title: WT Rep2

status: Public on Feb 04 2019

city: Smithville

first: Evangelia

last: Koutelou

address: 1808 Park Rd 1C

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on May 23, 2014) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: Placenta

extract_protocol:
Placentas at E9.5 were collected, the maternal decidua was carefully peeled off, the tissue was homogenized through a syringe and total RNA was isolated using an RNeasy mini plus kit (Qiagen, 74134) following the manufacturer’s instructions.
The libraries were prepared using the Illumina TruSeq stranded total RNA kit according to the manufacturer’s protocol

tag: embryonic stage

value: Placenta at embryonic day E9.5

tag: genotypes

value: wild-type


title: WT Rep3

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: Mutant Rep2


title: Mutant Rep1


title: N3

status: Public on Feb 05 2019

type: RNA

city: Changsha

first: Pengpeng

last: Zhang

state: Hunan

address: No.138 Tongzipo Road

country: China

institute: The Third Xiangya Hospital of Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. When Data was extracted, Quantile normalization and subsequent data processing were conducted to use the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through fold change and p-value (fold change ≥2.0 and p-value <0.05)

source_name: liver

label_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was extracted from 9 frozen mouse liver tissues (selected 3 samples from each group randomly) using TRIzol (Invitrogen, USA) according to manufacturer’s instructions.

tag: treatment

value: control mouse

tag: tissue

value: liver

tag: gender

value: male

tag: age

value: 8 week


title: blastocyst_19

city: Sha Tin

first: Shangli

last: Cheng

address: No. 15 Science Park West Avenue

department: Ming Wai Lau Centre for Reparative Medicine

country: Hong Kong

institute: Karolinska Institutet

data_processing:
The sequencing fregments were aligned to the mm10 genome assembly using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include "Read counts" and RPKM values for each Sample

source_name: Embryo

growth_protocol: 21 cells from E4.5 which are CAST/EiJ (CAST) female mice mated to C57 male mice.

extract_protocol:
These embryos were dissociated in TrypLE (Life technologies) for 15mins through trituration and single cells were manually picked with fine glass capillaries dispensing in lysis buffer.
Libraries generated for sequencing was carried out on Illumina sequencer based on Smart-seq2 protocol.
RNA libraries were prepared for sequencing using  Smart-seq2

treatment_protocol: Embryos were dissected from decidua shelled out from uterus. Attached basement membrane and ectoplacental core were carefully removed and fine dissected embryos with visceral endoderm (VE), extraembryonic endoderm (ExE) and epiblast were washed twice with DMEM medium.

tag: genotype

value: CAST/EiJ (F) x C57BL/6J (M)

value: embryonic day 4.5

tag: embryo

value: Embryo


title: blastocyst_21


title: N2


title: blastocyst_18


title: Primary rat small hepatocytes LN111-2

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

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction. Expression profiles were analyzed using an oligo microarray (SurePrint G3 Rat Gene Expression v2 G4853B).

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction

organism: Rattus norvegicus

source_name: Passaged and cultured cells on LN111-coated dishes

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: LN111 were passaged and cultured cells on laminin111-coated dishes. LN511 were passaged and cultured cells on laminin511-coated dishes. Mat were passaged and cultured cells on matrigel-coated dishes.

extract_protocol: Total RNAs of prepared cells were extracted using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were suspended in serum-free Dulbecco’s modified Eagle’s medium/Nutrient Mixture Ham F-12 (DMEM/F12; Sigma-Aldrich Co., St.Louis, MO) supplemented with 20 mM HEPES (Dojindo Laboratories, Kumamoto, Japan), 25 mM NaHCO3 (Kanto Chemical Co. Inc., Tokyo, Japan), 30 mg/L L-proline (Sigma-Aldrich Co.), 0.1% bovine serum albumin (BSA; Serologicals Proteons Inc., Kankakee, IL), 10 mM nicotinamide (Sigma-Aldrich Co.), 1 mM ascorbic acid-2 phosphate (Asc2P; Wako Pure Chem. City, Japan), 10−7 M dexamethasone (Dex; Wako Pure Chem.), 0.5 mg/L insulin-transferrin-selenium (ITS-X; GIBCO-BRL Invitrogen, Grand Island, NY), 10 ng/mL epidermal growth factor (EGF; BD Biosciences, San Jose, CA) and antibiotics.

value: F344 [dipeptidylpeptidase IV (DPPIV)+ strain; Sankyo Lab Service Corp.Inc., Tokyo, Japan]

value: Liver

tag: cell type

value: small hepatocytes


title: N1


title: blastocyst_20


title: blastocyst_15


title: blastocyst_16


title: blastocyst_17


title: blastocyst_14


title: blastocyst_10


title: blastocyst_12


title: blastocyst_13


title: WT Rep1


title: blastocyst_9


title: blastocyst_8


title: blastocyst_7


title: blastocyst_11


title: bisulphite converted DNA from control placenta 5

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi package for the R statistical software and in-house R scripts

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: placenta 5 control

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: placenta

tag: iugr

value: no

tag: pre-eclampsia


title: blastocyst_6


title: blastocyst_5


title: blastocyst_4


title: blastocyst_2


title: blastocyst_3


title: blastocyst_1


title: Brain_female_GFP-GR100_1.5_months_GR107

city: Jacksonville

first: Mark

last: Ebbert

state: FL

address: 4500 San Pablo Rd

department: Neuroscience

institute: Mayo Clinic

description:
GR107
1.5M_mice-combined_count_and_rpkm_by_gene.txt

data_processing:
The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina by the Mayo Clinic Bioinformatics Core (Rochester, MN).
Reads were aligned to mm10 using TopHat v. 2.1.0.
Transcript counts were normalized using conditional quantile normalization for transcript length and GC content. We then normalized for hippocampal and cortical brain weight to account for cell death between GFP and GFP-(GR)100 mice. We then tested for differential expression between the GFP and GFP-(GR)100 mice using the Wald test in DESeq2, after performing the regularized logarithm (rlog) transformation. We used a strict false discovery rate (FDR) < 0.01. We followed up with a weighted gene co-expression network analysis (WGCNA) and Gene Ontology overrepresentation test to provide biologically meaningful context for gene sets using only the significantly differentially-expressed genes. To make WGCNA modules as specific as possible, we set WGCNA “mergeCutHeight” to 0.01. Clusters were made using “pheatmap” in R (v. 3.4.1) with Euclidean clustering distance.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited file containing both raw counts and RPKM per gene for each sample.

source_name: Cortex and Hippocampus

extract_protocol:
To extract total RNA in mouse brain, 1 volume of the homogenate was immediately mixed with 3 volumes of Trizol LS Reagent (Thermo Fisher Scientific), and then frozen on dry ice. One day later, total RNA was extracted using the Direct-zol™ RNA MiniPrep kit (Zymo Research) according to the manufacturer’s instructions, combined with an in-column DNase I digestion step. cDNA was obtained after RT-PCR using 1000 ng of RNA with random primers and the High Capacity cDNA Transcription Kit (Applied Biosystems) according to the manufacturer’s instructions.
The library preparation and RNA-Seq was performed by the Mayo Clinic Sequencing Core Facility (Rochester, MN). A total of 200 ng of RNA in a 50 μl volume was used for preparation of paired-end sequencing libraries using the TruSeq Stranded Total Sample Preparation kit (Illumina). Afterward, samples were subjected to quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform.

treatment_protocol: A gene fragment containing 100 GR dipeptide repeats were synthesized by GeneArt, and then ligated to the HindIII and BamHI restriction sites of a pAAV-EGFP fusion vector in frame with the EGFP coding sequence, respectively. The sequence of all plasmids was verified by sequence analysis.

value: Cortex and Hippocampus

tag: Sex

value: F

tag: age (months)

tag: cortex and hippocampus brain weight (mg)


title: Brain_male_GFP_1.5_months_GR195

description:
GR195
1.5M_mice-combined_count_and_rpkm_by_gene.txt

value: GFP

value: M


title: Brain_male_GFP-GR100_1.5_months_GR109

description:
GR109
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Brain_male_GFP-GR100_1.5_months_GR103

description:
GR103
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Brain_female_GFP_1.5_months_GR65

description:
GR65
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Brain_female_GFP_1.5_months_GR68

description:
GR68
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Brain_male_GFP_1.5_months_GR197

description:
GR197
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Mouse embryo cell EB_2360

growth_protocol: We designed three types of mice crossing: 1) C57BL/6J (C57) female mice mated to C57 male mice; 2) CAST/EiJ (CAST) female mice mated to C57 male mice; 3) C57 female mice mated to CAST male mice. The embryos were collected at embryonic day (E) 5.25, E5.5, E6.25 and E6.5.

extract_protocol:
These embryos were dissociated in TrypLE (Life technologies) for 15mins through trituration and single cells were manually picked with fine glass capillaries dispensing in lysis buffer.
Libraries generated for sequencing was carried out on Illumina sequencer based on Smart-seq2 protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic day 6.5

