title: Activated MuSCs isolated from CTX injured muscle, Trpm7cKO_5, 3 days post injury

city: Shizuoka

first: Kotaro

last: Hirano

state: Shizuoka

address: Suruga Ward 52-1 Yada

country: Japan

institute: University of Shizuoka

description: Library name: ASC5_Trpm7cKO_2879-2

data_processing: Cell barcode and UMI in Read1 was extracted by using UMI-tools (ver: 1.1.4) with following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq –bc pattern=NNNNNNNNNNCCCCCCCCC”. Adaptor sequence and low-quality sequence were removed and read length below 20 bp were discarded by using Trim Galore (ver:  0.6.10), and reads were mapped to the GRCm38 reference using HISAT2 (ver: 2.2.1). Read  counts for each gene were obtained by featureCounts (ver: 2.0.6) and UMI duplications were removed by UMI-tools. Four cell barcodes “ATGCAATGC, GACACGACA, CGATGCGAT, TCTGGTCTG” were assigned to each sample and differentially expressed genes were extracted by DESeq2 (ver.1.30.1) using |log2FC| > 1.5 and padj < 0.05 as threshold values.

source_name: Skeletal muscle

extract_protocol:
Three thousand cells were sorted into 40 μL of 1x direct lysis buffer (TaKaRa, #635013) with RNase Inhibitor (TaKaRa, #2313A) and lysate was used for reverse transcription.
Library preparation was performed using the CEL-Seq2 protocol with a modification that Second Strand Synthesis Module (NEB) was used for double-stranded cDNA synthesis. Library was amplified by PCR without any sample pooling.

value: Skeletal muscle

tag: cell line

value: muscle satellite cell

value: Trpm7 knockout

value: CTX 3 days


title: 206530730006_R03C01 Methylation

status: Public on Apr 04 2025

type: genomic

city: Rochester

first: ARIJIT

last: PANDA

state: MINNESOTA

address: 200 1st street SW

country: USA

institute: MAYO CLINIC

hyb_protocol: Bisulphite converted DNA was subjected to Illumina FFPE restoration and hybridized to Illumina 450K EPICIllumina arrays

scan_protocol: We scanned the chips using Illumina’s iScan instrument with version 4.2.1 software.

data_processing:
The data package that we returned included the raw scan data (.idat files), as well as some preliminary reports that we generate with Illumina’s GenomeStudio v2011.1 software with the methylation module.
*processed value definition: average methylation

label: green (Cy3) and red (Cy5)

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain Tumor

label_protocol: Standard Illumina protocol

extract_protocol: Qiagen FFPE DNA isolation

tag: tissue

value: Brain Tumor

tag: age

tag: gender

value: F

value: Oligodendroglioma


title: Brain, CD3+ SS2 KO A15 mouse 2 scRNAseq

type: SRA

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
SmartSeq2
44_7_A15

library_source: transcriptomic single cell

data_processing:
alignment was performed using kallisto v0.44.0
The transcript abundance files in hdf5 format (Hoefling and Annau 2020) from the pseudo alignment via kallisto v0.44.0 (Bray et al. 2016) were merged and converted into Transcripts per Kilobase Million (TPM) normalised gene expression matrices, with additional length scaling (”lengthScaledTPM”) and otherwise default parameters, via the package tximport v.1.18.0 (Soneson et al. 2015). For that purpose, the transcript to gene annotation file (tx2genes.csv) found in the sequencing results folders was used to associate the corresponding transcript ID to gene ID. The Ensembl IDs were transformed into gene symbols using biomaRt v.2.46.0 (Durinck et al. 2005; Durinck et al. 2009).
Assembly: mm10
Supplementary files format and content: all samples merged to one matrix: tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
To isolate immune cells, after perfusion, brains were digested for 45 min in RPMI containing 10 mM HEPES, 0.5 mg/ml Collagenase Type IV (Sigma Aldrich) and 0.05 mg/ml DNase I (Sigma Aldrich) at 37°C. Cells were then isolated using density gradient centrifugation. The isolated brain cells were directly sorted on an BD Aria III cell sorter for sequencing experiments. The left hemisphere was used to sort CD45+ cells to perform scRNAseq with SeqWell v3 (Aicher et al. 2019). The right hemisphere was used for index sorting of CD3+ cells into 384 well plates (Penter et al. 2018) for scRNAseq with SmartSeq2 (Picelli et al. 2014). Only cells isolated with a purity of > 98% were used for further analysis.
CNS T cells from the brains of B57BL/6 Zfyve26-/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 or Zfyve26+/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 animals were isolated as described above. Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN) and transcriptome analysis was performed by SmartSeq2 (Picelli et al. 2014). Per sample, 500 pg RNA was denatured for 2 min at 95°C in 0.1% Triton X-100 containing 0.05 mM dNTP, 2 μM anchored oligodT (Smart dT30VN) primer and 1 U/μl RNase Inhibitor (Takara). Reverse transcription was carried out at 42°C for 90 min followed by 15 min inactivation at 70°C using 5 U/μl Superscript II reverse transcriptase (Thermo Fisher Scientific) in 1X Superscript II Buffer supplemented with 5 mM DTT, 1 M Betaine, 14 mM MgCl2, 1 μM Template Switching Oligo and 1 U/μl RNase Inhibitor. cDNA was then pre-amplified using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) containing 1 nM ISPCR Primer. Amplification was carried out for 16 cycles consisting of 20 s denaturation at 98°C, 20 s annealing at 67°C and 6 min elongation at 72°C each after an initial denaturing at 98°C for 3 min. The pre-amplification reaction was then purified by using a 0.8:1 ratio of AMPure XP beads (Beckman Coulter). DNA was allowed to bind to beads for 3 min at RT followed by one wash in 80% Ethanol for 30 s. cDNA was then eluted from the beads in 15 μl of water before checking for cDNA quality on a Tapestation 2200 using a HighSensitivity D5000 assay (Agilent Genomics) according to manufacturer’s instructions. Tagmentation, PCR amplification and indexing of samples was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturer’s recommendations. After library preparation, DNA was purified with a 1:1 ratio of AMPure XP beads and sample. Quantification and quality check of libraries was done on a Tapestation 2200 using a HighSensitivity D5000 Assay. Library concentrations were adjusted to 2nM and pooled prior to sequencing SR 75 bp with two 8 bp index reads on an Illumina NextSeq 500 instrument using High Output v2 chemistry. RNA-seq data was demultiplexed using bcl2fastq2 v2.20 and pseudo aligned to Mus_musculus.GRCm38.cdna.all.fa.gz transcriptome using kallisto v0.44.0 (Bray et al. 2016). The sequences of all oligos used for SmartSeq2 can be found in Table S7. All oligos were biotinylated at the 5′ end to avoid the formation of concatemers.

value: Brain

tag: strain

tag: Sex

value: male

tag: genotype

value: KO

value: 15 months


title: Brain, CD3+ SS2 KO A14 mouse 2 scRNAseq

description:
SmartSeq2
44_7_A14


title: Activated MuSCs isolated from CTX injured muscle, Trpm7cKO_3, 3 days post injury

description: Library name: ASC3_Trpm7cKO_2883-1

library_source: transcriptomic

tag: cell type

tag: treatment


title: Brain, CD3+ SS2 KO A22 mouse 2 scRNAseq

description:
SmartSeq2
44_7_A22


title: 206530730006_R02C01 Methylation

value: M


title: Brain, CD3+ SS2 KO A20 mouse 2 scRNAseq

description:
SmartSeq2
44_7_A20


title: Activated MuSCs isolated from CTX injured muscle, Trpm7cKO_1, 3 days post injury

description: Library name: ASC1_Trpm7cKO_2995-3


title: 206530730006_R01C01 Methylation

value: Astrocytoma (Grades 2, 3, 4)


title: Activated MuSCs isolated from CTX injured muscle, control_5, 3 days post injury

description: Library name: ASC5_control_3015-1

value: control


title: Brain, CD3+ SS2 KO A1 mouse 2 scRNAseq

description:
SmartSeq2
44_7_A1


title: 206530730005_R08C01 Methylation


title: Brain, CD3+ SS2 KO P9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P9


title: Activated MuSCs isolated from CTX injured muscle, control_1, 3 days post injury

description: Library name: ASC1_control_2851-3


title: Activated MuSCs isolated from CTX injured muscle, control_3, 3 days post injury

description: Library name: ASC3_control_2923-1


title: 206530730006_R04C01 Methylation


title: Brain, CD3+ SS2 KO P8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P8


title: 206530730005_R07C01 Methylation

value: Mixed Oligodendroglioma-Astrocytoma


title: Activated MuSCs isolated from CTX injured muscle, control_2, 3 days post injury

description: Library name: ASC2_control_2853-3


title: 206530730006_R05C01 Methylation


title: Soybean leaf sample 49a

city: Urbana

first: Katy

middle: D

last: Heath

state: IL

address: 1201 W. Gregory Dr

department: Plant Biology

institute: University of Illinois

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adapters were trimmed from the 3' end of reads using Trimmomatic.
Salmon version 1.2.1 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon, then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates, and --validateMappings to perform selective alignment.
Gene-level counts were estimated based on transcript-level abundances using the tximport R package v1.16.1 with the "lengthScaledTPM" option.
TMM normalization was performed with the edgeR R package v3.30.3.
Genes were filtered that did not have at least 0.5 counts-per-million in at least samples.  TMM normalization was performed again after filtering.
Assembly: GCF_000004515.5_Glycine_max_v2.1
Supplementary files format and content: Tab-delimited text listing raw counts for each gene.
Supplementary files format and content: Tab-delimited text listing log2-counts-per-million for each filtered gene.

molecule: polyA RNA

organism: Glycine max

source_name: leaf

growth_protocol: Soybeans were grown in chambers in sterile soil. Soybeans were inoculated  at growth stage R1 and allowed to grow for 8 days before leaf punches were taken for RNA sequence data.

extract_protocol:
Leaf punches were taken from top leaves, middle leaves, and bottom leaves. RNA was extracted using RNeasy plant mini kit.
RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Plants were inoculated with Methylobacteria, Colletotrichum sp. 1 and 2, and combinations of both by spraying leaves with endophytes suspended in sterile water, covering with a plastic bag overnight to increase humidity and encourage infection, and then allowed to grow with careful watering to avoid splashing and transfer of endophytes.

