title: WGBS_DNMT3A+DNMT3L-ADD_Sperm_Rep2

city: Fukuoka

first: Naoki

last: Kubo

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

description: whole-genome bisulfite sequencing (PBAT)

data_processing:
The reads were mapped to mouse genome mm10 using Bismark and bismark_methylation_extractor (Krueger et al. 2011). Only CG methylation data with coverage between 5 to 500 was used.
Assembly: mm10
Supplementary files format and content: bedGraph format

source_name: Sperm

extract_protocol:
FGOs were harvested from adult ovaries (10 to 12 weeks old) by needle puncture and cumulus cells were removed by capillary washing. Sperms were released from the cauda epididymides of adult male mice and collected by swim-up method. For the 3a/3L DM sperm, viable sperms were selected by mouth pipetting
Sample with unmethylated lambda phage DNA was subjected to bisulfite treatment and library construction by the post-bisulfite adaptor tagging (PBAT) method (Miura et al., 2012).
Bisulfite-seq (PBAT method)

value: Sperm

value: Dnmt3aADA/ADA + Dnmt3LD124A/D124A


title: RNA-seq of chromatin associated RNAs with FP treatment, Rep2

status: Public on Mar 17 2024

type: SRA

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using Hisat2.
Assembly: GRCm39
Supplementary files format and content: coverage files containing read coverage at individual sites, which are seperated by comma

molecule: nuclear RNA

organism: Mus musculus

source_name: mouse embryonic fibroblasts cells

growth_protocol: MEF cells were grown in DMEM (BI) medium containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Cells were washed with chilled PBS and pelleted by centrifugation before they were subjected to cell membrane lysis buffer (0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25 μM α-amanitin, 10 U SUPERase_In) and incubated on ice for 5 min. Cell lysates were then added to 2.5 volumes of chilled sucrose cushion (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose, 25 μM α-amanitin, 20 U SUPERase_In) and the mixture was centrifuged at 4 °C with 16,000 ×g for 10 min. The supernatant was the cytoplasmic fraction, and the pellet was regarded as cell nuclei. The nuclear pellet was then washed with nuclear wash buffer (0.1% Triton X-100, 1 mM EDTA, in 1× PBS, 25 μM α-amanitin, 10 U SUPERase In, and protease inhibitor mix) twice and pelleted by centrifugation at 1150 ×g for 2 min. The supernatant was discarded, and the pellet was subjected to chilled glycerol buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT, 25 μM α-amanitin, 10 U SUPERase_In). Equal volumes of chilled nuclei lysis buffer (1% NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1 M urea, 0.2 mM EDTA, 1 mM DTT, 25 μM α-amanitin, 10 U SUPERase_In) were then added to the nuclei suspension and incubated on ice for 2 min followed by centrifugation at 4 °C at 18,500 ×g for 2 min. The pellet was subjected to chilled chromatin resuspension solution (25 µM α-amanitin, 20 units SUPERase_In, 1× protease inhibitor mix (in 1× PBS)) to obtain the insoluble chromatin-associated fraction and subjected to RNA extraction using TRIzol Reagent.
For m6A immunoprecipitation, 50 μg chrRNA samples were fragmented by RNA fragmentation buffer (100 mM Tris-HCl pH 7.0 and 100 mM ZnCl2) at 94 °C for 30 s. Flowing standard ethanol precipitation and 1/20 of the fragmented RNA was saved as the input. The remaining fragmented RNA was immunoprecipitated with anti-m6A antibody (Abcam) in IP buffer (0.1% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl) at 4 °C for 4 h. Dynabeads protein A/G (NEB) were washed, added to the mixture and incubated for 2 h at 4 °C with rotation. The m6A-containing RNA fragment was eluted twice with 6.7 mM N6-methyladenosine 5’-monophosphate sodium salt at 4 °C for 1 h and precipitated with ethanol at -80 °C overnight. RNA was dissolved in 10 μl nuclease-free water and subjected to reverse transcription for qPCR (see reverse transcription and quantitative Real Time-PCR). For chrRNA m6A-seq, cDNA library construction and sequencing were performed at LC-BIO Biotech Ltd. (Hangzhou, China). Paired-end 2 × 150 bp sequencing on an Illumina NovaSeq™ 6000 platform was also performed on libraries.

treatment_protocol: For flavopiridol treatment assays, MEF cells at around 80% confluence were replenished with fresh medium 2 hours before harvesting. Subsequently, the cells were treated with 300 nM flavopiridol for a duration of 30 min.

tag: cell line

value: mouse embryonic fibroblasts cells

tag: treatment

value: 300 nM flavopiridol , 30 min


title: RNA-seq of chromatin associated RNAs without FP treatment, Rep2

value: DMSO


title: PP_B_brain_injury_6 [RNA_S5219Nr12]

city: Essen

first: Vikramjeet

last: Singh

state: Nordrhein-Westfalen

address: Universitätsstr. 2

department: Institute for Experimental Immunology and Imaging

country: Germany

institute: University Duisburg-Essen

data_processing:
The quality of sequenced reads was determined with FastQC (version v0.11.9) 7 and Illumina adapters and low-quality reads -Phred score under 20- were trimmed with Trimmomatic (version 0.39) 8. Kallisto (version 0.48.01) 7 was used to pseudo-align reads to the GRCm38 release 102 genome assembly from ENSEMBL 9 and subsequently to quantify transcript expression as transcripts per million (TPM).  Transcripts with less than 1 TPM across all 12 samples were removed and in R (version 4.1.2) 10, a Wald Test from package Sleuth (version 0.30.0) 11 was used to analyze differential expression between the sham-operated and brain injured sample groups at the gene level, with significance set at a p-value < 0.05. Gene Ontology (GO) 12, 13. Biological Process enrichment analysis was also performed in R, with package clusterprofiler (version 4.0.5) 14, 15 and significance was defined as FDR-adjusted p-value < 0.05. In gene set enrichment analysis (GSEA), the dot size indicates the ratio of the overlap of differentially expressed genes with single GO term gene sets to the overlap of differentially expressed genes with the sum of all unique GO term genes queried.
Assembly: GRCm38 release 102
Supplementary files format and content: Delimited file containing normalized expression values per sample in TPM (Transcripts Per Kilobase Million).

molecule: total RNA

source_name: B cell

extract_protocol:
RNA was isolated from MACS-purified B cells using RNeasy Micro Kit according to the protocols provided by the supplier (Cat. 74004, Qiagen). Briefly, cells were lysed in lysis buffer on ice and centrifuged to remove cell debris. RNA was precipitated with 70% ethanol and passed through the RNA columns. After two washing steps, genomic DNA was removed using RNase-free DNase set (Cat. 9254, Qiagen). The columns containing RNA were washed with buffers and supplemented with centrifugation steps. In the end, RNA from columns was collected using RNase-free water in new Eppendorf tubes and stored at -80°C until further used for the analysis.
cDNA

tag: strain

tag: cell type

value: B cell

value: Brain injury


title: m6A-seq of chromatin associated RNAs with FP treatment, Rep1


title: RNA-seq of chromatin associated RNAs without FP treatment, Rep1


title: WT, 9gg, rep1

city: Trento

first: Fulvio

last: Chiacchiera

address: Via Sommarive  9

department: Department of Cellular, Computational and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

description:
ALB_WT_DMSO_9gg_rep1
Normalized_counts.tsv
Raw_counts.tsv

data_processing:
Pair-end raw reads were trimmed using fastp with parameters “-t 1 -A -Q -L”
Trimmed reads were aligned with STAR v2.7.3.
Duplicated reads were removed with samblaster.
We quantified gene expression using featureCounts with parameters “-s 0 -t exon -p -g gene_name”
The annotation file (gtf) for the counting was downloaded from Gencode (Release M21 – GRCm38.p6)
Assembly: mm10
Supplementary files format and content: Tab-delimited file with raw counts (samples on columns)
Supplementary files format and content: Tab-delimited file with normalized counts (samples on columns)

molecule: polyA RNA

source_name: Liver

extract_protocol:
Total RNA has been extracted using Trizol (Life tech., 15596018) coupled with RNAeasy extraction kit (Qiagen, 74106).
Libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina, 20020595) following manufacturer instructions.

tag: tissue

value: Liver

value: hepatocytes

tag: genotype

value: WT

tag: time


title: WT, 9gg, TC, rep2

description:
ALB_WT_TC_30gg_rep2
Normalized_counts.tsv
Raw_counts.tsv

value: NR1L3 agonist


title: Arid1a KO, 30gg, TC, rep1

description:
A1A_KO_TC_30gg_rep1
Normalized_counts.tsv
Raw_counts.tsv

value: Arid1a KO


title: WT, 9gg, TC, rep1

description:
ALB_WT_TC_30gg_rep1
Normalized_counts.tsv
Raw_counts.tsv


title: WT, 30gg, rep1

description:
ALB_WT_DMSO_30gg_rep1
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a KO/BcatEXON, rep1

description:
A1A_KO_EXON_TUMOR_rep1
Normalized_counts.tsv
Raw_counts.tsv

source_name: Liver tumor

value: Liver tumor

value: Arid1a KO/BcatEXON


title: PP_B_sham_6 [RNA_S5219Nr6]

value: Sham


title: Arid1a/b DKO, 9gg, rep1

description:
A1A_B_DKO_DMSO_9gg_rep1
Normalized_counts.tsv
Raw_counts.tsv

value: Arid1a/b DKO


title: WT, 9gg, rep2

description:
ALB_WT_DMSO_9gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a KO, 30gg, rep1

description:
A1A_KO_DMSO_30gg_rep1
Normalized_counts.tsv
Raw_counts.tsv


title: Hepatocytes, A1ABDKO, H3K4me1, ChIP, rep2

library_source: genomic

data_processing:
Pair-end raw reads were trimmed using fastp with parameters “-t 1 -A -Q -L”. Trimmed reads were aligned with bowtie to mm10  with parameters “--chunkmbs 1024 -m 1 --best -S --no-unal -q -I 10 -X 1000”.
The bam files from the replicates (N=2) were merged with samtools. Peak calling was performed with MACS2 in narrow mode (with parameters “--keep-dup all -m 3 30 --format BAMPE --pvalue 1e-05”).
Called peaks were further filtered with a p-value threshold of 1e-10. Peaks found on blacklisted regions (mm10-blacklist.v2) and over non-canonical chromosomes were excluded.
TMM scaling was applied to normalise the differences in signal-to-noise ratio between samples. The calculated scaling factors were provided to deeptools for bigWig files creation
Assembly: mm10
Supplementary files format and content: Normalized bigWig files

molecule: genomic DNA

extract_protocol:
Purified hepatocytes were immediately fixed in 1% formaldehyde for 10 minutes. Cells were washed and resuspended in SDS buffer (50 mM Tris pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA, and protease inhibitors). The pellet was resuspended in IP buffer (100 mM Tris pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and sonicated to an average length of 500–1000 bp. Sonicated chromatin was incubated with 10 μg primary antibody (see Suppl.Table 2) overnight, and the immunocomplexes recovered using protein A–conjugated Sepharose beads (Life Tech., 101090). After extensive washes chromatin was de-crosslinked overnight in 0.1 M NaHCO3 and 1% SDS. DNA was purified using PCR purification kit (Qiagen, 28004)
Libraries were prepared as described in Blecher-Gonen, R., Barnett-Itzhaki, Z., Jaitin, D. et al. Nat Protoc 8, 539–554 (2013). volume 8 issue 3 pag 539-554.

tag: chip antibody


title: WT, 30gg, rep2

description:
ALB_WT_DMSO_30gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a KO, 30gg, TC, rep2

description:
A1A_KO_TC_30gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a KO/BcatEXON, rep2

description:
A1A_KO_EXON_TUMOR_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a KO, 9gg, rep1

description:
A1A_KO_DMSO_9gg_rep1
Normalized_counts.tsv
Raw_counts.tsv


title: Hepatocytes, A1AKO, H3K4me1, ChIP, rep1


title: Arid1a KO, 9gg, rep2

description:
A1A_KO_DMSO_9gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Arid1a/b DKO, 9gg, rep2

description:
A1A_B_DKO_DMSO_9gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: Hepatocytes, A1ABDKO, H3K4me1, ChIP, rep1


title: m6A-seq of chromatin associated RNAs without FP treatment, Rep1


title: Arid1a KO, 30gg, rep2

description:
A1A_KO_DMSO_30gg_rep2
Normalized_counts.tsv
Raw_counts.tsv


title: WGBS_DNMT3A+DNMT3L-ADD_Sperm_Rep1

country: Japan

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_Sperm_3A3L_mCG_10kb.bedGraph

extract_protocol:
FGOs were harvested from adult ovaries (10 to 12 weeks old) by needle puncture and cumulus cells were removed by capillary washing. Sperms were released from the cauda epididymides of adult male mice and collected by swim-up method. For the 3a/3L DM sperm, viable sperms were selected by mouth pipetting
Sample with unmethylated lambda phage DNA was subjected to bisulfite treatment and library construction by the post-bisulfite adaptor tagging (PBAT) method (Miura et al., 2012).