value: embryo 29


title: Mouse embryo cell EB_2361


title: Mouse embryo cell EB_2365


title: Mouse embryo cell EB_2358


title: Mouse embryo cell EB_2359


title: Brain_female_GFP-GR100_1.5_months_GR106

description:
GR106
1.5M_mice-combined_count_and_rpkm_by_gene.txt


title: Primary rat small hepatocytes LN511-3

source_name: Passaged and cultured cells on LN511-coated dishes


title: Mouse embryo cell EB_2355


title: Mouse embryo cell EB_2362


title: Mouse embryo cell EB_2354


title: Mouse embryo cell EB_2350


title: Mouse embryo cell EB_2353


title: Mouse embryo cell EB_2357


title: Mouse embryo cell EB_2351


title: Mouse embryo cell EB_2348


title: Mouse embryo cell EB_2347


title: Mouse embryo cell EB_2345


title: Mouse embryo cell EB_2341


title: Mouse embryo cell EB_2344


title: Mouse embryo cell EB_2340


title: Mouse embryo cell EB_2342


title: Mouse embryo cell EB_2363


title: Mouse embryo cell EB_2339


title: Mouse embryo cell EB_2336


title: Mouse embryo cell EB_2338


title: Mouse embryo cell EB_2335


title: Mouse embryo cell EB_2330


title: Mouse embryo cell EB_2337


title: Mouse embryo cell EB_2328


title: Mouse embryo cell EB_2329


title: Mouse embryo cell EB_2327


title: Mouse embryo cell EB_2326


title: Mouse embryo cell EB_2332


title: Mouse embryo cell EB_2331


title: Mouse embryo cell EB_2333


title: Mouse embryo cell EB_2319


title: Mouse embryo cell EB_2320


title: Mouse embryo cell EB_2322


title: Mouse embryo cell EB_2356


title: Mouse embryo cell EB_2313


title: Mouse embryo cell EB_2318


title: Mouse embryo cell EB_2311


title: Mouse embryo cell EB_2312


title: Mouse embryo cell EB_2309


title: Mouse embryo cell EB_2303


title: Mouse embryo cell EB_2301


title: Mouse embryo cell EB_2302


title: Mouse embryo cell EB_2304


title: Mouse embryo cell EB_2297


title: Mouse embryo cell EB_2296


title: Mouse embryo cell EB_2300


title: Mouse embryo cell EB_2298


title: Mouse embryo cell EB_2299


title: Mouse embryo cell EB_2293


title: Mouse embryo cell EB_2292


title: Mouse embryo cell EB_2289


title: Mouse embryo cell EB_2287


title: Mouse embryo cell EB_2288


title: Mouse embryo cell EB_2316


title: Mouse embryo cell EB_2314


title: Mouse embryo cell EB_2291


title: Mouse embryo cell EB_2284


title: Mouse embryo cell EB_2286


title: Mouse embryo cell EB_2283


title: Mouse embryo cell EB_2281


title: Mouse embryo cell EB_2280


title: Mouse embryo cell EB_2290


title: Mouse embryo cell EB_2282


title: Mouse embryo cell EB_2307


title: Mouse embryo cell EB_2279


title: Mouse embryo cell EB_2305


title: Mouse embryo cell EB_2276


title: Mouse embryo cell EB_2274


title: Mouse embryo cell EB_2278


title: Mouse embryo cell EB_2275


title: Mouse embryo cell EB_2270


title: Mouse embryo cell EB_2272


title: Mouse embryo cell EB_2271


title: Mouse embryo cell EB_2273


title: Mouse embryo cell EB_2277


title: Mouse embryo cell EB_2267


title: Mouse embryo cell EB_2266


title: Mouse embryo cell EB_2265


title: Mouse embryo cell EB_2264


title: Mouse embryo cell EB_2261


title: Mouse embryo cell EB_2262


title: Mouse embryo cell EB_2259


title: Mouse embryo cell EB_2258


title: Mouse embryo cell EB_2257


title: Mouse embryo cell EB_2253


title: Mouse embryo cell EB_2256


title: Mouse embryo cell EB_2251


title: Mouse embryo cell EB_2254


title: Mouse embryo cell EB_2249


title: Mouse embryo cell EB_2247


title: Mouse embryo cell EB_2252


title: Mouse embryo cell EB_2244


title: Mouse embryo cell EB_2245


title: Mouse embryo cell EB_2246


title: Mouse embryo cell EB_2237


title: Mouse embryo cell EB_2242


title: Mouse embryo cell EB_2260


title: Mouse embryo cell EB_2235


title: Mouse embryo cell EB_2240


title: Mouse embryo cell EB_2233


title: Mouse embryo cell EB_2241


title: Mouse embryo cell EB_2236


title: Mouse embryo cell EB_2225


title: Mouse embryo cell EB_2238


title: Mouse embryo cell EB_2255


title: Mouse embryo cell EB_2230


title: Mouse embryo cell EB_2226


title: Mouse embryo cell EB_2223


title: Mouse embryo cell EB_2227


title: Mouse embryo cell EB_2232


title: Mouse embryo cell EB_2219


title: Mouse embryo cell EB_2222


title: Mouse embryo cell EB_2250


title: Mouse embryo cell EB_2220


title: Mouse embryo cell EB_2215


title: Mouse embryo cell EB_2217


title: Mouse embryo cell EB_2218


title: Mouse embryo cell EB_2214


title: Mouse embryo cell EB_2213


title: Mouse embryo cell EB_2216


title: Mouse embryo cell EB_2221


title: Mouse embryo cell EB_2234


title: Mouse embryo cell EB_2211


title: Mouse embryo cell EB_2202


title: Mouse embryo cell EB_2204


title: Mouse embryo cell EB_2201


title: Mouse embryo cell EB_2197


title: Mouse embryo cell EB_2194


title: Mouse embryo cell EB_2198


title: Mouse embryo cell EB_2200


title: Mouse embryo cell EB_2206


title: Mouse embryo cell EB_2195


title: Mouse embryo cell EB_2199


title: Mouse embryo cell EB_2185


title: Mouse embryo cell EB_2191


title: Mouse embryo cell EB_2184


title: Mouse embryo cell EB_2187


title: Mouse embryo cell EB_2189


title: Mouse embryo cell EB_2183


title: Mouse embryo cell EB_2190


title: Mouse embryo cell EB_2188


title: Mouse embryo cell EB_2179


title: Mouse embryo cell EB_2180


title: Mouse embryo cell EB_2210


title: Mouse embryo cell EB_2177


title: Mouse embryo cell EB_2208


title: Mouse embryo cell EB_2182


title: Mouse embryo cell EB_2174


title: Mouse embryo cell EB_2203


title: Mouse embryo cell EB_2239


title: Mouse embryo cell EB_2181


title: Mouse embryo cell EB_1847

value: embryo 26


title: Mouse embryo cell EB_1845


title: Mouse embryo cell EB_2170


title: Mouse embryo cell EB_2166


title: Mouse embryo cell EB_1841


title: Mouse embryo cell EB_2171


title: Mouse embryo cell EB_2172


title: Mouse embryo cell EB_2176


title: Mouse embryo cell EB_1836


title: Mouse embryo cell EB_1838


title: Mouse embryo cell EB_1842


title: Mouse embryo cell EB_1843


title: Mouse embryo cell EB_1835


title: Mouse embryo cell EB_1834


title: Mouse embryo cell EB_1844


title: Mouse embryo cell EB_1846


title: Mouse embryo cell EB_1832


title: Mouse embryo cell EB_1840


title: Mouse embryo cell EB_1837


title: Mouse embryo cell EB_1833


title: Mouse embryo cell EB_2175


title: Mouse embryo cell EB_1830


title: Mouse embryo cell EB_1831


title: Mouse embryo cell EB_1829


title: Mouse embryo cell EB_1826


title: Mouse embryo cell EB_1828


title: Mouse embryo cell EB_2173


title: Mouse embryo cell EB_2167


title: Mouse embryo cell EB_1849


title: Mouse embryo cell EB_1825


title: Mouse embryo cell EB_1822


title: Mouse embryo cell EB_1815


title: Mouse embryo cell EB_1827


title: Mouse embryo cell EB_1812


title: Mouse embryo cell EB_1811


title: Mouse embryo cell EB_1810


title: Mouse embryo cell EB_1823


title: Mouse embryo cell EB_1824


title: Mouse embryo cell EB_1821


title: Mouse embryo cell EB_1814


title: Mouse embryo cell EB_1813


title: Mouse embryo cell EB_1807


title: Mouse embryo cell EB_1805


title: Mouse embryo cell EB_1809


title: Mouse embryo cell EB_1804


title: Mouse embryo cell EB_1803


title: Mouse embryo cell EB_1819


title: Mouse embryo cell EB_1816


title: Mouse embryo cell EB_1801


title: Mouse embryo cell EB_1802


title: Mouse embryo cell EB_1799


title: Mouse embryo cell EB_1797


title: Mouse embryo cell EB_1808


title: Mouse embryo cell EB_1796


title: Mouse embryo cell EB_1795


title: Mouse embryo cell EB_1794


title: Mouse embryo cell EB_1793


title: Mouse embryo cell EB_1818


title: Mouse embryo cell EB_1786


title: Mouse embryo cell EB_1785


title: Mouse embryo cell EB_1791


title: Mouse embryo cell EB_1784


title: Mouse embryo cell EB_1777


title: Mouse embryo cell EB_1779


title: Mouse embryo cell EB_1781


title: Mouse embryo cell EB_1776


title: Mouse embryo cell EB_1770


title: Mouse embryo cell EB_1780


title: Mouse embryo cell EB_1775


title: Mouse embryo cell EB_1806


title: Mouse embryo cell EB_2160

value: embryo 28


title: Mouse embryo cell EB_2158


title: Mouse embryo cell EB_2153


title: Mouse embryo cell EB_1774


title: Mouse embryo cell EB_1778


title: Mouse embryo cell EB_2151


title: Mouse embryo cell EB_2156


title: Mouse embryo cell EB_2163


title: Mouse embryo cell EB_2155


title: Mouse embryo cell EB_1772


title: Mouse embryo cell EB_1771


title: Mouse embryo cell EB_2159


title: Mouse embryo cell EB_2149


title: Mouse embryo cell EB_2150


title: Mouse embryo cell EB_2147


title: Mouse embryo cell EB_2148


title: Mouse embryo cell EB_2145


title: Mouse embryo cell EB_2142


title: Mouse embryo cell EB_2144


title: Mouse embryo cell EB_2143


title: Mouse embryo cell EB_2139


title: Mouse embryo cell EB_2136


title: Mouse embryo cell EB_2140


title: Mouse embryo cell EB_2152


title: Mouse embryo cell EB_2133


title: Mouse embryo cell EB_2138


title: Mouse embryo cell EB_2132


title: Mouse embryo cell EB_2128


title: Mouse embryo cell EB_2135


title: Mouse embryo cell EB_2123


title: Mouse embryo cell EB_2115


title: Mouse embryo cell EB_2118


title: Mouse embryo cell EB_2130


title: Mouse embryo cell EB_2113


title: Mouse embryo cell EB_2126


title: Mouse embryo cell EB_2107


title: Mouse embryo cell EB_2124


title: Mouse embryo cell EB_2110


title: Mouse embryo cell EB_2108


title: Mouse embryo cell EB_2112


title: Mouse embryo cell EB_2137


title: Mouse embryo cell EB_2119


title: Mouse embryo cell EB_2106


title: Mouse embryo cell EB_2103


title: Mouse embryo cell EB_2134


title: Mouse embryo cell EB_2111


title: Mouse embryo cell EB_2102


title: Mouse embryo cell EB_2101


title: Mouse embryo cell EB_2105


title: Mouse embryo cell EB_2121


title: Mouse embryo cell EB_2125


title: Mouse embryo cell EB_2100


title: Mouse embryo cell EB_2097


title: Mouse embryo cell EB_2095


title: Mouse embryo cell EB_2099


title: Mouse embryo cell EB_2094


title: Mouse embryo cell EB_2116


title: Mouse embryo cell EB_2091


title: Mouse embryo cell EB_2090


title: Mouse embryo cell EB_2098


title: Mouse embryo cell EB_2093


title: Mouse embryo cell EB_2087


title: Mouse embryo cell EB_2089


title: Mouse embryo cell EB_2088


title: Mouse embryo cell EB_2083


title: Mouse embryo cell EB_2082


title: Mouse embryo cell EB_2079


title: Mouse embryo cell EB_2081


title: Mouse embryo cell EB_2080


title: Mouse embryo cell EB_2078


title: Mouse embryo cell EB_2075


title: Mouse embryo cell EB_2076


title: Mouse embryo cell EB_2077


title: Mouse embryo cell EB_2104


title: Mouse embryo cell EB_2074


title: Mouse embryo cell EB_2072


title: Mouse embryo cell EB_2070


title: Mouse embryo cell EB_2069


title: Mouse embryo cell EB_2092


title: Mouse embryo cell EB_2073


title: Mouse embryo cell EB_2068


title: Mouse embryo cell EB_2071


title: Mouse embryo cell EB_2067


title: Mouse embryo cell EB_2065


title: Mouse embryo cell EB_2064


title: Mouse embryo cell EB_2063


title: Mouse embryo cell EB_2066


title: Mouse embryo cell EB_2060


title: Mouse embryo cell EB_2059


title: Mouse embryo cell EB_2086


title: Mouse embryo cell EB_2062


title: Mouse embryo cell EB_2061


title: Mouse embryo cell EB_2058


title: Mouse embryo cell EB_2057


title: Mouse embryo cell EB_2055


title: Mouse embryo cell EB_2056


title: Mouse embryo cell EB_2051


title: Mouse embryo cell EB_2052


title: Mouse embryo cell EB_2048


title: Mouse embryo cell EB_2049


title: Mouse embryo cell EB_2047


title: Mouse embryo cell EB_2053


title: Mouse embryo cell EB_2042


title: Mouse embryo cell EB_2054


title: Mouse embryo cell EB_2041


title: Mouse embryo cell EB_2046


title: Mouse embryo cell EB_2038


title: Mouse embryo cell EB_2043


title: Mouse embryo cell EB_2040


title: Mouse embryo cell EB_2045


title: Mouse embryo cell EB_2036


title: Mouse embryo cell EB_2030


title: Mouse embryo cell EB_2039


title: Mouse embryo cell EB_2035


title: Mouse embryo cell EB_2037


title: Mouse embryo cell EB_2034


title: Mouse embryo cell EB_2044


title: Mouse embryo cell EB_2029


title: Mouse embryo cell EB_2031


title: Mouse embryo cell EB_2028


title: Mouse embryo cell EB_2026


title: Mouse embryo cell EB_2033


title: Mouse embryo cell EB_2025


title: Mouse embryo cell EB_2027


title: Mouse embryo cell EB_2050


title: Mouse embryo cell EB_2023


title: Mouse embryo cell EB_2022


title: Mouse embryo cell EB_2014


title: Mouse embryo cell EB_2024


title: Mouse embryo cell EB_2020


title: Mouse embryo cell EB_2018


title: Mouse embryo cell EB_2017


title: Mouse embryo cell EB_2012


title: Mouse embryo cell EB_2013


title: Mouse embryo cell EB_2015


title: Mouse embryo cell EB_2010


title: Mouse embryo cell EB_2007


title: Mouse embryo cell EB_2011


title: Mouse embryo cell EB_2009


title: Mouse embryo cell EB_2008


title: Mouse embryo cell EB_2001


title: Mouse embryo cell EB_2005


title: Mouse embryo cell EB_1995


title: Mouse embryo cell EB_2004


title: Mouse embryo cell EB_1991


title: Mouse embryo cell EB_1993


title: Mouse embryo cell EB_1996


title: Mouse embryo cell EB_2032


title: Mouse embryo cell EB_1994


title: Mouse embryo cell EB_1992


title: Mouse embryo cell EB_1989


title: Mouse embryo cell EB_1990


title: Mouse embryo cell EB_1987


title: Mouse embryo cell EB_2016


title: Mouse embryo cell EB_1983


title: Mouse embryo cell EB_1984


title: Mouse embryo cell EB_1988


title: Mouse embryo cell EB_1980


title: Mouse embryo cell EB_1985


title: Mouse embryo cell EB_1982


title: Mouse embryo cell EB_2003


title: Mouse embryo cell EB_1977


title: Mouse embryo cell EB_2002


title: Mouse embryo cell EB_1976


title: Mouse embryo cell EB_1981


title: Mouse embryo cell EB_1979


title: Mouse embryo cell EB_1978


title: Mouse embryo cell EB_1999


title: Mouse embryo cell EB_1962


title: Mouse embryo cell EB_1963


title: Mouse embryo cell EB_1970


title: Mouse embryo cell EB_1968


title: Mouse embryo cell EB_1965


title: Mouse embryo cell EB_1973


title: Mouse embryo cell EB_1972


title: Mouse embryo cell EB_1974


title: Mouse embryo cell EB_1969


title: Mouse embryo cell EB_1966


title: Mouse embryo cell EB_1964


title: Mouse embryo cell EB_1958


title: Mouse embryo cell EB_1955

value: embryo 27


title: Mouse embryo cell EB_1951

value: CAST/EiJ (F) x C57BL/6J (M)


