title: Cortex2.CCJ15ANXX.SM2_052318p2_F6

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements


title: 4h_Long_C

status: Public on Jun 01 2019

type: SRA

city: La Jolla

first: Andrew

last: McCulloch

state: CA

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Quality scores of each sample were analyzed with FastQC.
The final 6 bases of each read were trimmed off of the 3' end of reads using FastX-Toolkit.
Reads were mapped to UCSC mm9 with TopHat v1.4.1.
Gene abundance and differential expression were calculated using Cufflinks v2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: Data was summarized in an .xlsx file, which lists the RPKM value for each sample, plus the fold change and p-value between each stretch condition and control.

molecule: total RNA

organism: Mus musculus

source_name: Neonatal cardiac myocytes

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy mini kit.
Libraries were prepared according to TruSeq RNA Sample Prep Kit v2. The first step was to purify the poly-A–containing mRNA molecules using poly-T oligo-attached magnetic beads. The mRNA was then fragmented into 120–210 bp pieces by incubating at 94 °C for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random hexamers. Second strand cDNA synthesis utilized DNA Polymerase I and RNase H. These fragments then went through an end repair process to blunt the ends. A single “A” base was added to the 3' end of the fragment, and then indexed adapters were ligated to the ends. Each adapter had a 7 bp sequence that was unique to one of the fifteen samples. The products were purified and amplified with PCR. This cDNA was quantified using an Agilent Technologies 2100 Bioanalyzer and then subjected to high-throughput sequencing by Illumina HiSeq 2000.

treatment_protocol: Static, biaxial stretch was applied to PDMS with attached cardiac myocytes for up to 4 hours. Stretch magnitude was 14% in the primary stretch axis and 3.6% in the orthogonal axis.

tag: strain


title: 4h_Long_A


title: Cortex2.CCJ15ANXX.SM2_052318p2_E4

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
scRNA-seq
full-length
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

source_name: Cortex

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Male

tag: age

value: one month

tag: library construction


title: Cortex2.CCJ15ANXX.SM2_052318p2_E5


title: 4h_Trans_C


title: 4h_Trans_B


title: 4h_Trans_A


title: 30m_Long_B


title: Cortex2.CCJ15ANXX.SM2_052318p2_E2


title: Cortex2.CCJ15ANXX.SM2_052318p2_E12


title: Cortex2.CCJ15ANXX.SM2_052318p2_E1


title: 30m_Long_A


title: 30m_Long_C


title: B9_H3K9me3_ChIP

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

description: ChIP

library_source: genomic

data_processing:
Reads were mapped to the mouse genome (mm10) appended with tandem repeat sequences using Bowtie version 1.0.1 allowing up to two mismatches.
Before peaks were called using MACS2, mapped bamfiles were downsampled using Picard tools to match total read counts. BigWig file were generated from MACS2 pileup bedgraph output using UCSC tools.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated from MACS2 pileup bedgraph output using UCSC tools.

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with antibody.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: mouse embryonic stem cells

tag: cell line

tag: antibody

value: Rabbit polyclonal H3K9me3 abcam ab8898


title: E7_WCE

description: Whole Cell Extracts


title: Cortex2.CCJ15ANXX.SM2_052318p2_E11


title: 30m_Trans_C


title: Cortex2.CCJ15ANXX.SM2_052318p2_E10


title: Cortex2.CCJ15ANXX.SM2_052318p2_F2


title: B9_H3K27me3_ChIP

description: ChIP

value: Mouse monoclonal H3K27me3 abcam ab6002


title: Cortex2.CCJ15ANXX.SM2_052318p2_D9


title: Control_C


title: Cortex2.CCJ15ANXX.SM2_052318p2_D8


title: 30m_Trans_B


title: 30m_Trans_A


title: Cortex2.CCJ15ANXX.SM2_052318p2_D7


title: Control_B


title: Cortex2.CCJ15ANXX.SM2_052318p2_D6


title: Cortex2.CCJ15ANXX.SM2_052318p2_D5


title: Control_A


title: MYC-8

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: rRNA depleted RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to dr7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: dr7
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

organism: Danio rerio

source_name: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYC transgenic zebrafish.

growth_protocol: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN and MYC transgenic zebrafish. Tumors were mechanically homogenized and EGFP+ cells were sorted directly into Trizol-LS

extract_protocol:
Sorted EGFP+ cells were sorted, then total RNA was extracted with Trizol-LS.
Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

value: EGFP+ neuroblasts


title: MYC-7

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_E3


title: MYC-6

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_D3


title: Cortex2.CCJ15ANXX.SM2_052318p2_D2


title: MYC-5

description: rRNA depleted RNA


title: MYC-3

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_D11


title: MYC-2

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_D12


title: MYC-1

description: rRNA depleted RNA


title: MYC-4

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_C8


title: MYCN-4

description: rRNA depleted RNA

source_name: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN transgenic zebrafish.


title: Cortex2.CCJ15ANXX.SM2_052318p2_D10


title: MYCN-3

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_C7


title: MYCN-2

description: rRNA depleted RNA


title: Cortex2.CCJ15ANXX.SM2_052318p2_C9


title: Cortex2.CCJ15ANXX.SM2_052318p2_D4


title: Cortex2.CCJ15ANXX.SM2_052318p2_C3


title: Cortex2.CCJ15ANXX.SM2_052318p2_C5


title: Cortex2.CCJ15ANXX.SM2_052318p2_C6


title: Cortex2.CCJ15ANXX.SM2_052318p2_C4


title: Cortex2.CCJ15ANXX.SM2_052318p2_C2


title: Cortex2.CCJ15ANXX.SM2_052318p2_C1


title: Cortex2.CCJ15ANXX.SM2_052318p2_C12


title: R39_07

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Sample collection protocol: Cryopreserved mononuclear cells were thawed and rested for 1 hour at 37℃. Cell types were pre-enriched using MagniSort® CD19 Positive Selection followed by flow sorting. Fc receptors on all cells were blocked using human IgG, followed by staining with panels outlined in Table 1 and separation on BD Influx sorter. A dump channel consisting of viability dye and antibodies to CD14, CD16, and CD3 was used to exclude unwanted cell types

data_processing:
Libraries were sequenced on the Illumina Miseq platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Processing and analysis of the V(D)J sequencing reads of ASCs was done using migec and MiXCR as described in (Bolotin et al., Nature Methods, 2015) but with some changes. Briefly, ‘migec Histogram’ was used as described but omitting the ‘--only-first-read’ command. the recommended MIG group size thresholding from this was used to select MIG groups with sufficient oversequencing to allow efficient error correction in the subsequent ‘migec Assemblebatch’ process and ‘--only-first-read’was again omitted from ‘migec Assemblebatch’. Oversequencing thresholds used ranged from 3-16 with the majority (27/30) being ≥4. The ‘kaligner’ alignment algorithm was used in ‘mixcr align’ to map reads to the ‘VTranscipt’ feature as recommended for full length VDJ data.
Genome_build: GRCm38
Supplementary_files_format_and_content: MiXCR file: The file is the default clonotype output of the MiXCR software (please refer to https://mixcr.readthedocs.io/en/master/ for detailed information). The file is tab delimited and contains the following categories: cloneId, cloneCount, cloneFraction, clonalSequence, quenceQuality, allVHitsWithScore, allDHitsWithScore, allJHitsWithScore, allCHitsWithScore, allVAlignments, allDAlignments, allJAlignments, allCAlignments, nSeqFR1, minQualFR1, nSeqCDR1, minQualCDR1, nSeqFR2 minQualFR2, nSeqCDR2, minQualCDR2, nSeqFR3, minQualFR3, nSeqCDR3, minQualCDR3, nSeqFR4, minQualFR4, aaSeqFR1, aaSeqCDR1, aaSeqFR2, aaSeqCDR2, aaSeqFR3, aaSeqCDR3, aaSeqFR4, refPoints

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA was isolated from circulating plasma cells (CD19+IgD-CD27+CD71+CD38+CD20- cells) sorted into and stored in RNAlater.
IGH VDJ-RNAseq was performed using a modified version of Turchaninova et al. (2016) - see methods

tag: tissue

value: Blood

tag: adjuvant

value: GLA-SE


title: R39_00


title: R40_07


title: R37_07


title: R37_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_C11


title: R36_07


title: Cortex2.CCJ15ANXX.SM2_052318p2_D1


title: Cortex2.CCJ15ANXX.SM2_052318p2_B9


title: R36_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_B8


title: R35_07


title: MYCN-1

description: rRNA depleted RNA


title: R35_00


title: R32_07


title: Cortex2.CCJ15ANXX.SM2_052318p2_B6


title: R40_00


title: R31_07


title: Cortex2.CCJ15ANXX.SM2_052318p2_B5


title: R32_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_B4


title: Cortex2.CCJ15ANXX.SM2_052318p2_B3


title: R10_07

value: Alum


title: Cortex2.CCJ15ANXX.SM2_052318p2_B7


title: R31_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_B1


title: R09_07


title: R10_00


title: R09_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_B12


title: Cortex2.CCJ15ANXX.SM2_052318p2_B10


title: Cortex2.CCJ15ANXX.SM2_052318p2_B11


title: R08_07


title: Cortex2.CCJ15ANXX.SM2_052318p2_A9


title: Cortex2.CCJ15ANXX.SM2_052318p2_C10


title: R05_07


title: Cortex2.CCJ15ANXX.SM2_052318p2_A8


title: Cortex2.CCJ15ANXX.SM2_052318p2_A7


title: R05_00


title: Cortex2.CCJ15ANXX.SM2_052318p2_A5


title: Cortex2.CCJ15ANXX.SM2_052318p2_A6


title: Cortex2.CCJ15ANXX.SM2_052318p2_A4


title: Cortex2.CCJ15ANXX.SM2_052318p2_B2


title: amplicon.ET01.CALR

city: New York

first: Kyu-Tae

last: Kim

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
10x data was processed using Cell Ranger 2.1.0 using default parameters. RNA reads were aligned to the human or mouse referece genome, or human and mouse reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, and 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data.
Output matrices processed from amplicon data have three columns: barcodes (BC), number of wildtype calls (num.WT.call), and number of mutant calls (num.MUT.call).
Genome_build: GRCh38 or hg19/mm10

