title: Streptomyces coelicolor_M1146_cAMP_2h_3

city: Suita

first: Katsuaki

last: Nitta

state: Osaka

address: Yamadaoka 2-1

country: Japan

institute: Osaka University

data_processing:
Generating reference genome by software STAR ver. 2.7
Read mapping to reference genome by software STAR ver. 2.7
Read counting by R-package feature counts
RLE normalized counts were generated by R-package DESeq2
Genome_build: ASM20383v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor

growth_protocol: Bacterial strains were grown in 50 mL liquid minimum nutrition medium with same composition as previous study in well siliconized 250 mL flasks containing stainless-steel springs. For inoculation, 1×109 CFU of spores were inoculated to the 50 mL medium. Incubation speed and temperature was set to 220 rpm and 30°C respectively.

extract_protocol:
Cells were disaggregated by double autoclaved empty tip and 0.17 mL of 15 mg/mL lysozyme was added to the cells and incubated at 30°C for 10 minutes. The solution including cells were transferred to tube containing lysing matrix E (MPbio medicals) and 0.6 mL RLT buffer (Qiagen) supplemented with beta-mercaptoethanol (100: 1, v/v), and vortexed for 5 seconds. Three pulses were applied to the tube by Fast Prep (6.5 m/s, 30s) while the tubes were kept on ice between pulses for 30 seconds. The tubes were centrifuged at 10000 rpm and 4°C for 1 minute and the lysate was recovered. After centrifuging heavy PLG tube to pack the resine for 1min, 0.65 mL recovered lysate was transferred to the heavy PLG tube. 0.65 mL chloroform, isoamyl alcohol and acid phenol mixture was added to the lysate in heavy PLG tube and mixed by inversion for 1 minute. The heavy PLG tubes containing extracts were centrifuged for 5 minutes and superior aqueous phase was recovered. RNA purification was performed with Direct-zol RNA MiniPrep Plus (Zymo research). After 0.6 mL ethanol was added to recovered 0.6 mL of aqueous phase and mixing by pipette, Zymo-spin ⅢCG column was assembled to collection tube, and 0.6 mL mixture solution was transferred to the assembled column-collection tube, and centrifuged at 10000 rpm for 30 seconds. Flow through from the collection tube was discarded and remaining 0.6 mL of mixture of aqueous extract and ethanol was transferred to the assembled column-collection tube, consequently centrifuged at 10000 rpm for 30 seconds. The flow through in the collection tube was discarded again. RNA wash buffer completed with ethanol (0.4 mL) was added to the column, centrifuged at 10000 rpm for 30 seconds and the flow-through was discarded. To the column matrix, 80 µL of DNase (6 U/µL) was added and incubated at 30°C for 15 minutes. After incubation, two cycles of RNA washing (Adding 0.4 mL of Direct-zol RNA prewash to the column, centrifuging at 10000 rpm for 30 seconds and discarding the flow through). To the column, 0.7 mL RNA wash buffer was added and centrifuged for 2 minutes to ensure complete removal of wash buffer. Consequently, the column was transferred to new RNase-free tube, 50 µL of DNase/RNase-free water was added and incubated at room temperature for 1 minute. The column with sample containing water was centrifuged at 10000 rpm for 1 minute, and tube with RNA sample was frozen by liquid nitrogen until next step.
The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at　4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand　cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The　first-strand cDNA was purified and the 5' Illumina HiSeq sequencing adapter was ligated to the 3' end　of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high　fidelity DNA polymerase. The HiSeq barcode sequences,　which are part of the 5' and 3' HiSeq sequencing adapters, are included in Table 2. The cDNA was　purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by　capillary electrophoresis

treatment_protocol: cAMP was supplemented at 20h and samples were collected at 0h, 1h and 2h after cAMP supplementation. Before sampling, all materials for sampling was autoclaved two times to avoid RNase contamination. Based on growth curve, expectedly more than 2.0 mg DCW cell cultures was sampled and mixed with the twice amount of RNA protection reagent (Qiagen) immediately. The cells were vortexed for 10 seconds, kept for 5 minutes at room temperature and centrifuged at 10000 rpm, 20°C for 10 minutes. Supernatant was eliminated as much as possible, and the cells were quenched by liquid nitrogen immediately and kept at -80°C until RNA isolation.

tag: time

tag: treatment

value: cAMP


title: Streptomyces coelicolor_M1146_cAMP_2h_1

status: Public on Nov 27 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: Streptomyces coelicolor_M1146_cAMP_2h_2


title: Streptomyces coelicolor_M1146_cAMP_1h_3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B6_AD001

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: age

tag: tissue

value: brain

tag: source

value: AI

tag: target

value: TH

tag: gender

value: male


title: Streptomyces coelicolor_M1146_cAMP_1h_2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B3_AD007

value: Pons

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B3_AD010


title: Streptomyces coelicolor_M1146_cAMP_1h_1


title: Streptomyces coelicolor_M1146_cAMP_0h_3

value: control


title: Streptomyces coelicolor_M1146_cAMP_0h_2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B1_AD012


title: Streptomyces coelicolor_M1146_cAMP_0h_1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B3_AD012


title: pSer2 RNA Polymerase II ChIP-Seq DMSO 2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

organism: Homo sapiens

growth_protocol: S phase synchronized IMR-5 cells by double Thymidine block

extract_protocol:
For spike-in experiments (ChIP-Rx) 10% of fixed NIH-3T3 mouse cell lines were added before lysis. Cells were treated with 1% formaldehyde for 5 min at RT following 5 min of incubation with glycine. After cell lysis (5 mM PIPES pH 8.8, 5 mM KCl, 0.5% NP40), nuclei were resuspended in RIPA buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1% Triton-X-100, 0.1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA containing protease and phosphatase inhibitor cocktail) and DNA was fragmented to a size <500 bp using a Covaris M220 sonifier. Antibodies were bound to Protein A/G-Dynabeads® (Invitrogen) and immunoprecipitated. After extensive washing, chromatin was eluted with 1% SDS and crosslinking was reverted overnight. Chloroform/phenol extraction was used for DNA purification. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with a gel extraction kit. DNA fragments were amplified by 16 cycles of PCR and library size and amount of library was specified with the Fragment Analyzer (Agilent). The library was subjected to Illumina NextSeq 500 sequencing according to the manufacturer’s instructions. After base calling with Illumina’s FASTQ Generation software v1.0.0 (NextSeq 500 sequencing), high quality PF-clusters were selected for further analyses.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 4 h treatment with 1 µM MK5108

tag: cell type

value: neuroblastoma cells

tag: cell line

tag: chip antibody

value: pSer2 RNA Polymerase II (ab5095, Abcam, Lot-Nr. CR3231908-1)


title: total RNA Polymerase II ChIP-Seq DMSO 2

value: total RNA Polymerase II (A10, sc17798, Santa Cruz, J1617)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_C10_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B2_AD008


title: PB CD8+CD45RO+ T cell 1

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: Peripheral blood CD8+CD45RO+ T cells from JIA patient

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.0.2 was used for demultiplexing, barcode processing and assembly of the TCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id.