title: Mouse embryo cell EB_1960


title: Mouse embryo cell EB_1959


title: Mouse embryo cell EB_1948


title: Mouse embryo cell EB_1946


title: Mouse embryo cell EB_1954


title: Mouse embryo cell EB_1940


title: Mouse embryo cell EB_1938


title: Mouse embryo cell EB_1939


title: Mouse embryo cell EB_1945


title: Mouse embryo cell EB_1947


title: Mouse embryo cell EB_1943


title: Mouse embryo cell EB_1935


title: Mouse embryo cell EB_1930


title: Mouse embryo cell EB_1919


title: Mouse embryo cell EB_1928


title: Mouse embryo cell EB_1933


title: Mouse embryo cell EB_1952


title: Mouse embryo cell EB_1920


title: Mouse embryo cell EB_1929


title: Mouse embryo cell EB_1924


title: Mouse embryo cell EB_1916


title: Mouse embryo cell EB_1921


title: Mouse embryo cell EB_1917


title: Mouse embryo cell EB_1914


title: Mouse embryo cell EB_1915


title: Mouse embryo cell EB_1922


title: Mouse embryo cell EB_1937


title: Mouse embryo cell EB_1923


title: Mouse embryo cell EB_1907


title: Mouse embryo cell EB_1912


title: Mouse embryo cell EB_1908


title: Mouse embryo cell EB_1911


title: Mouse embryo cell EB_1909


title: Mouse embryo cell EB_1895


title: Mouse embryo cell EB_1913


title: Mouse embryo cell EB_1891


title: Mouse embryo cell EB_1899


title: Mouse embryo cell EB_1894


title: Mouse embryo cell EB_1897


title: Mouse embryo cell EB_1893


title: Mouse embryo cell EB_1925


title: Mouse embryo cell EB_1892


title: Mouse embryo cell EB_1889


title: Mouse embryo cell EB_1896


title: Mouse embryo cell EB_1887


title: Mouse embryo cell EB_1888


title: Mouse embryo cell EB_1886


title: Mouse embryo cell EB_1885


title: Mouse embryo cell EB_1880


title: Mouse embryo cell EB_1882


title: Mouse embryo cell EB_1884


title: Mouse embryo cell EB_1875


title: Mouse embryo cell EB_1881


title: Mouse embryo cell EB_1878


title: Mouse embryo cell EB_1874


title: Mouse embryo cell EB_1877


title: Mouse embryo cell EB_1971


title: Mouse embryo cell EB_1871


title: Mouse embryo cell EB_1866


title: Mouse embryo cell EB_1870


title: Mouse embryo cell EB_1867


title: Mouse embryo cell EB_1872


title: Mouse embryo cell EB_1865


title: Mouse embryo cell EB_1863


title: Mouse embryo cell EB_1890


title: Mouse embryo cell EB_1859


title: Mouse embryo cell EB_1862


title: Mouse embryo cell EB_1869


title: Mouse embryo cell EB_1860


title: Mouse embryo cell EB_1864


title: Mouse embryo cell EB_1883


title: Mouse embryo cell EB_1857


title: Mouse embryo cell EB_1856


title: Mouse embryo cell EB_1876


title: Mouse embryo cell EB_1873


title: Mouse embryo cell EB_1852


title: Mouse embryo cell EB_1853


title: Mouse embryo cell EB_1767


title: Mouse embryo cell EB_1766


title: Mouse embryo cell EB_1765


title: Mouse embryo cell EB_1763


title: Mouse embryo cell EB_1758


title: Mouse embryo cell EB_1760


title: Mouse embryo cell EB_1759


title: Mouse embryo cell EB_1757


title: Mouse embryo cell EB_1755


title: Mouse embryo cell EB_1761


title: Mouse embryo cell EB_1753


title: Mouse embryo cell EB_1754


title: Mouse embryo cell EB_1756


title: Mouse embryo cell EB_1751


title: Mouse embryo cell EB_1850


title: Mouse embryo cell EB_1858


title: Mouse embryo cell EB_1752


title: Mouse embryo cell EB_1749


title: Mouse embryo cell EB_1769


title: Mouse embryo cell EB_1744


title: Mouse embryo cell EB_1748


title: Mouse embryo cell EB_1768


title: Mouse embryo cell EB_1747


title: Mouse embryo cell EB_1743


title: Mouse embryo cell EB_1762


title: Mouse embryo cell EB_1740


title: Mouse embryo cell EB_1746


title: Mouse embryo cell EB_1745


title: Mouse embryo cell EB_1742


title: Mouse embryo cell EB_1764


title: Mouse embryo cell EB_1739


title: Mouse embryo cell EB_1736


title: Mouse embryo cell EB_1735


title: Mouse embryo cell EB_1741


title: Mouse embryo cell EB_1731


title: Mouse embryo cell EB_1730


title: Mouse embryo cell EB_1728


title: Mouse embryo cell EB_1737


title: Mouse embryo cell EB_1750


title: Mouse embryo cell EB_1727


title: Mouse embryo cell EB_1726


title: Mouse embryo cell EB_1732


title: Mouse embryo cell EB_1724


title: Mouse embryo cell EB_1722


title: Mouse embryo cell EB_1723


title: Mouse embryo cell EB_1721


title: Mouse embryo cell EB_1720


title: Mouse embryo cell EB_1725


title: Mouse embryo cell EB_1713


title: Mouse embryo cell EB_1717


title: Mouse embryo cell EB_1714


title: Mouse embryo cell EB_1716


title: Mouse embryo cell EB_1719


title: Mouse embryo cell EB_1715


title: Mouse embryo cell EB_1712


title: Mouse embryo cell EB_1710


title: Mouse embryo cell EB_1709


title: Mouse embryo cell EB_1718


title: Mouse embryo cell EB_1711


title: Mouse embryo cell EB_1706


title: Mouse embryo cell EB_1702


title: Mouse embryo cell EB_1703


title: Mouse embryo cell EB_1701


title: Mouse embryo cell EB_1707


title: Mouse embryo cell EB_822

value: embryo 10


title: Mouse embryo cell EB_825

value: Embryo


title: Mouse embryo cell EB_817


title: Mouse embryo cell EB_1729


title: Mouse embryo cell EB_816


title: Mouse embryo cell EB_815


title: Mouse embryo cell EB_812


title: Mouse embryo cell EB_811


title: Mouse embryo cell EB_1705


title: Mouse embryo cell EB_805


title: Mouse embryo cell EB_803


title: Mouse embryo cell EB_802


title: Mouse embryo cell EB_792


title: Mouse embryo cell EB_798


title: Mouse embryo cell EB_786


title: Mouse embryo cell EB_784


title: Mouse embryo cell EB_783


title: Mouse embryo cell EB_780


title: Mouse embryo cell EB_782


title: Mouse embryo cell EB_776


title: Mouse embryo cell EB_777


title: Mouse embryo cell EB_779


title: Mouse embryo cell EB_775


title: Mouse embryo cell EB_774


title: Mouse embryo cell EB_773


title: Mouse embryo cell EB_768


title: Mouse embryo cell EB_762


title: Mouse embryo cell EB_760


title: Mouse embryo cell EB_758


title: Mouse embryo cell EB_767


title: Mouse embryo cell EB_759


title: Mouse embryo cell EB_818


title: Mouse embryo cell EB_756


title: Mouse embryo cell EB_826


title: Mouse embryo cell EB_823


title: Mouse embryo cell EB_737


title: Mouse embryo cell EB_742


title: Mouse embryo cell EB_747


title: Mouse embryo cell EB_736


title: Mouse embryo cell EB_785


title: Mouse embryo cell EB_729


title: Mouse embryo cell EB_727


title: Mouse embryo cell EB_769


title: Mouse embryo cell EB_743


title: Mouse embryo cell EB_722


title: Mouse embryo cell EB_724


title: Mouse embryo cell EB_723


title: Mouse embryo cell EB_745


title: Mouse embryo cell EB_761


title: Mouse embryo cell EB_720


title: Mouse embryo cell EB_721


title: Mouse embryo cell EB_719


title: Mouse embryo cell EB_746


title: Mouse embryo cell EB_741


title: Mouse embryo cell EB_715


title: Mouse embryo cell EB_714


title: Mouse embryo cell EB_716


title: Mouse embryo cell EB_710


title: Mouse embryo cell EB_709


title: Mouse embryo cell EB_707


title: Mouse embryo cell EB_706


title: Mouse embryo cell EB_699


title: Mouse embryo cell EB_700


title: Mouse embryo cell EB_697


title: Mouse embryo cell EB_748


title: Mouse embryo cell EB_698


title: Mouse embryo cell EB_696


title: Mouse embryo cell EB_692


title: Mouse embryo cell EB_718


title: Mouse embryo cell EB_687


title: Mouse embryo cell EB_695


title: Mouse embryo cell EB_413

value: embryo 8


title: Mouse embryo cell EB_414


title: Mouse embryo cell EB_411


title: Mouse embryo cell EB_412


title: Mouse embryo cell EB_410


title: Mouse embryo cell EB_691


title: Mouse embryo cell EB_415


title: Mouse embryo cell EB_713


title: Mouse embryo cell EB_499


title: Mouse embryo cell EB_495


title: Mouse embryo cell EB_409


title: Mouse embryo cell EB_497


title: Mouse embryo cell EB_408


title: Mouse embryo cell EB_496


title: Mouse embryo cell EB_494


title: Mouse embryo cell EB_500


title: Mouse embryo cell EB_488


title: Mouse embryo cell EB_490


title: Mouse embryo cell EB_703


title: Mouse embryo cell EB_491


title: Mouse embryo cell EB_492


title: Mouse embryo cell EB_493


title: Mouse embryo cell EB_487


title: Mouse embryo cell EB_483


title: Mouse embryo cell EB_480


title: Mouse embryo cell EB_484


title: Mouse embryo cell EB_482


title: Mouse embryo cell EB_481


title: Mouse embryo cell EB_479


title: Mouse embryo cell EB_477


title: Mouse embryo cell EB_498


title: Mouse embryo cell EB_474


title: Mouse embryo cell EB_471


title: Mouse embryo cell EB_475


title: Mouse embryo cell EB_473


title: Mouse embryo cell EB_470


title: Mouse embryo cell EB_476


title: Mouse embryo cell EB_468


title: Mouse embryo cell EB_464


title: Mouse embryo cell EB_467


title: Mouse embryo cell EB_453


title: Mouse embryo cell EB_461


title: Mouse embryo cell EB_462


title: Mouse embryo cell EB_466


title: Mouse embryo cell EB_465


title: Mouse embryo cell EB_459


title: Mouse embryo cell EB_463


title: Mouse embryo cell EB_455


title: Mouse embryo cell EB_449


title: Mouse embryo cell EB_452


title: Mouse embryo cell EB_456


title: Mouse embryo cell EB_457


title: Mouse embryo cell EB_450


title: Mouse embryo cell EB_448


title: Mouse embryo cell EB_447


title: Mouse embryo cell EB_451


title: Mouse embryo cell EB_444


title: Mouse embryo cell EB_439


title: Mouse embryo cell EB_441


title: Mouse embryo cell EB_442


title: Mouse embryo cell EB_437


title: Mouse embryo cell EB_435


title: Mouse embryo cell EB_460


title: Mouse embryo cell EB_432


title: Mouse embryo cell EB_431


title: Mouse embryo cell EB_426


title: Mouse embryo cell EB_430


title: Mouse embryo cell EB_458


title: Mouse embryo cell EB_454


title: Mouse embryo cell EB_429


title: Mouse embryo cell EB_425


title: Mouse embryo cell EB_427


title: Mouse embryo cell EB_446


title: Mouse embryo cell EB_424


title: Mouse embryo cell EB_423


title: Mouse embryo cell EB_422


title: Mouse embryo cell EB_420


title: Mouse embryo cell EB_333

value: embryo 6


title: Mouse embryo cell EB_417


title: Mouse embryo cell EB_419


title: Mouse embryo cell EB_335


title: Mouse embryo cell EB_332


title: Mouse embryo cell EB_330


title: Mouse embryo cell EB_329


title: Mouse embryo cell EB_328


title: Mouse embryo cell EB_334


title: Mouse embryo cell EB_327


title: Mouse embryo cell EB_323


title: Mouse embryo cell EB_325


title: Mouse embryo cell EB_324


title: Mouse embryo cell EB_320


title: Mouse embryo cell EB_319


title: Mouse embryo cell EB_321


title: Mouse embryo cell EB_322


title: Mouse embryo cell EB_428


title: Mouse embryo cell EB_318


title: Mouse embryo cell EB_421


title: Mouse embryo cell EB_317


title: Mouse embryo cell EB_316


title: Mouse embryo cell EB_418


title: Mouse embryo cell EB_315


title: Mouse embryo cell EB_314


title: Mouse embryo cell EB_313


title: Mouse embryo cell EB_301


title: Mouse embryo cell EB_307


title: Mouse embryo cell EB_303


title: Mouse embryo cell EB_304


title: Mouse embryo cell EB_308


title: Mouse embryo cell EB_305


title: Mouse embryo cell EB_312


title: Mouse embryo cell EB_306


title: Mouse embryo cell EB_297


title: Mouse embryo cell EB_296


title: Mouse embryo cell EB_290


title: Mouse embryo cell EB_295


title: Mouse embryo cell EB_293


title: Mouse embryo cell EB_302


title: Mouse embryo cell EB_283


title: Mouse embryo cell EB_286


title: Mouse embryo cell EB_284


title: Mouse embryo cell EB_288


title: Mouse embryo cell EB_277

value: embryo 5


title: Mouse embryo cell EB_279


title: Mouse embryo cell EB_278


title: Mouse embryo cell EB_280


title: Mouse embryo cell EB_276


title: Mouse embryo cell EB_291


title: Mouse embryo cell EB_274


title: Mouse embryo cell EB_273


title: Mouse embryo cell EB_269


title: Mouse embryo cell EB_263


title: Mouse embryo cell EB_271


title: Mouse embryo cell EB_294


title: Mouse embryo cell EB_289


title: Mouse embryo cell EB_275


title: Mouse embryo cell EB_262


title: Mouse embryo cell EB_268


title: Mouse embryo cell EB_272


title: Mouse embryo cell EB_261


title: Mouse embryo cell EB_260


title: Mouse embryo cell EB_256


title: Mouse embryo cell EB_255


title: Mouse embryo cell EB_265


title: Mouse embryo cell EB_259


title: Mouse embryo cell EB_258


title: Mouse embryo cell EB_257


title: Mouse embryo cell EB_251


title: Mouse embryo cell EB_254


title: Mouse embryo cell EB_250


title: Mouse embryo cell EB_253


title: Mouse embryo cell EB_247


title: Mouse embryo cell EB_249


title: Mouse embryo cell EB_245


title: Mouse embryo cell EB_243


title: Mouse embryo cell EB_237


title: Mouse embryo cell EB_242


title: Mouse embryo cell EB_239


title: Mouse embryo cell EB_248


title: Mouse embryo cell EB_240


title: Mouse embryo cell EB_244


title: Mouse embryo cell EB_235


title: Mouse embryo cell EB_241


title: Mouse embryo cell EB_234


title: Mouse embryo cell EB_230


title: Mouse embryo cell EB_236


title: Mouse embryo cell EB_228


title: Mouse embryo cell EB_233


title: Mouse embryo cell EB_227


title: Mouse embryo cell EB_231


title: Mouse embryo cell EB_232


title: Mouse embryo cell EB_225


title: Mouse embryo cell EB_224


title: Mouse embryo cell EB_221


title: Mouse embryo cell EB_218


title: Mouse embryo cell EB_223


title: Mouse embryo cell EB_217


title: Mouse embryo cell EB_216


title: Mouse embryo cell EB_229


title: Mouse embryo cell EB_1694

value: C57BL/6J (F)x CAST/EiJ (M)