value: leaf


title: Brain, CD3+ SS2 KO P7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P7


title: Activated MuSCs isolated from CTX injured muscle, Trpm7cKO_4, 3 days post injury

description: Library name: ASC4_Trpm7cKO_2879-1


title: 206530730005_R06C01 Methylation


title: Soybean leaf sample 40a


title: Activated MuSCs isolated from CTX injured muscle, Trpm7cKO_2, 3 days post injury

description: Library name: ASC2_Trpm7cKO_2877-3


title: Brain, CD3+ SS2 KO P6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P6


title: Soybean leaf sample 37a

value: Control


title: Activated MuSCs isolated from CTX injured muscle, control_4, 3 days post injury

description: Library name: ASC4_control_2945-1

value: Skeletal muscle


title: Soybean leaf sample 34a


title: Brain, CD3+ SS2 KO P5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P5


title: Soybean leaf sample 30a


title: 206530730005_R03C01 Methylation


title: Brain, CD3+ SS2 KO P4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P4


title: 206530730005_R04C01 Methylation


title: Soybean leaf sample 28a


title: 206530730005_R05C01 Methylation


title: Brain, CD3+ SS2 KO P3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P3


title: 206530730005_R02C01 Methylation


title: Soybean leaf sample 27a


title: 206530730005_R01C01 Methylation


title: Brain, CD3+ SS2 KO P24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P24


title: 206530720154_R05C01 Methylation


title: Soybean leaf sample 32a


title: Soybean leaf sample 24b

value: Meth


title: Soybean leaf sample 26a


title: Soybean leaf sample 25a


title: Brain, CD3+ SS2 KO P23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P23


title: alligator genital tubercle st15-16 ISL1 ChIP

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

department: Genetics

institute: University of Georgia

description:
PE150 sequencing
am_GT_st15-16_ISL1_qval0.01_4fold.narrowPeak
am_GT_st15-16_ISL1.bw

library_source: genomic

data_processing:
Libraries were sequenced by the Georgia Genomics and Bioinformatics Core (SE75) or by Genewiz (PE150). The GGBC provided pre-trimmed reads, while Genewiz reads were subsequently trimmed using cutadapt using the settings -O 1, -m 25
RNA-seq reads were aligned to mm10 using STAR (v. 2.7.3a). Transcripts were counted using HTSeq (v. 0.13.5). Differential gene expression was determined using DESeq2 (Galaxy v. 2.11.40.6).
ChIP-seq data were processed using the AQUAS Transcription Factor and Histone ChIP-seq pipeline. We used the pipeline's default bwa aligner to align mouse reads to mm10 (UCSC), chick to galGal6 (UCSC), alligator to allMis0.2/allMis1 (UCSC), turtle to CAS_Tse_1.0 NCBI RefSeq), and lizard to AnoSag2.0 (local genome build). Fragment size was set to 175 (-speak_spp 175, -extsize_macs2 175).
SPP was used to call IDR peaks using the default cutoff (0.05) in ISL1 ChIP-seq experiments performed in duplicate, while MACS2 peaks were used from individual experiments and from H3K27ac datasets. In H3K27ac datasets, the naive overlap peaks were used, while MACS2 peaks from ISL1 ChIP-seq in alligator, turtle, and lizard were filtered using a q-value cutoff of 0.01 and fold-enrichment cutoff of 4. bigWig files were generated using MACS2 and represent fold-enrichment values of ChIP vs control samples.
Mouse forelimb ISL1 ChIP-seq IDR peaks were used as a negative control to filter false-positive peaks from ISL1 peak sets, generating "FL_filtered" files
Assembly: varied by species (see above)
Supplementary files format and content: DESeq2 tabular files, SPP or MACS2 peak files, and MACS2 bigWig files

organism: Alligator mississippiensis

source_name: genital tubercle

extract_protocol:
For RNA-seq, genital tubercle samples were placed in RNA-Later, which was then removed before freezing samples at -80C. For hindlimb field samples, both sides from each embryo were placed directly into mirVana Lysis/Binding buffer and frozen. RNA was extracted using the mirVana miRNA isolation kit. For ChIP-seq, tissues form multiple embryos were sonified using a probe sonifier followed by a bath sonifier. Lysates were then incubated with the antibody with a portion kept as input DNA.
RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina); ChIP-seq libraries were constructed using the NEBNext Ultra II Library Prep Kit

tag: developmental stage

value: WT

tag: chip antibody


title: Soybean leaf sample 23a


title: Soybean leaf sample 29a


title: Brain, CD3+ SS2 KO P21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P21


title: 206530720154_R04C01 Methylation

value: Gliosarcoma


title: Brain, CD3+ SS2 KO P20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P20


title: Soybean leaf sample 20a


title: Soybean leaf sample 21a


title: Soybean leaf sample 22a


title: Soybean leaf sample 18a


title: Brain, CD3+ SS2 KO P18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P18


title: 206530720154_R01C01 Methylation

value: Brain Tumor


title: Brain, CD3+ SS2 KO P15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P15


title: Soybean leaf sample 17a


title: Brain, CD3+ SS2 KO P14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P14


title: Soybean leaf sample 15a


title: Soybean leaf sample 16a


title: Brain, CD3+ SS2 KO P13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P13


title: 206530720146_R07C01 Methylation


title: 206530720146_R04C01 Methylation

value: F


title: Soybean leaf sample 12a


title: 206530720146_R05C01 Methylation


title: Soybean leaf sample 11a


title: Soybean leaf sample 14b


title: 206530720146_R03C01 Methylation


title: Soybean leaf sample 13a


title: Brain, CD3+ SS2 KO P12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P12


title: 206530720154_R02C01 Methylation


title: Soybean leaf sample 10a


title: Brain, CD3+ SS2 KO P11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P11


title: Soybean leaf sample 9a


title: Brain, CD3+ SS2 KO P10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_P10


title: Soybean leaf sample 8a


title: Soybean leaf sample 19a


title: Soybean leaf sample 7a


title: Soybean leaf sample 6a


title: Soybean leaf sample 33a


title: 206530720061_R05C01 Methylation


title: Brain, CD3+ SS2 KO O7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O7


title: Soybean leaf sample 5a


title: Soybean leaf sample 4a


title: 206530720061_R04C01 Methylation


title: Brain, CD3+ SS2 KO O5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O5


title: Soybean leaf sample 2a


title: Soybean leaf sample 1a


title: Brain, CD3+ SS2 KO O4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O4


title: 206530720061_R02C01 Methylation


title: PBMC_Critical_Patient_pool

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

description: Library name: Critical

data_processing:
Droplet libraries were processed using 10x Genomics Cell Ranger 4.0.0. Reads were aligned to the GRCh38 human genome. The filtered feature matrices were used.
Assembly: GRCh38
Supplementary files format and content: Raw counts in h5 format

source_name: blood cells

extract_protocol:
PBMCs were isolated from patient blood samples using  Ficol. Isolates PBMCs were washed twice with 0.5% BSA/PBS.
Each sample pool was loaded into a different lane of a 10× chip (Single Cell G Chip Kit for v3.1). The 10x Chromium controller (10x Genomics), in combination with v3.1 reagents, was used to capture the single cells and generate Single-Indexed sequencing libraries, according to the manufacturer’s instructions (document CG000204, RevD).Sequencing was performed with a 150 bp paired-end kit using a custom program (28-8-0-150) on the Illumina NextSeq 500/550.

value: blood cells

tag: disease state


title: 206530720022_R05C01 Methylation


title: 206530720061_R01C01 Methylation


title: PBMC_Healthy_Patient_pool

description: Library name: Healthy

value: Healthy


title: PBMC_Mild_Patient_pool

description: Library name: Mild


title: Soybean leaf sample 3a


title: Brain, CD3+ SS2 KO O3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O3

value: Brain

value: male


title: PBMC_Severe_Patient_pool

description: Library name: Severe


title: Brain, CD3+ SS2 KO O24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O24

value: KO

value: 15 months


title: 206530720146_R02C01 Methylation

value: Astrocytoma (Grades 2, 3, 4)


title: CD45+ WT mouse 2 replicate 2_abs 3' CITEseq

description:
SeqWell v3
WT_2_pool_2_abs

library_source: other

data_processing:
The demultiplexing, gene counting and aggregation were made using an adapted version of dropSeqPipe v0.4. (https://github.com/Hoohm/dropSeqPipe)
Assembly: mm10
Supplementary files format and content: tar archives containing tab-separated values files and matrix files
Library strategy: CITE-Seq

molecule: other

extract_protocol:
To isolate immune cells, after perfusion, brains were digested for 45 min in RPMI containing 10 mM HEPES, 0.5 mg/ml Collagenase Type IV (Sigma Aldrich) and 0.05 mg/ml DNase I (Sigma Aldrich) at 37°C. Cells were then isolated using density gradient centrifugation. The isolated brain cells were directly sorted on an BD Aria III cell sorter for sequencing experiments. The left hemisphere was used to sort CD45+ cells to perform scRNAseq with SeqWell v3 (Aicher et al. 2019). The right hemisphere was used for index sorting of CD3+ cells into 384 well plates (Penter et al. 2018) for scRNAseq with SmartSeq2 (Picelli et al. 2014). Only cells isolated with a purity of > 98% were used for further analysis.
CNS CD45+ cells from the brains of B57BL/6 Zfyve26-/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 or Zfyve26+/- 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 animals were isolated as described above. These cells were labeled with ADT antibodies (Biolegend) according to the manufacturer’s protocol for TotalSeq™-A antibodies. 50μL cell suspension with 1x106 cells were resuspended in staining buffer (2% BSA, Jackson Immuno Research; 0.01% Tween-20, Sigma-Aldrich; 1x DPBS, GIBCO) and 5 μL mouse TruStain FcX™ FcBlocking (Biolegend) reagent were added. The blocking was performed for 10 min at 4°C. In the next step 1μg unique TotalSeq-A antibody was added to each sample and incubated for 30 min at 4°C. After the incubation time 1.5mL staining buffer were added and centrifuged for 5min at 350 g and 4°C. Washing was repeated for a total of 3 washes. Subsequently, the cells were resuspended in an appropriate volume of 1x DPBS (GIBCO), passed through a 40 μm mesh (Flowmi™ Cell Strainer, Merck) and counted, using a Neubauer Hemocytometer (Marienfeld). Cell counts were adjusted and hashtagged cells were pooled equally. The cell suspension was loaded, with 25,000 cells to 1.1x105 beads per SeqWell array. RT-transcription cDNA amplification and library generation were performed according to recommendations from Aicher et al. Aicher et al..

