title: miRNA sequencing of Rongchang pig VM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
VM-1

data_processing:
High-quality reads were then mapped to the corresponding reference genome with stringent criteria (0 mismatch in the whole length) using Bowtie.
Mappable reads were submitted to miRDeep (version 2.0.0.7) to detect miRNAs with default parameters, while annotated mature miRNA sequences of pig and all other mammalian and avian species in miRbase11 (release 22) were selected as reference.
Read counts were normalized by the total count of mappable reads of each sample, also known as RPM or TPM, for unbiased comparisons among samples.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: miRNA expression level (TPM) text file

organism: Sus scrofa

source_name: Vastus medialis

extract_protocol:
All libraries were conducted following TruSeq Small RNA Library Prep Kit protocol.
All libraries were sequenced on Hiseq 2500 (Illumina) or BGISEQ-500 (BGI) platform to produce average ~13.4 million 50-bp single-end raw reads and ~11.91 million high-quality reads (after removing low-quality reads, repeated sequences and adaptor sequences) for each library.

value: Rongchang

value: Vastus medialis

tag: developmental stage

value: adult


title: miRNA sequencing of Rongchang pig VM-3

status: Public on Apr 20 2021

type: SRA

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

description:
pig_miRNA.all_exp_tpm_gene.txt
VM-3

library_source: transcriptomic

molecule: total RNA

tag: breed

tag: tissue

tag: age

tag: Sex

value: female


title: E_hep_9_20

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

data_processing:
Sequencing reads were aligned to the Homo sapiens reference genome (hg38) with TopHat (v2.1.0).
HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene.
Gene expression levels were evaluated as transcripts per million (TPM).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: SmartSeq2.ReadCount.txt: Tab-delimited text file includes read count values for each sample.
Supplementary_files_format_and_content: SmartSeq2.TPM.txt: Tab-delimited text file includes TPM values for each sample.

organism: Homo sapiens

source_name: EnSC

growth_protocol: Human endoderm stem cells were generated from hPSCs and maintained in serum-free conditions as described previously (Cheng et al., 2012). For the hepatocyte differentiation, the EnSCs were dissociated into a single-cell suspension with 0.25% trypsin-EDTA, and then the cells were suspended in a 500 mL spinner flask at a density of 1×10e6 cells per milliliter in 300 mL hepatic specification medium, mixed with Matrigel at the final concentration of 4%, that contained ascorbic acid (Wako), MTG (Sigma), bFGF (10 ng/ml), TGF-α (20 ng/ml), EGF (10 ng/ml), VEGF (10 ng/ml), BMP4 (50 ng/ml), HGF (25 ng/ml), dexamethasone (Dex) (40 ng/ml, Sigma), and 1% DMSO (Sigma) (from day 0 to day 6, Stage I). From day 6 to day 12 (Stage II), the medium was replaced with hepatoblast formation medium containing ascorbic acid, MTG, bFGF (10 ng/ml), HGF (25 ng/ml), EGF (20 ng/ml), VEGF (10 ng/ml), oncostatin M (OSM) (20 ng/ml), Dex (40 ng/ml), 1% DMSO, Compound E (0.1 μM, Millipore), A83-01 (0.5 μM, Selleck), and Vitamin K1 (6 g/ml, Sangon). Then, the medium was changed to maturation medium, which contained ascorbic acid, MTG, HGF (25 ng/ml), OSM (20 ng/ml, PeproTech), Dex (40 ng/ml), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and erlotinib HCl (EGFi) (2 μM, Stemgent) (from day 12 to day 24, Stage 3H). The above differentiation medium was SFD-based (Cheng et al., 2012). From day 24, the hepatic spheres were cultured in hepatocyte culture medium (HCM, Lonza) that consisted of ascorbic acid, MTG, 8 bromo-cAMP (1 mM, Biolog), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and EGFi (2 μM) (from day 24 to day 30, Stage 4H). The medium was changed every 2 days. The cells were maintained in a 5% CO2, 5% O2, 90% N2 environment (from day 0 to day 18), and then in a 5% CO2/ambient air environment (from day 18 to day 30). The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise. For the cholangiocyte differentiation, the hepatoblasts were generated from EnSCs using the method as aforementioned. After hepatoblast formation, the hepatic spheres were cultured in SFD-based cholangiocyte specification medium containing ascorbic acid, MTG, FGF10 (50 ng/ml), Activin A (50 ng/ml), and retinoic acid (3 μM, Sigma) (from day 12 to day 15, Stage 3C). Then, the medium was changed to maturation medium, which contained HGF (25 ng/ml), EGF (50 ng/ml), TGF-β (5 ng/ml, PeproTech), Dex (40 ng/ml), and TPPB (0.5 μM, Calbiochem) (from day 16 to day 21, Stage 4C). The basic medium used for this final stage was biliary differentiation medium (BDM) (Sampaziotis et al., 2015). The cells were cultured in a 5% CO2, 5% O2, 90% N2 environment. The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise.

extract_protocol:
Single-cell RNA-seq was performed according to the Smart-seq2 protocol as reported previously (Picelli et al., 2014). After the cells were digested into a single-cell suspension, each single-cell sample was manually selected under a microscope with a mouth pipette and transferred into lysis buffer containing 1.9 µl of 0.2% Triton X-100 (Sigma), 1 µl of 10 µM oligo (dT) primer, 1 µl of 10 mM dNTP mix (New England Biolabs), 0.1 µl of 40 U/µl RNase inhibitor (New England Biolabs) and 0.05 µl of ERCC spike-in RNA (a dilution of 1:300,000, Life Technologies). After single-cell lysis, the sample was mixed with 0.29 µl H2O, 2 µl of 5× Superscript II first-strand buffer, 2 µl of 5 M Betaine (Sigma), 0.5 µl of 100 mM DTT, 0.06 µl of 1 M MgCl2, 0.1 µl of 100 µM TSO primer, 0.25 µl of 40 U/µl RNase inhibitor and 0.5 µl of 200 U/µl SuperScript II reverse transcriptase (Invitrogen). After reverse transcription was performed, 2.25 µl H2O, 12.5 µl KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 0.25 µl of 10 µM IS PCR primer were added to the sample. Then, PCR preamplification was conducted for 18 cycles. Next, cDNA samples were purified with VAHTS DNA Clean Beads XP beads (Vazyme).
Purified cDNA (2 ng) was prepared for library construction using a TruePrep DNA Library Prep Kit (Vazyme) with a 0.4× standard reaction system, and PCR amplification was conducted for 8 cycles. Finally, the library was purified and size-selected, and fragments with a peak size of ~350 bp were analyzed with an Advanced Analytical Fragment Analyzer.

tag: cell type

value: EnSC-derived hepatocyte


title: miRNA sequencing of Rongchang pig VM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
VM-2


title: miRNA sequencing of Rongchang pig VL-2

description:
pig_miRNA.all_exp_tpm_gene.txt
VL-2

source_name: Vastus lateralis

value: Vastus lateralis


title: E_hep_9_19


title: E13_FJW161012002_C04

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: EWF-E13_FJW161012002_C04_CGGAGCC-CCTAGAG_L002

data_processing:
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 42 -l 36 -k 4.0 -q 30' for HiSeq 1500, '-L 50 -l 36 -k 4.0 -q 30' for HiSeq 2500 and '-L 75 -l 36 -k 4.0 -q 30' for NextSeq. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '-p 4 --end-to-end'. Transcript levels were quantified as Transcripts Per Kilobase Million (TPM) with Sailfish (version 0.10.0) using GENCODE vM14 annotation file.
outside of the mean minus three standard deviations of the number of mapped reads to a sailfish index (Sailfish) or the number of assigned reads to gene regions (featureCounts, function of Subread version 1.5.0); over 10% reads assigning to mitochondrial RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
for count table, after convert Ensemble transcript_id to Gene_id, each isoform expression were summarized on gene level.
Genome_build: mm10
Supplementary_files_format_and_content: txt

organism: Mus musculus

source_name: E13.5_whisker follicles cells

extract_protocol:
Single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa).
RamDA-seq sequencing libraries were prepared by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0).

tag: Stage

value: whisker follicles cells

tag: data quality

value: ok


title: E12_FJW160809004_BE02

source_name: E12.0_whisker follicles cells


title: E12_FJW160809004_BE03


title: E13_FJW161012002_C03

description: EWF-E13_FJW161012002_C03_GCGTAGT-CCTAGAG_L002


title: E_hep_9_18


title: E13_FJW161012002_C02

description: EWF-E13_FJW161012002_C02_GGAGCTA-CCTAGAG_L002


title: E12_FJW160809004_BD12


title: miRNA sequencing of Rongchang pig VI-3

description:
pig_miRNA.all_exp_tpm_gene.txt
VI-3

source_name: Vastus intermedius

value: Vastus intermedius


title: E12_FJW160809004_BD11


title: miRNA sequencing of Rongchang pig VI-2

description:
pig_miRNA.all_exp_tpm_gene.txt
VI-2


title: E_hep_9_15


title: miRNA sequencing of Rongchang pig VL-3

description:
pig_miRNA.all_exp_tpm_gene.txt
VL-3


title: E_hep_9_16


title: E_hep_9_17


title: E13_FJW161012002_C01

description: EWF-E13_FJW161012002_C01_ACTCGCT-CCTAGAG_L002


title: E13_FJW161012002_B10

description: EWF-E13_FJW161012002_B10_CGATCAG-TTCTAGC_L002


title: miRNA sequencing of Rongchang pig VI-1

description:
pig_miRNA.all_exp_tpm_gene.txt
VI-1


title: E12_FJW160809004_BD10


title: E_hep_9_14


title: E12_FJW160809004_BD09


title: miRNA sequencing of Rongchang pig Uterus-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Uterus-3

source_name: Uterus

value: Uterus


title: E13_FJW161012002_B09

description: EWF-E13_FJW161012002_B09_CCTAAGA-TTCTAGC_L002


title: miRNA sequencing of Rongchang pig VL-1

description:
pig_miRNA.all_exp_tpm_gene.txt
VL-1


title: E13_FJW161012002_B12

description: EWF-E13_FJW161012002_B12_TCGACGT-TTCTAGC_L002


title: E_hep_9_13


title: E_hep_9_12


title: E13_FJW161012002_B08

description: EWF-E13_FJW161012002_B08_ACTGAGC-TTCTAGC_L002


title: E12_FJW160809004_BD08


title: miRNA sequencing of Rongchang pig Uterus-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Uterus-2


title: Endoderm_Stem_Cell_1_01

value: Endoderm stem cell (EnSC)


title: miRNA sequencing of Rongchang pig Uterus-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Uterus-1


title: Endoderm_Stem_Cell_1_02


title: E12_FJW160809004_BD07


title: E12_FJW160809004_BE01


title: E13_FJW161012002_B07

description: EWF-E13_FJW161012002_B07_TAGCGCT-TTCTAGC_L002


title: miRNA sequencing of Rongchang pig ULB-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ULB-3

source_name: Upper layer of backfat

value: Upper layer of backfat


title: miRNA sequencing of Rongchang pig ULB-2

description:
pig_miRNA.all_exp_tpm_gene.txt
ULB-2


title: E12_FJW160809004_BD06


title: E_hep_9_10


title: E13_FJW161012002_B06

description: EWF-E13_FJW161012002_B06_ATGCGCA-TTCTAGC_L002


title: E_hep_9_11


title: E13_FJW161012002_C06

description: EWF-E13_FJW161012002_C06_ATGCGCA-CCTAGAG_L002


title: E12_FJW160809004_BD05


title: chimeric mouse with rat hepatocytes, 0 ppm (control) for 7 days, biological rep3

type: RNA

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co., Ltd.

description: gene expression data from liver of chimeric mouse with rat hepatocytes fed diets containing 0 ppm (control) for 7 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, mixtures were hybridized to SurePrint G3 Rat Gene Expression 8x60K Microarrays, SurePrint G3 Mouse GE 8x60K Microarrays or SurePrint G3 Human GE v2 8x60K Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent) using one color scan setting for 8x60K array slides. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The processed signal intensities were log2-transformed and normalized to the 75th percentile using GeneSpring software (version 14.9.1) (Agilent).