source_name: ET01, amplicon, straight

extract_protocol:
Cryopreserved patient samples approved by the Institutional Review Board of Memorial Sloan-Kettering Cancer Center were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx. For the species mixing experiment, human MPL expressing Ba/F3 and UT-7 cell lines were generated by retroviral transduction, after which they were subjected to infection with CALR  variant lentiviral supernatants. Wildtype UT7 cells and mutant Ba/F3 cells were mixed in equal proportions.
The standard 10x Genomics Chromium v.2 protocol was carried out according to manufacturer’s recommendations (10x Genomics, Pleasanton, CA) until after emulsion breakage and recovery of first strand cDNA. If the targeted gene of interest, e.g. SF3B1, was not robustly detected by the standard 10x procedure (i.e. if <60% of the expected cells showed expression) based on a priori knowledge in a similar dataset, a gene-specific primer was spiked into 10x primer mix at 1% of the concentration of the cDNA amplification primers for the initial cDNA PCR step. Then, during the amplification step, the 10x cDNA library underwent an extra cycle of PCR beyond the manufacturer’s recommended number of cycles. After cleanup with SPRIselect, a small portion of the cDNA library, 3 µL (~10% of total) was aliquoted for targeted genotyping, and the remaining cDNA underwent the standard 10x protocol. The cDNA set aside for GoT was amplified for 3 to 4 additional cycles using KAPA HiFi HotStart ReadyMix (KAPABiosystems) and 10x primer mix to provide sufficient material for the enrichment step. After clean-up, locus-specific reverse primers and the generic forward SI-PCR were used to amplify the site of interest of the cDNA template (Supplementary Table 3) using ~10 PCR cycles. The locus-specific reverse primers contain a partial Illumina read 2 handle, a stagger to increase the complexity of the library for optimal sequencing and a gene specific region to allow specific priming. The SI-PCR oligo (10x) anneals to the partial Illumina read 1 sequence at the 3’ end of the molecule, preserving the cell barcode (CB) and UMI. After the initial amplification and SPRI purification to remove unincorporated primers, a second PCR was performed with a generic forward PCR primer (P5_generic) to retain the CB and UMI together with an RPI-x primer (Illumina) to complete the P7 end of the library and add a sample index. The targeted amplicon library was subsequently spiked into the remainder of the 10x library to be sequenced together on a HiSeq 2500 or sequenced separately on MiSeq with v3 chemistry (Illumina). The cycle settings were as follows: 26 cycles for read 1, 98 or 130 cycles for read 2, and 8 cycles for sample index.

tag: source

value: BMMC

tag: targeted mutation

tag: vaf (targeted exon sequencing)

value: 15% (source:CD34+ cells)

value: Female

tag: diagnosis

value: ET

tag: wbc(k/mcl)

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

tag: bm blast count

tag: bm fibrosis

tag: treatment

value: Aspirin; previously hydroxyurea


title: amplicon.MF05.NFE2

source_name: MF05, amplicon, straight

value: PBMC

value: NFE2 exon3 p.Glu261fs (c.782_785delAGAG)

value: 33% (source:CD34+ cells)

tag: Sex

tag: age

value: Myelofibrotic myeloid neoplasm

value: Indeterminate

value: Procrit; previously hydroxyurea and anagrelide


title: amplicon.ET02.CALR

source_name: ET02, amplicon, straight

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 26% (source:CD34- cells)

value: Male

value: Aspirin


title: Cortex2.CCJ15ANXX.SM2_052318p2_A3

value: one month

tag: strain

tag: library construction


title: Cortex2.CCJ15ANXX.SM2_052318p2_A2


title: Cortex2.CCJ15ANXX.SM2_052318p2_A1


title: Oxy_MNase-seq_naked_nomethylDNA

first: Leslie

last: Beh

state: NY

department: Biochemistry & Molecular Biophysics

institute: Columbia University

description: Biological replicate A

data_processing:
All Illumina sequencing data were quality trimmed (minimum quality score = 20) and length-filtered (minimum read length = 40 nt) using Galaxy. MNase-seq and 6mA IP-seq reads were mapped to the Oxytricha trifallax JRB310 (August 2013 build) macronuclear reference genome using Bowtie 2 with default settings, while poly(A)+ RNA-seq and TSS-seq reads were mapped using TopHat2 with August 2013 Oxytricha gene models.
Reads from all biological replicates from each dataset were merged before downstream processing. The per-basepair coverage of Oxytricha MNase-seq read pair centers (termed “nucleosome occupancy”) and full 6mA IP-seq reads were respectively computed across the genome.  Subsequently, the per-basepair coverage values were normalized by the average coverage within each chromosome to account for differences in DNA copy number (and hence, read depth) between Oxytricha chromosomes. The per-bp coverage values were then smoothed using a Gaussian filter of standard deviation = 15 . For RNA-seq data, the number of reads per kilobase of chromosome per million mapped reads (RPKM) was calculated for each chromosome without normalization by DNA copy number since there is no known correlation between Oxytricha DNA and transcript levels. Oxytricha TSS-seq data were processed using CAGEr; with clusterCTSS parameters (threshold = 1.6, thresholdIsTpm = TRUE, nrPassThreshold = 1, method = "paraclu", removeSingletons = TRUE, keepSingletonsAbove = 5). Only TSSs with tags per million counts > 0.1 were used for downstream analysis. All processed data files (.txt) format were generated using these normalization procedures.
Genome_build: Oxytricha trifallax JRB310 macronuclear genome (August 2013 build)
SMRT-seq data were processed with SMRTPipe v1.87.139483 in the SMRT Analysis 2.3.0 environment using, in order, the P_Fetch, P_Filter (with minLength = 50, minSubreadLength = 50, readScore = 0.75, and artifact = -1000), P_FilterReports, P_Mapping (with gff2Bed = True, pulsemetrics = DeletionQV, IPD, InsertionQV, PulseWidth, QualityValue, MergeQV, SubstitutionQV, DeletionTag, and loadPulseOpts = byread), P_MappingReports, P_GenomicConsensus (with algorithm = quiver, outputConsensus = True, and enableMapQVFilter = True), P_ConsensusReports, and P_ModificationDetection (with identifyModifcations = True, enableMapQVFilter = False, and mapQvThreshold = 10) modules. All other parameters were set to the default. Tetrahymena SMRT-seq reads were mapped to the June 2014 reference genome build.
Genomic coordinates of all epigenetic modifications are listed in "L920_allminus_020318_m6A_modifications.gff", "L920_allplus_012918_m6A_modifications.gff","Tth_PacBio_modifications_all_021716.gff". Only "m6A" calls were used for downstream analysis.
Genome_build: SMRT-seq - Tetrahymena thermophila SB210 macronuclear genome (June 2014 build).

organism: Oxytricha trifallax

source_name: PCR-Amplified genomic DNA

extract_protocol:
Naked MNase-digested DNA. MNase digest protocol: Native (methylated) or PCR-amplified (no methyl) gDNA was digested with MNase to approximately mononucleosome-sized fragments. Note that naked DNA was used: no histones were present. Mononucleosome-sized DNA fragments were gel-purified using a QIAquick gel extraction kit (QIAGEN) for subsequent paired-end sequencing on an Illumina HiSeq 2500 according to manufacturer’s instructions.
Naked gDNA-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

tag: cell type

value: in vitro

tag: presence of n6-methyladenine on dna template

value: No

tag: source of histones used for chromatin assembly

tag: amount of histones used for chromatin assembly

tag: extent of mnase digestion


title: Oxy_WT_MNase-seq_naked_DNA

description: Biological replicate A,B,C

source_name: Native genomic DNA

value: Yes


title: Oxy_Mut_MNase-seq_naked_DNA

description: Biological replicate A,B,C


title: Oxy_MNase-seq_naked_methylDNA

description: Biological replicate A


title: Oxy_Mut_MNase-seq_invivo_HeavyDigest_replAB

description: Biological replicate A,B,C

source_name: Purified nuclei

extract_protocol:
Oxytricha in vivo MNase-seq protocol: Vegetative Oxytricha cells were fixed in 1% (w/v) formaldehyde for 10 min at room temperature with gentle shaking, and then quenched with 125 mM glycine. Macronuclei were subsequently isolated by sucrose gradient centrifugation from fixed cells as previously described25. Purified nuclei were pelleted by centrifugation at 4000 x g, washed in 50 ml TMS buffer (10 mM Tris pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.25 M sucrose), resuspended in a final volume of 300 μl, and equilibriated at 37oC for 5 min. Chromatin was then digested with MNase (New England BioLabs) at a final concentration of 15.7 Kunitz Units / μl at 37oC for 1 min 15 sec, 3 min, 5 min, 7 min 30sec, 10 min 30 sec, and 15 min respectively. Reactions were stopped by adding 1/2 volume of PK buffer (300 mM NaCl, 30 mM Tris pH 8, 75 mM EDTA pH 8, 1.5% (w/v) SDS, 0.5 mg/ml Proteinase K). Each sample was incubated at 65oC overnight to reverse crosslinks and deproteinate samples. Subsequently, nucleosomal DNA was purified through phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.  Each sample was loaded on a 2% agarose-TAE gel to check the extent of MNase digestion. The sample exhibiting ~80% mononucleosomal species was selected for MNase-seq analysis. Mononucleosome-sized DNA was gel-purified using a QIAquick gel extraction kit (QIAGEN) for subsequent paired-end sequencing on an Illumina HiSeq 2500 according to manufacturer’s instructions.
MNase-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

