title: 11C_M_1213


title: 11C_M_1210

status: Public on Apr 20 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

tag: Sex

value: male


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title: 11B_M_2544


title: 11B_M_2543


title: 11B_M_2541


title: 11B_M_2542


title: 11B_M_2562


title: 11B_M_2538


title: 11B_M_2539


title: 11B_M_2536


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title: 11B_M_2532


title: 11B_M_2531


title: 11B_M_2530


title: 11B_M_2529


title: 11B_M_2528


title: 11B_M_2527


title: 11B_M_2525


title: 11B_M_2524


title: 11B_M_2526


title: 11B_M_2523


title: 11B_M_2522


title: 11B_M_2521


title: 11B_M_2519


title: 11B_M_2517


title: 11B_M_2515


title: 11B_M_2516


title: 11B_M_2514


title: 11B_M_2520


title: 11B_M_2574


title: 11B_M_2511


title: 11B_M_2512


title: 11B_M_2513


title: 11B_M_2533


title: 11B_M_2510


title: 11B_M_2509


title: 11B_M_2507


title: 11B_M_2508


title: 11B_M_2505


title: 11B_M_2506


title: 11B_M_2501


title: 11B_M_2503


title: 11B_M_2502


title: 11B_M_2496


title: 11B_M_2499


title: 11B_M_2495


title: 11B_M_2493


title: 11B_M_2494


title: 11B_M_2500


title: 11B_M_2498


title: 11B_M_2492


title: 11B_M_2491


title: 11B_M_2490


title: 11B_M_2485


title: 11B_M_2488


title: 11B_M_2487


title: 11B_M_2486


title: 11B_M_2484


title: 11B_M_2481


title: 11B_M_2480


title: 11B_M_2483


title: 11B_M_2479


title: 11B_M_2482


title: 11B_M_2478


title: 11B_M_2504


title: 11B_M_2476


title: 11B_M_2477


title: 11B_M_2474


title: 11B_M_2497


title: 11B_M_2475


title: 11B_M_2473


title: 11B_M_2472


title: 11B_M_2471


title: 11B_M_2470


title: 11B_M_2468


title: 11B_M_2467


title: 11B_M_2464


title: 11B_M_2465


title: 11B_M_2461


title: 11B_M_2462


title: 11B_M_2466


title: 11B_M_2463


title: 11B_M_2459


title: 11B_M_2460


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title: 11B_M_2453


title: 11B_M_2451


title: 11B_M_2454


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title: 11B_M_2427


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title: 11B_M_2083


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title: 11B_M_2027


title: 11B_M_2026


title: 11B_M_2022


title: 11B_M_2025


title: 11B_M_2020


title: 11B_M_2019


title: 11B_M_2018


title: 11B_M_2017


title: 11B_M_2016


title: 11B_M_2006


title: 11B_M_2012


title: 11B_M_2014


title: 11B_M_2009


title: 11B_M_2008


title: 11B_M_2028


title: 11B_M_2015


title: 11B_M_2010


title: 11B_M_2005


title: 11B_M_2011


title: 11B_M_2013


title: 11B_M_2003


title: 11B_M_2031


title: 11B_M_2004


title: 11B_M_2023


title: 11B_M_1999


title: 11B_M_2000


title: 11B_M_1998


title: 11B_M_2024


title: 11B_M_1997


title: 11B_M_1996


title: 11B_M_1995


title: 11B_M_2007


title: 11B_M_1994


title: 11B_M_1989


title: 11B_M_1991


title: 11B_M_1993


title: 11B_M_1990


title: 11B_M_2001


title: 11B_M_1987


title: 11B_M_1988


title: 11B_M_1983


title: 11B_M_1979


title: 11B_M_1980


title: 9_1_quadriceps

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description:
quad.counts.txt
quad.TPM.txt

library_source: transcriptomic

data_processing:
Quality inspection of raw RNA-Seq reads was performed with FastQC v0.11.9.
Counts and TPM values were obtained using kallisto v0.45 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

molecule: polyA RNA

source_name: quadriceps

extract_protocol:
Whole quadriceps, gonadal white adipose tissue, heart, brown adipose tissue, and a portion of  the liver were pulverized at the temperature of liquid nitrogen. Tissue was homogenized in Trizol  (Invitrogen, Carlsbad, CA, USA), RNA was isolated using the RNeasy Isolation Kit (Qiagen, Hilden,  Germany), and RNA concentration and quality were assessed (RIN > 7.0 used in downstream  applications)
Libraries were prepared using KAPA mRNA HyperPrep Kits and KAPA Dual Index Adapters (Roche, Basel, Switzerland) per manufacturer’s instructions. A total of 800-1000 ng of RNA was used for library preparation with settings 200-300 bp and 12 PCR cycles. The resultant libraries were tested for quality.

tag: tissue

value: quadriceps

value: female

value: SWR/J

tag: exercise group

value: Exercised


title: 11B_M_1986


title: 11B_M_1985


title: 11B_M_1978


title: 11B_M_1984


title: 11B_M_1982


title: 11B_M_1976


title: 9_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: Sedentary


title: 11B_M_1977


title: 11B_M_1975


title: 8_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: FVB/NJ


title: 8_15_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1972


title: 6_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: BALB/cJ


title: 11B_M_1971


title: 6_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1969


title: 7_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: PL/J


title: 7_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1974


title: 50_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: LP/J


title: 11B_M_1968


title: 11B_M_1970


title: 11B_M_1992


title: 50_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1973


title: 49_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: NZB/BlNJ


title: 5_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: CBA/J


title: 11B_M_1967


title: 5_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1965


title: 11B_M_1964


title: 47_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: NZW/LacJ


title: 47_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 48_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: BTBR T<+> tf/J


title: 11B_M_1963


title: 11B_M_1961


title: 48_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1960


title: 46_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: NOD/ShiLtJ


title: 11B_M_1959


title: 44_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 46_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1966


title: 43_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 45_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1954


title: 11B_M_1953


title: 11B_M_1958


title: 11B_M_1957


title: 11B_M_1951


title: 42_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1955


title: 11B_M_1950


title: 43_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1956


title: 40_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 40_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 42_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 49_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 41_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1962


title: 11B_M_1949


title: 11B_M_1948


title: 39_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1947


title: 11B_M_1945


title: 11B_M_1944


title: 38_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 44_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1943


title: 11B_M_1946


title: 39_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 37_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1939


title: 11B_M_1952


title: 4_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: AKR/J


title: 11B_M_1942


title: 4_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1938


title: 37_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 41_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1937


title: 38_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 36_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 35_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 35_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1940


title: 33_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 34_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: SJL/J


title: 11B_M_1935

value: male


title: 11B_M_1936


title: 32_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: quadriceps


title: 34_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: female


title: 11B_M_1932


title: 33_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1931


title: 11B_M_1941


title: 31_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: I/LnJ


title: 31_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1928


title: 11B_M_1927


title: 11B_M_1926


title: 11B_M_1925


title: 36_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 30_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: Exercised


title: 30_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: Sedentary


title: 3_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: A/J


title: 11B_M_1934


title: 3_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1923


title: 29_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 29_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 28_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 32_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1920


title: 11B_M_1922


title: 11B_M_1919


title: 11B_M_1930


title: 11B_M_1921


title: 27_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: SEA/GnJ


title: 28_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1924


title: 27_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 26_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: RIIIS/J


title: 11B_M_1918


title: 11B_M_1917


title: 11B_M_1914


title: 11B_M_1929


title: 11B_M_1916


title: 25_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1915


title: 11B_M_1911


title: 25_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 23_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1908