value: embryonic day 6.25

value: embryo 25


title: Mouse embryo cell EB_1688


title: Mouse embryo cell EB_1690


title: Mouse embryo cell EB_226


title: Mouse embryo cell EB_1692


title: Mouse embryo cell EB_1682


title: Mouse embryo cell EB_1683


title: Mouse embryo cell EB_1687


title: Mouse embryo cell EB_1681


title: Mouse embryo cell EB_222


title: Mouse embryo cell EB_219


title: Mouse embryo cell EB_220


title: Mouse embryo cell EB_1684


title: Mouse embryo cell EB_1678


title: Mouse embryo cell EB_1676


title: Mouse embryo cell EB_1674


title: Mouse embryo cell EB_1696


title: Mouse embryo cell EB_1673


title: Mouse embryo cell EB_1691


title: Mouse embryo cell EB_1689


title: Mouse embryo cell EB_1672


title: Mouse embryo cell EB_1670


title: Mouse embryo cell EB_1666


title: Mouse embryo cell EB_1668


title: Mouse embryo cell EB_1685


title: Mouse embryo cell EB_1667


title: Mouse embryo cell EB_1671


title: Mouse embryo cell EB_1669


title: Mouse embryo cell EB_1686


title: Mouse embryo cell EB_1658


title: Mouse embryo cell EB_1656


title: Mouse embryo cell EB_1657


title: Mouse embryo cell EB_1655


title: Mouse embryo cell EB_1653

value: embryo 24


title: Mouse embryo cell EB_1665


title: Mouse embryo cell EB_1660


title: Mouse embryo cell EB_1652


title: Mouse embryo cell EB_1661


title: Mouse embryo cell EB_1675


title: Mouse embryo cell EB_1680


title: Mouse embryo cell EB_433


title: Mouse embryo cell EB_434


title: Mouse embryo cell EB_1650


title: Mouse embryo cell EB_1659


title: Mouse embryo cell EB_1654


title: Mouse embryo cell EB_1648


title: Mouse embryo cell EB_1647


title: Mouse embryo cell EB_1645


title: Mouse embryo cell EB_1643


title: Mouse embryo cell EB_1640


title: Mouse embryo cell EB_1642


title: Mouse embryo cell EB_1641


title: Mouse embryo cell EB_1635


title: Mouse embryo cell EB_1639


title: Mouse embryo cell EB_1637


title: Mouse embryo cell EB_1633


title: Mouse embryo cell EB_1632


title: Mouse embryo cell EB_1630


title: Mouse embryo cell EB_1634


title: Mouse embryo cell EB_1631


title: Mouse embryo cell EB_1636


title: Mouse embryo cell EB_1651


title: Mouse embryo cell EB_1628


title: Mouse embryo cell EB_1621


title: Mouse embryo cell EB_1624


title: Mouse embryo cell EB_1626


title: Mouse embryo cell EB_1625


title: Mouse embryo cell EB_1627


title: Mouse embryo cell EB_1623


title: Mouse embryo cell EB_1629


title: Mouse embryo cell EB_1618


title: Mouse embryo cell EB_1617


title: Mouse embryo cell EB_1615


title: Mouse embryo cell EB_1619


title: Mouse embryo cell EB_1614


title: Mouse embryo cell EB_1616


title: Mouse embryo cell EB_1599

value: embryo 23


title: Mouse embryo cell EB_1600


title: Mouse embryo cell EB_1604


title: Mouse embryo cell EB_1603


title: Mouse embryo cell EB_1597


title: Mouse embryo cell EB_1620


title: Mouse embryo cell EB_1598


title: Mouse embryo cell EB_1592


title: Mouse embryo cell EB_1589


title: Mouse embryo cell EB_1593


title: Mouse embryo cell EB_1591


title: Mouse embryo cell EB_1588


title: Mouse embryo cell EB_1594


title: Mouse embryo cell EB_1585


title: Mouse embryo cell EB_1622


title: Mouse embryo cell EB_1582


title: Mouse embryo cell EB_1587


title: Mouse embryo cell EB_1581


title: Mouse embryo cell EB_1576


title: Mouse embryo cell EB_1575


title: Mouse embryo cell EB_1577


title: Mouse embryo cell EB_1580


title: Mouse embryo cell EB_1574


title: Mouse embryo cell EB_1573


title: Mouse embryo cell EB_1613


title: Mouse embryo cell EB_1568


title: Mouse embryo cell EB_1571


title: Mouse embryo cell EB_1572


title: Mouse embryo cell EB_1570


title: Mouse embryo cell EB_1569


title: Mouse embryo cell EB_1590


title: Mouse embryo cell EB_1566


title: Mouse embryo cell EB_1565


title: Mouse embryo cell EB_1586


title: Mouse embryo cell EB_1554


title: Mouse embryo cell EB_1579


title: Mouse embryo cell EB_1559


title: Mouse embryo cell EB_1556


title: Mouse embryo cell EB_1558


title: Mouse embryo cell EB_1555


title: Mouse embryo cell EB_1563


title: Mouse embryo cell EB_1557


title: Mouse embryo cell EB_1562


title: Mouse embryo cell EB_1550


title: Mouse embryo cell EB_1549


title: Mouse embryo cell EB_1547


title: Mouse embryo cell EB_1545


title: Mouse embryo cell EB_1548


title: Mouse embryo cell EB_1546


title: Mouse embryo cell EB_1541


title: Mouse embryo cell EB_1543


title: Mouse embryo cell EB_1539


title: Mouse embryo cell EB_1540


title: Mouse embryo cell EB_1535


title: Mouse embryo cell EB_1536


title: Mouse embryo cell EB_1567


title: Mouse embryo cell EB_1534


title: Mouse embryo cell EB_1527


title: Mouse embryo cell EB_1528


title: Mouse embryo cell EB_1111

value: embryo 16


title: Mouse embryo cell EB_1529


title: Mouse embryo cell EB_436

value: embryonic day 6.5


title: Mouse embryo cell EB_1109


title: Mouse embryo cell EB_1105


title: Mouse embryo cell EB_1551


title: Mouse embryo cell EB_1104


title: Mouse embryo cell EB_1103


title: Mouse embryo cell EB_1108


title: Mouse embryo cell EB_1107


title: Mouse embryo cell EB_1095


title: Mouse embryo cell EB_1094


title: Mouse embryo cell EB_1096


title: Mouse embryo cell EB_1101


title: Mouse embryo cell EB_1098


title: Mouse embryo cell EB_1097


title: Mouse embryo cell EB_1102


title: Mouse embryo cell EB_1106


title: Mouse embryo cell EB_1092


title: Mouse embryo cell EB_1093


title: Mouse embryo cell EB_1544


title: Mouse embryo cell EB_1538


title: Mouse embryo cell EB_1090


title: Mouse embryo cell EB_1089


title: Mouse embryo cell EB_1078


title: Mouse embryo cell EB_1086


title: Mouse embryo cell EB_1091


title: Mouse embryo cell EB_1076


title: Mouse embryo cell EB_1073


title: Mouse embryo cell EB_1071


title: Mouse embryo cell EB_1072


title: Mouse embryo cell EB_1065


title: Mouse embryo cell EB_1070


title: Mouse embryo cell EB_1069


title: Mouse embryo cell EB_1068


title: Mouse embryo cell EB_1066


title: Mouse embryo cell EB_1064


title: Mouse embryo cell EB_652

value: embryo 9


title: Mouse embryo cell EB_650


title: Mouse embryo cell EB_647


title: Mouse embryo cell EB_649


title: Mouse embryo cell EB_646


title: Mouse embryo cell EB_1067


title: Mouse embryo cell EB_639


title: Mouse embryo cell EB_642


title: Mouse embryo cell EB_641


title: Mouse embryo cell EB_636


title: Mouse embryo cell EB_635


title: Mouse embryo cell EB_643


title: Mouse embryo cell EB_634


title: Mouse embryo cell EB_633


title: Mouse embryo cell EB_632


title: Mouse embryo cell EB_631


title: Mouse embryo cell EB_637


title: Mouse embryo cell EB_628


title: Mouse embryo cell EB_630


title: Mouse embryo cell EB_627


title: Mouse embryo cell EB_626


title: Mouse embryo cell EB_625


title: Mouse embryo cell EB_624


title: Mouse embryo cell EB_623


title: Mouse embryo cell EB_645


title: Mouse embryo cell EB_644


title: Mouse embryo cell EB_619


title: Mouse embryo cell EB_616


title: Mouse embryo cell EB_622


title: Mouse embryo cell EB_618


title: Mouse embryo cell EB_617


title: Mouse embryo cell EB_621


title: Mouse embryo cell EB_613


title: Mouse embryo cell EB_603


title: Mouse embryo cell EB_612


title: Mouse embryo cell EB_605


title: Mouse embryo cell EB_606


title: Mouse embryo cell EB_614


title: Mouse embryo cell EB_610


title: Mouse embryo cell EB_609


title: Mouse embryo cell EB_602


title: Mouse embryo cell EB_608


title: Mouse embryo cell EB_601


title: Mouse embryo cell EB_611


title: Mouse embryo cell EB_600


title: Mouse embryo cell EB_599


title: Mouse embryo cell EB_597


title: Mouse embryo cell EB_596


title: Mouse embryo cell EB_620


title: Mouse embryo cell EB_594


title: Mouse embryo cell EB_593


title: Mouse embryo cell EB_591


title: Mouse embryo cell EB_615


title: Mouse embryo cell EB_590


title: Mouse embryo cell EB_589


title: Mouse embryo cell EB_607


title: Mouse embryo cell EB_586


title: Mouse embryo cell EB_587


title: Mouse embryo cell EB_585


title: Mouse embryo cell EB_577


title: Mouse embryo cell EB_580


title: Mouse embryo cell EB_579


title: Mouse embryo cell EB_574


title: Mouse embryo cell EB_584


title: Mouse embryo cell EB_573


title: Mouse embryo cell EB_575


title: Mouse embryo cell EB_677


title: Mouse embryo cell EB_680


title: Mouse embryo cell EB_663


title: Mouse embryo cell EB_666


title: Mouse embryo cell EB_664


title: Mouse embryo cell EB_576


title: Mouse embryo cell EB_675


title: Mouse embryo cell EB_581


title: Mouse embryo cell EB_667


title: Mouse embryo cell EB_659


title: Mouse embryo cell EB_662


title: Mouse embryo cell EB_660


title: Mouse embryo cell EB_668


title: Mouse embryo cell EB_661


title: Mouse embryo cell EB_657


title: Mouse embryo cell EB_658


title: Mouse embryo cell EB_656


title: Mouse embryo cell EB_588


title: Mouse embryo cell EB_654


title: Mouse embryo cell EB_578


title: Mouse embryo cell EB_215

value: embryo 4


title: Mouse embryo cell EB_213


title: Mouse embryo cell EB_209


title: Mouse embryo cell EB_211


title: Mouse embryo cell EB_207


title: Mouse embryo cell EB_210


title: Mouse embryo cell EB_208


title: Mouse embryo cell EB_206


title: Mouse embryo cell EB_212


title: Mouse embryo cell EB_204


title: Mouse embryo cell EB_205


title: Mouse embryo cell EB_202


title: Mouse embryo cell EB_192


title: Mouse embryo cell EB_653


title: Mouse embryo cell EB_201


title: Mouse embryo cell EB_190


title: Mouse embryo cell EB_191


title: Mouse embryo cell EB_203


title: Mouse embryo cell EB_184


title: Mouse embryo cell EB_187


title: Mouse embryo cell EB_186


title: Mouse embryo cell EB_189


title: Mouse embryo cell EB_188


title: Mouse embryo cell EB_185


title: Mouse embryo cell EB_181


title: Mouse embryo cell EB_183


title: Mouse embryo cell EB_180


title: Mouse embryo cell EB_182


title: Mouse embryo cell EB_214


title: Mouse embryo cell EB_177


title: Mouse embryo cell EB_178


title: Mouse embryo cell EB_168


title: Mouse embryo cell EB_174


title: Mouse embryo cell EB_172


title: Mouse embryo cell EB_176


title: Mouse embryo cell EB_167


title: Mouse embryo cell EB_173


title: Mouse embryo cell EB_158


title: Mouse embryo cell EB_169


title: Mouse embryo cell EB_170


title: Mouse embryo cell EB_163


title: Mouse embryo cell EB_162


title: Mouse embryo cell EB_171


title: Mouse embryo cell EB_165


title: Mouse embryo cell EB_164


title: Mouse embryo cell EB_156


title: Mouse embryo cell EB_161


title: Mouse embryo cell EB_151


title: Mouse embryo cell EB_152


title: Mouse embryo cell EB_150


title: Mouse embryo cell EB_148


title: Mouse embryo cell EB_149


title: Mouse embryo cell EB_144


title: Mouse embryo cell EB_179


title: Mouse embryo cell EB_143


title: Mouse embryo cell EB_145


title: Mouse embryo cell EB_142


title: Mouse embryo cell EB_135


title: Mouse embryo cell EB_175


title: Mouse embryo cell EB_139


title: Mouse embryo cell EB_134


title: Mouse embryo cell EB_130


title: Mouse embryo cell EB_995

value: C57BL/6J (F) x CAST/EiJ (M)