value: Vegetative

value: Oxytricha trifallax

value: Heavy


title: R08_00

tag: tissue

value: Blood

tag: adjuvant

value: Alum


title: Cortex2.CCJ15ANXX.SM2_052318p2_A11


title: Cortex2.CCJ15ANXX.SM2_052318p2_A10


title: Oxy_Mut_MNase-seq_invivo_LightDigest_replAB

description: Biological replicate A,B,C

value: Light


title: Oxy_WT_MNase-seq_invivo_HeavyDigest_replAB

description: Biological replicate A,B,C


title: Cortex2.CCJ15ANXX.SM2_052318p1_H8


title: Oxy_WT_MNase-seq_invivo_MediumDigest_replAB

description: Biological replicate A,B,C

value: Medium


title: Cortex2.CCJ15ANXX.SM2_052318p1_H7


title: Cortex2.CCJ15ANXX.SM2_052318p1_H9


title: Oxy_MNase-seq_invivo_replB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_H6


title: Oxy_WT_MNase-seq_invivo_LightDigest_replAB

description: Biological replicate A,B,C


title: Oxy_MNase-seq_invivo_replA

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_H4


title: Cortex2.CCJ15ANXX.SM2_052318p1_H5


title: Cortex2.CCJ15ANXX.SM2_052318p2_A12


title: Cortex2.CCJ15ANXX.SM2_052318p1_H2


title: Oxy_Mutant_polyA_RNAseq_replC

description:
Biological replicate C
L945_DESeq2_WTvsMut.txt

source_name: Whole cells

extract_protocol:
Oxytricha polyA+ RNAseq protocol: Vegetative Oxytricha cells were lysed in TRIzol reagent (Thermo Fisher Scientific) for total RNA isolation according to manufacturer’s instructions. Poly(A)+ RNA was then purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). The Oxytricha poly(A)+ RNA was prepared for RNA-seq using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina).
polyA+ RNAseq (Single-read sequencing); ScriptSeq v2 RNA-Seq library preparation protocol


title: Oxy_Mutant_polyA_RNAseq_replB

description:
Biological replicate B
L945_DESeq2_WTvsMut.txt


title: Oxy_WT_polyA_RNAseq_replC


title: Oxy_Mutant_polyA_RNAseq_replA

description:
Biological replicate A
L945_DESeq2_WTvsMut.txt


title: Cortex2.CCJ15ANXX.SM2_052318p1_H3


title: Oxy_WT_polyA_RNAseq_replB


title: Cortex2.CCJ15ANXX.SM2_052318p1_H11


title: Oxy_MNase-seq_invitroNap1_miACF_miATP_methylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B

source_name: in vitro reconstituted chromatin

growth_protocol: Vegetative Oxytricha trifallax strain JRB310 was cultured at a density of 1.5 × 107 cells/L to 2.5 × 107 cells/L in Pringsheim media (0.11 mM Na2HPO4, 0.08 mM MgSO4, 0.85 mM Ca(NO3)2, 0.35 mM KCl, pH 7.0) and fed daily with Chlamydomonas reinhardtii. Cells were filtered through cheesecloth to remove debris and collected on a 10 μm Nitex mesh for subsequent experiments.  Either whole cells or nuclei were used for genomic DNA purification. To obtain native genomic DNA (containing methylation), macronuclei were purified from vegetative Oxytricha trifallax strain JRB310 using a Nucleospin Tissue kit (Macherey-Nagel). gDNA was processed further by sucrose gradient ultracentrifugation in preparation for chromatin assembly, but not for 6mA IP-seq and MNase digest of naked DNA. Ultracentrifugation protocol: gDNA was loaded on a 15%-40% linear sucrose gradient and centrifuged in a SW40Ti rotor (Beckman Coulter) at 160,070 x g for 22.5hr at 20oC. Sucrose solutions were in 1 M NaCl, 20 mM Tris pH 7.5, 5 mM EDTA. Individual fractions from the sucrose gradient were analyzed on 0.9% agarose-TAE gels. Fractions containing high molecular weight DNA that migrated at the mobility limit were discarded as such DNA species were found to interfere with downstream chromatin assembly. All other fractions were pooled, ethanol precipitated, and adjusted to 0.5mg/mL DNA. To obtain genomic DNA lacking methylation for in vitro reconstitution, 98 chromosomes were individually PCR-amplified and purified using a MinElute PCR purification kit (QIAGEN), then mixed in equimolar ratios to obtain “mini-genome” DNA. The sample was concentrated by ethanol precipitation and adjusted to a final concentration of ~1.6 mg/ml. Xenopus histones were recombinantly expressed and purified, while Oxytricha histones were acid-extracted from purified nuclei. Xenopus or Oxytricha histones were combined in equimolar amounts in 6 M guanidine hydrochloride, 20 mM Tris pH 7.5 and the final concentration was adjusted to 1 mg/mL. The solution was dialyzed against 2 M NaCl, 10 mM Tris, 1 mM EDTA, and the octamers were purified from the tetramers and dimer species using size-exclusion chromatography on a Superdex 200 10/300 column (GE Healthcare Life Sciences). The purity of the fractions was analyzed by SDS-PAGE and pure fractions were combined, concentrated and stored in 50% glycerol at -20°C.

extract_protocol:
Oxytricha in vitro MNase-seq protocol: Chromatin was reconstituted in vitro through salt gradient dialysis or Nap1 histone chaperone (+/- ACF +/- ATP). Assembled chromatin was adjusted to 50 mM Tris pH 7.9, 5 mM CaCl2 and digested with a titration of MNase (New England BioLabs) to mainly mononucleosomal DNA. Mononucleosome-sized DNA was gel-purified and used for paired-end sequencing on an Illumina HiSeq 2500, according to manufacturer’s instructions.
MNase-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

value: in vitro (+Nap1 -ACF -ATP)

value: Xenopus laevis


title: Oxy_WT_polyA_RNAseq_replA


title: Cortex2.CCJ15ANXX.SM2_052318p1_G9


title: Cortex2.CCJ15ANXX.SM2_052318p1_G8


title: Oxy_MNase-seq_invitroNap1_miACF_miATP_methylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroNap1_miACF_miATP_nomethylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_G6


title: Oxy_MNase-seq_invitroNap1_miACF_miATP_nomethylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroNap1_plACF_miATP_methylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B

value: in vitro (+Nap1 +ACF -ATP)


title: Cortex2.CCJ15ANXX.SM2_052318p1_G4


title: Cortex2.CCJ15ANXX.SM2_052318p1_G3


title: Oxy_MNase-seq_invitroNap1_plACF_miATP_nomethylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroNap1_plACF_miATP_methylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroNap1_plACF_miATP_nomethylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_H12


title: Cortex2.CCJ15ANXX.SM2_052318p1_G2


title: Cortex2.CCJ15ANXX.SM2_052318p1_H1


title: Oxy_MNase-seq_invitroNap1_plACF_plATP_methylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B

value: in vitro (+Nap1 +ACF +ATP)


title: Cortex2.CCJ15ANXX.SM2_052318p1_G11

value: Male


title: Cortex2.CCJ15ANXX.SM2_052318p1_G12


title: Oxy_MNase-seq_invitroNap1_plACF_plATP_methylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_G10


title: Cortex2.CCJ15ANXX.SM2_052318p1_H10


title: Cortex2.CCJ15ANXX.SM2_052318p1_G1


title: Oxy_MNase-seq_invitroNap1_miACF_plATP_methylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B

value: in vitro (+Nap1 -ACF +ATP)


title: Oxy_MNase-seq_invitroNap1_plACF_plATP_nomethylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_F8

value: one month


title: Cortex2.CCJ15ANXX.SM2_052318p1_F9


title: Oxy_MNase-seq_invitroNap1_miACF_plATP_methylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroNap1_miACF_plATP_nomethylDNA_XenOctamers_HeavyDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_G7


title: Oxy_MNase-seq_invitroNap1_miACF_plATP_nomethylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_G5


title: Cortex2.CCJ15ANXX.SM2_052318p1_F5


title: Oxy_MNase-seq_invitroSalt_methylDNA_XenOctamers_HighOct_HeavyDigest_replAB

description: Biological replicate A,B

value: in vitro (salt dialysis)

value: High


title: Oxy_MNase-seq_invitroSalt_methylDNA_XenOctamers_LowOct_LightDigest_replAB 2

description: Biological replicate A,B

value: Yes


title: Cortex2.CCJ15ANXX.SM2_052318p1_F4


title: Oxy_MNase-seq_invitroSalt_methylDNA_XenOctamers_LowOct_LightDigest_replAB 1

description: Biological replicate A,B

value: Low


title: Cortex2.CCJ15ANXX.SM2_052318p1_F3


title: Oxy_MNase-seq_invitroSalt_methylDNA_OxyOctamers_LowOct_LightDigest_replAB 2

description: Biological replicate A,B

value: Oxytricha trifallax


title: Oxy_MNase-seq_invitroSalt_methylDNA_XenOctamers_LowOct_HeavyDigest_replAB

description: Biological replicate A,B

value: Heavy


title: Oxy_MNase-seq_invitroNap1_plACF_plATP_nomethylDNA_XenOctamers_LightDigest_ReplAB

description: Biological replicate A,B

value: No


title: Cortex2.CCJ15ANXX.SM2_052318p1_F1


title: Oxy_MNase-seq_invitroSalt_methylDNA_OxyOctamers_HighOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroSalt_methylDNA_OxyOctamers_LowOct_LightDigest_replAB 1

