title: rhTCR BOB18879_2

description:
BOB18879_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: GR-ZIF, rep3

status: Public on Mar 13 2024

type: SRA

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

library_source: transcriptomic

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.2.7, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 Gene level summaries were prepared using tximport version 1.20.0 running under R version 4.1.0
Assembly: mm10 with ensembl version 101 annotation
Supplementary files format and content: seban_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: seban_l2tpm.txt.gz is a tab delimited text file of log 2 tpm with a plus1 offset

molecule: total RNA

organism: Mus musculus

source_name: brachial lymph node

extract_protocol:
RNA MiniPrep Kit (QIAGEN)
RNAseq libraries were created from 400ng of total RNA using the NEBNext UltraII Directional RNA Library Prep kit (New England Biolabs) using half volume reagents and 17 cycles of PCR. Illumina library quality was confirmed using the Fragment Analyzer and qPCR

treatment_protocol: Mice were injected with RBD-trimer (3 ug), ZIF-8 or GR-ZIF (containing 0.9  ug of RBD-trimer) at week 0, 3 and 6. RNA was extracted from harvested brachial lymph node (3 biological replicate/condition) at week 5, after the first booster dose.

tag: tissue

value: brachial lymph node

tag: treatment

value: GR-ZIF immunization


title: LI_m330_GEX

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

department: Institut für Molekulare Medizin

country: Germany

institute: RWTH Aachen University Hospital

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs were generated in vitro before injection, replicate 1, GEX

library_source: genomic single cell

data_processing:
The hashtag library was demultiplexed using CellRanger software (version 7.1.0). Raw data was demultiplexed with cellranger mkfastq (10x Genomics v7.1.0) to generate fastq files. The fastq files were then analyzed by the cellranger multi with default parameters using refdata-gex-mm10-2020-A as reference. Subsequent data analysis was conducted by our custom pipeline written in R (v4.2.1). We used Seurat (v4.1.1) to perform quality controls, data scaling and normalization, cell filtering, cell cycle scoring, PCA /UMAP dimension reductions and data integration. Briefly, any cells whose nCount_RNA < 100 or nFeature_RNA < 50 were excluded. Gene expression matrices were scaled and normalized to remove technical cell-specific variation. Doublet detection was done by DoubletFinder (v.2.0.3, PMID: 30954475) with default parameters and prior estimate percentage of doublets provided by 10X Genomics. Cell cycle was scored by default built-in function of Seurat, however, we did not perform cell cycle regression since the effect was negligible. For dimensional reductions, gene expression matrices were transformed to top-25 principal components. These principal components were subsequently used to transformed to 2D UMAP coordinates. Cells were clustered by Seurat’s built-in algorithm with a resolution of 0.5. Differential gene expression between clusters were conducted by Wilcoxon test and Benjamin-Hochberg correction to remove false discovery rate.Cell type annotation was done manually based on the differentially expressed genes of each cluster, and we kept only clusters of interest for further analysis.
Assembly: mm10
Supplementary files format and content: CSV
Supplementary files format and content: H5

molecule: genomic DNA

source_name: large intestine

extract_protocol:
T cells were sorted from LI 7 to 8 weeks after adoptive T cell transfer as CD45+TCRβ+CD45.2+Foxp3/GFP+ or CD45+TCRβ+CD45.1+Foxp3/hCD2 Tregs, or CD45+TCRβ+CD45.1+ Teff with FACSAria II (Becton Dickenson). Sorted cells were encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI).
cDNA libraries were generated using the Chromium™ Next GEM Single Cell 5’ Reagent Kit v1 or v2 (10x Genomics) following the detailed protocol provided by the manufacturer. Libraries were quantified by Quantus (Promega) and quality was checked using TapeStatoin 4200 with High Sensitivity DNA kit (Agilent). Libraries were sequenced with NextSeq 500 platform (NextSeq 500/550 Mid Output Kit v2.5 (150 cycles), Illumina)  with paired-end mode or NovaSeq 6000 platform (SP Reagent Kit v1.5, Illumina) in 50 bp paired-end mode.

value: large intestine


title: rhTCR BOB18843_4

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
BOB18843_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

data_processing:
Demultiplexing of raw sequencing data
Separation of TCR alpha and beta reads using BLAST
Assembly and annotation of reads using MiXCR
Quality control and error correction
Quantification of T cell clonotypes
Assembly: GRCh38
Supplementary files format and content: excel files include T cell clonotype count values for each Sample

