title: 14C_M_1684


title: 14C_M_1678

status: Public on May 25 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: PCG

tag: age

tag: strain


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title: 14C_M_1942


title: 14C_M_1947


title: 14C_M_1948


title: 14C_M_1935


title: 14C_M_1937


title: 14C_M_1931


title: 14C_M_1932


title: 14C_M_1925


title: 14C_M_1926


title: 14C_M_1933


title: 14C_M_1927


title: 14C_M_1924


title: 14C_M_1923


title: 14C_M_1922


title: 14C_M_1920


title: 14C_M_1921


title: 14C_M_1928


title: 14C_M_1929


title: 14C_M_1919


title: 14C_M_1918


title: 14C_M_1914


title: 14C_M_1917


title: 14C_M_1913


title: 14C_M_1915


title: 14C_M_1916


title: 14C_M_1911


title: 14C_M_1909


title: 14C_M_1908


title: 14C_M_1910


title: 14C_M_1912


title: 14C_M_1930


title: 14C_M_1904


title: 14C_M_1903


title: 14C_M_1902


title: 14C_M_1905


title: 14C_M_1906


title: 14C_M_1901


title: 14C_M_1895


title: 14C_M_1892


title: 14C_M_1899


title: 14C_M_1898


title: 14C_M_1896


title: 14C_M_1891


title: 14C_M_1900


title: 14C_M_1907


title: 14C_M_1886


title: 14C_M_1889


title: 14C_M_1885


title: 14C_M_1884


title: 14C_M_1882


title: 14C_M_1879


title: 14C_M_1880


title: 14C_M_1881


title: 14C_M_1878


title: 14C_M_1897


title: 14C_M_1894


title: 14C_M_1893


title: 14C_M_1887


title: 14C_M_1890


title: 14C_M_1888


title: 14C_M_1883


title: Sperm,  WGBS, replicate 1

city: Sydney

first: Allegra

last: Angeloni

state: NSW

address: 384 Victoria St Darlinghurst

department: Genomics and Epigenetics Division

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Methylome analysis was performed using methods described in Skvortsova et al. Nat Commun 2019. Briefly, sequenced reads in FASTQ format were trimmed using the fastp v0.12.5 tool (https://github.com/OpenGene/fastp) with the following settings: (fastp -i ${read_1} -I ${read_2} -o ${trimmed_read_1} -O ${trimmed_read_2} -f 10 -t 10 -F 10 -T 10). Trimmed reads were mapped (petMar3 genome reference, containing the lambda genome as chrL) using WALT with the following settings: -m 10 -t 24 -N 10000000 -L 2000. PCR and optical duplicates were removed using Picard tools v2.3.0. Genotype and methylation bias correction was performed using MethylDackel software (https://github.com/dpryan79/MethylDackel). The number of methylated and unmethylated calls at each genomic CpG position were determined using MethylDackel (MethylDackel extract genome_lambda.fa $input_bam --mergeContext --minOppositeDepth 10 --maxVariantFrac 0.5 $input_bam -@ 32 --OT 0,0,0,0 --OB 10,0,0,0). Bisulfite conversion efficiency was estimated from the lambda phage spike-ins.
Assembly: petMar3
Supplementary files format and content: bedGraph

organism: Petromyzon marinus

source_name: Sperm

extract_protocol:
For DNA extraction, lamprey embryos were lysed in buffer containing 20 mM Tris, pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS and 0.5 mg/ml proteinase K for 3 h at 55 °C. Lysis was followed by two phenol:chloroform:isoamyl alcohol (25:24:1) extractions and subsequent centrifugation (5 min at 17,949g). DNA was then precipitated by adding 0.2 volumes of 4 M ammonium acetate and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 min. The DNA precipitate was centrifuged for 20 min at 4 °C (17,949g), and the pellet was washed with 500 μl of 70% ethanol and centrifuged for 5 min (17,949g) at room temperature. The pellet was then resuspended in 200 μl of TE buffer, and 1 μl of RNase A (20 μg/μl) was added. The reaction was left to proceed for 30 min at room temperature, after which time the DNA was precipitated with 0.1 volumes of 4 M ammonium acetate and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 min at 4 °C (17,949g), and the pellet was resuspended in TE buffer.
WGBS was performed on genomic DNA extracted from egg, sperm, day 1, day 2, brain, muscle and PBMC in replicate using methods described in Skvortsova et al. Nat Commun 2019. Briefly, DNA was spiked with unmethylated lambda phage fragments (Promega) and sonicated to approximately 300 base pairs. Sonicated DNA was concentrated in a vacuum centrifuge concentrator to the final volume of 20µL, required for bisulfite conversion with the EZ DNA Methylation-Gold Kit (Zymo Research). Bisulfite-converted DNA was then subjected to low input library preparation using the Accel-NGS Methyl-seq DNA Kit (Swift Biosciences). Briefly, the single-stranded, bisulfite-converted DNA was subjected to an adaptase reaction, followed by primer extension, adapter ligation (Methyl-seq Set A Indexing Kit-Swift Biosciences), and indexing PCR. Libraries were quantified using KAPA qPCR Library Quantification Kit (KAPA Biosystems) according to manufacturer instructions. Methylome libraries were sequenced on the Illumina HiSeqX platform (high-throughput mode, 150_bp, PE).

tag: tissue

value: Sperm

tag: developmental stage

value: Adult


title: Egg, WGBS, replicate 1

source_name: Egg

value: Egg


title: Day 2,  WGBS, replicate 1

source_name: Day 2

value: Day 2

value: Embryonic day 2


title: Day 1,  WGBS, replicate 2

source_name: Day 1

value: Day 1

value: Embryonic day 1


title: PBMC,  WGBS, replicate 1

source_name: PBMC

value: PBMC


title: Sperm,  WGBS, replicate 2


title: PBMC,  WGBS, replicate 2


title: Day 1,  WGBS, replicate 1


title: Muscle,  WGBS, replicate 2

source_name: Muscle

value: Muscle


title: Day 2,  WGBS, replicate 2


title: Muscle,  WGBS, replicate 1


title: Brain, WGBS, replicate 2

source_name: Brain

value: Brain


title: Brain, WGBS, replicate 1


title: 14C_M_1874


title: 14C_M_1869


title: 14C_M_1876


title: 14C_M_1872


title: 14C_M_1875


title: 14C_M_1877


title: 14C_M_1868


title: experiment 2, Aged mouse, Treated treated, replicate 4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

library_source: transcriptomic

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file include counts for each sample

molecule: polyA RNA

source_name: ovary

extract_protocol:
RNA was extracted using RNeasy mini Kit (Qiagen, cat. no. 74106) and digested with DNase I (Qiagen, cat. no. 79254)
The libraries were prepared using a Lexogen Quantseq kit

