title: K562_H3K27me3_20181120_icell8_226_(20181120_HK_Hs_K562_me3_CCAACACGCTCTCTAT)


title: K562_H3K27me3_20181120_icell8_219_(20181120_HK_Hs_K562_me3_TACTTGAATGGAAATC)

status: Public on Apr 29 2019

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Single-cell CUT&Tag for H3K27me3 in K562 cells using ICELL8 platform

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We extracted fragments from properly paired reads (Supplementary file(s) .bed) .

molecule: genomic DNA

organism: Homo sapiens

source_name: Single cell CUT&Tag

extract_protocol: Single-cell CUT&Tag: Approximately 50,000 exponentially growing K562 cells were processed by centrifugation between buffer and reagent exchanges in low-retention tubes throughout. Centrifugations were performed at 600g for 3 min in a swinging bucket rotor for the initial wash and incubation steps, and then at 300g for 3 min after pA-Tn5 binding.  Cells were collected and washed twice with 1ml Wash Buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM Spermidine, 1X Protease inhibitor cocktail) at room temperature. Nuclei were isolated by permeabilizing cells in NP40-Digitonin Wash Buffer (0.01% NP40, 0.01% Digitonin in wash buffer) and resuspended in 1 mL of NP40-Digitonin Wash buffer with 1mM EDTA. Antibody was added at a 1:50 dilution and incubated on a rotator at 4°C overnight. Permeabilized cells were then rinsed once with NP40-Digitonin Wash buffer and incubated with anti-Rabbit IgG antibody (1:50 dilution) in 1 ml of NP40-Digitonin Wash buffer on a rotator at room temperature for 30 min. Nuclei were then washed 3x for 5 min in 1 ml NP40-Digitonin Wash buffer to remove unbound antibodies. For pA-Tn5 binding, a 1:100 dilution of pA-Tn5 adapter complex was prepared in 1 mL NP40-Dig-med-buffer (0.01% NP40, 0.01% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail), and permeabilized cells were incubated with the pA-Tn5 adapter complex on a rotator at RT for 1 hr. Cells were washed 3x for 5 min in 1 ml NP40-Dig-med-buffer to remove excess pA-Tn5 protein. Cells were resuspended in 150 µL Tagmentation buffer (10 mM MgCl2 in NP40-Dig-med-buffer) and incubated at 37 for 1h. Tagmentation was stopped by adding 50 µL of 4X Stop Buffer (40.4 mM EDTA and 2 mg/ml DAPI) and the sample was held on ice for 30 minutes. The SMARTer ICELL8 single-cell system (Takara Bio USA, Cat. #640000) was used to array single cells as described for scATAC-seq12. DAPI-stained nuclei were visualized under the microscope and if there were clumps, they were strained through 10 micron cell strainers. Cells were counted using a hematocytometer and diluted at 25 cells/µL in 0.5X PBS and 1X Second Diluent (Takara Bio USA, Cat. # 640196). Cells were loaded to a source loading plate. Control wells containing 0.5X PBS (25 µl) and fiducial mix (25 µl) (Takara Bio USA, Cat.  #640196) were also included in the source loading plate. Using the ICELL8 MultiSample NanoDispenser (MSND) FLA program, cells were dispensed into a SMARTer ICELL8 350v chip (Takara Bio USA, Cat. # 640019) at 35 nanoliter per well. After cell dispense was complete, chips were sealed with the imaging film (Takara Bio USA, Cat. #640109) and centrifuged at 400 xg for 5 min at room temperature and imaged using the ICELL8 imaging station (Takara Bio USA). Images were analyzed using automated microscopy image analysis software (CellSelect, Takara Bio USA). Since cells were stained only with DAPI, they were propidium iodide negative, so that permeabilized cells would not be excluded by default software settings. Additional single cells were manually selected for dispensing using a manual triaging procedure. Immediately following imaging, the filter file, which notes single-cell containing wells and control wells, was generated. We typically obtained ~1000 single cells per chip. All of the following reagents were added to the selected set of wells which contained single cells. To index the whole chip, 72 i5 and 72 i7 unique indices [Buenostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486-U264 (2015)] were dispensed at 7.32 µM using ICELL8 MSND FLA program using the index 1 and index 2 filtered dispense tool respectively at 35 nanoliter per well. NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L) was dispensed twice using the ICELL8 MSND Single Cell / TCR program for the filtered dispense tool at 50 nanoliter per well. The chip was sealed and centrifuged at 2250 xg at 4◦C for at least 5 min after each dispense. The chip was sealed with a TE Sealing film (Takara Bio USA, Cat. #640109) and on-chip PCR was performed using a SMARTer ICELL8 Thermal Cycler (Takara Bio USA) as follows: 5 min at 72 ◦C and 2 min at 98 ◦C followed by 15 cycles of 10 sec at 98 ◦C, 30 sec at 60 ◦C, and 5 s at 72 ◦C, with a final extension at 72 ◦C for 1 min. PCR products were collected by centrifugation at ~2250 xg for 20 min using the supplied SMARTer ICELL8 Collection Kit (Takara Bio USA, Cat.#640048). Pooled libraries were purified using Ampure XP beads (Beckman Counter) in a 1:1.1 ratio. Briefly, libraries were incubated with beads for 15 min at RT, washed twice in 80% ethanol, and eluted in 10 mM Tris pH 8.0. Paired-end 25x8x8x25 bp Illumina sequencing was performed on the pooled barcoded libraries following the manufacturer’s instructions.

tag: antibody

value: H3K27me3 Cell Signalling #9733

tag: cell line

tag: cell type

value: human immortalised myelogenous leukemia cell line


title: K562_H3K27me3_20181120_icell8_216_(20181120_HK_Hs_K562_me3_GGGAATGAGCAAATTT)


title: K562_H3K27me3_20181120_icell8_246_(20181120_HK_Hs_K562_me3_GTGATAGCTGGAAATC)


title: K562_H3K27me3_20181120_icell8_215_(20181120_HK_Hs_K562_me3_ATAAGTTATGATGAAA)


title: K562_H3K27me3_20181120_icell8_217_(20181120_HK_Hs_K562_me3_TTGCTAAGAGAGATCT)


title: K562_H3K27me3_20181120_icell8_221_(20181120_HK_Hs_K562_me3_CAAGAATTACATTCGT)


title: K562_H3K27me3_20181120_icell8_218_(20181120_HK_Hs_K562_me3_GCGTTAAACGCCAGAT)


title: K562_H3K27me3_20181120_icell8_240_(20181120_HK_Hs_K562_me3_GAGCACGTAGAGATCT)


title: K562_H3K27me3_20181120_icell8_214_(20181120_HK_Hs_K562_me3_CCAAATAAGTAAGGAG)


title: K562_H3K27me3_20181120_icell8_212_(20181120_HK_Hs_K562_me3_GGAGTAAGTCACATGG)


title: K562_H3K27me3_20181120_icell8_213_(20181120_HK_Hs_K562_me3_TTTCGTCATATCCTCT)


title: K562_H3K27me3_20181120_icell8_234_(20181120_HK_Hs_K562_me3_CTTGGGTCCCACCGTT)


title: K562_H3K27me3_20181120_icell8_211_(20181120_HK_Hs_K562_me3_ATAAGTTACTCTCTAT)


title: K562_H3K27me3_20181120_icell8_207_(20181120_HK_Hs_K562_me3_TGGGTTTCACGCGCAG)


title: K562_H3K27me3_20181120_icell8_209_(20181120_HK_Hs_K562_me3_TTCGCGGCTGGGCGGT)


title: K562_H3K27me3_20181120_icell8_208_(20181120_HK_Hs_K562_me3_GCGTTAAATAACCAAG)


title: K562_H3K27me3_20181120_icell8_210_(20181120_HK_Hs_K562_me3_ATAAGTTAGCAAATTT)


title: K562_H3K27me3_20181120_icell8_205_(20181120_HK_Hs_K562_me3_CTTGGGTCGAGACGTG)


title: K562_H3K27me3_20181120_icell8_225_(20181120_HK_Hs_K562_me3_GTATTCGGGCAGCCTC)


title: K562_H3K27me3_20181120_icell8_206_(20181120_HK_Hs_K562_me3_CCGTTTGTCCTGCGGG)


title: K562_H3K27me3_20181120_icell8_204_(20181120_HK_Hs_K562_me3_CATCCTGTACTTGTTG)


title: K562_H3K27me3_20181120_icell8_201_(20181120_HK_Hs_K562_me3_AATTCGTTTCAAGAGC)


title: K562_H3K27me3_20181120_icell8_200_(20181120_HK_Hs_K562_me3_TTGACCCTACGCGCAG)


title: K562_H3K27me3_20181120_icell8_202_(20181120_HK_Hs_K562_me3_GGAGTAAGAGTCCGAG)


title: K562_H3K27me3_20181120_icell8_203_(20181120_HK_Hs_K562_me3_ATAAGTTAGGCACGGA)


title: K562_H3K27me3_20181120_icell8_197_(20181120_HK_Hs_K562_me3_TCTTATTATAAGTTAC)


title: K562_H3K27me3_20181120_icell8_199_(20181120_HK_Hs_K562_me3_CCGTTTGTTCACATGG)


title: K562_H3K27me3_20181120_icell8_189_(20181120_HK_Hs_K562_me3_TGTGCCTTACTTGTTG)


title: K562_H3K27me3_20181120_icell8_192_(20181120_HK_Hs_K562_me3_AAATACAGACTTAGAA)


title: K562_H3K27me3_20181120_icell8_193_(20181120_HK_Hs_K562_me3_GCGTTAAATAAGTTAC)


title: K562_H3K27me3_20181120_icell8_195_(20181120_HK_Hs_K562_me3_GGGAATGACGATAGGG)


title: K562_H3K27me3_20181120_icell8_190_(20181120_HK_Hs_K562_me3_GAGCACGTATTACCGT)


title: K562_H3K27me3_20181120_icell8_188_(20181120_HK_Hs_K562_me3_GCGTTAAACTTTAACA)


title: K562_H3K27me3_20181120_icell8_187_(20181120_HK_Hs_K562_me3_ATCACTCGTTCGTGCA)


title: K562_H3K27me3_20181120_icell8_220_(20181120_HK_Hs_K562_me3_CGCGGACATAACCAAG)


title: K562_H3K27me3_20181120_icell8_185_(20181120_HK_Hs_K562_me3_TGGGTTTCAGAGTAGA)


title: K562_H3K27me3_20181120_icell8_186_(20181120_HK_Hs_K562_me3_AGTAGATTCGTACCAA)


title: K562_H3K27me3_20181120_icell8_184_(20181120_HK_Hs_K562_me3_CTTGGGTCATGGTCAT)


title: K562_H3K27me3_20181120_icell8_183_(20181120_HK_Hs_K562_me3_CCAACACGCCCTTGGA)


title: K562_H3K27me3_20181120_icell8_180_(20181120_HK_Hs_K562_me3_GACGCTCCACCGGCCC)


title: K562_H3K27me3_20181120_icell8_182_(20181120_HK_Hs_K562_me3_CTCATGGGAGAGATCT)


title: K562_H3K27me3_20181120_icell8_181_(20181120_HK_Hs_K562_me3_AAATACAGTATCCTCT)