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_F11


title: Cortex2.CCJ15ANXX.SM2_052318p1_F10


title: Oxy_MNase-seq_invitroSalt_methylDNA_OxyOctamers_LowOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_F7


title: Cortex2.CCJ15ANXX.SM2_052318p1_E9


title: Cortex2.CCJ15ANXX.SM2_052318p1_F2


title: Cortex2.CCJ15ANXX.SM2_052318p1_F6


title: Cortex2.CCJ15ANXX.SM2_052318p1_E8


title: Oxy_Mut_MNase-seq_invivo_MediumDigest_replAB

description: Biological replicate A,B,C

value: Vegetative


title: Cortex2.CCJ15ANXX.SM2_052318p1_E7


title: Cortex2.CCJ15ANXX.SM2_052318p1_E6


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_XenOctamers_LowOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_E5


title: Cortex2.CCJ15ANXX.SM2_052318p1_E4


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_OxyOctamers_HighOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_OxyOctamers_LowOct_LightDigest_replAB 1

description: Biological replicate A,B

value: Light


title: Cortex2.CCJ15ANXX.SM2_052318p1_E3


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_XenOctamers_LowOct_LightDigest_replAB 1

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_E1


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_OxyOctamers_LowOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_XenOctamers_LowOct_LightDigest_replAB 2

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_E12


title: Cortex2.CCJ15ANXX.SM2_052318p1_F12


title: Cortex2.CCJ15ANXX.SM2_052318p1_E11


title: Cortex2.CCJ15ANXX.SM2_052318p1_E10


title: Cortex2.CCJ15ANXX.SM2_052318p1_D9


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_XenOctamers_HighOct_HeavyDigest_replAB

description: Biological replicate A,B


title: Cortex2.CCJ15ANXX.SM2_052318p1_D8


title: Cortex2.CCJ15ANXX.SM2_052318p1_E2


title: RA CD4Nv 61 (excluded from processed data)

type: genomic

city: San Francisco

first: Lindsey

middle: A.

last: Criswell

address: 513 Parnassus Avenue

institute: UCSF

description: RA CD4Nv sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the HiScan Reader under standard recommended Illumina scanner settings.

data_processing:
We processed the raw IDAT files (for each of the four cell sub-types separately) according to a normalization pipeline by Lenhe et al. (2015) using the “minfi” R package as follows. We removed 65 SNP markers and applied the Illumina background correction to all intensity values, while analyzing probes coming from autosomal and non-autosomal chromosomes separately. We set the threshold for detection p-value of intensity values to be 10−16; probes with p-values higher than this threshold were treated as missing values, and samples with call rate < 95% and probes with call rate < 90% were excluded. We then performed a quantile normalization of the methylation intensity levels, subdivided by probe type, probe sub-type, and color channel, and imputed missing values using the "impute" R package (impute.knn). Finally, we calculated Beta-normalized methylation levels based on the normalized intensity levels (according to the recommendation by Illumina) and discarded probes from non-autosomal chromosomes and polymorphic probes according to Chen et al. (2013), we well as a small batch of only 4 individuals. The final numbers of processed samples are n=89, n=88, n=90, and n=86 for the CD4+ memory cells, CD4+ naive cells, CD14+ monocytes, and CD19+ B cells, respectively.
Average Beta

label: Cy5 and Cy3

source_name: genomic DNA from peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Whole blood was collected from each subject into four 10‐ml EDTA collection tubes. A Ficoll‐Paque density gradient was used for isolating PBMCs and for staining with conjugated monoclonal antibodies against CD45 (fluorescein isothiocyanate conjugated), CD19 (phycoerythrin [PE] conjugated), CD45RA (PE–Cy7 conjugated) (all from BD PharMingen), CD3 (Brilliant Violet 421 conjugated), CD4 (CF594 conjugated) (both from BD Horizon), CD14 (allophycocyanin [APC] conjugated) (BD Biosciences), and CD27 (APC–eFlour 780 conjugated) (ebioscience). Cells were stored overnight in a buffer at 4°C and then sorted the following day using a BD Biosciences FACSAria fluorescence‐activated cell sorter (FACS). The populations that were gated for sorting following exclusion of debris and doublets are monocytes (CD45+CD14+), B cells (CD45+CD14 −CD3 −CD19+), naive CD4+ T cells (CD45+CD14 −CD19 −CD3+CD4+CD27+CD45RA+), and memory CD4+ T cells (CD45+CD14 −CD19 −CD3+CD4+CD45RA−). Purity checks and cell counts were performed following sorting, and then cells were stored frozen as a pellet at −80°C. The cells were extracted using Gentra Puregene Kit and quantified with Nanodrop.

tag: ethnicity

value: Caucasian

tag: subjecttype

tag: gender

value: Female

tag: ageatblooddraw

tag: smokerever


title: RA CD14 63 (excluded from processed data)

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D7


title: RA CD14 62 (excluded from processed data)

description: RA CD14 sample


title: Oxy_MNase-seq_invitroSalt_nomethylDNA_OxyOctamers_LowOct_LightDigest_replAB 2

description: Biological replicate A,B


title: RA CD4Mem 62 (excluded from processed data)

description: RA CD4Mem sample


title: RA CD4Mem 63 (excluded from processed data)

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D6


title: RA CD4Nv 59 (excluded from processed data)

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D5


title: RA CD19 60 (excluded from processed data)

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D4


title: RA CD14 61 (excluded from processed data)

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D2


title: RA CD4Mem 61 (excluded from processed data)

description: RA CD4Mem sample


title: RA CD14 60 (excluded from processed data)

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D1


title: RA CD4Mem 60 (excluded from processed data)

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D12


title: RA CD4Nv 58 (excluded from processed data)

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D11


title: Cortex2.CCJ15ANXX.SM2_052318p1_D10


title: Cortex2.CCJ15ANXX.SM2_052318p1_C9


title: control CD4Mem 31

description: control CD4Mem sample


title: RA CD19 58 (excluded from processed data)

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C5


title: control CD4Mem 30

description: control CD4Mem sample


title: control CD4Nv 31

description: control CD4Nv sample


title: control CD14 31

description: control CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C3


title: Cortex2.CCJ15ANXX.SM2_052318p1_C8


title: Cortex2.CCJ15ANXX.SM2_052318p1_C7


title: control CD14 30

description: control CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_D3


title: control CD19 30

description: control CD19 sample


title: control CD14 29

description: control CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C6


title: Cortex2.CCJ15ANXX.SM2_052318p1_C4


title: RA CD19 59 (excluded from processed data)

description: RA CD19 sample


title: control CD4Nv 30

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C2


title: Cortex2.CCJ15ANXX.SM2_052318p1_C1


title: Cortex2.CCJ15ANXX.SM2_052318p1_C12


title: control CD4Mem 29

description: control CD4Mem sample


title: RA CD4Nv 57

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C11


title: RA CD4Nv 56

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_C10


title: RA CD4Mem 59

description: RA CD4Mem sample


title: RA CD4Nv 55

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B9


title: Cortex2.CCJ15ANXX.SM2_052318p1_B8


title: control CD19 29

description: control CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B5


title: RA CD19 56

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B4


title: RA CD4Nv 54

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B6


title: RA CD19 57

description: RA CD19 sample


title: RA CD4Nv 53

description: RA CD4Nv sample


title: control CD4Nv 29

description: control CD4Nv sample


title: control CD19 28

description: control CD19 sample


title: control CD4Mem 28

description: control CD4Mem sample


title: RA CD19 61 (excluded from processed data)

description: RA CD19 sample


title: RA CD14 59

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B12


title: control CD14 28

description: control CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_B3


title: Cortex2.CCJ15ANXX.SM2_052318p1_B1


title: Cortex2.CCJ15ANXX.SM2_052318p1_B2


title: Cortex2.CCJ15ANXX.SM2_052318p1_B11


title: Cortex2.CCJ15ANXX.SM2_052318p1_B10


title: control CD19 27

description: control CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A9


title: control CD4Nv 28

description: control CD4Nv sample


title: control CD4Mem 27

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A8


title: Cortex2.CCJ15ANXX.SM2_052318p1_B7


title: Cortex2.CCJ15ANXX.SM2_052318p1_A7


title: control CD14 26

description: control CD14 sample


title: control CD19 26

description: control CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A4


title: Cortex2.CCJ15ANXX.SM2_052318p1_A6


title: Cortex2.CCJ15ANXX.SM2_052318p1_A3


title: Cortex2.CCJ15ANXX.SM2_052318p1_A2


title: control CD4Nv 27

description: control CD4Nv sample


title: RA CD14 58

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A1


title: RA CD4Mem 58

description: RA CD4Mem sample


title: RA CD14 57

description: RA CD14 sample


title: RA CD19 54

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A12


title: Cortex2.CCJ15ANXX.SM2_052318p1_A11


title: Cortex2.CCJ15ANXX.SM2_052318p1_A10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H9

description:
scRNA-seq
3'-end
cortex_mm10_count_matrix.mtx, cortex_mm10_gene.tsv, cortex_mm10_cell.tsv

value: sci-RNA-seq


title: RA CD14 56

description: RA CD14 sample


title: RA CD4Mem 57

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H8


title: RA CD19 53

description: RA CD19 sample


title: RA CD4Mem 56

description: RA CD4Mem sample


title: RA CD14 55

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H6


title: RA CD14 54

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H5


title: control CD4Mem 26

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.SM2_052318p1_A5


title: RA CD19 55

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H3


title: RA CD19 52

description: RA CD19 sample


title: RA CD4Nv 52

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H4


title: RA CD19 51

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H10


title: RA CD4Nv 51

description: RA CD4Nv sample


title: RA CD14 52

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G9


title: RA CD19 50

description: RA CD19 sample


title: RA CD4Mem 54

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_H7


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G7


title: RA CD4Nv 50

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G6


title: RA CD14 51

description: RA CD14 sample


title: RA CD4Mem 53

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G5


title: RA CD19 49

description: RA CD19 sample


title: RA CD4Nv 49

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G4


title: RA CD4Mem 55

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G3


title: RA CD4Mem 52

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G2


title: RA CD14 53

description: RA CD14 sample


title: RA CD14 50

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G12


title: RA CD4Mem 51

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F9


title: RA CD4Nv 47

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F7


title: RA CD19 48

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_G10


title: RA CD4Mem 50

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F3


title: RA CD19 47

description: RA CD19 sample


title: RA CD14 48

description: RA CD14 sample


title: RA CD4Nv 46

description: RA CD4Nv sample


title: RA CD19 46

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F1


title: RA CD4Mem 49

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F12


title: RA CD4Nv 48

description: RA CD4Nv sample


title: RA CD14 49

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F4


title: RA CD4Mem 48

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F11


title: RA CD4Nv 45

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F10


title: RA CD14 47

description: RA CD14 sample


title: RA CD14 46

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E8


title: RA CD4Mem 47

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E7


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_F6


title: RA CD19 45

description: RA CD19 sample


title: RA CD4Mem 46

description: RA CD4Mem sample


title: control CD14 27

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E9


title: RA CD4Nv 60 (excluded from processed data)