title: Hepatocytes, ALB, H3K4me1, ChIP, rep2


title: Hepatocytes, A1ABDKO, H3K27ac, ChIP, rep1


title: Hepatocytes, A1ABDKO, Input


title: Hepatocytes, A1ABDKO, H3K27ac, ChIP, rep2


title: Hepatocytes, ALB, H3K27ac, ChIP, rep1


title: Hepatocytes, A1AKO, H3K27ac, ChIP, rep2


title: Hepatocytes, A1AKO, Input


title: Hepatocytes, ALB, Input


title: WGBS_DNMT3L-ADD_FGO_Rep2

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_FGO_3A_mCG_10kb.bedGraph

source_name: Fully grown oocyte

value: Fully grown oocyte


title: Hepatocytes, A1AKO, H3K4me1, ChIP, rep2


title: WGBS_DNMT3A+DNMT3L-ADD_FGO_Rep2

description:
whole-genome bisulfite sequencing (PBAT)
Processed data file on Rep1 sample: WGBS_FGO_3A3L_mCG_10kb.bedGraph


title: WGBS_DNMT3A+DNMT3L-ADD_FGO_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_FGO_3A3L_mCG_10kb.bedGraph


title: WGBS_DNMT3A-ADD_Sperm_Rep2

description:
whole-genome bisulfite sequencing (PBAT)
Processed data file on Rep1 sample: WGBS_Sperm_3A_mCG_10kb.bedGraph

value: Sperm


title: WGBS_DNMT3L-ADD_FGO_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_FGO_3L_mCG_10kb.bedGraph


title: Hepatocytes, A1AKO, H3K27ac, ChIP, rep1


title: WGBS_WT_FGO_Rep2

description:
whole-genome bisulfite sequencing (PBAT)
Processed data file on Rep1 sample: WGBS_FGO_wt_mCG_10kb.bedGraph

value: Wild type


title: Hepatocytes, ALB, H3K4me1, ChIP, rep1


title: WGBS_DNMT3L-ADD_Sperm_Rep2

description:
whole-genome bisulfite sequencing (PBAT)
Processed data file on Rep1 sample: WGBS_Sperm_3L_mCG_10kb.bedGraph


title: WGBS_DNMT3A-ADD_Sperm_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_Sperm_3A_mCG_10kb.bedGraph


title: RNA_WT_MII_Rep10

description: SMART-seq (single cell)

data_processing:
RNA-seq reads were aligned against the mouse mm10 genome assembly using STAR (Dobin et al. 2013). The mapped reads were counted using HTSeq (Anders et al. 2015)
Assembly: mm10
Supplementary files format and content: text file format

source_name: MII oocyte

extract_protocol:
FGOs were harvested from adult ovaries (10 to 12 weeks old) by needle puncture and cumulus cells were removed by capillary washing.
RNA-seq library was generated from a single FGO or MII oocyte using SMART-SeqHT Kit (Takara) according to the manufacturer's instructions.

value: MII oocyte


title: RNA_WT_MII_Rep8

description: SMART-seq (single cell)


title: WGBS_WT_Sperm_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_Sperm_wt_mCG_10kb.bedGraph


title: WGBS_DNMT3L-ADD_Sperm_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_Sperm_3L_mCG_10kb.bedGraph


title: RNA_DNMT3A+DNMT3L-ADD_E9_embryo_Rep3

description: processsed data available on Rep 1 Sample (GSM7660788)

source_name: mouse embryo

value: mouse embryo

value: maternal allele:Dnmt3aADA/ADA + Dnmt3LD124A/D124A, paternal allele:Wild type


title: Hepatocytes, ALB, H3K27ac, ChIP, rep2


title: m6A-seq of chromatin associated RNAs without FP treatment, Rep2

value: mouse embryonic fibroblasts cells

value: DMSO


title: RNA_WT_MII_Rep7

description: SMART-seq (single cell)


title: RNA_WT_MII_Rep6

description: SMART-seq (single cell)


title: RPE-1 cells, 5hr, translation, rep4

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

country: USA

institute: University of Utah

data_processing:
Reads were aligned to the reference genome using STAR (version 2.5.4a) with the following parameters: --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapNmax 50 --winAnchorMultimapNmax 200 --seedSearchStartLmax 13 --alignIntronMax 1 --outWigType bedGraph --outWigStrand Unstranded.
We focused on the core CDS region from the 15th codon till last 6th codon for each transcript. Uniquely mapped, non-duplicated reads were counted using featureCounts version 1.5.1 with parameters -T 8 -s 1 --largestOverlap --ignoreDup -t 'CDS'.
Assembly: Homo_sapiens.GRCh38 (Ensembl release 90)
Supplementary files format and content: Raw counts of sequencing reads on the core coding region (15th codon till last 6th codon) for individual transcript
Library strategy: Ribo-Seq

organism: Homo sapiens

source_name: human RPE-1

extract_protocol:
RNA was extracted using Qiazol and miRNeasy Mini kits (Qiagen)
rRNA was depleted using Ribo-Zero Gold rRNA Removal Kit (Illumina). Libraries were constructed using Qiagen QIAseq miRNA library kit following manufacturer's protocols.

value: human RPE-1

value: retinal pigment epithelial cells

value: Serum stimulation for 5hr

tag: fraction

value: Ribosome protected RNA fragments


title: RNA_WT_MII_Rep9

description: SMART-seq (single cell)


title: RNA_DNMT3A+DNMT3L-ADD_E9_embryo_Rep1


title: RNA_DNMT3A+DNMT3L-ADD_E9_embryo_Rep2


title: RPE-1 cells, 15hr, translation, rep4

value: WT

value: Serum stimulation for 15hr


title: RNA_WT_MII_Rep2

description: SMART-seq (single cell)


title: RNA_WT_MII_Rep5

description: SMART-seq (single cell)


title: RPE-1 cells, 0hr, translation, rep3

value: Serum stimulation for 0 hr


title: RPE-1 cells, 0hr, translation, rep4


title: RNA_WT_MII_Rep4

description: SMART-seq (single cell)


title: RPE-1 cells, 15hr, translation, rep3


title: RNA_WT_MII_Rep3

description: SMART-seq (single cell)


title: RPE-1 cells, 10hr, translation, rep3

value: Serum stimulation for 10hr


title: WGBS_WT_FGO_Rep1

description:
whole-genome bisulfite sequencing (PBAT)
WGBS_FGO_wt_mCG_10kb.bedGraph


title: RPE-1 cells, 10hr, translation, rep2


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep7

description: SMART-seq (single cell)

value: Dnmt3aADA/ADA + Dnmt3LD124A/D124A


title: RPE-1 cells, 5hr, translation, rep3


title: RNA_WT_MII_Rep1

description: SMART-seq (single cell)


title: RPE-1 cells, 15hr, translation, rep2


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep8

description: SMART-seq (single cell)

value: Fully grown oocyte


title: RPE-1 cells, 5hr, translation, rep2


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep4

description: SMART-seq (single cell)


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep6

description: SMART-seq (single cell)


title: RPE-1 cells, 15hr, translation, rep1


title: RPE-1 cells, 0hr, translation, rep2


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep3

description: SMART-seq (single cell)


title: RPE-1 cells, 5hr, translation, rep1


title: RPE-1 cells, 0hr, translation, rep1


title: RNA_DNMT3A-ADD_FGO_Rep8

description: SMART-seq (single cell)


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep2

description: SMART-seq (single cell)


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep1

description: SMART-seq (single cell)


title: biol rep 4 YA larval stage (hermaphrodite) of N2 wildtype grown at 25oC

city: Rehovot

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

department: Brain Sciences

country: Israel

institute: Weizmann Institute of Science

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2YAB4.raw

data_processing:
Raw next-generation sequencing (NGS) data in the FASTQ format were analyzed using user-friendly transcriptome analysis pipeline (UTAP).
Briefly, reads were trimmed using cutadapt and mapped to the C. elegans reference genome WBcel235 using STAR v2.4.2a.
UMI counting was done using HTSeq-count after marking duplicates in union mode. Differential gene expression analysis and normalization of the counts was performed using DESeq2 using the rld (log2 normalized) gene expression values on a per-developmental stage basis between sexes.
Assembly: C. elegans reference genome WBcel235
Supplementary files format and content: Tab-delimited file include raw counts for each sample
Supplementary files format and content: Tab-delimited file include processed counts for each sample

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Worms were grown and maintained at 25C

extract_protocol:
Worms pellet were collected in 500 µL of Trizol and flash frozen in liquid nitrogen and stored at -80oC until further processing. Total RNA was prepared from the frozen worm pellets following the instructions for the TRIzol LS (Invitrogen) protocol. After the isopropanol precipitation step, the RNA was re-suspended in the extraction buffer of the RNA isolation kit (PicoPure, Arcturus), and further isolation was carried out in accordance with the manufacturer's instructions.
RNA libraries for RNA seq were prepared using a bulk version of the MARS-Seq procedure was employed. Briefly, reverse transcription was used to barcode and pool 18 ng of input RNA from each sample. The pooled samples underwent second strand synthesis after Agencourt Ampure XP beads cleanup (Beckman Coulter), and they were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and then converted into final library by tagging the samples with Illumina sequences during ligation, RT, and PCR

value: Whole animal

value: N2 wild-type

value: Grown at 25 degrees


title: RPE-1 cells, 15hr, transcription, rep4

data_processing:
Reads were aligned to the reference genome using STAR (version 2.5.4a) with the following parameters: --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapNmax 50 --winAnchorMultimapNmax 200 --seedSearchStartLmax 13 --alignIntronMax 1 --outWigType bedGraph --outWigStrand Unstranded.
We focused on the core CDS region from the 15th codon till last 6th codon for each transcript. Uniquely mapped, non-duplicated reads were counted using featureCounts version 1.5.1 with parameters -T 8 -s 1 --largestOverlap --ignoreDup -t 'CDS'.
Assembly: Homo_sapiens.GRCh38 (Ensembl release 90)
Supplementary files format and content: Raw counts of sequencing reads on the core coding region (15th codon till last 6th codon) for individual transcript

value: Total RNA


title: RPE-1 cells, 10hr, translation, rep1


title: RPE-1 cells, 10hr, transcription, rep4


title: RPE-1 cells, 5hr, transcription, rep4


title: biol rep 3 YA larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2YAB3.raw


title: RNA_DNMT3A-ADD_FGO_Rep7

description: SMART-seq (single cell)


title: 08_GBM229

city: San Francisco

first: Hideho

last: Okada

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

description:
nanopore full-length transcript amplicon sequencing
barcode08

data_processing:
The sequencing data was acquired using the MinKNOW software (v4.0.20) with high-accuracy mode. The generated Fast5 data were analyzed, excluding the Fast5_fail data and only focusing solely on the Fast5_pass data. Base calling was performed using Guppy basecaller (4.2.2+effbaf8).
The generated FASTQ files were analyzed using FLAIR (v2.0.0) [40] in the Python 3.9.16 environment. For the FLAIR analyses, a customized reference genome was prepared by extracting the chromosome 7 region where PTPRZ1 gene is located in the human genome hg19 (GRCh37). Additionally, the GTF annotation file was also narrowed down to the chromosome 7 region from the file ‘Homo_sapiens.GRCh37.87.chr.gtf,’ and each of the expected AS patterns of PTPRZ1 was concatenated.  The first module, ‘flair align,’ was performed for the FASTQ files with the reference genome, generating BED files. The second module, ‘flair correct,’ was performed with the BED files using the following command: flair correct -q $BED -g $GENOME -t $N -f $GTF -o $OUT_PREFIX. The third module, ‘flair collapse,’ was conducted with the concatenated single FASTQ file and the concatenated single BED file of all tested samples using the following command: flair collapse -g $GENOME -q $BED -r $FQ -t $N -f $GTF -o $OUT_PREFIX --keep_intermediate --generate_map --check_splice --annotation_reliant generate --trust_ends. Based on the defined high-confidence isoforms, the fourth module, ‘flair quantify,’ was performed to obtain the read count data of each isoform in each sample using the following command: flair quantify -r $MANIFEST -i $ISOFORM -o $OUT_PREFIX2 -t $N --generate_map --sample_id_only --trust_ends.
Assembly: human genome hg19 (GRCh37) chromosome 7 region
Supplementary files format and content: tsv file containing the count data matrix of each of the identified isotypes
Library strategy: amplicon-sequencing

growth_protocol: cells were maintained in complete NeuroCult media, which consisted of NS-A Basal Medium (Human) (STEMCELL Technologies, 05750) supplemented with 10% NeuroCult™ Proliferation Supplement (Human) (STEMCELL Technologies, 05753), heparin solution (final concentration, 2 µg/mL, STEMCELL Technologies, 07980), recombinant human EGF (20 ng/mL, PeproTech, AF-100-15), recombinant human FGF-basic (20 ng/mL, PeproTech, 100-18B), and 1% Penicillin-Streptomycin (Gibco, 15070063). The cells were cultured in spheroid form on culture dishes with an ultra-low attachment surface (Corning, 3471, 3473 , 3814, or 4616) and maintained in a humidified incubator at 37°C with 5% CO2. Passaging of the cells was performed by dissociating them using Accutase (Innovative Cell Technologies, AT104) and then plating them onto new culture dishes. EGF and FGF-basic were directly supplemented to the media twice a week during maintenance. Regular testing for mycoplasma infection was conducted every 3–4 months using the PlasmoTest mycoplasma detection kit (InvivoGen, catalog # rep-pt1). No other authentication assay was performed.