molecule: polyA RNA

source_name: Peripheral blood CD8+CD45RO+ T cells

extract_protocol:
Mononuclear cells from the peripheral blood (PBMCs) were isolated by Ficoll density‐gradient centrifugation and subsequent collection of the leukocyte-containing interphase. For the isolation of leukocytes from the synovial fluid, we diluted the viscous fluid with 5 mM ethylenediaminetetraacetic acid (EDTA)-containing phosphate-buffered saline (PBS) and filtered the cells using a 70 μm cell strainer (BD). Subsequently, cells were centrifuged at 300 g at 4 °C and resuspended in PBS containing 0.2% bovine serum albumin (PBS/BSA). Following an additional filtration step through a 70 μm cell strainer, cells were resuspended in PBS/BSA prior to depletion of CD15+ neutrophils by magnetic cell separation (MACS, Miltenyi Biotec). Single cell suspensions of PBMCs and CD15-depleted SF cells were blocked with human FcR blocking reagent (Miltenyi Biotec) and labeled for 15 min at 4 °C with antibodies for fluorescent activated cell sorting (FACS) using a FACS-Aria II (BD). Cells were sorted to obtain antigen-experienced (memory) CD4+CD45RO+CD25- T cells (Tcon), CD4+CD45RO+CD127loCD25+ regulatory T cells (Treg), and CD8+CD45RO+ T cells. Sorted cells then were subjected to single-cell sequencing by applying them to the 10X Genomics platform.
For single cell library preparation, FACS-sorted human T cells were applied to the 10X Genomics platform using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics) and following the manufacturer’s instructions for capturing ~3000 cells. The amplified cDNA was used for simultaneous 5’ gene expression (GEX) and TCR library preparation. TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX and TCR libraries was assessed by Qubit quantification, Bioanalyzer fragment analysis (HS DNA Kit, Agilent) and KAPA library quantification qPCR (Roche). The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for TCR libraries (read1: 150nt, read2: 150nt, index1: 8nt, index2: n.a., 20% PhiX spike-in). Raw Illumina-NextSeq 500 data were processed using cellranger-2.1.1. Mkfastq, count commands and vdj commands were used with default parameter settings. The genome reference was refdata-cellranger-hg19-1.2.0. The vdj-reference was refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0. In both cases, the number of expected cells was set to 3000.

value: Peripheral Blood

tag: patient id

value: JIA patient 1


title: PB CD8+CD45RO+ T cell 5

value: JIA patient 5


title: PB CD8+CD45RO+ T cell 4

value: JIA patient 4


title: PB CD8+CD45RO+ T cell 7

value: JIA patient 7


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_C10_AD006


title: SF CD8+CD45RO+ T cell 7

description: Synovial fluid CD8+CD45RO+ T cells from JIA patient

source_name: Synovial fluid CD8+CD45RO+ T cells

value: Synovial Fluid


title: SF CD8+CD45RO+ T cell 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B2_AD007


title: PB CD8+CD45RO+ T cell 2

value: JIA patient 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD001

value: brain


title: PB CD8+CD45RO+ T cell 6

value: JIA patient 6


title: SF CD8+CD45RO+ T cell 6


title: SF CD8+CD45RO+ T cell 4


title: SF CD8+CD45RO+ T cell 3

value: JIA patient 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B11_AD012

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B1_AD004

value: TH


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B11_AD010

value: Pons

value: female


title: SF CD8+CD45RO+ T cell 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B12_AD002

value: male


title: SF CD8+CD45RO+ T cell 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B11_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD006


title: PB CD4+ Treg 7

description: Peripheral blood CD4+CD45RO+CD127loCD25+ T cells from JIA patient


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD010


title: PB CD4+ Treg 6

source_name: Peripheral blood CD4+CD45RO+CD127loCD25+ T cells


title: PB CD4+ Treg 4


title: PB CD4+ Treg 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD012


title: PB CD4+ Treg 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B10_AD004


title: PB CD4+ Treg 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD010


title: SF CD4+ Treg 7

description: Synovial fluid CD4+CD45RO+CD127loCD25+ T cells from JIA patient


title: SF CD4+ Treg 6

source_name: Synovial fluid CD4+CD45RO+CD127loCD25+ T cells


title: SF CD4+ Treg 5


title: PB CD4+ Treg 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_B11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD008


title: SF CD4+ Treg 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A9_AD002


title: SF CD4+ Treg 1


title: SF CD4+ Treg 4


title: PB CD4+ Tcon 6

description: Peripheral blood CD4+CD45RO+CD25- T cells from JIA patient


title: PB CD4+ Tcon 7

source_name: Peripheral blood CD4+CD45RO+CD25- T cells


title: PB CD4+ Tcon 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD001


title: PB CD4+ Tcon 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD004


title: SF CD4+ Treg 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD007


title: PB CD4+ Tcon 2


title: SF CD4+ Tcon 7

description: Synovial fluid CD4+CD45RO+CD25- T cells from JIA patient

source_name: Synovial fluid CD4+CD45RO+CD25- T cells


title: PB CD4+ Tcon 1


title: SF CD4+ Tcon 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD008


title: SF CD4+ Tcon 2


title: SF CD4+ Tcon 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A7_AD010


title: SF CD4+ Tcon 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD012


title: SF CD4+ Tcon 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A5_AD008


title: Human Bone Marrow NK cells from Healthy donor 3

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

data_processing:
Cell Ranger software 3.0.1
Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed, and cells expressing more than 2500 genes. Additional QC has been performed
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files (gene/cell matrix)

source_name: NK cells

extract_protocol: 10x Genomics Chromium Single-Cell 3’ v2 protocol

value: bone marrow

value: NK cells

tag: patient diagnosis

value: healthy

tag: donor number


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A7_AD001


title: Human Bone Marrow NK cells from Healthy donor 7


title: Human Bone Marrow NK cells from Healthy donor 8


title: Human Bone Marrow NK cells from Healthy donor 5


title: Human Bone Marrow NK cells from Healthy donor 6


title: Human Bone Marrow NK cells from Healthy donor 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A5_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A5_AD010


title: Human Bone Marrow NK cells from Healthy donor 2


title: SF CD4+ Tcon 1

value: JIA patient 1


title: Human Bone Marrow NK cells from Healthy donor 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A4_AD006


title: Human Bone Marrow NK cells from AML donor 7

value: AML


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A4_AD002


title: Human Bone Marrow NK cells from AML donor 8


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A4_AD001


title: Human Bone Marrow NK cells from AML donor 1


title: Human Bone Marrow NK cells from AML donor 6


title: Human Bone Marrow NK cells from AML donor 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A4_AD010


title: Human Bone Marrow NK cells from AML donor 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD007


title: iCell neurons (CW20049), Total RNA, 4hr post-KCl stim, biorep 1, tech rep 1