title: 11B_M_1913


title: 24_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 21_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1912


title: 21_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 23_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1910


title: 24_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1909


title: 22_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1904


title: 20_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1903


title: 11B_M_1907


title: 11B_M_1906


title: 11B_M_1902


title: 2_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 26_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1905


title: 11B_M_1933


title: 11B_M_1901


title: 20_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1900


title: 2_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1899


title: 19_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 18_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 18_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1897


title: 22_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1898


title: 17_4_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 17_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1896


title: 11B_M_1894


title: 16_8_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 16_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 15_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt

value: SM/J


title: 19_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1889


title: 15_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1891


title: 11B_M_1888


title: 14_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 13_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 14_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1892


title: 11B_M_1890


title: 11B_M_1887


title: 11B_M_1886


title: 12_5_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 13_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1895


title: 11B_M_1884


title: 11B_M_1885


title: 11_2_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 10_7_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 12_3_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11_6_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1883


title: 11B_M_1879


title: 9_1_liver

description:
liver.counts.txt
liver.TPM.txt

source_name: liver

value: liver

value: SWR/J


title: 11B_M_1880


title: 8_3_liver

description:
liver.counts.txt
liver.TPM.txt

value: FVB/NJ


title: 8_15_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1877


title: 10_1_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 9_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 1_26_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 1_34_quadriceps

description:
quad.counts.txt
quad.TPM.txt


title: 11B_M_1881


title: 11B_M_1871


title: 11B_M_1876


title: 11B_M_1878


title: 11B_M_1872


title: 11B_M_1874


title: 6_6_liver

description:
liver.counts.txt
liver.TPM.txt

value: BALB/cJ


title: 7_7_liver

description:
liver.counts.txt
liver.TPM.txt

value: PL/J


title: 11B_M_1873


title: 11B_M_1868


title: 7_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1867


title: 11B_M_1866


title: 11B_M_1869


title: 6_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1870


title: 5_4_liver

description:
liver.counts.txt
liver.TPM.txt

value: CBA/J


title: 50_1_liver

description:
liver.counts.txt
liver.TPM.txt

value: LP/J


title: 50_8_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1865

value: male


title: 11B_M_1864


title: 11B_M_1863


title: 11B_M_1862


title: 49_5_liver

description:
liver.counts.txt
liver.TPM.txt

value: NZB/BlNJ


title: 48_7_liver

description:
liver.counts.txt
liver.TPM.txt

value: female

value: BTBR T<+> tf/J


title: 11B_M_1859


title: 11B_M_1861


title: 48_1_liver

description:
liver.counts.txt
liver.TPM.txt

value: Exercised


title: 47_5_liver

description:
liver.counts.txt
liver.TPM.txt

value: NZW/LacJ

value: Sedentary


title: 11B_M_1857


title: 47_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1860


title: 5_8_liver

description:
liver.counts.txt
liver.TPM.txt


title: 46_2_liver

description:
liver.counts.txt
liver.TPM.txt

value: NOD/ShiLtJ


title: 44_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1854


title: 11B_M_1858


title: 11B_M_1856


title: 45_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1855


title: 49_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 45_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1852


title: 11B_M_1853


title: 44_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 46_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1850


title: 11B_M_1851


title: 11B_M_1849


title: 11B_M_1847


title: 42_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1848


title: 11B_M_1845


title: 11B_M_1844


title: 41_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 4_8_liver

description:
liver.counts.txt
liver.TPM.txt

value: AKR/J


title: 41_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 40_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 43_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 40_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 4_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 39_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1843


title: 11B_M_1846


title: 43_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 39_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1842


title: 11B_M_1839


title: 11B_M_1841


title: 38_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 38_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1837


title: 42_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1838


title: 37_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1836


title: 36_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 36_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 34_8_liver

description:
liver.counts.txt
liver.TPM.txt

value: SJL/J


title: 35_5_liver

description:
liver.counts.txt
liver.TPM.txt

value: liver


title: 11B_M_1834


title: 11B_M_1833


title: 35_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 34_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1829


title: 11B_M_1832


title: 33_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1827


title: 33_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1840


title: 11B_M_1824


title: 31_6_liver

description:
liver.counts.txt
liver.TPM.txt

value: I/LnJ


title: 32_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1825


title: 11B_M_1823


title: 31_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 32_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1821


title: 30_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1820


title: 30_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 37_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 3_5_liver

description:
liver.counts.txt
liver.TPM.txt

value: A/J


title: 11B_M_1835


title: 11B_M_1817


title: 11B_M_1818


title: 3_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1815


title: 11B_M_1826


title: 29_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 29_4_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1814


title: 11B_M_1813


title: 11B_M_1810


title: 11B_M_1808


title: 26_5_liver

description:
liver.counts.txt
liver.TPM.txt

value: RIIIS/J


title: 11B_M_1807


title: 27_1_liver

description:
liver.counts.txt
liver.TPM.txt

value: SEA/GnJ


title: 11B_M_1806


title: 11B_M_1804


title: 28_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1803


title: 11B_M_1802


title: 11B_M_1812


title: 22_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 28_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1819


title: 22_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 25_8_liver

description:
liver.counts.txt
liver.TPM.txt


title: 26_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1811


title: 21_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1798


title: 25_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1805


title: 24_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 21_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 24_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1800


title: 11B_M_1801


title: 23_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 20_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1799


title: 27_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1797


title: 11B_M_1796


title: 11B_M_1795


title: 20_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 2_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 2_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1792


title: 11B_M_1794


title: 11B_M_1793


title: 23_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1789


title: 19_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1791


title: 18_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: Meevs.untreated.24hr.rep3

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving, Crocker Science Center Receiving

department: Biological Sciences

institute: University of Utah

data_processing:
Optical duplicates were removed using clumpify with the following command "clumpify.sh in1=R1.fq.gz in2=R2.fq.gz out1=SAMPLE.clump1.fq.gz out2=SAMPLE.clump2.fq.gz dupedist=12000 dedupe=t optical=t"
Illumina adapters were trimmed using cutadapt v1.16 using the following command "cutadapt -j 24 -O 6 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o SAMPLE.1.fq -p SAMPLE.2.fq SAMPLE.clump1.fq.gz SAMPLE.clump2.fq.gz"
Reads were aligned for each sample with the following command (STAR v2.7.9a) "STAR --genomeDir star125 --runThreadN 24 --readFilesIn SAMPLE.R1.fq SAMPLE.R2.fq --twopassMode Basic --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outWigType bedGraph --outWigStrand Unstranded"
Uniquely aligned reads were counted using featureCounts v1.6.3 with the following command "featureCounts -T 24 -p -s 2  --largestOverlap -a Danio_rerio.GRCz11.104.gtf SAMPLE.counts SAMPLE.bam"
Differentially expressed genes were detected using DESeq2 v1.36.0
Assembly: Zv11, Ensembl 104
Supplementary files format and content: DESeq2 output of differential expression between all conditions

organism: Danio rerio

source_name: Whole embryos

growth_protocol: Embryos were grown in the dark at 28.5C until point of treatment; after treatment, they were placed back in the dark incubator

extract_protocol:
Total RNA was extracted using Trizol protocol
Libraries were constructed using NEBNext Ultra II Directional RNA Prep with poly(A) mRNA selection