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop 2000/2000c Spectrophotometer.

growth_protocol: The animals were housed in a barrier maintained animal room. The environmental conditions in the animal room were set to maintain a temperature range of 22 - 26°C and a relative humidity range of 40 - 70%, and a 12 hour light (8:00 - 20:00)/ 12 hour dark (20:00 - 8:00) illumination cycle. A commercially available pulverized diet and filtered tap water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (Life Technologies Corporation, Carlsbad, CA) at -20°C. Total RNA was prepared using Isogen solution (Nippon Gene) and RNeasy Mini Kits (Qiagen) following the manufacturer's instructions. Total RNA was quantified using a NanoDrop 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male chimeric mice with rat hepatocytes, Crl:CD(SD) rats and CAR KO rats (4-7 animals/dose) were fed diets containing 0 (control) or 1000 ppm PB for 7 days.

tag: gender

value: male

value: liver


title: E13_FJW161012002_B05

description: EWF-E13_FJW161012002_B05_TACGCTG-TTCTAGC_L002


title: miRNA sequencing of Rongchang pig ULB-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ULB-1


title: miRNA sequencing of Rongchang pig TRC-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TRC-2

source_name: Trapezius cervicis

value: Trapezius cervicis


title: E13_FJW161012002_B03

description: EWF-E13_FJW161012002_B03_GCGTAGT-TTCTAGC_L002


title: E12_FJW160809004_BD04


title: E13_FJW161012002_B04

description: EWF-E13_FJW161012002_B04_CGGAGCC-TTCTAGC_L002


title: E_hep_9_08


title: E12_FJW160809004_BD03


title: E_hep_9_09


title: E12_FJW160809004_BD02


title: E_hep_9_07


title: miRNA sequencing of Rongchang pig TRC-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TRC-1


title: E13_FJW161012002_B02

description: EWF-E13_FJW161012002_B02_GGAGCTA-TTCTAGC_L002


title: E12_FJW160809004_BD01


title: E_hep_9_06


title: miRNA sequencing of Rongchang pig TM-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TM-3

source_name: Teres major

value: Teres major


title: E13_FJW161012002_B01

description: EWF-E13_FJW161012002_B01_ACTCGCT-TTCTAGC_L002


title: miRNA sequencing of Rongchang pig TM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TM-2


title: E12_FJW160809004_BC12


title: E_hep_9_04


title: E13_FJW161012002_A10

description: EWF-E13_FJW161012002_A10_CGATCAG-TCGACTA_L002


title: E13_FJW161012002_A11

description: EWF-E13_FJW161012002_A11_TGCAGCT-TCGACTA_L002

value: low


title: miRNA sequencing of Rongchang pig TM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TM-1

value: Rongchang


title: E12_FJW160809004_BC11


title: E12_FJW160809004_BC10


title: E_hep_9_03


title: E_hep_9_02


title: E13_FJW161012002_A09

description: EWF-E13_FJW161012002_A09_CCTAAGA-TCGACTA_L002


title: miRNA sequencing of Rongchang pig TIC-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TIC-2

source_name: Tibialis cranialis

value: Tibialis cranialis


title: E_hep_8_24


title: E13_FJW161012002_A07

description: EWF-E13_FJW161012002_A07_TAGCGCT-TCGACTA_L002


title: E12_FJW160809004_BC08


title: miRNA sequencing of Rongchang pig TIC-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TIC-3

value: adult


title: E12_FJW160809004_BC07


title: E_hep_8_23


title: E13_FJW161012002_A06

description: EWF-E13_FJW161012002_A06_ATGCGCA-TCGACTA_L002


title: E12_FJW160809004_BC06


title: miRNA sequencing of Rongchang pig TFL-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TFL-2

source_name: Tensor fasciae latae

value: Tensor fasciae latae

value: female


title: E13_FJW161012002_A05

description: EWF-E13_FJW161012002_A05_TACGCTG-TCGACTA_L002


title: E_hep_9_01

value: EnSC-derived hepatocyte


title: E_hep_9_05


title: E_hep_8_22


title: miRNA sequencing of Rongchang pig TFL-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TFL-3


title: miRNA sequencing of Rongchang pig TFL-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TFL-1


title: E12_FJW160809004_BC05

value: whisker follicles cells


title: E13_FJW161012002_D06

description: EWF-E13_FJW161012002_D06_ATGCGCA-GCGTAAG_L002

value: ok


title: E13_FJW161012002_A04

description: EWF-E13_FJW161012002_A04_CGGAGCC-TCGACTA_L002


title: E_hep_8_21


title: miRNA sequencing of Rongchang pig Testis-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Testis-3

source_name: Testis

value: Testis


title: miRNA sequencing of Rongchang pig Testis-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Testis-2


title: E13_FJW161012002_A03

description: EWF-E13_FJW161012002_A03_GCGTAGT-TCGACTA_L002


title: E12_FJW160809004_BC09


title: E13_FJW161012002_A08

description: EWF-E13_FJW161012002_A08_ACTGAGC-TCGACTA_L002


title: E_hep_8_20


title: miRNA sequencing of Rongchang pig TIC-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TIC-1


title: E12_FJW160809004_BC03


title: E_hep_8_19


title: E13_FJW161012002_A02

description: EWF-E13_FJW161012002_A02_GGAGCTA-TCGACTA_L002


title: miRNA sequencing of Rongchang pig Testis-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Testis-1


title: E_hep_8_18


title: E12_FJW160809004_BC02


title: E13_FJW161012002_A01

description: EWF-E13_FJW161012002_A01_ACTCGCT-TCGACTA_L002


title: miRNA sequencing of Rongchang pig TB-M-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-M-3

source_name: Triceps brachii caput mediale

value: Triceps brachii caput mediale


title: E12_FJW160809004_BC01


title: E13_FJW150126001_H12

description: mEWF-E13_FJW150126001_H12_TCGACGT-TTATGCG_L007

source_name: E13.0_whisker follicles cells


title: E12_FJW160809004_BB12


title: E_hep_8_17


title: miRNA sequencing of Rongchang pig TB-M-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-M-2


title: E_hep_8_16


title: E13_FJW150126001_H11

description: mEWF-E13_FJW150126001_H11_TGCAGCT-TTATGCG_L007


title: E12_FJW160809004_BC04


title: miRNA sequencing of Rongchang pig TB-LO-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-LO-3

source_name: Triceps brachii caput longum

value: Triceps brachii caput longum


title: E13_FJW150126001_H10

description: mEWF-E13_FJW150126001_H10_CGATCAG-TTATGCG_L007


title: miRNA sequencing of Rongchang pig TB-M-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-M-1


title: E_hep_8_15


title: E12_FJW160809004_BB10


title: E13_FJW150126001_H09

description: mEWF-E13_FJW150126001_H09_CCTAAGA-TTATGCG_L007


title: E_hep_8_13


title: E12_FJW160809004_BB09


title: E13_FJW150126001_H08

description: mEWF-E13_FJW150126001_H08_ACTGAGC-TTATGCG_L007


title: miRNA sequencing of Rongchang pig TB-LO-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-LO-1


title: E13_FJW150126001_H07

description: mEWF-E13_FJW150126001_H07_TAGCGCT-TTATGCG_L007


title: miRNA sequencing of Rongchang pig TB-LA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-LA-2

source_name: Triceps brachii caput laterale

value: Triceps brachii caput laterale


title: miRNA sequencing of Rongchang pig TB-LO-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-LO-2


title: miRNA sequencing of Rongchang pig TB-LA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TB-LA-1


title: E12_FJW160809004_BB06


title: E_hep_8_11


title: E_hep_8_14


title: E13_FJW150126001_H05

description: mEWF-E13_FJW150126001_H05_TACGCTG-TTATGCG_L007


title: E12_FJW160809004_BB08


title: E_hep_8_10


title: E12_FJW160809004_BB05


title: E13_FJW150126001_H04

description: mEWF-E13_FJW150126001_H04_CGGAGCC-TTATGCG_L007


title: E_hep_8_09


title: E12_FJW160809004_BB11


title: miRNA sequencing of Rongchang pig TA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
TA-2

source_name: Transversus abdominis

value: Transversus abdominis


title: E12_FJW160809004_BB04


title: miRNA sequencing of Rongchang pig TA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
TA-3


title: E13_FJW150126001_H03

description: mEWF-E13_FJW150126001_H03_GCGTAGT-TTATGCG_L007


title: E_hep_8_08

source_name: EnSC


title: miRNA sequencing of Rongchang pig TA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
TA-1


title: E_hep_8_07


title: E12_FJW160809004_BB07


title: miRNA sequencing of Rongchang pig SUB-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SUB-3

source_name: Subscapularis

value: Subscapularis


title: E12_FJW160809004_BB02


title: E_hep_8_12


title: E13_FJW150126001_H02

description: mEWF-E13_FJW150126001_H02_GGAGCTA-TTATGCG_L007


title: E13_FJW150126001_H01

description: mEWF-E13_FJW150126001_H01_ACTCGCT-TTATGCG_L007


title: E12_FJW160809004_BB01


title: E13_FJW150126001_H06

description: mEWF-E13_FJW150126001_H06_ATGCGCA-TTATGCG_L007


title: E13_FJW150126001_G11

description: mEWF-E13_FJW150126001_G11_TGCAGCT-GAGCCTT_L007


title: E13_FJW150126001_G12

description: mEWF-E13_FJW150126001_G12_TCGACGT-GAGCCTT_L007


title: miRNA sequencing of Rongchang pig SUB-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SUB-1


title: miRNA sequencing of Rongchang pig SUB-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SUB-2


title: E12_FJW160809004_BA11


title: E_hep_8_04


title: miRNA sequencing of Rongchang pig Stomach-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Stomach-1

source_name: Stomach

value: Stomach


title: E12_FJW160809004_BA10

source_name: E12.0_whisker follicles cells


title: miRNA sequencing of Rongchang pig ST-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ST-3

source_name: Semitendinosus

value: Semitendinosus


title: E12_FJW160809004_BA09


title: E13_FJW150126001_G10

description: mEWF-E13_FJW150126001_G10_CGATCAG-GAGCCTT_L007


title: E12_FJW160809004_BB03


title: E_hep_8_02


title: miRNA sequencing of Rongchang pig ST-2

description:
pig_miRNA.all_exp_tpm_gene.txt
ST-2


title: E_hep_8_06


title: E12_FJW160809004_BA08


title: E_hep_8_01


title: E13_FJW150126001_G08

description: mEWF-E13_FJW150126001_G08_ACTGAGC-GAGCCTT_L007


title: miRNA sequencing of Rongchang pig ST-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ST-1


title: E_hep_8_05


title: E12_FJW160809004_BA07


title: E13_FJW150126001_G06

description: mEWF-E13_FJW150126001_G06_ATGCGCA-GAGCCTT_L007


title: E12_FJW160809004_BA06


title: E_hep_7_12


title: E13_FJW150126001_G07

description: mEWF-E13_FJW150126001_G07_TAGCGCT-GAGCCTT_L007


title: E_hep_7_13


title: miRNA sequencing of Rongchang pig SSP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SSP-3

source_name: Supraspinatus

value: Supraspinatus


title: miRNA sequencing of Rongchang pig SSP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SSP-2

value: Rongchang


title: miRNA sequencing of Rongchang pig SSP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SSP-1


title: E_hep_7_11


title: E12_FJW160809004_BA05


title: E_hep_8_03


title: E12_FJW160809004_BA04


title: E13_FJW150126001_G04

description: mEWF-E13_FJW150126001_G04_CGGAGCC-GAGCCTT_L007


title: E_hep_7_10


title: E13_FJW150126001_G09

description: mEWF-E13_FJW150126001_G09_CCTAAGA-GAGCCTT_L007

value: low


title: miRNA sequencing of Rongchang pig Spleen-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Spleen-3

source_name: Spleen

value: Spleen

value: adult


title: E13_FJW150126001_G03

description: mEWF-E13_FJW150126001_G03_GCGTAGT-GAGCCTT_L007


title: miRNA sequencing of Rongchang pig Spleen-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Spleen-2

value: female


title: E12_FJW160809004_BA03


title: E12_FJW160809004_BA02


title: E_hep_7_09

value: EnSC-derived hepatocyte


title: E_hep_7_08


title: E13_FJW150126001_G01

description: mEWF-E13_FJW150126001_G01_ACTCGCT-GAGCCTT_L007

value: whisker follicles cells


title: E_hep_7_07


title: E_hep_7_06


title: E13_FJW150126001_G05

description: mEWF-E13_FJW150126001_G05_TACGCTG-GAGCCTT_L007

value: ok


title: miRNA sequencing of Rongchang pig SP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SP-3

source_name: Splenius

value: Splenius


title: E13_FJW150126001_F12

description: mEWF-E13_FJW150126001_F12_TCGACGT-AAGGCTA_L007


title: E12_FJW160809003_BH12


title: E12_FJW160809003_BH11


title: E13_FJW150126001_F11

description: mEWF-E13_FJW150126001_F11_TGCAGCT-AAGGCTA_L007


title: E_hep_7_05


title: E12_FJW160809004_BA01


title: miRNA sequencing of Rongchang pig SP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SP-1


title: E_hep_7_04


title: E12_FJW160809003_BH09


title: E12_FJW160809003_BH10


title: E13_FJW150126001_F10

description: mEWF-E13_FJW150126001_F10_CGATCAG-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig SOL-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SOL-3

source_name: Soleus

value: Soleus


title: E_hep_7_03


title: miRNA sequencing of Rongchang pig SOL-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SOL-2