value: female


title: 206530720022_R04C01 Methylation

value: Mixed Oligodendroglioma-Astrocytoma


title: Brain, CD3+ SS2 KO O23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O23


title: CD45+ WT mouse 1 replicate 2_abs 3' CITEseq

description:
SeqWell v3
WT_1_pool_2_abs


title: CD45+ WT mouse 2 replicate 1_abs 3' CITEseq

description:
SeqWell v3
WT_2_pool_1_abs


title: CD45+ WT mouse 1 replicate 1_abs 3' CITEseq

description:
SeqWell v3
WT_1_pool_1_abs


title: 206530720022_R03C01 Methylation


title: CD45+ KO mouse 2 replicate 2_abs 3' CITEseq

description:
SeqWell v3
KO_2_pool_2_abs


title: 206530720022_R02C01 Methylation

value: Oligodendroglioma


title: Brain, CD3+ SS2 KO O2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O2


title: CD45+ KO mouse 2 replicate 1_abs 3' CITEseq

description:
SeqWell v3
KO_2_pool_1_abs


title: FFPE DNA from SM-like #6

city: New York

first: Yiying

last: Yang

state: NY

address: 240 E 38th St

department: Pathology

institute: NYU Langone Health

description: FFPE DNA from SM-like #6

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to the Illumina Infinium Methylation EPIC v1.0 Beachip array using the standard Illumina hybridization protocol.

scan_protocol: Beadchip arrays were scanned and imaged using the iScan microarray scanner system.

data_processing:
R package "minfi" was used to analyze the raw intensity IDATs. Data was preprocessed, poor samples and probes were removed based on mean detection P-values. Then subsequent data was quantile normalized. Probes with SNPs were removed.
processed_beta_values_GCT-STM.txt - a table with minfi-calculated beta values of samples from case 1-30 with GCT-STM and Conventional GCT; processed_beta_values_STM-like_GCT.txt - a table with minfi calculated beta values of samples from case #1-#6 with SM like and Conventional GCT annotations

label: Cy5 and Cy3

source_name: SM-like #6

label_protocol: Standard illumina protocol

extract_protocol: Genomic DNA was extracted from macrodissected formalin-fixed paraffin-embedded (FFPE) tumor sections using the automated Maxwell system (Promega, Madison, WI, USA).

value: SM-like #6

value: SM-like


title: CD45+ KO mouse 1 replicate 2_abs 3' CITEseq

description:
SeqWell v3
KO_1_pool_2_abs


title: CD45+ KO mouse 1 replicate 1_abs 3' CITEseq

description:
SeqWell v3
KO_1_pool_1_abs


title: FFPE DNA from Conventional GCT #6

description: FFPE DNA from Conventional GCT #6

source_name: Conventional GCT #6

value: Conventional GCT #6

value: Conventional GCT


title: CD45+ WT mouse 2 replicate 3 3' scRNAseq

description:
SeqWell v3
WT_2_pool_3

data_processing:
The demultiplexing, gene counting and aggregation were made using an adapted version of dropSeqPipe v0.4. (https://github.com/Hoohm/dropSeqPipe)
Assembly: mm10
Supplementary files format and content: tar archives containing tab-separated values files and matrix files

value: WT


title: Brain, CD3+ SS2 KO O19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O19


title: CD45+ WT mouse 2 replicate 1 3' scRNAseq

description:
SeqWell v3
WT_2_pool_1


title: CD45+ WT mouse 1 replicate 2 3' scRNAseq

description:
SeqWell v3
WT_1_pool_2


title: FFPE DNA from Conventional GCT #5

description: FFPE DNA from Conventional GCT #5

source_name: Conventional GCT #5

value: Conventional GCT #5


title: CD45+ WT mouse 1 replicate 1 3' scRNAseq

description:
SeqWell v3
WT_1_pool_1


title: CD45+ WT mouse 2 replicate 2 3' scRNAseq

description:
SeqWell v3
WT_2_pool_2


title: Brain, CD3+ SS2 KO O17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O17


title: Brain, CD3+ SS2 KO O20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O20


title: FFPE DNA from SM-like #5

description: FFPE DNA from SM-like #5

source_name: SM-like #5

value: SM-like #5


title: FFPE DNA from SM-like #4

description: FFPE DNA from SM-like #4

source_name: SM-like #4

value: SM-like #4


title: CD45+ KO mouse 2 replicate 3 3' scRNAseq

description:
SeqWell v3
KO_2_pool_3


title: Brain, CD3+ SS2 KO O14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O14


title: FFPE DNA from Conventional GCT #4

description: FFPE DNA from Conventional GCT #4

source_name: Conventional GCT #4

value: Conventional GCT #4


title: CD45+ KO mouse 1 replicate 3 3' scRNAseq

description:
SeqWell v3
KO_1_pool_3

value: Brain


title: CD45+ KO mouse 2 replicate 2 3' scRNAseq

description:
SeqWell v3
KO_2_pool_2


title: Brain, CD3+ SS2 KO O18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O18

value: male


title: Brain, CD3+ SS2 KO O13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O13

value: KO


title: CD45+ KO mouse 2 replicate 1 3' scRNAseq

description:
SeqWell v3
KO_2_pool_1

value: 15 months


title: Brain, CD3+ SS2 KO O16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O16


title: CD45+ KO mouse 1 replicate 1 3' scRNAseq

description:
SeqWell v3
KO_1_pool_1


title: Brain, CD3+ SS2 WT P9 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P9


title: CD45+ KO mouse 1 replicate 2 3' scRNAseq

description:
SeqWell v3
KO_1_pool_2


title: FFPE DNA from Conventional GCT #3

description: FFPE DNA from Conventional GCT #3

source_name: Conventional GCT #3

value: Conventional GCT #3


title: Brain, CD3+ SS2 WT P7 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P7


title: Brain, CD3+ SS2 WT P5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P5


title: FFPE DNA from SM-like #2

description: FFPE DNA from SM-like #2

source_name: SM-like #2

value: SM-like #2


title: Brain, CD3+ SS2 WT P8 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P8


title: Brain, CD3+ SS2 WT P22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P22


title: FFPE DNA from SM-like #1

description: FFPE DNA from SM-like #1

source_name: SM-like #1

value: SM-like #1


title: Brain, CD3+ SS2 KO N9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N9


title: Brain, CD3+ SS2 KO O1 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O1


title: Brain, CD3+ SS2 WT P3 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P3


title: Brain, CD3+ SS2 WT P2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P2


title: Brain, CD3+ SS2 KO N8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N8


title: Brain, CD3+ SS2 WT P18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P18


title: FFPE DNA from GCT-STM Case 18

description: FFPE DNA from GCT-STM Case 18

source_name: GCT-STM Case 18

value: GCT-STM Case 18

value: GCT-STM


title: Brain, CD3+ SS2 WT P19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P19


title: Brain, CD3+ SS2 WT P15 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P15


title: Brain, CD3+ SS2 KO N6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N6


title: FFPE DNA from Conventional GCT #1

description: FFPE DNA from Conventional GCT #1

source_name: Conventional GCT #1

value: Conventional GCT #1


title: Brain, CD3+ SS2 KO N7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N7


title: Brain, CD3+ SS2 WT P16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P16


title: Brain, CD3+ SS2 KO O11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O11


title: FFPE DNA from SM-like #3

description: FFPE DNA from SM-like #3

source_name: SM-like #3

value: SM-like #3

value: SM-like


title: FFPE DNA from GCT-STM Case 17

description: FFPE DNA from GCT-STM Case 17

source_name: GCT-STM Case 17

value: GCT-STM Case 17


title: Brain, CD3+ SS2 KO O10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_O10

source_name: Brain


title: Brain, CD3+ SS2 WT P13 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P13

value: WT


title: Brain, CD3+ SS2 WT P4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P4


title: Brain, CD3+ SS2 KO N5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N5


title: FFPE DNA from Conventional GCT #2

description: FFPE DNA from Conventional GCT #2

source_name: Conventional GCT #2

value: Conventional GCT #2

value: Conventional GCT


title: FFPE DNA from GCT-STM Case 25

description: FFPE DNA from GCT-STM Case 25

source_name: GCT-STM Case 25

value: GCT-STM Case 25


title: Brain, CD3+ SS2 WT P24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P24

value: Brain


title: Brain, CD3+ SS2 WT P10 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P10

value: male


title: Brain, CD3+ SS2 KO N4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N4

value: KO


title: turtle genital tubercle st16-17 H3K27ac ChIP rep2

description:
SE75 sequencing
ts_GT_st16-17_H3K27ac_naive_overlap.narrowPeak.gz

organism: Trachemys scripta

source_name: genital tubercle

value: H3K27ac (Millipore or Cosmo Bio, CMA309)


title: FFPE DNA from GCT-STM Case 21

description: FFPE DNA from GCT-STM Case 21

source_name: GCT-STM Case 21

value: GCT-STM Case 21


title: Brain, CD3+ SS2 WT P1 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P1

value: 15 months


title: Brain, CD3+ SS2 KO N3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N3


title: FFPE DNA from Conventional GCT Case 8

description: FFPE DNA from Conventional GCT Case 8

source_name: Conventional GCT Case 8

value: Conventional GCT Case 8


title: Brain, CD3+ SS2 WT O8 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O8


title: Brain, CD3+ SS2 KO N23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N23


title: Brain, CD3+ SS2 WT O6 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O6


title: Brain, CD3+ SS2 WT O4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O4


title: Brain, CD3+ SS2 WT O3 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O3


title: Brain, CD3+ SS2 WT O24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O24


title: FFPE DNA from GCT-STM Case 22

description: FFPE DNA from GCT-STM Case 22

source_name: GCT-STM Case 22

value: GCT-STM Case 22


title: Brain, CD3+ SS2 KO N21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N21


title: Brain, CD3+ SS2 WT P14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P14


title: Brain, CD3+ SS2 WT O23 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O23


title: Brain, CD3+ SS2 WT O2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O2