value: ovary

tag: group

value: experiment 2

tag: mouse

value: Aged

value: Treated

tag: treatment

value: Auranofin

tag: replicate


title: Egg, WGBS, replicate 2


title: 14C_M_1871


title: 14C_M_1867


title: 14C_M_1870


title: 14C_M_1873


title: 14C_M_1865


title: 14C_M_1864


title: 14C_M_1866


title: experiment 2, Aged mouse, Treated treated, replicate 3


title: experiment 2, Aged mouse, untreated, replicate 5

value: untreated

value: control


title: experiment 2, Aged mouse, Treated treated, replicate 1


title: 14C_M_1858

value: PCG


title: 14C_M_1862


title: experiment 2, Aged mouse, Treated treated, replicate 2


title: 14C_M_1863


title: 14C_M_1859


title: 14C_M_1860


title: experiment 2, Aged mouse, untreated, replicate 3


title: 14C_M_1857


title: experiment 2, Aged mouse, untreated, replicate 2


title: experiment 2, Aged mouse, untreated, replicate 1


title: experiment 2, Young mouse, untreated, replicate 3

value: Young


title: experiment 2, Young mouse, untreated, replicate 4


title: experiment 2, Young mouse, untreated, replicate 2


title: 14C_M_1855


title: 14C_M_1856


title: 14C_M_1849


title: experiment 2, Young mouse, untreated, replicate 5


title: 14C_M_1851


title: experiment 2, Young mouse, untreated, replicate 1


title: experiment 2, Aged mouse, untreated, replicate 4


title: 14C_M_1854


title: experiment 1, Aged mouse, Treated treated, replicate 4

value: experiment 1


title: experiment 1, Aged mouse, Treated treated, replicate 3


title: 14C_M_1848


title: 14C_M_1861


title: experiment 1, Aged mouse, Treated treated, replicate 1


title: 14C_M_1843


title: experiment 1, Aged mouse, untreated, replicate 4


title: 14C_M_1845


title: 14C_M_1844


title: 14C_M_1846


title: 14C_M_1842


title: experiment 1, Aged mouse, untreated, replicate 3


title: 14C_M_1841


title: experiment 1, Aged mouse, Treated treated, replicate 2


title: 14C_M_1840


title: experiment 1, Aged mouse, untreated, replicate 2


title: experiment 1, Aged mouse, untreated, replicate 1


title: 14C_M_1853


title: experiment 1, Young mouse, untreated, replicate 5


title: 14C_M_1838


title: 14C_M_1839


title: 14C_M_1837


title: experiment 1, Young mouse, untreated, replicate 4


title: 14C_M_1836


title: experiment 1, Young mouse, untreated, replicate 2


title: experiment 1, Young mouse, untreated, replicate 3


title: 14C_M_1834


title: 14C_M_1835


title: 14C_M_1833


title: experiment 1, Young mouse, untreated, replicate 1


title: 14C_M_1831


title: 14C_M_1829


title: 14C_M_1830


title: 14C_M_1827


title: 14C_M_1832


title: 14C_M_1828


title: 14C_M_1826


title: 14C_M_1821


title: 14C_M_1819


title: 14C_M_1820


title: 14C_M_1825


title: 14C_M_1824


title: 14C_M_1822


title: 14C_M_1823


title: Dien F 319

city: Urbana

first: Tina

last: Barbasch

address: 505 S Goodwin Ave

department: Evolution, Ecology, and Behavior

institute: University of Illinois Urbana Champaign

data_processing: Reads were aligned to the stickleback reference genome using STAR and read counts generated using HTSeq

molecule: total RNA

organism: Gasterosteus aculeatus

source_name: Diencephalon

growth_protocol: All experiments were conducted during the summer breeding season (June – August) of 2020 using lab-reared individuals at the University of Illinois Urbana Champaign. Parents of the F1 individuals were wild caught from a population of the “white” ecotype (Blouw and Hagen 1990; Samuk 2016) of threespined stickleback (Gasterosteus aculeatus) from Canal Lake, Nova Scotia, CA . Laboratory conditions were maintained at 20°C and a 16:8 light / dark photoperiod to stimulate male nesting behavior. All individuals were fed ad libitum once a day with a mixture of brine shrimp (Artemia sp.), mysis shrimp (Mysis sp.), bloodworms (Chironomus sp.), and Cyclop-Eeze. Prior to experimental trials, males and females were housed socially (5-20/tank, 53L x 33W x 24H cm), but focal males were moved to individual tanks at least 24 hours prior to experimental trials. N=17 focal males were used in this experiment.

extract_protocol:
Sixty minutes after their final trial (n=4 males after a courtship opportunity, n=5 males after a territorial intrusion, n=4 males after the tradeoff treatment, and n=4 males after the control treatment), the diencephalon and telencephalon were rapidly dissected, preserved in RNAlater, and deep frozen at -80°C until extraction. RNA was extracted using Invitrogen PureLink RNA extraction kits (Invitrogen Corporation, Carlsbad, CA) and quality was checked using Agilent Bioanalyzer chips.
Libraries were prepped using TruSeq Stranded mRNA sample prep kits and samples were sequenced to a depth of >30M reads on a Novaseq 6000 S4 flow cell

treatment_protocol: Behavioral trials consisted of four treatments: a courtship opportunity (F), a territorial challenge (M), simultaneous courtship opportunity and territorial challenge (hereafter referred to as the “tradeoff” treatment, MF), and a control (C). At the start of each trial, the focal male was acclimated to the presence of the observer for five minutes, then two flasks were introduced into the tank. In the courtship opportunity treatment, a gravid female was confined to one of the flasks, in the territorial challenge treatment, a rival male displaying breeding coloration was confined to one of the flasks, and in the tradeoff treatment, a gravid female to one and a rival male to the other flask. The control consisted of two empty flasks. Each male was exposed to all four treatments in a random order, followed by all four treatments in a random order a second time, for a total of eight trials per male. Each male was exposed to one treatment per day. For each trial, the side of the tank with the flask containing a stimulus was randomized (excepting the control, which consisted of an empty flask on each side).

value: Diencephalon

tag: Sex

value: male

value: F


title: Dien M 330

value: M


title: Dien M 322


title: Dien F 320


title: Dien MF 321

value: MF


title: Dien F 329


title: Dien MF 323


title: MRSL_Control 9SR47437A

type: RNA

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 295 Duck Pond Dr

institute: Virginia Tech

hyb_protocol: Performed by ThermoFisher ClariomS services

data_processing: Data provided by ThermoFisher ClariomS services, analyzed by researchers using ThermoFisher's Transcriptome Analysis Console (TAC)

label: Biotin

source_name: Mouse RNA MRSL Control from ThermoFisher

growth_protocol: Transduced Pan02 cells were seeded at 1 x 10^5 cells per well in a 6 well plate. Cells were cultured in complete media (RPMI + 10% FBS +1% PS) +/- H2O2. RNA was collected with TRIxol and stored at -80C until it was submitted to Thermo Fisher for transcriptomics analysis.

extract_protocol: TRIzol

treatment_protocol: +/- 24 hours of low-dose H2O2 challenge.

tag: cell line

tag: genotype

tag: culture conditions


title: Dien M 317


title: Dien C 308

value: C


title: 14C_M_1815


title: 14C_M_1818


title: 14C_M_1816


title: 14C_M_1814


title: 14C_M_1813


title: 14C_M_1812


title: Dien C 304


title: Dien MF 306


title: Dien C 303


title: Dien C 307


title: 14C_M_1817


title: Dien M 318


title: Dien F 299


title: Dien M 298


title: Dien MF 302


title: 14C_M_1811


title: Tel M 330

source_name: Telencephalon

value: Telencephalon


title: Tel F 329


title: Tel MF 323


title: Tel M 322


title: Tel MF 321


title: Tel F 320


title: 14C_M_1808


title: 14C_M_1809


title: 14C_M_1807


title: 14C_M_1810


title: 14C_M_1806


title: Tel M 318


title: 14C_M_1799


title: 14C_M_1802


title: 14C_M_1800


title: 14C_M_1801


title: 14C_M_1798


title: 14C_M_1797


title: Tel C 308


title: 14C_M_1796


title: 14C_M_1803


title: Tel C 307


title: Tel F 319


title: Tel MF 306


title: Pan02OE_NormalMedia

scan_protocol: Performed by ThermoFisher ClariomS services

source_name: Pan02 cells overexpressing NLRX1 cultured in normal media

value: Pan02OE (overexpression NLRX1)

value: Normal culture conditions


title: Tel C 304


title: Tel MF 302


title: Tel M 317


title: Tel C 303


title: Tel F 299


title: Tel M 298


title: siUHRF1, RNA-seq rep2 [VS752]

city: Bethesda

first: Vinutha

last: Balachandra

state: MD

address: 10 Center Drive

department: National Cancer Institute, Genetics Branch

institute: National Institute for Health

data_processing:
Basecalls were performed using bcl2fastq for NextSeq output.
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using cudadapt v1.18, discarding reads left with < 20 bp
RNA-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2-2.4.2.
Assembly: hg38

organism: Homo sapiens

source_name: squamous cell carcinoma of head and neck

growth_protocol: Cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 2nM L-glutamine.

extract_protocol:
RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA).
Libraries were constructed according to the Illumina TruSeq Stranded mRNA Library Prep kit (cat# 20020594).

treatment_protocol: Cells were treated with human IFN-β at 1000U/ml (R&D systems Inc, 8499-IF-010/CF) for 24h prior to cell collection.

