title: SSCL_M1_ocSSC_p05c12r02_C23_24m_TCATTCACCTCT-ATTGTCCCATTT


title: WT_SNK170425005_D03

status: Public on Jun 11 2021

type: SRA

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: RNA from single nuclei

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 75 -l 36 -k 4.0 -q 30'. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '--no-softclip -p 4'. Gene expression levels were counted with featureCounts, function of Subread (version 1.5.0) using GENCODE vM15 annotation file.
We then removed samples outside of the mean minus three standard deviations of the total read number (FastQC) or the number of assigned reads to gene regions (featureCounts); over 5% reads assigning to ribosomal RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
We performed dimensional reduction of the count data (RPKM) and removed samples that were presumed to be immature and for which no cell type could be estimated.
Genome_build: mm10
Supplementary_files_format_and_content: txt

molecule: total RNA

organism: Mus musculus

source_name: nuclei from mice cortical region

extract_protocol:
Nuclei were isolated from adult mice brain (3 mice for each genotypes). After collection of nuclei by iodixanol density gradient. Single nuclei were directly sorted into the 96-well or 384-well plate pre-dispensed with the cell lysis buffer.
Single-nucleus RNA-seq was carried out according to the advanced method of RamDA-seq (https://doi.org/10.1038/s41467-018-02866-0).

treatment_protocol: Tamoxifen treatment at 3 weeks old (2 times)

tag: condition

value: WT (96 wel)

tag: strain

tag: tissue

value: brain cortex

tag: age

value: 14 weeks old

tag: celltype

value: Neuron

tag: genotype

value: wild type (Ehmt1+/+)

tag: treatment

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: WT_SNK170425003_H02

description: RNA from single nuclei

value: Microglia


title: WT_SNK170425005_A02

description: RNA from single nuclei

value: Oligodendrocyte


title: SSCL_M1_ocSSC_p05c09r05_I17_24m_TCAGCGAACTTT-ACAGCGTGGAGA

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

country: USA

institute: UC Davis

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome h38 using STAR 2.4 (Dobin et al., 2013)
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Genome_build: GRCm38.p6.gencode.vM20
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: Long bones

growth_protocol: freshly purified cells without prior in vitro culture

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and SSC populations purified via FACS.
SmartSeq2 pipeline (Picelli et al.)

treatment_protocol: no treatment

value: Aged 24 months

tag: batch

tag: Sex

value: male


title: SSCL_M1_ocSSC_p05c12r05_I23_24m_TCGCAATACATC-CGGAGCAAGGGC


title: WT_SNK170425005_E12

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c11r04_G21_24m_TCCAGCAAGTGG-TCCTCTGGCATC


title: SSCL_M1_ocSSC_p05c09r03_E17_24m_TCATAGTTTCAC-AACGAAGACCTT


title: WT_SNK170425003_D03

description: RNA from single nuclei


title: WT_SNK170425005_D04

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c05r01_A09_24m_TTACCGAGCGGA-CGGAAGCGTCAG


title: SSCL_M1_ocSSC_p05c04r05_I07_24m_TCAGGTCTACTA-GCACTTTCGCCT


title: WT_SNK170425005_E06

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c10r07_M19_24m_TATGACTTGTTG-TATGGCTCTTCG


title: SSCL_M1_ocSSC_p05c12r04_G23_24m_TCAGCAGCAAGG-ACCACGAGGTAG


title: WT_SNK170425005_H09

description: RNA from single nuclei


title: WT_SNK170425003_A08

description: RNA from single nuclei


title: WT_SNK170425003_E10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c05r02_C09_24m_TCACAGAGTTTG-TGATGTAGACAC


title: SSCL_M1_ocSSC_p05c02r02_C03_24m_TCAAGCACTTCC-GTTATGATTAGA


title: SSCL_M1_ocSSC_p05c01r03_E01_24m_TATCCCTATCGG-ATACAAGGTCTA


title: WT_SNK170425003_F10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c03r08_O05_24m_TAGGATAGGTGC-TGGAACAAACAA


title: WT_SNK170425005_H10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c01r02_C01_24m_TAGCGGTTGGTG-CAATAGTCACGA


title: WT_SNK170425005_C06

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c10r06_K19_24m_TAACACTAAAGC-AACCGAGCAATA


title: WT_SNK170425003_F08

description: RNA from single nuclei


title: WT_SNK170425005_E05

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r05_I13_24m_GTCTTGGCTGAG-CGATACAAAGAA


title: SSCL_M1_ocSSC_p05c04r01_A07_24m_TAGAGCGGGCGG-ATACAACGCTCG


title: SSCL_M1_ocSSC_p05c12r06_K23_24m_GTATTCTTCAGA-CTCAAATAAGAG


title: SSCL_M1_ocSSC_p05c01r01_A01_24m_TCAATGACTAAA-CGTCAAACAACA


title: WT_SNK170425003_H08

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c06r04_G11_24m_GGTCCAAGTCCC-TTTCTGAATAGC


title: WT_SNK170425003_F06

description: RNA from single nuclei


title: WT_SNK170425005_G06

description: RNA from single nuclei


title: WT_SNK170425003_B11

description: RNA from single nuclei


title: SSCk_M1_ocSSC_p12c05r03_F10_24m_TAGTTACAGGCG-GGCGAGCGTTCA


title: SSCL_M1_ocSSC_p05c07r02_C13_24m_GTATGAAGCCAA-ATGGGACCAGGT


title: SSCL_M1_ocSSC_p05c08r05_I15_24m_GCACACTGATAA-TGCTAAGAAATC


title: SSCL_M1_ocSSC_p05c07r07_M13_24m_TACCGATGTGAG-ACTCCACTGGGC


title: WT_SNK170425005_F02

description: RNA from single nuclei


title: WT_SNK170425003_B04

description: RNA from single nuclei


title: WT_SNK170425005_G01

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c09r01_A17_24m_GCGGGCTACTCG-ATTCACGACGCT


title: WT_SNK170425005_F04

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c01r05_I01_24m_GATAACGGGCAA-ACCCTCTAAATG


title: SSCL_M1_ocSSC_p05c12r08_O23_24m_GGGTGATTGACA-AAATGTGACAAT


title: SSCL_M1_ocSSC_p05c08r03_E15_24m_GAAGTTCTCGTC-AACTCAATGTAA


title: WT_SNK170425005_C08

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c04r04_G07_24m_GAACATCTTTGC-ATGCTATCTGAC


title: SSCL_M1_ocSSC_p05c03r04_G05_24m_GCCGAATCGCCG-AGTAGAGAAGGG


title: SSCL_M1_ocSSC_p05c05r05_I09_24m_GTTGTATCATTC-ATTAGCAAGTCC


title: WT_SNK170425003_H10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c12r03_E23_24m_GACTTCTCTTAG-GCTCACTCGGTC


title: SSCL_M1_ocSSC_p05c02r06_K03_24m_GCCAACCAGTAG-CAAGATACGGTG


title: SSCL_M1_ocSSC_p05c03r07_M05_24m_GAGGAGGGCGTT-TGGCGAGTCTAT


title: WT_SNK170425005_B11

description: RNA from single nuclei


title: WT_SNK170425003_B06

description: RNA from single nuclei


title: WT_SNK170425005_F10

description: RNA from single nuclei


title: WT_SNK170425003_C07

description: RNA from single nuclei


title: WT_SNK170425003_F02

description: RNA from single nuclei


title: WT_SNK170425003_G09

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c02r01_A03_24m_CTCTTGTATCTT-GTCTGTCAAGGC


title: SSCL_M1_ocSSC_p05c06r02_C11_24m_CTTCTATCTAAA-CGCATTCCCATT


title: WT_SNK170425005_H03

description: RNA from single nuclei


title: WT_SNK170425005_H07

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c08r01_A15_24m_CGGGATGGCTGG-CTGAAAGAGATT


title: WT_SNK170425005_G02

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r06_K13_24m_CGACTGTCATCT-TCTGGTCAGCCC


title: SSCL_M1_ocSSC_p05c06r01_A11_24m_CGATGCGTGAGG-ATAATCTTGCGT


title: WT_SNK170425003_C05

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r01_A13_24m_CGAGGAGTCCGA-GACGGGTGCGAG


title: WT_SNK170425005_B08

description: RNA from single nuclei


title: WT_SNK170425003_B02

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c04r06_K07_24m_CCTGTCAATGCT-AACACTCAGTAA


title: WT_SNK170425005_G05

description: RNA from single nuclei


title: WT_SNK170425003_E08

description: RNA from single nuclei


title: WT_SNK170425003_D08

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r03_E13_24m_CGACACCCAATC-TAATGTATTCCT


title: SSCL_M1_ocSSC_p05c05r06_K09_24m_CGAAGAAGTTAC-CGAAGATGACGA


title: SSCL_M1_ocSSC_p05c05r04_G09_24m_CCGAACACATTT-ACATACGACTGT


title: WT_SNK170425005_E01

description: RNA from single nuclei


title: WT_SNK170425005_A08

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c06r06_K11_24m_CCCGCTACAGTA-TCGCACTCACAC


title: SSCL_M1_ocSSC_p05c01r07_M01_24m_CTAACTCGGTTC-CCTTCACGGGTG


title: SSCL_M1_ocSSC_p05c10r01_A19_24m_CCTCCGCCTCAT-CAGGACCCGCAT


title: WT_SNK170425005_D08

description: RNA from single nuclei


title: WT_SNK170425003_C01

description: RNA from single nuclei


title: WT_SNK170425005_F01

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c01r04_G01_24m_CCAGCAAATGAT-AGAGTGTGCCTC


title: SSCL_M1_ocSSC_p05c08r07_M15_24m_CCCATTAGGCTA-GTTAGAGAGGAA


title: SSCL_M1_ocSSC_p05c11r02_C21_24m_CAGCGACTCCGT-ATAACTCGCCGT


title: WT_SNK170425003_G07

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c03r05_I05_24m_CCCATTCCCAGC-GACTTTCAAACG


title: SSCL_M1_ocSSC_p05c05r08_O09_24m_CAGACATCAAAC-ATAGGCAGTTAT


title: WT_SNK170425003_E01

description: RNA from single nuclei


title: WT_SNK170425003_G12

description: RNA from single nuclei


title: WT_SNK170425003_D01

description: RNA from single nuclei


title: WT_SNK170425005_E10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c09r06_K17_24m_CCGCTTGATACA-ACCCGATGTGCC


title: SSCL_M1_ocSSC_p05c06r07_M11_24m_CATAAATCGCAA-CGATGAGCCTGG


title: WT_SNK170425003_A09

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r04_G13_24m_CACGGATACAGA-ACCCGTGTATCG


title: WT_SNK170425003_G10

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c04r03_E07_24m_CAATACGGGCAC-GACACGCCCTGA


title: SSCL_M1_ocSSC_p05c03r01_A05_24m_ATGTGTATCCTC-AGGTCGCTTGGG


title: WT_SNK170425003_C02

description: RNA from single nuclei


title: WT_SNK170425005_A06

description: RNA from single nuclei


title: WT_SNK170425005_D07

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c11r06_K21_24m_ATGAAAGCATTT-TATCCGAAGTTG


title: WT_SNK170425005_G10

description: RNA from single nuclei


title: WT_SNK170425005_C04

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c02r07_M03_24m_ATCCTCGTTCAA-ACATTATTTGTG


title: WT_SNK170425005_E09

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c01r08_O01_24m_CAAGTAGTTGAC-AGAATCGGGCAG


title: WT_SNK170425003_G01

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c06r08_O11_24m_AGGGCGACTTTG-CGAGACTACCGT


title: SSCL_M1_ocSSC_p05c08r04_G15_24m_CAGAAGGATAGA-GATGGTAACGGT


title: SSCL_M1_ocSSC_p05c06r05_I11_24m_AGGCGATTTAGG-GGACGGCGTTCT


title: WT_SNK170425003_G03

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c12r01_A23_24m_ACTTGCTGGTGT-ACGGACCAGCGA


title: SSCL_M1_ocSSC_p05c04r08_O07_24m_ACTGCGTCCGTG-ATAAGCGTAGAA


title: WT_SNK170425003_C09

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c05r07_M09_24m_CACTATTTGTTC-TTATGCCAATCC


title: SSCL_M1_ocSSC_p05c09r07_M17_24m_ACCGCCCGTATT-ACCTCAAATGGC


title: WT_SNK170425003_E03

description: RNA from single nuclei


title: WT_SNK170425005_D09

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c07r08_O13_24m_AGGTGGTGAGTT-TGATGCCTAAGA


title: SSCL_M1_ocSSC_p05c11r03_E21_24m_AAACTTCCAGCA-AACCGCCTGTTG


title: WT_SNK170425005_E11

description: RNA from single nuclei


title: WT_SNK170425003_C11

description: RNA from single nuclei


title: WT_SNK170425005_C01

description: RNA from single nuclei


title: SSCb_M_ocSSC_P9_2m_72

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome h38 using STAR 2.4 (Dobin et al., 2013)
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Genome_build: GRCm38.p6.gencode.vM20
Supplementary_files_format_and_content: comma-separated text file with raw gene counts for every gene and every sample