title: Brain, CD3+ SS2 KO N20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N20


title: Brain, CD3+ SS2 WT O20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O20


title: Brain, CD3+ SS2 WT O19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O19


title: Brain, CD3+ SS2 WT P12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_P12


title: FFPE DNA from Conventional GCT Case 15

description: FFPE DNA from Conventional GCT Case 15

source_name: Conventional GCT Case 15

value: Conventional GCT Case 15


title: Brain, CD3+ SS2 KO N19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N19


title: Brain, CD3+ SS2 WT O18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O18


title: Brain, CD3+ SS2 WT O16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O16


title: FFPE DNA from GCT-STM Case 15

description: FFPE DNA from GCT-STM Case 15

source_name: GCT-STM Case 15

value: GCT-STM Case 15

value: GCT-STM


title: Brain, CD3+ SS2 WT O7 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O7


title: Brain, CD3+ SS2 WT O17 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O17


title: Brain, CD3+ SS2 WT O15 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O15


title: FFPE DNA from Conventional GCT Case 10

description: FFPE DNA from Conventional GCT Case 10

source_name: Conventional GCT Case 10

value: Conventional GCT Case 10


title: Brain, CD3+ SS2 WT O14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O14


title: Brain, CD3+ SS2 KO N15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N15


title: Brain, CD3+ SS2 KO N12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N12


title: Brain, CD3+ SS2 WT O13 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O13


title: FFPE DNA from GCT-STM Case 8

description: FFPE DNA from GCT-STM Case 8

source_name: GCT-STM Case 8

value: GCT-STM Case 8


title: FFPE DNA from Conventional GCT Case 13

description: FFPE DNA from Conventional GCT Case 13

source_name: Conventional GCT Case 13

value: Conventional GCT Case 13


title: Brain, CD3+ SS2 WT O12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O12

value: WT


title: FFPE DNA from GCT-STM Case 13

description: FFPE DNA from GCT-STM Case 13

source_name: GCT-STM Case 13

value: GCT-STM Case 13


title: Brain, CD3+ SS2 KO N10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N10


title: FFPE DNA from GCT-STM Case 6

description: FFPE DNA from GCT-STM Case 6

source_name: GCT-STM Case 6

value: GCT-STM Case 6


title: Brain, CD3+ SS2 WT O1 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O1

value: Brain


title: Brain, CD3+ SS2 KO N1 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N1

value: male


title: Brain, CD3+ SS2 WT N9 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N9


title: FFPE DNA from GCT-STM Case 19

description: FFPE DNA from GCT-STM Case 19

source_name: GCT-STM Case 19

value: GCT-STM Case 19


title: Brain, CD3+ SS2 KO N16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_N16

value: KO


title: Brain, CD3+ SS2 KO M9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M9


title: FFPE DNA from GCT-STM Case 23

description: FFPE DNA from GCT-STM Case 23

source_name: GCT-STM Case 23

value: GCT-STM Case 23


title: Brain, CD3+ SS2 WT N7 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N7

value: 15 months


title: Brain, CD3+ SS2 WT N5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N5


title: Brain, CD3+ SS2 WT N4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N4


title: Brain, CD3+ SS2 KO M8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M8


title: FFPE DNA from GCT-STM Case 4

description: FFPE DNA from GCT-STM Case 4

source_name: GCT-STM Case 4

value: GCT-STM Case 4


title: FFPE DNA from GCT-STM Case 20

description: FFPE DNA from GCT-STM Case 20

source_name: GCT-STM Case 20

value: GCT-STM Case 20


title: Brain, CD3+ SS2 WT N3 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N3

source_name: Brain


title: Brain, CD3+ SS2 WT N22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N22


title: Brain, CD3+ SS2 KO M6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M6


title: Brain, CD3+ SS2 WT N21 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N21


title: Brain, CD3+ SS2 WT O11 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_O11


title: FFPE DNA from Conventional GCT Case 30

description: FFPE DNA from Conventional GCT Case 30

source_name: Conventional GCT Case 30

value: Conventional GCT Case 30

value: Conventional GCT


title: Brain, CD3+ SS2 KO M7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M7


title: Brain, CD3+ SS2 WT N20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N20


title: Brain, CD3+ SS2 WT N19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N19


title: Brain, CD3+ SS2 KO M5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M5


title: FFPE DNA from Conventional GCT Case 29

description: FFPE DNA from Conventional GCT Case 29

source_name: Conventional GCT Case 29

value: Conventional GCT Case 29


title: Brain, CD3+ SS2 WT N16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N16


title: FFPE DNA from Conventional GCT Case 27

description: FFPE DNA from Conventional GCT Case 27

source_name: Conventional GCT Case 27

value: Conventional GCT Case 27


title: Brain, CD3+ SS2 KO M4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M4


title: Brain, CD3+ SS2 WT N2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N2


title: Brain, CD3+ SS2 WT N15 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N15


title: Brain, CD3+ SS2 WT N14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N14


title: Brain, CD3+ SS2 KO M3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M3


title: FFPE DNA from GCT-STM Case 3

description: FFPE DNA from GCT-STM Case 3

source_name: GCT-STM Case 3

value: GCT-STM Case 3

value: GCT-STM


title: Brain, CD3+ SS2 WT N13 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N13

value: WT


title: FFPE DNA from Conventional GCT Case 16

description: FFPE DNA from Conventional GCT Case 16

source_name: Conventional GCT Case 16

value: Conventional GCT Case 16


title: Brain, CD3+ SS2 KO M24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M24


title: Brain, CD3+ SS2 WT N12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N12


title: Brain, CD3+ SS2 WT N24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N24


title: Brain, CD3+ SS2 WT N11 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N11


title: Brain, CD3+ SS2 KO M22 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M22


title: Brain, CD3+ SS2 WT N1 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N1


title: FFPE DNA from GCT-STM Case 16

description: FFPE DNA from GCT-STM Case 16

source_name: GCT-STM Case 16

value: GCT-STM Case 16


title: Brain, CD3+ SS2 KO M21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M21

value: Brain


title: FFPE DNA from Conventional GCT Case 9, 2

description: FFPE DNA from Conventional GCT Case 9

source_name: Conventional GCT Case 9

value: Conventional GCT Case 9


title: Brain, CD3+ SS2 WT M4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M4

value: male


title: Brain, CD3+ SS2 WT M9 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M9


title: Brain, CD3+ SS2 WT N17 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_N17


title: Brain, CD3+ SS2 WT M5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M5


title: Brain, CD3+ SS2 KO M18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M18

value: KO


title: Brain, CD3+ SS2 WT M24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M24


title: FFPE DNA from Conventional GCT Case 28

description: FFPE DNA from Conventional GCT Case 28

source_name: Conventional GCT Case 28

value: Conventional GCT Case 28


title: FFPE DNA from Conventional GCT Case 9

description: FFPE DNA from Conventional GCT Case 9


title: Brain, CD3+ SS2 WT M23 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M23

value: 15 months


title: Brain, CD3+ SS2 WT M21 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M21


title: Brain, CD3+ SS2 WT M22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M22


title: FFPE DNA from GCT-STM Case 9

description: FFPE DNA from GCT-STM Case 9

source_name: GCT-STM Case 9

value: GCT-STM Case 9


title: Brain, CD3+ SS2 KO M15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M15


title: Brain, CD3+ SS2 KO M19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M19


title: Brain, CD3+ SS2 WT M20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M20


title: Brain, CD3+ SS2 KO M14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M14


title: Brain, CD3+ SS2 WT M19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M19


title: Brain, CD3+ SS2 WT M18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M18


title: Brain, CD3+ SS2 WT M17 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M17


title: FFPE DNA from GCT-STM Case 11

description: FFPE DNA from GCT-STM Case 11

source_name: GCT-STM Case 11

value: GCT-STM Case 11


title: Brain, CD3+ SS2 KO M12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_M12


title: Brain, CD3+ SS2 WT M16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M16


title: Brain, CD3+ SS2 KO L9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L9


title: Brain, CD3+ SS2 WT M15 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M15


title: Brain, CD3+ SS2 WT M14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M14


title: Brain, CD3+ SS2 KO L8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L8


title: Brain, CD3+ SS2 WT M13 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M13


title: FFPE DNA from GCT-STM Case 24

description: FFPE DNA from GCT-STM Case 24

source_name: GCT-STM Case 24

value: GCT-STM Case 24


title: Brain, CD3+ SS2 WT M12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M12


title: Brain, CD3+ SS2 KO L7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L7


title: Brain, CD3+ SS2 WT M11 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M11


title: Brain, CD3+ SS2 WT M10 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_M10


title: Brain, CD3+ SS2 WT L8 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L8


title: FFPE DNA from GCT-STM Case 14

description: FFPE DNA from GCT-STM Case 14

source_name: GCT-STM Case 14

value: GCT-STM Case 14


title: Brain, CD3+ SS2 WT L5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L5


title: Brain, CD3+ SS2 KO L6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L6


title: FFPE DNA from Conventional GCT Case 11

description: FFPE DNA from Conventional GCT Case 11

source_name: Conventional GCT Case 11

value: Conventional GCT Case 11

value: Conventional GCT


title: Brain, CD3+ SS2 KO L5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L5


title: FFPE DNA from Conventional GCT Case 12

description: FFPE DNA from Conventional GCT Case 12

source_name: Conventional GCT Case 12

value: Conventional GCT Case 12


title: Brain, CD3+ SS2 WT L24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L24


title: Brain, CD3+ SS2 WT L23 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L23


title: FFPE DNA from GCT-STM Case 1

description: FFPE DNA from GCT-STM Case 1

source_name: GCT-STM Case 1

value: GCT-STM Case 1

value: GCT-STM


title: Brain, CD3+ SS2 WT L22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L22

value: WT


title: Brain, CD3+ SS2 KO L24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L24


title: Brain, CD3+ SS2 WT L21 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L21


title: Brain, CD3+ SS2 WT L4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L4


title: FFPE DNA from GCT-STM Case 12

description: FFPE DNA from GCT-STM Case 12

source_name: GCT-STM Case 12

value: GCT-STM Case 12


title: FFPE DNA from Conventional GCT Case 26

description: FFPE DNA from Conventional GCT Case 26

source_name: Conventional GCT Case 26

value: Conventional GCT Case 26


title: Brain, CD3+ SS2 WT L20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L20

