title: MT2 snATAC-seq

description: Tn5 tagmented C2C12 myotube nuclei from myotubes filtered through a 40uM strainer were collected for snATAC-seq (technical rep 2). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.


title: MB2 snATAC-seq

status: Public on Apr 27 2021

type: SRA

city: Irvine

first: Elisabeth

last: Rebboah

state: California

address: 2300E Biological Sciences 3

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description: Tn5 tagmented C2C12 myoblast nuclei were collected for snATAC-seq (technical rep 2). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.

library_source: genomic

data_processing:
Use Docker container to run FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and generate HTML report for each fastq file in input directory. docker run --rm -v $1:/data/ bioraddbg/atac-seq-fastqc:v1.0.0  -i /data/ -o /data/fastqc_results --name fastqc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run BAP (https://github.com/caleblareau/bap) and debarcode fastq files. Barcodes are parsed from read 1 and appended to read name for valid barcodes only. docker run --rm -v $1:/data/ bioraddbg/atac-seq-debarcode-dbg:v1.0.0  -i /data/  -o /data/debarcoded_reads  --name debarcode. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run BWA (http://bio-bwa.sourceforge.net) to align to mm10. docker run --rm -v $1:/data/ -v /path/to/mm10/bwa/:/genome/ bioraddbg/atac-seq-bwa:v1.0.0 -i /data/debarcoded_reads/ -o /data/alignments/ -r /genome/ --name align. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run QC on aligned file with Picard (https://broadinstitute.github.io/picard/) CollectAlignmentSummaryMetrics and writes a text file with alignment summary metrics. docker run --rm -v $1:/data/ -v /path/to/mm10/:/genome/ bioraddbg/atac-seq-alignment-qc:v1.0.0  -i /data/alignments/  -r /genome/mm10.fa -o /data/alignment_qc --name alignment_qc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to filter beads (barcodes) from cell-free nanodroplets, and identify beads that ended up in the same nanodroplet with a nucleus using Jaccard indexing. docker run --rm -v $1:/data/ bioraddbg/atac-seq-filter-beads:v1.0.0 -i /data/alignments/  -o /data/bead_filtration/  -r mm10  --name bead_filtration --cpus="10". (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to merge beads that ended up in the same nanodroplet with a nucleus using BAP (https://github.com/caleblareau/bap) . docker run --rm -v $1:/data/ bioraddbg/atac-seq-deconvolute:v1.0.0 -i /data/alignments/ -f /data/bead_filtration/ -r mm10  -o /data/deconvoluted_data --name deconv_${2}. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to filter out cells with low read depth using a UMI- (unique molecular identifier) based "knee call". Outputs bam file and cell list included in this submission. docker run --rm -v $1:/data/  bioraddbg/atac-seq-cell-filter:v1.0.0 -i /data/deconvoluted_data/  -o /data/cells_filtered/ -r mm10  --name cell_filtration. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run MACS2 (https://github.com/taoliu/MACS). Outputs peaks included in this submission. docker run --rm -v $1:/data/ bioraddbg/atac-seq-macs2:v1.0.0  -i /data/deconvoluted_data/ -r mm10  -o /data/peaks  --name peak_calling. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run QC on deconvoluted alignment data, generating a FRIP score, insert size metrics histogram, and TSS score. In v.1.0.1, docker tool is fixed to run chromVar and generate peaks-by-cells counts matrix; v. 1.0.0 crashed at this step, hence our custom code. docker run --rm -v $1:/data/  bioraddbg/atac-seq-qc:v1.0.0  -r mm10 -d /data/deconvoluted_data/ -p /data/peaks  -o /data/atac_qc --name atac_qc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to generate an HTML and PDF report of all the outputs using MultiQC (https://multiqc.info). (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Merge peaks across all samples (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline). For example, python merge_peaks.py -p peakfiles.csv --o merged_peaks
Use custom script to generate CSV file of peaks-by-cells matrix using merged peaks, cell list, and alignments (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline). For example, python gen_count_matrix.py -p merged_peaks.bed  -b  MB1/MB1.bam  -bc MB1/MB1.aboveKneeBarcodes.csv -e MB1 --o MB1/ --full_csv
Genome_build: mm10
Supplementary_files_format_and_content: Peak calls from MACS2.
Supplementary_files_format_and_content: CSV file of cell IDs passing UMI cutoff.
Supplementary_files_format_and_content: Peaks-by-cells matrix generated using custom code (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline) and provided processed files: peaks, barcodes, and aligned reads.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: C2C12 cells  (ATCC, CRL-1772) were cultured on 10 cm plates  in 10 mL myoblast growth media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 20% fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin. Cells were maintained at 20-50% confluency at 37C with 5% CO2 and passaged at 1:3 or 1:4 every 2 to 3 days.

extract_protocol:
Cells were rinsed with 1X PBS and incubated with 2 mL TrypLE-Express for 5 minutes at 37C, which was then neutralized with 8 mL myoblast growth media. Nuclei were prepared following Bio-Rad's SureCell WTA 3' Nuclei Isolation protocol (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/surecell/surecell-wta3-nuclei-demonstrated-protocol-1000000044178-00.pdf). Myotubes were both filtered (3 samples) and not filtered (2 samples) through a 40uM strainer before nuclei isolation but data were very similar between the two different nuclei preps. Tagmented DNA was barcoded and amplified in nanodroplets, then extracted following Bio Rad's SureCell ATAC-seq library kit (cat. #17004620; protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf).
Bio-Rad's SureCell ATAC-seq library kit (cat. #17004620; protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf)

treatment_protocol: To differentiate myoblasts to myotubes, cells at 90-100% confluency were rinsed with 1X PBS and myoblast growth media was replaced with 10 mL differentiation media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 2% donor horse serum, 100 units/mL penicillin, 100 ug/mL streptomycin, and freshly-added 1uM insulin. Differentiation media was replaced every 24 hours for 3 days. ENCODE protocol: https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf

tag: cell type

value: myoblast

tag: cell line

tag: treatment protocol

value: Differentiation of C2C12, ENCODE (https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf)

tag: library prep protocol

value: snATAC-seq protocol; SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620).


title: MT1 snATAC-seq

description: Tn5 tagmented C2C12 myotube nuclei from myotubes filtered through a 40uM strainer were collected for snATAC-seq (technical rep 1). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.

value: myotube


title: MB1 snATAC-seq

description: Tn5 tagmented C2C12 myoblast nuclei were collected for snATAC-seq (technical rep 1). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.


title: Sample303.Killer whale.203531420079_R04C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Skin species=Killer whale

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

organism: Orcinus orca

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: canbeusedforagingstudies

value: yes

tag: Sex

value: Male

tag: tissue

value: Skin


title: Sample302.Killer whale.203531420079_R03C01


title: FMT snATAC-seq

description: Tn5 tagmented C2C12 myotube nuclei from myotubes filtered through a 40uM strainer were collected for snATAC-seq (bio rep to 2 technical reps of filtered myotubes). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.


title: Sample300.Killer whale.203531420079_R01C01

value: Female


title: Sample301.Killer whale.203531420079_R02C01


title: Sample297.Killer whale.203531420047_R04C02


title: MB_2 snATAC-seq

description: Tn5 tagmented C2C12 myoblast nuclei were collected for snATAC-seq (bio rep to 2 technical reps of myoblasts). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.


title: Sample299.Killer whale.203531420047_R06C02


title: Sample298.Killer whale.203531420047_R05C02


title: Sample292.Killer whale.203531420047_R05C01


title: Sample296.Beluga whale.203531420047_R03C02

description: genomic DNA methylation from tissue=Skin species=Beluga whale

organism: Delphinapterus leucas


title: Sample295.Beluga whale.203531420047_R02C02


title: Sample290.Killer whale.203531420047_R03C01


title: Sample291.Killer whale.203531420047_R04C01


title: Sample248.Bottlenose dolphin.203531420008_R03C02

description: genomic DNA methylation from tissue=Blood species=Bottlenose dolphin

organism: Tursiops truncatus

source_name: Blood

value: Blood


title: Sample281.Bottlenose dolphin.203531420041_R06C01


title: Sample286.Beluga whale.203531420041_R05C02

description: genomic DNA methylation from tissue=Blood species=Beluga whale


title: Sample254.Bottlenose dolphin.203531420054_R03C01


title: Sample293.Killer whale.203531420047_R06C01


title: Sample287.Bottlenose dolphin.203531420041_R06C02


title: Sample247.Bottlenose dolphin.203531420008_R02C02


title: Sample294.Killer whale.203531420047_R01C02


title: Sample238.Commerson's dolphin.203524370004_R05C02

description: genomic DNA methylation from tissue=Blood species=Commerson's dolphin