tag: cell type

value: cell line


title: 14C_M_1791


title: 14C_M_1792


title: 14C_M_1661


title: 14C_M_1793


title: 14C_M_1660


title: siUHRF1, RNA-seq rep3 [VS753]

value: squamous cell carcinoma of head and neck


title: 14C_M_1662


title: 14C_M_1794


title: 14C_M_1656


title: 14C_M_1659


title: 14C_M_1658


title: 14C_M_1655


title: 14C_M_1654


title: siUHRF1, RNA-seq rep1 [VS751]


title: siNC, RNA-seq rep1 [VS748]


title: siNC, RNA-seq rep2 [VS749]


title: siNC, RNA-seq rep3 [VS750]


title: 14C_M_1653


title: 14C_M_1652


title: 14C_M_1651


title: Pan02OECTL_NormalMedia

source_name: Pan02 cells (overexpression controls) cultured in normal media

label_protocol: Performed by ThermoFisher ClariomS services

value: Pan02OECTL (overexpression controls)


title: Pan02KD_H2O2

source_name: Pan02 cells with knocked-down NLRX1 challenged with low dose hydrogen peroxide

value: Pan02 KD (knockdown of NLRX1)

value: Low dose H2O2 challenge


title: 14C_M_1650

value: PCG


title: 14C_M_1649


title: 14C_M_1648


title: Pan02OE_H2O2

source_name: Pan02 cells overexpressing NLRX1 challenged with low dose hydrogen peroxide


title: 14C_M_1647

source_name: C57BL/6J Male P56 Mouse Brain


title: 14C_M_1646


title: 14C_M_1645


title: 14C_M_1644


title: 14C_M_1642


title: 14C_M_1643


title: 14C_M_1641


title: Pan02KDCTL_NormalMedia

source_name: Pan02 cells (knockdown controls) cultured in normal media

value: Pan02 KDCTL (knockdown controls)


title: 14C_M_1640


title: 14C_M_1638


title: 5-3, H3K4me3, rep1, CS029689 [VS413]

data_processing:
Basecalls were performed using bcl2fastq for NextSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using cudadapt v1.18, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2-2.4.2.
Peaks were called uing GoPeaks v2.1.0 with the significance cut-off q-value <=0.01. broadPeaks settings were used.
Assembly: hg38
Supplementary files format and content: bed, broadPeak (except for Input sample)
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

extract_protocol:
The 14-1048 CUT&RUN kit by EpiCypher was utilized according to EpiCypher’s protocol.
Libraries were constructed according to Illumina TruSeq ChIP (cat# IP-202-1012) (H4K20me3 for siNC/siSMYD3 treated cells) and IDT 2S Plus (cat#10009878) (H4K20me3, H3K4me3, SMYD3 for SMYD3 KO cells) DNA library prep kits.

value: SMYD3 KO 5-3

value: HNSCC cancer cells

tag: chip antibody

value: anti-H3K4me3, EpiCypher, 13-0041


title: HN-6, negative control, rep1  [VS669]

value: IgG negative control


title: HN-6, SMYD3, rep3, CS031308 [VS673]

value: anti-SMYD3, Abcam 187149


title: 5-3, H3K4me3, rep2, CS029689 [VS414]


title: 5-3, H3K4me3, rep3, CS029689 [VS415]


title: 14C_M_1637


title: HN-6, SMYD3, rep1, CS031308 [VS671]


title: HN-6, siSMYD3, H4K20me3, rep1, CS030666 [VS542]

value: anti-H4K20me3, ThermoFisher, MA5-36090


title: HN-6, siSMYD3, H4K20me3, rep2, CS030666 [VS543]


title: HN6, siNC, H4K20me3, rep2, CS030666 [VS540]


title: HN6, siNC, H4K20me3, rep3, CS030666 [VS541]


title: 5-3, SMYD3, rep1, CS031308 [VS674]


title: HN-6, siSMYD3, H4K20me3, rep3, CS030666 [VS544]


title: HN6, siNC, H4K20me3, rep1, CS030666 [VS539]


title: Pan02KDCTL_H2O2

source_name: Pan02 cells (knockdown controls) challenged with low dose hydrogen peroxide


title: 14C_M_1636


title: 14C_M_1639


title: HN-6, H3K4me3, rep2, CS029689 [VS411]


title: HN-6, H3K4me3, rep3, CS029689 [VS412]


title: HN-6, H3K4me3, rep1, CS029689 [VS410]


title: Pan02KD_NormalMedia

source_name: Pan02 cells with knocked-down NLRX1 cultured in normal media


title: HN-6, SMYD3, rep2, CS031308 [VS672]


title: Pan02OECTL_H2O2

source_name: Pan02 cells (overexpression controls) challenged with low dose hydrogen peroxide


title: 14C_M_1635


title: HN-6, negative control, rep1 [VS409]


title: 14C_M_1634


title: 5-3, H4K20me3, rep3, CS029758 [VS440]


title: 14C_M_1633


title: 5-3, H4K20me3, rep2, CS029758 [VS439]


title: 14C_M_1632


title: 14C_M_1631


title: HN-6, H4K20me3, rep2, CS029758 [VS436]


title: HN-6, H4K20me3, rep3, CS029758 [VS437]


title: 14C_M_1629


title: HN-6, H4K20me3, rep1, CS029758 [VS435]


title: 14C_M_1630


title: 5-3, H4K20me3, rep1, CS029758 [VS438]


title: 14C_M_1628


title: 14C_M_1626


title: 14C_M_1627


title: 14C_M_1625


title: Human airway epithelium organoids, infected by pCoV-GD01 sample 3, 24h

city: Suzhou

first: Hang-Yu

last: Zhou

state: Jiangsu

address: 100 Chongwen Road

country: China

institute: Institute of Systems Medicine, Chinese Academy of Systems Medicine

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are:  1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed );  2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads);  3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads);  4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads count values for each Sample

source_name: airway epithelium airway epithelium organoids

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Viral RNA was extracted from the culture supernatant using the QIAamp Viral RNA Kit (Qiagen) and detected using RT-qPCR. The determination of the detection limit was based on the lowest level at which viral RNA was detected and remained within the range of linearity of a standard curve (Ct value of 35).
(1) Library examination: RNA concentration of library was measured using Qubit® RNA Assay Kit in  Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlusTM Real-Time PCR System (Library valid concentration>10 nM); (2) Library clustering and sequencing: The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: primary cell

value: infected by pCoV-GD01, 24h


title: 14C_M_1623


title: Human airway epithelium organoids, infected by pCoV-GD01 sample 2, 24h

value: airway epithelium airway epithelium organoids


title: 14C_M_1622


title: Human airway epithelium organoids, infected by pCoV-GD01 sample 1, 24h


title: Human airway epithelium organoids, infected by SARS-CoV-2 sample 2, 24h

value: infected by SARS-CoV-2, 24h


title: 14C_M_1621


title: Human airway epithelium organoids, infected by SARS-CoV-2 sample 1, 24h


title: Human airway epithelium organoids, infected by SARS-CoV-2 sample 3, 24h


title: 14C_M_1620


title: Human airway epithelium organoids, Control-repeat3

value: control


title: Human airway epithelium organoids, Control-repeat2


title: HN-6, negative control, rep1  [VS531]

value: squamous cell carcinoma of head and neck


title: 14C_M_1619


title: Human airway epithelium organoids, Control-repeat1


title: 14C_M_1618


title: 14C_M_1617


title: 14C_M_1624


title: 14C_M_1616


title: HN-6, negative control, rep1 [VS427]


title: 14C_M_1615


title: 14C_M_1614


title: 14C_M_1613


title: 14C_M_1612


title: 14C_M_1611


title: 14C_M_1607


title: 14C_M_1605


title: 14C_M_1609


title: 14C_M_1606


title: 14C_M_1608


title: 14C_M_1603


title: 14C_M_1610


title: 14C_M_1602


title: 14C_M_1601


title: 14C_M_1600


title: 14C_M_1604


title: 14C_M_1598


title: 14C_M_1597


title: 14C_M_1596


title: 14C_M_1599


title: 14C_M_1594


title: 14C_M_1593


title: 14C_M_1595


title: 14C_M_1592


title: 14C_M_1591


title: 14C_M_1589


title: 14C_M_1588


title: 236_CTRL02_med

city: Stockholm

first: Joy

last: Roy

address: BioClinicum J8:20, Karolinska University Hospital

department: Department of Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Standard Affymetrix,Thermo Fisher hyb protocol

scan_protocol: Standard Affymetrix,Thermo Fisher scan protocol

data_processing: Data were normalized by Guanine Cytosine Count Normalization, Signal Space Transformation, and Robust Multi-Array Average by use of Transcriptome Analysis Console software (Thermo Fisher Scientific)

label: biotin

source_name: Human abdominal aorta

label_protocol: Standard Affymetrix,Thermo Fisher labeling protocol

extract_protocol: Tissue RNA was extracted by use of Qiazol Lysis Reagent and purified using the RNeasy or miRNeasy minikits (both Qiagen, Venlo, the Netherlands). RNA concentration was measured using Nanodrop ND 1000 (Thermo Fisher Scientific, Waltham, MA) and quality was verified using Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease state