source_name: Brain

value: Brain


title: Brain, CD3+ SS2 KO L23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L23

value: male


title: FFPE DNA from GCT-STM Case 5

description: FFPE DNA from GCT-STM Case 5

source_name: GCT-STM Case 5

value: GCT-STM Case 5


title: FFPE DNA from Conventional GCT Case 14

description: FFPE DNA from Conventional GCT Case 14

source_name: Conventional GCT Case 14

value: Conventional GCT Case 14


title: Brain, CD3+ SS2 WT L2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L2

value: 15 months


title: Brain, CD3+ SS2 WT L19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L19


title: Brain, CD3+ SS2 KO L21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L21

value: KO


title: FFPE DNA from GCT-STM Case 2

description: FFPE DNA from GCT-STM Case 2

source_name: GCT-STM Case 2

value: GCT-STM Case 2


title: Brain, CD3+ SS2 WT L6 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L6


title: Brain, CD3+ SS2 WT L17 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L17


title: FFPE DNA from GCT-STM Case 7

description: FFPE DNA from GCT-STM Case 7

source_name: GCT-STM Case 7

value: GCT-STM Case 7


title: Brain, CD3+ SS2 WT L16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L16


title: Brain, CD3+ SS2 KO L4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L4


title: Brain, CD3+ SS2 KO L20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L20


title: Brain, CD3+ SS2 KO L19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L19


title: Brain, CD3+ SS2 WT L14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L14


title: FOXC2 NHE1-KO input rep 3

city: San Francisco

first: Kyle

last: Kisor

address: 505 parnassus Ave

institute: UC San Francisco

description: Library name: FOXC2_NHE1KO_input_3

data_processing:
Data processing of raw data including for peak calling was performed by Azenta
Assembly: hg38
Supplementary files format and content: bigwig

source_name: breast

growth_protocol: MDA-MB-436 cells were maintained at 37°C and 5% CO2 in RPMI 1640 (Gibco:11875085) supplemented with Penicillin/Streptomycin (100U/mL each), and 10% FBS.

extract_protocol:
Cells were fixed for 5 minutes with 1% formaldahyde, stopped with glycine, and washed. Cells were lysed and sheared with sonication cycles of 30 seconds on/off for 40-cycles. Effective shearing with samples between 200-1000bp were confirmed via agarose gel and chromatin frozen on dry ice and stored at -80C.  10µg of FLAG antibody (Sigma F1804) was used to bind Flag-FOXC2 and Protein G Dynabeads used for immunoprecipitation. After washes, chromatin was decrosslinked and DNA quantified via Qubit and stored at -80C.
ChIP samples were sent to Azenta for library construction and sequencing.

treatment_protocol: NHE1-KO were generated via CRISPR/Cas9 resulting in decreased pHi. Cells were either untransfected or transfected with 1 µg of FOXC2-WT, -H122K, or -H122N with medium changed 8 h after transfection

value: breast


title: Brain, CD3+ SS2 KO L17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L17


title: FOXC2 NHE1-KO input rep 2

description: Library name: FOXC2_NHE1KO_input_2


title: Brain, CD3+ SS2 WT L11 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L11


title: Brain, CD3+ SS2 WT L1 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L1


title: Brain, CD3+ SS2 WT K9 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K9


title: Brain, CD3+ SS2 KO L16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L16


title: Brain, CD3+ SS2 KO L15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L15


title: FOXC2 NHE1-KO input rep 1

description: Library name: FOXC2_NHE1KO_input_1


title: Brain, CD3+ SS2 WT K7 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K7


title: Brain, CD3+ SS2 WT K5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K5


title: FOXC2 control input rep 3

description: Library name: FOXC2_cntl_input_3


title: Brain, CD3+ SS2 WT L18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L18


title: Brain, CD3+ SS2 KO L14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L14


title: Brain, CD3+ SS2 KO L13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L13


title: Brain, CD3+ SS2 WT K23 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K23


title: Brain, CD3+ SS2 WT L15 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L15


title: Brain, CD3+ SS2 WT K4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K4


title: Brain, CD3+ SS2 KO L12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L12


title: Brain, CD3+ SS2 WT K22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K22


title: FOXC2 control input rep 2

description: Library name: FOXC2_cntl_input_2


title: Brain, CD3+ SS2 WT L12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_L12


title: Brain, CD3+ SS2 WT K24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K24


title: Brain, CD3+ SS2 KO L10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_L10


title: FOXC2 NHE1-KO rep 3

description: Library name: FOXC2_NHE1KO_IP_3


title: FOXC2 control input rep 1

description: Library name: FOXC2_cntl_input_1


title: Brain, CD3+ SS2 WT K21 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K21


title: Brain, CD3+ SS2 WT K2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K2


title: Brain, CD3+ SS2 WT K19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K19


title: Brain, CD3+ SS2 WT K8 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K8


title: FOXC2 NHE1-KO rep 2

description: Library name: FOXC2_NHE1KO_IP_2


title: Brain, CD3+ SS2 KO K9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K9


title: FOXC2 NHE1-KO rep 1

description: Library name: FOXC2_NHE1KO_IP_1


title: Brain, CD3+ SS2 KO K8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K8


title: Brain, CD3+ SS2 WT K18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K18


title: Brain, CD3+ SS2 WT K16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K16


title: Brain, CD3+ SS2 WT K3 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K3


title: Brain, CD3+ SS2 WT K17 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K17


title: Brain, CD3+ SS2 KO K7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K7


title: FOXC2 control rep 3

description: Library name: FOXC2_cntl_IP_3


title: Brain, CD3+ SS2 WT K12 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K12


title: Brain, CD3+ SS2 KO K5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K5


title: Patient 65 (tumor CD4) T-cell receptor

first: David

last: Oh

state: CA

address: 513 Parnassus Ave, HSE301, Box 0519

institute: University of California, San Francisco

description:
Library name: b65_t_cd4_gex_tcr
Illumina NovaSeq 6000

data_processing:
Single-cell RNAseq analysis. 10X sequencing data was processed through the Cell Ranger pipeline (version 1.1, hg19 genome assembly) with default settings and filtered gene-barcode matrices were analyzed using the scanpy toolkit (Wolf FA et al. Genome Biol 2018). The gene expression values were log2 plus one transformed and normalized to 10,000 counts per cell. Cells with mitochondrial gene expression of >10% were filtered out. The resulting matrix was batch corrected by regressing out total UMI counts and percent mitochondrial genes using the scanpy function followed by scanpy implementation of ComBat (Johnson WE et al. Biostat Oxf Eng 2007). The adjusted matrix was scaled to a mean of zero and variance of 1. Highly variable genes were selected using the scanpy function followed by principal component analysis (PCA), Leiden clustering and UMAP plotting with default settings. CD4+ and CD8+ T cells were clustered together at a resolution of 0.9. DE analysis was carried out to identify marker genes that were upregulated in each individual cluster relative to all other single cells. Annotation of each unbiased population was performed by manual DE gene inspection.  Single-cell TCRseq analysis. For our overall patient TCR sequencing strategy, 10X barcodes of TCR were matched with 10X barcodes from cells with RNA sequences that passed filtering in the Cell Ranger pipeline. TRA and TRB CDR3s reads were aligned against known TRA and TRB CDR3 sequences and assembled into clonotype families using miXCR (Bolotin DA et al. Nat Methods 2015). For any given 10X barcode, the most abundant TRA or TRB clonotype was accepted for further analysis; if 2 TRA or TRB clonotypes were equally abundant for a given 10X barcode, the clonotype with the highest sequence alignment score was used for further analysis. Cells with paired TRA and TRB were used for further downstream analysis. For the specific results validating enrichment of tumor-matched TCRab clones in sorted KLRG1+ CD4+ T cells from PBMC (Patients 50 and 65, Supplemental Data 10), 10X Genomics Cell Ranger pipeline v8.0.1 was used.
Assembly: hg19
Supplementary files format and content: Gene expression: 10X Cellranger 1.1 outputs (barcodes.tsv, matrix.mtx, genes.tsv). TCR sequencing: processed TCRa and TCRb CDR3 and associated 10X GEX barcode (.csv). TCR sequencing from patients 50 and 65 (10X VDJ, Supplemental Data 10): filtered contig annotations (.csv)
Library strategy: scTCR-Seq

source_name: Tumor

extract_protocol:
Blood processing. Whole blood was collected in heparinized tubes and processed within 24h. Whole blood was diluted 1:1 with PBS (Ca2+ and Mg2+ free) and centrifuged with Ficoll. PMBC was removed from the white cell interface and washed 2x with PBS before freezing in 10% DMSO and 12.5% of human serum albumin in RPMI-1640.  Tumor processing. Cystectomy surgical specimens were obtained fresh from the operating field, and dissected in pathology where grossly apparent tumor or adjacent bladder not grossly affected by tumor (“normal” adjacent tissue) were isolated, minced, and transported at room temperature in L15 media with 15 mM HEPES and 600 g/L glucose. These were further minced and digested using freshly prepared 200 mg/ml Liberase and 100 mg/ml DNAse in RPMI-1640 at 37°C for 1 h with the gentleMACS dissociator (Milteny Biotec). Cells were washed with 10% heat inactivated FBS in RPMI-1640 and passed through a 100 mm cell strainer. Single cell suspensions were counted for viability and stained for cell sorting.
Single-cell RNA sequencing. CD3+CD4+ and CD3+CD8+ T cells were sorted from digested tumor and non-malignant tissues, or Ficoll-purified and previously cryopreserved PBMC from the same patients, into 500 ml of PBS with 0.04% BSA. Double-positive (ie CD4+ and CD8+ by protein expression) cells were excluded from the sort strategy and therefore do not contribute to the observed population of cytotoxic CD4+ (single-positive) T cells. Cells were centrigued and resuspended into a concentration of 1000 cells/ml and all cells sorted were used when not exceeding the maximum number recommended by manufacturer. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell 3′ platform, version 1, according to manufacturer’s instructions. Following library preparation, sequencing was performed on an Illumina HiSeq 2500 (Rapid Run mode).  Single-cell TCR sequencing. For our overall patient TCR sequencing strategy, targeted PCR with NEBNext Ultra II Q5 Master Mix (New England Biolabs) used a pool of forward Va and Vb primers containing the TruSeq Read 1 primer sequence with a reverse P7 primer to amplify CDR3 sequences as well as the 10X Genomics barcodes. A second PCR with forward primers containing the Illumina P5, i5 and TruSeq Read 1 sequences was used with reverse P7 primer to generate TCR libraries for sequencing. Sequencing used an Illumina NovaSeq S1 with separate lanes for TCRa and TCRb sequencing. Read 1 contained 280 bp of the TCRa and TCRb CDR3 sequence, and the i7 read contained the 14 bp 10X Genomics barcode. For the specific results validating enrichment of tumor-matched TCRab clones in sorted KLRG1+ CD4+ T cells from PBMC (Patients 50 and 65, Supplemental Data 10), 10X Genomics Human Single Cell V(D)J reagents were used.