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
Total RNA of peripheral blood was extracted from 400 μl of each blood sample using Quick-DNA/RNA miniprep plus kit
Bulk TCR-sequencing was performed with 200 ng of total RNA by the Dana-Farber Cancer Institute Translational Immunogenomics Laboratory following the protocol of RNase H-dependent PCR enabled T-cell receptor sequencing

value: blood


title: rhTCR BOB20410WB_1

description:
BOB20410WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: GR-ZIF, rep1


title: RBD-trimer, rep2

value: RBD-trimer immunization


title: RBD-trimer, rep3


title: rhTCR BOB18762_4

description:
BOB18762_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18789_4

description:
BOB18789_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: RBD-trimer, rep1


title: rhTCR BOB18759_5

description:
BOB18759_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18662_2

description:
BOB18662_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_ATAC_R3

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: genomic

data_processing:
ATACseq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: mm10
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: narrowPeak files generated by MACS2

extract_protocol:
Cells were harvested and then washed by PBS. Lysis with ATAC resuspension buffer(TRIS-HCl-pH7.4, 10mM; NaCl,10mM;MgCl2,3mM) plus 0.1% NP40, 0.1%Twwen-20,0.01%Digitonin.
Libraries were generated using NEBNext Ultra II kits.

tag: cell line

tag: cell type

value: mesenchymal progenitor cells

tag: genotype

value: WT


title: rhTCR BOB18553_5

description:
BOB18553_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_ATAC_R1


title: ZIF-8, rep1

value: ZIF-8 immunization


title: rhTCR BOB18657_4

description:
BOB18657_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18550_2

description:
BOB18550_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_ATAC_R2


title: G7_ATAC_R3

value: Atrx knockout


title: G7_ATAC_R1


title: rhTCR BOB18541_3

description:
BOB18541_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_ATAC_R3


title: rhTCR BOB18540_2

description:
BOB18540_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18528_4

description:
BOB18528_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18833_5

description:
BOB18833_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: GR-ZIF, rep2


title: B10_ATAC_R1


title: rhTCR BOB1848_3

description:
BOB1848_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_ATAC_R2


title: rhTCR BOB18479_2

description:
BOB18479_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_IgG_forATRX_R4

data_processing:
Cut and run reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software.
Assembly: mm10
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: bed files generated by SEACR

extract_protocol:
For histone marks, cells were collected by trypsin. Washed by PBS. For ATRX, cells were gently fixed using 0.1% PFA in PBS for 1 min at room temperature, followed by nuclei extraction with NE buffer (20 mM HEPES (pH7.9), 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MnCl2, 1×cOmplete Mini-Tablet (1 tablet), 0.5 mM Spermidine) according to the protocol from EpiCypher.
Libraries were generated using NEBNext Ultra II kits.

tag: chip antibody


title: rhTCR BOB18410_2

description:
BOB18410_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_IgG_forATRX_R3


title: rhTCR BOB18401_4

description:
BOB18401_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_forATRX_R4


title: rhTCR BOB18293_2

description:
BOB18293_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_forATRX_R3


title: G7_ATAC_R2


title: B10_IgG_forATRX_R4


title: rhTCR BOB18107_3

description:
BOB18107_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18193_2

description:
BOB18193_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18535_2

description:
BOB18535_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_forATRX_R3


title: rhTCR BOB18106_2

description:
BOB18106_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18096_2

description:
BOB18096_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_forATRX_R1


title: WT_ATRX_R4

value: ATRX(Abcam, ab97508)


title: rhTCR BOB18065_4

description:
BOB18065_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17932_2

description:
BOB17932_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18043_4

description:
BOB18043_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_ATRX_R1


title: WT_ATRX_R3


title: rhTCR BOB17730_4

description:
BOB17730_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB18412_2

description:
BOB18412_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_ATRX_R3


title: G7_ATRX_R4


title: WT_IgG_forATRX_R1


title: rhTCR BOB18269_2

description:
BOB18269_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17715_3

description:
BOB17715_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_ATRX_R1


title: rhTCR BOB17704_2

description:
BOB17704_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_ATRX_R3


title: G7_IgG_forATRX_R1


title: B10_ATRX_R4


title: rhTCR BOB17641_2

description:
BOB17641_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_IgG_forH33_R3