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and SSC populations purified via FACS.
SmartSeq2 single cell  pipeline (Picelli et al.)

value: bone

tag: cell type

value: ocSSC

value: Adult


title: SSCb_M_ocSSC_P8_2m_65


title: WT_SNK170425003_A01

description: RNA from single nuclei


title: SSCb_M_ocSSC_P7_2m_214


title: WT_SNK170425003_H04

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c10r08_O19_24m_AAGTCACCGAAT-GAGCAACCAAAG


title: WT_SNK170425003_B09

description: RNA from single nuclei


title: WT_SNK170425003_D11

description: RNA from single nuclei


title: SSCL_M1_ocSSC_p05c01r06_K01_24m_ACATCTCTACAT-ATCTCCTCGCCC


title: WT_SNK170425003_F12

description: RNA from single nuclei


title: WT_SNK170425003_G04

description: RNA from single nuclei


title: WT_SNK170425003_F04

description: RNA from single nuclei


title: SSCb_M_ocSSC_P5_2m_40


title: SSCb_M_ocSSC_P6_2m_129


title: WT_SNK170425003_H06

description: RNA from single nuclei


title: SSCb_M_ocSSC_P4_2m_76


title: WT_SNK170425003_A03

description: RNA from single nuclei


title: SSCb_M_ocSSC_P23_2m_24


title: WT_SNK170425005_D06

description: RNA from single nuclei


title: SSCb_M_ocSSC_P22_2m_219


title: WT_SNK170425003_E04

description: RNA from single nuclei


title: WT_SNK170425005_G11

description: RNA from single nuclei


title: SSCb_M_ocSSC_P24_2m_330


title: WT_SNK170425005_C05

description: RNA from single nuclei


title: SSCb_M_ocSSC_P20_2m_109


title: SSCb_M_ocSSC_P21_2m_110


title: SSCb_M_ocSSC_P3_2m_263


title: WT_SNK170425005_E08

description: RNA from single nuclei


title: WT_SNK170425003_D04

description: RNA from single nuclei


title: SSCb_M_ocSSC_P18_2m_196


title: WT_SNK170425003_A11

description: RNA from single nuclei


title: WT_SNK170425003_A07

description: RNA from single nuclei


title: SSCb_M_ocSSC_P2_2m_144


title: WT_SNK170425003_E06

description: RNA from single nuclei


title: SSCb_M_ocSSC_P16_2m_115


title: SSCb_M_ocSSC_P15_2m_318


title: WT_SNK170425005_C09

description: RNA from single nuclei


title: SSCb_M_ocSSC_P17_2m_177


title: WT_SNK170425005_G07

description: RNA from single nuclei


title: WT_SNK170425005_H02

description: RNA from single nuclei


title: SSCb_M_ocSSC_P13_2m_355


title: WT_SNK170425005_F05

description: RNA from single nuclei


title: SSCb_M_ocSSC_P14_2m_380


title: WT_SNK170425003_F07

description: RNA from single nuclei


title: SSCb_M_ocSSC_P12_2m_149


title: WT_SNK170425003_B12

description: RNA from single nuclei


title: SSCb_M_pvSSC_O9_2m_39

value: pvSSC


title: SSCb_M_ocSSC_P11_2m_12


title: SSCb_M_ocSSC_P1_2m_176


title: SSCb_M_ocSSC_P10_2m_3


title: SSCb_M_ocSSC_P19_2m_335


title: WT_SNK170425003_F09

description: RNA from single nuclei


title: SSCb_M_pvSSC_O7_2m_190


title: WT_SNK170425003_B10

description: RNA from single nuclei


title: WT_SNK170425005_F11

description: RNA from single nuclei


title: WT_SNK170425003_H03

description: RNA from single nuclei


title: SSCb_M_pvSSC_O5_2m_223


title: SSCb_M_pvSSC_O6_2m_282


title: WT_SNK170425005_H06

description: RNA from single nuclei


title: SSCb_M_pvSSC_O3_2m_339


title: SSCb_M_pvSSC_O4_2m_42


title: WT_SNK170425005_B09

description: RNA from single nuclei


title: WT_SNK170425003_C12

description: RNA from single nuclei


title: SSCb_M_pvSSC_O23_2m_181


title: SSCb_M_pvSSC_O24_2m_244


title: SSCb_M_pvSSC_O22_2m_32


title: WT_SNK170425003_D07

description: RNA from single nuclei


title: WT_SNK170425005_G03

description: RNA from single nuclei


title: WT_SNK170425003_F11

description: RNA from single nuclei


title: SSCb_M_pvSSC_O20_2m_163


title: WT_SNK170425005_A03

description: RNA from single nuclei


title: SSCb_M_pvSSC_O21_2m_331


title: SSCb_M_pvSSC_O2_2m_116


title: WT_SNK170425003_B05

description: RNA from single nuclei


title: SSCb_M_pvSSC_O8_2m_46


title: WT_SNK170425003_A05

description: RNA from single nuclei


title: SSCb_M_pvSSC_O19_2m_253


title: SSCb_M_pvSSC_O18_2m_246


title: SSCb_M_pvSSC_O17_2m_33


title: WT_SNK170425005_A09

description: RNA from single nuclei


title: SSCb_M_pvSSC_O16_2m_43


title: WT_SNK170425005_A07

description: RNA from single nuclei


title: WT_SNK170425003_E11

description: RNA from single nuclei


title: WT_SNK170425004_D09

description: RNA from single nuclei


title: WT_SNK170425002_C03

description: RNA from single nuclei


title: SSCb_M_pvSSC_O15_2m_135


title: WT_SNK170425005_C10

description: RNA from single nuclei


title: WT_SNK170425002_G02

description: RNA from single nuclei


title: SSCb_M_pvSSC_O13_2m_10


title: SSCb_M_pvSSC_O12_2m_277


title: WT_SNK170425002_D10

description: RNA from single nuclei


title: SSCb_M_pvSSC_O11_2m_222


title: BeWo total gDNA

type: genomic

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description:
1360
Input DNA

hyb_protocol: The labeled DNA was hybridized to the Affymetrix GeneChip human promoter arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cDNA. The staining was further amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody, followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was performed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings.

data_processing: Affymetrix Human Tiling 1.0R Promoter Arrays were analyzed using Tiling Array Software (v 1.1.02, Affymetrix). The Raw data (intensity) were scaled to a target intensity of 100, normalized by quantile normalization, and log2 transformed.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: BeWo 50 mM forskolin, 24hr total input

label_protocol: DNA fragments were pulled down by sequential chromatin immunoprecipitation. Amplification of dUTP-incorporated DNA was performed by ligand-mediated PCR (LMPCR). Libraries were prepared according to Affymetrix instructions (Chromatin Immunoprecipitation Assay Protocol). Amplified ChIP targets were cut with Uracil DNA Glycosylase (UDG) and APE1 restriction enzyme treatment into short fragments (~70-80bp). The samples were to be used for fragmentation analysis using a Bioanalyzer. Finally, DNA fragments were labeled by Terminal Deoxynucleotidyl Transferase and ready for chip hybridization.

growth_protocol: BeWo31 cell was cultured in 15% FBS F12K medium containing 1X Penicillin-Streptomycin-Glutamine.

extract_protocol: Cells were treated with 4% formaldehyde to crosslink DNA and proteins. Lysates were sonicated and GCM1-DNA complexes were isolated with antibody.

treatment_protocol: BeWo31 was treated 50mM forskolin for 24 hours.

tag: cell line

value: BeWo cells stably expressing HA-GCM1 (BeWo34)

value: 50 mM forskolin, 24hr

tag: chip antibody


title: SSCb_M_pvSSC_O10_2m_241


title: SSCb_M_pvSSC_O1_2m_272


title: WT_SNK170425004_E11

description: RNA from single nuclei


title: WT_SNK170425004_C01

description: RNA from single nuclei


title: SSCb_M_ocSSC_N9_2m_187


title: WT_SNK170425005_G04

description: RNA from single nuclei


title: SSCb_M_ocSSC_N7_2m_37


title: WT_SNK170425002_G06

description: RNA from single nuclei


title: BeWo HA-GCM1 IP DNA rep2

description:
1359
IP DNA

source_name: BeWo 50 mM forskolin, 24hr HA-bead IP 2

value: BeWo cells stably expressing HA-GCM1 (BeWo33)

value: Monoclonal Anti-HA-Agarose (Sigma, A2095)


title: SSCb_M_ocSSC_N8_2m_118


title: WT_SNK170425003_D02

description: RNA from single nuclei

value: WT (96 wel)

value: brain cortex


title: SSCb_M_pvSSC_O14_2m_240


title: SSCb_M_ocSSC_N5_2m_158


title: WT_SNK170425002_H12

description: RNA from single nuclei

value: 14 weeks old


title: SSCb_M_ocSSC_N4_2m_194


title: SSCb_M_ocSSC_N6_2m_324


title: BeWo IgG IP DNA

description:
1357
IP DNA

source_name: BeWo 50 mM forskolin, 24hr IgG-bead IP

value: BeWo cells stably expressing HA-GCM1 (BeWo31)

value: Mouse IgG-Agarose (Sigma, A0919)


title: WT_SNK170425004_D06

description: RNA from single nuclei

value: Neuron

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: TRSPZ012105

city: Penzberg

first: Henrik

last: Failmezger

address: Nonnenwald 2

country: Germany

institute: Roche Diagnostics GmbH

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq2 version 2.20.0 (Illumina).
FASTQ files were quality checked with FastQC version 0.11.5
Aligned reads were quality checked with MultiQC version 1.7
Genome_build: RNASeq paired-end reads were mapped onto the human genome (build hg38) with read aligner STAR version 2.5.2a using default mapping parameters
Supplementary_files_format_and_content: Numbers of mapped reads for all RefSeq and/or Ensembl transcript variants of a gene were combined into a single value (i. e. count) by SAMTools version 1.9  and normalized as rpkm (library size and transcript length normalized counts )

source_name: Intestine large colon

extract_protocol:
The AllPrep DNA/RNA FFPE Kit (Qiagen Cat No./ID: 80234) was used to purify genomic DNA and total RNA from 10 μm FFPET curls, according to the manufacturers instructions. RNA samples were then assessed for quality and quantity using the Qubit instrument and the Agilent Bioanalyzer to determine the degradation of the RNA samples (DV200 value).
To generate the sequencing library, the hybridization-based Illumina TruSeq RNA Access method was performed according to the manufacturers instructions, with first preparation of the total RNA library and second library enrichment for coding RNA. Finally, normalized libraries were sequenced using the Illumina sequencing-by-synthesis platform, with a  sequencing protocol of 50 bp paired-end sequencing and total read depth of 25M reads per sample

tag: tumor type

value: primary tumor

tag: tumor stage

value: IVA

tag: tumor grade


title: SSCb_M_ocSSC_N23_2m_352

value: bone

value: ocSSC

value: male


title: SSCb_M_ocSSC_N22_2m_357

value: Adult


title: TRSPZ012103

value: IIA


title: SSCb_M_ocSSC_N3_2m_75


title: BeWo HA-GCM1 IP DNA rep1

description:
1358
IP DNA

source_name: BeWo 50 mM forskolin, 24hr HA-bead IP 1

value: BeWo cells stably expressing HA-GCM1 (BeWo32)

value: 50 mM forskolin, 24hr


title: SSCb_M_ocSSC_N20_2m_4


title: WT_SNK170425002_G11

description: RNA from single nuclei

value: WT (96 wel)


title: WT_SNK170425004_C05

description: RNA from single nuclei

value: brain cortex


title: WT_SNK170425004_G11

description: RNA from single nuclei

value: 14 weeks old


title: SSCb_M_ocSSC_N21_2m_367


title: SSCb_M_ocSSC_N2_2m_261


title: TRSPZ012102

value: IIIB


title: TRSPZ012101


title: SSCb_M_ocSSC_N18_2m_257


title: SSCb_M_ocSSC_N17_2m_67


title: TRSPZ012100

value: I


title: SSCb_M_ocSSC_N16_2m_199


title: WT_SNK170425004_E08

description: RNA from single nuclei

value: Microglia


title: SSCb_M_ocSSC_N19_2m_125


title: WT_SNK170425002_A02

description: RNA from single nuclei

value: Neuron

value: wild type (Ehmt1+/+)