value: Donor abdominal aorta

tag: tunica

value: Media

tag: thrombus

value: Thrombus-free

value: Human abdominal aorta


title: 255_CTRL26_adv

value: Adventitia


title: 258_CTRL27_med


title: 248_CTRL15_med


title: 250_CTRL17_med


title: 14C_M_1587

tag: brain region

value: PCG

tag: age


title: 240_CTRL05_med

tag: tissue


title: 234_CTRL01_med


title: 238_CTRL03_med


title: 14C_M_1586

tag: strain


title: 252_CTRL20_med


title: 253_CTRL24_adv


title: 256_CTRL26_med


title: 251_CTRL20_adv


title: 14C_M_1585


title: 241_CTRL10_adv


title: 249_CTRL17_adv


title: 246_CTRL13_med


title: 254_CTRL24_med


title: 237_CTRL03_adv


title: 257_CTRL27_adv


title: 235_CTRL02_adv


title: 247_CTRL15_adv


title: 245_CTRL13_adv


title: 14C_M_1583


title: 14C_M_1581


title: 243_CTRL12_adv


title: 14C_M_1582


title: 14C_M_1580


title: 14C_M_1578


title: 14C_M_1576


title: 14C_M_1579


title: 239_CTRL05_adv


title: 14C_M_1584


title: 14C_M_1575


title: 232_3A399_TH_med

value: Abdominal aortic aneurysm

value: Thrombus-covered


title: 14C_M_1573


title: 14C_M_1574


title: 14C_M_1571


title: 220_3A333_TH_med


title: 224_3A341_TH_med


title: 244_CTRL12_med


title: 233_CTRL01_adv


title: 14C_M_1570


title: 222_3A341_NTH_med


title: 14C_M_1569


title: 14C_M_1572


title: 14C_M_1568


title: 14C_M_1567


title: 14C_M_1566


title: 14C_M_1564


title: 14C_M_1563


title: 14C_M_1565


title: 14C_M_1562


title: 231_3A399_TH_adv


title: 230_3A399_NTH_med


title: 221_3A341_NTH_adv


title: 228_3A383_TH_med


title: 14C_M_1560


title: 14C_M_1561


title: 14C_M_1559


title: 14C_M_1558


title: 14C_M_1557


title: 14C_M_1556


title: 215_3A305_TH_adv


title: 14C_M_1555


title: 209_3A284_NTH_adv


title: 229_3A399_NTH_adv


title: 218_3A333_NTH_med


title: 219_3A333_TH_adv


title: 207_3A274_TH_adv


title: 216_3A305_TH_med


title: 217_3A333_NTH_adv


title: 213_3A305_NTH_adv


title: 14C_M_1554


title: 205_3A274_NTH_adv


title: 214_3A305_NTH_med


title: 14C_M_1553


title: 242_CTRL10_med


title: 211_3A284_TH_adv


title: 204_3A269_TH_med


title: 227_3A383_TH_adv


title: 14C_M_1552


title: 212_3A284_TH_med


title: 206_3A274_NTH_med


title: 14C_M_1551


title: 226_3A383_NTH_med


title: 14C_M_1550


title: 14C_M_1549


title: 14C_M_1546


title: 14C_M_1548


title: 14C_M_1543


title: 14C_M_1544


title: 14C_M_1545


title: 198_3A267_NTH_med


title: 203_3A269_TH_adv


title: 14C_M_1541


title: 200_3A267_TH_med


title: 223_3A341_TH_adv


title: 14C_M_1540


title: 14C_M_1538


title: 201_3A269_NTH_adv


title: 199_3A267_TH_adv


title: 225_3A383_NTH_adv


title: 196_3A262_TH_med


title: 210_3A284_NTH_med


title: 14C_M_1536


title: 202_3A269_NTH_med


title: 14C_M_1471


title: 14C_M_1537


title: 14C_M_1469


title: 14C_M_1468


title: 14C_M_1470


title: 194_3A262_NTH_med


title: 14C_M_1465


title: 14C_M_1467


title: 14C_M_1464


title: 14C_M_1462


title: 14C_M_1461


title: 14C_M_1460


title: 14C_M_1463


title: 208_3A274_TH_med


title: 190_3A260_NTH_med


title: 192_3A260_TH_med


title: 188_3A258_TH_med


title: 14C_M_1458


title: 14C_M_1459


title: 14C_M_1457


title: 14C_M_1456


title: 197_3A267_NTH_adv


title: 186_3A258_NTH_med


title: 14C_M_1455


title: 189_3A260_NTH_adv


title: 195_3A262_TH_adv


title: 179_3A227_TH_adv


title: 183_3A253_TH_adv


title: 181_3A253_NTH_adv


title: 175_3A219_TH_adv


title: 187_3A258_TH_adv


title: 14C_M_1454


title: 14C_M_1453


title: 193_3A262_NTH_adv


title: 173_3A219_NTH_adv


title: 170_3A206_NTH_med


title: 191_3A260_TH_adv


title: 185_3A258_NTH_adv


title: 14C_M_1451


title: 14C_M_1450


title: 14C_M_1448


title: 177_3A227_NTH_adv


title: 14C_M_1452


title: 174_3A219_NTH_med


title: 14C_M_1447


title: 168_3A203_TH_med


title: 14C_M_1446


title: 172_3A206_TH_med


title: 184_3A253_TH_med


title: 178_3A227_NTH_med


title: 182_3A253_NTH_med


title: 14C_M_1445


title: 180_3A227_TH_med


title: 14C_M_1444


title: 14C_M_1440


title: 14C_M_1442


title: 14C_M_1443


title: 14C_M_1441


title: 14C_M_1438


title: 171_3A206_TH_adv


title: 14C_M_1439


title: 14C_M_1437


title: 14C_M_1434


title: 14C_M_1436


title: 14C_M_1435


title: 176_3A219_TH_med


title: 14C_M_1432


title: 164_3A179_TH_med


title: 14C_M_1431


title: 14C_M_1430


title: 162_3A179_NTH_med


title: 148_3A117_TH_med


title: 163_3A179_TH_adv


title: 165_3A203_NTH_adv


title: 14C_M_1429


title: 167_3A203_TH_adv


title: 14C_M_1428


title: 169_3A206_NTH_adv


title: 153_3A121_NTH_adv


title: 160_3A141_TH_med


title: 14C_M_1427


title: 151_3A118_TH_adv


title: 166_3A203_NTH_med


title: 155_3A121_TH_adv


title: 159_3A141_TH_adv


title: 146_3A117_NTH_med


title: 157_3A141_NTH_adv


title: 161_3A179_NTH_adv


title: 14C_M_1426


title: 14C_M_1425


title: 14C_M_1424


title: 14C_M_1423


title: 14C_M_1422


title: 152_3A118_TH_med


title: 149_3A118_NTH_adv


title: 14C_M_1421


title: 154_3A121_NTH_med


title: 147_3A117_TH_adv


title: 150_3A118_NTH_med


title: 14C_M_1419


title: 158_3A141_NTH_med


title: 14C_M_1418


title: 156_3A121_TH_med


title: 14C_M_1420


title: 14C_M_1417


title: 14C_M_1416


title: 14C_M_1413


title: 14C_M_1415


title: 14C_M_1412


title: 14C_M_1411


title: 14C_M_1410


title: 14C_M_1414


title: 14C_M_1408


title: 135_3A102_TH_adv


title: 144_3A115_TH_med


title: 14C_M_1279


title: 14C_M_1409


title: 14C_M_1277


title: 14C_M_1278


title: 136_3A102_TH_med


title: 14C_M_1276


title: 134_3A102_NTH_med


title: 142_3A115_NTH_med


title: 140_3A104_TH_med


title: 123_3A082_TH_adv


title: 138_3A104_NTH_med


title: 132_3A096_TH_med


title: 121_3A082_NTH_adv


title: 133_3A102_NTH_adv


title: 145_3A117_NTH_adv


title: 14C_M_1274


title: 14C_M_1275


title: 119_3A075_TH_adv


title: 131_3A096_TH_adv


title: 115_3A073_TH_adv


title: 139_3A104_TH_adv


title: 117_3A075_NTH_adv


title: 124_3A082_TH_med


title: 130_3A096_NTH_med


title: 114_3A073_NTH_med


title: 143_3A115_TH_adv


title: 116_3A073_TH_med


title: 14C_M_1272


title: 14C_M_1273


title: 14C_M_1271


title: 14C_M_1267


title: 14C_M_1270


title: 122_3A082_NTH_med


title: 14C_M_1269


title: 14C_M_1268


title: 129_3A096_NTH_adv


title: 118_3A075_NTH_med


title: 113_3A073_NTH_adv


title: 137_3A104_NTH_adv


title: 141_3A115_NTH_adv


title: 112_3A056_TH_med


title: 120_3A075_TH_med


title: 111_3A056_TH_adv


title: 105_3A014_NTH_adv


title: 14C_M_1265


title: 104_3A011_TH_med


title: 14C_M_1262


title: 14C_M_1263


title: 14C_M_1266


title: 14C_M_1261


title: 14C_M_1264


title: 103_3A011_TH_adv


title: 102_3A011_NTH_med


title: 14C_M_1260


title: 107_3A014_TH_adv


title: 100_3A008_TH_med


title: 109_3A056_NTH_adv