title: E12_FJW160809003_BH08


title: E13_FJW150126001_F08

description: mEWF-E13_FJW150126001_F08_ACTGAGC-AAGGCTA_L007


title: E_hep_7_02


title: miRNA sequencing of Rongchang pig Spleen-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Spleen-1


title: miRNA sequencing of Rongchang pig SOL-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SOL-1


title: E12_FJW160809003_BH06


title: E13_FJW150126001_G02

description: mEWF-E13_FJW150126001_G02_GGAGCTA-GAGCCTT_L007


title: E13_FJW150126001_F07

description: mEWF-E13_FJW150126001_F07_TAGCGCT-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig SP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SP-2


title: miRNA sequencing of Rongchang pig Small Intestine-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Small Intestine-3

source_name: Small Intestine

value: Small Intestine


title: E_hep_7_01


title: E12_FJW160809003_BH05


title: E13_FJW150126001_F06

description: mEWF-E13_FJW150126001_F06_ATGCGCA-AAGGCTA_L007


title: E_hep_6_30


title: E12_FJW160809003_BH04


title: E13_FJW150126001_F05

description: mEWF-E13_FJW150126001_F05_TACGCTG-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig Small Intestine-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Small Intestine-2


title: E12_FJW160809003_BH03


title: E_hep_6_28


title: E_hep_6_29


title: E13_FJW150126001_F03

description: mEWF-E13_FJW150126001_F03_GCGTAGT-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig Small Intestine-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Small Intestine-1


title: miRNA sequencing of Rongchang pig SM-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SM-3

source_name: Semimembranosus

value: Semimembranosus


title: E13_FJW150126001_F09

description: mEWF-E13_FJW150126001_F09_CCTAAGA-AAGGCTA_L007


title: E_hep_6_27


title: E12_FJW160809003_BH02


title: E12_FJW160809003_BH01


title: E13_FJW150126001_F02

description: mEWF-E13_FJW150126001_F02_GGAGCTA-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig SM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SM-2


title: E12_FJW160809003_BG12


title: E13_FJW150126001_F01

description: mEWF-E13_FJW150126001_F01_ACTCGCT-AAGGCTA_L007


title: miRNA sequencing of Rongchang pig SM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SM-1


title: E_hep_6_25


title: E13_FJW150126001_E12

description: mEWF-E13_FJW150126001_E12_TCGACGT-CTATTAA_L007


title: miRNA sequencing of Rongchang pig SAR-3

description:
pig_miRNA.all_exp_tpm_gene.txt
SAR-3

source_name: Sartorius

value: Sartorius


title: E_hep_6_24


title: E12_FJW160809003_BG11


title: E13_FJW150126001_E11

description: mEWF-E13_FJW150126001_E11_TGCAGCT-CTATTAA_L007


title: E12_FJW160809003_BG10


title: E_hep_6_23


title: E13_FJW150126001_F04

description: mEWF-E13_FJW150126001_F04_CGGAGCC-AAGGCTA_L007


title: E13_FJW150126001_E10

description: mEWF-E13_FJW150126001_E10_CGATCAG-CTATTAA_L007


title: miRNA sequencing of Rongchang pig SAR-1

description:
pig_miRNA.all_exp_tpm_gene.txt
SAR-1


title: E12_FJW160809003_BG09


title: E_hep_6_22


title: E13_FJW150126001_E09

description: mEWF-E13_FJW150126001_E09_CCTAAGA-CTATTAA_L007


title: miRNA sequencing of Rongchang pig Right Ventricle-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Right Ventricle-3

source_name: Right Ventricle

value: Right Ventricle


title: E12_FJW160809003_BG08


title: miRNA sequencing of Rongchang pig Right Ventricle-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Right Ventricle-1


title: E_hep_6_26


title: E13_FJW150126001_E08

description: mEWF-E13_FJW150126001_E08_ACTGAGC-CTATTAA_L007

source_name: E13.0_whisker follicles cells


title: E12_FJW160809003_BG06


title: E13_FJW150126001_E07

description: mEWF-E13_FJW150126001_E07_TAGCGCT-CTATTAA_L007


title: E_hep_6_19


title: miRNA sequencing of Rongchang pig Right Atrium-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Right Atrium-3

source_name: Right Atrium

value: Right Atrium


title: E12_FJW160809003_BG05


title: miRNA sequencing of Rongchang pig SAR-2

description:
pig_miRNA.all_exp_tpm_gene.txt
SAR-2


title: E12_FJW160809003_BG04


title: E_hep_6_18


title: E13_FJW150126001_E06

description: mEWF-E13_FJW150126001_E06_ATGCGCA-CTATTAA_L007


title: E13_FJW150126001_E05

description: mEWF-E13_FJW150126001_E05_TACGCTG-CTATTAA_L007


title: E_hep_6_17


title: miRNA sequencing of Rongchang pig RHO-3

description:
pig_miRNA.all_exp_tpm_gene.txt
RHO-3

source_name: Rhomboideus

value: Rhomboideus


title: E12_FJW160809003_BG03


title: E12_FJW160809003_BG02


title: miRNA sequencing of Rongchang pig RHO-1

description:
pig_miRNA.all_exp_tpm_gene.txt
RHO-1


title: E12_FJW160809003_BG07


title: miRNA sequencing of Rongchang pig Right Ventricle-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Right Ventricle-2


title: E_hep_6_15


title: E_hep_6_21


title: E_hep_6_16


title: E12_FJW160809003_BG01


title: E13_FJW150126001_E03

description: mEWF-E13_FJW150126001_E03_GCGTAGT-CTATTAA_L007


title: E_hep_6_20


title: miRNA sequencing of Rongchang pig RF-3

description:
pig_miRNA.all_exp_tpm_gene.txt
RF-3

source_name: Rectus femoris

value: Rectus femoris


title: E_hep_6_14

source_name: EnSC


title: E12_FJW160809003_BF12


title: E13_FJW150126001_E02

description: mEWF-E13_FJW150126001_E02_GGAGCTA-CTATTAA_L007


title: miRNA sequencing of Rongchang pig RF-2

description:
pig_miRNA.all_exp_tpm_gene.txt
RF-2

value: Rongchang


title: miRNA sequencing of Rongchang pig Right Atrium-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Right Atrium-1


title: E_hep_6_13


title: E13_FJW150126001_E01

description: mEWF-E13_FJW150126001_E01_ACTCGCT-CTATTAA_L007


title: miRNA sequencing of Rongchang pig RF-1

description:
pig_miRNA.all_exp_tpm_gene.txt
RF-1


title: E_hep_6_12


title: E12_FJW160809003_BF11


title: E13_FJW150126001_D12

description: mEWF-E13_FJW150126001_D12_TCGACGT-GCGTAAG_L007

value: low


title: E13_FJW150126001_D11

description: mEWF-E13_FJW150126001_D11_TGCAGCT-GCGTAAG_L007


title: E13_FJW150126001_E04

description: mEWF-E13_FJW150126001_E04_CGGAGCC-CTATTAA_L007


title: E12_FJW160809003_BF10


title: miRNA sequencing of Rongchang pig Retina-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Retina-1

source_name: Retina

value: Retina


title: E_hep_6_11


title: miRNA sequencing of Rongchang pig RAD-3

description:
pig_miRNA.all_exp_tpm_gene.txt
RAD-3

source_name: Retroperitoneal adipose

value: Retroperitoneal adipose

value: adult


title: E13_FJW150126001_D10

description: mEWF-E13_FJW150126001_D10_CGATCAG-GCGTAAG_L007


title: E_hep_6_10

value: EnSC-derived hepatocyte


title: miRNA sequencing of Rongchang pig RAD-2

description:
pig_miRNA.all_exp_tpm_gene.txt
RAD-2

value: female


title: E13_FJW150126001_D09

description: mEWF-E13_FJW150126001_D09_CCTAAGA-GCGTAAG_L007

value: whisker follicles cells

value: ok


title: E_hep_6_08


title: E12_FJW160809003_BF08

source_name: E12.0_whisker follicles cells


title: E_hep_6_09


title: E12_FJW160809003_BF07


title: E13_FJW150126001_D08

description: mEWF-E13_FJW150126001_D08_ACTGAGC-GCGTAAG_L007


title: E_hep_6_07


title: miRNA sequencing of Rongchang pig RA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
RA-3

source_name: Rectus abdominis

value: Rectus abdominis


title: miRNA sequencing of Rongchang pig RA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
RA-2


title: miRNA sequencing of Rongchang pig PS-2

description:
pig_miRNA.all_exp_tpm_gene.txt
PS-2

source_name: Pectoralis superficialis

value: Pectoralis superficialis


title: E_hep_6_06


title: E12_FJW160809003_BF05


title: E13_FJW150126001_D05

description: mEWF-E13_FJW150126001_D05_TACGCTG-GCGTAAG_L007


title: E13_FJW150126001_D04

description: mEWF-E13_FJW150126001_D04_CGGAGCC-GCGTAAG_L007


title: E12_FJW160809003_BF06


title: E_hep_6_05


title: E12_FJW160809003_BF04


title: miRNA sequencing of Rongchang pig PS-1

description:
pig_miRNA.all_exp_tpm_gene.txt
PS-1


title: E12_FJW160809003_BF03


title: E_hep_6_04


title: miRNA sequencing of Rongchang pig PP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
PP-3

source_name: Pectoralis profundus

value: Pectoralis profundus


title: E13_FJW150126001_D03

description: mEWF-E13_FJW150126001_D03_GCGTAGT-GCGTAAG_L007


title: E12_FJW160809003_BF09


title: E12_FJW160809003_BF02


title: E13_FJW150126001_D02

description: mEWF-E13_FJW150126001_D02_GGAGCTA-GCGTAAG_L007


title: E_hep_6_03


title: miRNA sequencing of Rongchang pig PP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
PP-2


title: E13_FJW150126001_D07

description: mEWF-E13_FJW150126001_D07_TAGCGCT-GCGTAAG_L007


title: E12_FJW160809003_BF01


title: E13_FJW150126001_D01

description: mEWF-E13_FJW150126001_D01_ACTCGCT-GCGTAAG_L007


title: E_hep_6_02


title: E12_FJW160809003_BE12


title: E_hep_6_01


title: E13_FJW150126001_C12

description: mEWF-E13_FJW150126001_C12_TCGACGT-CCTAGAG_L007


title: miRNA sequencing of Rongchang pig PP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
PP-1


title: miRNA sequencing of Rongchang pig PM-3

description:
pig_miRNA.all_exp_tpm_gene.txt
PM-3

source_name: Psoas major

value: Psoas major


title: E13_FJW150126001_C11

description: mEWF-E13_FJW150126001_C11_TGCAGCT-CCTAGAG_L007


title: E_hep_5_24


title: miRNA sequencing of Rongchang pig RA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
RA-1


title: miRNA sequencing of Rongchang pig PM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
PM-2


title: E12_FJW160809003_BE11


title: E13_FJW150126001_C10

description: mEWF-E13_FJW150126001_C10_CGATCAG-CCTAGAG_L007


title: E12_FJW160809003_BE10


title: E12_FJW160809003_BE09


title: miRNA sequencing of Rongchang pig PM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
PM-1


title: E_hep_5_22


title: E13_FJW150126001_C09

description: mEWF-E13_FJW150126001_C09_CCTAAGA-CCTAGAG_L007


title: E_hep_5_23


title: E12_FJW160809003_BE08


title: miRNA sequencing of Rongchang pig PK15

description:
pig_miRNA.all_exp_tpm_gene.txt
PK15

source_name: Iliac endothelial cells

value: Iliac endothelial cells


title: E13_FJW150126001_C08

description: mEWF-E13_FJW150126001_C08_ACTGAGC-CCTAGAG_L007


title: miRNA sequencing of Rongchang pig PEIC

description:
pig_miRNA.all_exp_tpm_gene.txt
PEIC

source_name: Kidney epithelial cells

value: Kidney epithelial cells


title: E12_FJW160809003_BE07


title: E_hep_5_21


title: E13_FJW150126001_C07

description: mEWF-E13_FJW150126001_C07_TAGCGCT-CCTAGAG_L007


title: E_hep_5_20


title: miRNA sequencing of Rongchang pig Ovary-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Ovary-3

source_name: Ovary

value: Ovary


title: E12_FJW160809003_BE06


title: E13_FJW150126001_C06

description: mEWF-E13_FJW150126001_C06_ATGCGCA-CCTAGAG_L007


title: miRNA sequencing of Rongchang pig Ovary-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Ovary-1


title: E12_FJW160809003_BE05


title: E_hep_5_18


title: E_hep_5_19


title: E12_FJW160809003_BE04


title: E13_FJW150126001_C04

description: mEWF-E13_FJW150126001_C04_CGGAGCC-CCTAGAG_L007


title: miRNA sequencing of Rongchang pig OEA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
OEA-3

