title: pTh7_cells, Orai 1/2/3 TKO, 6 hrs, techincal rep 2

city: Los Angeles

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave

institute: Univeristy of California-Los Angeles

description:
Library name: Sample8
Column names in raw_count file: OraiTKO2-pTh17-6h_S5

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the mouse Ensembl GRCm39.107 GTF file.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Assembly: mm10
Supplementary files format and content: tab-delimited files include RAW and CPM normalized counts for each sample

source_name: Lymph nodes, Spleen

growth_protocol: Naive CD4+ T-cells were isolated and purified from wild-type (control) and ORAI 1/2/3 TKO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech), 10 ng/ml IL-23 (R&D Systems) and 10 ng/ml IL-1β (R&D Systems) for pathogenic Th17 differentiation and cultured in T cell medium. At 6h and 24 hrs post isolation, ~3 million control and ORAI 1/2/3 TKO pathogenic Th17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.

extract_protocol:
~3 million control  and ORAI 1/2/3 TKO Pathogenic  Th17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.  4 Biological replicates per genotype were pooled after harvesting and divided into 3 technical replicates per condition. RNA was isolated using RNA purification kit (ThermoFisher Scientific), quantified and used for purification of mRNA, cDNA synthesis and library preparation using  KAPA stranded RNA seq-kit Sample following manufacturer’s instructions.
Libraries for RNA-Seq were prepared with KAPA mRNA HyperPrep Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase. Next steps include mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporating dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeq6000 for a paired-end 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Wild-type vs ORAI TKO (Genetic System)

value: Lymph nodes, Spleen

value: CD4 T Cells

value: ORAI 1/2/3 TKO

tag: time

value: 6 hrs

tag: batch


title: pTh7_cells, Orai 1/2/3 TKO, 6 hrs, techincal rep 3

status: Public on Feb 10 2025

type: SRA

country: USA

description:
Library name: Sample9
Column names in raw_count file: OraiTKO3-pTh17-6h_S6

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age

tag: Sex

value: Female

tag: cell type

tag: genotype

tag: treatment


title: pTh7_cells, Orai 1/2/3 TKO, 24 hrs, technical rep 2

description:
Library name: Sample11
Column names in raw_count file: OraiTKO2-pTh17-24h_S11

value: 24 hrs


title: pTh7_cells, Orai 1/2/3 TKO, 24 hrs, technical rep 3

description:
Library name: Sample12
Column names in raw_count file: OraiTKO3-pTh17-24h_S12


title: WT-A-2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: Raw gene count matrix (rawCounts.tsv)

source_name: Bone marrow

growth_protocol: BM HSPCs were FACS sorted from indicated mice using conventional cell surface markers (Lin-Sca-1+cKit+).

extract_protocol:
RNA was extracted using the Qiagen RNAeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either water (H2O) or ADP-heptose for 90mins in vitro

value: Bone marrow

tag: cell line

value: Primary cells

value: LSK

value: ADP-heptose


title: pTh7_cells, Orai 1/2/3 TKO, 6 hrs, techincal rep 1

description:
Library name: Sample7
Column names in raw_count file: OraiTKO1-pTh17-6h_S4


title: WT Cortex male mRNA rep2 [Tcerg1]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
Tcerg7_4CTX
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Semicolon-delimited csv files include FPKM and Count values for each Sample.

source_name: Cerebral Cortex

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Cerebral Cortex

value: Wild type

tag: strain/background

value: 6 months

value: male

tag: well address


title: pTh17 cells, Control, 24 hrs, technical rep 2

description:
Library name: Sample5
Column names in raw_count file: Control2-pTh17-24h_S8

value: Wild-type


title: Het (Q140) KI Striatum Male rep3 [Msh3]

library_source: genomic

data_processing:
Libraries for ATAC-seq were sequenced using an Illumina Novaseq S4.
Burrows-Wheeler Aligner (BWA) was used for alignment with default parameters to mouse genome GRCm38,
Samtools and Picard were used for marking and removing duplicates,
MACS2 was used to identify peaks with parameter nomodel,
and featureCounts was used to quantify the reads.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Msh3_striatum_12month_combined.narrowPeak_counts_annot.txt: Tab-delimited text file includes the count matrix.

molecule: genomic DNA

source_name: Striatum

extract_protocol:
Brain tissues were dissected from mice at 12 months of age. Nuclei were dissociated from frozen striatal tissues and labeled with Alexa 488-conjugated anti-NeuN antibody. Neuronal nuclei were then harvested by flow cytometric sorting. 50,000 nuclei for each sample were used for transposition reactions and library prep.
The transposition reactions and ATAC-seq library preparation generally followed the steps set out in the original ATAC-seq paper using Nextera DNA Library Preparation Kit.

value: Striatum

value: Het (Q140) KI

value: 12 months

value: Male


title: pTh17 cells, Control, 24 hrs, technical rep 3

description:
Library name: Sample6
Column names in raw_count file: Control3-pTh17-24h_S9

value: Lymph nodes, Spleen

value: CD4 T Cells


title: WT Cortex female mRNA rep4 [Tcerg1]

description:
Tcerg22_3CTX
mRNA

value: female


title: WT Cortex male mRNA rep3 [Tcerg1]

description:
Tcerg10_1CTX
mRNA


title: pTh17_cells, Control, 6 hrs, technical rep 3

description:
Library name: Sample3
Column names in raw_count file: Control3-pTh17-6h_S3

value: Female

value: 6 hrs


title: WT Cortex female mRNA rep2 [Tcerg1]

description:
Tcerg15_1CTX
mRNA


title: WT Cortex female mRNA rep1 [Tcerg1]

description:
Tcerg12_2CTX
mRNA


title: pTh17_cells, Control, 6 hrs, technical rep 2

description:
Library name: Sample2
Column names in raw_count file:  Control2-pTh17-6h_S2


title: WT-H-1

value: Bone marrow

value: Primary cells


title: pTh17 cells, Control, 24 hrs, technical rep 1

description:
Library name: Sample4
Column names in raw_count file: Control1-pTh17-24h_S7

value: 24 hrs


title: Het (Q140) KI Striatum male mRNA rep3 [Tcerg1]

description:
Tcerg13_2STR
mRNA

source_name: Corpus Striatum

value: Corpus Striatum


title: pTh17_cells, Control, 6 hrs, technical rep 1

description:
Library name: Sample1
Column names in raw_count file: Control1-pTh17-6h_S1


title: Het (Q140) KI Striatum male mRNA rep4 [Tcerg1]

description:
Tcerg18_1STR
mRNA


title: Ly8_KO_G6_2

city: Planegg

first: Maria

last: Solovey

address: Grosshadernerstr 9

department: Department of Physiological Chemistry

country: Germany

institute: Ludwigs Maximillians University

description:
clone G6; technical replicate 2
barcode: TTTTAG

library_source: transcriptomic single cell

data_processing:
Raw data was demultiplexed using deML (Renaud et. al.) and further processed using the zUMIs pipeline (2.5.4, Parekh et al.) with STAR (2.6, Dobin et al.)
Assembly: GRCh38.84
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: lymph node

growth_protocol: Cells were grown in IMDM supplemented with 10% FBS

extract_protocol:
RNA was isolated using Direct-zolTM RNA MicroPrep kit (Zymo Research) and each sample was normalized to 10 ng/µl.
A total of 10 ng of RNA per sample were subjected to RNA sequencing using a version of the prime-seq protocol (Janjic et. al. BioRXiv, 2021). A full step-by-step protocol can be found on protocols.io (https://www.protocols.io/view/prime-seq-s9veh66). Prime-seq is a three prime counting method that introduces a sample specific barcode sequence and unique molecular identifiers (UMI) for accurate quantification of gene expression. Illumina paired end sequencing was performed on an HiSeq 1500 instrument, where the first read was 16 bases long and covered the sample barcode and UMI, and the second read was 50 bases long and was used to identify the gene.

value: lymph node

value: Human B cell Lymphoma

value: ARID1A knock out


title: pTh7_cells, Orai 1/2/3 TKO, 24 hrs, technical rep 1

description:
Library name: Sample10
Column names in raw_count file: OraiTKO1-pTh17-24h_S10

value: ORAI 1/2/3 TKO


title: Ly8_KO_G6_1

description:
clone G6; technical replicate 1
barcode: TATCAT


title: Het (Q140) KI Striatum male mRNA rep2 [Tcerg1]

description:
Tcerg7_3STR
mRNA

value: 6 months

value: male


title: WT Cortex male mRNA rep1 [Tcerg1]

description:
Tcerg7_1CTX
mRNA

value: Cerebral Cortex

value: Wild type


title: Ly8_het_G5_2

description:
clone G5; technical replicate 2
barcode: TTGTTA

value: ARID1A heterozygous


title: Het (Q140) KI Striatum female mRNA rep4 [Tcerg1]

description:
Tcerg19_3STR
mRNA

value: Het (Q140) KI


title: Ly8_het_G10_1

description:
clone G10; technical replicate 1
barcode: TATAAG


title: Ly8_het_G10_2

description:
clone G10; technical replicate 2
barcode: TTTATG


title: Het (Q140) KI Striatum female mRNA rep3 [Tcerg1]

description:
Tcerg17_2STR
mRNA

value: female


title: WT Cortex female mRNA rep3 [Tcerg1]

description:
Tcerg15_2CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Tcerg1]

description:
Tcerg18_1CTX
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Tcerg1]

description:
Tcerg11_3STR
mRNA


title: Ly8_het_A9_1

description:
clone A9; technical replicate 1
barcode: TACAAA


title: Ly8_het_A9_2

description:
clone A9; technical replicate 2
barcode: TTCATA


title: Het (Q140) KI Cortex male mRNA rep2 [Tcerg1]

description:
Tcerg7_3CTX
mRNA


title: Ly8_cas9_6_2

description:
clone 6; technical replicate 2
barcode: TTACTA

value: control


title: Het (Q140) KI Cortex male mRNA rep3 [Tcerg1]

description:
Tcerg13_2CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Tcerg1]

description:
Tcerg6_3CTX
mRNA


title: Ly8_cas9_3_2

description:
clone 3; technical replicate 2
barcode: TTAACT


title: Ly8_cas9_6_1

description:
clone 6; technical replicate 1
barcode: TAACAA


title: Ly8_cas9_3_1

description:
clone 3; technical replicate 1
barcode: TAAAAC


title: Het (Q140) KI Cortex female mRNA rep3 [Tcerg1]

description:
Tcerg17_2CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Tcerg1]

description:
Tcerg11_3CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Tcerg1]

description:
Tcerg19_3CTX
mRNA


title: Ly8_cas9_11_2

description:
clone 11; technical replicate 2
barcode: TTATCA


title: Ly8_cas9_11_1

description:
clone 11; technical replicate 1
barcode: TAATAG


title: Ly1_KO_H3_2

description:
clone H3; technical replicate 2
barcode: CTAAAA


title: Het (Q140) KI Cortex female mRNA rep1 [Tcerg1]

description:
Tcerg11_2CTX
mRNA


title: Het (Q140) KI X Tcerg1+/- Striatum male mRNA rep4 [Tcerg1]

description:
Tcerg20_4STR
mRNA

value: Het (Q140) KI X Tcerg1+/-


title: Ly8_het_G5_1

description:
clone G5; technical replicate 1
barcode: TAGAAT


title: Ly1_KO_H3_1

description:
clone H3; technical replicate 1
barcode: ACTAAA


title: Het (Q140) KI X Tcerg1+/- Striatum male mRNA rep3 [Tcerg1]

description:
Tcerg20_2STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Tcerg1]

