title: STP_1_G

organism: Podothecus accipenserinus


title: STP_1_G_uc

status: Public on Jun 18 2022

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Sequencing data were processed with illumina2bam-tools v. 1.12
BAM files were converted to fastq format using SamToFastq.jar (picard-tools v1.100) with the INCLUDE_NON_PF_READS parameter set to FALSE (implemented in RefFreeDMA)
All reads were trimmed for adapter sequences and low-quality sequences using trimgalore v0.3.3 with the following command: trim_galore -q 20 --phred33 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --stringency 1 -e 0.1 --length 16 --output_dir $output_dir $input_fastq.
Reference-free processing (creation of the deduced genomes and processing) was performed using the RefFreeDMA software/pipeline (http://RefFreeDMA.computational-epigenetics.org)
Bisulfite alignment of the RRBS reads to the deduced genomes and to the reference genomes was performed using BSMAP v2.74 with the following command line: bsmap -a $input_fastq -d $ref_genome_fasta -o $output_bam -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -S 1 -f 5 –u (implemented in RefFreeDMA).
DNA methylation calling was performed using the biseqMethCalling.py software (Bock, 2010)(implemented in RefFreeDMA).
Genome_build: processed files list contains consensus genomes for each of 580 species
Supplementary_files_format_and_content: Tab-delimited text files include CpG methylation calls for each sample. The columns in the file correspond to thr chromosome, start and end of a CpG region, rationof methylated/non metylated, mean methylation in ‰ and the strand.

molecule: genomic DNA

source_name: Gills

extract_protocol:
Reduced representation bisulfite sequencing (RRBS) was performed as described in Klughammer et al., Cell Reports 2015, using 100 ng of genomic DNA for most samples, while occasionally going down to 1 ng for samples with low DNA amounts (Supplementary Table 1). To assess the bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added at a concentration of 0.1%. For most samples, DNA was digested using the restriction enzymes MspI and TaqI in combination (as opposed to only MspI in the original protocol) in order to increase genome-wide coverage. For certain older samples, only MspI was used
Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. Fi-nally, the libraries were size selected by performing a 0.75× cleanup with AMPure XP beads (Beckman Coulter, A63881) retaining fragments of about 100 bp to 1000 bp length. The amount of effective li-brary was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion, followed by library enrichment with PCR. Enrichment cycles were determined using qPCR and ranged from 6 to 18 (median: 11). After con-firming adequate fragment size distributions on Bioanalyzer High Sensitivity DNA chips (Agilent),

tag: tissue

value: Gills

tag: Sex

tag: individual

tag: age

value: adult

tag: sample type

value: unconverted


title: BEG_1_G_uc

organism: Rhinogobiops nicholsii


title: MCF7-6SA

type: RNA

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

description: Gene expression data from MCF7 with 6SA-Snail mutant

hyb_protocol: ~10ug labelled cRNA hybridization followed the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Functional annotation and identiﬁcation of over-represented functional themes were performed using Reactome database of GSEA.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7-6SA cells

label_protocol: The generation of labelled cRNA and its hybridization to Human U133 Plus 2 GeneChip arrays (Affymetrix, Santa Clara, CA) were carried out at the genomic core facilities in the National Yang-Ming University (Taipei, Taiwan) according to the standard procedures.

growth_protocol: MCF7 cell lines were obtained from ATCC and grown in DMEM/F12 (Gibco, Grand Island, NY) containing 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: MCF7 cells were transfected with control vector (CV, pCMV-Tag 2B) or vector carrying 6SA-Snail mutant (Nat Cell Biol 2004, 6, 931-940), followed by microarray analysis investigating gene expression proﬁles and subsequent pathway analysis.

tag: cell line

tag: transfection

value: 6SA-Snail mutant


title: SJD_2_S

organism: Zenopsis conchifer

source_name: Spleen

value: Spleen

value: converted


title: MCF7-CV

description: Gene expression data from MCF7 with control vector

source_name: MCF7-CV cells

value: control vector, pCMV-Tag 2B


title: SJD_1_K

source_name: Kidney

value: Kidney


title: PAG_3_G

organism: Coryphaenoides acrolepis

value: f


title: BLF_1_BL_uc

organism: Pomatomus saltator

source_name: Blood

value: Blood


title: PAG_2_G


title: PAG_1_G


title: CC_277242

city: Nanjing

first: Wei

last: Sun

state: Jiangsu

address: Nanjing, Jiangsu, China

country: China

institute: Jiangsu People's Hospital

library_source: transcriptomic

data_processing:
Star Matching Transcripts
StringTie splice transcripts and merge transcripts
Htseq quantitative
Assembly: Human hg38：  BSgenome.Hsapiens.UCSC.hg38  EnsDb.Hsapiens.v86
Supplementary files format and content: counts

source_name: Cervical

extract_protocol:
After the samples are qualified, the total RNA library preparation and library inspection are carried out according to the following experimental steps: (1) rRNA removal: Ribo-zero kit was used to remove rRNA, followed by high temperature and metal ions. (2) Synthesis and purification of cDNA: using RNA as a template, a six-base random primer is used to synthesize a strand of cDNA,Then add buffer, dNTPs, and enzyme to synthesize double-stranded cDNA, and then use VAHTSTM DNA Clean Beads Purification of double-stranded cDNA; (3) Fragment screening: the purified double-stranded cDNA is first subjected to end repair, A-tail, and sequencing ligation  head, followed by fragment screening with VAHTSTM DNA Clean Beads; (4) PCR enrichment: UDG enzyme degrades the second strand of cDNA containing U, and performs PCR enrichment, Finally, use VAHTSTM DNA Clean eads to purify the PCR product; (5) Library inspection: use Qubit to accurately quantify the library concentration, and Agilent 2100 Bioanalyzer to determine Library fragment size distribution to assess suitability for onboarding.
Ribo-zero kit for rRNA removal;One-stranded cDNA was synthesized using RNA as a template and six-base random primers; The second-stranded cDNA was synthesised by adding buffer, dNTPs and enzymes, followed by purification of the double-stranded cDNA using VAHTSTM DNA Clean Beads. purification of double-stranded cDNA;Accurate quantification of library concentrations with Qubit, determination of library fragment size distribution with Agilent 2100 Bioanalyzer

value: Cervical

tag: tissue type

value: primary cervical cancer

tag: molecule subtype

value: circRNA


title: PAG_1_G_uc


title: CA_277322

value: paracancerous tissue


title: BEG_1_G


title: PRF_1_G

organism: Zaprora silenus


title: PRF_1_G_uc


title: NRS_1_G

organism: Lepidopsetta polyxystra


title: CC_277322


title: CP_273020


title: NRS_1_G_uc


title: NSR_1_BL

organism: Prionotus carolinus


title: CC_273020


title: CHC_1_BL_uc

organism: Hypselecara coryphaenoides


title: NRS_2_G


title: NRS_3_G


title: CP_273233


title: BLF_1_BL


title: CHC_1_BL


title: CP_1103118


title: NSL_3_K

organism: Ammodytes dubius


title: CCS_1_BL_uc

organism: Scyliorhinus retifer

value: m

value: juvenil


title: NSR_1_BL_uc


title: NSL_3_SK

source_name: Skin

value: Skin


title: NSL_3_G

value: Gills


title: CC_273233


title: NSL_3_KF


title: CP_275320


title: NSL_3_H

source_name: Heart

value: Heart


title: NSL_2_SK


title: NSL_2_H


title: CC_275320


title: SFP_2_G

organism: Diodon hystrix


title: CCS_1_BL


title: SFP_1_BL_uc

value: adult

value: unconverted


title: NSL_2_F_uc

source_name: Fin

value: Fin


title: NSL_1_S

value: converted


title: CP_277251


title: NSL_1_M

source_name: Muscle

value: Muscle


title: CA_277251


title: ORT_2_W

organism: Ecteinascidia turbinata


title: NSL_2_K

value: Kidney


title: CP_277511


title: NSL_1_H


title: NSL_1_F


title: ORT_1_W


title: RSS_1_T

organism: Ascidiella aspersa

source_name: Tentacle

value: Tentacle


title: NSL_2_F


title: CA_277511


title: RSS_1_EN

source_name: Endostyle

value: Endostyle


title: RSS_1_EN_uc


title: ATE_2_G

organism: Lethrinus atkinsoni


title: ORT_1_W_uc


title: CAT_1_H

organism: Felis catus

value: f


title: CAT_1_L_uc

source_name: Liver

value: Liver


title: ATE_1_G


title: SUF_1_F

organism: Paralichthys dentatus


title: CAT_2_H


title: ATE_1_G_uc


title: SUF_1_G


title: CAT_1_L


title: SFP_1_BL

value: Blood


title: NSL_1_K


title: WSC_3_DT

organism: Apostichopus parvimensis


title: WSC_2_DT


title: BSB_1_F_uc

organism: Centropristis striata


title: JSS_2_H

organism: Ovis aries


title: BSB_1_F


title: JSS_2_L


title: WSC_1_DT


title: JSS_1_L_uc


title: JSS_1_L


title: BLC_2_O

organism: Ostorhinchus moluccensis

source_name: Operculum

value: Operculum


title: BLC_2_F


title: CAT_2_L


title: WSC_1_DT_uc


title: JSS_1_H


title: BLC_1_M_uc


title: BRS_2_AR

organism: Ophiothrix spiculata

source_name: Arm

value: Arm


title: BRS_3_AR


title: BRS_1_AR_uc


title: BLC_1_M


title: BRS_1_AR


title: BLC_1_F


title: SUF_1_F_uc


title: GKS_3_TF

organism: Pisaster giganteus


title: CAA_1_F

organism: Pseudanthias


title: MOU_2_L_uc

organism: Mus musculus


title: GKS_2_TF


title: MOU_1_H

value: m


title: MOU_2_H


title: MOU_1_L


title: GKS_1_TF_uc


title: CAA_2_CF


title: zr2149_2

status: Public on Jun 19 2022

city: Munich

first: sharmilee

last: vetrivel

state: Bayern

address: ziemssenstraße 1, DG

country: Germany

institute: Ludwig Maximilian University of Munich (Universität München)

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: E10.5 heads

extract_protocol:
ChIP pull-downs are prepared using snap-frozen mice embryo heads
ChIP-Seq libraries are quantified using 2200 Tape Station
Next-Gen Sequencing platform – HiSeq

tag: cell type

value: E10.5 heads

tag: chip antibody


title: human urine-derived stem cells

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Sequencing base quality control using illumina Casava 1.8
The small RNA tags were mapped to reference sequence by Bowtie
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al, 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA
The known and predicted miRNAs in each sample were counted and normalized with TPM.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Homo sapiens

source_name: urine

growth_protocol: Human urine-derived stem cells were maintained in in Dulbecco’s modified Eagle medium supplemented with 2% (v/v) fetal bovine serum, 10 ng/mL human epidermal growth factor, 2 ng/mL platelet-derived growth factor, 1 ng/mL transforming growth factor, 2 ng/mL basic fibroblast growth factor, 0.5 μM hydrocortisone, 25μg/mL insulin, 20 μg/mL transferrin, 549 ng/mL epinephrine, 50 ng/mL triiodothyronine (T3), L-glu, and antibiotics. in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
For exosomal miRNA sequencing, total RNA was extracted and purified from exosomes secreted by human USCs cells via an exoRNeasy Maxi Kit (Qiagen, Germany). 1.3 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNextRMultiplex Small RNA Library Prep Set for IlluminaR(NEB, USA.) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Exosomes secreted by human USCs cells were isolated from the supernatant of  human USCs cells by differential centrifugation and ultracentrifugation.

value: urine

value: urine-derived stem cells


title: GKS_1_TF


title: CAA_2_CF_uc

value: adult


title: RAT_2_L_uc

organism: Rattus rattus

value: unconverted


title: HLJ_1_G_uc

organism: Cantherhines pardalis

source_name: Gills

value: Gills


title: RAT_2_H

value: Heart

value: converted


title: RAT_2_L


title: FLF_1_BI

organism: Photoblepharon palpebratum

source_name: Biolum

value: Biolum


title: HLJ_1_G


title: MOU_2_L


title: FLF_1_BI_uc


title: RAT_1_L


title: FLF_1_F

value: Fin


title: OCP_1_F_uc

organism: Zoarces americanus


title: RAT_1_H


title: TMB_1_G_uc

organism: Scolopsis bilineata


title: WTF_1_G_uc

organism: Rhinecanthus aculeatus


title: OCP_2_M

value: Muscle


title: TMB_1_G


title: ATS_1_M_uc

organism: Salmo salar


title: ATS_1_M


title: WTF_1_G


title: OCP_1_F


title: YFS_2_F

organism: Centropomus robalito


title: WTF_3_G


title: NBD_1_F_uc

organism: Pomacentrus coelestis


title: NBD_3_F


title: WTF_2_G


title: YFS_1_M_uc


title: NBD_1_F


title: FPF_1_G_uc

organism: Onuxodon fowleri


title: STT_3_P

organism: Styela montereyensis

source_name: Pharynx

value: Pharynx


title: STT_2_P


title: HLJ_2_G


title: STT_1_P_uc


title: FPF_1_G


title: GFS_2_T

organism: Stichopus chloronotus

value: Tentacle


title: GFS_1_T


title: BCF_1_G

organism: Fistularia commersonii


title: STT_1_P


title: CLW_2_G_uc

organism: Oxycheilinus digramma


title: PLJ_1_G

organism: Pseudomonacanthus peroni


title: BCF_1_G_uc


title: U266 siBCMA 2 [RNA]

city: Houston

first: Dadi

last: Jiang

state: TX

address: 6565 MD Anderson Blvd, Unit 1052

department: Radiation Oncology

country: USA

institute: The University of Texas MD Anderson Cancer Center

data_processing:
.fastq files were processed with AfterQC ((https://github.com/OpenGene/AfterQC) and the good reads were analyzed with Salmon 1.2.1 and tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) to get the unnormalized counts.
Assembly: hg38
Supplementary files format and content: A single tab-delimited text file (.txt) with raw counts per gene

source_name: Plasma cell

growth_protocol: U266 cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in standing flasks and a humidified 37 °C, 5% CO2 incubator.

extract_protocol:
Briefly, snap frozen cell pellets (100 million cells per sample) were lysed in polysome lysis buffer (20 mM Tris-HCl pH 7.5, 250 mM NaCl, 15mM MgCl2, 1mM DTT, 0.5% Triton X-100, 0.024 U/ml TurboDNase, 0.48 U/ml RNasin, and 0.1 mg/ml cycloheximide). Lysates were centrifuged for 10 minutes at 4C, 14,000 x g. The supernatant was used for the isolation of total RNA.
RNA libraries for RNA-seq were prepared using SMARTER smRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: BCMA siRNA (SMARTPool Cat. No. L-011217-00-0005) constructs were purchased through GE Dharmacon Horizon (Cambridge, UK). For siRNA, transfection procedures were carried out using Lonza 4D-Nucleofactor device and kits in accordance with manufacturers protocol (Basal, Switzerland).