title: WT_SNK170425004_A01

description: RNA from single nuclei

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: TRSPZ011982

value: primary tumor


title: SSCb_M_ocSSC_N15_2m_57

value: bone


title: SSCb_M_ocSSC_N14_2m_338

value: ocSSC


title: TRSPZ012099

value: IV


title: SSCb_M_ocSSC_N13_2m_243

value: Adult

value: male


title: SSCb_M_ocSSC_N24_2m_184


title: SSCb_M_ocSSC_N12_2m_215


title: WT_SNK170425002_B03

description: RNA from single nuclei


title: SSCb_M_ocSSC_N10_2m_169


title: TRSPZ011980

value: IIA


title: SSCb_M_ocSSC_N1_2m_26


title: WT_SNK170425002_E02

description: RNA from single nuclei


title: TRSPZ011978

value: IIIC


title: SSCb_M_pvSSC_M8_2m_264

value: pvSSC


title: SSCb_M_pvSSC_M9_2m_205


title: WT_SNK170425002_F03

description: RNA from single nuclei

value: WT (96 wel)

value: brain cortex

value: Oligodendrocyte


title: SSCb_M_pvSSC_M7_2m_254


title: SSCb_M_pvSSC_M5_2m_293


title: WT_SNK170425004_F11

description: RNA from single nuclei

value: 14 weeks old


title: SSCb_M_pvSSC_M4_2m_80


title: TRSPZ011976


title: WT_SNK170425004_H02

description: RNA from single nuclei


title: SSCb_M_pvSSC_M3_2m_343


title: TRSPZ011975


title: SSCb_M_pvSSC_M23_2m_248


title: SSCb_M_pvSSC_M24_2m_237


title: WT_SNK170425002_D09

description: RNA from single nuclei

value: Microglia


title: TRSPZ011981

value: IIIB


title: SSCb_M_pvSSC_M22_2m_148


title: WT_SNK170425004_F05

description: RNA from single nuclei

value: wild type (Ehmt1+/+)


title: SSCb_M_pvSSC_M21_2m_161


title: TRSPZ011973


title: TRSPZ011974


title: SSCb_M_pvSSC_M2_2m_262


title: SSCb_M_pvSSC_M20_2m_81


title: WT_SNK170425004_G07

description: RNA from single nuclei

value: Neuron

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: WT_SNK170425002_E09

description: RNA from single nuclei


title: TRSPZ011979

value: primary tumor


title: SSCb_M_pvSSC_M19_2m_25

value: bone


title: TRSPZ011972

value: IIB


title: SSCb_M_pvSSC_M6_2m_92

value: Adult


title: WT_SNK170425004_C09

description: RNA from single nuclei


title: WT_SNK170425002_B01

description: RNA from single nuclei


title: TRSPZ011971


title: SSCb_M_pvSSC_M17_2m_221

value: male


title: SSCb_M_pvSSC_M15_2m_157


title: WT_SNK170425002_A06

description: RNA from single nuclei


title: TRSPZ011970


title: SSCb_M_pvSSC_M16_2m_286


title: WT_SNK170425002_H09

description: RNA from single nuclei


title: TRSPZ011967


title: SSCb_M_pvSSC_M12_2m_68


title: SSCb_M_pvSSC_M14_2m_322


title: SSCb_M_pvSSC_M11_2m_283


title: TRSPZ011969


title: WT_SNK170425002_A04

description: RNA from single nuclei


title: SSCb_M_pvSSC_M10_2m_182


title: TRSPZ011966

value: IIA


title: SSCb_M_ocSSC_N11_2m_206

value: ocSSC


title: WT_SNK170425002_C04

description: RNA from single nuclei


title: SSCb_M_pvSSC_M1_2m_208

value: pvSSC


title: SSCb_M_ocSSC_L9_2m_249


title: SSCb_M_ocSSC_L6_2m_162


title: SSCb_M_ocSSC_L7_2m_82


title: SSCb_M_ocSSC_L8_2m_96


title: SSCb_M_pvSSC_M18_2m_252


title: WT_SNK170425002_H11

description: RNA from single nuclei

value: WT (96 wel)


title: TRSPZ011962

value: IIIC


title: SSCb_M_ocSSC_L5_2m_301


title: SSCb_M_ocSSC_L4_2m_155


title: WT_SNK170425004_G03

description: RNA from single nuclei

value: brain cortex


title: WT_SNK170425004_A07

description: RNA from single nuclei

value: 14 weeks old


title: TRSPZ011960


title: SSCb_M_pvSSC_M13_2m_166


title: TRSPZ011959

value: IIIA


title: SSCb_M_ocSSC_L3_2m_251


title: SSCb_M_ocSSC_L24_2m_123


title: TRSPZ011958


title: SSCb_M_ocSSC_L23_2m_230


title: WT_SNK170425004_H06

description: RNA from single nuclei


title: WT_SNK170425002_B07

description: RNA from single nuclei


title: WT_SNK170425004_A09

description: RNA from single nuclei


title: SSCb_M_ocSSC_L2_2m_211


title: TRSPZ011957


title: TRSPZ011965

value: IIC


title: SSCb_M_ocSSC_L21_2m_70


title: SSCb_M_ocSSC_L20_2m_23


title: SSCb_M_ocSSC_L19_2m_370


title: WT_SNK170425004_G04

description: RNA from single nuclei

value: wild type (Ehmt1+/+)


title: TRSPZ011954

value: IIIB


title: TRSPZ011955


title: TRSPZ011952


title: SSCb_M_ocSSC_L15_2m_302


title: SSCb_M_ocSSC_L16_2m_337


title: SSCb_M_ocSSC_L18_2m_132


title: SSCb_M_ocSSC_L17_2m_351


title: WT_SNK170425002_G08

description: RNA from single nuclei

value: Neuron

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: SSCb_M_ocSSC_L22_2m_41

value: bone


title: SSCb_M_ocSSC_L12_2m_145


title: WT_SNK170425002_C06

description: RNA from single nuclei


title: SSCb_M_ocSSC_L10_2m_364


title: SSCb_M_ocSSC_L13_2m_121


title: SSCb_M_ocSSC_L14_2m_288


title: TRSPZ003461

value: primary tumor

value: IV


title: SSCb_M_pvSSC_K9_2m_279

value: Adult

value: male


title: WT_SNK170425002_D06

description: RNA from single nuclei


title: SSCb_M_pvSSC_K7_2m_342


title: SSCb_M_pvSSC_K8_2m_333


title: TRSPZ003457


title: TRSPZ003456

source_name: Intestine large rectum


title: TRSPZ003454


title: WT_SNK170425004_F10

description: RNA from single nuclei

value: Oligodendrocyte


title: WT_SNK170425004_C10

description: RNA from single nuclei


title: SSCb_M_ocSSC_L1_2m_45

value: ocSSC


title: SSCb_M_pvSSC_K5_2m_133

value: pvSSC


title: SSCb_M_pvSSC_K6_2m_58


title: SSCb_M_pvSSC_K4_2m_265


title: WT_SNK170425004_B09

description: RNA from single nuclei

value: WT (96 wel)


title: TRSPZ003453


title: WT_SNK170425004_G01

description: RNA from single nuclei

value: brain cortex


title: TRSPZ003452


title: SSCb_M_pvSSC_K24_2m_36


title: SSCb_M_pvSSC_K3_2m_217


title: WT_SNK170425004_G06

description: RNA from single nuclei

value: 14 weeks old


title: TRSPZ011951

value: IIA


title: SSCb_M_pvSSC_K23_2m_103


title: SSCb_M_ocSSC_L11_2m_307


title: TRSPZ003451


title: SSCb_M_pvSSC_K22_2m_201


title: TRSPZ003450


title: SSCb_M_pvSSC_K20_2m_281


title: SSCb_M_pvSSC_K21_2m_142


title: TRSPZ003449


title: WT_SNK170425002_D03

description: RNA from single nuclei


title: WT_SNK170425004_H03

description: RNA from single nuclei


title: WT_SNK170425002_E10

description: RNA from single nuclei


title: SSCb_M_pvSSC_K2_2m_365


title: TRSPZ003448


title: SSCb_M_pvSSC_K17_2m_212


title: SSCb_M_pvSSC_K19_2m_247


title: SSCb_M_pvSSC_K18_2m_186


title: WT_SNK170425002_F10

description: RNA from single nuclei


title: SSCb_M_pvSSC_K14_2m_15


title: SSCb_M_pvSSC_K15_2m_101


title: SSCb_M_pvSSC_K13_2m_22


title: TRSPZ003447


title: SSCb_M_pvSSC_K16_2m_227


title: TRSPZ003446


title: WT_SNK170425002_F06

description: RNA from single nuclei

value: Microglia


title: SSCb_M_pvSSC_K11_2m_98


title: TRSPZ003445


title: WT_SNK170425002_F08

description: RNA from single nuclei

value: wild type (Ehmt1+/+)