title: K562_H3K27me3_20181120_icell8_194_(20181120_HK_Hs_K562_me3_TTCCATATCCTTATGT)


title: K562_H3K27me3_20181120_icell8_196_(20181120_HK_Hs_K562_me3_AGTAGATTGCCCACGT)


title: K562_H3K27me3_20181120_icell8_191_(20181120_HK_Hs_K562_me3_CGGTTCCCCTAAGCCT)


title: K562_H3K27me3_20181120_icell8_179_(20181120_HK_Hs_K562_me3_TTGACCCTCGCCAGAT)


title: K562_H3K27me3_20181120_icell8_178_(20181120_HK_Hs_K562_me3_TGGGTTTCTCACATGG)


title: K562_H3K27me3_20181120_icell8_177_(20181120_HK_Hs_K562_me3_AATGGTAGTCCATCAA)


title: K562_H3K27me3_20181120_icell8_176_(20181120_HK_Hs_K562_me3_AGTAGATTTGCATACT)


title: K562_H3K27me3_20181120_icell8_175_(20181120_HK_Hs_K562_me3_CCAACACGTTCGTGCA)


title: K562_H3K27me3_20181120_icell8_172_(20181120_HK_Hs_K562_me3_TTTCGTCACCTGCGGG)


title: K562_H3K27me3_20181120_icell8_173_(20181120_HK_Hs_K562_me3_ATGGGAACAGAGATCT)


title: K562_H3K27me3_20181120_icell8_198_(20181120_HK_Hs_K562_me3_CGGTTCCCCTCTCTAT)


title: K562_H3K27me3_20181120_icell8_169_(20181120_HK_Hs_K562_me3_CCAAATAAACGCGCAG)


title: K562_H3K27me3_20181120_icell8_163_(20181120_HK_Hs_K562_me3_CTCTCTACTGGAAATC)


title: K562_H3K27me3_20181120_icell8_168_(20181120_HK_Hs_K562_me3_TCAGCTATAGCCGTTC)


title: K562_H3K27me3_20181120_icell8_165_(20181120_HK_Hs_K562_me3_GACGCTCCCGCCAGAT)


title: K562_H3K27me3_20181120_icell8_167_(20181120_HK_Hs_K562_me3_TTCGCGGCCTAAGCCT)


title: K562_H3K27me3_20181120_icell8_162_(20181120_HK_Hs_K562_me3_GGGAATGAGAGACGTG)


title: K562_H3K27me3_20181120_icell8_166_(20181120_HK_Hs_K562_me3_TTCCATATGGCACGGA)


title: K562_H3K27me3_20181120_icell8_158_(20181120_HK_Hs_K562_me3_CAATCTTATGATTGTT)


title: K562_H3K27me3_20181120_icell8_159_(20181120_HK_Hs_K562_me3_ATGATGATCAGCAACG)


title: K562_H3K27me3_20181120_icell8_160_(20181120_HK_Hs_K562_me3_ACCGGCTAACTGCATA)


title: K562_H3K27me3_20181120_icell8_161_(20181120_HK_Hs_K562_me3_GTATTCGGTCCATCAA)


title: K562_H3K27me3_20181120_icell8_174_(20181120_HK_Hs_K562_me3_TGGTCACACGGACTGC)


title: K562_H3K27me3_20181120_icell8_155_(20181120_HK_Hs_K562_me3_CATCGACCGGTGAAGG)


title: K562_H3K27me3_20181120_icell8_156_(20181120_HK_Hs_K562_me3_CTTGGGTCGTAAGGAG)


title: K562_H3K27me3_20181120_icell8_151_(20181120_HK_Hs_K562_me3_GTATTCGGGGGCTTGG)


title: K562_H3K27me3_20181120_icell8_154_(20181120_HK_Hs_K562_me3_GGGAATGACTTTAACA)


title: K562_H3K27me3_20181120_icell8_153_(20181120_HK_Hs_K562_me3_CATCGACCCTCTCTAT)


title: K562_H3K27me3_20181120_icell8_152_(20181120_HK_Hs_K562_me3_GTTAACAGCTCTCTAT)


title: K562_H3K27me3_20181120_icell8_171_(20181120_HK_Hs_K562_me3_ATGATGATAGAGTAGA)


title: K562_H3K27me3_20181120_icell8_157_(20181120_HK_Hs_K562_me3_AAGAGGCATGATGAAA)


title: K562_H3K27me3_20181120_icell8_164_(20181120_HK_Hs_K562_me3_TCTTATTAACTTAGAA)


title: K562_H3K27me3_20181120_icell8_144_(20181120_HK_Hs_K562_me3_ATTGCCGGAACATGAT)


title: K562_H3K27me3_20181120_icell8_170_(20181120_HK_Hs_K562_me3_ATAAGTTATCCATCAA)


title: K562_H3K27me3_20181120_icell8_150_(20181120_HK_Hs_K562_me3_TTCGCGGCTTTCTAGC)


title: K562_H3K27me3_20181120_icell8_145_(20181120_HK_Hs_K562_me3_CATCGACCTAAGTTAC)


title: K562_H3K27me3_20181120_icell8_146_(20181120_HK_Hs_K562_me3_GGTAAACCATTGGGTC)


title: K562_H3K27me3_20181120_icell8_143_(20181120_HK_Hs_K562_me3_TCCTGAGCCTAGAAGT)


title: K562_H3K27me3_20181120_icell8_148_(20181120_HK_Hs_K562_me3_TGTGCCTTTGATGAAA)


title: K562_H3K27me3_20181120_icell8_147_(20181120_HK_Hs_K562_me3_CTCATGGGACTTAGAA)


title: K562_H3K27me3_20181120_icell8_149_(20181120_HK_Hs_K562_me3_CATCGACCAATCTACA)


title: K562_H3K27me3_20181120_icell8_142_(20181120_HK_Hs_K562_me3_TAACAACAGGGCTTGG)


title: K562_H3K27me3_20181120_icell8_141_(20181120_HK_Hs_K562_me3_ATTGCCGGTGATGAAA)


title: K562_H3K27me3_20181120_icell8_140_(20181120_HK_Hs_K562_me3_GACGCTCCCTTTAACA)


title: K562_H3K27me3_20181120_icell8_139_(20181120_HK_Hs_K562_me3_TACTTGAACTTTAACA)


title: K562_H3K27me3_20181120_icell8_135_(20181120_HK_Hs_K562_me3_TTATGAAAAACATGAT)


title: K562_H3K27me3_20181120_icell8_133_(20181120_HK_Hs_K562_me3_TTCCATATGACGTGGC)


title: K562_H3K27me3_20181120_icell8_136_(20181120_HK_Hs_K562_me3_TGGGTTTCGTGTATCG)


title: K562_H3K27me3_20181120_icell8_137_(20181120_HK_Hs_K562_me3_TAACAACAATGGTCAT)


title: K562_H3K27me3_20181120_icell8_138_(20181120_HK_Hs_K562_me3_TGCTGGGTGAGACGTG)


title: K562_H3K27me3_20181120_icell8_132_(20181120_HK_Hs_K562_me3_AGTAGATTAAGGAGTA)


title: K562_H3K27me3_20181120_icell8_131_(20181120_HK_Hs_K562_me3_TACTTGAATGTTCCTG)


title: K562_H3K27me3_20181120_icell8_130_(20181120_HK_Hs_K562_me3_CTCTCTACTAACCAAG)


title: K562_H3K27me3_20181120_icell8_134_(20181120_HK_Hs_K562_me3_GGTCATTTCTTTAACA)


title: K562_H3K27me3_20181120_icell8_129_(20181120_HK_Hs_K562_me3_ATAAGTTAGTAAGGAG)


title: K562_H3K27me3_20181120_icell8_126_(20181120_HK_Hs_K562_me3_GATCCAAACCACCGTT)


title: K562_H3K27me3_20181120_icell8_125_(20181120_HK_Hs_K562_me3_CGGCCAATACGCGCAG)


title: K562_H3K27me3_20181120_icell8_124_(20181120_HK_Hs_K562_me3_GATCCAAACGGACTGC)


title: K562_H3K27me3_20181120_icell8_123_(20181120_HK_Hs_K562_me3_TTGCTAAGGGGCTTGG)


title: K562_H3K27me3_20181120_icell8_128_(20181120_HK_Hs_K562_me3_GTATTCGGTTAACTTG)


title: K562_H3K27me3_20181120_icell8_122_(20181120_HK_Hs_K562_me3_GGTAAACCAGCCGTTC)


title: K562_H3K27me3_20181120_icell8_120_(20181120_HK_Hs_K562_me3_TTCGCGGCCGCCAGAT)


title: K562_H3K27me3_20181120_icell8_116_(20181120_HK_Hs_K562_me3_TTTAATGCTGTTCCTG)


title: K562_H3K27me3_20181120_icell8_117_(20181120_HK_Hs_K562_me3_TACTTGAATTAACTTG)


title: K562_H3K27me3_20181120_icell8_121_(20181120_HK_Hs_K562_me3_GTATTCGGTGATTGTT)


title: K562_H3K27me3_20181120_icell8_118_(20181120_HK_Hs_K562_me3_GACGCTCCAGAGTAGA)


title: K562_H3K27me3_20181120_icell8_114_(20181120_HK_Hs_K562_me3_CGCGGACAAGAGATCT)


title: K562_H3K27me3_20181120_icell8_115_(20181120_HK_Hs_K562_me3_CATCCTGTTAACCAAG)


title: K562_H3K27me3_20181120_icell8_113_(20181120_HK_Hs_K562_me3_TGGGTTTCGCATTAAG)


title: K562_H3K27me3_20181120_icell8_112_(20181120_HK_Hs_K562_me3_CCAACACGCGATAGGG)


title: K562_H3K27me3_20181120_icell8_107_(20181120_HK_Hs_K562_me3_TCAGCTATGCAAATTT)


title: K562_H3K27me3_20181120_icell8_109_(20181120_HK_Hs_K562_me3_GTGATAGCAATCTACA)


title: K562_H3K27me3_20181120_icell8_106_(20181120_HK_Hs_K562_me3_TGGTCACACGTAGACC)


title: K562_H3K27me3_20181120_icell8_108_(20181120_HK_Hs_K562_me3_AAATACAGAGAGATCT)


title: K562_H3K27me3_20181120_icell8_105_(20181120_HK_Hs_K562_me3_GAAATGCCCTTTAACA)


title: K562_H3K27me3_20181120_icell8_127_(20181120_HK_Hs_K562_me3_AGACCAGCGTCGGACT)


title: K562_H3K27me3_20181120_icell8_104_(20181120_HK_Hs_K562_me3_TACTTGAACTCTCTAT)


title: K562_H3K27me3_20181120_icell8_100_(20181120_HK_Hs_K562_me3_CAAGAATTACTGCATA)


title: K562_H3K27me3_20181120_icell8_103_(20181120_HK_Hs_K562_me3_GATCCAAATGGGCGGT)


title: K562_H3K27me3_20181120_icell8_99_(20181120_HK_Hs_K562_me3_GATCCAAAGAGACGTG)


title: K562_H3K27me3_20181120_icell8_102_(20181120_HK_Hs_K562_me3_GGGAATGACCTTATGT)


title: K562_H3K27me3_20181120_icell8_98_(20181120_HK_Hs_K562_me3_TGGGTTTCTCCATCAA)