value: Plasma cell

value: Multiple myeloma

tag: genotype

value: BCMA knockdown

tag: treatment

value: siBCMA transfection


title: U266 siBCMA 3 [RNA]


title: BLR_1_G

organism: Sebastes mystinus


title: YFS_1_M


title: BLR_2_G


title: BLR_2_M


title: PLJ_2_G_uc


title: BLR_1_M


title: GFS_2_T_uc


title: U266 siBCMA 1 [RNA]

organism: Homo sapiens


title: FBS_3_AR

organism: Ophiopteris papillosa

value: Arm


title: FLC_1_G_uc

organism: Cheilodipterus quinquelineatus


title: FBS_2_AR


title: FBS_1_AR_uc


title: U266 siScramble 2 [RNA]

value: Control knockdown

value: siScramble transfection


title: BLR_2_BL

source_name: Blood

value: Blood

value: adult


title: CLW_1_G

value: Gills


title: U266 siScramble 3 [RNA]


title: BLR_2_BL_uc

value: unconverted


title: FLC_2_G

value: converted


title: SQR_3_G

organism: Sebastes hopkinsi


title: U266 siScramble 1 [RNA]


title: FLC_1_G


title: SQR_3_M


title: CLW_2_G


title: SQR_3_BL


title: CW_1_A

organism: Alitta succinea

source_name: Anterior

value: Anterior


title: BTR_2_G

organism: Pseudobalistes fuscus


title: FBS_1_AR


title: PSS_3_TF

organism: Pisaster brevispinus


title: PSS_1_TF_uc


title: PSS_2_TF


title: PSS_1_TF


title: BTR_1_G_uc


title: U288 siBCMA 3 [Ribo]

description: ribosome-protected mRNA fragments

data_processing:
The sequencing files for ribosome profiling and RNA-Seq data were processed using RiboFlow (Ozadam et al., 2020). All source code is freely available at https://github.com/ribosomeprofiling. Briefly, 3’ adapter sequence (AAAAAAAAAA) was removed from all reads using cutadapt. The 5’ end of each read includes 3 bases from the template switching reaction and also removed before alignment. We used a sequential alignment strategy to first filter out rRNA and tRNA mapping reads followed by mapping to representative isoforms for each as defined in the APPRIS database (Rodriguez et al., 2018). Next, PCR duplicates were removed from the ribosome profiling data using the 5’end of the sequence alignment coordinates.
The processed .fastq files were further processed using the BRB-SeqTools suite (https://brb.nci.nih.gov/seqtools/) with Tophat2 as the aligner and HTSeq-count as the gene counting tool.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files (.count) with raw counts per gene
Library strategy: Ribo-seq

extract_protocol:
Cells were pelleted and lysed in buffer (20 mM Tris-HCl, pH 7.4, 100 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1 % Triton X-100, 0.1 % NP-40, 100 μg/ml CHX, 20 U/ml TurboDNase I, complete protease inhibitor EDTA-free) in nuclease-free water. After lysis, RNA concentrations were measured using Nanodorop UV spectrophotometer and normalized amounts of RNA were layered onto a sucrose gradient (25-50% sucrose (w/v), 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, 15 mM MgCl2, 100 μg/ml CHX) in nuclease-free water and centrifuged in a SW41Ti rotor (Beckman) for 2.5 hr at 40,000 rpm at 4°C. Sixteen fractions were collected by the Density Gradient Fraction System (Brandel). To each fraction, 0.1 ml of 10 % SDS was added and mixed. 0.1 ml of 3 M NaOAc, pH 5.5 and 0.1 ml of water were added to each SDS containing fraction. For normalization, 500 pg of bioistronic firefly luciferase mRNA was added to each fraction. Total RNA from each fraction was extracted using acid-phenol:chloroform. Briefly, to each fraction, 900 μl of acid-phenol:chloroform was added and mixed thoroughly. The mixture was heated at 65 °C for 5 min, and centrifuged at 21,000 g for 10 min, RT. The aqueous phase (700 μl) was removed and precipitated overnight at -80 °C with 700 μl isopropanol and 1.5 μl GlycoBlue Coprecipitate (Invitrogen). The samples were centrifuged at 21,000 g, 30 min, 4 °C, supernatant was discarded, and the RNA pellet was washed twice with 500 μl cold 75 % ethanol. Pellets were dried for 15 min, RT and resuspended in nuclease free water. Total RNA from each fraction was treated with 2 U/μl TurboDNase I, incubated at 37 °C for 30min and column purified using the RNA Clean and Concentrator-5 (Zymo) according to the manufacturer’s instructions. RNA was eluted in 6 μl, twice. Except for the first fraction (F1), RNA was pooled from every three subsequent fractions (F2-4, F5-7, F8-10, F11-13, F14-16) and measured using Nanodorop UV spectrophotometer.
RNA libraries for RNA-seq were prepared using SMARTER smRNA-Seq Library Prep Kit following manufacturer's protocols.


title: U288 siBCMA 1 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: U288 siBCMA 3 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: BTR_1_G


title: U288 siBCMA 2 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: U288 siBCMA 2 [Ribo]

description: ribosome-protected mRNA fragments


title: SBS_2_AR

organism: Ophioderma panamensis


title: SQR_2_G


title: SQR_2_BL_uc


title: SBS_1_AR_uc


title: PLJ_2_G


title: BLR_1_BL


title: CW_1_A_uc


title: STC_1_G

organism: Coris caudimacula


title: U266 siScramble 3 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: SQR_2_BL


title: SQR_1_G


title: SBS_3_AR


title: SQR_1_M


title: SBS_1_AR


title: STC_3_G


title: U266 siScramble 3 [Ribo]

description: ribosome-protected mRNA fragments


title: U288 siBCMA 1 [Ribo]

description: ribosome-protected mRNA fragments


title: STC_1_G_uc


title: U266 siScramble 2 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: SEC_3_T

organism: Holothuria


title: SEC_2_T


title: STC_2_G


title: SEC_1_T


title: U266 siScramble 2 [Ribo]

description: ribosome-protected mRNA fragments


title: RBF_2_G

organism: Chaetodon lunula


title: U266 siScramble 1 replicate [Ribo]

description: ribosome-protected mRNA fragments


title: SCC_1_TF

organism: Thyonella gemmata


title: SEC_1_T_uc


title: GTW_1_V

organism: Riftia pachyptila

source_name: Vestimentum

value: Vestimentum


title: SES_3_AR_uc

organism: Nardoa novaecaledoniae


title: FLA_3_W

organism: Branchiostoma floridae


title: FLA_1_M

value: Muscle


title: SES_2_AR


title: SES_1_TF


title: COT_1_F

organism: Acanthurus triostegus

value: Fin


title: SQR_2_M


title: SCC_1_ME

source_name: Mesentary

value: Mesentary


title: U266 siScramble 1 [Ribo]

