title: Stimulated naïve CD4+ T cell treated as a control rep3

city: Bangkoknoi

first: Thamrong

last: Wongchang

state: Bangkok

address: 2 Wanglang, Siriaj

department: Pharmacology

country: Thailand

data_processing:
Paired-end libraries were sequenced using an Illumina HiSeqTM system
The original raw data were transformed to sequenced reads via base-calling
Raw data were recorded in a FASTQ file that contained sequence information (reads) and corresponding sequencing quality information
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference human genome (hg38) using Hisat2 v2.0.5
Supplementary files format and content: xlx files include RPKM values for each Sample

source_name: Blood

growth_protocol: Human naïve CD4+ T cells were stimulated with anti-CD3 (coated plate) and soluble anti-CD28 with IL-2 and TGF-beta  and were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using an Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: In DYRK1B treatment group, a selective DYRK1B inhibtor (AZ-DYRK1B-33) was added on day 0 and the cell were harvested after 24 hour for RNA extraction.

value: Blood

value: Primary cell

value: Leukocyte

value: Healthy adult human

value: control


title: HT1080-H4WT-S3-IP

status: Public on Apr 08 2023

type: SRA

city: Chaoyang

first: Liting

last: Lan

state: Beijing

address: Datun 15 Road

department: Institute of biophysics

country: China

institute: University of Chinese Academy of Sciences

library_source: genomic

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt (Martin 2011) with parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any, and then mapped to hg38 using Bowtie2 (Langmead, Trapnell et al. 2009) with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal. Duplicates were marked using picard MarkDuplicates (https://broadinstitute.github.io/picard/) with default parameters and removed using samtools view (Li, Handsaker et al. 2009) with parameters: -f 2 -F 1024 -q 10. Replication timing profile and timing domain were analyzed as described in (Ryba, Battaglia et al. 2011, Marchal, Sasaki et al. 2018). Briefly, in each 50 kb genome window, replication timing were calculated as log2((S1+S2)/(S3+S4))), then normalized with R function normalize.quantiles.use.target() from R package ‘preprocessCore’. The quantile normalized replication timing value were used for replication timing domain segmentation by R function CNA() from R package ‘DNAcopy’ and for timing domain annotation using HOMER (Heinz, Benner et al. 2010). Heatmap was produced using Java Treeview (Saldanha 2004). For IGV (Integrative Genomics Viewer) (Robinson, Thorvaldsdóttir et al. 2011) visualization, the normalized value was Loess-smoothed using R function loess() from R package ‘stats’.
Assembly: hg19, mm10
Supplementary files format and content: bedGraph
Library strategy: Repli-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Connective tissue

extract_protocol: HEK293T and HT1080 cells were cultured in the presence of 100 μM BrdU (sigma) for 2 h. To obtain four sub-populations of S phase cells, including S1, S2, S3 and S4, cells were fixed, stained with PI and sorted by FACS according to their DNA content. Next, isolated cells were lysed immediately in lysis buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1 M NaCl, 0.5% SDS, 0.1 mg/mL RNase A, 0.2 mg/mL Protease K) and incubated at 37 °C for 3 h, then at 55 °C for 8 h. Genomic DNA was extracted with phenol: chloroform: isoamyl (25:24:1) and chloroform: Isoamyl alcohol (24:1) and precipitated with 75% ethanol and 300 mM NaAc. DNA pellet was dissolved in TE (10 mM Tris, pH 8.0, 1 mM EDTA) before being sonicated using Bioruptor to 200-500 bp. The sonicated DNA was end-repaired, dA-tailed, and adapter-ligated. The adapter-ligated DNA was boiled for 10 min and cooled on ice immediately for 2 min. DNA solution was incubated with BrdU antibody (BD Bioscience, BD44) and rotated at 4 °C overnight. The mixture was incubated with protein G Dynabeads (Life Technology, 10009D) and rotated at 4 °C for another 8 h. After washing five times with washing buffer (PBS with 0.05% (v/v) Triton-X100) and once with TE, the beads were eluted by elution buffer (TE with 0.5% (w/v) SDS) at 65 °C for 10 min. After extraction with DNA Clean & Concentrator-5 kit (ZYMO, D4014), DNA was subjected to library amplification using Next Q5 Hot Start HiFi PCR Master Mix (NEB, M0543) and NEBNext Multiplex Oligos for Illumina (NEB, E7600). The libraries were purified with Ampure beads (0.9 ×) (Beckman, A633881) and sequenced using DNBSEQ-T7 platforms.

tag: tissue

value: Connective tissue

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

value: H4WT overexpression


title: HT1080-H4WT+PUG-S1-IP

description: HT1080-H4WT+PUG_target_qnor.Loess.bedGraph

tag: treatment

value: PUGNAc


title: mutant_gill_6

city: Hong Kong

first: Zilong

last: WEN

address: Rm6319, HKUST, Clear water bay, Kowloon

department: Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description:
mut_gill_6
data_TPM_progenitor_mut_sib.csv

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCz11.94 (danRer11) zebrafish reference genome using the STAR package, and gene counts were calculated using feature Counts.
The count tables were normalized to produce transcripts per million (TPM) tables.
Principal component analysis (PCA) was carried out using the R Stats package.
Differential expression genes (DEGs) were assessed with the R DESeq2 package.
Assembly: danRer11
Supplementary files format and content: comma-separated values file of TPM values for each sample

molecule: total RNA

organism: Danio rerio

source_name: gill

extract_protocol:
The EGFP+DsRedx- progenitor cells for RNA-seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted.
cDNA library was prepared according to the standard Smart-seq2 protocol with minor modifications. Briefly, 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo-dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase (18064071, Invitrogen). The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit (50-196-5217, Roche) for 23 cycles and purified with the Ampure XP beads (A63881, Beckman). The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

value: gill

tag: strain

value: Tg(spic:EGFP; mpeg1:DsRedx)

value: spic:EGFP+mpeg1:DsRedx- cells

value: mutant

tag: Stage

value: adult


title: HEK293T-H4S47A-S3-IP_rep2

description: HEK293T-H4S47A_target_qnor.Loess.bedGraph

source_name: kidney; Embryo

value: kidney; Embryo

value: H4S47A overexpression


title: Stimulated naïve CD4+ T cell treated as a control rep1


title: mutant_gill_5

description:
mut_gill_5
data_TPM_progenitor_mut_sib.csv


title: HT1080-H4S47A-S2-IP

description: HT1080-H4S47A_target_qnor.Loess.bedGraph


title: mutant_gill_3

description:
mut_gill_3
data_TPM_progenitor_mut_sib.csv


title: HT1080-H4S47A+PUG-S3-IP

description: HT1080-H4S47A+PUG_target_qnor.Loess.bedGraph


title: Stimulated naïve CD4+ T cell treated as a control rep2


title: HT1080-H4S47A+PUG-S1-IP


title: mutant_gill_2

description:
mut_gill_2
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4S47A-S1-IP_rep2


title: HT1080-H4S47A+PUG-S2-IP


title: HEK293T-H4S47A-S2-IP_rep2


title: Stimulated naïve CD4+ T cell treated with DYRK1B inhibitor rep3

value: treatment


title: mutant_gill_4

description:
mut_gill_4
data_TPM_progenitor_mut_sib.csv


title: sibling_gill_5

description:
sib_gill_5
data_TPM_progenitor_mut_sib.csv

value: sibling


title: mutant_gill_1

description:
mut_gill_1
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4S47A+PUG-S4-IP_rep2

description: HEK293T-H4S47A+PUG_target_qnor.Loess.bedGraph


title: Stimulated naïve CD4+ T cell treated with DYRK1B inhibitor rep2

value: Blood

value: Primary cell


title: HEK293T-H4S47A+PUG-S3-IP_rep2


title: HEK293T-H4S47A-S4-IP_rep1


title: HEK293T-H4S47A+PUG-S2-IP_rep2


title: HEK293T-H4S47A+PUG-S1-IP_rep2


title: Stimulated naïve CD4+ T cell treated with DYRK1B inhibitor rep1

value: Leukocyte

value: Healthy adult human


title: HEK293T-H4S47A-S3-IP_rep1


title: sibling_gill_4

description:
sib_gill_4
data_TPM_progenitor_mut_sib.csv


title: Alcoholic hepatitis HDN S34

city: Boston

first: Ioannis

middle: S

last: Vlachos

state: MA

address: 330 Brookline Ave. 519A, Dana Building

department: Pathology

country: USA

institute: Beth Israel Deaconess Medical Center

description:
high-density neutrophils exhibiting an activated phenotype
190529Sza_D19-6034

data_processing:
Gene expression was quantified using Salmon v.0.91 and gene annotations were derived from the Ensembl database 98.
Gene expression data were normalized using DESeq2 v1.25.12.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: tab-delimited matrix containing raw gene expression per sample.
Supplementary_files_format_and_content: tab-delimited matrix containing DESeq2 normalized gene expression.