title: WT_IgG_forH33_R2


title: rhTCR BOB17481_4

description:
BOB17481_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17448_2

description:
BOB17448_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_forH33_R3


title: G7_IgG_forH33_R2


title: G7_IgG_forH33_R1


title: rhTCR BOB17141_4

description:
BOB17141_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17208_2

description:
BOB17208_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17464_3

description:
BOB17464_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_forH33_R3


title: rhTCR BOB17914_3

description:
BOB17914_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_forH33_R2


title: rhTCR BOB17103_4

description:
BOB17103_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_forH33_R1


title: rhTCR BOB17369_3

description:
BOB17369_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_H33_R3


title: rhTCR BOB17056_4

description:
BOB17056_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17094_5

description:
BOB17094_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17012_4

description:
BOB17012_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB176892_2

description:
BOB176892_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_ATRX_R1


title: rhTCR BOB16475_2

description:
BOB16475_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB17502_4

description:
BOB17502_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_H33_R3


title: WT_H33_R1


title: rhTCR BOB16460_2

description:
BOB16460_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_IgG_forH33_R1


title: rhTCR BOB16459_2

description:
BOB16459_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_H33_R1


title: rhTCR BOB16450_2

description:
BOB16450_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_H33_R2


title: B10_H33_R2


title: rhTCR BOB16424_2

description:
BOB16424_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_H33_R3


title: rhTCR BOB16401_2

description:
BOB16401_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB16364_2

description:
BOB16364_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_IgG_R3


title: WT_IgG_R4


title: WT_H33_R2


title: rhTCR BOB16346_2

description:
BOB16346_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB16360_2

description:
BOB16360_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_H33_R1


title: rhTCR BOB16393_2

description:
BOB16393_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_R4


title: WT_IgG_R2


title: rhTCR BOB16286_2

description:
BOB16286_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_R3


title: rhTCR BOB16300_2

description:
BOB16300_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_R2


title: rhTCR BOB16289_2

description:
BOB16289_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_IgG_R1


title: rhTCR BOB16273_2

description:
BOB16273_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_R4


title: B10_IgG_R3


title: rhTCR BOB16201_4

description:
BOB16201_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB1602WB_1

description:
BOB1602WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_IgG_R1


title: rhTCR BOB15934_3

description:
BOB15934_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15932_3

description:
BOB15932_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15806_2

description:
BOB15806_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_K4me3_R4

value: H3K4me3(Active motif,39159)


title: WT_K4me3_R2


title: WT_IgG_R1


title: rhTCR BOB15800_2

description:
BOB15800_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15676_3

description:
BOB15676_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_K4me3_R1


title: rhTCR BOB15786_2

description:
BOB15786_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15655_3

description:
BOB15655_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15670_2

description:
BOB15670_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K4me3_R2


title: G7_K4me3_R1


title: G7_K4me3_R4


title: rhTCR BOB16124_4

description:
BOB16124_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K4me3_R4


title: B10_K4me3_R2


title: rhTCR BOB15650_2

description:
BOB15650_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15638_2

description:
BOB15638_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K4me3_R3


title: B10_IgG_R2


title: WT_K9me3_R1


title: rhTCR BOB15272_4

description:
BOB15272_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_K9me3_R3


title: rhTCR BOB15460_4

description:
BOB15460_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15227_5

description:
BOB15227_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K9me3_R3


title: G7_K9me3_R2


title: G7_K9me3_R1


title: rhTCR BOB15185_5

description:
BOB15185_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15749_2

description:
BOB15749_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14897_4

description:
BOB14897_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K9me3_R3


title: rhTCR BOB1483WB_1

description:
BOB1483WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14826_5

description:
BOB14826_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14758_2

description:
BOB14758_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_K9me3_R2


title: rhTCR BOB1479WB_1

description:
BOB1479WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB15515_2

description:
BOB15515_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14795_4

description:
BOB14795_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14638_2

description:
BOB14638_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K27ac_R1

value: H3K27Ac(Active motif,39133)


title: WT_K27ac_R1


title: WT_K27ac_R2


title: rhTCR BOB14747_2

description:
BOB14747_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K27ac_R3


title: WT_K27ac_R3


title: rhTCR BOB14679_4

description:
BOB14679_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14633_2

description:
BOB14633_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K27ac_R3


title: rhTCR BOB14628_4

description:
BOB14628_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14621_2

description:
BOB14621_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K27ac_R2