value: Tumor

value: bladder cancer

value: T cells

value: untreated

tag: timepoint

value: pre-treatment


title: Brain, CD3+ SS2 KO K4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K4


title: Brain, CD3+ SS2 WT K14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K14

value: WT


title: Patient 65 (blood CD4 KLRG1 positive) T-cell receptor

description:
Library name: b65_p_cd4k_plus_gex_tcr
Illumina NovaSeq 6000

source_name: PBMC

value: PBMC


title: Brain, CD3+ SS2 WT J4 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J4


title: Brain, CD3+ SS2 WT K20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K20


title: FOXC2 control rep 2

description: Library name: FOXC2_cntl_IP_2


title: Brain, CD3+ SS2 KO K3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K3


title: Brain, CD3+ SS2 WT J23 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J23


title: Patient 50 (blood CD4 KLRG1 positive) T-cell receptor

description:
Library name: b50_p_cd4k_plus_gex_tcr
Illumina NovaSeq 6000


title: Brain, CD3+ SS2 KO K6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K6


title: FOXC2 control rep 1

description: Library name: FOXC2_cntl_IP_1


title: Brain, CD3+ SS2 WT J20 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J20


title: Brain, CD3+ SS2 WT J18 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J18


title: Brain, CD3+ SS2 KO K20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K20


title: Brain, CD3+ SS2 WT K11 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_K11


title: Brain, CD3+ SS2 WT J7 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J7


title: Brain, CD3+ SS2 WT J13 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J13


title: Brain, CD3+ SS2 WT J14 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J14


title: Brain, CD3+ SS2 WT J6 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J6


title: Brain, CD3+ SS2 WT J3 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J3


title: Brain, CD3+ SS2 WT J8 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J8


title: Patient 65 (blood CD4 KLRG1 negative) T-cell receptor

description:
Library name: b65_p_cd4k_minus_gex_tcr
Illumina NovaSeq 6000


title: Brain, CD3+ SS2 WT J24 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J24


title: Brain, CD3+ SS2 WT J1 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J1


title: Brain, CD3+ SS2 KO K24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K24


title: Patient 50 (tumor CD4) T-cell receptor

description:
Library name: b50_t_cd4_gex_tcr
Illumina NovaSeq 6000


title: Brain, CD3+ SS2 WT J21 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J21


title: Untreated B (normal CD4) T-cell receptor

description:
Library name: untreated_b_normal_cd4_gex_tcr
Illumina NovaSeq S1

source_name: Normal adjacent tissue

value: Normal adjacent tissue


title: Brain, CD3+ SS2 KO K22 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K22

value: Brain


title: Brain, CD3+ SS2 KO K15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K15

value: male


title: Brain, CD3+ SS2 KO I7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I7


title: Brain, CD3+ SS2 KO K14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K14


title: Brain, CD3+ SS2 WT J2 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J2


title: Brain, CD3+ SS2 KO I6 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I6


title: Patient 50 (blood CD4 KLRG1 negative) T-cell receptor

description:
Library name: b50_p_cd4k_minus_gex_tcr
Illumina NovaSeq 6000


title: Brain, CD3+ SS2 WT J5 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J5


title: Brain, CD3+ SS2 KO I3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I3


title: Brain, CD3+ SS2 KO K19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K19


title: Untreated B (tumor CD8) T-cell receptor

description:
Library name: untreated_b_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 WT J16 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J16


title: Brain, CD3+ SS2 WT J22 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J22


title: Untreated B (tumor CD4) T-cell receptor

description:
Library name: untreated_b_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO K17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K17


title: Brain, CD3+ SS2 KO K12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K12


title: Untreated A (tumor CD8) T-cell receptor

description:
Library name: untreated_a_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO K16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K16


title: Brain, CD3+ SS2 KO I24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I24


title: Brain, CD3+ SS2 KO I23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I23


title: Brain, CD3+ SS2 WT J10 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J10


title: Untreated B (normal CD8) T-cell receptor

description:
Library name: untreated_b_normal_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 WT J19 mouse 2 scRNAseq

description:
SmartSeq2
SS2_20_017_5_J19


title: Brain, CD3+ SS2 KO I21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I21


title: Brain, CD3+ SS2 KO K13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K13


title: Untreated B (blood CD8) T-cell receptor

description:
Library name: untreated_b_blood_cd8_gex_tcr
Illumina NovaSeq S1


title: Untreated A (normal CD4) T-cell receptor

description:
Library name: untreated_a_normal_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I5


title: Brain, CD3+ SS2 KO I19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I19


title: Untreated B (blood CD4) T-cell receptor

description:
Library name: untreated_b_blood_cd4_gex_tcr
Illumina NovaSeq S1


title: Untreated A (blood CD8) T-cell receptor

description:
Library name: untreated_a_blood_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I16


title: Brain, CD3+ SS2 KO I8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I8


title: Brain, CD3+ SS2 KO I22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I22


title: Brain, CD3+ SS2 KO I12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I12


title: Brain, CD3+ SS2 KO I11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I11


title: Brain, CD3+ SS2 KO K11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_K11


title: Brain, CD3+ SS2 KO J5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J5


title: Untreated A (tumor CD4) T-cell receptor

description:
Library name: untreated_a_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I10 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I10


title: Brain, CD3+ SS2 KO I20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I20


title: Brain, CD3+ SS2 KO J4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J4


title: Healthy Blood (CD8 replicate 1) T-cell receptor

description:
Library name: healthy_blood_cd8_replicate1_gex_tcr
Illumina NovaSeq S1

value: healthy


title: Brain, CD3+ SS2 KO J9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J9


title: Healthy Blood (CD4 replicate 3) T-cell receptor

description:
Library name: healthy_blood_cd4_replicate3_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I2 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I2


title: Brain, CD3+ SS2 KO J8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J8


title: Brain, CD3+ SS2 KO I17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I17


title: Brain, CD3+ SS2 KO I18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I18


title: Brain, CD3+ SS2 KO J7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J7


title: Untreated A (blood CD4) T-cell receptor

description:
Library name: untreated_a_blood_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I15


title: Brain, CD3+ SS2 KO J6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J6


title: Healthy Blood (CD8 replicate 3) T-cell receptor

description:
Library name: healthy_blood_cd8_replicate3_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I14


title: Healthy Blood (CD8 replicate 2) T-cell receptor

description:
Library name: healthy_blood_cd8_replicate2_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H22


title: Brain, CD3+ SS2 KO I1 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_I1


title: Brain, CD3+ SS2 KO J2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J2


title: Chemo (tumor CD4) T-cell receptor

description:
Library name: chemo_tumor_cd4_gex_tcr
Illumina NovaSeq S1

value: chemo

value: post-chemotherapy


title: Brain, CD3+ SS2 KO H8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H8

value: KO

value: 15 months


title: Brain, CD3+ SS2 KO H20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H20


title: Brain, CD3+ SS2 KO H5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H5


title: Brain, CD3+ SS2 KO J24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J24


title: Healthy Blood (CD4 replicate 2) T-cell receptor

description:
Library name: healthy_blood_cd4_replicate2_gex_tcr
Illumina NovaSeq S1


title: Chemo (normal CD8) T-cell receptor

description:
Library name: chemo_normal_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H18


title: Brain, CD3+ SS2 KO H4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H4


title: Brain, CD3+ SS2 KO H23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H23


title: Brain, CD3+ SS2 KO H3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H3


title: Chemo (normal CD4) T-cell receptor

description:
Library name: chemo_normal_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO J3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J3


title: Healthy Blood (CD4 replicate 1) T-cell receptor

description:
Library name: healthy_blood_cd4_replicate1_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO J23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J23


title: Brain, CD3+ SS2 KO J20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J20


title: Chemo (tumor CD8) T-cell receptor

description:
Library name: chemo_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H12


title: Brain, CD3+ SS2 KO H9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H9


title: Brain, CD3+ SS2 KO H19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H19


title: Brain, CD3+ SS2 KO G9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G9


title: Brain, CD3+ SS2 KO J14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J14


title: Brain, CD3+ SS2 KO J13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J13


title: Anti-PD-L1 E (blood CD8 pre) T-cell receptor

description:
Library name: anti_pdl1_e_blood_cd8_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO J19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J19


title: Brain, CD3+ SS2 KO H15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H15


title: Brain, CD3+ SS2 KO H24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H24


title: Brain, CD3+ SS2 KO J17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J17


title: Brain, CD3+ SS2 KO J16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J16


title: Brain, CD3+ SS2 KO H14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H14


title: Brain, CD3+ SS2 KO H21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H21


title: Anti-PD-L1 E (blood CD8 post) T-cell receptor

description:
Library name: anti_pdl1_e_blood_cd8_post_gex_tcr
Illumina NovaSeq S1

value: post-atezolizumab


title: Brain, CD3+ SS2 KO H17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H17


title: Chemo (blood CD8) T-cell receptor

description:
Library name: chemo_blood_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H11


title: Brain, CD3+ SS2 KO G5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G5


title: Anti-PD-L1 E (blood CD4 pre) T-cell receptor

description:
Library name: anti_pdl1_e_blood_cd4_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H13 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H13


title: Chemo (blood CD4) T-cell receptor

description:
Library name: chemo_blood_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H1 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_H1


title: Brain, CD3+ SS2 KO J15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J15


title: Anti-PD-L1 E (blood CD4 post) T-cell receptor

description:
Library name: anti_pdl1_e_blood_cd4_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO G8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G8


title: Brain, CD3+ SS2 KO G3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G3