city: Boston

first: Gabriella

middle: Lutz

last: Boulting

state: MA

address: 200 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School

data_processing:
For total RNA sequencing of human iCell cultures, strand-specific single-end reads nominally sequenced at 75 bp but occasionally shorter were 3'-truncated to 70bp and filtered to include only reads with unambiguous base calls (the ~0.1% of reads shorter than 70bp were discarded). Reads were then aligned mapped to the hg19 or hg38 genome using BWA (v.0.7.8) allowing up to 2 mismatches, zero gaps, and otherwise default parameters. The usual 24 chromosomal alignment targets were supplemented with ~6.1 million short sequences comprising all possible intragenic subsets of ordered exons from the GRCh37.p5 RefSeq annotation, such that each sequence is of minimal length yet accommodates a 70-bp read spanning all junctions between consecutive exons within a subset; likewise, ~ 9.6 million such splice-junction sequences were added for the GRCh38.p2 RefSeq annotation. Typically 85-95% of all reads in each library were mappable and ~85-90% of these aligned uniquely; nonuniquely mapped reads were discarded.
Aligned total RNA-Seq reads were further analyzed using an in-house code MAPtoFeatures (M2F) that produces expression levels for individual genes and their exons. The following applies separately to the RefSeq annotations for human Build 37.3 assembly (7 Sept 2011) GRCh37.p5 and human assembly GRCh37.p2 (12 March 2015). The exons for all transcripts assigned to a gene based on RefSeq were merged (unioned); along with the constructed library of splice-junction sequences, these defined each gene's mature-RNA target region. The total number of bases of all reads that overlapped a gene's exonic region was divided bythe  region's total length to yield an average read Density (coverage). Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/70) (for 70-bp reads), where R = total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements. (RPKM units are proportional to normalized Density units: RPKM = Density/0.35). Relevant genic expression levels in M2F tables appear in column S_EXN_Density.
Differential-expression analysis was performed in R (v. 3.6.2) using edgeR to compare total RNA iCell samples that were stimulated with KCl to unstimulated samples. Stim time points at 15 minutes (3 or 4 samples, referring to non-G4 and G4 data, respectively), 1 hour (3 or 3), 2 hours (6 or 4), and 4 hours (3 or 4) were each compared to 6 or 4 samples at 0hr (i.e., unstim).  To produce a balanced normalization of Densities for each comparison, all RefSeq-annotated genes (23,202 in hg19; 24,681 in hg38) in all samples at each later time point were quantile normalized together with all samples at 0hr. These processed Densities were then converted back to read counts for edgeR input as follows:  divide each gene's Density by its sample's original normalization factor (10M/R)*(35/70), multiply by the gene's number of exonic bases, divide by read length 70, and round up to the nearest integer. These counts were input into edgeR using all defaults (removing genes with zero expression) and the BH correction for multiple comparisons to obtain q-values to be measured against a desired false discovery rate (FDR).
Genome_build: GRCh37  (hg19; Feb, 2009)
Genome_build: GRCh38  (hg38; Dec, 2013)
Supplementary_files_format_and_content: MAPtoFeatures (M2F) tables have rows that list genes and TAB-separated columns for various genic parameters, gene feature counts (for exons, introns, etc., individually and in total), and, for each feature and feature type, read counts, read-base counts, and normalized read Densities, all for reads that map sense or antisense to each gene. M2F LOG files document each run's read totals and summary statistics. Differential-expression tables from edgeR analyses have rows for genes and TAB-separated columns for: genic parameters, calculated fold-change (FC) ratios for KCl-stim at a time point, whether the mean change went up or down (UP.or.dn), inferred mean counts per million (CPM), reported p-value and BH-corrected q-value, various filtering results, numbers of samples with non0 expression and mean and SE log-RPKM values converted back to linear scale at each time, and read counts per sample input into edgeR. Single-cell counts tables list genes in rows, individual cells in TAB-separated columns; each entry is a UMI for a gene in a cell.

source_name: iCell GABANeurons

growth_protocol: Manufacturer's protocol.

extract_protocol:
Trizol, RNeasy Micro Kit (Qiagen), RiboMinus Eukaryote Kit for RNA-seq (ThermoFisher)
SE RNA-seq library kit (Illumina) or the NEBNext Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: KCl membrane depolarization

value: cultured human iPSC-derived neurons at ~DIV16

tag: time post-kcl stimulation

value: 4 hours

tag: biological replicate

tag: technical replicate

tag: chip epitope


title: Human Bone Marrow NK cells from AML donor 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD012


title: iCell neurons (1434), Total RNA, 4hr post-KCl stim, biorep 4, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD004


title: Human Bone Marrow NK cells from AML donor 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD001


title: iCell neurons (1501), Total RNA, 2hr post-KCl stim, biorep 1, tech rep 1

value: 2 hours


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD002


title: iCell neurons (1505), Total RNA, 2hr post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A8_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD001


title: iCell neurons (1505), Total RNA, 4hr post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD006


title: iCell neurons (CW20049), Total RNA, 15min post-KCl stim, biorep 1, tech rep 1

value: 15 minutes


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A4_AD004

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A12_AD004


title: iCell neurons (CW20049), Total RNA, 2hr post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD010


title: iCell neurons (1505), Total RNA, 15min post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A1_AD004


title: iCell neurons (CW20049), Total RNA, 1hr post-KCl stim, biorep 1, tech rep 1

value: 1 hour


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A3_AD002


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 7, tech rep 1


title: iCell neurons (1501), Total RNA, 4hr post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A12_AD012


title: iCell neurons (1505), Total RNA, 1hr post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A12_AD001


title: iCell neurons (1434), Total RNA, 1hr post-KCl stim, biorep 4, tech rep 1


title: iCell neurons (1501), Total RNA, 15min post-KCl stim, biorep 1, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD012


title: iCell neurons (1434), Total RNA, unstimulated, biorep 7, tech rep 1

value: unstimulated


title: iCell neurons (1501), Total RNA, unstimulated, biorep 1, tech rep 1


title: iCell neurons (1434), Total RNA, 4hr post-KCl stim, biorep 3, tech rep 1


title: iCell neurons (CW20049), Total RNA, unstimulated, biorep 1, tech rep 1


title: iCell neurons (1505), Total RNA, unstimulated, biorep 1, tech rep 1


title: iCell neurons (1434), Total RNA, 4hr post-KCl stim, biorep 1, tech rep 1


title: iCell neurons (1434), Total RNA, 15min post-KCl stim, biorep 4, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD004

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H9_AD008

value: ACA


title: iCell neurons (1434), Total RNA, 4hr post-KCl stim, biorep 2, tech rep 1


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 4, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A10_AD004

value: TH


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H9_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A10_AD012

value: Pons

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H9_AD012

value: male


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 3, tech rep 1, sequencing runs 1 & 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H8_AD012


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 6, tech rep 1


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 2, tech rep 1, sequencing runs 1 & 2


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 5, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H9_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H8_AD004


title: iCell neurons (1434), Total RNA, 2hr post-KCl stim, biorep 1, tech rep 1, sequencing runs 1 & 2


title: iCell neurons (1434), Total RNA, 15min post-KCl stim, biorep 3, tech rep 1, sequencing runs 1 & 2


title: iCell neurons (1434), Total RNA, 1hr post-KCl stim, biorep 1, tech rep 1


title: iCell neurons (1434), Total RNA, 1hr post-KCl stim, biorep 2, tech rep 1


title: iCell neurons (1434), Total RNA, 1hr post-KCl stim, biorep 3, tech rep 1


title: iCell neurons (1434), Total RNA, 15min post-KCl stim, biorep 2, tech rep 1, sequencing runs 1 & 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H6_AD004


title: iCell neurons (1434), Total RNA, 15min post-KCl stim, biorep 1, tech rep 1, sequencing runs 1 & 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A11_AD008


title: H3.3 ChIP-Seq Dox rep2

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
chromosome ideagrams were drawn with RIdeogram v0.2.2
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: neuroblastoma cell line

growth_protocol: S phase synchronized IMR-5 cells with inducible RNaseH1 by double Thymidine block

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol:
24 h treatment with 1 µg/ml Doxycycline
Where indicated in the file names, the input samples were obtained from cells that had been incubated for 4 h with 1 µM MLN8237 or DMSO before harvest.