extract_protocol:
Total RNA was extracted from tumor cell culture pellets using the RNeasy Mini Kit (Qiagen, 74106) and the RNase-Free DNase Set (Qiagen, 79254) following the manufacturer’s protocol. The RNA integrity was evaluated using the Agilent Bioanalyzer 2100 and confirmed to be RIN ≥ 7 (range, 7.3–9.9). Subsequently, complementary DNA (cDNA) was synthesized from the total RNA samples using the TaKaRa PrimeScript 1st strand cDNA Synthesis Kit (TaKaRa, 6110A).
To obtain the amplicons of the entire coding sequence (CDS) region of PTPRZ1 transcripts, the following oligo primers were designed to bind to the 5’-UTR and 3’-UTR of PTPRZ1 transcripts, respectively: Fwd: 5’- ACCGTCTGGAAATGCGAATC-3’; Rev: 5’- TGGTCCATGGAGACACTAGG-3’. Polymerase chain reaction (PCR) was performed using PrimeSTAR GXL DNA Polymerase (TaKaRa, R050A), following the recommended Rapid PCR protocol, consisting of 35 cycles of 98℃ for 10 sec, 60℃ for 15 sec, and 68℃ for 80sec. The amplicons (PCR products) were imaged after electrophoresis on a 0.8% agarose gel. Gel pieces of each lane were excised from the agarose gel, digested, and purified using the NucleoSpin® Gel and PCR Clean-Up kit (TaKaRa, 740609), according to the manufacturer’s protocols. The library preparation of the nanopore full-length transcript amplicon was conducted following the protocol “native-barcoding-amplicons-NBA_9093_v109_revD_12Nov2019-minion,” provided by Oxford Nanopore Technologies (ONT). The following materials were used: Ligation Sequencing Kit (ONT, SQK-LSK109); Native Barcoding Expansion 1-12 (PCR-free) (ONT, EXP-NBD104); Flow Cell Priming Kit (ONT, EXP-FLP002); Agencourt AMPure XP beads (Beckman Coulter, A63880); Blunt/TA Ligase Master Mix (New England Biolabs, M0367S); NEBNext Quick Ligation Reaction Buffer (New England Biolabs, B6058S); NEBNext Companion Module for Oxford Nanopore Technologies Ligation (New England Biolabs, E7180S). As per the recommended protocol, the sample concentration was measured using the Qubit™ dsDNA HS Assay Kit (Invitrogen, Q32854) and Qubit Fluorometer (Invitrogen), and was adjusted accordingly at each step. After barcode ligation, all the individual libraries were pooled. Subsequently, following adapter ligation and the concentration measurement, 50 fmol of the pooled library was loaded to the R9.4.1 flow cells (ONT, FLO-MIN106D) on the MinION Mk1B sequencer.
nanopore full-length transcript amplicon sequencing

value: PDX cell line

value: unknown


title: biol rep 2 YA larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2YAB2.raw


title: 07_GBM126

description:
nanopore full-length transcript amplicon sequencing
barcode07


title: RPE-1 cells, 10hr, translation, rep4


title: RNA_DNMT3A-ADD_FGO_Rep5

description: SMART-seq (single cell)


title: RPE-1 cells, 15hr, transcription, rep3


title: RPE-1 cells, 0hr, transcription, rep4


title: biol rep 4 L4 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L4B4.raw


title: 06_GBM117

description:
nanopore full-length transcript amplicon sequencing
barcode06


title: biol rep 1 YA larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2YAB1.raw


title: RNA_DNMT3A-ADD_FGO_Rep6

description: SMART-seq (single cell)


title: RPE-1 cells, 10hr, transcription, rep3


title: 05_GBM75

description:
nanopore full-length transcript amplicon sequencing
barcode05


title: RNA_DNMT3A-ADD_FGO_Rep4

description: SMART-seq (single cell)


title: biol rep 3 L4 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L4B3.raw


title: 04_GBM64

description:
nanopore full-length transcript amplicon sequencing
barcode04


title: biol rep 2 L4 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L4B2.raw


title: 02_GBM39

description:
nanopore full-length transcript amplicon sequencing
barcode02


title: RNA_DNMT3A-ADD_FGO_Rep2

description: SMART-seq (single cell)


title: RPE-1 cells, 0hr, transcription, rep3


title: RNA_DNMT3A-ADD_FGO_Rep3

description: SMART-seq (single cell)


title: RPE-1 cells, 5hr, transcription, rep3


title: RNA_DNMT3A-ADD_FGO_Rep1

description: SMART-seq (single cell)


title: biol rep 1 L4 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L4B1.raw


title: 03_GBM43

description:
nanopore full-length transcript amplicon sequencing
barcode03


title: 01_GBM6

description:
nanopore full-length transcript amplicon sequencing
barcode01


title: RNA_DNMT3A+DNMT3L-ADD_FGO_Rep5

description: SMART-seq (single cell)


title: biol rep 3 L3 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L3B3.raw


title: RPE-1 cells, 10hr, transcription, rep2


title: RNA_DNMT3L-ADD_FGO_Rep7

description: SMART-seq (single cell)


title: biol rep 4 L3 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L3B4.raw


title: Mouse gingival fibroblasts, Irradiated, 3h [L3]

city: Bunkyo City

first: Hiromi

last: Niimi

state: Tokyo

address: Yushima 1-5-45

department: Periodontology

institute: Tokyo Medical and Dental University

data_processing:
Data (26.7M reads/13.3M pairs per sample) was processed using packages based on R.
Low-quality and adapter sequences from the paired-end reads were trimmed using Trimmomatic v0.39
The quality of the trimmed reads was assessed using FastQC v0.11.9.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using HISAT2 v2.2.1.
Assembly: StringTie v2.1.7 was used to assemble transcripts and estimate abundance based on GRCm39 gene annotations.
Supplementary files format and content: Comma-separated spreadsheet files include raw counts for each sample (concluded by tissue type).

source_name: Gingival

growth_protocol: Primary mouse gingival fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Total RNA (tRNA) was extracted from irradiated and non-irradiated cells with NucleoSpin® RNA kit (TaKaRa Bio, Shiga, Japan) according to the manufacturer’s instructions.

treatment_protocol: The cells at the bottom of the 35-mm culture dish were irradiated with Er:YAG laser (energy density: 3.9 J/cm2) positioned at a distance of 25 cm.

value: Gingival

value: Primary cells

value: Fibroblasts

tag: strain background

value: Er:YAG laser irradiation


title: biol rep 2 L3 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L3B2.raw


title: RNA_DNMT3L-ADD_FGO_Rep8

description: SMART-seq (single cell)


title: Mouse gingival fibroblasts, Irradiated, 3h [L2]


title: RPE-1 cells, 5hr, transcription, rep2

value: human RPE-1

value: retinal pigment epithelial cells

value: Serum stimulation for 5hr


title: RPE-1 cells, 0hr, transcription, rep2

value: WT

value: Serum stimulation for 0 hr


title: RPE-1 cells, 15hr, transcription, rep1

value: Serum stimulation for 15hr


title: RNA_DNMT3L-ADD_FGO_Rep5

description: SMART-seq (single cell)

value: Fully grown oocyte


title: biol rep 4 L2 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L2B4.raw

value: Whole animal


title: Mouse gingival fibroblasts, Irradiated, 3h [L1]


title: Mouse gingival fibroblasts, Non-irradiated, 3h [C3]


title: RNA_DNMT3L-ADD_FGO_Rep4

description: SMART-seq (single cell)


title: RPE-1 cells, 10hr, transcription, rep1

value: Serum stimulation for 10hr


title: RPE-1 cells, 15hr, transcription, rep2


title: biol rep 3 L2 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L2B3.raw

value: N2 wild-type

value: Grown at 25 degrees


title: Mouse gingival fibroblasts, Non-irradiated, 3h [C1]


title: RPE-1 cells, 5hr, transcription, rep1

value: Total RNA


title: RNA_DNMT3L-ADD_FGO_Rep3

description: SMART-seq (single cell)


title: Mouse gingival fibroblasts, Non-irradiated, 3h [C2]


title: RNA_DNMT3L-ADD_FGO_Rep2

description: SMART-seq (single cell)


title: biol rep 2 L2 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L2B2.raw


title: RPE-1 cells, 0hr, transcription, rep1


title: biol rep 1 L3 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L3B1.raw


title: Donor6_Day0_TEM_TCRB

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

data_processing:
Processing of raw Illumina sequence reads, filtering, demultiplexing, clustering and mapping of CDR3 sequences and annotation of VDJ genes were done by Adaptive Biotechnologies
Assembly: IMGT
Supplementary files format and content: tab-delimited text file contains repertoire characteristics for each sample

source_name: CD4+T cell

extract_protocol:
Genomic DNA was extracted from sorted CD4+T cells using QIAamp DNA Micro Kit (QIAGEN).
Done by Adaptive Biotechnologies, Human CDR3B assay

tag: individual

value: CD4+T cell

tag: cell subset


title: biol rep 1 L2 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2L2B1.raw


title: RNA_DNMT3L-ADD_FGO_Rep6

description: SMART-seq (single cell)


title: Donor6_Day0_TCM_TCRB


title: RNA_DNMT3L-ADD_FGO_Rep1

description: SMART-seq (single cell)


title: tail, WT_3

city: Guangzhou

first: Luping

last: Wang

address: East Wai-huan Road, Guangzhou 510006, Guangdong, China.

institute: South China University of Technology

data_processing:
The generated fastq files were subjected to FastQC  to check sequencing quality.
The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 (v2.0.5).
The mapped reads were then counted using FeatureCounts.
The counts matrix was applied to DESeq2 for normalization, differentially expressed genes identification.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .
Assembly: GRCz11
Supplementary files format and content: gene_fpkm.txt

organism: Danio rerio

source_name: tail

extract_protocol:
Larvae were collected at 3 dpf, then grouped into sirt6 mutant and WT groups through genotyping, total RNA was extracted with TRIzol (Invitrogen) from the tails including hematopoietic tissue.
The poly-A selected RNA was applied to the NGS RNA Library Prep kits (Novogene) to construct Sequencing libraries.

value: tail

tag: developmental stage

value: larvae at 3 dpf


title: biol rep 4 L1 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2B4.raw


title: biol rep 3 L1 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2B3.raw


title: tail, WT_2


title: Donor6_Day0_Naive_TCRB


title: tail, WT_1


title: RNA_WT_FGO_Rep17

description: SMART-seq (single cell)

value: Wild type


title: Donor6_APOB_AIMpos_TCRB


title: RNA_WT_FGO_Rep16

description: SMART-seq (single cell)


title: biol rep 2 L1 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2B2.raw


title: biol rep 1 L1 larval stage (hermaphrodite) of N2 wildtype grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
N2B1.raw


title: tail, S6M_3

value: sirt6 mutant


title: tail, S6M_2


title: RNA_WT_FGO_Rep15

description: SMART-seq (single cell)


title: Donor5_Day0_TEM_TCRB


title: biol rep 4 YA larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MYAB4.raw


title: RNA_WT_FGO_Rep14

description: SMART-seq (single cell)


title: Donor5_Day0_TCM_TCRB


title: biol rep 3 YA larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MYAB3.raw


title: RNA_WT_FGO_Rep18

description: SMART-seq (single cell)


title: biol rep 2 YA larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MYAB2.raw


title: RNA_WT_FGO_Rep12

description: SMART-seq (single cell)


title: Donor5_APOB_AIMpos_TCRB


title: Donor5_Day0_Naive_TCRB


title: P10_CTRL_1

city: GUANGZHOU

first: LEI

last: SUN

state: GUANGDONG

address: XIAOGUWEI STREET

department: School of Pharmacy 619

institute: Sun Yat-sen University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt.
The reference genome alignment was performed using Hisat2.
Stringtie was used to reconstruct transcripts and calculate all gene expression levels in each sample.
Assembly: human_hg38
Supplementary files format and content: The Excel file contains the gene count values for each sample.

source_name: liver cancer

growth_protocol: PDC medium and cells were cultured at 37℃ at 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were performed using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: PDCs were treated with 1uM Romidepsin or 2uM Romidepsin for 48h.

value: liver cancer

value: liver cancer cell

value: lenvatinib resistance

value: CTRL


title: biol rep 1 YA larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MYAB1.raw


title: P10_2uM_2

value: 2uM Romidepsin treatment


title: Donor5_APOB_AIMneg_TCRB


title: biol rep 4 L4 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML4B4.raw


title: RNA_WT_FGO_Rep10

description: SMART-seq (single cell)


title: RNA_WT_FGO_Rep11

description: SMART-seq (single cell)


title: P10_1uM_2

value: 1uM Romidepsin treatment


title: biol rep 3 L4 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML4B3.raw


title: RNA_WT_FGO_Rep9

description: SMART-seq (single cell)

value: Fully grown oocyte


title: Donor6_APOB_AIMneg_TCRB


title: Donor4_Day0_TCM_TCRB


title: Donor4_Day0_TEM_TCRB


title: P10_2uM_1


title: biol rep 2 L4 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML4B2.raw

value: Whole animal


title: RNA_WT_FGO_Rep8

description: SMART-seq (single cell)


title: RNA_WT_FGO_Rep13

description: SMART-seq (single cell)


title: biol rep 1 L4 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML4B1.raw


title: P10_1uM_1


title: RNA_WT_FGO_Rep7

description: SMART-seq (single cell)


title: P5_CTRL_2


title: Donor4_Day0_Naive_TCRB


title: tail, S6M_1


title: biol rep 4 L3 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML3B4.raw


title: P5_CTRL_1


title: Donor4_APOB_AIMneg_TCRB


title: RNA_WT_FGO_Rep6

description: SMART-seq (single cell)


title: Donor4_APOB_AIMpos_TCRB


title: P10_CTRL_2


title: P5_2uM_2


title: biol rep 3 L3 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML3B3.raw


title: Donor3_Day0_TEM_TCRB


title: RNA_WT_FGO_Rep5

description: SMART-seq (single cell)


title: biol rep 2 L3 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML3B2.raw


title: RNA_WT_FGO_Rep4

description: SMART-seq (single cell)


title: Donor3_Day0_TCM_TCRB


title: P5_2uM_1


title: P5_1uM_2


title: biol rep 1 L3 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML3B1.raw


title: biol rep 4 L2 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML2B4.raw


title: Donor3_Day0_Naive_TCRB


title: Donor3_APOB_AIMpos_TCRB


title: biol rep 3 L2 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML2B3.raw


title: Donor3_APOB_AIMneg_TCRB


title: RNA_WT_FGO_Rep2

description: SMART-seq (single cell)


title: RNA_WT_FGO_Rep1

description: SMART-seq (single cell)


title: biol rep 2 L2 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML2B2.raw


title: P5_1uM_1


title: vancomcycin_30mins_3

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
prepocessing using BBDuk. BBDuk was used to trim the 5’ adapter sequence of the raw data using the parameters ‘ktrim=l k=23 mink=11 hdist=1’ followed by quality trimming with the parameters ‘qtrim=rl trimq=30’(Bushnell, 2014). After trimming, BBmerge was used to merge the paired-end reads using the default parameters (Bushnell et al, 2017)
mapped using BBMap
Read counts for each feature was computed using bedtools coverage (https://bedtools.readthedocs.io/en/latest/)(PMID: 25199790)
Differential gene expression analysis was performed using DESeq2 (Love et al, 2014)(PMID: 25516281)
Assembly: GCF_000145595.1
Supplementary files format and content: gene count table (raw reads counts)
Supplementary files format and content: Deseq2 output table of differentially expressed genes

organism: Staphylococcus aureus subsp. aureus str. JKD6008

source_name: whole cell

growth_protocol: S. aureus str. JKD6008 was grown in Muller-Hinton media to an OD600 of 0.8 before treatment

extract_protocol:
GTF-phenol (Tollervey & Mattaj EMBO J 1987; PMID: 2953599)
Libraries prepared by Novagene using prokaryotic directional mRNA library preparation (with rRNA removal).