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E5


title: RA CD14 45

description: RA CD14 sample


title: RA CD19 44

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E3


title: RA CD19 43

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E1


title: RA CD4Nv 43

description: RA CD4Nv sample


title: RA CD4Nv 42

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_E10


title: RA CD4Nv 44

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D9


title: RA CD4Mem 45

description: RA CD4Mem sample


title: RA CD14 43

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D8


title: RA CD19 42

description: RA CD19 sample


title: RA CD14 42

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D7


title: RA CD4Mem 44

description: RA CD4Mem sample


title: RA CD4Nv 41

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D3


title: RA CD4Mem 43

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D4


title: RA CD4Nv 40

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D2


title: RA CD14 41

description: RA CD14 sample


title: RA CD14 44

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D1


title: RA CD19 40

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_D10


title: RA CD19 39

description: RA CD19 sample


title: RA CD4Mem 42

description: RA CD4Mem sample


title: RA CD4Nv 39

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C9


title: RA CD4Nv 38

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C7


title: RA CD14 40

description: RA CD14 sample


title: RA CD4Nv 37

description: RA CD4Nv sample


title: RA CD19 41

description: RA CD19 sample


title: RA CD4Mem 40

description: RA CD4Mem sample


title: RA CD19 38

description: RA CD19 sample


title: RA CD4Nv 36

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C3


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C5


title: RA CD14 39

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C4


title: RA CD4Mem 39

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C11


title: RA CD19 36

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B8


title: RA CD4Mem 38

description: RA CD4Mem sample


title: RA CD4Mem 37

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B7


title: RA CD14 37

description: RA CD14 sample


title: RA CD4Mem 41

description: RA CD4Mem sample


title: RA CD4Nv 35

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C6


title: control CD14 25

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B5


title: control CD19 25

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B4


title: RA CD19 37

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B2


title: control CD19 24

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B12


title: control CD4Nv 25

description: control CD4Nv sample


title: control CD4Nv 26

description: control CD4Nv sample


title: RA CD14 38

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B11


title: control CD14 24

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B3


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_C10


title: control CD14 23

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_B6


title: control CD19 22

description: control CD19 sample


title: control CD19 23

description: control CD19 sample


title: control CD14 22

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A7


title: control CD4Mem 24

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A5


title: control CD19 21

description: control CD19 sample


title: control CD4Mem 25

description: control CD4Mem sample


title: control CD4Nv 24

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A3


title: RA CD14 36

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A4


title: RA CD19 35

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A2


title: RA CD4Nv 34

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A10


title: RA CD4Nv 33

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H9


title: RA CD4Mem 35

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H7


title: RA CD19 33

description: RA CD19 sample


title: RA CD14 34

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p3_A6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H6


title: RA CD4Mem 34

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H3


title: RA CD19 32 (excluded from processed data)

description: RA CD19 sample


title: RA CD4Nv 32

description: RA CD4Nv sample


title: RA CD4Nv 31

description: RA CD4Nv sample


title: RA CD4Mem 33

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H12


title: RA CD14 35

description: RA CD14 sample


title: RA CD19 34

description: RA CD19 sample


title: RA CD4Mem 32

description: RA CD4Mem sample


title: RA CD4Mem 36

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_H11


title: RA CD14 32

description: RA CD14 sample


title: RA CD19 31

description: RA CD19 sample


title: RA CD14 33

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G7


title: RA CD4Nv 29

description: RA CD4Nv sample


title: RA CD19 30

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G5


title: RA CD14 30

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G4


title: RA CD14 31

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G3


title: RA CD14 29

description: RA CD14 sample


title: RA CD4Nv 28

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G2


title: RA CD4Mem 31

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G12


title: RA CD4Nv 30

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G11


title: RA CD4Nv 27

description: RA CD4Nv sample


title: RA CD4Nv 26

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G10


title: RA CD14 28

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F8


title: RA CD19 28

description: RA CD19 sample


title: RA CD4Mem 30

description: RA CD4Mem sample


title: RA CD4Mem 29

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F7


title: RA CD14 27

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F2


title: RA CD4Nv 25

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F1


title: RA CD4Mem 28

description: RA CD4Mem sample


title: RA CD19 27

description: RA CD19 sample


title: RA CD14 26

description: RA CD14 sample


title: RA CD19 29

description: RA CD19 sample


title: RA CD4Mem 27 (excluded from processed data)

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_G1


title: RA CD14 25

description: RA CD14 sample


title: RA CD19 26

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E9


title: RA CD14 24

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F11


title: RA CD4Mem 26

description: RA CD4Mem sample


title: control CD19 20

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_F3


title: RA CD4Nv 24

description: RA CD4Nv sample


title: control CD4Nv 23

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E4


title: RA CD19 25

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E7


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E3


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E2


title: control CD4Mem 22

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E12


title: control CD4Nv 21

description: control CD4Nv sample


title: control CD4Mem 23

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E5


title: control CD4Mem 21

description: control CD4Mem sample


title: control CD4Nv 22

description: control CD4Nv sample


title: control CD14 21

description: control CD14 sample


title: control CD14 20

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D9


title: control CD19 18

description: control CD19 sample


title: control CD19 19

description: control CD19 sample


title: control CD4Nv 20

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_E6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D6


title: control CD4Mem 20

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D7


title: control CD4Mem 19

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D3


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D1


title: control CD19 16

description: control CD19 sample


title: control CD19 17

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D11


title: control CD14 19

description: control CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_D10


title: control CD4Nv 18

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C8


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C6


title: control CD4Nv 17

description: control CD4Nv sample


title: control CD4Mem 17

description: control CD4Mem sample


title: control CD19 14

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C7


title: control CD14 17

description: control CD14 sample


title: control CD4Mem 18

description: control CD4Mem sample


title: control CD19 13

description: control CD19 sample


title: control CD4Nv 16

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C12


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C3


title: control CD14 16

description: control CD14 sample


title: control CD19 12

description: control CD19 sample


title: control CD4Nv 19

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C10


title: control CD14 18

description: control CD14 sample


title: control CD4Mem 16

description: control CD4Mem sample


title: control CD19 11

description: control CD19 sample


title: control CD19 15

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B8


title: control CD14 15

description: control CD14 sample


title: control CD4Mem 15

description: control CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B9


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B6


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B7


title: control CD4Nv 15

description: control CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B5


title: control CD4Nv 14

description: control CD4Nv sample


title: control CD19 9

description: control CD19 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B3


title: RA CD4Mem 25

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B2


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B12


title: RA CD4Nv 23

description: RA CD4Nv sample


title: RA CD14 23

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_C11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B11


title: RA CD14 22

description: RA CD14 sample


title: RA CD4Mem 23

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B10


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A8


title: control CD19 10

description: control CD19 sample


title: RA CD14 21

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A9


title: RA CD14 20

description: RA CD14 sample


title: RA CD4Nv 22

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A7


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A5


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A4


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_B4


title: RA CD19 24

description: RA CD19 sample


title: RA CD4Nv 21

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A3


title: RA CD4Mem 21

description: RA CD4Mem sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A2


title: RA CD19 23

description: RA CD19 sample


title: RA CD4Mem 24

description: RA CD4Mem sample


title: RA CD14 19

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A1


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A12


title: RA CD4Nv 20

description: RA CD4Nv sample


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A11


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A10


title: Cortex2.CCLBDANXX.68.052318-DroNcSeq_3B

value: DroNc-seq


title: RA CD14 18

description: RA CD14 sample


title: Cortex2.CCKVLANXX.10X_3D

value: 10x Chromium (v2)