description: ribosome-protected mRNA fragments

value: Plasma cell


title: RBF_1_G_uc


title: STA_2_M_uc

organism: Sebastes constellatus


title: STA_1_M


title: SCC_1_TF_uc


title: RBF_1_G


title: SQR_1_BL


title: SES_3_AR


title: LBF_1_F

organism: Chaetodon lineolatus

source_name: Fin


title: SSR_1_BL_uc

organism: Hypanus americanus

value: f


title: SCC_1_M

source_name: Muscle


title: COT_1_F_uc


title: FLA_1_HE_uc

source_name: Head

value: Head


title: CNR_1_BL

organism: Rhinoptera bonasus


title: COT_2_M


title: LBF_2_F


title: STA_2_M


title: CNR_1_BL_uc


title: STA_1_G


title: CAA_2_DF

organism: Pseudanthias

value: m


title: FLA_1_HE


title: LBF_3_F


title: SSR_1_BL


title: LBT_1_F

organism: Ctenochaetus striatus


title: LBF_1_F_uc


title: TSW_3_F

organism: Halichoeres trimaculatus


title: WB_1_H

organism: Sus scrofa

source_name: Heart

value: Heart


title: MAS_1_G

organism: Lutjanus mahogoni


title: STA_2_G


title: STA_1_BL


title: TSW_1_F_uc


title: GTW_1_V_uc


title: WB_2_L

source_name: Liver

value: Liver


title: WTD_1_F

organism: Dascyllus aruanus


title: LBT_3_F


title: LBT_2_F


title: WB_2_H


title: WB_1_L_uc


title: MAS_1_GO

source_name: Gonad

value: Gonad


title: DSH_2_F

organism: Mustelus canis


title: STA_2_BL

value: Blood


title: DSH_1_BL_uc

value: juvenil


title: LBT_1_F_uc


title: WTD_2_F


title: WB_1_L

value: adult


title: TSW_2_F


title: DSH_1_BL


title: UO_2_H

organism: Strix uralensis


title: UO_2_B

source_name: Brain

value: Brain


title: MAS_1_G_uc

value: Gills

value: unconverted


title: UO_2_LU

source_name: Lung

value: Lung

value: converted


title: TSW_1_F

value: Fin


title: RTC_1_G

organism: Ostorhinchus aureus


title: UO_2_L


title: SIS_1_L

organism: Corucia zebrata


title: UO_2_S

source_name: Spleen

value: Spleen


title: VER_2_M

organism: Sebastes miniatus

value: Muscle


title: WTD_3_F


title: VER_1_G

source_name: Gills


title: VER_2_G


title: OWL_1_L

organism: Strigiformes


title: SIS_1_H

value: f


title: UO_1_LU


title: WTD_1_F_uc


title: RTC_1_G_uc


title: SIS_1_H_uc


title: BSH_1_G

organism: Paracirrhites forsteri


title: VER_2_G_uc


title: RTC_3_G


title: BSH_1_G_uc


title: VER_2_BL


title: OWL_1_H


title: UO_1_S


title: RTC_2_G


title: GD_2_L_uc

organism: Eliomys quercinus


title: VER_1_M


title: CRF_2_G

organism: Sebastes caurinus


title: UO_1_B


title: CRF_1_G_uc


title: UO_1_B_uc


title: OWL_1_H_uc


title: PAJ_3_G

organism: Monacanthidae


title: RT_1_L

organism: Astrochelys radiata


title: CRF_1_G


title: UO_1_H


title: GD_1_H


title: RT_1_H_uc


title: PAJ_2_G_uc


title: UO_1_L


title: GD_2_H


title: GD_1_L


title: PAJ_1_G


title: VER_1_BL


title: CRF_1_BL


title: PAJ_2_G


title: RC_1_LU

organism: Grus japonensis


title: RT_1_H


title: CRF_2_BL


title: GD_2_L


title: COH_2_G

organism: Cephalopholis miniata


title: RC_1_B


title: RC_1_L


title: SSC_1_G

organism: Mya arenaria


title: RC_1_S


title: NCL_1_H_uc

organism: Dracaena guianensis


title: COH_3_G


title: NCL_1_L


title: ARC_1_M

organism: Salvelinus alpinus


title: RC_1_H


title: SSC_1_G_uc


title: COH_1_G_uc


title: NCL_2_L


title: KER_1_M

organism: Sebastes atrovirens


title: KER_2_M


title: STS_1_GO_uc

organism: Carcharias taurus


title: RC_2_S


title: KER_1_BL


title: NCL_2_LU


title: KER_1_BL_uc


title: EB_2_LU

organism: Merops apiaster


title: SME_1_G

organism: Gymnothorax moringa


title: EB_2_L


title: COH_1_G


title: EB_2_H


title: NCL_1_H


title: STS_1_GO


title: ARC_1_M_uc


title: EB_2_B


title: KER_2_G


title: KER_1_G


title: RC_2_H


title: SME_1_GO


title: GRP_2_L

organism: Perdix perdix


title: GRP_2_H


title: EB_2_S


title: RC_2_L


title: WSD_1_G_uc

organism: Phyllopteryx taeniolatus


title: STS_1_G


title: RC_2_LU_uc


title: RC_2_LU


title: KER_2_BL


title: GRP_1_L


title: HAR_1_BL

organism: Sebastes semicinctus


title: EB_1_H


title: SME_1_BL


title: SME_1_BL_uc


title: EB_1_LU


title: HAR_1_BL_uc


title: HAR_2_M


title: GRP_2_L_uc


title: VSU_2_TF

organism: Lytechinus variegatus


title: HAR_1_M


title: EB_1_B


title: VSU_1_C

source_name: Coelom

value: Coelom


title: VSU_1_C_uc


title: GRP_1_H

value: m


title: EB_1_S


title: EB_1_L


title: TRS_1_H

organism: Scandentia

value: Heart


title: EB_1_B_uc


title: TRS_1_L_uc

value: Liver


title: HAR_2_G


title: WSD_1_G


title: HAR_1_G


title: POL_1_GO_uc

organism: Pollachius virens

value: Gonad


title: EJ_1_H

organism: Garrulus glandarius


title: EJ_1_H_uc


title: BRF_1_M

organism: Sebastes paucispinis


title: MSB_1_H_uc

organism: Nectariniidae


title: VSU_1_GO


title: HAR_2_BL

value: Blood


title: TRS_1_L

value: juvenil


title: MSB_1_L


title: EJ_1_L

value: adult


title: MSB_1_H


title: PD_2_H_uc

organism: Cynomys


title: BRF_1_BL_uc


title: WRS_2_L

organism: Copsychus malabaricus


title: POL_1_GO


title: BRF_1_G


title: WRS_2_H


title: PD_2_L


title: POL_1_M


title: BRF_1_BL


title: BL_2_S

organism: Heloderma


title: BL_2_LU


title: POL_1_G


title: PD_1_L


title: WRS_1_L


title: EV_2_LU

organism: Vipera berus


title: PD_1_H


title: BYR_2_M_uc

organism: Sebastes chrysomelas


title: BL_2_L_uc


title: BL_2_L


title: PD_2_H


title: ABU_4_L

organism: Hoplobatrachus tigerinus


title: BYR_1_M


title: WRS_1_H


title: EV_2_L


title: EV_1_L_uc


title: BYR_1_BL


title: WRS_1_H_uc


title: ABU_4_H


title: BYR_2_G


title: ABU_3_H


title: BL_1_S


title: COL_1_L

organism: Laemanctus


title: BL_1_L


title: ABU_3_H_uc


title: BL_2_H


title: BYR_2_M


title: LSH_1_BL_uc

organism: Negaprion brevirostris


title: BL_1_LU


title: LT_1_L

organism: Leontopithecus


title: LSH_1_BL


title: BYR_2_BL


title: ABU_2_H


title: LT_1_H_uc


title: ABU_3_L


title: COL_2_L


title: BL_1_H


title: LSH_1_F


title: BYR_1_G


title: EV_1_H


title: LT_1_H


title: ABU_1_H


title: EV_1_L


title: TSH_1_BL_uc

organism: Galeocerdo cuvier


title: COL_1_LU


title: DS_3_LU

organism: Natrix tessellata


title: TSH_1_F


title: COL_1_L_uc


title: TSH_1_BL


title: COL_2_H


title: DS_3_L


title: EGF_1_L

organism: Chloris chloris


title: TRF_2_M

organism: Cornufer guentheri


title: ABU_2_L


title: EGF_1_H_uc


title: GST_1_Z

organism: Botryllus schlosseri

source_name: Zooids

value: Zooids


title: DS_3_H


title: EGF_1_H


title: TRF_2_L


title: GST_1_Z_uc


title: TRF_1_H_uc


title: DS_2_LU


title: ABU_1_L


title: DS_2_L


title: AFP_1_GO

organism: Alectis ciliaris


title: AFP_1_GO_uc


title: DS_2_H


title: TRF_1_H


title: CRH_1_H

organism: Tockus alboterminatus


title: DS_1_LU


title: MS_2_L

organism: Ambystoma


title: TRF_1_L


title: CRH_1_L


title: DS_1_L


title: FRG_1_M

organism: Haemulon flavolineatum


title: AFP_1_G

value: Gills


title: DS_1_H_uc

value: unconverted


title: FRG_1_G


title: TAP_1_H

organism: Tapirus


title: DS_1_H


title: CRH_1_H_uc


title: TAP_1_L


title: MS_2_LU_uc

value: Lung


title: MS_1_L

value: converted


title: MS_1_H


title: FRG_1_GO_uc


title: MS_2_LU


title: XEN_1_H

organism: Xenagama wilmsi


title: COR_2_H_uc

organism: Corvus corax


title: CHU_1_L

organism: Sauromalus


title: XEN_1_H_uc


title: TAP_1_H_uc


title: CHU_1_H_uc


title: CHU_1_H


title: CK_1_H

organism: Falco tinnunculus


title: COR_2_H


title: FDO_1_H

organism: Ptilinopus


title: MS_1_LU


title: FDO_1_H_uc


title: FDO_1_L


title: STO_1_H_uc

organism: Ciconiidae


title: NG_2_L

organism: Astur gentilis


title: CAM_1_H_uc

organism: Cebinae


title: RA_2_L

organism: Procyon lotor


title: STO_1_L


title: STO_1_H


title: TUR_1_L

organism: Musophagidae


title: TUR_1_H


title: NG_2_H


title: CAM_1_L


title: XEN_1_L


title: FRG_1_GO


title: RA_1_L


title: UG_1_L

organism: Cyanoloxia brissonii


title: RA_1_H


title: CK_1_L


title: COR_2_L


title: CK_1_H_uc


title: COR_1_H


title: CAM_1_H


title: COR_1_L


title: UG_1_LU


title: TUR_1_H_uc


title: NG_2_H_uc


title: RA_2_H


title: UG_1_L_uc


title: NG_1_H


title: VIS_2_L

organism: Lagostomus maximus


title: TM_2_H

organism: Ara


title: PR_2_S

organism: Cricetomyinae


title: NG_1_L


title: PR_2_LU_uc


title: RA_2_H_uc


title: TM_1_L

value: old


title: TM_2_H_uc


title: AN_2_L_uc

organism: Eunectes


title: PR_2_LU


title: VIS_2_H


title: TM_2_L


title: PR_2_LN

source_name: Lymphnode

value: Lymphnode


title: ASL_1_L_uc

organism: Ambystoma andersoni


title: YS_2_S

organism: Trachemys scripta scripta

value: Spleen


title: ASL_1_L

value: f


title: PR_1_S


title: AN_2_L


title: PR_2_L


title: VIS_1_H_uc


title: AN_2_H


title: TM_1_H


title: VIS_1_H


title: BTS_1_L

organism: Lamprotornis chalcurus


title: AN_1_L


title: ASL_1_LU


title: PR_2_B

value: Brain


title: AN_1_H

value: m


title: VIS_1_L


title: PR_1_LU


title: BTS_1_H_uc

value: Heart


title: BTS_1_H


title: YS_2_M

value: Muscle


title: PR_1_L

value: Liver


title: PR_1_H


title: RHI_1_L_uc

organism: Rhinocerotidae


title: ACT_1_L

organism: Duttaphrynus melanostictus


title: YS_2_LU


title: PR_2_H


title: RHI_1_L


title: YS_2_K

source_name: Kidney

value: Kidney


title: ACT_1_H


title: EHA_2_H_uc

organism: Lepus europaeus


title: RHI_1_LU


title: ACT_2_L


title: YS_2_L_uc


title: HAG_1_H_uc

organism: Tetrastes bonasia


title: YS_2_L


title: EHA_2_L


title: HAG_1_L


title: ESB_1_H_uc

organism: Tiliqua rugosa


title: YS_1_S


title: YS_2_H


title: ACT_2_H


title: HAG_1_H


title: YS_1_L


title: ACT_1_H_uc


title: YS_2_D

source_name: Duodenum

value: Duodenum


title: SV_1_H

organism: Vipera ammodytes

value: adult


title: YS_1_H


title: ESB_1_L


title: EHA_1_L


title: SV_1_L


title: JCH_1_L_uc

organism: Trioceros jacksonii


title: EHA_1_H


title: SV_2_LU


title: YS_1_K


title: SV_1_LU


title: BNS_1_L

organism: Cygnus melancoryphus

value: juvenil


title: ESB_1_H


title: BNS_1_H


title: YS_3_S


title: JCH_1_LU


title: EHA_2_H


title: YS_3_M


title: FG_1_H

organism: Pachyuromys


title: BNS_1_H_uc


title: YS_1_D


title: CTT_2_S

organism: Saguinus oedipus


title: SV_2_L


title: FG_1_L


title: YS_1_LU


title: SV_2_S


title: YS_3_LU


title: SV_2_L_uc


title: GGC_1_H

organism: Callocephalon fimbriatum


title: GGC_1_H_uc


title: GGC_1_L


title: WCA_1_LU

organism: Felis silvestris


title: YS_3_L


title: GEL_1_L

organism: Theropithecus gelada


title: SV_2_H


title: JCH_1_L


title: GEL_1_H_uc


title: YS_3_H


title: FG_1_H_uc


title: YS_3_D


title: NAR_1_H_uc

organism: Rhyticeros narcondami


title: CTT_2_LN


title: WWD_1_H_uc

organism: Dendrocygna viduata


title: CTT_2_B


title: WCA_1_H


title: GF_1_L_uc

organism: Heleophrynidae


title: BBM_2_L

organism: Chiroxiphia pareola


title: CTT_2_L


title: SPB_1_L

organism: Antidorcas


title: BBM_2_H


title: CTT_2_H


title: GEL_1_H


title: WCA_2_H_uc


title: WCA_2_L


title: NAR_1_H


title: CTT_2_LU


title: CTT_1_S


title: WCA_2_H


title: SSN_1_L

organism: Coronella austriaca


title: SSN_1_H_uc


title: CTT_1_LU


title: WWD_1_L


title: YS_3_K

organism: Trachemys scripta scripta


title: CTT_1_B


title: WWD_1_H


title: CTT_1_LN


title: GF_1_L


title: CTH_1_H

organism: Coccothraustes


title: NAR_1_L


title: CTH_1_H_uc


title: SAB_1_L

organism: Hippotragus


title: CTT_1_L


title: NBI_2_L

organism: Geronticus eremita


title: CTT_1_H


title: SPB_1_H_uc


title: SSN_1_H


title: SPB_1_H


title: KP_1_L

organism: Aptenodytes patagonicus


title: CTH_1_L


title: BBM_1_H


title: WA_3_L

organism: Macropus


title: BBM_1_H_uc


title: GF_1_LU


title: KP_2_L


title: SF_1_H

organism: Falco cherrug


title: CTT_1_B_uc

organism: Saguinus oedipus


title: SAB_1_H


title: SAB_1_H_uc


title: NBI_2_H


title: SF_1_L_uc


title: NBI_2_B


title: WA_3_S


title: CAC_1_H

organism: Corvus corone


title: KP_1_H_uc


title: NBI_2_LU


title: NBI_2_LU_uc


title: SF_1_L


title: KP_1_H


title: NBI_2_S


title: ET_2_L

organism: Saguinus imperator


title: WA_3_LU


title: WA_2_S


title: WA_3_H


title: CAC_1_L


title: ET_2_H


title: WA_2_LU


title: KP_2_H


title: CA_1_S

organism: Hydrochoerus hydrochaeris


title: NBI_1_H


title: CAC_1_H_uc


title: NBI_1_L


title: ET_2_H_uc


title: ET_1_H


title: ET_1_L


title: NBI_1_LU


title: WA_1_H_uc


title: CA_1_H


title: WA_2_H


title: CA_1_S_uc


title: CA_1_LU


title: NBI_1_S