treatment_protocol: Where applicable, cultures were treated with 8ug/ml of vancomycin for 30mins and then harvested into GTC-phenol buffer.

value: whole cell

value: strain JKD6008 (vancomycin intermediate, VISA)

value: VISA

value: 8 ug/ml vancomycin for 30 mins


title: biol rep 1 L2 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
ML2B1.raw

value: Grown at 25 degrees


title: Donor2_Day0_TEM_TCRB

value: CD4+T cell


title: NC_2

city: Qingdao

first: Zhihua

last: Wu

address: Yushan 5rd

institute: Ocean university of China

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method.
RSEM (http://deweylab.biostat.wisc.edu/rsem/)was used to quantify gene abundances.
Assembly: Assembly: ENSMUSG
Supplementary files format and content: gene_id, gene_name,
Supplementary files format and content: sample name, etc

source_name: peritoneal

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

value: peritoneal

value: peritoneal macrophages

value: macrophages

value: Vehicle 24h


title: vancomycin_30mins_2


title: biol rep 4 L1 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MOSB4.raw


title: NC_1


title: LUP_2

value: 0.5 mg/ml LUP 24h


title: vancomcyin_30mins_1


title: Donor2_Day0_TCM_TCRB


title: RNA_WT_FGO_Rep3

description: SMART-seq (single cell)

value: Wild type


title: Donor2_APOB_AIMpos_TCRB


title: Donor2_Day0_Naive_TCRB


title: control_30mins_1

value: no treatment


title: control_30mins_2


title: LUP_1


title: biol rep 1 L1 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MOSB1.raw


title: Donor2_APOB_AIMneg_TCRB


title: Membrane 29

type: RNA

city: Palo Alto

first: Theodore

last: Leng

address: 2452 Watson Ct

department: Ophthalmology

institute: Stanford University

data_processing: Geometric mean was used to normalize the number of hybridized reads of each miR to spiked internal positive controls, and to the top 100 reads mean (nSolver Analysis Software 4.0, version 4.0.62, NanoString Technologies Inc.). The mean of negative controls plus 3 standard deviations (3σ) was used to determine significant difference

source_name: Epiretinal membrane

label_protocol: miR profiling was performed via NanoStringTM nCounter microarray analysis (NanoString Technologies Inc., WA, USA)

extract_protocol: Samples of ERMs from patients and separate patients with normal vitreous for controls were collected aseptically during surgery in RNAase free 1.5 ml collection tubes and were immediately frozen with dry ice. Total RNA was isolated from ERM tissue and from non-ERM vitreous using TRIzol® (ThermoFisher Scientific, Waltham, MA)

tag: age

value: 70 years old

tag: Sex

value: Female


title: HeLa PolyA RNA, Replicate 2

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

data_processing:
Low quality reads were trimmed and adaptor contamination were removed using Trim Galor
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2
Raw read counts were generated using StringTie and converted to Transcripts per million (TPM) values
Assembly: hg38
Supplementary files format and content: CSV text file includes includes TPM values for each sample

source_name: HeLa

extract_protocol:
RNA was extracted using Trizol using the manufacturer's protocol. 1ug of RNA was depleted with rRRR or NEBnext rRNA depletion kit
RNA-seq libraries were prepared using  NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. 90 ng of RNA was used for every library

value: HeLa

value: Epithelial cells derived from cervix

value: WT


title: Donor1_Day0_TEM_TCRB


title: WT t6h of meiotic time course

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: HiC bank

data_processing:
Alignment of paired-end reads and processing of the contact data were done with Hicstuff pipeline on the CBS10367_SNP_inferred reference genome, using with the following parameters: aligning with bowtie2, filtering out spurious 3C events and PCR duplicates based on read positions.
Assembly: CBS10367_SNP_inferred reference genome
Supplementary files format and content: 1kb cool format matrix

organism: Lachancea kluyveri

source_name: yeast cell

growth_protocol: Hi-C experiments were performed using the CBS 10367 isolate. To harvest enough cells per time point (ie ca 2 x 10^9 cells), four independent 200 ml cultures in 2 l flasks were used. Equal samples were harvested from the four flasks at 0, 2, 3, 4, 5, 6, 7 and 8 hours post meiosis induction and treated with 3% formaldehyde for 20 minutes under constant shaking. Samples were quenched using 0.35M glycine at 4°C for 20 minutes. Cells were harvested by centrifugation at 4000 g for 4 minutes at 4°C, washed once with potassium acetate 1% (sporulation medium), transferred to 1.5 ml tubes and pellets were flash frozen using liquid nitrogen.

extract_protocol: Hi-C experiments were performed as in Piazza et al 2021. Hi-C DNA libraries were generated and sequenced as in Dauban et al 2020.

tag: isolate

value: yeast cell

value: meiosis induction

value: hour 6


title: biol rep 3 L1 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MOSB3.raw

value: Whole animal

value: Grown at 25 degrees


title: WT t5h of meiotic time course

description: HiC bank

value: hour 5


title: HeLa total RNA treated with NEBNext for rRNA depletion, Replicate 2

value: NEBNext


title: Membrane 34

value: 68 years old


title: control_30mins_3

value: whole cell

value: strain JKD6008 (vancomycin intermediate, VISA)

value: VISA


title: Membrane 31

value: Male


title: WT t4h of meiotic time course

description: HiC bank

value: hour 4


title: Donor1_APOB_AIMpos_TCRB

value: CD4+T cell


title: WT t3h of meiotic time course

description: HiC bank

value: hour 3


title: WT t2h of meiotic time course

description: HiC bank

value: hour 2


title: HeLa total RNA treated with rRRR for rRNA depletion, Replicate 2

value: HeLa

value: Epithelial cells derived from cervix

value: WT

value: rRRR


title: Membrane 15

value: 51 years old

value: Female


title: biol rep 2 L1 larval stage (male) of dpy-28(y1);him-8(e1489) grown at 25oC

description:
DESeq2_MOS_N2_umi_counts_20210422_160738.xlsx
MOSB2.raw

value: Whole animal

value: Grown at 25 degrees


title: HeLa total RNA treated with NEBNext for rRNA depletion, Replicate 1

value: NEBNext


title: Control 6

source_name: Vitreous

value: 76 years old


title: Donor1_Day0_TCM_TCRB


title: WT t0h of meiotic time course

description: HiC bank

value: yeast cell

value: control

value: hour 0


title: Control 4

value: 60 years old

value: Male


title: Membrane 28

value: 54 year old


title: HeLa PolyA RNA, Replicate 1


title: HeLa total RNA treated with rRRR for rRNA depletion, Replicate 1


title: Donor1_Day0_Naive_TCRB

value: CD4+T cell


title: Donor1_APOB_AIMneg_TCRB


title: Psoriasis patient skin-8

status: Public on Mar 16 2024

city: Sakado

first: Madoka

last: Kage

address: 1-1 Keyakidai

institute: Josai University

description: Gene expression data from psoriasis patient skin

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

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Gene Spring v14.9.1 (Agilent) using Affymetrix default analysis settings and global scaling as normalization method. A given gene was analyzed if its normalized intensity was more than 0.2.

label: biotin

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

extract_protocol: After freezing and crushing the skin tissue, Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Human skin


title: ATAC TSS Rep1

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

data_processing:
ATAC-seq reads were aligned to reference genome hg19 with Bowtie2105 (version 2.3.4.1) using parameter --very-sensitive. Data was filtered to remove mitochondrial reads, retain proper pairs (-f 0x2), and remove ambiguously mapped reads (MAPQ>10, -q 10).
Bam files were sorted and indexed with Samtools (version 1.8).
Bedgraph coverage files were generated using bamCoverage from deepTools (version 3.3.1_py36)106 with parameters -- numberOfProcessors 10 --binSize 50 --normalizeUsing CPM --region chr4.
For quantification, data was further normalized by the total signal for chr4 per sample using a pseudocount of 1e-4 and scaled to 1e6.
Assembly: hg19
Supplementary files format and content: bedgraph coverage

source_name: Jurkat

extract_protocol:
Cells were sorted by FACS for live cells and for the cell populations expressing the constructs of interest. ATAC-seq was performed according to published protocols as referenced in Methods.
Lbrary construction for ATAC-seq was performed according to published protocols as referenced in Methods.

treatment_protocol: Lentiviral infection of perturbation and non-targeting control gRNAs, doxycycline

value: Jurkat

value: T cell

value: expresses dCas9 and gRNA


title: Psoriasis patient skin-5


title: Patient4 OM-85+ISO

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
sequencing reads were processed using the Cellranger pipeline (v6.1.2) and aligned on the human reference genome (GRCh38)
Assembly: GRCh38
Supplementary files format and content: gene expression, filtered h5 files

source_name: Bronchoalveolar lavage fluid

extract_protocol:
Single-cell suspensions were processed with Single Cell 3′ Reagent Kit v2 (Chromium Single Cell 3′ Library& Gel Bead Kit v2, Chromium Single CellGChip Kit, 10x Genomics) and Chromium Controller (10x Genomics) according to the protocol at theBIOS+Genomics FacilityinBellinzona.
Single-cell suspensions were processed with Single Cell 3′ Reagent Kit v2 (Chromium Single Cell 3′ Library& Gel Bead Kit v2, Chromium Single CellGChip Kit, 10x Genomics) and Chromium Controller (10x Genomics) according to the protocol at theBIOS+Genomics FacilityinBellinzona.The generated libraries were sequenced using Illumina NextSeq2000 Systems accordingly with the 10x Genomics manual.

treatment_protocol: Bronchoalveolar lavage (BAL) cells were stimulated or not with isotype control antibody (mIgG1k) or a combination of Anti-hTLR2 and Anti-hTLR4 (10ug/ml each) for 90 min, followed by stimulation with bacterial lysate OM-85 (150ug/ml) for 3hr.

value: Bronchoalveolar lavage fluid

value: BAL cells

value: OM-85 150ug/ml+Isotype control Ab


title: Patient2 UT

description: 10x Genomics

value: UT


title: Patient2 OM-85+ISO

description: 10x Genomics


title: Patient1 UT

description: 10x Genomics


title: Patient4 UT

description: 10x Genomics


title: Patient3 OM-85+T2/4

description: 10x Genomics

value: OM-85 150ug/ml+Anti-TLR2/4 Abs


title: Psoriasis patient skin-4


title: Patient2 OM-85+T2/4

description: 10x Genomics


title: Patient3 UT

description: 10x Genomics


title: Patient3 OM-85+ISO

description: 10x Genomics


title: Healthy control skin

description: Gene expression data from healthy human skin


title: Psoriasis patient skin-6


title: Patient4 OM-85+T2/4

description: 10x Genomics


title: Psoriasis patient skin-1


title: ATAC E6 Rep1


title: Psoriasis patient skin-3


title: Psoriasis patient skin-7


title: Patient1 OM-85+T2/4

description: 10x Genomics


title: Psoriasis patient skin-2


title: Patient1 OM-85+ISO

description: 10x Genomics


title: ATAC E9 Rep2


title: ATAC E9 Rep1


title: ATAC E4 Rep2


title: ATAC TSS Rep2


title: ATAC NTC Rep2


title: ATAC E4 Rep1


title: ATAC NTC Rep1


title: ATAC E2 Rep1


title: ATAC E2 Rep2


title: ATAC E6 Rep2


title: RNA-Seq S38-CT

city: Beijing

first: Ze

last: Yan

address: No.2, Yuanmingyuan Road (West), HaiDian District

institute: China Agricultural University

data_processing:
Sequence reads were trimmed for adaptor sequencing / low-quality bases using fastp software with default parameters.
Trimmed clean reads were mapped to Oar_rambouillet_v1.0 (GCA_002742125.1) by the program STAR (v2.7.9a)(parameter: -quantMode GeneCounts, -outFilterMismatchNmax 3, -outFilterMultimapNmax 10)
Properly paired and uniquely mapped reads were extracted by using SAMtools (v1.11)112 with the command “view -f 2”
Gene counts were generated by the featureCounts program from the Subread package suite (v2.0.3)
Assembly: Oar_rambouillet_v1.0 (GCA_002742125.1)
Supplementary files format and content: tab-delimited next file includes raw counts for each sample

organism: Ovis aries

source_name: pituitary

extract_protocol:
Total RNA was extracted from flash-frozen tissues with RNA TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
libraries were constructed by the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, CA, USA)