organism: Cephalorhynchus commersonii


title: Sample241.Bottlenose dolphin.203531420008_R02C01


title: Sample236.Commerson's dolphin.203524370004_R03C02


title: Sample261.Bottlenose dolphin.203531420054_R04C02


title: Sample237.Commerson's dolphin.203524370004_R04C02


title: Sample245.Commerson's dolphin.203531420008_R06C01


title: Sample228.Bottlenose dolphin.203524370004_R01C01


title: Sample246.Bottlenose dolphin.203531420008_R01C02


title: Sample218.Bottlenose dolphin.203531420072_R03C01


title: Sample223.Bottlenose dolphin.203531420072_R02C02


title: Sample227.Bottlenose dolphin.203531420072_R06C02


title: Sample222.Bottlenose dolphin.203531420072_R01C02


title: Sample226.Bottlenose dolphin.203531420072_R05C02


title: Sample217.Bottlenose dolphin.203531420072_R02C01


title: Sample205.Bottlenose dolphin.203531420027_R02C01


title: Sample207.Bottlenose dolphin.203531420027_R04C01


title: Sample225.Bottlenose dolphin.203531420072_R04C02


title: Sample208.Bottlenose dolphin.203531420027_R05C01


title: Sample200.Beluga whale.203531420063_R03C02


title: Sample196.Bottlenose dolphin.203531420063_R05C01


title: Sample216.Bottlenose dolphin.203531420072_R01C01


title: Sample203.Bottlenose dolphin.203531420063_R06C02


title: Sample209.Bottlenose dolphin.203531420027_R06C01


title: Sample197.Bottlenose dolphin.203531420063_R06C01


title: Sample202.Beluga whale.203531420063_R05C02


title: Sample199.Bottlenose dolphin.203531420063_R02C02


title: Sample201.Beluga whale.203531420063_R04C02


title: Sample194.Bottlenose dolphin.203531420063_R03C01


title: Sample198.Bottlenose dolphin.203531420063_R01C02


title: Sample189.Bottlenose dolphin.203531420011_R04C02


title: Sample193.Bottlenose dolphin.203531420063_R02C01


title: Sample204.Bottlenose dolphin.203531420027_R01C01


title: Sample190.Bottlenose dolphin.203531420011_R05C02


title: Sample188.Bottlenose dolphin.203531420011_R03C02


title: Sample191.Bottlenose dolphin.203531420011_R06C02


title: Sample195.Bottlenose dolphin.203531420063_R04C01


title: Sample182.Bottlenose dolphin.203531420011_R03C01


title: Sample224.Bottlenose dolphin.203531420072_R03C02


title: Sample180.Bottlenose dolphin.203531420011_R01C01


title: Sample181.Bottlenose dolphin.203531420011_R02C01


title: Sample187.Bottlenose dolphin.203531420011_R02C02


title: Sample184.Bottlenose dolphin.203531420011_R05C01


title: Sample185.Bottlenose dolphin.203531420011_R06C01


title: Sample179.Bottlenose dolphin.203531420070_R06C02


title: Sample183.Bottlenose dolphin.203531420011_R04C01


title: Sample177.Bottlenose dolphin.203531420070_R04C02


title: Sample172.Bottlenose dolphin.203531420070_R05C01


title: Sample166.Bottlenose dolphin.203531420015_R05C02


title: Sample186.Bottlenose dolphin.203531420011_R01C02


title: Sample178.Bottlenose dolphin.203531420070_R05C02


title: Sample174.Bottlenose dolphin.203531420070_R01C02


title: Sample175.Bottlenose dolphin.203531420070_R02C02


title: Sample173.Bottlenose dolphin.203531420070_R06C01


title: Sample168.Bottlenose dolphin.203531420070_R01C01


title: Sample167.Bottlenose dolphin.203531420015_R06C02


title: Sample171.Killer whale.203531420070_R04C01

description: genomic DNA methylation from tissue=Blood species=Killer whale


title: Sample169.Bottlenose dolphin.203531420070_R02C01


title: Sample176.Bottlenose dolphin.203531420070_R03C02


title: Sample164.Bottlenose dolphin.203531420015_R03C02


title: Sample163.Bottlenose dolphin.203531420015_R02C02


title: Sample170.Bottlenose dolphin.203531420070_R03C01


title: Sample161.Bottlenose dolphin.203531420015_R06C01


title: Sample162.Bottlenose dolphin.203531420015_R01C02


title: Sample156.Bottlenose dolphin.203531420015_R01C01


title: Sample159.Killer whale.203531420015_R04C01


title: Sample157.Bottlenose dolphin.203531420015_R02C01


title: Sample160.Bottlenose dolphin.203531420015_R05C01


title: Sample155.Bottlenose dolphin.203531420018_R06C02


title: C2C12 myoblast-derived extracellualr vesicles with fluid flow shear stress rep1

city: Osaka-Sayama

first: YOSHIMASA

last: TAKAFUJI

state: Osaka

address: 377-2 Ohno-Higashi

department: Facluty of Medicine

country: Japan

institute: Kindai University

description:
Total RNA from culture media exosome fraction was preocessed to small-RNA sequencing
KIN_003_05_LAB_191_05

library_source: transcriptomic

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen, Germantown, MD, USA).
Reads were grouped by sequence and counted with small RNA analysis tool, and the read groups were matched to miR-base annotated micro RNAs.
Raw counts of each sample were converted by total count 1,000,000 at first,  and the converted counts were further normalized by scaling method with means as normalization values, median mean as reference and trimming percentage 5 for comparing multiple samples.
Genome_build: mm10
Supplementary_files_format_and_content: Gene name, raw counts and normalized counts are shown in a tab-deliminated txt file.

molecule: total RNA

source_name: Culture media

growth_protocol: For analysis of the effects of endocrine factors on physiological action of Myo-EV, C2C12 cells in the 10 cm culture plate were cultured in fresh DMEM supplemented with 10% EV-depleted FBS with or without 1, 25-dihydroxyvitamin D3 (1, 25(OH)2D3) or dexamethasone for 48 hr at 37 °C.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent following product manual.
90 ng of total RNA was converted to sequencing library with NEBNext Small RNA Library Prep Kit (E7330, New England Biolabs) and single-index primers.
Small-RNA-seq

treatment_protocol: EVs were isolated from conditioned medium by ultracentrifugation. The conditioned medium of C2C12 cell was centrifuged at 3,000 g for 5 min for removing dead cells, filtered with a Stericup filter unit with a 0.22-um PVDF filter for removing cell debris. Then, the medium was ultracentrifuged at 130,000 g for 70 min at 4 C with a Himac CP80NX system for isolating pellet of Myo-EVs.

tag: strains

value: C2C12 myoblast-derived extracellular vesicles (Myo-EVs)

tag: stress

value: fluid flow shear stress


title: C2C12 myoblast-derived extracellualr vesicles with fluid flow shear stress rep2

description:
Total RNA from culture media exosome fraction was preocessed to small-RNA sequencing
KIN_003_06_LAB_191_06


title: 4_Rat_Heart_Old

type: RNA

city: Milwaukee

first: Arshad

last: Jahangir

state: WI

address: 2801 Kinnic Kinnic River Parkway, Suite 777

department: Cardiology

institute: Advocate Aurora Health

hyb_protocol: Labeled cRNA, synthesized and amplified from the double-stranded cDNA template, was fragmented and hybridized onto GeneChip® Rat Genome 230 2.0 arrays (Affymetrix, Santa Clara, CA) according to manufacturer’s protocol. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and BSA to the hybridization buffer. The hybridization mixture was heated at 99°C for 5 min followed by incubation at 45°C for 5 min, before sample was injected into the microarray. Hybridization was carried out at 45°C for 16 hours, mixing on a rotisserie at 60 rpm. After hybridization, solutions were removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Invitrogen Corporation, Carlsbad, CA).

scan_protocol: After washes, probe arrays were scanned using the GeneChip 3000 scanner (Affymetrix, Santa Clara, CA). The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated before hybridization onto the GeneChip® Rat Genome 230 2.0 array by hybridizing onto a test-3 array, and analyzed as a measure of quality control. Intensity values for each probe cell in the arrays were calculated by GeneChip software.

data_processing: Data normalization and analysis was performed using GeneSpring GX 7.3 (Agilent Technologies). Probe cell intensities were used to calculate an average intensity for each set of probe pairs representing a gene. Quality control filtering was performed on the normalized intensity values and entities were clustered into conditions. Gene expression profiles for each condition were visualized as volcano plots to identify genes significantly upregulated or downregulated in each group. Statistical analysis was performed using the unpaired unequal variance t-test (Welch test). The hierarchical clustering for groups and entities was performed using Euclidean distance metric and Ward’s linkage algorithm.

label: Biotin

organism: Rattus norvegicus

source_name: Rat heart old

label_protocol: Total isolated RNA (100 ng) from each sample was converted to cDNA following instructions provided in the Two-Cycle cDNA synthesis kit and Target Labeling Protocols (Affymetrix, Santa Clara, CA). The obtained cDNA was purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction and used as a template for the in vitro transcription reaction. Biotinylated cRNA was then synthesized using an RNA transcript labeling reagent (Affymetrix, Santa Clara, CA).

growth_protocol: Whole hearts were extracted from male Fischer-344 rats, which were maintained on a standard chow diet and housed in a controlled environment for one week before being sacrificed.

extract_protocol: Total RNA was extracted from the whole heart with TRIzol and purified using an affinity resin column (Qiagen RNeasy Mini kit, Germantown, MD) according to manufacturer’s protocol.

treatment_protocol: Male Fischer-344 rats were maintained on a standard chow diet and housed in a controlled environment prior to extraction of hearts.

value: male

tag: strain

tag: developmental stage

value: 24 month old

value: heart


title: 2_Rat_Heart_Old


title: 2_Rat_Heart_Young

source_name: Rat heart young

value: 6 month old


title: 3_Rat_Heart_Old


title: 6_Rat_Heart_Old


title: 3_Rat_Heart_Young


title: Sample152.Killer whale.203531420018_R03C02


title: C2C12 myoblast-derived extracellualr vesicles rep2

description:
Total RNA from culture media exosome fraction was preocessed to small-RNA sequencing
KIN_003_04_LAB_191_04

value: control


title: 4_Rat_Heart_Young


title: 5_Rat_Heart_Old


title: C2C12 myoblast-derived extracellualr vesicles rep1

description:
Total RNA from culture media exosome fraction was preocessed to small-RNA sequencing
KIN_003_03_LAB_191_03


title: 6_Rat_Heart_Young


title: 1_Rat_Heart_Young


title: Sample154.Bottlenose dolphin.203531420018_R05C02


title: Sample148.Beluga whale.203531420018_R05C01


title: Sample150.Beluga whale.203531420018_R01C02


title: Sample149.Beluga whale.203531420018_R06C01


title: Sample151.Bottlenose dolphin.203531420018_R02C02


title: Ws after salt treatment rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

description: Gene expression of Ws accession after salt treatment

hyb_protocol: cRNA was hybridized to the Arabidopsis arrays according to manufacturer’s instructions.