title: 110_3A056_NTH_med


title: 14C_M_1259


title: 14C_M_1256


title: 108_3A014_TH_med


title: 14C_M_1257


title: 14C_M_1255


title: 14C_M_1258


title: 101_3A011_NTH_adv


title: 099_3A008_TH_adv


title: 14C_M_1254


title: 14C_M_1248


title: 14C_M_1250


title: 14C_M_1247


title: 14C_M_1249


title: 14C_M_1253


title: 14C_M_1251


title: 14C_M_1252


title: 106_3A014_NTH_med


title: 14C_M_1246


title: 097_3A008_NTH_adv


title: 14C_M_1245


title: 098_3A008_NTH_med


title: 14C_M_1244


title: 084_3A380_TH_med


title: 090_3A384_TH_med


title: 14C_M_1242


title: 095_3A007_TH_adv


title: 092_3A417_TH_med


title: 14C_M_1241


title: 096_3A007_TH_med


title: 14C_M_1240


title: 089_3A384_TH_adv


title: 094_3A007_NTH_med


title: 086_3A400_TH_med


title: 14C_M_1238


title: 14C_M_1239


title: 088_3A404_TH_med


title: 085_3A400_TH_adv


title: 093_3A007_NTH_adv


title: 14C_M_1236


title: 14C_M_1237


title: 091_3A417_TH_adv


title: 14C_M_1235


title: 14C_M_1234


title: 087_3A404_TH_adv


title: 14C_M_1243


title: 083_3A380_TH_adv


title: 072_3A322_TH_med


title: 14C_M_1230


title: 14C_M_1229


title: 14C_M_1232


title: 14C_M_1231


title: 076_3A338_TH_med


title: 14C_M_1233


title: 070_3A314_TH_med


title: 14C_M_1228


title: 081_3A378_TH_adv


title: 075_3A338_TH_adv


title: 14C_M_1227


title: 14C_M_1226


title: 074_3A331_TH_med


title: 066_3A302_TH_med


title: 073_3A331_TH_adv


title: 069_3A314_TH_adv


title: 071_3A322_TH_adv


title: 060_3A273_TH_med


title: 064_3A287_TH_med


title: 14C_M_1225


title: 14C_M_1223


title: 063_3A287_TH_adv


title: 14C_M_1224


title: 14C_M_1221


title: 062_3A282_TH_med


title: 082_3A378_TH_med


title: 14C_M_1220


title: 14C_M_1219


title: 065_3A302_TH_adv


title: 14C_M_1222


title: 061_3A282_TH_adv


title: 14C_M_1218


title: 059_3A273_TH_adv


title: 14C_M_1215


title: 14C_M_1217


title: 055_3A264_TH_adv


title: 14C_M_1214


title: 14C_M_1212


title: 14C_M_1213


title: 050_3A254_TH_med


title: 056_3A264_TH_med


title: 049_3A254_TH_adv


title: 053_3A261_TH_adv


title: 14C_M_1211


title: 14C_M_1210


title: 14C_M_1216


title: 048_3A233_TH_med


title: 051_3A255_TH_adv


title: 14C_M_1207


title: 047_3A233_TH_adv


title: 046_3A228_TH_med


title: 14C_M_1206


title: 14C_M_1205


title: 054_3A261_TH_med


title: 052_3A255_TH_med


title: 045_3A228_TH_adv


title: 14C_M_1203


title: 14C_M_1204


title: 14C_M_1202


title: 14C_M_1209


title: 14C_M_1201


title: 042_3A210_TH_med


title: 14C_M_1208


title: 040_3A167_TH_med


title: 043_3A225_TH_adv


title: 039_3A167_TH_adv


title: 041_3A210_TH_adv


title: 14C_M_1200


title: 038_3A140_TH_med


title: 14C_M_1198


title: 037_3A140_TH_adv


title: 044_3A225_TH_med


title: 036_3A127_TH_med


title: 14C_M_1195


title: 14C_M_1196


title: 14C_M_1194


title: 034_3A126_TH_med


title: 14C_M_1192


title: 14C_M_1193


title: 14C_M_1199


title: 14C_M_1191


title: 029_3A101_TH_adv


title: 032_3A122_TH_med


title: 035_3A127_TH_adv


title: 033_3A126_TH_adv


title: 14C_M_1197


title: 027_3A099_TH_adv


title: 031_3A122_TH_adv


title: 14C_M_1190


title: 14C_M_1189


title: 030_3A101_TH_med


title: 14C_M_1188


title: 028_3A099_TH_med


title: 025_3A092_TH_adv


title: 14C_M_1187


title: 026_3A092_TH_med


title: 023_3A068_TH_adv


title: 14C_M_1185


title: 14C_M_1184


title: 021_3A066_TH_adv


title: 024_3A068_TH_med


title: 14C_M_1186


title: 022_3A066_TH_med


title: 019_3A059_TH_adv


title: 14C_M_1181


title: 14C_M_1182


title: 020_3A059_TH_med


title: 14C_M_1179


title: 14C_M_1180


title: 14C_M_1183


title: 14C_M_1178


title: 14C_M_1176


title: 018_3A057_TH_med


title: 14C_M_1175


title: 017_3A057_TH_adv


title: 14C_M_1174


title: 015_3A042_TH_adv


title: 14C_M_1173


title: 016_3A042_TH_med


title: 013_3A031_TH_adv


title: 14C_M_1170


title: 14C_M_1172


title: PBS_1

city: Cambridge

first: Jigar

last: Desai

state: MA

address: 733 Concord Avenue

institute: Wave Life Science

data_processing:
Reads were trimmed using cutadapt v1.15. Reads were trimmed for both adapter sequencing as well as poly-A sequences.
Mapping was done with hisat2 v2.1.0
Alignment files were then processed using Rsubread v2.0.1 using featureCounts to extract counts per gene
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Primary Mouse Hepatocyte

extract_protocol:
Total RNA Isolation kit (Promega, Cat No. Z3505), and eluted with 100 µl of nuclease-free H2O.
QuantSeq 3′-mRNA-Seq library preparation kit (Lexogen GmbH, Vienna, Austria) was used to prepare the library according to manufacturer’s protocol

value: Primary Mouse Hepatocyte

value: WT

value: PBS

tag: time

value: Day 1


title: PBS_3


title: PBS_2


title: 014_3A031_TH_med


title: 14C_M_1171


title: 14C_M_1169


title: TTR-1186_2uM_2


title: TTR-1186_2uM_3


title: 008_3A012_TH_med


title: 14C_M_1168


title: 010_3A013_TH_med


title: 011_3A027_TH_adv


title: 009_3A013_TH_adv


title: 14C_M_1167


title: 012_3A027_TH_med


title: TTR-1186_0.2uM_2


title: TTR-1186_0.2uM_3


title: 14C_M_1165


title: 14C_M_1164


title: 006_3A005_TH_med


title: TTR-1186_0.2uM_1


title: Reference_4_2uM_2

value: Reference 4, 2uM


title: Reference_4_2uM_3


title: 14C_M_1162


title: 14C_M_1160


title: Reference_4_2uM_1


title: TTR-1186_2uM_1


title: 007_3A012_TH_adv


title: Reference_4_0.2uM_3

value: Reference 4, 0.2uM


title: 004_3A004_TH_med


title: Reference_4_0.2uM_2


title: 14C_M_1166


title: 14C_M_1155


title: 14C_M_1156


title: 14C_M_1157


title: Reference_4_0.2uM_1


title: 003_3A004_TH_adv


title: TTR-1236_2uM_3


title: 002_3A003_TH_med


title: 14C_M_1163


title: TTR-1236_2uM_1


title: TTR-1236_2uM_2


title: 14C_M_1154


title: 14C_M_1153


title: 14C_M_1159


title: TTR-1236_0.2uM_2


title: TTR-1236_0.2uM_1


title: 14C_M_895


title: 14C_M_894


title: ATAC_18h2 [ATAC-seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Basecalls performed using CASAVA version 1.4.
The ATAC-seq reads were trimmed to remove adaptor content using Trimmomatic (version 0.33) and mapped to mouse genome mm9 using Bowtie2 (version 2.9.2). Reads with mapping quality score (MAPQ) < 10 were filtered out using samtools (version 1.9) and PCR duplicates were removed using Picard tools (version 1.127).
Reads with mapping quality score (MAPQ) < 10 were filtered out using samtools (version 1.9) and PCR duplicates were removed using Picard tools (version 1.127).
Peaks were called using MACS2 version 2.2.6.
wig files were generated using deeptools.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: .bw: bigwig files

source_name: Spleen

growth_protocol: B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol.

