title: 14A_M_2135


title: 14A_M_2134

status: Public on May 24 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


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title: 14A_M_2435


title: 14A_M_2434


title: 14A_M_2433


title: 14A_M_2438


title: 14A_M_2432


title: 14A_M_2430


title: 14A_M_2426


title: 14A_M_2428


title: 14A_M_2431


title: 14A_M_2427


title: 14A_M_2425


title: 14A_M_2422


title: 14A_M_2424


title: 14A_M_2423


title: 14A_M_2421


title: 14A_M_2419


title: 14A_M_2440


title: 14A_M_2420


title: 14A_M_2417


title: 14A_M_2418


title: 14A_M_2416


title: 14A_M_2415


title: 14A_M_2413


title: 14A_M_2411


title: 14A_M_2414


title: 14A_M_2410


title: 14A_M_2429


title: 14A_M_2409


title: 14A_M_2408


title: 14A_M_2405


title: 14A_M_2407


title: 14A_M_2403


title: 14A_M_2404


title: 14A_M_2401


title: 14A_M_2400


title: 14A_M_2397


title: 14A_M_2398


title: 14A_M_2406


title: 14A_M_2402


title: 14A_M_2399


title: 14A_M_2395


title: 14A_M_2394


title: 14A_M_2396


title: 14A_M_2412


title: 14A_M_2392


title: 14A_M_2387


title: 14A_M_2389


title: 14A_M_2390


title: 14A_M_2391


title: 14A_M_2386


title: 14A_M_2393


title: 14A_M_2388


title: 14A_M_2384


title: 14A_M_2385


title: 14A_M_2381


title: 14A_M_2382


title: 14A_M_2380


title: 14A_M_2379


title: 14A_M_2377


title: 14A_M_2378


title: 14A_M_2376


title: 14A_M_2374


title: 14A_M_2383


title: 14A_M_2369


title: 14A_M_2372


title: 14A_M_2373


title: 14A_M_2370


title: 14A_M_2367


title: 14A_M_2368


title: 14A_M_2230


title: 14A_M_2227


title: 14A_M_2365


title: 14A_M_2366


title: 14A_M_2361


title: 14A_M_2362


title: 14A_M_2363


title: 14A_M_2231


title: 14A_M_2226


title: 14A_M_2225


title: 14A_M_2371


title: 14A_M_2229


title: 14A_M_2364


title: 14A_M_2222


title: 14A_M_2224


title: 14A_M_2220


title: 14A_M_2218


title: 14A_M_2375


title: 14A_M_2217


title: 14A_M_2223


title: 14A_M_2216


title: 14A_M_2213


title: 14A_M_2360


title: 14A_M_2228


title: 14A_M_2221


title: 14A_M_2214


title: 14A_M_2215


title: 14A_M_2219


title: 14A_M_2212


title: 14A_M_2209


title: 14A_M_2208


title: 14A_M_2211


title: 14A_M_2207


title: 14A_M_2200


title: 14A_M_2199


title: 14A_M_2198


title: 14A_M_2204


title: 14A_M_2196


title: 14A_M_2203


title: 14A_M_2195


title: 14A_M_2192


title: 14A_M_2193


title: 14A_M_2202


title: 14A_M_2194


title: 14A_M_2191


title: 14A_M_2206


title: 14A_M_2190


title: 14A_M_2201


title: 14A_M_2189


title: 14A_M_2187


title: 14A_M_2185


title: 14A_M_2186


title: 14A_M_2184


title: 14A_M_2188


title: 14A_M_2210


title: 14A_M_2205


title: 14A_M_2179


title: 14A_M_2181


title: 14A_M_2178


title: 14A_M_2177


title: 14A_M_2176


title: 14A_M_2197


title: 14A_M_2182


title: 14A_M_2173


title: 14A_M_2103


title: 14A_M_2174


title: 14A_M_2168


title: 14A_M_2175


title: 14A_M_2098


title: 14A_M_2170


title: 14A_M_2102


title: 14A_M_2101


title: 14A_M_2094


title: 14A_M_2096


title: 14A_M_2169


title: 14A_M_2100


title: 14A_M_2183


title: 14A_M_2099


title: 14A_M_2180


title: 14A_M_2091


title: 14A_M_2171


title: 14A_M_2089


title: 14A_M_2172


title: 14A_M_2088


title: 14A_M_2090


title: 14A_M_2084


title: 14A_M_2097


title: 14A_M_2079


title: 14A_M_2078


title: 14A_M_2081


title: 14A_M_2095


title: 14A_M_2092


title: 14A_M_2076


title: 14A_M_2093


title: 14A_M_2075


title: 14A_M_2086


title: 14A_M_2087


title: 14A_M_2085


title: 14A_M_2080


title: 14A_M_2082


title: 14A_M_2077


title: 14A_M_2074


title: 14A_M_2064


title: 14A_M_2073


title: 14A_M_2062


title: 14A_M_2061


title: 14A_M_2071


title: 14A_M_2070


title: 14A_M_2072


title: 14A_M_2060


title: 14A_M_2069


title: 14A_M_2059


title: 14A_M_2057


title: 14A_M_2058


title: 14A_M_2068


title: 14A_M_2067


title: 14A_M_2066


title: 14A_M_2083


title: 14A_M_2054


title: 14A_M_2049


title: 14A_M_2052


title: 14A_M_2065


title: 14A_M_2063


title: 14A_M_2056


title: 14A_M_2055


title: 14A_M_2047


title: 14A_M_2045


title: 14A_M_2053


title: 14A_M_2050


title: 14A_M_2042


title: 14A_M_2048


title: 14A_M_2040


title: 14A_M_1911


title: 14A_M_2051


title: 14A_M_2046


title: 14A_M_2041


title: 14A_M_1904


title: 14A_M_2044


title: 14A_M_1909


title: 14A_M_1902


title: 14A_M_1910


title: 14A_M_1908


title: 14A_M_1905


title: 14A_M_1907


title: 14A_M_1895


title: 14A_M_1899


title: 14A_M_1896


title: 14A_M_1893


title: 14A_M_1903


title: 14A_M_1892


title: 14A_M_1901


title: 14A_M_2043


title: 14A_M_1894


title: 14A_M_1906


title: 14A_M_1891


title: CD8 T cells, GFP control, chronic, donor 1, day 14

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

data_processing:
Read quality was assessed with FastQC and adapters were trimmed with Trimmomatic.
Trimmed reads were aligned to the hg38 reference genome using Bowtie (v1.0.0) using parameters -v 2 --best --strata -m 1.
Reads mapping to the ENCODE hg38 blacklisted regions were removed using bedtools2 intersect (v2.25.0).
Duplicate reads were excluded using Picard MarkDuplicates (v1.130).
Count per million normalized bigWig files were generated for visualization using deeptools bamCoverage (v3.0.1).
Peak calling was performed using MACS2 narrowPeak and filtered for an adjusted P value < 0.001.
Peak calls were merged across samples to make a union-peak set. A count matrix containing the number of reads in peaks for each sample was generated using feature Counts (subread v1.4.6) and used for differential analysis in DESeq2.
Assembly: hg38
Supplementary files format and content: NarrowPeak files with peak information and signal.
Supplementary files format and content: bigWig files normalized by library size.

organism: Homo sapiens

source_name: CD8 T cells

growth_protocol: CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicillin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).

extract_protocol:
50,000 transduced CD8 T cells were sorted for ATAC-seq.
ATAC-seq libraries were prepared according to the Omni ATAC-seq protocol.

tag: cell type

value: CD8 T cells

tag: genotype

value: GFP control

tag: condition

value: chronic stimulation

tag: time point

value: day 14

tag: donor


title: 14A_M_1889


title: CD8 T cells, BATF3, chronic, donor 1, day 14

value: BATF3 overexpression


title: CD8 T cells, GFP control, chronic, donor 2, day 14


title: CD8 T cells, BATF3, acute, donor 3, day 14

value: acute stimulation


title: 14A_M_1888


title: 14A_M_1897


title: 14A_M_1887


title: CD8 T cells, BATF3, acute, donor 2, day 14


title: 14A_M_1885


title: 14A_M_1898


title: CD8 T cells, BATF3, acute, donor 1, day 14


title: CD8 T cells, GFP control, acute, donor 3, day 14


title: CD8 T cells, GFP control, acute, donor 2, day 14


title: 14A_M_1900


title: CD8 T cells, BATF3, chronic, donor 2, day 14


title: 14A_M_1884


title: 14A_M_1883


title: 14A_M_1886


title: 14A_M_1881


title: CD8 T cells, GFP control, acute, donor 1, day 14


title: case33, PER

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
case33_PER
Cat
Sex type: MN

library_source: transcriptomic

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: FelCat9 (Ensembl gene build)
Supplementary files format and content: AllSamples_rawCounts.txt: Matrix table with raw gene counts for every gene and every sample.