title: rhTCR BOB14620_2

description:
BOB14620_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K27ac_R2


title: B10_K27ac_R1


title: WT_K27me3_R3


title: WT_K27me3_R2


title: B10_K9me3_R2


title: rhTCR BOB14605_2

description:
BOB14605_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB1456WB_1

description:
BOB1456WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14552_4

description:
BOB14552_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_K27me3_R1


title: B10_K9me3_R1


title: G7_K27me3_R3


title: rhTCR BOB14400_2

description:
BOB14400_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K27me3_R2


title: rhTCR BOB14386_2

description:
BOB14386_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_K27me3_R1


title: rhTCR BOB14348_2

description:
BOB14348_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K27me3_R3


title: WT_rRNAdeplete_3

data_processing:
For the poly A RNAseq, transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
For the rRNA depleted RNAseq, reads were aligned to the mm10 genome with STAR (v2.27.10a) setting the ‘—winAnchorMultimapNmax’ and ‘—outFilterMultimapNmax’ arguments to 100. Reads in repeats was then counted with the TElocal function from TEtranscripts and differential abundance calculated with DESeq2.
Assembly: mm10
Supplementary files format and content: Counts tables contain the raw counts quantified by Salmon and DESeq2 (ploy A) or TE transcripts (rRNA depleted).

extract_protocol:
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. Cell pelet were sent to MSKCC integrated Genomics Operation for library prep.
Libraries were generated using NEBNext Ultra II kits.


title: rhTCR BOB1400WB_1

description:
BOB1400WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13773_4

description:
BOB13773_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB14224_4

description:
BOB14224_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13692_3

description:
BOB13692_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_rRNAdeplete_2


title: B10_K27me3_R2


title: rhTCR BOB14366_3

description:
BOB14366_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_rRNAdeplete_2


title: G7_rRNAdeplete_3


title: WT_rRNAdeplete_1


title: rhTCR BOB13703_5

description:
BOB13703_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13497_3

description:
BOB13497_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13511_3

description:
BOB13511_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_K27me3_R1


title: B10_rRNAdeplete_2


title: rhTCR BOB13431_4

description:
BOB13431_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_rRNAdeplete_3


title: rhTCR BOB13499_2

description:
BOB13499_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: B10_rRNAdeplete_1


title: rhTCR BOB13352_4

description:
BOB13352_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_R3


title: rhTCR BOB13250_4

description:
BOB13250_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT_R1


title: WT_R2


title: rhTCR BOB13079_3

description:
BOB13079_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13076_3

description:
BOB13076_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: sg6_B10_R3


title: sg6_B10_R2


title: sg6_B10_R1


title: rhTCR BOB12691_2

description:
BOB12691_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: sg5_G7_R3


title: rhTCR BOB12560_2

description:
BOB12560_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13000_5

description:
BOB13000_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: G7_rRNAdeplete_1


title: rhTCR BOB13046_2

description:
BOB13046_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: sg5_G7_R2


title: rhTCR BOB12540_4

description:
BOB12540_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB13645_4

description:
BOB13645_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: sg5_G7_R1


title: rhTCR BOB12409_3

description:
BOB12409_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 6

city: Philadelphia

first: Jesse

last: Lee

state: PA

address: South Pavilion, Room 8-326

institute: University of Pennsylvania

description: 25451_Alb-Cre+/+ STAT3f/f_PDAC_Tumor

data_processing:
FASTQ files were uploaded to the BaseSpace Suite (Illumina) and aligned using its RNA-Seq Alignment application (version 2.0.2), in which STAR was selected to align sequences with maximum mismatches set to 14 as recommended by Lexogen.
Assembly: mm10
Supplementary files format and content: csv sheet with raw counts

source_name: Tumor

growth_protocol: Cell lines were cultured in DMEM (Corning) supplemented with 10% FBS (VWR), 83 μg/mL gentamicin (Thermo Fisher Scientific), and 1% GlutaMAX (Thermo Fisher Scientific) at 37°C, 5% CO2

extract_protocol:
RNA was isolated from tumors by scraping FFPE tissue from slides and isolating RNA according to the RNeasy FFPE kit (Qiagen) instructions
Libraries were prepared using a Quantseq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen)

value: Tumor

value: KPC derived Tcelllow PDAC

value: Alb-Cre+/+ STAT3f/f


title: rhTCR BOB12371_4

description:
BOB12371_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB12339_2