title: SSCb_M_pvSSC_K12_2m_292


title: WT_SNK170425004_C08

description: RNA from single nuclei


title: WT_SNK170425004_A06

description: RNA from single nuclei


title: SSCb_M_pvSSC_K1_2m_304


title: TRSPZ003444


title: SSCb_M_pvSSC_K10_2m_233


title: WT_SNK170425004_G02

description: RNA from single nuclei


title: SSCb_M_ocSSC_J8_2m_362


title: TRSPZ003443


title: TRSPZ003442


title: WT_SNK170425004_H07

description: RNA from single nuclei


title: WT_SNK170425004_A08

description: RNA from single nuclei


title: WT_SNK170425004_G05

description: RNA from single nuclei


title: SSCb_M_ocSSC_J5_2m_381


title: WT_SNK170425002_B04

description: RNA from single nuclei


title: SSCb_M_ocSSC_J24_2m_259


title: SSCb_M_ocSSC_J6_2m_13


title: SSCb_M_ocSSC_J3_2m_126


title: TRSPZ003440


title: SSCb_M_ocSSC_J22_2m_20


title: SSCb_M_ocSSC_J21_2m_299


title: SSCb_M_ocSSC_J23_2m_276


title: TRSPZ003438


title: WT_SNK170425004_C11

description: RNA from single nuclei


title: SSCb_M_ocSSC_J9_2m_280


title: SSCb_M_ocSSC_J19_2m_53


title: TRSPZ003437


title: SSCb_M_ocSSC_J18_2m_38


title: SSCb_M_ocSSC_J2_2m_112


title: TRSPZ003441


title: WT_SNK170425002_B11

description: RNA from single nuclei


title: SSCb_M_ocSSC_J7_2m_285


title: WT_SNK170425004_F01

description: RNA from single nuclei


title: TRSPZ003436


title: SSCb_M_ocSSC_J15_2m_180


title: SSCb_M_ocSSC_J16_2m_197


title: TRSPZ003435


title: TRSPZ003439


title: WT_SNK170425004_B08

description: RNA from single nuclei


title: WT_SNK170425002_E05

description: RNA from single nuclei


title: SSCb_M_ocSSC_J14_2m_250


title: TRSPZ003434


title: WT_SNK170425002_A10

description: RNA from single nuclei


title: SSCb_M_ocSSC_J13_2m_350


title: SSCb_M_ocSSC_J17_2m_108


title: SSCb_M_ocSSC_J4_2m_321


title: SSCb_M_ocSSC_J11_2m_295


title: SSCb_M_ocSSC_J10_2m_85


title: WT_SNK170425002_A08

description: RNA from single nuclei


title: TRSPZ003432


title: WT_SNK170425004_D08

description: RNA from single nuclei


title: SSCb_M_pvSSC_I9_2m_170


title: TRSPZ003431

value: II


title: WT_SNK170425002_D05

description: RNA from single nuclei

value: Neuron


title: SSCb_M_pvSSC_I7_2m_207


title: TRSPZ003433


title: SSCb_M_pvSSC_I6_2m_216


title: TRSPZ003430


title: SSCb_M_ocSSC_J1_2m_183


title: SSCb_M_pvSSC_I8_2m_334


title: SSCb_M_pvSSC_I4_2m_298


title: WT_SNK170425002_E07

description: RNA from single nuclei

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: SSCb_M_pvSSC_I5_2m_312

value: bone


title: TRSPZ003429

value: primary tumor


title: SSCb_M_pvSSC_I3_2m_303


title: SSCb_M_pvSSC_I24_2m_377


title: WT_SNK170425004_E10

description: RNA from single nuclei


title: TRSPZ003428

value: IV


title: WT_SNK170425002_H01

description: RNA from single nuclei


title: TRSPZ003427


title: WT_SNK170425002_E12

description: RNA from single nuclei


title: TRSPZ003426


title: SSCb_M_pvSSC_I20_2m_325

value: Adult


title: SSCb_M_pvSSC_I2_2m_28

value: male


title: SSCb_M_pvSSC_I22_2m_62


title: SSCb_M_pvSSC_I19_2m_195


title: SSCb_M_pvSSC_I23_2m_119


title: TRSPZ003425


title: SSCb_M_pvSSC_I18_2m_238


title: TRSPZ003424


title: WT_SNK170425002_C10

description: RNA from single nuclei


title: SSCb_M_pvSSC_I17_2m_191


title: SSCb_M_pvSSC_I16_2m_8


title: WT_SNK170425002_H05

description: RNA from single nuclei


title: WT_SNK170425002_G05

description: RNA from single nuclei

value: Oligodendrocyte


title: SSCb_M_pvSSC_I15_2m_156


title: TRSPZ003423


title: SSCb_M_pvSSC_I14_2m_314


title: WT_SNK170425004_H12

description: RNA from single nuclei


title: TRSPZ003422


title: SSCb_M_pvSSC_I10_2m_345


title: SSCb_M_pvSSC_I11_2m_59


title: TRSPZ003421


title: WT_SNK170425002_B08

description: RNA from single nuclei


title: SSCb_M_pvSSC_I21_2m_239


title: TRSPZ003420


title: SSCb_M_pvSSC_I1_2m_366


title: SSCb_M_ocSSC_H9_2m_140

value: ocSSC


title: WT_SNK170425002_C08

description: RNA from single nuclei


title: SSCb_M_ocSSC_H8_2m_360


title: WT_SNK170425004_G10

description: RNA from single nuclei


title: TRSPZ003419


title: SSCb_M_ocSSC_H7_2m_87


title: TRSPZ003418


title: WT_SNK170425004_C04

description: RNA from single nuclei


title: SSCb_M_ocSSC_H6_2m_384


title: SSCb_M_ocSSC_H5_2m_55


title: SSCb_M_pvSSC_I13_2m_83

value: pvSSC


title: SSCb_M_ocSSC_H4_2m_375


title: TRSPZ003417


title: SSCb_M_pvSSC_I12_2m_52


title: WT_SNK170425002_F05

description: RNA from single nuclei

value: WT (96 wel)


title: WT_SNK170425004_E09

description: RNA from single nuclei

value: brain cortex


title: TRSPZ003415


title: SSCb_M_ocSSC_H23_2m_188


title: WT_SNK170425002_H07

description: RNA from single nuclei

value: 14 weeks old


title: WT_SNK170425002_E01

description: RNA from single nuclei


title: SSCb_M_ocSSC_H24_2m_226


title: SSCb_M_ocSSC_H21_2m_359


title: TRSPZ003412


title: SSCb_M_ocSSC_H22_2m_379


title: NC-HDAC1

city: Beijing

first: Zihan

last: Zhang

address: No. 38 Xuyuan Stress

country: China

institute: Peking University

library_source: genomic

data_processing:
Aligned to the unmasked human reference genome using Bowtie2
further analyzed by MACS (Model-based Analysis for ChIP-Seq)
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: bigwig files were generated

source_name: Breast cancer cells

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
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: MCF-7 cells stably expressing vector and FLAG-TRIM46 were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5×10^7 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by either normal rabbit IgG (control) or polyclonal antibodies against HDAC1.

value: breast cancer cells

tag: genotype/variation

value: stably expressing vector

value: Anti-HDAC1 antibody (Abcam, ab7028, GR225006-11)


title: SSCb_M_ocSSC_H2_2m_48


title: SSCb_M_ocSSC_H19_2m_305


title: NC_Input DNA

value: rabbit IgG (control)


title: WT_SNK170425004_B07

description: RNA from single nuclei

value: Neuron

value: wild type (Ehmt1+/+)


title: SSCb_M_ocSSC_H18_2m_218

value: bone


title: SSCb_M_ocSSC_H17_2m_204


title: SSCb_M_ocSSC_H16_2m_17


title: FLAG-TRIM46-HDAC1

value: stably expressing FLAG-TRIM46


title: SSCb_M_ocSSC_H15_2m_224


title: SSCb_M_ocSSC_H3_2m_317


title: SSCb_M_ocSSC_H14_2m_69


title: FLAG-TRIM46_Input DNA


title: WT_SNK170425002_G07

description: RNA from single nuclei

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: WT_SNK170425002_G12

description: RNA from single nuclei


title: MEF Trp53-/-; Zfp871-/-

city: Davis

first: Xinbin

last: Chen

state: CA

address: One Shields Avenue

institute: University of California Davis

description: MEF Trp53-/-; Zfp871-/-

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Embryo

growth_protocol: The MEFs were cultured in DMEM supplemented with 10% FBS (Hyclone Laboratories, Erie, PA, USA) 55 μM β-mercaptoethanol and 1x non-essential amino acids solution (Cellgro, Manassas, VA, USA). Exponentially growing primary MEFs at passage 4 were used for RNA extraction and RNA-sequencing.

extract_protocol:
Mouse embryonic fibroblasts (MEFs) were isolated from 12.5–13.5 days post-coitum mouse embryos.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse embryonic fibroblasts


title: SSCb_M_ocSSC_H12_2m_200

value: Adult

value: male


title: MEF Zfp871-/-

description: MEF Zfp871-/-


title: WT_SNK170425004_H01

description: RNA from single nuclei

value: Oligodendrocyte


title: WT_SNK170425002_E03

description: RNA from single nuclei


title: SSCb_M_ocSSC_H1_2m_168

value: ocSSC


title: WT_SNK170425004_F08

description: RNA from single nuclei

value: WT (96 wel)

value: Microglia


title: SSCb_M_ocSSC_H20_2m_77


title: SSCb_M_ocSSC_H13_2m_154


title: SSCb_M_ocSSC_H10_2m_150


title: SSCb_M_pvSSC_G8_2m_193

value: pvSSC


title: WT_SNK170425004_F06

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old


title: SSCb_M_pvSSC_G9_2m_16


title: MEF Trp53-/-

description: MEF Trp53-/-


title: MEF WT

description: MEF WT

value: Wild type


title: WT_SNK170425004_B12

description: RNA from single nuclei


title: SSCb_M_pvSSC_G6_2m_372


title: SSCb_M_pvSSC_G7_2m_179


title: SSCb_M_pvSSC_G24_2m_122


title: SSCb_M_pvSSC_G4_2m_79


title: WT_SNK170425004_B03

description: RNA from single nuclei


title: RNA-PRC-5e-7M-rep3

city: Stanford

first: Christopher

middle: Michael

last: Weber

address: B209 Beckman Center

department: Pathology

institute: Stanford University

data_processing:
Transcriptome: Ensembl v96 transcriptome (https://github.com/pachterlab/kallisto-transcriptome-indices/releases)
The first three bases from read 1 were trimmed with cutadapt 1.16 using -u 3 option. Transcripts were quantified using Kallisto version 0.44.0 using -l 280-s 20 (or paired-end) and --fr-stranded.
Trimmed reads were aligned to mm10 genome build with hisat2 using --rna-strandness FR (version 2.1.0), .bam files were merged with samtools merge (version 1.7), .bw files were generated using deeptools --binSize 10 --normalizeUsing RPKM (version 3.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: Kallisto abundance estimates and merged .bw files

source_name: mESC TC1 (129) passage 25-30

growth_protocol: Cells were treated with DMSO, 0.5mM auxin, or dTAG13 (5x10^-11 to 5x10^-7M) for indicated time.

extract_protocol:
SMARTer Stranded Total RNA Sample Prep Kit - HI
Ribosomal RNA depleted total RNA

treatment_protocol: Cells were washed 1x with PBS and resuspended in Trisure. RNA was extracted and DNase I digested. The reaction was cleaned up with acid phenol and the RNA was precipitated.

tag: drug

tag: time treated

value: mESC


title: SSCb_M_pvSSC_G3_2m_86


title: SSCb_M_ocSSC_H11_2m_47


title: RNA-PRC-5e-7M-rep2


title: WT_SNK170425002_G10

description: RNA from single nuclei

tag: condition

tag: strain

value: Neuron


title: SSCb_M_pvSSC_G22_2m_202

tag: tissue

tag: age


title: WT_SNK170425004_D04

description: RNA from single nuclei

tag: celltype

tag: genotype

value: wild type (Ehmt1+/+)


title: RNA-PRC-5e-9M-rep4


title: SSCb_M_pvSSC_G19_2m_234

value: bone

tag: batch


title: SSCb_M_pvSSC_G2_2m_130

tag: Sex


title: SSCb_M_pvSSC_G20_2m_99

tag: cell type


title: SSCb_M_pvSSC_G17_2m_185


title: WT_SNK170425002_G01

description: RNA from single nuclei

tag: treatment


title: RNA-PRC-5e-7M-rep4

tag: cell line


title: WT_SNK170425004_B04

description: RNA from single nuclei


title: WT_SNK170425002_C02

description: RNA from single nuclei


title: RNA-PRC-5e-9M-rep2


title: SSCb_M_pvSSC_G5_2m_64


title: RNA-PRC-5e-7M-rep1


title: SSCb_M_pvSSC_G18_2m_131


title: WT_SNK170425004_D03

description: RNA from single nuclei


title: SSCb_M_pvSSC_G16_2m_376


title: RNA-PRC-5e-9M-rep3


title: SSCb_M_pvSSC_G13_2m_141


title: SSCb_M_pvSSC_G14_2m_236


title: WT_SNK170425004_G09

description: RNA from single nuclei


title: SSCb_M_pvSSC_G21_2m_245


title: SSCb_M_pvSSC_G12_2m_93


title: SSCb_M_pvSSC_G11_2m_289


title: RNA-PRC-5e-9M-rep1


title: SSCb_M_pvSSC_G23_2m_374


title: WT_SNK170425004_A04

description: RNA from single nuclei


title: RNA-PRC-5e-10M-rep3


title: SSCb_M_pvSSC_G10_2m_271


title: RNA-PRC-5e-10M-rep2


title: SSCb_M_pvSSC_G1_2m_84


title: SSCb_M_ocSSC_F8_2m_61


title: WT_SNK170425004_H05

description: RNA from single nuclei


title: SSCb_M_pvSSC_G15_2m_89


title: RNA-PRC-5e-11M-rep4


title: SSCb_M_ocSSC_F5_2m_229


title: SSCb_M_ocSSC_F4_2m_268


title: RNA-PRC-5e-10M-rep1


title: RNA-PRC-5e-11M-rep3


title: SSCb_M_ocSSC_F3_2m_152


title: WT_SNK170425004_E03

description: RNA from single nuclei


title: WT_SNK170425004_A10

description: RNA from single nuclei


title: WT_SNK170425002_D11

description: RNA from single nuclei


title: SSCb_M_ocSSC_J20_2m_27


title: SSCb_M_ocSSC_F7_2m_232


title: SSCb_M_ocSSC_F23_2m_146


title: WT_SNK170425004_E06

description: RNA from single nuclei


title: RNA-PRC-5e-11M-rep2


title: SSCb_M_ocSSC_F22_2m_97


title: RNA-PRC-5e-11M-rep1


title: SSCb_M_ocSSC_F21_2m_260


title: SSCb_M_ocSSC_F20_2m_90


title: RNA-PRC-DMSO-rep4

value: DMSO control


title: WT_SNK170425002_C05

description: RNA from single nuclei

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: SSCb_M_ocSSC_F2_2m_347


title: SSCb_M_ocSSC_F6_2m_231


title: WT_SNK170425002_A09

description: RNA from single nuclei


title: SSCb_M_ocSSC_F19_2m_373


title: SSCb_M_ocSSC_F9_2m_326


title: RNA-PRC-5e-10M-rep4


title: WT_SNK170425002_H10

description: RNA from single nuclei


title: RNA-PRC-DMSO-rep2


title: WT_SNK170425002_H08

description: RNA from single nuclei


title: SSCb_M_ocSSC_F18_2m_228


title: WT_SNK170425002_G03

description: RNA from single nuclei


title: RNA-PRC-DMSO-rep1


title: RNA-PRC-DMSO-rep3


title: SSCb_M_ocSSC_F24_2m_66


title: WT_SNK170425002_C07

description: RNA from single nuclei


title: SSCb_M_ocSSC_F15_2m_266


title: SSCb_M_ocSSC_F13_2m_346


title: RNA-Brg1-8h-aux-rep4

source_name: mESC TC1 (129) passage 15-20

value: 0.5mM Auxin


title: SSCb_M_ocSSC_F12_2m_74

value: Adult


title: SSCb_M_ocSSC_F11_2m_106

value: male


title: SSCb_M_ocSSC_F14_2m_29


title: RNA-Brg1-8h-aux-rep3


title: WT_SNK170425004_E12

description: RNA from single nuclei


title: WT_SNK170425002_G09

description: RNA from single nuclei


title: SSCb_M_ocSSC_F16_2m_344


title: RNA-Brg1-4h-aux-rep4


title: SSCb_M_pvSSC_E9_2m_242


title: WT_SNK170425004_H09

description: RNA from single nuclei


title: WT_SNK170425002_B06

description: RNA from single nuclei

value: Oligodendrocyte


title: SSCb_M_pvSSC_E7_2m_139


title: RNA-Brg1-4h-aux-rep3


title: SSCb_M_ocSSC_F17_2m_340

value: ocSSC


title: SSCb_M_pvSSC_E8_2m_220


title: SSCb_M_pvSSC_E6_2m_1


title: RNA-Brg1-2h-aux-rep4


title: WT_SNK170425004_D10

description: RNA from single nuclei

value: WT (96 wel)