description:
Tcerg11_2STR
mRNA


title: Ly1_KO_G1_2

description:
clone G1; technical replicate 2
barcode: CATAAA


title: Het (Q140) KI X Tcerg1+/- Striatum male mRNA rep2 [Tcerg1]

description:
Tcerg7_2STR
mRNA


title: Ly1_KO_G1_1

description:
clone G1; technical replicate 1
barcode: AATTTC


title: Het (Q140) KI X Tcerg1+/- Striatum male mRNA rep1 [Tcerg1]

description:
Tcerg6_2STR
mRNA


title: Ly1_KO_E8_1

description:
clone E8; technical replicate 1
barcode: AATGTA


title: Ly1_KO_E8_2

description:
clone E8; technical replicate 2
barcode: ATTTTG


title: Ly1_het_F9_2

description:
clone F9; technical replicate 2
barcode: ATTATC


title: Het (Q140) KI X Tcerg1+/- Striatum female mRNA rep4 [Tcerg1]

description:
Tcerg29_2STR
mRNA


title: Het (Q140) KI X Tcerg1+/- Striatum female mRNA rep3 [Tcerg1]

description:
Tcerg19_1STR
mRNA


title: Het (Q140) KI X Tcerg1+/- Striatum female mRNA rep2 [Tcerg1]

description:
Tcerg17_1STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Tcerg1]

description:
Tcerg6_3STR
mRNA


title: Ly1_het_F9_1

description:
clone F9; technical replicate 1
barcode: AAGTTA


title: Het (Q140) KI X Tcerg1+/- Striatum female mRNA rep1 [Tcerg1]

description:
Tcerg8_3STR
mRNA


title: Het (Q140) KI X Tcerg1+/- Cortex male mRNA rep4 [Tcerg1]

description:
Tcerg20_4CTX
mRNA


title: Ly1_het_F10_1

description:
clone F10; technical replicate 1
barcode: AATATG


title: Het (Q140) KI X Tcerg1+/- Cortex male mRNA rep3 [Tcerg1]

description:
Tcerg20_2CTX
mRNA


title: Ly1_cas9_9_2

description:
clone 9; technical replicate 2
barcode: ATGTAA


title: Ly1_het_F10_2

description:
clone F10; technical replicate 2
barcode: ATTGTT


title: Het (Q140) KI X Tcerg1+/- Cortex male mRNA rep2 [Tcerg1]

description:
Tcerg7_2CTX
mRNA


title: Ly1_cas9_9_1

description:
clone 9; technical replicate 1
barcode: AACATA


title: Het (Q140) KI X Tcerg1+/- Cortex male mRNA rep1 [Tcerg1]

description:
Tcerg6_2CTX
mRNA


title: Het (Q140) KI X Tcerg1+/- Cortex female mRNA rep3 [Tcerg1]

description:
Tcerg19_1CTX
mRNA


title: Ly1_cas9_1_2

description:
clone 1; technical replicate 2
barcode: ATATGA


title: Het (Q140) KI X Tcerg1+/- Cortex female mRNA rep2 [Tcerg1]

description:
Tcerg17_1CTX
mRNA


title: Ly1_cas9_7_2

description:
clone 7; technical replicate 2
barcode: ATCTAT


title: Het (Q140) KI X Tcerg1+/- Cortex female mRNA rep1 [Tcerg1]

description:
Tcerg8_3CTX
mRNA


title: Ly1_cas9_1_1

description:
clone 1; technical replicate 1
barcode: AAACAT


title: HCCLM3 cells, CRTC2-R>A

city: tianjin

first: meixi

last: wang

address: Tianjin Sports Institute North Road Huanhu West Road

country: China

institute: Tianjin Medical University Cancer Hospital

description: Library name: RNAseq-3

data_processing:
For RNA-seq, read counts were performed using STAR.
Assembly: hg38
Supplementary files format and content: For RNA-seq, an XLS file includes raw counts for each sample.

source_name: Liver

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol reagent kit according to the manufacturer’s protocol.
For RNA-seq, mRNA was enriched with magnetic beads containing Oligo (dT). Subsequently, a fragmentation buffer was added to break the mRNA into short fragments. Using mRNA as a template, a single strand of cDNA was synthesized using six base random primers. Then, buffer, dNTPs, and DNA polymerase I and RNase H were added to synthesize a double stranded cDNA. The double stranded cDNA was purified using AMPure XP beads. The purified double stranded cDNA is first subjected to end repair, followed by adding an A-tail and connecting to a sequencing adapter, followed by AMPure XP beads for fragment size selection. Finally, PCR amplification was performed and the PCR product was purified using AMPure XP beads to obtain the final sequencing library.

value: Liver

value: CRTC2-R>A overexpression


title: HCCLM3 cells, CRTC2-WT

description: Library name: RNAseq-2

value: CRTC2-WT overexpression


title: Tcerg1+/- Striatum male mRNA rep3 [Tcerg1]

description:
Tcerg18_2STR
mRNA

value: Corpus Striatum


title: HCCLM3 cells, Control

description: Library name: RNAseq-1

value: WT


title: Tcerg1+/- Striatum male mRNA rep2 [Tcerg1]

description:
Tcerg13_1STR
mRNA


title: Tcerg1+/- Striatum male mRNA rep4 [Tcerg1]

description:
Tcerg27_4STR
mRNA


title: Tcerg1+/- Striatum male mRNA rep1 [Tcerg1]

description:
Tcerg10_3STR
mRNA


title: Tcerg1+/- Striatum female mRNA rep3 [Tcerg1]

description:
Tcerg22_1STR
mRNA


title: Tcerg1+/- Striatum female mRNA rep4 [Tcerg1]

description:
Tcerg29_3STR
mRNA


title: Tcerg1+/- Striatum female mRNA rep2 [Tcerg1]

description:
Tcerg19_2STR
mRNA


title: Ly1_cas9_7_1

description:
clone 7; technical replicate 1
barcode: AAATCA

value: lymph node

value: Human B cell Lymphoma


title: total RNA-seq from sample MUC23195_S13

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: Library name: MUC23195_S13

data_processing:
Quality control with FastQC version 0.11.8 Unique Molecular Identifiers extraction with UMI-tools version 1.1.1 Adapter trimming with cutadapt version 2.10 Read aligning to the reference genome with STAR version 2.7.7a Read deduplication with UMI-tools version 1.1.1 Quantification of gene and transcript expression with RSEM version 1.3.3 Batch correction and differential analysis using Limma.
Assembly: GRCh38.p12
Supplementary files format and content: genes.results and isoforms.results files containing count data from RSEM

source_name: PBMCs

extract_protocol:
Blood was collected in the morning under fasted conditions, peripheral blood mononuclear cells (PBMCs) were extracted and stored at in the gas phase of liquid nitrogen. The RNA was extracted automatically with the chemagic 360 instrument by using the chemagic RNA Kit according to the manufacturer's instructions and 25µl eluate stored in a PCR plate at -80°C until further processing.
200ng RNA was used for rRNA depletion with the RiboCop rRNA Depletion Kit V1.3. 10µl of the depleted RNA was used for library preparation with the Lexogen CORALL total RNA-Seq Library Prep Kit with UDIs 12 nt Sets A1-A4. The library was sequenced on an NovaSeq 6000 using an S4 200 flow cell with paired-end 100bp reads.

tag: bmi

tag: total pairs

tag: gc content

tag: status

value: affected

value: PBMCs


title: total RNA-seq from sample MUC23380_S198

description: Library name: MUC23380_S198

value: male


title: total RNA-seq from sample MUC23356_S174

description: Library name: MUC23356_S174


title: Tcerg1+/- Cortex male mRNA rep4 [Tcerg1]

description:
Tcerg27_4CTX
mRNA

value: Cerebral Cortex

value: 6 months


title: total RNA-seq from sample MUC23365_S183

description: Library name: MUC23365_S183


title: Tcerg1+/- Striatum female mRNA rep1 [Tcerg1]

description:
Tcerg8_2STR
mRNA


title: total RNA-seq from sample MUC23392_S210

description: Library name: MUC23392_S210


title: Tcerg1+/- Cortex male mRNA rep3 [Tcerg1]

description:
Tcerg18_2CTX
mRNA


title: Het (Q140) KI X Tcerg1+/- Cortex female mRNA rep4 [Tcerg1]

description:
Tcerg29_2CTX
mRNA


title: total RNA-seq from sample MUC23550_S368

description: Library name: MUC23550_S368


title: total RNA-seq from sample MUC23391_S209

description: Library name: MUC23391_S209


title: total RNA-seq from sample MUC23564_S382

description: Library name: MUC23564_S382


title: Tcerg1+/- Cortex male mRNA rep1 [Tcerg1]

description:
Tcerg10_3CTX
mRNA


title: total RNA-seq from sample MUC23314_S132

description: Library name: MUC23314_S132


title: total RNA-seq from sample MUC23396_S214

description: Library name: MUC23396_S214


title: Tcerg1+/- Cortex female mRNA rep4 [Tcerg1]

description:
Tcerg29_3CTX
mRNA


title: Tcerg1+/- Cortex female mRNA rep3 [Tcerg1]

description:
Tcerg22_1CTX
mRNA


title: total RNA-seq from sample MUC23337_S155

description: Library name: MUC23337_S155


title: total RNA-seq from sample MUC23490_S308

description: Library name: MUC23490_S308


title: total RNA-seq from sample MUC23245_S63

description: Library name: MUC23245_S63


title: total RNA-seq from sample MUC23502_S320

description: Library name: MUC23502_S320


title: Tcerg1+/- Cortex female mRNA rep1 [Tcerg1]

description:
Tcerg8_2CTX
mRNA


title: WT Striatum male mRNA rep3 [Polq]

description:
Polq15_1STR
mRNA

value: Wild type


title: total RNA-seq from sample MUC23347_S165

description: Library name: MUC23347_S165


title: WT Striatum male mRNA rep4 [Polq]

description:
Polq15_2STR
mRNA


title: WT Striatum male mRNA rep2 [Polq]

description:
Polq13_4STR
mRNA


title: WT Striatum male mRNA rep1 [Polq]

description:
Polq13_2STR
mRNA


title: total RNA-seq from sample MUC23515_S333

description: Library name: MUC23515_S333


title: WT Striatum female mRNA rep3 [Polq]

description:
Polq16_3STR
mRNA


title: WT Striatum female mRNA rep4 [Polq]

description:
Polq23_3STR
mRNA


title: total RNA-seq from sample MUC23244_S62

description: Library name: MUC23244_S62


title: Tcerg1+/- Cortex male mRNA rep2 [Tcerg1]

description:
Tcerg13_1CTX
mRNA


title: total RNA-seq from sample MUC23233_S51

description: Library name: MUC23233_S51


title: total RNA-seq from sample MUC23456_S274

description: Library name: MUC23456_S274


title: WT Striatum female mRNA rep2 [Polq]

description:
Polq11_1STR
mRNA


title: total RNA-seq from sample MUC23421_S239

description: Library name: MUC23421_S239


title: total RNA-seq from sample MUC23420_S238

description: Library name: MUC23420_S238


title: WT Striatum female mRNA rep1 [Polq]

description:
Polq10_2STR
mRNA


title: total RNA-seq from sample MUC23207_S25

description: Library name: MUC23207_S25


title: Tcerg1+/- Cortex female mRNA rep2 [Tcerg1]

description:
Tcerg19_2CTX
mRNA


title: total RNA-seq from sample MUC23435_S253

description: Library name: MUC23435_S253


title: total RNA-seq from sample MUC23464_S282

description: Library name: MUC23464_S282


title: total RNA-seq from sample MUC23288_S106

description: Library name: MUC23288_S106


title: WT Cortex female mRNA rep3 [Polq]