source_name: Peripheral blood neutrophils

extract_protocol:
40-50ml of whole blood from the AH patients and healthy subjects were collected and diluted with warm RPMI including 1% Anti-anti to 1:1. 36ml of the diluted blood was layered on 12ml of gradient medium Ficoll and centrifuged at 585 xg for 20 minutes. PBMCs were harvested from interphase between plasma and Ficoll and washed with 2% FBS HBSS. After Ficoll was aspirated, red blood cell lysis buffer (BD Bioscience) was added into the RBC/neutrophil fraction. After 15 minutes incubation at room temperature, the tube was centrifuged at 200 xg for 5 minutes and the pellet was washed with PBS and harvested for neutrophils (HDNs). LDNs were isolated from PBMCs using EasySep Human Neutrophil Isolation kit (Stemcell). RNA was extracted from each group of neutrophils through miRNeasy kit (Qiagen).
cDNA library was prepared after rRNA removal, using Kapa RNA RiboErase.

value: peripheral blood

value: neutrophils

tag: density

value: high

tag: diagnosis

value: acute alcoholic hepatitis

tag: subject id


title: HEK293T-H4S47A-S4-IP_rep2

value: epithelial cell


title: HEK293T-H4S47A-S2-IP_rep1


title: HEK293T-H4S47A+PUG-S4-IP_rep1

value: PUGNAc


title: Alcoholic hepatitis HDN S33

description:
high-density neutrophils exhibiting an activated phenotype
190529Sza_D19-6033


title: sibling_gill_2

description:
sib_gill_2
data_TPM_progenitor_mut_sib.csv

value: gill

value: Tg(spic:EGFP; mpeg1:DsRedx)

value: spic:EGFP+mpeg1:DsRedx- cells


title: sibling_gill_1

description:
sib_gill_1
data_TPM_progenitor_mut_sib.csv

value: adult


title: Alcoholic hepatitis HDN S32

description:
high-density neutrophils exhibiting an activated phenotype
190529Sza_D19-6032


title: sibling_gill_3

description:
sib_gill_3
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4S47A+PUG-S2-IP_rep1

value: kidney; Embryo

value: H4S47A overexpression


title: mutant_epidermis_6

description:
mut_epi_6
data_TPM_progenitor_mut_sib.csv

source_name: epidermis

value: epidermis

value: mutant


title: HEK293T-H4WT-S4-IP_rep2

value: H4WT overexpression


title: HEK293T-H4WT-S3-IP_rep2


title: Alcoholic hepatitis HDN S31

description:
high-density neutrophils exhibiting an activated phenotype
190529Sza_D19-6031


title: HEK293T-H4WT-S2-IP_rep2


title: HEK293T-H4S47A+PUG-S1-IP_rep1


title: Alcoholic hepatitis LDN S30

description:
low-density neutrophils exhibiting an exhausted phenotype
190529Sza_D19-6030

value: low


title: HEK293T-H4S47A-S1-IP_rep1

description: HEK293T-H4S47A_target_qnor.Loess.bedGraph


title: Alcoholic hepatitis LDN S29

description:
low-density neutrophils exhibiting an exhausted phenotype
190529Sza_D19-6029


title: HEK293T-H4WT+PUG-S3-IP_rep2

description: HEK293T-H4WT+PUG_target_qnor.Loess.bedGraph


title: mutant_epidermis_5

description:
mut_epi_5
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4WT+PUG-S4-IP_rep2


title: HEK293T-H4WT+PUG-S1-IP_rep2


title: HEK293T-H4WT-S1-IP_rep2


title: HEK293T-H4S47A+PUG-S3-IP_rep1


title: mutant_epidermis_3

description:
mut_epi_3
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4WT+PUG-S2-IP_rep2


title: Alcoholic hepatitis LDN S28

description:
low-density neutrophils exhibiting an exhausted phenotype
190529Sza_D19-6028


title: Alcoholic hepatitis LDN S27

description:
low-density neutrophils exhibiting an exhausted phenotype
190529Sza_D19-6027


title: HEK293T-H4WT-S4-IP_rep1


title: mutant_epidermis_7

description:
mut_epi_7
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4WT-S3-IP_rep1


title: mutant_epidermis_2

description:
mut_epi_2
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4WT-S2-IP_rep1


title: HEK293T-H4WT-S1-IP_rep1


title: Control HDN S26

description:
healthy control high-density neutrophils
190529Sza_D19-6026

value: healthy


title: mutant_epidermis_1

description:
mut_epi_1
data_TPM_progenitor_mut_sib.csv


title: HEK293T-H4WT+PUG-S2-IP_rep1


title: HEK293T-H4WT+PUG-S4-IP_rep1


title: sibling_epidermis_6

description:
sib_epi_6
data_TPM_progenitor_mut_sib.csv

value: sibling


title: HEK293T-H4WT+PUG-S3-IP_rep1


title: sibling_epidermis_7

description:
sib_epi_7
data_TPM_progenitor_mut_sib.csv


title: Control HDN S25

description:
healthy control high-density neutrophils
190529Sza_D19-6025

value: peripheral blood

value: neutrophils


title: HEK293T-H4WT+PUG-S1-IP_rep1


title: mutant_epidermis_4

description:
mut_epi_4
data_TPM_progenitor_mut_sib.csv


title: sibling_epidermis_5

description:
sib_epi_5
data_TPM_progenitor_mut_sib.csv


title: 12m SNCA TG mice housed in EE, bio rep 4, BS

city: Vancouver

first: Michael

last: Kobor

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
CCJM1ANXX_6_ACTTGA
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

data_processing:
Raw fastq files aligned to mm10 reference genome
Aligned files sorted and filtered for MAPQ > 10 with SAMtools
Methylation ratios calculated with BSMAP
Data filtered to CpG or CpH sites, minimum 10X coverage, maximum 99.9% quantile of coverage across all samples
Beta values calculated as the number of methylated reads divided by the number of total reads per cytosine
Outlier samples removed (failing 3 or more of the following: PCA clustering, median coverage < 20X, sample-sample correlation < 0.8, abnormal beta distribution, detectOutlier from lumi R package, outlyx from wateRmelon R package)
Assembly: mm10
Supplementary files format and content: Matrices containing methylation levels for cytosines passing read coverage filters, and samples passing outlier detection

organism: Mus musculus

source_name: Hippocampus

extract_protocol: RRBS libraries for were prepared according to published protocols (Gu et al., 2011, PMID 21412275), and paired bisulfite/oxidative bisulfite conversion were performed with the NuGen TrueMethyl oxBS Kit according to manufacturer's instructions.