title: SSCb_M_pvSSC_E5_2m_356


title: WT_SNK170425004_C02

description: RNA from single nuclei


title: SSCb_M_pvSSC_E3_2m_35


title: SSCb_M_pvSSC_E4_2m_114


title: SSCb_M_pvSSC_E24_2m_309


title: SSCb_M_ocSSC_F10_2m_5


title: RNA-Brg1-1h-aux-rep4


title: SSCb_M_pvSSC_E23_2m_78


title: WT_SNK170425004_B11

description: RNA from single nuclei


title: WT_SNK170425004_F02

description: RNA from single nuclei


title: RNA-Brg1-1h-aux-rep3


title: RNA-Brg1-1h-aux-rep2


title: SSCb_M_pvSSC_E22_2m_9


title: WT_SNK170425002_B02

description: RNA from single nuclei


title: SSCb_M_ocSSC_F1_2m_178


title: RNA-Brg1-2h-aux-rep3


title: SSCb_M_pvSSC_E21_2m_124


title: SSCb_M_pvSSC_E19_2m_290


title: SSCb_M_pvSSC_E2_2m_332


title: RNA-Brg1-1h-aux-rep1


title: WT_SNK170425004_H10

description: RNA from single nuclei


title: SSCb_M_pvSSC_E18_2m_49


title: SSCb_M_pvSSC_E16_2m_378


title: WT_SNK170425002_F02

description: RNA from single nuclei


title: SSCb_M_pvSSC_E15_2m_175


title: RNA-Brg1-05h-aux-rep3


title: RNA-Brg1-05h-aux-rep2


title: SSCb_M_pvSSC_E14_2m_382


title: SSCb_M_pvSSC_E12_2m_383


title: WT_SNK170425004_C06

description: RNA from single nuclei


title: SSCb_M_pvSSC_E20_2m_310


title: WT_SNK170425002_D08

description: RNA from single nuclei


title: SSCb_M_pvSSC_E13_2m_153


title: SSCb_M_pvSSC_E10_2m_159


title: SSCb_M_pvSSC_E11_2m_120


title: WT_SNK170425004_E07

description: RNA from single nuclei


title: SSCb_M_ocSSC_D9_2m_105


title: RNA-Brg1-DMSO-rep4


title: SSCb_M_ocSSC_D8_2m_138


title: RNA-Brg1-DMSO-rep3


title: SSCb_M_ocSSC_D7_2m_104


title: WT_SNK170425002_F11

description: RNA from single nuclei


title: RNA-Brg1-05h-aux-rep1


title: RNA-Brg1-05h-aux-rep4


title: SSCb_M_ocSSC_D6_2m_225


title: SSCb_M_pvSSC_E17_2m_308


title: D4 AGN Replicate 3

city: New York

first: Deepak

last: Kaji

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
merged_df.csv
D4-AGN-3

data_processing:
STAR compiler was run on raw fastq files
featureCounts was run on the aligned fastqs
Feature Counted files were concatenated into one file
Concatenated file was processed in edgeR (including normalization, estimation of dispersion effects, ENSEMBLE ID to MGI symbol conversion, and differential gene expression)
Genome_build: GRCmm38
Supplementary_files_format_and_content: normalized counts table (CSV)

source_name: Monolayer (cell culture)

growth_protocol: ES derived cultures were obtained, briefly, by growing stem cells, and subsequently differentiating for 10 days.

extract_protocol:
RNA extraction was performed using Qiagen’s RNeasy Plus Universal mini kit according to the manufacturer’s instructions.
Libraries were prepared using the NEB Next Ultra NRA Library Prep Kit for Illumina Sequencing in accordance with manufacturer's instructions

treatment_protocol: Somite was captured or plated in monolayer with CD1530 or AGN 193109 and isolated at D0, D0.25, D0.75, D1.5, D2.5, D4

tag: time

value: Day 4

value: Monolayer (cell culture)


title: D4 AGN Replicate 2

description:
merged_df.csv
D4-AGN-2


title: WT_SNK170425002_A01

description: RNA from single nuclei

value: brain cortex


title: SSCb_M_ocSSC_D4_2m_113


title: WT_SNK170425002_F09

description: RNA from single nuclei

value: 14 weeks old


title: D4 AGN Replicate 1

description:
merged_df.csv
D4-AGN-1


title: SSCb_M_ocSSC_D3_2m_319


title: SSCb_M_pvSSC_E1_2m_137

value: pvSSC


title: SSCb_M_ocSSC_D23_2m_198


title: WT_SNK170425002_D01

description: RNA from single nuclei


title: WT_SNK170425002_B12

description: RNA from single nuclei


title: D4 CD1530 Replicate 3

description:
merged_df.csv
D4-CD1530-3


title: WT_SNK170425002_F07

description: RNA from single nuclei


title: SSCb_M_ocSSC_D24_2m_56


title: SSCb_M_ocSSC_D22_2m_151


title: SSCb_M_ocSSC_D21_2m_11


title: D4 CD1530 Replicate 2

description:
merged_df.csv
D4-CD1530-2


title: SSCb_M_ocSSC_D20_2m_174


title: WT_SNK170425002_B05

description: RNA from single nuclei


title: SSCb_M_ocSSC_D2_2m_21


title: SSCb_M_ocSSC_D18_2m_189


title: WT_SNK170425002_B10

description: RNA from single nuclei


title: D2.5 AGN Replicate 3

description:
merged_df.csv
D2-5-AGN-3

value: Day 2.5


title: SSCb_M_ocSSC_D17_2m_164


title: SSCb_M_ocSSC_D16_2m_306


title: D4 CD1530 Replicate 1

description:
merged_df.csv
D4-CD1530-1


title: SSCb_M_ocSSC_D5_2m_273


title: SSCb_M_ocSSC_D15_2m_256


title: WT_SNK170425004_H08

description: RNA from single nuclei

value: Neuron


title: D2.5 AGN Replicate 2

description:
merged_df.csv
D2-5-AGN-2


title: SSCb_M_ocSSC_D14_2m_51


title: WT_SNK170425002_C12

description: RNA from single nuclei

value: Microglia

value: wild type (Ehmt1+/+)


title: SSCb_M_ocSSC_D13_2m_363

value: bone


title: D2.5 AGN Replicate 1

description:
merged_df.csv
D2-5-AGN-1


title: SSCb_M_ocSSC_D11_2m_323


title: WT_SNK170425004_F12

description: RNA from single nuclei

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: D2.5 CD1530 Replicate 3

description:
merged_df.csv
D2-5-CD1530-3


title: SSCb_M_ocSSC_D10_2m_14


title: SSCb_M_ocSSC_D1_2m_278


title: WT_SNK170425004_C03

description: RNA from single nuclei


title: D2.5 CD1530 Replicate 1

description:
merged_df.csv
D2-5-CD1530-1


title: SSCb_M_pvSSC_C8_2m_143


title: SSCb_M_pvSSC_C7_2m_269


title: SSCb_M_pvSSC_C9_2m_100


title: WT_SNK170425002_D07

description: RNA from single nuclei


title: D1.5 AGN Replicate 2

description:
merged_df.csv
D1-5-AGN-2

value: Day 1.5


title: SSCb_M_pvSSC_C4_2m_60

value: Adult


title: SSCb_M_pvSSC_C3_2m_328

value: male


title: WT_SNK170425004_D11

description: RNA from single nuclei

value: Oligodendrocyte


title: WT_SNK170425004_A03

description: RNA from single nuclei


title: WT_SNK170425004_B10

description: RNA from single nuclei


title: SSCb_M_pvSSC_C24_2m_274


title: WT_SNK170425002_H03

description: RNA from single nuclei


title: SSCb_M_pvSSC_C23_2m_88


title: SSCb_M_pvSSC_C22_2m_167


title: D1.5 CD1530 Replicate 3

description:
merged_df.csv
D1-5-CD1530-3


title: SSCb_M_ocSSC_D12_2m_287

value: ocSSC


title: SSCb_M_pvSSC_C21_2m_267


title: D1.5 AGN Replicate 3

description:
merged_df.csv
D1-5-AGN-3


title: D2.5 CD1530 Replicate 2

description:
merged_df.csv
D2-5-CD1530-2


title: D1.5 CD1530 Replicate 2

description:
merged_df.csv
D1-5-CD1530-2


title: SSCb_M_pvSSC_C20_2m_311


title: SSCb_M_pvSSC_C6_2m_192


title: SSCb_M_pvSSC_C2_2m_284


title: SSCb_M_pvSSC_C5_2m_50


title: WT_SNK170425004_G12

description: RNA from single nuclei

value: WT (96 wel)


title: D1.5 AGN Replicate 1

description:
merged_df.csv
D1-5-AGN-1


title: SSCb_M_pvSSC_C19_2m_54


title: WT_SNK170425004_H11

description: RNA from single nuclei


title: SSCb_M_pvSSC_C18_2m_354


title: D0.75 AGN Replicate 3

description:
merged_df.csv
D0-75-AGN-3


title: WT_SNK170425002_D02

description: RNA from single nuclei


title: D1.5 CD1530 Replicate 1

description:
merged_df.csv
D1-5-CD1530-1


title: SSCb_M_pvSSC_C17_2m_147


title: SSCb_M_pvSSC_C16_2m_136


title: SSCb_M_ocSSC_D19_2m_44


title: D0.75 AGN Replicate 2

description:
merged_df.csv
D0-75-AGN-2


title: SSCb_M_pvSSC_C15_2m_71


title: WT_SNK170425004_D12

description: RNA from single nuclei


title: SSCb_M_pvSSC_C14_2m_336


title: SSCb_M_pvSSC_C13_2m_165


title: WT_SNK170425002_E11

description: RNA from single nuclei


title: SSCb_M_pvSSC_C12_2m_173


title: D0.75 CD1530 Replicate 3

description:
merged_df.csv
D0-75-CD1530-3


title: WT_SNK170425002_A03

description: RNA from single nuclei


title: SSCb_M_pvSSC_C10_2m_275


title: SSCb_M_pvSSC_C11_2m_348


title: WT_SNK170425004_C07

description: RNA from single nuclei


title: SSCb_M_pvSSC_C1_2m_107


title: D0.75 AGN Replicate 1

description:
merged_df.csv
D0-75-AGN-1


title: WT_SNK170425004_B01

description: RNA from single nuclei


title: SSCb_M_ocSSC_B8_2m_341


title: D0.75 CD1530 Replicate 1

description:
merged_df.csv
D0-75-CD1530-1


title: WT_SNK170425002_G04

description: RNA from single nuclei


title: mG1_3m

city: Paris

first: Julia

last: FUCHS SEBE

address: 11, Macelin Berthelot

department: CIRB

country: France

institute: Collège de France

data_processing:
Quality control FastQC version 0.11.8
Adaptor removal Trim Galore
Alignment bismark v0.20.0
infer the methylation state of all cytosines cytosine2coverage and bismark_methylation_extractor modules of Bismark
differential methylation analysis  Methylkit v1.7.0
annotation R/Bioconductor package annotation
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: methylation state of all cytosines (for every single uniquely  mappable read)

source_name: mouse ventral midbrain

extract_protocol:
DNA was also extracted during the same process of RNA extraction using the AllPrep DNA/RNA Micro Kit (Qiagen 80284). The DNA was then purified, treated with RNase H (ThermoFischer, 18021071) and Proteinase K (PCR grade, Roche, 3115836001) and concentrated with the DNA Clean & Concentrator-5 kit (Zymo, D4013). DNA concentration of each sample was measured using the Qubit® fluorometer with dsDNA BR Assay Kit (Thermo Fisher Scientific). DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-488 High Sensitivity genomic DNA Analysis Kit (Agilent).
RRBS libraries were prepared using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode) which uses the Mspl restriction enzyme and size selection to enrich for CpG-rich regions (coverage of about 4 million CpGs). 100ng of genomic DNA were used to start library preparation for each sample. Following library preparation, samples were pooled together by 8. PCR clean-up after the final library amplification was performed using a 1.45x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). DNA concentration of the pools was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The profile of the pools was checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent).