extract_protocol:
About 50,000 spleen cells were lysed with 50 mL of Lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, protease inhibitor). After centrifuging at 500 g for 10 min at 4oC, pellets (nuclei) were resuspended with 50 ul of transposition mix (Illumina; 1X Tagment DNA buffer, Tn5 Transposase, nuclease-free H2O) and incubated for 30 min at 37 oC in the Thermomixer.
Transposed DNA was purified using QIAgen MinElute columns, subsequently amplified with Nextera sequencing primers and NEB high fidelity 2X PCR master mix for 12 cycles (New England Biolabs). PCR-amplified DNA was purified using QIAgen MinElute columns and sequenced using Illumina platform with paired-end reads of 75 bases.

treatment_protocol: Two replicates were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0, 1, 4 or 18 hours.

value: B cell

value: 10ug/ml goat anti-mouse IgM Fab'2

tag: time point

value: 18 hours


title: ATAC_18h1 [ATAC-seq]

tag: treatment


title: 14C_M_1158


title: 14C_M_893


title: 001_3A003_TH_adv


title: 14C_M_892


title: 14C_M_891


title: ATAC_4h2 [ATAC-seq]

value: 4 hours


title: ATAC_4h1 [ATAC-seq]


title: ATAC_1h1 [ATAC-seq]

value: 1 hour


title: 14C_M_888


title: ATAC_1h2 [ATAC-seq]


title: TTR-1236_0.2uM_3


title: 14C_M_889


title: ATAC_0h2 [ATAC-seq]

value: untreated

value: 0 hour


title: 14C_M_890


title: 14C_M_887


title: 14C_M_1152


title: 14C_M_886


title: H3K4me3 18h_1 [ChIP-seq]

data_processing:
Basecalls performed using CASAVA version 1.4.
Bowtie software was used to map quality-filtered reads from demultiplexed FASTQ files to mouse genome assembly mm9 (Ensembl v67) with default options.
CisGenome software was used for peak calling with a window size of 200 bases and a threshold of 4 reads (2 from each strand), FDR<0.1 and fold change >2. Peaks separated by less than 200 bases were merged into one peak.
HOMER annotatePeaks.pl to annotate peaks with default parameters (promoter regions were defined from −1 kb to +100 bp). We then combined the two annotated gene lists together. Motif finding was carried out with HOMER using the de novo setting.
findMotifs-Genome.pl and findMotifs.pl were used to identify transcription factor binding motifs within peaks or promoter regions (−400 to +100 bp from TSSs).
All samples were normalized to 10 million reads for visualization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig in WashU Epigenome Browser.

source_name: spleen B cell

growth_protocol: B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol during treatment.

extract_protocol:
Cells were washed twice with PBS and then were fixed at room temperature with either 1% formaldehyde in PBS for 10 min (for H3K27ac and H3K4me3 ChIP) or 1.5mM EGS (Pierce Cat # 21565) for 30 min followed by 1% formaldehyde (Sigma-Aldrich) at room temperature for 15 min in PBS (RelA and Rel ChIP). Reactions were quenched by adding glycine to a final concentration of 0.125 M, and cells were washed twice with cold PBS. Nuclei were isolated and lysed in buffer containing 50 mM Hepes-KOH, pH7.5; 150 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; and protease inhibitors. The crosslinked chromatin was subjected to fragmentation by sonication (Branson Sonicator). ChIP was performed with 2.5 μg anti-RelA or anti-Rel antibody (Santa Cruz) and 3 μg H3K27ac and H3K4me3 antibody (Abcam) prebound to 50 μl Protein A or G Dynabeads (Invitrogen). Sonicated chromatin was added to antibody-bound beads and incubated at 4C overnight. Beads were collected by centrifugation, washed, and incubated at 65C for 4 h in elution buffer (50 mM Tris-HCl, pH 7.5; 10 mM EDTA; 1% SDS) to reverse cross-linking. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Two replicates were treated with 10ug/ml goat anti-IgM Fab`2 for 0, 1, 4 or 18 hours.

value: 10ug/ml goat anti-IgM Fab'2

value: H3K4me3  (ab8580, Abcam)


title: H3K4me3 18h_2 [ChIP-seq]


title: ATAC_0h1 [ATAC-seq]


title: H3K4me3 1h_1 [ChIP-seq]


title: H3K4me3 1h_2 [ChIP-seq]


title: 14C_M_884

value: PCG


title: 14C_M_883


title: 14C_M_881


title: 14C_M_879


title: 14C_M_878


title: 14C_M_880


title: H3K4me3 0h_2 [ChIP-seq]


title: H3K4me3 0h_1 [ChIP-seq]


title: H3K4me1 0h_2 [ChIP-seq]

value: H3K4me1 (ab8895, Abcam)


title: H3K4me1 0h_1 [ChIP-seq]


title: 14C_M_877


title: H3K27ac 0h_2 [ChIP-seq]

value: H3K27ac (ab4729, Abcam)


title: Rel 18h_2 [ChIP-seq]

value: WT

value: cRel (sc-71, Santa Cruz)


title: Rel 18h_1 [ChIP-seq]


title: Rel 1h_1 [ChIP-seq]


title: Rel 1h_2 [ChIP-seq]


title: 14C_M_872


title: 14C_M_873


title: H3K27ac 0h_1 [ChIP-seq]


title: 14C_M_875


title: 14C_M_876


title: 14C_M_885


title: 14C_M_870


title: 14C_M_871


title: Rel 0h_2 [ChIP-seq]


title: 14C_M_869


title: Rel 0h_1 [ChIP-seq]


title: RelA 4h_2 [ChIP-seq]

value: RelA (sc-372, Santa Cruz)


title: RelA 4h_1 [ChIP-seq]


title: RelA 1h_2 [ChIP-seq]


title: RelA 1h_1 [ChIP-seq]


title: 14C_M_864


title: 14C_M_866


title: 14C_M_868


title: 14C_M_867


title: RelA 0h_2 [ChIP-seq]


title: RelA 0h_1 [ChIP-seq]


title: 14C_M_862


title: Rel KO 18h [scRNA-seq]

data_processing:
Demultiplexing of raw base call files into FASTQ files was completed with 10X Genomics Cell Ranger (v.3.0.2) mkfastq.
Cell Ranger count combine was used to aggregate multiple sequencing run reads to achieve increased sequencing depth.
Combined Cell Ranger count data were processed in R v3.6.3 with Seurat v3.2.3 (Stuart, Butler et al. 2019) using default parameters.
Quality control filtering was applied to each sample to eliminate downstream analysis of empty droplets, low-quality cells, and potential doublets.
Further barcode filtering was conducted based on % mitochondrial genes, genes detected and reads per barcode; see methods for details.
Each sample was normalized using NormalizeData function.
Principal Component Analysis (PCA) was performed, then 20 dimensions were used for the FindNeighbors and RunUMAP functions to generate Uniform Manifold Approximation and Projection (UMAP).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .h5 files are binary matrix format files containing barcode, feature and matrix information.

extract_protocol:
Follow 10X Genomics Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).
Cells were encapsulated into GEMs and barcoded; cDNA was generated and amplified, fragmented, end repaired, A-tailed, size selected, adapters added, indexed and then sequenced.
10X Genomics single cell 3' gene expression, V.3.0.

treatment_protocol: Cells were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0, 1 hour, 4 hours or 18 hours.

value: Rel-/-


title: Rel KO 1h [scRNA-seq]

value: 1 hours


title: WT 18h [scRNA-seq]

value: B cell


title: WT 1h [scRNA-seq]

value: 10ug/ml goat anti-mouse IgM Fab'2


title: Rel KO 0h [scRNA-seq]


title: WT 0h [scRNA-seq]


title: RelA cKO 4h [scRNA-seq]

value: RelA-flfl x Cd19-cre


title: 14C_M_865


title: RelA cKO 1h [scRNA-seq]


title: 14C_M_863


title: RelA-flfl 4h [scRNA-seq]

value: RelA-flfl

value: 4 hours


title: RelA-flfl 1h [scRNA-seq]

value: 1 hour


title: RelA-flfl 0h [scRNA-seq]

value: 0 hour


title: 14C_M_853


title: 14C_M_861


title: 14C_M_857


title: 14C_M_851


title: 14C_M_852


title: 14C_M_859


title: 14C_M_858


title: 14C_M_855


title: 14C_M_850


title: 14C_M_854


title: Rel KO 18h2 [RNA-seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
RSEM (Li and Dewey 2011) was used to align RNA-Seq reads to the mouse genome and to quantify transcript abundance.
EBSeq (Leng, Dawson et al. 2013) was used to compare the aligned reads from multiple conditions to find differentially expressed genes in wild type using a cutoff of FDR <0.05.
Comparisons between WT and Rel KO or RelA cKO or BAY11-7082-treated samples were carried out DESeq2 (Love, Huber et al. 2014).
Differentially expressed genes were identified using DESeq2.
Two filtering steps were followed to define differentially expressed genes in cells with modified NF-kB expression.
First, all differentially changed genes were selected based on an FDR <0.05 after DESeq2 analysis; Second, only those genes were selected that were more than 2-fold up or down-regulated in wild samples after anti-IgM treatment.
k-means analysis of RNA expression data was carried out in MATLAB using fold change compared with 0h, with correlation as the distance metric, repeat clustering set to 5, and other parameters set to default.
All samples were normalized to 1 million aligned reads for visualization.
For visualization, bigwig files were generated.
CON and RelA cKO samples were aligned to mouse genome assembly mm10, all other bigwig files were aligned to mm9.
Genome_build: mm9 (MGSCv37) or mm10 (GRCm38)
Supplementary_files_format_and_content: .bw: bigwig indexed binary format files used for visualization.
Supplementary_files_format_and_content: RelA_flfl_cKO_WT_Bay_Rel_KO_0h_1h_4h_18h.txt: Tab-delimited text file.