title: RA CD4Nv 19

description: RA CD4Nv sample


title: RA CD4Mem 22

description: RA CD4Mem sample


title: RA CD19 21

description: RA CD19 sample


title: RA CD14 17

description: RA CD14 sample


title: Cortex2.CCKVLANXX.10X_3B

value: Male


title: RA CD19 22

description: RA CD19 sample


title: Cortex2.CCKVLANXX.10X_3C


title: RA CD4Mem 20

description: RA CD4Mem sample


title: RA CD14 16

description: RA CD14 sample


title: RA CD4Mem 19

description: RA CD4Mem sample


title: Cortex2.CCKVLANXX.052318-DroNcSeq_3B


title: Cortex2.CCKVLANXX.10X_3A


title: RA CD19 19

description: RA CD19 sample


title: Cortex2.CCLBDANXX.68.052318-DroNcSeq_3A


title: RA CD19 20

description: RA CD19 sample


title: Cortex2.CCKVLANXX.052318-DroNcSeq_3A


title: Cortex2.CCJ15ANXX.052318-SciSeq-p2_A6


title: Cortex2.CCJ15ANXX.10X_3C


title: RA CD14 15

description: RA CD14 sample


title: Cortex2.CCJ15ANXX.10X_3B


title: RA CD4Nv 18

description: RA CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H9


title: RA CD19 17

description: RA CD19 sample


title: RA CD14 14

description: RA CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H8


title: RA CD4Mem 18

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H7


title: RA CD14 13

description: RA CD14 sample


title: RA CD4Nv 17

description: RA CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H6


title: Cortex1.CCKVLANXX.SM2_042518p4_H5


title: RA CD4Nv 16

description: RA CD4Nv sample


title: RA CD19 16

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H3


title: Cortex1.CCKVLANXX.SM2_042518p4_H4


title: Cortex2.CCJ15ANXX.10X_3D


title: RA CD19 18

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H2


title: Cortex1.CCKVLANXX.SM2_042518p4_H1


title: RA CD4Mem 16

description: RA CD4Mem sample


title: RA CD4Mem 17

description: RA CD4Mem sample


title: RA CD14 12

description: RA CD14 sample


title: RA CD14 11

description: RA CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H12


title: RA CD19 15

description: RA CD19 sample


title: Cortex2.CCJ15ANXX.10X_3A


title: RA CD4Mem 15

description: RA CD4Mem sample


title: RA CD4Nv 15

description: RA CD4Nv sample


title: RA CD14 10

description: RA CD14 sample


title: RA CD4Mem 14

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H10


title: kidney organoid, single cells, Day14rep1

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

description: single cell

data_processing:
Cellranger analysis pipeline (version 2.2.0) was used to align reads generated to GRCh38 and the subsequent aggregation of generated outputs across all samples.
Quality control and filtering was conducted with Seurat (version 2.3.0) to retain cells with mitochondrial gene content < 5%, total genes expressed between 200 and 7000, as well as number of detected unique molecules < 50,000. Gene expression measurements for retained cells were log-transformed, normalized by total expression per cell, and scaled to 10,000 molecules per cell. We regressed out nonbiological interesting variation in gene expression that is driven by processing batch, number of detected molecules, and mitochondrial gene content. Highly variable genes across the single cells were then identified and principal components (PCs) analysis was conducted. 8 PCs were selected as input for t-Distributed Stochastic Neighbor Embedding (tSNE) for day10, day12, day14 cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix of raw gene counts across all single cells captured from Day10, Day12 and Day14 human pluripotent stem cell-derived kidney organoid. Single cell id in row 1. Corresponding sample type of single cell in row 2. Raw gene count for specific genes in individual single cell from row 3 onwards.

source_name: Human pluripotent stem cells

growth_protocol: Induction of kidney organoids from human pluripotent stem cells (hPSCs) hPSCs were dissociated into single cells with Accutase (STEMCELL Technologies), and plated onto Matrigel (BD Biosciences)-coated plates at a density of ~15,000 to ~24,000 cells/cm2. The plated cells were cultured in TeSR supplemented with 10 μM Y-27632 (Sigma) for 24 hours, followed by another 48-72 hours culture in TeSR to reach a confluence of 50-60%. To induce primitive streak, cells were cultured in basic differentiation medium (Advanced RPMI 1640, 1x L-GlutaMAX, 1 x NEAA) (Life Technologies) supplemented with 10 μM CHIR99021 (Sigma) for 4 days with daily media change. Next, to induce nephrogenic intermediate mesoderm, cells were cultured in basic differentiation medium, without any growth factor for 3 days with daily media change. Subsequently, to induce nephron progenitors, cells were cultured in basic differentiation media supplemented with 50 ng/mL FGF9 (Peprotech) and 3 μM CHIR99021 with daily media change for 2 days. From day 10 of differentiation onward, cells were cultured in basic differentiation media supplemented with 50 ng/mL FGF9 until day 20. On day 14 of differentiation, cells were pulsed with 1 μM CHIR99021 (patterning CHIR) for 24 hours. From day 20 of differentiation onward, basic differentiation medium was used for organoid culture.

extract_protocol:
Day 10, Day 12 and Day 14 kidney organoids were dissociated into single cells with accutase treatment, followed by passing through a 40 μm filter thrice to remove cell clumps. Dissociated cells were subsequently stained with trypan blue and found to have at least 80% viability.
A minimum of 7000 dissociated cells were loaded per well for single cell RNA-seq library preparation with the Chromium Single Cell 3’ Gene Expression Solution according to the manufacturer’s recommendations. Libraries generated were sequenced on Illumina HiSeq 4000 platform.

treatment_protocol: To generate 3D kidney organoids, day 10-12 differentiating cells were dissociated into single cells by Accutase. 2.5-5 x 104 cells (per well) were aggregated in basic differentiation media supplemented with 50 ng/mL FGF9 and 10 μM Y-27632 using round bottom ultra-low attachment 96-well plates (Corning). 24 hours later, Y-27632 was removed. To generate kidney organoids with a high glomerulus-to-tubule ratio, no patterning CHIR was needed. To generate kidney organoids with a high tubule-to-glomerulus ratio, 10 days patterning CHIR was applied from day 14 to day 24 of differentiation. 3D kidney organoids were transferred onto the upper chamber of transwell (Corning) for liquid-air interface culture on day 16-18 of differentiation (5-7 days after aggregation), with daily medium change at the bottom chamber. Taking H9 ESCs as an example, we seeded ~21,000 cells per cm2, and started differentiation when the cells reached 50-60% confluence. On day 10-12 of differentiation, we dissociated the differentiation culture into single cells, and re-aggregated into cell clusters with a gradient of cell numbers (5,000-75,000 cells per organoid). One million starting human ESCs could give rise to approximately 3,500 kidney organoids that were aggregated with 35,000 cells per organoid. hPSC-derived 3D kidney organoids were implanted beneath the renal capsule of left kidney of NSG mice for easier manipulation. After 2-4 weeks mice were sacrificed, and implants were isolated for further analysis.

value: Human pluripotent stem cells

value: Kidney organoid

tag: developmental stage


title: kidney organoid, single cells, Day14rep2

description: single cell


title: kidney organoid, single cells, Day10rep2

description: single cell


title: kidney organoid, single cells, Day12

description: single cell


title: Cortex1.CCKVLANXX.SM2_042518p4_G9

tag: Sex

value: one month


title: RA CD19 14

description: RA CD19 sample


title: kidney organoid, single cells, Day10rep1

description: single cell


title: RA CD14 9

description: RA CD14 sample


title: RA CD4Nv 14

description: RA CD4Nv sample


title: RA CD4Mem 13

description: RA CD4Mem sample


title: RA CD4Nv 13

description: RA CD4Nv sample


title: RA CD4Nv 12

description: RA CD4Nv sample


title: Cell body 5

city: Houston

first: Pengchao

last: zhang

state: TX

address: 6670 Bertner Ave

department: Nanomedicine

institute: Houston Methodist Research Institute

description:
sample name in processed data file:
S10

data_processing:
Firstly, Cutadapt v1.10 and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Then sequence quality was verified using FastQC 0.10.1.
HISAT2.0 was used to map reads to the genome of human. The mapped reads of each sample were assembled using StringTie v1.3.
Then, all transcriptomes from sample S1-S10 were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie v1.3 and Ballgown v2016.06.29 was used to estimate the expression levels of all transcripts.
StringTie v1.3 was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package Ballgown v2016.09.29.
Genome_build: v88
Supplementary_files_format_and_content: Excel file includes statistics and RPKM values for each Sample.

molecule: polyA RNA

source_name: Breast cancer

growth_protocol: By applying a vacuum (approximately 1 psi) from the outlet of the PG-Chips, cell suspensions with a concentration of approximately 5 × 10^6 cells/mL at the inlet flowed into the channels, and single cells were trapped by the micro-hooks, forming single-cell arrays. The formation of a uniform cell protrusion array was achieved after incubation the single cell array for 6 hours at at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
mRNAs were isolated according to the newly developed protocol (E. R. Thomsen, et al. Nat. Meth. 2016, 13, 87-93). cDNA synthesis and amplification were performed following the protocol of SMART-Seq v4 Ultra Low Input RNA Kit; Takara Bio USA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell protrusion arrays were fixed in a paraformaldehyde solution (4% in PBS) on ice for 15 min. Then, cell protrusion and body samples were isolated using a ArcturusXT Laser Capture Microdissection System.

tag: cell line

value: Breast

tag: cell compartment

value: Cell body


title: Cortex1.CCKVLANXX.SM2_042518p4_G7

tag: age

tag: strain

tag: library construction


title: Cortex1.CCKVLANXX.SM2_042518p4_G8


title: Cell protrusion 5

description:
sample name in processed data file:
S9

value: Cell protrusion


title: control CD4Nv 13

description: control CD4Nv sample


title: Cell body 4

description:
sample name in processed data file:
S8


title: control CD4Mem 14

description: control CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_G6


title: RA CD4Mem 12

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_H11


title: control CD14 14

description: control CD14 sample


title: Cell protrusion 4

description:
sample name in processed data file:
S7


title: Cortex1.CCKVLANXX.SM2_042518p4_G4


title: control CD14 13

description: control CD14 sample


title: control CD4Mem 13

description: control CD4Mem sample


title: Cell protrusion 3

description:
sample name in processed data file:
S5


title: Cell body 3

description:
sample name in processed data file:
S6


title: Cortex1.CCKVLANXX.SM2_042518p4_G3


title: Cortex1.CCKVLANXX.SM2_042518p4_G2


title: Cortex1.CCKVLANXX.SM2_042518p4_G1


title: Cell body 2

description:
sample name in processed data file:
S4


title: control CD19 6

description: control CD19 sample


title: RA CD19 13

description: RA CD19 sample


title: control CD14 12

description: control CD14 sample


title: control CD4Mem 12

description: control CD4Mem sample


title: control CD4Nv 11

description: control CD4Nv sample


title: control CD14 11

description: control CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_G12


title: control CD4Nv 10

description: control CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_G5


title: Cortex1.CCKVLANXX.SM2_042518p4_G11


title: Cortex1.CCKVLANXX.SM2_042518p4_G10


title: Cell body 1

description:
sample name in processed data file:
S2


title: Cell protrusion 1

description:
sample name in processed data file:
S1


title: control CD4Mem 11

description: control CD4Mem sample


title: control CD19 5

description: control CD19 sample


title: control CD19 8

description: control CD19 sample


title: control CD14 10

description: control CD14 sample


title: control CD19 7

description: control CD19 sample


title: control CD4Nv 9

description: control CD4Nv sample


title: control CD14 9

description: control CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F9


title: Cortex1.CCKVLANXX.SM2_042518p4_F8


title: siE1A_YAP_TAZ_mRNAseq_rep1

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Sequences were aligned to the hg19 human genome sequence using TopHat v2.
FPKM (fragments per kb per million mapped reads) for each annotated hg19 RefSeq gene ID was determined using Cuffdiff v2 from Cufflinks RNA-Seq analysis tools at http://cufflinks.cbcb.umd.edu.
Bedgraph files were generated using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig. Cuffdiff output on the series record.