source_name: Obiliquus extensor abdominis

value: Obiliquus extensor abdominis


title: E13_FJW150126001_C05

description: mEWF-E13_FJW150126001_C05_TACGCTG-CCTAGAG_L007


title: E12_FJW160809003_BE03


title: miRNA sequencing of Rongchang pig OEA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
OEA-2

value: Rongchang


title: E_hep_5_17


title: E13_FJW150126001_C03

description: mEWF-E13_FJW150126001_C03_GCGTAGT-CCTAGAG_L007


title: E12_FJW160809003_BE02


title: miRNA sequencing of Rongchang pig OEA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
OEA-1


title: miRNA sequencing of Rongchang pig MAS-3

description:
pig_miRNA.all_exp_tpm_gene.txt
MAS-3

source_name: Masseter

value: Masseter


title: E_hep_5_15


title: E_hep_5_16


title: E12_FJW160809003_BE01


title: E13_FJW150126001_C02

description: mEWF-E13_FJW150126001_C02_GGAGCTA-CCTAGAG_L007

source_name: E13.0_whisker follicles cells


title: E_hep_5_14


title: E12_FJW160809003_BD12


title: E13_FJW150126001_B12

description: mEWF-E13_FJW150126001_B12_TCGACGT-TTCTAGC_L007


title: E_hep_5_13


title: miRNA sequencing of Rongchang pig MAD-3

description:
pig_miRNA.all_exp_tpm_gene.txt
MAD-3

source_name: Mesenteric adipose

value: Mesenteric adipose


title: E12_FJW160809003_BD11


title: miRNA sequencing of Rongchang pig MAS-1

description:
pig_miRNA.all_exp_tpm_gene.txt
MAS-1


title: E13_FJW150126001_B11

description: mEWF-E13_FJW150126001_B11_TGCAGCT-TTCTAGC_L007


title: miRNA sequencing of Rongchang pig MAD-1

description:
pig_miRNA.all_exp_tpm_gene.txt
MAD-1


title: E_hep_5_12


title: E13_FJW150126001_B10

description: mEWF-E13_FJW150126001_B10_CGATCAG-TTCTAGC_L007


title: E_hep_5_11


title: miRNA sequencing of Rongchang pig Lung-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Lung-3

source_name: Lung

value: Lung


title: E12_FJW160809003_BD09


title: E13_FJW150126001_B09

description: mEWF-E13_FJW150126001_B09_CCTAAGA-TTCTAGC_L007


title: miRNA sequencing of Rongchang pig Lung-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Lung-2

value: adult


title: E12_FJW160809003_BD08


title: E13_FJW150126001_B08

description: mEWF-E13_FJW150126001_B08_ACTGAGC-TTCTAGC_L007


title: E_hep_5_10

value: EnSC-derived hepatocyte


title: E13_FJW150126001_C01

description: mEWF-E13_FJW150126001_C01_ACTCGCT-CCTAGAG_L007


title: E12_FJW160809003_BD06


title: E13_FJW150126001_B07

description: mEWF-E13_FJW150126001_B07_TAGCGCT-TTCTAGC_L007


title: E_hep_5_08


title: E12_FJW160809003_BD05


title: miRNA sequencing of Rongchang pig Liver-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Liver-2

source_name: Liver

value: Liver

value: female


title: miRNA sequencing of Rongchang pig Lung-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Lung-1


title: miRNA sequencing of Rongchang pig Liver-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Liver-3


title: E_hep_5_06

source_name: EnSC


title: E13_FJW150126001_B05

description: mEWF-E13_FJW150126001_B05_TACGCTG-TTCTAGC_L007

value: whisker follicles cells

value: ok


title: E12_FJW160809003_BD04


title: E12_FJW160809003_BD10


title: E12_FJW160809003_BD03


title: miRNA sequencing of Rongchang pig Liver-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Liver-1


title: E12_FJW160809003_BD02


title: E_hep_5_05


title: E13_FJW150126001_B06

description: mEWF-E13_FJW150126001_B06_ATGCGCA-TTCTAGC_L007


title: E13_FJW150126001_B02

description: mEWF-E13_FJW150126001_B02_GGAGCTA-TTCTAGC_L007


title: miRNA sequencing of Rongchang pig LIN-3

description:
pig_miRNA.all_exp_tpm_gene.txt
LIN-3

source_name: Lingualis

value: Lingualis


title: E_hep_5_04


title: E_hep_5_09


title: miRNA sequencing of Rongchang pig LIN-1

description:
pig_miRNA.all_exp_tpm_gene.txt
LIN-1


title: E12_FJW160809003_BD01


title: E13_FJW150126001_A11

description: mEWF-E13_FJW150126001_A11_TGCAGCT-TCGACTA_L007


title: E13_FJW150126001_B01

description: mEWF-E13_FJW150126001_B01_ACTCGCT-TTCTAGC_L007


title: E_hep_5_02


title: E_hep_5_03


title: E_hep_5_07


title: miRNA sequencing of Rongchang pig Left Ventricle-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Left Ventricle-3

source_name: Left Ventricle

value: Left Ventricle


title: E12_FJW160809003_BC12

source_name: E12.0_whisker follicles cells


title: miRNA sequencing of Rongchang pig Left Ventricle-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Left Ventricle-2


title: E12_FJW160809003_BC11


title: E12_FJW160809003_BC10


title: E13_FJW150126001_A10

description: mEWF-E13_FJW150126001_A10_CGATCAG-TCGACTA_L007


title: E_hep_5_01


title: E13_FJW150126001_B03

description: mEWF-E13_FJW150126001_B03_GCGTAGT-TTCTAGC_L007


title: E_hep_4_08


title: miRNA sequencing of Rongchang pig Left Atrium-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Left Atrium-3

source_name: Left Atrium

value: Left Atrium


title: E13_FJW150126001_A09

description: mEWF-E13_FJW150126001_A09_CCTAAGA-TCGACTA_L007


title: E12_FJW160809003_BC09


title: E13_FJW150126001_A08

description: mEWF-E13_FJW150126001_A08_ACTGAGC-TCGACTA_L007


title: miRNA sequencing of Rongchang pig Left Atrium-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Left Atrium-1


title: E12_FJW160809003_BC08


title: E13_FJW150126001_A07

description: mEWF-E13_FJW150126001_A07_TAGCGCT-TCGACTA_L007


title: E_hep_4_07


title: E_hep_4_05


title: miRNA sequencing of Rongchang pig LDM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
LDM-1

source_name: Longissimus dorsi muscle

value: Longissimus dorsi muscle


title: E13_FJW150126001_A05

description: mEWF-E13_FJW150126001_A05_TACGCTG-TCGACTA_L007


title: E13_FJW150126001_A06

description: mEWF-E13_FJW150126001_A06_ATGCGCA-TCGACTA_L007


title: E12_FJW160809003_BC06


title: miRNA sequencing of Rongchang pig LD-2

description:
pig_miRNA.all_exp_tpm_gene.txt
LD-2

source_name: Latissimus dorsi

value: Latissimus dorsi


title: E_hep_4_03


title: E_hep_4_02


title: E13_FJW150126001_A03

description: mEWF-E13_FJW150126001_A03_GCGTAGT-TCGACTA_L007


title: miRNA sequencing of Rongchang pig Kidney-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Kidney-3

source_name: Kidney

value: Kidney


title: E_hep_4_06


title: miRNA sequencing of Rongchang pig LDM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
LDM-2


title: E_hep_4_04


title: E13_FJW150126001_A04

description: mEWF-E13_FJW150126001_A04_CGGAGCC-TCGACTA_L007


title: miRNA sequencing of Rongchang pig Left Ventricle-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Left Ventricle-1


title: E13_FJW150126001_A02

description: mEWF-E13_FJW150126001_A02_GGAGCTA-TCGACTA_L007


title: miRNA sequencing of Rongchang pig LD-1

description:
pig_miRNA.all_exp_tpm_gene.txt
LD-1


title: miRNA sequencing of Rongchang pig Kidney-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Kidney-2


title: E12_FJW160809003_BC02


title: E_hep_3_16


title: E_hep_4_01


title: E12_FJW160809003_BC07


title: E12_FJW160809003_BC03


title: miRNA sequencing of Rongchang pig Kidney-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Kidney-1


title: E12_FJW160809001_H12

description: EWF-E12_FJW160809001_H12_TCGACGT-TTATGCG_L001

value: low


title: E12_FJW160809003_BC01


title: E12_FJW160809001_H11

description: EWF-E12_FJW160809001_H11_TGCAGCT-TTATGCG_L001


title: miRNA sequencing of Rongchang pig ISP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ISP-3

source_name: Infraspinatus

value: Rongchang

value: Infraspinatus


title: E12_FJW160809003_BC05


title: E12_FJW160809003_BB12


title: E_hep_3_14


title: miRNA sequencing of Rongchang pig ISP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
ISP-2


title: E12_FJW160809001_H10

description: EWF-E12_FJW160809001_H10_CGATCAG-TTATGCG_L001


title: E12_FJW160809003_BC04


title: E12_FJW160809003_BB11


title: E_hep_3_13


title: miRNA sequencing of Rongchang pig ISP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ISP-1


title: miRNA sequencing of Rongchang pig ILB-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ILB-3

source_name: Inner layer of backfat

value: Inner layer of backfat


title: E12_FJW160809003_BB09


title: E12_FJW160809001_H08

description: EWF-E12_FJW160809001_H08_ACTGAGC-TTATGCG_L001


title: E12_FJW160809001_H07

description: EWF-E12_FJW160809001_H07_TAGCGCT-TTATGCG_L001


title: E_hep_3_11


title: E12_FJW160809003_BB08


title: E12_FJW160809001_H06

description: EWF-E12_FJW160809001_H06_ATGCGCA-TTATGCG_L001


title: miRNA sequencing of Rongchang pig ILB-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ILB-1


title: E_hep_3_10


title: E_hep_3_09


title: E12_FJW160809001_H05

description: EWF-E12_FJW160809001_H05_TACGCTG-TTATGCG_L001


title: E12_FJW160809003_BB07


title: E_hep_3_15


title: miRNA sequencing of Rongchang pig GRA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
GRA-3

source_name: Gracillis

value: Gracillis


title: E12_FJW160809003_BB06


title: miRNA sequencing of Rongchang pig GRA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
GRA-2

value: adult


title: E12_FJW160809003_BB05


title: E12_FJW160809001_H09

description: EWF-E12_FJW160809001_H09_CCTAAGA-TTATGCG_L001


title: E_hep_3_07

value: EnSC-derived hepatocyte


title: E_hep_3_08


title: E12_FJW160809001_H02

description: EWF-E12_FJW160809001_H02_GGAGCTA-TTATGCG_L001


title: miRNA sequencing of Rongchang pig GRA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
GRA-1


title: E12_FJW160809003_BB04


title: E12_FJW160809003_BB10


title: E_hep_3_12


title: E_hep_3_06


title: miRNA sequencing of Rongchang pig GOM-3

description:
pig_miRNA.all_exp_tpm_gene.txt
GOM-3

source_name: Greater omentum

value: Greater omentum


title: E12_FJW160809001_H03

description: EWF-E12_FJW160809001_H03_GCGTAGT-TTATGCG_L001


title: miRNA sequencing of Rongchang pig ILB-2

description:
pig_miRNA.all_exp_tpm_gene.txt
ILB-2

value: female


title: E12_FJW160809003_BB03

value: whisker follicles cells


title: E_hep_3_05


title: E12_FJW160809001_H01

description: EWF-E12_FJW160809001_H01_ACTCGCT-TTATGCG_L001

value: ok


title: E12_FJW160809003_BB02


title: miRNA sequencing of Rongchang pig GOM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
GOM-1