title: K562_H3K27me3_20181120_icell8_96_(20181120_HK_Hs_K562_me3_CGGCCAATTAAGTTAC)


title: K562_H3K27me3_20181120_icell8_95_(20181120_HK_Hs_K562_me3_TTCCATATATGGTCAT)


title: K562_H3K27me3_20181120_icell8_97_(20181120_HK_Hs_K562_me3_TTATGAAAACATTCGT)


title: K562_H3K27me3_20181120_icell8_94_(20181120_HK_Hs_K562_me3_TTATGAAATTAACTTG)


title: K562_H3K27me3_20181120_icell8_119_(20181120_HK_Hs_K562_me3_AAGAGGCAGGTTCAAT)


title: K562_H3K27me3_20181120_icell8_92_(20181120_HK_Hs_K562_me3_TTGCTAAGCCAGTTTA)


title: K562_H3K27me3_20181120_icell8_93_(20181120_HK_Hs_K562_me3_TGGGTTTCACGATAAC)


title: K562_H3K27me3_20181120_icell8_89_(20181120_HK_Hs_K562_me3_AACGCCATTAACCAAG)


title: K562_H3K27me3_20181120_icell8_111_(20181120_HK_Hs_K562_me3_ATCACTCGAGCCGTTC)


title: K562_H3K27me3_20181120_icell8_88_(20181120_HK_Hs_K562_me3_ATGGGAACTTGCCTAA)


title: K562_H3K27me3_20181120_icell8_110_(20181120_HK_Hs_K562_me3_GTAGAGGATGGGCGGT)


title: K562_H3K27me3_20181120_icell8_87_(20181120_HK_Hs_K562_me3_TACACCTCTTAACTTG)


title: K562_H3K27me3_20181120_icell8_85_(20181120_HK_Hs_K562_me3_CATCCTGTTAAGTTAC)


title: K562_H3K27me3_20181120_icell8_90_(20181120_HK_Hs_K562_me3_GTATTCGGCTAAGCCT)


title: K562_H3K27me3_20181120_icell8_86_(20181120_HK_Hs_K562_me3_GGCGTCGAGCAAATTT)


title: K562_H3K27me3_20181120_icell8_83_(20181120_HK_Hs_K562_me3_TAACAACAACGATAAC)


title: K562_H3K27me3_20181120_icell8_101_(20181120_HK_Hs_K562_me3_TTTAATGCCCCTTGGA)


title: K562_H3K27me3_20181120_icell8_81_(20181120_HK_Hs_K562_me3_CTTGGGTCCGTACCAA)


title: K562_H3K27me3_20181120_icell8_80_(20181120_HK_Hs_K562_me3_TCAGCTATCGTAGACC)


title: K562_H3K27me3_20181120_icell8_82_(20181120_HK_Hs_K562_me3_ATGGGAACGCATTAAG)


title: K562_H3K27me3_20181120_icell8_79_(20181120_HK_Hs_K562_me3_TCCTGAGCGGCACGGA)


title: K562_H3K27me3_20181120_icell8_78_(20181120_HK_Hs_K562_me3_AGTAGATTGACGTGGC)


title: K562_H3K27me3_20181120_icell8_77_(20181120_HK_Hs_K562_me3_GGCGTCGAGGCACGGA)


title: K562_H3K27me3_20181120_icell8_91_(20181120_HK_Hs_K562_me3_TTGCTAAGCCTGCGGG)


title: K562_H3K27me3_20181120_icell8_69_(20181120_HK_Hs_K562_me3_GATCCAAAATGGTCAT)


title: K562_H3K27me3_20181120_icell8_72_(20181120_HK_Hs_K562_me3_CAAGAATTCGCCAGAT)


title: K562_H3K27me3_20181120_icell8_73_(20181120_HK_Hs_K562_me3_ATGATGATGAGACGTG)


title: K562_H3K27me3_20181120_icell8_75_(20181120_HK_Hs_K562_me3_AGTAGATTTCCGAGTT)


title: K562_H3K27me3_20181120_icell8_76_(20181120_HK_Hs_K562_me3_CCAACACGGACGTGGC)


title: K562_H3K27me3_20181120_icell8_70_(20181120_HK_Hs_K562_me3_AGACCAGCCTAAGCCT)


title: K562_H3K27me3_20181120_icell8_74_(20181120_HK_Hs_K562_me3_GACGCTCCTGATTGTT)


title: K562_H3K27me3_20181120_icell8_71_(20181120_HK_Hs_K562_me3_AGGCAGAAGGTTCAAT)


title: K562_H3K27me3_20181120_icell8_67_(20181120_HK_Hs_K562_me3_ATGGGAACCCCTTGGA)


title: K562_H3K27me3_20181120_icell8_65_(20181120_HK_Hs_K562_me3_CGGTTCCCAACATGAT)


title: K562_H3K27me3_20181120_icell8_66_(20181120_HK_Hs_K562_me3_TTTCGTCAGGCACGGA)


title: K562_H3K27me3_20181120_icell8_68_(20181120_HK_Hs_K562_me3_TCAGCTATTCCATCAA)


title: K562_H3K27me3_20181120_icell8_84_(20181120_HK_Hs_K562_me3_TTGCTAAGTCCATCAA)


title: K562_H3K27me3_20181120_icell8_62_(20181120_HK_Hs_K562_me3_CATCGACCTCCATCAA)


title: K562_H3K27me3_20181120_icell8_64_(20181120_HK_Hs_K562_me3_GTAGAGGACTAGAAGT)


title: K562_H3K27me3_20181120_icell8_61_(20181120_HK_Hs_K562_me3_CGGCCAATCCAGTTTA)


title: K562_H3K27me3_20181120_icell8_60_(20181120_HK_Hs_K562_me3_TTGACCCTTTAACTTG)


title: K562_H3K27me3_20181120_icell8_63_(20181120_HK_Hs_K562_me3_CCAACACGAGCCGTTC)


title: K562_H3K27me3_20181120_icell8_59_(20181120_HK_Hs_K562_me3_AGTAGATTATCCAGGA)


title: K562_H3K27me3_20181120_icell8_58_(20181120_HK_Hs_K562_me3_AATTCGTTGCATTAAG)


title: K562_H3K27me3_20181120_icell8_56_(20181120_HK_Hs_K562_me3_CTTGGGTCCGTAGACC)


title: K562_H3K27me3_20181120_icell8_55_(20181120_HK_Hs_K562_me3_GGTAAACCGTGTATCG)


title: K562_H3K27me3_20181120_icell8_57_(20181120_HK_Hs_K562_me3_ATCACTCGACGCGCAG)


title: K562_H3K27me3_20181120_icell8_53_(20181120_HK_Hs_K562_me3_GTGATAGCTATTTGCG)


title: K562_H3K27me3_20181120_icell8_52_(20181120_HK_Hs_K562_me3_GGAGTAAGCCCTTGGA)


title: K562_H3K27me3_20181120_icell8_51_(20181120_HK_Hs_K562_me3_TTCCATATATTGGGTC)


title: K562_H3K27me3_20181120_icell8_54_(20181120_HK_Hs_K562_me3_GTATTCGGTCCGAGTT)


title: K562_H3K27me3_20181120_icell8_49_(20181120_HK_Hs_K562_me3_ATTGCCGGCGTACCAA)


title: K562_H3K27me3_20181120_icell8_50_(20181120_HK_Hs_K562_me3_GCGTTAAAGACGTGGC)


title: K562_H3K27me3_20181120_icell8_48_(20181120_HK_Hs_K562_me3_ATGGGAACCCACCGTT)


title: K562_H3K27me3_20181120_icell8_43_(20181120_HK_Hs_K562_me3_CTTGGGTCTACTGACC)


title: K562_H3K27me3_20181120_icell8_41_(20181120_HK_Hs_K562_me3_GGTAAACCTGGGCGGT)


title: K562_H3K27me3_20181120_icell8_47_(20181120_HK_Hs_K562_me3_TACACCTCTGGAAATC)


title: K562_H3K27me3_20181120_icell8_46_(20181120_HK_Hs_K562_me3_TGGTCACAGGTTCAAT)


title: K562_H3K27me3_20181120_icell8_40_(20181120_HK_Hs_K562_me3_TGGGTTTCGACGTGGC)


title: K562_H3K27me3_20181120_icell8_42_(20181120_HK_Hs_K562_me3_GGCGTCGAAGTCCGAG)


title: K562_H3K27me3_20181120_icell8_45_(20181120_HK_Hs_K562_me3_CCAAATAACTAAGCCT)


title: K562_H3K27me3_20181120_icell8_38_(20181120_HK_Hs_K562_me3_TGGTCACAACTTAGAA)


title: K562_H3K27me3_20181120_icell8_35_(20181120_HK_Hs_K562_me3_CCAAATAATTGCCTAA)


title: K562_H3K27me3_20181120_icell8_39_(20181120_HK_Hs_K562_me3_TTGACCCTCGTAGACC)


title: K562_H3K27me3_20181120_icell8_37_(20181120_HK_Hs_K562_me3_ATTGCCGGCTAGAAGT)


title: K562_H3K27me3_20181120_icell8_32_(20181120_HK_Hs_K562_me3_TTTAATGCGAGACGTG)


title: K562_H3K27me3_20181120_icell8_30_(20181120_HK_Hs_K562_me3_GCGTTAAACGTAGACC)


title: K562_H3K27me3_20181120_icell8_29_(20181120_HK_Hs_K562_me3_GGTAAACCAAGGAGTA)


title: K562_H3K27me3_20181120_icell8_36_(20181120_HK_Hs_K562_me3_GATCCAAATATCCTCT)


title: K562_H3K27me3_20181120_icell8_24_(20181120_HK_Hs_K562_me3_TGTGCCTTTGCATACT)


title: K562_H3K27me3_20181120_icell8_28_(20181120_HK_Hs_K562_me3_ATTGCCGGACTTGTTG)


title: K562_H3K27me3_20181120_icell8_26_(20181120_HK_Hs_K562_me3_GGTAAACCGTAAGGAG)


title: K562_H3K27me3_20181120_icell8_25_(20181120_HK_Hs_K562_me3_ATCACTCGTGATTGTT)


title: K562_H3K27me3_20181120_icell8_27_(20181120_HK_Hs_K562_me3_CAATCTTAGCCCACGT)


title: K562_H3K27me3_20181120_icell8_22_(20181120_HK_Hs_K562_me3_TTCCATATACATTCGT)


title: K562_H3K27me3_20181120_icell8_21_(20181120_HK_Hs_K562_me3_CGGCCAATCAGCAACG)


title: K562_H3K27me3_20181120_icell8_23_(20181120_HK_Hs_K562_me3_CATCCTGTTGGGCGGT)


title: K562_H3K27me3_20181120_icell8_20_(20181120_HK_Hs_K562_me3_GGGAATGAGATTCCCA)


title: K562_H3K27me3_20181120_icell8_19_(20181120_HK_Hs_K562_me3_AGTAGATTCGTAGACC)


title: K562_H3K27me3_20181120_icell8_18_(20181120_HK_Hs_K562_me3_TTATGAAATGATTGTT)


title: K562_H3K27me3_20181120_icell8_17_(20181120_HK_Hs_K562_me3_CCGTTTGTGGTGAAGG)