value: Whole embryos

tag: developmental stage

value: 48 hpf

tag: genotype

value: Meevs mutant

tag: treatment

value: mock

tag: time


title: 18_3_liver

description:
liver.counts.txt
liver.TPM.txt

value: female


title: 17_8_liver

description:
liver.counts.txt
liver.TPM.txt


title: 19_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1790

value: male


title: 11B_M_1788


title: Meevs.untreated.24hr.rep1


title: 11B_M_1786


title: Meevs.UVR.24hr.rep1

value: 450 J UVB


title: sh-2

type: RNA

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

country: China

institute: Sun Yat-sen University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SNU638 cells were obtained from KCLB, and maintained at 37℃ and 5% CO2. Cells were maintained in Dulbecco modified Eagle medium media supplemented with 10% (v/v) fetal bovine serum (FBS).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: We screened four hairpin shRNAs targeting human ACTL6A transcripts and found shACTL6A-1 and shACTL6A-2 that reduced mRNA levels by >70%. The shRNA was in the pLKO.1 vector.Cells were infected twice with culture medium containing 2ml lentivirus expressing shACTL6A-1 and shACTL6A-2, 200ul FBS and 5 mg/ml polybrene (Sigma) at 37℃ for 24 hr and 48 hr. To increase the knockdown efficiency, infected cells were under several days of puromycin selection.

tag: cell line

value: gastric cancer cell line SNU638

tag: transfection


title: scramble-1

value: scramble RNA


title: Meevs.untreated.5hr.rep3

value: 29 hpf


title: scramble-2


title: sh-1


title: Meevs.UVR.24hr.rep2


title: 11B_M_1784


title: Meevs.untreated.5hr.rep1


title: Meevs.untreated.5hr.rep2


title: 11B_M_1785


title: 15_7_liver

description:
liver.counts.txt
liver.TPM.txt

value: SM/J

value: Sedentary


title: Meevs.UVR.5hr.rep3


title: 11B_M_1787


title: Meevs.UVR.5hr.rep2


title: 11B_M_1783


title: Meevs.untreated.24hr.rep2


title: 17_4_liver

description:
liver.counts.txt
liver.TPM.txt

value: liver

value: Exercised


title: Meevs.UVR.24hr.rep3


title: Meevs.UVR.5hr.rep1


title: 16_8_liver

description:
liver.counts.txt
liver.TPM.txt


title: 14_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: wildtype.untreated.24hr.rep3

value: wild type


title: 15_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: wildtype.UVR.24hr.rep1


title: 11B_M_1782


title: 14_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: wildtype.untreated.24hr.rep2


title: wildtype.UVR.24hr.rep3


title: wildtype.UVR.24hr.rep2


title: 11B_M_1780


title: 16_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 13_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1781


title: 11B_M_1779


title: wildtype.untreated.5hr.rep3


title: wildtype.untreated.24hr.rep1


title: wildtype.UVR.5hr.rep3


title: wildtype.UVR.5hr.rep1


title: 13_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 11B_M_1778


title: wildtype.UVR.5hr.rep2


title: 11B_M_1777


title: 12_3_liver

description:
liver.counts.txt
liver.TPM.txt


title: 12_5_liver

description:
liver.counts.txt
liver.TPM.txt


title: wildtype.untreated.5hr.rep1


title: 11B_M_1776


title: 11B_M_1775


title: 11_2_liver

description:
liver.counts.txt
liver.TPM.txt


title: 73-7

city: Minneapolis

first: Chris

middle: H

last: Wendt

state: MN

address: 420 Delaware St SE

department: Medicine

institute: University of Minnesota

data_processing:
FastQ PE reads for samples (n = 28.4M reads/sample) were trimmed using Trimmomatic (version 0.40) (38) enabled with the optional “-q” option: 3 base pair (bp) sliding window trimming 3’ requiring minimum Q30
Quality control on raw sequence data for each sample was performed using FastQC and read mapping was done with Hisat (v2.1.0) using the rat genome (RGSC v6.0) as reference
Gene quantification was done via Feature Counts for raw read counts. Finally, differentially expressed genes (DEGs) were identified using the EdgeR feature in CLCGWB (Qiagen, Hilden, Germany) using raw read counts with p value < 0.05 and false discovery rate (FDR) < 0.05 to adjust for multiple comparisons
Assembly: Rnor_6.0
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Rat hippcampus - Iron deficiency - intranasal insulin treated

growth_protocol: Gestational and neonatal ID was induced by starting pregnant dams on a purified ID diet containing 3-6 ppm iron from G3 to P7

extract_protocol:
Rats were euthanized using sodium pentobarbital (100 mg/kg, i.p.) on P7 or P21. Hematocrit, blood glucose, and body weight were measured. The brain was removed and weighed.
Total RNA was isolated (MONARCH Total RNA Miniprep Kit; NEB, Ipswich, MA) from one hippocampus of each rat following the manufacturer’s protocol

treatment_protocol: Intranasal insulin was administered to the pups in the IS-INS and ID-INS groups twice daily from P8 to P21 using the dose and protocol described in our previous study

value: Hippocampus

value: WT

value: Intranasal insulin


title: 73-8


title: 11B_M_1774


title: 73-4


title: 10_7_liver

description:
liver.counts.txt
liver.TPM.txt


title: 73-3


title: 73-9


title: 73-10


title: 73-1


title: 73-2


title: 11B_M_1772


title: 10_1_liver

description:
liver.counts.txt
liver.TPM.txt


title: 1_34_liver

description:
liver.counts.txt
liver.TPM.txt


title: wildtype.untreated.5hr.rep2

value: Whole embryos


title: 72-10

source_name: Rat hippcampus - Iron sufficiency - intranasal insulin treated


title: 72-5


title: 72-7


title: 11B_M_1771


title: 11B_M_1769


title: 1_26_liver

description:
liver.counts.txt
liver.TPM.txt


title: 72-4


title: 11_6_liver

description:
liver.counts.txt
liver.TPM.txt


title: 72-3


title: 72-2


title: 11B_M_1768


title: 9_5_heart

description:
heart.counts.txt
heart.TPM.txt

source_name: heart

value: heart

value: SWR/J


title: 9_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: female


title: 71-10

source_name: Rat hippcampus - Iron sufficiency - control

value: Control


title: 11B_M_1773

value: male


title: 11B_M_1767


title: 8_3_heart

description:
heart.counts.txt
heart.TPM.txt

value: FVB/NJ


title: 71-7


title: 71-5


title: 8_15_heart

description:
heart.counts.txt
heart.TPM.txt


title: 72-8


title: 7_7_heart

description:
heart.counts.txt
heart.TPM.txt

value: PL/J


title: 11B_M_1765


title: 11B_M_1764


title: 7_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1763


title: 70-2

source_name: Rat hippcampus - Iron deficiency - control


title: 6_6_heart

description:
heart.counts.txt
heart.TPM.txt

value: BALB/cJ


title: 71-1


title: 70-4


title: 70-3


title: 70-1


title: 6_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1762


title: 71-4


title: 71-3


title: 71-8


title: 69-5


title: 11B_M_1761


title: 50_8_heart

description:
heart.counts.txt
heart.TPM.txt

value: LP/J


title: 69-3


title: 11B_M_1766


title: 69-4


title: 50_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: 71-6


title: 69-1


title: 11B_M_1760


title: 11B_M_1759


title: 5_8_heart

description:
heart.counts.txt
heart.TPM.txt

value: CBA/J

value: Sedentary


title: RP-63

city: Frederick

first: Venkat

last: Pannala

state: Maryland

address: 2405 Whittier Dr, #200

department: DoD BHSAI

institute: Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.