title: E12_FJW160809001_H04

description: EWF-E12_FJW160809001_H04_CGGAGCC-TTATGCG_L001


title: miRNA sequencing of Rongchang pig GM-3

description:
pig_miRNA.all_exp_tpm_gene.txt
GM-3

source_name: Gluteus medius

value: Gluteus medius


title: E12_FJW160809003_BB01


title: miRNA sequencing of Rongchang pig GM-2

description:
pig_miRNA.all_exp_tpm_gene.txt
GM-2


title: E12_FJW160809003_BA11


title: E_hep_3_03


title: E_hep_3_02


title: E12_FJW160809001_G10

description: EWF-E12_FJW160809001_G10_CGATCAG-GAGCCTT_L001


title: E12_FJW160809003_BA10


title: E12_FJW160809001_G09

description: EWF-E12_FJW160809001_G09_CCTAAGA-GAGCCTT_L001


title: E12_FJW160809003_BA09


title: miRNA sequencing of Rongchang pig GM-1

description:
pig_miRNA.all_exp_tpm_gene.txt
GM-1


title: miRNA sequencing of Rongchang pig GAS-M-3

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-M-3

source_name: Gastrocnemius-mediale

value: Gastrocnemius-mediale


title: miRNA sequencing of Rongchang pig GAS-M-2

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-M-2


title: E12_FJW160809001_G08

description: EWF-E12_FJW160809001_G08_ACTGAGC-GAGCCTT_L001


title: E_hep_2_08


title: E12_FJW160809003_BA08


title: E12_FJW160809001_G07

description: EWF-E12_FJW160809001_G07_TAGCGCT-GAGCCTT_L001


title: E_hep_2_07


title: miRNA sequencing of Rongchang pig GAS-M-1

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-M-1


title: E12_FJW160809003_BA07


title: E12_FJW160809001_G06

description: EWF-E12_FJW160809001_G06_ATGCGCA-GAGCCTT_L001


title: E_hep_2_06


title: E12_FJW160809001_G12

description: EWF-E12_FJW160809001_G12_TCGACGT-GAGCCTT_L001


title: E12_FJW160809001_G11

description: EWF-E12_FJW160809001_G11_TGCAGCT-GAGCCTT_L001


title: E12_FJW160809001_G05

description: EWF-E12_FJW160809001_G05_TACGCTG-GAGCCTT_L001


title: E12_FJW160809003_BA06


title: E_hep_3_04


title: E_hep_2_05


title: miRNA sequencing of Rongchang pig GAS-L-2

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-L-2

source_name: Gastrocnemius-laterale

value: Gastrocnemius-laterale


title: E12_FJW160809001_G04

description: EWF-E12_FJW160809001_G04_CGGAGCC-GAGCCTT_L001


title: miRNA sequencing of Rongchang pig GAS-L-1

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-L-1


title: miRNA sequencing of Rongchang pig GAS-L-3

description:
pig_miRNA.all_exp_tpm_gene.txt
GAS-L-3


title: E12_FJW160809003_BA05


title: E_hep_2_04


title: E12_FJW160809001_G03

description: EWF-E12_FJW160809001_G03_GCGTAGT-GAGCCTT_L001


title: E_hep_3_01


title: miRNA sequencing of Rongchang pig FDS-H-3

description:
pig_miRNA.all_exp_tpm_gene.txt
FDS-H-3

source_name: Flexor digitorum superficialis

value: Flexor digitorum superficialis


title: E_hep_2_03


title: E12_FJW160809001_G02

description: EWF-E12_FJW160809001_G02_GGAGCTA-GAGCCTT_L001


title: E12_FJW160809003_BA02


title: miRNA sequencing of Rongchang pig FDS-H-2

description:
pig_miRNA.all_exp_tpm_gene.txt
FDS-H-2


title: E_hep_2_02


title: E12_FJW160809003_BA04


title: E_hep_2_01


title: miRNA sequencing of Rongchang pig FDS-H-1

description:
pig_miRNA.all_exp_tpm_gene.txt
FDS-H-1


title: E_hep_1_30


title: E12_FJW160809001_F11

description: EWF-E12_FJW160809001_F11_TGCAGCT-AAGGCTA_L001


title: miRNA sequencing of Rongchang pig FDS-F-2

description:
pig_miRNA.all_exp_tpm_gene.txt
FDS-F-2


title: E11_FJW180312003_CH12

source_name: E11.5_whisker follicles cells


title: E12_FJW160809001_G01

description: EWF-E12_FJW160809001_G01_ACTCGCT-GAGCCTT_L001


title: E_hep_1_29

source_name: EnSC


title: E12_FJW160809001_F10

description: EWF-E12_FJW160809001_F10_CGATCAG-AAGGCTA_L001


title: E12_FJW160809003_BA03


title: miRNA sequencing of Rongchang pig FDS-F-1

description:
pig_miRNA.all_exp_tpm_gene.txt
FDS-F-1


title: E11_FJW180312003_CH11


title: miRNA sequencing of Rongchang pig FDP-H-3

description:
pig_miRNA.all_exp_tpm_gene.txt
FDP-H-3

source_name: Flexor digitorum profundus

value: Flexor digitorum profundus


title: miRNA sequencing of Rongchang pig FDP-H-1

description:
pig_miRNA.all_exp_tpm_gene.txt
FDP-H-1


title: E11_FJW180312003_CH10


title: E12_FJW160809001_F08

description: EWF-E12_FJW160809001_F08_ACTGAGC-AAGGCTA_L001


title: E12_FJW160809001_F09

description: EWF-E12_FJW160809001_F09_CCTAAGA-AAGGCTA_L001


title: E_hep_1_27


title: E_hep_1_26


title: E_hep_1_28


title: E11_FJW180312003_CH09


title: miRNA sequencing of Rongchang pig FDP-F-3

description:
pig_miRNA.all_exp_tpm_gene.txt
FDP-F-3


title: E11_FJW180312003_CH07


title: E12_FJW160809003_BA01


title: E12_FJW160809001_F07

description: EWF-E12_FJW160809001_F07_TAGCGCT-AAGGCTA_L001


title: E12_FJW160809001_F12

description: EWF-E12_FJW160809001_F12_TCGACGT-AAGGCTA_L001


title: E12_FJW160809001_F06

description: EWF-E12_FJW160809001_F06_ATGCGCA-AAGGCTA_L001


title: E_hep_1_24


title: miRNA sequencing of Rongchang pig FDP-F-2

description:
pig_miRNA.all_exp_tpm_gene.txt
FDP-F-2


title: E12_FJW160809001_F05

description: EWF-E12_FJW160809001_F05_TACGCTG-AAGGCTA_L001


title: E11_FJW180312003_CH05


title: E_hep_1_22


title: E11_FJW180312003_CH06


title: E12_FJW160809001_F04

description: EWF-E12_FJW160809001_F04_CGGAGCC-AAGGCTA_L001


title: E12_FJW160809001_F03

description: EWF-E12_FJW160809001_F03_GCGTAGT-AAGGCTA_L001


title: E11_FJW180312003_CH04


title: miRNA sequencing of Rongchang pig EDL-H-2

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-H-2

source_name: Extensor digitorum lateralis

value: Extensor digitorum lateralis


title: miRNA sequencing of Rongchang pig EDL-H-1

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-H-1


title: E11_FJW180312003_CH08


title: E12_FJW160809001_F02

description: EWF-E12_FJW160809001_F02_GGAGCTA-AAGGCTA_L001

source_name: E12.0_whisker follicles cells


title: E_hep_1_25


title: E_hep_1_19


title: E11_FJW180312003_CH02


title: E12_FJW160809001_F01

description: EWF-E12_FJW160809001_F01_ACTCGCT-AAGGCTA_L001


title: E11_FJW180312003_CH03


title: miRNA sequencing of Rongchang pig EDL-F-3

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-F-3


title: miRNA sequencing of Rongchang pig EDL-F-2

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-F-2


title: miRNA sequencing of Rongchang pig FDP-F-1

description:
pig_miRNA.all_exp_tpm_gene.txt
FDP-F-1


title: miRNA sequencing of Rongchang pig EDL-H-3

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-H-3


title: E_hep_1_23


title: E11_FJW180312003_CH01


title: miRNA sequencing of Rongchang pig EDL-F-1

description:
pig_miRNA.all_exp_tpm_gene.txt
EDL-F-1


title: E12_FJW160809001_E12

description: EWF-E12_FJW160809001_E12_TCGACGT-CTATTAA_L001


title: E11_FJW180312003_CG12


title: E_hep_1_21


title: E12_FJW160809001_E11

description: EWF-E12_FJW160809001_E11_TGCAGCT-CTATTAA_L001

value: low


title: E12_FJW160809001_E10

description: EWF-E12_FJW160809001_E10_CGATCAG-CTATTAA_L001


title: E11_FJW180312003_CG11


title: miRNA sequencing of Rongchang pig EDC-3

description:
pig_miRNA.all_exp_tpm_gene.txt
EDC-3

source_name: Extensor digitorum communis

value: Rongchang

value: Extensor digitorum communis


title: miRNA sequencing of Rongchang pig EDC-2

description:
pig_miRNA.all_exp_tpm_gene.txt
EDC-2


title: E_hep_1_17


title: E_hep_1_20


title: E11_FJW180312003_CG10


title: E_hep_1_16


title: E12_FJW160809001_E09

description: EWF-E12_FJW160809001_E09_CCTAAGA-CTATTAA_L001


title: miRNA sequencing of Rongchang pig EDC-1

description:
pig_miRNA.all_exp_tpm_gene.txt
EDC-1


title: E11_FJW180312003_CG09


title: E_hep_1_15


title: E_hep_1_14


title: E12_FJW160809001_E07

description: EWF-E12_FJW160809001_E07_TAGCGCT-CTATTAA_L001


title: E11_FJW180312003_CG08


title: miRNA sequencing of Rongchang pig DSP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
DSP-2

source_name: Deltoideus scapular part

value: Deltoideus scapular part


title: E_hep_1_18


title: E_hep_1_13


title: miRNA sequencing of Rongchang pig DSP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
DSP-3


title: E11_FJW180312003_CG07


title: E12_FJW160809001_E06

description: EWF-E12_FJW160809001_E06_ATGCGCA-CTATTAA_L001


title: E_hep_1_12


title: miRNA sequencing of Rongchang pig DSP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
DSP-1


title: E11_FJW180312003_CG06


title: E12_FJW160809001_E05

description: EWF-E12_FJW160809001_E05_TACGCTG-CTATTAA_L001


title: E_hep_1_11


title: E11_FJW180312003_CG05


title: E12_FJW160809001_E04

description: EWF-E12_FJW160809001_E04_CGGAGCC-CTATTAA_L001


title: E_hep_1_10


title: E11_FJW180312003_CG04


title: miRNA sequencing of Rongchang pig DAP-2

description:
pig_miRNA.all_exp_tpm_gene.txt
DAP-2

source_name: Deltoideus acromial part

value: Deltoideus acromial part


title: E12_FJW160809001_E03

description: EWF-E12_FJW160809001_E03_GCGTAGT-CTATTAA_L001


title: E11_FJW180312003_CG03


title: miRNA sequencing of Rongchang pig DAP-1

description:
pig_miRNA.all_exp_tpm_gene.txt
DAP-1

value: adult


title: E_hep_1_09

value: EnSC-derived hepatocyte


title: E12_FJW160809001_E08

description: EWF-E12_FJW160809001_E08_ACTGAGC-CTATTAA_L001


title: E_hep_1_08


title: E12_FJW160809001_E02

description: EWF-E12_FJW160809001_E02_GGAGCTA-CTATTAA_L001


title: E_hep_1_07


title: E11_FJW180312003_CG02


title: miRNA sequencing of Rongchang pig Colon-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Colon-3

source_name: Colon

value: Colon


title: E12_FJW160809001_E01

description: EWF-E12_FJW160809001_E01_ACTCGCT-CTATTAA_L001


title: miRNA sequencing of Rongchang pig Colon-2

description:
pig_miRNA.all_exp_tpm_gene.txt
Colon-2

value: female


title: E12_FJW160809001_D12

description: EWF-E12_FJW160809001_D12_TCGACGT-GCGTAAG_L001

value: whisker follicles cells


title: miRNA sequencing of Rongchang pig Colon-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Colon-1


title: E11_FJW180312003_CF12

value: ok


title: E_hep_1_06


title: E_hep_1_05


title: E12_FJW160809001_D11

description: EWF-E12_FJW160809001_D11_TGCAGCT-GCGTAAG_L001


title: E11_FJW180312003_CG01


title: miRNA sequencing of Rongchang pig Cerebrum-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Cerebrum-1

source_name: Cerebrum

value: Cerebrum


title: E11_FJW180312003_CF11


title: E12_FJW160809001_D10

description: EWF-E12_FJW160809001_D10_CGATCAG-GCGTAAG_L001


title: miRNA sequencing of Rongchang pig Cerebellum-3

description:
pig_miRNA.all_exp_tpm_gene.txt
Cerebellum-3

source_name: Cerebellum

value: Cerebellum


title: E_hep_1_04


title: E11_FJW180312003_CF10


title: E12_FJW160809001_D09

description: EWF-E12_FJW160809001_D09_CCTAAGA-GCGTAAG_L001


title: E_hep_1_03


title: miRNA sequencing of Rongchang pig BRA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
BRA-3

source_name: Brachiocephalicus

value: Brachiocephalicus


title: miRNA sequencing of Rongchang pig Cerebellum-1

description:
pig_miRNA.all_exp_tpm_gene.txt
Cerebellum-1


title: E_hep_1_02


title: E11_FJW180312003_CF09


title: E12_FJW160809001_D07

description: EWF-E12_FJW160809001_D07_TAGCGCT-GCGTAAG_L001


title: miRNA sequencing of Rongchang pig DAP-3

description:
pig_miRNA.all_exp_tpm_gene.txt
DAP-3


title: E11_FJW180312003_CF08


title: E_hep_1_01


title: E12_FJW160809001_D08

description: EWF-E12_FJW160809001_D08_ACTGAGC-GCGTAAG_L001


title: E12_FJW160809001_D06

description: EWF-E12_FJW160809001_D06_ATGCGCA-GCGTAAG_L001


title: miRNA sequencing of Rongchang pig BRA-2

description:
pig_miRNA.all_exp_tpm_gene.txt
BRA-2


title: miRNA sequencing of Rongchang pig BRA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
BRA-1