title: K562_H3K27me3_20181120_icell8_34_(20181120_HK_Hs_K562_me3_GCTACGCTTAGATCGC)


title: K562_H3K27me3_20181120_icell8_11_(20181120_HK_Hs_K562_me3_TTGACCCTTGATGAAA)


title: K562_H3K27me3_20181120_icell8_15_(20181120_HK_Hs_K562_me3_AGTAGATTACGCGCAG)


title: K562_H3K27me3_20181120_icell8_13_(20181120_HK_Hs_K562_me3_GAGCACGTACATTCGT)


title: K562_H3K27me3_20181120_icell8_33_(20181120_HK_Hs_K562_me3_ACAAAGTGACTTAGAA)


title: K562_H3K27me3_20181120_icell8_31_(20181120_HK_Hs_K562_me3_TTGCTAAGCGATAGGG)


title: K562_H3K27me3_20181120_icell8_10_(20181120_HK_Hs_K562_me3_GGGAATGATAAGTTAC)


title: K562_H3K27me3_20181120_icell8_9_(20181120_HK_Hs_K562_me3_GATCCAAAAAGGAGTA)


title: K562_H3K27me3_20181120_icell8_8_(20181120_HK_Hs_K562_me3_CCAACACGACGCGCAG)


title: LPS+A10_711P

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Sample 15

library_source: transcriptomic

data_processing:
Reads were aligned to the Ovis aries transcriptome, Oar_3.1, downloaded from NCBI on 2/27/2017, using the salmon aligner, version 0.8.0
Counts per transcript were imported into R using the Bioconductor tximport package, version 1.2.0, and then summarized to the gene level based on transcript to gene mappings from the Ensembl release-85 gtf file, Ovis_aries.Oar_v3.1.85.gtf.gz
Genes were filtered based on the sum of the log counts/million being larger than zero.
Genome_build: Oar_3.1
Supplementary_files_format_and_content: Tab-delimited text file of the counts/gene. The row names are Ensembl Gene IDs.

molecule: total RNA

organism: Ovis aries

source_name: Astrocytes

growth_protocol: The detailed protocol has been presented elsewhere. (2) Briefly, astrocytes are the major adherent cell population in flask. Astrocytes were purified by passage into a new T75 flask for 4-5 times before any manipulations and treatments. After floating microglia collection, the adherent cells were detached by trypsinization (Trypsine 0.25% + EDTA 0.1%, Wisent Cat. No 325-043-EL) and re-plated into a new flask. Cells were cultured for another 7 days with 10% all-dressed DMEM. The cell passage procedure took 4-5 weeks until purified astrocytes could be used for the in vitro experiment. Pure astrocytes were plated into a 24-well plate at 1 x 105 cells/mL with 10% DMEM for another 7 days, and then treated with or without LPS for 6h.

extract_protocol:
We used Qiagen RNeasy Mini Kit (Cat no 74104) for RNA extraction. RNA quantity and quality (RNA integrity number, RIN) was established by using a RNA Nano Chip (Agilent RNA 6000 Nano Chips) with Agilent 2100 BioAnalyzer. All samples had an acceptable RIN value ranging from 8.4 to 9.6. A total of twelve naïve astrocyte cultures from four sets of replicates was selected for RNA sequencing at high throughput, as well as three second hit astrocyte cultures, including SHC, SHL and antagonist-exposed astrocytes (SHB).
RNA-seq libraries were prepared using the TruSeq stranded mRNA kit (Illumina cat #20020594) and quality control was performed on the Agilent TapeStation and using the KAPA SYBRFAST qPCR kit.  Single read 100-bp sequencing was performed in rapid mode on a HiSeq 2500 at the University of Washington Northwest Clinical Genomics Lab (Department of Pathology).

treatment_protocol: Prior to exposure to LPS, cells were pretreated for 1 hour with either 10nM AR-R17779 hydrochloride (Tocris Bioscience Cat# 3964), a selective α7nAChR agonist, or 100 nM α-Bungarotoxin (Tocris Bioscience Cat# 2133), a selective α7nAChR antagonist. Optimal dose of AR-R17779 (A) or α-Bungarotoxin (B) was chosen based on a dose-response experiment with LPS; AR-R17779 hydrochloride was dissolved in DMSO into a stock solution. α-Bungarotoxin was reconstituted with culture media into a stock solution and underwent serial dilutions. AR-R17779 and α-Bungarotoxin preparations were added well by well; the same volume of vehicle (either DMSO or cell culture media) was added in control wells. Therefore, in a complete cell culture experiment, we had four experimental groups: Control (naïve control or NC), LPS (naïve LPS or NL), LPS+B (naïve LPS+B or NB) and LPS +A (naïve LPS+A or NA).

tag: treatment

value: LPS+Agonist

tag: animal id

tag: Sex

value: M

tag: number lps treatment


title: K562_H3K27me3_20181120_icell8_7_(20181120_HK_Hs_K562_me3_AGTAGATTGGGCTTGG)


title: K562_H3K27me3_20181120_icell8_6_(20181120_HK_Hs_K562_me3_TGGATCTGCCAGTTTA)


title: LPS+B100_711P

description: Sample 14

value: LPS+Antagonist


title: K562_H3K27me3_20181120_icell8_4_(20181120_HK_Hs_K562_me3_TACTTGAAACTGCATA)


title: LPS+B100_4502P

description: Sample 11


title: K562_H3K27me3_20181120_icell8_5_(20181120_HK_Hs_K562_me3_TCAGCTATCGATAGGG)


title: LPS100_711P

description: Sample 13

value: LPS


title: K562_H3K27me3_20181120_icell8_3_(20181120_HK_Hs_K562_me3_CCAACACGCGTAGACC)


title: K562_H3K27me3_20181120_icell8_2_(20181120_HK_Hs_K562_me3_TCTTATTAGGCACGGA)


title: LPS100_4502P

description: Sample 10


title: K562_H3K27me3_20181120_icell8_12_(20181120_HK_Hs_K562_me3_GGAGTAAGGGTTCAAT)


title: K562_H3K27me3_20181120_icell8_14_(20181120_HK_Hs_K562_me3_GATCCAAATCAAGAGC)


title: K562_H3K27me3_20181120_icell8_16_(20181120_HK_Hs_K562_me3_ATGGGAACGGCACGGA)


title: K562_H3K27me3_20181120_icell8_1_(20181120_HK_Hs_K562_me3_GCGTTAAAGGTTCAAT)


title: LPS+A10_4414T2

description: Sample 8

value: F


title: K562_PolSer7P_(20180919_HK_Hs_K5I_PolSer7P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser7) in 100000 K562 cells

data_processing:
Library strategy:  High-throughput CUT&Tag
assembly: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We extracted fragments from properly paired reads (Supplementary file(s) .bed) .

source_name: CUT&Tag

extract_protocol: High-throughput CUT&Tag: Cells were washed twice with Wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1X Protease inhibitor cocktail) and resuspended in Dig-wash (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1X Protease inhibitor cocktail; 0.05% Digitonin) containing 2mM EDTA and arrayed in a 96-well plate, 25 µL per well. Permeabilization before antibody incubation varied from 1 to 5 hours. Then, 25 µL 1:25 dilutions of appropriate antibodies in Dig-wash-EDTA were added. Cells were incubated with primary antibodies overnight at 4 oC. Concanavalin A (ConA) coated magnetic beads (Bangs Laboratories) were prepared as described [Skene, P.J. & Henikoff, S. Elife 6:e21856 (2017)]. Ten µL of activated ConA-coated magnetic beads were added to each sample, mixed gently and incubated at room temperature for 10 minutes. The plate was placed on a magnetic plate holder and supernatants were discarded. An appropriate secondary antibody (Guinea Pig anti-Rabbit IgG Heavy & Light Chain antibody, Antibodies-Online ABIN101961) was prepared as a 1:50 dilution in Dig-wash and added to each well. Cells were washed 3 times with Dig-wash and then incubated with a 1:200 dilution of pA-Tn5 adapter complex (Kaya-Okur et al.,  CUT&Tag for efficient epigenomic profiling of small samples and single cells, manuscript submitted) in Dig-med (0.05% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail) at RT for 1 hr. Cells were washed 3x for 5 min in Dig-med, resuspended in 50 µL Tagmentation buffer (Dig-med + 10 mM MgCl2) and incubated at 37 for 1h. To stop tagmentation, 2.25 µL 0.5M EDTA, 2.75 µL 10% SDS and 0.5 µL 20 mg/ml Proteinase K was added to the sample, which was incubated at 55 oC for 30 min and then at 70 oC for 20 min to inactivate the Proteinase K. Samples were held at 4oC overnight until ready to continue. A 1.1x volume of AMPure XP beads was added to each well, vortexed and incubated at room temperature for 10-15 min. The plate was placed on magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol, and DNA was eluted with 35 µL of 10 mM Tris-HCl pH 8. A 21 µL sample was mixed with 2 μL of a universal i5 and a uniquely barcoded i7 primer [Buenostro, J.D. et al. Nature 523, 486-U264 (2015)], using a different barcode for each sample. A volume of 25 μL NEBNext HiFi 2x PCR Master mix was added and mixed. The sample was placed in a Thermocycler with heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 sec; 14 cycles of 98 °C for 10 sec and 63 °C for 30 sec; final extension at 72°C for 1 min and hold at 8 oC. Post-PCR clean-up was performed by adding a 1.1X volume of Ampure XP beads (Beckman Counter), and libraries were incubated with the beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 μL 10 mM Tris pH 8.0. All 96 individually i7-barcoded libraries were mixed in equal proportions for sequencing on an Illumina HiSeq 2500 2-lane (Turbo) flow-cell.

value: Phospho-Rpb1 CTD (Ser7) Cell Signaling cat# 13780

value: K562 human immortalised myelogenous leukemia cell line


title: LPS+A10_4502P

description: Sample 12


title: LPS+B100_4414T2

description: Sample 7


title: K562_PolSer5P_(20180919_HK_Hs_K5I_PolSer5P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser5) in 100000 K562 cells

value: Phospho-Rpb1 CTD (Ser5) Cell Signaling cat# 13523


title: LPS100_4414T2

description: Sample 6


title: K562_PolSer2P_(20180919_HK_Hs_K5I_PolSer2P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser2) in 100000 K562 cells

value: Phospho-Rpb1 CTD (Ser2) Cell Signaling cat# 13499


title: K562_PolSer25P_(20180919_HK_Hs_K5I_PolSer25P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser2/Ser5) in 100000 K562 cells

value: Phospho-Rpb1 CTD (Ser2/Ser5) Cell Signaling cat# 13546


title: Ctrl_4502P

description: Sample 9

value: Ctrl


title: Ctrl_4414T2

description: Sample 5


title: LPS+A10_4414T1

description: Sample 4


title: K562_NPAT_(20181120_HK_Hs_K5I_NPAT_0912)

description: CUT&Tag for NPAT in 100000 K562 cells

value: NPAT Thermo Fisher cat# PA5-66839


title: LPS+B100_4414T1

description: Sample 3


title: LPS100_4414T1

description: Sample 2


title: K562_K4me3_(20180919_HK_Hs_K5I_K4me3_0912)

description: CUT&Tag for H3K4me3 in 100000 K562 cells

value: H3K4me3 Active Motif cat# 39159


title: K562_K4me1_(20180919_HK_Hs_K5I_K4me1_0912)