value: rabbit monoclonal H3.3 (EPR17899) Lot N° GR3263393-3)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H8_AD006


title: Input H3.3 rep2


title: pS2 ChIP-Seq Dox rep2


title: iCell neurons (1434), Total RNA, unstimulated, biorep 6, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H7_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H6_AD007


title: iCell neurons (1434), Total RNA, unstimulated, biorep 5, tech rep 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H4_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H4_AD006


title: iCell neurons (1434), Total RNA, unstimulated, biorep 4, tech rep 1


title: iCell neurons (1434), Total RNA, unstimulated, biorep 3, tech rep 1, sequencing runs 1 & 2


title: iCell neurons (1434), Total RNA, unstimulated, biorep 2, tech rep 1, sequencing runs 1 & 2


title: Input A10 S2P rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H5_AD008


title: iCell neurons (1434), Total RNA, unstimulated, biorep 1, tech rep 1, sequencing runs 1 & 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H4_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H5_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H5_AD004


title: H3.3 ChIP-Seq EtOH rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H4_AD008


title: pS2 ChIP-Seq EtOH rep2


title: A10 ChIP-Seq EtOH rep2

value: A10 Antibody, Santa Cruz Lot No:J2219


title: histone H3.3 ChIP-Seq DMSO rep2

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

extract_protocol:
For spike-in experiments (ChIP-Rx) 10% of fixed NIH-3T3 mouse cell lines were added before lysis. Cells were treated with 1% formaldehyde for 5 min at RT following 5 min of incubation with glycine. After cell lysis (5 mM PIPES pH 8.8, 5 mM KCl, 0.5% NP40), nuclei were resuspended in RIPA buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1% Triton-X-100, 0.1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA containing protease and phosphatase inhibitor cocktail) and DNA was fragmented to a size <500 bp using a Covaris M220 sonifier. Antibodies were bound to Protein A/G-Dynabeads® (Invitrogen) and immunoprecipitated. After extensive washing, chromatin was eluted with 1% SDS and crosslinking was reverted overnight. Chloroform/phenol extraction was used for DNA purification. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with a gel extraction kit. DNA fragments were amplified by 16 cycles of PCR and library size and amount of library was specified with the Fragment Analyzer (Agilent). The library was subjected to Illumina NextSeq 500 sequencing according to the manufacturer’s instructions. After base calling with Illumina’s FASTQ Generation software v1.0.0 (NextSeq 500 sequencing), high quality PF-clusters were selected for further analyses.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
spike normalized ChIP-Sequencing (ChIP-rx)

treatment_protocol: 4 h treatment with 1 µM MLN8237 or DMSO

value: neuroblastoma cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H4_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H3_AD004


title: pS2 ChIP-Seq MLN rep2

treatment_protocol:
4 h treatment with 1 µM MLN8237 or DMSO
Where indicated in the file names, the input samples were obtained from cells that had been incubated for 4 h with 1 µM MLN8237 or 1 µM MK5108 before harvest.


title: histone H3.3 ChIP-Seq MLN rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P5_180801_P6_A6_AD010


title: A10 ChIP-Seq Dox rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H3_AD010


title: Input IR180 rep2


title: A10 ChIP-Seq MLN rep2


title: pS2 ChIP-Seq DMSO rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H3_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H3_AD006


title: 4SU sample, Pladienolide B, repeat 3

data_processing:
Library strategy: 4sU-Sequencing with pulse and chase
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were aligned with Tophat v2.1.1  to hg19
reads were identified as "spliced" or "unspliced" based on their CIGAR strings
the number of unspliced reads mapping to various features (only exons, exons + introns, only introns, only intergenic) was determined with intersectBed
calculated percentages are averages of all replicates; for "pulse" the average of all "pulse" samples
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph file

extract_protocol:
For 4sU labelled nascent RNA sequencing, IMR-5 cells were cell cycle synchronized using double thymidine block. At timepoint of release indicated inhibitors were added. 2 h before harvest cells were incubated with 500 µM of 4sU (Sigma-Aldrich) in RPMI to label nascent RNA. After 15 min medium was changed. RNA was harvested using Qiagen miRNeasy kit. After extraction and quantification of total RNA by Nanodrop, equal amount was labelled with biotin (Pierce) in presence of DMF-HPDP buffer. Free biotin removal was carried out by chloroform-isoamyl alcohol extraction after which RNA was resuspended into nuclease free water. DynabeadsTM MyOneTM Streptavidin C1 beads (Life Technologies) were used for enrichment of biotinylated RNA, which was then eluted by 100 mM DTT and cleaned by RNeasy MinElute cleanup kit. Nascent RNA concentration was then measured using RiboGreen RNA assay kit and equal amount was used for library preparation. Before library preparation, rRNA was depleted using NEBNext® rRNA Depletion Kit and then all eluted material was used for NEB Ultra Directional kit with 14 PCR cycles. The libraries were then finally sequenced for 75 cycles using Illumina NextSeq 500 system.
Libraries were prepared according to Illumina's instructions; rRNA was depleted using NEBNext® rRNA Depletion Kit (Part# E6350) and Library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Part# E7765).

treatment_protocol: 4 h treatment with 1 µM MLN8237, 1 µM MK5108, 1 µM Pladienolide B, 2 h before harvest cells were pulsed for 15 min with 500 µM 4sU and then chased for 2 h


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H2_AD012


title: A10 ChIP-Seq DMSO rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H1_AD010


title: 4SU sample, Pladienolide B, repeat 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H2_AD007


title: Input rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H1_AD007


title: 4SU sample, MLN8237, repeat 2


title: 4SU pulse early, Pladienolide B


title: 4SU sample, MLN8237, repeat 3


title: 4SU pulse late, Pladienolide B


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H12_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H12_AD008


title: 4SU pulse late, MLN8237


title: 4SU sample, MLN8237, repeat 1


title: 4SU pulse early, MLN8237


title: 4SU sample, MK5108, repeat 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H11_AD010


title: 4SU sample, Pladienolide B, repeat 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H12_AD004


title: 4SU sample, MK5108, repeat 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H11_AD007


title: 4SU sample, DMSO, repeat 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H1_AD008


title: 4SU sample, DMSO, repeat 1


title: 4SU pulse late, DMSO


title: 4SU sample, DMSO, repeat 3


title: PDX model treated for 14 d, combination treatment, repeat 3

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
RNAseq reads were aligned with Tophat v2.1.1 to hg19
reads were counted using the “summarizeOverlaps” function from the R package “GenomicAlignments"
differentially expressed genes were called with edgeR
differential exon usage was determined with DEXseq after mapping with hisat2
gene set enrichment analysis was carried out with GSEA and the MSigDB gene sets Hallmarks, C2, C5
Genome_build: hg19
Supplementary_files_format_and_content: count files were generated with edgeR

source_name: PDX

extract_protocol:
s.c. tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Patient-derived cells were used as published previously, e.g. in Henssen et al. (2017). Sci Transl Med 9.