title: ALB_Pos_CYP3A4_Pos_E_hep_5_12

value: Sorted ALB+; CYP3A4+ EnSC-derived hepatocyte


title: E12_FJW160809001_D05

description: EWF-E12_FJW160809001_D05_TACGCTG-GCGTAAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_13


title: miRNA sequencing of Rongchang pig BF-3

description:
pig_miRNA.all_exp_tpm_gene.txt
BF-3

source_name: Biceps femoris

value: Biceps femoris


title: E12_FJW160809001_D04

description: EWF-E12_FJW160809001_D04_CGGAGCC-GCGTAAG_L001


title: E11_FJW180312003_CF06


title: ALB_Pos_CYP3A4_Pos_E_hep_5_11


title: E11_FJW180312003_CF05


title: E11_FJW180312003_CF07


title: miRNA sequencing of Rongchang pig BF-2

description:
pig_miRNA.all_exp_tpm_gene.txt
BF-2


title: E11_FJW180312003_CF04


title: E12_FJW160809001_D03

description: EWF-E12_FJW160809001_D03_GCGTAGT-GCGTAAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_10


title: miRNA sequencing of Rongchang pig BF-1

description:
pig_miRNA.all_exp_tpm_gene.txt
BF-1


title: E11_FJW180312003_CF03


title: E12_FJW160809001_D02

description: EWF-E12_FJW160809001_D02_GGAGCTA-GCGTAAG_L001


title: miRNA sequencing of Rongchang pig BB-3

description:
pig_miRNA.all_exp_tpm_gene.txt
BB-3

source_name: Biceps brachii

value: Biceps brachii


title: E11_FJW180312003_CF02


title: E12_FJW160809001_D01

description: EWF-E12_FJW160809001_D01_ACTCGCT-GCGTAAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_09


title: miRNA sequencing of Rongchang pig BB-1

description:
pig_miRNA.all_exp_tpm_gene.txt
BB-1


title: ALB_Pos_CYP3A4_Pos_E_hep_5_08


title: E11_FJW180312003_CE12


title: E12_FJW160809001_C12

description: EWF-E12_FJW160809001_C12_TCGACGT-CCTAGAG_L001


title: miRNA sequencing of Rongchang pig ASA-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ASA-3

source_name: Abdominal subcutaneous adipose

value: Abdominal subcutaneous adipose


title: E11_FJW180312003_CE11


title: ALB_Pos_CYP3A4_Pos_E_hep_5_06


title: E12_FJW160809001_C11

description: EWF-E12_FJW160809001_C11_TGCAGCT-CCTAGAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_07


title: E11_FJW180312003_CE10


title: miRNA sequencing of Rongchang pig ADD-2

description:
pig_miRNA.all_exp_tpm_gene.txt
ADD-2

source_name: Adductores

value: Rongchang

value: Adductores


title: E12_FJW160809001_C09

description: EWF-E12_FJW160809001_C09_CCTAAGA-CCTAGAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_04


title: E11_FJW180312003_CE08


title: E12_FJW160809001_C08

description: EWF-E12_FJW160809001_C08_ACTGAGC-CCTAGAG_L001


title: miRNA sequencing of Rongchang pig ADD-3

description:
pig_miRNA.all_exp_tpm_gene.txt
ADD-3


title: E12_FJW160809001_C10

description: EWF-E12_FJW160809001_C10_CGATCAG-CCTAGAG_L001


title: E11_FJW180312003_CE09


title: ALB_Pos_CYP3A4_Pos_E_hep_5_03


title: miRNA sequencing of Rongchang pig ADD-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ADD-1


title: E12_FJW160809001_C07

description: EWF-E12_FJW160809001_C07_TAGCGCT-CCTAGAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_5_02


title: MNaseseq_eda16-dHc_mock_rep2

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

library_source: genomic

data_processing:
For RNA-seq, STAR was used to generate genome indices from GTF genome from emsembl Genome assembly TAIR10 (STAR --runThreadN 4 --runMode genomeGenerate --sjdbOverhang 75) and map reads from raw fastq files (STAR --runThreadN 4 --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate) to generate sorted BAM files.
For RNA-seq sorted BAM files, Htseq-count through LiBiNorm was used to produce tab delimited count files (count --order=pos --minaqual=10 --mode=intersection-nonempty --idattr=gene_id --type=exon --stranded=reverse)
For MNase-seq, raw reads from fastq files were trimmed with Trimmomatic (trimmomatic SE -threads 8 -phred33 LEADING:5 TRAILING:5 MINLEN:30)
For MNase-seq, trimmed reads were mapped with bowtie2 (-p 8 --very-sensitive -x) to TAIR10 genome version and sort with samtools and create a bigwig file for easy visualization
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq data as tab-delimited text files with count values for each sample. MNase-seq data as bigWig files generated using samtools from sorted bam files

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Arabidopsis seeds were sterilised with diluted bleach in 70% EtOH for 7 minutes. Seedlings were grown in ½ Murashige and Skoog medium 0.5% Phytagel, long day photoperiod (16 h light)

extract_protocol:
flg22-treated and mock-treated seedlings were harvested onto lab tissue before freezing inmediatelly in liquid nitrogen. Frozen tissue was thoroughly ground to fine powder in liquid nitrogen using a pre-chilled pestle and mortar. RNA was extracted with the NucleoSpin® RNA kit (Macherey-Nagel) starting from ~100 mg of powder, following manufacturer’s specifications. For MNase-seq experiments, 2 g of frozen powder were used for nuclei extraction with 10 mL of nuclei extraction buffer 1 (0.4 M sucrose, 10 mM Tris/HCl, pH 8.00, 10 mM MgCl2, 5 mM ß-mercapto-EtOH, 0.1 mM PMSF and Protease Inhibitor Mix P, 39103 Serva), filtering debris out through a 200 μm filter and centrifuging supernatant at 1000 g for 10 min at 4 °C. Nuclei pellet was washed in 5ml of nuclei extraction buffer 2 (25 mM Sucrose, 10 mM Tris/HCl pH 8.00, 10 mM MgCl2, 1% Triton X-100, 5 mM ß-mercapto-EtOH, 0.1 mM PMSF and Protease Inhibitor Mix P, 39103 Serva), mixed by vortex, filtered using a using a 60 μm filter and centrifuged at 1000 g for 10 min at 4 °C. Nuclei pellet was rinsed with Mnase buffer (10 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2, 0.15 mM Spermine and 0.5 mM Spermidine) and re-suspended in 250 μL of MNase buffer. DNA concentration was quantified with a NanoDrop, and samples were diluted to 400 ng/μL. 1 μl of 25 U/μL micrococcal nuclease (MNase) was added to 125 μL per sample and incubated at 37 °C for 10 minutes. To stop the reaction, 125 μL of Stop Buffer 2x (50 mM EDTA, 50 mM EGTA and 1% SDS) Tris/HCl pH 6.50 and 4 μL of proteinase K (stock 10 mg/ml) were added and incubated at 45 °C for 1h. Samples were purified with a QIAquick PCR Purification Kit (Qiagen) and eluted with 15 μL water. Eluate was loaded onto a 1% agarose gel (without loading buffer dye) and the lowest band (mono-nucleosomal DNA) was excised and gel-purified with QIAquick® Gel Extraction Kit (Qiagen).
RNA library prep was carried out with a #E7420 S/L NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (New England Biolabs) following manufacturer’s instructions. Agencourt® AMPure® XP Beads (#A63881, Beckman Coulter, Inc.) magnetic beads were used for RNA purification. Genomic libraries for MNase-seq were prepared starting from 50 ng of DNA per sample. DNA library prep was carried out with a NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645S/L, NEB) following manufacturer’s instructions. Agencourt® AMPure® XP Beads (#A63881, Beckman Coulter, Inc.) magnetic beads were used for DNA purification.

treatment_protocol: 200 2-week-old seedlings per genotype and biological replicate were pre-conditioned to liquid 1/2 MS 24 hours before replacing medium with 100 mM flg22 in 1/2 MS (liquid) or 1/2 MS (liquid) as mock treatment for 2 hours

value: 2-week-old seedlings

tag: ecotype

tag: genotype

value: SAIL_735_G06 homozygous

tag: treatment

value: mock-treated, 2 hours


title: E11_FJW180312003_CE06

source_name: E11.5_whisker follicles cells


title: ALB_Pos_CYP3A4_Pos_E_hep_5_01

source_name: EnSC


title: E12_FJW160809001_C06

description: EWF-E12_FJW160809001_C06_ATGCGCA-CCTAGAG_L001


title: E11_FJW180312003_CE05


title: MNaseseq_eda16-dHc_mock_rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_4_14


title: miRNA sequencing of Rongchang pig ASA-1

description:
pig_miRNA.all_exp_tpm_gene.txt
ASA-1

value: adult


title: E11_FJW180312003_CE04


title: MNaseseq_eda16-dHc_flg22_rep2

value: 100 nM flg22, 2 hours


title: ALB_Pos_CYP3A4_Pos_E_hep_5_05


title: E12_FJW160809001_C04

description: EWF-E12_FJW160809001_C04_CGGAGCC-CCTAGAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_4_13


title: E11_FJW180312003_CE03


title: MNaseseq_eda16-dHc_flg22_rep1


title: E11_FJW180312003_CE07


title: E12_FJW160809001_C03

description: EWF-E12_FJW160809001_C03_GCGTAGT-CCTAGAG_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_4_12


title: ALB_Pos_CYP3A4_Pos_E_hep_4_11


title: MNaseseq_eda16-OE_mock_rep1

value: SAIL_40_F09 homozygous


title: E11_FJW180312003_CE02

value: whisker follicles cells


title: E12_FJW160809001_C02

description: EWF-E12_FJW160809001_C02_GGAGCTA-CCTAGAG_L001

value: ok


title: MNaseseq_eda16-OE_mock_rep2


title: ALB_Pos_CYP3A4_Pos_E_hep_4_10


title: MNaseseq_eda16-OE_flg22_rep2


title: E12_FJW160809001_C01

description: EWF-E12_FJW160809001_C01_ACTCGCT-CCTAGAG_L001


title: E11_FJW180312003_CD12


title: E12_FJW160809001_C05

description: EWF-E12_FJW160809001_C05_TACGCTG-CCTAGAG_L001


title: E12_FJW160809001_B12

description: EWF-E12_FJW160809001_B12_TCGACGT-TTCTAGC_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_4_09


title: MNaseseq_eda16-OE_flg22_rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_4_08


title: E11_FJW180312003_CD11


title: E12_FJW160809001_B11

description: EWF-E12_FJW160809001_B11_TGCAGCT-TTCTAGC_L001


title: E12_FJW160809001_B10

description: EWF-E12_FJW160809001_B10_CGATCAG-TTCTAGC_L001


title: E11_FJW180312003_CD10


title: MNaseseq_Col-0_mock_rep2

value: wild type


title: E12_FJW160809001_B09

description: EWF-E12_FJW160809001_B09_CCTAAGA-TTCTAGC_L001


title: E11_FJW180312003_CD09


title: MNaseseq_Col-0_mock_rep1


title: E11_FJW180312003_CD08


title: E11_FJW180312003_CE01


title: E12_FJW160809001_B08

description: EWF-E12_FJW160809001_B08_ACTGAGC-TTCTAGC_L001


title: E11_FJW180312003_CD07


title: ALB_Pos_CYP3A4_Pos_E_hep_4_06


title: E12_FJW160809001_B07

description: EWF-E12_FJW160809001_B07_TAGCGCT-TTCTAGC_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_4_04


title: MNaseseq_Col-0_flg22_rep2


title: E11_FJW180312003_CD06


title: MNaseseq_Col-0_flg22_rep1


title: E12_FJW160809001_B06

description: EWF-E12_FJW160809001_B06_ATGCGCA-TTCTAGC_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_4_03