value: Hippocampus

value: SNCA TG

value: Enriched environment

tag: molecule subtype

value: Bisulfite-converted DNA


title: SIRT2 knockout, Cold exposure [T20]

city: Beijing

first: Shuang

last: Li

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

description:
T20
Unknown_AQ668-01T0020

data_processing:
After the construction of the library, Qubit2.0 and Agilent 2100 were used to detect the concentration and Insert Size of the library, and Q-PCR was used to accurately quantify the effective concentration of the library, so as to ensure the quality of the library.
After qualified, high-throughput sequencing was performed with NovaSeq 6000, and the sequencing read length was PE150.
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

source_name: liver

extract_protocol:
Advanced molecular biology equipment was used to detect the purity, concentration and integrity of RNA samples to ensure the use of qualified samples for transcriptome sequencing.
Eukaryotic mRNA was enriched by magnetic beads with Oligo (dT). mRNA was randomly interrupted by Fragmentation Buffer. The first cDNA strand was synthesized by random hexamers using mRNA as template. Then the second cDNA strand was synthesized by adding buffer solution, dNTPs, RNase H and DNA polymerase I. The cDNA strand was purified by AMPure XP beads. The purified double-stranded cDNA was end-repaired, A tail was added and sequencing connectors were connected. AMPure XP beads were used for segment size selection. Finally, cDNA library was obtained by PCR enrichment.

value: liver

value: SIRT2 knockout

value: Cold exposure


title: 12m SNCA TG mice housed in EE, bio rep 3, BS

description:
CCJM1ANXX_6_CAGATC
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: sibling_epidermis_4

description:
sib_epi_4
data_TPM_progenitor_mut_sib.csv

value: Tg(spic:EGFP; mpeg1:DsRedx)

value: spic:EGFP+mpeg1:DsRedx- cells

value: adult


title: SIRT2 knockout, Cold exposure [T17]

description:
T17
Unknown_AQ668-01T0017


title: SIRT2 knockout, Cold exposure [T18]

description:
T18
Unknown_AQ668-01T0018


title: 12m SNCA TG mice housed in EE, bio rep 2, BS

description:
CCJM1ANXX_6_GCCAAT
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: sibling_epidermis_3

description:
sib_epi_3
data_TPM_progenitor_mut_sib.csv

value: epidermis


title: 12m SNCA TG mice housed in EE, bio rep 1, BS

description:
CCJM1ANXX_6_ACAGTG
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: SIRT2 knockout, Cold exposure [T16]

description:
T16
Unknown_AQ668-01T0016


title: sibling_epidermis_2

description:
sib_epi_2
data_TPM_progenitor_mut_sib.csv


title: SIRT2 knockout, control [T15]

description:
T15
Unknown_AQ668-01T0015

value: control


title: Control HDN S24

description:
healthy control high-density neutrophils
190529Sza_D19-6024

value: high


title: 12m SNCA TG mice housed in SE, bio rep 4, BS

description:
CCJM1ANXX_6_TGACCA
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

value: Standard housing


title: SIRT2 knockout, control [T13]

description:
T13
Unknown_AQ668-01T0013


title: sibling_epidermis_1

description:
sib_epi_1
data_TPM_progenitor_mut_sib.csv

value: sibling


title: HEK293T, H4S47A+ PUG, RNase-treated-NS_rep2

data_processing:
library strategy: short nascent-strand sequencing (SNS-seq)
150 bp paired-end reads sequenced with Illumina Nova-seq were first cleaned using Cutadapt (Version 2.10)
Cleaned data were mapped to a mixed hg38-mm10 genome using Bowtie2 (Version 2.2.5)
The concordantly mapped read pairs were filtered using a custom python script to retain those with mapq > 10
PCR duplicates and reads mapped to mitochondrial or alternate contigs regions were filtered out. NS-seq peaks were detected using MACS (Version 1.4.1)
The fold enrichment between the samples not treated with RNase A and the samples treated with RNase A within the peak regions were then calculated with getDifferentialPeaks from Homer (Version 4.11).Peaks with higher signal before RNase A digestion were retained as firing origins (fold change ≥ 1.5 and p value < 0.05).
For spike-in normalization, the unique reads mapped to mouse genome (mm10) were counted for each library, and the unique hg38 reads were scaled to one million unique mm10 reads, represented in the form of reference-adjusted reads per million (RRPM)
Heatmaps were generated using Deeptools (Version 3.4.3).
Venn diagrams were plotted using Venn Plot in R (Version 4.0.2)
Assembly: hg38, mm10
Supplementary files format and content: tdf, genome coverage bedgraph files

growth_protocol: DMEM, 10% fetal bovine serum, 4 mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37 ℃ at 5% CO2.

extract_protocol:
HEK293T cells were collected and lysed with DNAzol (Invitrogen, 10503027) at room temperature for 5 min. Genomic DNA with 1% spike-in mouse DNA (R1 cells) was precipitated with 100% ethanol, denatured by boiling for 10 min at 100 °C and then loaded onto 40 mL neutral 5-30% sucrose gradients prepared in TEN500 (10 mM Tris pH 7.9, 2 mM EDTA, 500 mM NaCl) in ultra-clear tubes. Gradients was centrifuged in SW28 rotor at 25,000 rpm for 20 h. A 1 mL-fraction was withdrawn from the top of the gradients. DNA fragments ranging from 0.5-2.5 kb were collected and purified with ethanol. Half of the total purified DNA was treated with RNase A. Subsequently, all DNA was treated with lambda exonuclease (NEB, MO262L) three times and purified with Illustra GFX PCR DNA and Gel Band Purification Kit (GE Healthcare, 28903470). Using Klenow Fragment (NEB, M0212L) and random primers (Invitrogen, 48190011), ssDNA was converted to dsDNA and then subjected to DNA library preparation using Next Ultra DNA Library Prep Kit (NEB, E7645) according to the manufactory’s instructions.
DNA library preparation using Next Ultra DNA Library Prep Kit (NEB, E7645) according to the manufactory’s instructions.

treatment_protocol: HEK293T cells were transfected with Flag-H4WT or -H4S47A for 24 h and incubated with or without PUG for another 24 h.

value: Human embryonic kidney

value: Transfected with Flag-H4S47A  and incubated with PUG


title: HEK293T, H4S47A+ PUG, NS_rep2


title: HEK293T, H4S47A+ PUG, RNase-treated-NS_rep1


title: SIRT2 knockout, Cold exposure [T19]

description:
T19
Unknown_AQ668-01T0019


title: HEK293T, H4S47A+ PUG, NS_rep1


title: F107 FS EoE

city: Aurora

first: Calies

last: Menard-Katcher

state: CO

department: Pediatrics

institute: University of Colorado School of Medicine

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

molecule: polyA RNA

source_name: esophageal mucosal biopsy

extract_protocol:
Total RNA was isolated from esophageal mucosal biopsies using RNeasy Mini Kit (Qiagen)
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

tag: phenotype

value: FS EoE


title: 12m SNCA TG mice housed in SE, bio rep 3, BS

description:
CCJM1ANXX_6_TTAGGC
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

value: Hippocampus

value: SNCA TG


title: 12m SNCA TG mice housed in SE, bio rep 2, BS

description:
CCJM1ANXX_6_CGATGT
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

value: Bisulfite-converted DNA


title: SIRT2 knockout, control [T12]

description:
T12
Unknown_AQ668-01T0012

value: liver


title: F096 FS EoE


title: SIRT2 knockout, control [T11]

description:
T11
Unknown_AQ668-01T0011

value: SIRT2 knockout


title: HEK293T, H4S47A, RNase-treated-NS_rep2

value: Transfected with Flag-H4S47A


title: F090 FS EoE


title: F094 FS EoE


title: WT, Cold exposure [T10]

description:
T10
Unknown_AQ668-01T0010

value: WT

value: Cold exposure


title: WT, Cold exposure [T09]

description:
T09
Unknown_AQ668-01T0009


title: F085 FS EoE


title: WT, Cold exposure [T08]

description:
T08
Unknown_AQ668-01T0008


title: SIRT2 knockout, control [T14]

description:
T14
Unknown_AQ668-01T0014


title: 12m WT mice housed in EE, bio rep 3, BS

description:
CCJM1ANXX_5_CAGATC
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

value: Enriched environment


title: HEK293T, H4S47A, RNase-treated-NS_rep1


title: HEK293T, H4S47A, NS_rep2


title: 12m SNCA TG mice housed in SE, bio rep 1, BS

description:
CCJM1ANXX_6_ATCACG
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: 12m WT mice housed in EE, bio rep 4, BS