value: pituitary


title: RNA-Seq S36-ZW

source_name: abomasum

value: abomasum


title: RNA-Seq S29-ZW


title: RNA-Seq S35-ZW


title: RNA-Seq S32-ZW


title: RNA-Seq S30-ZW


title: RNA-Seq S34-ZW


title: RNA-Seq S28-ZW


title: RNA-Seq S39-CT


title: RNA-Seq S37-ZW


title: RNA-Seq S41-ZW


title: RNA-Seq S42-ZW


title: RNA-Seq S38-ZW


title: RNA-Seq S40-ZW


title: RNA-Seq S45-ZW


title: RNA-Seq S48-ZW


title: RNA-Seq S46-ZW


title: RNA-Seq S39-ZW


title: RNA-Seq S43-ZW


title: RNA-Seq S40-CT


title: RNA-Seq S44-ZW


title: RNA-Seq S31-ZW


title: RNA-Seq S50-ZW


title: RNA-Seq S49-ZW


title: RNA-Seq S17-BJ

source_name: muscle

value: muscle


title: RNA-Seq S33-ZW


title: RNA-Seq S12-heart

source_name: heart

value: heart


title: RNA-Seq S13-heart


title: RNA-Seq S16-heart


title: RNA-Seq S15-heart


title: RNA-Seq S20-heart


title: RNA-Seq S17-heart


title: RNA-Seq S14-heart


title: RNA-Seq S18-BJ


title: RNA-Seq S21-heart


title: RNA-Seq S47-ZW


title: RNA-Seq S29-heart


title: RNA-Seq S24-heart


title: RNA-Seq S23-heart


title: RNA-Seq S28-heart


title: RNA-Seq S26-heart


title: RNA-Seq S22-heart


title: RNA-Seq S30-heart


title: RNA-Seq S25-heart


title: RNA-Seq S31-heart


title: RNA-Seq S36-heart


title: RNA-Seq S27-heart


title: RNA-Seq S37-heart


title: RNA-Seq S11-heart


title: RNA-Seq S38-heart


title: RNA-Seq S32-heart


title: RNA-Seq S33-heart


title: RNA-Seq S39-heart


title: RNA-Seq S18-heart


title: RNA-Seq S34-heart


title: RNA-Seq S19-heart


title: RNA-Seq S19-BJ


title: RNA-Seq S40-heart


title: RNA-Seq S49-JC

source_name: colon

value: colon


title: RNA-Seq S48-JC


title: RNA-Seq S50-JC


title: RNA-Seq S02-KC

source_name: jejunum

value: jejunum


title: RNA-Seq S03-KC


title: RNA-Seq S04-KC


title: RNA-Seq S01-KC


title: RNA-Seq S26-BJ


title: RNA-Seq S05-KC


title: RNA-Seq S06-KC


title: RNA-Seq S07-KC


title: RNA-Seq S09-KC


title: RNA-Seq S12-KC


title: RNA-Seq S15-KC


title: RNA-Seq S08-KC


title: RNA-Seq S10-KC


title: RNA-Seq S27-BJ


title: RNA-Seq S14-KC


title: RNA-Seq S16-KC


title: RNA-Seq S19-KC


title: RNA-Seq S13-KC


title: RNA-Seq S18-KC


title: RNA-Seq S20-KC


title: RNA-Seq S21-KC


title: RNA-Seq S28-BJ


title: RNA-Seq S23-KC


title: RNA-Seq S22-KC


title: RNA-Seq S24-KC


title: RNA-Seq S26-KC


title: RNA-Seq S35-kidney

source_name: kidney

value: kidney


title: RNA-Seq S37-kidney


title: RNA-Seq S38-kidney


title: RNA-Seq S25-KC


title: RNA-Seq S36-kidney


title: RNA-Seq S39-kidney


title: RNA-Seq S41-kidney


title: RNA-Seq S11-KC


title: RNA-Seq S35-BJ


title: RNA-Seq S42-kidney


title: RNA-Seq S43-kidney


title: RNA-Seq S17-KC


title: RNA-Seq S44-kidney


title: RNA-Seq S47-kidney


title: RNA-Seq S48-kidney


title: RNA-Seq S46-kidney


title: RNA-Seq S45-kidney


title: RNA-Seq S47-heart


title: RNA-Seq S49-kidney


title: RNA-Seq S48-heart


title: RNA-Seq S50-kidney


title: RNA-Seq S49-heart


title: RNA-Seq S01-liver

source_name: liver

value: liver


title: RNA-Seq S03-BJ


title: RNA-Seq S40-kidney


title: RNA-Seq S01-JC


title: RNA-Seq S02-JC


title: RNA-Seq S07-JC


title: RNA-Seq S03-JC


title: RNA-Seq S50-heart


title: RNA-Seq S10-JC


title: RNA-Seq S21-BJ


title: RNA-Seq S05-JC


title: RNA-Seq S13-JC


title: RNA-Seq S04-JC


title: RNA-Seq S12-JC


title: RNA-Seq S06-JC


title: RNA-Seq S14-JC


title: RNA-Seq S11-JC


title: RNA-Seq S09-JC


title: RNA-Seq S27-KC


title: RNA-Seq S22-BJ


title: RNA-Seq S30-KC


title: RNA-Seq S15-JC


title: RNA-Seq S08-JC


title: RNA-Seq S18-JC


title: RNA-Seq S16-JC


title: RNA-Seq S17-JC


title: RNA-Seq S32-KC


title: RNA-Seq S34-KC


title: RNA-Seq S31-KC


title: RNA-Seq S29-BJ


title: RNA-Seq S28-KC


title: RNA-Seq S33-KC


title: RNA-Seq S36-KC


title: RNA-Seq S47-KC


title: RNA-Seq S38-KC


title: RNA-Seq S48-KC


title: RNA-Seq S40-KC


title: RNA-Seq S44-KC


title: RNA-Seq S46-KC


title: RNA-Seq S37-KC


title: RNA-Seq S41-KC


title: RNA-Seq S50-KC


title: RNA-Seq S49-KC


title: RNA-Seq S42-KC


title: RNA-Seq S39-KC


title: RNA-Seq S29-KC


title: RNA-Seq S30-BJ


title: RNA-Seq S45-KC


title: RNA-Seq S35-KC


title: RNA-Seq S04-BJ


title: RNA-Seq S31-BJ


title: RNA-Seq S02-kidney


title: RNA-Seq S03-kidney


title: RNA-Seq S04-kidney


title: RNA-Seq S14-liver


title: RNA-Seq S43-KC


title: RNA-Seq S15-liver


title: RNA-Seq S16-liver


title: RNA-Seq S17-liver


title: RNA-Seq S18-liver


title: RNA-Seq S01-kidney


title: RNA-Seq S19-liver


title: RNA-Seq S20-liver


title: RNA-Seq S23-liver


title: RNA-Seq S26-liver


title: RNA-Seq S27-liver


title: RNA-Seq S21-liver


title: RNA-Seq S30-liver


title: RNA-Seq S31-liver


title: RNA-Seq S25-liver


title: RNA-Seq S38-BJ


title: RNA-Seq S29-liver


title: RNA-Seq S33-liver


title: RNA-Seq S28-liver


title: RNA-Seq S32-liver


title: RNA-Seq S39-BJ


title: RNA-Seq S38-liver


title: RNA-Seq S36-liver


title: RNA-Seq S35-liver


title: RNA-Seq S43-liver


title: RNA-Seq S41-liver


title: RNA-Seq S37-liver


title: RNA-Seq S22-liver


title: RNA-Seq S36-LW

source_name: rumen

value: rumen


title: RNA-Seq S24-liver


title: RNA-Seq S40-liver


title: RNA-Seq S47-LW


title: RNA-Seq S46-LW


title: RNA-Seq S38-LW


title: RNA-Seq S40-BJ


title: RNA-Seq S48-LW


title: RNA-Seq S50-BJ


title: RNA-Seq S39-liver


title: RNA-Seq S40-LW


title: RNA-Seq S49-BJ


title: RNA-Seq S35-LW


title: RNA-Seq S42-LW


title: RNA-Seq S04-QN

source_name: hypothalamus

value: hypothalamus


title: RNA-Seq S43-LW


title: RNA-Seq S41-LW


title: RNA-Seq S34-LW


title: RNA-Seq S34-liver


title: RNA-Seq S45-LW


title: RNA-Seq S44-LW


title: RNA-Seq S01-QN


title: RNA-Seq S02-QN


title: RNA-Seq S06-BJ


title: RNA-Seq S49-LW


title: RNA-Seq S03-QN


title: RNA-Seq S09-QN


title: RNA-Seq S07-QN


title: RNA-Seq S05-QN


title: RNA-Seq S50-RNA-Seq Spleen

source_name: spleen

value: spleen


title: RNA-Seq S06-QN


title: RNA-Seq S11-QN


title: RNA-Seq S01-WBC

source_name: blood (leukocyte)

value: blood (leukocyte)