molecule: total RNA

organism: Felis catus

source_name: Gingiva

extract_protocol:
Tissue samples were homogenized in Trizol and RNA was extracted from the aqueous phase using the Quick-RNA Prep Kit (Zymo Research). Samples were treated with DNase on an RNA Clean & Concentrator column (Zymo Research) if high molecular weight material was observed on a Fragment Analyzer trace.
Ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat; New England Biolabs) using 500 ng input total RNA and RNA-seq libraries were generated with the NEBNext Ultra II Directional library prep kit (New England Biolabs).

tag: tissue

value: Gingiva

tag: disease

value: Periodontitis (PER)

tag: Sex

value: Male

tag: neutered status

value: Neutered

tag: age (years)

tag: breed

value: Domestic Shorthair (DSH)


title: case32, PER

description:
case32_PER
Cat
Sex type: MN


title: 14A_M_1879


title: case31, PER

description:
case31_PER
Cat
Sex type: MN

value: Siamese


title: case30, PER

description:
case30_PER
Cat
Sex type: MN


title: 14A_M_1877


title: 14A_M_1878


title: case26, HGIN

description:
case26_HGIN
Cat
Sex type: M

value: Healthy


title: 14A_M_1875


title: case22, HGIN

description:
case22_HGIN
Cat
Sex type: M


title: 14A_M_1874


title: 14A_M_1890


title: 14A_M_1872


title: 14A_M_1880


title: 14A_M_1882


title: 14A_M_1871


title: case23, HOM sample 1

description:
case23_HOM1
Cat
Sex type: F

source_name: Oral mucosa

value: Oral mucosa

value: Female


title: 14A_M_1870


title: case23, HOM sample 2

description:
case23_HOM2
Cat
Sex type: F


title: 14A_M_1869


title: case28, PER

description:
case28_PER
Cat
Sex type: FS

value: Spayed


title: 14A_M_1867


title: 14A_M_1876


title: case22, HOM

description:
case22_HOM
Cat
Sex type: M


title: case21, HOM sample 2

description:
case21_HOM2
Cat
Sex type: FS


title: case21, HOM sample 1

description:
case21_HOM1
Cat
Sex type: FS


title: 14A_M_1866


title: case25, HGIN

description:
case25_HGIN
Cat
Sex type: M


title: 14A_M_1865


title: case19, FCGS

description:
case19_FCGS
Cat
Sex type: MN

value: Feline chronic gingivostomatitis (FCGS)


title: case20, FCGS

description:
case20_FCGS
Cat
Sex type: MN


title: case17, FCGS

description:
case17_FCGS
Cat
Sex type: FS


title: case25, HOM

description:
case25_HOM
Cat
Sex type: M


title: 14A_M_1873


title: case15, FCGS

description:
case15_FCGS
Cat
Sex type: FS


title: case24, HOM sample 2

description:
case24_HOM2
Cat
Sex type: M


title: 14A_M_1860


title: 14A_M_1858


title: case12, FCGS

description:
case12_FCGS
Cat
Sex type: FS


title: case11, FCGS

description:
case11_FCGS
Cat
Sex type: MN


title: case29, PER

description:
case29_PER
Cat
Sex type: FS


title: 14A_M_1857


title: 14A_M_1855


title: case5, FCGS

description:
case5_FCGS
Cat
Sex type: MN


title: 14A_M_1868


title: case8, FCGS

description:
case8_FCGS
Cat
Sex type: FS


title: case18, FCGS

description:
case18_FCGS
Cat
Sex type: FS


title: 14A_M_1863


title: 14A_M_1854


title: Wild type 24h after LPS treatment, replicate 4

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

data_processing:
Raw read QC was done using FastQC (v0.11.9)
Adapter and quality trimming was done using cutadapt (v3.7)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.10a)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.2)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3)
Assembly: Mus musculus GRCm39 (Ensembl release 109)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: bone marrow

growth_protocol: BMDMs were generated by culturing bone-marrow cells in IMDM containing 10% heat-inactivated FBS, 30% L929 cell-conditioned medium, 1% non-essential amino acids, 100 U/ml penicillin, and 100 mg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2. Six days later, cells were collected and seeded in 12-well plates (700 000 cells/well) in the same medium.

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy mini kits per manufacturer (Qiagen) protocol.
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: BMDMs were stimulated with 500 ng/ml Ultrapure LPS from Salmonella minnesota (Invivogen) for indicated hours.

value: bone marrow

value: primary bone marrow-derived macrophage

value: OtulinFL/FL

tag: treatment

value: LPS

tag: time


title: case24, HOM sample 1

description:
case24_HOM1
Cat
Sex type: M


title: 14A_M_1852


title: 14A_M_1862


title: 14A_M_1849


title: Wild type 12h after LPS treatment, replicate 4


title: 14A_M_1859


title: case14, FCGS

description:
case14_FCGS
Cat
Sex type: MN


title: case10, FCGS

description:
case10_FCGS
Cat
Sex type: MN

value: Domestic Longhair (DLH)


title: 14A_M_1864


title: 14A_M_1717


title: 14A_M_1716


title: Wild type 24h after LPS treatment, replicate 3


title: Wild type before LPS treatment, replicate 4

value: no LPS


title: case16, FCGS

description:
case16_FCGS
Cat
Sex type: FS


title: 14A_M_1856


title: Wild type 12h after LPS treatment, replicate 3


title: Wild type 6h after LPS treatment, replicate 3


title: WT cDC1, 2

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: splenic cDC1 were sorted from wild-type mice

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Spleens were digested, and denritic cells were enriched with anti-CD11c MicroBeads prior to sorting. Splenic cDC1 (CD11c+CD8α+CD24+TCRβ−CD49b−B220−) were sorted from naïve WT and Flcn∆DC mice.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with RLT lysis buffer of Rneasy Micro kit from Qiagen.