description:
CCJM1ANXX_5_ACTTGA
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: HEK293T, H4S47A, NS_rep1


title: 12m WT mice housed in EE, bio rep 2, BS

description:
CCJM1ANXX_5_GCCAAT
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: HEK293T, H4WT+ PUG, RNase-treated-NS_rep2

value: Transfected with Flag-H4WT and incubated with PUG


title: F070 FS EoE


title: HEK293T, H4WT+ PUG, RNase-treated-NS_rep1


title: 12m WT mice housed in EE, bio rep 1, BS

description:
CCJM1ANXX_5_ACAGTG
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: WT, Cold exposure [T07]

description:
T07
Unknown_AQ668-01T0007


title: 12m WT mice housed in SE, bio rep 4, BS

description:
CCJM1ANXX_5_TGACCA
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: WT, Cold exposure [T06]

description:
T06
Unknown_AQ668-01T0006


title: F051a FS EoE


title: WT, control [T05]

description:
T05
Unknown_AQ668-01T0005

value: control


title: WT, control [T04]

description:
T04
Unknown_AQ668-01T0004


title: 12m WT mice housed in SE, bio rep 3, BS

description:
CCJM1ANXX_5_TTAGGC
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: F044a FS EoE


title: HEK293T, H4WT+ PUG, NS_rep1


title: HEK293T, H4WT+ PUG, NS_rep2


title: 12m WT mice housed in SE, bio rep 2, BS

description:
CCJM1ANXX_5_CGATGT
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv


title: WT, control [T03]

description:
T03
Unknown_AQ668-01T0003


title: E091 EoE

value: non-fs EoE


title: HEK293T, H4WT, RNase-treated-NS_rep2

value: Transfected with Flag-H4WT


title: WT, control [T02]

description:
T02
Unknown_AQ668-01T0002


title: HEK293T, H4WT, RNase-treated-NS_rep1


title: E081 EoE


title: 12m SNCA TG mice housed in EE, bio rep 3, oxBS

description:
CCJM1ANXX_3_CAGATC
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Oxidative bisulfite-converted DNA


title: 12m SNCA TG mice housed in EE, bio rep 4, oxBS

description:
CCJM1ANXX_3_ACTTGA
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: HEK293T, H4WT, NS_rep2

value: Human embryonic kidney


title: E083 EoE


title: WT, control [T01]

description:
T01
Unknown_AQ668-01T0001


title: 12m WT mice housed in SE, bio rep 1, BS

description:
CCJM1ANXX_5_ATCACG
BS_beta_matrix_CpG_noout.csv
BS_beta_matrix_CpH_noout.csv

value: Standard housing


title: Glucose oxidase (5 mU/mL, 30 min) + Ethyl-2-hydroxybenzylamine (0.2 mM, 24h)

city: Nashville

first: Nestor

last: de la Visitacion

state: TN

address: 2213 GARLAND AVE

institute: Vanderbilt University Medical Center

data_processing:
Sequencing was performed at Paired-End 150 bp on the Illumina NovaSeq 6000 targeting an average of 50M reads per sample.
An average of 50M reads per sample was targeted.
The data was aligned to mm10 genome by STAR softwatre. .
The reads were extracted by FeatureCount software.
Differential detection was performed byDESeq2 software
Assembly: mm10
Supplementary files format and content: csv files with differential detection

source_name: Aorta

growth_protocol: Mouse aorta endothelial cells and their complete media purchased from Cell biologics

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Stranded mRNA (NEB) Library prep

value: Aorta

value: Endothelilal cells (MAECs)


title: 12m SNCA TG mice housed in EE, bio rep 2, oxBS

description:
CCJM1ANXX_3_GCCAAT
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Hippocampus

value: SNCA TG


title: p12_2

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

description: adult human dental pulp stromal cells

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: passage 12 of hDPCs

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

value: hDPCs

tag: passage

value: passage 12


title: F006c FS EoE

value: FS EoE


title: HEK293T, H4WT, NS_rep1


title: 12m SNCA TG mice housed in EE, bio rep 1, oxBS

description:
CCJM1ANXX_3_ACAGTG
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: E065 EoE


title: p12_1

description: adult human dental pulp stromal cells


title: 12m SNCA TG mice housed in SE, bio rep 4, oxBS

description:
CCJM1ANXX_3_TGACCA
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: E068 EoE


title: 12m SNCA TG mice housed in SE, bio rep 3, oxBS

description:
CCJM1ANXX_3_TTAGGC
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: Input_ChIPSeq (LONP1_AKO_H3K4me1 control)

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description: adipocytes DNA input control

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.2.5 with the default parameters.
peaks were called using macs2 version 2.2.1 with the default parameters.
Assembly: mm10
Supplementary files format and content: Bedgraph and excel files including tag density and peak information were generated using macs2.

source_name: adipocytes input control

extract_protocol:
Lysates were clarified from sonicated nuclei, H3K4me-DNA complexes were isolated with antibody.
NEBNext® UNEBNext DNA Library Prep Master Mix Set for Illumina (cat# E6040L) was used with ChIP-DNA for the construction of sequencing libraries. ChIP libraries were prepared for sequencing using standard Illumina protocols

value: adipocytes input control

tag: chip antibody

value: Wild-type mouse

tag: Sex

value: Male


title: E062 EoE


title: p5

description: adult human dental pulp stromal cells

source_name: passage 6 of hDPCs

value: passage 6


title: LONP1_AKO_H3K4me1_ChIPSeq

description: adipocytes DNA from LONP1 adipocyte specific knockout mouse

source_name: adipocytes from LONP1 adipocyte specific knockout mouse

value: LONP1 adipocyte specific knockout  mouse


title: E078 EoE

value: non-fs EoE


title: E057c EoE


title: E053 EoE


title: WT_H3K4me1_ChIPSeq

description: adipocytes DNA from wild-type mouse - control mouse for adipocyte specific knockout LONP1 mouse

source_name: adipocytes from wild-type mouse - control mouse for adipocyte specific knockout LONP1 mouse


title: 12m SNCA TG mice housed in SE, bio rep 1, oxBS

description:
CCJM1ANXX_3_ATCACG
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: p3_2

description: adult human dental pulp stromal cells

source_name: passage 3 of hDPCs

value: passage 3


title: 12m SNCA TG mice housed in SE, bio rep 2, oxBS

description:
CCJM1ANXX_3_CGATGT
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Oxidative bisulfite-converted DNA


title: E048 EoE


title: Glucose oxidase (5 mU/mL, 30 min)

treatment_protocol: Glucose oxidase (5 mU/mL, 30 min) + Ethyl-2-hydroxybenzylamine (0.2 mM, 24h)

value: Glucose oxidase (5 mU/mL, 30 min)


title: E021a EoE


title: 3D spheriod, titanium dioxide treated, replicate 2, scRNAseq

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 610 Charles E. Young Drive East

institute: University of California, Los Angeles

description:
10x Genomics
XY-3D1-T2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were all done using the Cell Ranger software version 3.0.2. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver cell line

extract_protocol:
The cultured 3D liver spheroids were collected in a 1.5 mL tube and washed with PBS three times to remove cell debris and nanoparticles and then centrifuged at 1400 rpm for 5 min. The obtained spheroids were dissociated using 5 mg/mL collagenase for 2 hours at 37°C. The cells were then washed and collected by centrifugation and resuspended in ~500-1000 μL of 0.04% BSA/PBS solution. Subsequently, the cell suspension was filtered through a 40 μm strainer. Cells then underwent one more centrifugation step and were resuspended in a 60 μL of 0.04% BSA/PBS.
Library was performed according to the 10x 3′ single-cell RNA-seq V3.1 manufacter’s protocol . Briefly, the master mix which contained the single cell suspensions of hepatocyte and Kupffer cells, partitioning oil and gel beads were loaded into the Chromium Next GEM Chip G to generate the gel bead-in-emulsions (GEMs). The poly-A RNA from the cell lysate in the GEM was converted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The resulting pooled barcoded cDNA was then cleaned up with the provided DynaBeads then amplified by PCR. The fragments were then size selected using SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
scRNA-seq using the 10x 3′ single-cell RNA-seq V3.1 protocol