title: RNA-Seq S39-LW


title: RNA-Seq S01-CT


title: RNA-Seq S10-QN


title: RNA-Seq S50-LW


title: RNA-Seq S08-QN


title: RNA-Seq S02-WBC


title: RNA-Seq S07-BJ


title: RNA-Seq S49-RNA-Seq Spleen


title: RNA-Seq S09-WBC


title: RNA-Seq S07-WBC


title: RNA-Seq S03-WBC


title: RNA-Seq S05-WBC


title: RNA-Seq S04-WBC


title: RNA-Seq S12-WBC


title: RNA-Seq S11-CT


title: RNA-Seq S12-CT


title: RNA-Seq S08-WBC


title: RNA-Seq S04-liver


title: RNA-Seq S02-liver


title: RNA-Seq S14-WBC


title: RNA-Seq S06-WBC


title: RNA-Seq S05-liver


title: RNA-Seq S37-LW


title: RNA-Seq S13-WBC


title: RNA-Seq S36-BJ


title: RNA-Seq S06-liver


title: RNA-Seq S03-liver


title: RNA-Seq S16-WBC


title: RNA-Seq S09-liver


title: RNA-Seq S12-liver


title: RNA-Seq S07-liver


title: RNA-Seq S37-BJ


title: RNA-Seq S10-liver


title: RNA-Seq S11-liver


title: RNA-Seq S11-WBC


title: RNA-Seq S06-LW


title: RNA-Seq S07-LW


title: RNA-Seq S13-liver


title: RNA-Seq S09-LW


title: RNA-Seq S11-LW


title: RNA-Seq S12-LW


title: RNA-Seq S13-LW


title: RNA-Seq S14-LW


title: RNA-Seq S15-LW


title: RNA-Seq S47-BJ


title: RNA-Seq S16-LW


title: RNA-Seq S08-liver


title: RNA-Seq S17-LW


title: RNA-Seq S19-LW


title: RNA-Seq S05-LW


title: RNA-Seq S18-LW


title: RNA-Seq S20-LW


title: RNA-Seq S46-BJ


title: RNA-Seq S23-LW


title: RNA-Seq S24-LW


title: RNA-Seq S48-BJ


title: RNA-Seq S08-LW


title: RNA-Seq S22-LW


title: RNA-Seq S27-LW


title: RNA-Seq S29-LW


title: RNA-Seq S28-LW


title: RNA-Seq S15-WBC


title: RNA-Seq S30-LW


title: RNA-Seq S10-LW


title: RNA-Seq S31-LW


title: RNA-Seq S33-LW


title: RNA-Seq S32-LW


title: RNA-Seq S21-RNA-Seq Spleen


title: RNA-Seq S22-RNA-Seq Spleen


title: RNA-Seq S10-WBC


title: RNA-Seq S23-RNA-Seq Spleen


title: RNA-Seq S08-CT


title: RNA-Seq S21-LW


title: RNA-Seq S25-RNA-Seq Spleen


title: RNA-Seq S26-RNA-Seq Spleen


title: RNA-Seq S27-RNA-Seq Spleen


title: RNA-Seq S28-RNA-Seq Spleen


title: RNA-Seq S29-RNA-Seq Spleen


title: RNA-Seq S30-RNA-Seq Spleen


title: RNA-Seq S26-LW


title: RNA-Seq S36-RNA-Seq Spleen


title: RNA-Seq S33-RNA-Seq Spleen


title: RNA-Seq S31-RNA-Seq Spleen


title: RNA-Seq S34-RNA-Seq Spleen


title: RNA-Seq S35-RNA-Seq Spleen


title: RNA-Seq S39-RNA-Seq Spleen


title: RNA-Seq S40-RNA-Seq Spleen


title: RNA-Seq S25-LW


title: RNA-Seq S20-RNA-Seq Spleen


title: RNA-Seq S41-RNA-Seq Spleen


title: RNA-Seq S42-RNA-Seq Spleen


title: RNA-Seq S24-RNA-Seq Spleen


title: RNA-Seq S43-RNA-Seq Spleen


title: RNA-Seq S44-RNA-Seq Spleen


title: RNA-Seq S45-RNA-Seq Spleen


title: RNA-Seq S10-CT


title: RNA-Seq S48-RNA-Seq Spleen


title: RNA-Seq S46-RNA-Seq Spleen


title: RNA-Seq S16-CT


title: RNA-Seq S47-RNA-Seq Spleen


title: RNA-Seq S38-RNA-Seq Spleen


title: RNA-Seq S07-XDM

source_name: artery

value: artery


title: RNA-Seq S10-XDM


title: RNA-Seq S32-RNA-Seq Spleen


title: RNA-Seq S08-XDM


title: RNA-Seq S11-XDM


title: RNA-Seq S09-CT


title: RNA-Seq S12-XDM


title: RNA-Seq S37-RNA-Seq Spleen


title: RNA-Seq S13-XDM


title: RNA-Seq S15-XDM


title: RNA-Seq S14-XDM


title: RNA-Seq S16-XDM


title: RNA-Seq S19-XDM


title: RNA-Seq S18-XDM


title: RNA-Seq S17-XDM


title: RNA-Seq S23-XDM


title: RNA-Seq S20-XDM


title: RNA-Seq S21-XDM


title: RNA-Seq S25-XDM


title: RNA-Seq S24-XDM


title: RNA-Seq S09-XDM


title: RNA-Seq S26-XDM


title: RNA-Seq S28-XDM


title: RNA-Seq S30-XDM


title: RNA-Seq S31-XDM


title: RNA-Seq S29-XDM


title: RNA-Seq S33-XDM


title: RNA-Seq S34-XDM


title: RNA-Seq S27-XDM


title: RNA-Seq S32-XDM


title: RNA-Seq S23-ZC

source_name: duodenum

value: duodenum


title: RNA-Seq S26-ZC


title: RNA-Seq S35-XDM


title: RNA-Seq S24-ZC


title: RNA-Seq S28-CT


title: RNA-Seq S25-ZC


title: RNA-Seq S17-CT


title: RNA-Seq S29-ZC


title: RNA-Seq S22-XDM


title: RNA-Seq S32-ZC


title: RNA-Seq S30-ZC


title: RNA-Seq S31-ZC


title: RNA-Seq S18-CT


title: RNA-Seq S35-ZC


title: RNA-Seq S33-ZC


title: RNA-Seq S37-ZC


title: RNA-Seq S34-ZC


title: RNA-Seq S29-CT


title: RNA-Seq S36-ZC


title: RNA-Seq S40-ZC


title: RNA-Seq S44-ZC


title: RNA-Seq S39-ZC


title: RNA-Seq S45-ZC


title: RNA-Seq S38-ZC


title: RNA-Seq S41-ZC


title: RNA-Seq S42-ZC


title: RNA-Seq S28-ZC


title: RNA-Seq S46-ZC


title: RNA-Seq S30-CT


title: RNA-Seq S43-ZC


title: RNA-Seq S48-ZC


title: RNA-Seq S49-ZC


title: RNA-Seq S50-ZC


title: RNA-Seq S27-ZC


title: RNA-Seq S02-ZF

source_name: adipose

value: adipose


title: RNA-Seq S04-ZF


title: RNA-Seq S47-ZC


title: RNA-Seq S01-ZF


title: RNA-Seq S03-ZF


title: RNA-Seq S41-CT


title: RNA-Seq S05-ZF


title: RNA-Seq S10-BJ


title: RNA-Seq S44-CT


title: RNA-Seq S42-CT


title: RNA-Seq S45-CT


title: RNA-Seq S49-CT


title: RNA-Seq S47-CT


title: RNA-Seq S46-CT


title: RNA-Seq S20-BJ


title: RNA-Seq S43-heart


title: RNA-Seq S44-heart


title: RNA-Seq S48-CT


title: RNA-Seq S41-heart


title: RNA-Seq S42-heart


title: RNA-Seq S45-heart


title: RNA-Seq S01-BJ


title: RNA-Seq S50-CT


title: RNA-Seq S02-BJ


title: RNA-Seq S01-DN

source_name: cerebrum

value: cerebrum


title: RNA-Seq S46-heart


title: RNA-Seq S43-CT


title: RNA-Seq S11-BJ


title: RNA-Seq S03-DN


title: RNA-Seq S06-DN


title: RNA-Seq S02-DN


title: RNA-Seq S07-DN


title: RNA-Seq S05-DN


title: RNA-Seq S04-DN


title: RNA-Seq S14-DN


title: RNA-Seq S10-DN


title: RNA-Seq S08-DN


title: RNA-Seq S12-DN


title: RNA-Seq S13-DN


title: RNA-Seq S15-DN


title: RNA-Seq S09-DN


title: RNA-Seq S17-DN


title: RNA-Seq S11-DN


title: RNA-Seq S19-DN


title: RNA-Seq S20-DN


title: RNA-Seq S12-BJ


title: RNA-Seq S18-DN


title: RNA-Seq S16-DN


title: RNA-Seq S22-DN


title: RNA-Seq S21-DN


title: RNA-Seq S13-BJ


title: RNA-Seq S24-DN


title: RNA-Seq S26-DN


title: RNA-Seq S25-DN


title: RNA-Seq S27-DN


title: RNA-Seq S23-DN


title: RNA-Seq S28-DN


title: RNA-Seq S29-DN


title: RNA-Seq S30-DN


title: RNA-Seq S14-BJ


title: RNA-Seq S46-liver


title: RNA-Seq S47-liver


title: RNA-Seq S45-liver


title: RNA-Seq S48-liver


title: RNA-Seq S49-liver


title: RNA-Seq S02-lung

source_name: lung

value: lung


title: RNA-Seq S06-lung


title: RNA-Seq S05-lung


title: RNA-Seq S08-lung


title: RNA-Seq S41-BJ


title: RNA-Seq S01-lung


title: RNA-Seq S05-BJ


title: RNA-Seq S50-liver


title: RNA-Seq S03-lung


title: RNA-Seq S04-lung


title: RNA-Seq S07-lung


title: RNA-Seq S10-lung


title: RNA-Seq S14-lung


title: RNA-Seq S11-lung


title: RNA-Seq S42-BJ


title: RNA-Seq S15-lung


title: RNA-Seq S17-lung


title: RNA-Seq S19-lung


title: RNA-Seq S18-lung


title: RNA-Seq S21-lung


title: RNA-Seq S20-lung


title: RNA-Seq S22-lung


title: RNA-Seq S23-lung


title: RNA-Seq S12-QN


title: RNA-Seq S13-QN


title: RNA-Seq S09-lung


title: RNA-Seq S14-QN


title: RNA-Seq S02-CT

source_name: pituitary

value: pituitary


title: RNA-Seq S13-lung


title: RNA-Seq S17-QN


title: RNA-Seq S22-QN


title: RNA-Seq S24-QN


title: RNA-Seq S15-QN


title: RNA-Seq S19-QN


title: RNA-Seq S12-lung


title: RNA-Seq S23-QN


title: RNA-Seq S25-QN


title: RNA-Seq S18-QN


title: RNA-Seq S21-QN


title: RNA-Seq S26-QN


title: RNA-Seq S16-lung


title: RNA-Seq S03-CT


title: RNA-Seq S20-QN


title: RNA-Seq S29-QN


title: RNA-Seq S32-QN


title: RNA-Seq S27-QN


title: RNA-Seq S34-QN


title: RNA-Seq S35-QN


title: RNA-Seq S30-QN


title: RNA-Seq S31-QN


title: RNA-Seq S33-QN


title: RNA-Seq S04-CT


title: RNA-Seq S16-QN


title: RNA-Seq S36-QN


title: RNA-Seq S39-QN


title: RNA-Seq S30-WBC


title: RNA-Seq S28-WBC


title: RNA-Seq S37-QN


title: RNA-Seq S27-WBC


title: RNA-Seq S31-WBC


title: RNA-Seq S14-CT


title: RNA-Seq S40-QN


title: RNA-Seq S32-WBC


title: RNA-Seq S34-WBC


title: RNA-Seq S28-QN


title: RNA-Seq S35-WBC


title: RNA-Seq S40-WBC


title: RNA-Seq S37-WBC


title: RNA-Seq S39-WBC


title: RNA-Seq S38-WBC


title: RNA-Seq S43-WBC


title: RNA-Seq S45-WBC


title: RNA-Seq S41-WBC


title: RNA-Seq S44-WBC


title: RNA-Seq S38-QN


title: RNA-Seq S46-WBC


title: RNA-Seq S29-WBC


title: RNA-Seq S15-CT


title: RNA-Seq S42-WBC


title: RNA-Seq S33-WBC


title: RNA-Seq S36-WBC


title: RNA-Seq S47-WBC


title: RNA-Seq S48-WBC


title: RNA-Seq S50-WBC


title: RNA-Seq S49-WBC


title: RNA-Seq S01-XDM


title: RNA-Seq S02-XDM


title: RNA-Seq S05-XDM


title: RNA-Seq S03-XDM


title: RNA-Seq S06-XDM


title: RNA-Seq S04-XDM


title: RNA-Seq S15-XN

source_name: cerebrellum

value: cerebrellum


title: RNA-Seq S20-XN


title: RNA-Seq S19-XN


title: RNA-Seq S22-CT


title: RNA-Seq S16-XN


title: RNA-Seq S18-XN


title: RNA-Seq S17-XN


title: RNA-Seq S21-XN


title: RNA-Seq S24-XN


title: RNA-Seq S23-XN


title: RNA-Seq S27-XN


title: RNA-Seq S23-CT


title: RNA-Seq S22-XN


title: RNA-Seq S25-XN


title: RNA-Seq S31-XN


title: RNA-Seq S26-XN


title: RNA-Seq S29-XN


title: RNA-Seq S28-XN


title: RNA-Seq S36-XN


title: RNA-Seq S40-XN


title: RNA-Seq S33-XN


title: RNA-Seq S41-XN


title: RNA-Seq S38-XN


title: RNA-Seq S37-XN


title: RNA-Seq S42-XN


title: RNA-Seq S38-ZF


title: RNA-Seq S34-CT


title: RNA-Seq S30-XN


title: RNA-Seq S34-XN


title: RNA-Seq S48-ZF


title: RNA-Seq S35-XN


title: RNA-Seq S24-CT


title: RNA-Seq S39-XN


title: RNA-Seq S14-XN


title: RNA-Seq S01-ZW

source_name: abomasum

value: abomasum


title: RNA-Seq S06-ZW


title: RNA-Seq S39-ZF


title: RNA-Seq S10-ZW


title: RNA-Seq S09-ZW


title: RNA-Seq S41-ZF


title: RNA-Seq S42-ZF


title: RNA-Seq S43-ZF


title: RNA-Seq S45-ZF


title: RNA-Seq S35-CT


title: RNA-Seq S47-ZF


title: RNA-Seq S46-ZF


title: RNA-Seq S12-ZW


title: RNA-Seq S32-XN


title: RNA-Seq S16-ZW


title: RNA-Seq S14-ZW


title: RNA-Seq S49-ZF


title: RNA-Seq S36-CT


title: RNA-Seq S04-ZW


title: RNA-Seq S50-ZF


title: RNA-Seq S17-ZW


title: RNA-Seq S02-ZW


title: RNA-Seq S08-ZW


title: RNA-Seq S40-ZF


title: RNA-Seq S05-ZW


title: RNA-Seq S03-ZW


title: RNA-Seq S34-DN


title: RNA-Seq S44-ZF


title: RNA-Seq S36-DN


title: RNA-Seq S39-DN


title: RNA-Seq S13-ZW


title: RNA-Seq S41-DN


title: RNA-Seq S42-DN


title: RNA-Seq S15-ZW


title: RNA-Seq S43-DN


title: RNA-Seq S07-ZW


title: RNA-Seq S45-DN


title: RNA-Seq S18-ZW


title: RNA-Seq S47-DN


title: RNA-Seq S11-ZW


title: RNA-Seq S35-DN


title: RNA-Seq S31-DN


title: RNA-Seq S46-DN


title: RNA-Seq S32-DN


title: RNA-Seq S02-heart

source_name: heart

value: heart


title: RNA-Seq S37-DN


title: RNA-Seq S50-DN


title: RNA-Seq S40-DN


title: RNA-Seq S44-DN


title: RNA-Seq S15-BJ

source_name: muscle

value: muscle


title: RNA-Seq S48-DN


title: RNA-Seq S33-DN


title: RNA-Seq S49-DN


title: RNA-Seq S10-heart


title: RNA-Seq S01-heart


title: RNA-Seq S16-BJ


title: RNA-Seq S24-JC

source_name: colon

value: colon


title: RNA-Seq S38-DN


title: RNA-Seq S03-heart


title: RNA-Seq S04-heart


title: RNA-Seq S37-CT


title: RNA-Seq S05-heart


title: RNA-Seq S06-heart


title: RNA-Seq S27-JC


title: RNA-Seq S07-heart


title: RNA-Seq S20-JC


title: RNA-Seq S19-JC


title: RNA-Seq S08-heart


title: RNA-Seq S09-heart


title: RNA-Seq S23-BJ


title: RNA-Seq S32-JC


title: RNA-Seq S21-JC


title: RNA-Seq S26-JC


title: RNA-Seq S33-JC


title: RNA-Seq S28-JC


title: RNA-Seq S29-JC


title: RNA-Seq S34-JC


title: RNA-Seq S35-JC


title: RNA-Seq S23-JC


title: RNA-Seq S30-JC


title: RNA-Seq S39-JC


title: RNA-Seq S31-JC


title: RNA-Seq S25-JC


title: RNA-Seq S38-JC


title: RNA-Seq S24-BJ


title: RNA-Seq S36-JC


title: RNA-Seq S43-JC


title: RNA-Seq S22-JC


title: RNA-Seq S37-JC


title: RNA-Seq S40-JC


title: RNA-Seq S05-kidney

source_name: kidney

value: kidney


title: RNA-Seq S47-JC


title: RNA-Seq S41-JC


title: RNA-Seq S25-BJ


title: RNA-Seq S42-JC


title: RNA-Seq S45-JC


title: RNA-Seq S06-kidney


title: RNA-Seq S09-kidney


title: RNA-Seq S46-JC


title: OD_STAGE13_024_10HPF_JUVENILE

city: Shanghai

first: Kaile

last: Zhang

address: No. 600 Yishan Road

department: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to OSAKA2016 whole transcriptome using hisat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a clustromlized Perl script
Genome_build: OSAKA2016

organism: Oikopleura dioica

source_name: Whole embryo

growth_protocol: O. dioica were collected at Sakoshi Bay and Tossaki Port in Hyodo, Japan, and cultured over 180 generations for more than three years in the inland laboratory, as previously described (Nishida, 2008; Omotezako et al., 2013). Animals were cultured at 20?C. At this condition, O.dioica hatches at 3 h after fertilization (hpf) and complete organogenesis and forms fully functional body by 10 hpf. Animals mature sexually and spawn at the fifth days.