title: RNAseq_eda16-dHc_mock_rep1


title: RNAseq_eda16-dHc_mock_rep2


title: ALB_Pos_CYP3A4_Pos_E_hep_4_02


title: E11_FJW180312003_CD05


title: E11_FJW180312003_CD04


title: RNAseq_eda16-dHc_flg22_rep2


title: ALB_Pos_CYP3A4_Pos_E_hep_4_07


title: E12_FJW160809001_B05

description: EWF-E12_FJW160809001_B05_TACGCTG-TTCTAGC_L001


title: RNAseq_eda16-dHc_flg22_rep1


title: E12_FJW160809001_B03

description: EWF-E12_FJW160809001_B03_GCGTAGT-TTCTAGC_L001


title: E11_FJW180312003_CD03


title: ALB_Pos_CYP3A4_Pos_E_hep_4_01


title: ALB_Pos_CYP3A4_Pos_E_hep_4_05


title: RNAseq_eda16-OE_mock_rep2


title: E12_FJW160809001_B02

description: EWF-E12_FJW160809001_B02_GGAGCTA-TTCTAGC_L001


title: E11_FJW180312003_CD02


title: ALB_Pos_CYP3A4_Pos_E_hep_3_13


title: ALB_Pos_CYP3A4_Pos_E_hep_3_14


title: E11_FJW180312003_CD01


title: RNAseq_eda16-OE_mock_rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_3_12


title: E12_FJW160809001_A11

description: EWF-E12_FJW160809001_A11_TGCAGCT-TCGACTA_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_3_11


title: E11_FJW180312003_CC11


title: E12_FJW160809001_B01

description: EWF-E12_FJW160809001_B01_ACTCGCT-TTCTAGC_L001

value: low


title: E12_FJW160809001_A10

description: EWF-E12_FJW160809001_A10_CGATCAG-TCGACTA_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_3_10


title: RNAseq_Col-0_mock_rep2


title: E12_FJW160809001_B04

description: EWF-E12_FJW160809001_B04_CGGAGCC-TTCTAGC_L001


title: E11_FJW180312003_CC10


title: E12_FJW160809001_A09

description: EWF-E12_FJW160809001_A09_CCTAAGA-TCGACTA_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_3_09


title: RNAseq_Col-0_mock_rep1


title: E11_FJW180312003_CC09


title: E12_FJW160809001_A08

description: EWF-E12_FJW160809001_A08_ACTGAGC-TCGACTA_L001


title: RNAseq_Col-0_flg22_rep2


title: E12_FJW160809001_A07

description: EWF-E12_FJW160809001_A07_TAGCGCT-TCGACTA_L001


title: E11_FJW180312003_CC08


title: E11_FJW180312003_CC07


title: ALB_Pos_CYP3A4_Pos_E_hep_3_07


title: E12_FJW160809001_A06

description: EWF-E12_FJW160809001_A06_ATGCGCA-TCGACTA_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_3_08


title: RNAseq_eda16-OE_flg22_rep2


title: E11_FJW180312003_CC06


title: RNAseq_eda16-OE_flg22_rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_3_06


title: RNAseq_Col-0_flg22_rep1


title: E12_FJW160809001_A05

description: EWF-E12_FJW160809001_A05_TACGCTG-TCGACTA_L001


title: E11_FJW180312003_CC12


title: ALB_Pos_CYP3A4_Pos_E_hep_3_04


title: E12_FJW160809001_A04

description: EWF-E12_FJW160809001_A04_CGGAGCC-TCGACTA_L001


title: Nomal week-5 rep1

city: Chongqing

first: Zhenxing

last: Yang

state: Chongqing

address: No.183, Xinqiao main street,

department: Urology

institute: Army Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: Rat
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance (fpkm) for each sample

source_name: Bladder

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bladder tissues

tag: strain

value: Sprague-Dawley

tag: disease state

value: normal

tag: time

value: week 5


title: E12_FJW160809001_A03

description: EWF-E12_FJW160809001_A03_GCGTAGT-TCGACTA_L001


title: E11_FJW180312003_CC04


title: E11_FJW180312003_CC03


title: BOO model week-5 rep2

value: BOO


title: ALB_Pos_CYP3A4_Pos_E_hep_3_02

value: Sorted ALB+; CYP3A4+ EnSC-derived hepatocyte


title: E11_FJW180312003_CC02


title: ALB_Pos_CYP3A4_Pos_E_hep_3_03


title: Nomal week-5 rep3


title: E12_FJW160809001_A01

description: EWF-E12_FJW160809001_A01_ACTCGCT-TCGACTA_L001


title: ALB_Pos_CYP3A4_Pos_E_hep_3_05


title: ALB_Pos_CYP3A4_Pos_E_hep_2_11


title: Nomal week-4 rep2

value: week 4


title: Nomal week-5 rep2


title: E11_FJW180312003_CB12


title: BOO model week-5 rep1


title: E11_FJW180312003_CC01


title: Single_cell_RNAseq_K5SmoM2Tot rep2

city: Anderlecht

first: Alizee

last: Vercauteren Drubbel

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: All living cells have been sorted

data_processing:
Data were demuliplexed using cellranger demux with Illumina bcl2fastq to generate FASTQs for R1 and R2 paired-end as well as the sample index.
Cell Ranger version 3.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome with EYFP custom reference added.
Genome_build: mm10 + EYFP
Supplementary_files_format_and_content: H5 binary format. Feature Barcode Matrix of single cell sequencing in hierarchical data format

source_name: Esophagus

extract_protocol:
Tissues were digested and sorted in 1ml PBS 0.04% BSA. Samples were loaded on a chromium chip and processed using the Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) following manufacturer’s recommendations.
Multiplexed libraries were obtained following manufacturer’s recommendations of Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) and loaded on a Novaseq 6000 (Illumina).

value: Esophagus

tag: processed sample name


title: E11_FJW180312003_CC05


title: ALB_Pos_CYP3A4_Pos_E_hep_2_10


title: Nomal week-4 rep3


title: Single_cell_RNAseq_K5SmoM2Tot rep1

description: All living cells have been sorted

value: SmoTot


title: Nomal week-4 rep1


title: RNA-seq_K5SmoM2Sox9cKO rep4

description: Cells have been sorted on high expression of EpCam

data_processing:
Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample and genome annotations

extract_protocol:
Tissues were digested, sorted in TRK lysis buffer and extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)

tag: raw name


title: ALB_Pos_CYP3A4_Pos_E_hep_2_09


title: E11_FJW180312003_CB10


title: E12_FJW160809001_A02

description: EWF-E12_FJW160809001_A02_GGAGCTA-TCGACTA_L001

source_name: E12.0_whisker follicles cells


title: ALB_Pos_CYP3A4_Pos_E_hep_2_08


title: BOO model week-4 rep2


title: RNA-seq_K5SmoM2Sox9cKO rep2


title: RNA-seq_K5SmoM2Sox9cKO rep3


title: ALB_Pos_CYP3A4_Pos_E_hep_2_07


title: E11_FJW180312003_CB09


title: BOO model week-4 rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_3_01


title: E11_FJW180312003_CB08


title: RNA-seq_K5SmoM2Sox9cKO rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_2_06


title: ALB_Pos_CYP3A4_Pos_E_hep_2_05


title: RNA-seq_K5SmoM2 7w epLo rep4

description: Cells have been sorted on low expression of EpCam


title: E11_FJW180312003_CB11


title: RNA-seq_K5SmoM2 7w epLo rep3


title: E11_FJW180312003_CB07


title: E11_FJW180312003_CB06


title: ALB_Pos_CYP3A4_Pos_E_hep_2_04


title: E11_FJW180312003_CB05


title: ALB_Pos_CYP3A4_Pos_E_hep_2_03


title: BOO model week-4 rep3


title: RNA-seq_K5SmoM2 7w epLo rep2


title: E11_FJW180312003_CB04


title: RNA-seq_K5SmoM2 7w epLo rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_2_02


title: E11_FJW180312003_CB03


title: RNA-seq_K5SmoM2 7w epHi rep4


title: E11_FJW180312003_CB02


title: ALB_Pos_CYP3A4_Pos_E_hep_1_15


title: E11_FJW180312003_CB01


title: P25 WT naïve sample 6

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

description: SC341-2WT-P25 (2nd batch)

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq and differential gene expression analysis was carried out using R/Bioconductor DEseq2 package.
The P-values were first corrected by applying empirical estimation of the null distribution using the R fdrtool (v.1.2.15) package and then were adjusted for multiple testing with the Benjamini–Hochberg correction
Genome_build: GRCm38
Supplementary_files_format_and_content: [.txt] tab-delimited, normalized read count matrix calculated by using DESeq2.

source_name: P25 WT naïve

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: WT

tag: treatment (drug)

value: naïve


title: RNA-seq_K5SmoM2 7w epHi rep2


title: P25 WT naïve sample 5

description: SC321-13WT-P25 (2nd batch)


title: RNA-seq_K5SmoM2 7w epHi rep1


title: P25 WT naïve sample 4

description: SC28-3WT-P25 (2nd batch)


title: ALB_Pos_CYP3A4_Pos_E_hep_1_14


title: E11_FJW180312003_CA11


title: E11_FJW180312003_CA09


title: P25 KO naïve sample 6

description: SC341-1KO-P25 (2nd batch)

source_name: P25 KO naïve

value: KO


title: E11_FJW180312003_CA10

value: whisker follicles cells


title: RNA-seq_K5SmoM2 3w epLo rep4


title: ALB_Pos_CYP3A4_Pos_E_hep_1_11


title: ALB_Pos_CYP3A4_Pos_E_hep_1_12


title: ALB_Pos_CYP3A4_Pos_E_hep_1_13


title: RNA-seq_K5SmoM2 3w epLo rep3


title: P25 KO naïve sample 5

description: SC321-12KO-P25 (2nd batch)


title: ALB_Pos_CYP3A4_Pos_E_hep_2_01


title: RNA-seq_K5SmoM2 7w epHi rep3


title: E11_FJW180312003_CA07

value: ok


title: RNA-seq_K5SmoM2 3w epLo rep1


title: P14 WT naïve sample 6

description: SC312-1WT-P14 (2nd batch)

source_name: P14 WT naïve


title: RNA-seq_K5SmoM2 3w epHi rep4


title: E11_FJW180312003_CA06


title: ALB_Pos_CYP3A4_Pos_E_hep_1_08


title: ALB_Pos_CYP3A4_Pos_E_hep_1_09


title: P14 WT naïve sample 5

description: SC309-14WT-P14 (2nd batch)


title: RNA-seq_K5SmoM2 3w epHi rep3


title: E11_FJW180312003_CA08


title: ALB_Pos_CYP3A4_Pos_E_hep_1_07


title: P14 WT naïve sample 4

description: SC309-13WT-P14 (2nd batch)


title: RNA-seq_K5SmoM2 3w epLo rep2


title: P14 KO naïve sample 6

description: SC312-6KO-P14 (2nd batch)

source_name: P14 KO naïve


title: E11_FJW180312003_CA03


title: RNA-seq_K5SmoM2 3w epHi rep1


title: ALB_Pos_CYP3A4_Pos_E_hep_1_10


title: E11_FJW180312003_CA04


title: RNA-seq_K5SmoM2 3w epHi rep2


title: P25 KO naïve sample 4

description: SC28-4KO-P25 (2nd batch)


title: P14 KO naïve sample 5

description: SC309-19KO-P14 (2nd batch)


title: ALB_Pos_CYP3A4_Pos_E_hep_1_05


title: ALB_Pos_CYP3A4_Pos_E_hep_1_06


title: E11_FJW180312003_CA02


title: E11_FJW180312003_CA05


title: RNA-seq_Junction squamous rep3

description: Cells have been sorted on high expression of EpCam and negative expression of YFP

source_name: Squamous part of the junction

value: Squamous part of the junction


title: P14 KO naïve sample 4

description: SC309-17KO-P14 (2nd batch)


title: ALB_Pos_CYP3A4_Pos_E_hep_1_04


title: E11_FJW180312003_CA01


title: RNA-seq_Junction squamous rep2


title: ALB_Pos_CYP3A4_Pos_E_hep_1_03


title: RNA-seq_Junction squamous rep1


title: P25 KO naïve sample 2


title: ALB_Pos_CYP3A4_Pos_E_hep_1_02


title: ATAC-seq_Embryo rep1

description: The cells have been sorted based on YFP expression

data_processing:
ATACseq paired-end reads of 50 bp were trimmed for adaptor sequences (using Trimmomatic).
ATAC-seq paired-end reads were then aligned to the mouse GRCm38 genome (using Bowtie2)
Mitochondrial reads and reads aligned to scaffolds and undefined chromosomes were excluded from downstream analysis.
Duplicated reads were removed by Picard tools.
Read start sites were adjusted to represent the center of the transposon binding event as described in Li et al., 2009.
Peak calling was performed on each individual sample using Macs2.
TDF files were generated using igv.
bigWig files were generated using bamCoverage from deepTools in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: TDF binary files generated using igv. BigWig indexed binary file format generated using deepTools (bin size=50pb, scaling factor=1.0), files normalized for sequencing depth.

source_name: Embryonic esophagus E13

extract_protocol:
Tissues were digested, sorted in 1ml PBS 3% FBS. Nuclei were isolated to proceed to transposase reaction (Illumina). DNA was purified using the MinElute purification kit.
DNA libraries were PCR amplified (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), indexed using primers described by Buenrostro et al. (2013), and double size selected (from 150 to 1200 bp) using AmpureXP magnetic beads (Beckman) following the manufacturer's recommendations. The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) using a S2 flow cell and paired-end sequences were produced using a 200 Cycle Kit.