value: Liver cell line

value: Hepa 1-6 and KUP5

value: Hepatocyte and Kupffer cells

value: titanium dioxide


title: siLPS_2

description: adult human dental pulp stromal cells

source_name: hDPCs transfected with YAP siRNAs+LPS treatment

tag: tranfection

value: YAP siRNAs

tag: agent

value: LPS treatment


title: p6

description: adult human dental pulp stromal cells

value: hDPCs


title: 3D spheriod, titanium dioxide treated, replicate 1, scRNAseq

description:
10x Genomics
XY-3D2-T1

tag: tissue


title: C104 Control

value: healthy control


title: 12m WT mice housed in EE, bio rep 3, oxBS

description:
CCJM1ANXX_2_CAGATC
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Hippocampus

value: WT

value: Enriched environment


title: siLPS_1

description: adult human dental pulp stromal cells


title: 3D spheriod, graphene oxide treated, replicate 2, scRNAseq

description:
10x Genomics
XY-3D1-O2

tag: cell line

value: graphene oxide


title: NCLPS_2

description: adult human dental pulp stromal cells

source_name: hDPCs transfected with scrambled RNAs+LPS treatment

tag: cell type

value: scrambled RNAs


title: C101 Control


title: NCLPS_1

description: adult human dental pulp stromal cells


title: 12m WT mice housed in EE, bio rep 1, oxBS

description:
CCJM1ANXX_2_ACAGTG
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

tag: genotype


title: 3D spheriod, graphene oxide treated, replicate 1, scRNAseq

description:
10x Genomics
XY-3D2-O1

tag: treatment


title: Control cells

value: Aorta

value: Endothelilal cells (MAECs)

value: Control


title: 12m WT mice housed in EE, bio rep 2, oxBS

description:
CCJM1ANXX_2_GCCAAT
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

tag: strain

value: Oxidative bisulfite-converted DNA


title: 12m WT mice housed in SE, bio rep 4, oxBS

description:
CCJM1ANXX_2_TGACCA
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Standard housing


title: p3_1

description: adult human dental pulp stromal cells

value: passage 3


title: 3D spheriod, vanadium pentoxide treated, replicate 2, scRNAseq

description:
10x Genomics
XY-3D1-V2

value: Liver cell line

value: Hepa 1-6 and KUP5

value: Hepatocyte and Kupffer cells

value: vanadium pentoxide


title: siYAP_2

description: adult human dental pulp stromal cells

source_name: hDPCs transfected with YAP siRNAs

value: hDPCs

value: YAP siRNAs


title: 12m WT mice housed in SE, bio rep 3, oxBS

description:
CCJM1ANXX_2_TTAGGC
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: Hippocampus


title: 12m WT mice housed in EE, bio rep 4, oxBS

description:
CCJM1ANXX_2_ACTTGA
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv

value: WT


title: siYAP_1

description: adult human dental pulp stromal cells


title: 3D spheriod, vanadium pentoxide treated, replicate 1, scRNAseq

description:
10x Genomics
XY-3D2-V1


title: C087 Control

value: healthy control


title: C080 Control


title: 3D spheriod, Control, replicate 2, scRNAseq

description:
10x Genomics
XY-3D1-C2

value: No treatment


title: 12m WT mice housed in SE, bio rep 2, oxBS

description:
CCJM1ANXX_2_CGATGT
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: C084 Control


title: hDPCs transfected with scrambled RNAs [NC_2]

description: adult human dental pulp stromal cells

source_name: hDPCs transfected with scrambled RNAs

value: scrambled RNAs


title: 3D spheriod, Control, replicate 1, scRNAseq

description:
10x Genomics
XY-3D2-C1


title: C076 Control


title: 12m WT mice housed in SE, bio rep 1, oxBS

description:
CCJM1ANXX_2_ATCACG
oxBS_beta_matrix_CpG_noout.csv
oxBS_beta_matrix_CpH_noout.csv


title: hDPCs transfected with scrambled RNAs [NC_1]

description: adult human dental pulp stromal cells


title: C073 Control


title: RNAseq Adult Skate Liver replicate 2

status: Public on Apr 07 2023

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Alignment with STAR
Filtering of duplicated and not valid reads
Read count per gene with htseq-count
Assembly: custom assembly (uploaded in the same Bioproject)
Supplementary files format and content: Tabular file, contains Gene ID, gene position and counts for each sample

organism: Leucoraja erinaceus

source_name: Liver

extract_protocol:
total RNA was extracted from frozen samples by using the QIAGEN RNeasy Plus Micro Kit
polyA-selected standard Illumina libraries

value: Liver

tag: developmental timing

value: Adult


title: RNAseq Adult Skate Intestine replicate 2

source_name: Intestine

value: Intestine


title: RNAseq Adult Skate Pancreas replicate 2

source_name: Pancreas

value: Pancreas


title: RNAseq Adult Skate Testis replicate 1

source_name: Testis

value: Testis


title: RNAseq Adult Skate Kidney replicate 2

source_name: Kidney

value: Kidney


title: RNAseq Adult Skate Midbrain replicate 1

source_name: Midbrain

value: Midbrain


title: RNAseq Adult Skate Midbrain replicate 2


title: RNAseq Adult Skate Muscle replicate 2

source_name: Muscle

value: Muscle


title: RNAseq Adult Skate Ovary replicate 1

source_name: Ovary

value: Ovary


title: RNAseq Adult Skate Testis replicate 2


title: RNAseq Adult Skate Ovary replicate 2


title: RNAseq Adult Skate Hindbrain replicate 2

source_name: Hindbrain

value: Hindbrain


title: RNAseq Adult Skate Intestine replicate 1


title: RNAseq Adult Skate Heart replicate 1

source_name: Heart

value: Heart


title: RNAseq Adult Skate Gills replicate 1

source_name: Gills

value: Gills


title: RNAseq Adult Skate Gills replicate 2


title: RNAseq Adult Skate Heart replicate 2


title: RNAseq Adult Skate Liver replicate 1


title: RNAseq Adult Skate Pancreas replicate 1


title: RNAseq Adult Skate Kidney replicate 1


title: RNAseq Adult Skate Muscle replicate 1


title: Ehmt2_K182R_Dex 1

city: Berkeley

first: Jen-Chywan

last: Wang

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

data_processing:
Reads from BGI were trimmed using TrimGalore! (v0.6.6) to remove adaptors
Mapped to the ensemble transcriptome (Mus_musculus.GRCm38.cdna.all.fa.gz) using Salmon (v1.3.0: salmon quant -i GRCm38_index  -l A  -r sample_1_trimmed.fq.gz -p 4 --validateMappings --seqBias --gcBias --numBootstraps 50 -o quants/sample_1_quant)
Count Tables were imported into R using tximeta (v 1/9/3) using gene model Mus_musculus.GRCm38.101.gtf.gz
differential expression perfomred using DESeq2 (v 1.30.1, and fit to the model ~dex + mutant + dex:mutant)
Genome_build: mm10
Supplementary_files_format_and_content: Count Table

extract_protocol:
Mouse livers were harvested and were snap frozen in liquid nitrogen. RNA was then extracted using the Zymogen RNA extraction microprep kit. RNA was eluted with RNAse free water and 1ug of RNA was used in constrution of the libraries.
DNB seq platform was used for sequncing

tag: age

value: 8 weeks old


title: RNAseq Adult Skate Cerebellum replicate 2

source_name: Cerebellum

value: Cerebellum

value: WT


title: RNAseq Adult Skate Cerebellum replicate 1


title: Ehmt2_K182R_Dex 3


title: RNAseq Adult Skate Hindbrain replicate 1


title: RNAseq Adult Skate Forebrain replicate 1

source_name: Forebrain

value: Forebrain


title: RNAseq Adult Skate Forebrain replicate 2


title: WT_Dex 3


title: Ehmt2_K182R_PBS 1


title: Ehmt2_K182R_PBS 2


title: Ehmt2_K182R_PBS 3


title: WT_PBS 1


title: E.coli_RedC_rep2

city: Moscow

first: Grigory

last: Evko

address: Vavilova str., 34/5

country: Russia

institute: Institute of Gene Biology of the Russian Academy of Sciences

library_source: other

data_processing:
For raw data processing RedClib pipeline was used (github: https://github.com/agalitsyna/RedClib)
Supplementary files format and content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts. Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Library strategy: RedC

molecule: other

organism: Escherichia coli

growth_protocol:
E. coli DH5α and B. subtilis 168 strains were grown overnight in Luria-Bertani broth at 37 °C and 180 rpm to a final OD600 ~ 1.7.
T. adornatum 1910bT strain was grown on strictly anaerobic modified Pfennig medium supplemented with 0.1 g/L of yeast extract, 1/100 (v/v) of sterile culture broth filtrate of Desulfurococcus sp. 1910a and 1.0 g/L of glucose as the substrate under N2 in the gas phase at 80°C and pH 5.75 to a final growth yield of 3×10^7 cells/mL.