description: Control

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the rat transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o Rat/"$sample" $DATA_DIR/2516-"$p"_R1_001.fastq.gz $DATA_DIR/2516-"$p"_R2_001.fastq.gz -t 14
Genome_build: Rattus norvegicus Rnor6.0 Release 92
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

source_name: Kidney

extract_protocol:
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (New England BioLabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (KAPA Biosystems). Pooled libraries were subjected to 150-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Sprague Dawley

value: Kidney

tag: time point (duration after exposure)

value: 5 h

tag: agent

value: Vehicle


title: RP-64

description: Treatment

value: Bromobenzene


title: 11B_M_1758


title: RP-62

description: Control


title: 5_4_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: 11B_M_1757


title: 49_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: NZB/BlNJ


title: 11B_M_1756


title: RP-58

description: Treatment


title: RP-61

description: Treatment


title: 49_2_heart

description:
heart.counts.txt
heart.TPM.txt

value: female


title: 11B_M_1755


title: 48_7_heart

description:
heart.counts.txt
heart.TPM.txt

value: BTBR T<+> tf/J


title: RP-57

description: Treatment


title: RP-55

description: Treatment


title: 69-2

value: Hippocampus

value: WT

value: Control


title: RP-56

description: Treatment


title: 11B_M_1754

value: male


title: RP-60

description: Control


title: RP-54

description: Control


title: RP-53

description: Control


title: RP-59

description: Treatment


title: RP-51

description: Treatment


title: 11B_M_1752


title: 48_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1753


title: 47_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: NZW/LacJ


title: RP-50

description: Control


title: 47_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-49

description: Control


title: 11B_M_1751


title: RP-48

description: Control


title: 46_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: NOD/ShiLtJ


title: 11B_M_1750


title: RP-47

description: Control


title: RP-46

description: Control


title: 11B_M_1749


title: RP-45

description: Control


title: RP-44

description: Treatment


title: 46_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: 45_6_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: 11B_M_1748


title: RP-41

description: Treatment

value: Sprague Dawley


title: RP-43

description: Treatment

value: Kidney


title: RP-39

description: Control

value: 5 h


title: RP-42

description: Treatment


title: RP-40

description: Treatment


title: RP-52

description: Treatment


title: RP-37

description: Control

value: Vehicle


title: 45_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1747


title: 11B_M_1746


title: 11B_M_1745


title: 43_6_heart

description:
heart.counts.txt
heart.TPM.txt


title: 44_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 44_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-38

description: Control


title: RP-36

description: Control


title: RP-35

description: Control


title: RP-34

description: Treatment

value: Bromobenzene


title: 11B_M_1743


title: 43_4_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: RP-32

description: Treatment

source_name: Liver

value: Liver


title: 42_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart


title: RP-30

description: Control


title: 42_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: female


title: RP-29

description: Treatment


title: 11B_M_1741


title: 11B_M_1740


title: RP-28

description: Control


title: 11B_M_1739


title: 41_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 41_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1738


title: RP-22

description: Control


title: RP-21

description: Control


title: RP-23

description: Treatment


title: 11B_M_1736


title: RP-26

description: Treatment


title: RP-20

description: Treatment


title: RP-25

description: Treatment


title: 11B_M_1737


title: 4_8_heart

description:
heart.counts.txt
heart.TPM.txt

value: AKR/J


title: 40_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-24

description: Treatment


title: RP-19

description: Treatment


title: RP-33

description: Treatment


title: RP-27

description: Treatment


title: RP-18

description: Control


title: RP-31

description: Control


title: 11B_M_1735


title: 4_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1742


title: RP-17

description: Control


title: 39_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-15

description: Control


title: 11B_M_1734


title: RP-16

description: Control


title: 11B_M_1733


title: RP-14

description: Control


title: 40_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 39_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1732


title: RP-13

description: Control


title: 38_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-12

description: Treatment


title: 38_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-10

description: Treatment


title: 11B_M_1731


title: RP-9

description: Treatment


title: 11B_M_1730


title: RP-8

description: Treatment


title: RP-11

description: Treatment


title: 37_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 37_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-6

description: Control


title: RP-7

description: Control


title: RP-5

description: Control


title: 11B_M_1728


title: 11B_M_1727


title: 36_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: RP-3

description: Control


title: RP-2

description: Treatment


title: 36_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 35_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1725


title: 35_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1724


title: 11B_M_1729


title: 34_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: SJL/J


title: 11B_M_1723


title: 33_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: 22RV1, DMSO, rep3

first: Ralph

last: White

address: 420 Delaware Street SE

data_processing:
Read trimming with Trimmomatic (0.33)
Alignment to GRCh38 reference genome using HISAT2 (2.1.0)
Sorting BAM files with SAMTools (1.7)
Mapping raw read counts to genes using Subread FeatureCounts
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file including gene level raw count data for all 8 samples.

source_name: prostate cancer cell line

growth_protocol: Cells were grown in complete media containing 10% FBS and antibodies for 24 hours, then switched for media containing charcoal stripped FBS at 5% and antibodies for 72 hours, prior to treatment.

extract_protocol:
Extracted via Rneasy Mini Kit (Qiagen, no. 74106)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using hexamers primers followed by second strand cDNA synthesis. The library was ready after end repair, poly A tailing, adapter ligation, size selection, amplification, and further purification.

treatment_protocol: Synthetic androgen R1881 and epidermal growth factor (EGF) is given at 10nM for 48 hours. Given in tandem are DMSO, Enzalutmide, Saracatinib, or Enzalutamide plus Saracatinib. Cells are harvested for RNA in duplicate

value: prostate cancer cell line

tag: cell type

value: prostate epithelium

value: WT

value: DMSO (untreated)


title: 22RV1, Enzalutamide, rep3

value: Enzalutamide


title: 22RV1, Enzalutamide + Saracatinib, rep3

value: Enzalutamide + Saracatinib


title: 22RV1, Enzalutamide + Saracatinib, rep2


title: 22RV1, Saracatinib, rep3

value: Saracatinib


title: 22RV1, Enzalutamide, rep2


title: 22RV1, Saracatinib, rep2


title: 11B_M_1722

value: male


title: RP-4

description: Control

value: Sprague Dawley

value: 5 h


title: 11B_M_1721


title: 33_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1720


title: RP-1

description: Treatment

value: Bromobenzene


title: 32_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: 11B_M_1726


title: synovial stromal cells,resolved_1

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

library_source: transcriptomic single cell

data_processing:
CellRanger (10x Genomics: v2.1.1) was employed to align to mm10
Assembly: mm10
Supplementary files format and content: CellRanger processed data files (barcode, gene, matrix)

source_name: CD45neg synovial tissue

extract_protocol:
Intact joints were dissected and transferred into RPMI-1640 (+2% FCS) having collagenase D (Roche) 0.1g/ml and 0.01g/ml of DNAse I (Sigma-Aldrich). Obtained samples were then incubated for 40min at 37 °C. This was followed by incubation for 20mins with medium incorporated with  0.1 g/ml collagenase dispase (Roche) and 0.01 g/ml DNase I. Synovial CD45 negative cells obtained from hind limbs at day 0, day 7 to 9 peak, day 15 resolving, or day 22 resolved,  of STIA murine joints (biological replicates n = 3, each was made from of cells extracted from the joints of three different animals) were sorted and subsequently purified using the BD ARIA and finally acquired with the 10x Genomics Chromium system.
3’-scRNAseq was completed using the 10x Genomics Chromium system. Sequencing libraries were generated using the 10x Genomics Single Cell 3′ Solution (version 2) kit and subjected to Illumina sequencing