value: mouse ventral midbrain

value: OF1 wildtype

tag: time after injection

value: 92 days


title: SSCb_M_ocSSC_B7_2m_117


title: mG4_3m

value: 93 days


title: WT_SNK170425002_C11

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old


title: D0.25 AGN Replicate 3

description:
merged_df.csv
D0-25-AGN-3

value: Monolayer (cell culture)


title: WT_SNK170425004_F09

description: RNA from single nuclei

value: Neuron


title: SSCb_M_ocSSC_B6_2m_127


title: D0.25 AGN Replicate 2

description:
merged_df.csv
D0-25-AGN-2


title: mC1_3m

value: 90 days


title: mG6_2w

value: 17 days


title: D0.25 AGN Replicate 1

description:
merged_df.csv
D0-25-AGN-1


title: WT_SNK170425004_B06

description: RNA from single nuclei

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: SSCb_M_ocSSC_B5_2m_294

value: bone

value: Adult


title: WT_SNK170425002_H04

description: RNA from single nuclei

value: Oligodendrocyte


title: D0.25 CD1530 Replicate 3

description:
merged_df.csv
D0-25-CD1530-3


title: mG1_2w

value: 16 days


title: WT_SNK170425004_D01

description: RNA from single nuclei

value: WT (96 wel)


title: D0.75 CD1530 Replicate 2

description:
merged_df.csv
D0-75-CD1530-2


title: SSCb_M_ocSSC_B3_2m_349

value: ocSSC

value: male


title: mC4_2w

value: mouse ventral midbrain

value: OF1 wildtype

value: 15 days


title: D0.25 CD1530 Replicate 1

description:
merged_df.csv
D0-25-CD1530-1


title: D0.25 CD1530 Replicate 2

description:
merged_df.csv
D0-25-CD1530-2


title: SSCb_M_ocSSC_B9_2m_172


title: SSCb_M_ocSSC_B24_2m_235


title: D0 Paraxial Mesoderm Replicate 3

description:
merged_df.csv
D0-SOM-3

source_name: Embryoid bodies (cell culture)

value: Day 0

value: None (paraxial mesoderm)

value: Embryoid bodies (cell culture)


title: mC3_3m

value: 91 days


title: WT_SNK170425004_F07

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old

value: Neuron


title: mC1_2w

value: 14 days


title: SSCb_M_ocSSC_B22_2m_327

value: bone

value: Adult


title: WT_SNK170425002_F04

description: RNA from single nuclei

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: 6-ACU-LFES

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq version1 was used for demultiplexing.
read adapter trimming was performed with cutadapt v1.6
reads were aligned with the SHRiMP (v2.2.3) short read mapper
Normalized abundace was caluclated with DESeq2 R Package (version 1.26.0)
Genome_build: miRBase release 21 ( http://www.mirbase.org/index.shtml )
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each miRNA (in rows).

source_name: acupuncture treatment_exosome

extract_protocol:
Qiagen miRNeasy Mini with DNase digest
Seqmatic TailorMix miRNA Sample Preparation Kit V2

value: three months

value: ACU-LFES

value: Exosome from blood


title: D0 Paraxial Mesoderm Replicate 1

description:
merged_df.csv
D0-SOM-1


title: SSCb_M_ocSSC_B4_2m_358

value: ocSSC

value: male


title: 5-ACU-LFES


title: SSCb_M_ocSSC_B20_2m_255


title: WGBS SL_C

city: shenzhen

first: Donge

last: Tang

state: Guangdong

address: NO.1017 Dongmen North, Shenzhen People’s Hospital, Shenzhen, Guangdong

institute: shenzhen people's hospital

data_processing:
Firstly, Cutadapt[1] and perl scripts in house were used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads that passed quality control were mapped to reference genome using WALT[2]. After alignment, reads were further deduplicated using samtool.
For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using per scripts in house and MethPipe.
Differentially methylated regions (DMRs) were calculated by R package-MethylKit[5] with default parameters (1000 bp slide windows, 500 bp overlap, p value<0.05).
Genome_build: GRCh38
Supplementary_files_format_and_content: methyGeneTable

source_name: Blood

extract_protocol:
PBMCs from each donor were obtained by using the Ficoll density gradient separation method (Sigma, USA). Then PBMCs was stored at –80 °C for further treatment. Moreover, genomic DNA was extracted from PBMCs using a DNA isolation kit for cells.
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure.The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments.. Finally, we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences.

tag: disease state

value: systemic lupus erythematous (SLE)

value: PBMCs


title: WT_SNK170425002_C09

description: RNA from single nuclei

source_name: nuclei from mice cortical region

value: WT (96 wel)

value: Microglia


title: 3-Control

source_name: sham treatment_exosome

value: sham


title: 4-ACU-LFES


title: SSCb_M_ocSSC_B21_2m_63

source_name: Long bones


title: WT_SNK170425002_H06

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old


title: WGBS H_C

value: control


title: SSCb_M_ocSSC_B2_2m_31

value: bone


title: SSCb_M_ocSSC_B19_2m_73

value: Adult


title: 2-Control


title: SSCb_M_ocSSC_B23_2m_210


title: H2_eso1-D147N_pol2-P287R_G200

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
S. pombe (ASM294v2.20 assembly) reference Genome was indexed from Bowtie2.  And sequence reads were aligned using Bowtie2 with ‘--fr -X 1000 -I 0 -N 0 --local -k 1’ parameters..
PCR/Sequencing duplicates were marked with samtools MarkDuplicates. For the variant calling process, the bam files were processed with mpileup from samtools and the calling process were executed with VarScan2.
Supplementary_files_format_and_content: bigWig file with counts after de-duplication.
Genome_build: S. pombe (ASM294v2.20 assembly)

organism: Schizosaccharomyces pombe

growth_protocol: cell culture: Strains were woken up from -70°C, then for each variant examined, 2-3 random single colonies were picked up and used to start 2-3 lineages. One colony was grown up on YE3S to prepare DNA for sequencing (generation 0). Each of the colonies was restreaked on a fresh YES plate, and after the colonies had grown up (3 days), a single colony was restreaked on a second YES plate. This process was repeated until the cells had gone through approximately 200 generations (11 passages). At the end of the experiment a single colony from each of the lineages was grown up on YE3S to prepare DNA for sequencing (generation 200).

extract_protocol:
20 mL of a saturated culture were pelleted (centrifugation 5 minutes at 1600 g) and washed in 1 mL of 10 mM of EDTA pH 8.9. Then, 250 μL of EDTA/ß-mercapto-ethanol/zymolase (EDTA 10 mM pH 8.9, 1% ß-mercapto-ethanol, 2 mg/mL zymolase) were added to the cell pellet and incubated at 37°C for 1 hour with shaking 400 rpm (ThermomixerC – Eppendorf). Equal amount of glass beads acid-washed (Sigma G8772) and cell pellet were added prior to 4 cycles of 15 seconds at 4 m/s on the FastPrep-24 from mpbioTM to help to break cell wall. Following mechanistic cell break, a 10 minutes heat shock at 65°C was performed. gDNA was then extracted and purified according to manufacturer guidelines for the DNeasy Plant Mini Kit from QIAGEN®.
Total DNA were used to generate barcoded, Illumina compatible, libraries. Basically, adapters are ligated to DNA followed by an amplification and clean up. The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis paired reads of 150 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. DNA-Seq was performed at Novogene (21F, Tower B, Jinma Building, No.38 Xueqing Road, Haidian District, Beijing, China).

tag: genotype/variation

tag: generation

tag: library type

value: DNA-Seq


title: FSL-R8-5682_rep3_planktonic

city: Burlington

first: Andrea

last: Etter

state: VT

address: 109 Carrigan Drive

department: Nutrition and Food Science

institute: University of Vermont

description: Listeria innocua from retail deli

data_processing:
Criteria for removal of bases/reads were: Phred33 score <30 or read length <50 bases
Trimmed reads were mapped to  L. monocytogenes 10403S using Bowtie2 (v. 2.2.8) (Sciences 2016)
HTSeq (v. 0.6.1) (Lemon and others 2010) determined read counts
DESeq2 (v. 2.1.2) (Love and others 2014) was used to determine significant differences between biofilm and planktonic samples for each isolate
Supplementary_files_format_and_content: HTSeq files for each sample containg gene counts after mapping to 10403S

organism: Listeria innocua

source_name: Bacteria

extract_protocol:
Following incubation, coupons were washed three times with sterile PBS to remove non-adherent cells, then immediately mixed with 1:10 volume ice-cold 10% acidified phenol:chloroform (Life Technologies, Grand Island, NY) in ethanol. Biofilm cells were detached from the coupons in stop solution using a spatula and subsequent vortexing. Cells were pelleted (15,300 x g, 20 min, 4°C), coupons removed, and pellets re-suspended in 1 mL TRIzol® (Life Technologies). RNA extraction proceeded as previously described in biological triplicate (Pleitner and others 2014; Raengpradub and others 2008). Sample quality was assessed via the 2100 Bioanalyzer system (Agilent, Foster City, CA). DNA removal was evaluated  via qRT-PCR as previously described (Pleitner and others 2014)
RNA libraries were prepared using the Epicentre ScriptSeqTM complete kit (Illumina) and ScriptSeqTM Index PCR primers (Illumina)

treatment_protocol: Early stationary phase cells (8ml; OD600=0.7-0.8) were incubated statically with sterile coupons (n= 20 coupons/isolate) in a sterile petri dish with BHI (20°C for 2 hours) (Chavant and others 2002). Coupons were rinsed three times in PBS to remove non-adherent cells, placed in a new sterile petri dish containing 8 ml BHI broth, and incubated for three days; BHI was replaced daily. For planktonic controls, overnight cultures were diluted with BHI to OD600 0.7-0.8  (total volume: 8 ml) (Chavant and others 2002), and then incubated in test tubes at 20oC, 200 rpm for 24 hours.

tag: sample type

value: Planktonic

tag: Stage

value: Early stationary phase

tag: medium

value: BHI


title: H1_eso1-D147N_pol2-P287R_G200


title: 1-Control

tag: strain

tag: age

value: three months

tag: tissue

value: Exosome from blood


title: SSCb_M_ocSSC_B18_2m_270

value: ocSSC

tag: batch

value: male


title: H2_eso1-D147N_pol2-P287R_G0


title: WT_SNK170425002_F12

description: RNA from single nuclei

tag: condition

tag: celltype

value: Neuron

tag: genotype

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: FSL-R8-5682_rep1_planktonic

description: Listeria innocua from retail deli


title: H1_eso1-D147N_pol2-P287R_G0


title: WT_SNK170425002_A05

description: RNA from single nuclei

value: WT (96 wel)

value: Microglia

tag: treatment


title: SSCb_M_ocSSC_B15_2m_316

tag: cell type

tag: Sex


title: FSL-R8-5682_rep2_planktonic

description: Listeria innocua from retail deli


title: SSCb_M_ocSSC_B16_2m_369


title: SSCb_M_ocSSC_B17_2m_7


title: WT_SNK170425004_D02

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old


title: WT_SNK170425004_B02

description: RNA from single nuclei


title: FSL-R8-5682_rep2_bf

description: Listeria innocua from retail deli

value: Biofilm


title: WT_SNK170425002_B09

description: RNA from single nuclei


title: SSCb_M_ocSSC_B13_2m_300

value: bone

value: Adult


title: SSCb_M_ocSSC_B14_2m_258


title: WT_SNK170425002_E04

description: RNA from single nuclei


title: WT_SNK170425002_A11

description: RNA from single nuclei

value: Oligodendrocyte


title: FSL-R8-5682_rep1_bf

description: Listeria innocua from retail deli

value: Early stationary phase


title: WT_SNK170425004_B05

description: RNA from single nuclei


title: G1_eso1-D147N_G200

value: DNA-Seq


title: SSCb_M_ocSSC_B12_2m_102


title: WT_SNK170425004_G08

description: RNA from single nuclei


title: FSL-R8-7802_rep3_planktonic

description: Transient non-food contact isolate from retail deli

value: Planktonic

value: BHI


title: SSCb_M_ocSSC_B11_2m_203

value: ocSSC


title: F2_kpa1-KO_pol2-P287R_G200


title: D0 Paraxial Mesoderm Replicate 2

description:
merged_df.csv
D0-SOM-2

tag: time

value: Day 0

value: None (paraxial mesoderm)

value: Embryoid bodies (cell culture)