description: CUT&Tag for H3K4me1 in 100000 K562 cells

value: H3K4me1 Abcam cat# ab8895


title: K562_K4me2_(20180919_HK_Hs_K5I_K4me2_0912)

description: CUT&Tag for H3K4me2 in 100000 K562 cells

value: H3K4me2 Upstate cat# 07-030


title: K562_K27me3_(20180919_HK_Hs_K5I_K27me3_0912)

description: CUT&Tag for H3K27me3 in 100000 K562 cells

value: H3K27me3 Cell Signalling #9733


title: K562_K27ac_(20180919_HK_Hs_K5I_K27ac_0912)

description: CUT&Tag for H3K27ac in 100000 K562 cells

value: Millipore cat# MABE647


title: K562_H3K27me3_6k_(20180919_HK_Hs_K5II_K27me5_6k_0912)

description: CUT&Tag for H3K27me3 in 6000 K562 cells


title: K562_H3K27me3_200_(20180919_HK_Hs_K5II_K27me8_200_0912)

description: CUT&Tag for H3K27me3 in 200 K562 cells


title: K562_H3K27me3_2k_(20180919_HK_Hs_K5II_K27me6_2k_0912)

description: CUT&Tag for H3K27me3 in 2000 K562 cells


title: K562_H3K27me3_60_(20180919_HK_Hs_K5II_K27me9_60_0912)

description: CUT&Tag for H3K27me3 in 60 K562 cells


title: K562_H3K27me3_20k_(20180919_HK_Hs_K5II_K27me4_20k_0912)

description: CUT&Tag for H3K27me3 in 20000 K562 cells


title: K562_H3K27me3_600_(20180919_HK_Hs_K5II_K27me7_600_0912)

description: CUT&Tag for H3K27me3 in 600 K562 cells


title: H1_PolSer5P_(20180919_HK_Hs_H1I_PolSer5P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser5) in 100000 H1 ES cells

value: H1 human embryonic stem cells


title: K562_H3K27me3_60k_(20180919_HK_Hs_K5II_K27me3_60k_0912)

description: CUT&Tag for H3K27me3 in 60000 K562 cells


title: H1_Sox2_(20180919_HK_Hs_H1I_Sox2_0912)

description: CUT&Tag for Sox2 in 100000 H1 ES cells

value: Sox2 Abcam cat# ab92494


title: H1_PolSer2P_(20180919_HK_Hs_H1I_PolSer2P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser2) in 100000 H1 ES cells


title: H1_PolSer25P_(20180919_HK_Hs_H1I_PolSer25P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser2/Ser5) in 100000 H1 ES cells


title: H1_K4me1_(20180919_HK_Hs_H1I_K4me1_0912)

description: CUT&Tag for H3K4me1 in 100000 H1 ES cells


title: H1_K4me2_(20180919_HK_Hs_H1I_K4me2_0912)

description: CUT&Tag for H3K4me2 in 100000 H1 ES cells


title: Ctrl_4414T1

description: Sample 1


title: H1_K4me3_(20180919_HK_Hs_H1I_K4me3_0912)

description: CUT&Tag for H3K4me3 in 100000 H1 ES cells


title: H1_K27me3_(20180919_HK_Hs_H1I_K27me3_0912)

description: CUT&Tag for H3K27me3 in 100000 H1 ES cells


title: H1_K27ac_(20180919_HK_Hs_H1I_K27ac_0912)

description: CUT&Tag for H3K27ac in 100000 H1 ES cells


title: H1_PolSer7P_(20180919_HK_Hs_H1I_PolSer7P_0912)

description: CUT&Tag for Phospho-Rpb1 CTD (Ser7) in 100000 H1 ES cells


title: cultured bovine granulosa cells untreated rep 5

type: RNA

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Raw data were processed with the Expression Console (V1.4.1.46; Affymetrix), where normalization, background reduction and a gene-level summary was done using the RMA method (Robust Multichip Average).

label: Biotin

organism: Bos taurus

source_name: cultured bovine granulosa cells, untreated

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

extract_protocol: Total RNA was prepared using the NucleoSpin RNA Kit including removal of genomic DNA with RNAse free rDNAse (Macherey-Nagel).

treatment_protocol: Bovine ovaries were obtained from a local abattoir. Antral granulosa cells were aspirated from small to medium sized follicles (<6mm), collected in phosphate buffered saline (PBS, pH 7.4) and isolated by centrifugation from the buffer.  Living cells were counted using the trypan blue exclusion method and cryo-preserved in freezing media (fetal calf serum containing 10 % DMSO; Roth, Karlsruhe, Germany). For seeding, the GC were thawed and immediately transferred into α-MEM and centrifuged at 500 x g for 3 min to ensure fast removing of the freezing media. Afterwards the cell pellet was diluted in α-MEM containing L-Glutamin (2 mM), sodium bicarbonate (0.084%), BSA (0.1%), HEPES (20 mM), sodium selenite (4 ng/ml), transferrin (5 µg/ml), insulin (10 ng/ml), non-essential amino acids (1 mM), penicillin (100 IU/ml) and streptomycin (0.1 mg/ml), FSH (20 ng/ml; Sigma Aldrich, Steinheim, Germany), R3 IGF-1 (50 ng/ml; Sigma Aldrich), and androstenedione (2 µM; Sigma Aldrich). Improved attachment of plated GC was achieved with Collagen R coated wells (0.02%; Serva, Heidelberg, Germany). Cells were cultured at a density of 1.0x10E5 living cells per well. Cells were additionally treated with sodium L-lactate (30 mM; Sigma Aldrich), sodium chloride as vehicle control (30 mM; Sigma Aldrich) or left untreated. If not stated otherwise all reagents were purchased from Merck Millipore (Berlin, Germany). GC were cultured for 8 days at 37 °C and 5% CO2 and two-third of the media with or without L-lactate or vehicle was exchanged every other day.

value: cultured bovine granulosa cells

value: untreated


title: BS_DKO_72h

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

data_processing:
OxBS-seq reads were mapped to both the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC and the phage Lambda genome (GenBank: J02459.1) using bsmap-2.90 (" -v 15 -w 3 -p 4 -S 1921 -q 20 -A AGATCGGAAGAGC -r 0 -R -V 2 ").
The mapping results were separated into reads belonging to the mm10 genome and each of the three loci from lambda used for oxidation and conversion efficiency calculation.
Methylation calls from lambda- and mm10-derived reads were obtained using bsmap-2.90 function methratio.py (" -u -p -g -i "correct" -x CG,CHG,CHH ").
To calculate conversion efficiencies as well as posterior probabilities of methylation, hydroxymethylation and unmodified Cytosine we used luxGLM v.0.666 (prior probabilities used for for C, hmC and mC "998,1,1", "6,2,72" and "1,998,1" respectively)
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Posterior probabilities for C, hmC and mC for each timepoint (00h/72h) for each condition (WT/DKO) on each of the 18 queried cytosine

organism: Mus musculus

extract_protocol:
DNA was purified using DNaeasy Qiagen blood and tissue kit (Qiagen). Three PCR products containing C, mC, or hmC pertaining to different regions of ʎ phage genome were used as spike-ins at a ratio of 1:200 of the genomic DNA. 1.5 µg of genomic DNA mixed with spike-ins was precipitated with ethanol and 1 µg of the precipitated DNA was oxidized with potassium perruthenate (KRuO4; Sigma) followed by bisulfite treatment (for oxBS). As control, 0.5 µg of DNA was directly used for bisulfite treatment.
The BS and oxBS treated DNA were amplified using respective PCR primers and as well as primers specific to the spike-in PCR products with KAPA Uracil+ PCR mix (Roche). The amplified products were pooled and libraries were prepared using the NEB Ultra II library preparation kit (NEB) according the manufacturer.
Bisulfite-seq, paired-end 250 with Miseq

treatment_protocol: Cells were either unstimulated or activated with LPS (25ug/mL) and IL-4 (10ng/mL)

tag: strain

tag: age

value: 8-12 weeks

tag: genotype/variation

value: Tet2/3-DKO (CreERT2, Tet2-flox, Tet3-flox, Rosa26-LSL-YFP)

tag: timepoint

tag: tissue

value: Spleen

tag: molecule subtype

value: Bisulfite-treated genomic DNA


title: OxBS_DKO_72h

value: Oxidative bisulfite-treated genomic DNA


title: BS_DKO_00h


title: OxBS_WT_72h

value: Tet2/3-WT (Tet2-flox, Tet3-flox, Rosa26-LSL-YFP)


title: cultured bovine granulosa cells untreated rep 1


title: cultured bovine granulosa cells untreated rep 4


title: cultured bovine granulosa cells untreated rep 3


title: cultured bovine granulosa cells treated with NaCl rep 5

source_name: cultured bovine granulosa cells, NaCl

value: NaCl


title: cultured bovine granulosa cells treated with NaCl rep 2


title: BS_WT_00h


title: WT_0h_BATF_rep1

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
Single end reads (50bp) were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC with  Bowtie (V.1.1.2).
Reads were sorted and PCR duplicates were removed using SortSam and MarkDuplicates,  respectively from Picard Tools (V.2.7.1).
Tag directories were created with makeTagDirectory (-genome mm10  –checkGC) from HOMER (Heinz et al., 2010), and bigwig was created with makeBigWig.pl.
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Bigwig file that can be uploaded to the genome browser track for visualization of reads

extract_protocol:
Cells were fixed with 1% formaldehyde (ThermoFisher) at room temperature for 10 mins at 1E6 cell/mL in media, quenched with 125 mM glycine, washed twice with ice cold PBS. Cells were pelleted, snap-froze with liquid nitrogen. To isolate nuclei for sonication, cell pellets were thawed on ice and lysed with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 mins at 4°C with rotation, washed once with washing buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and twice with shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS). Nuclei were resuspended in 1mL shearing buffer and sonicated with Covaris E220 using 1 mL milliTUBE (Covaris, Woburn, MA) for 18-20 minutes (Duty Cycle 5%, intensity 140 Watts, cycles per burst 200). After sonication, insoluble debris was removed by centrifugation at 20,000 x g. Buffer for chromatin was adjusted with 1 volume of 2x conversion buffer (10 mM Tris-HCl pH 7.5, 280 mM NaCl, 1 mM EDTA, 1mM EGTA, 0.2% sodium deoxycholate, 0.2% Triton-X100, 1% Halt protease inhibitors). Chromatin was pre-cleared with washed protein A dynabeads  (ThermoFisher) for 2 hours, incubated with rabbit polyclonal anti-BATF (pab4003, Brookwood Biochemical) and protein A dynabeads overnight (all procedures were at 4°C with rotation). Bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5% sodium deoxycholate, 1% NP-40), once with high salt wash buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% NP-40), and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/mL RNaseA; Qiagen) twice for 30 mins each at 37°C with constant shaking. NaCl and proteinase K (Ambion) were added to the eluted chromatin at concentrations of 250 mM and 0.5 mg/mL, respectively, and de-crosslinked at 65°C overnight with constant shaking. DNA was purified with Zymo ChIP DNA Clean & Concentrator-Capped Column (Zymo Research, Irvine, CA).
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacture’s instruction.