value: splenic cDC1

value: wild-type


title: 14A_M_1853


title: 14A_M_1713


title: 14A_M_1851


title: Flcn_KO cDC1, 1

source_name: splenic cDC1 were sorted from  Flcn∆DC mice


title: 14A_M_1850


title: 14A_M_1709


title: 14A_M_1848


title: Otulin knock-out before LPS treatment, replicate 4

value: OtulinFL/FL LysMCreTg/WT


title: 14A_M_1719


title: 14A_M_1706


title: Wild type before LPS treatment, replicate 3


title: WT cDC1, 1


title: Wild type 12h after LPS treatment, replicate 2


title: Wild type 6h after LPS treatment, replicate 4


title: Otulin knock-out 12h after LPS treatment, replicate 4


title: 14A_M_1718


title: 14A_M_1705


title: Wild type 6h after LPS treatment, replicate 2


title: 14A_M_1703


title: Wild type 3h after LPS treatment, replicate 2


title: 14A_M_1702


title: 14A_M_1715


title: 14A_M_1714


title: 14A_M_1861


title: Wild type 3h after LPS treatment, replicate 3


title: 14A_M_1700


title: Wild type 3h after LPS treatment, replicate 4


title: 14A_M_1698


title: 14A_M_1699


title: Wild type 12h after LPS treatment, replicate 1


title: 14A_M_1712


title: Otulin knock-out 24h after LPS treatment, replicate 4


title: 14A_M_1710


title: 14A_M_1708


title: Otulin knock-out 6h after LPS treatment, replicate 4


title: 14A_M_1695


title: Otulin knock-out 12h after LPS treatment, replicate 3


title: Flcn_KO cDC1, 3


title: Otulin knock-out 3h after LPS treatment, replicate 4


title: Wild type 24h after LPS treatment, replicate 2


title: Otulin knock-out 3h after LPS treatment, replicate 3


title: 14A_M_1711


title: 14A_M_1691


title: 14A_M_1690


title: Flcn_KO cDC1, 2


title: 14A_M_1704


title: Wild type before LPS treatment, replicate 2


title: Otulin knock-out 12h after LPS treatment, replicate 2


title: 14A_M_1689


title: Otulin knock-out 3h after LPS treatment, replicate 2


title: 14A_M_1701


title: Wild type 24h after LPS treatment, replicate 1


title: 14A_M_1687


title: Otulin knock-out 24h after LPS treatment, replicate 2


title: 14A_M_1686


title: Wild type 6h after LPS treatment, replicate 1


title: 14A_M_1697


title: Wild type before LPS treatment, replicate 1


title: Otulin knock-out 6h after LPS treatment, replicate 1


title: 14A_M_1696


title: Wild type 3h after LPS treatment, replicate 1


title: Otulin knock-out 3h after LPS treatment, replicate 1


title: Otulin knock-out before LPS treatment, replicate 1


title: 14A_M_1681


title: 14A_M_1685


title: 14A_M_1684


title: Otulin knock-out 24h after LPS treatment, replicate 3


title: Otulin knock-out 6h after LPS treatment, replicate 3


title: 14A_M_1680


title: 14A_M_1693


title: Otulin knock-out before LPS treatment, replicate 3


title: 14A_M_1692


title: E12 FL-EC

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the mm10 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.2.3.0) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable.
Assembly: mm10
Supplementary files format and content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs.
Supplementary files format and content: Monocle cell data set files: "SampleX.RDS" contains monocle cell data sets for sample(s) X imported from 10Xoutput files; "SampleX_P.RDS" contains cell data set for sample(s) X following pre-processing, dimensionality reduction, and clustering steps.

molecule: polyA RNA

source_name: Fetal Liver

extract_protocol:
FACS-isolated primary cells or cultured cells harvested by trypsinization (for FL-EC) or pipetting (for co-cultured hematopoietic cells) were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller.
The 10X Genomics Version 3.1 single cell 3’ kit was used to prepare single cell mRNA libraries for freshly isolated primary cells or FL-EC, while the 10X Genomics Version 3.1 with Feature Barcoding technology for Cell Surface Protein Sequencing was used for co-cultured cells. Both kits were used according to manufacturer protocols with the Index Kit T Set A. Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 75 cycle, high output kit.

value: Endothelium

value: Fetal Liver

tag: cell fraction


title: E13.5 FL SE-hi coculture

description: 10x Genomics

value: Hematopoietic cells, cocultured


title: Sema4B transduced immortalized brown adipocytes, Stimulated with NE, 3

city: Belfast

first: Colin

last: Adrain

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Raw fastq reads were processed using FastQ Screen to identify any non-murine reads prior to alignment.
Reads passing were aligned to the mouse genome (mm10, GRCm38.p4) using STAR v2.7.9a.
Counts per gene were calculated using htseq-count.
Differential gene expression analysis was performed with DESeq2, with an adjusted p-value cut‐off of ≤0.05 and a foldchange cut-off of ≥ 1
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text file includes DESeq2 normalised counts values for each Sample

source_name: Adipose tissue

growth_protocol: SV40-immortalized preadipocytes were maintained in complete medium (DMEMF12 supplemented with 1 % penicillin-streptomycin solution 100X, 2.5 μg/ml amphotericin B (Life Tech), 10 μg/ml gentamycin sulphate (Sigma), and 10% new-born calf serum (Biowest)

extract_protocol:
Total RNA was extracted from matured adipocytes using the NZYTech total RNA extraction kit
Nextera

treatment_protocol: Differentiation of immortalizedd preadipocytes to mature adipocytes was induced by exposing confluent preadipocytes to differentiation medium (complete medium supplemented with 1 mM 3-isobutyl methylxanthine (AppliChem), 2 μM rosiglitazone (Cayman), 10 μM dexamethasone (Cayman), 1 μg/ml insulin (Sigma), and 2 nM 3,3’,5-Triiodo-L-thyronine (Sigma)) on day 0 and day 2. On day 4 and day 6 post induction, differentiating cells were exposed to maintenance medium (complete medium supplemented with 1 μg/ml insulin (Sigma), and 2 nM 3,3’,5-Triiodo-L-thyronine (Sigma)). On day 8 post induction, the cells were used for relevant experiments

value: Adipose tissue

value: SV40 Lge T-immortalized brown adipocye

value: WT

value: Norepinephrine


title: Otulin knock-out 6h after LPS treatment, replicate 2


title: 14A_M_1677

tag: brain region


title: 14A_M_1688

tag: age


title: Sema4B transduced immortalized brown adipocytes, Stimulated with NE, 2


title: 14A_M_1694

tag: strain


title: Sema4B transduced immortalized brown adipocytes, Stimulated with NE, 1

tag: cell type


title: 14A_M_1675


title: Otulin knock-out before LPS treatment, replicate 2

tag: genotype


title: Otulin knock-out 24h after LPS treatment, replicate 1


title: Sema4B transduced immortalized brown adipocytes, Unstimulated, 1

value: Untreated


title: Otulin knock-out 12h after LPS treatment, replicate 1

value: bone marrow


title: 14A_M_1682


title: 14A_M_1668


title: 14A_M_1679


title: E13.5 FL SE-hi primary

description: 10x Genomics

value: Hematopoietic cells, primary


title: 14A_M_1666


title: 14A_M_1683


title: 14A_M_1678


title: mutant mouse brain 2, infratentorial, Smarcb11148del/1148del

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

description: 10x Genomics

data_processing:
The samples were demultiplexed and processed with the 10x Genomics CellRanger v3.0.2 program suite.
Raw 10X scRNA-seq data was converted to the standard fastq format with CellRanger's mkfastq function.
The CellRanger count algorithm was subsequently used to align the sample data against the murine reference transcriptome mm10 v3.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain, infratentorial

extract_protocol:
Isolated brains from two Smarcb11148del/1148del and two Smarcb1+/+ P0 mice were divided into a supratentorial and an infratentorial part and each minced with scalpels on ice. For enzymatic dissociation, 2-3 mL of a solution composed of 1 vial Papain (Worthington), 5 mL pre-equilibrated DMEM:F12 and 34 µL DNAse I diluted in 250 µL DMEM:F12 were added to each sample, followed by incubation at 37 °C in 5 % CO2 for 30 min. Afterwards, the cell solution was transferred onto a 40 µm cell strainer. The reaction was stopped with 2 mL PBS / 10 % BSA before washing with 10 mL PBS. The obtained single-cell suspensions were stained with 7-Aminoactinmycin D (7-AAD) (eBioscience). Non-viable, 7-AAD-positive cells were removed by Fluorescence-activated cell sorting (BD FACS Aria II), followed by manual counting with Trypan Blue staining.
Approximately 25,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2000 (Agilent Technologies). Indexed libraries were sequenced separately by the Illumina NextSeq 500 sequencing platform (v 2.5 chemistry, 75 cycle kit). For all samples, the same library was sequenced a second time to increase sequencing saturation.

value: brain, infratentorial

value: 0 days

value: Male


title: 14A_M_1676


title: 14A_M_1669


title: Empty vector transduced immortalized brown adipocytes, Stimulated with NE, 2


title: 14A_M_1674


title: 14A_M_1663


title: 14A_M_1673


title: Empty vector transduced immortalized brown adipocytes, Stimulated with NE, 1


title: 14A_M_1662


title: Sema4B transduced immortalized brown adipocytes, Unstimulated, 3


title: Sema4B transduced immortalized brown adipocytes, Unstimulated, 2


title: 14A_M_1671


title: mouse brain 2, infratentorial, Smarcb1+/+

description: 10x Genomics


title: 14A_M_1670


title: 14A_M_1657


title: Empty vector transduced immortalized brown adipocytes, Unstimulated, 2


title: mouse brain 1, infratentorial, Smarcb1+/+

description: 10x Genomics

value: Female


title: Cocoa butter diet, E-FABP Knockout, replicate 2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Basecalling was performed in BaseSpace using bcl2fastq.
Sequences were directly aligned to the mouse mm10 reference genome assembly using tophat2 (version 2.0.13). The Ensembl GRCm38 v84 gtf was used to guide transcript expression.
Differential expression analysis between  pairwise conditions was performed using the Tuxedo Suite program cuffdiff2 (version 2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: cuffnorm normalized FPKM values

source_name: skin

growth_protocol: Wild type C57b/6 mice were fed with 10% LFD, 45% HFD with saturated fatty acids, 45% HFD with n-3 fatty acids for 4-6 months.  E-FABP knockout mice were fed with 45% HFD with saturated fatty acids, 45% HFD with n-3 fatty acids for 4-6 months.  Skin RNA (n=3/group) from above groups (total 15 samples) was extracted for RNA sequencing.

