title: 8K_M_2246


title: 8K_M_2245

status: Public on Jul 17 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-seq2

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


title: 8K_M_2244


title: 8K_M_2248


title: 8K_M_2242


title: 8K_M_2238


title: 8K_M_2240


title: 8K_M_2241


title: 8K_M_2237


title: 8K_M_2234


title: 8K_M_2239


title: 8K_M_2233


title: 8K_M_2232


title: 8K_M_2230


title: 8K_M_2258


title: 8K_M_2231


title: 8K_M_2228


title: 8K_M_2229


title: 8K_M_2227


title: 8K_M_2226


title: 8K_M_2222


title: 8K_M_2224


title: 8K_M_2225


title: 8K_M_2247


title: 8K_M_2243


title: 8K_M_2221


title: 8K_M_2219


title: 8K_M_2218


title: 8K_M_2235


title: 8K_M_2236


title: 8K_M_2217


title: 8K_M_2214


title: 8K_M_2215


title: 8K_M_2211


title: 8K_M_2212


title: 8K_M_2213


title: 8K_M_2210


title: 8K_M_2223


title: 8K_M_2209


title: 8K_M_2205


title: 8K_M_2206


title: 8K_M_2204


title: 8K_M_2208


title: 8K_M_2207


title: 8K_M_2203


title: 8K_M_2201


title: 8K_M_2199


title: 8K_M_2220


title: 8K_M_2197


title: 8K_M_2200


title: 8K_M_2202


title: 8K_M_2195


title: 8K_M_2198


title: 8K_M_2196


title: 8K_M_2216


title: 8K_M_2194


title: 8K_M_2193


title: 8K_M_2251


title: 8K_M_2189


title: 8K_M_2191


title: 8K_M_2192


title: 8K_M_2190


title: 8K_M_2187


title: 8K_M_2186


title: 8K_M_2185


title: 8K_M_2182


title: 8K_M_2180


title: 8K_M_2183


title: 8K_M_2179


title: 8K_M_2184


title: 8K_M_2178


title: 8K_M_2181


title: 8K_M_2176


title: 8K_M_2177


title: 8K_M_2175


title: 8K_M_2174


title: 8K_M_2171


title: 8K_M_2169


title: 8K_M_2173


title: 8K_M_2172


title: 8K_M_2168


title: 8K_M_2170


title: 8K_M_2167


title: 8K_M_2164


title: 8K_M_2163


title: 8K_M_2188


title: 8K_M_2166


title: 8K_M_2161


title: 8K_M_2160


title: 8K_M_2159


title: 8K_M_2157


title: 8K_M_2158


title: 8K_M_2156


title: 8K_M_2154


title: 8K_M_2151


title: 8K_M_2153


title: 8K_M_2148


title: 8K_M_2149


title: 8K_M_2150


title: 8K_M_2147


title: 8K_M_2165


title: 8K_M_2141


title: 8K_M_2146


title: 8K_M_2142


title: 8K_M_2143


title: 8K_M_2144


title: 8K_M_2140


title: 8K_M_2162


title: 8K_M_2145


title: 8K_M_2136


title: 8K_M_2134


title: 8K_M_2138


title: 8K_M_2137


title: 8K_M_2135


title: 8K_M_2155


title: 8K_M_2133


title: 8K_M_2132


title: 8K_M_2152


title: 8K_M_2130


title: 8K_M_2139


title: 8K_M_2128


title: 8K_M_2126


title: 8K_M_2127


title: 8K_M_2125


title: 8K_M_2123


title: 8K_M_2122


title: 8K_M_2121


title: 8K_M_2119


title: 8K_M_2120


title: 8K_M_2124


title: 8K_M_2118


title: 8K_M_2117


title: 8K_M_2113


title: 8K_M_2114


title: 8K_M_2111


title: 8K_M_2116


title: 8K_M_2112


title: 8K_M_2115


title: 8K_M_2107


title: 8K_M_2110


title: 8K_M_2129


title: 8K_M_2109


title: 8K_M_2106


title: 8K_M_2105


title: 8K_M_2108


title: 8K_M_2104


title: 8K_M_2103


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title: 8K_M_2100


title: 8K_M_2099


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title: 8K_M_2092


title: 8K_M_2095


title: 8K_M_2093


title: 8K_M_2091


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title: 8K_M_2086


title: 8K_M_2084


title: 8K_M_2087


title: 8K_M_2083


title: 8K_M_2082


title: 8K_M_2081


title: 8K_M_2075


title: 8K_M_2078


title: 8K_M_2079


title: 8K_M_2101


title: 8K_M_2077


title: 8K_M_2073


title: 8K_M_2074


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title: 8K_M_2071


title: 8K_M_2069


title: 8K_M_2072


title: 8K_M_2068


title: 8K_M_2067


title: 8K_M_2063


title: 8K_M_2085


title: 8K_M_2070


title: 8K_M_2066


title: 8K_M_2065


title: 8K_M_2064


title: 8K_M_2060


title: 8K_M_2058


title: 8K_M_2080


title: 8K_M_2056


title: 8K_M_2061


title: 8K_M_2057


title: 8K_M_2055


title: 8K_M_2054


title: 8K_M_2053


title: 8K_M_2051


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title: 8K_M_2047


title: 8K_M_2048


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title: 8K_M_2045


title: 8K_M_2041


title: 8K_M_2062


title: 8K_M_2040


title: 8K_M_2042


title: 8K_M_2043


title: 8K_M_2059


title: 8K_M_2038


title: 8K_M_2044


title: 8K_M_2034


title: 8K_M_2033


title: 8K_M_2036


title: 8K_M_2031


title: 8K_M_2035


title: 8K_M_2027


title: 8K_M_2029


title: 8K_M_2030


title: 8K_M_2028


title: 8K_M_2025


title: 8K_M_2024


title: 8K_M_2023


title: 8K_M_2022


title: 8K_M_2021


title: 8K_M_2019


title: 8K_M_2018


title: 8K_M_2026


title: 8K_M_2016


title: 8K_M_2015


title: 8K_M_2014


title: 8K_M_2012


title: 8K_M_2017


title: 8K_M_2037


title: 8K_M_2032


title: 8K_M_2010


title: 8K_M_2020


title: 8K_M_2006


title: 8K_M_2008


title: 8K_M_2005


title: 8K_M_2004


title: 8K_M_2007


title: 8K_M_2011


title: 8K_M_2003


title: 8K_M_1998


title: 8K_M_2000


title: 8K_M_1999


title: 8K_M_2001


title: 8K_M_1996


title: 8K_M_1994


title: 8K_M_1993


title: 8K_M_1991


title: 8K_M_1990


title: 8K_M_1989


title: 8K_M_1997


title: 8K_M_1988


title: 8K_M_1984


title: 8K_M_1987


title: 8K_M_1986


title: 8K_M_1981


title: 8K_M_1982


title: 8K_M_1983


title: 8K_M_1979


title: 8K_M_1976


title: 8K_M_1977


title: 8K_M_1978


title: 8K_M_1980


title: 8K_M_1974


title: 8K_M_2009


title: 8K_M_1992


title: 8K_M_2013


title: 8K_M_1971


title: 8K_M_1969


title: 8K_M_1970


title: 8K_M_1965


title: 8K_M_1966


title: 8K_M_1964


title: 8K_M_1963


title: 8K_M_1985


title: 8K_M_1962


title: 8K_M_1959


title: 8K_M_1958


title: 8K_M_1960


title: 8K_M_1961


title: 8K_M_1956


title: 8K_M_1973


title: 8K_M_1957


title: 8K_M_1955


title: 8K_M_1972


title: 8K_M_1952


title: 8K_M_1968


title: 8K_M_1949


title: 8K_M_1948


title: 8K_M_1945


title: 8K_M_1944


title: 8K_M_1951


title: 8K_M_1950


title: 8K_M_1947


title: 8K_M_1975


title: 8K_M_1953


title: 8K_M_1967


title: 8K_M_1954


title: 8K_M_1946


title: 8K_M_1942


title: 8K_M_1940


title: 8K_M_1939


title: 8K_M_1938


title: 8K_M_1937


title: 8K_M_1941


title: 8K_M_1933


title: 8K_M_1934


title: 8K_M_1935


title: 8K_M_1936


title: 8K_M_1932


title: 8K_M_1943


title: 8K_M_1925


title: 8K_M_1927


title: 8K_M_1930


title: 8K_M_1928


title: 8K_M_1931


title: 8K_M_1924


title: 8K_M_1929


title: 8K_M_1926


title: 8K_M_1920


title: 8K_M_1918


title: 8K_M_1919


title: 8K_M_1921


title: 8K_M_1923


title: 8K_M_1915


title: 8K_M_1912


title: 8K_M_1913


title: 8K_M_1911


title: 8K_M_1909


title: 8K_M_1916


title: 8K_M_1908


title: 8K_M_1907


title: 8K_M_1904


title: 8K_M_1902


title: 8K_M_1901


title: 8K_M_1917


title: 8K_M_1900


title: 8K_M_1898


title: 8K_M_1899


title: 8K_M_1897


title: 8K_M_1891


title: 8K_M_1894


title: 8K_M_1895


title: 8K_M_1896


title: 8K_M_1893


title: 8K_M_1890


title: 8K_M_1889


title: 8K_M_1887


title: 8K_M_1888


title: 8K_M_1886


title: 8K_M_1884


title: 8K_M_1906


title: 8K_M_1905


title: 8K_M_1882


title: 8K_M_1903


title: 8K_M_1880


title: 8K_M_1878


title: 8K_M_1885


title: 8K_M_1881


title: 8K_M_1877


title: 8K_M_1876


title: 8K_M_1875


title: 8K_M_1874


title: 8K_M_1873


title: 8K_M_1871


title: 8K_M_1883


title: 8K_M_1872


title: 8K_M_1867


title: 8K_M_1868


title: 8K_M_1866


title: 8K_M_1869


title: 8K_M_1870


title: 8K_M_1879


title: 8K_M_1863


title: 8K_M_1865


title: 8K_M_1862


title: 8K_M_1861


title: 8K_M_1859


title: 8K_M_1855


title: 8K_M_1857


title: 8K_M_1864


title: 8K_M_1858


title: 8K_M_1856


title: 8K_M_1854


title: 8K_M_1853


title: 8K_M_1850


title: 8K_M_1851


title: 8K_M_1849


title: 8K_M_1852


title: 8K_M_1846


title: 8K_M_1842


title: 8K_M_1847


title: 8K_M_1844


title: 8K_M_1838


title: 8K_M_1843


title: 8K_M_1840


title: 8K_M_1860


title: 8K_M_1845


title: 8K_M_1839


title: 8K_M_1841


title: 8K_M_1834


title: 8K_M_1837


title: 8K_M_1836


title: 8K_M_1835


title: 8K_M_1827


title: 8K_M_1828


title: 8K_M_1826


title: 8K_M_1829


title: 8K_M_1832


title: 8K_M_1825


title: 8K_M_1824


title: 8K_M_1823


title: 8K_M_1822


title: 8K_M_1821


title: 8K_M_1820


title: 8K_M_1819


title: 8K_M_1815


title: 8K_M_1818


title: 8K_M_1833


title: 8K_M_1830


title: 8K_M_1814


title: 8K_M_1812


title: 8K_M_1816


title: 8K_M_1811


title: 8K_M_1922


title: 8K_M_1813


title: 8K_M_1808


title: 8K_M_1810


title: 8K_M_1809


title: 8K_M_1807


title: 8K_M_1806


title: 8K_M_1804


title: 8K_M_1801


title: 8K_M_1805


title: 8K_M_1802


title: 8K_M_1800


title: 8K_M_1799


title: 8K_M_1798


title: 8K_M_1797


title: 8K_M_1796


title: 8K_M_1794


title: 8K_M_1795


title: 8K_M_1817


title: 8K_M_1793


title: 8K_M_1790


title: 8K_M_1791


title: 8K_M_1789


title: 8K_M_1787


title: 8K_M_1788


title: 8K_M_1785


title: 8K_M_1803


title: 8K_M_1786


title: 8K_M_1780


title: 8K_M_1784


title: 8K_M_1781


title: Control3

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

country: China

institute: Shenzhen Institute of Science and Technology

library_source: transcriptomic

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Assembly: GCF_000002285.5_Dog10K_Boxer_Tasha
Supplementary files format and content: excel

molecule: total RNA

organism: Canis lupus familiaris

source_name: kidney