description:
Polq16_3CTX
mRNA


title: total RNA-seq from sample MUC23375_S193

description: Library name: MUC23375_S193


title: WT Cortex female mRNA rep4 [Polq]

description:
Polq23_3CTX
mRNA


title: WT Cortex male mRNA rep1 [Polq]

description:
Polq13_2CTX
mRNA


title: total RNA-seq from sample MUC23399_S217

description: Library name: MUC23399_S217


title: WT Cortex female mRNA rep2 [Polq]

description:
Polq11_1CTX
mRNA


title: WT Cortex male mRNA rep4 [Polq]

description:
Polq15_2CTX
mRNA


title: total RNA-seq from sample MUC23304_S122

description: Library name: MUC23304_S122


title: WT Cortex male mRNA rep2 [Polq]

description:
Polq13_4CTX
mRNA


title: total RNA-seq from sample MUC23434_S252

description: Library name: MUC23434_S252


title: Het (Q140) KI Striatum male mRNA rep1 [Polq]

description:
Polq17_4STR
mRNA

value: Het (Q140) KI


title: Het (Q140) KI Striatum female mRNA rep4 [Polq]

description:
Polq27_3STR
mRNA

value: female


title: total RNA-seq from sample MUC23530_S348

description: Library name: MUC23530_S348


title: Het (Q140) KI Striatum female mRNA rep3 [Polq]

description:
Polq19_3STR
mRNA


title: total RNA-seq from sample MUC23512_S330

description: Library name: MUC23512_S330


title: total RNA-seq from sample MUC23185_S3

description: Library name: MUC23185_S3


title: Het (Q140) KI Striatum male mRNA rep4 [Polq]

description:
Polq26_2STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Polq]

description:
Polq22_1STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Polq]

description:
Polq20_3STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Polq]

description:
Polq14_5STR
mRNA


title: total RNA-seq from sample MUC23292_S110

description: Library name: MUC23292_S110


title: total RNA-seq from sample MUC23507_S325

description: Library name: MUC23507_S325


title: WT Cortex male mRNA rep3 [Polq]

description:
Polq15_1CTX
mRNA


title: total RNA-seq from sample MUC23362_S180

description: Library name: MUC23362_S180


title: WT Cortex female mRNA rep1 [Polq]

description:
Polq10_2CTX
mRNA


title: total RNA-seq from sample MUC23495_S313

description: Library name: MUC23495_S313


title: Het (Q140) KI Cortex male mRNA rep1 [Polq]

description:
Polq17_4CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Polq]

description:
Polq19_3CTX
mRNA


title: total RNA-seq from sample MUC23364_S182

description: Library name: MUC23364_S182


title: total RNA-seq from sample MUC23556_S374

description: Library name: MUC23556_S374


title: Het (Q140) KI Cortex female mRNA rep2 [Polq]

description:
Polq14_5CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Polq]

description:
Polq14_3CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Polq]

description:
Polq26_2CTX
mRNA


title: total RNA-seq from sample MUC23482_S300

description: Library name: MUC23482_S300


title: total RNA-seq from sample MUC23557_S375

description: Library name: MUC23557_S375


title: total RNA-seq from sample MUC23533_S351

description: Library name: MUC23533_S351


title: Het (Q140) KI Striatum female mRNA rep1 [Polq]

description:
Polq14_3STR
mRNA


title: total RNA-seq from sample MUC23350_S168

description: Library name: MUC23350_S168


title: total RNA-seq from sample MUC23302_S120

description: Library name: MUC23302_S120


title: total RNA-seq from sample MUC23461_S279

description: Library name: MUC23461_S279


title: Het (Q140) KI X Polq+/- Striatum male mRNA rep3 [Polq]

description:
Polq26_3STR
mRNA

value: Het (Q140) KI X Polq+/-


title: Het (Q140) KI Cortex male mRNA rep3 [Polq]

description:
Polq22_1CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Polq]

description:
Polq20_3CTX
mRNA


title: Het (Q140) KI X Polq+/- Striatum female mRNA rep3 [Polq]

description:
Polq18_3STR
mRNA


title: total RNA-seq from sample MUC23377_S195

description: Library name: MUC23377_S195


title: total RNA-seq from sample MUC23285_S103

description: Library name: MUC23285_S103


title: Het (Q140) KI Cortex female mRNA rep4 [Polq]

description:
Polq27_3CTX
mRNA


title: total RNA-seq from sample MUC23349_S167

description: Library name: MUC23349_S167


title: total RNA-seq from sample MUC23223_S41

description: Library name: MUC23223_S41


title: Het (Q140) KI X Polq+/- Striatum female mRNA rep1 [Polq]

description:
Polq10_1STR
mRNA


title: Het (Q140) KI X Polq+/- Cortex male mRNA rep4 [Polq]

description:
Polq7_2CTX
mRNA


title: Het (Q140) KI X Polq+/- Cortex male mRNA rep2 [Polq]

description:
Polq26_1CTX
mRNA


title: Het (Q140) KI X Polq+/- Cortex male mRNA rep1 [Polq]

description:
Polq13_3CTX
mRNA


title: total RNA-seq from sample MUC23561_S379

description: Library name: MUC23561_S379


title: total RNA-seq from sample MUC23397_S215

description: Library name: MUC23397_S215


title: total RNA-seq from sample MUC23470_S288

description: Library name: MUC23470_S288


title: total RNA-seq from sample MUC23282_S100

description: Library name: MUC23282_S100


title: Het (Q140) KI X Polq+/- Cortex female mRNA rep4 [Polq]

description:
Polq23_4CTX
mRNA


title: total RNA-seq from sample MUC23415_S233

description: Library name: MUC23415_S233


title: Het (Q140) KI X Polq+/- Striatum male mRNA rep1 [Polq]

description:
Polq13_3STR
mRNA


title: total RNA-seq from sample MUC23253_S71

description: Library name: MUC23253_S71


title: Polq+/- Striatum male mRNA rep2 [Polq]

description:
Polq13_5STR
mRNA

value: Polq+/-


title: Het (Q140) KI X Polq+/- Striatum female mRNA rep4 [Polq]

description:
Polq23_4STR
mRNA


title: Polq+/- Striatum female mRNA rep4 [Polq]

description:
Polq18_4STR
mRNA


title: total RNA-seq from sample MUC23455_S273

description: Library name: MUC23455_S273


title: Het (Q140) KI X Polq+/- Striatum male mRNA rep4 [Polq]

description:
Polq7_2STR
mRNA


title: Het (Q140) KI X Polq+/- Striatum female mRNA rep2 [Polq]

description:
Polq12_3STR
mRNA


title: Het (Q140) KI X Polq+/- Cortex male mRNA rep3 [Polq]

description:
Polq26_3CTX
mRNA


title: total RNA-seq from sample MUC23338_S156

description: Library name: MUC23338_S156


title: total RNA-seq from sample MUC23388_S206

description: Library name: MUC23388_S206


title: total RNA-seq from sample MUC23417_S235

description: Library name: MUC23417_S235


title: Het (Q140) KI X Polq+/- Striatum male mRNA rep2 [Polq]

description:
Polq26_1STR
mRNA


title: Polq+/- Striatum female mRNA rep2 [Polq]

description:
Polq14_4STR
mRNA


title: total RNA-seq from sample MUC23524_S342

description: Library name: MUC23524_S342


title: total RNA-seq from sample MUC23451_S269

description: Library name: MUC23451_S269


title: total RNA-seq from sample MUC23412_S230

description: Library name: MUC23412_S230


title: total RNA-seq from sample MUC23230_S48

description: Library name: MUC23230_S48


title: total RNA-seq from sample MUC23373_S191

description: Library name: MUC23373_S191


title: Het (Q140) KI X Polq+/- Cortex female mRNA rep3 [Polq]

description:
Polq18_3CTX
mRNA


title: total RNA-seq from sample MUC23224_S42

description: Library name: MUC23224_S42


title: total RNA-seq from sample MUC23191_S9

description: Library name: MUC23191_S9


title: total RNA-seq from sample MUC23323_S141

description: Library name: MUC23323_S141


title: total RNA-seq from sample MUC23355_S173

description: Library name: MUC23355_S173


title: Polq+/- Cortex female mRNA rep4 [Polq]

description:
Polq18_4CTX
mRNA


title: Polq+/- Cortex female mRNA rep3 [Polq]

description:
Polq16_2CTX
mRNA


title: total RNA-seq from sample MUC23458_S276

description: Library name: MUC23458_S276


title: Polq+/- Cortex female mRNA rep2 [Polq]

description:
Polq14_4CTX
mRNA


title: Het (Q140) KI X Polq+/- Cortex female mRNA rep2 [Polq]

description:
Polq12_3CTX
mRNA


title: total RNA-seq from sample MUC23538_S356

description: Library name: MUC23538_S356


title: Polq+/- Cortex female mRNA rep1 [Polq]

description:
Polq14_2CTX
mRNA


title: total RNA-seq from sample MUC23346_S164

description: Library name: MUC23346_S164


title: WT Striatum male mRNA rep4 [Msh3_striatum]

description:
Mh3Q25_1_STR
mRNA

value: 12 months


title: Het (Q140) KI X Polq+/- Cortex female mRNA rep1 [Polq]

description:
Polq10_1CTX
mRNA


title: WT Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q22_3_STR
mRNA


title: total RNA-seq from sample MUC23254_S72

description: Library name: MUC23254_S72


title: total RNA-seq from sample MUC23479_S297

description: Library name: MUC23479_S297


title: Polq+/- Striatum male mRNA rep4 [Polq]

description:
Polq21_4STR
mRNA


title: WT Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q22_1_STR
mRNA


title: total RNA-seq from sample MUC23486_S304

description: Library name: MUC23486_S304


title: Polq+/- Striatum male mRNA rep3 [Polq]

description:
Polq21_1STR
mRNA


title: Polq+/- Striatum male mRNA rep1 [Polq]

description:
Polq13_1STR
mRNA


title: total RNA-seq from sample MUC23196_S14

description: Library name: MUC23196_S14


title: WT Striatum female mRNA rep4 [Msh3_striatum]

description:
PQ71_4_STR
mRNA


title: total RNA-seq from sample MUC23462_S280

description: Library name: MUC23462_S280


title: total RNA-seq from sample MUC23543_S361

description: Library name: MUC23543_S361


title: Polq+/- Striatum female mRNA rep3 [Polq]

description:
Polq16_2STR
mRNA


title: WT Striatum female mRNA rep3 [Msh3_striatum]

description:
MQC72_4_STR
mRNA


title: total RNA-seq from sample MUC23262_S80

description: Library name: MUC23262_S80


title: total RNA-seq from sample MUC23326_S144

description: Library name: MUC23326_S144


title: total RNA-seq from sample MUC23361_S179

description: Library name: MUC23361_S179


title: total RNA-seq from sample MUC23312_S130

description: Library name: MUC23312_S130


title: total RNA-seq from sample MUC23494_S312

description: Library name: MUC23494_S312


title: WT Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q19_1_STR
mRNA


title: total RNA-seq from sample MUC23210_S28

description: Library name: MUC23210_S28


title: total RNA-seq from sample MUC23339_S157

description: Library name: MUC23339_S157


title: Het (Q140) KI Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q35_2_STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q25_2_STR
mRNA


title: total RNA-seq from sample MUC23198_S16

description: Library name: MUC23198_S16


title: Het (Q140) KI Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q14_2_STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q19_3_STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Msh3_striatum]

description:
Mh3Q37_5_STR
mRNA


title: total RNA-seq from sample MUC23551_S369

description: Library name: MUC23551_S369


title: Polq+/- Cortex male mRNA rep4 [Polq]