title: Brain, CD3+ SS2 KO J12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J12


title: Brain, CD3+ SS2 KO J11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J11


title: Brain, CD3+ SS2 KO G21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G21


title: Anti-PD-L1 D (tumor CD8) T-cell receptor

description:
Library name: anti_pdl1_d_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO G22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G22


title: Brain, CD3+ SS2 KO G24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G24


title: Brain, CD3+ SS2 KO J10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_J10


title: Brain, CD3+ SS2 KO G20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G20


title: Brain, CD3+ SS2 KO G4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G4


title: Brain, CD3+ SS2 KO G17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G17


title: Anti-PD-L1 D (normal CD4) T-cell receptor

description:
Library name: anti_pdl1_d_normal_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO G16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G16


title: Anti-PD-L1 D (tumor CD4) T-cell receptor

description:
Library name: anti_pdl1_d_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I7


title: Brain, CD3+ SS2 KO G19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G19


title: Brain, CD3+ SS2 KO G13 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G13


title: Brain, CD3+ SS2 KO G12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G12


title: Brain, CD3+ SS2 KO F8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F8


title: Brain, CD3+ SS2 KO F7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F7


title: Anti-PD-L1 D (blood CD8 post) T-cell receptor

description:
Library name: anti_pdl1_d_blood_cd8_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F5


title: Brain, CD3+ SS2 KO I6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I6


title: Brain, CD3+ SS2 KO G23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_G23


title: Brain, CD3+ SS2 KO I5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I5


title: Brain, CD3+ SS2 KO F3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F3


title: Anti-PD-L1 D (blood CD4 pre) T-cell receptor

description:
Library name: anti_pdl1_d_blood_cd4_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F24


title: Brain, CD3+ SS2 KO I4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I4


title: Brain, CD3+ SS2 KO I9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I9


title: Brain, CD3+ SS2 KO I8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I8


title: Anti-PD-L1 D (blood CD4 post) T-cell receptor

description:
Library name: anti_pdl1_d_blood_cd4_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F22


title: Anti-PD-L1 C (tumor CD8) T-cell receptor

description:
Library name: anti_pdl1_c_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F20


title: Brain, CD3+ SS2 KO I24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I24


title: Brain, CD3+ SS2 KO I3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I3


title: Brain, CD3+ SS2 KO F2 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F2


title: Anti-PD-L1 C (tumor CD4) T-cell receptor

description:
Library name: anti_pdl1_c_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F21


title: Anti-PD-L1 D (blood CD8 pre) T-cell receptor

description:
Library name: anti_pdl1_d_blood_cd8_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I21


title: Brain, CD3+ SS2 KO F18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F18


title: Brain, CD3+ SS2 KO F17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F17


title: Anti-PD-L1 C (normal CD4) T-cell receptor

description:
Library name: anti_pdl1_c_normal_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F16


title: Brain, CD3+ SS2 KO I20 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I20


title: Anti-PD-L1 C (blood CD8 pre) T-cell receptor

description:
Library name: anti_pdl1_c_blood_cd8_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F13 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F13


title: Brain, CD3+ SS2 KO F14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F14


title: Anti-PD-L1 C (blood CD4 pre) T-cell receptor

description:
Library name: anti_pdl1_c_blood_cd4_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F12


title: Brain, CD3+ SS2 KO I19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I19


title: Brain, CD3+ SS2 KO F1 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F1


title: Anti-PD-L1 C (blood CD8 post) T-cell receptor

description:
Library name: anti_pdl1_c_blood_cd8_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F23


title: Brain, CD3+ SS2 KO I18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I18


title: Brain, CD3+ SS2 KO E9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E9


title: Brain, CD3+ SS2 KO E7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E7


title: Brain, CD3+ SS2 KO E8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E8


title: Brain, CD3+ SS2 KO I17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I17


title: Anti-PD-L1 B (tumor CD4) T-cell receptor

description:
Library name: anti_pdl1_b_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Anti-PD-L1 C (blood CD4 post) T-cell receptor

description:
Library name: anti_pdl1_c_blood_cd4_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO E24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E24


title: Brain, CD3+ SS2 KO E23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E23


title: Anti-PD-L1 B (tumor CD8) T-cell receptor

description:
Library name: anti_pdl1_b_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I15


title: Brain, CD3+ SS2 KO E5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E5


title: Brain, CD3+ SS2 KO I10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I10


title: Brain, CD3+ SS2 KO I12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I12


title: Brain, CD3+ SS2 KO E3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E3


title: Brain, CD3+ SS2 KO F19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F19


title: Anti-PD-L1 B (normal CD4) T-cell receptor

description:
Library name: anti_pdl1_b_normal_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO I11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_I11


title: Brain, CD3+ SS2 KO E22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E22


title: Brain, CD3+ SS2 KO E20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E20


title: Brain, CD3+ SS2 KO E2 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E2


title: Brain, CD3+ SS2 KO H9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H9


title: Anti-PD-L1 B (blood CD8 post) T-cell receptor

description:
Library name: anti_pdl1_b_blood_cd8_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO F15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_F15


title: Brain, CD3+ SS2 KO E21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E21


title: Anti-PD-L1 B (blood CD4 pre) T-cell receptor

description:
Library name: anti_pdl1_b_blood_cd4_pre_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO E17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E17


title: Brain, CD3+ SS2 KO E18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E18


title: Brain, CD3+ SS2 KO H8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H8


title: Brain, CD3+ SS2 KO E15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E15


title: Anti-PD-L1 B (blood CD4 post) T-cell receptor

description:
Library name: anti_pdl1_b_blood_cd4_post_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO H7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H7


title: Brain, CD3+ SS2 KO H5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H5


title: Anti-PD-L1 A (tumor CD8) T-cell receptor

description:
Library name: anti_pdl1_a_tumor_cd8_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO E14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E14


title: Brain, CD3+ SS2 KO E11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E11


title: Brain, CD3+ SS2 KO E12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E12


title: Anti-PD-L1 B (blood CD8 pre) T-cell receptor

description:
Library name: anti_pdl1_b_blood_cd8_pre_gex_tcr
Illumina NovaSeq S1


title: Anti-PD-L1 A (tumor CD4) T-cell receptor

description:
Library name: anti_pdl1_a_tumor_cd4_gex_tcr
Illumina NovaSeq S1


title: Brain, CD3+ SS2 KO D9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D9


title: Brain, CD3+ SS2 KO E19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_E19


title: Brain, CD3+ SS2 KO H4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H4


title: Brain, CD3+ SS2 KO D8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D8


title: Brain, CD3+ SS2 KO H23 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H23


title: Brain, CD3+ SS2 KO H24 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H24


title: Brain, CD3+ SS2 KO D5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D5


title: Brain, CD3+ SS2 KO D6 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D6


title: Brain, CD3+ SS2 KO D7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D7


title: Brain, CD3+ SS2 KO D24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D24


title: Brain, CD3+ SS2 KO H2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H2


title: Brain, CD3+ SS2 KO H21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H21


title: Single-nucleus RNA-seq of cortical organoid from 16p11.2 deletion iPSC line DELD3 at 2 months

city: La Jolla

first: Summer

middle: R

last: Fair

address: 2880 Torrey Pines Scenic Drive

institute: UC San Diego

description: Library name: DELD3_2m

data_processing:
Sequencing BCL files were demultiplexed using `cellranger mkfastq` (10x Genomics Cell Ranger v6.1.1) to generate FASTQ files.
FASTQs were processed using `cellranger count` with default parameters and the 10x-provided GRCh38 v2020-A reference (based on Ensembl release 98).
Filtered gene-barcode matrices (`filtered_feature_bc_matrix.h5`) were generated by Cell Ranger for each sample.
Matrices were imported into Python and analyzed using Scanpy. Quality control filters were applied to exclude nuclei with low UMI counts, high mitochondrial RNA content, or likely doublets.
Downstream analyses including normalization, dimensionality reduction, clustering, and cell type annotation were performed in Scanpy.
Assembly: GRCh38 (10x Genomics reference v2020-A, based on Ensembl release 98)
Supplementary files format and content: Filtered HDF5 matrix files (`filtered_feature_bc_matrix.h5`) containing gene expression counts for high-quality nuclei.

molecule: nuclear RNA

source_name: Human iPSC Cortical Organoid

growth_protocol: Cortical organoids were generated from human iPSC lines using a guided differentiation protocol and maintained in ultra-low attachment 6-well plates in BrainPhys-based medium. Organoids were cultured up to 4 months, and samples for this dataset were harvested at 2 months. All lines were differentiated in parallel under identical conditions, with media changes every 2–3 days.

extract_protocol:
Nuclei were isolated from individual organoids using the 10x Genomics demonstrated protocol for single-nucleus RNA-seq. Organoids were gently dissociated in lysis buffer to release nuclei, which were filtered through a 40 µm strainer, pelleted by centrifugation, and resuspended in nuclei buffer.
Single-nucleus libraries were prepared using the 10x Genomics Chromium Single Cell 3’ v3.1 kit according to the manufacturer’s protocol. Approximately 8,000–10,000 nuclei per sample were loaded onto each Chromium chip channel. Libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: No drug treatments or exogenous perturbations were applied. Samples reflect unmanipulated differentiation from iPSC lines with 16p11.2 CNVs or wild-type controls.

value: Human iPSC Cortical Organoid

value: 16p11.2 deletion

tag: batch


title: Single-nucleus RNA-seq of cortical organoid from 16p11.2 duplication iPSC line DUP3 at 2 months

description: Library name: DUP3_2m

value: 16p11.2 duplication


title: Single-nucleus RNA-seq of cortical organoid from 16p11.2 deletion iPSC line DELA9 at 2 months

description: Library name: DELA9_2m


title: Brain, CD3+ SS2 KO D3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D3


title: Brain, CD3+ SS2 KO D23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D23


title: Brain, CD3+ SS2 KO D22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D22


title: Single-nucleus RNA-seq of cortical organoid from 16p11.2 duplication iPSC line DUP1 at 2 months

description: Library name: DUP1_2m


title: Brain, CD3+ SS2 KO D21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D21


title: Brain, CD3+ SS2 KO H17 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H17


title: Brain, CD3+ SS2 KO D20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D20


title: Brain, CD3+ SS2 KO D19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D19


title: Brain, CD3+ SS2 KO D18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D18


title: MRD229_04_CD45Neg

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

description: Library name: MRD229_04_CD45Neg

data_processing:
cellranger-8.0.0/cellranger mkfastq --run=. --samplesheet=cellRanger.csv --output-dir ./cellRanger --jobmode=slurm --localcores=24 --localmem=120
cellranger-8.0.0/cellranger count --fastqs=./fastq_path --create-bam true --jobmode=local --maxjobs=5 --transcriptome=cellranger-8.0.0/refdata-gex-GRCh38-2024-A --project=PROJECT_NAME --id=Sample_SAMPLE --sample=SAMPLE
Assembly: GRCh38
Supplementary files format and content: MEX format compressed folder containing a file corresponding to the genes, barcodes, and counts matrix as generated by cellranger count