growth_protocol: MDCK cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: MDCK cells  were treated with or without antivirals at their EC50 values for 24 h and then collected for bulk RNA sequencing.

tag: tissue

value: kidney

tag: cell line

value: MDCK cell

tag: treatment


title: Control2


title: Coptisine1

value: Coptisine 50 uM, 24 h


title: 8K_M_1782


title: 8K_M_1783


title: 8K_M_1779


title: Control1


title: Coptisine2


title: 8K_M_1777


title: 8K_M_1776


title: 8K_M_1792


title: Coptisine3


title: 8K_M_1774


title: 8K_M_1773


title: 8K_M_1770


title: Ctrl-20

type: RNA

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 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 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

data_processing: Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

source_name: lung tissue-Control

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Wistar

value: lung tissue

tag: gender

value: male

value: 8  week


title: 8K_M_1768


title: 8K_M_1767


title: Ctrl-18


title: 8K_M_1765


title: 8K_M_1775


title: 8K_M_1766


title: 8K_M_1764


title: 8K_M_1914


title: 8K_M_1763


title: 8K_M_1772


title: 8K_M_1771


title: 8K_M_1760


title: 8K_M_1761


title: 8K_M_1778


title: Ctrl-17


title: 8K_M_1759


title: 8K_M_1758


title: Ctrl-15


title: Ctrl-16


title: 8K_M_1757


title: LPS-3

source_name: lung tissue-LPS


title: LPS-5


title: LPS-7


title: LPS-1


title: 8K_M_1769


title: 8K_M_1762


title: LPS-6


title: 8K_M_1756


title: Uninfected control, 24 hr

city: Aurora

first: Reid

middle: V

last: Wilkening

state: CO

department: Department of Pediatrics, Section of Critical Care Medicine

institute: University of Colorado

description:
NZ bacteria 5hr results.csv
NZ bacteria 24 hr results.csv

data_processing:
CLC Genomics Workbench V 20.0.4 was used to import and trim data. Read were sequentially aligned to first the M musculus genome, than the S pyogenes NZ131 genome.
Uniquely mapped mouse or bacterial transcripts were normalized and used for differential gene expression analysis using R (v4.2.2), Rstudio (v2022.12.0+353, RRID: SCR_000432), and DESeq2 (v1.36.0, RRID: SCR_015687)
Differentially expressed genes were filtered based on an absolute log2 fold change cutoff and Benjamini-Hochberg False Discovery Rate (FDR) cutoff.
Assembly: mm10, NC_011375.1
Supplementary files format and content: CSV files including raw counts for each sample.
Supplementary files format and content: CSV files including processed data for each sample.

source_name: Epithelium

extract_protocol:
Skin was excised at indicated time point after euthanizing mice. Bead beating was used to lyse both murine and bacterial cells and RNA was extracted using the Qiagen RNAeasy kit. To obtain sufficient bacterial RNA, each sample represents 5 mice treated as technical replicates.
Ribozero RNA depletion followed by Illumina stranded library preparation.

value: Epithelium

value: Uninfected epithelium


title: usp7 knockdown FGSCs control rep3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: difgene_1vs2_counts.xls, difgene_3vs4_counts.xls: Excel files include abundance measurements.

source_name: FGSC

extract_protocol:
FGSCs were extracted RNA using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: genotype/variation

value: control

tag: cell type

value: Female germline stem cells (FGSCs)


title: usp7 knockdown FGSCs control rep1


title: 8K_M_1755


title: usp7 knockdown FGSCs rep2

value: usp7 knockdown


title: usp7 knockdown FGSCs control rep2


title: 8K_M_1754


title: 8K_M_1752


title: usp7 knockdown FGSCs rep1


title: usp7 overexpression FGSCs control rep3


title: 8K_M_1750


title: 8K_M_1751


title: 8K_M_1748


title: usp7 knockdown FGSCs rep3


title: 8K_M_1747


title: 8K_M_1746


title: Uninfected control, 5 hr


title: usp7 overexpression FGSCs control rep1


title: usp7 overexpression FGSCs rep3

value: usp7 overexpression


title: usp7 overexpression FGSCs rep2


title: 8K_M_1745


title: 8K_M_1743


title: 8K_M_1753


title: usp7 overexpression FGSCs rep1


title: 8K_M_1742


title: 8K_M_1744


title: 8K_M_1749


title: NZ131 Input 3

organism: Streptococcus pyogenes NZ131

source_name: Planktonic culture

value: Planktonic culture


title: 8K_M_1741


title: NZ131 Input 2


title: NZ131 Input 1


title: 8K_M_1740


title: 8K_M_1738


title: Si-CircRREB1_1

city: Hangzhou

first: shuying

last: shen

state: Zhejiang

address: 3 East Qingchun Road

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances
Essentially, differential expression analysis was performed using the DESeq2/DEGseq[6]/edgeR/Limm/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Homo sapiens

source_name: articular sample

extract_protocol:
Total RNA was extracted from the cell using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara)
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA

value: articular sample

value: chondrocyte

value: Primary generation chondrocyte

tag: genotype

value: wild type

value: CircRREB1 SiRNA transfection


title: Si-NC_3 (CircRREB1 control)

value: Negetive SiRNA transfection


title: Si-CircRREB1_3


title: 8K_M_1736


title: Si-NC_2 (CircRREB1 control)


title: 8K_M_1739


title: 8K_M_1735


title: 8K_M_1737


title: Si-NC_1 (CircRREB1 control)


title: 8K_M_1734


title: Cell-only hepatic [N_MH]

city: Chuncheon-si

first: Kim

last: Wijin

address: Kangwondaehak-gil

country: South Korea

institute: kangwon national university

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform.
Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Homo sapiens (GRCh38) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw read count and Normalized values for each Sample

source_name: iPSC

growth_protocol: The spheroids were cultured in a TeSR–E8™ medium supplemented with 10 nM ROCK I for 2 days.

extract_protocol:
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).
The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

treatment_protocol: After 2 days, the TeSR–E8™ medium was replaced with RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 100 ng/mL activin A (R&D Systems, Minneapolis, MN, USA), 2.0% B27 supplement (Thermo Fisher Scientific), and 3 µM CHIR 99021 (Sigma-Aldrich), primocin (InvivoGen, San Diego, CA, USA) for 4 days. Subsequently, RPMI-1640 medium supplemented with 2.0% B27, 20 ng/mL bone morphogenic protein 4 (R&D Systems), 5 ng/mL basic fibroblast growth factor (Pepro Tech, Rocky Hill, NJ, USA), 0.5% DMSO, and primocin was used for 5 days. Then, spheroids were cultured in a hepatocyte culture medium (Lonza, Basel, Switzerland) supplemented with 20 ng/mL oncostatin M (OSM) and hepatocyte growth factor (HGF, Peprotech) for 10 days. All cultures were maintained in a 5% CO2-humidified incubator at 37 °C.

value: CTRL

value: iPSC

value: Hepatic differentiated


title: 8K_M_1733


title: 8K_M_1731


title: Incorporating cell-adhesive nanofibrils [YI_MH]

value: cell-adhesive nanofibrils

value: Hepatic differentiated iPSCs


title: 8K_M_1732


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 H689A/F667I, replicate 2

city: Columbus

first: Julian

last: Aldana

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

data_processing:
CUT&Tag reads were trimmed using TrimGalore v.0.6.5
CUT&Tag reads were aligned to the human genome assembly (GRCh38/hg38) using BWA v0.7.17
Trimmed Mean of M-values (TMM) normalization and reformatting to bigWig were performed using deepTools v3.5.1
Peaks were called using MACS v2.2.7.1 to generate broadPeak files
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicilin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were centrifuged, resuspended in nuclear extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1X EDTA-free protease inhibitor) and incubated for 10 min at 4C. Extracted nucleai were conjugated to activated concanavalin A–coated beads from Epichypher
CUT&Tag libraries were prepared using i5/i7 Nextera index primers and CUTANA High Fidelity 2x PCR Master Mix from EpiCypher. Libraries were amplified using 17 cycles in a Real-Time PCR System. PCR products were purified by adding a 1.3X volume of Ampure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA kit

value: Human embryonic kidney

tag: cut&tag antibody


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 H689A/F667I, replicate 1


title: 8K_M_1729


title: 8K_M_1728


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 Y641F, replicate 1

value: EZH2 Y641F


title: 8K_M_1730


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 A677G, replicate 2

value: EZH2 A677G


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 A677G, replicate 1


title: 8K_M_1727


title: Si-CircRREB1_2


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 Y641F, replicate 2


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 WT, replicate 2

value: WT


title: H3K27me3, CUT_Tag, HEK293T cells, EZH2 WT, replicate 1


title: 8K_M_1725


title: 8K_M_1724


title: ATACSeq, HEK293T cells, EZH2 A677G, replicate 2

data_processing:
ATAC-Seq reads were trimmed using TrimGalore v.0.6.5
ATAC-Seq reads were aligned to the human genome assembly (GRCh38/hg38) using BWA v0.7.17
Reads Per Kilobase per Million mapped reads (RPKM) normalization and reformatting to bigWig were performed using deepTools v3.5.1
Peaks were called using MACS v2.2.7.1 to generate broadPeak files
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak

extract_protocol:
Cells were centrifuged, resuspended in lysisi buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40)  and incubated for 5 min at 4C.Transposition reaction was performed with Tagment DNA Enzyme from Nextera with incubation for 30 min at 37C.
CUT&Tag libraries were prepared using i5/i7 Nextera index primers and NEBNext High-Fidelity PCR Master Mix. Libraries were amplified using 17 cycles in a Real-Time PCR System. PCR products were purified by adding a 1.3X volume of Ampure XP beads from Beckman Coulter.LIbabries were validated using the Agilent High Sensitivity DNA kit


title: ATACSeq, HEK293T cells, EZH2 H689A/F667I, replicate 1


title: ATACSeq, HEK293T cells, EZH2 A677G, replicate 1


title: 8K_M_1723


title: 8K_M_1722


title: 8K_M_1721


title: 8K_M_1720


title: 8K_M_1719


title: 8K_M_1726


title: 8K_M_1717


title: ATACSeq, HEK293T cells, EZH2 Y641F, replicate 1


title: ATACSeq, HEK293T cells, EZH2 Y641F, replicate 2


title: 8K_M_1718


title: ATACSeq, HEK293T cells, EZH2 H689A/F667I, replicate 2


title: ATACSeq, HEK293T cells, EZH2 WT, replicate 1


title: HT-29 cells, shAPC_Rep3

city: Cambridge

first: Sellers

last: Lab

state: MA

address: 415 Main St

institute: Broad Institute

description:
STAR_Gene_TPM.csv
shRNA-NT1vshRNA-APC.limma_star.annot.csv

data_processing:
Sequenced reads were aligned to the UCSC hg38 reference genome assembly
gene counts were quantified using STAR (v2.7.3a)
RNAseq analysis was performed using the VIPER snakemake pipeline.
Differential gene expression testing was performed by LIMMA.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Differential gene expression testing performed by LIMMA.

source_name: Colorectal

growth_protocol: HT29 cells were maintained in McCoy supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: HT29 cells were infected with lentivirus encoded with corresponding ORFs or shRNAs. For ORFs, cells were collceted 2 days after infection. For shRNAs, cells were collected 1 day after 2uM doxycycline induction

value: Colorectal

value: Colon adenocarcinoma

value: APC mutant

value: shRNA-APC


title: HT-29 cells, shAPC_Rep2


title: 8K_M_1716


title: 8K_M_1714


title: 8K_M_1712


title: HT-29 cells, shNT1_Rep3

value: shNT1 ctr


title: HT-29 cells, shAPC_Rep1


title: HT-29 cells, shNT1_Rep2


title: 8K_M_1711


title: HT-29 cells, shNT1_Rep1


title: HT-29 cells, CTNNB1_Rep3

description:
STAR_Gene_TPM.csv
CTNNB1vGFP.limma_star.annot.csv

value: CTNNB1 overexpression


title: HT-29 cells, CTNNB1_Rep2


title: ATACSeq, HEK293T cells, EZH2 WT, replicate 2


title: 8K_M_1710


title: 8K_M_1715


title: 8K_M_1708


title: 8K_M_1709


title: HT-29 cells, GFP_Rep3

value: GFP overexpression


title: 8K_M_1707


title: 8K_M_1706


title: 8K_M_1713


title: 8K_M_1704


title: 8K_M_1703


title: HT-29 cells, GFP_Rep2


title: 8K_M_1705


title: 8K_M_1702


title: MDA-MB-231-Glucose_2

city: Wuhan

first: Li

last: Mei-Xin

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

institute: Wuhan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MDA-MB-231 cells were treated with glucose-glutamine-deficient medium(starvation) or supplemented with inosine(16.67mM)  or glucose(16.67mM) for 12h.The cell pellets were collected and subjected to RNA-seq.

value: breast cancer epithelial cell

value: Starvation treatment supplement with glucose

tag: time


title: MDA-MB-231-Glucose_1


title: 8K_M_1701


title: HT-29 cells, CTNNB1_Rep1


title: MDA-MB-231-Inosine_3

value: Starvation treatment supplement with inosine


title: 8K_M_1699


title: MDA-MB-231-Glucose_3


title: MDA-MB-231-Inosine_2


title: 8K_M_1700


title: MDA-MB-231-Inosine_1


title: 8K_M_1696


title: MDA-MB-231-G-Q_1

value: Starvation treatment


title: 8K_M_1698


title: MDA-MB-231-G-Q_2


title: 8K_M_1694


title: 8K_M_1695


title: Sample_3_T-cells, CD38-/CD39+

first: Ann

last: Strange

address: 12801 E. 17th Ave, 8th floor

department: Division of Medical Oncology

institute: CU Anschutz

data_processing:
FastQC was used to determine the quality of the reads, presence of contaminating adapter sequences and other quality control metrics. Low quality reads (Phred score < 20), reads < 20bp in length, and contaminating adapter sequences were removed with TrimGalore
Resulting reads were then aligned to the human genome (GRCH38, release 84) with HISAT2
Mapped reads were sorted and indexed with SAMtools
Counts aggregated with FeatureCounts with options: -p and -s 0
Differential gene expression analysis was conducted with DESeq2. Genes with a count < 50 were removed. Next, the CD38+CD39+ samples were contrasted against the other three populations in DESeq2 accounting for the paired nature of the data with: “design = ~patient + population”. Differentially expressed genes (DEGs) were considered as those with a log2FC of > |1| and an adjusted p-value of < 0.01.
Assembly: GRCH38, release 84

source_name: melanoma tumor

extract_protocol:
CD4+ cells were flow sorted into CD4+ CD127-GARP-CD38-CD39-, CD4+ CD127-GARP-CD38+CD39-, CD4+ CD127-GARP-CD38-CD39+, or CD4+ CD127-GARP-CD38+CD39+. Total RNA was isolated from the sorted cells with either a Qiagen RNAEasy Plus Micro kit or a Qiagen RNAEasy Mini kit.
RNA integrity numbers (RIN) for each sample were determined for each sample with an Agilent 2100 Bioanalyzer. Only samples with a RIN ≥ 8.0 were used to prepare cDNA libraries with a CloneTech SMARTer HT kit. Sequencing was performed by the NYU Langone’s Genome Technology Center (RRID: SCR_017929) on an Illumina NovaSeq 6000, generating approximately 50 million 100bp paired reads per sample.

value: melanoma tumor

value: T cells

tag: patient id

value: Pre-treatment

value: immune checkpoint inhibitor


title: HT-29 cells, GFP_Rep1


title: Sample_3_T-cells, CD38+/CD39-


title: 8K_M_1692


title: 8K_M_1691


title: Sample_2_T-cells, CD38+/CD39+


title: Sample_3_T-cells, CD38+/CD39+


title: Sample_3_T-cells, CD38-/CD39-


title: 8K_M_1697


title: Sample_2_T-cells, CD38+/CD39-


title: MDA-MB-231-G-Q_3


title: 8K_M_1689


title: 8K_M_1687


title: Sample_2_T-cells, CD38-/CD39+


title: 8K_M_1688


title: Sample_2_T-cells, CD38-/CD39-


title: Sample_1_T-cells, CD38-/CD39+


title: Sample_1_T-cells, CD38+/CD39+


title: 8K_M_1690


title: Sample_1_T-cells, CD38+/CD39-


title: 8K_M_1686


title: 8K_M_1685


title: 8K_M_1684


title: Sample_1_T-cells, CD38-/CD39-


title: HeLa S3, KO+WT, input

first: Yueyu

last: Kong

state: Hubei

address: Wuhan University

data_processing:
Sequencing adapters were trimmed by Trim galore (v0.6.7)
The chimeric H.sapiens-Drosophila genome (GRCh38- GCF_000001215.4) was generated by STAR (v2.7.10a)
The clean reads were mapped to chimeric genome using STAR
Peaks were called by Macs2 (v2.1.1)
assembly: hg38
narrowPeak files (except for Input sample)

source_name: Human cervical carcinoma

growth_protocol: Human cervical carcinoma cell (HeLa S3) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the sonication was performed using a Bioruptor (Minichiller 300, Diagenode) with 30 cycles (30 s on, 30 s off).
ChIP-seq libraries were generated using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607, Vazyme)

value: Human cervical carcinoma

value: HeLa S3

value: Human cervical carcinoma cell

value: knockout G9a transfect WT G9a


title: HeLa S3, KO+WT,IP-1

value: WT


title: HeLa S3,KO+T1045E, IP-2

value: knockout G9a transfect T1045E G9a


title: 8K_M_1693


title: HeLa S3, KO+WT,IP-2


title: HeLa S3,KO+T1045E, input


title: HeLa S3,KO+T1045E, IP-1


title: 8K_M_1683


title: HeLa S3, KO G9a, IP-1

value: KO G9a

value: knockout G9a


title: HeLa S3, KO G9a, input


title: HeLa S3, KO G9a, IP-2


title: 8K_M_1681


title: 8K_M_1680


title: 8K_M_1677


title: 8K_M_1678


title: HeLa S3, KO+WT,rep2

data_processing:
The raw reads were removed adapters by Trim galore (v0.6.7)
The clean reads were mapped to the hg38 using Bowtie2 (v2.3.5.1).
The bam files should be sorted by SAMtools (v1.3.1), and PCR replication removed by Sambamba (v0.8.1).
Reads mapped to the chrM and low quality reads(samtools view -q 30) were dicarded. Narrow peaks were called by Macs2 (v2.1.1) using the parameter (–nomodel –shift -100 –extsize 200).
assembly: hg38
narrowPeak files

extract_protocol:
Cells were lysed with ATAC lysis buffer (10 mM Tris·Cl(pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) NP-40 ) on the ice for 10 minutes. The lysate was centrifuged at 500g for 5 min at 4℃. Nuclei was resuspended in 35 μl ddH20.
ATAC libraries were prepared using Hieff NGS Fast Tagment DNA Library Prep Kit for Illumina Cat. 12207, Yeasen


title: HeLa S3, KO+WT,rep1


title: HeLa S3,KO+T1045E, rep2


title: 8K_M_1679


title: 8K_M_1676


title: 8K_M_1674


title: 8K_M_1672


title: 8K_M_1671


title: 8K_M_1682


title: 8K_M_1670


title: HeLa S3,KO+T1045E, rep1


title: HeLa S3, KO G9a, rep2


title: HeLa S3, KO G9a, rep1


title: 8K_M_1669


title: 8K_M_1668


title: HEK293T, WT, rep2

data_processing:
Libraries passing quality control was trimmed by Trim galore (v0.6.7)
Trimmed reads were mapped to the human genome hg38 using Hisat2 (v7.5.0).
The reads counting was used featureCounts(v2.0.1).
assembly: hg38
txt file include counts in each gene

source_name: Human Embryonic Kidney

growth_protocol: Human Embryonic Kidney 293T were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNA isolater Total RNA Extraction Reagent (Vazyme,R401-01). 1ug total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 (ABclonal，Cat. RK20306) following manufacturer's protocols.

