title: TSC-FF-Rocki-5

status: Public on Mar 11 2022

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Science

institute: Cornell University

data_processing:
The quality of raw reads was checked using FastQC before aligning to bovine reference genome using TOPHAT
Differentially expressed genes were identified using R package EdgeR

organism: Bos taurus

source_name: bovine blastocysts

growth_protocol: TSC were grown with or without feeders

extract_protocol:
Total RNA was isolated using RNAqueous Micro Total RNA isolation kit.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina)

treatment_protocol: Treatment with TGFB1 10ng/ml or ROCK inhibitor 10 µM Y-27632

value: bovine trophoblast stem cells

value: Rho kinase inhibition


title: SAMPLE 4_AC16-L10-D12

status: Public on Mar 12 2022

type: RNA

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

description: Gene expression data from AC16 cells treated with exosomes isolated from blood of astronaut D12 10 days before flight.

hyb_protocol: Human Clariom S chips were hybridized with 2.5 µg of fragmented biotin-labeled cDNA in 100 µl hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000 using Command Console Software (Thermo Fisher Scientific, Waltham, MA).

data_processing: Arrays were processed and RMA normalized using oligo, pd.clariom.s.human, annotate and clariomsmousetranscriptcluster.db BioConductor packages. Probe IDs were converted to ENSEMBL gene IDs.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: AC16 cell line treated with exosomes of D12 austronaut at L-10

label_protocol: 100 ng of RNA was used from each sample to prepare fragmented biotin-labeled cDNA by GeneChip WT PLUS reagent kit

growth_protocol: Exosomes were isolated from blood plasma samples of 3 astronauts (D12, D13, and D14) at L-10 and R+3 using the ExoQuick Plasma prep and exosome precipitation kit (Cat # EXOQ5TM, System Biosciences, CA, USA).

extract_protocol: Total RNA was extracted from AC16 cells treated with astronaut-derived exosomes (ExoL-10 and ExoR+3) for 24 hrs using the RNeasy Mini Kit (Qiagen), according to the manufacturer's protocol. High-quality RNA was isolated using RNeasy Mini spin columns and eluted using molecular-grade water (RNAse/DNAse free).

treatment_protocol: AC16 cells, were cultured in DMEM/F12 containing 2 mM L‐Glutamine, 10% exosomes-free FBS, and 1% Penicillin/Streptomycin Solution.

tag: treatment

value: treated

tag: cell line

tag: time point


title: TSC-FF-Rocki-4

type: SRA

country: USA

library_source: transcriptomic

tag: cell type


title: TSC-FF-Rocki-3


title: TSC-FF-Rocki-2


title: shVHL61-1 activated Macrophage

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.39)
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1)
A user-friendly software RSEM (version 1.2.28) was applied for the quantification of the transcript abundance
Differentially expressed genes (DEGs) were identified by EBSeq (version 1.16.0)
The functional enrichment analysis of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among gene clusters was implemented in an R package called clusterProfiler (version 3.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized count of mapped reads (FPKM) for every gene and every sample

source_name: Macrophage precursor THP-1

extract_protocol:
Using miRNeasy Mini Kit (QIAGEN, #217004)
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads with 20M clean reads per sample generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan

treatment_protocol: Macrophage was induced from THP-1 by treatment with 50 ng/ml phorbol 12-myristate-13-acetate (PMA; Sigma Aldrich #P8139) for 24 hrs, and subsequently cultured in RPMI-1640 containing 10% FBS for 24 hrs. The macrophages were seeded in the lower chamber of a Boyden chamber at 80% confluency; then human kidney tubukle cells HK-2 expressing either short-hairpin (sh) RNA specific for Luciferase (as control) or VHL (shVHL61, as VHL knockdown) were seeded in the upper chamber. Macrophages were collected for RNA purification 48 hr later.

tag: tissue

value: Peripheral blood

tag: age

value: 1 year

tag: Sex

value: male


title: SAMPLE 2_AC16-NT

description: Gene expression data from untreated AC16 cells.

source_name: AC16 cell line untreated

value: untreated


title: TSC-FF-Rocki-1


title: SAMPLE 8_AC16-R3-D13

description: Gene expression data from  AC16 cells treated with exosomes isolated from blood of astronaut D13 3 days after return.