tag: strain background

value: wild type

value: unstimulated B cells

tag: time point

tag: chip antibody


title: CHD4_WT_1 [Ctrl_rep1039]

city: Denver

middle: R

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

data_processing:
Raw data from the sequencer was demultiplexed and FASTQ files were generated using Illumina bcl2fastq conversion software (version 2.17).
ATAC-seq reads were trimmed of Nextera TruSight adapters and poor sequence by skewer (version 0.2.2).
BAM files were generated by mapping to the mm9 mouse genome with Bowtie2 (versoin 2.3.2) with max fragment length set to –X 2000.
The resulting BAM files were filtered for chrM, PCR duplicates and the ATAC-seq Blacklist from Encode (https://www.encode.org/files/ENCFF299EZH/@@download/ENCFF299EZH.bed.gz)  using picardtools (version 2.12.1, http://broadinstitute.github.io/picard/) and samtools (version 1.5).
Peaks were called for each sample using MACS2 (version 2.1.1) with -B --SPMR --nomodel --nolambda --call-summits options.
A bed file of peak summits +/- 200bp was generated using the bedtools2 (version 2.26.0) slopbed tool and using bedops (version 2.4.14) merged across samples to create a common reference peak list.
A count table of the number of fragments intersecting each reference peak was then generated with the Bedtools2 multiBamCov tool for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: gzipped tab-separated text; output from bedtools2 multiBamCov, showing peak coordinates and for each sample the number of reads overlapping each peak

source_name: CHD4_WT_pro-B cells

extract_protocol:
Pro-B cells (Lin–CD19+c-Kit+IgM–IgD–CD25–) were isolated from the bone marrow of Chd4fl/flCd79a-CreTg/+ or wild-type littermate controls using the Synergy Sorter (iCyt). Cells were lysed to extract nuclei. Nuclei were resuspended in 50 μL 1× TD buffer containing 2.5 μL transposase (Nextera, Illumina). The transposase reaction was conducted for 40 min at 37 °C.
Library amplification and barcoding were performed using Illumina compatible index primers purchased from IDTdna.com. PCR was conducted for 12-15 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and size selection was using AMPureXP beads (Beckman Coulter). Libraries were quantified and size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Paired-end sequencing was performed on a HiSeq 2500 (Illumina) with 50 cycles for each read.

value: 4-6 weeks

value: bone marrow


title: CHD4_WT_2 [Ctrl_rep1035]


title: K562_H3K27me3_20181120_icell8_44_(20181120_HK_Hs_K562_me3_TTCGCGGCCCCTTGGA)

description: Single-cell CUT&Tag for H3K27me3 in K562 cells using ICELL8 platform

value: H3K27me3 Cell Signalling #9733

value: human immortalised myelogenous leukemia cell line


title: cultured bovine granulosa cells treated with NaCl rep 3


title: cultured bovine granulosa cells treated with NaCl rep 4


title: CHD4_cKO_2 [Chd4_rep1036]

source_name: CHD4_cKO_pro-B cells

value: Chd4 conditional knockout (Chd4fl/flCd79a-CreTg/+)


title: cultured bovine granulosa cells untreated rep 2


title: CHD4_cKO_1 [Chd4_rep1042]


title: CHD4_WT_3 [Ctrl_rep1274]

data_processing:
Raw sequence data was demultiplexed and FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the mm9 (NCBI  build 37) assembly of the mouse genome using gene using gene annotations from Ensembl version 67 (http://may2012.archive.ensembl.org/).
Reads mapping to each gene of the Ensembl 67 annotation were counted with the featureCounts program from the Subread software package (v1.5.2).
Genome_build: mm9
Supplementary_files_format_and_content: counts per gene (Ensembl 67 mouse annotation) for each sample (gzipped output from featureCounts program)

molecule: polyA RNA

extract_protocol:
Pro-B cells (Lin–CD19+c-Kit+IgM–IgD–CD25–) were isolated from the bone marrow of Chd4fl/flCd79a-CreTg/+ or wild-type littermate controls using the Synergy Sorter (iCyt). RNA from these cells (~100,000-200,000 total cells per biological replicate) was isolated using the RNeasy Micro kit (Qiagen), with on-column treatment with RNase-free DNaseI, according to manufacturer’s instructions.
RNA analysis, cDNA synthesis and library preparation were performed by the Genomics Core in the Center for Genes, Environment and Health at National Jewish Health. RNA quality was assessed using the Qubit RNA assay (Life Technologies) and Bioanalyzer using the Nano RNA kit (Agilent). mRNA was captured by two rounds of magnetic Oligo-dT beads. Libraries were prepared with 50 ng of total RNA using the KAPA stranded mRNA-seq kit for the Illumina platform. Library quality was assessed using the QubitÒ DNA assay and High Sensitivity Bioanalyzer DNA (Agilent).


title: OxBS_DKO_00h


title: OxBS_WT_00h


title: cultured bovine granulosa cells treated with NaCl rep 1


title: BS_WT_72h


title: cultured bovine granulosa cells treated with L-Lactate rep 1

source_name: cultured bovine granulosa cells, L-Lactate

value: L-Lactate


title: cultured bovine granulosa cells treated with L-Lactate rep 4

value: cultured bovine granulosa cells


title: cultured bovine granulosa cells treated with L-Lactate rep 3


title: CHD4_cKO_3 [Chd4_rep1273]


title: cultured bovine granulosa cells treated with L-Lactate rep 5


title: CHD4_cKO_2 [Chd4_rep1241]


title: CHD4_WT_2 [Ctrl_rep1240]


title: CHD4_cKO_1 [Chd4_rep1237]


title: CHD4_WT_1 [Ctrl_rep1238]


title: B6WT_72h_DSG_Ig

data_processing:
Single end 50bp reads were mapped to mm10 using bowtie 2 (v2.1.0) with “-very-sensitive”
Mapped SAM files were converted to BAM using Samtools (v1.7) view –h –F 4
Duplicates were removed using Picard (v2.7.1) "MarkDuplicates"
Mapped read counts were obtained using samtools view -b -c
Bam files were converted to bedGraph normalized to read per 10,000,000 reads using bedtools genomecov -bg -scale
bedGraph files were converted to BigWig using bedGraphToBigWig (v4)
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: bigWig file that contains all the reads that map to the genome; reads are normalized to 10M reads

extract_protocol:
Cells were centrifugation at 250 x g for 5 mins and cell pellets were resuspended in 37°C PBS with 2mM disuccinimidyl glutarate (ThermoFisher) to crosslink proteins for 30 mins at room temperature. Formaldehyde was added to a final concentration of 1% and the cells were incubated at room temperature for 10 mins. Fixation was quenched with 125 mM glycine and cells were washed twice with ice cold PBS. Cells were pelleted, snap-froze with liquid nitrogen. To isolate nuclei for sonication, cell pellets were thawed on ice and lysed with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 mins at 4°C with rotation, washed once with washing buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and twice with shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS). Nuclei were resuspended in 1mL shearing buffer and sonicated with Covaris E220 using 1 mL milliTUBE (Covaris, Woburn, MA) for 18-20 minutes (Duty Cycle 5%, intensity 140 Watts, cycles per burst 200). After sonication, insoluble debris was removed by centrifugation at 20,000 x g. Buffer for chromatin was adjusted with 1 volume of 2x conversion buffer (10 mM Tris-HCl pH 7.5, 280 mM NaCl, 1 mM EDTA, 1mM EGTA, 0.2% sodium deoxycholate, 0.2% Triton-X100, 1% Halt protease inhibitors with 0.1% SDS). Chromatin was pre-cleared with washed protein A dynabeads  (ThermoFisher) for 2 hours, incubated with rabbit polyclonal anti-Tet2 (ab124297;  Abcam) and protein A dynabeads overnight (all procedures were at 4°C with rotation). Bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS), once with high salt wash buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS), and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/mL RNaseA; Qiagen) twice for 30 mins each at 37°C with constant shaking. NaCl and proteinase K (Ambion) were added to the eluted chromatin at concentrations of 250 mM and 0.5 mg/mL, respectively, and de-crosslinked at 65°C overnight with constant shaking. DNA was purified with Zymo ChIP DNA Clean & Concentrator-Capped Column (Zymo Research, Irvine, CA).
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacture’s instruction.
ChIP-seq, 50bp single end with HiSeq2500

treatment_protocol: Cells were activated with LPS (25ug/mL) and IL-4 (10ng/mL) for 72h

tag: antibody rrid


title: cultured bovine granulosa cells treated with L-Lactate rep 2


title: WT.48.Input.E1

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
Single end reads (50bp) were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC with  Bowtie (V.1.1.2).
Reads were sorted and PCR duplicates were removed using SortSam and MarkDuplicates,  respectively from Picard Tools (V.2.7.1).
Tag directories were created with makeTagDirectory (-genome mm10  –checkGC) from HOMER, and peaks were called with findPeaks (-region).
Peaks from all samples were  merged with mergePeaks from HOMER into a master table.
Quantile normalization was applied to all raw  counts files and differentially enriched 5hmC regions were identified with edgeR (Robinson et al., 2010); a p  adjusted value of <= 0.05
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Tab separated file with the quantile normalized counts

extract_protocol:
Cells were fixed with 1% formaldehyde (ThermoFisher) at room temperature for 10 mins at 1E6 cell/mL in media, quenched with 125 mM glycine, washed twice with ice cold PBS. Cells were pelleted, snap-froze with liquid nitrogen. To isolate nuclei for sonication, cell pellets were thawed on ice and lysed with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 mins at 4°C with rotation, washed once with washing buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and twice with shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS). Nuclei were resuspended in 1mL shearing buffer and sonicated with Covaris E220 using 1 mL milliTUBE (Covaris, Woburn, MA) for 18-20 minutes (Duty Cycle 5%, intensity 140 Watts, cycles per burst 200). After sonication, insoluble debris was removed by centrifugation at 20,000 x g. Buffer for chromatin was adjusted with 1 volume of 2x conversion buffer (10 mM Tris-HCl pH 7.5, 280 mM NaCl, 1 mM EDTA, 1mM EGTA, 0.2% sodium deoxycholate, 0.2% Triton-X100, 1% Halt protease inhibitors with 0.1% SDS). Chromatin was pre-cleared with washed protein A dynabeads  (ThermoFisher) for 2 hours, incubated with rabbit polyclonal anti-H3K27Ac (ab4729, Abcam) and protein A dynabeads overnight (all procedures were at 4°C with rotation). Bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS), once with high salt wash buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS), and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/mL RNaseA; Qiagen) twice for 30 mins each at 37°C with constant shaking. NaCl and proteinase K (Ambion) were added to the eluted chromatin at concentrations of 250 mM and 0.5 mg/mL, respectively, and de-crosslinked at 65°C overnight with constant shaking. DNA was purified with Zymo ChIP DNA Clean & Concentrator-Capped Column (Zymo Research, Irvine, CA).
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacture’s instruction.
ChIP-seq, 50bp single end with HiSeq2500


title: WT.48.Input.E2


title: WT.48.IP.E1

value: Abcam Cat# ab4729,RRID:AB_211829


title: B6WT_72h_DSG_Tet2

value: 8-12 weeks


title: WT.0.Input.E2


title: WT.48.IP.E2


title: Tet2/3-DKO_72h_BATF_rep1

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
Single end reads (50bp) were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC with  Bowtie (V.1.1.2).
Reads were sorted and PCR duplicates were removed using SortSam and MarkDuplicates,  respectively from Picard Tools (V.2.7.1).
Tag directories were created with makeTagDirectory (-genome mm10  –checkGC) from HOMER (Heinz et al., 2010), and peaks were called with findPeaks (-style factor -o auto).
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Raw and quantile normalized counts in a CSV format