value: tumor

tag: recipient mouse strain

value: NOD.Cg-Prkdcscid Il2rgtm1Sug/JicTac


title: 4SU pulse early, DMSO


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD010

tag: strain


title: PDX model treated for 14 d, vehicle-treated, repeat 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD012

tag: age


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD008

tag: tissue


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD007

tag: source


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD004

tag: target


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD010

tag: gender


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD007


title: PDX model treated for 24 h, combination treatment, repeat 2


title: PDX model treated for 24 h, combination treatment, repeat 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD008


title: PDX model treated for 24 h, combination treatment, repeat 3


title: PDX model treated for 24 h, vehicle-treated, repeat 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD004


title: PDX model treated for 24 h, vehicle-treated, repeat 2


title: PDX model treated for 24 h, vehicle-treated, repeat 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD002


title: pSer2 RNA Polymerase II ChIP-Seq MLN

description: spike normalized ChIP-Sequencing (ChIP-rx)

tag: cell type

value: pSer2 RNA Polymerase II (ab5095, Abcam, Lot-Nr. CR3231908-1)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_H10_AD006


title: PDX model treated for 14 d, combination treatment, repeat 1


title: PDX model treated for 14 d, vehicle-treated, repeat 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD008


title: PDX model treated for 14 d, combination treatment, repeat 2


title: pSer2 RNA Polymerase II ChIP-Seq DMSO

tag: cell line


title: total RNA Polymerase II ChIP-Seq MLN

tag: chip antibody

value: total RNA Polymerase II (A10, sc17798, Santa Cruz, J1617)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD006


title: H3S10 S MLN

growth_protocol: synchronized IMR-5 cells with double thymidine block in S  phase

treatment_protocol: treat with DMSO, NVP2 or MLN8237

value: neuroblastoma cell line

value: pH3S10 (rabbit, Abcam, ab177218)


title: H3 S MLN

value: H3 (rabbit, Abcam, ab1791)


title: H3S10 S DMSO


title: total RNA Polymerase II ChIP-Seq DMSO


title: H3 S DMSO


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD010

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD008

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD012

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD006


title: H3S10 S MLN rep2


title: Input S


title: Input


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD001


title: H3 S MLN rep2


title: H3S10 S DMSO rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G7_AD002


title: H3 S DMSO rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD004


title: H3S10 S DMSO NVP2


title: H3 S DMSO NVP2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD012


title: Input NVP2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD008


title: H3S10 S NVP2


title: TCR-seq_P23-M1-PD1

city: SEATTLE

first: Sylvain

last: Simon

state: WA

address: 1100 Fairview Ave

department: Clinical Research

institute: Fred Hutchinson cancer research center

data_processing:
Library strategy: TCR-seq
TCR sequence analysis was performed using R (v3.5.2). The input data consisted of the observed number of each TCR (alpha or beta) sequence in each sample. Within each fraction, Fisher exact tests to calculate differential abundance of each TRBC (or TRAC) between two time points (T0 vs M1) were performed. The clonality score is derived from the Shannon entropy, which is calculated from the frequencies of all sequences divided by the logarithm of the total number of unique productive sequences. This normalized entropy value was then inverted (1 - normalized entropy) to produce the clonality metric. Differentially abundant sequences (FDR 5%) were then divided into 4 clusters (emerging, expanding, contracting and non-expanding/contracting) according to their signs of the fold-change (negative or positive) between T0 - M1 and whether or not the sequence was present at T0. Differential expression analyses were performed using the limma statistical framework and associated R package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics (2-tailed) were used to assess differences in expression. Contrasts comparing time points, fractions and/or outcomes were tested. When needed, intraclass correlations were estimated to account for measures originating from the same patients. An absolute log2-fold change cutoff of 1 and an FDR cutoff of 5% were used to determine DEGs.  Gene set enrichment analysis (GSEA) was performed using the R function Camera implemented within the limma R package. The same contrasts as above were investigated. A FDR cutoff of 5% was used to determine significant gene sets. KEGG, Hallmark, immunologic signatures (c7) and curated pathways were used as gene sets. Those gene sets were downloaded from MSigDB database60.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv-delimited table

source_name: Human PBMC

extract_protocol:
Total RNA were extracted from sorted T cells using RNeasy Kit (QIAGEN). Total RNA quality and quantity were assessed using high sensitivity RNA 6000 pico kit (Agilent) and Agilent 2100 Bioanalyzer. RNA with RIN>7 were obtained for all samples. Total RNA were stored at -80 °C until TCR and gene expression profiling.
cDNA librairies for TCR-seq analysis were prepared from 15ng of total RNA using Human TCR Panel QIAseq™ Immune Repertoire RNA Library Kit (QIAGEN) according to manufacturer’s instructions and was described previously.     Sequencing libraries were quantified with QIAseq Library Quant System (QIAGEN) and quality control was performed by capillary electrophoresis on a TapeStation System (Agilent Technologies). For sequencing, each library was diluted to 4nM, pooled and denatured. Denatured library pool with 1.0 pM concentration was run on a NextSeq Mid Output V2 kit (Illumina) for asymmetrical pair-end 261x41 base read. FASTQ files were analyzed in the QIAGEN GeneGlobe Data Analysis Center as described previously).

value: CD8 T cell

value: melanoma

tag: subject id

value: Melanoma patient number 23

tag: cell population

value: PD1 (PD1+TIGIT-)

tag: time

value: Month 1 after anti-PD-1 therapy


title: TCR-seq_P23-M1-DNEG

tag: patient diagnosis

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G6_AD002

value: Pons

value: female


title: TCR-seq_P23-T0-PD1

value: Baseline


title: TCR-seq_P23-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD002


title: H3 S NVP2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD012

value: male


title: TCR-seq_P22-M2-PD1

value: Melanoma patient number 22

value: Month 2 after anti-PD-1 therapy


title: TCR-seq_P22-M2-DNEG


title: TCR-seq_P23-T0-TIGIT

value: TIGIT (PD1-TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD002


title: TCR-seq_P22-M2-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD001

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD004


title: TCR-seq_P23-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G3_AD010

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD007

value: ACA


title: TCR-seq_P23-M1-DPOS

value: CD8 T cell


title: TCR-seq_P22-M1-PD1

value: melanoma


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G3_AD006


title: TCR-seq_P22-M1-DNEG


title: TCR-seq_P22-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G4_AD008


title: TCR-seq_P22-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G3_AD001


title: TCR-seq_P22-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G2_AD012


title: TCR-seq_P22-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G2_AD010


title: TCR-seq_P22-M2-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G2_AD007


title: Input MLN rep2

value: neuroblastoma cell line


title: TCR-seq_P22-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G2_AD004


title: TCR-seq_P21-M2-TIGIT

value: Melanoma patient number 21


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G1_AD010


title: TCR-seq_P22-T0-DNEG


title: TCR-seq_P21-M1-DNEG

value: Month 1 after anti-PD-1 therapy


title: TCR-seq_P21-M2-PD1

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G1_AD001

value: Pons


title: TCR-seq_P21-M2-DNEG

value: DNEG (PD1-TIGIT-)


title: TCR-seq_P21-M2-DPOS


title: TCR-seq_P21-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G1_AD002

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G12_AD012

value: male


title: TCR-seq_P21-T0-DNEG

value: Baseline


title: TCR-seq_P21-T0-PD1


title: TCR-seq_P21-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G11_AD006


title: TCR-seq_P21-M1-DPOS


title: TCR-seq_P21-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G12_AD004


title: TCR-seq_P19-M2PD1

value: Melanoma patient number 19

value: Month 2 after anti-PD-1 therapy


title: TCR-seq_P19-M2-TIGIT

value: TIGIT (PD1-TIGIT+)


title: TCR-seq_P19-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD010

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD012

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G1_AD004

value: ACA


title: TCR-seq_P19-T0-PD1

value: CD8 T cell


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD007


title: TCR-seq_P19-M2-DNEG

value: melanoma


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD008


title: TCR-seq_P19-M1-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G11_AD004


title: TCR-seq_P19-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G12_AD007


title: TCR-seq_P19-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F8_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD002


title: TCR-seq_P18-M2-TIGIT

value: Melanoma patient number 18


title: TCR-seq_P19-M1-TIGIT

value: Month 1 after anti-PD-1 therapy


title: TCR-seq_P18-M1-PD1

value: PD1 (PD1+TIGIT-)


title: TCR-seq_P18-M2-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G5_AD006