title: WA_1_H


title: NIM_1_H

organism: Aotidae


title: CA_1_LN


title: NBI_1_B


title: PP_2_L

organism: Erythrura


title: PP_2_LU


title: WA_2_L


title: PP_2_H


title: DG_1_L

organism: Nanger dama


title: NIM_1_L


title: NIM_1_H_uc


title: CA_2_S


title: DG_1_H_uc


title: PP_2_B_uc


title: CA_1_L


title: DG_1_H


title: PP_2_B


title: CA_2_LU


title: PTO_1_L

organism: Astrochelys yniphora


title: PP_1_L


title: WA_1_L


title: CRG_1_H

organism: Correlophus ciliatus


title: CRG_1_H_uc


title: CA_2_LN


title: CRG_1_L


title: CA_2_H


title: CP_2_L

organism: Rollulus


title: LTM_1_L_uc

organism: Macaca silenus


title: LTM_1_L


title: PTO_1_H_uc


title: PDO_1_H_uc

organism: Geopelia placida


title: PDO_1_H


title: LTM_1_H


title: PDO_1_L


title: CP_2_H


title: EGW_1_L

organism: Picus viridis


title: PP_1_H


title: WEC_1_L

organism: Tetrao urogallus


title: CP_1_H_uc


title: LTB_2_L

organism: Psarisomus dalhousiae


title: WEC_2_H


title: PTO_1_H


title: WEC_2_L


title: WEC_1_H


title: CA_2_L


title: WEC_2_H_uc


title: TW_1_H

organism: Canis lupus lycaon


title: LTB_2_H


title: EGW_1_H_uc


title: TW_1_LU


title: CP_1_L


title: FBI_1_L

organism: Brachylophus


title: LTB_2_H_uc


title: EGW_1_H


title: BD_2_LU

organism: Pogona barbata


title: BD_2_L


title: TW_2_H


title: LTB_1_L


title: LTB_1_H


title: FBI_1_H


title: TW_2_LU


title: BAB_1_L

organism: Papio


title: BD_2_L_uc


title: YCL_2_H

organism: Agapornis personatus


title: FBI_2_H


title: YCL_1_L


title: YCL_2_LU


title: BD_2_H


title: CP_1_H


title: BD_1_LU


title: BAB_1_H_uc


title: FBI_2_L


title: YCL_1_L_uc


title: BD_1_L


title: TUT_2_L

organism: Testudinidae


title: BAB_1_H


title: TUT_2_H


title: BD_1_H


title: YCL_1_H


title: MOS_1_L

organism: Varanus exanthematicus


title: WEA_2_H_uc

organism: Mustela


title: FBI_2_H_uc


title: BP_1_H_uc

organism: Python regius


title: MOS_1_H


title: TUT_1_L


title: BP_1_H


title: TW_2_H_uc


title: MOS_1_H_uc


title: TUT_1_H


title: WEA_2_H


title: BP_1_L


title: BP_2_L


title: BTL_1_L

organism: Tiliqua scincoides


title: FF_2_H

organism: Pteropus


title: WEA_1_H


title: FF_2_L


title: BP_2_H


title: BTL_1_H_uc


title: BTL_1_H


title: WEA_1_L


title: TUT_1_L_uc


title: FF_1_H_uc


title: AL_1_L

organism: Panthera pardus


title: SU_1_LU

organism: Eurypygidae


title: SU_1_H


title: WEA_2_L


title: ASQ_1_L

organism: Tamiops


title: FF_1_H


title: AL_1_H


title: FF_1_L


title: ASQ_1_H_uc


title: AL_1_H_uc


title: SU_1_L


title: ASQ_1_H


title: BLL_1_H_uc

organism: Vanellus armatus


title: SU_1_S


title: SU_1_LU_uc


title: BBR_1_L

organism: Coracias cyanogaster


title: PIG_3_H

organism: Columbidae


title: BLL_1_L


title: SU_2_LU


title: PIG_2_H


title: BLL_1_H


title: SU_2_S


title: BBR_1_H_uc


title: BBR_1_H


title: PIG_3_L


title: PIG_2_L


title: SIL_1_L

organism: Gallus


title: BB_1_H_uc

organism: Ursus arctos


title: SU_2_L


title: SIL_1_H_uc


title: BB_1_H


title: PIG_2_H_uc


title: SU_2_H


title: PIG_1_H


title: BB_1_L


title: ALP_2_L_uc

organism: Vicugna pacos


title: SIL_1_H


title: AI_1_L_uc

organism: Capra


title: COQ_2_L

organism: Coturnix coturnix


title: BB_2_L


title: AI_1_L


title: ALP_2_L


title: BB_2_H


title: COQ_1_L


title: ALP_1_L


title: AI_1_H


title: ST_1_LU

organism: Panthera tigris


title: COQ_1_H_uc


title: ST_1_H_uc


title: AI_2_H


title: ALP_1_H


title: AI_2_L


title: COQ_1_H


title: SKI_1_L

organism: Scincidae


title: SKI_1_L_uc


title: YC_1_L_uc

organism: Caiman yacare


title: ST_1_H


title: RAD_2_H_uc

organism: Nyctereutes


title: RAD_2_L


title: LEC_2_L

organism: Kobus leche


title: RAD_2_H


title: COQ_2_H


title: YC_1_H


title: PF_1_H_uc

organism: Falco peregrinus


title: LEC_2_H


title: ALP_2_H


title: LEC_2_H_uc


title: LEC_1_L


title: RAD_1_L


title: SKI_1_M


title: LEC_1_LU


title: PF_1_L


title: RO_1_H_uc

organism: Corvus frugilegus


title: NM_2_S

organism: Heterocephalus


title: NM_2_LU


title: NM_2_L


title: YC_1_L


title: RBU_1_L

organism: Buteo lagopus


title: ANW_1_H

organism: Bos


title: RBU_1_H_uc


title: ANW_1_L


title: RO_1_L


title: ANW_1_H_uc


title: NM_2_LU_uc


title: RL_2_S

organism: Lemur


title: NM_2_H


title: NM_1_H


title: RO_1_H


title: EEO_1_H

organism: Bubo bubo


title: ABB_1_H_uc

organism: Ursus


title: ABB_1_L


title: RL_2_S_uc


title: RBU_1_H


title: EEO_1_L


title: NM_1_LU


title: PF_1_H


title: NM_1_S


title: EEO_2_L


title: RAD_1_H


title: ABB_1_H


title: NM_1_L


title: RL_2_LN


title: BCC_2_H

organism: Balearica pavonina


title: ABB_2_LU


title: BCC_2_L_uc


title: RL_2_L


title: RL_2_H


title: BW_2_L

organism: Notamacropus rufogriseus


title: AC_1_L

organism: Serinus


title: RL_2_LU


title: RL_1_S


title: BW_2_H


title: BCC_2_L


title: AC_1_H_uc


title: AC_1_H


title: BCC_1_H


title: RL_1_LU


title: BW_1_H


title: BW_1_H_uc


title: RS_2_LU

organism: Crotalus


title: RL_1_H


title: EEO_2_H


title: AC_2_LU


title: BCC_1_L


title: RL_1_B


title: RS_2_H_uc


title: RL_1_L


title: AC_2_L


title: ABB_2_L


title: EEO_2_H_uc


title: RUL_1_L

organism: Varecia


title: RS_2_H


title: NAP_2_H

organism: Erethizon


title: MBI_2_L_uc

organism: Coliiformes


title: RUL_1_H


title: NAP_2_L


title: MBI_2_L


title: RS_2_L


title: RUL_1_H_uc


title: BW_1_L


title: RS_1_LU


title: RS_1_L


title: MBI_2_H


title: CDH_1_H

organism: Phodopus campbelli


title: CDH_1_H_uc


title: CDH_1_L


title: RS_1_H


title: MBI_1_L


title: SRP_1_H_uc

organism: Eudyptes chrysocome


title: RS_1_S


title: NAP_1_L


title: COE_2_L

organism: Taurotragus


title: NAP_1_H


title: SE_2_S_uc

organism: Phocidae


title: NAP_1_H_uc


title: SE_2_S


title: COE_2_H_uc


title: WBW_1_H_uc

organism: Dinemellia


title: WBW_1_H


title: SRP_1_L


title: SE_2_H


title: SRP_2_L


title: COE_2_H


title: SRP_2_H


title: FD_2_S

organism: Glis glis


title: MBI_1_H


title: SE_2_B


title: WBW_1_L


title: COE_1_H


title: FD_2_LU


title: SRP_1_H


title: DHU_2_H

organism: Capromys pilorides


title: SE_2_L


title: FD_2_L


title: FD_2_H


title: RIN_1_H

organism: Cyclura


title: DHU_2_L


title: SE_1_S


title: RIN_1_H_uc


title: SE_1_H


title: COE_1_L


title: FD_2_B


title: RIN_1_L


title: LPW_1_H_uc

organism: Vidua paradisaea


title: SE_1_B


title: FD_1_B


title: FD_1_LU


title: FD_1_S


title: CM_2_L

organism: Callithrix jacchus


title: KCO_2_L

organism: Colobus polykomos


title: DHU_1_H_uc


title: LPW_1_L


title: LPW_1_H


title: CM_2_H


title: KCO_2_H_uc


title: KCO_2_H


title: WFB_2_L

organism: Merops bullockoides


title: FD_1_B_uc


title: DHU_1_H


title: DHU_1_L


title: FD_1_L


title: WFB_2_H


title: FD_1_H


title: CM_1_L_uc


title: SE_1_L


title: CM_1_L


title: WFB_1_H


title: KCO_1_H


title: WFB_1_H_uc


title: HH_2_L

organism: Circus cyaneus


title: AS_1_H_uc

organism: Zamenis longissimus


title: CM_1_H


title: OS_3_L

organism: Struthio camelus


title: OS_3_H


title: HH_2_H_uc


title: WFB_1_L


title: AS_1_H


title: HH_2_H


title: TH_1_H

organism: Bycanistes bucinator


title: AS_1_L


title: HH_1_L


title: CIK_2_H

organism: Tamias


title: OS_2_H


title: CIK_2_L


title: KCO_1_L


title: OS_1_L


title: OS_2_L


title: TH_1_H_uc


title: EUS_2_H

organism: Accipiter nisus


title: TH_1_L


title: HH_1_H


title: WFA_2_H

organism: Amazona


title: EUS_1_L


title: WFA_2_L


title: CIK_1_L


title: OS_1_H_uc


title: CIK_1_H


title: EUS_2_H_uc


title: HFP_1_L

organism: Columba livia


title: OS_1_H


title: CIK_1_H_uc


title: WFA_2_L_uc


title: KT_1_H

organism: Testudo kleinmanni


title: KT_1_H_uc


title: WFA_1_H


title: EH_2_H

organism: Cricetus


title: EUS_2_L


title: SI_2_L

organism: Plegadis falcinellus


title: HFP_1_H


title: BRL_2_LU

organism: Oplurus


title: BWP_1_L

organism: Pitta moluccensis


title: EH_2_H_uc


title: EH_2_L


title: SI_2_H


title: BRL_2_LU_uc


title: SI_2_H_uc


title: BRL_2_L


title: HFP_1_H_uc


title: GSQ_2_H

organism: Spermophilus


title: EUS_1_H


title: WFA_1_L


title: GSQ_2_L


title: SID_1_L

organism: Cervus nippon


title: EH_1_H


title: SI_1_H


title: HAQ_2_L

organism: Coturnix delegorguei


title: BWP_1_H


title: GSQ_1_L_uc


title: SID_2_L


title: BRL_2_H


title: GSQ_1_L


title: SID_1_L_uc


title: SI_1_L


title: EH_1_L


title: HAQ_1_L_uc


title: HAQ_2_H


title: GSQ_1_H


title: BRL_1_H


title: BRL_1_LU


title: SID_1_H


title: BRL_1_L


title: BWP_1_H_uc


title: SPM_1_L

organism: Acomys


title: PI_2_S

organism: Recurvirostra avosetta


title: HAQ_1_H


title: HAQ_1_L


title: SID_2_H


title: BEA_1_H_uc

organism: Haliaeetus leucocephalus


title: PI_2_LU


title: COK_2_H

organism: Nymphicus hollandicus


title: PI_1_S


title: BEA_1_L


title: PI_2_H


title: COK_2_L


title: SPM_1_H


title: PI_2_L


title: COK_1_H


title: RSH_1_L

organism: Macroscelides proboscideus


title: PI_1_H


title: SPM_1_H_uc


title: CHM_1_H

organism: Dolichotis


title: BEA_1_H


title: CHM_1_L


title: COK_1_L


title: HT_2_L

organism: Calyptocephallela gayi


title: RSH_1_H_uc


title: CHM_1_H_uc


title: COK_2_H_uc


title: PI_1_LU_uc


title: HT_2_H


title: PI_1_L


title: RSH_1_H


title: VG_2_S

organism: Acryllium vulturinum


title: SM_3_LU

organism: Martes foina


title: HT_2_LU


title: PI_1_LU


title: SM_3_S


title: WG_2_L_uc

organism: Capra aegagrus


title: HT_1_L


title: VG_2_LU


title: HT_1_H


title: WG_2_L


title: SM_3_LN


title: WG_2_H


title: SM_3_L


title: HT_1_H_uc


title: VG_2_H


title: WG_1_L


title: SM_3_H


title: VG_2_B


title: HT_1_LU


title: WG_1_H


title: SM_3_B


title: VG_1_B_uc


title: KOA_1_H_uc

organism: Phascolarctos cinereus


title: EYV_1_H

organism: Bothriechis schlegelii


title: SM_2_S


title: VG_2_L


title: VG_1_S


title: SM_2_LU


title: EYV_1_L


title: KOA_1_H


title: KOA_1_L


title: VG_1_L


title: SM_2_B


title: EYV_1_H_uc


title: RP_1_LU

organism: Ailurus fulgens


title: SM_2_L


title: VG_1_LU


title: HB_1_L

organism: Papio hamadryas


title: HB_1_H_uc


title: VG_1_B


title: SM_2_LN


title: RP_1_L


title: VG_1_H


title: RP_1_S


title: SM_2_H


title: BAS_1_L

organism: Ammotragus


title: SR_2_L

organism: Psammomys obesus


title: RP_1_H_uc


title: SM_1_B

value: 1 j


title: SR_2_H_uc

value: unconverted


title: BAS_1_H_uc


title: RP_1_LN


title: SM_1_S


title: BAS_1_H


title: SM_1_L_uc


title: RP_1_H


title: SR_2_H


title: SR_1_L


title: BAS_2_L


title: SM_1_LU

value: Lung


title: BAS_2_H

value: converted


title: SM_1_LN


title: SM_1_H


title: RP_2_S


title: HB_1_H


title: SR_1_H


title: RP_2_L


title: RED_1_H_uc

organism: Cervus elaphus

value: old


title: RP_2_H


title: PHL_2_L

organism: Phloeomys


title: RED_2_L


title: RP_2_B


title: RED_1_H


title: PHL_1_L_uc


title: CO_3_L

organism: Puma concolor


title: RP_2_LU


title: RED_1_L


title: CO_3_H


title: PHL_1_L


title: GUP_2_L

organism: Caviidae


title: PHL_2_H


title: GUP_2_H


title: AGH_1_H_uc

organism: Tockus nasutus


title: CO_1_LU


title: GUP_2_H_uc


title: CTL_2_L

organism: Leiocephalus


title: CTL_2_LU_uc


title: AGH_1_L


title: CO_2_LU


title: PHL_1_H


title: SM_1_L


title: GUP_1_L


title: GUP_1_H


title: HAM_1_L

organism: Cricetinae


title: HAM_1_H


title: AGH_1_H


title: CTL_1_H


title: BLB_2_L_uc

organism: Antilope


title: BUD_1_L

organism: Melopsittacus


title: BLB_2_L


title: CTL_2_LU


title: CO_1_H


title: RCB_2_L_uc

organism: Uraeginthus bengalus


title: HAM_1_H_uc


title: AB_1_H

organism: Abronia anzuetoi


title: BLB_2_H


title: BUD_1_H


title: AB_1_L


title: BLB_1_L


title: RCB_2_L


title: AB_2_L


title: RCB_2_H


title: CTL_1_L


title: BLB_1_H


title: RCB_1_L


title: BUD_2_L_uc


title: AB_2_LU


title: AB_2_L_uc


title: CO_2_H_uc


title: BT_2_L_uc

organism: Geoemyda spengleri


title: BUD_2_H


title: CO_2_H


title: LOB_1_H_uc

organism: Agapornis


title: BT_2_L


title: BT_2_H


title: RCB_1_LU


title: ANT_1_H_uc

organism: Vermilingua


title: RKI_2_H_uc

organism: Milvus milvus


title: LOB_1_L


title: ANT_1_H


title: LOB_1_H


title: BUD_2_L


title: RKI_2_H


title: BT_1_H


title: ANT_2_H


title: KT_1_L

organism: Testudo kleinmanni


title: VI_2_L

organism: Vicugna


title: RKI_1_L


title: RKI_1_H


title: VI_2_H