extract_protocol: RedC uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.


title: WT_PBS 3


title: WT_Dex 1


title: WT_Dex 2


title: WT_PBS 2


title: E.coli_RedC_rep1


title: MH-3

type: RNA

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

country: Japan

institute: Sapporo Medical University School of Medicine

description: Extracellar vesicles separated form culture media

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Toray) according to manufacturer's instruction. Expression profiles were analyzed using an oligo microarray (Rat_miRNA_V20).

scan_protocol: Array was scanned with an Toray 3D-Gene Scanner.

data_processing: Digitalizing analysis  Software was used for background subtraction

organism: Rattus norvegicus

source_name: rat liver parenchymal cells

label_protocol: Total miRNA was labeled using a3D-Gene miRNA labeling kit(Toray) according to manufacturer's instruction.

growth_protocol: Thy1 and MSC were cultured on plastic culture dishes. SHs were cultured on hyaruronic acid-coated dishes. MHs were cultured on type I collagen coat dishes.

extract_protocol: MicroRNAs (miRNAs) were extracted from EVs using the Qiazol lysis reagent and miRNeasy mini kit (Qiagen).

treatment_protocol: Cells were suspended with FBS free DMEM for 2 days for EVs isolation.

value: rat liver parenchymal cells


title: MSC-2

source_name: Bone marrow mesenchymal cells

value: Bone marrow mesenchymal cells


title: Ehmt2_K182R_Dex 2

value: Liver


title: MH-2


title: MH-1


title: SH-2

source_name: rat liver progenitor cells

value: rat liver progenitor cells


title: MSC-3


title: Thy1-3

source_name: rat liver stem cells

value: rat liver stem cells


title: Thy1-2


title: run_28_PD-12G_S383

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

source_name: sci-RNA-seq3 of mouse organogenesis and fetal development

growth_protocol: For the newly generated mouse embryo data (ranging from E8 to P0), we employed a combination of staging methodologies depending on gestational age of harvest. To maximize temporal coherence, resolution, and accuracy, we sought to stage individual embryos based on well-defined morphological criteria, rather than by gestational day alone. Embryos harvested between E8.0 - E10.0 were staged based upon the number of somites counted at the time of harvest and further characterized by morphological features. Based upon an estimated 1.5 to 2 hour periodicity for somite formation, E8.0 - E10.0 embryos were grouped into 4 somite bins. For E10.25-E14.75 embryos, developmental age was determined using the embryonic Mouse Ontogenetic Staging System (eMOSS, https://limbstaging.embl.es/), which leverages dynamic changes in hindlimb bud morphology and landmark-free based morphometry to estimate the absolute developmental stage of a sample. A modified staging tool, implemented in python, with increased performance on E14.0-E15.0 samples was used to confirm staging of samples within this window (documentation and python scripts available at: https://github.com/marcomusy/welsh_embryo_stager). To distinguish samples staged via eMOSS, these samples are designated with “mE” for morphometric embryonic day (e.g. mE13.5). Due to the increased complexity of limb morphology at later stages automated staging beyond ~E15.0 is not possible. As a consequence, harvests for all remaining embryonic samples (E15.0-E18.75) were performed precisely at 00:00, 06:00, 12:00, and 18:00 on the targeted day. From close inspection of limbs in this sample set we defined additional dynamics related to digit morphogenesis that allowed further binning of samples collected on Days 15 and 16. Therefore, amongst samples profiled in this study only the E17.0-E18.75 samples were staged solely by gestational age. Lastly, P0 samples were harvested from litters at noon of the day of birth (parturition for C57BL/6NJ occurs between E18.75 and E19.0).

extract_protocol: To generate the dataset, we used the optimized sci-RNA-seq3 protocol, adjusting the volume and type of lysis buffer to the size of the embryos. Briefly, frozen embryos were pulverized on dry ice and cells were lysed with a phosphate-based, hypotonic lysis buffer containing magnesium chloride, Igepal, diethyl pyrocarbonate (DEPC) as an RNase inhibitor, and either sucrose or bovine serum albumin (BSA). Lysate is passed over a 20um filter, and the nuclei-containing flow-through is fixed with a mixture of methanol and dithiobis (succinimidyl propionate) (DSP). Nuclei are rehydrated and washed in a sucrose/PBS/triton/magnesium chloride buffer (SPBSTM), then counted and distributed into 96-well plates for reverse transcription with indexed oligo-dT primers.

tag: developmental stage

value: birth-series


title: run_28_PD-12E_S381

description: sci-RNA-seq3 library


title: run_28_PD-12H_S384

description: sci-RNA-seq3 library


title: run_28_PD-12D_S380

description: sci-RNA-seq3 library


title: run_28_PD-11H_S376

description: sci-RNA-seq3 library


title: run_28_PD-12C_S379

description: sci-RNA-seq3 library


title: Thy1-1


title: run_28_PD-11G_S375

description: sci-RNA-seq3 library


title: run_28_PD-11F_S374

description: sci-RNA-seq3 library


title: run_28_PD-12F_S382

description: sci-RNA-seq3 library


title: SH-3


title: run_28_PD-11D_S372

description: sci-RNA-seq3 library


title: run_28_PD-11C_S371

description: sci-RNA-seq3 library


title: SH-1


title: MSC-1


title: run_28_PD-12A_S377

description: sci-RNA-seq3 library


title: run_28_PD-12B_S378

description: sci-RNA-seq3 library


title: PZ3 PBMCs

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: basal Peripheral Blood Mononuclear Cells (PBMC) (day 1)

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

label: biotin

label_protocol: Gene expression profile (GEP) was performed on total RNA purified from PBMC and CIK cells obtained from three oncologic patients. Briefly, biotinylated cRNA were synthesized from 100ng of total RNA by using GeneAtlas 3´ IVT Plus Reagent Kit (P/N 703210, Affymetrix) according to the standard protocol supplied by Affymetrix. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

extract_protocol: Total cellular RNA was isolated from 3x10^6 of PBMC (day 1, absence of INF- γ) and CIK cells (day 14) obtained from 3 GIST patients, using the Invitrogen™ TRIzol™ (Thermo Fisher Scientific). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: CIK cells were expanded from peripheral blood mononuclear cells (PBMC) collected from 3 patients with histologic confirmed Gastrointestinal Stromal Tumors (GIST). Cryopreserved PBMC were seeded at a concentration of 2x10^6 cells/ml according to the standard protocol (Gammaitoni, L., L. Giraudo, V. Leuci,et al. Clin Cancer Res 2013; Sangiolo, D., G. Mesiano, L. Gammaitoni, Cancer Res 2014), including 21 days of culture in RPMI-1640 medium (Gibco BRL Life Technologies Italia, Monza, Italy) supplemented with 10% fetal bovine serum (Sigma Aldrich, MI, Italy) 100 U/ml penicillin, and 100 U/ml streptomycin (Gibco BRL Life Technologies Italia) at 37°C and 5% CO2, with the timed addition of IFN-γ (1000 U/ml on day 0), Ab anti-CD3 OKT3 (50 ng/ml on day 1) and IL-2 (300 U/ml on day 1 up to the end, refreshing the medium every 2-3 days) (all factors are from Miltenyi Biotec S.r.l., Calderara di Reno, BO, Italy). At day 0 a small number of each PBMC culture (7 x 106) were seeded at the same concentration and culture conditions (2 x 106 cells/ml in RPMI-1640 medium with 10% fetal bovine serum, 100 U/ml penicillin and streptomycin at 37°C and 5% CO2) but without the addition of INF-γ.

