% fetal calf serum and supplied with 1× ITS liquid media supplement (10 μg/mL recombinant human insulin, 5.5 μg/mL human transferrin (substantially iron-free) and 5 ng/mL sodium selenite, Sigma), dexamethasone (40 ng/mL) (Sigma), Penicillin-Streptomycin (100 U/mL) (Gibco) at 37°C for 48 h. Then, the cells were dissociated with 0.25% trypsin to suspend for replating. For the 2D cultures, cells were replated in 10 cm dishes. For the 3D cultures, cells were grown in Matrigel-embedded 3D cultures in the 10 cm dish. When the cells in the 2D cultures were 50% confluent and the cells in the 3D cultures had grown for 24 h, 1 mM hydroxyurea was added to the medium for 24 h (2D) or 36 h (3D) to arrest the cells in G1/S boundary.

extract_protocol:
The Hi-C chimeric DNA were prepared by "in-situ Hi-C" method with minor modifications, Briefly, nuclei released from ten million crosslinked cells were digested with Mbo I (NEB). After biotin fill-in and ligation in nuclei, biotin labeled ligation product were fragmented with Cavrios M220, the molecular with size ranging from 300bp to 500bp were selected for the generation of library.
The Hi-C libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina with modifications. Briefly, after end-repair and adaptor ligation with NEB modules, biotin labeled validated chimeric DNA were selected with Streptavidin C1 beads (Invitrogen). Hi-C library was amplified after DNA elution by incubating at 98° C.

tag: cell line

tag: drug for synchronization

value: Hydroxyurea


title: 3HH27_Lung_S14

tag: strain

tag: treatment

value: HH


title: Plasma, liver_cancer_7

value: liver cancer patient

value: M

tag: tissue


title: 3HH29_Lung_S35


title: 3HH25_Lung_S13


title: Plasma, liver_cancer_4


title: 2D Hi-C rep1


title: 3HH23_Lung_S12


title: Plasma, liver_cancer_5


title: 3HH21_Lung_S22


title: 3D RNA-seq rep2

data_processing:
We removed adapters and low quality reads using cutadapt (v1.8.3) and Trimmomatic (v0.36) with default parameters. The remaining valid paired reads were mapped to the GRCm38 mouse reference genome by HISAT2 (v2.0.5) with options “--rna-strandness RF --no-softclip”. We assembled and quantified the transcripts using Stringtie (v1.3.4), with the Mus_musculus.GRCm38.93.chr GTF file downloaded from Ensembl database. Read counts of genes were extracted from output files of Stringtie through a Python script “prepDE.py” provided online (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py). To evaluate the difference of gene expression between 2D and 3D cultured cells, we used an R package “DESeq2” to calculate the fold change of the transcription level and assigned a statistical significance for each pair of genes.
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file contain 11 columns, representing gene_ID, gene_name, strand, chrom, start position, end position, tpm_2d_1, tpm_2d_2, tpm_3d_1, tpm_3d_2, log2 fold change of 2d vs 3d, p-value and gene annotation, respectively.

growth_protocol: AML12 (alpha mouse liver 12) cells were cultured in a mix of Dulbecco`s modified Eagle’s medium and Ham’s F12 medium (1:1) containing 10% fetal calf serum and supplied with 1× ITS liquid media supplement (10 μg/mL recombinant human insulin, 5.5 μg/mL human transferrin (substantially iron-free) and 5 ng/mL sodium selenite, Sigma), dexamethasone (40 ng/mL) (Sigma), Penicillin-Streptomycin (100 U/mL) (Gibco) at 37°C for 48 h. Then, the cells were dissociated with 0.25% trypsin to suspend for replating. For the 2D cultures, cells were replated in 10 cm dishes. For the 3D cultures, cells were grown in Matrigel-embedded 3D cultures in the 10 cm dish. When the cells in the 2D cultures were 50% confluent and the cells in the 3D cultures had grown for 24 h, 1 mM hydroxyurea was added to the medium for 24 h (2D) or 36 h (3D).