treatment_protocol: STIA was induced by intravenous injection of 100 μl arthritogenic serum from KRN mice (K/BxN)

value: CD45neg synovial tissue

value: stromal cells

value: STIA (resolved, d22)


title: synovial stromal cells,resolved_2


title: synovial stromal cells,resolving_3

value: STIA (resolving, d15)


title: synovial stromal cells,resolving_2


title: synovial stromal cells,resolving_1


title: synovial stromal cells,resolved_3


title: synovial stromal cells,peak_3

value: STIA (peak, d7-9)


title: 11B_M_1719


title: 34_8_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: female

value: SJL/J


title: 22RV1, DMSO, rep1

value: prostate cancer cell line

value: prostate epithelium

value: WT

value: DMSO (untreated)


title: synovial stromal cells,peak_2


title: 11B_M_1717

value: male


title: 31_6_heart

description:
heart.counts.txt
heart.TPM.txt

value: I/LnJ


title: 30_6_heart

description:
heart.counts.txt
heart.TPM.txt


title: synovial stromal cells,rest_2

value: none (rest, d0)


title: 31_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: 11B_M_1718


title: T8.TN.Input_1.ChIP

first: Ananda

last: Goldrath

address: 9500 Gilman Drive

institute: UCSD

data_processing:
ENCODE ChIPSeq Pipeline and MSPC to combine with Cut&Run
Assembly: mm10
Supplementary files format and content: Peak set in bed file format

source_name: spleen

extract_protocol: Cells were sort purified, crosslinked, sonicated, pulled down with antibody, ligated to Illumina adaoters, amplified by PCR, and sequenced

value: spleen

value: OT-I

value: Day 0


title: 30_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: synovial stromal cells,rest_3

value: CD45neg synovial tissue

value: stromal cells


title: T8.TN.Input_2.ChIP


title: T8.TN.CTCF_3.ChIP

tag: chip antibody

value: CTCF (Sigma Aldrich #07-729-25UL)


title: synovial stromal cells,rest_1


title: T8.TN.CTCF_1.ChIP


title: T8.TE.Input_4.ChIP

value: Lm-OVA

value: Day 7


title: 11B_M_1713


title: 11B_M_1712


title: T8.TN.CTCF_2.ChIP


title: 3_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: female

value: A/J

value: Sedentary


title: 11B_M_1714


title: 32_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: 29_6_heart

description:
heart.counts.txt
heart.TPM.txt


title: T8.TE.Input_3.ChIP


title: T8.TE.CTCF_6.ChIP


title: T8.TE.CTCF_5.ChIP


title: synovial stromal cells,peak_1

value: WT

value: STIA (peak, d7-9)


title: 3_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1711

value: male


title: 11B_M_1716


title: T8.TE.CTCF_4.ChIP


title: 29_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1715


title: T8.TE.CTCF_3.ChIP


title: 11B_M_1710


title: T8.MP.Input_2.ChIP


title: T8.MP.Input_1.ChIP


title: 28_6_heart

description:
heart.counts.txt
heart.TPM.txt


title: T8.TN.CTCF_4.ChIP


title: 11B_M_1709


title: T8.MP.CTCF_1.ChIP


title: 28_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: T8.MP.CTCF_2.ChIP


title: T8.InVitro.shCTCF_2.ATAC

description: InVitro.shCTCF.ATAC.optimalpeak.bed

data_processing:
ENCODE ATACSeq Pipeline
Assembly: mm10
Supplementary files format and content: Peak set in bed file format

extract_protocol: Omni-ATAC was performed on sort purified cells and DNA was PCR amplified for sequencing.

value: anti-CD3+anti-CD28 and 100U/mL IL-2

value: Day 4


title: 11B_M_1708


title: T8.InVitro.shCTCF_1.ATAC

description: InVitro.shCTCF.ATAC.optimalpeak.bed

value: spleen


title: T8.InVitro.shCD19_2.ATAC

value: OT-I


title: 27_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: SEA/GnJ

value: Exercised


title: 26_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: RIIIS/J


title: 27_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1706


title: 11B_M_1707


title: 11B_M_1705


title: Neg_OVA_1

city: ILLKIRCH

first: Mei

last: Li

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

description: Mice were treated with LMP/OVA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 96 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: Lang- migratory dendritic cells from lymph nodes

extract_protocol:
Lymph node cell were incubated 30minutes at 37°C in 2mg/mL collagenase D, 0,25mg/mL Dnase I, 2.5% FCS prior mechanical disruption. Cells were stained with anti-B220, anti-CD11c, anti-I-A/I-E, and propidium iodide for viability. Lang+ and Lang- migratory dendritic cells (DC) were FACS sorted. RNA was extracted using RNeasy Micro Kit (Qiagen).
Full length cDNA were generated from 1ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: LangGFP C57BL/6J

value: Ear draining lymph nodes

tag: cell population

value: Lang- migratory DC

value: OVA


title: Neg_OVA_2

description: Mice were treated with LMP/OVA


title: Neg_OVA_3

description: Mice were treated with LMP/OVA


title: 11B_M_1703

tag: brain region


title: 25_8_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: female


title: 11B_M_1704

tag: age


title: 25_3_heart

description:
heart.counts.txt
heart.TPM.txt

tag: strain


title: Neg_MC_3

description: Mice were treated with MC903


title: Mm_PMC_8M-2-1

city: Boston

first: Stefano

last: Nardone

state: MASSACHUSETTS

address: 3,blackfan circle

department: Endocrinology

institute: Beth Israel Deaconess Medical Center

description: snRNA-seq (DroNc-seq)

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0). Digital expression matrices (DGE) were generated using the Drop-Seq tools pipeline (https://github.com/broadinstitute/Drop-seq, version 2.4.0) as follows. Cell and UMI barcodes were extracted from read 1 and tagged onto read 2 --- barcodes with any base quality score <10 were filtered out. Subsequently, reads were trimmed at the 5′ end to remove any TSO sequence and at the 3′ end to remove poly(A) tails and/or (reverse complemented) barcodes and adapters. Tagged and trimmed reads were aligned with STAR (version 2.7.3) against the GRCm38 genome assembly using the GENCODE M20 primary assembly genomic annotation, pre-filtered to remove pseudogenes. Gene counts were obtained on a per-barcode basis by summarizing the unique read alignments across exons and introns, collapsing UMI barcodes at hamming distance 1.
Assembly: GRCm38 - mm10
Supplementary files format and content: Digital expression matrices (DGE)

