title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD004_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_89_AD002_indexed

status: Public on Dec 12 2019

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Read mapping and the partitioning of transcriptome and methylome reads   To map methylome reads, sequencing reads were mapped to in-silico bisulfite converted hg19 reference genome as previously described (Luo et al., 2017). Mapped reads with MAPQ > 10 were retained for further analyses. Sequencing reads with non-CG methylation level < 0.5 and number of cytosine ≥ 3 were considered as true methylome reads. Tab-delimited (allc) files containing methylation level for every cytosine positions was generated using methylpy call_methylated_sites function (Schultz et al., 2015).     To map transcriptome reads, sequencing reads were mapped to Gencode V19 transcriptome index using STAR 2.5.2b with the following parameters: --alignEndsType EndToEnd --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --sjdbOverhang 100 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattrRGline ID:4 PL:Illumina. Mapped reads with MAPQ > 10 were retained for further analyses. Non-CG methylation levels for each STAR mapped read  was determined from the MD tag. Mapped reads with non-CG methylation levels greater than 0.9 and number of cytosine ≥ 3 were considered as true transcriptome reads. Transcriptome reads were counted across gene annotations using featureCount 1.6.4 (Liao et al. 2014) with the default parameters. Gene expression was quantified using either only exonic reads with -t exon, or both exonic and intronic reads with -t gene. For snATAC-seq data - Using a custom python script, we first de-multicomplexed FASTQ files by integrating the cell barcode (concatenate reads pair in I1.fastq and I2.fastq) into the read name (R1.fastq and R2 fastq) in the following format: "@"+"barcode"+":"+"original_read_name".  Demulticomplexed reads were aligned to the corresponding reference genome (hg19) using bwa (0.7.13-r1126) in pair-end mode with default parameter settings. Alignments were then sorted based on the read name using samtools (v1.9). Pair-end reads were converted into fragments and only those that are 1) properly paired (according to SMA flag value); 2) uniquely mapped (MAPQ > 30); 3) with length less than 1000bp were kept.  Since fragments were sorted by barcode (integrated into the read name), fragments belonging to the same cell (or barcode) were automatically grouped together which allowed for removing PCR duplicates for each cell separately.  Using remaining fragments, a snap-format (Single-Nucleus Accessibility Profiles) file was generated.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines). snap file is hierarchically structured hdf5 file that contains the following sessions: header (HD), cell-by-bin matrix (BM), cell-by-peak matrix (PM), cell-by-gene matrix (GM), barcode (BD) and fragment (FM). HD session contains snap-file version, date, alignment and reference genome information. BD session contains all unique barcodes and corresponding meta data. BM session contains cell-by-bin matrices of different resolutions (or bin sizes). PM session contains cell-by-peak count matrix. PM session contains cell-by-gene count matrix. FM session contains all usable fragments for each cell. Fragments are indexed for fast search. A detailed documentation of snap file can be found here (https://docs.google.com/document/d/1AGyn_WJTr0A1SKcfrEgum-jvAJjWd84jZ6DwbwiGRaQ/edit?usp=sharing)

molecule: genomic DNA

organism: Homo sapiens

source_name: human embryonic stem cell

growth_protocol: HEK293T cells were cultured in DMEM with 15% FBS and 1% Penicillin-Streptomycin and dissociated with 1X TrypLE. H1 human ESCs (WA01, WiCell Research Institute) were maintained in feeder-free mTesR1 medium (Stemcell Technologies). hESCs (passage 26) were dispersed with 1U/ml Dispase and collected for single-cell sorting or nuclei isolation. Postmortem human brain biospecimens GUID: NDARKD326LNK and NDARKJ183CYT were obtained from NIH NeuroBioBank at University of Miami Brain Endowment Bank. Postmortem human brain biospecimens UMB4540, UMB5577 and UMB5580 are obtained from NIH NeuroBioBank at University of Maryland Brain and Tissue Bank.

extract_protocol:
Nuclei isolation from cultured cells for snmCT-seq: Cell pellets containing 1 million cells were resuspended in 600 µl NIBT [250 mM Sucrose, 10 mM Tris-Cl pH=8, 25 mM KCl, 5mM MgCl2, 0.1% Triton X-100, 1mM DTT, 1:100 Proteinase inhibitor (Sigma-Aldrich P8340), 1:1000 SUPERaseIn RNase Inhibitor (ThermoFisher Scientific AM2694), 1:1000 RNaseOUT RNase Inhibitor (ThermoFisher Scientific 10777019)]. The lysate was transferred to a pre-chilled 2 ml dounce homogenizer (Sigma-Aldrich D8938) and dounced using loose and tight pestles for 20 times each. The lysate was then mixed with 400 µl of 50% Iodixanol (Sigma-Aldrich D1556) and gently pipetted on top of 500 µl 25% Iodixanol cushion. Nuclei were pelleted by centrifugation at 10,000 x g at 4°C for 20 min using a swing rotor. The pellet was resuspended in 2 ml of DPBS supplemented with 1:1000 SUPERaseIn RNase Inhibitor and 1:1000 RNaseOUT RNase Inhibitor. Hoechst 33342 was added to the sample to a final concentration of 1.25 nM and incubated on ice for 5 min for nuclei staining. Nuclei were pelleted by 1,000 x g at 4°C for 10 min and resuspended in 1 ml of DPBS supplemented with RNase inhibitors.   Nuclei isolation from human brain tissues and GpC methyltransferase treatment  Brain tissue samples were ground in liquid nitrogen with cold mortar and pestle, and then aliquoted and store at -80°C. Approximately 100mg of ground tissue was resuspended in 3 ml NIBT (250 mM Sucrose, 10 mM Tris-Cl pH=8, 25 mM KCl, 5mM MgCl2, 0.2% IGEPAL CA-630, 1mM DTT, 1:100 Proteinase inhibitor (Sigma-Aldrich P8340), 1:1000 SUPERaseIn RNase Inhibitor (ThermoFisher Scientific AM2694), 1:1000 RNaseOUT RNase Inhibitor (ThermoFisher Scientific 10777019)). The lysate was transferred to a pre-chilled 7 ml dounce homogenizer (Sigma-Aldrich D9063) and dounced using loose and tight pestles for 40 times each. The lysate was then mixed with 2 ml of 50% Iodixanol (Sigma-Aldrich D1556) to generate a nuclei suspension with 20% Iodixanol. Gently pipet 1 ml of the nuclei suspension on top of 500 µl 25% Iodixanol cushion in each of the 5 freshly prepared 2ml microcentrifuge tubes. Nuclei were pelleted by centrifugation at 10,000 x g at 4°C for 20 min using a swing rotor. The pellet was resuspended in 1ml of DPBS supplemented with 1:1000 SUPERaseIn RNase Inhibitor and 1:1000 RNaseOUT RNase Inhibitor. A 10 µl aliquot of the suspension was taken for nuclei counting using a Biorad TC20 Automated Cell Counter. One million nuclei aliquots were pelleted by 1,000 x g at 4°C for 10 min and resuspended in 200 µl of GpC methyltransferase M.CviPI (NEB M0227L) reaction containing 1X GC Reaction Buffer, 0.32 nM S-Adenoslylmethionime, 80U 4U/µl M.CviPI, 1:100 SUPERaseIn RNase Inhibitor and 1:100 RNaseOUT RNase Inhibitor and incubated at 37°C for 8 min. The reaction was stopped by adding 800 µl of ice-cold DPBS with 1:1000 RNase inhibitors and mixing. Hoechst 33342 was added to the sample to a final concentration of 1.25 nM and incubated on ice for 5 min for nuclei staining. Nuclei were pelleted by 1,000 x g at 4°C for 10 min, resuspended in 900 µl of DPBS supplemented with 1:1000 RNase inhibitors and 100 µl of 50mg/ml UltrapureTM BSA (Ambion AM2618) and incubated on ice for 5 min for blocking. Neuronal nuclei were labeled by adding 1 µl of AlexaFluor488-conjugated anti-NeuN antibody (clone A60, MilliporeSigma MAB377XMI) for 20 min. For snATAC-seq, nuclei were isolated from frozen mouse brain sections and permeabilized. Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR.
Reverse transcription for snmC2T-seq Single cells or single nuclei were sorted into 384-well PCR plates (ThermoFisher 4483285) containing 1 µl mCT-seq reverse transcription reaction per well. The mCT-seq reverse transcription reaction contained 1X Superscript II First-Strand Buffer, 5mM DTT, 0.1% Triton X-100, 2.5 mM MgCl2, 500 µM each of 5’-methyl-dCTP (NEB N0356S), dATP, dTTP and dGTP, 1.2 µM dT30VN_4 oligo-dT primer (5’-AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3’ was used the cultured cell experiments; 5’-/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3’ was used for human brain experiments), 2.4 µM TSO_3 template switching oligo (/5SpC3/AAGCAGUGGUAUCAACGCAGAGUGAAUrGrG+G), 1U RNaseOUT RNase inhibitor, 0.5 U SUPERaseIn RNase inhibitor, 10U Superscript II Reverse Transcriptase (ThermoFisher 18064-071). For snmC2T-seq, the reaction further included 2 µM N6_2 random primer (/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACNNNNNN). After sorting, the PCR plates were vortexed and centrifuged at 2000 x g. The plates were placed in a thermocycler and incubated using the following program: 25°C for 5 min, 42°C for 90min, 70°C 15min followed by 4°C. cDNA amplification for snmC2T-seq 3 µl of mCT-seq cDNA amplification mix was added into each mCT-seq reverse transcription reaction. mCT-seq cDNA amplification reaction contains 1X KAPA 2G Buffer A, 600 nM ISPCR23_2 PCR primer (/5SpC3/AAGCAGUGGUAUCAACGCAGAGU), 0.08U KAPA2G Robust HotStart DNA Polymerase (5 U/μL, Roche KK5517). PCR reactions were performed using a thermocycler with the following conditions: 95°C 3min -> [95°C 15 sec -> 60°C 30 sec -> 72°C 2min] -> 72°C 5min -> 4°C. The cycling steps were repeated for 12 cycles for scmCT-seq using H1 or HEK293 cells, 15 cycles for snmCT-seq using H1 or HEK293 cells and 14 cycles for snmC2T-seq using human brain tissues. Digestion of unincorporated DNA oligos for snmCT-seq For scmCT-seq and snmCT-seq using H1 and HEK293 cells, 1 µl uracil cleavage mix was added to into cDNA amplification reaction. Each 1 µl uracil cleavage mix contains 0.25 µl Uracil DNA Glycosylase (Enzymatics G5010) and 0.25 µl Endonuclease VIII (Enzymatics Y9080) and 0.5 µl Elution Buffer (Qiagen 19086). Unincorporated DNA oligos were digested at 37°C for 30 min using a thermocycler. We have found that Endonuclease VIII is dispensable for the digestion of unincorporated DNA oligos since the alkaline condition during the desulfonation step of bisulfite conversion can effective cleave abasic sites created by Uracil DNA Glycosylase (Greenberg, 2014). Therefore for snmC2T-seq using human brain tissues, each cDNA amplification reaction was treated with 1µl uracil cleavage mix containing 0.5 µl Uracil DNA Glycosylase (Enzymatics G5010-1140) and 0.5 µl Elution Buffer (Qiagen 19086). For snATAC-seq, nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR. Libraries were sequenced on a HiSeq2500 (Illumina) with following read lengths: 50 + 14 + 14 + 50 (Read1 + Index1 + Index2 + Read2).