title: WT_SNK170425004_A05

description: RNA from single nuclei

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: F1_kpa1-KO_pol2-P287R_G0

tag: genotype/variation


title: FSL-R8-5682_rep3_bf

description: Listeria innocua from retail deli


title: E2_kpa1-KO_pol2-P287R_G200

tag: generation


title: G1_eso1-D147N_G0

tag: library type


title: WT_SNK170425002_E06

description: RNA from single nuclei

value: WT (96 wel)

value: Neuron


title: SSCb_M_ocSSC_B1_2m_329

value: male


title: E1_kpa1-KO_pol2-P287R_G0


title: WT_SNK170425004_A11

description: RNA from single nuclei

value: brain cortex

value: 14 weeks old


title: WT_SNK170425004_H04

description: RNA from single nuclei


title: F1_kpa1-KO_pol2-P287R_G200


title: SSCb_M_pvSSC_A9_2m_361

value: bone

value: pvSSC

value: Adult


title: SSCb_M_pvSSC_A8_2m_2


title: WT_SNK170425004_E02

description: RNA from single nuclei

value: Oligodendrocyte


title: WT_SNK170425002_D12

description: RNA from single nuclei


title: D2_kpa1-KO_G0

value: DNA-Seq


title: D2_kpa1-KO_G200


title: D1_kpa1-KO_G200


title: SSCb_M_ocSSC_B10_2m_160


title: SSCb_M_pvSSC_A7_2m_291


title: WT_SNK170425004_C12

description: RNA from single nuclei


title: D1_kpa1-KO_G0


title: SSCb_M_pvSSC_A5_2m_95


title: E1_kpa1-KO_pol2-P287R_G200


title: SSCb_M_pvSSC_A6_2m_297


title: SSCb_M_pvSSC_A4_2m_94


title: Leaf-ASM-rep3-3d_Cy3

type: RNA

city: Angers

first: Alexandre

last: Degrave

address: André Lenôtre

institute: Agrocampus Ouest

description:
raw data file:
256467710024_Ary00075_scan_2015-02-06_532_635_GE2_1105_Oct12_1_1.txt

hyb_protocol: The hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple seedling leaf tissue, sampled 3 days after ASM treatment (0.4 g/L)

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Plants were grown under greenhouse conditions (natural photoperiod supplemented with artificial light if needed during a 16 h photophase, 23–25°C day, 17°C night)

extract_protocol: Each sample corresponds to a pool of 10 leaf discs (diam 9mm) punched out from the parenchyma of the youngest expanded leaf from 5 replicate plants per condition. Samples were snap-frozen in liquid nitrogen and further ground to a fine powder in liquid nitrogen using a tissue lyser (Retsch, Haan, Germany) and total RNA were extracted using the Nucleospin® RNA Plant Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s procedure, and by adding 2% PVP-40 in the extraction buffer. The quality of total RNAs was verified in 1.2% agarose gel before amplification steps. Purity and concentration of samples were assayed with a NanoDrop® One.

treatment_protocol: To assess ASM action, plants were sprayed to runoff (with a pressurized hand sprayer) with the commercial product Bion 50WG (Syngenta, Basel, Switzerland; 50% of ASM) prepared in reverse osmosis water at a final concentration of 0.4 g/L. The same water was used as control.

value: Leaf

value: ASM

tag: sampling time

value: 3 days post treatment


title: C2_pol2-P287R_G200


title: SSCb_M_pvSSC_A3_2m_313


title: Pln R14Del mutant - PLN-ASO Treated  - 24 weeks (rep1)

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description: Treatment consisted of a 4-week loading phase with weekly dosing of 100mg/kg and a 20wk maintenance phase with dosing of 50mg/kg once every 4 weeks. Treatment was initiated at the age of 3 weeks.

data_processing:
aligment - STAR 2.4.2a
readcount analysis - HTSEQ COUNT 0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: PLN_ASO_Readcounts_raw.txt -> Matrix table with raw readcounts per gene for all samples

source_name: heart - left ventricle

extract_protocol:
Trizol extraction
Truseq stranded mRNA (Illumina)

value: Pln R14Del/R14Del

value: treated

value: female


title: Leaf-ASM-rep1-3d_Cy3

description:
raw data file:
256467710011_Ary00047_scan_2014-07-04_532_635_GE2_1105_Oct12_1_1.txt


title: Pln R14Del mutant - PLN-ASO Treated  - 26 weeks (rep2)


title: Hela_mono layer_2

city: Jeddah

first: Mohammed Razeeth

middle: Shait

last: Mohammed

state: Makkah

address: Department of biochemistry, faculty of science, King Abdulaziz University

department: Department of biochemistry

country: Saudi Arabia

institute: KIng Abdulaziz UNiversity

data_processing: Result table 6day vs j4 based on DESeq2

source_name: Cervix

growth_protocol: cells were grown in ultra-low attachment plate obtained from Corning (Sigma) in a CO2 incubator at 37°C. The assessments of matrix detachment were done in cell suspension culture. Cells were dislodged by simple agitation in the presence of trypsin, followed with washing with PBS, resuspended at 0.5×106 cells/ml in serum-free culture media containing BSA, and finally were cultured in ultra-low attachment plate for at 37°C for various time points, which results in the formation of spheroids

extract_protocol:
Briefly, RNA was extracted from all the cell lines at the end of different experimental conditions using RNAeasy kit (Qiagen)
NovaSeq6000 SP/S1/S2 SBS Cartridge 300cycles, Illumina cat # 20013076, lot # 20443236). Approximately 120ng/mL of total RNA fragmented was used for Library Preparation for Paired End Total RNASeq. Bioanalyzer 2100 Analysis for Quality Check for all the RNA Samples. Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus, Illumina cat # 20040529. For analysis software Analysis Viewer (SAV), Illumina version 2.4 were used

tag: culture method

value: ECM attached

tag: cell line

value: HeLa


title: Hela_mono layer_1


title: Pln R14Del mutant - PLN-ASO Treated  - 26 weeks (rep1)

tag: strain


title: Leaf-ASM-rep4-3d_Cy5

description:
raw data file:
256467710024_Ary00075_scan_2015-02-06_532_635_GE2_1105_Oct12_1_3.txt


title: Hela_spheroid_2

value: ECM detached


title: Pln R14Del mutant - PLN-ASO Treated  - 22 weeks (rep3)

tag: age

value: male


title: WT_SNK170425002_D04

description: RNA from single nuclei

data_processing:
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 75 -l 36 -k 4.0 -q 30'. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '--no-softclip -p 4'. Gene expression levels were counted with featureCounts, function of Subread (version 1.5.0) using GENCODE vM15 annotation file.
We then removed samples outside of the mean minus three standard deviations of the total read number (FastQC) or the number of assigned reads to gene regions (featureCounts); over 5% reads assigning to ribosomal RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
We performed dimensional reduction of the count data (RPKM) and removed samples that were presumed to be immature and for which no cell type could be estimated.
Genome_build: mm10
Supplementary_files_format_and_content: txt

extract_protocol:
Nuclei were isolated from adult mice brain (3 mice for each genotypes). After collection of nuclei by iodixanol density gradient. Single nuclei were directly sorted into the 96-well or 384-well plate pre-dispensed with the cell lysis buffer.
Single-nucleus RNA-seq was carried out according to the advanced method of RamDA-seq (https://doi.org/10.1038/s41467-018-02866-0).

value: WT (96 wel)

tag: tissue

value: brain cortex

value: Neuron

value: wild type (Ehmt1+/+)

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old


title: SSCb_M_pvSSC_A23_2m_128

value: bone

value: pvSSC

value: Adult

tag: batch


title: C1_pol2-P287R_G200

value: DNA-Seq


title: Hela_spheroid_1


title: C3_pol2-P287R_G200


title: C2_pol2-P287R_G0


title: SSCb_M_pvSSC_A22_2m_371


title: Leaf-Water-rep4-3d_Cy3

source_name: Apple seedling leaf tissue, sampled 3 days after water treatment

value: Leaf

value: Water

value: 3 days post treatment


title: C1_pol2-P287R_G0


title: Leaf-ASM-rep2-3d_Cy5

description:
raw data file:
256467710011_Ary00047_scan_2014-07-04_532_635_GE2_1105_Oct12_1_3.txt

value: ASM


title: Leaf-Water-rep3-3d_Cy5


title: Leaf-Water-rep1-3d_Cy5


title: Pln R14Del mutant - PLN-ASO Treated  - 22 weeks (rep2)

value: Pln R14Del/R14Del

value: treated

value: female


title: SSCb_M_pvSSC_A24_2m_6

value: male


title: SSCb_M_pvSSC_A20_2m_34


title: SSCb_M_pvSSC_A21_2m_315


title: Pln R14Del mutant - PLN-ASO Treated  - 22 weeks (rep1)


title: B2_pol2-D276A-E278A_G200


title: B2_pol2-D276A-E278A_G0


title: Leaf-Water-rep2-3d_Cy3


title: B1_pol2-D276A-E278A_G200


title: Pln R14Del mutant - PLN-ASO Treated  - 18 weeks (rep3)


title: Rh30 48 hr PTC-028 rep 2

first: Karmella

middle: A

last: Haynes

address: 1760 Haygood Dr NE

department: Wallace H. Coulter Department of Biomedical Engineering

institute: Emory University

data_processing:
Bases were called using Illumina CASAVA
Reference genome and gene model annotation files were downloaded from UCSC. Indexes of the reference genome were built using STAR (v2.5) and paired-end clean reads were aligned to the reference genome. 1) Reads with remaining adapter sequences were removed. 2) Reads with >10% uncertain nucleotides were removed. 3) Reads with low quality nucleotide (base quality <20 >50% of read) were removed.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene, and the number of reads mapped to the gene.
Differential expression analysis between DMSO versus PTC-028 was performed using the DESeq2 R package (2_1.6.3).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read counts

source_name: Rhabdomyosarcoma cells

growth_protocol: All cells were incubated at 37C with 5% CO2 in a humidified environment. Rh28 was grown in RPMI with 10% FBS and supplemented with 2 mM L-glutamine. Rh30 was grown in DMEM with 10% FBS and 2 mM L-glutamine.

extract_protocol:
Total RNA was stored in TRIzol then extracted with Qiagen RNAeasy.
RNA-sequencing was performed by Novogene Co., Ltd (150 PE, 50-60M read pairs per sample). RNA libraries were prepared for sequencing using standard Illumina protocols. Concentration was quantified and run on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were plated the day prior to treatment at 70-80% confluence. DMSO PTC-028 was mixed into the cell culture media at the necessary concentration and then added to cells for 24 or 48 hr.


title: Pln R14Del mutant - PLN-ASO Treated  - 18 weeks (rep2)


title: Rh30 48 hr PTC-028 rep 1


title: Rh30 48 hr PTC-028 rep 3


title: SSCb_M_pvSSC_A19_2m_19

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome h38 using STAR 2.4 (Dobin et al., 2013)
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Genome_build: GRCm38.p6.gencode.vM20
Supplementary_files_format_and_content: comma-separated text file with raw gene counts for every gene and every sample

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and SSC populations purified via FACS.
SmartSeq2 single cell  pipeline (Picelli et al.)


title: B1_pol2-D276A-E278A_G0


title: Pln R14Del mutant - PLN-ASO Treated  - 18 weeks (rep1)


title: A2_WT_G200

value: WT


title: SSCb_M_pvSSC_A18_2m_368


title: Pln R14Del mutant - PLN-ASO Treated  - 7 weeks (rep4)

description: Treatment consisted of a 4-week loading phase with weekly dosing of 100mg/kg. Treatment was initiated at the age of 3 weeks.


title: SSCb_M_pvSSC_A2_2m_213


title: Pln R14Del mutant - PLN-ASO Treated  - 7 weeks (rep3)


title: Rh30 24 hr PTC-028 rep 1


title: A2_WT_G0


title: Rh30 DMSO rep 3

value: Dimethyl sulfoxide (DMSO) 0.1%


title: Pln R14Del mutant - PLN-ASO Treated  - 7 weeks (rep2)


title: A1_WT_G200


title: SSCb_M_pvSSC_A16_2m_111


title: A1_WT_G0


title: Rh30 24 hr PTC-028 rep 3


title: Pln R14Del mutant - PBS  - 7 weeks (rep4)

description: Control treatment consisted of 4 times a weekly dosing of PBS with a comparable volume to the PLN-ASO treated animals (+/- 10ul/g). Treatment was initiated at the age of 3 weeks.