extract_protocol:
RNA was extracted from the skin of mice using the Qiagen mRNA extraction kit, per the manufacturer's instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina Cat# 20020594), TruSeq RNA Single Indexes Set A (Illumina Cat# 20020492) and Set B (Illumina Cat # 20020493) per the manufacturer's instructions.

tag: diet

value: Cocoa butter

tag: knockout status

value: KO


title: Cocoa butter diet, E-FABP Knockout, replicate 3


title: 14A_M_1667


title: Cocoa butter diet, E-FABP Knockout, replicate 1


title: Empty vector transduced immortalized brown adipocytes, Stimulated with NE, 3


title: 14A_M_1653


title: Omega 3 diet, E-FABP Knockout, replicate 2

value: Omega 3


title: 14A_M_1664


title: Cocoa butter diet, Wild Type, replicate 2


title: Cocoa butter diet, Wild Type, replicate 1


title: mutant mouse brain 1, supratentorial, Smarcb11148del/1148del

description: 10x Genomics

source_name: brain, supratentorial

value: brain, supratentorial


title: Empty vector transduced immortalized brown adipocytes, Unstimulated, 3


title: 14A_M_1649


title: mutant mouse brain 1, infratentorial, Smarcb11148del/1148del

description: 10x Genomics


title: Omega 3 diet, Wild Type, replicate 3


title: Omega 3 diet, Wild Type, replicate 2


title: mutant mouse brain 2, supratentorial, Smarcb11148del/1148del

description: 10x Genomics


title: Empty vector transduced immortalized brown adipocytes, Unstimulated, 1


title: 14A_M_1661


title: 14A_M_1665


title: mouse brain 2, supratentorial, Smarcb1+/+

description: 10x Genomics


title: 14A_M_1644


title: 14A_M_1660


title: mouse brain 1, supratentorial, Smarcb1+/+

description: 10x Genomics


title: 14A_M_1643


title: ebc1-sh-rep3

city: Shanghai

first: mengdi

last: dai

state: China

address: 555 Zuchongzhi Rd, Bldg. 2, RM.409  shanghai, P.R. China

country: China

institute: SIMM

description:
E_663
SYK knockdown of EBC-1.
processed data file: EBC1_fpkm.txt

data_processing:
Illumina Casava software was used for basecalling.
Data filtering were performed as follows: 1) Remove reads with adaptor sequences; 2) Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3) Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 20) is greater than 50% in a read, this read is defined as low quality.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008).
Hisat2 (Kim D et al., 2015) was used to map clean reads to the reference genome of GRCh37 or GRch38 to map clean reads to reference gene.
Genome_build: GRCh38 (hg38) for HCC827, GRCh37 (hg19) for EBC-1 and PC-9
Supplementary_files_format_and_content: *_fpkm.txt: Tab-delimited text file includes FPKM values.

source_name: cancer cells

growth_protocol: SYK in HCC827, PC-9 and EBC-1 cells was knocked down by an shRNA targeting SYK (shSYK, TRCN0000003166) engineered and packaged using a lentiviral delivery system. Corresponding negative controls were also generated. Cells were cultured as instructed.

extract_protocol:
RNA was harvested using Trizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: shRNA

value: shSYK

tag: gene abnormality

value: MET amplification


title: ebc1-sh-rep1

description:
E_661
SYK knockdown of EBC-1.
processed data file: EBC1_fpkm.txt


title: 14A_M_1658


title: 14A_M_1656


title: 14A_M_1655


title: 14A_M_1640


title: ebc1-nc-rep3

description:
E_nc3
Negative control of EBC-1.
processed data file: EBC1_fpkm.txt

value: Negative control


title: Omega 3 diet, E-FABP Knockout, replicate 3


title: 14A_M_1639


title: ebc1-nc-rep2

description:
E_nc2
Negative control of EBC-1.
processed data file: EBC1_fpkm.txt


title: 14A_M_1659


title: 14A_M_1654


title: ebc1-sh-rep2

description:
E_662
SYK knockdown of EBC-1.
processed data file: EBC1_fpkm.txt


title: Omega 3 diet, E-FABP Knockout, replicate 1


title: 14A_M_1652


title: 14A_M_1707


title: ebc1-nc-rep1

description:
E_nc1
Negative control of EBC-1.
processed data file: EBC1_fpkm.txt


title: pc9-sh-rep3

description:
S9S3
SYK knockdown of PC-9.
processed data file: PC9_fpkm.txt

value: EGFR exon 19 deletion


title: Cocoa butter diet, Wild Type, replicate 3

value: WT


title: 14A_M_1636


title: 14A_M_1650


title: 14A_M_1651


title: pc9-sh-rep2

description:
S9S2
SYK knockdown of PC-9.
processed data file: PC9_fpkm.txt


title: 14A_M_1648


title: 14A_M_1647


title: 14A_M_1634


title: pc9-sh-rep1

description:
S9S1
SYK knockdown of PC-9.
processed data file: PC9_fpkm.txt


title: pc9-nc-rep3

description:
S9N3
Negative control of PC-9.
processed data file: PC9_fpkm.txt


title: 14A_M_1633


title: 827-sh-rep3

description:
H827S3
Y2_3
SYK knockdown of HCC827.
processed data file: HCC827_fpkm.txt


title: 14A_M_1630


title: 14A_M_1629


title: Omega 3 diet, Wild Type, replicate 1


title: Low fat diet, Wild Type, replicate 3

value: Low fat


title: 14A_M_1626


title: 14A_M_1646


title: 14A_M_1625


title: 14A_M_1624


title: 14A_M_1645


title: Low fat diet, Wild Type, replicate 2


title: 14A_M_1623


title: 14A_M_1642


title: Low fat diet, Wild Type, replicate 1


title: HEK293 T-Rex Flp-In cells, BRD4-p300(HI), biol rep 2

city: Dallas

first: Michael

last: Rosen

state: TX

address: 6001 Forest Park Rd., ND8.124

department: Biophysics

institute: UT Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Fastq files were mapped to human genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes from igenomes
Differential expression results were generated using edgeR
Assembly: hg19
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: kidney; embryo

growth_protocol: The cells were grown in DMEM medium with addition of 10% heat-inactivated Fetal Bovine Serum, 1% penicillin – streptomycin, 15μg/mL blasticidin and either 100μg/mL zeocin (control cell line) or 100μg/mL hygromycin B (developed stable cell lines).

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen).

treatment_protocol: Induction of protein expression was performed by treating cells with 5ng/mL doxycycline for 2h, followed by 4h washout with medium with no added antibiotics.

tag: tissue

value: kidney; embryo

value: epithelial

value: 2h 5ng/mL doxycycline + 4h washout


title: 14A_M_1621


title: 14A_M_1672


title: 14A_M_1638


title: 14A_M_1637


title: 14A_M_1635


title: HEK293 T-Rex Flp-In cells, BRD4-p300(H*IT), biol rep 1


title: 14A_M_1641


title: 14A_M_1620


title: HEK293 T-Rex Flp-In cells, BRD4-p300(H*IT), biol rep 2


title: HEK293 T-Rex Flp-In cells, BRD4-p300, biol rep 2


title: 14A_M_1619


title: pc9-nc-rep2

description:
S9N2
Negative control of PC-9.
processed data file: PC9_fpkm.txt


title: 14A_M_1617


title: 14A_M_1632


title: pc9-nc-rep1

description:
S9N1
Negative control of PC-9.
processed data file: PC9_fpkm.txt


title: 14A_M_1622


title: 14A_M_1631


title: 14A_M_1616


title: 14A_M_1615


title: 14A_M_1613


title: 827-sh-rep2

description:
H827S2
Y2_2
SYK knockdown of HCC827.
processed data file: HCC827_fpkm.txt


title: HEK293 T-Rex Flp-In cells, BRD4-NUT, biol rep 1


title: HEK293 T-Rex Flp-In cells, BRD4-NUT, biol rep 2


title: 827-sh-rep1

description:
H827S1
Y2_1
SYK knockdown of HCC827.
processed data file: HCC827_fpkm.txt


title: 14A_M_1610


title: 14A_M_1628


title: 827-nc-rep3

description:
H827N3
Y1_3
Negative control of HCC827.
processed data file: HCC827_fpkm.txt


title: 14A_M_1627


title: 14A_M_1607


title: 827-nc-rep2

description:
H827N2
Y1_2
Negative control of HCC827.
processed data file: HCC827_fpkm.txt


title: 14A_M_1612


title: 14A_M_1604


title: 827-nc-rep1

description:
H827N1
Y1_1
Negative control of HCC827.
processed data file: HCC827_fpkm.txt


title: HEK293 T-Rex Flp-In cells, BRD4-p300(I), biol rep 2


title: HEK293 T-Rex Flp-In cells, BRD4-p300(I), biol rep 1


title: HEK293 T-Rex Flp-In cells, BRD4-p300(HI), biol rep 1


title: 14A_M_1618


title: 14A_M_1602


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), input 2

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to reference genome using Bowtie2
Duplicates were removed using picard-tools (v1.127)
Peaks were called using MACS2
Peak annotation was performed using Homer
Assembly: hg19
Supplementary files format and content: tab dellimted text file which contains peak calls

growth_protocol: The cells were grown in DMEM medium with addition of 10% heat-inactivated Fetal Bovine Serum, 1% penicillin – streptomycin, 15μg/mL blasticidin and 100μg/mL hygromycin B.