source_name: AC16 cell line treated with exosomes of D13 austronaut at R+3


title: TSC-TGFB1-4

value: Transforming growth factor beta 1 treatment


title: TSC-TGFB1-1


title: TSC-TGFB1-2


title: TSC-TGFB1-3


title: TSC-TGFB1+Rocki-3

value: Transforming growth factor beta 1 treatment and Rho kinase inhibition


title: TSC-TGFB1+Rocki-1


title: TSC-TGFB1+Rocki-2


title: TSC-Rocki-4


title: TSC-Rocki-1


title: TSC-Rocki-3


title: SAMPLE 1_AC16-NT


title: Lamin AC WT cells, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description:
The GM12878 cell line is EBV positive.
Lamin AC WT cells, replicate 1
WT.1

library_source: genomic

data_processing:
HiC data preprocessing done using HiC-Pro using EBV genome version NC_007605.1 with 1kb resolution.
Assembly: NC_007605.1
Supplementary files format and content: Processed data files contain the HiC-Pro output: count matrices (*_1000.matrix) and regions file (1000_abs.bed).

molecule: genomic DNA

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: GM12878 cell line

extract_protocol:
5x10^6 cells per condition were collected for in situ Hi-C.
Libraries of total ligation products were produced using Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol.

tag: genotype

value: Lamin A/C WT

tag: replicate


title: Lamin AC KO cells, replicate 2

description:
The GM12878 cell line is EBV positive.
Lamin AC KO cells, replicate 2
KO.2

value: Lamin A/C KO


title: Lamin AC WT cells, replicate 2

description:
The GM12878 cell line is EBV positive.
Lamin AC WT cells, replicate 2
WT.2


title: Lamin AC KO cells under treated with G9a inhibitor, replicate 2

data_processing:
RNA-Seq data analysis was done with bowtie2 and rsem (ver. 1.2.3) using EBV genome version NC_007605.1
DESeq2 was used for differentail expression analysis
Genome_build: NC_007605.1
Supplementary_files_format_and_content: Prosessed files contains the raw counts for EBV genes

molecule: polyA RNA

extract_protocol:
RNA was extracted with Trizol (Invitrogen) for all RNA preparations, then subsequently cleaned and DNase treated using RNeasy columns (Qiagen)
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: lamins

value: KO

value: trt


title: TSC-Rocki-2


title: Lamin AC KO cells, replicate 1

description:
The GM12878 cell line is EBV positive.
Lamin AC KO cells, replicate 1
KO.1


title: Lamin AC KO cells under treated with G9a inhibitor, replicate 1


title: Lamin AC KO cells under untreated condition, replicate 2

value: unt


title: Lamin AC WT cells under treated with G9a inhibitor, replicate 3

value: WT


title: Lamin AC WT cells under treated with G9a inhibitor, replicate 2


title: Lamin AC WT cells under untreated condition, replicate 3


title: Lamin AC WT cells under untreated condition, replicate 1


title: Lamin AC WT cells under untreated condition, replicate 2


title: Diesel T24

city: Genova

first: Alessandra

last: Pulliero

state: Genova

address: Via A. Pastore 1

country: Italy

institute: Dipartimento di Scienze della Salute UNIGE

description: miRNA profiling

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies).

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number: G2565CA) and data extracted using Agilent feature extraction v.10. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: GeneSpring software (GeneSpring Multi-Omic Analysis version 14.9 – Build 11939 by Agilent Technologies) was used for analysis of miRNA expression. miRNA raw data files from Agilent Technologies Microarray Scanner System G2505C were imported to GeneSpring using miRNA analysis type, AgilentmiRNA,  Threshold: 1.0, Logbase: 2, Technology: Agilent.miRNA.70156_v21_0, Normalization: None, Baseline Transformation: None .

label: Cyanine 3-pCp

source_name: Human skin biopsy

label_protocol: 50 ng of total RNA was processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The, the Cy3-labeled RNA was purified using Micro Bio-Spin P-6 Gel Column (Bio-Rad Laboratories, Inc., Hercules, CA, USA).