description:
Polq21_4CTX
mRNA


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q29_4_STR
mRNA

value: Het (Q140) KI X Msh3-/-


title: total RNA-seq from sample MUC23354_S172

description: Library name: MUC23354_S172


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q20_5_STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh3_striatum]

description:
Msh3Q9_4_STR
mRNA


title: Polq+/- Cortex male mRNA rep3 [Polq]

description:
Polq21_1CTX
mRNA


title: total RNA-seq from sample MUC23414_S232

description: Library name: MUC23414_S232


title: total RNA-seq from sample MUC23183_S1

description: Library name: MUC23183_S1


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep4 [Msh3_striatum]

description:
Mh3Q40_5_STR
mRNA


title: total RNA-seq from sample MUC23325_S143

description: Library name: MUC23325_S143


title: Polq+/- Striatum female mRNA rep1 [Polq]

description:
Polq14_2STR
mRNA


title: Polq+/- Cortex male mRNA rep2 [Polq]

description:
Polq13_5CTX
mRNA


title: Polq+/- Cortex male mRNA rep1 [Polq]

description:
Polq13_1CTX
mRNA


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep3 [Msh3_striatum]

description:
Mh3Q39_2_STR
mRNA


title: total RNA-seq from sample MUC23357_S175

description: Library name: MUC23357_S175


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q26_5_STR
mRNA


title: total RNA-seq from sample MUC23532_S350

description: Library name: MUC23532_S350


title: total RNA-seq from sample MUC23430_S248

description: Library name: MUC23430_S248


title: total RNA-seq from sample MUC23322_S140

description: Library name: MUC23322_S140


title: Msh3-/- Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q24_2_STR
mRNA


title: WT Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q16_2_STR
mRNA


title: total RNA-seq from sample MUC23265_S83

description: Library name: MUC23265_S83


title: WT Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q21_2_STR
mRNA


title: Msh3-/- Striatum female mRNA rep3 [Msh3_striatum]

description:
Mh3Q26_2_STR
mRNA


title: total RNA-seq from sample MUC23287_S105

description: Library name: MUC23287_S105


title: total RNA-seq from sample MUC23478_S296

description: Library name: MUC23478_S296


title: Het (Q140) KI Striatum male mRNA rep4 [Msh3_striatum]

description:
Msh3Q16_1_STR
mRNA


title: total RNA-seq from sample MUC23501_S319

description: Library name: MUC23501_S319


title: total RNA-seq from sample MUC23360_S178

description: Library name: MUC23360_S178


title: Het (Q140) KI Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q26_3_STR
mRNA


title: total RNA-seq from sample MUC23445_S263

description: Library name: MUC23445_S263


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep4 [Msh3_striatum]

description:
Mh3Q51_2_STR
mRNA


title: total RNA-seq from sample MUC23487_S305

description: Library name: MUC23487_S305


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q29_3_STR
mRNA

value: Het (Q140) KI X Msh3+/-


title: Msh3-/- Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q19_2_STR
mRNA

value: Corpus Striatum


title: total RNA-seq from sample MUC23249_S67

description: Library name: MUC23249_S67


title: Het (Q140) KI X Msh3-/- Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q36_5_STR
mRNA


title: total RNA-seq from sample MUC23208_S26

description: Library name: MUC23208_S26


title: total RNA-seq from sample MUC23213_S31

description: Library name: MUC23213_S31


title: total RNA-seq from sample MUC23332_S150

description: Library name: MUC23332_S150


title: Msh3-/- Striatum male mRNA rep4 [Msh3_striatum]

description:
Mh3Q44_4_STR
mRNA


title: total RNA-seq from sample MUC23209_S27

description: Library name: MUC23209_S27


title: total RNA-seq from sample MUC23411_S229

description: Library name: MUC23411_S229


title: Het (Q140) KI X Msh3-/- Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q30_3_STR
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q21_4_STR
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q18_2_STR
mRNA


title: total RNA-seq from sample MUC23263_S81

description: Library name: MUC23263_S81


title: Msh3-/- Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q20_1_STR
mRNA


title: Msh3-/- Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q17_3_STR
mRNA


title: total RNA-seq from sample MUC23476_S294

description: Library name: MUC23476_S294


title: total RNA-seq from sample MUC23358_S176

description: Library name: MUC23358_S176


title: Msh3-/- Striatum female mRNA rep4 [Msh3_striatum]

description:
Mh3Q36_1_STR
mRNA


title: total RNA-seq from sample MUC23542_S360

description: Library name: MUC23542_S360


title: Msh3+/- Striatum male mRNA rep4 [Msh3_striatum]

description:
Mh3Q55_5_STR
mRNA


title: Msh3+/- Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q22_2_STR
mRNA


title: total RNA-seq from sample MUC23423_S241

description: Library name: MUC23423_S241


title: total RNA-seq from sample MUC23348_S166

description: Library name: MUC23348_S166


title: total RNA-seq from sample MUC23522_S340

description: Library name: MUC23522_S340


title: total RNA-seq from sample MUC23499_S317

description: Library name: MUC23499_S317


title: total RNA-seq from sample MUC23333_S151

description: Library name: MUC23333_S151

value: unaffected


title: Msh3+/- Striatum female mRNA rep4 [Msh3_striatum]

description:
Mh3Q36_2_STR
mRNA


title: total RNA-seq from sample MUC23448_S266

description: Library name: MUC23448_S266


title: total RNA-seq from sample MUC23267_S85

description: Library name: MUC23267_S85


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q29_2_STR
mRNA


title: total RNA-seq from sample MUC23193_S11

description: Library name: MUC23193_S11


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep4 [Msh3_striatum]

description:
Mh3Q31_1_STR
mRNA


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep4 [Msh3_striatum]

description:
Mh3Q39_1_STR
mRNA


title: Msh3+/- Striatum male mRNA rep3 [Msh3_striatum]

description:
Mh3Q44_2_STR
mRNA


title: total RNA-seq from sample MUC23528_S346

description: Library name: MUC23528_S346


title: Het (Q140) KI X Msh3+/- Striatum male mRNA rep1 [Msh3_striatum]

description:
Mh3Q22_4_STR
mRNA


title: total RNA-seq from sample MUC23359_S177

description: Library name: MUC23359_S177


title: total RNA-seq from sample MUC23517_S335

description: Library name: MUC23517_S335


title: WT Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q22_3_CTX
mRNA


title: total RNA-seq from sample MUC23527_S345

description: Library name: MUC23527_S345


title: total RNA-seq from sample MUC23334_S152

description: Library name: MUC23334_S152


title: Het (Q140) KI X Msh3+/- Striatum female mRNA rep3 [Msh3_striatum]

description:
Mh3Q30_4_STR
mRNA


title: total RNA-seq from sample MUC23537_S355

description: Library name: MUC23537_S355


title: Msh3-/- Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q18_3_STR
mRNA


title: total RNA-seq from sample MUC23496_S314

description: Library name: MUC23496_S314


title: total RNA-seq from sample MUC23475_S293

description: Library name: MUC23475_S293


title: WT Cortex female mRNA rep4 [Msh3_cortex]

description:
PQ71_4_CTX
mRNA


title: Msh3+/- Striatum male mRNA rep2 [Msh3_striatum]

description:
Mh3Q33_1_STR
mRNA


title: total RNA-seq from sample MUC23228_S46

description: Library name: MUC23228_S46


title: total RNA-seq from sample MUC23309_S127

description: Library name: MUC23309_S127


title: WT Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q19_1_CTX
mRNA


title: total RNA-seq from sample MUC23477_S295

description: Library name: MUC23477_S295


title: total RNA-seq from sample MUC23232_S50

description: Library name: MUC23232_S50


title: total RNA-seq from sample MUC23407_S225

description: Library name: MUC23407_S225


title: Msh3+/- Striatum female mRNA rep2 [Msh3_striatum]

description:
Mh3Q21_3_STR
mRNA


title: Msh3+/- Striatum female mRNA rep3 [Msh3_striatum]

description:
Mh3Q26_4_STR
mRNA


title: Msh3+/- Striatum female mRNA rep1 [Msh3_striatum]

description:
Mh3Q19_4_STR
mRNA


title: WT Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q16_2_CTX
mRNA


title: WT Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q22_1_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q25_2_CTX
mRNA


title: total RNA-seq from sample MUC23308_S126

description: Library name: MUC23308_S126


title: WT Cortex female mRNA rep3 [Msh3_cortex]

description:
MQC72_4_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q35_2_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh3_cortex]

description:
Mh3Q37_5_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q26_3_CTX
mRNA


title: WT Cortex male mRNA rep4 [Msh3_cortex]

description:
Mh3Q25_1_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Msh3_cortex]

description:
Msh3Q9_4_CTX
mRNA


title: total RNA-seq from sample MUC23503_S321

description: Library name: MUC23503_S321


title: Het (Q140) KI Cortex male mRNA rep4 [Msh3_cortex]

description:
Msh3Q16_1_CTX
mRNA


title: total RNA-seq from sample MUC23558_S376

description: Library name: MUC23558_S376


title: total RNA-seq from sample MUC23331_S149

description: Library name: MUC23331_S149


title: total RNA-seq from sample MUC23457_S275

description: Library name: MUC23457_S275


title: total RNA-seq from sample MUC23297_S115

description: Library name: MUC23297_S115


title: Het (Q140) KI X Msh3 -/- Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q36_5_CTX
mRNA

value: Het (Q140) KI X Msh3 -/-


title: Het (Q140) KI X Msh3 -/- Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q29_4_CTX
mRNA


title: total RNA-seq from sample MUC23264_S82

description: Library name: MUC23264_S82


title: WT Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q21_2_CTX
mRNA


title: Het (Q140) KI X Msh3 -/- Cortex female mRNA rep4 [Msh3_cortex]

description:
Mh3Q40_5_CTX
mRNA


title: total RNA-seq from sample MUC23317_S135

description: Library name: MUC23317_S135


title: total RNA-seq from sample MUC23293_S111

description: Library name: MUC23293_S111


title: total RNA-seq from sample MUC23398_S216

description: Library name: MUC23398_S216


title: total RNA-seq from sample MUC23492_S310

description: Library name: MUC23492_S310


title: Het (Q140) KI Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q14_2_CTX
mRNA


title: total RNA-seq from sample MUC23242_S60

description: Library name: MUC23242_S60


title: Het (Q140) KI X Msh3 -/- Cortex female mRNA rep3 [Msh3_cortex]

description:
Mh3Q39_2_CTX
mRNA


title: total RNA-seq from sample MUC23425_S243

description: Library name: MUC23425_S243


title: total RNA-seq from sample MUC23220_S38

description: Library name: MUC23220_S38


title: total RNA-seq from sample MUC23409_S227

description: Library name: MUC23409_S227


title: Het (Q140) KI X Msh3 -/- Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q26_5_CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q19_3_CTX
mRNA


title: total RNA-seq from sample MUC23363_S181

description: Library name: MUC23363_S181


title: Het (Q140) KI X Msh3 -/- Cortex male mRNA rep4 [Msh3_cortex]

description:
Mh3Q51_2_CTX
mRNA


title: total RNA-seq from sample MUC23218_S36

description: Library name: MUC23218_S36


title: total RNA-seq from sample MUC23186_S4

description: Library name: MUC23186_S4


title: Msh3 -/- Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q17_3_CTX
mRNA


title: Het (Q140) KI X Msh3 -/- Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q20_5_CTX
mRNA


title: Msh3 -/- Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q18_3_CTX
mRNA


title: total RNA-seq from sample MUC23465_S283

description: Library name: MUC23465_S283


title: total RNA-seq from sample MUC23212_S30

description: Library name: MUC23212_S30


title: total RNA-seq from sample MUC23493_S311

description: Library name: MUC23493_S311


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep4 [Msh3_cortex]