source_name: spleen

growth_protocol: B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol for 30 minutes.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN, 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Two replicates were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 1 hour, 4 hours or 18 hours.

value: 18 hr


title: 14C_M_849


title: 14C_M_848


title: 14C_M_847


title: Rel KO 18h1 [RNA-seq]


title: Rel KO 4h2 [RNA-seq]

value: 4 hr


title: 14C_M_846

value: PCG


title: 14C_M_1177


title: 14C_M_845


title: 14C_M_844


title: 14C_M_843


title: RelA cKO 0h [scRNA-seq]


title: Rel KO 1h2 [RNA-seq]

value: 1 hr


title: Rel KO 1h1 [RNA-seq]


title: 14C_M_842


title: 14C_M_841


title: Rel KO 0h1 [RNA-seq]

value: 0 hr


title: 14C_M_838


title: BAY 18h2 [RNA-seq]

value: 1uM BAY 11-7082; 10ug/ml goat anti-mouse IgM Fab'2

value: I hr inhibitor followed by 18 hr anti IgM


title: BAY 1h1 [RNA-seq]

value: I hr inhibitor followed by 1 hr anti IgM


title: 14C_M_837


title: 14C_M_834


title: 14C_M_835


title: 14C_M_840


title: BAY 1h2 [RNA-seq]


title: BAY 0h2 [RNA-seq]


title: Rel KO 4h1 [RNA-seq]

value: Rel-/-


title: 14C_M_836


title: BAY 18h1 [RNA-seq]


title: BAY 4h2 [RNA-seq]

value: I hr inhibitor followed by 4 hr anti IgM


title: 14C_M_833


title: BAY 4h1 [RNA-seq]

value: B cell


title: 14C_M_832


title: BAY 0h1 [RNA-seq]


title: WT 4h2 [RNA-seq]

value: 10ug/ml goat anti-mouse IgM Fab'2


title: WT 18h2 [RNA-seq]


title: WT 1h2 [RNA-seq]


title: WT 1h1 [RNA-seq]


title: 14C_M_831


title: WT 18h1 [RNA-seq]


title: 14C_M_825


title: 14C_M_827


title: 14C_M_824


title: 14C_M_830


title: 14C_M_826


title: 14C_M_828


title: 14C_M_829


title: RelA cKO 18h2 [RNA-seq]

value: RelA-flfl x Cd19-cre


title: 14C_M_823


title: WT 0h1 [RNA-seq]


title: RelA cKO 4h2 [RNA-seq]


title: 14C_M_822


title: 14C_M_821


title: 14C_M_820


title: RelA cKO 4h1 [RNA-seq]


title: RelA cKO 18h1 [RNA-seq]


title: 14C_M_819


title: RelA cKO 1h2 [RNA-seq]


title: WT 4h1 [RNA-seq]


title: RelA cKO 1h1 [RNA-seq]


title: 14C_M_817


title: 14C_M_816


title: 14C_M_814


title: RelA cKO 0h2 [RNA-seq]


title: 14C_M_813


title: RelA-flfl 18h1 [RNA-seq]

value: RelA-flfl


title: 14C_M_812


title: RelA-flfl 4h2 [RNA-seq]


title: WT 0h2 [RNA-seq]


title: RelA-flfl 4h1 [RNA-seq]


title: RelA-flfl 18h2 [RNA-seq]


title: 14C_M_808


title: 14C_M_811


title: 14C_M_806


title: 14C_M_803


title: 14C_M_809


title: ASO081, RNA-seq rep2 [VS217]

value: squamous cell carcinoma of head and neck

value: cell line


title: 14C_M_807


title: RelA-flfl 1h2 [RNA-seq]


title: RelA cKO 0h1 [RNA-seq]


title: Rel KO 0h2 [RNA-seq]


title: 14C_M_805


title: RelA-flfl 0h2 [RNA-seq]


title: RelA-flfl 0h1 [RNA-seq]


title: RelA-flfl 1h1 [RNA-seq]


title: Stress, replicate 3, snRNAseq

city: Aachen

first: Kai Markus

last: Schneider

address: Pauwelsstraße 30

country: Germany

institute: University Hospital RWTH Aachen

description: 10x Genomics

data_processing:
Cellranger V5
BCL files were demultiplexed, aligned to mouse mm10 genome.
UMI counted using CellRanger software v5.0 (10X Genomics)
Assembly: mouse mm10 genome

source_name: C57BL/6J, ENS nuclei

extract_protocol:
Nuclei were isolated as described in manuscript, sorted on a BD FACSAria Fusion sorter (BD Biosciences)  based on DAPI and INTACT positivity, and loaded into 10X Genomics platform  10X Genomics according to manufacturers protocol
Libraries were prepared using the 10X Genomics platform

value: C57BL/6J, ENS nuclei

value: ENS cells

value: WT

value: 7 days restraint stress


title: 14C_M_810

value: PCG


title: 14C_M_802


title: 14C_M_804


title: ASO081, RNA-seq rep1 [VS213]


title: 14C_M_797


title: 14C_M_796


title: Stress, replicate 2, snRNAseq

description: 10x Genomics


title: PBS, RNA-seq rep1 [VS212]


title: Control, replicate 1, snRNAseq

description: 10x Genomics

value: Control


title: 14C_M_801


title: PBS, RNA-seq rep2 [VS216]


title: 14C_M_795


title: 14C_M_800


title: si1SMYD3, RNA-seq rep3 [VS14]


title: 005_3A005_TH_adv

value: Abdominal aortic aneurysm

value: Adventitia

value: Thrombus-covered

value: Human abdominal aorta


title: Stress, replicate 2, scRNASeq

description: 10x Genomics

library_source: transcriptomic single cell

source_name: primary leukocytes

extract_protocol: CD45+ Leukocytes were isolated as described in manuscript, sorted on a BD FACSAria Fusion sorter (BD Biosciences), and loaded into 10X Genomics platform  10X Genomics according to manufacturers protocol

value: CD45+ Leukocytes

value: primary leukocytes


title: si1SMYD3, RNA-seq rep2 [VS11]

source_name: squamous cell carcinoma of head and neck


title: Stress, replicate 1, scRNASeq

description: 10x Genomics


title: Stress, replicate 1, snRNAseq

description: 10x Genomics


title: 14C_M_799


title: 14C_M_794


title: Control, replicate 2, snRNAseq

description: 10x Genomics


title: Dexa, replicate 1, snRNAseq

description: 10x Genomics

value: 7 days of dexa treatment


title: 14C_M_792


title: 14C_M_786


title: 14C_M_788


title: siNC, RNA-seq rep2 [VS10]

value: siNC


title: 14C_M_790


title: 14C_M_784


title: 14C_M_791


title: si1SMYD3, RNA-seq rep1 [VS8]


title: S.TRi1.3

description: Senescent cells, Tri-1 treated, replicate 3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Assembly: hg19
Supplementary files format and content: Prosessed files contains the raw counts for each gene

source_name: IMR90 cell line

extract_protocol:
IMR90 cells were harvested, and the RNA was extracted using RNeasy mini Kit (Qiagen, cat. no. 74106) and digested with DNase I (Qiagen, cat. no. 79254)
The libraries were prepared using a KAPA RNA HyperPrep kit (Roche, cat. no: 07962312001) and sequenced in a 75-bp paired-end run at the Wistar Genomics Facility using an Illumina NextSeq 500 system

tag: cells

value: senescent

tag: group

tag: replicate


title: Control, replicate 2, scRNAseq

description: 10x Genomics

tag: genotype


title: siNC, RNA-seq rep3 [VS13]