scan_protocol: The arrays were scanned using the high resolution array scanner (Agilent technologies) with the appropriate settings for the one color gene expression arrays after hybridization.

data_processing: Array images were acquired with Agilent's dual-laser microarray scanner and signal intensities were extracted from the scanned images with dedicated Agilent Feature Extraction software (Agilent technologies). The outliers and the abnormal features were flagged and the data was normalized using the intra-array percentile shift normalization (threshold of 75 and above) and median based inter-array normalization. The GeneSpring software (Agilent technologies) was used to calculate the intensity ratios and fold changes.  All the genes with a P value below 0.01 and a fold change above 2 were chosen for further analysis.

organism: Arabidopsis thaliana

source_name: Ws after salt treatment rep2

label_protocol: Microarray analysis was performed using Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version). In total 150ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe with the help of low RNA input linear amplification/labeling kit  (Agilent technologies) and 1.65µg of Labeled cRNA probes were fragmented using fragmentation buffer (Agilent Technologies).

growth_protocol: Arabidopsis seeds of C24, Col, Ler, Sha, and Ws ecotype were sown in MS plates and grown at 23/18°C in a growth room with a 16-h light/8-h dark cycle at 150 μmol m-2s-1 and 70% relative humidity

extract_protocol: Total RNA was extracted and purified from leaves of at least 30 seedlings per plate using QIAGEN-RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to guidelines specified by the manufacturer. Two biological replicates were prepared for each combination. RNA was quantified using a Nanodrop-ND 8000 spectrophotometer (Thermo Fisher Scientific) and RNA quality was assessed by agarose gel analysis and using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol. Samples with the RNA integrity number of 7.5 and above were chosen for further analysis.

treatment_protocol: Two-week-old seedlings were transferred to either 100mM NaCl or -0.7MPa PEG for 48 h. Plant materials were then collected for RNA extraction.

tag: ecotype

value: Ws

value: whole seedling

tag: age

value: 2 weeks


title: Ws after PEG treatment rep2

description: Gene expression of Ws accession after PEG treatment

source_name: Ws after PEG treatment rep2


title: Ws after salt treatment rep1

source_name: Ws after salt treatment rep1


title: Ws after PEG treatment rep1

source_name: Ws after PEG treatment rep1


title: Ws control rep2

description: Gene expression of Ws accession under control condition

source_name: Ws control rep2


title: Sample147.Beluga whale.203531420018_R04C01


title: Sample146.Short-finned pilot whale.203531420018_R03C01

description: genomic DNA methylation from tissue=Blood species=Short-finned pilot whale

organism: Globicephala macrorhynchus


title: Mouse primary osteoblasts

description:
Total RNA from mouse primary osteoblasts was preocessed to small-RNA sequencing
KIN_003_01_LAB_191_01

source_name: Osteoblasts

value: primary osteoblasts

value: 8-10 weeks


title: Sha after salt treatment rep2

description: Gene expression of Sha accession after salt treatment

source_name: Sha after salt treatment rep2

value: Sha


title: Sha after salt treatment rep1

source_name: Sha after salt treatment rep1


title: Per2KO.d5

city: Minneapolis

first: Nobuaki

last: Kikyo

state: Minnesota

department: Stem Cell Institute

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using hisat2 v2.1.0
Read assignments were performed using hisat2 v2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expression count assigned raw reads for each sample.

source_name: Whole Muscle

growth_protocol: C2C12 cells were maintained in 10% FBS in DMEM. Differentiation was induced with 5% horse serum in DMEM.

extract_protocol:
Used Quick RNA Microprep (Zymo)
Total RNA was prepared from KO C2C12 cells before differentiation (day 0) and day 3 and 5 during differentiation. RNA concentration and RNA Integrity Number (RIN) were measured with an Agilent BioAnalyzer 2100. Samples with RIN over 8 were used to create sequencing libraries at University of Minnesota Genomics Center. One microgram of total RNA was used to create each sequencing library using Truseq RNA Sample Preparation Kit (Illumina, RS-122-2001). Briefly, poly-adenylated RNA was first purified using oligo-dT-coated magnetic beads. RNA was then fragmented and reverse-transcribed into cDNA. The cDNA was further fragmented, blunt-ended, and ligated to barcoded adaptors and amplified. Final library size distribution was validated with capillary electrophoresis and quantified with a Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, P11496) and qPCR. Indexed libraries were pooled and size-selected to 320 bp ± 5% with a LabChip XT (PerkinElmer). Libraries were loaded onto a single read flow cell and amplified on a cBot (Illumina) before sequencing using a HiSeq 2500 (Illumina).

tag: differentiation day

tag: inducible gene

value: Per2 KO

value: Whole Muscle


title: Per2KO.d3


title: Ws control rep1

source_name: Ws control rep1


title: Per2KO.d0


title: Sample145.Bottlenose dolphin.203531420018_R02C01

value: yes

value: Male


title: Sha after PEG treatment rep1

description: Gene expression of Sha accession after PEG treatment

source_name: Sha after PEG treatment rep1


title: Sha control rep1

description: Gene expression of Sha accession under control condition

source_name: Sha control rep1


title: Sha control rep2

source_name: Sha control rep2


title: Per1KO.d5

value: Per1 KO


title: Ler after salt treatment rep2

description: Gene expression of Ler accession after salt treatment

source_name: Ler after salt treatment rep2

value: Ler


title: Per1KO.d3


title: Sha after PEG treatment rep2

source_name: Sha after PEG treatment rep2


title: Sample137.Bottlenose dolphin.202897220153_R06C01

description: genomic DNA methylation from tissue=Blood species=Bottlenose dolphin

source_name: Blood

value: Blood


title: Sample136.Short-finned pilot whale.202897220153_R05C01


title: Ler after salt treatment rep1

source_name: Ler after salt treatment rep1


title: Ler after PEG treatment rep1

description: Gene expression of Ler accession after PEG treatment

source_name: Ler after PEG treatment rep1


title: Sample144.Beluga whale.203531420018_R01C01

description: genomic DNA methylation from tissue=Blood species=Beluga whale

value: Female


title: Ler after PEG treatment rep2

source_name: Ler after PEG treatment rep2


title: Ler control rep2

description: Gene expression of Ler accession under control condition

source_name: Ler control rep2


title: Ler control rep1

source_name: Ler control rep1


title: Tumor Th1

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

data_processing:
The abundance of transcripts from RNA-seq data was quantified through the Kallisto program. This program is based on pseudo alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. The Kallisto transcript index used as reference was built from merged mouse cDNA and ncDNA files from mm10. Gene-level count matrices were then created with the DESeq2 library. Low-count genes were pre-filtered by removing genes with too few reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv

source_name: Th1 cells from B16-F10 tumor

growth_protocol: CD4 T + cells were isolated from C57/Bl6 WT spleen, lymph nodes, draining lymph nodes and B16-F10 tumor

extract_protocol:
Total RNA was extracted from 300,000 CD4+ T cells with Trireagent by following manufacturer protocol.
Libraries were prepared from 12 µl of total RNA with the TruSeq Stranded Total RNA using Ribo-Zero (Illumina) following manufacturer instructions. Once qualified, paired-end libraries were sequenced using 2 × 75 bp output on a NextSeq 500 device (Illumina).

value: 7 weeks

tag: genotype

value: Wild-type

value: Th1 cells

value: B16-F10 tumor


title: Mouse primary bone marrow cells

description:
Total RNA from bone marrow cells was preocessed to small-RNA sequencing
KIN_003_02_LAB_191_02

source_name: Bone marrow

tag: cell type

value: primary bone marrow cells

value: control


title: Col after salt treatment rep1

description: Gene expression of Col accession after salt treatment

source_name: Col after salt treatment rep1

value: Col

value: whole seedling

value: 2 weeks


title: Sample135.Short-finned pilot whale.202897220153_R04C01


title: Sample133.Bottlenose dolphin.202897220153_R02C01


title: Col after PEG treatment rep2

description: Gene expression of Col accession after PEG treatment

source_name: Col after PEG treatment rep2


title: Per1KO.d0

source_name: Whole Muscle

tag: cell line


title: Col after salt treatment rep2

source_name: Col after salt treatment rep2


title: Spleen 2 Th1

source_name: Th1 cells from spleen, lymph nodes, draining lymph nodes


title: Sample132.Beluga whale.202897220153_R01C01


title: Col after PEG treatment rep1

source_name: Col after PEG treatment rep1


title: Col control rep1

description: Gene expression of Col accession under control condition

source_name: Col control rep1


title: Col control rep2

source_name: Col control rep2


title: Spleen 1 Th1

value: spleen, lymph nodes, draining lymph nodes


title: Sample134.Short-finned pilot whale.202897220153_R03C01


title: C24 after salt treatment rep2

description: Gene expression of C24 accession after salt treatment

source_name: C24 after salt treatment rep2


title: Normal 165 CD10+CD44+

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
base calling were performed on Illumina Solexa 1G platform
reads were collected as 17bp nucleotides in front of the PCR adaptor
raw reads were mapped to best gene using SAGE genie database long tag files (ftp://ftp1.nci.nih.gov/pub/SAGE/HUMAN/)
reads were normalized to counts per 10 million
Genome_build: hg19
Supplementary_files_format_and_content: tab delimilted txt file with columns of gene, count, and normalized count (read per 10M)