tag: cell type

value: human embryonic stem cell

tag: Sex

value: Male

tag: donor

tag: protocol

value: scmCT-seq


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD002_indexed

description: snmC2T-seq.gene_rna_counts.4358cell.60606gene.csv.gz

source_name: Human frontal cortex

value: Human frontal cortex


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD007_indexed


title: 171009_mCT_hs_hek293_hek293_mCT_pool_13_AD008_indexed

source_name: human embryonic kidney cell

value: human embryonic kidney cell

value: Female


title: 171009_mCT_hs_h1_h1_mCT_pool_83_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_76_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD001_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD012_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD010_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_68_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_68_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_66_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD007_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_66_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_58_AD008_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD004_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD002_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD012_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_92_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_75_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD007_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_50_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_4_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_36_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD004_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_49_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_34_AD006_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_2_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD012_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_26_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD010_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_51_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_20_AD010_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_25_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD007_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_57_AD008_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD004_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_1_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_19_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD001_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_11_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_10_AD010_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_10_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD012_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD007_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD008_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_28_AD010_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD001_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD002_indexed


title: 171009_mCT_hs_h1_h1_mCT_pool_20_AD008_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD008_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD006_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD001_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD004_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD007_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD002_indexed


title: UMB4540_snATAC-seq

value: snATAC-seq


title: M263_Control_RNA-seq

status: Public on Oct 16 2019

city: Los Angeles

first: Xiang

last: Lu

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

library_source: transcriptomic

data_processing:
For UCLA samples, we are uncertain about the precise base calling procedures; For COH RNA-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.1.8.4; For COH ChIP-Seq / ATAC-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.2.18
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).  For unstranded counts (with anti-sense, AS, genes removed), strand was to "no" for "Unstranded" counts / FPKM (and strand was set to "reverse" for "Stranded" counts / FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

molecule: total RNA

growth_protocol: M-series patient derived cell lines used in this study were generated under UCLA institutional review board approval # 11–003254. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (Omega), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza). The cell lines were tested for mycoplasma and were periodically authenticated to its early passage using GenePrint 10 System (Promega).

extract_protocol:
total RNA was extracted from cell pellets using RNeasy Mini Kit (Qiagen).
for UCLA Samples: Libraries were prepared using the IlluminaTruSeq RNA sample preparation kit, for COH RNA-Seq 160607 Batch Samples: TruSeq unstranded polyA kit, for COH RNA-Seq 160916+160930 Batch Samples: KAPA stranded polyA kit

treatment_protocol: BRAF inhibitor (vemurafenib) from Selleck Chemicals LLC, were dissolved in DMSO at designated concentrations before applying to cell culture media. Cells were plated in 10cm tissue culture plate at 60% confluency and treated with certain drugs for the specified numbers of days. M397 cells were treated with 3uM of vemurafenib for 59days and at day29, drug were removed and cells were cultured with normal medium for another 35days

value: Patient-derived melanoma cell line M263

tag: treatment

value: M263 Cells untreated with BRAF inhibitor

tag: batch

value: UCLA

tag: library strandedness

value: stranded

tag: facility


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD004_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD002_indexed


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD012_indexed


title: M263_D21_RNA-seq

value: M263 Cells treated with BRAF inhibitor 21 days


title: M229_D3_RNA-seq

value: Patient-derived melanoma cell line M229

value: M229 Cells treated with BRAF inhibitor 3 days


title: M229_D21_RNA-seq

value: M229 Cells treated with BRAF inhibitor 21 days


title: 190305_mCTseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD010_indexed


title: M229_Control_RNA-seq

value: M229 Cells untreated with BRAF inhibitor


title: 171009_mCT_hs_h1_h1_mCT_pool_59_AD002_indexed


title: M249_D21_RNA-seq

value: Patient-derived melanoma cell line M249

value: M249 Cells treated with BRAF inhibitor 21 days

value: COH


title: M263_D3_RNA-seq

value: M263 Cells treated with BRAF inhibitor 3 days


title: M249_D3_RNA-seq

value: M249 Cells treated with BRAF inhibitor 3 days


title: M249_Control_RNA-seq

value: M249 Cells untreated with BRAF inhibitor


title: M262_D21_RNA-seq

value: Patient-derived melanoma cell line M262

value: M262 Cells treated with BRAF inhibitor 21 days


title: M262_D3_RNA-seq

value: M262 Cells treated with BRAF inhibitor 3 days


title: M262_Control_RNA-seq

value: M262 Cells untreated with BRAF inhibitor


title: M233_D21_RNA-seq

value: Patient-derived melanoma cell line M233

value: M233 Cells treated with BRAF inhibitor 21 days


title: miR-1253_2

status: Public on Oct 23 2019

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was extracted using Trizol (Trizol Reagent, Invitrogen) according to manufacturer’s instructions. RNA was evaluated by Nanodrop and RNA concentration and integrity was assessed by Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: Experimental protocol: Primary human aortic endothelial cells (HAEC) were grown in EMB-2 supplemented with the EGM-2 SingleQuot Kit (Lonza; Walkersville, MD), and were transfected with pre-miR miRNA precursors for hsa-miR-103a-2-5p, miR-585-5p, miR-1253, or a scrambled negative control (Life Technologies) using Lipofectamine 2000 (Life Technologies).