title: RKI_2_L


title: DE_1_LU

organism: Cervidae


title: ANT_1_L


title: BT_1_L


title: ANT_2_L


title: RNP_2_L_uc

organism: Phasianus colchicus


title: WMH_2_H

organism: Circus aeruginosus


title: VI_2_L_uc


title: RNP_2_L


title: DE_2_H


title: DE_1_L


title: BGR_2_H

organism: Lyrurus tetrix


title: WMH_2_L


title: BGR_2_L


title: DE_2_L


title: VI_1_H


title: RNP_1_L


title: DE_2_H_uc


title: WMH_1_H


title: WMH_1_H_uc


title: RNP_2_H


title: ROD_2_L

organism: Capreolus capreolus


title: ROD_2_H


title: VI_1_L


title: BPA_1_H

organism: Cyanoliseus patagonus


title: BGR_1_LU_uc


title: BGR_1_LU


title: WMH_1_L


title: CHD_1_H_uc

organism: Charadriidae


title: EPC_2_H

organism: Mustela putorius


title: ROD_1_H


title: ROD_1_L_uc


title: CHD_1_H


title: BPA_2_H_uc


title: BGR_1_H


title: ROD_1_L


title: BPA_1_L


title: BPA_2_L


title: DFP_1_H

organism: Cyclopsitta diophthalma


title: EPC_1_S


title: EPC_2_L


title: BPA_2_H


title: DFP_1_L


title: CHD_1_L


title: MU_3_LN

organism: Ovis orientalis

value: Lymphnode


title: OBW_1_L

organism: Amandava subflava


title: MU_3_L


title: MU_3_H


title: OBW_1_LU


title: RNP_1_H


title: MU_3_S

value: Spleen


title: EPC_1_LU_uc


title: SEM_2_H

organism: Cariamidae


title: EPC_1_LU


title: CR_2_LU

organism: Corvus

value: f


title: DFP_1_H_uc


title: SEM_2_L


title: GWP_2_L

organism: Pytilia melba


title: OBW_1_L_uc


title: MU_3_B

value: Brain


title: CR_2_S_uc


title: MU_2_LN


title: GWP_2_L_uc


title: SEM_1_H


title: SEM_2_H_uc

value: m


title: PCO_1_L

organism: Probosciger aterrimus


title: GWP_2_H

value: Heart


title: PCO_1_H


title: CR_2_B


title: MU_2_LU


title: MU_2_H


title: CR_2_S


title: GWP_1_M

value: Muscle


title: SEM_1_L

value: Liver


title: MU_2_L


title: CHA_2_L

organism: Chamaeleonidae


title: MU_2_B


title: PCO_1_H_uc


title: CR_2_L


title: CHA_2_H


title: MU_1_L

value: 2 j


title: MU_2_S


title: CHA_1_LU


title: CR_2_H


title: CR_1_H


title: GWP_1_L


title: KAN_3_L

organism: Macropodidae


title: MU_1_S


title: CR_1_LU


title: CHA_1_LU_uc


title: KAN_3_H


title: CR_1_L


title: MU_1_LU


title: CHA_1_L


title: CR_1_S


title: MUS_1_H_uc

organism: Musophaga


title: KAN_2_L


title: MU_1_H


title: MU_1_LN


title: MF_2_L

organism: Theloderma


title: KAN_1_L


title: MUS_1_L


title: KAN_1_H


title: MUS_1_H


title: MF_2_H


title: MU_1_B


title: KBT_2_L

organism: Cuora mouhotii


title: MF_2_L_uc


title: KAN_1_H_uc


title: MU_1_B_uc


title: CBU_2_L

organism: Buteo buteo


title: WHE_1_L

organism: Zosteropidae


title: MF_2_LU


title: KBT_1_H_uc


title: CBU_2_H_uc


title: MF_2_B


title: KAN_2_H


title: CBU_2_H


title: KBT_1_H


title: WHE_1_H


title: CR_1_B


title: CBU_1_L


title: MF_1_L


title: MAT_1_L

organism: Mustelidae


title: WHE_2_L


title: CBU_1_H


title: MF_1_M


title: KBT_1_L


title: MF_3_LU


title: WHE_2_H


title: WHE_1_H_uc


title: MAT_1_H


title: RI_2_LU

organism: Cyclura cornuta


title: MAC_1_H_uc

organism: Macaca


title: MAT_2_H_uc


title: MAT_2_L


title: RI_2_H


title: MAC_1_H


title: RI_2_L


title: MF_3_M


title: MF_3_H


title: BFD_2_L

organism: Ptilinopus pulchellus


title: MAT_2_H


title: BFD_2_H


title: RI_1_LU


title: HHO_1_H

organism: Erinaceidae


title: RI_1_L


title: HHO_1_L


title: STL_2_H

organism: Uromastyx ocellata


title: RI_1_H


title: BFD_1_L


title: STL_2_L


title: BFD_1_H_uc


title: MF_3_L


title: MAC_1_L


title: STL_1_L


title: BFD_1_H


title: RI_1_S_uc


title: RI_1_S


title: STL_1_H


title: HHO_3_L


title: HHO_2_L


title: HHO_2_H


title: STL_2_H_uc


title: HHO_3_H


title: UR_2_H

organism: Uromastyx


title: MT_2_L

organism: Muntiacus


title: MT_2_LU


title: FL_2_L

organism: Phoenicopteriformes


title: FL_2_LU


title: FL_2_H


title: HHO_3_L_uc


title: MT_2_LN


title: BOA_1_H_uc

organism: Boa constrictor


title: BOA_1_H


title: UR_2_LU


title: FL_2_S


title: MT_2_S


title: WFS_2_H

organism: Pithecia pithecia


title: MT_2_H


title: UR_1_LU


title: WFS_2_L


title: UR_1_L


title: MT_1_S


title: UR_2_L


title: BOA_1_L


title: MT_1_LU_uc


title: FL_2_B


title: WFS_1_L


title: MT_1_LU


title: WFS_1_H_uc


title: FL_1_H


title: FL_1_S


title: FL_1_L


title: AFB_3_H

organism: Irena puella


title: UR_1_L_uc


title: WFS_1_H


title: MT_1_H


title: UR_1_H


title: AFB_3_L


title: LO_1_H

organism: Asio otus


title: FL_1_B


title: CH_2_S

organism: Acinonyx


title: LO_2_H_uc


title: LO_1_L


title: LO_2_L


title: FL_1_B_uc


title: MT_1_B


title: CH_2_LU_uc


title: CHI_2_L

organism: Axis axis


title: LO_2_H


title: AFB_2_H


title: CHI_2_H


title: CHI_1_L_uc


title: AFB_2_L


title: FL_1_LU


title: AFB_1_L


title: AFB_1_L_uc


title: CHI_1_L


title: PW_1_L

organism: Canis lupus


title: AFB_1_H


title: CH_2_L


title: PW_1_H


title: CHI_1_H


title: CH_2_H


title: STB_2_LU

organism: Carollia perspicillata


title: CH_1_S


title: PW_2_LU_uc


title: CH_2_LU


title: STB_2_L


title: MCL_1_L

organism: Polychrus marmoratus


title: PW_2_LU


title: PW_2_H


title: CH_1_LN


title: MCL_1_H


title: STB_2_LU_uc


title: STB_1_LU


title: CH_1_LU


title: BSN_2_LU

organism: Bison bonasus


title: MCB_1_L

organism: Cuora mccordi


title: PW_3_LU


title: TAO_2_L_uc

organism: Strix aluco


title: TAO_1_H


title: MCB_1_H_uc


title: CH_1_H


title: NH_1_L

organism: Equus


title: NH_1_H_uc


title: MCL_1_H_uc


title: BSN_1_L_uc


title: TAO_2_H


title: BSN_2_L


title: MCB_1_H


title: TAO_1_L


title: TS_2_L

organism: Erpeton


title: BSN_1_L


title: NH_1_H


title: VW_2_L_uc

organism: Ploceus cucullatus


title: TS_2_H


title: BSN_1_H


title: PY_1_H

organism: Pythonidae


title: TS_1_L


title: PY_1_L


title: PW_3_H


title: SGO_1_H

organism: Varanus gouldii


title: VW_1_H


title: VW_2_L


title: STB_1_L


title: TAO_2_L


title: JAK_2_L

organism: Jaculus


title: JAK_2_H


title: PY_2_H_uc


title: SGO_1_H_uc


title: EM_1_H_uc

organism: Dromaius novaehollandiae


title: VW_2_H


title: PY_2_H


title: TS_1_L_uc


title: TS_1_LU


title: BMT_2_L

organism: Leontocebus fuscicollis


title: VW_1_L


title: PC_2_LU_uc

organism: Pelecanus


title: PY_2_L


title: PC_2_S


title: SGO_1_L


title: JAK_2_H_uc


title: BMT_1_H_uc


title: EM_1_L


title: GAC_1_L

organism: Gallicolumba


title: EM_1_H


title: JAK_1_H


title: BMT_1_L


title: JAK_1_L


title: PC_2_LU


title: BMT_2_H


title: PC_2_L


title: BMT_1_H


title: HOO_1_L

organism: Upupa epops


title: GAC_1_H


title: PC_1_H


title: HOO_1_H_uc


title: MT_1_L

organism: Muntiacus


title: SRB_2_L_uc

organism: Euplectes orix


title: GAC_1_H_uc


title: SRB_2_L


title: PC_1_L


title: SRB_2_H


title: SRB_1_H


title: CH_2_LN

organism: Acinonyx


title: HOO_1_H


title: PC_2_H


title: SRB_1_L


title: PC_1_S


title: HOO_2_H


title: CRS_2_L

organism: Tringa totanus


title: KIS_1_L

organism: Lampropeltis


title: HOO_2_L


title: MUT_1_L

organism: Saguinus mystax


title: PC_1_LU


title: KIS_1_H_uc


title: PIP_2_H

organism: Ducula bicolor


title: PIP_2_L


title: YM_1_L

organism: Cynictis


title: CRS_2_H_uc


title: YM_1_H_uc


title: PIP_1_H


title: YM_1_H


title: IFT_1_H_uc

organism: Lissemys punctata


title: PIP_1_H_uc


title: IFT_1_L


title: CRS_1_L


title: KIS_1_H


title: MUT_1_H_uc


title: NIL_2_L

organism: Boselaphus tragocamelus


title: IFT_1_H


title: SEV_2_H_uc

organism: Leptailurus


title: CRS_1_H


title: SEV_2_L


title: PIP_1_L


title: CRS_2_H


title: NMO_1_H_uc

organism: Mimus polyglottos


title: NMO_1_H


title: SEV_1_LU


title: GU_2_L

organism: Cercopithecus


title: SEV_2_H


title: GU_2_H


title: NIL_1_L_uc


title: MUT_1_H


title: NMO_1_L


title: NIL_2_H


title: SEV_1_H


title: SC_1_L

organism: Casuarius casuarius


title: GU_1_L_uc


title: FED_2_L

organism: Dama dama


title: NIL_1_L


title: GU_1_L


title: NIL_1_H


title: GU_1_H


title: EL_1_L

organism: Elephas maximus indicus


title: FED_2_H


title: FED_1_L


title: OG_1_L

organism: Paroedura picta


title: FED_1_H_uc


title: OG_1_L_uc


title: SC_1_H


title: MAR_2_H

organism: Marmota


title: EL_1_H


title: MAR_2_L


title: FED_1_H


title: MAR_1_L


title: EAS_1_H

organism: Spinus spinus


title: MAR_1_H_uc


title: OG_1_H


title: SLT_2_H

organism: Trachemys


title: SC_1_H_uc


title: EAS_1_L


title: DR_1_L

organism: Camelus dromedarius


title: DR_1_H_uc


title: SLT_1_L


title: BAT_1_L_uc

organism: Yangochiroptera


title: EAS_1_H_uc


title: GT_1_L

organism: Parus major


title: MAR_1_H


title: DR_1_H


title: SLT_1_H_uc


title: EL_1_H_uc


title: SLT_1_H


title: WHS_1_L

organism: Cygnus cygnus


title: BAT_1_L


title: GT_1_H_uc


title: WHS_1_H


title: BAT_1_H


title: SLT_2_L


title: GT_1_H


title: PBP_2_H

organism: Sus scrofa domesticus


title: PCA_1_H

organism: Furcifer pardalis


title: BOT_1_L

organism: Terrapene


title: PCA_1_L


title: PCA_2_H


title: BOT_1_H


title: PBP_1_H_uc


title: BOT_2_L


title: WHS_2_H


title: PBP_1_H


title: PCA_2_H_uc


title: PCA_2_L


title: PS_2_L

organism: Hemisphaeriodon


title: BOT_2_H_uc


title: BM_2_S

organism: Macaca sylvanus


title: LB_3_L

organism: Chloropsis


title: GA_2_L_uc

organism: Spatula querquedula


title: PS_2_H


title: GA_2_L


title: LB_3_H


title: BM_2_LU


title: PS_2_LU_uc


title: WHS_2_H_uc


title: PBP_1_L


title: GA_2_H


title: GA_1_H


title: PS_1_H


title: WHS_2_L


title: BM_2_LN


title: BM_2_L


title: GA_1_L


title: PS_2_LU


title: RAB_2_L_uc

organism: Oryctolagus cuniculus


title: PS_1_L


title: RAB_2_L


title: BM_2_H


title: LB_2_S


title: PS_1_LU


title: LB_2_H


title: RAB_2_H


title: BM_1_S


title: LB_2_B


title: LB_2_S_uc


title: SQM_3_H

organism: Saimiriinae


title: BM_2_B


title: SQM_3_L


title: PBP_2_L


title: BOT_2_H


title: RAB_1_L


title: LB_3_S


title: LB_2_LU


title: RAB_1_H


title: SQM_2_L


title: LB_3_LU


title: BM_1_LN


title: SL_1_L_uc

organism: Folivora


title: SQM_2_H


title: BM_2_B_uc


title: BM_1_LU


title: LB_2_L


title: LB_1_L


title: SL_1_H


title: LB_1_H


title: BM_1_L


title: SQM_2_L_uc


title: BM_1_H


title: OU_1_L

organism: Pongo


title: SL_1_L


title: BM_1_B


title: SQM_1_L


title: AGS_1_H_uc

organism: Aplonis panayensis


title: AGS_1_H


title: LB_1_LU


title: SQM_1_H


title: JS_2_H_uc

organism: Lonchura oryzivora


title: CT_3_H

organism: Incilius alvarius


title: AGS_1_L


title: CT_3_LU


title: BTF_1_L

organism: Rhacophorus reinwardtii


title: JS_2_H


title: OU_1_H


title: YNM_1_H_uc

organism: Apodemus flavicollis


title: CT_3_M


title: BTF_1_H_uc


title: YNM_1_L


title: JS_2_L


title: YNM_1_H


title: BTF_1_H


title: CT_3_L


title: CT_2_H


title: LB_1_B


title: BTF_2_L


title: JS_1_LU


title: JS_1_H


title: OU_1_H_uc


title: MOL_1_H

organism: Varanus


title: CT_2_L


title: LYN_2_L

organism: Lynx lynx


title: EO_2_H

organism: Lutra lutra


title: MOL_1_H_uc


title: LYN_2_H_uc


title: EO_2_L_uc


title: EAB_1_H

organism: Sylvia atricapilla


title: CT_1_L


title: CT_1_M


title: EAB_1_L


title: LYN_2_H


title: LYN_1_L


title: EAB_5_LU


title: EO_1_L


title: CT_1_LU


title: EAB_5_H


title: LYN_1_LU


title: CT_1_L_uc


title: EO_1_H


title: CT_1_H


title: MOL_1_L


title: BHP_2_L

organism: Loriculus galgulus


title: MEE_1_L

organism: Suricata


title: BHP_2_L_uc


title: EAB_5_M


title: BHP_2_H


title: MEE_1_H_uc


title: CT_2_M


title: EAB_5_B


title: MST_1_H

organism: Leptoptilos crumenifer


title: MEE_1_H


title: MST_1_L


title: EO_2_L


title: EAB_4_M_uc


title: BHP_1_H


title: MEE_2_H


title: BHP_1_L


title: EAB_4_H


title: MST_2_L


title: MEE_2_L


title: MST_2_H_uc


title: EAB_4_M


title: TUP_2_L

organism: Tupaia


title: BA_2_L

organism: Meles meles


title: BA_2_H


title: MST_2_H


title: EAB_4_LU


title: TUP_2_L_uc


title: TUP_2_H


title: BA_1_L


title: HS_1_H_uc

organism: Passer domesticus


title: EAB_3_M


title: HS_1_H


title: TUP_1_L


title: HS_1_L


title: BA_1_H


title: EAB_3_B


title: BA_1_H_uc


title: EAB_4_B


title: TUP_1_H


title: SER_1_L

organism: Capricornis


title: MAA_2_H

organism: Dolichotis patagonum


title: BBA_1_LU

organism: Amazona agilis


title: EAB_3_H


title: SER_1_H


title: EAB_3_LU


title: BBA_1_H


title: MAA_2_L


title: SER_2_L_uc


title: EAB_2_B


title: BBA_2_LU