treatment_protocol: 293T cells were transfected with the plasmid(vector, T1045E G9a and WT G9a)

value: Human Embryonic Kidney

value: HEK 293T

value: Human Embryonic Kidney 293T

value: transfect WT G9a


title: 8K_M_1667


title: 8K_M_1675


title: HEK293T, WT, rep1


title: 8K_M_1673


title: 8K_M_1665


title: HEK293T, T1045E, rep2

value: transfect T1045E G9a


title: HEK293T, T1045E, rep1


title: HEK293T, vector, rep2

value: vector

value: transfect empty vector


title: usp7 overexpression FGSCs control rep2

value: control

value: Female germline stem cells (FGSCs)


title: 8K_M_1661


title: DMRT1 Cut-And-Run d8 DAZL+ PGCLC replicate 1

first: SUN MIN

last: LEE

state: Cambridgeshire

address: Gurdon Institute, Tennis Court Road

country: United Kingdom

institute: Gurdon Institute

description: DMRT1 CUT&RUN in d8 DZ+PGCLC

data_processing:
Cut-And-Run : leeHom package (with ---ancientdna option) were used to trim adaptor sequences and short fragments. The trimmed reads were aligned to the human reference genome (GENCODE, GRCh38.p13) using Bowtie2 2.2.5.
bigWig files were generated using MACS2 --bdg
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: DMRT1_CR_peaks_in_d8_DZ+PGCLCs.xlsx
Library strategy: Cut&Run

extract_protocol:
DZ+PGCLCs cells were bound to activated 10ul Concanavalin A -coated magnetic beads and incubated with DMRT1 antibody (Abcam, ab126741) or rabbit IgG(Cell Signaling, #2729) in Wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and protease inhibitor) containing 0.1% Digitonin for 2hr at 4°C. After two washes, beads were incubated with Protein A/G-MNase fusion protein at 70 ng/mL in Digitonin-wash buffer for 1 hr at 4°C. After two washes, MNase activity was induced by addition of 3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.1% Digitonin and stopped by addition of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4mM EGTA, 0.1% Digitonin, RNAse A 100 ul/mL, Glycogen 50 ug/mL). Beads were incubated at 37°C for 30 min, supernatants were removed to a fresh tube and incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. DNA was extracted with phenol-chloroform extraction.
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) for Illumina with KAPA HiFi™ Real-Time PCR Library Amplification Kit (Roche, KK2702)

value: Primordial germ cell-like cells

tag: chip antibody

value: DMRT1 antibody (Abcam, ab126741)


title: 8K_M_1664


title: HEK293T, vector, rep1


title: IgG Cut-And-Run d8 DAZL+ PGCLC

description: IgG CUT&RUN in d8 DZ+PGCLC

value: rabbit IgG (Cell Signaling, #2729)


title: 8K_M_1663


title: 8K_M_1660


title: 8K_M_1666


title: 8K_M_1658


title: DMRT1 Cut-And-Run d8 DAZL+ PGCLC replicate 2

description: DMRT1 CUT&RUN in d8 DZ+PGCLC


title: 8K_M_1659


title: CAPS_d8DZPGCLC_2

description: CAPS

data_processing:
Trim Galore was used to remove the low-quality reads and Samtools rmdup function was used to remove PCR duplicates. Trimmed reads were mapped to a genome and modified bases were called by asTair ( https://bitbucket.org/bsblabludwig/astair/src/master/). CpG methylation levels of bigWig files  were calculated considering only information from CpGs with >5X coverage.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: Differentially_methylated_regions.xlsx

extract_protocol:
Genomic DNA was purified using Quick-DNA mini prep kit (ZYMO research). DNA was spiked with spike-in control DNA and sonicated to 300-500 bp, before ligated with NEBNext Adaptor for Illumina using KAPA HyperPrep Kit according to the manufacturer’s protocol.
The uracil in the loop of NEBNext Adaptor was removed by USER Enzyme (New England Biolabs). 100 ng ligated DNA was used for both TAPSβ and CAPS. For TAPSβ, the ligated library was subjected to βGT (Thermo Fisher) blocking, two rounds of mTet1 oxidation, and borane reduction. For CAPS, the ligated library was subjected to chemical oxidation and borane reduction. Converted DNA from TAPSβ and CAPS was amplified with NEBNext Multiplex Oligos for Illumina and KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit for 4 cycles according to the manufacturer’s protocol. The PCR product was purified with Ampure XP beads and quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher) according to the manufacturer’s protocol. Libraries were sequenced for 150 cycles in paired-end mode on the NovaSeq platform.


title: CAPS_N3PGCLC_2

description: CAPS


title: 8K_M_1655

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-seq2

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: CAPS_d8DZPGCLC_1

description: CAPS


title: 8K_M_1654


title: 8K_M_1657


title: CAPS_4iESC_1

description: CAPS

value: embroynic stem cells


title: 8K_M_1653


title: 8K_M_1662


title: 8K_M_1656


title: 8K_M_1652


title: CAPS_N3PGCLC_1

description: CAPS


title: 8K_M_1651


title: TAPSbeta_d8DZPGCLC_2

description: TAPSbeta


title: 8K_M_1650


title: 8K_M_1649


title: TAPSbeta_N3PGCLC_2

description: TAPSbeta


title: TAPSbeta_N3PGCLC_1

description: TAPSbeta


title: 8K_M_1648


title: TAPSbeta_d8DZPGCLC_1

description: TAPSbeta


title: TAPSbeta_4iESC_1

description: TAPSbeta


title: TAPSbeta_4iESC_2

description: TAPSbeta


title: 10xscRNAseq_d8 DAZL+PGCLC

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The reads were demultiplexed and aligned to the 10X Genomics’ GRCh38-2020-A reference genomes using the Cell Ranger Software (v.7.0.0, 10X Genomics) using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: DEGs_from_scRNA-seq.xlsx

source_name: Primordial germ cell-like cells

extract_protocol:
Reporter or cell surface marker positive cells were sorted by FACS.
Cells loading and library preparation were carried out according to the manufacturer’s protocol for the  Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index). Libraries were sequenced using the sequencing format: read 1, 28 cycles; i7 index, 10 cycles; i5 index, 10 cycles; read 2, 90 cycles on Novaseq 6000 system.

value: d8 DAZL+PGCLC


title: 8K_M_1645


title: 8K_M_1647


title: 8K_M_1646


title: 8K_M_1644


title: 10xscRNAseq_DMRT1+PGCLC

description: 10x Genomics


title: 10xscRNAseq_NANOS3+PGCLC

description: 10x Genomics


title: 10xscRNAseq_4i ESC

description: 10x Genomics

source_name: embroynic stem cells

value: 4i ESC


title: 8K_M_1643


title: 8K_M_1641


title: 8K_M_1640


title: 8K_M_1638


title: 8K_M_1639


title: snRNA, Control donor C4, Motor cortex

city: New York

first: Stella

last: Dracheva

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School Of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
snRNA-seq reads were mapped to the human GRCh38 genome using 10x Genomics Cell Ranger (v3.0.2).
CellBender (v0.2.0) was used to distinguish cell-containing from cell-free droplets and retrieve noise-free cell-by-gene quantification tables.
Scublet (v0.2.3) was used to compute the doublet score for each nucleus. Nuclei with fewer than 500 detected genes, more than 1% reads that mapped to the mitochondrial genome, or a doubtlet score greater than 0.2 were excluded from further analysis.
Seurat (v4.0.4) was used to perform Sctransform normalization, Principal component analysis (PCA), Harmony integration, Leiden clustering, and UMAP (Uniform Manifold Approximation and Projection) visualization.
Clusters were annotated using the expression of selected marked genes. See Suppl. Methods in the paper for details.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files that include unfiltered barcodes from Cell Ranger for each sample.
Supplementary files format and content: Tab-delimited text files that include unfiltered features (genes) from Cell Ranger for each sample.
Supplementary files format and content: Raw (unfiltered) sparse matrices with genes on the rows and cells on the columns from Cell Ranger for each sample.
Supplementary files format and content: H5 format files from CellBender that includes filtered cell-by-gene matrices with ambient RNA and non-cell droplets removed for each sample. Not available for sample "snRNA_C9FTD_F2_FrontalCortex" as it failed QC in CellBender.

molecule: nuclear RNA

source_name: motor cortex

extract_protocol:
Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407).
Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3’ system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of  ~10,870 unique molecular identifiers (UMIs) per nucleus.

value: motor cortex

tag: donor id

tag: disease

value: Control

tag: Sex

value: Male


title: snRNA, Control donor C6, Frontal cortex

description: 10x Genomics

source_name: frontal cortex

value: frontal cortex

value: Female


title: snRNA, Control donor C5, Frontal cortex

description: 10x Genomics


title: snRNA, Control donor C6, Motor cortex

description: 10x Genomics


title: snRNA, Control donor C4, Frontal cortex

description: 10x Genomics


title: 8K_M_1637

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: snRNA, Control donor C3, Frontal cortex