extract_protocol:
total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols, AVW(non-strand specific), staged RNA-Seq (strand-specific)

tag: population

value: Japanese

value: embryo

value: wild type


title: OD_STAGE13_023_10HPF_JUVENILE


title: OD_STAGE10_033_3HPF_HATCHED_LARVAE


title: OD_STAGE11_020_5HPF_EARLY_ORGANOGENESIS


title: OD_STAGE12_021_8HPF_LATE_ORGANOGENESIS


title: OD_STAGE10_005_3HPF_HATCHED_LARVAE


title: OD_STAGE11_007_5HPF_EARLY_ORGANOGENESIS


title: OD_STAGE12_035_8HPF_LATE_ORGANOGENESIS


title: OD_STAGE12_008_8HPF_LATE_ORGANOGENESIS


title: OD_STAGE09_004_2.5HPF_TADPOLE_LARVAE


title: OD_STAGE09_032_2.5HPF_TADPOLE_LARVAE


title: OD_STAGE08_031_1.5HPF


title: OD_STAGE08_002_1.5HPF


title: OD_STAGE08_019_1.5HPF


title: OD_STAGE11_006_5HPF_EARLY_ORGANOGENESIS


title: OD_STAGE07_001_32CELL


title: OD_STAGE06_017_16CELL


title: OD_STAGE10_034_3HPF_HATCHED_LARVAE


title: RNA-Seq S07-kidney


title: RNA-Seq S44-JC


title: OD_STAGE05_044_8CELL


title: OD_STAGE09_003_2.5HPF_TADPOLE_LARVAE


title: RNA-Seq S08-kidney


title: OD_STAGE06_018_16CELL


title: OD_STAGE07_047_32CELL


title: OD_STAGE07_048_32CELL


title: OD_STAGE05_030_8CELL


title: OD_STAGE13_022_10HPF_JUVENILE


title: OD_STAGE06_046_16CELL


title: OD_STAGE04_036_4CELL


title: OD_STAGE02_042_FERTILIZED_EGG


title: OD_STAGE05_045_8CELL


title: OD_STAGE03_013_2CELL


title: OD_STAGE02_010_FERTILIZED_EGG


title: OD_STAGE04_037_4CELL


title: OD_STAGE04_043_4CELL


title: OD_STAGE03_014_2CELL


title: OD_STAGE01_009_UNFERTILIZED_EGG


title: OD_STAGE02_011_FERTILIZED_EGG


title: OD_STAGE03_012_2CELL


title: OD_ADULT_FEMALE_028


title: OD_STAGE01_029_UNFERTILIZED_EGG


title: OD_STAGE01_041_UNFERTILIZED_EGG


title: OD_ADULT_FEMALE_027


title: OD_Whole_embryo_No5_12HPF_S42

value: 12 hpf


title: OD_Whole_embryo_No4_8CELL_S33

value: 8 cell


title: OD_ADULT_MALE_026


title: OD_Vegetal_No6_8CELL_S44

source_name: Vegetal hemisphere


title: OD_Vegetal_No6_12HPF_S47


title: OD_ADULT_MALE_025


title: OD_Vegetal_No5_12HPF_S41


title: OD_Whole_embryo_No6_12HPF_S48


title: OD_Whole_embryo_No6_8CELL_S45


title: OD_Whole_embryo_No5_8CELL_S39


title: OD_Whole_embryo_No3_8CELL_S27


title: OD_Whole_embryo_No4_12HPF_S36


title: OD_Vegetal_No3_12HPF_S29


title: OD_Animal_No5_8CELL_S37

source_name: Animal hemisphere


title: OD_Animal_No5_12HPF_S40


title: OD_Animal_No6_8CELL_S43


title: OD_Vegetal_No5_8CELL_S38


title: OD_Animal_No3_12HPF_S28


title: OD_Animal_No3_8CELL_S25


title: OD_Whole_embryo_No3_12HPF_S30


title: OD_Vegetal_No3_8CELL_S26


title: OD_Vegetal_No4_12HPF_S35


title: OD_Vegetal_No4_8CELL_S32


title: RNA-Seq S61-XDM

value: artery


title: RNA-Seq S10-HC

source_name: ileum

value: ileum


title: OD_Animal_No6_12HPF_S46


title: RNA-Seq S65-XDM


title: OD_Animal_No4_8CELL_S31


title: RNA-Seq S75-XDM


title: OD_Animal_No4_12HPF_S34


title: RNA-Seq S76-XDM


title: RNA-Seq S73-XDM


title: RNA-Seq S62-XDM


title: RNA-Seq S51-XN

source_name: cerebellum

value: cerebellum


title: RNA-Seq S54-XN


title: RNA-Seq S63-XDM

source_name: artery


title: RNA-Seq S66-XDM


title: RNA-Seq S64-XDM


title: RNA-Seq S30-HC


title: RNA-Seq S53-XN


title: RNA-Seq S35-HC


title: RNA-Seq S32-HC


title: RNA-Seq S34-HC


title: RNA-Seq S38-HC


title: RNA-Seq S87-BJ


title: RNA-Seq S11-HC


title: RNA-Seq S40-HC


title: RNA-Seq S55-XN


title: RNA-Seq S33-HC


title: RNA-Seq S52-XN


title: RNA-Seq S36-HC


title: RNA-Seq S31-HC


title: RNA-Seq S43-HC


title: RNA-Seq S41-HC


title: RNA-Seq S37-HC


title: RNA-Seq S39-HC


title: RNA-Seq S48-HC


title: RNA-Seq S50-HC


title: RNA-Seq S89-BJ


title: RNA-Seq S42-HC


title: RNA-Seq S84-HC


title: RNA-Seq S88-BJ


title: RNA-Seq S83-HC


title: RNA-Seq S44-HC


title: RNA-Seq S45-HC


title: RNA-Seq S46-HC


title: RNA-Seq S47-HC


title: RNA-Seq S81-HC


title: RNA-Seq S86-HC


title: RNA-Seq S82-HC


title: RNA-Seq S82-BJ


title: RNA-Seq S88-JC


title: RNA-Seq S87-JC


title: RNA-Seq S88-HC


title: RNA-Seq S81-KC

source_name: jejunum

value: jejunum


title: RNA-Seq S85-HC


title: RNA-Seq S89-JC


title: RNA-Seq S82-KC


title: RNA-Seq S84-KC


title: RNA-Seq S89-HC


title: RNA-Seq S82-CT


title: RNA-Seq S81-BJ


title: RNA-Seq S83-CT


title: RNA-Seq S87-KC


title: RNA-Seq S88-KC


title: RNA-Seq S82-kidney


title: RNA-Seq S87-HC


title: RNA-Seq S86-kidney


title: RNA-Seq S84-kidney


title: RNA-Seq S85-KC


title: RNA-Seq S83-KC


title: RNA-Seq S86-KC


title: RNA-Seq S89-kidney


title: RNA-Seq S85-kidney


title: RNA-Seq S81-kidney


title: RNA-Seq S83-kidney


title: RNA-Seq S82-liver

source_name: liver

value: liver


title: RNA-Seq S83-liver


title: RNA-Seq S85-liver


title: RNA-Seq S89-liver


title: RNA-Seq S81-liver


title: RNA-Seq S87-liver


title: RNA-Seq S84-CT

value: pituitary


title: RNA-Seq S81-lung

value: lung


title: RNA-Seq S85-CT


title: RNA-Seq S81-ZC

source_name: duodenum

value: duodenum


title: RNA-Seq S88-XN


title: RNA-Seq S86-ZC


title: RNA-Seq S89-XN


title: RNA-Seq S82-ZC


title: RNA-Seq S82-DN

source_name: cerebrum

value: cerebrum


title: RNA-Seq S88-ZC


title: RNA-Seq S83-BJ

value: muscle


title: RNA-Seq S83-ZC


title: RNA-Seq S88-kidney


title: RNA-Seq S85-ZC


title: RNA-Seq S83-ZF

source_name: adipose

value: adipose


title: RNA-Seq S84-ZC


title: RNA-Seq S83-DN


title: RNA-Seq S86-liver


title: RNA-Seq S84-liver


title: RNA-Seq S82-ZF


title: RNA-Seq S84-ZF


title: RNA-Seq S88-liver


title: RNA-Seq S82-lung

source_name: lung


title: RNA-Seq S84-DN


title: RNA-Seq S82-ZW

source_name: abomasum

value: abomasum


title: RNA-Seq S87-ZF


title: RNA-Seq S87-ZC


title: RNA-Seq S84-ZW


title: RNA-Seq S85-ZW


title: RNA-Seq S89-ZF


title: RNA-Seq S86-ZF


title: RNA-Seq S88-ZF


title: RNA-Seq S86-ZW


title: RNA-Seq S87-ZW


title: RNA-Seq S81-ZW


title: RNA-Seq S88-ZW


title: RNA-Seq S83-ZW


title: RNA-Seq S52-BJ


title: RNA-Seq S85-DN


title: RNA-Seq S89-ZC


title: RNA-Seq S89-ZW


title: RNA-Seq S53-BJ


title: RNA-Seq S81-ZF


title: RNA-Seq S61-BJ


title: RNA-Seq S54-BJ


title: RNA-Seq S51-BJ


title: RNA-Seq S55-BJ


title: RNA-Seq S56-BJ


title: RNA-Seq S63-BJ


title: RNA-Seq S64-BJ


title: RNA-Seq S62-BJ


title: RNA-Seq S74-BJ


title: RNA-Seq S76-BJ


title: RNA-Seq S65-BJ


title: RNA-Seq S71-BJ


title: RNA-Seq S86-DN


title: RNA-Seq S66-BJ


title: RNA-Seq S72-BJ


title: RNA-Seq S54-DN


title: RNA-Seq S55-DN


title: RNA-Seq S73-BJ


title: RNA-Seq S87-DN


title: RNA-Seq S61-DN


title: RNA-Seq S75-BJ


title: RNA-Seq S71-DN


title: RNA-Seq S65-DN


title: RNA-Seq S51-DN


title: RNA-Seq S72-DN


title: RNA-Seq S52-DN


title: RNA-Seq S56-DN


title: RNA-Seq S53-DN


title: RNA-Seq S62-DN


title: RNA-Seq S63-DN


title: RNA-Seq S88-DN


title: RNA-Seq S66-DN


title: RNA-Seq S64-DN


title: RNA-Seq S84-heart

source_name: heart

value: heart


title: RNA-Seq S86-heart


title: RNA-Seq S81-CT

source_name: pituitary


title: RNA-Seq S89-heart


title: RNA-Seq S87-heart


title: RNA-Seq S85-heart


title: RNA-Seq S74-DN


title: RNA-Seq S83-heart


title: RNA-Seq S84-lung


title: RNA-Seq S83-lung


title: RNA-Seq S86-lung


title: RNA-Seq S81-LW

source_name: rumen

value: rumen


title: RNA-Seq S73-DN


title: RNA-Seq S82-heart


title: RNA-Seq S81-heart


title: RNA-Seq S82-LW


title: RNA-Seq S81-JC

source_name: colon

value: colon


title: RNA-Seq S88-heart


title: RNA-Seq S84-LW


title: RNA-Seq S83-JC


title: RNA-Seq S87-lung


title: RNA-Seq S85-JC


title: RNA-Seq S89-lung


title: RNA-Seq S83-LW


title: RNA-Seq S86-LW


title: RNA-Seq S86-CT


title: RNA-Seq S82-JC


title: RNA-Seq S84-QN

source_name: hypothalamus

value: hypothalamus


title: RNA-Seq S84-JC


title: RNA-Seq S87-CT


title: RNA-Seq S85-QN


title: RNA-Seq S83-QN


title: RNA-Seq S85-lung


title: RNA-Seq S87-LW


title: RNA-Seq S86-JC


title: RNA-Seq S82-QN


title: RNA-Seq S81-RNA-Seq Spleen

source_name: spleen

value: spleen


title: RNA-Seq S82-RNA-Seq Spleen


title: RNA-Seq S88-lung


title: RNA-Seq S88-LW


title: RNA-Seq S87-RNA-Seq Spleen


title: RNA-Seq S87-QN


title: RNA-Seq S89-LW


title: RNA-Seq S89-QN


title: RNA-Seq S89-RNA-Seq Spleen


title: RNA-Seq S84-RNA-Seq Spleen


title: RNA-Seq S85-LW


title: RNA-Seq S86-RNA-Seq Spleen


title: RNA-Seq S88-RNA-Seq Spleen


title: RNA-Seq S88-CT


title: RNA-Seq S83-WBC

source_name: blood (leukocyte)

value: blood (leukocyte)