source_name: dorsal pontine tegmentum

extract_protocol:
5-6 bilateral tissue dissections were placed in a dounce homogenizer with 1 mL cold (4C°) Lysis Buffer containing 10 mM trisHCl pH 8 (Sigma-Aldrich), 250 mM Sucrose (Sigma-Aldrich), 25 mM KCl, 5mM MgCl2 (Sigma-Aldrich), 0.1% Triton x100 (Sigma-Aldrich), 0.5% RNasin Plus RNase Inhibitor (Promega), 0.1 mM Dithiothreitol (DTT) (Sigma-Aldrich) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). After douncing for 20 times, the solution was filtered through a sterile 20 µm Cell Strainer (pluriSelect), collected in 1.5 mL DNA LoBind® Tubes (Eppendorf), and centrifuged for 10 min at 900 g (rcf) at 4 C. The "slow sedimenting" component (debris and membranes) was aspirated and discarded while the "fast sedimenting" component (nuclear fraction) was gently resuspended in a 1 mL of Working Solution containing 1X pH 7.4 RNase free PBS (Thermo Fisher Scientific), 0.01% Albumin Bovine Serum (BSA) (Sigma-Aldrich), 0.5% RNasin Plus RNase inhibitor (Promega) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). Nuclei were kept on ice while transferred to the BNORC Functional Genomics and Bioinformatics (FGB) Core for DroNc-seq assay.
DroNc-seq was performed as per Habib et al. 2017, with minor modifications. Briefly, nuclei stained with Hoechst 33342 (ThermoFisher, cat. R37605) were counted on a hemocytometer and diluted in NSB to ~250,000 nuclei/ml. Barcoded beads (Chemgenes, Cat # Macosko-2011-10) were size-selected using a 40 μm strainer, diluted to 350,000 per ml, and loaded onto 70 μm wide and 75 μm deep microfluidic device (Nanoshift). The nuclei and barcoded bead suspensions were loaded and run at 35 ml/hr each, along with carrier oil (BioRad Sciences, Cat # 186-4006) at 200 ul/min, to co-encapsulate single nuclei and beads in ~75 μm drops (vol. ~ 200 pl) at 4,500 drops/sec and double Poisson loading concentrations. The microfluidic emulsion was collected into 50 ml Falcon tubes for 10-25 min each and placed on ice 2h before droplet disruption. Individual 200µl reverse transcription (RT) reactions were performed on up to 90K beads. After further exonuclease digestion, aliquots of 800-5K beads were PCR amplified for 10 cycles, and PCR products were pooled in batches of 4 wells or 16 wells for library construction. Purified cDNA was quantified, and 550 pg of each sample was fragmented, tagged, and amplified in each Nextera reaction. Libraries were sequenced on the Illumina NextSeq500 using between 1.6–1.7 pM and 0.3 μM Read1CustSeqB (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) using a 20 × 8 × 60 read structure to a depth of 60,000 reads/nucleus.

value: dorsal pontine tegmentum

tag: region-based dissection

value: Bar

tag: batch

value: neuronal/ non-neuronal/ glial cells

value: 8-10 weeks old

tag: diet

value: NCD

tag: schedule

value: ad libitum

tag: Sex

tag: co2 treatment

value: neg


title: Mm_PMC_9M-2-1

description: snRNA-seq (DroNc-seq)

tag: tissue

value: male


title: Neg_MC_2

description: Mice were treated with MC903

tag: treatment


title: 24_5_heart

description:
heart.counts.txt
heart.TPM.txt

tag: exercise group

value: Sedentary


title: Mm_PMC_8M-1-1

description: snRNA-seq (DroNc-seq)


title: Mm_PMC_9M-1-1

description: snRNA-seq (DroNc-seq)


title: Neg_MC_1

description: Mice were treated with MC903


title: 11B_M_1701


title: 11B_M_1700


title: Neg_NT_3

description: Mice were non-treated

value: Non treated


title: T8.InVitro.shCD19_1.ATAC

value: spleen

value: OT-I

tag: genotype

value: anti-CD3+anti-CD28 and 100U/mL IL-2

tag: time

value: Day 4


title: 23_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: 11B_M_1699


title: 23_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart


title: Mm_PMC_9F-1-1

description: snRNA-seq (DroNc-seq)

tag: cell type

value: female


title: Neg_NT_2

description: Mice were non-treated

value: LangGFP C57BL/6J

value: Ear draining lymph nodes

value: Lang- migratory DC


title: Mm_PMC_8M-3-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: Bar

value: neuronal/ non-neuronal/ glial cells

value: 8-10 weeks old


title: Neg_NT_1

description: Mice were non-treated


title: 26_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: RIIIS/J


title: 11B_M_1698

value: male


title: 22_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: 11B_M_1702


title: 11B_M_1697


title: Pos_OVA_3

description: Mice were treated with LMP/OVA

source_name: Lang+ migratory dendritic cells from lymph nodes

value: Lang+ migratory DC

value: OVA


title: Mm_PMC_8F-1-1

description: snRNA-seq (DroNc-seq)

value: NCD

value: ad libitum

value: neg


title: 21_5_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart


title: Mm_PMC_8F-2-1

description: snRNA-seq (DroNc-seq)

value: female


title: 22_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: Pos_OVA_2

description: Mice were treated with LMP/OVA

value: LangGFP C57BL/6J

value: Ear draining lymph nodes


title: 11B_M_1696

source_name: C57BL/6J Male P56 Mouse Brain


title: 24_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: Mm_PMC_7M-3AB-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum


title: 11B_M_1695


title: Pos_OVA_1

description: Mice were treated with LMP/OVA


title: Mm_PMC_9F-2-1

description: snRNA-seq (DroNc-seq)

value: Bar


title: Pos_MC_3

description: Mice were treated with MC903


title: Mm_PMC_7M-2AB-1

description: snRNA-seq (DroNc-seq)

value: neuronal/ non-neuronal/ glial cells


title: Pos_MC_2

description: Mice were treated with MC903


title: 20_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: Pos_MC_1

description: Mice were treated with MC903


title: 21_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: 20_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1692


title: Mm_PMC_7F-2C-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old


title: 2_6_heart

description:
heart.counts.txt
heart.TPM.txt


title: Pos_NT_3

description: Mice were non-treated

value: Non treated


title: 11B_M_1691

value: male


title: Mm_PMC_7F-2A-1

description: snRNA-seq (DroNc-seq)


title: Mm_PMC_7F-2B-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1690


title: 2_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: 19_7_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: 11B_M_1689


title: Mm_PMC_7F-1A-1

description: snRNA-seq (DroNc-seq)


title: 19_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: Pos_NT_1

description: Mice were non-treated

value: Lang+ migratory DC


title: Mm_PMC_7F-1B-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1688


title: Mm_PMC_6M-3B-1

description: snRNA-seq (DroNc-seq)


title: 18_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1693


title: Mm_PMC_6M-3A-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1686


title: Mm_PMC_7M-1AB-1

description: snRNA-seq (DroNc-seq)


title: 18_3_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1694


title: 17_8_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1687


title: 11B_M_1685


title: Mm_PMC_6M-2B-1

description: snRNA-seq (DroNc-seq)


title: 17_4_heart

description:
heart.counts.txt
heart.TPM.txt


title: Mm_PMC_6M-2A-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1684


title: Pos_NT_2

description: Mice were non-treated


title: Mm_PMC_6M-1AB-1

description: snRNA-seq (DroNc-seq)


title: Mm_PMC_6F-2B-1

description: snRNA-seq (DroNc-seq)


title: 16_8_heart

description:
heart.counts.txt
heart.TPM.txt


title: 11B_M_1683


title: 16_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: Plasma methamphetamine4

city: Ningbo

first: Wenjin

last: Xu

state: Zhejiang Province

address: 42 Xibei Street

institute: School of Medicine, Ningbo University,

description: Total miRNAs from plasma from methamphetamine addicts

hyb_protocol: Sample hybridization was performed as per the manufacturer’s standard protocols by using the Agilent miRNA Complete Labeling and Hyb Kit. Resuspend the dried sample in nuclease-free water. Add 4.5 μL of the 10X GE Blocking Agent to each sample. Add 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45 μL. Mix well but gently on a vortex mixer. Incubate at 100°C for 5 minutes. Immediately transfer to an ice water bath for 5 minutes. Quickly spin in a centrifuge to collect any condensation at the bottom of the tube, followed by preparing the hybridization assembly to process the miRNA system microarray. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. Slowly dispense all of the volume of the hybridization sample onto the gasket well in the center. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Firmly hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set your hybridization rotator to rotate at 20 rpm. Hybridize at 55°C for 20 hours.

