title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1763_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD006_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

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

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 frontal cortex

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 frontal cortex

tag: Sex

value: Male

tag: donor

tag: protocol


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1761_AD010_indexed

value: snmC-seq


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1762_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1761_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1762_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1761_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1761_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1760_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1760_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1760_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B9_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1759_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD004_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1759_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1759_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B8_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1758_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1758_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1758_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1758_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1757_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B7_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1757_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1757_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1759_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1757_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1756_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B6_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1755_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD012_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1756_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1754_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1755_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD004_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B5_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1753_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1753_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1753_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1753_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1752_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1751_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1751_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1751_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1754_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1754_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1750_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1749_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1750_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1749_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1749_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1748_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1748_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD012_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B4_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1748_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1751_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1747_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1747_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1747_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1746_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD001_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD004_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B3_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1746_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1746_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1745_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1745_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1745_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1749_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1744_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD007_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B2_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1744_AD008_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1744_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1744_AD002_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD004_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B1_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1743_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B12_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1743_AD006_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B12_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B12_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1742_AD010_indexed


title: 190321_mCTseq_hs_21yr_BA10_UMB5577_3_UMB5577_4_B12_AD007_indexed


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title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H8_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H8_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H8_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1713_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1713_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1714_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H8_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H8_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H9_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1713_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1712_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1712_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1711_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1712_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1712_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1711_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H7_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1711_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H6_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1711_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1710_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1710_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1709_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H4_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H4_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H4_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1709_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1708_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1709_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H5_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1708_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1707_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1708_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1707_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1707_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H4_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1709_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1706_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H4_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H3_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H2_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1706_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1706_AD002_indexed


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title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1706_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1704_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1705_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1704_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H1_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1703_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1703_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1703_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1702_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1702_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H12_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1702_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H10_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1701_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_H11_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1701_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1700_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1699_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G9_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1700_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1699_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1701_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G8_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1698_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1698_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1699_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1698_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G7_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1698_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1697_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1697_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1699_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD004_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1696_AD010_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1697_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD012_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1696_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD008_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1696_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1695_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD007_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1695_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G4_AD001_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1694_AD006_indexed


title: AB5665

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Brain cortex

extract_protocol:
Single-cell libraries were prepared as previously described (Keren-Shaul, Nature Protocols, 2019). In brief, mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier (Keren-Shaul, Nature Protocols, 2019).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

tag: tissue

value: Brain

value: Immune cells

tag: selection marker

tag: source

value: BioLegend

tag: catalog#

tag: age


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1694_AD002_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1696_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G6_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G3_AD008_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G5_AD006_indexed


title: 170512_NDARKD326LNK_hs_58yr_BA10_pool_1693_AD010_indexed


title: AB5663


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title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_G3_AD007_indexed


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title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H8_AD002_indexed

source_name: mixture of human embryonic stem cell and human embryonic kidney cell

value: Unknown

value: H1 or HEK293

value: snmCT-seq


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H9_AD006_indexed

value: mixture of human embryonic stem cell and human embryonic kidney cell


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H9_AD004_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H8_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD008_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H7_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD007_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H7_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B9_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD008_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H6_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD007_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H7_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD004_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H6_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD010_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H6_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD002_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H5_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B7_AD006_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H5_AD001_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H5_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD010_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD007_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD008_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H7_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B8_AD001_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H4_AD006_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H4_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD002_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B5_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B5_AD008_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H4_AD002_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H4_AD001_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B5_AD007_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H3_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B5_AD006_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B5_AD004_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H3_AD004_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B4_AD012_indexed


title: 190305_mCTseq_hs_29yr_BA10_UMB5580_1_UMB5580_2_B6_AD006_indexed


title: 180615_mCT_hs_h1-hek293_h1-hek293_random2_H2_AD006_indexed