tag: tissue

value: Primary human aortic endothelial cells (HAECs)

tag: transfected pre-mir


title: miR-1253_1


title: miR-585_3


title: NEG-3

value: Scrambled, negative control


title: miR-103a_2


title: miR-585_1


title: miR-585_2


title: miR-103a_1


title: miR-103a_3


title: NEG-2


title: M233_Control_RNA-seq

value: M233 Cells untreated with BRAF inhibitor

value: stranded


title: M233_D3_RNA-seq

value: M233 Cells treated with BRAF inhibitor 3 days


title: M381_D21_RNA-seq

value: Patient-derived melanoma cell line M381

value: M381 Cells treated with BRAF inhibitor 21 days


title: M381_D3_RNA-seq

value: Patient-derived melanoma cell line M281

value: M281 Cells treated with BRAF inhibitor 3 days

value: COH


title: NEG-1


title: 24plusI_IN_rep2

status: Public on Oct 04 2019

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

organism: Mus musculus

source_name: primary myoblasts derived from mouse satellite cells isolated from leg muscle of 3-6 week old wild type C57Bl/6 mice

growth_protocol:
Mouse satellite cells were isolated from leg muscle of 3-6 week old wild type C57Bl/6 mice. The muscle was extracted and cut into small pieces, washed with Hank’s Balanced Salt Solution (HBSS; ThermoFisher Scientific) and incubated with 0.1% Pronase for 1 h at 37 ºC. The cells were then filtered using a 100 μm cell sieve and resuspended in 3 ml of growild typeh media (1:1 v/v DMEM:F-12, 20% FBS, 2% chick embryo extract and 25 ng/ml of basic FGF). Cells were filtered again using a 40 µm cell sieve and centrifuged at 1,000 x g for 1 min at room temperature. The cells were placed in the top of a Percoll gradient (35 and 70%) and centrifuged 20 min at 1,850 x g at room temperature. The myoblasts were contained in the lower interface of the 70% Percoll fraction was washed with HBSS, centrifuged 5 min at 1,000 x g, and resuspended in growth wild type media for plating. Myoblasts were grown and differentiated on plates coated with 0.02% collagen (Advanced BioMatrix) (42). The different treatments were: presence and absence of CuSO4.
DMEM, 2% Horse Serum (HS), 100 U/ml1 penicillin and 100 mg/ml streptomycin and 1% Insulin–Transferrin–Selenium-A supplement (Invitrogen)

extract_protocol:
Differentiating (24 h) primary myoblasts were crosslinked with 1% Formaldehyde and incubated for 10 min at room temperature in an orbital shaker. To inactivate the formaldehyde, 1 ml of 1M glycine was added and cells were incubated for 5 minutes in an orbital shaker at room temperature. Cells were washed 3 times with 10 ml of ice cold PBS supplemented with Complete Protease Inhibitor (Roche). Crosslinked myoblasts were resuspended in 1 ml of ice cold PBS supplemented with Complete. The cell suspension was transferred to a 1.5 ml microcentrifuge tube and centrifuged for 5 minutes at 5,000 x g at 4 ºC. The PBS was removed and the cell pellet was resuspended in 200 µl of ice cold SDS lysis buffer (50 mM Tris pH 8; 10 mM EDTA, 1% SDS) for 10 min. Proliferating myoblasts were sonicated three times for 5 min 30” by 30” at mild intensity for and five times for nascent myotubes using a Bioruptor UCD-200 (Diagenode). The samples were diluted to a final volume of 1 ml in IP buffer (16 mM Tris pH 8.1; 1.2 mM EDTA; 0.01% SDS; 1.1% Triton X100; 167 mM NaCl). ChIP was performed using a rabbit anti-MTF1 antibody (Santa Cruz biotechnologies). Samples were incubated for 2 h at 4 ºC in agitation and 80 µl of Magna ChIP protein A+G Magnetic Beads (Millipore, Sigma) were added to each sample and incubated overnight in agitation at 4 C. The samples were then placed in a magnetic rack and washed using 1 ml of the wash buffer sequence A-D (Buffer A: 20 mM Tris pH 8.1, 2 mM EDTA, 0.1% SDS, 1% Triton-X100, 167 NaCl, Buffer B: 20 mM Tris pH 8.1, 2 mM EDTA, 0.1% SDS, 1% Triton-X100, 500 NaCl; Buffer C: 10 mM Tris pH 8.1, 1 mM EDTA, 1% NP40, 1% Sodium deoxicholate, 0.25 M LiCl2; Buffer D: 10 mM Tris pH 8.1, 1 mM EDTA). Immune complexes were eluted in 100 µl of buffer containing 0.1 M NaHCO3, 1% SDS, 1 µg/µl proteinase K. Samples were then reverse-crosslinked using 20 µl of 5M NaCl and incubated overnight at 65 ºC. The reverse crosslinked DNA was purified using the ChIP DNA clean concentrator, following the manufacturer’s instructions (Zymo Research).
Samples were end-repaired, A-tailed, and adaptor-ligated using barcoded inline adaptors according to the manufacturer’s instructions (Illumina). DNA was purified over a Zymo Research PCR purification column between each enzymatic reaction (Zymo Research). DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected for 200-300 bp fragments on a 1.5% agarose gel and the library concentrations were determined using a QuBit 3.0 Fluorometer (Thermo Scientific). Libraries were sequenced on an Illumina HiSeq2000 using single-end 50bp sequencing at the UMass Medical School deep sequencing core facility
Libraries of ChIP-enriched DNA were prepared following Illumina strategy

treatment_protocol: Primary myoblasts were plated at 4 x 10^4 cells per cm2 for experimentation. Cells were maintained in growth media (GM: 1 : 1 mixture of DMEM: Ham’s F10, 20% FBS, 5 ng/ml bFGF, 100 U/ml penicillin G, 100 mg/ml streptomycin) in a humidified 5% CO2 incubator at 37 C on collagen-coated dishes. Cells were induced to differentiated when they reached 90% confluency.

tag: strain

tag: age

value: 3-6 week old

tag: genotype

value: wild type

value: primary myoblasts

tag: primary antibody

tag: secondary antibody


title: 24noICu_IP_rep1

growth_protocol:
Mouse satellite cells were isolated from leg muscle of 3-6 week old wild type C57Bl/6 mice. The muscle was extracted and cut into small pieces, washed with Hank’s Balanced Salt Solution (HBSS; ThermoFisher Scientific) and incubated with 0.1% Pronase for 1 h at 37 ºC. The cells were then filtered using a 100 μm cell sieve and resuspended in 3 ml of growild typeh media (1:1 v/v DMEM:F-12, 20% FBS, 2% chick embryo extract and 25 ng/ml of basic FGF). Cells were filtered again using a 40 µm cell sieve and centrifuged at 1,000 x g for 1 min at room temperature. The cells were placed in the top of a Percoll gradient (35 and 70%) and centrifuged 20 min at 1,850 x g at room temperature. The myoblasts were contained in the lower interface of the 70% Percoll fraction was washed with HBSS, centrifuged 5 min at 1,000 x g, and resuspended in growth wild type media for plating. Myoblasts were grown and differentiated on plates coated with 0.02% collagen (Advanced BioMatrix) (42). The different treatments were: presence and absence of CuSO4.
DMEM, 2% Horse Serum (HS), 100 U/ml1 penicillin and 100 mg/ml1 streptomycin

extract_protocol:
Differentiating (24 h) primary myoblasts were crosslinked with 1% Formaldehyde and incubated for 10 min at room temperature in an orbital shaker. To inactivate the formaldehyde, 1 ml of 1M glycine was added and cells were incubated for 5 minutes in an orbital shaker at room temperature. Cells were washed 3 times with 10 ml of ice cold PBS supplemented with Complete Protease Inhibitor (Roche). Crosslinked myoblasts were resuspended in 1 ml of ice cold PBS supplemented with Complete. The cell suspension was transferred to a 1.5 ml microcentrifuge tube and centrifuged for 5 minutes at 5,000 x g at 4 ºC. The PBS was removed and the cell pellet was resuspended in 200 µl of ice cold SDS lysis buffer (50 mM Tris pH 8; 10 mM EDTA, 1% SDS) for 10 min. Proliferating myoblasts were sonicated three times for 5 min 30” by 30” at mild intensity for and five times for nascent myotubes using a Bioruptor UCD-200 (Diagenode). The samples were diluted to a final volume of 1 ml in IP buffer (16 mM Tris pH 8.1; 1.2 mM EDTA; 0.01% SDS; 1.1% Triton X100; 167 mM NaCl). ChIP was performed using a rabbit anti-MTF1 and antibody (Santa Cruz biotechnologies). Samples were incubated for 2 h at 4 ºC in agitation and 80 µl of Magna ChIP protein A+G Magnetic Beads (Millipore, Sigma) were added to each sample and incubated overnight in agitation at 4 C. The samples were then placed in a magnetic rack and washed using 1 ml of the wash buffer sequence A-D (Buffer A: 20 mM Tris pH 8.1, 2 mM EDTA, 0.1% SDS, 1% Triton-X100, 167 NaCl, Buffer B: 20 mM Tris pH 8.1, 2 mM EDTA, 0.1% SDS, 1% Triton-X100, 500 NaCl; Buffer C: 10 mM Tris pH 8.1, 1 mM EDTA, 1% NP40, 1% Sodium deoxicholate, 0.25 M LiCl2; Buffer D: 10 mM Tris pH 8.1, 1 mM EDTA). Immune complexes were eluted in 100 µl of buffer containing 0.1 M NaHCO3, 1% SDS, 1 µg/µl proteinase K. Samples were then reverse-crosslinked using 20 µl of 5M NaCl and incubated overnight at 65 ºC. The reverse crosslinked DNA was purified using the ChIP DNA clean concentrator, following the manufacturer’s instructions (Zymo Research).
Samples were end-repaired, A-tailed, and adaptor-ligated using barcoded inline adaptors according to the manufacturer’s instructions (Illumina). DNA was purified over a Zymo Research PCR purification column between each enzymatic reaction (Zymo Research). DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected for 200-300 bp fragments on a 1.5% agarose gel and the library concentrations were determined using a QuBit 3.0 Fluorometer (Thermo Scientific). Libraries were sequenced on an Illumina HiSeq2000 using single-end 50bp sequencing at the UMass Medical School deep sequencing core facility
Libraries of ChIP-enriched DNA were prepared following Illumina strategy