value: squamous cell carcinoma of head and neck

tag: cell line


title: 14C_M_787

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: 14C_M_789


title: 14C_M_780


title: Control, replicate 1, scRNAseq

description: 10x Genomics

tag: cell type


title: 14C_M_785


title: 14C_M_793


title: Colon stress, replicate 5

description: illumina TruSeq stranded mRNA kit

data_processing:
Raw reads were mapped to the mouse reference transcriptome (Ensembl; Mus musculus version 67) using Kallisto61 version 0.46.
Assembly: Ensembl; Mus musculus version 67

source_name: total Colon

extract_protocol:
Total RNA was extracted using TRIzolTM (Invitrogen, 15596026) according to the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq stranded mRNA kit with Illumina TruSeq unique dual indices according to the manufacturer’s instructions. Quality and quantity control of RNA and libraries were performed using an Agilent 4200 TapeStation and Qubit 4, respectively. Libraries were sequenced on an Illumina NextSeq 550

value: total Colon


title: Colon stress, replicate 3

description: illumina TruSeq stranded mRNA kit


title: Colon stress, replicate 4

description: illumina TruSeq stranded mRNA kit


title: 14C_M_783

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


title: siNC, RNA-seq rep1 [VS7]

value: cell line


title: 14C_M_782


title: S.DMSO.3

description: Senescent cells, DMSO treated, replicate 3

value: DMSO


title: Colon stress, replicate 1

description: illumina TruSeq stranded mRNA kit

value: WT


title: 14C_M_777


title: 14C_M_781


title: 14C_M_775


title: 14C_M_778


title: S.TRi1.2

description: Senescent cells, Tri-1 treated, replicate 2


title: S.DMSO.2

description: Senescent cells, DMSO treated, replicate 2


title: 14C_M_779


title: Colon control, replicate 5

description: illumina TruSeq stranded mRNA kit


title: Colon control, replicate 4

description: illumina TruSeq stranded mRNA kit


title: 14C_M_776


title: S.DMSO.1

description: Senescent cells, DMSO treated, replicate 1


title: 14C_M_773


title: 14C_M_772


title: Colon control, replicate 3

description: illumina TruSeq stranded mRNA kit


title: 14C_M_770


title: 14C_M_769


title: 14C_M_771


title: Colon control, replicate 2

description: illumina TruSeq stranded mRNA kit


title: Colon stress, replicate 2

description: illumina TruSeq stranded mRNA kit

value: 7 days restraint stress


title: S.TRi1.1

description: Senescent cells, Tri-1 treated, replicate 1


title: S.shTR.1

description: Senescent cells, shTXNRD1 condition, replicate 1


title: 14C_M_701

value: PCG


title: 14C_M_703


title: 14C_M_702


title: S.ctrl.2

description: Senescent cells, control condition, replicate 2

value: control


title: S.ctrl.3

description: Senescent cells, control condition, replicate 3


title: 14C_M_700


title: 14C_M_699


title: Growing cells, control condition, replicate 3

value: growing


title: S.ctrl.1

description: Senescent cells, control condition, replicate 1


title: S.shTR.3

description: Senescent cells, shTXNRD1 condition, replicate 3


title: Growing cells, control condition, replicate 1


title: 14C_M_694


title: 14C_M_693


title: 14C_M_695


title: 14C_M_692


title: 14C_M_698


title: 14C_M_691


title: 14C_M_696


title: 14C_M_688


title: Growing cells, control condition, replicate 2


title: 14C_M_689


title: 14C_M_690


title: 14C_M_685


title: 14C_M_687


title: S.shTR.2

description: Senescent cells, shTXNRD1 condition, replicate 2


title: CCMCL1-sgFOXO1.2

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: sgFOXO1.2 infected

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM value of each gene in each sample

source_name: CCMCL1 MCL cells

growth_protocol: Cells were acttively growing in RPMI1640 media witth 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 96 hr prior to the lysis of cells were infected with lentivirus particles encoding respective sgRNA.

value: B cell lymphoma

value: Mantle cell lymphoma

tag: tumor origin

value: Mature B cell

tag: sgrna


title: 14C_M_686

source_name: C57BL/6J Male P56 Mouse Brain


title: CCMCL1-sgROSA

description: sgROSA infected

value: sgROSA


title: 14C_M_684


title: 14C_M_683


title: CCMCL1-sgFOXO1.1

description: sgFOXO1.1 infected


title: 14C_M_680


title: Colon control, replicate 1

description: illumina TruSeq stranded mRNA kit

value: Control


title: 14C_M_681


title: H3K27Ac

description: H3K27Ac ChIP

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm9 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: hg19
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

growth_protocol: We harvested mouse brains at indicated ages and cross-linked with 1% paraformaldehyde.

extract_protocol:
After isolation of nucleus with lysis buffer (50 mM HEPES-KOH, 135 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% TritonX100), the chromatin was digested with micrococcal nuclease. The pellet was resuspended with IP buffer (50 mM Tris-HCl, 100 mM NaCl, 10 mM EDTA, 0.1% SDS, and 1% TritonX100) and the nuclear membrane was broken with sonication. IP was performed with respective antibody overnight at  cold room. The antibody-antigen was precipitated with magnetic beads. The ChIPed DNA was eluted and extracted with DNA extraction kit (MN #740609.250).
Libraries were made using KAPA Hyper Prep kit (KAPABiosystems #KR0961) following manufacturer’s instructions. Briefly, 30 ng from each immunoprecipitated or Input DNA, were end-repaired, phosphorylated, A-tailed and ligated to adaptors (Roche SeqCap Adapter kit A #07141530001). Ligated products were size selected with 0.8X SPRI beads to obtain 250~350 bp of DNA. After purification, 8-cycle PCR amplification reaction was performed. PCR product was cleaned by the use of 1X SPRI beads. Final product was resuspended in 30 ul of Tris buffer.

value: blood

tag: disease

tag: chip antibody

value: abcam #ab4729


title: 14C_M_682

tag: brain region


title: 14C_M_678

tag: age


title: IRF4

description: IRF4 ChIP

tag: tissue

value: Cell Signaling Technology #4964


title: 14C_M_677

tag: strain


title: 14C_M_675


title: EBF1

description: EBF1 ChIP

value: millipore #ABE1294


title: 14C_M_673


title: FOXO1

description: FOXO1 ChIP

value: Home-made


title: 14C_M_672


title: 14C_M_671


title: 14C_M_668


title: PAX5

description: PAX5 ChIP

value: MyBioSource #MBS8542987


title: 14C_M_676


title: neclei isolated from control (PBS)-treated mouse tongue epithelium

first: Hong

last: Wang

address: 3500 Market Street

institute: Monell Chemical Senses Center

library_source: genomic single cell

data_processing:
Demultiplexed raw base call files generated from sequencing were processed using the 10x Genomics Cell Ranger ATAC pipeline (version 1.2.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: circumvallate papillae

extract_protocol:
To isolate the nuclei for scATAC-seq, the peeled tongue epithelia from PBS- and LPS-treated mice were prepared. Six mice per group were used. Epithelia from the circumvallate papillae were cut off and rinsed in calcium-free Tyrode’s buffer (140 mM NaCl, 5 mM KCl, 10 mM HEPES, 1 mM MgCl2, 10 mM glucose, 10 mM Na-pyruvate, 2 mM EGTA, pH 7.4). Circumvallate epithelia were then transferred to a solution containing 0.25% trypsin-EDTA (Fisher Scientific) and incubated at 37˚C for 15 min. Cold Opti-MEM with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific) was added to the mixture, and cells were further dissociated by gentle pipetting. Cells were centrifuged, rinsed with cold Opti-MEM with 10% FBS, passed through a 40 µm cell strainer, and rinsed once with wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% bovine serum albumin (BSA), and 0.1% Tween-20). Dissociated cells were then resuspended in 0.1x Lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.9% BSA, 0.01% Tween-20, 0.01% NP40, 0.001% digitonin) and incubated on ice for 5 min. Cell lysis was monitored by staining with trypan blue solution (0.4%; Thermo Fisher Scientific). Nuclei were rinsed with wash buffer, centrifuged, resuspended in 1x nuclei buffer (10x Genomics), and counted. About 4000 nuclei per group were used for downstream ATAC-seq procedures.
The chromatin transposition reaction, nuclei partitioning, barcoding, and library construction were carried out using 10x Genomics Chromium scATAC reagent kits, following the manufacturer’s protocols. High-throughput sequencing was also performed at the NGSC using Illumina HiSeq 4000 instruments.
Cell Ranger ATAC 1.2.0

tag: developmental stage

value: adult

value: circumvallate papillae

value: PBS


title: 14C_M_669

value: PCG


title: 14C_M_670


title: 14C_M_679