description: 10x Genomics


title: snRNA, Control donor C3, Motor cortex

description: 10x Genomics


title: 8K_M_1634

tag: age


title: 8K_M_1633

tag: strain


title: snRNA, Control donor C1, Motor cortex

description: 10x Genomics

tag: tissue


title: 8K_M_1631


title: snRNA, Control donor C2, Motor cortex

description: 10x Genomics


title: 8K_M_1632


title: 8K_M_1629


title: 8K_M_1628


title: snRNA, C9-FTD donor F5, Motor cortex

description: 10x Genomics


title: snRNA, Control donor C2, Frontal cortex

description: 10x Genomics


title: snRNA, C9-FTD donor F4, Motor cortex

description: 10x Genomics


title: 8K_M_1630


title: snRNA, C9-FTD donor F5, Frontal cortex

description: 10x Genomics


title: snRNA, Control donor C1, Frontal cortex

description: 10x Genomics


title: 8K_M_1636


title: 8K_M_1635


title: 8K_M_1626


title: 8K_M_1625


title: snRNA, C9-FTD donor F3, Frontal cortex

description: 10x Genomics


title: snRNA, Control donor C5, Motor cortex

description: 10x Genomics


title: snRNA, C9-FTD donor F3, Motor cortex

description: 10x Genomics


title: snRNA, C9-FTD donor F2, Frontal cortex

description: 10x Genomics


title: 8K_M_1624


title: 8K_M_1622


title: 8K_M_1623


title: snRNA, C9-FTD donor F2, Motor cortex

description: 10x Genomics


title: snRNA, C9-FTD donor F1, Motor cortex

description: 10x Genomics


title: snRNA, C9-FTD donor F4, Frontal cortex

description: 10x Genomics


title: 8K_M_1619


title: 8K_M_1627


title: 8K_M_1618


title: 8K_M_1621


title: 8K_M_1617


title: snRNA, C9-ALS donor A6, Frontal cortex

description: 10x Genomics


title: 8K_M_1614


title: snRNA, C9-ALS donor A4, Frontal cortex

description: 10x Genomics


title: snRNA, C9-ALS donor A4, Motor cortex

description: 10x Genomics


title: snRNA, C9-ALS donor A5, Frontal cortex

description: 10x Genomics


title: 8K_M_1613


title: CAPS_4iESC_2

description: CAPS

tag: cell line


title: snRNA, C9-ALS donor A3, Motor cortex

description: 10x Genomics


title: snRNA, C9-ALS donor A3, Frontal cortex

description: 10x Genomics


title: 8K_M_1611


title: snRNA, C9-ALS donor A2, Motor cortex

description: 10x Genomics


title: 8K_M_1609


title: snRNA, C9-ALS donor A6, Motor cortex

description: 10x Genomics


title: 8K_M_1610


title: 8K_M_1608


title: 8K_M_1620


title: snRNA, C9-ALS donor A1, Motor cortex

description: 10x Genomics


title: snRNA, C9-ALS donor A2, Frontal cortex

description: 10x Genomics


title: snRNA, C9-ALS donor A5, Motor cortex

description: 10x Genomics


title: snATAC, Control donor C6, Motor cortex

description: 10x Genomics

library_source: genomic single cell

data_processing:
snATAC-seq reads were mapped to the human GRCh38 genome using 10x Genomics Cell Ranger ATAC (v1.1.0).
ArchR (v1.0.2) was used in the downstream analysis. Fragment size distribution in each sample was inspected for nucleosomal periodicity, and nuclei with TSS (Transcription Start Site) enrichment score less than 4 and a number of unique fragments less than 1000 were removed.
After doublet inference and removal, a cell-by-tile matrix containing insertion counts across genome-wide 500-bp bins was created. Dimensionality reduction with iterative Latent Semantic Indexing (LSI), Louvain clustering and UMAP visualization were then performed.
Gene activity scores were computed using the model implemented in ArchR, accounting for both the accessibility within the entire gene body and the activity of putative distal regulatory elements.
Clusters were annotated using labels transferred from our snRNA-seq dataset.
Reproducible peaks were called using MACS2 (v2.2.7.1).
Differential chromatin accessibility was accessed with Wilcoxon test in both gene-based levels (with gene activity scores) and peak-based levels.
ChromVAR was used to estimate chromatin accessibility within peaks sharing the same transcription factor (TF) motif while controlling for technical biases. See Suppl. Methods for details.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files from Cell Ranger ATAC that include the coordinates, barcode and number of supported read pairs for each unique fragment captured for each sample.
Supplementary files format and content: Tabix index of the fragment intervals

extract_protocol:
Nuclei were isolated from 50-70 mg frozen brain tissue mostly as described in Velmeshev et al. (Science 2019). For each donor, brain tissues from the motor cortex and frontal cortex were dissected with a scalpel blade. The tissues were then homogenized on ice in 5mL lysis buffer (0.32 M sucrose, 3 mM Mg(Ac)2, 3 mM CaCl2, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton-X, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water), containing 0.4 U/μl freshly added Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A) until no chunks of tissue were visible in the tissue suspension (~20 strokes) using a glass Dounce homogenizer (Thomas Scientific; Cat. # 3431D76; size A). The homogenized tissues were filtered through a 40 μm strainer (Thermofisher; Cat. # 22-363-547) and transferred to a 30 mL thick polycarbonate ultracentrifuge tube (Beckman Coulter; Cat. # 355631). Nine mL of the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0 in DEPC-treated water) were added to the bottom of the tubes with the tissue homogenate, and the tubes were centrifuged at 34,400 RPM (107,164 FCF) for 2.5 hours at 4°C, using a swing bucket rotor (SW28). The supernatant was aspirated, and the nuclear pellet was submerged on ice for 20 min in 250 uL of DEPC-treated water-based PBS, containing 1% BSA and 0.4 U/μL RRI. The nuclear pellet was then resuspended and filtered twice through a 30 μm cell strainer (Miltenyi Pre-separation Filters; Cat. # 130-041-407).
Nuclei were counted using a hemocytometer and diluted to ~2,000 nuclei/μL before performing single-nucleus capture on the 10X Genomics Single-Cell 3’ system. The 10X capture and library preparation protocols were used without modification. Matched control, C9-ALS and C9-FTD samples were loaded on the same 10X chip to minimize potential batch effects. Single-nucleus libraries from individual samples were pooled and sequenced on the NovaSeq 6000 machine with an average depth of  ~8,223 unique fragments nucleusper nucleus.


title: snRNA, C9-ALS donor A1, Frontal cortex

description: 10x Genomics


title: 8K_M_1607


title: 8K_M_1606


title: snATAC, Control donor C5, Motor cortex

description: 10x Genomics


title: 8K_M_1605


title: snATAC, Control donor C5, Frontal cortex

description: 10x Genomics


title: snATAC, Control donor C4, Motor cortex

description: 10x Genomics


title: snATAC, Control donor C4, Frontal cortex

description: 10x Genomics


title: 8K_M_1603


title: 8K_M_1602


title: 8K_M_1612


title: snATAC, Control donor C3, Motor cortex

description: 10x Genomics


title: snATAC, Control donor C3, Frontal cortex

description: 10x Genomics


title: 8K_M_1601


title: 8K_M_1600


title: snATAC, Control donor C2, Motor cortex

description: 10x Genomics


title: Donor_25_OSE230

city: NANTES

first: Isabelle

last: Girault

state: PAYS-DE-LA-LOIRE

address: 22 BOULEVARD BENONI GOULIN

country: France

institute: OSE IMMUNOTHERAPEUTICS

description: RNA extraction

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument.

data_processing: Data from the NanoString nCounter system was standardized to the internal positive controls and housekeeping genes using the recommended settings in the nSolver 4.0 software normalization module (NanoString Technologies). Standardized not log2 transformed data was exported and differential expression analysis was performed using DESEq2 R package  for the R programming language.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: macrophages

growth_protocol: Monocytes were treated in vitro with M-CSF at 50ng/ml (Isokine, 01-A0220) to obtain M(M-CSF) (M2-like) macrophages

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen)

treatment_protocol: After 3 days in culture, macrophages were incubated with 10µg/ml of antiChemR23 or hIgG1

tag: treatment

tag: donor

value: macrophages


title: 8K_M_1599


title: Donor_24_hIgG1

description: RNA extraction

label_protocol: Capture probe-3'biotin, Reporter probe-5' barcode signal


title: 8K_M_1604


title: Donor_26_OSE230

description: RNA extraction


title: snATAC, Control donor C2, Frontal cortex

description: 10x Genomics


title: 8K_M_1598


title: Donor_23_OSE230

description: RNA extraction


title: Donor_23_hIgG1

description: RNA extraction


title: Donor_24_OSE230

description: RNA extraction


title: 8K_M_1597


title: Donor_22_OSE230

description: RNA extraction


title: Donor_21_hIgG1

description: RNA extraction


title: snATAC, Control donor C1, Frontal cortex

description: 10x Genomics


title: 8K_M_1596


title: snATAC, C9-FTD donor F4, Motor cortex

description: 10x Genomics


title: 8K_M_1595


title: 8K_M_1615


title: snATAC, C9-FTD donor F4, Frontal cortex

description: 10x Genomics


title: 8K_M_1594


title: Donor_22_hIgG1

description: RNA extraction


title: snATAC, Control donor C1, Motor cortex

description: 10x Genomics


title: snATAC, C9-FTD donor F3, Motor cortex

description: 10x Genomics


title: snATAC, C9-FTD donor F3, Frontal cortex

description: 10x Genomics


title: 8K_M_1593


title: Donor_21_OSE230

description: RNA extraction


title: KP with LP-diet 2

first: Gian Luca

last: Rampioni Vinciguerra

state: OH

address: 460W 12th Avenue

department: Cancer Biology and Genetics

institute: The Ohio State University

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The analysis of the Clariom™ S Mouse Affymetrix panel (of ~22K genes) was carried out by Transcriptome Analysis Console (TAC) software (v4 - Thermo Fisher Scientific) and consisted of three main steps: 1) data quality control; 2) normalization (signal space transformation robust multiple-array average); 3) differentially expression analysis employing the eBayes method from limma R package included in TAC software.

label: biotin

source_name: KP mouse with low protein diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (GeneChip WT PLUS Reagent Kit, 2013, Affymetrix).

growth_protocol: PDAC were extracted from KPP and GL mice after 60 days from the induction

extract_protocol: RNA was collected and isolated with Trizol and RNA clean-up and concentration kit Norgen. Total RNA was treated with RNase-free DNase I Kit by Norgen, in order to avoid DNA contamination.