growth_protocol: HEK293 (human embryonic kidney cell line) were maintained at 37°C in a 5% CO2 incubator in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum.

extract_protocol:
1X10^6 HEK293 were transfected with indicated siRNAs for 4, 8, or 16 days. RNA was isolated using QIAGEN RNeasy Plus Mini Kit. Eluted RNA was treated with Ambion DNA-free™ DNA Removal Kit and then Ambion TRIzol reagent, precipitated with isopropanol, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer.
One microgram of RNA was fragmented and copied into DNA then PCR amplified with bar-coded primers for separate samples to prepare sequencing libraries using the Illumina TruSeq RNA Sample Preparation procedure.

treatment_protocol: siRNA transfections were performed using Invitrogen RNAiMAX reverse transfection protocol. Cells were plated in antibiotic free 10% FBS DMEM containing indicated Ambion/ThermoFisher Silencer Select siRNA for a final concentration of 10nM that was pre-incubated in lipofectamine RNAiMAX reagent in Opti-MEM.

value: embryonic

value: kidney

tag: sirna transfection

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM; Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572; Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: control CD4Nv 12

description: control CD4Nv sample


title: siE1A_YAP_TAZ_mRNAseq_rep2


title: Cell protrusion 2

description:
sample name in processed data file:
S3


title: control CD19 4

description: control CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F7


title: control CD14 8

description: control CD14 sample


title: control CD4Nv 8

description: control CD4Nv sample


title: control CD19 3

description: control CD19 sample


title: siE1A_YAP_mRNAseq

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM; Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572


title: Cortex1.CCKVLANXX.SM2_042518p4_F6


title: Cortex1.CCKVLANXX.SM2_042518p4_F5


title: control CD4Nv 7

description: control CD4Nv sample


title: siE1A_mRNAseq_rep1

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM


title: control CD14 7

description: control CD14 sample

value: Caucasian


title: control CD14 6

description: control CD14 sample

value: Female


title: siE1A_mRNAseq_rep2


title: control CD4Mem 9

description: control CD4Mem sample


title: control CD4Nv 6

description: control CD4Nv sample


title: siYAP_TAZ_mRNAseq

value: Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572; Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: Cortex1.CCKVLANXX.SM2_042518p4_F4


title: control CD19 2

description: control CD19 sample


title: control CD4Mem 10

description: control CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F3


title: control CD4Mem 8

description: control CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F2


title: siTAZ_mRNAseq

value: Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: control CD4Mem 7

description: control CD4Mem sample


title: control CD19 1

description: control CD19 sample


title: siE1A_TAZ_mRNAseq

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM; Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: control CD4Mem 6

description: control CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F1

value: Male


title: control CD14 5

description: control CD14 sample


title: siCtrl_mRNAseq_rep2

value: Silencer Negative Control No. 2 siRNA, ThermoFisher Cat#AM4613


title: Cortex1.CCKVLANXX.SM2_042518p4_F12


title: control CD4Mem 5

description: control CD4Mem sample


title: siCtrl_mRNAseq_rep1


title: control CD4Mem 4

description: control CD4Mem sample


title: siE1A_16d_mRNAseq_rep2

tag: duration


title: control CD4Mem 3

description: control CD4Mem sample


title: control CD14 4

description: control CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F10


title: siE1A_16d_mRNAseq_rep1


title: Cortex1.CCKVLANXX.SM2_042518p4_E9


title: control CD4Nv 4

description: control CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_F11


title: control CD4Nv 3

description: control CD4Nv sample


title: control CD14 3

description: control CD14 sample


title: siYAP_mRNAseq

value: Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572


title: control CD4Mem 2

description: control CD4Mem sample


title: siCtrl_16d_mRNAseq_rep1


title: siCtrl_16d_mRNAseq_rep2


title: control CD14 2

description: control CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E7

value: one month


title: siE1A_8d_mRNAseq_rep2


title: Cortex1.CCKVLANXX.SM2_042518p4_E8


title: Cortex1.CCKVLANXX.SM2_042518p4_E6


title: siE1A_8d_mRNAseq_rep1


title: control CD14 1

description: control CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E5


title: control CD4Nv 5

description: control CD4Nv sample


title: control CD4Nv 1

description: control CD4Nv sample


title: siCtrl_8d_mRNAseq_rep2


title: RA CD4Nv 11

description: RA CD4Nv sample


title: RA CD19 12

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E4


title: RA CD19 11

description: RA CD19 sample


title: RA CD19 10

description: RA CD19 sample


title: control CD4Nv 2

description: control CD4Nv sample


title: RA CD4Nv 10

description: RA CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E3


title: Cortex1.CCKVLANXX.SM2_042518p4_E2


title: RA CD4Mem 11

description: RA CD4Mem sample


title: RA CD4Mem 10

description: RA CD4Mem sample


title: control CD4Mem 1

description: control CD4Mem sample


title: RA CD19 9

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E1


title: RA CD19 8

description: RA CD19 sample


title: RA CD4Nv 9

description: RA CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E12


title: RA CD14 8

description: RA CD14 sample


title: siE1A_4d_mRNAseq_rep2


title: siCtrl_4d_mRNAseq_rep1


title: RA CD4Nv 8

description: RA CD4Nv sample


title: RA CD4Mem 9

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E11


title: RA CD4Mem 8

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_E10


title: siE1A_YAP_TAZ_RAD21_INP

data_processing:
Reads were mapped to the hg19 human genome reference using Bowtie2 software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled into 50 base pair windows and each read was extended by 150 bases and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other.
Wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIP-seq was performed using 1x107 siRNA transfected HEK293. Cells were transfected for 1 or 4 days for H3K18ac (814) and H3K27ac (Active Motif) ChIP, 4 days for H3K4me1 (abcam), RAD21 (abcam), and 8 days for YAP (CST D8H1X), TEAD1 (BD Transduction Laboratories), and TEAD4 (Santa Cruz N-G2). For H3K18ac, H3K27ac, H3K4me1 and RAD21 ChIP-seqs cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of mostly ~200-600 base pairs. Samples were normalized for equal amounts of DNA as measured by Qubit fluorometer in sonicated, cross-linked chromatin prior to pre-clear and IP. Up to 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and 2ug of antibody or 5uL of H3K18ac anti-rabbit sera. 50uL of protein A dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer. YAP, TEAD1, and TEAD4 ChIP-seqs were performed similarly with the following modifications: cells were double-crosslinked with 4mM DSG in PBS for 30min then 1% formaldehyde for 10 min, crosslinking was quenched in 500mM Tris pH7.9 for 20min and cell pellets were lysed in 1mL lysis buffer 1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche cOmplete protease inhibitors) for 10min on ice. Lysate was pelleted at 3000 rpm 5min 4°C then resuspended in 1mL lysis buffer 2 (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, Roche complete protease inhibitors) and placed on nutator 10min 4°C and pelleted as before, then resuspended in 125uL of lysis buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, Roche complete protease inhibitors) and sonicated, 2ug of antibody was used, magnetic beads were washed and blocked in 0.5% BSA in PBS.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

tag: chip antibody

value: none (input)


title: siE1A_4d_mRNAseq_rep1

tag: tissue


title: RA CD19 7

description: RA CD19 sample


title: siYAP_TAZ_RAD21_INP


title: RA CD14 7

description: RA CD14 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D9


title: siCtrl_8d_mRNAseq_rep1


title: RA CD4Nv 7

description: RA CD4Nv sample


title: RA CD4Mem 7

description: RA CD4Mem sample


title: RA CD4Mem 6

description: RA CD4Mem sample


title: siE1A_RAD21_INP


title: siCtrl_4d_mRNAseq_rep2


title: siCtrl_RAD21_INP


title: RA CD14 6

description: RA CD14 sample


title: RA CD4Nv 5

description: RA CD4Nv sample


title: RA CD4Nv 6

description: RA CD4Nv sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D7


title: Cortex1.CCKVLANXX.SM2_042518p4_D6


title: siE1A_YAP_TAZ_H3K27_K18ac_INP


title: RA CD4Mem 4

description: RA CD4Mem sample


title: RA CD4Mem 5

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D5


title: RA CD4Nv 4

description: RA CD4Nv sample


title: RA CD19 6

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D4


title: Cortex1.CCKVLANXX.SM2_042518p4_D3


title: RA CD14 5

description: RA CD14 sample


title: RA CD4Nv 3

description: RA CD4Nv sample


title: RA CD19 5

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D8


title: RA CD4Mem 3

description: RA CD4Mem sample


title: Cortex1.CCKVLANXX.SM2_042518p4_D2


title: siCtrl_H3K27_K18ac_INP


title: siE1A_H3K27_K18ac_INP


title: RA CD14 4

description: RA CD14 sample


title: RA CD4Nv 2

description: RA CD4Nv sample


title: RA CD4Mem 2

description: RA CD4Mem sample


title: RA CD19 4

description: RA CD19 sample


title: siE1A_4d_H3K27_K18ac_INP


title: siYAP_TAZ_H3K27_K18ac_INP


title: Cortex1.CCKVLANXX.SM2_042518p4_D12


title: siCtrl_4d_H3K27_K18ac_INP


title: siCtrl_H3K4me1_INP


title: siE1A_H3K4me1_INP


title: Cortex1.CCKVLANXX.SM2_042518p4_D1


title: Cortex1.CCKVLANXX.SM2_042518p4_D10


title: siE1A_1d_H3K27_K18ac_INP


title: siCtrl_1d_H3K27_K18ac_INP


title: RA CD4Nv 1

description: RA CD4Nv sample


title: RA CD19 3

description: RA CD19 sample


title: Cortex1.CCKVLANXX.SM2_042518p4_C9


title: RA CD14 3

description: RA CD14 sample


title: RA CD4Mem 1

description: RA CD4Mem sample


title: RA CD14 2

description: RA CD14 sample


title: RA CD19 2

description: RA CD19 sample


title: CAF_HiP culture rep1

city: Los Angeles

first: Neil

last: Bhowmick

state: California

address: 8750 Beverly Blvd., Atrium Building Room#103

department: Hematology/Oncology

institute: Cedars Sinai Medical Center

data_processing: Primary analysis for AmpliSeq sequencing data of all samples was performed using the ampliSeqRNA plugin available for Ion Torrent™ sequencing platforms. This plugin uses the Torrent Mapping Alignment Program (TMAP) for aligning raw sequencing reads against a hg19-based custom reference sequence set containing all human transcripts targeted by the AmpliSeq kit as described previously (Li et al., 2015). As part of the ampliSeqRNA plugin, raw read counts of the targeted genes were performed using Samtools and then were normalized in RPM (Reads Per Millions).