organism: Homo sapiens

source_name: normal reduction

extract_protocol:
mRNA isolated from atleast 50-100K cells were captured on oligo(dT) beads followed by cDNA synthesis
cDNA was cleaved with anchoring enzyme NlAIII followed by ligation of adapter 1. cDNA was then released by tagging enzyme MmeI and ligated to adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were from Illumina
SAGE-seq

value: mammary gland

tag: mutation

tag: parity

value: parous


title: Normal 136 CD10+CD44+

value: nulliparous


title: Normal 132 CD10+CD44+


title: Normal 117 CD10+CD44+


title: CD4 tumor 3

source_name: CD4+ T cells from tumor

growth_protocol: CD4 T + cells were isolated from C57/Bl6 WT spleen and  MC38 tumor

value: CD4+ T cells

value: MC38 tumor


title: CD4 tumor 2


title: Sample131.Short-finned pilot whale.202897220152_R06C02

source_name: Blood

tag: basename

value: yes

value: Blood


title: Normal 102 CD10+CD44+


title: Normal 108 CD10+CD44+


title: Normal 165 CD10+CD44-


title: CD4 spleen 3

source_name: CD4+ T cells from spleen

value: 7 weeks

value: spleen


title: Normal 136 CD10+CD44-


title: Normal 117 CD10+CD44-


title: CD4 spleen 2

value: Wild-type


title: Normal 108 CD10+CD44-


title: CD4 spleen 1


title: Normal 102 CD10+CD44-


title: Sample129.Bottlenose dolphin.202897220152_R04C02

tag: canbeusedforagingstudies

value: Male


title: Sample130.Bottlenose dolphin.202897220152_R05C02

tag: Sex


title: Normal 132 CD10+CD44-

tag: tissue


title: Sample128.Bottlenose dolphin.202897220152_R03C02

value: Female


title: Normal 174 total CD10

source_name: normal prophylactic


title: C24 after PEG treatment rep1

description: Gene expression of C24 accession after PEG treatment

source_name: C24 after PEG treatment rep1


title: Sample127.Bottlenose dolphin.202897220152_R02C02


title: C24 control rep2

description: Gene expression of C24 accession under control condition

source_name: C24 control rep2


title: Sample120.Killer whale.202897220152_R01C01

description: genomic DNA methylation from tissue=Blood species=Killer whale


title: uterine leiomyoma cell treated with 32.0 μmol/L NP rep3

city: haikou

first: Feng

middle: Tao

last: Zhang

state: hainan

address: 58 Renmin Avenue, Meilan District

department: School of  Life and  Pharmaceutical Sciences

institute: Hainan University

data_processing:
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Comparative analysis:These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match were further analyzed and annotated based on the reference genome. HISAT2 soft were used to map with reference genome.
Gene functional annotation:Gene function was annotated based on the following databases:NR(non- redundant protein sequence database);Swiss-Prot(A manually annotated, non- redundant protein sequence database);GO(Gene Ontology database);COG(Th   e database  of Clusters of Orthologous Groups of proteins);KOG(The  databas    e of Clusters of Protein homology);Pfam(The  database of Homologous protei     n family);KEGG(The database of Kyoto Encyclopedia of Genes  and  Genomes)
Quantification of gene expression levels: Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.Differential expression analysis of two conditions/groups was performed using the DESeq R package. DESeq provide statistical routines for determining differential expressionin digital gene expression data using a model based on the negative binomial distribution.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited text files includes FPKM values for each sample
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample

source_name: uterine leiomyoma cell lines

growth_protocol: The third generation of uterine leiomyoma cells was chosen and seeded on three 96-well culture plates at a density of 100 μl/well. The 96-well cell culture plate was incubated at 37 ° C with 5% CO2 for 48 h. Following that, 10μl of CCK-8 reagent(APExBIO, Houston, USA)was added to each well incubated for 2 h at 37 °C.

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was examined on 1.5% agarose gels. RNA concentration and purity were measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and reads were generated. Three biological replicates were sequenced per condition.

treatment_protocol: three representative primary cultured cell lines were selected, and cells were treated with 0.1% DMSO (Sigma, USA), 10.0 μmol/L BPA(Sigma, USA), and 32.0 μmol/L NP(Sigma, USA) for different times (24 h, 48 h, and 72 h), respectively. Each group had 5 complex holes. At the end of the culture, the absorbance (A450 value) was detected with an automatic fluorescence microplate reader, and the operation was repeated 3 times.nextly,the cells treated with  0.1% DMSO， 10.0μmol/L BPA, 32.0 μmol / L NP for 48h were fixed with cold 70% ethanol overnight prior to being stained with propidium iodide (PI) for cell cycle analysis.

value: Leiomyoma

tag: treatment

value: treated with 32.0 umol/L NP for 48h

tag: gender

value: female


title: Sample121.Beluga whale.202897220152_R02C01


title: uterine leiomyoma cell treated with 10.0 μmol/L BPA rep3

value: treated with 10.0 umol/L BPA for 48h


title: C24 control rep1

source_name: C24 control rep1

value: whole seedling

value: 2 weeks


title: Sample113.Bottlenose dolphin.202897220040_R06C01


title: Sample126.Bottlenose dolphin.202897220152_R01C02


title: uterine leiomyoma cell treated with 32.0 μmol/L NP rep1


title: uterine leiomyoma cell treated with 10.0 μmol/L BPA rep2


title: uterine leiomyoma cell treated with 32.0 μmol/L NP rep2


title: Normal 171 total CD10

value: mammary gland

value: parous


title: Sample112.Short-finned pilot whale.202897220040_R05C01

description: genomic DNA methylation from tissue=Blood species=Short-finned pilot whale


title: uterine leiomyoma cell treated with 10.0 μmol/L BPA rep1


title: C24 after salt treatment rep1

source_name: C24 after salt treatment rep1


title: Normal 105 total CD10


title: C24 after PEG treatment rep2

source_name: C24 after PEG treatment rep2


title: Sample110.Short-finned pilot whale.202897220040_R03C01


title: uterine leiomyoma cell treated with 0.1% DMSO rep3

value: untreated


title: uterine leiomyoma cell treated with 0.1% DMSO rep2


title: Trigeminal ganglia LgDel rep4 [LD_3]

city: Roanoke

first: Thomas

last: Maynard

state: VA

address: 2 Riverside Circle

institute: Virginia Tech Carilion/FBRI

data_processing:
Illumina RTA and Casava software used for basecalling.
Alignment to GRCm38/mm10 using HISAT2 v.2.1.0
Alignments indexed using SAMtools v.1.4
Assembly into transcripts using Cufflinks v.2.2.1
Differential expression analysis was using CuffDiff utility of Cufflinks v.2.2.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Trigeminal ganglia LgDel

extract_protocol:
Trigeminal ganglia were harvested by microdissection from E10.5 WT and LgDel embryosand stored in RNAlater until each embryo was genotyped. Pooled CNgV samples were generated to yield five biological replicates for each genotype (WT, LgDel); each pool contained at least six ganglia from at least three embryos of the same genotype over several litters. Pools contained approximately 30 000–36 000 cells. Accordingly, we used all of the RNAs isolated from each pool for subsequent transcriptome sequencing. Total RNA from each pool was extracted using by the acid guanidinium thiocyanate-phenol-chloroform method.  Samples all passed QC with RIN scores ≥8 via Agilent 2100 Bioanalyzer. were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: LgDel

value: embryonic day 10.5

value: Trigeminal ganglia


title: Trigeminal ganglia LgDel rep1 [LD_0]

tag: developmental stage


title: Trigeminal ganglia LgDel rep5 [LD_4]


title: Trigeminal ganglia LgDel rep2 [LD_1]


title: Trigeminal ganglia LgDel rep3 [LD_2]


title: Trigeminal ganglia WT rep5 [WT_4]

source_name: Trigeminal ganglia WT

value: WT


title: Trigeminal ganglia WT rep4 [WT_3]


title: Sample109.Bottlenose dolphin.202897220040_R02C01

value: yes

value: Blood


title: H69-d10-2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: biotin

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: Total RNA from each time point was extracted using Trizol (Invitrogen) and purified using RNeasy columns (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. After processing with DNase digestion and clean-up procedures, RNA samples were quantified, aliquoted, and stored at −80 °C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis (OD 260/280 ratio) and analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: cholangiocyte

value: ESP-treated


title: H69-d10-1


title: H69-d05-2


title: H69-d00-1

value: Untreated


title: uterine leiomyoma cell treated with 0.1% DMSO rep1

value: Leiomyoma


title: Trigeminal ganglia WT rep3 [WT_2]


title: Sample111.Short-finned pilot whale.202897220040_R04C01

value: Female


title: H69-d05-1


title: Trigeminal ganglia WT rep2 [WT_1]


title: Trigeminal ganglia WT rep1 [WT_0]


title: H69-d00-2


title: WT_Non treated 3

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with genes identified by Entrez id

source_name: Mesenteric lymph node

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

value: Sorted ILC2s

value: Mesenteric lymph node


title: RanG22V D3_rep1

city: Wonju-si

first: Soo-Hwan

state: Gangwon-do

address: 1, Yeonsedae-gil, Heungeop-myeon

department: DIVISION OF BIOLOGICAL SCIENCE AND TECHNOLOGY

institute: Yonsei University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10(NCBI) whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Leaves

growth_protocol: Arabidopsis thaliana Col-0 wild-type and Ran-GDP, Ran-GTP overexpression transgenic plants were grown in greenhouse operating under a cycle of 16 h light (100–150 µmol m–2 s–1) and 8 h dark at 22°C

extract_protocol:
Total RNA was extracted from the leaves using iNtRON easy spin IIp plant RNA extraction kit.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The fifth and sixth leaves of 4 week-old Ran-GDP and Ran-GTP overexpression transgenic plants were detached and harvested for D0 samples. Those of the same leaves set incubated 3 days in darkness were harvested for D3 samples.