description:
Mh3Q31_1_CTX
mRNA


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q29_3_CTX
mRNA


title: total RNA-seq from sample MUC23260_S78

description: Library name: MUC23260_S78


title: Msh3 -/- Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q20_1_CTX
mRNA


title: total RNA-seq from sample MUC23472_S290

description: Library name: MUC23472_S290


title: total RNA-seq from sample MUC23281_S99

description: Library name: MUC23281_S99


title: total RNA-seq from sample MUC23315_S133

description: Library name: MUC23315_S133


title: total RNA-seq from sample MUC23410_S228

description: Library name: MUC23410_S228


title: total RNA-seq from sample MUC23248_S66

description: Library name: MUC23248_S66


title: Msh3 -/- Cortex female mRNA rep3 [Msh3_cortex]

description:
Mh3Q26_2_CTX
mRNA


title: Het (Q140) KI X Msh3 -/- Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q30_3_CTX
mRNA


title: Msh3 -/- Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q19_2_CTX
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q21_4_CTX
mRNA


title: total RNA-seq from sample MUC23294_S112

description: Library name: MUC23294_S112


title: total RNA-seq from sample MUC23424_S242

description: Library name: MUC23424_S242


title: Msh3 -/- Cortex male mRNA rep4 [Msh3_cortex]

description:
Mh3Q44_4_CTX
mRNA


title: total RNA-seq from sample MUC23341_S159

description: Library name: MUC23341_S159


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q29_2_CTX
mRNA


title: total RNA-seq from sample MUC23467_S285

description: Library name: MUC23467_S285


title: total RNA-seq from sample MUC23416_S234

description: Library name: MUC23416_S234


title: Msh3+/- Cortex male mRNA rep4 [Msh3_cortex]

description:
Mh3Q55_5_CTX
mRNA


title: total RNA-seq from sample MUC23200_S18

description: Library name: MUC23200_S18


title: Msh3+/- Cortex male mRNA rep2 [Msh3_cortex]

description:
Mh3Q33_1_CTX
mRNA


title: total RNA-seq from sample MUC23199_S17

description: Library name: MUC23199_S17


title: Het (Q140) KI X Msh3+/- Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q22_4_CTX
mRNA


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep4 [Msh3_cortex]

description:
Mh3Q39_1_CTX
mRNA


title: Msh3+/- Cortex female mRNA rep4 [Msh3_cortex]

description:
Mh3Q36_2_CTX
mRNA


title: total RNA-seq from sample MUC23500_S318

description: Library name: MUC23500_S318


title: Msh3 -/- Cortex female mRNA rep4 [Msh3_cortex]

description:
Mh3Q36_1_CTX
mRNA


title: total RNA-seq from sample MUC23463_S281

description: Library name: MUC23463_S281


title: total RNA-seq from sample MUC23483_S301

description: Library name: MUC23483_S301


title: Msh3+/- Cortex female mRNA rep3 [Msh3_cortex]

description:
Mh3Q26_4_CTX
mRNA


title: total RNA-seq from sample MUC23197_S15

description: Library name: MUC23197_S15


title: total RNA-seq from sample MUC23190_S8

description: Library name: MUC23190_S8


title: WT Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ113_3STR
mRNA


title: total RNA-seq from sample MUC23216_S34

description: Library name: MUC23216_S34


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep3 [Msh3_cortex]

description:
Mh3Q30_4_CTX
mRNA


title: total RNA-seq from sample MUC23431_S249

description: Library name: MUC23431_S249


title: total RNA-seq from sample MUC23438_S256

description: Library name: MUC23438_S256


title: Het (Q140) KI X Msh3+/- Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q18_2_CTX
mRNA


title: total RNA-seq from sample MUC23531_S349

description: Library name: MUC23531_S349


title: total RNA-seq from sample MUC23184_S2

description: Library name: MUC23184_S2


title: Msh3+/- Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q44_2_CTX
mRNA


title: WT Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ117_4STR
mRNA


title: Msh3 -/- Cortex male mRNA rep3 [Msh3_cortex]

description:
Mh3Q24_2_CTX
mRNA


title: WT Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ117_4CTX
mRNA


title: total RNA-seq from sample MUC23484_S302

description: Library name: MUC23484_S302


title: total RNA-seq from sample MUC23520_S338

description: Library name: MUC23520_S338


title: WT Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ100_1CTX
mRNA


title: total RNA-seq from sample MUC23553_S371

description: Library name: MUC23553_S371


title: total RNA-seq from sample MUC23374_S192

description: Library name: MUC23374_S192


title: WT Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ116_5CTX
mRNA


title: total RNA-seq from sample MUC23320_S138

description: Library name: MUC23320_S138


title: WT Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ121_4STR
mRNA


title: Msh3+/- Cortex female mRNA rep2 [Msh3_cortex]

description:
Mh3Q21_3_CTX
mRNA


title: total RNA-seq from sample MUC23226_S44

description: Library name: MUC23226_S44


title: Msh3+/- Cortex male mRNA rep1 [Msh3_cortex]

description:
Mh3Q22_2_CTX
mRNA


title: total RNA-seq from sample MUC23310_S128

description: Library name: MUC23310_S128


title: WT Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ100_1STR
mRNA


title: WT Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ116_3CTX
mRNA


title: WT Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ101_5STR
mRNA


title: WT Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ108_2CTX
mRNA


title: WT Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ116_5STR
mRNA


title: total RNA-seq from sample MUC23437_S255

description: Library name: MUC23437_S255


title: WT Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ116_3STR
mRNA


title: total RNA-seq from sample MUC23460_S278

description: Library name: MUC23460_S278


title: Het (Q140) KI Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ113_4STR
mRNA


title: total RNA-seq from sample MUC23250_S68

description: Library name: MUC23250_S68


title: total RNA-seq from sample MUC23378_S196

description: Library name: MUC23378_S196


title: WT Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ108_2STR
mRNA


title: total RNA-seq from sample MUC23328_S146

description: Library name: MUC23328_S146


title: total RNA-seq from sample MUC23215_S33

description: Library name: MUC23215_S33


title: Het (Q140) KI Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ110_4STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ108_3STR
mRNA


title: total RNA-seq from sample MUC23403_S221

description: Library name: MUC23403_S221


title: Het (Q140) KI Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ115_4CTX
mRNA


title: total RNA-seq from sample MUC23269_S87

description: Library name: MUC23269_S87


title: Msh3+/- Cortex female mRNA rep1 [Msh3_cortex]

description:
Mh3Q19_4_CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ113_4CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ110_5CTX
mRNA


title: total RNA-seq from sample MUC23446_S264

description: Library name: MUC23446_S264


title: Het (Q140) KI Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ112_5CTX
mRNA


title: total RNA-seq from sample MUC23386_S204

description: Library name: MUC23386_S204


title: WT Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ121_4CTX
mRNA


title: WT Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ113_3CTX
mRNA


title: total RNA-seq from sample MUC23504_S322

description: Library name: MUC23504_S322


title: total RNA-seq from sample MUC23231_S49

description: Library name: MUC23231_S49


title: total RNA-seq from sample MUC23324_S142

description: Library name: MUC23324_S142


title: total RNA-seq from sample MUC23219_S37

description: Library name: MUC23219_S37


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ73_2STR
mRNA

value: Het (Q140) KI X Rgs9+/- X Msh2-/-


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ70_4STR
mRNA


title: total RNA-seq from sample MUC23256_S74

description: Library name: MUC23256_S74


title: WT Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ101_5CTX
mRNA


title: total RNA-seq from sample MUC23319_S137

description: Library name: MUC23319_S137


title: total RNA-seq from sample MUC23261_S79

description: Library name: MUC23261_S79


title: Het (Q140) KI Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ115_4STR
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ106_1STR
mRNA


title: total RNA-seq from sample MUC23384_S202

description: Library name: MUC23384_S202


title: total RNA-seq from sample MUC23560_S378

description: Library name: MUC23560_S378


title: Het (Q140) KI Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ110_5STR
mRNA


title: total RNA-seq from sample MUC23541_S359

description: Library name: MUC23541_S359


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ97_4STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ112_5STR
mRNA


title: total RNA-seq from sample MUC23521_S339

description: Library name: MUC23521_S339

value: affected


title: total RNA-seq from sample MUC23439_S257

description: Library name: MUC23439_S257

value: PBMCs


title: Het (Q140) KI Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ111_5STR
mRNA


title: total RNA-seq from sample MUC23535_S353

description: Library name: MUC23535_S353

value: male


title: Het (Q140) KI Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ101_1STR
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ73_2CTX
mRNA

value: Cerebral Cortex


title: total RNA-seq from sample MUC23241_S59

description: Library name: MUC23241_S59


title: total RNA-seq from sample MUC23563_S381

description: Library name: MUC23563_S381


title: total RNA-seq from sample MUC23379_S197

description: Library name: MUC23379_S197


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ71_1CTX
mRNA

value: 6 months


title: Het (Q140) KI Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ110_4CTX
mRNA


title: total RNA-seq from sample MUC23345_S163

description: Library name: MUC23345_S163


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ70_4CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ111_5CTX
mRNA


title: total RNA-seq from sample MUC23376_S194

description: Library name: MUC23376_S194


title: total RNA-seq from sample MUC23382_S200

description: Library name: MUC23382_S200


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ97_4CTX
mRNA


title: total RNA-seq from sample MUC23257_S75

description: Library name: MUC23257_S75


title: total RNA-seq from sample MUC23400_S218

description: Library name: MUC23400_S218


title: total RNA-seq from sample MUC23329_S147

description: Library name: MUC23329_S147


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ77_2CTX
mRNA


title: total RNA-seq from sample MUC23480_S298

description: Library name: MUC23480_S298


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ133_3STR
mRNA

value: Het (Q140) KI X Rgs9+/-


title: total RNA-seq from sample MUC23235_S53

description: Library name: MUC23235_S53


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ133_1STR
mRNA


title: total RNA-seq from sample MUC23405_S223

description: Library name: MUC23405_S223


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ106_1CTX
mRNA


title: total RNA-seq from sample MUC23278_S96

description: Library name: MUC23278_S96


title: Het (Q140) KI Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ108_3CTX
mRNA

value: Het (Q140) KI


title: total RNA-seq from sample MUC23447_S265

description: Library name: MUC23447_S265


title: Het (Q140) KI Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ101_1CTX
mRNA

value: female


title: total RNA-seq from sample MUC23188_S6

description: Library name: MUC23188_S6


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ127_5STR
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ71_1STR
mRNA


title: total RNA-seq from sample MUC23534_S352

description: Library name: MUC23534_S352


title: total RNA-seq from sample MUC23286_S104

description: Library name: MUC23286_S104


title: total RNA-seq from sample MUC23321_S139

description: Library name: MUC23321_S139


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ68_1STR
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ97_1STR
mRNA


title: total RNA-seq from sample MUC23368_S186

description: Library name: MUC23368_S186


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ133_3CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ77_2STR
mRNA


title: total RNA-seq from sample MUC23343_S161

description: Library name: MUC23343_S161


title: total RNA-seq from sample MUC23429_S247

description: Library name: MUC23429_S247


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ91_3CTX
mRNA


title: total RNA-seq from sample MUC23505_S323

description: Library name: MUC23505_S323


title: total RNA-seq from sample MUC23529_S347

description: Library name: MUC23529_S347


title: total RNA-seq from sample MUC23344_S162

description: Library name: MUC23344_S162


title: total RNA-seq from sample MUC23433_S251

description: Library name: MUC23433_S251


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ122_3CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ68_1CTX
mRNA


title: total RNA-seq from sample MUC23413_S231

description: Library name: MUC23413_S231


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ97_1CTX
mRNA


title: total RNA-seq from sample MUC23238_S56

description: Library name: MUC23238_S56


title: total RNA-seq from sample MUC23485_S303

description: Library name: MUC23485_S303


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ91_3STR
mRNA


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ129_2CTX
mRNA


title: WT Striatum male mRNA rep4 [Msh2]