scan_protocol: Slides were scanned immediately after washing. Assemble the slides into slide holder of the Agilent Scanner G2505C. Verify scan settings for miRNA. Select the protocol AgilentG3_miRNA for the 8x60K format. All the appropriate settings are set as default s (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood plasma

label_protocol: Sample labeling was performed as per the manufacturer’s standard protocols by using the Agilent miRNA Complete Labeling and Hyb Kit. After the 16°C labeling reaction or sample purification, samples were completely dried by using a vacuum concentrator.

extract_protocol: total RNA

treatment_protocol: Peripheral blood samples (2 ml) were collected into EDTA-containing tubes. Whole blood was centrifuged at 1200 g for 15 min at room temperature within 30 min after blood collection, and the supernatant fluid was transferred into microcentrifuge tubes, followed by a second centrifugation at 12, 000 g for 10 min at 4°C to remove cellular debris. Plasma was then aliquoted and stored at −80°C until use.

value: plasma

tag: gender


title: Plasma methamphetamine2


title: Plasma methamphetamine5


title: 11B_M_1682


title: Plasma methamphetamine1


title: 15_7_heart

description:
heart.counts.txt
heart.TPM.txt

value: SM/J


title: Mm_PMC_6F-2A-1

description: snRNA-seq (DroNc-seq)

value: NCD

value: ad libitum


title: 11B_M_1681


title: Mm_PMC_6F-1B-1

description: snRNA-seq (DroNc-seq)

value: neg


title: 15_2_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: female


title: 11B_M_1678


title: 11B_M_1679


title: 14_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: Mm_PMC_5F-2B-1

description: snRNA-seq (DroNc-seq)


title: Plasma Control2

description: Total miRNAs from plasma from healthy control


title: Plasma Control3


title: Mm_PMC_6F-1A-1

description: snRNA-seq (DroNc-seq)


title: Mm_PMC_5F-2A-1

description: snRNA-seq (DroNc-seq)


title: 13_7_heart

description:
heart.counts.txt
heart.TPM.txt


title: 14_1_heart

description:
heart.counts.txt
heart.TPM.txt

value: Exercised


title: 11B_M_1677


title: 11B_M_1676


title: Mm_PMC_5F-1B-1

description: snRNA-seq (DroNc-seq)


title: 13_2_heart

description:
heart.counts.txt
heart.TPM.txt


title: Plasma Control1


title: 12_5_heart

description:
heart.counts.txt
heart.TPM.txt


title: Plasma Control5


title: Nanhui511_LN [S04]

city: Chongqing

first: Xiaojian

last: Qin

state: --- Select One ---

address: No.37, Daxuecheng Middle Road, Shapingba District, Chongqing

institute: Chongqing Normal University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to rice cultivar 93-11 whole genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_000004655.2/).
Known and novel miRNAs were identified using the miRDeep2 software, which is a comprehensive software package for miRNA identification that matches reads to the genome based on the distribution information of reads on the precursor sequence.
Cufflinks are used for assemble transcripts and remap and quanity gene-expression level, which is estimate by FPKM value
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: 6 days seedlings

extract_protocol:
RNA was harvested using the mirVana™ RNA Isolation Kits (Thermo Fisher). 1.5 ug of total RNA was used for the construction of sequencing libraries by small RNA Sample Pre Kit.
RNA libraries for RNA-seq were prepared using standard illumila protocols by NEB Next Ultra small RNA Sample Library Prep Kit.

value: 6 days seedlings

tag: cultivar

value: low nitrogen (LN)

value: WT


title: Plasma Control4


title: Mm_PMC_5F-1A-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: Bar

value: neuronal/ non-neuronal/ glial cells


title: Nanhui511_HN [S03]

value: high nitrogen (HN)


title: 11B_M_1675

tag: brain region

value: male


title: 11B_M_1674

tag: age


title: RBD bio rep 1

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

description:
RBD_peak_summerized_table_rev1.csv
750_rev1.bed

data_processing:
Raw reads were demultiplexed using bcl2fastq version 2.19.0.
Raw reads were filtered with CLIP Tool Kit (CTK) built-in function and processed by cutadapt/b1to remove adapters.
Alignment was performed using bowtie/1.2.1.1/b1.
Clustering and peak calling were performed on aligned reads with CTK built-in functions using the 'valley seeking' algorithm.
Summarized tables containing peak information were generated by bedtools/2.30.0 and R-4.1.2 from bed files.
Assembly: GRCh38, hg38
Supplementary files format and content: comma-delimited tables containing peak information
Supplementary files format and content: bed files containing peak information

growth_protocol: Human HEK293T cells were propagated in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were treated with 800 mM 4sU 16 hours before crosslinking by 312 nm ultraviolet exposure using Stratagene Stratalinker UV 1800. Crosslinked cells were lysed in a native lysis buffer with 50 mM HEPES, pH 7.5, 150 mM KCl, 2 mM EDTA, 1 mM NaF, 0.1% (v/v) Nonidet P-40, 1 mM DTT, 25 ml/ml protease inhibitor cocktail for mammalian tissues (Sigma-Aldrich), and 1U/ml RNase T1. Immunoprecipitation was performed using anti-DYKDDDDK magnetic agarose (ThermoFisher) followed by on-bead RNA digestion with 5U/ml RNase T1, on-bead dephosphorylation with calf intestinal alkaline phosphatase (CIP), and on-bead phosphorylation with T4 PNK and 32[P]-ATP or non-radioactive ATP. Radio-labeled RNA-protein complexes were extracted from beads by boiling in 70 ml of SDS loading buffer (Bio-Rad), separated on a 4-12% Bis-Tris gel, and imaged with phosphorimager. Bands corresponding to the protein size were cut off from the gel, subjected to proteinase K digestion and RNA purification by phenol-chloroform. The purified non-radioactive RNAs were run on 15% denaturing polyacrylamide gel and purified for deep sequencing.
Sequencing libraries were constructed using the NEBNext® Small RNA Library Prep Set following the manufacturer’s instructions.
PAR-CLIP-seq

treatment_protocol: FLAG-tagged full-length and truncated PRRC2B were overexpressed in HEK293T cells.