value: the fifth and sixth leaves of 4 week-old plants

value: 3 days dark incubation


title: WT_Non treated 2


title: RanT27N D3_rep1


title: RanT27N D3_rep2


title: Sample107.Short-finned pilot whale.202897220070_R06C02


title: Sample106.Bottlenose dolphin.202897220070_R05C02

value: Male


title: RanG22V D0_rep2

value: untreated


title: RanG22V D3_rep2


title: RanG22V D0_rep1


title: Sample103.Bottlenose dolphin.202897220070_R02C02


title: Sample104.Bottlenose dolphin.202897220070_R03C02


title: Sample105.Bottlenose dolphin.202897220070_R04C02


title: WT_Non treated 1


title: Sample102.Bottlenose dolphin.202897220070_R01C02


title: RanT27N D0_rep2


title: RanT27N D0_rep1


title: Col D0_rep2

value: wildtype


title: Col D0_rep1


title: Young LepR+ rep3

first: Philipp

last: Leucht

address: 550 First Avenue

department: Orthopedic Surgery, Cell Biology

institute: NYU Grossman School of Medicine

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 sequencer.  demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The sequencing
Sequencing results were reads were aligned to the mouse genome (build mm10/GRCm38) using Sequencing results were the splice-aware STAR
The featureCounts program [https://www.ncbi.nlm.nih.gov/pubmed/24227677] was utilized to generate counts for each gene based on how many aligned reads overlap its exons. These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package [http://www.ncbi.nlm.nih.gov/pubmed/25516281]. Normalized counts were used for Gene Set Enrichment Analysis (GSEA) [http://software.broadinstitute.org/gsea/index.jsp].
Genome_build: mm10
Supplementary_files_format_and_content: excel file includes normalized gene counts for each sample

source_name: Tibiae and femurs

extract_protocol:
Tibiae and femurs were harvested and subjected to collagenase digestion to retrieve skeletal stem and progintors from the bone marrow and bone-lining cells. LepR+ cells were isolated from the nonhematopoeitic compartmentment by florcytometry
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LepR+ Skeletal cell and progenitors

value: young

value: Tibiae and femurs


title: Young LepR+ rep1


title: Middle-aged-treated LepR+ rep3

value: middle aged

value: sodium salicylate


title: Sample93.Bottlenose dolphin.202897220159_R04C02

value: yes

value: Blood


title: Sample96.Killer whale.202897220070_R01C01


title: Sample97.Beluga whale.202897220070_R02C01


title: Sample92.Bottlenose dolphin.202897220159_R03C02


title: DPSC3

city: Serdang

first: Pooi Ling

last: Mok

state: Selangor

address: Universiti Putra Malaysia

department: Department of Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

data_processing:
The BaseSpace Onsite Hub in the NextSeq 500 System was used to generate output data from the run
The protocol was adapted from Love et al., F1000Res, 2018. In brief, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor 6.0 transcriptome using Salmon with example parameters: salmon quant -i r.norv_index -l A -1 Example_R1.fastq -2 Example_R2.fastq -p 8 --validateMappings -o Example_quant. k-mer was designated as 31
Transcript abundance obtained with Salmon (v1.1.0) were converted to the gene level with Tximport and used as an input for DESeq2 (v3.2) for normalization and quantification.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each sample

source_name: Retina

growth_protocol: MSC, DPSC, and MSCEPO cells were routinely generated by re-plating the adherent cultures (typically around 5 × 10^5 cells into a T75 flask) on uncoated plastic in DMEM-F12 medium (Thermofisher, MA, USA).

extract_protocol:
Retinas were removed and preserved in RNALater. The RNA was harvested using the RNeasy mini kit (Qiagen, Hilden, Germany). The qiaseq stranded mrna select kit (Cat No./ID: 180773) was with 1 ug of total RNA to produce the sequencing libaries.
RNA libraries were prepared for sequencing using standard Qiagen protocols that are made compatible with the Illumina system

treatment_protocol: The stem cells were transplanted intravitreally at a desired concentration of 1 x 10^5 cells/ul (suspended in Hank's balanced saline solution) using a Hamilton syringe. The retinal degeneration model was developed with a systemic administration of sodium iodate at a 40 mg/kg dose. Rats with xenograft transplants were given intraperitoneal dexamethasone immunosuppressant (2 mg/kg) before the surgery. After the surgery, the regime was changed to oral cyclosporin immunosuppresant at a dose of 10 mg/kg/day until the end of the study.

value: Sprague-Dawley

value: Retinal tissue

value: Post natal week 12

value: Wild type

value: Post transplant day 31


title: Middle-aged LepR+ rep3


title: Young LepR+ rep2


title: Middle-aged LepR+ rep1


title: Sample89.Bottlenose dolphin.202897220159_R06C01

value: Female


title: Sample91.Bottlenose dolphin.202897220159_R02C02


title: EPO1


title: Middle-aged LepR+ rep2


title: Sample87.Bottlenose dolphin.202897220159_R04C01


title: DPSC2


title: HIF2_8

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

data_processing:
Raw sequencing read quality was assessed utilizing FastQC.
Reads were aligned to the reference mouse transcriptome (UCSC mm10) using Bowtie v 2.1.0.0 and TopHat v 2.0.9. Default parameters were used for the alignment, with the exception of “-b2-very-sensitive,” “-no-coverage-search,” and “-no-novel-juncs.” Mate inner pair distances were estimated by TopHat, and the values were used in the alignment.
Expression quantification and differential expression analysis between Hif-2αLSL and Hif-2α+/+ mice were conducted using CuffDiff v 2.1.1 with the parameter settings “-multi-read-correct,” “-compatible-hits-norm,” and “-upper-quartile-norm” for normalization of expression calculations across samples. For the CuffDiff analysis, we used UCSC mm10.fa as the reference genome and UCSC mm10.gtf as the reference transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM matrix of all samoples generated by Cufflinks

molecule: polyA RNA

source_name: Colon tissue

growth_protocol: This was all perfromed in vivo.

extract_protocol:
RNA was isolated from fresh or frozen tissue using Isol-RNA lysis reagent
RNA sequencing libraries were prepared using the TruSeq RNA library prep kit v2 (Illumina) following the manufacturer's recommended protocol.

treatment_protocol: These mice were untreated, comparing WT mice to mice overexpresing HIF2 in the colon

tag: genotype/variation

value: Hif2a LFL

value: colon


title: DPSC1

tag: age


title: EPO3


title: MSC3

value: sodium iodate-administered, MSC-treated


title: Sample86.Bottlenose dolphin.202897220159_R03C01


title: Middle-aged-treated LepR+ rep2


title: Middle-aged-treated LepR+ rep1


title: Sample90.Bottlenose dolphin.202897220159_R01C02

description: genomic DNA methylation from tissue=Skin species=Bottlenose dolphin

source_name: Skin

value: Skin


title: Sample85.Bottlenose dolphin.202897220159_R02C01

source_name: Blood


title: Sample83.Bottlenose dolphin.202897220157_R06C02


title: MSC2


title: HIF2_6


title: Sample84.Bottlenose dolphin.202897220159_R01C01

value: Male


title: HIF2_7


title: MSC1


title: EPO2


title: Sham3

value: Sodium iodate-administered


title: HIF2_4


title: Sample80.Bottlenose dolphin.202897220157_R03C02


title: Sham2


title: HIF2_3


title: HIF2_2


title: NT3

value: Healthy


title: HIF2_1


title: Sample82.Bottlenose dolphin.202897220157_R05C02


title: HIF2_0


title: Sample78.Killer whale.202897220157_R01C02


title: Sample81.Bottlenose dolphin.202897220157_R04C02


title: NT1


title: WT_8

value: Hif2a +/+


title: Sample76.Killer whale.202897220157_R05C01


title: WT_7


title: Sample79.Bottlenose dolphin.202897220157_R02C02


title: WT_6


title: Sample75.Killer whale.202897220157_R04C01


title: HIF2_5


title: NT2


title: Sample77.Killer whale.202897220157_R06C01


title: Sample73.Killer whale.202897220157_R02C01


title: Sample74.Killer whale.202897220157_R03C01


title: WT_5


title: Sample71.Bottlenose dolphin.202897220149_R06C02


title: Sham1


title: WT_3


title: Sample72.Bottlenose dolphin.202897220157_R01C01


title: WT_2


title: knock out, biological rep2

city: Chong Qing

first: zi hao

last: zhang

state: China/Chong Qing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

description: mouse bone marrow was rushed first, then single cell suspension samples were stained and sorted to harvest HSCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Clariom D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: 6-8 weeks old CDK19-/- mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The bone marrow cells in the mouse tibia, femur and ilium were gently flushed out by a syringe

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Lin- enrichment and fluorescent stain of HSC marker, samples were sorted by flow cytometry

value: bone marrow hematopoietic stem cells


title: knock out, biological rep3


title: WT_4


title: knock out, biological rep1


title: WT_0


title: A3 (experience group)

city: Dalian

first: Shuaijun

last: Zan

address: NO.2 of Linggong road

institute: Dalian university and technology

data_processing:
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Illumina Casava1.7 software used for basecalling.
Quality control.Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Quantification of gene expression level.HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways. For the SNP analysis, Picard-tools (v1.96) and samtools (v 0.1.18) were used to sort, mark duplicated reads and reorder the bam alignment results of each sample. GATK2 software was used to perform SNP calling.
Genome_build: CP058972.1 (https://www.ncbi.nlm.nih.gov/nuccore/CP058972.1/). FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample.