value: Pancreatic cancer (PDAC)

value: low protein diet


title: KP with LP-diet 3


title: KP with LP-diet 4


title: 8K_M_1591


title: KP with LP-diet 1


title: KP with LP-diet 5


title: snATAC, C9-FTD donor F2, Frontal cortex

description: 10x Genomics


title: 8K_M_1592


title: KP with C-diet 5

source_name: KP mouse with control diet

value: control diet


title: snATAC, C9-ALS donor A6, Motor cortex

description: 10x Genomics


title: 8K_M_1590


title: snATAC, C9-ALS donor A5, Motor cortex

description: 10x Genomics


title: 8K_M_1589


title: snATAC, C9-ALS donor A5, Frontal cortex

description: 10x Genomics


title: KP with C-diet 2


title: GL with LP-diet 3

source_name: GL mouse with low protein diet


title: snATAC, C9-ALS donor A6, Frontal cortex

description: 10x Genomics


title: KP with C-diet 3


title: GL with LP-diet 2


title: 8K_M_1588


title: GL with LP-diet 5


title: GL with C-diet 4

source_name: GL mouse with control diet


title: KP with C-diet 4


title: KP with C-diet 1


title: GL with C-diet 5


title: GL with LP-diet 4


title: GL with LP-diet 1


title: snATAC, C9-ALS donor A4, Motor cortex

description: 10x Genomics


title: 8K_M_1586


title: snATAC, C9-ALS donor A3, Motor cortex

description: 10x Genomics


title: snATAC, C9-ALS donor A4, Frontal cortex

description: 10x Genomics


title: GL with C-diet 2


title: GL with C-diet 3


title: 8K_M_1585


title: 8K_M_1584


title: 8K_M_1587


title: snATAC, C9-ALS donor A3, Frontal cortex

description: 10x Genomics


title: 8K_M_1582


title: 8K_M_1583


title: GL with C-diet 1


title: snATAC, C9-ALS donor A2, Frontal cortex

description: 10x Genomics


title: snATAC, C9-ALS donor A1, Motor cortex

description: 10x Genomics


title: 8K_M_1581


title: 8K_M_1580


title: snATAC, C9-ALS donor A1, Frontal cortex

description: 10x Genomics


title: 8K_M_1579


title: bulk RNA-seq, Control donor C6, Motor cortex, Other glia

data_processing:
FastQC (v0.11.8) was used to examine the quality of the RNA-seq reads.
Reads were then trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 20) using Trim Galore (v0.5.0) in paired-end mode. The first 3 bp from the 5′ end of read 1 were also removed.
Trimmed reads were then mapped to the human hg38 genome and the GENCODE annotated transcriptome (release V35) with STAR (v2.7.1a). Gene expression was estimated using RSEM (v1.2.30).
Gene-level ‘expected count’ from the RSEM results were rounded and fed into edgeR (v3.34.1) to perform differential expression tests separately for each sorted population in each brain region. Only genes that were expressed (with CPM > 2) in at least six samples were kept.
The read counts of the remaining genes were then normalized using the TMM method, and DEGs were called in the quasi-likelihood F-test mode with a cutoff of FDR < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw counts or TPM (Transcripts per million) values for each sample.

extract_protocol:
The isolation of brain nuclei prior to the flow cytometry separation was performed mostly as previously described in Kozlenkov et al. (Sci Adv. 2018). Tissue (~300 mg) was homogenized in ice-cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton X-100, 1 mM DTT, 1 U/µl Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A), and 10mM Tris-HCl, pH 8.0), underlaid with the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, 0.4 U/µl RRI, and 10 mM Tris-HCl pH 8.0), and centrifuged for 1h at 24,000 rpm. The nuclear pellets were then resuspended in the antibody-incubation buffer (0.5% BSA, 3mM MgCl2, 1 U/µl RRI, and 10 mM Tris-HCl, pH 8.0) and incubated with antibodies against NeuN and SOX10 for 1 hr at 4°C. Fluorescence-activated nuclei sorting (FANS) was then used to isolate neurons (NeuN+SOX10- population), oligodendrocyte lineage cells (NeuN-SOX10+ population), consisting of mature oligodendrocytes and a smaller population of OPCs, and a third population (NeuN-SOX10-; hereafter “other glia”) that mostly consisted of astrocytes and microglia. Alexa488-conjugated anti-NeuN antibodies (1:1000 dilution, Millipore, Cat. # MAB377x) and anti-SOX10 antibodies (R&D Systems, Cat. # AF2864) that were custom conjugated to Alexa647 (1:150 dilution, Cat# FCMAB317PE, Millipore) were used. DNA stain DAPI was used to label intact nuclei. From each sample, 250-300K nuclei of neurons, 250-300K of oligodendrocytes, and 150-200K nuclei of other glia were collected. Nuclei were collected directly to the lysis buffer from PicoPure RNA Isolation Kit (ThermoFisher Scientific, Cat. # KIT024), which was then used for RNA isolation.
RNA-seq libraries were prepared with the SMARTer Stranded Total RNA-seq Kit, Pico-Input v2 (Takara, Cat. # 634414) from 10ng of the RNA. Libraries were sequenced on a NovaSeq 6000 instrument (Illumina), using paired-end 100 cycles protocol to an average of 120 million read pairs per sample.

value: other glia (NeuN-SOX10-)


title: snATAC, C9-ALS donor A2, Motor cortex

description: 10x Genomics


title: Leptin overexpression ovary, diestrus, 2

city: Jinan

first: Rusong

last: Zhao

state: Shandong

address: 44 Wenhua xi Road

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Data preprocessing and follow-up analysis were performed DESeq2 software. The lists of DEGs between WT and leptin pigs cases were generated using the edgeR package (version 3.32.0) (Robinson et al., 2010). To normalize the raw data, the genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes between the leptin and WT groups.
Assembly: Ensembl_release103
Supplementary files format and content: excel file includes raw counts and FPKM values for each Sample

organism: Sus scrofa

source_name: Ovary

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Ovary

value: Leptin overexpression


title: 8K_M_1578

first: Joseph

last: Ecker


title: GnT-IX-deficient_cuprizone 12 weeks, biological rep 1

city: Fukushima City

first: Shinobu

last: Kitazume

state: Fukushima

address: 1 Hikariga-oka

country: Japan

institute: Fukushima Medical University

hyb_protocol: Fragmentated and labeled cDNA was hybridized on Clariom S Mouse Array according to GeneChip 3' IVT Pico Kit (Thermo Fisher Scientific) guide.

scan_protocol: GeneChips were scanned using the GneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The data were analyzed with Affymetrix GeneChip Command Console (AGCC) Ver 4.1 and Expression Console 1.4 with the RMA procedure.

source_name: white matter astrocytes, GnT-IX-deficient mouse fed cuprizone for 12 weeks

label_protocol: Double-stranded cDNA prepared from total RNA was labeled using Affymetrix GeneChip 3' IVT Pico Kit (Thermo Fisher Scientific) according to the manufacture's instructions.

growth_protocol: At 8–12 weeks of age, wild-type and GnT-IX-deficient mice were fed a powdered diet containing 0.2% (w/w) cuprizone (Sigma) for 0, 3, or 12 weeks. White matter was isolated from mouse brain and dissociated using a Papain Dissociation System (Worthington Biochemical Corporation). Neural cells, suspended in Hank’s balanced salt solution (Thermo Fisher Scientific) containing 0.5% BSA (Sigma), 0.8 mM kynurenic acid (Sigma), 0.05 mM DL-2-Amino-5-phosphonopentanoic acid (Tocris Bioscience), and 10% trehalose (Sigma), were incubated with FcR Blocking Regent (Miltenyi Biotec) to prevent contamination by Fc receptor-expressing cells, such as microglia. Astrocytes were then isolated using anti-GLAST microbeads (Miltenyi Biotec).

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen) or NucleoSpin RNA XS (Takara).

value: GnT-IX-deficient

tag: cuprizone administration term

value: 12 weeks

value: white matter astrocytes


title: wild-type_cuprizone 12 weeks, biological rep 2

source_name: white matter astrocytes, wild-type mouse fed cuprizone for 12 weeks

value: wild-type


title: wild-type_cuprizone 3 weeks, biological rep 1

source_name: white matter astrocytes, wild-type mouse fed cuprizone for 3 weeks

value: 3 weeks


title: wild-type_cuprizone 12 weeks, biological rep 1


title: wild-type_cuprizone 0 weeks, biological rep 3

source_name: white matter astrocytes, wild-type mouse fed cuprizone for 0 weeks

value: 0 weeks


title: wild-type_cuprizone 3 weeks, biological rep 2


title: HFL1 cells, H2O2-control, biol rep1

city: Zografou

first: Dionysia

last: Skea

address: Zografou Campus, 9, Iroon Polytechniou str

country: Greece

institute: NTUA

data_processing:
To trimming and map the reads to the GRCh38 human reference genome, we used Bbduk and STAR, respectively
raw bam files were summarized to a 3’UTR read counts table, using the Bioconductor package Genomic Ranges
The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package EDASeq after removing genes that had zero counts over all samples
Assembly: GRCh38
Supplementary files format and content: normalized_counts_table which contains a table with the normalized read counts for each sample

growth_protocol: BJ and HFL1 fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Trizol protocol following manufacturer's instructions was used for total RNA isolation. 500ng were used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library prep Kit following manufacturer's protocols.

treatment_protocol: Proteasome inhibition-induced premature senescence was induced in HFL1 and BJ cells following treatment with bortezomib for 9 and 10 days, respectively. Stress-induced premature senescence was induced following treatment with subcytotoxic doses of H2O2, followed by 72 hours recovery of cells in complete culture media.

tag: cell type

value: Normal Lung fibroblasts

value: WT

value: hydrogen peroxide


title: HFL1 cells, H2O2-control, biol rep3

tag: genotype


title: HFL1 cells, H2O2-treated, biol rep2


title: HFL1 cells, H2O2-treated, biol rep3


title: HFL1 cells, H2O2-treated, biol rep1


title: GnT-IX-deficient_cuprizone 12 weeks, biological rep 2


title: GnT-IX-deficient_cuprizone 12 weeks, biological rep 3


title: wild-type_cuprizone 0 weeks, biological rep 1


title: HFL1 cells, H2O2-control, biol rep2


title: wild-type_cuprizone 12 weeks, biological rep 3


title: bulk RNA-seq, Control donor C6, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Control

value: Female


title: wild-type_cuprizone 3 weeks, biological rep 3


title: wild-type_cuprizone 0 weeks, biological rep 2


title: 8K_M_1577

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: HFL1 cells, Bortezomib-control, biol rep3

value: bortezomib


title: bulk RNA-seq, Control donor C6, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)


title: WT ovary, diestrus, 2

value: Ovary


title: HFL1 cells, Bortezomib-control, biol rep2


title: bulk RNA-seq, Control donor C6, Frontal cortex, Other glia

value: frontal cortex

value: other glia (NeuN-SOX10-)


title: snRNA, C9-FTD donor F1, Frontal cortex

description: 10x Genomics


title: 8K_M_1575


title: HFL1 cells, Bortezomib-control, biol rep1


title: HFL1 cells, Bortezomib-treated, biol rep3


title: bulk RNA-seq, Control donor C6, Frontal cortex, Oligodendrocyte lineage cells


title: bulk RNA-seq, Control donor C6, Frontal cortex, Neurons


title: 8K_M_1573


title: 8K_M_1574


title: Leptin overexpression ovary, diestrus, 1

value: Leptin overexpression


title: Ngn2 Day6 VenusNeg Rep1 RNAseq

city: Vienna

first: Gintautas

last: Vainorius

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

data_processing:
Reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
Read mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c
Reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Differential expression analysis and variance stabilized transformation for PCA analysis was performed using R package Deseq2
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files with RPM normalized values

source_name: mESC

growth_protocol: mESC grown in Serum-LIF; Differentiation is done in Neurobasal, DMEM-F12, N2 supplement, B27 supplement, L-Glutamate, Na-Pyruvate, Penicilin-Streptomycin, Non-essential amino acids, 20 µg/ml Insulin. Cells were grown at 37 ºC, 5% CO2.