value: Mtf1, Santa Cruz biotechnologies


title: 24plusI_IP_rep1

value: Magna ChIP protein A+G Magnetic Beads (Millipore, Sigma)


title: 24plusI_IP_rep2


title: 24plusCu_IP_rep1

growth_protocol:
Mouse satellite cells were isolated from leg muscle of 3-6 week old wild type C57Bl/6 mice. The muscle was extracted and cut into small pieces, washed with Hank’s Balanced Salt Solution (HBSS; ThermoFisher Scientific) and incubated with 0.1% Pronase for 1 h at 37 ºC. The cells were then filtered using a 100 μm cell sieve and resuspended in 3 ml of growild typeh media (1:1 v/v DMEM:F-12, 20% FBS, 2% chick embryo extract and 25 ng/ml of basic FGF). Cells were filtered again using a 40 µm cell sieve and centrifuged at 1,000 x g for 1 min at room temperature. The cells were placed in the top of a Percoll gradient (35 and 70%) and centrifuged 20 min at 1,850 x g at room temperature. The myoblasts were contained in the lower interface of the 70% Percoll fraction was washed with HBSS, centrifuged 5 min at 1,000 x g, and resuspended in growth wild type media for plating. Myoblasts were grown and differentiated on plates coated with 0.02% collagen (Advanced BioMatrix) (42). The different treatments were: presence and absence of CuSO4.
DMEM, 2% Horse Serum (HS), 100 U/ml1 penicillin and 100 mg/ml1 streptomycin, 100 uM CuSO4


title: 24plusI_IN_rep1


title: 24noICu_IP_rep2


title: 24plusCu_IP_rep2


title: M381_Control_RNA-seq

value: M381 Cells untreated with BRAF inhibitor


title: M397_DR_ATAC-seq

status: Public on Sep 23 2019

description: DR

data_processing:
For UCLA samples, we are uncertain about the precise base calling procedures; For COH RNA-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.1.8.4; For COH ChIP-Seq / ATAC-Seq samples: .bcl files were produced using Real-time analysis (RTA) 2.2.38 and base calling was performed using bcl2fastq v.2.18
ChIP-seq and ATAC-seq Reads were aligned to hg19 with bowtie2
Peaks were called on the merged set of bam files using MACS2
Differential accessibility or enrichment of histone mark were measured using diffReps/DESeq2
Differentially accessible or enrichmental regions were called if the absolute log value of the fold change was more than 1 at an FDR <0.05
RNA-seq reads were aligned against the human genome (hg19) using TopHat2. Read counts were quantified using htseq-count (Anders et al., 2015), with UCSC known gene annotations (Hsu et al., 2006) with anti-sense (AS) genes removed.  Fold-change values were calculated from Fragments Per Kilobase per Million reads(FPKM) (Warden et al., 2013) normalized expression values, which were also used for visualization (following a log2 transformation). Aligned reads were counted using GenomicRanges (Lawrence et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, bigwig files. To visualize peaks in each sample, bed graph file was generated using MACS2 with following parametes: --nomodel, --broad, --bdg, --SPMR. Then the generated bed graph file was converted into bigwig file by bedGraphToBigWig tool. For RNA-seq, tab-delimited text files include RPKM values for each sample.

extract_protocol:
Briefly, cells were cultured to ~80% confluency in a petri dish containing 10 mL of growth media, and then fixed in 1% formaldehyde by adding 275 μl of 37% formaldehyde for 10 minutes to cross-link protein–DNA complexes at room temperature. The unreacted formaldehyde was quenched by adding Glycine to a final concentration 0.125 M. Gently swirl dish to mix. The nuclear pellet was isolated with Cell Lysis Buffer. The pellet was resuspended with 500 μl SDS Lysis Buffer containing 1X Protease Inhibitor Cocktail II before sonication for 4 min (10 s on, 30 s off, 10% strength in a Bioruptor to yield DNA fragments of 0.2-1.0 kb in length. The lysates were cleared by centrifugation (12,000g for 10 min at 4 °C) and diluted tenfold in ChIP dilution buffer to decrease the concentration of SDS. After keeping 10% of the sample as input, 500 μl supernatant was incubated overnight at 4 °C with antibody and 20 μL of fully resuspended protein A/G magnetic beads. The washing, elution, reverse cross-linking, and purification steps were performed according to manufacturer’s description. ChIPed Eluted DNA was quantified by Qubit dsDNA HS Assay Kit.  As for ATAC-seq, the previous published protocol (Buenrostro et al., 2015) were used for cell lysis, tagmentation and DNA purification. For RNA-seq, total RNA was extracted from cell pellets using RNeasy Mini Kit (Qiagen).
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Kapa, Cat KK 8700) according to the manufacturer's protocol. Briefly, 5-10 ng of immunoprecipitated DNA was underwent end-repaired, A tailing and adaptor ligation. A 10 cycles of PCR was performed to produce the final sequencing library. As for ATAC, the Tn5 treated DNA was amplified with a 5-cycle PCR in 50µl reaction volume. The tubes were removed from thermocycler and used 5 µl of partially amplified library to perform qPCR to determine how many additional PCR cycles were needed. For the samples in this study, an additional 4-5 cycles of PCR was performed on the remaining 45ul of each partially amplified product. 1.8X AmpurXP beads purification was used for the final PCR cleanup. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit, and quantified with qPCR. For RNA-seq, sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, USA) with minor modifications.

treatment_protocol: BRAF inhibitor (vemurafenib) from Selleck Chemicals LLC, were dissolved in DMSO at designated concentrations before applying to cell culture media. Cells were plated in 10cm tissue culture plate at 60% confluency and treated with certain drugs for the specified numbers of days. M397 cells were treated with 3uM of vemurafenib for 59days and at day29, drug were removed and cells were cultured with normal medium for another 35days.

tag: cell line

value: Patient-derived melanoma cell line M397

value: M397 Cells treated with BRAF inhibitor 29 days, then untreated 35 days


title: M397_D32_ATAC-seq

value: M397 Cells treated with BRAF inhibitor 32 days


title: M397_D3_ATAC-seq

value: M397 cells treated with BRAF inhibitor 3 days


title: M397_D0_ATAC-seq

value: M397 Cells untreated with BRAF inhibitor


title: R3a - no treatment

status: Public on Aug 19 2019

city: Gif-sur-Yvette

first: Claire

last: Toffano-Nioche

address: Avenue de la Terrasse, b. 21

department: UFR des Sciences

country: France

institute: CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay

description: tRNA epitranscriptome not treated (- condition)

data_processing:
Library strategy: Dts-seq
Remove adapters and trim poly-A tails from R2 reads using cutadapt (version 1.11, with –adapter and --minimum-length options)
Map on E. coli genome using Bowtie2 (version 2.2.8, with –local option)
Filter mapped reads and with a CCA sequence motif at the 3’ end (awk command line ; see https://github.com/i2bc/dts-seq)
Compute stranded genomic coverages using samtools (version 1.4, depth command with -a and -d options)
Compute the termination signal for tRNA using a dedicaced R code (see https://github.com/i2bc/dts-seq)
Genome_build: GCF_000005845.2_ASM584v2
Supplementary_files_format_and_content: The txt files contain the number of reads at each genomic base position, the first column is for the forward strand while the second column is for the reverse strand.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: - treatment, C replicate

growth_protocol: grown at 37°C in standard LB medium, sampling at an OD 600 of ~4.0

extract_protocol:
Total RNA was extracted with a standard trizol protocol. Total RNA was either not treated (nD), or treated with DNase (NT), treated with DNase and deacylated (D), treated with DNase, oxydized an deacylated (OD), or treated with DNase, deacylated and oxydized (DO) prior to 3' adapter ligation. After reverse transcription, chimeric RNA/cDNA products were directly loaded on gel for size selection between 35 to 200 bp by electrophoresis, to eliminate the excess of 3’ adapters and select mid-size RNA transcripts.
Gel-extracted products were subjected to poly-A tailing by a TdT enzyme. A first round of selective pre-amplification of the cDNA was achieved with Illumina TruSeq sRNA RTP with TGG overhang and Illumina TruSeq sRNA 5’ adapter primer with polyT(20). A second amplification with Illumina RP1 and Illumina TruSeq sRNA Index primer (RPIX) that added a specific tag to each of the samples provided the final libraries.