organism: Pseudoalteromonas sp. JSTW

source_name: Marine Sediment

extract_protocol:
strain JSTW were centrifuged and collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Marine bacteria

value: anaerobic condition


title: A1 (experience group)


title: Sample70.Bottlenose dolphin.202897220149_R05C02

first: Steve

institute: University of California, Los Angeles

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

extract_protocol: genomic DNA was extracted

value: yes

value: Blood


title: WT_1


title: Sample108.Beluga whale.202897220040_R01C01


title: Sample69.Bottlenose dolphin.202897220149_R04C02


title: Heart sample H21 (HKII+/+)

first: Sander

middle: M

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.4.0 g1)
gene-level read quantification via featureCounts v1.4.4
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing read count per gene

source_name: heart

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture) and samples were run on an Illumina HiSeq 2500 sequencer to yield a total read depth of approximately 52 million 100 nucleotide single-end reads per sample

value: male

tag: age (months)

value: between 2 and 4

value: HKII+/+

tag: diet

value: chow


title: Heart sample H20 (HKII+/-)

tag: genotype

value: HKII+/-


title: Sample65.Pacific white-sided dolphin.202897220149_R06C01

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

description: genomic DNA methylation from tissue=Blood species=Pacific white-sided dolphin

organism: Sagmatias obliquidens

value: Female


title: Sample64.Bottlenose dolphin.202897220149_R05C01


title: RAS, low density, control, fish 4

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with GenePix 4100 microarray scanner

data_processing: Images were processed using GenePix Pro 6.0. After removal of flagged spots, lowess normalization was performed

organism: Salmo salar

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: culture method

value: RAS

tag: condition

value: control

tag: density

value: low


title: Heart sample H22 (HKII+/-)


title: Sample66.Killer whale.202897220149_R01C02

city: Los Angeles

description: genomic DNA methylation from tissue=Skin species=Killer whale

value: Skin


title: wild type, biological rep1

source_name: 6-8 weeks old WT mice

tag: cell type

value: wildtype


title: Sample62.Bottlenose dolphin.202897220149_R03C01

description: genomic DNA methylation from tissue=Blood species=Bottlenose dolphin

tag: basename

value: Male


title: RAS, low density, control, fish 3


title: B3 (experience group)

value: aerobic condition


title: B2 (experience group)

value: Marine bacteria


title: wild type, biological rep3

value: bone marrow hematopoietic stem cells


title: RAS, low density, control, fish 2


title: RAS, low density, control, fish 6


title: RAS, low density, control, fish 5


title: RAS, low density, control, fish 1


title: Sample61.Killer whale.202897220149_R02C01

tag: canbeusedforagingstudies

value: yes


title: Heart sample H18 (HKII+/+)

tag: Sex


title: wild type, biological rep2


title: Sample63.Bottlenose dolphin.202897220149_R04C01

tag: tissue

value: Blood


title: B1 (experience group)

tag: treatment


title: Heart sample H19 (HKII+/-)

value: male


title: A2 (experience group)

value: anaerobic condition


title: SJ3 (experience group)

value: untreated


title: Heart sample H17 (HKII+/+)

value: between 2 and 4

value: HKII+/+

value: chow


title: Heart sample H15 (HKII+/+)


title: SJ2 (experience group)


title: SJ1 (experience group)


title: Heart sample H16 (HKII+/-)

value: HKII+/-


title: Heart sample H14 (HKII+/+)


title: Cov2-MeRIP

city: La Jolla

last: Li

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the SARS-CoV-2 (NC_045512.2) genome or hg38 genome assembly using STAR or Bowtie2 aligner
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called by MACS2 using the following configuration:  p-value< 0.05, call-summit, keep-dup 1 --nomodel --extsize 200 or keep-dup all --nomodel --extsize 200 for SARS-CoV-2 alignment; p<1e-5, -keep-dup auto --extsize 200 nomodel for human alignment
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: SARS-CoV-2 (NC_045512.2), GRCh38, ChlSab1.1
Supplementary_files_format_and_content: xlsx: contains normailzed gene expression by DESeq2; bigBed: contains peaks detecting by MACS2 (1: keep-dup 1; all: keep-dup all)

organism:
Chlorocebus aethiops
Severe acute respiratory syndrome coronavirus 2

source_name: SARS-CoV-2 viral infected Vero cells

growth_protocol: The human colorectal adenocarcinoma Caco-2 cells were purchased from ATCC. Caco-2 cells were cultured in high-glucose MEM (Thermo Fisher Scientific) supplemented with 20% fetal bovine serum (FBS; Gibco), MEM NEAA (Thermo Fisher Scientific) and 50 U/ml penicillin-streptomycin (Gibco) in a humidified 5% CO2 atmosphere.  For SARS-CoV-2 live cell infection, SARS-CoV-2 isolate USA-WA1/2020 was obtained from BEI Resources. SARS-CoV-2 virus was propagated, and infectious units were quantified by plaque assay using Vero E6 cells.

extract_protocol:
supernatant RNA from infected Vero cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

treatment_protocol: Infected with SARS-CoV-2

tag: cell line

value: Kidney epithelial Vero E6 cells from an African green monkey

tag: infection

value: SARS-CoV-2 virus

tag: passages

tag: viral strain

value: Betacoronavirus

tag: merip antibody

value: anti-m6A polyclonal antibody (ab151230, abcam)


title: Cov2-Input

extract_protocol:
supernatant RNA from infected Vero cells were extracted and purified for input of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).


title: RAS, high density, control, fish 5

value: Skin

value: RAS

value: control

value: high


title: RAS, high density, control, fish 6


title: Heart sample H11 (HKII+/-)

description: Potential outlier

tag: strain

tag: age (months)


title: RAS, high density, control, fish 1


title: RAS, high density, control, fish 3


title: Heart sample H13 (HKII+/+)

description: Potential outlier

tag: genotype

tag: diet


title: RAS, high density, control, fish 2

tag: culture method

tag: condition


title: β-cell Ctrl, rep3

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

description:
β Ctrl Rep3
Sorted from 2-month-old RipCreER; R26YFP mice.
Normalized_Expression_table_SUMMARY.xlsx

data_processing:
Raw reads were trimmed to 60bp using fastx_trimmer from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Trimmed reads were aligned with the Tuxedo suite (Bowtie2 2.2.2.0 (Langmead et al. 2009), TopHat v2.0.12 (Trapnell et al. 2009), Cufflinks v2.2.1 (Trapnell et al. 2012)) using default settings and the UCSC mm10 annotation of the mouse genome, but changing the maximum number of fragments a locus may have before being skipped (--max-bundle-frags) to 1E8, to include quantification of highly expressed α- and β- cell genes. Transcript levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) generated by TopHat/Cufflinks.
Next, the Cuffnorm and Cuffdiff tools (Trapnell et al. 2012) were used to normalize gene expression data across samples and replicates used in this study and to detect differential gene expression in pairwise sample comparisons, respectively.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized_Expression_table_SUMMARY.xlsx: Excel file table with normalized gene expression for all samples and replicates.

source_name: Control FACS sorted Beta cells, Replicate 3

extract_protocol:
RNA from cells isolated by FACS was assessed for quality by Agilent bioanalyzer prior to library generation and sequencing.
Sequencing was performed at the iGE3 Genomic Platform using an HiSeq 2500 sequencer and we sequenced 100 single-end reads.

treatment_protocol: 1) α cells control and 5, 15, 30 days after DT (α 5dpDT, 15dpDT and 30dpDT): sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice (whose glucagon-expressing α-cells express the fluorescent reporter YFP and β-cells can be ablated by DT administration), injected with three doses of DT at 2 months of age. 2) mature β cells (β Ctrl): sorted from 2-month-old RipCreER; R26YFP mice (whose insulin expressing cells express YFP after tamoxifen (TAM) administration; TAM was injected when mice were 1-month-old).

tag: genotype/variation

value: RipCreER; R26YFP

tag: cell type

value: beta-cells

tag: age

value: 2 months


title: Sample55.Killer whale.202894750036_R02C02

tag: basename

tag: canbeusedforagingstudies

value: yes

tag: Sex

value: Female

value: Blood


title: β-cell Ctrl, rep2

description:
β Ctrl Rep2
Sorted from 2-month-old RipCreER; R26YFP mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: Control FACS sorted Beta cells, Replicate 2


title: Heart sample H12 (HKII+/-)

value: male

value: between 2 and 4


title: β-cell Ctrl, rep1

description:
β Ctrl Rep1
Sorted from 2-month-old RipCreER; R26YFP mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: Control FACS sorted Beta cells, Replicate 1


title: Sample57.Killer whale.202894750036_R04C02

tag: tissue


title: Sample60.Pacific white-sided dolphin.202897220149_R01C01


title: RAS, high density, control, fish 4

tag: density


title: Sample54.Pacific white-sided dolphin.202894750036_R01C02


title: Sample58.Bottlenose dolphin.202894750036_R05C02

value: Male


title: α-cell 30dpDT, rep5

description:
α 30dpDT Rep5
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 30 days after DT-induced β-cell loss, Replicate 5

value: Glucagon-rtTA, R26YFP, RIP-DTR

value: alpha-cells

tag: time point

value: 30 days after DT-induced beta-cell loss


title: Sample53.Pacific white-sided dolphin.202894750036_R06C01


title: Flowthrough, low density, control, fish 1

value: flowthrough

value: low


title: Flowthrough, low density, control, fish 5

value: Skin


title: Sample52.Pacific white-sided dolphin.202894750036_R05C01


title: Flowthrough, low density, control, fish 6

value: control


title: Flowthrough, low density, control, fish 2


title: Sample51.Beluga whale.202894750036_R04C01

description: genomic DNA methylation from tissue=Blood species=Beluga whale


title: Sample56.Killer whale.202894750036_R03C02


title: α-cell 30dpDT, rep2

description:
α 30dpDT Rep2
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 30 days after DT-induced β-cell loss, Replicate 2