tag: individual

value: GIST patient #3

value: Peripheral Blood

value: PBMCs


title: PZ2 PBMCs

source_name: Peripheral Blood Mononuclear Cells (PBMC)

value: GIST patient #2


title: PZ3 CIK cells

description: Cytokine Induced Killer (CIK) cells obtained from ex vivo expansion (day 14)

value: CIK cells


title: PZ2 CIK cells

source_name: Cytokine Induced Killer (CIK) cells obtained from ex vivo expansion


title: PZ4 PBMCs

value: GIST patient #4


title: PZ4 CIK cells


title: run_28_PD-10H_S368

description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


title: run_28_PB-06D_S140

description: sci-RNA-seq3 library


title: run_28_PB-06E_S141

description: sci-RNA-seq3 library


title: run_28_PB-06F_S142

description: sci-RNA-seq3 library


title: run_28_PB-05E_S133

description: sci-RNA-seq3 library


title: run_28_PB-05A_S129

description: sci-RNA-seq3 library


title: run_28_PB-05D_S132

description: sci-RNA-seq3 library


title: run_28_PB-06A_S137

description: sci-RNA-seq3 library


title: run_28_PB-05F_S134

description: sci-RNA-seq3 library


title: run_28_PB-05H_S136

description: sci-RNA-seq3 library


title: run_28_PB-05C_S131

description: sci-RNA-seq3 library


title: run_28_PB-06C_S139

description: sci-RNA-seq3 library


title: run_28_PB-04H_S128

description: sci-RNA-seq3 library


title: run_28_PB-05G_S135

description: sci-RNA-seq3 library


title: run_28_PB-05B_S130

description: sci-RNA-seq3 library


title: run_28_PB-06B_S138

description: sci-RNA-seq3 library


title: run_28_PB-04D_S124

description: sci-RNA-seq3 library


title: run_28_PB-04G_S127

description: sci-RNA-seq3 library


title: run_28_PB-04C_S123

description: sci-RNA-seq3 library


title: run_28_PB-04E_S125

description: sci-RNA-seq3 library


title: run_28_PB-04B_S122

description: sci-RNA-seq3 library


title: run_28_PB-04F_S126

description: sci-RNA-seq3 library


title: run_28_PB-04A_S121

description: sci-RNA-seq3 library


title: run_28_PB-03H_S120

description: sci-RNA-seq3 library


title: run_28_PB-03G_S119

description: sci-RNA-seq3 library


title: run_28_PB-03F_S118

description: sci-RNA-seq3 library


title: run_28_PB-03E_S117

description: sci-RNA-seq3 library


title: run_28_PB-03D_S116

description: sci-RNA-seq3 library


title: run_28_PB-03C_S115

description: sci-RNA-seq3 library


title: run_28_PB-02H_S112

description: sci-RNA-seq3 library


title: run_28_PB-02G_S111

description: sci-RNA-seq3 library


title: run_28_PB-02F_S110

description: sci-RNA-seq3 library


title: run_28_PB-02B_S106

description: sci-RNA-seq3 library


title: run_28_PB-02C_S107

description: sci-RNA-seq3 library


title: run_28_PB-02D_S108

description: sci-RNA-seq3 library


title: run_28_PB-02A_S105

description: sci-RNA-seq3 library


title: run_28_PB-01G_S103

description: sci-RNA-seq3 library


title: run_28_PB-01H_S104

description: sci-RNA-seq3 library


title: run_28_PB-01E_S101

description: sci-RNA-seq3 library


title: run_28_PB-01D_S100

description: sci-RNA-seq3 library


title: run_28_PB-01B_S98

description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


title: run_28_PB-01C_S99

description: sci-RNA-seq3 library


title: run_28_PA-12G_S95

description: sci-RNA-seq3 library


title: run_28_PA-11H_S88

description: sci-RNA-seq3 library


title: run_28_PA-12F_S94

description: sci-RNA-seq3 library


title: run_28_PA-12C_S91

description: sci-RNA-seq3 library


title: run_28_PA-12D_S92

description: sci-RNA-seq3 library


title: run_28_PA-11G_S87

description: sci-RNA-seq3 library


title: run_28_PA-12B_S90

description: sci-RNA-seq3 library


title: run_28_PA-12A_S89

description: sci-RNA-seq3 library


title: run_28_PB-03B_S114

description: sci-RNA-seq3 library


title: run_28_PB-03A_S113

description: sci-RNA-seq3 library


title: run_28_PA-11F_S86

description: sci-RNA-seq3 library


title: run_28_PB-02E_S109

description: sci-RNA-seq3 library


title: run_28_PA-11D_S84

description: sci-RNA-seq3 library


title: run_28_PA-11B_S82

description: sci-RNA-seq3 library


title: run_28_PA-12E_S93

description: sci-RNA-seq3 library


title: run_28_PA-11C_S83

description: sci-RNA-seq3 library


title: run_28_PB-01A_S97

description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library

value: mouse embryos spanning late gastrulation (E8) to birth (P0)


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


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description: sci-RNA-seq3 library