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G11_AD008


title: TCR-seq_P18-M2-PD1


title: TCR-seq_P18-M1-DNEG

value: DNEG (PD1-TIGIT-)


title: TCR-seq_P19-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD008

value: female


title: TCR-seq_P18-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G1_AD007


title: TCR-seq_P19-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD006


title: TCR-seq_P21-M1-TIGIT

value: Melanoma patient number 21


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_G10_AD004

value: male


title: TCR-seq_P18-T0-DNEG

value: Baseline


title: TCR-seq_P19-T0-DPOS

value: Melanoma patient number 19


title: TCR-seq_P18-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F9_AD004


title: TCR-seq_P16-M2-PD1

value: Melanoma patient number 16

value: Month 2 after anti-PD-1 therapy


title: TCR-seq_P18-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F8_AD010

value: brain

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD008

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F8_AD004


title: TCR-seq_P16-M2-DPOS

value: CD8 T cell

value: melanoma


title: TCR-seq_P18-M1-DPOS

value: Melanoma patient number 18

value: DPOS (PD1+TIGIT+)


title: TCR-seq_P16-M1-PD1

value: PD1 (PD1+TIGIT-)

value: Month 1 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD010


title: TCR-seq_P18-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD007


title: TCR-seq_P16-M1-DNEG

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD006

value: Pons

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD012

value: male


title: TCR-seq_P16-M2-DNEG


title: TCR-seq_P16-M2-TIGIT

value: TIGIT (PD1-TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F7_AD008


title: TCR-seq_P18-T0-TIGIT

value: Baseline


title: TCR-seq_P23-M1-TIGIT

value: Melanoma patient number 23


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD010


title: TCR-seq_P16-T0-TIGIT

value: Melanoma patient number 16


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD012

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD006


title: TCR-seq_P16-M1-TIGIT


title: TCR-seq_P16-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F6_AD004


title: TCR-seq_P15-M2-PD1

value: Melanoma patient number 15

value: Month 2 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD008

value: AI

value: ACA


title: TCR-seq_P16-T0-DNEG

value: CD8 T cell

value: melanoma


title: TCR-seq_P16-T0-DPOS

value: DPOS (PD1+TIGIT+)


title: TCR-seq_P15-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD004


title: TCR-seq_P15-M1-PD1

value: PD1 (PD1+TIGIT-)

value: Month 1 after anti-PD-1 therapy


title: TCR-seq_P15-M2-DNEG

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD001

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD007

value: female


title: TCR-seq_P16-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD010

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD004


title: TCR-seq_P15-M1-DPOS


title: TCR-seq_P15-M1-DNEG


title: TCR-seq_P15-M1-TIGIT

value: TIGIT (PD1-TIGIT+)


title: TCR-seq_P15-T0-PD1

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD006


title: TCR-seq_P15-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD010


title: TCR-seq_P15-T0-DNEG


title: TCR-seq_P14-M2-PD1

value: Melanoma patient number 14


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F5_AD002

value: brain


title: TCR-seq_P14-M2-DNEG


title: TCR-seq_P15-T0-TIGIT

value: Melanoma patient number 15


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD012


title: TCR-seq_P14-M2-TIGIT

value: Month 2 after anti-PD-1 therapy


title: TCR-seq_P14-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD002


title: TCR-seq_P14-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD008

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F2_AD007

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F2_AD006


title: TCR-seq_P14-T0-PD1

value: CD8 T cell


title: TCR-seq_P14-T0-TIGIT

value: melanoma


title: TCR-seq_P14-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F2_AD002


title: TCR-seq_P15-M2-TIGIT


title: TCR-seq_P14-M1-TIGIT


title: TCR-seq_P14-T0-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F12_AD010


title: TCR-seq_P8-M2-PD1

value: Melanoma patient number 8

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F12_AD008


title: TCR-seq_P8-M2-DNEG

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F12_AD006

value: Pons


title: TCR-seq_P14-M1-DNEG

value: Month 1 after anti-PD-1 therapy


title: TCR-seq_P14-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F3_AD004

value: male


title: TCR-seq_P8-M2-DPOS


title: TCR-seq_P8-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD010


title: TCR-seq_P8-M1-TIGIT

value: TIGIT (PD1-TIGIT+)


title: TCR-seq_P8-M2-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F12_AD002

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD007


title: TCR-seq_P8-M1-DPOS


title: TCR-seq_P8-M1-DNEG


title: TCR-seq_P8-T0-TIGIT

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD001

value: brain


title: TCR-seq_P8-T0-DPOS


title: TCR-seq_P7-M2-DNEG

value: Melanoma patient number 7


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD008


title: TCR-seq_P8-T0-DNEG


title: TCR-seq_P7-M2-DPOS

value: Month 2 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD006


title: TCR-seq_P7-M1-PD1


title: TCR-seq_P7-M2-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD007

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F11_AD004

value: ACA


title: TCR-seq_P7-M2-PD1

value: CD8 T cell


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD008


title: TCR-seq_P7-M1-DPOS

value: melanoma


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E9_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E9_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD001


title: TCR-seq_P7-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E9_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E9_AD007


title: TCR-seq_P8-T0-PD1


title: TCR-seq_P7-T0-DNEG


title: TCR-seq_P7-T0-TIGIT


title: TCR-seq_P7-T0-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E8_AD012


title: TCR-seq_P6-M1-PD1

value: Melanoma patient number 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_F10_AD006


title: TCR-seq_P7-M1-DNEG


title: TCR-seq_P6-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E8_AD004


title: TCR-seq_P6-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E8_AD002


title: TCR-seq_P6-T0-PD1

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E7_AD010


title: TCR-seq_P6-M1-DPOS


title: TCR-seq_P7-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E7_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E7_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E7_AD007


title: TCR-seq_P6-T0-DNEG

value: DNEG (PD1-TIGIT-)


title: TCR-seq_P6-T0-TIGIT


title: TCR-seq_P6-T0-DPOS


title: TCR-seq_P5-M2-DNEG

value: Melanoma patient number 5


title: TCR-seq_P5-M2-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E6_AD006

value: Pons


title: TCR-seq_P5-M2-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E6_AD004