value: embryonic day 5.5

value: embryo 13


title: Mouse embryo cell EB_132


title: Mouse embryo cell EB_166


title: Mouse embryo cell EB_996


title: Mouse embryo cell EB_988


title: Mouse embryo cell EB_997


title: Mouse embryo cell EB_989


title: Mouse embryo cell EB_994


title: Mouse embryo cell EB_992


title: Mouse embryo cell EB_982


title: Mouse embryo cell EB_983


title: Mouse embryo cell EB_985


title: Mouse embryo cell EB_990


title: Mouse embryo cell EB_984


title: Mouse embryo cell EB_987


title: Mouse embryo cell EB_972


title: Mouse embryo cell EB_993


title: Mouse embryo cell EB_986


title: Mouse embryo cell EB_975


title: Mouse embryo cell EB_979


title: Mouse embryo cell EB_980


title: Mouse embryo cell EB_137


title: Mouse embryo cell EB_141


title: Mouse embryo cell EB_133


title: Mouse embryo cell EB_140


title: Mouse embryo cell EB_977


title: Mouse embryo cell EB_131


title: Mouse embryo cell EB_976


title: Mouse embryo cell EB_978


title: Mouse embryo cell EB_974


title: Mouse embryo cell EB_965


title: Mouse embryo cell EB_969


title: Mouse embryo cell EB_964


title: Mouse embryo cell EB_970


title: Mouse embryo cell EB_963


title: Mouse embryo cell EB_962


title: Mouse embryo cell EB_959


title: Mouse embryo cell EB_954


title: Mouse embryo cell EB_949


title: Mouse embryo cell EB_968


title: Mouse embryo cell EB_956


title: Mouse embryo cell EB_951


title: Mouse embryo cell EB_955


title: Mouse embryo cell EB_950


title: Mouse embryo cell EB_948


title: Mouse embryo cell EB_944


title: Mouse embryo cell EB_945


title: Mouse embryo cell EB_943


title: Mouse embryo cell EB_942


title: Mouse embryo cell EB_953


title: Mouse embryo cell EB_939


title: Mouse embryo cell EB_898

value: embryo 11


title: Mouse embryo cell EB_947

value: Embryo


title: Mouse embryo cell EB_894


title: Mouse embryo cell EB_892


title: Mouse embryo cell EB_897


title: Mouse embryo cell EB_973


title: Mouse embryo cell EB_895


title: Mouse embryo cell EB_888


title: Mouse embryo cell EB_881


title: Mouse embryo cell EB_871


title: Mouse embryo cell EB_873


title: Mouse embryo cell EB_875


title: Mouse embryo cell EB_868


title: Mouse embryo cell EB_872


title: Mouse embryo cell EB_880


title: Mouse embryo cell EB_930

value: embryo 12


title: Mouse embryo cell EB_931


title: Mouse embryo cell EB_878


title: Mouse embryo cell EB_1525

value: embryo 22


title: Mouse embryo cell EB_136


title: Mouse embryo cell EB_926


title: Mouse embryo cell EB_1526


title: Mouse embryo cell EB_1521


title: Mouse embryo cell EB_1523


title: Mouse embryo cell EB_1524


title: Mouse embryo cell EB_1520


title: Mouse embryo cell EB_928


title: Mouse embryo cell EB_1522


title: Mouse embryo cell EB_1517


title: Mouse embryo cell EB_1518


title: Mouse embryo cell EB_1516


title: Mouse embryo cell EB_1515


title: Mouse embryo cell EB_879


title: Mouse embryo cell EB_1512


title: Mouse embryo cell EB_869


title: Mouse embryo cell EB_867


title: Mouse embryo cell EB_1511


title: Mouse embryo cell EB_1508


title: Mouse embryo cell EB_1506


title: Mouse embryo cell EB_1507


title: Mouse embryo cell EB_1505


title: Mouse embryo cell EB_1503


title: Mouse embryo cell EB_1504


title: Mouse embryo cell EB_903


title: Mouse embryo cell EB_1501


title: Mouse embryo cell EB_1502


title: Mouse embryo cell EB_1513


title: Mouse embryo cell EB_1499


title: Mouse embryo cell EB_1519


title: Mouse embryo cell EB_1500


title: Mouse embryo cell EB_1495


title: Mouse embryo cell EB_1498


title: Mouse embryo cell EB_1496


title: Mouse embryo cell EB_1493


title: Mouse embryo cell EB_1497


title: Mouse embryo cell EB_1490


title: Mouse embryo cell EB_1514


title: Mouse embryo cell EB_1491


title: Mouse embryo cell EB_1494


title: Mouse embryo cell EB_1492


title: Mouse embryo cell EB_1489


title: Mouse embryo cell EB_1510


title: Mouse embryo cell EB_1487


title: Mouse embryo cell EB_1486


title: Mouse embryo cell EB_1509


title: Mouse embryo cell EB_1485


title: Mouse embryo cell EB_1484


title: Mouse embryo cell EB_1483


title: Mouse embryo cell EB_1482


title: Mouse embryo cell EB_1481


title: Mouse embryo cell EB_1479


title: Mouse embryo cell EB_1480


title: Mouse embryo cell EB_1476


title: Mouse embryo cell EB_1474


title: Mouse embryo cell EB_1475


title: Mouse embryo cell EB_1478


title: Mouse embryo cell EB_1472


title: Mouse embryo cell EB_1473


title: Mouse embryo cell EB_1477


title: Mouse embryo cell EB_1488


title: Mouse embryo cell EB_1468

value: embryo 21


title: Mouse embryo cell EB_1470


title: Mouse embryo cell EB_1460


title: Mouse embryo cell EB_1467


title: Mouse embryo cell EB_1465


title: Mouse embryo cell EB_1457


title: Mouse embryo cell EB_1469


title: Mouse embryo cell EB_1455


title: Mouse embryo cell EB_1464


title: Mouse embryo cell EB_1451


title: Mouse embryo cell EB_1450


title: Mouse embryo cell EB_1454


title: Mouse embryo cell EB_1448


title: Mouse embryo cell EB_925


title: Mouse embryo cell EB_922


title: Mouse embryo cell EB_921


title: Mouse embryo cell EB_1471


title: Mouse embryo cell EB_920


title: Mouse embryo cell EB_919


title: Mouse embryo cell EB_916


title: Mouse embryo cell EB_918


title: Mouse embryo cell EB_1446


title: Mouse embryo cell EB_1445


title: Mouse embryo cell EB_1441


title: Mouse embryo cell EB_1466


title: Mouse embryo cell EB_1459


title: Mouse embryo cell EB_1443


title: Mouse embryo cell EB_1447


title: Mouse embryo cell EB_1444


title: Mouse embryo cell EB_1439


title: Mouse embryo cell EB_1437


title: Mouse embryo cell EB_1440


title: Mouse embryo cell EB_1434


title: Mouse embryo cell EB_1435


title: Mouse embryo cell EB_1433


title: Mouse embryo cell EB_1432


title: Mouse embryo cell EB_1436


title: Mouse embryo cell EB_1431


title: Mouse embryo cell EB_1438


title: Mouse embryo cell EB_1429


title: Mouse embryo cell EB_1428


title: Mouse embryo cell EB_1426


title: Mouse embryo cell EB_1427


title: Mouse embryo cell EB_1430


title: Mouse embryo cell EB_1418


title: Mouse embryo cell EB_1423


title: Mouse embryo cell EB_1416


title: Mouse embryo cell EB_1414


title: Mouse embryo cell EB_1412


title: Mouse embryo cell EB_1422


title: Mouse embryo cell EB_1411


title: Mouse embryo cell EB_914


title: Mouse embryo cell EB_1415


title: Mouse embryo cell EB_1410


title: Mouse embryo cell EB_912


title: Mouse embryo cell EB_910


title: Mouse embryo cell EB_1409


title: Mouse embryo cell EB_1408


title: Mouse embryo cell EB_911


title: Mouse embryo cell EB_904


title: Mouse embryo cell EB_905


title: Mouse embryo cell EB_909


title: Mouse embryo cell EB_907


title: Mouse embryo cell EB_906


title: Mouse embryo cell EB_94

value: embryo 2


title: Mouse embryo cell EB_1425


title: Mouse embryo cell EB_96


title: Mouse embryo cell EB_1417


title: Mouse embryo cell EB_1413


title: Mouse embryo cell EB_86


title: Mouse embryo cell EB_89


title: Mouse embryo cell EB_93


title: Mouse embryo cell EB_92


title: Mouse embryo cell EB_80


title: Mouse embryo cell EB_83


title: Mouse embryo cell EB_81


title: Mouse embryo cell EB_85


title: Mouse embryo cell EB_82


title: Mouse embryo cell EB_78


title: Mouse embryo cell EB_76


title: Mouse embryo cell EB_79


title: Mouse embryo cell EB_74


title: Mouse embryo cell EB_77


title: Mouse embryo cell EB_75


title: Mouse embryo cell EB_73


title: Mouse embryo cell EB_70


title: Mouse embryo cell EB_68


title: Mouse embryo cell EB_69


title: Mouse embryo cell EB_71


title: Mouse embryo cell EB_65


title: Mouse embryo cell EB_67


title: Mouse embryo cell EB_63


title: Mouse embryo cell EB_88


title: Mouse embryo cell EB_64


title: Mouse embryo cell EB_91


title: Mouse embryo cell EB_66


title: Mouse embryo cell EB_87


title: Mouse embryo cell EB_62


title: Mouse embryo cell EB_58


title: Mouse embryo cell EB_57


title: Mouse embryo cell EB_61


title: Mouse embryo cell EB_51


title: Mouse embryo cell EB_55


title: Mouse embryo cell EB_59


title: Mouse embryo cell EB_54


title: Mouse embryo cell EB_56


title: Mouse embryo cell EB_1063

value: embryo 15


title: Mouse embryo cell EB_49


title: Mouse embryo cell EB_50


title: Mouse embryo cell EB_1059


title: Mouse embryo cell EB_1056


title: Mouse embryo cell EB_1055


title: Mouse embryo cell EB_1061


title: Mouse embryo cell EB_1057


title: Mouse embryo cell EB_1053


title: Mouse embryo cell EB_1054


title: Mouse embryo cell EB_1037


title: Mouse embryo cell EB_1045


title: Mouse embryo cell EB_1046


title: Mouse embryo cell EB_1040


title: Mouse embryo cell EB_1038


title: Mouse embryo cell EB_1050


title: Mouse embryo cell EB_60


title: Mouse embryo cell EB_1031


title: Mouse embryo cell EB_1035


title: Mouse embryo cell EB_1051


title: Mouse embryo cell EB_1030


title: Mouse embryo cell EB_1036


title: Mouse embryo cell EB_1029


title: Mouse embryo cell EB_52


title: Mouse embryo cell EB_1026


title: Mouse embryo cell EB_1015


title: Mouse embryo cell EB_1010


title: Mouse embryo cell EB_1012


title: Mouse embryo cell EB_1007


title: Mouse embryo cell EB_1027


title: Mouse embryo cell EB_1018


title: Mouse embryo cell EB_1014


title: Mouse embryo cell EB_1025