title: RNA-Seq S88-QN


title: RNA-Seq S84-WBC


title: RNA-Seq S86-QN


title: RNA-Seq S83-RNA-Seq Spleen


title: RNA-Seq S85-WBC


title: RNA-Seq S87-WBC


title: RNA-Seq S83-XDM

value: artery


title: RNA-Seq S88-WBC


title: RNA-Seq S89-WBC


title: RNA-Seq S82-WBC


title: RNA-Seq S84-XDM


title: RNA-Seq S86-WBC


title: RNA-Seq S90-WBC


title: RNA-Seq S81-XDM


title: RNA-Seq S81-WBC


title: RNA-Seq S82-XDM


title: RNA-Seq S81-XN

value: cerebellum


title: RNA-Seq S85-XDM


title: RNA-Seq S86-XDM


title: RNA-Seq S81-DN


title: RNA-Seq S88-XDM


title: RNA-Seq S89-XDM


title: RNA-Seq S86-XN


title: RNA-Seq S82-XN


title: RNA-Seq S83-XN


title: RNA-Seq S76-DN


title: RNA-Seq S51-heart


title: RNA-Seq S84-XN


title: RNA-Seq S85-XN


title: RNA-Seq S89-CT


title: RNA-Seq S55-heart


title: RNA-Seq S85-RNA-Seq Spleen


title: RNA-Seq S53-heart


title: RNA-Seq S87-XN


title: RNA-Seq S89-DN


title: RNA-Seq S63-heart


title: RNA-Seq S75-DN


title: RNA-Seq S87-XDM


title: RNA-Seq S65-heart


title: RNA-Seq S61-heart


title: RNA-Seq S52-heart


title: RNA-Seq S54-heart


title: RNA-Seq S56-heart


title: RNA-Seq S62-heart


title: RNA-Seq S64-heart


title: RNA-Seq S72-heart


title: RNA-Seq S71-heart


title: RNA-Seq S74-heart


title: RNA-Seq S75-heart


title: RNA-Seq S01-HC

source_name: ileum

value: ileum


title: RNA-Seq S51-kidney

source_name: kidney

value: kidney


title: RNA-Seq S76-heart


title: RNA-Seq S52-kidney


title: RNA-Seq S54-kidney


title: RNA-Seq S73-heart


title: RNA-Seq S56-kidney


title: RNA-Seq S53-kidney


title: RNA-Seq S63-kidney


title: RNA-Seq S62-kidney


title: RNA-Seq S61-kidney


title: RNA-Seq S71-kidney


title: RNA-Seq S72-kidney


title: RNA-Seq S75-kidney


title: RNA-Seq S02-HC


title: RNA-Seq S64-kidney


title: RNA-Seq S53-liver

value: liver


title: RNA-Seq S03-HC


title: RNA-Seq S65-kidney


title: RNA-Seq S55-liver


title: RNA-Seq S54-liver


title: RNA-Seq S56-liver


title: RNA-Seq S74-kidney


title: RNA-Seq S73-kidney


title: RNA-Seq S63-liver


title: RNA-Seq S61-liver


title: RNA-Seq S55-kidney


title: RNA-Seq S76-kidney


title: RNA-Seq S62-liver


title: RNA-Seq S66-liver


title: RNA-Seq S65-liver


title: RNA-Seq S73-liver


title: RNA-Seq S74-liver


title: RNA-Seq S64-liver


title: RNA-Seq S75-liver


title: RNA-Seq S72-liver


title: RNA-Seq S71-liver


title: RNA-Seq S76-liver


title: RNA-Seq S51-lung

value: lung


title: RNA-Seq S66-kidney


title: RNA-Seq S53-lung


title: RNA-Seq S52-lung


title: RNA-Seq S54-lung


title: RNA-Seq S04-HC


title: RNA-Seq S05-HC


title: RNA-Seq S55-lung


title: RNA-Seq S56-lung


title: RNA-Seq S61-lung


title: RNA-Seq S65-lung


title: RNA-Seq S63-lung


title: RNA-Seq S73-lung


title: RNA-Seq S64-lung


title: RNA-Seq S72-lung


title: RNA-Seq S66-lung


title: RNA-Seq S74-lung


title: RNA-Seq S61-QN


title: RNA-Seq S62-QN


title: RNA-Seq S54-QN


title: RNA-Seq S75-lung


title: RNA-Seq S64-QN


title: RNA-Seq S06-HC


title: RNA-Seq S76-lung


title: RNA-Seq S53-QN


title: RNA-Seq S66-QN


title: RNA-Seq S65-QN


title: RNA-Seq S63-QN


title: RNA-Seq S07-HC


title: RNA-Seq S71-QN


title: RNA-Seq S62-lung


title: RNA-Seq S84-BJ

source_name: muscle


title: RNA-Seq S72-QN


title: RNA-Seq S73-QN


title: RNA-Seq S53-RNA-Seq Spleen


title: RNA-Seq S52-RNA-Seq Spleen


title: RNA-Seq S74-QN


title: RNA-Seq S75-QN


title: RNA-Seq S08-HC


title: RNA-Seq S51-RNA-Seq Spleen


title: RNA-Seq S76-QN


title: RNA-Seq S62-XN

source_name: cerebellum


title: RNA-Seq S55-RNA-Seq Spleen


title: RNA-Seq S66-heart


title: RNA-Seq S61-XN


title: RNA-Seq S56-XN


title: RNA-Seq S72-XN


title: RNA-Seq S66-XN


title: RNA-Seq S63-XN


title: RNA-Seq S12-HC


title: RNA-Seq S74-XN


title: RNA-Seq S64-XN


title: RNA-Seq S76-XN


title: RNA-Seq S71-XN


title: RNA-Seq S85-BJ


title: RNA-Seq S65-XN


title: RNA-Seq S13-HC


title: RNA-Seq S15-HC


title: RNA-Seq S73-XN


title: RNA-Seq S75-XN


title: RNA-Seq S17-HC


title: RNA-Seq S14-HC


title: RNA-Seq S16-HC


title: RNA-Seq S18-HC


title: RNA-Seq S20-HC


title: RNA-Seq S21-HC


title: RNA-Seq S23-HC


title: RNA-Seq S22-HC


title: RNA-Seq S19-HC


title: RNA-Seq S26-HC


title: RNA-Seq S27-HC


title: RNA-Seq S28-HC


title: RNA-Seq S86-BJ


title: RNA-Seq S24-HC


title: RNA-Seq S29-HC


title: RNA-Seq S61-RNA-Seq Spleen


title: RNA-Seq S62-RNA-Seq Spleen


title: RNA-Seq S65-RNA-Seq Spleen


title: RNA-Seq S56-RNA-Seq Spleen


title: RNA-Seq S64-RNA-Seq Spleen


title: RNA-Seq S66-RNA-Seq Spleen


title: RNA-Seq S63-RNA-Seq Spleen


title: RNA-Seq S71-RNA-Seq Spleen


title: RNA-Seq S72-RNA-Seq Spleen


title: RNA-Seq S73-RNA-Seq Spleen


title: RNA-Seq S75-RNA-Seq Spleen


title: RNA-Seq S74-RNA-Seq Spleen


title: RNA-Seq S54-XDM

source_name: artery


title: RNA-Seq S76-RNA-Seq Spleen


title: RNA-Seq S52-XDM


title: RNA-Seq S55-XDM


title: RNA-Seq S18-WBC


title: RNA-Seq S17-WBC


title: RNA-Seq S25-HC


title: RNA-Seq S21-WBC


title: RNA-Seq S19-WBC


title: RNA-Seq S22-WBC


title: RNA-Seq S24-WBC


title: RNA-Seq S26-WBC


title: RNA-Seq S13-CT

value: pituitary


title: RNA-Seq S23-WBC


title: RNA-Seq S25-WBC


title: RNA-Seq S19-CT


title: RNA-Seq S39-XDM


title: RNA-Seq S37-XDM


title: RNA-Seq S41-XDM


title: RNA-Seq S38-XDM


title: RNA-Seq S36-XDM


title: RNA-Seq S42-XDM


title: RNA-Seq S43-XDM


title: RNA-Seq S53-XDM


title: RNA-Seq S46-XDM


title: RNA-Seq S44-XDM


title: RNA-Seq S47-XDM


title: RNA-Seq S20-CT


title: RNA-Seq S20-WBC


title: RNA-Seq S48-XDM


title: RNA-Seq S49-XDM


title: RNA-Seq S50-XDM


title: RNA-Seq S04-XN

source_name: cerebrellum

value: cerebrellum


title: RNA-Seq S01-XN


title: RNA-Seq S06-XN


title: RNA-Seq S21-CT


title: RNA-Seq S02-XN


title: RNA-Seq S08-XN


title: RNA-Seq S07-XN


title: RNA-Seq S03-XN


title: RNA-Seq S31-CT


title: RNA-Seq S11-XN


title: RNA-Seq S08-ZF


title: RNA-Seq S40-XDM


title: RNA-Seq S10-ZF


title: RNA-Seq S07-ZF


title: RNA-Seq S13-XN


title: RNA-Seq S12-XN


title: RNA-Seq S12-ZF


title: RNA-Seq S15-ZF


title: RNA-Seq S10-XN


title: RNA-Seq S05-XN


title: RNA-Seq S09-ZF


title: RNA-Seq S11-ZF


title: RNA-Seq S09-HC


title: RNA-Seq S08-BJ

value: muscle


title: RNA-Seq S13-ZF

value: adipose


title: RNA-Seq S14-ZF


title: RNA-Seq S09-XN


title: RNA-Seq S20-ZF


title: RNA-Seq S32-CT


title: RNA-Seq S45-XDM


title: RNA-Seq S09-BJ


title: RNA-Seq S22-ZF


title: RNA-Seq S24-ZF


title: RNA-Seq S25-ZF


title: RNA-Seq S17-ZF


title: RNA-Seq S21-ZF


title: RNA-Seq S27-ZF


title: RNA-Seq S16-ZF


title: RNA-Seq S18-ZF


title: RNA-Seq S33-ZF


title: RNA-Seq S28-ZF


title: RNA-Seq S29-ZF


title: RNA-Seq S34-ZF


title: RNA-Seq S23-ZF


title: RNA-Seq S30-ZF


title: RNA-Seq S31-ZF


title: RNA-Seq S37-ZF


title: RNA-Seq S26-ZF


title: RNA-Seq S33-CT


title: RNA-Seq S04-RNA-Seq Spleen


title: RNA-Seq S01-RNA-Seq Spleen


title: RNA-Seq S19-ZF


title: RNA-Seq S11-RNA-Seq Spleen


title: RNA-Seq S35-ZF


title: RNA-Seq S49-QN


title: RNA-Seq S03-RNA-Seq Spleen


title: RNA-Seq S07-RNA-Seq Spleen


title: RNA-Seq S50-QN


title: RNA-Seq S06-CT


title: RNA-Seq S36-ZF


title: RNA-Seq S02-RNA-Seq Spleen


title: RNA-Seq S16-RNA-Seq Spleen


title: RNA-Seq S06-RNA-Seq Spleen


title: RNA-Seq S09-RNA-Seq Spleen


title: RNA-Seq S19-RNA-Seq Spleen


title: RNA-Seq S05-RNA-Seq Spleen


title: RNA-Seq S44-XN


title: RNA-Seq S12-RNA-Seq Spleen


title: RNA-Seq S10-RNA-Seq Spleen


title: RNA-Seq S08-RNA-Seq Spleen


title: RNA-Seq S13-RNA-Seq Spleen


title: RNA-Seq S07-CT


title: RNA-Seq S14-RNA-Seq Spleen


title: RNA-Seq S17-RNA-Seq Spleen


title: RNA-Seq S32-ZF


title: RNA-Seq S18-RNA-Seq Spleen


title: RNA-Seq S48-XN


title: RNA-Seq S45-XN


title: RNA-Seq S15-RNA-Seq Spleen


title: RNA-Seq S43-XN


title: RNA-Seq S04-ZC

source_name: duodenum

value: duodenum


title: RNA-Seq S47-XN


title: RNA-Seq S50-XN


title: RNA-Seq S49-XN


title: RNA-Seq S07-ZC


title: RNA-Seq S03-ZC


title: SM3762_4w CCl4

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
STAR v.2.4.1
Next-Generation Sequencing HOMER
Assembly: mm10
Supplementary files format and content: tab delimited file that contains raw counts for each sample

source_name: Liver

extract_protocol:
RNA column purification using the RNeasy Mini Kit (74106, Qiagen, Hilden, Germany)
Transcriptomic

value: Liver

value: Female

value: 4w CCl4


title: RNA-Seq S01-ZC


title: RNA-Seq S06-ZC


title: RNA-Seq S05-ZC


title: RNA-Seq S46-XN


title: SM3763_4w CCl4


title: RNA-Seq S08-ZC


title: RNA-Seq S09-ZC


title: RNA-Seq S25-CT


title: SM3761_4w CCl4


title: RNA-Seq S02-ZC


title: RNA-Seq S12-ZC


title: SM3759_4w CCl4


title: SM3758_4w CCl4


title: RNA-Seq S13-ZC


title: SM3757_2w CCl4

value: 2w CCl4


title: RNA-Seq S14-ZC


title: RNA-Seq S26-CT


title: RNA-Seq S15-ZC


title: SM3756_2w CCl4


title: RNA-Seq S27-CT


title: SM3754_2w CCl4


title: SM3753_2w CCl4


title: RNA-Seq S16-ZC


title: SM3755_2w CCl4


title: RNA-Seq S17-ZC


title: SM3752_2w CCl4


title: RNA-Seq S19-ZC


title: SM3751_4w Chow

value: 4w Chow


title: RNA-Seq S21-ZC


title: ZJ00-10_FRAS210076002-2

city: Hangzhou

first: lianyu

last: lin

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: Zhejiang University

description:
From isolate ZJ00-10, Biological Replicate 2
ZJ00-10-2r

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the 70-15 reference genome using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on the 70-15 reference genome annotations was determined using stringtie (v2.0) with the default parameter settings.
Transcripts per Million (TPM) were calculated for representing the expression of each gene.
Assembly: 70-15 reference genome
Supplementary files format and content: Matrix table with TPM for every gene and every sample

organism: Pyricularia oryzae

source_name: hypha

growth_protocol: For vegetative growth, the M. oryzae strains were cultured on a complete medium (CM, 6 g yeast extract, 6 g casein hydrolysate, 10 g sucrose, 20 g agar for solid medium) for 5 days at 25℃, then transfered in the liquid CM for 3 days in a shaking incubator at 25℃ and 110 rpm condition.

extract_protocol:
The RNA extraction was using a HiPure Universal RNA kit (r4130-02; Magen, China) according to the manufacturer’s instructions. 5 μg of total RNA was used for the construction of sequencing libraires.
RNA integrity and quantity were verified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and Qubit 2.0 (Life Tecnologies, China), respectively. The cDNA library was sequenced using IIIumina sequencing platform (NovaSqu 6000) with 150 bo pair-end reads length and 300 bp insert size by Novogene Co. (Tianjin, China).

value: hypha


title: RNA-Seq S10-ZC


title: YN072313_FRAS210075993-2

description:
From isolate YN072313, Biological Replicate 2
YN072313-2r


title: RNA-Seq S20-ZC


title: ZJ00-10_FRAS210076002-1

description:
From isolate ZJ00-10, Biological Replicate 1
ZJ00-10-1r


title: SM3760_4w CCl4


title: RNA-Seq S22-ZC


title: RNA-Seq S11-ZC


title: SM3750_4w Chow


title: RNA-Seq S19-ZW

source_name: abomasum

value: abomasum


title: RNA-Seq S20-ZW


title: RNA-Seq S22-ZW


title: RNA-Seq S23-ZW


title: SM3748_4w Chow


title: RNA-Seq S24-ZW


title: Sar-2-20-1_FRAS210075994-3

description:
From isolate Sar-2-20-1, Biological Replicate 2
Sar-2-20-1-3r


title: RNA-Seq S25-ZW


title: RNA-Seq S18-ZC


title: RNA-Seq S27-ZW