growth_protocol: Human skin biopsies (12 mm diameter) were obtained from three healthy Caucasian donors (40–45 years old) who underwent elective abdominoplasties at Hunstad/Kortesis/ Bharti Cosmetic Surgery clinic. In total, 24 punch iopsies were taken from the abdominal  skin of each donor, and subcutaneous fat was removed with sterile scissors and  a scalpel. The biopsies, comprising dermal and epidermal layers, were rapidly rinsed with  Phosphate-Buffered Saline (PBS, Gibco, New York, NY, USA). The biopsies were then  moved into 6-well dishes containing 2 mL of complete Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum (FBS) and 1% of antibiotics and antimycotics (100 U/mL penicillin and 100 μg/mL, Gibco, New York, NY, USA) added; then, they were  incubated at 37 °C in 5% CO2 for overnight recovery

extract_protocol: The total RNA extraction was performed using a miRNeasy Mini kit QIAGEN (Hilgen, DE, cat. 1038703) and Qiazol Lysis Reagent 50 QIAGEN (Hilgen, DE, cat. 1023537), according to the manufacturer’s protocol. Total RNA was quantified by Qubit 2.0 Fluorometer using the Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: A full 24 h after skin biopsy collection, ex vivo explants were allocated into a plexiglass  sealed chamber, connected to the ozone generator machine (ECO3 model CUV-01,  Model 306 Ozone Calibration Source, 2B Technologies, Ozone solution, ITA), and exposed to 0.2 ppm for 4 h. Sample biopsies were then collected following ozone exposure (T0) or after 24 h (T24).Another set of skin biopsies was exposed to diesel engine exhaust by letting the engine run for 10 s and allowing the exhaust to reach the sealed exposure chamber where the skin biopsies remained for 30 min. Specifically, the skin explants were placed into a  sealed plexiglass box connected to a Kubota RTV-X900 diesel engine (3-cylinder, 4-cycle diesel with overhead valves, 1123 cc with 24.8 HP at 3000 rpm).The other human skin biopsies were exposed to 200 milli Joule (mJ) UVA/UVB light, which equates to circa 2 h at solar apex and corresponding to 10 minimal erythemal doses (MED, 1 MED = 20 mJ/cm2) [22]. UVA/UVB light (exposure of circa 20 s) was generated by a Sol1A Class ABB Solar Simulator, equipped with a xenon lamp (Newport Oriel Sol1A, CA, USA). Samples were collected after UV exposure (T0), or after 24 h (T24).

value: Human skin biopsy

tag: exposure

value: human skin exposed to diesel at 24 h.


title: UV T0

description: miRNA profiling

value: treated UV samples at 0h


title: AIR T24

description: miRNA profiling

value: untreated skin at 24 h


title: O3 T24

description: miRNA profiling

value: skin explants will be collected 24 hours (T24) after the initial ozone exposure to 0.2 ppm for 4 h.


title: AIR T0

description: miRNA profiling

value: skin either unexposed (Air) at 0h


title: O3 T0

description: miRNA profiling

value: treated ozone samples at 0h


title: control_2

city: Shanghai

first: Yuxin

last: Tian

address: 399 Wanyuan Road

country: China

institute: Children's Hospital of Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Mus musculus

source_name: Intestine

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®2.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
One micrograms of RNA were used as input material for the RNA sample preparations.Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide

treatment_protocol: The induction of NEC involves gavage feeding of hyperosmolar formula milk (15g Similac and 75 mL Esbilac; 50l/kg body weight per day), exposure to hypoxia (5% O2 for 10 min, 3 times/day) for 4 days, and lipopolysaccharide (LPS) stimulation (4 mg/kg/day) with oral feeding on postnatal days 6 and 7.

tag: strain

value: terminal ileum

value: postnatal day 9


title: control_1


title: NEC_2


title: control_3


title: Lamin AC KO cells under untreated condition, replicate 1


title: NEC_1


title: Lamin AC WT cells under treated with G9a inhibitor, replicate 1


title: NEC_3


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10G

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 with E8.5 mouse embryo
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.
Genome_build: 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: mouse embryos

growth_protocol: For newly generated E8.5b data, C57BL/6 mice were obtained at The Jackson Laboratory. In brief, timed matings of mice were performed via standard husbandry procedures. On the morning of E8.5, individual decidua were removed and placed in ice cold PBS during the harvest. Individual embryos were dissected free of extraembryonic membranes, imaged, and the number of somites present were noted prior to snap freezing in liquid nitrogen. Samples were stored at -80C until further processing.

extract_protocol: We performed a simplified, optimized version of sci-RNA-seq3 (Cao et al. 2019). Briefly, to each tube, 100ul of a hypotonic, PBS-based lysis buffer was added with DEPC as an RNase inhibitor. The resulting nuclei were then fixed with 4 volumes of a mix of methanol and dithiobis (succinimidyl propionate) (DSP). After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton buffer (SPBST), the nuclei were distributed to a 96-well plate for reverse transcription, allocating 8 wells per embryo. After reverse transcription, nuclei were pooled, washed in SPBST and redistributed to a fresh plate for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to 5 final plates for second strand synthesis, extraction, tagmentation, and PCR to add the third index plus a plate index. Products were pooled by PCR plate, size-selected and sequenced on an Illumina NovaSeq.