title: Mouse embryo cell EB_1020


title: Mouse embryo cell EB_1022


title: Mouse embryo cell EB_1023


title: Mouse embryo cell EB_1019


title: Mouse embryo cell EB_1009


title: Mouse embryo cell EB_1006


title: Mouse embryo cell EB_1406

value: embryonic day 5.25

value: embryo 20


title: Mouse embryo cell EB_1400


title: Mouse embryo cell EB_1398


title: Mouse embryo cell EB_1401


title: Mouse embryo cell EB_1392


title: Mouse embryo cell EB_1397


title: Mouse embryo cell EB_1396


title: Mouse embryo cell EB_1402


title: Mouse embryo cell EB_1395


title: Mouse embryo cell EB_1390


title: Mouse embryo cell EB_1387


title: Mouse embryo cell EB_1405


title: Mouse embryo cell EB_1393


title: Mouse embryo cell EB_1386


title: Mouse embryo cell EB_1384


title: Mouse embryo cell EB_1011


title: Mouse embryo cell EB_1383


title: Mouse embryo cell EB_1382


title: Mouse embryo cell EB_1376


title: Mouse embryo cell EB_1378


title: Mouse embryo cell EB_1373


title: Mouse embryo cell EB_1377


title: Mouse embryo cell EB_1380


title: Mouse embryo cell EB_1375


title: Mouse embryo cell EB_1367


title: Mouse embryo cell EB_1372


title: Mouse embryo cell EB_1366


title: Mouse embryo cell EB_1374


title: Mouse embryo cell EB_1369


title: Mouse embryo cell EB_1362


title: Mouse embryo cell EB_1351

value: embryo 19


title: Mouse embryo cell EB_1346


title: Mouse embryo cell EB_1365


title: Mouse embryo cell EB_1348


title: Mouse embryo cell EB_1349


title: Mouse embryo cell EB_1347


title: Mouse embryo cell EB_1198

value: embryo 17


title: Mouse embryo cell EB_1188


title: Mouse embryo cell EB_1361


title: Mouse embryo cell EB_1363


title: Mouse embryo cell EB_1197


title: Mouse embryo cell EB_1199


title: Mouse embryo cell EB_1183


title: Mouse embryo cell EB_1182


title: Mouse embryo cell EB_1370


title: Mouse embryo cell EB_1368


title: Mouse embryo cell EB_1178


title: Mouse embryo cell EB_1175


title: Mouse embryo cell EB_1177


title: Mouse embryo cell EB_1173


title: Mouse embryo cell EB_1174


title: Mouse embryo cell EB_1170


title: Mouse embryo cell EB_1172


title: Mouse embryo cell EB_1169


title: Mouse embryo cell EB_1176


title: Mouse embryo cell EB_1171


title: Mouse embryo cell EB_1168


title: Mouse embryo cell EB_1165


title: Mouse embryo cell EB_1164


title: Mouse embryo cell EB_1161


title: Mouse embryo cell EB_1162


title: Mouse embryo cell EB_1156


title: Mouse embryo cell EB_1155


title: Mouse embryo cell EB_1163


title: Mouse embryo cell EB_1151


title: Mouse embryo cell EB_1153


title: Mouse embryo cell EB_1150


title: Mouse embryo cell EB_1149


title: Mouse embryo cell EB_1181


title: Mouse embryo cell EB_1179


title: Mouse embryo cell EB_1148


title: Mouse embryo cell EB_1146


title: Mouse embryo cell EB_1145


title: Mouse embryo cell EB_1147


title: Mouse embryo cell EB_1143


title: Mouse embryo cell EB_1144


title: Mouse embryo cell EB_1142


title: Mouse embryo cell EB_1167


title: Mouse embryo cell EB_1141


title: Mouse embryo cell EB_1166


title: Mouse embryo cell EB_1160


title: Mouse embryo cell EB_1140


title: Mouse embryo cell EB_1138


title: Mouse embryo cell EB_1139


title: Mouse embryo cell EB_1137


title: Mouse embryo cell EB_1132


title: Mouse embryo cell EB_1134


title: Mouse embryo cell EB_1133


title: Mouse embryo cell EB_1135


title: Mouse embryo cell EB_1130


title: Mouse embryo cell EB_1131


title: Mouse embryo cell EB_1129


title: Mouse embryo cell EB_1154


title: Mouse embryo cell EB_1127


title: Mouse embryo cell EB_1128


title: Mouse embryo cell EB_1126


title: Mouse embryo cell EB_1119


title: Mouse embryo cell EB_1124


title: Mouse embryo cell EB_1123


title: Mouse embryo cell EB_1121


title: Mouse embryo cell EB_1120


title: Mouse embryo cell EB_1118


title: Mouse embryo cell EB_1125


title: Mouse embryo cell EB_1116


title: Mouse embryo cell EB_1115


title: Mouse embryo cell EB_1117


title: Mouse embryo cell EB_1136


title: Mouse embryo cell EB_1345


title: Mouse embryo cell EB_1113


title: Mouse embryo cell EB_1337


title: Mouse embryo cell EB_1344


title: Mouse embryo cell EB_1336


title: Mouse embryo cell EB_1338


title: Mouse embryo cell EB_1333


title: Mouse embryo cell EB_1334


title: Mouse embryo cell EB_1330


title: Mouse embryo cell EB_1329


title: Mouse embryo cell EB_1332


title: Mouse embryo cell EB_1328


title: Mouse embryo cell EB_1327


title: Mouse embryo cell EB_1335


title: Mouse embryo cell EB_1325


title: Mouse embryo cell EB_1122


title: Mouse embryo cell EB_1323


title: Mouse embryo cell EB_1324


title: Mouse embryo cell EB_1311


title: Mouse embryo cell EB_1309


title: Mouse embryo cell EB_1312


title: Mouse embryo cell EB_1308


title: Mouse embryo cell EB_1305


title: Mouse embryo cell EB_1306


title: Mouse embryo cell EB_1339


title: Mouse embryo cell EB_1302


title: Mouse embryo cell EB_1331


title: Mouse embryo cell EB_1293


title: Mouse embryo cell EB_1303


title: Mouse embryo cell EB_1295


title: Mouse embryo cell EB_1294


title: Mouse embryo cell EB_1326


title: Mouse embryo cell EB_1291


title: Mouse embryo cell EB_1289


title: Mouse embryo cell EB_1288


title: Mouse embryo cell EB_97

value: embryo 3


title: Mouse embryo cell EB_99


title: Mouse embryo cell EB_1292


title: Mouse embryo cell EB_98


title: Mouse embryo cell EB_47

value: embryo 1


title: Mouse embryo cell EB_46


title: Mouse embryo cell EB_9


title: Mouse embryo cell EB_45


title: Mouse embryo cell EB_44


title: Mouse embryo cell EB_1310


title: Mouse embryo cell EB_1307


title: Mouse embryo cell EB_40


title: Mouse embryo cell EB_38


title: Mouse embryo cell EB_39


title: Mouse embryo cell EB_36


title: Mouse embryo cell EB_33


title: Mouse embryo cell EB_34


title: Mouse embryo cell EB_37


title: Mouse embryo cell EB_32


title: Mouse embryo cell EB_30


title: Mouse embryo cell EB_28


title: Mouse embryo cell EB_29


title: Mouse embryo cell EB_31


title: Mouse embryo cell EB_48


title: Mouse embryo cell EB_26


title: Mouse embryo cell EB_25


title: Mouse embryo cell EB_24


title: Mouse embryo cell EB_22


title: Mouse embryo cell EB_18


title: Mouse embryo cell EB_17


title: Mouse embryo cell EB_15


title: Mouse embryo cell EB_20


title: Mouse embryo cell EB_14


title: Mouse embryo cell EB_23


title: Mouse embryo cell EB_126


title: Mouse embryo cell EB_125


title: Mouse embryo cell EB_13


title: Mouse embryo cell EB_19


title: Mouse embryo cell EB_35


title: Mouse embryo cell EB_124


title: Mouse embryo cell EB_123


title: Mouse embryo cell EB_117


title: Mouse embryo cell EB_121


title: Mouse embryo cell EB_120


title: Mouse embryo cell EB_119


title: Mouse embryo cell EB_27


title: Mouse embryo cell EB_118


title: Mouse embryo cell EB_112


title: Mouse embryo cell EB_114


title: Mouse embryo cell EB_110


title: Mouse embryo cell EB_113


title: Mouse embryo cell EB_116


title: Mouse embryo cell EB_108


title: Mouse embryo cell EB_107


title: Mouse embryo cell EB_115


title: Mouse embryo cell EB_106


title: Mouse embryo cell EB_104


title: Mouse embryo cell EB_1286

value: embryo 18


title: Mouse embryo cell EB_100


title: Mouse embryo cell EB_111


title: Mouse embryo cell EB_1285


title: Mouse embryo cell EB_1284


title: Mouse embryo cell EB_1276


title: Mouse embryo cell EB_103


title: Mouse embryo cell EB_1279


title: Mouse embryo cell EB_1273


title: Mouse embryo cell EB_1272


title: Mouse embryo cell EB_1271


title: Mouse embryo cell EB_1201


title: Mouse embryo cell EB_101


title: Mouse embryo cell EB_1274


title: Mouse embryo cell EB_1278


title: Mouse embryo cell EB_1209


title: Mouse embryo cell EB_109


title: Mouse embryo cell EB_122


title: Mouse embryo cell EB_1205


title: Mouse embryo cell EB_1227


title: Mouse embryo cell EB_1250


title: Mouse embryo cell EB_102


title: Mouse embryo cell EB_1258


title: Mouse embryo cell EB_1234


title: Mouse embryo cell EB_1218


title: Mouse embryo cell EB_1213


title: Mouse embryo cell EB_1226


title: Mouse embryo cell EB_1204


title: Mouse embryo cell EB_1242


title: Mouse embryo cell EB_1241


title: Mouse embryo cell EB_1269


title: Mouse embryo cell EB_1249


title: Mouse embryo cell EB_1233


title: Mouse embryo cell EB_1225


title: Mouse embryo cell EB_1268


title: Mouse embryo cell EB_1256


title: Mouse embryo cell EB_1248


title: SCCOHT1_SMARCA4_1

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
Sequencing reads were mapped to reference human genome sequence (hg19) downloaded from Illumina iGenomes using STAR57 (version 2.4.2. --quantMode)
The number of fragments was counted with HTSeq58 (version 0.6.1p1)  based on known gene from RefSeq database on UCSC Genome Browser.
Differentially expressed gene (DEG) analysis was performed using DESeq2 (v 1.16.1) bioconductor R package.
Genome_build: hg19
Supplementary_files_format_and_content: Comma seperated values including raw counts

source_name: SCCOHT Cell line

growth_protocol: BIN-67 and SCCOHT-1 cells were all cultured in RPMI with 7% fetal bovine serum (FBS), 1% penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentiviral vectors (Control and SMACRA4) in triplicates for 8 hours followed by puromycin selection for 2 days before harvesting.