extract_protocol: Cells were grown in 15cm dishes to confluency and 2-3 plates were used for each experiment. After doxycycline treatments, cells were washed once with 20mL of PBS. Next, the cells were treated with 1% methanol-free formaldehyde diluted in PBS – 10mL per plate for 8 minutes, with gentle agitation. Formaldehyde was then quenched with 500μL of 2.5M glycine for another 8 minutes, with gentle agitation. After quenching, cells were scraped off the plates, transferred to 50mL conical tubes and centrifuged at 500xg at 4oC for 5 minutes. The supernatant was removed, and the cell pellet was washed with 5mL of cold PBS per plate. Following the wash, cells were again centrifuged at 500xg at 4oC for 5 minutes and then, the supernatant was removed. Pellets were finally snap-frozen in liquid nitrogen and stored at –80oC. Cell pellets were thawed and resuspended in LB1 buffer (50mM Hepes-KOH pH 7.9, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 1% TritonX-100 and 1x Complete, EDTA-free protease inhibitor cocktail) to obtain ~1x107 cells/mL suspension and they were then incubated on a rotator at 4oC for 20 minutes, for lysis. Lysis efficiency of at least 60% was determined using trypan blue. Next, the suspension was centrifuged at 1,350xg at 4oC for 5 minutes. The supernatant was removed, and the pellet was resuspended in LB2 buffer (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA and 1x Complete, EDTA-free protease inhibitor cocktail) to again obtain ~1x107 cells/mL suspension and they were then incubated on a rotator at 4oC for 5 minutes. Next, the suspension was centrifuged at 1,350xg at 4oC for 5 minutes. The supernatant was removed, and the pellet was resuspended in LB3 buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% SDS, 1% TritonX-100 and 1x Complete, EDTA-free protease inhibitor cocktail) to obtain ~1x107 cells/mL suspension, which was then passed through a 27G needle 3 times, to completely homogenize the pellet. The suspension was transferred to a Covaris millitube with AFA fiber and sonicated using Covaris M220 sonicator (average incident power 7.5 Watts, peak incident power 75 Watts, duty factor 10%, cycles: 200 count, duration: 18 minutes, minimum temperature: 5oC, temperature setpoint: 7oC, maximum temperature: 9oC). After sonication, samples were centrifuged at 15,000xg at 4oC for 10 minutes, soluble supernatant was transferred to a new tube, snap-frozen in liquid nitrogen and stored at –80oC. 10μL of each sample were incubated overnight at 65oC and treated with Proteinase K and RNAse A and DNA was purified to test the sonication efficiency. Protein G-conjugated Dynabeads (75uL of suspension per IP) were washed with 1mL of blocking buffer (0.5% BSA in PBS) 3 times and collected on a magnet stand each time. Beads were resuspended in 500μL blocking buffer and mixed with 7.5μg antibody (NUT monoclonal rabbit antibody or H3K27Ac monoclonal rabbit antibody) and incubated on a rotator at 4oC overnight. Next day, the beads were washed 3 times with the same blocking buffer to remove unbound antibody and then they were resuspended in 75μL of the blocking buffer. The resuspended beads bound to antibody were mixed with chromatin extract and mixed on a rotator at 4oC overnight. After that, the beads were washed 3 times in 1mL washing buffer 1 (50mM Hepes pH 7.0, 100mM LiCl, 1mM EDTA, 1% NP40, 0.7% sodium deoxycholate and 1x Complete, EDTA-free protease inhibitor cocktail). For the third wash, beads were incubated on a rotator at 4oC for 10 minutes. The washes were repeated with washing buffer 2 (20mM Tris pH 8.0, 350mM NaCl, 1% TritonX-100, 0.1% SDS, 2mM EDTA). Next, the beads were washed with 1mL TE buffer with 50mM NaCl and centrifuged shortly at 300xg and then placed on the magnet stand, to remove residual buffer. Then, 200μL of the elution buffer was added to the beads (50mM Tris pH 8.0, 10mM EDTA and 1% SDS) and the beads were incubated at 65oC for 30 min. with gentle agitation. The beads were next centrifuged at 300xg and placed on the magnet stand. The 200μL elution was then transferred to a new tube. The elution was incubated at 65oC overnight to reverse crosslinks. Next, samples were treated with RNase A for 1h at 37oC and then with Proteinase K for 2h at 55oC. DNA was then purified from these samples using the Qiagen PCR purification kit.

tag: chip antibody


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), NUT antibody, biol rep 1

value: NUT


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), biol rep 2


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), biol rep 1


title: 14A_M_1614


title: HEK293 T-Rex Flp-In cells, BRD4-p300, biol rep 1


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), input 1


title: 14A_M_1600


title: HEK293 T-Rex Flp-In cells, control, biol rep 2

value: no treatment


title: 14A_M_1611


title: 14A_M_1603


title: HEK293 T-Rex Flp-In cells, H3K27Ac antibody

value: histone H3 K27 acetyl


title: HEK293 T-Rex Flp-In cells, BRD4-p300, H3K27Ac antibody, biol rep 2


title: HEK293 T-Rex Flp-In cells, input


title: 14A_M_1608


title: 14A_M_1598


title: HEK293 T-Rex Flp-In cells, BRD4-NUT, input


title: HEK293 T-Rex Flp-In cells, BRD4-p300, H3K27Ac antibody, biol rep 1


title: HEK293 T-Rex Flp-In cells, BRD4-p300, input


title: 14A_M_1606


title: moderate COPD 2, scRNAseq

city: Chengdu

first: Yi

last: Li

state: Sichuan

address: 88# Keyuan South Road, Hi-Tech District

institute: West China Hospital

description:
A4-SI-GA-A4-01
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Freshly collected human lung tissue were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2). Single cells isolation was performed by incubation of tissue with digestion buffer (HBSSwo, Collagenase I & IV, Dispase, DNAse I) in a shaking incubator and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Cells were washed in HBSS and resuspended in HBSS supplemented with 0.04% w/v BSA for further research.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: disease state

value: moderate COPD

value: lung


title: HEK293 T-Rex Flp-In cells, control, biol rep 1


title: 14A_M_1529


title: 14A_M_1605


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), H3K27Ac antibody, biol rep 2


title: moderate COPD 3, scRNAseq

description:
2018jz39
10x Genomics


title: HEK293 T-Rex Flp-In cells, BRD4-NUT, NUT antibody, biol rep 2


title: 14A_M_1601


title: 14A_M_1594


title: 14A_M_1609


title: 14A_M_1595


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), H3K27Ac antibody, biol rep 1


title: mild COPD 4, scRNAseq

description:
2018jz63
10x Genomics

value: mild COPD


title: 14A_M_1528


title: HEK293 T-Rex Flp-In cells, BRD4-NUT, NUT antibody, biol rep 1


title: HEK293 T-Rex Flp-In cells, BRD4-NUT(MIN), NUT antibody, biol rep 2


title: 14A_M_1597


title: 14A_M_1599


title: mild COPD 2, scRNAseq

description:
2018jz15
10x Genomics


title: 14A_M_1527


title: 14A_M_1526


title: moderate COPD 1, scRNAseq

description:
2018jz14
10x Genomics


title: 14A_M_1596


title: moderate COPD 4, scRNAseq

description:
2018jz62
10x Genomics


title: mild COPD 1, scRNAseq

description:
2018jz13
10x Genomics


title: 14A_M_1525


title: wo COPD 4, scRNAseq

description:
C4
10x Genomics

value: no COPD


title: 14A_M_1524


title: wo COPD 3, scRNAseq

description:
2018jz36
10x Genomics


title: wo COPD 1, scRNAseq

description:
2018jz60
10x Genomics


title: 14A_M_1523


title: wo COPD 2, scRNAseq

description:
2018jz47
10x Genomics


title: 14A_M_1521


title: 14A_M_1522


title: LentiMPRA transfected NPC cells DNA-seq replicate 3

city: Piscataway

first: Justin

last: Koesterich

state: New Jersey

address: 679 Hoes Lane West

institute: Rutgers University

description: Files R1 and R3 are paired end reads. The R2 file is the association files to associate barcodes to candidate regulatory sequences