extract_protocol:
Total RNA were extracted with Trizol reagent.
RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit following the manufacturer’s instructions.


title: 2D RNA-seq rep2


title: 2D RNA-seq rep1


title: 3D RNA-seq rep1


title: Plasma, liver_cancer_2


title: Plasma, liver_cancer_3


title: 3HH20_Lung_S11


title: 0503L52b: Chimpanzee iPSCs rep 3

description: RNA sequencing_low input_50 cells

organism: Pan troglodytes

extract_protocol: The rhesus macaque blastocysts on day 5 post IVF was used for immunosurgery to remove zonae pellucidae and trophectoderm as explained elsewhere(Mitalipov et al., 2006). In summary, the zonae pellucidae of rhesus blastocysts will be removed by exposure to 0.5% pronase in TH3 medium for 45 seconds. For immunosurgical isolation of rhesus ICM to remove trophectoderm, zona pellucidae-free rhesus blastocysts were exposed to rabbit anti-rhesus spleen serum for 30 minutes at 37°C from VandeVoort laboratory at UC Davis. Subsequently, the blastocysts were washed in TH3 medium for 3 times and were incubated in guinea pig complement reconstituted with HECM-9 (1:2 vol/vol) at 37°C for 30 minutes(Mitalipov et al., 2006). After the incubation, the trophectoderm was removed mechanically using a small-bore pipette (125μM inner diameter) and the clumps of ICM cells from each blastocyst were washed in PBS and placed in a separate PCR tube containing 5μL of RNAse-free water with 5% RNAse inhibitor. The ICMs were quickly frozen on dry ice and were stored at -80°C for cDNA synthesis and RNA-seq library preparation. The cDNA synthesis and RNA-seq were conducted directly from ICM cells using SMART-Seq V4 Ultra Low input cDNA synthesis kit (Clonetech Inc.). The cDNA concentration was measured using Quibit kit and Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.). The cDNA from each ICM were used for library preparation following Illumina Nextera XT kit protocol (Illumina Inc.). The quality and the quantity of the final library were evaluated using Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.),Kappa kit, and the Agilent 2100 Bioanalyzer instrument. Dual index RNA-seq library from ICMs were pooled together with dual index RNAseq libraries of approximately 50 iPSCs for sequencing with dual index Illumia platform on a HiSeq 4000 sequencing machine. The low input cDNA synthesis and RNA-seq library preparation for ICMs and iPSCs were performed simultaneously on similar number of cells and pooled together to be sequenced in the same batch to minimize the potential batch effects. The sequencing coverage approximately 50 million reads per RNA-seq sample.

value: iPSCs derived from blood peripheral mononuclear cells

value: untreated


title: 0503L52a: Chimpanzee iPSCs rep 3

description: RNA sequencing_low input_50 cells


title: 0503L12a: Chimpanzee iPSCs rep 1

description: RNA sequencing_low input_50 cells


title: 0503L12b: Chimpanzee iPSCs rep 2

description: RNA sequencing_low input_50 cells


title: 2D Hi-C rep2


title: Fengycin treatment rep 3

city: Riverside

first: Alex

last: Blacutt

address: 3523 Webber Hall

institute: University of California, Riverside

data_processing:
Reads were uploaded to the UGA Galaxy server for trimming and quality control.
Reads were mapped to the F. verticillioides genome (GCF_000149565.1) via Tophat v2.0.14
Transcript assembly was conducted via Cufflinks v 2.21
Differential expression analysis was conducted through Cuffdiff (v2.2.1.3)
cummeRbund (v2.13.1) was used for data analysis
Genome_build: GCF_000149565.1
Supplementary_files_format_and_content: gene_exp_data is a cuffdiff output file for the experiment, saved as an excel spreadsheet

molecule: polyA RNA

organism: Fusarium verticillioides

source_name: Colony edge of strain FRC-M3125

growth_protocol: Cultures were inoculated as 5 uL of 1.5 x 10^6 conidia/mL suspensions onto 20mL plates of Potato Dextrose agar and incubated in the dark at 27 C for five days prior to treatment.