value: Cancer cells

tag: smacra4 status

value: ectopic expression


title: SCCOHT1_pR2

value: Deficient


title: SCCOHT1_SMARCA4_3


title: SCCOHT1_pR3


title: SCCOHT1_pR1


title: BIN67_SMARCA4_3


title: Mouse embryo cell EB_1232


title: Mouse embryo cell EB_1224


title: BIN67_SMARCA4_2


title: Mouse embryo cell EB_1267


title: BIN67_SMARCA4_1


title: Mouse embryo cell EB_1255


title: Mouse embryo cell EB_1257


title: Mouse embryo cell EB_1239


title: Mouse embryo cell EB_1208


title: Mouse embryo cell EB_1223


title: BIN67_pR2


title: Mouse embryo cell EB_1217


title: SCCOHT1_SMARCA4_2


title: BIN67_pR3


title: Plasmid_rep1

city: Kansas City

first: Shui

middle: Q

last: Ye

state: MO

address: 2411 Holmes Street

department: Departmetn of Biomedical and Health Informatics

institute: University of Missouri Kansas City School of Medicine

library_source: genomic

data_processing:
The sequence reads were demultiplexed and converted to fastQ with BCL2FastQ v2.17
The fastq files were trimmed in cutadapt 1.7.1 (with Python 2.7.6) to include only the 20bp sgRNA using the 5’ sequence GTGGAAAGGACGAAACACCG and the 3’ sequence GTTTTAGAGCTAGA
Trimmed reads were aligned to the index in Bowtie2 v2.1 with a 1bp mismatch allowance
Raw read counts were calculated in unix and combined across the 4 technical replicates per sample
Read counts were normalized to the median with T0 as control and analyzed using sgRNA and gene-level RRA (Robust Rank Aggregation) in MaGeCK v0.5.6
Genome_build: GeKOv2 sgRNA library index
Supplementary_files_format_and_content: tab-delimited text file of a matrix table of raw read counts.

organism: Escherichia coli

source_name: GeCKOv2 plasmid library

growth_protocol: HuH7 cells were maintained in DMEM (Thermo Fisher cat. 111885092) supplemented with 100 U/ml penicillin and streptomycin (Thermo Fisher cat. 15140122), non-essential amino acids (Thermo Fisher cat. 11140050), and 10% fetal bovine serum (Atlanta Biologicals cat. S11150) as previously described, with the addition of 2mM L-glutamine (Thermo Fisher cat. 25030081) and 1mM sodium pyruvate (Thermo Fisher)67. Cells were detached with trypsin-EDTA (Thermo Fisher cat. 25200056). All incubations were performed at 37°C and 5% CO2.

extract_protocol:
Genomic DNA was isolated from samples of a minimum of 2E7 cells using the Blood and Cell Culture Midi Kit (Qiagen cat. 13343, Valencia, CA)
5µl amplicon or 1µl diluted plasmid library was used as template in 13 50µl Herculase II DNA polymerase reactions per sample to attach pooled variable-length spacers and Illumina indexes (custom primers, see manuscript). 24 cycles were used to amplify DNA in the first and second PCR, respectively. The amplicon fragments after PCR 2 comprise a 354-362bp library with variable 20bp sgRNA sequence in the middle. DNA was pooled by sample and purified using the Nucleospin Gel and PCR Clean-up kit (Clontech cat. 740609.250, Mountain View, CA). DNA was quantified using a Qubit high-sensitivity DNA quantification assay (Thermo Fisher cat. Q32851) and Take3 microspot plate reader (BioTek). DNA quality was analyzed by Experion CHIP assay (BioRad cat. 7007-163, Hercules, CA). Clusters were generated on the flow cell using the HiSeq Rapid Duo CBot Sample Loading Kit (Illumina CT- cat. 403-2001, San Diego, CA).
A single-read rapid run of 75 cycles was performed on a HiSeq 1500 (Illumina cat. GD-402-4002) using the HiSeq Rapid SBS kit (Illumina cat. FC-402-4022) with 10% PhiX.

treatment_protocol: HuH7 were transduced with a Cas9 LLV and subsequently with control or sgRNA library LLV to produce gene knockouts. The pooled, transduced cells were selected with 1.5µg/ml puromycin (Invitrogen cat. Ant-pr-1) for 3 days alongside cells transduced with the empty vector lentiGuidePuro, positive fluorescent control PLJM1-EGFP. After 8 days of transduction a T0 sample was collected (N=2) and the remaining library-transduced cells were treated with 15mM APAP for 30 minutes up to 4 days (2 biological replicates for T0, 24 hour, and 4 day samples).  Samples that underwent 4 days of APAP treatment were outgrown for 21 days prior to collection.

tag: treatment dosage

value: no APAP treatment

value: untreated


title: DIV1_KO_2

city: Los Angeles

first: Liang

last: Chen

state: CA

address: 1050 Childs Way

institute: University of Southern California

data_processing:
The libraries were mapped to mouse reference genome (GRCm38/mm10) with the Gencode annotation (Release M12)  using the STAR aligner (Dobin et al., 2013). The parameters for STAR were specified as “--outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 ”.
The STAR alignment to the Gencode transcriptome was fed into RSEM (Li and Dewey, 2011) to obtain gene and transcript counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Gene/transcripts read counts output from RSEM were shown in Excel files

source_name: Cortical Culture

growth_protocol: Neurons were dissociated in warm plating media (20% heat inactivated horse serum, 25mM glucose, 1x GlutaMax in MEM), centrifuged, resuspended in fresh plating media and plated. Media were changed to feeding media (1x GlutaMax, 1x B-27 in Neurobasal) 6 hours after plating.

extract_protocol:
Total RNA from cultured primary neurons per sample were extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's instructions. DNase I (Thermo Fisher Scientific) was used to remove DNA contamination from RNA samples prior to cDNA synthesis.
RINs were determined by Bioanalyzer (Agilent). RNA-seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits.

tag: plating format

value: 1 million cells/35mm petri dish

value: cortical neurons

tag: days in vitro (div)

value: Ptbp2 KO


title: Mouse embryo cell EB_1200

value: Embryo


title: Mouse embryo cell EB_1212


title: DIV1_KO_1

tag: strain


title: Mouse embryo cell EB_1207


title: Mouse embryo cell EB_1263


title: BIN67_pR1


title: DIV3_WT_1

value: WT


title: DIV3_WT_2


title: Mouse embryo cell EB_1203

value: embryonic day 5.25


title: Mouse embryo cell EB_1254


title: Mouse embryo cell EB_1246


title: Mouse embryo cell EB_1247


title: Mouse embryo cell EB_1211


title: DIV1_WT_2


title: Mouse embryo cell EB_1265


title: Mouse embryo cell EB_1231


title: Mouse embryo cell EB_1245


title: DIV1_WT_1


title: Mouse embryo cell EB_1237


title: Plasmid_rep2

tag: treatment


title: Mouse embryo cell EB_1253

tag: tissue


title: Mouse embryo cell EB_1262


title: Mouse embryo cell EB_1221


title: Mouse embryo cell EB_1261


title: Mouse embryo cell EB_1236


title: Mouse embryo cell EB_1220


title: Mouse embryo cell EB_1228


title: Mouse embryo cell EB_1210


title: Mouse embryo cell EB_12


title: Mouse embryo cell EB_407

value: embryo 7


title: Mouse embryo cell EB_406


title: Mouse embryo cell EB_405


title: Mouse embryo cell EB_399


title: Mouse embryo cell EB_404


title: Mouse embryo cell EB_397


title: Mouse embryo cell EB_402


title: Mouse embryo cell EB_400


title: Mouse embryo cell EB_1244


title: Mouse embryo cell EB_398


title: Mouse embryo cell EB_384


title: Mouse embryo cell EB_401


title: Mouse embryo cell EB_387


title: Mouse embryo cell EB_395


title: Mouse embryo cell EB_390


title: Mouse embryo cell EB_1260


title: Mouse embryo cell EB_396


title: Mouse embryo cell EB_382


title: Mouse embryo cell EB_375


title: Mouse embryo cell EB_374


title: Mouse embryo cell EB_381


title: SR15R

city: Ankara

first: Gunseli

last: Cubukcuoglu Deniz

address: Ceyhun Atuf Kansu Cad. No: 169

department: Stem Cell Institute

country: Turkey

institute: Ankara University

description: Gene expression data from human atrium tissue

hyb_protocol: 15 μg of fragmented biotin-labeled cRNA were hybridized to Human Genome U133 Plus 2.0 Affymetrix GeneChips (P/N 900467 Affymetrix Inc., Santa Clara, CA, USA). Arrays were washed, stained using the GeneChip® Fluidics Station 450. (Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit, Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G according to the Affymetrix protocol.

data_processing: The raw array data in CEL format files were uploaded Partek Genomic Suite (PGS, V6.6, St. Louis, MO). Differentially regulated transcripts (Affy IDs) between persistant AFib and SR groups were uploaded to the WebGestalt (WEB-based Gene SeT AnaLysis Toolkit, http://www.webgestalt.org/) software for annotation, enrichment and visualization of these coding genes. Gene Ontology (GO) and pathway analysis were performed on WebGestalt toolkit.

label: biotin

source_name: right atrium tissue from SR patient

label_protocol: 500 ng of total RNA from each human atrium sample were used to generate amplified and biotinylated cRNA according to standart Affymetrix protocol (GeneChip® 3’ IVT Express Kit, P/N 901229 Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated from LA and RA with MELTTM Total Nucleic Acid Isolation System according to manufacturer's instructions (P/N AM1983 Ambion, Life Technologies, Thermo Fisher Scientific).

treatment_protocol: Patients who were scheduled to undergo mitral valve repair for chronic primary severe Mitral Regurgitation.

tag: disease state

value: sinus rhythm patient with severe mitral regurgitation

value: right atrium  - heart


title: SR13R


title: SR13L

source_name: left atrium tissue from SR patient

value: left atrium  - heart


title: SR14R


title: SR15L


title: Mouse embryo cell EB_380

tag: age


title: SR11R


title: SR14L


title: Mouse embryo cell EB_379

tag: genotype


title: SR11L


title: Mouse embryo cell EB_378

tag: embryo


title: SR16R


title: SR12R


title: SR12L


title: Mouse embryo cell EB_373


title: Mouse embryo cell EB_377


title: Mouse embryo cell EB_371


title: Mouse embryo cell EB_376


title: Mouse embryo cell EB_368


title: SR09L


title: Mouse embryo cell EB_367


title: Mouse embryo cell EB_369


title: Mouse embryo cell EB_365


title: SR09R


title: SR10L


title: Mouse embryo cell EB_363


title: SR10R


title: SR08L


title: SR08R


title: Mouse embryo cell EB_361


title: Mouse embryo cell EB_360


title: Mouse embryo cell EB_359


title: Mouse embryo cell EB_357


title: Mouse embryo cell EB_362


title: Mouse embryo cell EB_358


title: Mouse embryo cell EB_356


title: Mouse embryo cell EB_370


title: SR07R


title: Mouse embryo cell EB_355


title: SR07L


title: Mouse embryo cell EB_352


title: Mouse embryo cell EB_353


title: Mouse embryo cell EB_354


title: Mouse embryo cell EB_351


title: Mouse embryo cell EB_349


title: SR06R


title: SR05L


title: SR05R


title: SR04L


title: Mouse embryo cell EB_394


title: Mouse embryo cell EB_393


title: Mouse embryo cell EB_344


title: Mouse embryo cell EB_346


title: Mouse embryo cell EB_389


title: Mouse embryo cell EB_392


title: SR03R


title: Mouse embryo cell EB_388


title: SR04R


title: Mouse embryo cell EB_391


title: Mouse embryo cell EB_10

value: embryo 1


title: Mouse embryo cell EB_341


title: Mouse embryo cell EB_347


title: SR02L


title: SR01L


title: AF15L

source_name: left atrium tissue from AFib patient

value: atrial fibrillation patient with severe mitral regurgitation


title: Mouse embryo cell EB_339


title: SR06L


title: SR01R


title: Mouse embryo cell EB_345


title: Mouse embryo cell EB_337


title: SR03L


title: AF13R

source_name: right atrium tissue from AFib patient


title: AF14R


title: Mouse embryo cell EB_385


title: Mouse embryo cell EB_336


title: iE95

city: Palo Alto

first: Wu

last: Wei

address: 3165 Porter Dr.

institute: Stanford Genome Technology Center

description:
FACS sorted
normExpression_YJM_NatMicro.tab.gz

data_processing:
For 5’ cap sequencing reads, random barcodes were first extracted and added to the reads name. The reads were aligned to yeast genome  with Novoalign (http://www.novocraft.com) using default setting.
Reads with multiple alignments, or mapping quality <30, or carrying soft-clipped bases on the 5’ end were excluded from downstream analysis
5' end of reads passing quality filtering were extracted; total number of reads per genome location were calculated; total unique number of reads (or unique molecule, based on random barcode sequences) per genome location were calculated
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3), downloaded from SGD(http://www.yeastgenome.org/).
Supplementary_files_format_and_content: Table for normalized express value per gene per cell

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae single cell

growth_protocol: In short, BY4741 or YJM789 were pre-grown in rich media overnight. The next morning cells were diluted to OD(660) 0.05 and grown for at least two full divisions before sorting. Prior to sorting cells were diluted at a final OD of 0.01 and briefly sonicated for 3 pulses 0.5 seconds to remove aggregates (Sonicator Branson M1800).