value: Embryonic esophagus E13

tag: sample identification


title: P25 KO naïve sample 1

tag: tissue


title: ATAC-seq_Embryo rep2


title: P25 WT naïve sample 3

tag: age


title: U_PHH_5_11

source_name: Liver

value: Uncultured adult human primary hepatocyte


title: ALB_Pos_CYP3A4_Pos_E_hep_1_01


title: U_PHH_5_10


title: P25 WT naïve sample 2


title: ATAC-seq_K5SmoM2Sox9cKO rep3

description: The cells have been sorted based on high EpCam expression


title: ATAC-seq_K5SmoM2Sox9cKO rep2


title: Thymus_gdT_Gli2R Tg Rep1

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

data_processing:
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.

source_name: Adult thymus CD3+CD27+gdTCR+

extract_protocol:
Thymi were dissected from 4 week old mice for each genotype and stained for surface markers CD3, gdTCR, CD27. The cells positive for CD3, CD27 and gdTCR were sorted and RNA was extracted from these cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thymus

tag: cell markers

tag: developmental stage

value: 4 weeks old

value: Gli2R Tg


title: Thymus_gdT_Gli2A Tg Rep2

value: Gli2A Tg


title: Thymus_gdT_Shhfl/fl FoxN1Cre+ Rep1

value: Shhfl/fl FoxN1Cre+


title: Thymus_gdT_Gli2R Tg Rep2


title: U_PHH_5_09

tag: cell type


title: P25 WT naïve sample 1


title: Cadmium_W22_Cd-0.01mM_biological-replicate_rep2

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

country: Germany

institute: Friedrich-Schiller-University

description: blanks (only one single “T” nucleotide) are used for background corrections

hyb_protocol: Hybridization was done automatically over night (16 hours) at 45°C using RT-Analyzer from febit. The biotin labeling was detected with streptavidinphycoerythrin (SAPE), in combination with Consecutive Signal Enhancement (CSE) procedure from febit.

scan_protocol: The feature recognition, using Cy3 filter set, and signal calculation were done automatically within milliseconds using the Geniom RT Analyzer.

data_processing: Background correction was performed using the intensities of blank probes which consist only of one single ”T” nucleotide. The median background intensity was subtracted from spot intensity. After converting any negative values to a low positive value (7), signal intensities were log2-transformed. The obtained data were processed using quantile normalization, and duplicate spots were averaged. By R and Bioconductor computed log2 transformed and quantil normalized signal intensity

label: biotin

organism: Schizophyllum commune

source_name: strain W22, monokaryon

label_protocol: For each array 1 µg of total RNA was labeled using the MassageAmpTM-Biotin Enhanced RNA Kit from Ambion.

growth_protocol: The S. commune strains were grown on solid medium (CYM) at 28°C. Mycelium was transferred onto a cellophane membrane onto fresh CYM plates and grown for 3 days.

extract_protocol: Total RNA was isolated from < 100 mg tissue powder using “Qiagen Rneasy plant mini kit” (Qiagen, Hilden, Germany), quality controlled with Agilent 2100 Bioanalyzer, using RNA 6000 Nano Kit, and a NanoDropTM 1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: Mycelium was harvested, frozen in liquid nitrogen and ground with mortar and pestle to a powder.

value: monokaryon

tag: strain(s)

value: 0.01 mM cadmium

tag: mating type loci


title: P25 KO naïve sample 3


title: Thymus_gdT_Shhfl/fl FoxN1Cre+ Rep2


title: Thymus_gdT_Gli2A Tg Rep1


title: Cadmium_W22_Cd-0.01mM_biological-replicate_rep1


title: Monokaryon1_12-43_technical-replication_rep1

source_name: strain 12-43, monokaryon

value: ura-


title: Monokaryon1_12-43_technical-replication_rep2


title: HSW_12-43-Haldensickerwasser(1:10)_biological-replicate_rep2

value: 1:10 diluted contaminated seepage water


title: ATAC-seq_K5SmoM2Sox9cKO rep1

value: Esophagus


title: P14 KO naïve sample 3

value: brain

value: naïve


title: Thymus_gdT_WildType Rep2

value: WildType


title: HSW_12-43-Haldensickerwasser(1:10)_biological-replicate_rep1


title: P14 KO naïve sample 2

value: KO


title: WT_AngII_3

city: Kuopio

first: Nicholas

last: Downes

address: P.O.Box 1627 (Neulaniementie 2)

department: A.I.Virtanen Institute for Molecular Sciences

country: Finland

institute: UEF

data_processing:
Image analysis and base calling were performed using RTA 2.4.11, followed by demultiplexing of indexed reads and generation of FASTQ files using bcl2fastq v2.20.0.422
Paired-end reads were trimmed and filtered using Trim Galore (v.0.4.4) with Phred quality score cutoff 30
Processed reads were aligned to the genome assembly GRCm38 (mm10) using STAR version 2.5.4b with options --outFilterMismatchNoverLmax 0.04 and --outFilterMultimapNmax 10. Aligned reads mapping to features were assigned using featureCounts (Rsubread 1.32.4) with the Gencode M16 GTF
Aligned reads mapping to features were assigned using featureCounts (Rsubread 1.32.4) with the Gencode M16 GTF
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cardiac tissue, left ventricle

extract_protocol:
hearts were flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1ug of total RNA was rRNA depleted using Illumina Ribo-Zero Plus rRNA Depletion Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: VEGFR1_TK -/-

value: AngII induced LVH


title: WT_AngII_4


title: P14 KO naïve sample 1


title: WT_AngII_2


title: U_PHH_5_08

value: Uncultured adult human primary hepatocyte


title: U_PHH_5_06


title: U_PHH_5_07


title: U_PHH_5_05


title: 18Feb16_YL06-KO3

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

country: USA

institute: University of Southern California

description: Tgfbr2 CKO rep3

data_processing:
Cutadapt 1.13
Trimmomatic 0.35
RNA-star 2.5.2b
Htseq-count 0.6.1p2
EdgeR 3.16.5
Genome_build: Gencode 23 M8, GRCm38, Ensembl 83
Supplementary_files_format_and_content: 02Mar16_Raw_Data_RPKM_annotated.xlsx: Raw Counts and RPKM values for the entire genome
Supplementary_files_format_and_content: 04Mar16_WS_DE_edgeR_filtered_annotated.xlsx: Differential expression analysis with edgeR with annotation, counts, and RPKM
Supplementary_files_format_and_content: Data_Processing_Alignment_Statistics_WS.xls: Data Processing summary

source_name: Lung

growth_protocol: Tgfbr2 flox mice were crossed with Tbx4-rtTA/TetO-Cre transgenic mice

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and purified using the RNeasy Micro Kit (QIAGEN, Cat #74004).
Illumina TruSeq v2

treatment_protocol: Doxycycline was gived in drinking water (1mg/ml) and in food from E6.5 to E15.5.

value: Lung

value: embryonic day 15.5 (E15.5)

tag: genotype/variation


title: P14 WT naïve sample 2

tag: genotype

value: WT


title: U_PHH_5_04


title: P14 WT naïve sample 3


title: 17Feb16_YL06-KO3

description: Tgfbr2 CKO rep3


title: 18Feb16_YL05-KO2

description: Tgfbr2 CKO rep2


title: VEGFR_1_TK_KO_AngII_4

value: wildtype

tag: treatment


title: P14 WT naïve sample 1

tag: strain


title: U_PHH_5_03


title: 18Feb16_YL04-KO1

description: Tgfbr2 CKO rep1


title: VEGFR_1_TK_KO_AngII_3


title: VEGFR_1_TK_KO_AngII_2


title: Thymus_gdT_WildType Rep1

value: thymus

value: 4 weeks old


title: U_PHH_5_01


title: 17Feb16_YL05-KO2

description: Tgfbr2 CKO rep2


title: U_PHH_4_24


title: WT_AngII_1


title: 17Feb16_YL04-KO1

description: Tgfbr2 CKO rep1


title: U_PHH_5_02


title: 18Feb16_YL03-WT3

description: WT rep3

value: wild type


title: U_PHH_4_23


title: 17Feb16_YL03-WT3

description: WT rep3


title: AZD_G7NM

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the mouse genome ( mm10, Genome Reference Consortium GRCm38) using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated for the murine samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes log2 RPKM values for each sample

source_name: tumour

growth_protocol: The transplantable syngeneic high-grade serous mouse model 60577 was established by injecting the 60577 murine cell line intraperitoneally in syngeneic mice. The tumours were allowed to establish for 21 days.

extract_protocol:
Total RNA was extracted from frozen murine tumors and non-diseased omenta. The samples were transferred into RNAlater and homogenized with Miltenyi GentleMACS in RLT buffer and further processed using Qiagen RNeasy Mini kit with on-column DNAse digestion.
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

treatment_protocol: The animals were treated with Carboplatin for three cycles, once weekly, and then receiced AZD7507 by oral gavage daily for 84 days straight after the end of the three cycles of carboplatin. Tumours were collected at humane endpoint.

value: high-grade serous ovarian tumor

tag: treatment in vivo

tag: tumour stage

value: endpoint


title: AZD_G72R


title: AZD_G62R


title: U_PHH_4_20


title: 17Feb16_YL02-WT2

description: WT rep2


title: 18Feb16_YL02-WT2

description: WT rep2


title: U_PHH_4_21


title: U_PHH_4_22


title: VEGFR_1_TK_KO_AngII_1


title: 18Feb16_YL01-WT1

description: WT rep1


title: Ctrl_G21R

value: Vehicle


title: U_PHH_4_19


title: RNA sequencing sheep3-Spleen biological replicate 3

description:
sheep3-Spleen
sheep_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

organism: Ovis aries

source_name: Spleen

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Small-tail Han sheep

value: Spleen

value: Adult

tag: Sex

value: female


title: Ctrl_G11L


title: RNA sequencing sheep3-Skeletal-muscle biological replicate 3

description:
sheep3-Skeletal-muscle
sheep_exp.txt

source_name: Skeletal muscle

value: Skeletal muscle


title: Col-0-1

city: DAEJEON

first: Hyo-Jun

last: Lee

state: DAEJEON

address: 125 GWAHAK-RO YUSEONG-GU

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Sequencing adapters and low quality bases were trimmed by Skewer ver 0.2.2.
High quality reads were mapped to the reference genome by STAR ver 2.5 software
To quantify the mapped reads on the reference genome, Cuffquant in Cufflinks ver 2.2.1. was used
Genome_build: TAIR10
Supplementary_files_format_and_content: An excel file containing differentially expressed genes

source_name: Whole seedlings

growth_protocol: Seedlings were grown on MS-agar plates for 7 d under long-day conditions at light intensity of 154 mmol m-2 s-1

extract_protocol:
Total RNA was extracted using Trizol
MGIEasy RNA Directional Library PrepKit was used

treatment_protocol: Seedlings were harvested at ZT3

value: Whole seedlings

value: light intensity of 154 mmol m-2 s-1

value: 7 days after germination

value: control Col-0


title: fer-4-3


title: fer-4-2


title: Col-0-2


title: fer-4-1


title: Col-0-3


title: U_PHH_4_18

value: Uncultured adult human primary hepatocyte


title: Ctrl_G4NM


title: RNA sequencing sheep3-Lung biological replicate 3

description:
sheep3-Lung
sheep_exp.txt

value: Lung


title: Single_cell_RNAseq_K5SmoM2 rep2

source_name: Esophagus

value: Esophagus

tag: processed sample name

tag: cell sorting

value: The cells have been sorted based on high EpCam expression


title: Single_cell_RNAseq_K5SmoM2 rep1

tag: tissue

value: Smo-Hi


title: NN_33

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale with the edgeR package in Bioconductor.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated files with raw gene counts and TMM-CPM-log2 normalized values respectively for each gene in each sample
Supplementary_files_format_and_content: Comma seperated file with metadata,

molecule: polyA RNA

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads

tag: group

value: NN

tag: subjectid

value: Ectocervix


title: NN_32


title: RNA sequencing sheep3-Kidney biological replicate 3

description:
sheep3-Kidney
sheep_exp.txt

source_name: Kidney

value: Kidney

tag: age


title: NN_31


title: RNA-seq_Gut rep2

source_name: Gut

value: Gut

tag: raw name

value: mixed genetic background

value: Cells have been sorted on YFP expression


title: 17Feb16_YL01-WT1

description: WT rep1

tag: developmental stage

value: embryonic day 15.5 (E15.5)

value: wild type


title: RNA sequencing sheep3-Heart biological replicate 3

description:
sheep3-Heart
sheep_exp.txt

source_name: Heart

value: Small-tail Han sheep

value: Heart

value: Adult

value: female