title: MAA_1_H


title: SER_2_L


title: EAB_2_M


title: BBA_2_H_uc


title: MAA_1_L


title: SER_2_H


title: EAB_2_H


title: EAB_2_LU


title: MAA_1_L_uc


title: RAY_1_L

organism: Batoidea


title: KO_1_H_uc

organism: Naja


title: KO_1_L


title: GHL_1_L

organism: Agapornis canus


title: RAY_1_H_uc


title: EPO_2_M_uc

organism: Ostrea edulis


title: EPO_3_G

value: Gills


title: GHL_1_H_uc

value: adult


title: KO_1_H


title: EPO_3_M


title: RAY_1_H


title: PK_1_S

organism: Notamacropus parma


title: WE_1_L

organism: Haliaeetus albicilla


title: PK_1_M


title: BWL_1_H_uc

organism: Agapornis taranta


title: EPO_2_M


title: PK_1_LU


title: WE_1_B


title: BBA_2_H


title: EPO_2_G


title: GHL_1_H


title: WE_1_LU


title: WE_1_S


title: NIP_1_L

organism: Caloenas nicobarica


title: EPO_1_M


title: PK_1_K

value: Kidney


title: PK_1_D

value: Duodenum

value: 1 j


title: BWL_1_H


title: EPO_1_G


title: SRM_2_HK

organism: Mullus surmuletus

source_name: Headkidney

value: Headkidney


title: WE_1_B_uc

value: unconverted


title: NIP_1_H

value: converted


title: NIP_1_H_uc


title: PK_1_H


title: BCR_1_L

organism: Anthropoides paradiseus


title: SRM_3_ST

source_name: Stomach

value: Stomach


title: SRM_2_SK

source_name: Skin

value: Skin


title: BCR_1_H

value: f


title: BWL_1_L


title: WE_2_B

value: Brain


title: BCR_1_H_uc


title: PK_3_K


title: PK_3_S

value: Spleen


title: SRM_1_ST


title: WE_2_LU

value: Lung

value: m


title: SRM_1_H

value: Heart


title: EUR_1_L

organism: Coracias garrulus

value: Liver


title: PK_1_L


title: SRM_2_L


title: EUR_1_H


title: WE_2_H


title: WE_2_S


title: PK_3_LU


title: WE_1_H


title: EUR_1_H_uc


title: SRM_2_ST


title: PK_3_LN_uc

value: Lymphnode


title: SRM_3_HK

value: adult


title: PK_1_LN


title: PK_3_LN


title: MH_1_H

organism: Lepus timidus


title: GRE_1_L

organism: Ardea


title: GRE_1_H_uc


title: MH_1_L


title: SRM_3_E

source_name: Esophagus

value: Esophagus


title: PK_3_L


title: SRM_1_E


title: GRE_1_H


title: PK_3_M

source_name: Muscle

value: Muscle


title: WE_2_L


title: SRM_3_B


title: GRE_2_L


title: MH_2_H

source_name: Heart


title: PK_3_H


title: GRE_2_H


title: PK_3_D

value: Duodenum


title: SRM_1_HK

value: Headkidney


title: OSO_1_H

organism: Aonyx cinereus


title: PK_3_B


title: SRM_3_M


title: OSO_1_H_uc

value: unconverted


title: HP_3_S

organism: Spheniscus humboldti

value: converted


title: PK_2_H


title: PK_2_M


title: OSO_1_L

source_name: Liver


title: SBT_1_L

organism: Graptemys


title: SBT_1_H_uc


title: HP_3_LU


title: HP_3_L


title: MH_2_H_uc


title: PK_2_LU


title: SRM_1_L_uc


title: SRM_1_G

value: Gills


title: MH_2_L


title: SRM_3_G


title: PK_2_D


title: SBT_1_H


title: HP_3_B


title: HP_2_LU


title: SRM_1_SK

value: Skin


title: RES_2_L

organism: Trachemys scripta elegans

value: f


title: PK_2_L


title: HP_3_H


title: PK_2_B

value: Brain


title: HP_2_H


title: SRM_2_H


title: SRM_3_SK


title: PK_2_K

value: Kidney


title: RES_1_L


title: HP_2_S

value: Spleen


title: HP_2_B


title: SRM_3_L


title: HP_2_L


title: RES_1_H_uc


title: SRM_1_M


title: RES_1_H


title: VC_2_LU

organism: Chamaeleo calyptratus

value: Lung


title: VC_2_H

value: Heart


title: SRM_2_G


title: RES_2_H


title: HP_1_S


title: HP_2_H_uc


title: SRM_1_L

value: Liver


title: NY_2_H

organism: Tragelaphus angasii

value: m


title: PK_2_S

value: adult


title: HP_1_H


title: NY_2_S


title: VC_2_H_uc


title: SRM_2_E

value: Esophagus


title: NY_2_LU_uc


title: VC_1_LU


title: SRM_1_B


title: HP_1_L


title: VC_1_L


title: NY_2_LN

value: Lymphnode


title: NY_2_LU


title: HP_1_B


title: VC_1_H


title: SRM_2_M

value: Muscle


title: HA_2_LU

organism: Scopus umbretta


title: NY_2_B


title: HP_1_LU


title: LOW_2_H_uc

organism: Athene noctua


title: VC_2_L


title: NPI_3_SB

organism: Esox lucius

source_name: Swimbladder

value: Swimbladder


title: SRM_3_H


title: NY_2_L


title: LOW_2_H


title: NPI_3_L


title: NPI_3_K


title: NPI_3_S


title: NY_1_LN


title: NY_1_S


title: HA_1_H

value: juv


title: NY_1_LU

value: converted


title: LOW_1_L


title: LOW_2_L


title: HA_1_H_uc

value: unconverted


title: SSL_2_H_uc

organism: Otaria

value: juvenil


title: SRM_2_B

source_name: Brain


title: MAI_1_H

organism: Iguanidae

value: f


title: HA_1_L


title: NPI_2_SB


title: NY_1_L


title: NPI_3_H


title: SSL_2_L


title: HA_2_L


title: NY_1_H


title: NPI_2_S


title: NY_1_B

value: Brain


title: SSL_2_H


title: MAI_1_L


title: LOW_1_H


title: NPI_2_L


title: SSL_1_H


title: NPI_2_K

value: Kidney


title: TAH_2_L_uc

organism: Hemitragus


title: PEC_2_H

organism: Tayassuidae


title: MAI_1_H_uc


title: TAH_2_H


title: PEC_2_L


title: COB_1_H

organism: Pycnonotus barbatus


title: SSL_1_L


title: PEC_2_H_uc


title: NPI_1_S_uc

value: Spleen


title: PEC_1_M

value: old


title: COB_1_H_uc

value: Heart


title: TAH_1_L

value: Liver


title: COB_1_L

value: m


title: NPI_1_S

value: adult


title: NPI_1_SB


title: TAH_1_H


title: TAH_2_L


title: PEC_1_H


title: HE_1_S

organism: Testudo hermanni


title: HE_1_LU

source_name: Lung

value: Lung


title: NPI_1_L


title: NPI_1_K


title: WI_2_L

organism: Connochaetes


title: GI_1_H

organism: Giraffa giraffa


title: NPI_1_H


title: WI_2_H


title: NPI_2_H


title: WI_1_L


title: HE_1_H


title: GJ_1_H_uc

organism: Canis aureus


title: GI_1_H_uc


title: WI_1_H


title: CHR_3_SB

organism: Salvelinus umbla


title: HE_2_S

source_name: Spleen


title: WI_2_L_uc


title: HE_2_LU


title: RYB_1_L

organism: Trachyphonus erythrocephalus


title: CHR_3_L


title: CD_1_S

organism: Crocodylia


title: RYB_1_LU


title: HE_2_L_uc


title: GJ_1_H


title: HE_1_L


title: CHR_3_K


title: CD_1_LU


title: GJ_1_L


title: RYB_1_L_uc


title: HE_2_L


title: CD_1_L


title: CHR_3_S


title: CHR_2_SB


title: CD_1_H


title: AR_1_LU_uc

organism: Dasypodidae


title: AR_1_S


title: CHR_2_S


title: WAB_2_L

organism: Kobus


title: CD_1_LU_uc


title: AR_1_LU


title: WAB_2_H_uc


title: CD_2_S


title: WAB_2_H


title: HE_2_H


title: CHR_2_K


title: CHR_2_L


title: AR_1_LN

value: Lymphnode


title: CD_2_B


title: CHR_3_H


title: COY_1_L

organism: Myocastor coypus


title: AR_1_L


title: CHR_2_H


title: AR_2_S


title: CHR_1_S_uc


title: AR_1_H


title: AR_2_LU


title: OWP_2_L

organism: Hystricidae


title: COY_1_H


title: WAB_1_H


title: CHR_1_SB


title: OWP_2_H


title: COY_2_H


title: WAB_1_L


title: CHR_1_L


title: CD_2_L


title: CHR_1_S


title: AR_2_L


title: OWP_2_L_uc


title: CHR_1_K


title: COY_2_L_uc


title: OWP_1_L


title: CHR_1_H


title: COY_2_L


title: DP_2_L

organism: Pelecanus crispus


title: ES_2_LU

organism: Macroscelidea


title: ES_2_B


title: SSS_3_P_uc

organism: Boltenia ovifera

source_name: Pharynx

value: Pharynx


title: OWP_1_H


title: DP_2_H


title: DP_1_L


title: SSS_3_P


title: BYM_2_L

organism: Ara ararauna


title: ES_2_H


title: BYM_1_L


title: BYM_2_H_uc


title: BYM_1_H


title: SSS_2_P


title: ES_1_S


title: ES_1_L


title: ES_2_L


title: SEP_2_P

organism: Halocynthia pyriformis


title: ES_1_H


title: TD_7_TN

organism: Sarcophilus

source_name: Trigeminal Nerve

value: Trigeminal Nerve


title: DP_1_L_uc


title: BYM_2_H


title: SSS_1_P


title: TD_5_S


title: ES_1_H_uc


title: SEP_1_SI_uc

source_name: Siphon

value: Siphon


title: SEP_1_P

value: converted


title: TD_4_S


title: AR_2_H


title: TD_4_SK

value: Skin


title: PT_2_H

organism: Malacochersus


title: SEP_1_SI


title: CST_2_L

organism: Chelydra serpentina

value: juvenil


title: CST_2_L_uc

value: f

value: unconverted


title: TD_3_Tm_uc


title: TD_5_SK


title: CST_1_L


title: PT_2_S


title: GSU_3_TF

organism: Strongylocentrotus droebachiensis


title: CST_1_H


title: GSU_2_TF


title: LTR_1_L

organism: Jacanidae


title: LTR_1_H_uc


title: GSU_1_E_uc

value: Esophagus


title: TD_3_S

value: Spleen


title: TD_3_SK


title: PT_1_S_uc


title: PT_2_LU


title: PT_2_L


title: LTR_1_H

value: old


title: TD_2_S


title: TD_8_H

value: Heart


title: PT_1_S


title: GSU_1_E


title: GSU_1_TF


title: TD_2_SK


title: YBH_1_H_uc

organism: Tockus flavirostris


title: NOP_2_M

organism: Sphoeroides maculatus

value: Muscle


title: TD_10_LU


title: YBH_1_H


title: PT_1_L

value: Liver

value: m


title: NOP_2_K

value: Kidney


title: RSQ_2_L

organism: Sciurus vulgaris

value: adult


title: TD_9_L


title: PT_1_H


title: ROF_2_SK

organism: Sebastes norvegicus


title: NOP_2_S


title: YBH_1_L


title: NOP_2_G

source_name: Gills

value: Gills


title: JMD_1_H

organism: Tragulus javanicus


title: RSQ_2_H


title: RSQ_1_H


title: NOP_2_H


title: JMD_1_L


title: NOP_2_L


title: PT_1_LU

value: Lung


title: ROF_1_SK_uc


title: RSQ_1_L


title: RSQ_1_H_uc


title: NOP_2_L_uc


title: ROF_1_SK


title: ASH_2_M

organism: Pleoticus muelleri


title: JMD_2_L


title: JMD_2_H


title: NOP_1_M


title: ASH_1_SK


title: ZE_2_LN

organism: Equus zebra

source_name: Lymphnode

value: Lymphnode


title: NOP_1_K

source_name: Kidney

value: converted


title: ASH_2_GO

source_name: Gonad

value: Gonad


title: ZE_2_LU


title: ROF_2_M


title: GLT_1_L

organism: Leontopithecus chrysomelas


title: GLT_1_H_uc


title: NOP_1_S


title: ZE_2_L


title: ASH_1_M


title: ASH_1_GO


title: GLT_1_H


title: NOP_1_G


title: ZE_2_S


title: JMD_1_H_uc


title: CS_2_L_uc

organism: Sturnus vulgaris


title: ASH_2_SK

value: Skin


title: ZE_1_S


title: CS_2_H


title: AMP_2_S

organism: Hippoglossoides platessoides


title: CS_1_L


title: NOP_1_H


title: ZE_1_LU


title: AMP_2_K


title: ZE_1_H_uc


title: PRA_2_SK

organism: Penaeus


title: PRA_1_M


title: CS_4_L

value: juvenil


title: CS_1_H


title: AMP_2_M


title: ZE_1_L


title: AMP_2_L


title: ZE_1_H


title: PRA_2_M


title: NOP_1_L


title: ZE_1_LN


title: GCO_2_L

organism: Phalacrocorax carbo

value: f


title: AMP_2_G


title: ZE_2_H


title: CS_4_H


title: ASH_2_SK_uc

value: unconverted


title: PRA_1_SK


title: CS_2_L


title: AMP_1_K


title: AMP_1_L


title: CS_3_L


title: PRA_1_SK_uc


title: PA_2_LU

organism: Acanthosaura


title: GCO_2_H


title: CS_3_H


title: GCO_2_L_uc


title: AMP_1_M


title: AMP_1_G_uc


title: TRO_4_H

organism: Salmo trutta


title: TRO_4_L


title: TRO_4_K


title: AMP_1_G


title: BV_1_H

organism: Gypaetus


title: PA_2_L


title: AMP_1_S

value: Spleen


title: GCO_1_L


title: PA_1_H_uc


title: BV_1_H_uc


title: BV_1_L


title: WHH_2_SK_uc

organism: Urophycis tenuis


title: TRO_3_S


title: WHH_2_SK


title: GCO_1_H


title: WHH_2_K


title: PO_1_H

organism: Petauridae


title: PA_1_H


title: PO_1_S


title: TRO_3_K


title: PA_1_L


title: PA_2_H


title: TRO_3_L


title: TRO_3_H


title: WHH_2_SB

value: Swimbladder


title: MA_4_L

organism: Anas platyrhynchos

value: old


title: TRO_2_S


title: TRO_3_SB


title: PO_1_LU_uc


title: TRO_2_L_uc


title: WHH_2_S


title: PO_1_LU


title: MA_4_H

value: Heart


title: WHH_2_H


title: TRO_2_L

value: Liver


title: PA_1_LU


title: TRO_4_S

value: m


title: PO_2_B

value: Brain


title: MA_3_L


title: WHH_2_M

value: Muscle


title: TRO_2_K

value: Kidney

value: adult


title: WHH_2_F

source_name: Fin

value: Fin


title: PO_1_L

value: converted


title: PO_2_LU

value: Lung


title: TRO_2_H


title: TRO_1_SB


title: MA_2_H


title: MA_3_H


title: WHH_1_K


title: TRO_1_S


title: WHH_1_SB


title: PO_2_S


title: MA_1_L


title: TRO_1_L


title: MA_2_L


title: MA_1_H


title: WHH_1_L


title: PO_2_H


title: SIT_1_L

organism: Tragelaphus spekii


title: TRO_1_H


title: MA_4_L_uc


title: SIT_1_H_uc


title: WHH_1_H


title: CCA_3_SB

organism: Cyprinus carpio


title: COC_1_T

organism: Octopus vulgaris

source_name: Tentacle

value: Tentacle


title: COC_4_T


title: COC_5_T


title: CCA_3_L


title: WHH_2_G

value: Gills


title: PO_2_L

value: f


title: WHH_1_M


title: FOX_2_L

organism: Vulpes vulpes


title: CCA_3_S


title: WHH_1_F


title: COC_3_M_uc

value: unconverted


title: CCA_3_H


title: SIT_1_H

value: juvenil


title: WHH_1_G


title: FOX_2_H


title: WHH_1_S

value: Spleen


title: FOX_1_H


title: COC_2_M


title: CCA_2_L


title: CCA_2_S


title: CCA_2_SB

value: Swimbladder


title: COC_3_M


title: COC_2_SK

source_name: Skin

value: Skin


title: PSL_1_G_uc