tag: developmental stage

value: mouse embryo (E8.5), early somitogenesis


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-11A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10H


title: UV T24

description: miRNA profiling

value: human skin biopsies were exposed to 200 milli Joule (mJ) UVA/UVB light,


title: GLU_13

city: Johnson City

first: David

middle: L

last: Williams

state: TN

address: PO Box 70575

department: Surgery

institute: East Tennessee State University

data_processing:
Basecalls performed using CASAVA
Aligment performed using STAR V2.5
Reads containing adaptor contamination, uncertain nucleotides > 10%, and low quality nucleotides constituting > 50% of total read were removed.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3)
KEGG and GO analysis was performed using clusterProfiler
Genome_build: mm10
Supplementary_files_format_and_content: "TrainedvsControl.DEG.all.xls" is differential expression analysis generated using DESeq2
Supplementary_files_format_and_content: "TrainedvsControl.all.KEGGenrich.xls" is KEGG pathway enrichment analysis performed using clusterProfiler
Supplementary_files_format_and_content: "TrainedvsControl.all.GOenrich.xls" is gene ontology analysis performed using clusterProfiler

source_name: Bone marrow-derived macophages

growth_protocol: BMDMs generated by culturing BM cells in in RPMI 1640 with 25mM HEPES (ThermoFisher 22400071), 10% FBS, 1% Gibco antibiotic-antimycotic (ThermoFisher 15240062), and 10 ng/mL M-CSF (R&D systems 416-ML-050) for seven days.

extract_protocol:
RNA was isolated from BMDMs using the RNeasy Mini Kit (Qiagen# 74104) using manufacturer instructions
Library was contructed by Novogene using their standard protocol

treatment_protocol: After BMDMs were generated, BMDMs were treated with 10 μg/mL C. albicans-derived β-glucan or PBS for 24 hours. BMDMs were allowed to rest for 7 days with media being changed every other day.

value: Bone marrow-derived macophages

value: C. albicans-derived B-glucan


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10A


title: ND1

city: Boston

first: Zhekai

last: Hu

address: 1 Kneeland St

institute: TUFTS UNIVERSITY

description: ND bone, 18wks

hyb_protocol: The labeled samples were hybridized onto Arraystar Mouse LncRNA Array V2.0 in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). Only lncRNA probes were included, excluding the mRNAs in the array.

source_name: ND bone, 18wks, replicate 1

label_protocol: Total RNA from each sample was amplified and transcribed into cyanine-3 (Cy3) labeled cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Total RNA was extracted using TriZol reagent (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: 18-week old male high-fat-diet (HFD) mice (12-week high fat diet) and 18-week old male normal-diet (ND) mice  were used for microarray assay and comparison of the gene characteristics

value: male

value: bone

value: normal-diet


title: ND3

description: ND bone, 18wks

source_name: ND bone, 18wks, replicate 3


title: Diesel T0

description: miRNA profiling

value: skin biopsies was exposed to diesel engine exhaust t for 30 min


title: ND2

description: ND bone, 18wks

source_name: ND bone, 18wks, replicate 2


title: HFD2

description: HFD bone, 18wks

source_name: HFD bone, 18wks, replicate 2

value: 12-week high fat diet


title: HFD1

description: HFD bone, 18wks

source_name: HFD bone, 18wks, replicate 1


title: HFD3

description: HFD bone, 18wks

source_name: HFD bone, 18wks, replicate 3


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08B


title: Vector UM-UC-3 rep3

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen 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 whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: UM-UC-3 cells

growth_protocol: The human bladder cancer cell lines UM-UC-3 were purchased from American Type Culture Collection and cultured in an incubator with 5% CO2 at 37℃. UM-UC-3 cells were cultured in Dulbecco's modified eagle's medium contained 10% fetal bovine serum.

extract_protocol:
The indicated UM-UC-3 cells were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pcDNA3.1 expression vector with circNCOR1 gene were purchased from Genepharma company (Shanghai, China) and used to overexpress the circNCOR1 gene in UM-UC-3 cells. The transfections were conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

value: human bladder cancer UM-UC-3 cells

value: transfected with Vector plasmids


title: sci-RNA-seq3 with E8.5 mouse embryo PE-08A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-10B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-07C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-09A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-05A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-06E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-03A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02A