extract_protocol:
Treated colony edges were excised, flash frozen and homogenized via mortar and pestle. 100 mg of homogenized culture was extracted for total RNA using the Norgen Biotek plant/fungi total RNA kit and manufacturers protocol (Thorold, ON, Canada)
RNA quality (RIN value > 7.0) was determined via Agilent RNA Nano 6000 Chips on an Agilent 2100 bioanalyzer. Messenger RNA was isolated via poly-T magnetic bead purification before libraries were created using the Illumina TruSeq v2 library kit and manufacturers protocol. Libraries were indexed and quantified via fluorimetry before pooling for sequencing.
Illumina TruSeq v2

treatment_protocol: Treatments were applied in 100 uL of 0.2X PDB to colony edges and plates were allowed to dry for five minutes in a laminar hood, followed by incubation in the dark at 27C for 6 hours.

value: 5 day growth on PDA in the dark

tag: growth

value: filamentous radial growth


title: Plasma, liver_cancer_1


title: Fengycin treatment rep 2


title: Combined treatment rep 2


title: 3D Hi-C rep2

extract_protocol:
The Hi-C chimeric DNA were prepared by "in-situ Hi-C" method with minor modifications, Briefly, nuclei released from ten million crosslinked cells were digested with Mbo I (NEB). After biotin fill-in and ligation in nuclei, biotin labeled ligation product were fragmented with Cavrios M220, the molecular with size ranging from 300bp to 500bp were selected for the generation of library.
The Hi-C libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina with modifications. Briefly, after end-repair and adaptor ligation with NEB moduals, biotin labeled validated chimeric DNA were selected with Streptavidin C1 beads (Invitrogen). Hi-C library was amplified after DNA elution by incubating at 98° C.

tag: condition


title: Control rep 3


title: Ma2E8L3b: Pig-tailed macaque iPSCs rep 4

description: RNA sequencing_low input_50 cells

organism: Macaca nemestrina


title: Ma2E8L2b: Pig-tailed macaque iPSCs rep 2

description: RNA sequencing_low input_50 cells


title: Surfactin treatment rep 3


title: Fengycin treatment rep 1


title: Surfactin treatment rep 2


title: Combined treatment rep 1


title: Ma2E8L2a: Pig-tailed macaque iPSCs rep 1

description: RNA sequencing_low input_50 cells


title: Control rep 1


title: Control rep 2


title: Plasma, liver_cancer_6

value: F


title: Wild-type, 1BNe

status: Public on Sep 29 2020

city: Santiago

first: Melissa

last: Gómez

address: Las Palmeras 3425

department: Ciencias Ecológicas

country: Chile

institute: Universidad de Chile

description:
none
1ANe_1BNe_1CNe.txt

data_processing:
RNA-seq: The reads were mapped to protein coding genes obtained from the annotation of the genome assembly of the X. dendrorhous included in the BioPoject ID: PRJNA637109, using the RNA-seq analysis tools from the CLC Genomics Workbench 20 software to determine the count data values. Differentially Expressed Genes (DEGs) were estimated using the DESeq2 and edgeR packages of R/Bioconductor using the criteria |log2 fold change| ≥ 1, p-adjusted < 0.05 (DESeq2) or FDR < 0.05 (edgeR), and DEGs common to both analyses (DESeq2 and edgeR) were selected.
ChIP-exo: The reads obtained from Peconic LLC were mapped to the genome assembly of X. dendrorhous included in the BioPoject ID: PRJNA637109, using the aligner Bowtie2 version 2.3.5.1 with default settings for paired end reads. Reads were filtered to retain reads mapped in proper pairs using SAMtools. For the peak calling step, the MACS2 tool was used: the effective genome size was 20 Mb, the peak detection was based in a q-value of 0.05, and the control used for the treatment of BAM files was an IgG BAM file. The intersect function from the BEDtools tool was used to find overlap peaks among the MACS2 output files from each biological replicate. For comparative purposes, the Epigenetics Analysis tools from the CLC Genomics Workbench 20 software was also used for the peak calling step, using a maximum p-value of 0.01. To ensure the generation of a high confidence dataset, in addition to the standard computational analysis, a manual correction of the associated genes up- and downstream of some peaks was included. Additionally, common peaks between each FLAG-tagged strain and the untagged control strain were discarded.
Genome_build: PRJNA637109
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the counts for each sample. ChIP-exo: Coverage tracks in bigwig format were generated with the bamCoverage tool and visualized with the IGV software. Peak text files include the common peaks of three biological replicas (3BR) of each strain: CBS.FLAG.SRE1N and CBS.cyp61-.FLAG.SRE1, using the peak caller MACS2 (the text file includes all the common peaks) and the peak caller from the CLC Genomics Workbench 20 software (the text file includes only common peaks associated to DEGs).