data_processing:
We used the MPRAflow (Nature Protocols 2020) pipeline to associate barcodes to assayed sequences and count barcodes per sequence
We used the MPRAnalyze (Genome Biology 2019) pipeline to detect regulatory activity of sequences and identify motifs effects in the tested regions
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each associated barcode for each replicate
Supplementary files format and content: annotation of column names in counts file to associate column names with replicate number and condition
Supplementary files format and content: Log2 fold change of transcription values between reference and alternate allele sequence
Supplementary files format and content: FASTA file: Fasta File containing the sequence of the promoter sequence along with the sequence name and chromosome coordinates
Supplementary files format and content: PICKLE file: Gzipped Pickle file that contains a python dicitonary associating variant sequence name to the 15bp barcode sequences used for counting transcription rate.  The 1-686 barcode IDs in the annot file refers to the barcode at position 1-686 of this pickle dictionary.
Library strategy: Massively Parallel Reporter Assay

source_name: Brain

extract_protocol:
DNA and RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen)
RNA was treated with Turbo DNase (Thermo Fisher Scientific) to remove contaminating DNA, and reverse-transcribed with SuperScript II (Invitrogen, 18064022) using barcodes specific primer (P7-pLSmp-assUMI-gfp), which has a unique molecular identifier (UMI - 10bp index). Barcode DNA/cDNA from each replicate were amplified with 3-cycle PCR using specific primers (P7-pLSmp-assUMI-gfp and P5-pLSmP-5bc-i#) to add sample index and UMI. A second round of PCR was performed for 19 cycles using P5 and P7 primers (P5, P7). The fragments were purified and further sequenced with NextSeq 15PE with 10-cycle dual index reads, using custom primers (R1, pLSmP-ass-seq-ind1; R2 (index read1 for UMI), pLSmP-UMI-seq; R3, pLSmP-bc-seq; R4 (index read2 for sample index), pLSmP-5bc-seqR2).

value: Brain

value: H1 hESC-derived neural progenitor cells

value: neural progenitor cell

value: Intitated with noggin and supplemented with EGF and FGF


title: LentiMPRA transfected NPC cells RNA-seq replicate 3


title: 14A_M_1519


title: mild COPD 3, scRNAseq

description:
2018jz61
10x Genomics


title: LentiMPRA transfected NPC cells DNA-seq replicate 2


title: LentiMPRA transfected NPC cells RNA-seq replicate 1


title: 14A_M_1517


title: 14A_M_1518


title: LentiMPRA transfected NPC cells RNA-seq replicate 2


title: 14A_M_1513


title: LentiMPRA transfected NPC cells DNA-seq replicate 1


title: miRNA-seq_donor2_Mock_1

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Read quality was verified using FastQC (v. 0.11.9; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). UMI extraction and adapter removal was performed using UMI-Tools (v. 1.1.2); then reads shorter than 16 bp were removed using BBDuk (v. 38.92; sourceforge.net/projects/bbmap/).
Reads were subsequently aligned to the human reference genome (hg38) using STAR (v. 2.7.9a; Dobin et al., 2013). Alignments are then de-duplicated using UMI-Tools (v. 1.1.2).
UMI-based counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.6.4; Liao et al., 2014) and the miRBase annotation (v22; Kozomara et al., 2019)  for hg38 reference genome.
UMI-based counts were normalized to counts per million mapped reads (CPM) using the edgeR R package (v. 3.34.1; Robinson et al., 2010); only genes with a CPM greater than 1 in at least 2 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: CPM obtained using edgeR

source_name: erythroblasts (day 13) derived from SCD CD34+ HSPCs

growth_protocol: terminal erythroid differentiation day 13

extract_protocol:
RNA was harvested using Quick-RNA MicroPrep kit (Zymo Research). 50ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for miR-seq were prepared using QIAseq miRNA Library Kit (Qiagen)

value: SCD (SS)

value: Mock-transduced


title: 14A_M_1514

source_name: C57BL/6J Male P56 Mouse Brain


title: 14A_M_1511


title: miRNA-seq_donor2_AS3_2

value: erythroblasts (day 13) derived from SCD CD34+ HSPCs

value: transduced with BetaAS3-LV


title: 14A_M_1510


title: miRNA-seq_donor2_AS3_1


title: miRNA-seq_donor2_AS3m_miRnt_2

value: transduced with BetaAS3m/miRnt-LV


title: 14A_M_1509


title: miRNA-seq_donor2_AS3m_miRnt_1


title: miRNA-seq_donor2_AS3m_miRHBB_2

data_processing:
Read quality was verified using FastQC (v. 0.11.9; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). UMI extraction and adapter removal was performed using UMI-Tools (v. 1.1.2); then reads shorter than 16 bp were removed using BBDuk (v. 38.92; sourceforge.net/projects/bbmap/).
Reads were subsequently aligned to the human reference genome (hg38) using STAR (v. 2.7.9a; Dobin et al., 2013). Alignments are then de-duplicated using UMI-Tools (v. 1.1.2).
UMI-based counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.6.4; Liao et al., 2014) and the miRBase annotation (v22; Kozomara et al., 2019)  for hg38 reference genome.
UMI-based counts were normalized to counts per million mapped reads (CPM) using the edgeR R package (v. 3.34.1; Robinson et al., 2010); only genes with a CPM greater than 1 in at least 2 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: CPM obtained using edgeR; the expression values of the miR7m can be inspected in the gene expression matrix of AS3m_miRHBB samples looking for "miR7m".

value: transduced with BetaAS3m/miR7m-LV


title: 14A_M_1520


title: miRNA-seq_donor1_Mock_1


title: 14A_M_1508


title: 14A_M_1507


title: miRNA-seq_donor2_AS3m_miRHBB_1


title: 14A_M_1506


title: 14A_M_1516


title: miRNA-seq_donor1_AS3m_miRnt_1


title: LNCaP_pooled_Input

city: Houston

first: Ping

last: Yi

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the human genome build UCSC hg38 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in TDF format

source_name: LNCaP cells

growth_protocol: LNCaP control or TRAF4 stable cells were grown in RPMI1640 supplemented with 10% FBS and streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde before harvesting. Cell pellets were sent to Active Motif for extraction.
The library was constructed in Active Motif.

treatment_protocol: Cells were cultured in 10% charcoal-stripped serum containing phenol red free-RPMI1640 medium for 2 days before harvesting.

value: androgen-dependent prostate cancer cells

value: input


title: LNCaP__TRAF4_AR

value: AR (active motif)

value: Cells were cultured in charcoal-stripped serum medium for 2 days

tag: genotype/variation


title: 14A_M_1504

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: 14A_M_1500


title: 14A_M_1503


title: 14A_M_1502


title: 14A_M_1512


title: 14A_M_1499


title: LNCaP__vector_AR

tag: treatment

value: control


title: 14A_M_1505


title: 14A_M_1498


title: 14A_M_1501


title: miRNA-seq_donor1_AS3m_miRHBB_1


title: 14A_M_1497


title: miRNA-seq_donor1_AS3_1


title: 14A_M_1495


title: 14A_M_1494


title: 14A_M_1493


title: RBG32723_p53KO

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were mapped simultaneously to the Mus musculus genome (mm10) and the 92 ERCC sequences using STAR. FeatureCounts was used to count the number of reads mapped to each gene. Quality control was applied to exclude dead and dying cells as well as poor quality cells (using the parameters fGenes:Total > 12%, mit:mappedToGene < 20%, nNuclearReads > 150K, ercc:mapped < 20%). Data was pre-processed using the in-house pre-processing tool smqpp in Python analysed using Scanpy (1.7.1). Cells were normalised using the DESeq2 method and logged.
Assembly: mm10
Supplementary files format and content: a h5ad file that contains raw counts, metadata for each cell and gene annoataion information.