title: run_27_PG-03G_S215

description: sci-RNA-seq3 library


title: run_27_PG-05D_S228

description: sci-RNA-seq3 library


title: run_27_PG-03C_S211

description: sci-RNA-seq3 library


title: run_27_PG-02H_S208

description: sci-RNA-seq3 library


title: run_27_PG-02G_S207

description: sci-RNA-seq3 library


title: run_27_PG-02E_S205

description: sci-RNA-seq3 library


title: run_27_PG-03A_S209

description: sci-RNA-seq3 library


title: run_27_PG-02D_S204

description: sci-RNA-seq3 library


title: run_27_PG-03B_S210

description: sci-RNA-seq3 library


title: run_27_PG-05E_S229

description: sci-RNA-seq3 library


title: run_27_PG-02F_S206

description: sci-RNA-seq3 library


title: run_27_PG-02C_S203

description: sci-RNA-seq3 library


title: run_27_PG-02B_S202

description: sci-RNA-seq3 library


title: run_27_PG-01H_S200

description: sci-RNA-seq3 library


title: run_27_PG-01E_S197

description: sci-RNA-seq3 library


title: run_27_PG-01G_S199

description: sci-RNA-seq3 library


title: run_27_PG-02A_S201

description: sci-RNA-seq3 library


title: run_27_PG-01F_S198

description: sci-RNA-seq3 library


title: run_27_PG-01D_S196

description: sci-RNA-seq3 library


title: run_27_PF-12E_S189

description: sci-RNA-seq3 library


title: run_27_PG-01A_S193

description: sci-RNA-seq3 library


title: run_27_PF-12D_S188

description: sci-RNA-seq3 library


title: run_27_PF-12H_S192

description: sci-RNA-seq3 library


title: run_27_PG-01B_S194

description: sci-RNA-seq3 library


title: run_27_PG-01C_S195

description: sci-RNA-seq3 library


title: run_27_PF-12G_S191

description: sci-RNA-seq3 library


title: run_27_PF-12A_S185

description: sci-RNA-seq3 library


title: run_27_PF-12C_S187

description: sci-RNA-seq3 library


title: run_27_PF-11H_S184

description: sci-RNA-seq3 library


title: run_27_PF-12F_S190

description: sci-RNA-seq3 library


title: run_27_PF-11F_S182

description: sci-RNA-seq3 library


title: run_27_PF-12B_S186

description: sci-RNA-seq3 library


title: run_27_PF-11D_S180

description: sci-RNA-seq3 library


title: run_27_PF-11C_S179

description: sci-RNA-seq3 library


title: run_27_PF-11A_S177

description: sci-RNA-seq3 library


title: run_27_PF-10G_S175

description: sci-RNA-seq3 library


title: run_27_PF-10H_S176

description: sci-RNA-seq3 library


title: run_27_PF-11B_S178

description: sci-RNA-seq3 library


title: run_27_PF-11E_S181

description: sci-RNA-seq3 library


title: run_27_PF-10D_S172

description: sci-RNA-seq3 library


title: run_27_PF-10C_S171

description: sci-RNA-seq3 library


title: run_27_PF-10F_S174

description: sci-RNA-seq3 library


title: run_27_PF-10A_S169

description: sci-RNA-seq3 library


title: run_27_PF-10B_S170

description: sci-RNA-seq3 library


title: run_27_PF-09H_S168

description: sci-RNA-seq3 library


title: run_27_PF-09F_S166

description: sci-RNA-seq3 library


title: run_27_PF-09G_S167

description: sci-RNA-seq3 library


title: run_27_PF-09D_S164

description: sci-RNA-seq3 library


title: run_27_PF-09E_S165

description: sci-RNA-seq3 library


title: run_27_PF-11G_S183

description: sci-RNA-seq3 library


title: run_27_PF-09C_S163

description: sci-RNA-seq3 library


title: run_27_PF-09B_S162

description: sci-RNA-seq3 library


title: run_27_PF-08G_S159

description: sci-RNA-seq3 library


title: run_27_PF-09A_S161

description: sci-RNA-seq3 library


title: run_27_PF-08D_S156

description: sci-RNA-seq3 library


title: run_27_PF-08F_S158

description: sci-RNA-seq3 library


title: run_27_PF-08E_S157

description: sci-RNA-seq3 library


title: run_27_PF-10E_S173

description: sci-RNA-seq3 library


title: run_27_PF-08A_S153

description: sci-RNA-seq3 library


title: run_27_PF-07F_S150

description: sci-RNA-seq3 library


title: run_27_PF-07H_S152

description: sci-RNA-seq3 library


title: run_27_PF-07E_S149

description: sci-RNA-seq3 library


title: run_27_PF-07C_S147

description: sci-RNA-seq3 library


title: run_27_PF-07B_S146

description: sci-RNA-seq3 library


title: run_27_PF-07A_S145

description: sci-RNA-seq3 library


title: run_27_PF-06E_S141

description: sci-RNA-seq3 library


title: run_27_PF-06F_S142

description: sci-RNA-seq3 library


title: run_27_PF-06G_S143

description: sci-RNA-seq3 library


title: run_27_PF-08H_S160

description: sci-RNA-seq3 library


title: run_27_PF-06D_S140

description: sci-RNA-seq3 library


title: run_27_PF-06C_S139

description: sci-RNA-seq3 library


title: run_27_PF-05F_S134

description: sci-RNA-seq3 library


title: run_27_PF-06B_S138

description: sci-RNA-seq3 library


title: run_27_PF-06A_S137

description: sci-RNA-seq3 library


title: run_27_PF-05G_S135

description: sci-RNA-seq3 library


title: run_27_PF-05H_S136

description: sci-RNA-seq3 library


title: run_27_PF-05D_S132

description: sci-RNA-seq3 library


title: run_27_PF-05C_S131

description: sci-RNA-seq3 library


title: run_27_PF-08C_S155

description: sci-RNA-seq3 library


title: run_27_PF-05B_S130

description: sci-RNA-seq3 library


title: run_27_PF-05A_S129

description: sci-RNA-seq3 library


title: run_27_PF-08B_S154

description: sci-RNA-seq3 library


title: run_27_PF-07D_S148

description: sci-RNA-seq3 library


title: run_27_PF-07G_S151

description: sci-RNA-seq3 library


title: run_27_PF-04F_S126

description: sci-RNA-seq3 library


title: run_27_PF-04E_S125

description: sci-RNA-seq3 library


title: run_27_PF-04G_S127

description: sci-RNA-seq3 library


title: run_27_PF-04H_S128

description: sci-RNA-seq3 library


title: run_27_PF-04D_S124

description: sci-RNA-seq3 library


title: run_27_PF-04C_S123

description: sci-RNA-seq3 library


title: run_27_PF-06H_S144

description: sci-RNA-seq3 library


title: run_27_PF-04A_S121

description: sci-RNA-seq3 library


title: run_27_PF-04B_S122

description: sci-RNA-seq3 library


title: run_27_PF-03H_S120

description: sci-RNA-seq3 library


title: run_27_PF-03G_S119

description: sci-RNA-seq3 library


title: run_27_PF-03F_S118

description: sci-RNA-seq3 library


title: run_27_PF-03E_S117

description: sci-RNA-seq3 library


title: run_27_PF-03D_S116

description: sci-RNA-seq3 library


title: run_27_PF-05E_S133

description: sci-RNA-seq3 library


title: run_27_PF-03C_S115

description: sci-RNA-seq3 library


title: run_27_PF-03B_S114

description: sci-RNA-seq3 library


title: run_27_PF-02H_S112

description: sci-RNA-seq3 library


title: run_27_PF-02G_S111

description: sci-RNA-seq3 library


title: run_27_PF-02F_S110

description: sci-RNA-seq3 library


title: run_27_PF-02E_S109

description: sci-RNA-seq3 library


title: run_27_PF-02C_S107

description: sci-RNA-seq3 library


title: run_27_PF-03A_S113

description: sci-RNA-seq3 library


title: run_27_PF-02D_S108

description: sci-RNA-seq3 library


title: run_27_PF-02A_S105

description: sci-RNA-seq3 library


title: run_27_PF-01H_S104

description: sci-RNA-seq3 library


title: run_27_PF-01F_S102

description: sci-RNA-seq3 library


title: run_27_PF-01E_S101

description: sci-RNA-seq3 library


title: run_27_PF-01D_S100

description: sci-RNA-seq3 library


title: run_27_PE-12H_S96

description: sci-RNA-seq3 library


title: run_27_PF-01C_S99

description: sci-RNA-seq3 library


title: run_27_PF-02B_S106

description: sci-RNA-seq3 library


title: run_27_PE-12E_S93

description: sci-RNA-seq3 library


title: run_27_PF-01A_S97

description: sci-RNA-seq3 library


title: run_27_PE-12G_S95

description: sci-RNA-seq3 library


title: run_27_PF-01B_S98

description: sci-RNA-seq3 library


title: run_27_PE-12D_S92

description: sci-RNA-seq3 library


title: run_27_PE-12B_S90

description: sci-RNA-seq3 library


title: run_27_PE-12A_S89

description: sci-RNA-seq3 library


title: run_27_PE-11G_S87

description: sci-RNA-seq3 library


title: run_27_PE-11F_S86

description: sci-RNA-seq3 library


title: run_27_PE-11D_S84

description: sci-RNA-seq3 library


title: run_27_PE-11C_S83

description: sci-RNA-seq3 library


title: run_27_PE-11A_S81

description: sci-RNA-seq3 library


title: run_27_PE-10G_S79

description: sci-RNA-seq3 library


title: run_27_PE-11B_S82

description: sci-RNA-seq3 library


title: run_27_PE-10H_S80

description: sci-RNA-seq3 library


title: run_27_PE-10F_S78

description: sci-RNA-seq3 library


title: run_27_PF-01G_S103

description: sci-RNA-seq3 library


title: run_27_PE-12F_S94

description: sci-RNA-seq3 library


title: run_27_PE-10D_S76

description: sci-RNA-seq3 library


title: run_27_PE-10B_S74

description: sci-RNA-seq3 library


title: run_27_PE-10E_S77

description: sci-RNA-seq3 library


title: run_27_PE-09H_S72

description: sci-RNA-seq3 library


title: run_27_PE-09G_S71

description: sci-RNA-seq3 library