extract_protocol:
Cells were fixed with 1% formaldehyde (ThermoFisher) at room temperature for 10 mins at 1E6 cell/mL in media, quenched with 125 mM glycine, washed twice with ice cold PBS. Cells were pelleted, snap-froze with liquid nitrogen. To isolate nuclei for sonication, cell pellets were thawed on ice and lysed with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 mins at 4°C with rotation, washed once with washing buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and twice with shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS). Nuclei were resuspended in 1mL shearing buffer and sonicated with Covaris E220 using 1 mL milliTUBE (Covaris, Woburn, MA) for 18-20 minutes (Duty Cycle 5%, intensity 140 Watts, cycles per burst 200). After sonication, insoluble debris was removed by centrifugation at 20,000 x g. Buffer for chromatin was adjusted with 1 volume of 2x conversion buffer (10 mM Tris-HCl pH 7.5, 280 mM NaCl, 1 mM EDTA, 1mM EGTA, 0.2% sodium deoxycholate, 0.2% Triton-X100, 1% Halt protease inhibitors). Chromatin was pre-cleared with washed protein A dynabeads  (ThermoFisher) for 2 hours, incubated with rabbit polyclonal anti-BATF (pab4003, Brookwood Biochemical) and protein A dynabeads overnight (all procedures were at 4°C with rotation). Bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5% sodium deoxycholate, 1% NP-40), once with high salt wash buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% NP-40), and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/mL RNaseA; Qiagen) twice for 30 mins each at 37°C with constant shaking. NaCl and proteinase K (Ambion) were added to the eluted chromatin at concentrations of 250 mM and 0.5 mg/mL, respectively, and de-crosslinked at 65°C overnight with constant shaking. DNA was purified with Zymo ChIP DNA Clean & Concentrator-Capped Column (Zymo Research, Irvine, CA).
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacture’s instruction.
ChIP-seq, 50bp single end with HiSeq2500

value: Tet2/3-DKO (CreERT2, Tet2-flox, Tet3-flox, Rosa26-LSL-YFP)


title: Tet2/3-WT_72h_BATF_rep2

value: Spleen

value: rabbit polyclonal anti-BATF (pab4003, Brookwood Biochemical)


title: WT.0.IP.E2


title: WT.0.IP.E1


title: Tet2/3-DKO_72h_BATF_rep2


title: Tet2/3-WT_72h_BATF_rep1


title: WT.0.Input.E1


title: WT_96h_RNA-seq_Rep3

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
RNA-seq samples at four different time-points collected from WT and DKO conditions were first mapped to the mouse genome mm10/GRCm38 using both hisat2 (PMID: 26355784) (“--no-mixed --no-discordant --add-chrname –dta”) and tophat2 (PMID: 23618408) (“--no-novel-juncs”) alignment programs separately.
Aligned bam files obtained from both the programs were further used to generate the hisat2- and tophat2-specific counts using htseq-count program (PMID: 25260700) (default parameters).
Hisat2- and tophat2-specific count files at each time point for WT and DKO conditions were then used to identify the differentially expressed genes (FDR < 0.05) between matching time points using edgeR program (PMID: 19910308).
The common differentially expressed genes obtained from both hisat2- and tophat2-specific list were used to perform the downstream analysis.
Potential batch effects were removed using svaseq program (PMID: 25294822).
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: tabl delimited files with TPM values for each sample (columns). Column1: chromosome; column2:gene name; column3-22:samples, column23:gene length

extract_protocol:
Total RNA was isolated from naïve and activated B cells with Trizol (ThermoFisher) and the integrity of the RNA was accessed with TapeStation RNA Analysis ScreenTape or Bioanalyzer RNA pico kit (Agilent). 10ng of RNA was reverse transcribed using oligo-dT30 VN primer in the presence of Template Switching Oligo (TSO) with SuperScript II reverse transcriptase. cDNA was pre-amplified with IS PCR primers and PCR products were cleaned up with Ampure XP beads.
One ng of PCR product was used to generate library using NexteraXT library prep kit (Illumina) and tagmentated DNA was amplified with indexed primers for a 12 cycles PCR followed by purification with AmpureXP beads.
RNA-seq, 50bp single end with HiSeq2500


title: WT_72h_RNA-seq_Rep3


title: WT_96h_RNA-seq_Rep1


title: WT_72h_RNA-seq_Rep1


title: WT_48h_RNA-seq_Rep3


title: WT_48h_RNA-seq_Rep1


title: WT_0h_RNA-seq_Rep1


title: WT_0h_RNA-seq_Rep3


title: WT_24h_RNA-seq_Rep3


title: DKO_96h_RNA-seq_Rep3


title: DKO_72h_RNA-seq_Rep3


title: DKO_48h_RNA-seq_Rep3


title: DKO_96h_RNA-seq_Rep1


title: DKO_72h_RNA-seq_Rep1


title: DKO_48h_RNA-seq_Rep1


title: DKO_24h_RNA-seq_Rep3


title: DKO_24h_RNA-seq_Rep1


title: DKO_0h_RNA-seq_Rep1


title: DKO_72h_rep2

data_processing:
ATAC-seq Paired-End reads were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC using bowtie 1.0.0 ("-p 8 -m 1 --best --strata -X 2000 -S --fr --chunkmbs 1024.").
Reads that failed this alignment step were filtered for Illumina adapters and low quality using trim_galore ("--paired --nextera --length 37 --stringency 3 --three_prime_clip_R1 1 --three_prime_clip_R2 1") and re-mapped using the same parameters.
Both mapping resulst were merged and processed together to remove duplicates using picard-tools-1.94 MarkDuplicates; Mitochondrial and Chromosome Y reads were excluded as well.
Subnucleosomal fragments were obtained with samtools and awk ("'{if(sqrt(\$9*\$9)<100){print \$0}}’") to identify DNA fragments that were less equal than 100 nt in length.
These fragments were used to call peaks using HOMER (v4.9.1) findPeaks function per replicate ("-size 500 -region -center -P .1 -LP .1 -poisson .1 -style dnase") and all the peak sets were merged to generate a global set.
Peaks overlapping with ENCODE blacklisted regions (Consortium, 2012; Kundaje, 2013) were removed.
From each sample, Tn5 insertion sites were obtained by isolation of the initial 9bp of mapped reads (Buenrostro et al., 2013) which were used to compute the number of transposase insertions per peak using MEDIPS (Chavez et al., 2010).
Before differential coverage calculation, all of the raw reads were quantile normalized altogether.
For differential coverage, the quantile normalized data was given as input to edgeR, avoiding the TMM normalization to re-normalize, and incuding only those regions that added up to more than 32 normalized reads across the samples per comparison.
Differentially accessible regions were defined by an adjusted p value (FDR) lower than 0.05 and a log 2 fold enriichment higher equal than 1.
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Quantile Normalized Tn5 Insertion sites per sample on all the set of peaks (space-delimited)

extract_protocol:
50,000 cells were collected by centrifugation and washed once with 50uL ice-cold PBS and centrifuged at 600 xg for 5 mins at 4°C. Cell pellets were resuspended in 50 uL of cold lysis buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spin down immediately at 500 xg for 10 mins at 4°C. Supernatant was discarded and nuclei were resuspended in 50uL transposition reaction mix (25uL 1x TD buffer fom Illuminia, 2.5 uL Tn5 transposase, 22.5 uL H2O), incubated at 37°C for 30 mins, and DNA was purified with a Qiagen MinElute kit (Qiagen).
Library was amplified with KAPA HiFi HotStart Real-time PCR Master Mix (Roche) using indexed primers.
ATAC-seq, 50bp paired-end with HiSeq2500

value: Tn5 (ATAC)


title: DKO_0h_RNA-seq_Rep3


title: DKO_48h_rep2


title: DKO_72h_rep1


title: DKO_48h_rep1


title: DKO_24h_rep1


title: DKO_00h_rep2


title: WT_72h_rep1

value: Tet2/3-WT (Tet2-flox, Tet3-flox, Rosa26-LSL-YFP)


title: WT_48h_rep1


title: WT_72h_rep2


title: DKO_24h_rep2


title: WT_48h_rep2


title: DKO_00h_rep1


title: WT_24h_RNA-seq_Rep1


title: WT_00h_rep1


title: WT_24h_rep2


title: WT_00h_rep2


title: WT_24h_rep1


title: Sample 24_WT.72.IP.E3

description:
5hmC-enriched by CMSIP
WT-72-CMS_S32

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
Paired-end reads (50bp) were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC, using  BSMAP (V.2.74) (-v 4 -R -n 1 -w 2 -r 0 -q 20 -R -p 8).
Reads that mapped to the spike-in control  (chrPhagueLambda and Puro) were filtered out from the sam file using awk.
Tag directories were created with  the remaining reads using makeTagDirectory from HOMER (-genome mm10 -tbp 1 –checkGC).
Peaks were  called with findPeaks from HOMER (-style histone -o auto -i).
Quantile normalization was applied to all raw counts files and  differentially enriched 5hmC regions were identified with edgeR (Robinson et al., 2010); a p adjusted value of <= 0.05
Genome_build: mouse genome mm10 GRCm38 (Dec. 2011) from UCSC
Supplementary_files_format_and_content: Quantile normalized counts, in a csv format. Column1: chromosome; column2:start; column3:end; coulmn4-27:Samples1-24

extract_protocol:
Genomic DNA isolated from naïve and activated B cells was spiked with unmethylated lambda phage cI857 Sam7 DNA (Promega, Madison, WI) and a PCR amplicon from puromycin resistant gene at a ratio of 200:1 and 100,000:1, respectively. DNA (5-10 ug in 130 uL TE buffer) was sheared with a Covaris E220 (Covaris) using microTUBE for 4 mins. DNA was cleaned-up with AmureXP beads, processed with NEBNext End Repair and A-tail Modules (NEB, Ipswich, MA), and ligated to methylated Illumina adaptors (NEB). DNA was then bisulfite-treated, denatured, and immunoprecipitated with anti-CMS serum (in house) and mixture of protein A and G dynabeads (ThermoFisher).
Libraries for immunoprecipitated DNA were generated by PCR with barcoded primers (NEBNext Multiplex Oligos for Illumina, NEB) for 15 cycles using KAPA HiFi HotStart Uracil+ ReadyMix (Roche), followed by a cleanup with AmpureXP beads (Beckman Coulter).
Bisulfite-seq, 50bp paired-end with HiSeq 2500

value: Bisulfite-treated genomic DNA


title: Sample 20_WT.48.IP.E3

description:
5hmC-enriched by CMSIP
WT-48-CMS_S30


title: Sample 23_WT.72.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-13_S21


title: Sample 19_WT.48.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-11_S19


title: Sample 18_WT.48.IP.E1

description:
5hmC-enriched by CMSIP
BCSR-CMSIP-6_S6


title: Sample 17_WT.24.IP.E3

description:
5hmC-enriched by CMSIP
WT-24-CMS_S28


title: Sample 22_WT.72.IP.E1

description:
5hmC-enriched by CMSIP
BCSR-CMSIP-7_S7


title: Sample 16_WT.24.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-09_S17