treatment_protocol: Cells were not treated

tag: substrain


title: F-PHHs-3

status: Public on Sep 02 2019

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

country: China

institute: Peking University

data_processing:
The transcriptome reads were mapped using STAR.
The read counts for each gene were calculated using featureCounts. For microRNA, clean fasta format sequencing reads generated from the sequencer mapped against the human genome build hg19 and calculated read counts by miRDeep2.
Gene expression was normalized by DESeq2, and low expression genes with total counts across all samples less than 1 were excluded.
Genome_build: hg19 for human
Supplementary_files_format_and_content: CSV files include the expression values for each sample

source_name: primary human hepatocyte

extract_protocol:
Total RNA from each sample was isolated using Direct-zol RNA Miniprep kit (ZYMO RESEARCH) or TRNzol Universal (TIANGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.For microRNAs, RNA sequencing libraries were prepared using the NEB Next® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following the manufacturer’s recommendations.

treatment_protocol: hHPLCs  were cultured in HEM and collected from RNA extraction at indicated passages. hiHeps derived from hHPLCs of different passages were cultured in 2C medium for 10 days and then collected from RNA extraction. Primary huaman hepatocytes were fresh isolated.

tag: batch number

value: batch 1

value: fresh isolated

tag: cell type

value: primary human hepatocyte


title: F-PHHs-1


title: F-PHHs-2


title: R3b - DNase treatment

description: tRNA epitranscriptome treated with DNase (D condition)

source_name: D treatement, C replicate


title: R3c - DNase treatment and deacylation

description: tRNA epitranscriptome treated with DNase and deacylated (Dd condition)

source_name: Dd treatment, C replicate


title: LMNA_NULL4_replicate_3

status: Public on Oct 02 2019

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina Mouse Ref-8 v2 Expression Bead Chips (Illumina, San Diego, CA). The arrays were then rinsed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-conjugated Cy3.

source_name: mouse embryo fibroblasts (MEFs)

extract_protocol:
Spontaneously immortalized MEFs (wild-type (Lmna+/+) and Lmna knockout (Lmna-/-))  were generated in the laboratory of Colin L. Stewart and grown in Dulbecco Modified Eagle Medium (DMEM), supplemented with 10% FBS, 50 μg/ml streptomycin and 50 units/ml penicillin, at 37oC with 5% CO2.
Cells grown overnight were washed in cold PBS, and RNA was extracted using trizol (Invitrogen) according to the manufacturer’s instructions. RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: A total of 2x106 cells were seeded in 10 cm plates and grown overnight.

value: Fibroblasts

tag: Stage

value: Embryonic, immortalized

value: Lmna null


title: LMNA_WT4_replicate_3

value: Lmna WT


title: LMNA_WT1_replicate_1


title: R2b - DNase treatment

source_name: D treatement, B replicate


title: R3e - DNase treatment, deacylation, and oxidation

description: tRNA epitranscriptome treated with DNase, deacylated, and oxidated (DdO condition)

source_name: DO treatment, C replicate


title: LMNA_WT3_replicate_2


title: R2a - no treatment

source_name: - treatment, B replicate


title: R3d - DNase treatment, oxidation, and deacylation

description: tRNA epitranscriptome treated with DNase, oxidated, and deacylated (DOd condition)

source_name: OD treatment, C replicate


title: R2c - DNase treatment and deacylation

source_name: Dd treatment, B replicate


title: LMNA_NULL3_replicate_2


title: R1b - DNase treatment

source_name: D treatement, A replicate


title: R2e - DNase treatment, deacylation, and oxidation

source_name: DO treatment, B replicate


title: R1c - DNase treatment and deacylation

source_name: Dd treatment, A replicate


title: R1e - DNase treatment, deacylation, and oxidation

source_name: DO treatment, A replicate


title: R1d - DNase treatment, oxidation, and deacylation

source_name: OD treatment, A replicate


title: R2d - DNase treatment, oxidation, and deacylation

source_name: OD treatment, B replicate


title: F-PHHs-4

value: batch 2


title: R1a - no treatment

source_name: - treatment, A replicate


title: LMNA_NULL1_replicate_1


title: WRN-1_NR_D7_replicate_1

status: Public on Aug 16 2019

hyb_protocol: A total of 825 ng Cy3-labeled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 55 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent C. elegans (V2) 4×44K Gene Expression Microarrays (G2519F-020186) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2. A total of 1.65 micrograms Cy3-labelled cRNA

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data from four separate experiments were log-transformed. Three separate probe preparations were used individually or combined in equal amounts for the fourth hybridization. Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

organism: Caenorhabditis elegans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Caenorhabditis elegans (C. elegans) nematodes were cultured at 25°C on solid agar plates of standard nematode growth medium (NGM) with OP50 food source unless otherwise, and maintained following standard protocols previously described. The Bristol strain N2 (wild type) was from Caenorhabditis Genetics Center (CGC), while the wrn-1(gk99), a C. elegans model of Werner Syndrome with a 196bp deletion mutation resulting in the complete absence of the WRN-1 protein, was a gift from Dr. Hyeon-Sook Koo (Yonsei University, Korea).

extract_protocol: Four independent experiments per condition were collected, and stored at -80oC in lysis reagent (Qiagen Cat. no. 75142). Crude extracts were prepared by bead beating packed worm pellets with the Mini-Beadbeater 8 (Biospec Products, Oklahoma), and total RNA isolated using RNeasy Mini Kit on the QIAcube according to the manufacturer's protocol (Qiagen, California). RNA concentration and quality was measured by Nanodrop (ThermoFisher, Waltham, MA USA) and the Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: Both strains were treated with either vehicle control (CTR), NAD+ precursor nicotinamide riboside (NR, 1 mM), a SIRT1 activator (SRT1720, 10 µM), or a PARP inhibitor (Olaparib, 500 nM) from the L4 stage, followed by changing to fresh drug plate on adult Day 4, and collection for transcriptomic analysis on adult D7. Approximately 500 worms were used for each experiment, with four biological repeats per condition.

tag: disease state

value: model of WS

value: NR, 1 mM

tag: time

value: Day 7


title: WRN-1_NR_D7_replicate_3

tag: treatment


title: N2_Ola_D7_replicate_4

value: N2:wild type Bristol

value: control

value: Olaparib_500 nM


title: WRN-1_NR_D7_replicate_4


title: WRN-1_Ola_D7_replicate_1


title: WRN-1_SRIT1_D7_replicate_1


title: WRN-1_CTR_D7_replicate_1

value: CTR


title: WRN-1_Ola_D7_replicate_4


title: WRN-1_CTR_D7_replicate_3


title: WRN-1_SRIT1_D7_replicate_2


title: N2_SRIT1_D7_replicate_2


title: WRN-1_CTR_D7_replicate_4


title: WRN-1_Ola_D7_replicate_2


title: WRN-1_Ola_D7_replicate_3


title: WRN-1_CTR_D7_replicate_2


title: N2_SRIT1_D7_replicate_1


title: N2_SRIT1_D7_replicate_4


title: N2_Ola_D7_replicate_2


title: N2_NR_D7_replicate_3


title: N2_NR_D7_replicate_4


title: WRN-1_SRIT1_D7_replicate_4


title: N2_NR_D7_replicate_1


title: N2_SRIT1_D7_replicate_3


title: WRN-1_NR_D7_replicate_2


title: N2_NR_D7_replicate_2


title: N2_Ola_D7_replicate_3


title: WRN-1_SRIT1_D7_replicate_3


title: N2_Ola_D7_replicate_1


title: N2_CTR_D7_replicate_4


title: N2_CTR_D7_replicate_3


title: N2_CTR_D7_replicate_2


title: 12N2_RNA

status: Public on Jul 01 2019

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: RNA library from 12Z cells after non-targeting siRNA control treatment

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

source_name: 12Z cell line

growth_protocol: 12Z cells were grown in DMEM/F12 + 10% FBS, 1% pen/strep, 1% L-glutamine

extract_protocol:
72 hours after siRNA transfection, RNA was prepared using the Quick-RNA Miniprep Kit (Zymo Research).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 500 ng of total RNA material.

treatment_protocol: Cells were transfected with siRNAs using Lipofectamine RNAiMax reagent, and media was replaced after 24 hours.

value: 12Z endometriotic epithelial cells

tag: condition

value: non-targeting siRNA control


title: 12N3_RNA


title: Uwt2_RNA

description: RNA library. First flow cell. Cells from pooled mice.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 74’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting. Lexogen SIRVome was independently aligned and quantified for qualitative assessment of library concordancy.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

source_name: endometrial epithelium

growth_protocol: Mice were housed at the Van Andel Research Institute Animal Facility and the Michigan State University Grand Rapids Research Center in accordance with protocols approved by the Van Andel Research Institute and Michigan State University, under AUF# 01/16-099-00.