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E6_AD002


title: TCR-seq_P5-M2-DPOS


title: TCR-seq_P5-M1-DNEG

value: Month 1 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E6_AD001


title: TCR-seq_P5-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E5_AD007

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E5_AD002


title: TCR-seq_P5-M1-TIGIT

value: TIGIT (PD1-TIGIT+)


title: TCR-seq_P5-T0-DNEG

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E4_AD010

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E5_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD010


title: TCR-seq_P5-M1-DPOS


title: TCR-seq_P5-T0-PD1


title: TCR-seq_P5-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E4_AD007


title: TCR-seq_P5-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E6_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD006


title: P23-M2-TIGIT

data_processing:
FASTQ files were generated from Illumina’s NextSeq Sequencing run and analyzed on QIAGEN’s GeneGlobe Data Analysis Center (https://www.qiagen.com/us/shop/genes-and-pathways/data-analysis-center-overview-page). GeneGlobe provides the primary read alignment and demultiplexed UMI values.  Raw count data were imported into R (v3.5.2). The edgeR R package was used to calculate the normalization factors to scale the raw library sizes, followed by a voom transformation from the limma R package. Briefly, it transforms count data to log2 counts per million (log2 CPM), and estimates the mean-variance relationship to compute appropriate observation-level weights.  Differential expression analyses were performed using the limma statistical framework and associated R package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics (2-tailed) were used to assess differences in expression. Contrasts comparing time points, fractions and/or outcomes were tested. When needed, intraclass correlations were estimated to account for measures originating from the same patients. An absolute log2-fold change cutoff of 1 and an FDR cutoff of 5% were used to determine DEGs.  Gene set enrichment analysis (GSEA) was performed using the R function Camera implemented within the limma R package. The same contrasts as above were investigated. A FDR cutoff of 5% was used to determine significant gene sets. KEGG, Hallmark, immunologic signatures (c7) and curated pathways were used as gene sets. Those gene sets were downloaded from MSigDB database60.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv-delimitated table

extract_protocol:
Total RNA were extracted from sorted T cells using RNeasy Kit (QIAGEN). Total RNA quality and quantity were assessed using high sensitivity RNA 6000 pico kit (Agilent) and Agilent 2100 Bioanalyzer. RNA with RIN>7 were obtained for all samples. Total RNA were stored at -80 °C until TCR and gene expression profiling.     Gene expression analysis by RNAseq was done using 10ng of total RNA with QIAseq Targeted RNA Custom Panel (CRHS-10563Z-975 and CRHS-10707Z-977) with QIAseq Targeted RNA 96-Index kits (QIAGEN) according to manufacturer’s recommendations. Briefly, RNA is treated with DNase to remove any residual DNA, and the RNA is reverse transcribed into cDNA. In the first reactions a gene-specific primer with unique molecular indexes (UMIs) is used in a single primer extension reaction to capture the gene of interest. Next, a gene specific reverse primer and a universal primer is used to capture and amplify the region of interest. A unique sample dual index is then added using a PCR reaction.     Sequencing libraries were quantified with QIAGEN’s QIAseq Library Quant System and quality control was performed by capillary electrophoresis on a TapeStation System (Agilent Technologies) using a High Sensitivity D1000 Screen Tape. Each library was diluted and normalized to 4 nM according to the QIAseq Library Quant results prior to pooling equally and denaturing.  The denatured library pool with a final concentration of 1.2 pM was run on a NextSeq High Output V2 kit (Illumina) using dual indexing, single end sequencing with 150 cycles and a Custom Read 1 sequencing Primer.
Llibraries were prepared for sequencing using standard Illumina protocols

tag: subject number

value: Melanoma patient number 23

value: Month 2 after anti-PD-1 therapy


title: P23-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD004

value: ACA


title: P23-M2-DPOS

value: CD8 T cell


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E4_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD012

value: AI


title: P23-T0-DNEG

value: melanoma


title: P23-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD008


title: P23-M2-DNEG


title: P23-M1-DPOS

value: DPOS (PD1+TIGIT+)


title: P23-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD007


title: P23-M1-DNEG


title: P23-M2-PD1

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD002


title: P23-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E3_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD008


title: P22-M2-DPOS

value: Melanoma patient number 22


title: P22-M2-TIGIT


title: P23-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD010


title: P22-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD007


title: P22-M2-DNEG

value: DNEG (PD1-TIGIT-)


title: P22-M2-PD1


title: P22-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD006

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E2_AD001

value: male


title: P22-M1-DNEG

value: Month 1 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD001


title: P22-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD012


title: P22-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E1_AD012


title: P22-T0-PD1


title: P21-M2-TIGIT

value: Melanoma patient number 21


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD008

value: female


title: P22-T0-DPOS

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD004

value: brain


title: P21-M2-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E12_AD002


title: P22-T0-TIGIT

value: TIGIT (PD1-TIGIT+)


title: P21-M2-PD1

value: Month 2 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD010

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD002


title: P21-M1-TIGIT

value: CD8 T cell


title: P21-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD012

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD007


title: P21-M1-PD1

value: melanoma


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E12_AD008


title: P21-T0-PD1


title: P21-T0-DPOS

value: DPOS (PD1+TIGIT+)


title: P21-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD004


title: P21-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_E10_AD002


title: P19-M1-DNEG

value: Melanoma patient number 19


title: P19-M2-DPOS


title: P19-M2PD1

value: PD1 (PD1+TIGIT-)


title: P21-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD006


title: P21-M1-DNEG

value: DNEG (PD1-TIGIT-)


title: P19-M2-TIGIT


title: P19-M1-TIGIT


title: P19-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD001

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD004

value: male


title: P19-M2-DNEG


title: P19-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD010


title: P19-M1-PD1

value: Month 1 after anti-PD-1 therapy


title: P18-M2-PD1

value: Melanoma patient number 18


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD002

value: female


title: P18-M2-DNEG


title: P18-M2-DPOS


title: P19-T0-DPOS

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD008

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D9_AD012


title: P19-T0-TIGIT

value: TIGIT (PD1-TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD012


title: P19-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD004


title: P18-M1-TIGIT


title: P18-T0-DNEG


title: P18-M2-TIGIT

value: Month 2 after anti-PD-1 therapy


title: P18-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD001

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D6_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D7_AD006


title: P16-M2-PD1

value: CD8 T cell

value: Melanoma patient number 16


title: P16-M2-TIGIT

value: melanoma


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D6_AD006


title: P18-M1-DPOS

value: DPOS (PD1+TIGIT+)


title: P16-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D8_AD001


title: P18-T0-DPOS


title: P18-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD007

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD012


title: P16-M2-DPOS


title: P16-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D6_AD007


title: P18-M1-PD1

value: PD1 (PD1+TIGIT-)


title: P16-M2-DNEG

value: DNEG (PD1-TIGIT-)


title: P16-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD002

value: Pons


title: P18-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D6_AD001

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD001


title: P16-M1-TIGIT

value: Month 1 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD004


title: P16-T0-DPOS


title: P16-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D5_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD007


title: P15-M2-DNEG

value: Melanoma patient number 15


title: P15-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD004


title: P15-M2-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD002

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD008


title: P15-M1-TIGIT


title: P16-T0-DNEG

value: Baseline


title: P15-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD010

value: brain


title: P16-T0-TIGIT

value: TIGIT (PD1-TIGIT+)