tag: cell line

value: human embryonic kidney

value: Flag-tagged truncated PRRC2B overexpression

tag: clip antibody

value: anti-DYKDDDDK magnetic agarose

tag: fraction

value: CLIPed RNA


title: RBD bio rep 2


title: 12_3_heart

description:
heart.counts.txt
heart.TPM.txt

tag: strain


title: 11B_M_1673


title: Plasma methamphetamine3

value: plasma


title: 11_6_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: Mm_LPBN_07-2X-3

description: snRNA-seq (DroNc-seq)

tag: region-based dissection

value: PB

tag: batch

value: 8-10 weeks old

tag: diet

value: NCD

tag: schedule

value: refeed

value: neg


title: 11B_M_1672

tag: Sex


title: FL bio rep 1

description:
FL_peak_summerized_table_rev1.csv
2B_rev1.bed

value: Flag-tagged PRRC2B overexpression


title: 11_2_heart

description:
heart.counts.txt
heart.TPM.txt

tag: tissue

value: heart

value: female

tag: exercise group

value: Exercised


title: Mm_LPBN_07-2X-2

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: neuronal/ non-neuronal/ glial cells

tag: co2 treatment


title: Xrn1 ko A549 cells, PR8-PA(∆X), biol rep 3

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

data_processing:
cutadapt v3.5 (Martin, 2011) was used to trim Illumina adapters and UMI from each read sequence
Trimmed reads were aligned to the human genome version GRCh38/hg38, the PR8 genome and the ERCC spike sequences using HISAT2 v2.2.1 (Kim et al., 2019) with the following specific parameters: retain unique alignments only (-k 1 option), disallow softclipping (--no-softclip option), and select fr-secondstrand library type (--rna-strandness F option).
Reads with the same UMI mapping to the same genome region were collapsed into one, to eliminate read duplications that can arise from PCR amplification.
Uniquely aligned reads were used for the PyDegradome 2.0 pipeline to identify PA-X cut sites (https://github.com/mgaglia81/PyDegradome). Reads that aligned to the wrong strand (based on their strandness) and contained insertions or deletions were discarded for the PyDegradome analysis.
Assembly: hg38
Supplementary files format and content: Tab delimited files containing information about PA-X cut sites, obtained by comparing RNA fragments in WT PR8 samples vs. PR8-PA(∆X) samples using the PyDegradome 2.0 pipeline. One is PA-X cut sites shared across three biological replicates using PyDegradome 2.0 with parameters confidence interval (cl) = 99% / multiplication factor (mf) = 2 / window (w) = 4. Second file is PA-X cut sites when using each biological replicate concatenated together as input for PyDegradome 2.0 with parameters cl = 99.99% / mf = 2 / w = 4. Columns are: chromosome number, strand, genomic location of cut (hg38), EMSEMBL gene ID, gene name and -25 bp +25 bp sequence around the cut site.
Supplementary files format and content: Tab-delimited files listing PyDegradome peaks detected when using WT PR8 samples as the test samples and the PR8-PA(∆X) samples as controls, or viceversa as control. Each peak is represented by three lines, one giving the position and various parameters, the second listing read counts in control sample and the third listing the read counts in the test sample. Read counts are listed starting 25 nt before the 5' end of the detected peak and ending 25 nt after the 3' end of the peak. User-defined parameters for PyDegradome: cI = 99% for each replicate or 99.99% for concatenated analysis / mf = 2 / w = 4

source_name: Xrn1 ko A549 cells

growth_protocol: Xrn1 ko A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS, Gibco) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy Plus mini kit (Qiagen) and treated with Turbo DNase (Life Technologies). 3 ug of total DNase treated RNA was used for the construction of sequencing libraries.
3 µg RNA was mixed with 6 µl of ERCC ExFold RNA spike-in mixes diluted to 1:100 (Invitrogen). Ribosomal RNA was removed from each sample using Ribo-Zero Plus kit (Illumina). The rest of the RNA was ligated to a RACE-Seq adapter using T4 RNA ligase (Invitrogen) for 2 hours at 25C. The RACE-seq adapter contains a unique molecular identifier (UMI) in order to identify and remove reads that are the result of PCR duplication during the library preparation. Ligated RNA was then reverse transcribed to cDNA with SuperScript III RT (Invitrogen) using random primers of different lengths that also include a known sequence adapter. Finally, reads were amplified in two rounds of PCR of six cycles each to enrich for ligated fragments and add the Illumina adapters. Between the two PCRs, DNA fragments of 150-400 bp were selected using SPRIselect Reagent (Beckman Coulter).

treatment_protocol: Samples were washed twice with PBS then mock infected or infected with WT PR8 or PR8-PA(∆X) at a MOI of 1 in DMEM supplemented with 0.5% bovine serum albumin (BSA, Sigma-Aldrich) and 0.5 µg/ml TPCK-treated trypsin (Sigma-Aldrich)

value: Xrn1 ko A549 cells

tag: cell type

value: lung carcinoma epithelial cells

tag: genotype

value: Xrn1 knock out

tag: treatment

value: infected with influenza virus PR8-PA({delta}X)


title: 11B_M_1671

tag: brain region

value: male


title: Mm_LPBN_07-2X-1

description: snRNA-seq (DroNc-seq)

tag: age


title: 10_7_heart

description:
heart.counts.txt
heart.TPM.txt

value: Sedentary


title: Xrn1 ko A549 cells, WT PR8, biol rep 3

tag: cell line

value: infected with influenza virus WT PR8


title: 11B_M_1670


title: 10_1_heart

description:
heart.counts.txt
heart.TPM.txt


title: Mm_LPBN_07-1X-2

description: snRNA-seq (DroNc-seq)

value: PB

value: 8-10 weeks old


title: 11B_M_1669


title: Xrn1 ko A549 cells, mock, biol rep 3

value: mock infected


title: Xrn1 ko A549 cells, PR8-PA(∆X), biol rep 2


title: 1_34_heart

description:
heart.counts.txt
heart.TPM.txt


title: Mm_LPBN_08-1X-1

description: snRNA-seq (DroNc-seq)

value: NCD

value: ad libitum

value: neg


title: 1_26_heart

description:
heart.counts.txt
heart.TPM.txt

value: heart

value: female


title: Mm_LPBN_07-1X-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: refeed


title: Mm_LPBN_06-6X-1

description: snRNA-seq (DroNc-seq)

value: neuronal/ non-neuronal/ glial cells


title: FL bio rep 2

value: human embryonic kidney

value: Flag-tagged PRRC2B overexpression

tag: clip antibody

value: anti-DYKDDDDK magnetic agarose

value: CLIPed RNA


title: 11B_M_1668

value: male


title: Xrn1 ko A549 cells, WT PR8, biol rep 2

value: Xrn1 ko A549 cells

value: lung carcinoma epithelial cells

value: Xrn1 knock out

value: infected with influenza virus WT PR8


title: 11B_M_1667


title: Mm_LPBN_06-5X-1

description: snRNA-seq (DroNc-seq)

value: PB

value: 8-10 weeks old

value: NCD


title: 9_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

source_name: gonadal white adipose tissue

value: gonadal white adipose tissue

value: SWR/J

value: Sedentary


title: Xrn1 ko A549 cells, mock, biol rep 2

value: mock infected


title: Mm_LPBN_06-4X-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: neuronal/ non-neuronal/ glial cells

value: ad libitum

value: neg


title: 9_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female

value: Exercised


title: Xrn1 ko A549 cells, PR8-PA(∆X), biol rep 1

value: Xrn1 ko A549 cells

value: infected with influenza virus PR8-PA({delta}X)


title: 11B_M_1665

value: male


title: 8_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: FVB/NJ


title: Mm_LPBN_06-3X-1

description: snRNA-seq (DroNc-seq)

value: PB


title: Xrn1 ko A549 cells, WT PR8, biol rep 1

value: lung carcinoma epithelial cells

value: Xrn1 knock out

value: infected with influenza virus WT PR8


title: 8_15_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: 11B_M_1664


title: Xrn1 ko A549 cells, mock, biol rep 1


title: Mm_LPBN_06-2X-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old

value: NCD


title: 7_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: PL/J

value: Sedentary


title: 11B_M_1662


title: Mm_LPBN_06-1X-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: neuronal/ non-neuronal/ glial cells

value: ad libitum


title: 7_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female

value: Exercised


title: Mm_LPBN_05-3X-1

description: snRNA-seq (DroNc-seq)

value: neg


title: 6_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: BALB/cJ


title: 11B_M_1661

value: male