organism: Ammodytes hexapterus


title: CCA_2_H

value: Heart


title: PSL_1_G


title: FOX_1_L_uc

value: Liver

value: m


title: FOX_1_L


title: PSL_2_G


title: BE_2_H_uc

organism: Castoridae


title: ANG_1_SK

organism: Lophius piscatorius


title: BE_2_L


title: ANG_2_SK


title: SFI_1_G_uc

organism: Anoplopoma fimbria


title: CCA_1_SB


title: CCA_1_H_uc


title: SFI_1_G


title: CCA_1_H


title: YIL_2_G

organism: Hemilepidotus jordani


title: BE_1_L


title: PSL_3_G


title: ANG_2_M

source_name: Muscle

value: Muscle


title: YIL_1_G_uc


title: ANG_1_M


title: AX_4_H

organism: Ambystoma mexicanum

source_name: Heart


title: AX_4_BL

source_name: Blood

value: Blood


title: FS_3_L

organism: Chrysopelea

source_name: Liver


title: FS_3_LU


title: YIL_1_G

value: adult


title: YIL_3_G


title: FS_2_L


title: CCA_1_S


title: RH_2_L

organism: Rhea americana


title: BE_2_H


title: FHS_2_G

organism: Hippoglossoides elassodon


title: AX_4_S


title: FS_1_K

value: Kidney


title: AX_4_M

value: converted


title: RH_2_LN

value: Lymphnode


title: FHS_3_G


title: ANG_2_M_uc


title: FHS_1_G_uc


title: BE_1_H


title: FS_1_L_uc


title: AX_3_M


title: FS_1_L


title: RH_2_H


title: RH_1_H


title: AX_3_S


title: RH_2_LU

value: Lung


title: FHS_1_G

value: Gills


title: AX_3_H


title: RH_1_S

value: f


title: RH_2_S


title: RH_1_LU_uc

value: unconverted


title: AX_3_BL


title: TEN_3_L

organism: Tinca tinca


title: AX_2_S


title: RH_1_L


title: ATM_1_G_uc

organism: Pleurogrammus monopterygius


title: TEN_3_K


title: ATM_1_G


title: AX_2_H


title: RH_1_LU


title: TEN_3_H


title: AX_2_M


title: SNB_2_M

organism: Lumpenus lampretaeformis


title: TEN_2_SB

source_name: Swimbladder


title: SNB_2_K_uc


title: AST_2_L_uc

organism: Geochelone


title: AST_2_L


title: TEN_3_SB


title: AST_2_H


title: AX_1_BL


title: TEN_2_S_uc


title: ATM_3_G


title: SNB_2_K


title: TEN_3_S


title: ATM_2_G


title: AX_1_M


title: TEN_2_S


title: SNB_2_L


title: AX_1_S


title: TEN_2_K


title: TEN_2_L


title: SNB_2_G


title: AX_1_H


title: AST_1_H


title: AST_1_L


title: MB_2_LU_uc

organism: Yinpterochiroptera

source_name: Lung


title: AX_2_BL


title: TEN_2_H


title: SNB_1_M


title: SNB_1_H


title: MB_2_S

source_name: Spleen


title: AX_1_S_uc


title: SNB_1_L


title: TEN_1_SB


title: JB6-TPA (RNA)

city: Piscataway

first: Hsiao-Chen Dina

last: Kuo

address: 160 frelinghuysen road

department: Ernest Mario School of Pharmacy

institute: Rutgers University

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to hs19 using Hisat2 with default parameters
Duplicates removed by Picard
Reads overlapping gene features were counted by featureCounts.
Differential expression by DESeq in R
Assembly: mm10
Supplementary files format and content: Comma delimited tables with raw counts

organism: Mus musculus

source_name: JB6 P+

growth_protocol: JB6 cells were cultured in DMEM medium (10% Fetal Bovine Serum and 1% penicillin-streptomycin) and passaged every 2-3 days (typically 1*10^6 cells were seeded per 100mm plate every passage)

extract_protocol:
Qiagen Allprep DNA/RNA extraction
Standard Illumina protocols

treatment_protocol: Treated JB6 cells with 10 ng/mL TPA or 10 ng/mL TPA + 50 nM CDDO in 1% FBS medium every other day for five days

value: JB6 P+

value: skin epithelial cells

value: TPA, 10ng/mL


title: JB6-CDDO+TPA (RNA)

value: TPA, 10ng/mL, CDDO, 0.05uM


title: TEN_1_S

value: Spleen


title: SNB_1_G


title: JB6-Control (RNA)

value: Control


title: MB_2_LU

value: m


title: MB_2_L

value: Liver


title: TEN_1_L


title: MB_2_H

value: Heart


title: STR_1_M

organism: Morone saxatilis

value: Muscle

value: adult


title: JB6-CDDO+TPA (DNA)

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to hs19 using Bismark with default parameters
Duplicates removed by Picard
Reads overlapping gene features were counted by DMRfinder
Annotation by ChIPseeker
DMR analysis by DSS in R
Assembly: mm10
Supplementary files format and content: Comma delimited tables with raw counts
Supplementary files format and content: Tab delimited tables with CpG methylation ratio and gene annotation


title: TEN_1_K

value: Kidney

value: converted


title: STR_1_F

value: Fin


title: TEN_1_H


title: MB_2_B

source_name: Brain

value: Brain


title: SGS_2_TI

organism: Molgula citrina

source_name: Tissue

value: Tissue


title: STR_1_F_uc

value: unconverted


title: MB_1_B

value: juvenil


title: JB6-TPA (DNA)

value: JB6 P+

value: skin epithelial cells


title: MB_1_S


title: AFC_1_M

organism: Coris gaimard

value: juvenile


title: Prrx1 transduction, noDox3, bulk-RNAseq

city: St. Louis

first: Barak

last: Cohen

state: Missouri

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

data_processing:
Counts for each gene were obtained using Kallisto version 0.43.0 using the parameters -t 4 -b 200
Assembly: mm10
Supplementary files format and content: Tab-separated values files for abundances of each gene in each sample.

extract_protocol:
NIH3T3-CG cells were released from 6-well plates using Trypsin and we extracted total RNA using Qiagen RNEasy.
Library construction and sequencing was performed at Novogene corporation
bulk mRNA sequencing

value: Embryonic fibroblasts

value: Prrx1, no Doxycycline


title: JB6-Control (DNA)

value: Control


title: AFC_1_DF


title: SGS_2_P_uc

source_name: Pharynx

value: Pharynx


title: AFC_1_DF_uc


title: MB_1_L

value: Liver


title: MB_1_H

value: Heart


title: SGS_1_P


title: SGS_1_TI


title: Prrx1 transduction, noDox2, bulk-RNAseq


title: Prrx1 transduction, noDox1, bulk-RNAseq


title: AFC_1_CF


title: SGS_2_P


title: Prrx1 transduction, Dox3, bulk-RNAseq

value: Prrx1, Doxycycline


title: SOS_2_H

organism: Chauna torquata

value: m

value: adult


title: HTF_1_M_uc

organism: Choerodon fasciatus

value: Muscle


title: Prrx1 transduction, Dox1, bulk-RNAseq


title: OSC_3_TF

organism: Cucumaria frondosa

value: converted


title: Prrx1 transduction, Dox2, bulk-RNAseq


title: HTF_1_M


title: MB_1_LU

value: Lung


title: SOS_1_L

value: f


title: OSC_2_T

value: Tentacle


title: HTF_1_O

source_name: Operculum

value: Operculum


title: OSC_2_TF_uc

value: unconverted


title: SOS_1_H

value: juvenil


title: SOS_1_H_uc


title: OSC_3_T


title: SOS_2_L


title: OSC_2_TF


title: RBW_1_M

organism: Cirrhilabrus roseafascia


title: Rejuvenated Old biol rep 6

city: New Haven

first: George

last: Hung

state: Connecticut

address: 300 George Street Room 741

institute: Yale University

description: Old MSCs subject to co-culture with Young MSCs  day 7

data_processing:
The open source Galaxy pipeline was used for data processing and analysis
Raw sequencing reads were aligned to the UCSC mm10 genome using HISAT2
Transcript assembly with StringTie
Alignment quantification with featureCounts
Count normalization and differential expression analyses with DESeq2 and Genesis
Assembly: UCSC mm10
Supplementary files format and content: tab delimited text files with normalized gene expression

source_name: MSCs harvested from bone marrow

growth_protocol: All cells were incubated at 37°C in 5% CO2. MSCs were expanded in culture in alpha-MEM basal medium (Stemcell Technologies  Tukwila  WA) supplemented with 20% FBS (Gibco Invitrogen  Carlsbad  CA)  120 units/mL Penicillin  100 mcg/mL streptomycin  and 2mM L-glutamine

extract_protocol:
Qiagen miRNAeasy Mini kit and followed QiaCube miRNeasy mini protocol with on column DNase I digestion
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's protocols.

treatment_protocol: Replicates of 105 old MSCs were cultured separately  or in co-culture with young MSCs  for 7 days using a 0.4µm Transwell system in 6-well plates (Corning)  which allow transfer of soluble paracrine factors released by the cells  but not of the cells themselves.

value: MSCs harvested from bone marrow

value: Primary mouse MSCs

value: mesechymal stem cells

value: co-culture with young MSCs


title: HTF_1_F

value: Fin


title: Rejuvenated Old biol rep 5


title: RBW_1_CF_uc


title: OSC_1_TF


title: EPT_2_S

organism: Emydidae

value: Spleen


title: Rejuvenated Old biol rep 4


title: Rejuvenated Old biol rep 2


title: Rejuvenated Old biol rep 1


title: EPT_2_H

value: Heart


title: Old biol rep 6

description: Old MSCs  day 7

value: no treatment


title: EPT_1_H

value: adult


title: OSC_1_T


title: SAD_1_F

organism: Oxycercichthys veliferus

value: m


title: SAD_1_F_uc


title: Rejuvenated Old biol rep 3


title: EPT_2_LU

value: converted


title: WIF_2_H

organism: Glyptocephalus cynoglossus


title: RBW_1_DF


title: Old biol rep 4

description: Old MSCs  day 7


title: EPT_2_L

value: Liver


title: EPT_1_LU_uc

value: Lung

value: f


title: RBW_1_CF


title: WIF_2_K

source_name: Kidney

value: Kidney


title: WIF_2_S_uc

value: unconverted


title: AW_4_PR

organism: Saccoglossus kowalevskii

source_name: Proboscis

value: Proboscis


title: Old biol rep 2

description: Old MSCs  day 7

value: MSCs harvested from bone marrow


title: WIF_2_M

value: Muscle


title: BU_3_S

organism: Buteo


title: Old biol rep 5

description: Old MSCs  day 7

value: Primary mouse MSCs

value: mesechymal stem cells


title: Young biol rep 6

description: Young MSCs  day 7


title: WIF_2_S


title: AW_4_C

source_name: Collar

value: Collar


title: AW_3_PO

source_name: Posterior

value: Posterior


title: AW_3_PR


title: AW_4_PO


title: Old biol rep 3

description: Old MSCs  day 7


title: WIF_1_M

source_name: Muscle


title: EPT_1_S

value: Spleen


title: BU_3_LU


title: Young biol rep 5

description: Young MSCs  day 7

value: no treatment


title: WIF_2_L


title: BU_3_H

source_name: Heart

value: Heart

value: adult


title: EPT_1_LU

value: converted


title: WIF_1_S


title: AW_3_C


title: AW_2_PO


title: EPT_1_L

value: Liver


title: WIF_2_G

source_name: Gills

value: Gills


title: Old biol rep 1

description: Old MSCs  day 7


title: BU_3_L

source_name: Liver

value: f


title: WIF_1_H


title: Young biol rep 3

description: Young MSCs  day 7


title: Young biol rep 4

description: Young MSCs  day 7


title: AW_2_PR


title: BU_2_S


title: WIF_1_G


title: BU_2_LU

value: Lung


title: WIF_1_L


title: WIF_1_K

value: Kidney


title: AW_2_C


title: AW_1_GO

source_name: Gonad

value: Gonad

value: m


title: Young biol rep 1

description: Young MSCs  day 7

value: MSCs harvested from bone marrow


title: PLW_1_M

organism: Cirrhilabrus lineatus

value: Muscle


title: WRY_2_M

organism: Cryptacanthodes maculatus


title: AW_1_GO_uc

value: unconverted


title: DOG_2_H

organism: Canis lupus familiaris


title: BU_2_L


title: DOG_2_L


title: DOG_1_H


title: Young biol rep 2

description: Young MSCs  day 7

value: Primary mouse MSCs

value: mesechymal stem cells


title: BU_1_L


title: PLW_1_O_uc

value: Operculum


title: WRY_2_K


title: DOG_1_H_uc


title: PLW_1_F

source_name: Fin

value: Fin


title: PLW_1_O


title: BU_2_H

value: Heart


title: WRY_2_L


title: DOG_1_L

value: adult


title: BU_1_B_uc

value: Brain


title: BU_2_B

value: converted


title: WRY_2_H


title: TBF_1_G_uc

organism: Platax teira

value: Gills


title: TBF_1_G


title: WRY_2_S

source_name: Spleen

value: Spleen


title: WRY_1_K


title: WRY_2_G


title: BU_1_H

value: f


title: PLF_1_F

organism: Elops affinis


title: BU_1_LU

source_name: Lung

value: Lung


title: BU_1_B

source_name: Brain


title: WRY_1_S


title: BU_1_S


title: ROA_1_H_uc

organism: Hippotragus equinus


title: SVS_5_P

organism: Ciona intestinalis

value: Pharynx


title: WRY_1_L

value: Liver


title: WRY_1_M


title: WRY_1_H_uc


title: Normal Tissue 3

city: Chongqing

first: Junfeng

last: Zhang

address: Gaotan Yanzheng Street, Shapingba District

institute: First Affiliated Hospital of Army Medical University

hyb_protocol: Array hybridization and washing were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

organism: Homo sapiens

source_name: Normal Tissue 3

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit (Cat#902280, Affymetrix, Santa Clara, CA, US)/ Ovation FFPE WTA System (Cat#3403, NuGEN, San Carlos, CA, US) / Ovation® Pico WTA System V2 (Cat#3302, NuGEN, San Carlos, CA, US) and FL-Ovation™ cDNA Biotin Module V2 (Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Pancreatic ductal adenocarcinoma samples and normal tissue samples were obtained by surgery.