title: P15-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D4_AD001


title: P14-M2-PD1

value: Melanoma patient number 14

value: Month 2 after anti-PD-1 therapy


title: P15-T0-DPOS

value: CD8 T cell


title: P14-M2-DNEG


title: P14-M2-TIGIT


title: P14-M2-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD007

value: ACA


title: P15-M1-PD1

value: melanoma


title: P14-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD006


title: P14-M1-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD012

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD007


title: P15-M1-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD006


title: P15-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D3_AD004


title: P14-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD004


title: P15-T0-PD1

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD010


title: P15-M2-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD010


title: P8-M2-DPOS

value: Melanoma patient number 8


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D2_AD008


title: P8-M1-PD1


title: P14-M1-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD012


title: P8-M1-TIGIT


title: P14-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD008


title: P14-T0-PD1


title: P14-T0-DNEG

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD006

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD008


title: P14-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D1_AD001

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD006


title: P8-M2-PD1


title: P8-M2-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD008


title: P7-M2-PD1

value: Melanoma patient number 7


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD007

value: female


title: P8-M1-DNEG

value: Month 1 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD001

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D12_AD002


title: P8-M1-DPOS


title: P7-M2-DPOS


title: P8-T0-PD1

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD010


title: P8-M2-TIGIT

value: TIGIT (PD1-TIGIT+)


title: P8-T0-DNEG


title: P7-M1-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD007


title: P7-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD006


title: P8-T0-TIGIT


title: P7-T0-DNEG


title: P8-T0-DPOS


title: P6-M1-PD1

value: Melanoma patient number 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD002


title: P6-M1-DNEG

value: CD8 T cell


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD007

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD004


title: P7-M2-DNEG

value: melanoma

value: Month 2 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C8_AD012

value: AI


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C8_AD008


title: P7-M2-TIGIT


title: P6-T0-DNEG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C8_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D11_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C8_AD006


title: P5-M2-PD1

value: Melanoma patient number 5

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C7_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD010


title: P7-M1-PD1


title: P7-M1-DNEG

value: DNEG (PD1-TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD004

value: Pons


title: P7-M1-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD008


title: P5-M2-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_D10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD012

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD010


title: P7-T0-TIGIT

value: Melanoma patient number 7


title: P6-M1-TIGIT

value: Month 1 after anti-PD-1 therapy


title: P6-M1-DPOS


title: P7-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD008

value: brain

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C9_AD002


title: P5-M1-DNEG


title: P6-T0-DPOS

value: Baseline


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C8_AD001


title: P6-T0-PD1

value: Melanoma patient number 6


title: P5-M2-DNEG

value: CD8 T cell


title: P6-T0-TIGIT

value: TIGIT (PD1-TIGIT+)


title: P5-M1-TIGIT

value: melanoma


title: P5-M2-TIGIT

value: Month 2 after anti-PD-1 therapy


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C7_AD004

value: ACA


title: P5-T0-DNEG

value: Melanoma patient number 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD004


title: P5-T0-TIGIT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C5_AD012

value: AI


title: P5-M1-PD1

value: PD1 (PD1+TIGIT-)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C4_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD006

value: Pons


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD010


title: P5-M1-DPOS

value: DPOS (PD1+TIGIT+)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD012

value: male


title: P5-T0-PD1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C4_AD008


title: Monocytes 33

city: Oklahoma City

first: Judith

middle: A.

last: James

state: Oklahoma

address: 825 NE 13th Street

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Libraries were evaluated for poor sample quality using FASTQC (version 0.11.8)
Adaptors and contaminating non-specific reads removed using BBTools (version38.56)
Reads were aligned to the GENCODE release 28 transcriptome using STAR (version 2.5.3a)
BAM files were then converted to a gene count matrix using StringTie (version 1.3.6)
Counts were normalized using the DESeq2 package (version 1.24.0) in R and transformed using variance stabilizing transformation for visualizations
All low expressed genes were removed prior to analysis, and outliers were identified and removed using hierarchical clustering
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel comma seperated values file with transcript counts

source_name: PBMCs

extract_protocol:
PBMCs were sorted for CD66b-CD19-CD3+ T cells, CD66b-CD3-CD19+ B cells, CD66b-CD3-CD19-CD56-HLA-DR+CD14+CD16+/- monocytes using a FACS Aria III (BD Biosciences) and RNA was isolated using TRIZOL reagent (Invitrogen/Thermo Fischer (Waltham, MA), purified with Direct-zol RNA microprep kit (Zymo Research, Irvine, CA), and quantitated using 2100 Bioanalyzer (Agilent, Santa Clara, CA).
QuantSeq 3’ mRNA-sequencing library prep kit for Illumina (FWD) (Lexogen, Vienna, Austria) was used to create cDNA libraries, amplify and sequence 3 million reads/sample using NextSeq 550 (Illumina, San Diego, CA). 1 ug of total RNA was used for construction of the sequencing libraries and the manufacturer protocol was followed.

tag: manuscript subject id

tag: disease status

value: SLE

tag: race

value: EA

value: Monocytes


title: P5-T0-DPOS


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C6_AD007

tag: strain

value: brain

value: female


title: T cells 34

value: AA

value: T cells


title: Monocytes 35


title: T cells 35


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C5_AD004

tag: age


title: T cells 33


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD007

tag: tissue


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C4_AD001

tag: source


title: T cells 31


title: Monocytes 32


title: B cells 33

value: B cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C7_AD010

tag: target


title: T cells 32


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD004

tag: gender


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD006


title: B cells 32

tag: cell type


title: B cells 34


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C4_AD010


title: Monocytes 30


title: T cells 30


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD006


title: B cells 30


title: T cells 29

value: ANA+


title: Monocytes 29


title: B cells 29


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C3_AD008


title: T cells 28


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD012


title: Monocytes 28


title: T cells 27


title: Monocytes 27


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD004


title: B cells 31


title: B cells 28


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD006


title: T cells 26


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD010


title: Monocytes 26


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD004


title: B cells 26


title: B cells 27


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD006


title: T cells 25


title: B cells 25


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C12_AD004


title: B cells 23

value: ANA-


title: B cells 24


title: T cells 22


title: Monocytes 23


title: T cells 24


title: Monocytes 22


title: Monocytes 21


title: T cells 21


title: B cells 21


title: T cells 20


title: Monocytes 20


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD004

value: ACA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD007


title: B cells 20


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C11_AD002


title: Monocytes 19


title: B cells 19


title: B cells 18


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD004


title: T cells 17


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD010


title: B cells 17


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD012


title: T cells 16


title: Monocytes 16


title: T cells 18


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD007


title: T cells 15


title: B cells 15


title: B cells 16


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD004


title: B cells 14


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD008


title: T cells 19


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C10_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD008


title: Monocytes 14


title: Monocytes 15


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD012


title: T cells 13


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B9_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD010


title: Monocytes 12


title: B cells 10


title: Monocytes 13


title: Monocytes 9


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B5_AD012


title: T cells 12


title: B cells 13


title: Monocytes 11


title: T cells 9


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B8_AD006


title: T cells 14


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B4_AD010


title: B cells 12


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD004


title: B cells 9


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B7_AD001


title: B cells 8


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B5_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B6_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B6_AD004


title: T cells 7


title: Monocytes 8


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B4_AD008


title: T cells 8


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B4_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B4_AD006


title: Monocytes 7


title: T cells 10


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD007


title: B cells 7


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B4_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD008


title: T cells 4


title: T cells 5


title: Monocytes 6


title: B cells 6


title: Monocytes 5


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD002


title: Monocytes 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_C2_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD008


title: T cells 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B3_AD010


title: B cells 3


title: T cells 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD004


title: B cells 2


title: Monocytes 2


title: B cells 1


title: B cells 4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B2_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD010


title: T cells 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD006


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD008


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD012


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD007


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P3_180801_P4_B1_AD002