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Lexogen SIRV-set2 RNAs were spiked into RNA prior to library preparation at a concentration of 1% by mass. RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 100 ng of total RNA material.

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

value: EPCAM+ endometrial epithelium

value: Control wild-type

tag: phenotype

value: normal healthy


title: 12N1_RNA


title: Uwt3_RNA

tag: tissue


title: Zfp931

status: Public on Jun 27 2019

city: Bethesda

first: Gernot

last: Wolf

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
Reads were mapped using Bowtie or Bowtie2, as indicated in the sample information.
Mapped reads were converted to Bigwig files (normalized voverage to 1x) with DeepTools (control ChIPs were substracted from ChIP samples).
Peaks were called using MACS (version 1.4.2) with parameters as indicated in the sample information over Input and/or ChIP control samples, as indicated. For further analysis, the 200 bp region around the peak summit was used.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files and MACS14 peaks of all KRAB-ZFPs (200 bp core regions around peak summit)

source_name: B6 ES cells

growth_protocol: F9 EC cells were grown on gelatine coated plates in DMEM supplemented with 10% FBS, ES cells were grown in standard ES media with 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Chromatin was purified and immunoprecipitated according to previously described protocols as indicated in the sample information.
DNA SMART kit (Takara) or Truseq (Illumina)

treatment_protocol: Cells were cross-linked in 1% formaldehyde for 10 minutes before ChIP.

value: B6 ES cells

tag: overexpression

tag: chip antibody

value: HA (clone 16B12, Covance)

tag: tag

tag: ChIP

value: Imbeault et al. 2017

tag: mapping

value: Bowtie (--best)

tag: peak  calling parameters

value: p-value < 1e-5

tag: input


title: TI_443_Input


title: TI_339_Input


title: Uwt1_RNA

tag: strain

tag: genotype


title: Zfp882

source_name: F9 EC cells

tag: cell type

value: F9 EC cells

value: O'Geen et al. 2010

value: Bowtie (-5 3 --best)

value: p-value < 1e-10, enrichment > 10

value: F9_Input + FLAG_control


title: Zfp810

value: p-value < 1e-10, enrichment > 20


title: N2_CTR_D7_replicate_1

value: N2:wild type Bristol

value: control

value: CTR

value: Day 7


title: Gm14419


title: Gm14418

value: p-value < 1e-5, enrichment > 10


title: Gm14410


title: Zfp617


title: Gm8898


title: Gm14420


title: Gm14401


title: Gm6710


title: Gm14443


title: Gm14406


title: Gm4631


title: Gm14436


title: Gm14412


title: Gm14399


title: Gm14393


title: HA_control

value: O'Geen et al.


title: Gm14295

value: B6 ES cells


title: Gm14326


title: FLAG_control


title: Gm13157


title: EtOHi1


title: Zkscan17

value: F9_Input + HA_control


title: Zfp961


title: Zfp953


title: Zfp935


title: Zfp94


title: Zfp874b


title: Zfp933


title: Zfp874a


title: Zfp759


title: Gm14391


title: Zfp738


title: Zfp712


title: Zfp595


title: Zfp58


title: Zfp938


title: Fibroid [MP310F]

status: Public on Aug 07 2019

type: genomic

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

label: Cy5 and Cy3

source_name: Fibroid

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.  Array beadchips were scanned on the Illumina iScan platform. DNA methylome was captured by HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) using the manufacturer’s standard protocol.

tag: subject id

tag: tissue type

value: Fibroid


title: Zfp709


title: Zfp661


title: Zfp599


title: Zfp872


title: Zfp808


title: Zfp493


title: F9_Input


title: Zfp458


title: Zfp457


title: Zfp456


title: Zfp534


title: Zfp46


title: Fibroid [MP307F]


title: Zfp429


title: Stromal Cervix [MP311C]

source_name: Stromal Cervix

value: Stromal Cervix


title: Rex2


title: Gm14296_control


title: Fibroid [MP311F]


title: Zfp273


title: Stromal Cervix [MP310C]


title: Stromal Cervix [MP308C]


title: Normal Myometrium [MP308N]

source_name: Normal Myometrium

value: Normal Myometrium


title: Normal Myometrium [MP305N]


title: Fibroid [MP306F]


title: Gm30910

value: F9 EC cells


title: Stromal Cervix [MP306C]


title: Normal Myometrium [MP311N]


title: Gm13247

value: O'Geen et al. 2010


title: Gm13251

value: Bowtie (-5 3 --best)


title: Fibroid [MP308F]


title: LOC102638055


title: Gm13225

value: p-value < 1e-10, enrichment > 10


title: Gm13235


title: Normal Myometrium [MP306N]


title: Fibroid [MP305F]


title: Normal Myometrium [MP310N]


title: Gm13212

value: F9_Input + FLAG_control


title: Gm13051

value: p-value < 1e-10, enrichment > 20


title: Stromal Cervix [MP307C]


title: Gm13154


title: Gm13145


title: Gm13152


title: AW146154


title: Gm13139


title: 2610305D13Rik


title: CBMS1_Day7Diff_ESC_single_MidS_41 [scRepli-seq]

status: Public on Jun 26 2019

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: This is duplicated sample record of GSM2905074 with additional sequence reads and re-analyzed processed data.

data_processing:
Sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
Trimmed reads were mapped into mm9 and CBMS1-specific (CBA/MsM) diploid genome based on mm9 genomeby using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 were removed by using picard tool and the reads overlapped with mm9 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
Single-cell data (CBMS1, differentiated CBMS1, EpiSC un-resolved at 80-kb): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder's correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase), Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. "Repliscore" was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved chrX data (d0, d2, d7): after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder's correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"].
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Binarized 40kb data: Sample_Name_40k_100S_MAP_2HMM2_eps0.01.binary.bedGraph
Genome_build: mm9
Supplementary_files_format_and_content: We provide three types of processed data files. One is the binarized data (scRepliseq_data_884cells_G1_Sphase_binary_data_80kb.txt). Second is the sample information data (scRepliseq_data_sample_Info.txt). Third is the haplotype-resolved Mid-S binarized data of chrX (scRepliseq_d0_33_CBA_XX_chrX_only_400kb.txt, scRepliseq_d0_33_MsM_XX_chrX_only_400kb.txt, scRepliseq_d2_27_CBA_XX_chrX_only_400kb.txt, scRepliseq_d2_27_MsM_XX_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xa_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xi_chrX_only_400kb.txt). We also provide README file for the description of each processed file.
Supplementary_files_format_and_content: bedGraph

source_name: Day7 Differentiated CBMS1 ESC

growth_protocol: CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as discribed (Tesar et al. 2007).

extract_protocol:
For single cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80-bp length, single-read).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

value: CBA/MsM

value: day7 differentiated ESCs

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

value: MsM

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

value: CBA

tag: repliscore of 40–70%

value: TRUE

tag: cell cycle phase

value: MidS


title: CBMS1_Day7Diff_ESC_single_MidS_33 [scRepli-seq]

description: This is duplicated sample record of GSM2905066 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_39 [scRepli-seq]

description: This is duplicated sample record of GSM2905072 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_31 [scRepli-seq]

description: This is duplicated sample record of GSM2905064 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_28 [scRepli-seq]

description: This is duplicated sample record of GSM2905061 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_24 [scRepli-seq]

description: This is duplicated sample record of GSM2905057 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_30 [scRepli-seq]

description: This is duplicated sample record of GSM2905063 with additional sequence reads and re-analyzed processed data.


title: Gm13150

tag: overexpression

tag: chip antibody

value: F9_Input + HA_control


title: CBMS1_Day7Diff_ESC_single_MidS_25 [scRepli-seq]

description: This is duplicated sample record of GSM2905058 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_22 [scRepli-seq]

description: This is duplicated sample record of GSM2905055 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_15 [scRepli-seq]

description: This is duplicated sample record of GSM2905048 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_10 [scRepli-seq]

description: This is duplicated sample record of GSM2905043 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_20 [scRepli-seq]

description: This is duplicated sample record of GSM2905053 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_G1_02 [scRepli-seq]

description: This is duplicated sample record of GSM2905032 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_G1_03 [scRepli-seq]

description: This is duplicated sample record of GSM2905033 with re-analyzed processed data.