extract_protocol:
Cells were washed with PBS, trypsinized and FACS sorted where indicated. Cells then were processed using the Qiagen RNeasy mini kit. RNA was additionally treated with TURBO DNA-free™ kit (Invitrogen) according to the manufacturer’s protocols. Integrity of RNA was measured using Fragment Analyzer™.
RNAseq-Libraries were prepared using QuantSeq 3` mRNA-Seq Library Prep Kit (Lexogen GmbH).

treatment_protocol: 1 µg/ml Doxyciclin.

value: mESC

value: Ngn2 overexpression for 6 day, Venus negative


title: HFL1 cells, Bortezomib-treated, biol rep2


title: bulk RNA-seq, Control donor C5, Motor cortex, Oligodendrocyte lineage cells


title: 8K_M_1572


title: Ngn2 Day6 VenusPos Rep2 RNAseq

value: Ngn2 overexpression for 6 day, Venus positive


title: bulk RNA-seq, Control donor C5, Motor cortex, Other glia


title: Ngn2 Day6 VenusPos Rep1 RNAseq


title: 8K_M_1571


title: bulk RNA-seq, Control donor C5, Motor cortex, Neurons


title: Ngn2 Day4 VenusNeg Rep2 RNAseq

value: Ngn2 overexpression for 4 day, Venus negative


title: HFL1 cells, Bortezomib-treated, biol rep1

value: Normal Lung fibroblasts


title: BJ cells, H2O2-control, biol rep3

source_name: BJ

value: BJ

value: Normal skin fibroblasts

value: WT


title: 8K_M_1570


title: bulk RNA-seq, Control donor C5, Frontal cortex, Other glia


title: 8K_M_1576


title: BJ cells, H2O2-control, biol rep2

value: hydrogen peroxide


title: Ngn2 Day4 VenusNeg Rep1 RNAseq


title: 8K_M_1569


title: BJ cells, H2O2-control, biol rep1


title: WT ovary, diestrus, 1


title: Ngn2 Day6 VenusNeg Rep2 RNAseq


title: Ngn2 Day4 VenusPos Rep2 RNAseq

value: Ngn2 overexpression for 4 day, Venus positive


title: 8K_M_1568


title: bulk RNA-seq, Control donor C5, Frontal cortex, Neurons

value: Control

value: Female


title: BJ cells, H2O2-treated, biol rep3


title: BJ cells, H2O2-treated, biol rep2


title: bulk RNA-seq, Control donor C4, Motor cortex, Other glia

value: motor cortex

value: Male


title: BJ cells, Bortezomib-control, biol rep3

value: bortezomib


title: Ngn2 Day3 VenusNeg Rep1 RNAseq

value: Ngn2 overexpression for 3 day, Venus negative


title: Ngn2 Day3 VenusPos Rep2 RNAseq

value: Ngn2 overexpression for 3 day, Venus positive


title: 8K_M_1566


title: 8K_M_1564


title: bulk RNA-seq, Control donor C4, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: 8K_M_1567


title: Ngn2 Day4 VenusPos Rep1 RNAseq

value: mESC


title: BJ cells, Bortezomib-control, biol rep2


title: bulk RNA-seq, Control donor C4, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)


title: Ngn2 Day3 VenusPos Rep1 RNAseq


title: BJ cells, H2O2-treated, biol rep1


title: 8K_M_1565


title: bulk RNA-seq, Control donor C5, Frontal cortex, Oligodendrocyte lineage cells

value: frontal cortex


title: bulk RNA-seq, Control donor C4, Frontal cortex, Oligodendrocyte lineage cells


title: BJ cells, Bortezomib-control, biol rep1


title: Ngn2 Day2 Rep2 RNAseq

value: Ngn2 overexpression for 2 day


title: BJ cells, Bortezomib-treated, biol rep3

value: BJ


title: 8K_M_1563


title: bulk RNA-seq, Control donor C4, Frontal cortex, Neurons


title: 8K_M_1562


title: Ngn2 Day2 Rep1 RNAseq


title: bulk RNA-seq, Control donor C4, Frontal cortex, Other glia

value: other glia (NeuN-SOX10-)


title: Ngn2 Day3 VenusNeg Rep2 RNAseq

value: WT


title: 8K_M_1561


title: bulk RNA-seq, Control donor C3, Motor cortex, Other glia


title: Ngn2 ESC Rep2 RNAseq

value: mESC before Ngn2 induction


title: BJ cells, Bortezomib-treated, biol rep2

value: Normal skin fibroblasts


title: BJ cells, Bortezomib-treated, biol rep1


title: bulk RNA-seq, Control donor C3, Motor cortex, Oligodendrocyte lineage cells

value: Control


title: bulk RNA-seq, Control donor C3, Motor cortex, Neurons


title: Ascl1 Day6 VenusNeg Rep1 RNAseq

value: Ascl1 overexpression for 6 day, Venus negative


title: AG-221-treated replicate 1.

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
bcl2fastq v2.20.0
Sequencing reads were pre-processed and aligned to the mouse genome using the bcbio-nextgen pipeline (v. 19.03). Reads were first trimmed for quality and adapter using Atropos (v. 1.1.21), and aligned to the Mus musculus genome (mm10) using bwa (v. 0.7.17-r1188).
Reads were shifted to correct for the transposon event. Peak calling was performed using MACS2 (v. 2.1.1.20160309), using the --broad option, generating one broad peak list for Idh2i-treated samples, and one for the DMSO-treated samples
Genome_build: mm10
Supplementary_files_format_and_content: *_bampe_peaks.txt: Tab-delimited text files containing the output of Macs2 --broad peaks. One file per treatment (DMSO or AG-221-treated)

source_name: Splenic CD8 T cells

growth_protocol: Splenocytes were cultured in RPMI medium (Gibco 61870-01) supplemented with 10% FBS, (Gibco 10270-106), 1% Penicillin/Streptomycin (Gibco 15070-063), 50µM ß-mercaptoethanol, 1% HEPES (Gibco 15630-080), 1x Non-essential amino acids (Gibco 11140-035), 1% L-glutamine (Gibco 25030-081) and 1mM Sodium Pyruvate (Gibco 11360-039). Cells were additionally supplemented with recombinant human (rh) IL-2 100IU/ml (in house) and ovalbumin peptide (SIINFEKL) 1µg/ml and either with 20 µM UK5099 (Sigma Aldrich) or with their solvent DMSO as a control. Splenocytes were collected at day 3, washed and split, and cells were cultured for 4 additional days with 100U/ml rhIL-2 and 10ng/ml rhIL-7 (Peprotech 200-07) without small molecule inhibitor.

extract_protocol:
50 000 T cells were washed 1x with PBS and prepared for transposase treatment
T cell pellet was resuspended in 50 µl of ice-cold lysis buffer (10mM Tris-Cl (pH 7.4), 10mM NaCl, 3mM MgCl2 and 0.1% (v/v) of NP-40. Cells were centrifuged immediately and the resulting pellet (nuclei) was resuspended in 50 µl of transposase reaction mix  (Illumina), followed by incubation at 37°C for 30min. Tagmented DNA was cleaned using QIAGEN MinElute PCR Purification kit as described in the kit’s protocol. Library preparation was performed using Indexes (R#20027213) and NEBNext High-Fidelity 2X PCR Master Mix(M0541), using the following program: 5 min 72°C, 30 s 98°C; 10 cycles: 10 s 98°C, 30 s 63°C, 1 min 72C°. The libraries were then cleaned using Agencourt AMPure XP magnetic beads (A63880, Beckman).

treatment_protocol: T cells were treated for 7 days with either DMSO or 5µM AG-221

value: Splenic CD8 T cells


title: AG-221-treated replicate 2.


title: DMSO-treated replicate 2.

value: DMSO


title: bulk RNA-seq, Control donor C3, Frontal cortex, Oligodendrocyte lineage cells

value: Male


title: 8K_M_1557

city: La Jolla


title: 8K_M_1558


title: 8K_M_1555


title: bulk RNA-seq, Control donor C3, Frontal cortex, Neurons


title: Ascl1 Day6 VenusPos Rep1 RNAseq

value: Ascl1 overexpression for 6 day, Venus positive


title: DMSO-treated replicate 1.


title: Ascl1 Day6 VenusPos Rep2 RNAseq


title: bulk RNA-seq, Control donor C2, Motor cortex, Other glia

value: motor cortex


title: 8K_M_1554


title: Ascl1 Day4 VenusNeg Rep2 RNAseq

value: Ascl1 overexpression for 4 day, Venus negative


title: Ascl1 Day4 VenusNeg Rep1 RNAseq

value: mESC


title: bulk RNA-seq, Control donor C2, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: bulk RNA-seq, Control donor C2, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)


title: 8K_M_1553


title: 8K_M_1560


title: Ascl1 Day4 VenusPos Rep2 RNAseq

value: Ascl1 overexpression for 4 day, Venus positive


title: 8K_M_1552


title: Ngn2 ESC Rep1 RNAseq


title: Ascl1 Day6 VenusNeg Rep2 RNAseq


title: 8K_M_1559


title: bulk RNA-seq, Control donor C2, Frontal cortex, Other glia

value: frontal cortex


title: bulk RNA-seq, Control donor C3, Frontal cortex, Other glia

value: other glia (NeuN-SOX10-)


title: 8K_M_1551


title: Ascl1 Day4 VenusPos Rep1 RNAseq

value: WT


title: 8K_M_1556


title: bulk RNA-seq, Control donor C2, Frontal cortex, Oligodendrocyte lineage cells


title: Ascl1 Day3 VenusNeg Rep2 RNAseq

value: Ascl1 overexpression for 3 day, Venus negative


title: 8K_M_1550


title: 8K_M_1549


title: bulk RNA-seq, Control donor C1, Motor cortex, Other glia

value: Female


title: bulk RNA-seq, Control donor C1, Motor cortex, Oligodendrocyte lineage cells

value: Control


title: 8K_M_1548


title: 8K_M_1547


title: bulk RNA-seq, Control donor C1, Motor cortex, Neurons


title: Ascl1 Day3 VenusPos Rep2 RNAseq

value: Ascl1 overexpression for 3 day, Venus positive


title: bulk RNA-seq, Control donor C1, Frontal cortex, Other glia


title: CONTROL for DataSet2 (remaining IDs) [CONTROL17_GRP2]

description:
HistonePath
CONTROL for DataSet2 (remaining IDs)

data_processing:
Sequence quality and adapter contamination in the ChIP-seq libraries were evaluated with FASTQC
Reads were trimmed using “Trim Galore!”.
Reads were aligned to the human genome (GRCH38) using bowtie2.
Multimapping and duplicate reads removed with SAMtools and Picard tools.
Only analyze files containing CD8 in the filename, as CD4 is a different cell population and did not appear to be powereed in our analysis.
Assembly: ChIP enrichment peaks were called using macs28 and differential ChIP peaks identified with DiffBind
Supplementary files format and content: NCBI GRCh38 p14
Supplementary files format and content: count matrix

source_name: TIL ACT Product

extract_protocol: 5µg of chromatin was extracted from CD4+ and CD8+ sorted TIL and subjected to immunoprecipitation using 4µl of a H3 pan-acetyl antibody (Active Motif, cat #23139), per Active Motif’s standard protocols. Pooled, unprecipitated genomic DNA was used as an input control. These libraries were then sequenced on the Illumina NextSeq 500 v2 sequencer with a 75-base paired-end run in order to generate 30-40 million read pairs per sample.