source_name: prostate

growth_protocol: Fibroblast cultures were maintained in DME/F12 medium supplemented with 5% FBS, 5% NuSerum, Insulin, testosterone, and gentamicin. 5% CO2.

extract_protocol:
Cells were trypsinized and pelleted for total RNA extraction.
The AmpliSeq transcriptome libraries were prepared Ion AmpliSeq™ Transcriptome Human Gene Expression Kit. As described before (Li et al., 2015), A barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit from 10 ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Agilent Bioanalyzer High sensitivity chip. Libraries were then diluted to 100pM and pooled equally, with eight individual samples per pool. Pooled libraries were amplified using emulsion PCR on Ion Torrent OneTouch2 instruments (OT2) and enriched following manufactures instructions. Templated libraries were then sequenced on Ion Torrent Proton™ sequencing system, using Ion PI sequencing 200 kit v2.

treatment_protocol: none.

value: prostate

value: male

tag: cell type

value: high passage cancer associated fibroblast


title: RA CD19 1

description: RA CD19 sample

tag: ethnicity


title: Cortex1.CCKVLANXX.SM2_042518p4_C8

source_name: Cortex


title: siCtrl_YAP_TEAD1_TEAD4_INP

value: embryonic

value: kidney


title: siE1A_YAP_TEAD1_TEAD4_INP


title: Cortex1.CCKVLANXX.SM2_042518p4_D11


title: Cortex1.CCKVLANXX.SM2_042518p4_C7


title: Cortex1.CCKVLANXX.SM2_042518p4_C5


title: NAF culture rep1

value: normal associated fibroblast


title: Cortex1.CCKVLANXX.SM2_042518p4_C6


title: siYAP_TAZ_RAD21_ChIPseq

value: Rabbit polyclonal anti-RAD21 abcam Cat#ab992


title: Tuberculosis 1008

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human Omni-zhonghua chips

hyb_protocol: according to the manufacturer’s specifications

scan_protocol: chips were scanned using iScan instrument

data_processing: We used Genomestudio to call the genotypes of SNPs, and performed association study using plink.

label: biotin

source_name: Tuberculosis

growth_protocol: Extraction of genomic DNA from blood was performed using proteinase K and repeated phenol-chloroform extraction.

extract_protocol: genomic DNAs were extracted with DNA-extraction kits (Tiangen Biotech, Beijing, China)

treatment_protocol: the whole-blood was stored in -80 refrigerator

value: Blood


title: Tuberculosis 1007

label_protocol: according to the manufacturer’s specifications


title: Tuberculosis 1006


title: Tuberculosis 1001


title: Tuberculosis 1003


title: Cortex1.CCKVLANXX.SM2_042518p4_C3


title: siE1A_YAP_TAZ_H3K27ac_ChIPseq

value: Rabbit polyclonal anti-H3K27ac Active Motif Cat#39133  Lot#31814008

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM; Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572; Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: CAF culture rep1

value: cancer associated fibroblast


title: Cortex1.CCKVLANXX.SM2_042518p4_C4


title: siE1A_YAP_TAZ_RAD21_ChIPseq


title: Cortex1.CCKVLANXX.SM2_042518p4_C2


title: Tuberculosis 1005


title: Tuberculosis 1002


title: Tuberculosis 999


title: RA CD14 1

description: RA CD14 sample

value: Caucasian

tag: subjecttype

value: Female


title: Cortex1.CCKVLANXX.SM2_042518p4_C1

value: Male


title: Tuberculosis 998


title: Tuberculosis 997


title: siYAP_TAZ_H3K27ac_ChIPseq

value: Silencer Select siRNA YAP1, ThermoFisher Assay ID:s534572; Silencer Select siRNA WWTR1 ThermoFisher Assay ID:s24788


title: siE1A_H3K27ac_ChIPseq

value: Custom Select siRNA E1A, ThermoFisher Design ID:ADLJIAM


title: Tuberculosis 1004


title: siCtrl_RAD21_ChIPseq

value: Silencer Negative Control No. 2 siRNA, ThermoFisher Cat#AM4613


title: siE1A_RAD21_ChIPseq


title: Tuberculosis 996


title: Cortex1.CCKVLANXX.SM2_042518p4_C12

value: one month


title: Tuberculosis 994


title: Tuberculosis 995


title: Tuberculosis 1000


title: Cortex1.CCKVLANXX.SM2_042518p4_C11


title: Cortex1.CCKVLANXX.SM2_042518p4_C10


title: Tuberculosis 993


title: siE1A_YAP_TAZ_H3K18ac_ChIPseq

value: Rabbit polyclonal anti-H3K18ac (814) Grunstein/Kurdistani laboratories (Suka et al., 2001)


title: Tuberculosis 992


title: Cortex1.CCKVLANXX.SM2_042518p4_B9


title: siYAP_TAZ_H3K18ac_ChIPseq


title: Tuberculosis 989


title: Cortex1.CCKVLANXX.SM2_042518p4_B8


title: Tuberculosis 991


title: Tuberculosis 990


title: Cortex1.CCKVLANXX.SM2_042518p4_B7


title: siCtrl_H3K18ac_ChIPseq


title: Tuberculosis 988


title: Tuberculosis 987


title: Tuberculosis 984


title: Tuberculosis 986


title: siE1A_H3K18ac_ChIPseq


title: Tuberculosis 985


title: siE1A_H3K4me1_ChIPseq

value: Rabbit polyclonal anti-H3K4me1 abcam Cat#ab8895


title: Tuberculosis 983


title: siCtrl_H3K27ac_ChIPseq

value: embryonic


title: Tuberculosis 982


title: siCtrl_H3K4me1_ChIPseq

value: kidney


title: Tuberculosis 981


title: Tuberculosis 980


title: Cortex1.CCKVLANXX.SM2_042518p4_B5


title: Cortex1.CCKVLANXX.SM2_042518p4_B4


title: siE1A_4d_H3K27ac_ChIPseq


title: Tuberculosis 979


title: Tuberculosis 976


title: Tuberculosis 977


title: siCtrl_4d_H3K27ac_ChIPseq


title: Tuberculosis 978


title: Tuberculosis 975


title: siCtrl_4d_H3K18ac_ChIPseq


title: Tuberculosis 974


title: Cortex1.CCKVLANXX.SM2_042518p4_B1


title: Tuberculosis 972


title: Tuberculosis 973


title: Cortex1.CCKVLANXX.SM2_042518p4_B12


title: Cortex1.CCKVLANXX.SM2_042518p4_B6


title: Tuberculosis 971


title: siE1A_1d_H3K27ac_ChIPseq


title: siCtrl_1d_H3K27ac_ChIPseq


title: Cortex1.CCKVLANXX.SM2_042518p4_B3


title: Tuberculosis 969


title: Tuberculosis 968


title: Tuberculosis 967


title: Tuberculosis 970


title: Cortex1.CCKVLANXX.SM2_042518p4_B10


title: Tuberculosis 966


title: siE1A_1d_H3K18ac_ChIPseq


title: siCtrl_1d_H3K18ac_ChIPseq


title: Cortex1.CCKVLANXX.SM2_042518p4_B2


title: Tuberculosis 965


title: siE1A_4d_H3K18ac_ChIPseq


title: Tuberculosis 964


title: siE1A_TEAD4_ChIPseq

value: Mouse monoclonal anti-TEF-3 a.k.a. TEAD4 (N-G2) Santa Cruz Cat#sc-101184


title: Tuberculosis 963


title: Cortex1.CCKVLANXX.SM2_042518p4_A7


title: siCtrl_TEAD4_ChIPseq


title: Tuberculosis 962


title: Tuberculosis 961


title: Cortex1.CCKVLANXX.SM2_042518p4_A8


title: siE1A_TEAD1_ChIPseq

value: Mouse monoclonal anti-TEF1 a.k.a. TEAD1 (31/TEF1) BD Transduction Laboratories Cat#610922


title: Cortex1.CCKVLANXX.SM2_042518p4_A9


title: Cortex1.CCKVLANXX.SM2_042518p4_A6


title: Tuberculosis 958

value: Blood


title: Cortex1.CCKVLANXX.SM2_042518p4_A5


title: Cortex1.CCKVLANXX.SM2_042518p4_B11


title: Tuberculosis 959


title: Tuberculosis 956


title: Tuberculosis 955


title: Tuberculosis 954


title: siE1A_YAP_ChIPseq

value: Rabbit monoclonal anti-YAP (D8H1X) Cell Signaling Technology Cat#14074


title: siCtrl_YAP_ChIPseq


title: Tuberculosis 953


title: siCtrl_TEAD1_ChIPseq


title: Cortex1.CCKVLANXX.SM2_042518p4_A3


title: Cortex1.CCKVLANXX.SM2_042518p4_A4