source_name: Bone marrow

extract_protocol:
To harvest mouse bone marrow cells, spine, femurs, tibiae and pelvic bones were crushed with a pestle and mortar in 3 mL PBS + 2% FBS. Further 3 mL PBS + 2% FCS were used to wash the bones and the resulting cell suspension was filtered through a 0.75 uM filter. Cells were pelleted and resuspended in 3 mL PBS + 2% FBS. Red cell lysis was performed using cold ammonium chloride (StemCell Technologies cat. no 07800). PBS 2% FCS was added to dilute the red cell lysis buffer during subsequent centrifugation at 4 oC.   For lineage depletion, EasySep™ Mouse Hematopoietic Progenitor Cell Enrichment Kit from StemCell Technologies (cat no. 19816A) was used according to the manufacturer’s instructions but avoiding the use of rat serum. Samples were transferred into 5 ml polystyrene (352058) FACS tubes and incubated with 10 µl/ml EasySep mouse hematopoietic progenitor cell isolation cocktail labelled with biotin. 40 µl/ml of EasySep™ Streptavidin RapidSpheres were added and allowed to bind on ice for 10 minutes. The samples were subsequently diluted to 2.5 ml using PBS + 2% FBS and placed in the EasyStep magnet (StemCell Technologies cat no. 18000) for 3 minutes at room temperature. After incubation, samples were transferred into new tubes, spun down, and resuspended in 100 ul PBS + 2% FCS.   For antibody staining, a master mix was prepared as indicated in table 2 and cell suspensions were incubated on ice, in the dark for 30 minutes. After staining, cells were washed, pelleted, and resuspended in 100 ul PBS + 2% FCS. Were necessary, streptavidin conjugated antibody was added in a second step. Samples were pelleted and resuspended to a final volume of 500 ul PBS + 2% FCS. We used single colour, unstained, and full panel controls that were made using pooled BM cells from all mice before lineage depletion.
Primary single cells (LSK cells – Lin-Sca1+ckit+) were FACS index sorted into lysis buffer (0.2% Triton X-100 (Sigma), RNase inhibitor (SUPERase, Thermofisher), and nuclease-free water (Thermo Fisher)). scRNA sequencing was performed according to the Smart-Seq2 protocol.
Libraries were prepared using the Illumina nextera XT DNA preparation kit and sequenced on the Illumina Hi-Seq 2500.