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow aspirates were obtained from MDS/AML patients after written informed consent in accordance with the Declaration of Helsinki and approval of University of Rochester institutional review board (IRB). To isolate the bone spicules, the bone marrow aspirates were passed through 40mM filter. The filter containing spicules was washed with PBS and placed in a 6 well plate. The spicules were digested for 1 h in collagenase (Stem cell technologies) at 37°C. After filtering, the filtered aspirate was used to isolate bone marrow mononuclear cells (BMMNCs) by density centrifugation (Ficoll-Paque, GE healthcare). Digested bone cells and BMMNCs were magnetically depleted for CD45- cell fraction using LD columns (Miltenyi Biotech).
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher). The purified cDNA was further amplified by PCR to generate sufficient material for library construction. Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000. Samples were demultiplexed and counted using cellranger-8.0.0 mkfastq and count, using default parameters.

value: Bone marrow aspirate

value: MDS/ AML


title: Brain, CD3+ SS2 KO H15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H15


title: Brain, CD3+ SS2 KO D16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D16


title: Single-nucleus RNA-seq of cortical organoid from wild-type iPSC line at 2 months

description: Library name: CVB24_2m


title: Brain, CD3+ SS2 KO D4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D4


title: Brain, CD3+ SS2 KO D15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D15


title: Brain, CD3+ SS2 KO H14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H14


title: Brain, CD3+ SS2 KO D17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D17


title: MDS41_01_CD45Neg

description: Library name: MDS41_01_CD45Neg


title: Brain, CD3+ SS2 KO D14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D14


title: Brain, CD3+ SS2 KO D11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D11


title: Brain, CD3+ SS2 KO H18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H18


title: Brain, CD3+ SS2 KO H13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H13


title: HNTM55

city: Glasgow

first: Niranjan

last: Shirgaonkar

state: East Dunbartonshire

address: Switchback Rd, Garscube Estate

country: United Kingdom

institute: Cancer Research UK

description: Library name: HNTM55

data_processing:
Primary analysis of samples was performed using the bcbio-nextgen pipeline (version 1.0.9a)
RNASeq data were aligned with the RNASeq aligner STAR (version 2.5.4a)42 using 2-pass method, gene expression Transcript per Million (TPM) values were obtained from Salmon (version 0.9.1)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes TPM counts for each sample

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen)
RNA libraries for RNA-Seq were prepared using the TruSeq Stranded Total RNA LT with Ribo-Zero Gold.


title: Brain, CD3+ SS2 KO D12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D12


title: Brain, CD3+ SS2 KO H10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H10


title: Brain, CD3+ SS2 KO H12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H12


title: Brain, CD3+ SS2 KO C8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C8


title: Brain, CD3+ SS2 KO D13 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D13


title: HNTM49

description: Library name: HNTM49


title: HNTM38

description: Library name: HNTM38


title: Brain, CD3+ SS2 KO H11 mouse 1 scRNAseq

description:
SmartSeq2
43_6_H11


title: HNTM24

description: Library name: HNTM24


title: Brain, CD3+ SS2 KO C7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C7


title: MDS47_01_CD45Neg

description: Library name: MDS47_01_CD45Neg


title: Brain, CD3+ SS2 KO D10 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_D10


title: Brain, CD3+ SS2 KO C5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C5


title: Brain, CD3+ SS2 KO C6 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C6


title: HNTM17

description: Library name: HNTM17


title: Brain, CD3+ SS2 KO G9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G9


title: Brain, CD3+ SS2 KO C3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C3


title: Brain, CD3+ SS2 KO C24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C24


title: HNTC9REC

description: Library name: HNTC9REC


title: Brain, CD3+ SS2 KO G6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G6


title: Brain, CD3+ SS2 KO C4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C4


title: HNTC9

description: Library name: HNTC9


title: Brain, CD3+ SS2 KO G8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G8


title: Brain, CD3+ SS2 KO C23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C23


title: Brain, CD3+ SS2 KO C21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C21


title: Brain, CD3+ SS2 KO C9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C9


title: Brain, CD3+ SS2 KO C20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C20


title: HN182LN

description: Library name: HN182LN


title: Brain, CD3+ SS2 KO C19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C19


title: Brain, CD3+ SS2 KO G4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G4


title: HN160PRI

description: Library name: HN160PRI


title: Brain, CD3+ SS2 KO C18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C18


title: Brain, CD3+ SS2 KO C15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C15


title: HN160MET

description: Library name: HN160MET


title: Brain, CD3+ SS2 KO C17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C17


title: Brain, CD3+ SS2 KO C16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C16


title: Brain, CD3+ SS2 KO G2 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G2


title: Brain, CD3+ SS2 KO C14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C14


title: Brain, CD3+ SS2 KO C12 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C12


title: Brain, CD3+ SS2 KO G18 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G18


title: Brain, CD3+ SS2 KO C11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C11


title: Brain, CD3+ SS2 KO G19 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G19


title: Brain, CD3+ SS2 KO C13 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C13


title: HN159MET

description: Library name: HN159MET


title: Brain, CD3+ SS2 KO G16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G16


title: Brain, CD3+ SS2 KO C10 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C10


title: Brain, CD3+ SS2 KO C22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_C22


title: HNNPC7

description: Library name: HNNPC7


title: Brain, CD3+ SS2 KO B8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B8


title: HN148PRI

description: Library name: HN148PRI


title: Brain, CD3+ SS2 KO G5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G5


title: Brain, CD3+ SS2 KO B9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B9


title: Brain, CD3+ SS2 KO G15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G15


title: Brain, CD3+ SS2 KO G3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G3


title: Brain, CD3+ SS2 KO B7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B7


title: Brain, CD3+ SS2 KO B6 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B6


title: Brain, CD3+ SS2 KO B5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B5


title: HN137PRI

description: Library name: HN137PRI


title: HN159PRI

description: Library name: HN159PRI


title: Brain, CD3+ SS2 KO G14 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G14


title: Brain, CD3+ SS2 KO G13 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G13


title: Brain, CD3+ SS2 KO B3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B3


title: Brain, CD3+ SS2 KO G12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G12


title: Brain, CD3+ SS2 KO B24 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B24


title: Brain, CD3+ SS2 KO B22 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B22


title: Brain, CD3+ SS2 KO B20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B20


title: HN120PRI

description: Library name: HN120PRI


title: HN120MET

description: Library name: HN120MET


title: Brain, CD3+ SS2 KO G10 mouse 1 scRNAseq

description:
SmartSeq2
43_6_G10


title: Brain, CD3+ SS2 KO B23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B23


title: Brain, CD3+ SS2 KO F9 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F9


title: HN137MET

description: Library name: HN137MET


title: Brain, CD3+ SS2 KO B2 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B2


title: HCC9-2

description: Library name: HCC9-2


title: Brain, CD3+ SS2 KO B18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B18


title: HN148MET

description: Library name: HN148MET


title: Brain, CD3+ SS2 KO F8 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F8


title: Brain, CD3+ SS2 KO B17 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B17


title: HCCC008T3

description: Library name: HCCC008T3


title: Brain, CD3+ SS2 KO B16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B16


title: HCC26-1

description: Library name: HCC26-1


title: Brain, CD3+ SS2 KO B4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B4


title: Brain, CD3+ SS2 KO B15 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B15


title: Brain, CD3+ SS2 KO F7 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F7


title: Brain, CD3+ SS2 KO B10 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B10


title: Brain, CD3+ SS2 KO F6 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F6


title: Brain, CD3+ SS2 KO B1 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B1


title: Brain, CD3+ SS2 KO B11 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B11


title: Brain, CD3+ SS2 KO B21 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_B21


title: Brain, CD3+ SS2 KO A9 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A9


title: HCC1-6

description: Library name: HCC1-6


title: Brain, CD3+ SS2 KO F4 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F4


title: CRC976LVM

description: Library name: CRC976LVM


title: Brain, CD3+ SS2 KO A7 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A7


title: CRC948PRI

description: Library name: CRC948PRI


title: Brain, CD3+ SS2 KO A5 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A5


title: Brain, CD3+ SS2 KO A8 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A8


title: Brain, CD3+ SS2 KO F3 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F3


title: CRC851PRI

description: Library name: CRC851PRI


title: Brain, CD3+ SS2 KO A4 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A4


title: Brain, CD3+ SS2 KO F21 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F21


title: Brain, CD3+ SS2 KO A3 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A3


title: Brain, CD3+ SS2 KO A23 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A23


title: CRC826LVM

description: Library name: CRC826LVM


title: CRC623LVM

description: Library name: CRC623LVM


title: Brain, CD3+ SS2 KO A20 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A20


title: Brain, CD3+ SS2 KO F5 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F5


title: Brain, CD3+ SS2 KO A19 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A19


title: CRC2783PRI

description: Library name: CRC2783PRI


title: Brain, CD3+ SS2 KO F16 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F16


title: Brain, CD3+ SS2 KO A2 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A2


title: CRC2756PRI

description: Library name: CRC2756PRI


title: Brain, CD3+ SS2 KO F15 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F15


title: Brain, CD3+ SS2 KO A18 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A18


title: CRC2756OMET

description: Library name: CRC2756OMET


title: Brain, CD3+ SS2 KO A6 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A6


title: Brain, CD3+ SS2 KO A16 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A16


title: Brain, CD3+ SS2 KO A14 mouse 3 scRNAseq

description:
SmartSeq2
SS2_20_017_5_A14


title: Brain, CD3+ SS2 KO F12 mouse 1 scRNAseq

description:
SmartSeq2
43_6_F12