title: CBMS1_ESC_single_MidS_34 [scRepli-seq]

description: This is duplicated sample record of GSM2905016 with additional sequence reads and re-analyzed processed data.

source_name: CBMS1 ESC

value: embryonic stem cell


title: CBMS1_Day7Diff_ESC_single_G1_01 [scRepli-seq]

description: This is duplicated sample record of GSM2905031 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_42 [scRepli-seq]

description: This is duplicated sample record of GSM2905075 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_33 [scRepli-seq]

description: This is duplicated sample record of GSM2905015 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_31 [scRepli-seq]

description: This is duplicated sample record of GSM2905013 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_32 [scRepli-seq]

description: This is duplicated sample record of GSM2905014 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_30 [scRepli-seq]

description: This is duplicated sample record of GSM2905012 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_28 [scRepli-seq]

description: This is duplicated sample record of GSM2905010 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_29 [scRepli-seq]

description: This is duplicated sample record of GSM2905011 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_27 [scRepli-seq]

description: This is duplicated sample record of GSM2905009 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_26 [scRepli-seq]

description: This is duplicated sample record of GSM2905008 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_25 [scRepli-seq]

description: This is duplicated sample record of GSM2905007 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_19 [scRepli-seq]

description: This is duplicated sample record of GSM2905052 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_22 [scRepli-seq]

description: This is duplicated sample record of GSM2905004 with additional sequence reads and re-analyzed processed data.


title: CBMS1_Day7Diff_ESC_single_MidS_05 [scRepli-seq]

description: This is duplicated sample record of GSM2905038 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_19 [scRepli-seq]

description: This is duplicated sample record of GSM2905001 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_21 [scRepli-seq]

description: This is duplicated sample record of GSM2905003 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_16 [scRepli-seq]

description: This is duplicated sample record of GSM2904998 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_15 [scRepli-seq]

description: This is duplicated sample record of GSM2904997 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_18 [scRepli-seq]

description: This is duplicated sample record of GSM2905000 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_14 [scRepli-seq]

description: This is duplicated sample record of GSM2904996 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_12 [scRepli-seq]

description: This is duplicated sample record of GSM2904994 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_08 [scRepli-seq]

description: This is duplicated sample record of GSM2904990 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_07 [scRepli-seq]

description: This is duplicated sample record of GSM2904989 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_10 [scRepli-seq]

description: This is duplicated sample record of GSM2904992 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_11 [scRepli-seq]

description: This is duplicated sample record of GSM2904993 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_09 [scRepli-seq]

description: This is duplicated sample record of GSM2904991 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_04 [scRepli-seq]

description: This is duplicated sample record of GSM2904986 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_05 [scRepli-seq]

description: This is duplicated sample record of GSM2904987 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_MidS_06 [scRepli-seq]

description: This is duplicated sample record of GSM2904988 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_G1_02 [scRepli-seq]

description: This is duplicated sample record of GSM2904979 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_G1_03 [scRepli-seq]

description: This is duplicated sample record of GSM2904980 with additional sequence reads and re-analyzed processed data.


title: CBMS1_ESC_single_G1_01 [scRepli-seq]

description: This is duplicated sample record of GSM2904978 with re-analyzed processed data.


title: CBMS1_ESC_single_MidS_24 [scRepli-seq]

description: This is duplicated sample record of GSM2905006 with additional sequence reads and re-analyzed processed data.


title: Zfp600

tag: tag

tag: ChIP

value: p-value < 1e-5, enrichment > 10


title: CBMS1_ESC_single_MidS_20 [scRepli-seq]

description: This is duplicated sample record of GSM2905002 with additional sequence reads and re-analyzed processed data.


title: Gm21082

value: F9 EC cells

tag: mapping

tag: peak  calling parameters


title: CBMS1_ESC_single_G1_04 [scRepli-seq]

description: This is duplicated sample record of GSM2904981 with additional sequence reads and re-analyzed processed data.

tag: strain


title: 141426_PBMC_2

status: Public on May 26 2019

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description:
200373830105_J
SAMPLE 77

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

label: biotin

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA from PBMC, T Cell, B Cell samples was extracted using the RNeasy mini kit (Qiagen, CA)

tag: subject status

value: Healthy Adults receiving Influenza Vaccination

tag: age group

value: Frail

tag: blood draw date

value: after vaccination day 2

value: Peripheral Blood Mononuclear Cells (PBMC)


title: 141425_PBMC_2

description:
200373830119_B
SAMPLE 73

tag: cell type


title: 141426_PBMC_0

description:
200373830105_I
SAMPLE 76

value: day 0; prior to administration of vaccine


title: 141423_PBMC_2

description:
200373830101_F
SAMPLE 65


title: 141422_PBMC_0

description:
200373830101_A
SAMPLE 60

value: Young


title: 141424_PBMC_2

description:
200373830114_B
SAMPLE 69


title: 141425_PBMC_0

description:
200373830119_A
SAMPLE 72


title: 141426_PBMC_7

description:
200373830105_K
SAMPLE 78

value: after vaccination day 7


title: 141426_PBMC_28

description:
200373830105_L
SAMPLE 79

value: after vaccination day 28


title: 141425_PBMC_7

description:
200373830119_C
SAMPLE 74


title: 141423_PBMC_28

description:
200373830101_H
SAMPLE 67


title: 141424_PBMC_28

description:
200373830114_D
SAMPLE 71

value: after vaccination day 41


title: 141421_PBMC_28

description:
200373830101_L
SAMPLE 59


title: 141421_PBMC_2

description:
200373830101_J
SAMPLE 57


title: 141424_PBMC_0

description:
200373830114_A
SAMPLE 68


title: 141423_PBMC_0

description:
200373830101_E
SAMPLE 64


title: 141424_PBMC_7

description:
200373830114_C
SAMPLE 70


title: 141419_PBMC_2

description:
200373830119_F
SAMPLE 53


title: 141425_PBMC_28

description:
200373830119_D
SAMPLE 75


title: 141421_PBMC_0

description:
200373830101_I
SAMPLE 56


title: 141423_PBMC_7

description:
200373830101_G
SAMPLE 66


title: 141421_PBMC_7

description:
200373830101_K
SAMPLE 58


title: 141422_PBMC_7

description:
200373830101_C
SAMPLE 62


title: 141419_PBMC_28

description:
200373830119_H
SAMPLE 55


title: 141422_PBMC_2

description:
200373830101_B
SAMPLE 61


title: 141419_PBMC_7

description:
200373830119_G
SAMPLE 54


title: 141422_PBMC_28

description:
200373830101_D
SAMPLE 63


title: 141417_PBMC_28

description:
200373830107_H
SAMPLE 51


title: 141419_PBMC_0

description:
200373830119_E
SAMPLE 52


title: CBMS1_ESC_single_G1_05 [scRepli-seq]

description: This is duplicated sample record of GSM2904982 with additional sequence reads and re-analyzed processed data.

value: CBA/MsM

tag: sample state

value: Single cell

value: XX


title: 141415_PBMC_2

description:
200373830105_F
SAMPLE 41


title: 141416_PBMC_0

description:
200373830114_E
SAMPLE 44


title: 141417_PBMC_7

description:
200373830107_G
SAMPLE 50


title: 141417_PBMC_2

description:
200373830107_F
SAMPLE 49


title: 141414_PBMC_7

description:
200373830112_G
SAMPLE 38


title: 141417_PBMC_0

description:
200373830107_E
SAMPLE 48


title: 141416_PBMC_2

description:
200373830080_F
SAMPLE 45


title: 141412_PBMC_2

description:
200373830114_F
SAMPLE 33


title: 141415_PBMC_7

description:
200373830105_G
SAMPLE 42


title: 141414_PBMC_0

description:
200373830112_E
SAMPLE 36


title: 141409_PBMC_7

description:
200373830107_C
SAMPLE 30


title: 141415_PBMC_0

description:
200373830080_E
SAMPLE 40


title: 141412_PBMC_0

description:
200373830105_E
SAMPLE 32


title: 141409_PBMC_2

description:
200373830107_B
SAMPLE 29


title: 141409_PBMC_28

description:
200373830107_D
SAMPLE 31


title: 141407_PBMC_28

description:
200373830119_L
SAMPLE 27

value: after vaccination day 25


title: 141414_PBMC_2

description:
200373830112_F
SAMPLE 37


title: 141415_PBMC_28

description:
200373830105_H
SAMPLE 43

value: after vaccination day 37


title: 141416_PBMC_7

description:
200373830080_G
SAMPLE 46


title: 141403_PBMC_28

description:
200373830080_L
SAMPLE 23


title: 141407_PBMC_2

description:
200373830119_J
SAMPLE 25


title: 141409_PBMC_0

description:
200373830107_A
SAMPLE 28


title: 141416_PBMC_28

description:
200373830080_H
SAMPLE 47


title: 141414_PBMC_28

description:
200373830112_H
SAMPLE 39


title: 141412_PBMC_7

description:
200373830114_G
SAMPLE 34


title: 141407_PBMC_7

description:
200373830119_K
SAMPLE 26


title: 141403_PBMC_7

description:
200373830080_K
SAMPLE 22


title: 141407_PBMC_0

description:
200373830119_I
SAMPLE 24


title: 141397_PBMC_2

description:
200373830108_J
SAMPLE 17

value: Older


title: H-hepatocyte-1

status: Public on May 08 2019

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using BCL2Fastq version 1.8.4
Sequenced reads were trimmed for low-quality sequence by using Sickle (V1.33).
After preprocessing, the sequenced reads were mapped to hg19 human reference genome using RSEM (v.1.2.31) with STAR (v2.5.2b)
Merged expression level from paired end reads and orphan read and calculate merged transcript per million (TPM) by using in-house script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file which contains gene & transcript ID, transcript size, effective size, count, and TPM.