description:
MRQ4_1str
mRNA

value: Wild type


title: total RNA-seq from sample MUC23440_S258

description: Library name: MUC23440_S258


title: total RNA-seq from sample MUC23387_S205

description: Library name: MUC23387_S205


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ122_3STR
mRNA


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ116_4STR
mRNA


title: WT Striatum male mRNA rep2 [Msh2]

description:
MRQ23_2str
mRNA


title: total RNA-seq from sample MUC23508_S326

description: Library name: MUC23508_S326


title: total RNA-seq from sample MUC23418_S236

description: Library name: MUC23418_S236


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ129_2STR
mRNA


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ108_4STR
mRNA


title: WT Striatum female mRNA rep2 [Msh2]

description:
MRQ6_1str
mRNA


title: WT Striatum male mRNA rep3 [Msh2]

description:
MRQ23_5str
mRNA


title: total RNA-seq from sample MUC23436_S254

description: Library name: MUC23436_S254


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ133_1CTX
mRNA


title: total RNA-seq from sample MUC23246_S64

description: Library name: MUC23246_S64


title: total RNA-seq from sample MUC23217_S35

description: Library name: MUC23217_S35


title: WT Cortex male mRNA rep1 [Msh2]

description:
MRQ15_3CTX
mRNA


title: total RNA-seq from sample MUC23336_S154

description: Library name: MUC23336_S154


title: WT Cortex female mRNA rep1 [Msh2]

description:
MRQ23_2CTX
mRNA


title: total RNA-seq from sample MUC23206_S24

description: Library name: MUC23206_S24


title: total RNA-seq from sample MUC23381_S199

description: Library name: MUC23381_S199


title: Het (Q140) KI Striatum male mRNA rep4 [Msh2]

description:
MRQ8_4str
mRNA


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ127_5CTX
mRNA


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ116_4CTX
mRNA


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ108_4CTX
mRNA


title: WT Striatum female mRNA rep1 [Msh2]

description:
MRQ51_1str
mRNA


title: WT Striatum male mRNA rep5 [Msh2]

description:
MRQ7_2str
mRNA


title: total RNA-seq from sample MUC23279_S97

description: Library name: MUC23279_S97


title: Het (Q140) KI Striatum male mRNA rep3 [Msh2]

description:
MRQ30_2str
mRNA


title: total RNA-seq from sample MUC23229_S47

description: Library name: MUC23229_S47


title: total RNA-seq from sample MUC23548_S366

description: Library name: MUC23548_S366


title: total RNA-seq from sample MUC23546_S364

description: Library name: MUC23546_S364


title: WT Striatum male mRNA rep1 [Msh2]

description:
MRQ15_3str
mRNA


title: total RNA-seq from sample MUC23443_S261

description: Library name: MUC23443_S261


title: Het (Q140) KI Striatum male mRNA rep1 [Msh2]

description:
MRQ20_1str
mRNA


title: total RNA-seq from sample MUC23509_S327

description: Library name: MUC23509_S327


title: total RNA-seq from sample MUC23468_S286

description: Library name: MUC23468_S286


title: total RNA-seq from sample MUC23453_S271

description: Library name: MUC23453_S271


title: Het (Q140) KI Striatum female mRNA rep3 [Msh2]

description:
MRQ51_4str
mRNA


title: WT Cortex male mRNA rep2 [Msh2]

description:
MRQ51_1CTX
mRNA


title: WT Cortex male mRNA rep3 [Msh2]

description:
MRQ7_2CTX
mRNA


title: total RNA-seq from sample MUC23559_S377

description: Library name: MUC23559_S377


title: total RNA-seq from sample MUC23236_S54

description: Library name: MUC23236_S54


title: total RNA-seq from sample MUC23474_S292

description: Library name: MUC23474_S292


title: WT Cortex female mRNA rep3 [Msh2]

description:
MRQ4_1CTX
mRNA


title: WT Cortex female mRNA rep2 [Msh2]

description:
MRQ23_5CTX
mRNA


title: total RNA-seq from sample MUC23280_S98

description: Library name: MUC23280_S98


title: Het (Q140) KI Cortex male mRNA rep3 [Msh2]

description:
MRQ30_2CTX
mRNA


title: WT Cortex female mRNA rep4 [Msh2]

description:
MRQ6_1CTX
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Msh2]

description:
MRQ24_4str
mRNA


title: total RNA-seq from sample MUC23408_S226

description: Library name: MUC23408_S226


title: Het (Q140) KI Cortex male mRNA rep2 [Msh2]

description:
MRQ24_4CTX
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh2]

description:
MRQ52_2str
mRNA


title: total RNA-seq from sample MUC23372_S190

description: Library name: MUC23372_S190


title: Het (Q140) KI Cortex male mRNA rep1 [Msh2]

description:
MRQ20_1CTX
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Msh2]

description:
MRQ45_2str
mRNA


title: total RNA-seq from sample MUC23222_S40

description: Library name: MUC23222_S40


title: Het (Q140) KI Striatum female mRNA rep1 [Msh2]

description:
MRQ27_2str
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh2]

description:
MRQ52_2CTX
mRNA


title: total RNA-seq from sample MUC23340_S158

description: Library name: MUC23340_S158


title: total RNA-seq from sample MUC23513_S331

description: Library name: MUC23513_S331


title: Het (Q140) KI Cortex male mRNA rep4 [Msh2]

description:
MRQ51_4CTX
mRNA


title: total RNA-seq from sample MUC23283_S101

description: Library name: MUC23283_S101


title: total RNA-seq from sample MUC23545_S363

description: Library name: MUC23545_S363


title: Het (Q140) KI Cortex female mRNA rep2 [Msh2]

description:
MRQ45_2CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep1 [Msh2]

description:
MRQ12_5str
mRNA


title: total RNA-seq from sample MUC23330_S148

description: Library name: MUC23330_S148


title: total RNA-seq from sample MUC23426_S244

description: Library name: MUC23426_S244


title: Het (Q140) KI Cortex female mRNA rep4 [Msh2]

description:
MRQ8_4CTX
mRNA


title: total RNA-seq from sample MUC23202_S20

description: Library name: MUC23202_S20


title: total RNA-seq from sample MUC23497_S315

description: Library name: MUC23497_S315


title: Het (Q140) KI Cortex female mRNA rep1 [Msh2]

description:
MRQ27_2CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep2 [Msh2]

description:
MRQ39_3str
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep1 [Msh2]

description:
MRQ31_1str
mRNA


title: total RNA-seq from sample MUC23370_S188

description: Library name: MUC23370_S188


title: total RNA-seq from sample MUC23452_S270

description: Library name: MUC23452_S270


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep4 [Msh2]

description:
MRQ46_1str
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep4 [Msh2]

description:
MRQ9_3CTX
mRNA


title: total RNA-seq from sample MUC23192_S10

description: Library name: MUC23192_S10


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep3 [Msh2]

description:
MRQ46_1CTX
mRNA


title: total RNA-seq from sample MUC23547_S365

description: Library name: MUC23547_S365


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep2 [Msh2]

description:
MRQ42_3CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep3 [Msh2]

description:
MRQ42_3str
mRNA


title: total RNA-seq from sample MUC23390_S208

description: Library name: MUC23390_S208


title: total RNA-seq from sample MUC23187_S5

description: Library name: MUC23187_S5


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum male mRNA rep2 [Msh2]

description:
MRQ16_3str
mRNA


title: total RNA-seq from sample MUC23311_S129

description: Library name: MUC23311_S129


title: total RNA-seq from sample MUC23313_S131

description: Library name: MUC23313_S131


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep4 [Msh2]

description:
MRQ9_3str
mRNA


title: total RNA-seq from sample MUC23211_S29

description: Library name: MUC23211_S29


title: total RNA-seq from sample MUC23449_S267

description: Library name: MUC23449_S267


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Striatum female mRNA rep3 [Msh2]

description:
MRQ49_3str
mRNA


title: total RNA-seq from sample MUC23335_S153

description: Library name: MUC23335_S153


title: total RNA-seq from sample MUC23237_S55

description: Library name: MUC23237_S55


title: total RNA-seq from sample MUC23506_S324

description: Library name: MUC23506_S324


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep1 [Msh2]

description:
MRQ16_3CTX
mRNA


title: total RNA-seq from sample MUC23406_S224

description: Library name: MUC23406_S224


title: total RNA-seq from sample MUC23498_S316

description: Library name: MUC23498_S316


title: Rgs9+/- X Msh2-/- Striatum male mRNA rep3 [Msh2]

description:
MRQ59_2str
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep4 [Msh2]

description:
MRQ49_3CTX
mRNA


title: Rgs9+/- X Msh2-/- Striatum male mRNA rep2 [Msh2]

description:
MRQ3_3str
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep2 [Msh2]

description:
MRQ31_1CTX
mRNA


title: total RNA-seq from sample MUC23201_S19

description: Library name: MUC23201_S19


title: total RNA-seq from sample MUC23544_S362

description: Library name: MUC23544_S362


title: total RNA-seq from sample MUC23489_S307

description: Library name: MUC23489_S307


title: total RNA-seq from sample MUC23225_S43

description: Library name: MUC23225_S43


title: Rgs9+/- X Msh2-/- Striatum male mRNA rep1 [Msh2]

description:
MRQ24_1str
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex female mRNA rep3 [Msh2]

description:
MRQ39_3CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2-/- Cortex male mRNA rep1 [Msh2]

description:
MRQ12_5CTX
mRNA


title: total RNA-seq from sample MUC23259_S77

description: Library name: MUC23259_S77


title: Rgs9+/- X Msh2-/- Striatum female mRNA rep3 [Msh2]

description:
MRQ8_5str
mRNA


title: total RNA-seq from sample MUC23251_S69

description: Library name: MUC23251_S69


title: total RNA-seq from sample MUC23307_S125

description: Library name: MUC23307_S125


title: total RNA-seq from sample MUC23536_S354

description: Library name: MUC23536_S354


title: total RNA-seq from sample MUC23481_S299

description: Library name: MUC23481_S299


title: Rgs9+/- X Msh2-/- Striatum female mRNA rep2 [Msh2]

description:
MRQ44_1str
mRNA


title: total RNA-seq from sample MUC23432_S250

description: Library name: MUC23432_S250


title: Rgs9+/- X Msh2-/- Cortex male mRNA rep3 [Msh2]

description:
MRQ42_4CTX
mRNA


title: Rgs9+/- X Msh2-/- Striatum female mRNA rep1 [Msh2]

description:
MRQ42_4str
mRNA


title: Hepatocyte organoids, RGF +T3, Day 6, Dox+, 3

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: Comma delimited file include normalized CPM values for each sample

molecule: polyA RNA

source_name: liver

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma). The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. RGF +T3: 10nM Triiodothyronine(T3) in RGF medium;

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: AAV-TBG-Cre was mixed with fragmented HOs in BME at a concentration of 1x10^10 GC/ml during the passage before the maturation process. 200ng/ml Dox were added to the medium to induce YAP overexpression.