organism: Phaffia rhodozyma

source_name: Cell pellet

extract_protocol:
For RNA-seq assays, total RNA was extracted and shipped to Macrogen (Macrogen Inc., Seoul, South Korea) for library preparation and sequencing. For the ChIP-exo assays, formaldehyde-cross linked cell pellets were prepared and shipped to Peconic LLC (State College, PA, USA) for the library preparation and sequencing.
Libraries were prepared using Illumina protocols.

tag: parental strain

tag: genotype

value: wild-type strain


title: Wild-type, 1CNe

description:
none
1ANe_1BNe_1CNe.txt


title: Surfactin treatment rep 1


title: Mutant strain, 5CN

description:
FLAG epitope fused to Sre1 transcription factor
5AN_5BN_5CN.txt

value: FLAG.Sre1-tagged strain


title: Mutant strain, 2AN

description:
none
2AN_2BN_2CN.txt

value: SRE1 deletion


title: Mutant strain, 2BN

description:
none
2AN_2BN_2CN.txt


title: Mutant strain, 2CN

description:
none
2AN_2BN_2CN.txt


title: Wild-type, 1ANe

description:
none
1ANe_1BNe_1CNe.txt


title: Mutant strain, 4BN

description:
none
4AN_4BN_4CN.txt

value: SRE1 deletion - Interruption CYP61 locus


title: Mutant strain, 4CN

description:
none
4AN_4BN_4CN.txt


title: Combined treatment rep 3


title: Mutant strain, 5BN


title: Mutant strain, 5AN


title: Ma2E8L3a: Pig-tailed macaque iPSCs rep 3

description: RNA sequencing_low input_50 cells


title: Mutant strain, 4AN

description:
none
4AN_4BN_4CN.txt


title: Wild-type, 1BN

description:
none
1AN_1BN_1CN.txt


title: Wild-type, 1CN

description:
none
1AN_1BN_1CN.txt


title: Mutant strain, 3AN

description:
none
3AN_3BN_3CN.txt

value: Interruption CYP61 locus


title: QYZM_root

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
the raw reads for each sample were filtered, generating clean reads used in next analysis.
To estimate the expression level of ramie genes in various tissues, the clean reads from transcriptome sequencing of ZSZ1 and QYZM tissues were aligned to ramie genome (NCBI  accession PRJNA663427) using the Bowtie2 software, and read number of each transcript was calculated using the RSEM software. The fragments per kilobase of transcript sequence, per millions base pairs sequenced (FPKM) were estimated to measure the expression of each transcript.
Supplementary_files_format_and_content: ramie_fpkm.txt contains the gene name, sample name, and FPKM value

organism: Boehmeria nivea

source_name: wild tenacissima accession QYZM

extract_protocol:
The total RNA of roots, stems, and leaves were extracted from QYZM and ZSZ1. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol.
Total RNAs for all 6 samples were separately extracted and used to construct the cDNA library with fragment lengths of ~350 bp.

value: roots

tag: developmental stage

tag: wild tenacissima accession

value: QYZM


title: ZSZ1_stem

source_name: Cultivar ZSZ1

value: stems

tag: cultivar


title: Wild-type, 1AN

description:
none
1AN_1BN_1CN.txt


title: ZSZ1_root


title: QYZM_stem


title: QYZM_leaf

value: leaves