title: Sample59.Killer whale.202894750036_R06C02


title: α-cell 30dpDT, rep3

description:
α 30dpDT Rep3
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 30 days after DT-induced β-cell loss, Replicate 3


title: α-cell 30dpDT, rep4

description:
α 30dpDT Rep4
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 30 days after DT-induced β-cell loss, Replicate 4


title: Sample50.Beluga whale.202894750036_R03C01


title: Flowthrough, high density, control, fish 6

value: high


title: Flowthrough, low density, control, fish 3


title: Flowthrough, low density, control, fish 4


title: Flowthrough, high density, control, fish 4


title: Flowthrough, high density, control, fish 5


title: α-cell 30dpDT, rep1

description:
α 30dpDT Rep1
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 30 days after DT-induced β-cell loss, Replicate 1


title: Flowthrough, high density, control, fish 3


title: Sample47.Beluga whale.202894750035_R06C02


title: Sample46.Beluga whale.202894750035_R05C02


title: α-cell 15dpDT, rep3

description:
α 15dpDT Rep3
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 15 days after DT-induced β-cell loss, Replicate 3

value: 15 days after DT-induced beta-cell loss


title: Sample49.Beluga whale.202894750036_R02C01


title: Sample48.Beluga whale.202894750036_R01C01


title: Flowthrough, high density, control, fish 2


title: α-cell 15dpDT, rep2

description:
α 15dpDT Rep2
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 15 days after DT-induced β-cell loss, Replicate 2


title: α-cell 15dpDT, rep1

description:
α 15dpDT Rep1
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 15 days after DT-induced β-cell loss, Replicate 1


title: α-cell 5dpDT, rep2

description:
α 5dpDT Rep2
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 5 days after DT-induced β-cell loss, Replicate 2

value: 5 days after DT-induced beta-cell loss


title: α-cell 5dpDT, rep3

description:
α 5dpDT Rep3
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 5 days after DT-induced β-cell loss, Replicate 3


title: α-cell 5dpDT, rep1

description:
α 5dpDT Rep1
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: α-cells FACS sorted 5 days after DT-induced β-cell loss, Replicate 1


title: Flowthrough, high density, control, fish 1

source_name: Skin


title: α-cell Ctrl, rep3

description:
α Ctrl Rep3
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: Control FACS sorted α-cells, Replicate 3


title: α-cell Ctrl, rep2

description:
α Ctrl Rep2
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: Control FACS sorted α-cells, Replicate 2


title: α-cell Ctrl, rep1

description:
α Ctrl Rep1
Cells sorted from Glucagon-rtTA, R26YFP, RIP-DTR mice.
Normalized_Expression_table_SUMMARY.xlsx

source_name: Control FACS sorted α-cells, Replicate 1


title: RAS, low density, stress, fish 4

value: RAS

value: crowding stress


title: Sample44.Beluga whale.202894750035_R03C02

source_name: Blood

value: yes


title: RAS, low density, stress, fish 3


title: RAS, low density, stress, fish 5


title: RAS, low density, stress, fish 6


title: Dhx36_CLIP_Bio_Rep2

city: HONG KONG

first: Jie

last: Yuan

state: HONG KONG

address: Prince of Wales Hospital

department: Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

description:
CLIP-seq (single-end sequencing)
RNAs interacting with Dhx36

data_processing:
Library strategy: CLIP-seq
First 6nt low quality bases were trimmed and adapter sequences were removed by Trimmomatic.
After de-duplication, the remaining reads were aligned to the mouse genome mm9 using Bowtie2 software, allowing 2 insertions or deletions, 2 mismatches and only kept the reads with greater than 90% identity.
CLIP-Seq peaks were called using Piranha with the following parameters: -sort; -p_threshold 0.05; -b 100.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bed: The peak bed files were generated using Piranha software.

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
The cell pellet was resuspended in 1 ml of wash buffer (1xPBS, 0.1% SDS, 0.5% NP-40, 0.5% deoxycholate), mixed briefly and incubated on ice for 15 min. After sonicated twice for 10 sec each at the maximum setting (BRANSON, SONIFER cell disruptor 185) (output setting 4; timer Hold), cells were spun down at 13,000 rpm for 15 min at 4 °C. Then added the beads which coupled antibody to the cell lysate and incubate 4h at 4 °C. After immunoprecipitation, washed beads with wash buffer, high salt wash buffer (5xPBS, 0.1% SDS, 0.5% NP-40, 0.5% deoxycholate), and 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10mM MgCl2, 0.5% NP-40). And then the beads was briefly incubated with 200 μl of 1 × MN buffer (50 mM Tris-HCl pH 8.0, 5 mM CaCl2) plus 0.12 U micrococcal nuclease for 10 min at 37 °C. The reaction was stopped by washing twice with 1 × PNK + EGTA buffer (50 mM Tris- HCl pH7.4, 20 mM EGTA, 0.5% NP-40) and twice with 1 × PNK buffer. After the fragmentation, beads were treated with Fast alkaline phosphatase for 15 min at 37 °C. Then stopped the reaction by washing beads twice with 1 × PNK + EGTA buffer and 1 × PNK buffer. The target RNAs in bead then were ligated the 3' linker by the T4 RNA Ligase 2, truncated KQ. After the ligation, protein and the binding RNA were elute by 1xLDS sample buffer for 10min at 70 °C. And run the 4-12% bis-tris gel and transfer membrane. After recover the membrane, proteinase K treatment was carried out to release the RNAs, and the RNAs were extracted with acid Phenol: chloroform and precipitated at -20°C ethanol. RNAs were pelleted at 13,000 rpm and washed twice with 75% ETOH before resuspending in 6.5 μl of nuclease-free water. The 5' linker were ligated by T4 RNA ligase for 4h at 16°C. And the RNAs were extracted like above, and washed twice with 75% ETOH before resuspending in 8 μl of nuclease-free water.
Reverse transcription was performed by addition of 1 μl 10 mM dNTPs and 1 μl 10 mM RT primer, incubated at 65 °C for 5 min. And then added the 10 μl of RT mix (2 μl of 10 × Superscript RT buffer, 1 μl of 100 mM DTT, 1 μl of RNase inhibitor, 1 μl of Superscript III reverse transcriptase) to the mixture and incubation at 50 °C for 60 min, and then 80 °C for 5 min. The 1st round PCR was performed with 1 μl of 10 μM AD primer, 1 μl of 10 μM PB primer, 1 μl 10 mM dNTPs, 10 μl of 5 × phusion HF buffer, 0.5 μl of phusion taq polymerase. The 70 bp to 110 bp of PCR products were purified from TBE gel. Then the 2nd round PCR was performed with 0.5 μl of 10 μM index primer, 0.5 μl of 10 μM PB primer, 0.4 μl 10 mM dNTPs, 4 μl of 5 × phusion HF buffer, 0.15 μl of phusion taq polymerase and purified the 110 bp to 170 bp of PCR products. The DNA concentration was measured by Qubit and sequenced by Illumina single-end sequencing.

treatment_protocol: C2C12 myoblasts were washed twice with 10 ml ice-cold PBS per plate and then irradiated with 254 nm UV light in a Stratalinker 2400 (Stratagene). The crosslinked cells were scraped off and collected by centrifugation at 500 g.

tag: cell line

tag: developmental stage

value: GM 48 hours

tag: antibody


title: RAS, low density, stress, fish 2


title: RAS, low density, stress, fish 1


title: RAS, high density, stress, fish 5


title: Sample40.Bottlenose dolphin.202894750035_R05C01

department: Human Genetics

description: genomic DNA methylation from tissue=Blood species=Bottlenose dolphin

value: Blood


title: Sample39.Killer whale.202894750035_R04C01

description: genomic DNA methylation from tissue=Blood species=Killer whale


title: WT.d0.L002

city: Minneapolis

first: Nobuaki

last: Kikyo

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using hisat2 v2.1.0
Read assignments were performed using hisat2 v2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expression count assigned raw reads for each sample.

source_name: Whole Muscle

extract_protocol:
Used Quick RNA Microprep (Zymo)
Total RNA was prepared from KO C2C12 cells before differentiation (day 0) and day 3 and 5 during differentiation. RNA concentration and RNA Integrity Number (RIN) were measured with an Agilent BioAnalyzer 2100. Samples with RIN over 8 were used to create sequencing libraries at University of Minnesota Genomics Center. One microgram of total RNA was used to create each sequencing library using Truseq RNA Sample Preparation Kit (Illumina, RS-122-2001). Briefly, poly-adenylated RNA was first purified using oligo-dT-coated magnetic beads. RNA was then fragmented and reverse-transcribed into cDNA. The cDNA was further fragmented, blunt-ended, and ligated to barcoded adaptors and amplified. Final library size distribution was validated with capillary electrophoresis and quantified with a Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, P11496) and qPCR. Indexed libraries were pooled and size-selected to 320 bp ± 5% with a LabChip XT (PerkinElmer). Libraries were loaded onto a single read flow cell and amplified on a cBot (Illumina) before sequencing using a HiSeq 2500 (Illumina).