value: TIL ACT Product

value: Expanded TIL

value: H3 pan-acetyl

tag: dataset

value: TIL ACT


title: bulk RNA-seq, Control donor C2, Frontal cortex, Neurons

value: Male


title: Ascl1 Day2 Rep1 RNAseq

value: Ascl1 overexpression for 2 day


title: Ascl1 Day3 VenusNeg Rep1 RNAseq

value: mESC


title: 8K_M_1545


title: Ascl1 ESC Rep2 RNAseq

value: mESC before Ascl1 induction


title: bulk RNA-seq, Control donor C1, Frontal cortex, Neurons

value: neurons (NeuN+SOX10-)


title: Ascl1 Day3 VenusPos Rep1 RNAseq

value: Ngn2 overexpression for 3 day, Venus positive


title: Ascl1 Day2 Rep2 RNAseq


title: 8K_M_1546


title: Patient 23 CD8+ [Pt23_CD8]

description: HistonePath

tag: trial

tag: response

value: PR

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: gender

value: M


title: 8K_M_1543

tag: brain region

tag: age

tag: strain


title: bulk RNA-seq, C9-FTD donor F7, Motor cortex, Oligodendrocyte lineage cells

source_name: motor cortex

tag: tissue

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

tag: donor id

tag: disease

tag: Sex


title: CONTROL for DataSet1 (CONTROL13_GRP1)

description:
HistonePath
CONTROL for DataSet1 (Pt01_CD4, Pt01_CD8, Pt02_CD4, Pt04_CD4, Pt04_CD8, Pt05_CD8, Pt06_CD8, Pt09_CD8, Pt10_CD4, Pt10_CD8)

tag: cell line

tag: cell type

tag: chip antibody

tag: dataset

tag: treatment


title: bulk RNA-seq, Control donor C1, Frontal cortex, Oligodendrocyte lineage cells

source_name: frontal cortex

value: frontal cortex

tag: genotype

value: Female


title: Patient 21 CD8+ [Pt21_CD8]

description: HistonePath

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

value: F


title: Patient 24 CD8+ [Pt24_CD8]

description: HistonePath

tag: tissue

value: TIL ACT Product

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: gender


title: Ascl1 ESC Rep1 RNAseq

value: WT


title: Ngn2 Ctrl Day0 Rep3

extract_protocol:
Cells were washed with PBS and processed using the Qiagen RNeasy mini kit. RNA was additionally treated with TURBO DNA-free™ kit (Invitrogen) according to the manufacturer’s protocols. Integrity of RNA was measured using Fragment Analyzer™.
RNAseq-Libraries were prepared using QuantSeq 3` mRNA-Seq Library Prep Kit (Lexogen GmbH).
Quantseq

treatment_protocol: 1 day of 1 µg/ml Doxyciclin.

value: mESC before Ngn2 induction


title: Ngn2 Ctrl Day1 Rep1

value: Ngn2 overexpression for 1 day


title: Patient 20 CD8+ [Pt20_CD8]

description: HistonePath

tag: cell line

value: Expanded TIL

value: H3 pan-acetyl

value: PD

value: TIL ACT


title: 8K_M_1544

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: age

tag: strain


title: bulk RNA-seq, C9-FTD donor F7, Frontal cortex, Neurons

tag: cell type

value: neurons (NeuN+SOX10-)

tag: donor id

tag: disease

tag: Sex

value: Male


title: Ngn2 Ctrl Day0 Rep1

value: mESC

tag: genotype

tag: treatment


title: bulk RNA-seq, C9-FTD donor F6, Motor cortex, Other glia

value: other glia (NeuN-SOX10-)


title: Ascl1 Tcf7l1-KO Day1 RepD2

value: Tcf7l1 knockout

value: Ascl1 overexpression for 1 day


title: bulk RNA-seq, C9-FTD donor F7, Motor cortex, Other glia

value: motor cortex


title: 8K_M_1536


title: Patient 16 CD8+ [Pt16_CD8]

description: HistonePath

tag: chip antibody

tag: dataset

tag: trial

tag: response

value: PR

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months


title: Ngn2 Ctrl Day1 Rep3


title: Patient 23 CD4+ [Pt23_CD4]

description: HistonePath

tag: tissue

tag: cell line

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: gender

value: M


title: 8K_M_1541

tag: brain region

tag: age

tag: strain


title: Ngn2 Ctrl Day1Rep2

tag: cell type

tag: genotype

tag: treatment


title: 8K_M_1533


title: bulk RNA-seq, C9-FTD donor F6, Frontal cortex, Oligodendrocyte lineage cells

value: frontal cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

tag: donor id

tag: disease

tag: Sex

value: Female


title: Patient 22 CD8+ [Pt22_CD8]

description: HistonePath

value: TIL ACT Product

tag: chip antibody

tag: dataset

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months


title: bulk RNA-seq, C9-FTD donor F7, Motor cortex, Neurons

tag: tissue


title: bulk RNA-seq, C9-FTD donor F7, Frontal cortex, Other glia


title: 8K_M_1540

tag: brain region


title: 8K_M_1539

tag: age


title: Patient 21 CD4+ [Pt21_CD4]

description: HistonePath

tag: cell line

value: Expanded TIL

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: gender

value: F


title: 8K_M_1532

tag: strain


title: Patient 11 CD8+ [Pt11_CD8]

description: HistonePath

tag: cell type

tag: chip antibody

value: H3 pan-acetyl

value: PD

tag: treatment


title: Patient 10 CD8+ [Pt10_CD8]

description: HistonePath

tag: dataset

tag: trial

tag: response

value: TIL ACT


title: bulk RNA-seq, C9-FTD donor F7, Frontal cortex, Oligodendrocyte lineage cells

tag: genotype

tag: donor id

tag: disease

tag: Sex

value: Male


title: Ngn2 Ctrl Day0 Rep2

value: mESC

value: WT

value: mESC before Ngn2 induction


title: 8K_M_1538

tag: brain region

tag: age


title: bulk RNA-seq, C9-FTD donor F5, Motor cortex, Other glia

tag: tissue

value: other glia (NeuN-SOX10-)


title: 8K_M_1542


title: 8K_M_1537


title: bulk RNA-seq, C9-FTD donor F6, Frontal cortex, Neurons

value: neurons (NeuN+SOX10-)


title: Patient 20 CD4+ [Pt20_CD4]

description: HistonePath

tag: cell line

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4


title: Ascl1 Tcf7l1-KO Day0 RepA1

tag: cell type

value: Tcf7l1 knockout

tag: treatment

value: mESC before Ascl1 induction


title: DT 5 [PLUS5_S14]

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol, name and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Gingival epithelium

extract_protocol:
RNA was extracted using Rneasy Micro Kit (Qiagen) following manufacturer protocol
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000, using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: the samples are mice gingival epithelium samples taken from Langerin-DTR mice that were injected with either PBS or Diphtheria toxin, and therefore are either depleted (DT) or non depleted (PBS) of Langerhans cells.

value: Gingival epithelium

value: Langerin-DTR mice

value: injected with Diphtheria toxin


title: Patient 18 CD8+ [Pt18_CD8]

description: HistonePath

value: TIL ACT Product

tag: chip antibody

tag: dataset

tag: trial

tag: response

tag: infusion percent_cd8

tag: gender


title: bulk RNA-seq, C9-FTD donor F6, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

tag: genotype

tag: donor id

tag: disease

tag: Sex

value: Female


title: Ascl1 Tcf7l1-KO Day1 RepC4

value: Ascl1 overexpression for 1 day


title: bulk RNA-seq, C9-FTD donor F5, Motor cortex, Neurons

tag: tissue


title: DT 4 [PLUS4_S13]


title: DT 3 [PLUS3_S12]


title: 8K_M_1535

tag: brain region

tag: age

tag: strain


title: bulk RNA-seq, C9-FTD donor F6, Motor cortex, Neurons


title: Ascl1 Tcf7l1-KO Day1 RepA1


title: DT 2 [PLUS2_S11]


title: 8K_M_1534


title: Ascl1 Ctrl Day0 Rep1


title: DT 1 [PLUS1_S10]


title: Patient 7 CD8+ [Pt07_CD8]

description: HistonePath

tag: cell line

value: Expanded TIL

value: H3 pan-acetyl

value: PD

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

value: M

value: TIL ACT


title: PBS 5 [MINUS6_S9]

tag: treatment

value: injected with PBS


title: Patient 4 CD4+ [Pt04_CD4]

description: HistonePath

tag: cell type

tag: chip antibody

tag: dataset

tag: trial

tag: response

tag: infusion percent_cd8

tag: gender


title: Patient 15 CD4+ [Pt15_CD4]

description: HistonePath

tag: tissue


title: bulk RNA-seq, C9-FTD donor F6, Frontal cortex, Other glia

value: frontal cortex

value: other glia (NeuN-SOX10-)

tag: genotype

tag: donor id

tag: disease

tag: Sex


title: bulk RNA-seq, C9-FTD donor F5, Frontal cortex, Neurons

value: neurons (NeuN+SOX10-)

value: Male


title: bulk RNA-seq, C9-FTD donor F4, Motor cortex, Oligodendrocyte lineage cells


title: PBS 4 [MINUS4_S7]

value: Gingival epithelium

value: Langerin-DTR mice


title: bulk RNA-seq, C9-FTD donor F4, Motor cortex, Neurons


title: Ascl1 Tcf7l1-KO Day0 RepD2

value: mESC

value: Tcf7l1 knockout

value: mESC before Ascl1 induction


title: Patient 4 CD8+ [Pt04_CD8]

description: HistonePath

value: TIL ACT Product

tag: cell line

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months


title: Patient 14 CD8+ [Pt14_CD8]

description: HistonePath

value: CR

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

value: F

tag: treatment