value: liver

value: Hepatocyte organoids

value: hepatocytes

value: TetO-YAP

value: Dox


title: Rgs9+/- X Msh2-/- Cortex male mRNA rep4 [Msh2]

description:
MRQ44_1CTX
mRNA

value: 12 months


title: Hepatocyte organoids, RGF +T3, Day 6, Dox+, 2


title: Hepatocyte organoids, RGF +T3, Day 6, Dox-, 1

value: Control


title: Rgs9+/- X Msh2-/- Cortex male mRNA rep2 [Msh2]

description:
MRQ3_3CTX
mRNA


title: total RNA-seq from sample MUC23252_S70

description: Library name: MUC23252_S70

value: unaffected


title: Hepatocyte organoids, RGF +T3, Day 6, Dox-, 2


title: total RNA-seq from sample MUC23471_S289

description: Library name: MUC23471_S289

value: affected


title: CK18_D0

city: Hong Kong

first: Ying

last: NI

address: Tat Chee Avenue

institute: City University of Hong Kong

data_processing:
Modifications of 5-methylcytosine at each genomic site was determined with Megalodon pipeline (version 2.4.1) with the model configuration of “dna_r9.4.1_450bps_modbases_5mc_hac.cfg”. Methylation for promoter regions of each gene was determined by the average methylation level of CG sites before the transcriptional start site.
Assembly: hg38
Supplementary files format and content: methylation proportion in the promoter region of each gene, which included the Ensembl gene ID and the 5mC ratio generated from raw data. The 5mC ratio was calculated by the average of 5mC level on each CG site within the region.

extract_protocol:
Genomic DNA was extracted from diagnostic de novo AML bone marrow.
Around 0.2-1µg native genomic DNA were used to build the library with 1D ligation sequencing kit (LSK-110, ONT) according to the manufacturer’s protocol. The libraries were loaded to R9.4.1 flow cells (FLO-106, ONT).

value: Bone marrow

tag: subject status

value: Adult patients (age 18 to 65 years old) with newly diagnosed CK-AML

tag: group

value: nonresponder

tag: time point


title: Rgs9+/- X Msh2-/- Cortex male mRNA rep1 [Msh2]

description:
MRQ24_1CTX
mRNA

value: Cerebral Cortex

value: male


title: total RNA-seq from sample MUC23247_S65

description: Library name: MUC23247_S65

value: PBMCs


title: CK17_D10


title: Rgs9+/- X Msh2-/- Cortex female mRNA rep2 [Msh2]

description:
MRQ8_5CTX
mRNA

value: female


title: CK16_D10


title: CK16_D0


title: CK15_D10


title: total RNA-seq from sample MUC23419_S237

description: Library name: MUC23419_S237


title: CK17_D0


title: Rgs9+/- X Msh2-/- Cortex female mRNA rep1 [Msh2]

description:
MRQ59_2CTX
mRNA


title: CK15_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum male mRNA rep2 [Msh2]

description:
MRQ3_2str
mRNA

value: Corpus Striatum

value: Het (Q140) KI X Rgs9+/- X Msh2+/-


title: CK14_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum male mRNA rep4 [Msh2]

description:
MRQ5_3str
mRNA


title: total RNA-seq from sample MUC23422_S240

description: Library name: MUC23422_S240


title: CK14_D10


title: Hepatocyte organoids, RGF +T3, Day 6, Dox+, 1

value: liver

value: Hepatocyte organoids


title: CK12_D10


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum male mRNA rep1 [Msh2]

description:
MRQ25_2str
mRNA


title: CK13_D10


title: total RNA-seq from sample 23L002676_S28

description: Library name: 23L002676_S28

source_name: Whole Blood

extract_protocol:
RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
rRNA was depleted with RiboCop and libraries were prepared with the Lexogen CORALL total RNA-Seq V2 Library Prep Kit. Sequencing was performed on a NovaSeq 6000 with a target depth of 15.6 million reads per sample.

value: Whole Blood


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum male mRNA rep3 [Msh2]

description:
MRQ30_4str
mRNA


title: CK10_D10

value: responder


title: CK18_D10


title: total RNA-seq from sample 23L002694_S46

description: Library name: 23L002694_S46


title: CK9_D10


title: CK11_D10


title: CK13_D0


title: CK11_D0


title: total RNA-seq from sample MUC23510_S328

description: Library name: MUC23510_S328


title: Hepatocyte organoids, RGF +T3, Day 6, Dox-, 3

value: hepatocytes

value: TetO-YAP


title: CK10_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex male mRNA rep4 [Msh2]

description:
MRQ5_3CTX
mRNA

value: 12 months


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum female mRNA rep4 [Msh2]

description:
MRQ33_4str
mRNA


title: CK7_D10


title: CK7_D0


title: total RNA-seq from sample MUC23353_S171

description: Library name: MUC23353_S171

value: affected


title: total RNA-seq from sample 23L002725_S77

description: Library name: 23L002725_S77

value: unaffected


title: total RNA-seq from sample 23L002700_S52

description: Library name: 23L002700_S52


title: CK8_D10

value: Bone marrow

value: Adult patients (age 18 to 65 years old) with newly diagnosed CK-AML


title: CK12_D0

value: nonresponder


title: total RNA-seq from sample 23L002667_S19

description: Library name: 23L002667_S19


title: CK6_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex male mRNA rep3 [Msh2]

description:
MRQ30_4CTX
mRNA

value: Cerebral Cortex

value: male


title: CK9_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum female mRNA rep2 [Msh2]

description:
MRQ25_3str
mRNA

value: female


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum female mRNA rep1 [Msh2]

description:
MRQ24_2str
mRNA

value: Corpus Striatum


title: CK8_D0


title: CK5_D0


title: CK5_D10


title: total RNA-seq from sample 23L002653_S5

description: Library name: 23L002653_S5


title: CK4_D10


title: CK4_D0


title: total RNA-seq from sample 23L002688_S40

description: Library name: 23L002688_S40


title: CK6_D10


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Striatum female mRNA rep3 [Msh2]

description:
MRQ29_3str
mRNA

value: Het (Q140) KI X Rgs9+/- X Msh2+/-


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex male mRNA rep1 [Msh2]

description:
MRQ24_2CTX
mRNA


title: total RNA-seq from sample 23L002717_S69

description: Library name: 23L002717_S69


title: CK3_D10


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex male mRNA rep2 [Msh2]

description:
MRQ3_2CTX
mRNA


title: CK2_D0


title: total RNA-seq from sample MUC23268_S86

description: Library name: MUC23268_S86

value: PBMCs


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex female mRNA rep4 [Msh2]

description:
MRQ33_4CTX
mRNA


title: total RNA-seq from sample 23L002671_S23

description: Library name: 23L002671_S23


title: NBL-S P53 KO cells

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were aligned to the human reference genome (hg38) with STAR (version 2.7.5b) (--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated).
BAM files were imported into R using Rsubread featureCounts (1.32.4)
Assigned reads were then normalized and differentially expressed genes were identified using the R package DEseq2 (version 1.36.0) (Love et al. 2014)
Genes were considered expressed if the sum of raw counts was >10 for any given gene. Differentially expressed genes were called using an adjusted p value <= 0.05 and log2FC >= 0.75 or <= -0.75.
4 ATRX IFF clones were compared to 2 ATRX WT clones and the parental NBL-S P53 KO line the clones were generated from
Assembly: hg38
Supplementary files format and content: CSV files with lists of differentially expressed genes
Supplementary files format and content: CSV files with normalized counts

source_name: NBL-S

growth_protocol: NBL-S cells were cultured in DMEM supplemented with 10% FBS, 100 IU of penicillin and 100 μg/mL of streptomycin

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and the quality of RNA samples was assessed on a 2100 Agilent Bioanalyzer
mRNA was extracted from 2 ug of total RNA per sample using NEXTFLEX® Poly(A) Beads 2.0 (Perkin Elmer, Austin, Texas, USA). Libraries were prepared from mRNA samples using NEXTFLEX® Rapid Directional RNA-seq Kit 2.0 (Perkin Elmer, Austin, Texas, USA). Quality of library preparation was assessed on a 2100 Agilent Bioanalyzer or 4150 Tapestation

treatment_protocol: The ATRX wildtype P53 -/- cell clone NBL-S A9 was transfected with two CRISPR gRNAs encoded on pSpCas9(BB)-2A-GFP (PX458) and pSpCas9(BB)-2A-Puro (PX459) V2.0, respectively, to induce a deletion of exons 2-10 (fusion of exon 1-11). 24h post transfection cells were selected with puromycin (1 μg/ml) and sorted into a pool of GFP+ cells after 48 hours of selection. After 1-2 weeks, cells were sorted into single cells into a 96-well format. DNA was collected from single cell clones and screened via PCR for deletion of the region between the two target sites. IFF and WT clones were confirmed via targeted sequencing and Western blot for full-length ATRX or ATRX IFF.

value: NBL-S

value: Neuroblastoma

value: P53 KO, ATRX WT


title: CK2_D10

value: responder


title: total RNA-seq from sample 23L002735_S87

description: Library name: 23L002735_S87

value: Whole Blood


title: total RNA-seq from sample 23L002727_S79

description: Library name: 23L002727_S79


title: total RNA-seq from sample 23L002709_S61

description: Library name: 23L002709_S61


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep3 [Msh2]

description:
MRQ48_3str
mRNA

value: Het (Q140) KI X Rgs9+/-

value: 12 months


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex female mRNA rep3 [Msh2]

description:
MRQ29_3CTX
mRNA


title: CK1_D10


title: CK1_D0


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex female mRNA rep2 [Msh2]

description:
MRQ25_3CTX
mRNA


title: Het (Q140) KI X Rgs9+/- X Msh2+/- Cortex female mRNA rep1 [Msh2]

description:
MRQ25_2CTX
mRNA


title: total RNA-seq from sample 23L002664_S16

description: Library name: 23L002664_S16

value: unaffected


title: NBL-S P53 KO cells WT clone #46


title: NBL-S P53 KO cells WT clone #70


title: NBL-S P53 KO cells IFF clone #118

value: P53 KO, ATRX IFF


title: NBL-S P53 KO cells IFF clone #79


title: CK3_D0

value: Bone marrow

value: Adult patients (age 18 to 65 years old) with newly diagnosed CK-AML


title: total RNA-seq from sample 23L002662_S14

description: Library name: 23L002662_S14


title: NBL-S P53 KO cells IFF clone #141


city: Chicago

first: James

last: Mathew

state: IL

address: 300 E Superior

department: Department of Surgery, Division of Organ Transplantation, Comprehensive Transplant Center

institute: Northwestern University Feinberg School of Medicine

description: Library name: R70-Urine_Pellet-for_cause_Dec_31_2019_TCRB

data_processing:
raw data preprocessed by Adaptive Biotechnologies
Assembly: hg18 (NCBI 36)
Supplementary files format and content: sample level TSV files (unique per sample) are tab deliminated and contain the T-cell receptor rearrangement sequences, their observed counts and frequencies in the sample, as well as information relating to rearrangement length, V,D,J gene usage and their respective indices along the nucleotide rearrangement, and whether the sequence was in frame for transcription/translation and thus productive
Supplementary files format and content: project level TSV file (one containing data from all samples) is tab deliminated and contains sample level metrics including the numbers of T-cell receptor rearrangements and templates observed, the total number of nucleated cells observed, the T-cell content of the sample i.e. the fraction of T-cell templates observed divided by the total number of nucleated cells observed, the fraction of T-cell receptors that are productive or in-frame, Simpson clonality of the observed productive T-cells, the sequencing locus TCRB, and the estimated gDNA mass sequenced
Library strategy: TCR-Seq

source_name: Urine Pellet

extract_protocol:
QIAamp DNA blood Mini kit (Qiagen)
Bias-controlled multiplex PCR using forward and reverse primers specific to CDR3 Vβ and Jβ region (Adaptive Biotechnologies)