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

value: Normal pancreatic tissue


title: Normal Tissue 5

source_name: Normal Tissue 5


title: Normal Tissue 4

source_name: Normal Tissue 4


title: Normal Tissue 1

source_name: Normal Tissue 1


title: Normal Tissue 2

source_name: Normal Tissue 2


title: Pancreatic Ductal Adenocarcinoma 10

source_name: Pancreatic Cancer 10

value: Pancreatic ductal adenocarcinoma


title: SVS_4_P

source_name: Pharynx


title: PLF_1_F_uc

value: unconverted


title: SVS_4_H


title: ROA_1_L


title: WRY_1_H


title: GP_2_L

organism: Psittacus


title: ROA_1_H


title: WRY_1_G


title: SVS_2_SI_uc

source_name: Siphon

value: Siphon


title: SVS_3_P


title: GP_2_B


title: GP_2_H


title: YEF_2_K

organism: Myzopsetta ferruginea

source_name: Kidney

value: Kidney


title: YEF_2_L


title: SVS_2_SI


title: YEF_2_H

source_name: Heart


title: Pancreatic Ductal Adenocarcinoma 8

source_name: Pancreatic Cancer 8


title: GP_2_LU


title: Pancreatic Ductal Adenocarcinoma 9

source_name: Pancreatic Cancer 9


title: GP_1_S


title: YEF_2_M

source_name: Muscle

value: Muscle


title: SVS_1_P


title: GP_1_H


title: Pancreatic Ductal Adenocarcinoma 7

source_name: Pancreatic Cancer 7


title: GP_2_S

source_name: Spleen


title: YEF_2_F_uc

source_name: Fin

value: Fin


title: YEF_2_F


title: PGR_1_G

organism: Oxylebius pictus

source_name: Gills


title: YEF_2_S


title: GP_1_LU

source_name: Lung


title: Pancreatic Ductal Adenocarcinoma 5

source_name: Pancreatic Cancer 5


title: YEF_2_G


title: GP_1_LU_uc


title: PGR_1_G_uc


title: GP_1_B

source_name: Brain


title: BST_1_TF

organism: Patiria miniata


title: Pancreatic Ductal Adenocarcinoma 6

source_name: Pancreatic Cancer 6


title: BST_1_TF_uc


title: Pancreatic Ductal Adenocarcinoma 3

source_name: Pancreatic Cancer 3


title: BST_3_TF


title: Pancreatic Ductal Adenocarcinoma 2

source_name: Pancreatic Cancer 2


title: Pancreatic Ductal Adenocarcinoma 4

source_name: Pancreatic Cancer 4


title: YEF_1_K


title: BST_2_TF


title: YEF_1_H

value: Heart


title: GP_1_L

source_name: Liver

value: adult


title: YEF_1_M


title: OHH_1_G_uc

organism: Atherinomorus vaigiensis


title: ESQ_1_M

organism: Loligo vulgaris


title: BLS_3_T

organism: Holothuria atra

source_name: Tentacle

value: Tentacle


title: AP/NTS TRAP2 cDNA library

city: New York

first: Anoj

last: Ilanges

state: NY

address: 1230 York Avenue, Co Box 89

institute: Rockefeller University

description: 3' mRNA library

data_processing:
The FASTQ files for each sample was analyzed with Cell Ranger version 5.0. The following analysis was based on Orchestrating Single-Cell Analysis from Bioconductor (v 1.0.6; https://bioconductor.org/books/release/OSCA/) and Vignettes from Seurat (v 4.0; https://satijalab.org/seurat/). The ambient RNA contamination and doublets were estimated by using DropletUtils (https://bioconductor.org/packages/release/bioc/html/DropletUtils.html) and scDblFinder (https://bioconductor.org/packages/release/bioc/html/scDblFinder.html), respectively. After removing ambient RNA, doublets, and nuclei with >1% mitochondrial reads, the data from individual samples were integrated using canonical correlation analysis (CCA) from Seurat using the first 2,000 variable features of each sample. The counting matrix of the samples were then merged and re-scaled by using the common variable features of the samples. Finally, a single-cell dataset with 29329 (features) x 19918 (cell barcodes) was generated.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Mus musculus

extract_protocol:
Samples were dounce homogenized and FACS sorted. Refer to Ilanges, et al. 2022 for further details
10X single-cell from chromium v3

value: Brain

value: Neuron


title: AP/NTS TRAP2 HTO library

description: HTO library

library_source: other

molecule: protein


title: OHH_1_G

value: Gills

value: converted


title: AP/NTS baseline 2 HTO library

description: HTO library


title: ESQ_2_M


title: YEF_1_G

value: f


title: BLS_1_T


title: ESQ_1_M_uc


title: YEF_1_F


title: AP/NTS baseline 1 cDNA library

description: 3' mRNA library


title: BLS_1_T_uc


title: AP/NTS baseline 2 cDNA library

description: 3' mRNA library


title: LLA_2_Lymph

organism: Lama glama

source_name: Lymphocytes

value: Lymphocytes


title: ESS_1_AR

organism: Fromia

source_name: Arm

value: Arm


title: Pancreatic Ductal Adenocarcinoma 1

source_name: Pancreatic Cancer 1


title: LOS_2_M

organism: Myoxocephalus octodecemspinosus

source_name: Muscle


title: LLA_1_Lymph


title: LLA_2_Mono

source_name: Monocytes

value: Monocytes


title: LOS_2_K

source_name: Kidney


title: ESS_2_AR


title: LLA_2_Gran

source_name: Granulocytes

value: Granulocytes


title: LOS_2_G

source_name: Gills


title: LOS_1_M


title: BLS_2_T


title: Mock 6w Rep 3

city: Shreveport

first: Bailey

last: Mosher

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: Louisiana State University Health - Shreveport

description: S29_Mock-6wk Length, S29_Mock-6wk Effective Length, S29_Mock-6wk Expected Count, S29_Mock-6wk TPM, S29_Mock-6wk FPKM

data_processing:
Reads were aligned to a concatenated human and HCMV genome (chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19).
Transcripts were quantified with RSEM 1.3.0.
Sequence reads were mapped to chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19  using STAR 2.5.31.
Assembly: chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19
Supplementary files format and content: tab-delimited text files include raw counts, TPM, FPKM values for each Sample

source_name: Peripheral blood

growth_protocol: Monocytes were cultered ex-vivo on fibronectin-treated cell culture plates in 10% human serum/RPMI, with fresh media replaced every other day to maintain cell viability

extract_protocol:
RNA was harvested using the RNA STAT-60 protocol. Total RNA was used for construction of sequencing libaries.
RNA libraries for RNAseq were prepared with the NEBNextUltra directional library kit and the TruSeq stranded mRNA kit (Illumina). A 1.8pM library was spiked with 1% PhiX as an internal control and pair end sequenced with 101 x 51 cycles.

value: Peripheral blood

value: Primary

value: Monocyte

value: WT

tag: time

value: 6 wpi


title: PAO_5_M

organism: Magallana gigas

value: Muscle


title: LOS_1_K

value: Kidney


title: LLA_1_Mono

value: adult


title: ESS_1_AR_uc

value: unconverted


title: LOS_1_SK_uc

source_name: Skin

value: Skin


title: LLA_1_Gran


title: HCMV 6w Rep 3

description: S30_HCMV-6wk Length, S30_HCMV-6wk Effective Length, S30_HCMV-6wk Expected Count, S30_HCMV-6wk TPM, S30_HCMV-6wk FPKM

value: HCMV


title: PAO_6_G

value: Gills

value: converted


title: LAF_1_NA

organism: Loweina terminata


title: SQF_1_G

organism: Neoniphon sammara


title: LOS_2_F

source_name: Fin

value: Fin


title: LOS_1_F


title: LLA_1_Gran_uc


title: HCMV 4w Rep 3

description: S28_HCMV-4wk Length, S28_HCMV-4wk Effective Length, S28_HCMV-4wk Expected Count, S28_HCMV-4wk TPM, S28_HCMV-4wk FPKM

value: 4 wpi


title: SQF_1_G_uc


title: SQF_3_M

source_name: Muskle

value: Muskle


title: LAF_1_NA_uc


title: LOS_1_SK


title: SQF_2_M


title: SHR_1_G

organism: Sebastes borealis


title: HCMV 2w Rep 3

description: S26_HCMV-2wk Length, S26_HCMV-2wk Effective Length, S26_HCMV-2wk Expected Count, S26_HCMV-2wk TPM, S26_HCMV-2wk FPKM

value: 2 wpi


title: Mock 2w Rep 3

description: S25_Mock-2wk Length, S25_Mock-2wk Effective Length, S25_Mock-2wk Expected Count, S25_Mock-2wk TPM, S25_Mock-2wk FPKM

value: Peripheral blood


title: SHR_1_G_uc


title: PAO_2_G


title: SHR_3_G

value: m


title: HCMV 24h Rep 3

description: S24_HCMV-24h Length, S24_HCMV-24h Effective Length, S24_HCMV-24h Expected Count, S24_HCMV-24h TPM, S24_HCMV-24h FPKM

value: Primary

value: Monocyte

value: 24 hpi


title: PAO_1_M

value: Muscle


title: PAO_6_M


title: Mock 4w Rep 3

description: S27_Mock-4wk Length, S27_Mock-4wk Effective Length, S27_Mock-4wk Expected Count, S27_Mock-4wk TPM, S27_Mock-4wk FPKM

value: WT


title: SHR_2_G

value: adult


title: WBD_1_F

organism: Amblyglyphidodon leucogaster


title: WBD_2_F


title: WBD_3_F_uc

value: unconverted


title: PAO_5_G


title: Mock 24h Rep 3

description: S23_Mock-24h Length, S23_Mock-24h Effective Length, S23_Mock-24h Expected Count, S23_Mock-24h TPM, S23_Mock-24h FPKM

organism: Homo sapiens


title: SEA_2_G

organism: Bathymaster signatus


title: PAO_4_M


title: HCMV 4h Rep 3

description: S22_HCMV-4h Length, S22_HCMV-4h Effective Length, S22_HCMV-4h Expected Count, S22_HCMV-4h TPM, S22_HCMV-4h FPKM

value: 4 hpi


title: PAO_2_M


title: SEA_3_G


title: WBD_3_F


title: Mock 4h Rep 3

description: S21_Mock-4h Length, S21_Mock-4h Effective Length, S21_Mock-4h Expected Count, S21_Mock-4h TPM, S21_Mock-4h FPKM


title: FLS_1_G

organism: Lutjanus quinquelineatus


title: SEA_1_G_uc


title: PAO_3_M


title: PAO_2_G_uc


title: DAS_1_H

organism: Leptoclinus maculatus

source_name: Heart

value: Heart


title: HCMV 6w Rep 2

description: S20_HCMV-6wk Length, S20_HCMV-6wk Effective Length, S20_HCMV-6wk Expected Count, S20_HCMV-6wk TPM, S20_HCMV-6wk FPKM

value: HCMV

value: 6 wpi


title: FLS_3_G

value: Gills

value: converted


title: SEA_1_G


title: Mock 6w Rep 2

description: S19_Mock-6wk  Length, S19_Mock-6wk  Effective Length, S19_Mock-6wk  Expected Count, S19_Mock-6wk  TPM, S19_Mock-6wk  FPKM


title: PAO_1_G


title: PAO_4_G


title: Mock 4w Rep 2

description: S17_Mock-4wk Length, S17_Mock-4wk Effective Length, S17_Mock-4wk Expected Count, S17_Mock-4wk TPM, S17_Mock-4wk FPKM

value: 4 wpi


title: FLS_2_G


title: HCMV 2w Rep 2

description: S16_HCMV-2wk Length, S16_HCMV-2wk Effective Length, S16_HCMV-2wk Expected Count, S16_HCMV-2wk TPM, S16_HCMV-2wk FPKM

value: 2 wpi


title: HCMV 4w Rep 2

description: S18_HCMV-4wk Length, S18_HCMV-4wk Effective Length, S18_HCMV-4wk Expected Count, S18_HCMV-4wk TPM, S18_HCMV-4wk FPKM

value: Peripheral blood


title: PAO_3_G


title: DAS_1_M


title: FLS_1_G_uc


title: DAS_3_M


title: PSU_1_GO

organism: Strongylocentrotus purpuratus

source_name: Gonad

value: Gonad


title: BC_2_LU

organism: Camelus ferus

source_name: Lung

value: Lung

value: m


title: Mock 2w Rep 2

description: S15_Mock-2wk Length, S15_Mock-2wk Effective Length, S15_Mock-2wk Expected Count, S15_Mock-2wk TPM, S15_Mock-2wk FPKM

value: Primary

value: Monocyte


title: BC_2_L

source_name: Liver

value: Liver


title: DAS_3_F

value: Fin


title: DAS_3_H


title: HCMV 24h Rep 2

description: S14_HCMV-24h Length, S14_HCMV-24h Effective Length, S14_HCMV-24h Expected Count, S14_HCMV-24h TPM, S14_HCMV-24h FPKM

value: WT

value: 24 hpi


title: BC_2_H

value: Heart

value: adult


title: DAS_3_L


title: PSU_2_GO


title: BC_2_S

source_name: Spleen

value: Spleen


title: DAS_3_G_uc

value: Gills

value: unconverted


title: HCMV 4h Rep 2

description: S12_HCMV-4h Length, S12_HCMV-4h Effective Length, S12_HCMV-4h Expected Count, S12_HCMV-4h TPM, S12_HCMV-4h FPKM

value: HCMV

value: 4 hpi


title: BSG_2_G

organism: Parupeneus spilurus

value: converted


title: BC_1_S

value: f


title: Mock 4h Rep 2

description: S11_Mock-4h Length, S11_Mock-4h Effective Length, S11_Mock-4h Expected Count, S11_Mock-4h TPM, S11_Mock-4h FPKM

value: Peripheral blood


title: PSU_1_GO_uc

value: Gonad


title: BSG_1_G


title: BC_1_LU

value: Lung


title: DAS_3_G


title: BSG_1_G_uc


title: PSU_3_GO


title: DAS_2_S


title: GBG_1_G_uc

organism: Ostorhinchus rueppellii


title: HCMV 6w Rep 1

description: S10_HCMV-6wk Length, S10_HCMV-6wk Effective Length, S10_HCMV-6wk Expected Count, S10_HCMV-6wk TPM, S10_HCMV-6wk FPKM

value: Primary

value: Monocyte

value: 6 wpi


title: BC_1_L_uc

value: Liver


title: BC_1_LN

source_name: Lymphnode

value: Lymphnode


title: Mock 24h Rep 2

description: S13_Mock-24h Length, S13_Mock-24h Effective Length, S13_Mock-24h Expected Count, S13_Mock-24h TPM, S13_Mock-24h FPKM

value: WT

value: 24 hpi


title: Mock 6w Rep 1

description: S9_Mock-6wk Length, S9_Mock-6wk Effective Length, S9_Mock-6wk Expected Count, S9_Mock-6wk TPM, S9_Mock-6wk FPKM


title: DAS_2_L


title: BC_1_L

value: adult


title: GBG_3_G

value: Gills


title: HCMV 2w Rep 1

description: S6_HCMV-2wk Length, S6_HCMV-2wk Effective Length, S6_HCMV-2wk Expected Count, S6_HCMV-2wk TPM, S6_HCMV-2wk FPKM

value: 2 wpi


title: GBG_1_G


title: FTF_1_G_uc

organism: Sufflamen chrysopterum

value: unconverted