tag: differentiation day

tag: inducible gene

value: WT

value: Whole Muscle


title: Sample35.Killer whale.202897220027_R06C02

value: Male


title: Sample36.Killer whale.202894750035_R01C01


title: Sample37.Killer whale.202894750035_R02C01


title: Sample38.Killer whale.202894750035_R03C01

value: Female


title: Sample34.Killer whale.202897220027_R05C02


title: WT.d3.L002


title: RAS, high density, stress, fish 3


title: WT.d5.L002


title: RAS, high density, stress, fish 6


title: RAS, high density, stress, fish 4


title: Sample42.Beluga whale.202894750035_R01C02

description: genomic DNA methylation from tissue=Blood species=Beluga whale


title: Sample45.Beluga whale.202894750035_R04C02


title: Dhx36_CLIP_Bio_Rep1


title: Sample32.Killer whale.202897220027_R03C02


title: Flowthrough, low density, stress, fish 6


title: RAS, high density, stress, fish 2


title: Sample33.Killer whale.202897220027_R04C02


title: Sample31.Bottlenose dolphin.202897220027_R02C02


title: RAS, high density, stress, fish 1


title: Flowthrough, low density, stress, fish 5


title: Sample30.Bottlenose dolphin.202897220027_R01C02


title: Sample43.Beluga whale.202894750035_R02C02


title: Sample28.Killer whale.202897220027_R05C01

description: genomic DNA methylation from tissue=Spleen species=Killer whale

source_name: Spleen

value: Spleen


title: CJ_CG84-21_dRNA_R2_minus_TEX

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: -q 20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of reads longer than 11 nt to reference genome using segemehl version 0.2.0 with minimum accuracy 95% after poly(A)-trimming (parameters for reademption align: -l 12 -c -a 95 ) (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length); Normalization: coverage-tnoar_mil_normalized (counts divided by total number of aligned reads and multiplied by 1,000,000) (READemption 0.4.5, Förstner et al., 2014)
Genome_build: Campylobacter jejuni CG84-21 (Assembly acc.: GCF_000171795.2, Sequence ID: NZ_CP005388.1)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

organism: Campylobacter jejuni subsp. jejuni CG8421

source_name: Campylobacter jejuni CG84-21 cells

growth_protocol: Bacterial cells grown to mid-log in Brucella Broth media at 37° C, 140 rpm agitation in microaerobic environment (10% CO2, 5% O2, 85% N2) of HERAcell 150i incubator.

extract_protocol:
Total RNA was purified using Hot-Phenol RNA isolation method from C.jejuni CG84-21 cells and used for TEX treatment.
Briefly, total RNA isolated from CG84-21 was treated with DNase I, and equal amounts of Campylobacter RNA were incubated with Terminator™ 5′-phosphate-dependent exonuclease (TEX) (Epicentre, cat. #TER51020) for depletion of processed transcripts as previously described(2)(9). cDNA libraries for Illumina sequencing were then constructed by Vertis Biotechnologie AG, Germany (http://www.vertis-biotech.com) in a strand-specific manner (2)(9). In brief, RNA samples were poly(A)-tailed using poly(A) polymerase. Then, 5′-triphosphates were removed using tobacco acid pyrophosphatase (TAP), and an RNA adaptor was then ligated to the resulting 5′-monophosphate. First-strand cDNA was synthesized with an oligo(dT)-adaptor primer using M-MLV reverse transcriptase. A PCR-based amplification step was then conducted with a high-fidelity DNA polymerase to increase the cDNA concentration to 10-20 ng/μL. For all libraries, the Agencourt AMPure XP kit (Beckman Coulter Genomics) was used to purify the DNA, which was subsequently analyzed by capillary electrophoresis.  A library-specific barcode for multiplex sequencing was included as part of a 3′-sequencing adaptor. The following adaptor sequences flank the cDNA inserts:  TruSeq_Sense_primer:  5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′  TruSeq_Antisense_NNNNNN_primer:  5′-CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC(dT25)-3′  (NNNNNN = 6nt barcode for multiplexing):

treatment_protocol: No treatment applied during growth.

tag: strain

tag: tex

value: untreated

tag: replicate

value: replicate 2


title: Flowthrough, low density, stress, fish 2

value: Skin

tag: culture method

value: flowthrough

tag: condition

value: low


title: CJ_CG84-21_dRNA_R2_plus_TEX

value: exonuclease treated


title: Sample27.Killer whale.202897220027_R04C01

description: genomic DNA methylation from tissue=Liver species=Killer whale

source_name: Liver

value: Liver


title: Flowthrough, low density, stress, fish 3


title: Sample29.Bottlenose dolphin.202897220027_R06C01


title: Flowthrough, high density, stress, fish 6

value: high


title: Sample19.Killer whale.202897220080_R02C02

description: genomic DNA methylation from tissue=Blubber species=Killer whale

source_name: Blubber

value: Blubber


title: Flowthrough, low density, stress, fish 4

value: crowding stress


title: Sample25.Killer whale.202897220027_R02C01

value: yes


title: CJ_CG84-21_dRNA_R1_plus_TEX

value: replicate 1


title: CJ_CG84-21_dRNA_R1_minus_TEX


title: Flowthrough, high density, stress, fish 4


title: Sample21.Killer whale.202897220080_R04C02

description: genomic DNA methylation from tissue=Lung species=Killer whale

source_name: Lung

value: Lung


title: Sample26.Bottlenose dolphin.202897220027_R03C01

description: genomic DNA methylation from tissue=Skin species=Bottlenose dolphin


title: Flowthrough, high density, stress, fish 5


title: Flowthrough, low density, stress, fish 1


title: Sample20.Killer whale.202897220080_R03C02

description: genomic DNA methylation from tissue=Pancreas species=Killer whale

source_name: Pancreas

value: Pancreas


title: Granulosa_ZT20_3

city: Chengdu

first: Liang

state: Sichuan

address: Wenjiangqu huiminlu211hao sichuan nongyedaxue

institute: Sichuan agricultural university

data_processing:
Clean reads were mapped against chicken reference genome using STAR v2.6.0c and merged with Cuffmerge (Cufflinks v2.2.1).
Assemblyline and TACO to filter transcripts and merge all expressed transcripts
Remove transcripts of coding gene while comparing to annotated genome by Cuffcompare
The prediction and calculation of the coding potential of the remaining transcripts by CPC2
Comparing with the Pfam-31A database and trimming out transcripts with a p-value < 10-4 by Hmmscan
Genome_build: STAR v2.6.0c
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

organism: Gallus gallus

source_name: Granulosa cells

extract_protocol:
Granulosa cells were collected and put into liquid nitrogen immediately from preovulatory follicles (F1). For total RNA sequencing, about 4 μg total RNA was isolated from the granulosa cells (a total of 9 samples) by using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Chicken follicle

tag: cell type

value: Granulosa cells

tag: time


title: Granulosa_ZT20_2


title: Sample24.Killer whale.202897220027_R01C01

description: genomic DNA methylation from tissue=Kidney species=Killer whale

source_name: Kidney

tag: basename

tag: canbeusedforagingstudies

value: Female

value: Kidney


title: Sample23.Killer whale.202897220080_R06C02

description: genomic DNA methylation from tissue=LymphNode species=Killer whale

source_name: LymphNode

tag: Sex

tag: tissue

value: LymphNode


title: Flowthrough, high density, stress, fish 2

value: Skin

tag: density


title: Granulosa_ZT20_1


title: Flowthrough, high density, stress, fish 1

value: flowthrough


title: HAP1_PDCL3P4_NULL3_4

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

country: Australia

institute: Mater Research Institute-University of Queensland

description:
Null3_4
rnaseq_counts.txt

data_processing:
STAR 2.7.3a was used to align RNA-seq reads to GRCh38.3.
htseq-count 0.11.2 was used to quantify read counts against Ensembl genes GRCh38.8.
Genome_build: GRCh38.3
Supplementary_files_format_and_content: rnaseq_counts.txt: Tab-delimited text file containing counts for each replicate.

source_name: HAP1 cells

growth_protocol: Low passage (≤ p10) HAP1 cells (Horizon) were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco cat # 12440-053) supplemented with 10% Fetal Bovine Serum (Sigma Aldrich cat # F2442) and 1% Penicillin / Streptomycin (Gibco cat # 15140-122) and grown in a tissue culture incubator (37ºC, 5% CO2).

extract_protocol:
RNA was extracted from validated clones and wild-type HAP1 cells using the RNeasy Mini Kit (Qiagen cat # 74104) following the manufacturer’s instructions and then treated with TURBO DNA-free™ Kit (Life Technologies cat # AM1907) to remove genomic DNA.
Paired-end 150bp.

tag: cell line

tag: genotype/variation

value: PDCL3P4 null


title: Sample17.Killer whale.202897220080_R06C01

growth_protocol: DNA extracted from tissues


title: Sample15.Killer whale.202897220080_R04C01

description: genomic DNA methylation from tissue=Heart species=Killer whale

source_name: Heart

value: Heart


title: Sample22.Killer whale.202897220080_R05C02

value: Spleen


title: HAP1_PDCL3P4_NULL3_3

description:
Null3_3
rnaseq_counts.txt


title: Granulosa_ZT12_2


title: Sample16.Killer whale.202897220080_R05C01


title: HAP1_PDCL3P4_NULL3_2

description:
Null3_2
rnaseq_counts.txt


title: Sample18.Killer whale.202897220080_R01C02


title: Granulosa_ZT12_3


title: HAP1_PDCL3P4_NULL3_1

description:
Null3_1
rnaseq_counts.txt


title: Granulosa_ZT12_1


title: Granulosa_ZT0_3


title: HAP1_PDCL3P4_NULL2_2

description:
Null2_2
rnaseq_counts.txt


title: Granulosa_ZT0_2


title: HAP1_PDCL3P4_NULL2_3

description:
Null2_3
rnaseq_counts.txt