extract_protocol:
Cell lysis buffer was added into each well and lysis was performed for 10 minutes at 37ºC followed by 3 minutes at 72ºC
Library preparation has performed using in-house protocol (explained details in the method section)
Single-cell RNA seq

tag: growth media

value: YPD

tag: external control

value: ERCC


title: iE93


title: iE86


title: iE88


title: iE87


title: iE94


title: iE83


title: iE92


title: iE91


title: AF13L


title: AF11L


title: AF12R


title: AF12L


title: iE78


title: iE82


title: iE77


title: iE79


title: iE80


title: iE73


title: AF10R


title: AF10L


title: iE59


title: iE74


title: iE84


title: iE65


title: AF09R


title: iE69


title: iE57


title: iE75


title: iE55


title: iE52


title: AF11R


title: AF09L


title: iE50


title: iE51


title: AF08L


title: AF08R


title: AF07R


title: iE62


title: AF07L


title: iE25


title: iE48


title: iE35


title: iE21


title: iE30


title: iE39


title: iE23


title: iE15


title: iE18


title: iE22


title: pp7l_4d_3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 4-d-old seedlings

growth_protocol: seedlings were grown on 0.8% (w/v) agar (Sigma-Aldrich, Darmstadt, Germany) containing 1% (w/v) sucrose at 22 °C under 100 µmol photons m-2 sec-1 provided by white fluorescent lamps

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: long-day conditions

value: pp7l-1 mutant


title: iE19


title: iE14


title: iE9


title: iE11


title: AF06L


title: AF04L


title: AF06R


title: AF05R


title: pp7l_4d_2


title: AF05L


title: AF04R


title: AF03L


title: AF03R


title: AF02R


title: pp7l_4d_1


title: iE6


title: Col_4d_2

value: wild type


title: iE7


title: Col_4d_3


title: iE10


title: iI93

description:
FACS sorted
normExpression_YPD_NatMicro.tab.gz


title: iE8


title: iI92


title: iE5


title: iE4


title: iI87


title: iI91


title: iI88


title: AF01R


title: iI90


title: KS_10X_NPC_WT_C1-2_scRNA-seq

city: Baltimore

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

data_processing:
Sequencing output was processed through the Cell Ranger 2.1.0 preprocessing pipeline using default parameters with the exception of --expect-cells=5000 for `cellranger count` and --normalize=none for `cellranger aggr`. Reads were quantified against hg19 using the 10x reference genome and transcriptome builds (refdata-cellranger-GRCh38-1.2.0). The aggregated raw count matrix was then used as input for the Monocle2 single-cell RNAseq framework.
Differential gene expression analysis was performed on all NPCs and iPSCs with respect to genotype (KS1 patient vs healthy control) and was performed using the Monocle2(Trapnell et al., 2014) likelihood ratio test (0.1% FDR, Monocle2 LRT, Benjamini-Hochberg corrected) with `num_genes_expressed` added as a nuisance parameter to both the full and reduced models. The directionality of the differential gene test was determined by calculating the mean gene expression across all KS1 patient-derived and healthy control cells respectively, evaluating the relative fold change.
High-variance genes were selected as those with a positive residual to the estimated dispersion fit and a mean number of reads per cell >=0.0005.
Dimensionality reduction and visualization was performed via UMAP(McInnes et al., 2018) on the log10(counts + 1) of the high variance genes in the NPC dataset. The first 10 principal components were used as input for UMAP using the default parameters of the R/CRAN package umap. Cells were assigned to clusters using Monocle2’s implementation of the louvain community detection algorithm.
Genome_build: hg19

molecule: polyA RNA

growth_protocol: iPSCs and NPCs were plated at equal density and sampled at 60% confluency.

extract_protocol:
Single cell suspension was obtained using Accutase
Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics). Targeted cell recovery for each sample was 5,000 cells. Sufficient cDNA for library construction was achieved using 20 amplification cycles for iPSC libraries and 16 cycles for NPC libraries. Sample indexing was achieved using 11 PCR cycles for iPSC libraries and 5 cycles for NPC libraries.

treatment_protocol: NPCs were induced in parallel from each iPSC line under identical conditions, and passaged three times before sampling

tag: subject/sample type

value: Healthy Control 1

tag: genotype/variation

value: wild-type

tag: cell type

value: patient-derived NPC


title: KS_10X_NPC_WT_C3-1_scRNA-seq

value: Healthy Control 2


title: 5_cor_B2_R2_9wk

city: Toronto

first: James

last: Ellis

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

data_processing:
Reads were aligned to the human genome (Ensembl release 84 for GRCh38) using HISAT2 (version 2.1.0) with default parameters
Aligned reads overlapping protein coding genes were counted by featureCounts (subread package version 1.5.3) with default parameters, using GENCODE basic gene annotation from a release 27 for GRCh38.
Expression levels of genes in terms of transcript per million (TPM) was separately estimated by Sailfish (version 0.10.0) using an index prepared from a transcriptome of protein coding genes (Ensembl release 86 for GRCh38).
Differential gene expression analysis was carried out in DESeq2 using pairwise comparisons between R841X and R841X-C at each timepoint.
Genome_build: GRCh38 release 27
Supplementary_files_format_and_content: tab-delimited files of negative binomial normalized counts for each sample

source_name: Neurons

growth_protocol: Neurons were differentiated from neural precursor cells in 6x10 cm dishes per line per batch. For the first four weeks, they were grown in the presence of BDNF, GDNF, cAMP. Mouse astrocytes were added at 4 weeks until 9 weeks of age.

extract_protocol:
At 4 weeks of age, one-half of the cultures were dissociated with Accutase, and subjected to negative selection using magnetic activated cell sorting (MACS) as described previously in Djuric Mol Cell Prot 2017 to deplete NPCs and glia. The flow-through (neuronal fraction) from MACS was harvested, and total RNA was extracted using a standard Trizol-based protocol. The quality of RNA was checked by BioAnalyzer
Libraries prepared from the isolated RNA were sequenced on Illumina HiSeq 2500 with paired-end reads (125 bp each) to a depth of approximately 30 million reads per sample.

tag: cell-type

value: IPSC-derived neurons

tag: timepoint


title: 5_cor_B2_R1_9wk


title: 5_cor_B2_R2_4wk


title: iI85


title: 5_cor_B2_R1_4wk


title: iI84


title: KS_10X_NPC_KS1_K1-1_scRNA-seq

value: KS1 patient (clone 1)

value: Kmt2d +/mut


title: 5_cor_B1_R2_9wk


title: Col_4d_1


title: AF01L


title: KS_10X_iPSC_WT_C3-1_scRNA-seq

value: patient-derived iPSC


title: SR02R

value: sinus rhythm patient with severe mitral regurgitation


title: iI80


title: iI89


title: 5_cor_B1_R2_4wk


title: KS_10X_iPSC_WT_C1-2_scRNA-seq


title: KS_10X_iPSC_KS1_K1-1_scRNA-seq


title: iI77


title: iI81


title: 5_cor_B1_R1_9wk


title: Mouse embryo cell EB_386

value: embryonic day 5.25

value: embryo 7

value: Embryo


title: iI78


title: iI79


title: iI82


title: TTC642_idasanutlin_Rep3

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters (--outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000
Reads Per Kilobase of exon per Megabase of library size (RPKM) and ranscripts Per Kilobase Million (TPM) were calculated by using RSEM (Li et al, BMC bioinformatics, 2011)
Differential analysis was performed by DESeq2 (Love et al, Genome biology, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample ...

growth_protocol: TTC642 cells were cultured in RPMI with 10% FBS

extract_protocol:
Total RNA was extracted using TRIzol and purified using RNeasy MinElute Cleanup Kit (Qiagen)
1ug of RNA was used to make the libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: TTC642 cells were treated with Idasanutlin (1 uM) or DMSO (0.01%) for 24 hrs.

value: soft tissue rhabdoid tumor derived cell line

tag: treatment/condition

value: Idasanutlin


title: iI75

value: YPD

value: ERCC


title: 5_cor_B1_R1_4wk


title: iI73


title: TTC642_idasanutlin_Rep2


title: iI72


title: 5_B2_R2_9wk


title: TTC642_idasanutlin_Rep1


title: Mouse embryo cell EB_340


title: 5_B2_R2_4wk


title: 5_B2_R1_9wk


title: TTC642_DMSO_Rep2

value: DMSO


title: AF02L

value: atrial fibrillation patient with severe mitral regurgitation

value: left atrium  - heart


title: iI71


title: 5_B2_R1_4wk


title: iI70


title: TTC642_DMSO_Rep1


title: iI69


title: iI76


title: iI68


title: 5_B1_R2_4wk


title: TTC642_DMSO_Rep3


title: 5_B1_R1_9wk


title: R8-D13-16hSep6-9SR-T1-33N: Donor 4, ST2-transduced Treg + TCR + IL-33 (16h)

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

data_processing:
Within Illumina BaseSpace RNA-Seq Alignment App (v1.1.0): base-calls made with RTA (v2.1), demultiplexing with bcl2fastq2, read sequences aligned with STAR (v2.5.0a), gene expression quantified as raw counts by Illumina’s RnaReadCounter to generate the processed data files.
From raw counts, DESeq2 (v1.16.1) within R (v.3.4.2) used to identify differentially expressed genes by pairwise comparisons.
GSEAPreranked tool within GSEA software (v3.0) and MSigDB gene set collections (v6.1) used for gene set enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Per sample: raw counts of all genes, generated by RnaReadCounter

source_name: Peripheral blood naive Treg

growth_protocol: Day 0: Naive Tregs were flow-sorted (CD4+CD25hiCD127loCD45RA+) and expanded 1:1 with 75Gy-irradiated artificial antigen-presenting cells expressing CD32, CD52, CD80 + OKT3 (0.1μg/ml) + IL-2 (1000IU/ml). Day 1: Cell were transduced with a lentiviral vector encoding ST2 and NGFR (MOI = 10). Day 7: NGFR+ cells were bead-purified by positive selection and expanded as in day 0. Day 12: Cells were rested overnight in reduced IL-2 (100IU/ml). Cultured in X-VIVO 15 with 5% (v/v) human serum, 1% (v/v) penicillin-streptomycin, 2mM GlutaMAX.

extract_protocol:
Activated cells were pelleted (500g for 5 min), lysed and total RNA isolated with RNAzol RT per manufacturer's instructions. All samples used in this study had an RNA integrity number of 9.8-10.
mRNA enrichment and library preparation with NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNExt Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 13 day-expanded ST2-transduced Tregs were activated with IL-2 (100IU/ml) + 1:1 anti-CD3/CD28-coated beads ± IL-33 (20ng/ml) for 16 h. Cultured in X-VIVO 15 with 5% (v/v) human serum, 1% (v/v) penicillin-streptomycin, 2mM GlutaMAX.

tag: donor

tag: Sex

value: female

value: naive Treg

tag: transduction

tag: expansion time

value: 13 days

tag: culture condition

value: IL-2 + TCR + IL-33

tag: culture time


title: R8-D13-16hSep6-4SR-T1-33N: Donor 3, ST2-transduced Treg + TCR + IL-33 (16h)


title: iI66

tag: strain


title: R8-D13-16hSep6-4SR-T1N: Donor 3, ST2-transduced Treg + TCR (16h)

value: IL-2 + TCR


title: iI65


title: R7-D13-16hAug23-9SR-T1-33N: Donor 2, ST2-transduced Treg + TCR + IL-33 (16h)


title: 5_B1_R2_9wk

value: IPSC-derived neurons

tag: genotype


title: R7-D13-16hAug23-9SR-T1N: Donor 2, ST2-transduced Treg + TCR (16h)


title: iI64


title: R8-D13-16hSep6-9SR-T1N: Donor 4, ST2-transduced Treg + TCR (16h)


title: R7-D13-16hAug23-3SR-T1-33N: Donor 1, ST2-transduced Treg + TCR + IL-33 (16h)

value: male


title: iI63


title: iI60


title: iI67


title: R7-D13-16hAug23-3SR-T1n: Donor 1, ST2-transduced Treg + TCR (16h)


title: 5_B1_R1_4wk


title: iI56


title: iI57


title: iI59


title: iI55


title: iE58


title: iI58


title: iI52


title: iI54


title: iI48


title: iI53


title: 27036

city: Leioa

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

description: Complete biopsy.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan with standard recommended Illumina scanner settings.

data_processing: GenomeStudio v2011.1 and R/Bioconductor packages

source_name: duodenum biopsy, complete, celiac disease

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Nucleic acids from all samples were isolated with AllPrep DNA/RNA microkit (Qiagen, Hilden, Germany, Cat No 80284).

treatment_protocol: Not applicable

tag: disease status

value: Celiac Disease

tag: tissue

value: Duodenum

tag: individual identifier


title: 211073

description: Complete biopsy.

source_name: duodenum biopsy, complete, control

value: Non-celiac disease

tag: sample type

value: Control


title: 215026_326

description: CD326+ cells separated with anti-CD326 magnetic beads.

source_name: duodenum biopsy, epithelium, control

value: Epithelium


title: 215025_326

source_name: duodenum biopsy, epithelium, celiac disease


title: iI46

tag: growth media

value: YPD

tag: external control


title: 211084

description: Complete biopsy.


title: 27017

description: Complete biopsy.


title: iI50

value: ERCC


title: iI51


title: iI43


title: iI42