value: Urine Pellet

tag: subject

tag: visit

value: 6.3 Month

tag: diagnosis 3_months

value: Stable

tag: induction

value: Simulect


title: R70-Urine_Pellet-2W_TCRB

description: Library name: R70-Urine_Pellet-2W_TCRB

tag: tissue

value: 2 Week


title: R70-Urine_Pellet-3M_TCRB

description: Library name: R70-Urine_Pellet-3M_TCRB

value: 3 Month


title: total RNA-seq from sample 23L002680_S32

description: Library name: 23L002680_S32

tag: Sex

value: female

tag: age

tag: cell type


title: total RNA-seq from sample 23L002742_S94

description: Library name: 23L002742_S94


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep5 [Msh2]

description:
MRQ8_2str
mRNA

value: Corpus Striatum

tag: genotype

tag: strain/background


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep2 [Msh2]

description:
MRQ4_2str
mRNA

value: male

tag: well address


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep4 [Msh2]

description:
MRQ39_1str
mRNA


title: NBL-S P53 KO cells IFF clone #117

tag: cell line

value: NBL-S

value: Neuroblastoma


title: R70-PBMC-for_cause_Dec_31_2019_TCRB

description: Library name: R70-PBMC-for_cause_Dec_31_2019_TCRB

source_name: PBMC

value: PBMC


title: R70-PBMC-3M_TCRB

description: Library name: R70-PBMC-3M_TCRB


title: total RNA-seq from sample 23L002677_S29

description: Library name: 23L002677_S29

tag: bmi

tag: total pairs

tag: gc content

value: Whole Blood


title: Het (Q140) KI X Rgs9+/- Striatum male mRNA rep1 [Msh2]

description:
MRQ26_2str
mRNA

value: Het (Q140) KI X Rgs9+/-

value: 12 months


title: total RNA-seq from sample 23L002719_S71

description: Library name: 23L002719_S71

tag: status

value: unaffected


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep3 [Msh2]

description:
MRQ33_5str
mRNA


title: R70-PBMC-PreTx_TCRB

description: Library name: R70-PBMC-PreTx_TCRB

value: PreTx


title: R70-Kidney-12M_TCRB

description: Library name: R70-Kidney-12M_TCRB

source_name: Kidney

value: Kidney

value: 12 Month


title: total RNA-seq from sample 23L002730_S82

description: Library name: 23L002730_S82


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep2 [Msh2]

description:
MRQ12_4str
mRNA


title: total RNA-seq from sample 23L002695_S47

description: Library name: 23L002695_S47


title: R70-CD8-DRTC_TCRB

description: Library name: R70-CD8-DRTC_TCRB

source_name: DRTC

value: DRTC

value: Stable


title: R70-CD4-DRTC_TCRB

description: Library name: R70-CD4-DRTC_TCRB

value: Simulect


title: Het (Q140) KI X Rgs9+/- Striatum female mRNA rep1 [Msh2]

description:
MRQ12_2str
mRNA


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep4 [Msh2]

description:
MRQ48_3CTX
mRNA

value: Cerebral Cortex


title: total RNA-seq from sample 23L002660_S12

description: Library name: 23L002660_S12

value: female


description: Library name: R69-Urine_Pellet-for_cause_July_16_2019_TCRB

value: Urine Pellet

value: 1 Month

value: Campath


title: R69-Urine_Pellet-3M_TCRB

description: Library name: R69-Urine_Pellet-3M_TCRB

value: 3 Month


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep3 [Msh2]

description:
MRQ26_2CTX
mRNA

value: male


title: R69-PBMC-for_cause_Jul_16_2019_TCRB

description: Library name: R69-PBMC-for_cause_Jul_16_2019_TCRB

value: PBMC


title: R69-PBMC-PreTx_TCRB

description: Library name: R69-PBMC-PreTx_TCRB


title: R69-PBMC-3M_TCRB

description: Library name: R69-PBMC-3M_TCRB


title: R69-Urine_Pellet-2W_TCRB

description: Library name: R69-Urine_Pellet-2W_TCRB

value: 2 Week


title: total RNA-seq from sample 23L002721_S73

description: Library name: 23L002721_S73

value: Whole Blood


title: total RNA-seq from sample 23L002738_S90

description: Library name: 23L002738_S90

value: unaffected


title: R69-Kidney-PreTx_TCRB

description: Library name: R69-Kidney-PreTx_TCRB

value: PreTx


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep2 [Msh2]

description:
MRQ12_4CTX
mRNA

value: Het (Q140) KI X Rgs9+/-

value: 12 months


title: R69-CD8-DRTC_TCRB

description: Library name: R69-CD8-DRTC_TCRB

value: DRTC


title: R70-Kidney-PreTx_TCRB

description: Library name: R70-Kidney-PreTx_TCRB

value: Kidney

value: Stable


title: Het (Q140) KI X Rgs9+/- Cortex male mRNA rep1 [Msh2]

description:
MRQ12_2CTX
mRNA

value: Cerebral Cortex


title: R69-CD4-DRTC_TCRB

description: Library name: R69-CD4-DRTC_TCRB


title: R65-Urine_Pellet-12M_TCRB

description: Library name: R65-Urine_Pellet-12M_TCRB

value: 12 Month

value: Simulect


title: R70-Kidney-for_cause_Dec_31_2019_TCRB

description: Library name: R70-Kidney-for_cause_Dec_31_2019_TCRB

value: 6.3 Month


title: R69-Kidney-for_cause_Aug_2_2019_TCRB

description: Library name: R69-Kidney-for_cause_Aug_2_2019_TCRB

value: 1.7 Months

value: Campath


title: R65-Urine_Pellet-6M_TCRB

description: Library name: R65-Urine_Pellet-6M_TCRB

value: Urine Pellet

value: 6 Month


title: total RNA-seq from sample 23L002702_S54

description: Library name: 23L002702_S54

value: male


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep4 [Msh2]

description:
MRQ8_2CTX
mRNA

value: female


title: total RNA-seq from sample 23L002681_S33

description: Library name: 23L002681_S33

value: unaffected

value: Whole Blood


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep3 [Msh2]

description:
MRQ4_2CTX
mRNA

value: Het (Q140) KI X Rgs9+/-


title: R65-Urine_Pellet-3M_TCRB

description: Library name: R65-Urine_Pellet-3M_TCRB

value: 3 Month


title: R65-Urine_Pellet-2W_TCRB

description: Library name: R65-Urine_Pellet-2W_TCRB

value: 2 Week


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep2 [Msh2]

description:
MRQ39_1CTX
mRNA

value: 12 months


title: total RNA-seq from sample 23L002734_S86

description: Library name: 23L002734_S86


title: R65-PBMC-12M_TCRB

description: Library name: R65-PBMC-12M_TCRB

value: PBMC

value: Stable


title: total RNA-seq from sample 23L002683_S35

description: Library name: 23L002683_S35


title: R65-PBMC-6M_TCRB

description: Library name: R65-PBMC-6M_TCRB


title: total RNA-seq from sample 23L002685_S37

description: Library name: 23L002685_S37


title: R65-PBMC-3M_TCRB

description: Library name: R65-PBMC-3M_TCRB


title: total RNA-seq from sample 23L002691_S43

description: Library name: 23L002691_S43


title: R65-PBMC-PreTx_TCRB

description: Library name: R65-PBMC-PreTx_TCRB

value: PreTx


title: R65-Kidney-12M_TCRB

description: Library name: R65-Kidney-12M_TCRB

value: Kidney

value: 12 Month

value: Simulect


title: Rgs9+/- Striatum male mRNA rep4 [Msh2]

description:
MRQ8_3str
mRNA

value: Corpus Striatum


title: Het (Q140) KI X Rgs9+/- Cortex female mRNA rep1 [Msh2]

description:
MRQ33_5CTX
mRNA

value: Cerebral Cortex


title: R65-Kidney-PreTx_TCRB

description: Library name: R65-Kidney-PreTx_TCRB


title: R65-CD8-DRTC_TCRB

description: Library name: R65-CD8-DRTC_TCRB

value: DRTC


title: Rgs9+/- Striatum male mRNA rep3 [Msh2]

description:
MRQ5_4str
mRNA

value: male


title: R65-CD4-DRTC_TCRB

description: Library name: R65-CD4-DRTC_TCRB


title: total RNA-seq from sample 23L002714_S66

description: Library name: 23L002714_S66


title: total RNA-seq from sample 23L002689_S41

description: Library name: 23L002689_S41

value: female


title: Rgs9+/- Striatum male mRNA rep2 [Msh2]

description:
MRQ5_2str
mRNA


title: R62-Urine_Pellet-3M_TCRB

description: Library name: R62-Urine_Pellet-3M_TCRB

value: Urine Pellet

value: Reject


title: Rgs9+/- Striatum male mRNA rep1 [Msh2]

description:
MRQ4_3str
mRNA


title: R62-Urine_Pellet-6M_TCRB

description: Library name: R62-Urine_Pellet-6M_TCRB

value: 6 Month


title: total RNA-seq from sample 23L002650_S2

description: Library name: 23L002650_S2

value: unaffected

value: Whole Blood


description: Library name: R62-Urine_Pellet-for_cause_Feb_17_2020_TCRB

value: 9.3 Months

tag: rejection episode

value: Rejection 2


title: Rgs9+/- Striatum female mRNA rep4 [Msh2]

description:
MRQ7_3str
mRNA

value: 12 months


title: total RNA-seq from sample 23L002716_S68

description: Library name: 23L002716_S68


title: total RNA-seq from sample 23L002723_S75

description: Library name: 23L002723_S75


title: R62-Urine_Pellet-2W_TCRB

description: Library name: R62-Urine_Pellet-2W_TCRB

tag: subject

value: 2 Week


title: Rgs9+/- Striatum female mRNA rep3 [Msh2]

description:
MRQ35_1str
mRNA


title: R62-PBMC-6M_TCRB

description: Library name: R62-PBMC-6M_TCRB

value: PBMC

tag: visit


title: total RNA-seq from sample 23L002731_S83

description: Library name: 23L002731_S83


description: Library name: R62-Urine_Pellet-for_cause_May_30_2019_TCRB

value: 0.4 Month

tag: diagnosis 3_months

value: Rejection 1


title: R62-PBMC-for_cause_Feb_17_20_TCRB

description: Library name: R62-PBMC-for_cause_Feb_17_20_TCRB

tag: induction

value: Simulect


title: Rgs9+/- Striatum female mRNA rep2 [Msh2]

description:
MRQ23_4str
mRNA

tag: tissue

value: Corpus Striatum


title: R62-PBMC-3M_TCRB

description: Library name: R62-PBMC-3M_TCRB

value: 3 Month


title: Rgs9+/- Striatum female mRNA rep1 [Msh2]

description:
M2R22_1str
mRNA

tag: Sex


title: total RNA-seq from sample 23L002656_S8

description: Library name: 23L002656_S8

value: male

tag: age


title: total RNA-seq from sample 23L002669_S21

description: Library name: 23L002669_S21

tag: cell type


title: R62-PBMC-for_cause_May_30_19_TCRB

description: Library name: R62-PBMC-for_cause_May_30_19_TCRB


title: R62-PBMC-PreTx_TCRB

description: Library name: R62-PBMC-PreTx_TCRB

value: PreTx


title: R62-Kidney-for_cause_Feb_17_20_TCRB

description: Library name: R62-Kidney-for_cause_Feb_17_20_TCRB

value: Kidney


title: R62-Kidney-for_cause_Mar_30_19_TCRB

description: Library name: R62-Kidney-for_cause_Mar_30_19_TCRB

value: Reject


title: Rgs9+/- Cortex male mRNA rep2 [Msh2]

description:
MRQ5_2CTX
mRNA

value: Cerebral Cortex

tag: genotype


title: R62-Kidney-for_cause_Jun_18_19_TCRB

description: Library name: R62-Kidney-for_cause_Jun_18_19_TCRB

value: 1 Month

value: Borderline