value: Bone marrow

value: p53 knock-outs


title: RBG32720_p53KO


title: RBG32719_p53KO


title: RBG32724_WT

value: WT


title: RBG32721_p53KO


title: 14A_M_1492

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: RBG32716_WT


title: RBG32715_WT


title: RBG32717_WT


title: 14A_M_1491


title: 14A_M_1490


title: 14A_M_1489


title: RBG32722_p53KO


title: RBG32714_WT


title: 14A_M_1487


title: 14A_M_1488


title: RBG32712_WT


title: RBG32713_WT


title: RBG32711_p53KO


title: 14A_M_1496


title: 14A_M_1486


title: 14A_M_1485


title: RBG32710_p53KO


title: RBG32709_p53KO


title: RBG32708_p53KO


title: 14A_M_1483


title: RBG32718_p53KO


title: RBG32707_p53KO


title: RBG32706_p53KO


title: RBG32704_WT


title: 14A_M_1482


title: 14A_M_1481


title: 14A_M_1479


title: RBG32705_WT


title: 14A_M_1480


title: 14A_M_1476


title: 14A_M_1478


title: 14A_M_1475


title: RBG32703_WT


title: RBG32702_WT


title: 14A_M_1473


title: 14A_M_1484


title: RBG32701_WT


title: RBG32700_WT


title: RBG32698_p53KO


title: 14A_M_1472


title: RBG32697_p53KO


title: 14A_M_1471


title: 14A_M_1470


title: RBG32696_p53KO


title: RBG32695_p53KO


title: 14A_M_1469


title: RBG32694_p53KO


title: 14A_M_1468


title: RBG32693_WT


title: 14A_M_1467


title: RBG32691_WT


title: 14A_M_1272


title: RBG32689_WT


title: RBG32692_WT


title: RBG32690_WT


title: RBG32699_p53KO


title: 14A_M_1474


title: RBG32688_WT


title: 14A_M_1466


title: RBG32015_WT


title: 14A_M_1269


title: RBG32013_p53KO


title: 14A_M_1267


title: RBG32014_WT


title: 14A_M_1266


title: 14A_M_1268


title: RBG32012_p53KO


title: RBG32010_TKO

value: Aldh2 & Fancd2 & p53 triple knock-outs


title: 14A_M_1264


title: 14A_M_1265


title: RBG32011_p53KO


title: RBG32008_TKO


title: 14A_M_1263


title: RBG32009_TKO


title: 14A_M_1273


title: 14A_M_1261


title: RBG32007_TKO


title: 14A_M_1262


title: 14A_M_1271


title: RBG32005_DKO

value: Aldh2 & Fancd2 double knock-outs


title: RBG32006_TKO


title: 14A_M_1260


title: 14A_M_1258


title: 14A_M_1270


title: RBG32003_WT


title: 14A_M_1259


title: 14A_M_1257


title: RBG32002_WT


title: RBG32001_p53KO


title: RBG31999_p53KO


title: 14A_M_1256


title: RBG32000_p53KO


title: 14A_M_1253


title: RBG31998_TKO


title: 14A_M_1254


title: 14A_M_1252


title: RBG31997_TKO


title: 14A_M_1251


title: RBG31995_TKO


title: 14A_M_1250


title: RBG31996_TKO


title: 14A_M_1249


title: RBG31994_TKO


title: RBG32004_DKO


title: RBG31992_DKO


title: 14A_M_1247


title: RBG31991_WT


title: 14A_M_1245


title: RBG31993_DKO


title: RBG31990_WT


title: 14A_M_1244


title: RBG31989_p53KO


title: 14A_M_1248


title: 14A_M_1243


title: 14A_M_1255


title: RBG31984_TKO


title: RBG31985_TKO


title: RBG31981_DKO


title: RBG31982_TKO


title: RBG31980_DKO


title: 14A_M_1235


title: 14A_M_1242


title: 14A_M_1241


title: 14A_M_1236


title: 14A_M_1240


title: 14A_M_1237


title: 14A_M_1239


title: RBG31979_WT


title: 14A_M_1246


title: RBG31978_WT


title: RBG31977_p53KO


title: RBG31976_p53KO


title: 14A_M_1231


title: RBG31974_TKO


title: 14A_M_1234


title: 14A_M_1229


title: 14A_M_1230


title: RBG31975_p53KO


title: 14A_M_1228


title: 14A_M_1233


title: RBG31986_TKO


title: RBG31973_TKO


title: RBG31983_TKO


title: RBG31972_TKO


title: 14A_M_1227


title: 14A_M_1226


title: RBG31971_TKO


title: RBG31970_TKO


title: 14A_M_1223


title: 14A_M_1222


title: 14A_M_1224


title: 14A_M_1221


title: 14A_M_1232


title: RBG31968_DKO


title: RBG31967_WT


title: RBG31969_DKO


title: RBG31965_p53KO


title: RBG31988_p53KO


title: RBG31966_WT


title: 14A_M_1220


title: 14A_M_1218


title: 14A_M_1217


title: 14A_M_1216


title: RBG31962_TKO


title: 14A_M_1219


title: RBG31964_p53KO


title: RBG31963_TKO


title: 14A_M_1215


title: RBG31960_TKO


title: RBG31961_TKO


title: 14A_M_1214


title: RBG31959_TKO


title: 14A_M_1225


title: 14A_M_1213


title: RBG31958_DKO


title: 14A_M_1212


title: RBG31957_DKO


title: RBG31956_DKO


title: 14A_M_1210


title: RBG31955_WT


title: 14A_M_1209


title: 14A_M_1211


title: RBG31954_WT


title: 14A_M_1208


title: RBG31953_p53KO


title: 14A_M_1207


title: RBG31951_TKO


title: RBG31950_TKO


title: 14A_M_1204


title: 14A_M_1205


title: RBG31949_TKO


title: 14A_M_1203


title: 14A_M_1202


title: RBG31948_TKO


title: 14A_M_1206


title: RBG31946_DKO


title: RBG31945_DKO


title: 14A_M_1201


title: 14A_M_1200


title: RBG31944_DKO


title: 14A_M_1199


title: 14A_M_1198


title: RBG31943_WT


title: 14A_M_1197


title: 14A_M_1196


title: RBG31941_p53KO


title: RBG31952_p53KO


title: 14A_M_1195


title: RBG31938_TKO


title: RBG31940_p53KO


title: 14A_M_1193


title: 14A_M_1194


title: RBG31939_TKO


title: RBG31937_TKO


title: RBG31947_TKO


title: RBG31936_TKO


title: RBG31935_TKO


title: 14A_M_1190


title: 14A_M_1189


title: RBG31933_DKO


title: 14A_M_1187


title: RBG31934_DKO


title: 14A_M_1186


title: RBG31932_DKO


title: 14A_M_1192


title: 14A_M_1185


title: RBG31931_WT


title: RBG31929_p53KO


title: 14A_M_1188


title: RBG31942_WT


title: 14A_M_1183


title: RBG31930_WT


title: RBG31927_TKO


title: 14A_M_1184


title: RBG31928_p53KO


title: RBG31926_TKO


title: RBG31925_TKO


title: 14A_M_1181


title: 14A_M_1179


title: 14A_M_1191


title: 14A_M_1178


title: RBG31924_TKO


title: 14A_M_1176


title: 14A_M_1177


title: RBG31923_TKO


title: RBG31921_DKO


title: RBG31920_DKO


title: 14A_M_1173


title: RBG31919_DKO


title: 14A_M_1174


title: 14A_M_1180


title: 14A_M_1172


title: 14A_M_1171


title: RBG31916_TKO


title: 14A_M_1170


title: 14A_M_1182


title: 14A_M_1169


title: 14A_M_1167


title: 14A_M_1168


title: RBG31913_TKO


title: RBG31914_TKO


title: 14A_M_1165


title: RBG31906_DKO


title: RBG31912_TKO


title: 14A_M_1164


title: RBG31918_DKO


title: 14A_M_1163


title: 14A_M_1175


title: RBG31904_TKO


title: RBG31905_DKO


title: RBG31903_TKO


title: RBG31901_TKO


title: 14A_M_1162


title: RBG31917_DKO


title: RBG31915_TKO


title: RBG31902_TKO


title: RBG31907_DKO


title: 14A_M_1159


title: 14A_M_1161


title: 14A_M_1157


title: RBG31895_DKO


title: 14A_M_1158


title: RBG31894_DKO


title: 14A_M_1166


title: RBG31893_DKO


title: RBG31891_TKO


title: 14A_M_1155


title: RBG31890_TKO


title: RBG31889_TKO


title: 14A_M_1152


title: 14A_M_1154


title: 14A_M_1153


title: 14A_M_1160


title: RBG31883_DKO


title: RBG31882_DKO


title: 14A_M_1151


title: 14A_M_1149


title: RBG31880_TKO


title: RBG31879_TKO


title: 14A_M_1148


title: 14A_M_1150


title: RBG31878_TKO


title: 14A_M_892


title: 14A_M_893


title: RBG31874_WT


title: 14A_M_890


title: 14A_M_1156


title: RBG31875_WT


title: RBG31892_TKO


title: 14A_M_889


title: RBG31876_TKO


title: RBG31922_DKO


title: 14A_M_891


title: 14A_M_887


title: 14A_M_888


title: RBG31873_p53KO


title: RBG31871_DKO


title: RBG31870_DKO


title: RBG31869_TKO


title: RBG31877_TKO


title: RBG31868_TKO


title: RBG31866_TKO


title: RBG31867_TKO


title: 14A_M_883


title: 14A_M_882


title: 14A_M_886


title: 14A_M_881


title: RBG31865_TKO


title: 14A_M_884


title: RBG31864_WT


title: 14A_M_879


title: 14A_M_880


title: RBG31861_p53KO


title: RBG31863_WT


title: RBG31859_DKO


title: RBG31858_DKO


title: RBG31872_p53KO


title: RBG31857_TKO


title: 14A_M_876


title: 14A_M_875


title: 14A_M_874


title: 14A_M_873


title: RBG31855_TKO


title: RBG31854_TKO


title: 14A_M_872


title: RBG31856_TKO


title: RBG31853_TKO


title: RBG31852_WT


title: 14A_M_871


title: 14A_M_885


title: RBG31851_WT


title: 14A_M_866


title: 14A_M_868


title: 14A_M_867


title: 14A_M_878


title: 14A_M_877


title: RBG31850_p53KO


title: 14A_M_869


title: RBG31847_DKO


title: RBG31846_DKO


title: RBG31845_TKO


title: RBG31844_TKO


title: 14A_M_863


title: 14A_M_865


title: 14A_M_864


title: 14A_M_862


title: RBG31843_TKO


title: 14A_M_861


title: RBG31842_TKO


title: 14A_M_860


title: RBG31841_TKO


title: 14A_M_859


title: RBG31840_WT


title: 14A_M_858


title: 14A_M_870


title: RBG31839_WT


title: RBG31849_p53KO


title: RBG31837_p53KO


title: RBG31836_p53KO


title: 14A_M_856


title: RBG31833_TKO


title: 14A_M_852


title: RBG31831_TKO


title: 14A_M_855


title: RBG31830_TKO


title: 14A_M_853


title: RBG31829_TKO


title: RBG31832_TKO


title: 14A_M_851


title: RBG31828_WT


title: 14A_M_848


title: RBG31827_WT


title: 14A_M_849


title: RBG31825_p53KO


title: 14A_M_850


title: RBG31824_p53KO


title: 14A_M_847


title: 14A_M_846


title: RBG31823_TKO


title: 14A_M_845


title: RBG31822_TKO


title: 14A_M_857


title: 14A_M_844


title: RBG31821_TKO


title: 14A_M_843


title: 14A_M_854


title: RBG31819_WT


title: 14A_M_842


title: 14A_M_841


title: RBG31820_WT


title: 14A_M_840


title: 14A_M_839


title: RBG31818_p53KO


title: RBG31815_DKO


title: 14A_M_837


title: RBG31817_p53KO


title: RBG31814_DKO


title: 14A_M_838


title: RBG31813_TKO


title: RBG31812_TKO


title: 14A_M_835


title: 14A_M_834


title: RBG31810_TKO


title: RBG31811_TKO


title: RBG31809_TKO


title: 14A_M_832


title: RBG31816_DKO


title: RBG31806_p53KO


title: RBG31808_WT


title: 14A_M_767


title: RBG31804_DKO


title: 14A_M_764


title: 14A_M_762


title: RBG31807_WT


title: 14A_M_763


title: RBG31803_DKO


title: 14A_M_765


title: 14A_M_766


title: 14A_M_761


title: RBG31802_DKO


title: 14A_M_759


title: RBG31801_TKO


title: 14A_M_758


title: 14A_M_757


title: 14A_M_760


title: RBG31799_TKO


title: RBG31800_TKO


title: 14A_M_836


title: 14A_M_833


title: RBG31798_TKO


title: 14A_M_756


title: 14A_M_755


title: RBG31805_p53KO


title: RBG31795_WT


title: 14A_M_753


title: RBG31794_p53KO


title: 14A_M_749


title: RBG31790_DKO


title: 14A_M_751


title: RBG31793_p53KO


title: RBG31792_DKO


title: RBG31791_DKO


title: 14A_M_752


title: 14A_M_750


title: RBG31796_WT


title: 14A_M_745


title: RBG31787_TKO


title: 14A_M_748


title: RBG31784_WT


title: 14A_M_743


title: RBG31783_WT


title: 14A_M_744


title: 14A_M_742


title: 14A_M_754


title: RBG31788_TKO


title: 14A_M_747


title: RBG31785_TKO


title: 14A_M_746


title: RBG31797_TKO


title: RBG31786_TKO


title: RBG31782_p53KO


title: 14A_M_741


title: RBG31781_p53KO


title: 14A_M_740


title: RBG31789_TKO


title: 14A_M_739


title: RBG31780_DKO


title: 14A_M_737


title: 14A_M_738


title: RBG31779_DKO


title: 14A_M_735


title: RBG31777_TKO


title: RBG31778_DKO


title: 14A_M_736


title: RBG31776_TKO


title: 14A_M_734


title: RBG31771_p53KO


title: RBG31775_TKO


title: RBG31774_TKO


title: RBG31770_p53KO


title: RBG31772_WT


title: RBG31773_WT


title: RBG31769_p53KO


title: RBG31768_DKO


title: 14A_M_723