title: Sample 15_WT.24.IP.E1

description:
5hmC-enriched by CMSIP
BCSR-CMSIP-5_S5


title: Sample 14_WT.0.Input.E3

description:
Input for 5hmC-pulldown by CMSIP
WT-0-Input_S34


title: Sample 12_WT.0.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-07_S15


title: Sample 4_DKO.24.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-10_S18


title: Sample 3_DKO.0.Input.E3

description:
Input for 5hmC-pulldown by CMSIP
DKO-0-Input_S35


title: Sample 9_DKO.72.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-14_S22


title: Sample 8_DKO.48.Input.E3

description:
Input for 5hmC-pulldown by CMSIP
DKO-48-Input_S37


title: Sample 7_DKO.48.IP.E3

description:
5hmC-enriched by CMSIP
DKO-48-CMS_S31


title: Sample 10_DKO.72.IP.E3

description:
5hmC-enriched by CMSIP
DKO-72-CMS_S33


title: Sample 21_WT.48.Input.E3

description:
Input for 5hmC-pulldown by CMSIP
WT-48-Input_S36


title: dr18

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
pair-end reads are mapped using bowtie2
Read count for each gene is calculated by HT-seq
FPKM is calculated by cufflinks
Differential genes are calculated by DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: bw, bigwig format, contains the read density at each genomic position

growth_protocol: SF7761 was grown in neural stem cell medium as neuroshperes, SF8628 and SF9427 cells were grown in DNEM+10%FBS

extract_protocol:
RNeasy plus kit (Qiagen)
RNA-seq system v2 kit (NuGEN)

treatment_protocol: shRNAs were infected as standard protocol

tag: shRNA

tag: genotype


title: dr15


title: dr13


title: dr16


title: dr17


title: dr11


title: dr12


title: Sample 13_WT.0.IP.E3

description:
5hmC-enriched by CMSIP
WT-0-CMS_S26


title: Sample 11_WT.0.IP.E1

description:
5hmC-enriched by CMSIP
BCSR-CMSIP-1_S1


title: Sample 6_DKO.48.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-12_S20


title: Sample 5_DKO.24.IP.E3

description:
5hmC-enriched by CMSIP
DKO-24-CMS_S29


title: 128G: EXOME of homo sapiens, donor liver

type: genomic

city: Shanghai

first: Yuan

last: Liu

state: Shanghai

address: No.277 Chongqingnan Road, Huangpu Distict,Shanghai

country: China

institute: Shanghai Jiaotong University school of medicine

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.231 BeadChip.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: Illumina MiSeq® System

data_processing: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium ® Human Exome-12 v1.2 BeadChip (Illumina).

label: cy3, cy5

source_name: donor liver

label_protocol: 600ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Both donor and recipient genomic DNA were extracted from liver tissues (stored at -80°C) using an AllPrep DNA/RNA Mini Kit

value: donor liver

tag: gender

value: male


title: Sample 2_DKO.0.IP.E3

description:
5hmC-enriched by CMSIP
DKO-0-CMS_S27


title: SVEC4-10 cells Mical2 knock-down

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: SVEC4-10 cells transduced with lentiviral vector expressing anti-Mical2 shRNA. The sample was generated from pooling three biological replicas.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG-430 PM Array Strip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using Bioconductor affy library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

label: biotin

source_name: SVEC4-10 cells Mical2 knock-down

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions

growth_protocol: SVEC4-10 were kept in Dulbecco's modified Eagle medium (DMEM) added with 10% fetal bovine serum, 4mM L-glutamine, 1.5g/l sodium bicarbonate, 100U/ml penicillin, 100μg/ml streptomycin, in 5%CO2, 80% humidity, 37°C.

extract_protocol: Total RNA was extracted using TriPure (Roche) accordingly to manifacturer guidelines. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.

treatment_protocol: Wild Type SVEC4-10 cells were transduced with pLENTI6/Block-iT lentiviral vector (Invitrogen) expressing either of the following short hairpin RNAs. For Mical2: 5'-tttggaacatggcaggagcaggaagcacttcaagagagtgcttcctgctcctgccatgtttttttt-3'; for Mical3: 5'-tttggaagtggaggagattagtggcgtgttcaagagacacgccactaatctcctccactttttttt-3'.  Control: insert-free vector. Transduced cells were selected with blasticidin.

tag: cell line

tag: experimental condition

value: anti-Mical2 shRNA


title: 126G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.229 BeadChip.

value: female


title: 127G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.230 BeadChip.


title: 125G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.228 BeadChip.


title: 123G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.226 BeadChip.


title: SVEC4-10 cells transduced with insert-free vector

description: SVEC4-10 cells transduced with insert-free lentiviral vector. The sample was generated from pooling three biological replicas.

value: trasduced with insert-free vector


title: SVEC4-10 cells untreated

description: Untreated SVEC4-10 cells. The sample was generated from pooling three biological replicas.

source_name: SVEC4-10 cells untreated

value: untreated


title: Sample 1_DKO.0.IP.E2

description:
5hmC-enriched by CMSIP
2-7-17-Jlio-CMSIP-08_S16


title: SVEC4-10 cells Mical3 knock-down

description: SVEC4-10 cells transduced with lentiviral vector expressing anti-Mical3 shRNA. The sample was generated from pooling three biological replicas.

source_name: SVEC4-10 cells Mical3 knock-down

value: anti-Mical3 shRNA


title: 122G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.225 BeadChip.


title: 121G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.224 BeadChip.


title: 124G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.227 BeadChip.


title: 119G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.222 BeadChip.


title: 118G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.221 BeadChip.


title: 120G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.223 BeadChip.


title: dr14


title: dr10


title: 115G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.218 BeadChip.


title: 114G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.217 BeadChip.


title: 108G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.213 BeadChip.


title: 107G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.212 BeadChip.


title: 116G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.219 BeadChip.


title: 109G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.214 BeadChip.


title: 113G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.216 BeadChip.


title: 117G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.220 BeadChip.


title: 106G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.211 BeadChip.


title: 105G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.210 BeadChip.


title: 101G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.208 BeadChip.


title: 104G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.209 BeadChip.


title: 97G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.205 BeadChip.


title: 100G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.207 BeadChip.


title: 99G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.206 BeadChip.


title: 96G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.204 BeadChip.


title: 92G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.200 BeadChip.


title: 91G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.199 BeadChip.


title: 95G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.203 BeadChip.


title: 88G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.196 BeadChip.


title: 93G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.201 BeadChip.


title: 111G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.215 BeadChip.


title: 90G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.198 BeadChip.


title: 83G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.193 BeadChip.


title: 86G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.194 BeadChip.


title: 94G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.202 BeadChip.


title: 89G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.197 BeadChip.


title: 87G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.195 BeadChip.


title: 82G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.192 BeadChip.


title: 75G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.186 BeadChip.


title: 73G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.184 BeadChip.


title: 78G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.189 BeadChip.


title: 76G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.187 BeadChip.


title: 80G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.191 BeadChip.


title: 77G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.188 BeadChip.


title: 72G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.183 BeadChip.


title: 74G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.185 BeadChip.


title: 70G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.181 BeadChip.


title: 71G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.182 BeadChip.


title: 69G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.180 BeadChip.


title: 67G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.179 BeadChip.


title: 65G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.177 BeadChip.


title: 66G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.178 BeadChip.


title: 63G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.175 BeadChip.


title: 64G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.176 BeadChip.


title: 79G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.190 BeadChip.


title: 59G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.171 BeadChip.


title: 53G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.165 BeadChip.


title: 61G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.173 BeadChip.


title: 56G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.168 BeadChip.


title: 50G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.162 BeadChip.


title: 58G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.170 BeadChip.


title: 54G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.166 BeadChip.


title: 60G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.172 BeadChip.


title: 48G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.161 BeadChip.


title: 42G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.156 BeadChip.


title: 44G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.158 BeadChip.


title: 47G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.160 BeadChip.


title: 39G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.153 BeadChip.


title: 40G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.154 BeadChip.


title: 38G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.152 BeadChip.


title: 36G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.150 BeadChip.


title: 34G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.148 BeadChip.


title: 37G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.151 BeadChip.


title: 52G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.164 BeadChip.


title: 33G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.147 BeadChip.


title: 43G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.157 BeadChip.


title: 35G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.149 BeadChip.


title: 29G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.143 BeadChip.


title: 23G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.137 BeadChip.


title: 41G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.155 BeadChip.


title: 30G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.144 BeadChip.


title: 25G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.139 BeadChip.


title: 27G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.141 BeadChip.


title: 22G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.136 BeadChip.


title: 24G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.138 BeadChip.


title: 20G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.134 BeadChip.


title: 21G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.135 BeadChip.


title: 51G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.163 BeadChip.


title: 31G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.145 BeadChip.


title: 26G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.140 BeadChip.


title: 17G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.132 BeadChip.


title: 15G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.130 BeadChip.


title: 16G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.131 BeadChip.


title: 14G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.129 BeadChip.


title: 12G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.127 BeadChip.


title: 13G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.128 BeadChip.


title: 32G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.146 BeadChip.


title: 18G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.133 BeadChip.


title: 10G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.125 BeadChip.


title: 11G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.126 BeadChip.


title: 28G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.142 BeadChip.


title: 8G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.123 BeadChip.


title: 9G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.124 BeadChip.


title: 45G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.159 BeadChip.


title: 4G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.120 BeadChip.


title: 5G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.121 BeadChip.


title: 2G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.118 BeadChip.


title: 6G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.122 BeadChip.


title: 3G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.119 BeadChip.


title: Cuz_32

city: Los Angeles

first: Yuichiro

last: Itoh

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "Olig1.RiboTag_rawcounts.txt" has count values for each Sample

source_name: mice expressing HA-tagged ribosomal protein RPL22 in oligodendrocytes, Cuz

growth_protocol: Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.

extract_protocol:
Corpus callosum was collected and snap-frozen by liquid nitrogen. After RNA co-immunoprecipitation process, RNA was isolated using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

treatment_protocol: Young adult female mice (age 8-10 weeks) were fed with 0.2% bis-(cyclohexanone)-oxaldihydrazone (cuprizone) diet (TD.140803, Harlan Teklad) for 6 weeks or 9 weeks to induce demyelination, followed by a 3 week recovery period on global 18% protein rodent control diet (TD.00588, Harlan Teklad) to induce natural remyelination.

value: Corpus callosum

tag: cell type

value: oligodendrocytes

tag: treatment

tag: rip antibody

value: monoclonal  anti-HA antibody


title: Cuz_31

tag: strain

value: fed with 0.2% bis-(cyclohexanone)-oxaldihydrazone (cuprizone) diet


title: Cuz_30


title: 127S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.115 BeadChip.

source_name: recipient liver

value: recipient liver

tag: age


title: 126S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.114 BeadChip.


title: Vehicle_27

source_name: mice expressing HA-tagged ribosomal protein RPL22 in oligodendrocytes, Vehicle

value: Control


title: Vehicle_24


title: Vehicle_26


title: 124S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.112 BeadChip.


title: 122S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.110 BeadChip.


title: 121S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.109 BeadChip.


title: 128S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.116 BeadChip.


title: 1G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.117 BeadChip.


title: 120S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.108 BeadChip.