value: sham


title: Pln R14Del mutant - PLN-ASO Treated  - 7 weeks (rep1)


title: Rh28 48 hr PTC-028 rep 3


title: SSCb_M_pvSSC_A14_2m_209


title: Pln R14Del mutant - PBS  - 7 weeks (rep3)


title: Rh30 DMSO rep 2


title: Rh28 48 hr PTC-028 rep 2


title: WT_SNK170425002_A07

first: Itoshi

last: NIKAIDO

address: 2-1 Hirosawa

institute: RIKEN

description: RNA from single nuclei

tag: condition

value: WT (96 wel)

value: brain cortex

value: 14 weeks old

value: Neuron

value: wild type (Ehmt1+/+)


title: Rh30 DMSO rep 1


title: SSCb_M_pvSSC_A17_2m_134

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

value: bone

value: pvSSC

value: Adult


title: E14.5 Mouse Tail

description: EMB

data_processing:
CellRanger Suite aligned fastq files to mm38 genome
Gene-cell matrices were extracted and load into R software and further analyzed using the single cell RNA sequencing package, Seurat (version 3.0)
Genome_build: GRCmm38
Supplementary_files_format_and_content: Seurat gene cell matrix

source_name: Mouse Embryo (in vivo)

growth_protocol: mESC derived tenocytes and somites were differentiated from pluripotency. The E14.5 tail was isolated from the embryo with a scalpel.

extract_protocol:
Single cell suspensions of the samples were prepared with Trypsin and Collagenase and dead cell depletion was performed with the EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL) to enrich for live cells.
Live cells were input to a 10x Genomics Chromium device. Single cell RNA libraries were prepared using the Chromium Single Cell 3’ v3 Reagent Kit (10x Genomics) user guide. Sample libraries were pooled together at equimolar ratios

treatment_protocol: The samples differ by origin, not treatment. ES derived, in vitro somite and tenocytes differ in the time of isolation, not treatment.

tag: in vivo/in vitro

value: in vivo

value: Mouse Embryo (in vivo)


title: SSCb_M_pvSSC_A12_2m_171


title: SSCb_M_pvSSC_A15_2m_320


title: Differentiated Tenocytes

source_name: monolayer (cell culture)

value: In vitro

value: monolayer (cell culture)


title: Rh30 24 hr PTC-028 rep 2


title: Pln R14Del mutant - PBS  - 7 weeks (rep2)

tag: genotype

value: Pln R14Del/R14Del


title: Pln R14Del mutant - PBS  - 7 weeks (rep1)

tag: treatment

value: female


title: SSCb_M_pvSSC_A11_2m_18

tag: cell type

value: male


title: Rh28 24 hr PTC-028 rep 3


title: Rh28 48 hr PTC-028 rep 1


title: Spleen CD8T cells - RES_TCR

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

description: gene expression and TCR

data_processing:
BCL conversion and demultiplexing: Bcl2fastq and CellRanger
Mapping: CellRanger
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Spleen

growth_protocol: Liver mononuclear cells were separated by 40/75% percoll from liver tissue suspension,  then samples from four mice were pooled. Liver CD8T cells were separated by FACS sorting (CD45+TCRb+NK1.1-CD4-CD8+) using FACS (BD Aria III).

extract_protocol:
Target cells (CD45+TCRb+NK1.1-CD4-CD8+) were isolated from liver mononuclear cells via FACS.
scRNA-seq: Freshly sorted liver CD8 T cells (CD45+TCRb+NK1.1-CD4-CD8+) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Indexed libraries were multiplexed and sequenced on Illumina HiSeq X instruments according to the manufacturer's instructions.
scRNA/TCR-seq: Target liver CD8+ cells were isolated by FACS and libraries were prepared using single-cell  5' gene expression library preparation v1.1,  multiplex 1:9 = TCR : gene-expression according to manufacturer’s protocol (10X Genomics) and sequenced by DNBSEQ.

value: Spleen

value: CD8T cells

value: HFHC diet (24 wks) + normal diet (5wks) fed


title: SSCb_M_pvSSC_A10_2m_91

tag: Sex


title: Differentiated Paraxial Mesoderm

description: SOM

value: in vitro

value: Embryoid bodies (cell culture)


title: SSCb_M_pvSSC_A13_2m_30


title: WT-7weeks (rep3)

value: WT

value: untreated


title: Liver CD8T cells - RES_TCR

description: TCR

source_name: Liver

value: Liver


title: Spleen CD8T cells - RES_GEX

description: gene expression and TCR


title: WT-7weeks (rep2)


title: WT-7weeks (rep1)


title: s-4 LP-1 BR

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
ATAC-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Homo sapiens genome (hg19)
Regions of enrichments were called using the MACS2 (version 2.1.1) peak caller.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated by deeptools

growth_protocol: LP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Cells were resuspended in lysis buffer, centrifugated and resuspended for 60 min at 37℃ in Transposase reaction mix. The fragmented DNA was purified and added adaptor sequences by PCR. After DNA purification, DNA was sequenced on HiSeq X ten.
Construction of libraries were performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).

treatment_protocol: LP-1 cells were induced bortezomib resistance and infected with with overexpression HP1g plasmid or vector.

value: cell strain

value: myeloma


title: Rh28 24 hr PTC-028 rep 2


title: Liver CD8T cells - RES_GEX

description: gene expression


title: Rh28 DMSO rep 3

value: Dimethyl sulfoxide (DMSO) 0.1%


title: p00_fezf_enr_bc209

city: Santa Cruz

first: Bin

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
paired-end map to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
paired-end map (repeat-filtered reads) to mm10 with STAR
convert mappings to coverage of mm10 Gencode VM18 genes
differential expression analysis with DESeq on per-gene, per-sample read counts, 2-4 replicates per condition
use DESeq sizeFactors to report per-sample normalized read counts for significant genes
Genome_build: mm10
Supplementary_files_format_and_content: for each gene, the read counts, normalized by DESeq sizeFactors, are shown for all replicates.

source_name: cortex

growth_protocol: Fezf2+/- mice were bred with Fezf2+/-;Fezf2-EnR mice. P0 Fezf2+/+, Fezf2-/-, and Fezf2-/-; Fezf2-EnR pups were used for the study.

extract_protocol:
Qiagen RNAeasy protocol was followed to isolate total RNAs from the dissected cortices.
Illumina TruSeq RNA sample preparation protocol

treatment_protocol: Cerebral cortex was dissected out from 3 P0 Fezf2+/+,  4 Fezf2-/-, and 2 Fezf2-/-; Fezf2-EnR mice. Total RNAs from each brain were isolated using Qiagen RNAeasy kit. The sequencing libraries were generated following Illumina PolyA library prep protocol. The libraries were sequenced on an Illumina Novaseq4 platform. DESeq was used to identify genes differentially expressed in Fezf2-/- and Fezf2-/-;Fezf2-EnR cortices.

value: cortex

value: post-natal day 0

value: Fezf2-/-; Fezf2-EnR

tag: litter


title: Rh28 24 hr PTC-028 rep 1


title: p00_fezf_enr_bc208


title: Spleen CD8T cells - ND_TCR

description: TCR

value: normal diet (29 wks) fed


title: Spleen CD8T cells - ND_GEX

description: gene expression


title: p00_fezf_xxx_bc207


title: Rh28 DMSO rep 1


title: s-3 LP-1 BR


title: s-2 LP-1 WT


title: p00_fezf_xxx_bc205


title: s-1 LP-1 WT


title: Liver CD8T cells - ND_GEX

description: gene expression


title: Liver CD8T cells - ND_TCR

description: TCR


title: p00_wild_xxx_bc203

value: wild type


title: E+L.0uM

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
Reads were processed and aligned to the GRCh38 human reference genome using Cell Ranger (v3.1.0) pipeline (https://github.com/10XGenomics/cellranger). For each sample, a digital gene expression matrix was generated containing the raw UMI counts for each cell in a given sample.
Downstream analysis was performed using various functions in Seurat package (v3.1.1).
Differentially expressed genes (DEG) for clusters and MeHg treatments were detected using the R package edgeR on the corresponding read matrixes.
Genome_build: GRCh38 human reference genome
Supplementary_files_format_and_content: Files suffixed with "barcodes.tsv.gz", "features.tsv.gz" and "matrix.mtx.gz" are feature-barcode matrix generated by Cell Ranger. CellRanger represents the feature-barcode matrix using sparse formats (only the nonzero entries are stored) in order to minimize file size. Please see the link for details:   https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices
Supplementary_files_format_and_content: File "DE_detection_cluster_edgeR.tar" includes differential expression analysis using edgeR. A README file is included to explain the file content.

source_name: hiPSC line derived from dermal fibroblasts

extract_protocol:
To harvest the cells the cultures were washed twice with DMEM/F12 medium to remove dead cells and cell debris, dissociated with accutase for 12 minutes and collected in ice-cold DMEM/F12 containing 10 µM Rock-inhibitor. The cells were pelleted at 300 x g for 5 minutes at 4oC, resuspended in ice-cold DMEM/F12 containing glutamax, 0.04% BSA and 10 µM Rock-inhibitor and gently triturated using a 5 ml glass pipette. The cell suspensions were strained through a 40 µm filter, the viability of the harvested cells was approximately 90% for all samples as determined with trypan blue exclusion assay using an automated cell counter (Cellometer AutoT4 from Nexcelome Bioscience, Lawrence, MA).
The cell concentrations were adjusted to 550 cells/µl and approximately 10,000 cells per channel (to give estimated recovery of 5,000-8,000 cells per channel) were loaded onto a Chromium Single Cell 3′ Chip (10x Genomics, PN-2000168) and processed through the Chromium controller to generate single-cell gel beads in emulsion (GEMs). scRNA-seq  libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-1000075).  Each sample was ligated and barcoded prior to performing library QC.  The Agilent Bioanalyzer and QuantStudio 12K Flex were used to assess the library quality prior to sequencing. Libraries from different samples were pooled based on molar concentrations and sequenced on a NovaSeq 6000 instrument (Illumina) with 151 bases for read 1, 151 bases for read 2 and 8 bases for index 1. After the first round of sequencing, libraries were re-pooled on the basis of the actual number of cells in each and re-sequenced to give an equal number of reads per cell in each sample and to reach a sequencing saturation of at least 50%.
Chromium Single Cell Gene Expression

value: E+L, 0uM MeHg

tag: days of differentiation

value: 38 days


title: 4LP-1OECBX3


title: E+L.0.1uM

value: hiPSC line derived from dermal fibroblasts

value: E+L, 0.1uM MeHg


title: 3LP-1OECBX3


title: Rh28 DMSO rep 2


title: p00_fezf_xxx_bc204

last: Chen


title: p00_wild_xxx_bc201


title: p00_wild_xxx_bc202


title: E.0.1uM

value: E, 0.1uM MeHg


title: 1LP-1CON


title: E+L.1uM

value: E+L, 1uM MeHg


title: p00_fezf_xxx_bc206


title: WT-scrotum-3

status: Public on Jun 10 2021

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

data_processing:
High-throughput sequencing was performed on the NovaSeq system (Illumina).
Remove unqualified as well as adapter sequences by fastp with parameters “--detect_adapter_for_pe”
Porcine genome from NCBI (GCF_000003025.6) was used as the reference to which reads were mapped to using accessible gene annotation by hisat2 (version 2.1.0) with default parameters.
htseq-count (version 0.11.2) was used to quantify the gene expression levels, and custom scripts was used to generate gene expression matrices.
Genome_build: GCF_000003025.6
Supplementary_files_format_and_content: comma-delimited csv file includes Raw reads counts for each Sample ...

organism: Sus scrofa

source_name: normal tissues from wild type pig

growth_protocol: Three DIK founders with 7-month-old and age-matched wild-type were treated with Dox . Obvious tumors were gradually developed in the nose, mouth, and scrotum of one DIK founder. Eight month after induction, this founder and age-matched wild-type were sacrificed and the tissues of nose, mouse and scrotum were collected for RNA-seq analysis.

extract_protocol:
Total RNAs were extracted using TRIzol (Thermo Fisher) in accordance with the standard instructions.
The library were constructed by VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611) in accordance with the standard instructions.

treatment_protocol: The fresh collected tumor and normal tissues were stored in RNAlater™ Stabilization Solution (Thermo Fisher, AM7020) at -80°C before extraction of total RNA together.

value: scrotum

tag: tissue type

value: fresh normal tissue


title: WT-mouth-3

value: mouth


title: SSCb_M_pvSSC_A1_2m_353

city: Sacramento

value: bone

value: pvSSC

value: Adult

value: male


title: E.1uM

value: E, 1uM MeHg


title: WT-mouth-1


title: WT-nose-3

value: nose


title: WT-mouth-2


title: WT-nose-1


title: DIK-scrotum-2

source_name: tumors from DIK pig

value: fresh tumor tissue


title: WT-scrotum-1


title: 2LP-1CON

value: cell strain

value: myeloma