source_name: Human primary hepatocytes replicate #1

growth_protocol: Liver tissue samples were perfused via portal vein with a solution A containing 0.19 g/L EDTA (Gibco BRL Co, NY, USA), 8 g/L NaCl, 0.4 g/L KCl, 0.078 g/L NaH2PO4·2H2O, 0.151 g/L Na2HPO4·12H2O, and 0.19 g/L HEPES for 5 min at 37°C, followed by a solution B containing 0.3 g/L collagenase (Sigma, C5138USA), 0.56 g/L CaCl2, 8 g/L NaCl, 0.4 g/L KCl, 0.078 g/L NaH2PO4·2H2O, 0.151 g/L Na2HPO4·12H2O, 0.19 g/L HEPES for 8 min at 37°C. Viable hepatocytes were selected by isodensity centrifugation in Percoll (GE Healthcare, Little Chalfont, United Kingdom). Viability was 80-90% as judged by 0.4% trypan blue exclusion assay. CdH: Hepatocytes were seeded on collagen-coated dishes (STEMCELL Technologies, BC, Canada) at 5000 cells/cm2 in basic High Glucose DMEM/F-12 media (Gibco, CA, USA) containing 1% FBS (Gibco), 10 mM nicotinamide (Sigma-Aldrich, MO, USA), 0.1 μM dexamethasone (Sigma-Aldrich), 1% insulin-transferrin-selenium (ITS) (Gibco), 1% penicillin/streptomycin (Gibco), and 20 ng/ml epidermal growth factor (EGF) (Peprotech, NJ, USA). After overnight incubation, the basic medium was supplemented with 4 μM A83-01 (Gibco) and 3 μM CHIR99021 (STEMCELL Technologies), and 20 ng/ml of hepatocyte growth factor (Peprotech), designated reprogramming medium.

extract_protocol:
Total RNAs were isolated using Trizol Reagent (Gibco). 1-μg RNA samples were reverse transcribed using a Transcriptor First Strand cDNA Synthesis Kit (Roche, PA, USA).
A library was independently prepared with 1 µg of total RNA for each sample using an Illumina TruSeq Stranded mRNA Sample Prep Kit (#RS-122-2101, Illumina, Inc., San Diego, CA, USA). The initial step of library preparation involved purifying poly‐A containing mRNA molecules using poly‐T-attached magnetic beads. After this step, the purified mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved mRNA fragments were copied to the top strand of cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers, and the reverse complement strand of cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. These cDNA fragments underwent the ends repair process including the addition of a single ‘A’ base and adapter ligation. After these steps, the final cDNA libraries were created, purified, and enriched with PCR

value: primary hepatocytes


title: H-hepatocyte-2

source_name: Human primary hepatocytes replicate #2


title: 141394_PBMC_28

description:
200373830112_D
SAMPLE 15


title: 141393_PBMC_7

description:
200373830112_K
SAMPLE 10


title: 141394_PBMC_0

description:
200373830112_A
SAMPLE 12


title: 141397_PBMC_28

description:
200373830108_L
SAMPLE 19


title: 141392_PBMC_0

description:
200373830107_I
SAMPLE 5


title: 141394_PBMC_2

description:
200373830112_B
SAMPLE 13


title: 141397_PBMC_7

description:
200373830108_K
SAMPLE 18


title: 141392_PBMC_2

description:
200373830107_J
SAMPLE 6


title: 141403_PBMC_2

description:
200373830080_J
SAMPLE 21


title: 141393_PBMC_28

description:
200373830112_L
SAMPLE 11


title: U2OS_N_Replicate_3

status: Public on May 21 2019

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores is supplied.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: U2OS cells (ATCC) were cultured in DMEM-Glutamax (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: Total RNA was purified from 5 x 10^6 exponentially growing cells using the RNeasy Mini Kit (Qiagen). RNA quantity and integrity were evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: For APTX knock-out experiments, U2OS cells were seeded on a 6-well dish and transfected with an aprataxin double Nickase plasmid (sc-417083-NIC, Santa Cruz Biotechnology) using PolyJet transfection reagent (SignaGen Laboratories). Transfected cells were selected in medium with 2 µg/ml puromycin for one week, then harvested and reseeded on 150 mm dishes at 20 cells per dish. Single cell colonies were propagated. Disruption of APTX was verified by PCR amplification of the flanking target region and Western blot analysis. Cells were cultured for 3-4 weeks prior to RNA extraction.

tag: cell line

tag: genotype/variation

value: Control


title: 141388_PBMC_7

description:
200373830105_C
SAMPLE 3

value: Healthy Adults receiving Influenza Vaccination


title: APTX_KO_Replicate_3

value: APTX Knockout


title: U2OS_N_Replicate_1


title: 141388_PBMC_0

description:
200373830105_A
SAMPLE 1


title: U2OS_N_Replicate_2


title: 141388_PBMC_2

description:
200373830105_B
SAMPLE 2

value: after vaccination day 2


title: 141393_PBMC_2

description:
200373830112_J
SAMPLE 9

value: Peripheral Blood Mononuclear Cells (PBMC)


title: 141392_PBMC_28

description:
200373830107_L
SAMPLE 7


title: 141394_PBMC_7

description:
200373830112_C
SAMPLE 14

value: Frail


title: 141393_PBMC_0

description:
200373830112_I
SAMPLE 8

value: day 0; prior to administration of vaccine


title: APTX_KO_Replicate_1


title: APTX_KO_Replicate_2


title: 141388_PBMC_28

description:
200373830105_D
SAMPLE 4


title: 141412_PBMC_28

description:
200373830114_H
SAMPLE 35

value: Young


title: Lgr5eGFP+ uninfected

status: Public on Mar 25 2019

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

data_processing:
NextSeq data were demultiplexed using bcl2fastq v1.9
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation performed with 10X Cell Ranger (v2.0.0, 10X Genomics).
Cell Ranger R kit version 2.0.0 and Seurat version 2.3 was used for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction and t-SNE was used for clustering visualization. sSeq integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output:
*analysis.tar.gz: Several CSV files packed as tar.gz which contain automated secondary analysis results (Cell Ranger 2.1.0 output).
*filtered_gene_bc_matrices_h5.h5.gz: Filtered feature-barcode matrix. HDF5 Feature Barcode Matrix.
*filtered_gene_bc_matrices.tar.gz: Filtered feature-barcode matrix. Contains only detected cellular barcodes. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
*metrics_summary.csv.gz: Run summary CSV.
*molecule_info.h5.gz: HDF5 file containing per-molecule information for all molecules that contain a valid cell-barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
*raw_gene_bc_matrices_h5.h5.gz: Unfiltered feature-barcode matrix. HDF5 Feature Barcode Matrix.
*raw_gene_bc_matrices.tar.gz: Unfiltered feature-barcode matrix. Contains every barcode from fixed list of known-good barcode sequences. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).

molecule: polyA RNA

source_name: Lgr5+ cells from gastric gland base

growth_protocol: Lgr5eGFP+ cells were isolated form mouse antrum, sorted and processed for single cell analysis

extract_protocol:
PolyA selection based RNA capture (Chromium Single Cell 3’ Reagent Kit , v2 Chemistry, 10X Genomics) as per the manufacturer's instructions provided by 10X Genomics platform.   RNA-Seq
Libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform (https://www.10xgenomics.com/single-cell/)

tag: mouse status

value: uninfected

tag: tissue

value: antrum; gastric gland base

value: Lgr5eGFP+ cells