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01F


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01E


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01C


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01D


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01B


title: sci-RNA-seq3 with E8.5 mouse embryo PE-01A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12H


title: sci-RNA-seq3 with E8.5 mouse embryo PE-04A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-12A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-11A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10G


title: sci-RNA-seq3 with E8.5 mouse embryo PE-02B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-10A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-08B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07E


title: Ctrl3_RNA

city: Segrate

first: Ettore

last: Mosca

address: Via F.lli Cervi 93

institute: National Research Council - Institute of Biomedical Technologies

description:
CSV_S4
norm_smallRNA_counts.txt

data_processing:
smallRNA reads were checked for quality control using FastQC 0.11.4
smallRNA reads were filtered and trimmed with cutadapt 1.12
smallRNA reads were mapped against Arena-Idb 10/2020 with Bowtie 1.2.3 and RSEM 1.2.15
smallRNA reads were clustered with SEED 02/2018
Normalization size factors were computed with TMM on cluster cardinalities
smallRNA expressions were normalized using normalization size factors
edgeR 3.10 was applied to compute differential expression analyses
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including normalized smallRNA read counts (smallRNA id, normalized expressions)
Supplementary files format and content: tab-delimited text file including edgeR results for comparisons of one patient vs. all the healthy controls (smallRNA id, logFC, FDR, normalized expressions)

source_name: Stool

extract_protocol: RNA, including smallRNA, was extracted from stool samples (about 200mg) using RNeasy Power Microbiome kit (Qiagen) according to manufacturer's istruction. SmallRNA libraries were prepared for sequencing using the TruSeq Small RNA Library Illumina protocol.

tag: sample source

value: stool

tag: disease state

value: Neurotypical development

tag: age range


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-07A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-06C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-09A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02A


title: sci-RNA-seq3 with E8.5 mouse embryo PD-02B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-05H


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01F


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01B


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01C


title: sci-RNA-seq3 with E8.5 mouse embryo PD-01A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12E


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12D


title: sci-RNA-seq3 with E8.5 mouse embryo PD-03G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-09B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-10E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-12A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-05D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-08A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-07A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-06H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01G


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-02D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01F


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01D


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01B


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01C


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-04C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-12A


title: sci-RNA-seq3 with E8.5 mouse embryo PC-03C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10E


title: sci-RNA-seq3 with E8.5 mouse embryo PC-01H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-10C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09G


title: sci-RNA-seq3 with E8.5 mouse embryo PD-04F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-11A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-09E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05H


title: sci-RNA-seq3 with E8.5 mouse embryo PC-11F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-05A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-08A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-07H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-06H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-03C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02A


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01G


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01B


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01C


title: sci-RNA-seq3 with E8.5 mouse embryo PB-01A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12H


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12F


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12D


title: sci-RNA-seq3 with E8.5 mouse embryo PB-04A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-12A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11E


title: sci-RNA-seq3 with E8.5 mouse embryo PB-02G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-11A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-09A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-08A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-10H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-06A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-05A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-04C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-07E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-03A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02F


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01H


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02C


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01G


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01D


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01A


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01B


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01C


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-760

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
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.
Genome_build: 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 (using scanpy.read_loom to open)

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer.
The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%. Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping. The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi).
Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer. Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well.
Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes). After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including 4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.
After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen).
1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter).
In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate. For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.


title: sci-RNA-seq3 with E8.5 mouse embryo P2-02E


title: sci-RNA-seq3 with E8.5 mouse embryo P2-01F


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-756


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-758


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-757


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-753


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-754


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-755


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-751


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-752


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-750


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-748


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-749


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-747


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-746


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-744


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-745


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-743


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-742


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-740


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-738


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-737


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-734


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-735


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-731


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-733


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-732


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-729


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-727


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-725


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-726


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-724


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-719


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-720


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-718


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-722


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-721


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-717


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-716


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-715


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-713


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-712


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-714


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-711


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-710


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-741


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-739


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-709


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-736


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-708


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-705


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-707


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-706


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-704


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-728


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-703


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-701


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-702


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-699


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-700


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-698


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-693


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-694


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-696


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-695


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-692


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-690


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-688


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-687


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-686


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-685


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-673


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-669


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-648


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-652


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-649


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-645


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-647


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-643


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-670


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-642


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-651


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-621


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-617


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-618


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-646


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-599


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-561


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-560


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title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-253


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-252


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-248


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-250


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-251


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-247


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-246


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-244


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-243


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-242


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-241


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-238


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-239