description:
BOB12339_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 5

description: 25450_Alb-Cre+/+ STAT3f/f_PDAC_Tumor


title: rhTCR BOB12332_2

description:
BOB12332_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 4

description: 25449_Alb-Cre+/+ STAT3f/f_PDAC_Tumor


title: rhTCR BOB12308_2

description:
BOB12308_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB12268_2

description:
BOB12268_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 3

description: 25448_Alb-Cre+/+ STAT3f/f_PDAC_Tumor


title: rhTCR BOB12186_3

description:
BOB12186_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB12172_2

description:
BOB12172_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB12097_5

description:
BOB12097_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 2

description: 25447_Alb-Cre+/+ STAT3f/f_PDAC_Tumor


title: rhTCR BOB12090_4

description:
BOB12090_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Tumor 1

description: 25444_Alb-Cre+/+ STAT3f/f_PDAC_Tumor


title: rhTCR BOB12075_4

description:
BOB12075_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ovCHA092, scTCR-seq

city: seoul

first: hiram

last: kang

state: seoul

address: 222, Banpo-daero, Seocho-gu, Seoul

country: South Korea

institute: Catholic university of Korea

description: ovCHA092_TCR_filtered_contig_annotations.csv

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the GRCh38 human reference genome using the Cell Ranger toolkit (version 5.0.0).
Assembly: GRCh38
Supplementary files format and content: R object file

source_name: Ovary

extract_protocol:
Tumor tissues were minced and dissociated using the enzyme mix from Tumor Dissociation Kit, human (130-095-929, Miltenyi Biotec) with the h_tumor_02 program twice on the gentleMACS dissociator/C tube (130-093-237, Miltenyi Biotec). At the end of each program, the sample was incubated in a pre-warmed 37°C incubator for 30 minutes. The reaction was stopped with a medium containing penicillin-streptomycin and FBS. Then, the sample was filtered through a 70-μm strainer filter (352350, Life Technologies) and processed with Ficoll-Paque PLUS (17-1440-02, GE Healthcare) to remove dead cells. Cell pellets were washed and resuspended in a cell-freezing medium and stored in liquid nitrogen.
Single cell suspensions were subjected to 5' single-cell RNA sequencing using the Single Cell 5′ Library and Gel Bead Kit V1, Single Cell A Chip Kit, i7 Multiplex Kit (10x Genomics) according to the manufacturer's protocol. Library for T92 was constructed using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, and Chromium Next GEM Chip G Single Cell Kit (10x Genomics) instead. Each target for cell recovery was set at 5,000-7,000 cells. TCR-enriched and BCR-enriched libraries were prepared using the Single Cell V(D)J Enrichment Kit, Human T Cell, and Single Cell V(D)J Enrichment Kit, Human B Cell (10× Genomics) according to the manufacturer's protocol.

tag: patient

value: Ovary

tag: cancer stage

tag: metastatic/primary

value: Primary

tag: chemotherapy

value: N

tag: recurrent/primary

tag: platform

value: Single Cell TCR


title: Max floxed male PGC_E12.5 with Oct4-CreERT2

type: RNA

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

hyb_protocol: Affymetrix Standard WT Plus Protocol.

scan_protocol: AGCC Standard Protocol.

data_processing: The data were background-subtracted and normalized using the Transcriptome Analysis Console Software (TAC4.0, ThermoFisher, https://www.thermofisher.com/jp/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-transcriptome-analysis-console-software.html).

label: biotin

source_name: Max gene-floxed male PGCs at E12.5 with CreERT2 transgene

label_protocol: Affymetrix WT Plus Kit.

growth_protocol: Homozygous Max gene-floxed mouse embryos with or without CreERT2 transgene were generated by the intercross between Max floxed male mouse with CreERT2 transgene and female Max floxed female mouse without the transgene.

extract_protocol: Total RNAs were isolated from germ cells with RNeasy Micro Kit (QIAGEN, Cat# 74004)

treatment_protocol: Tamoxifen was intraperitoneally administered to mouse embryos at E8.5. Germ cells were recovered from genital ridges of those embryos at E12.5 for RNA preparation.

tag: Sex

value: Male

value: CreERT2 transgene

tag: strain

value: PGC

tag: developmental stage


title: WT PDAC Tumor 6


title: rhTCR BOB11738_2

description:
BOB11738_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

value: blood


title: ovCHA092, scRNA-seq

value: Single Cell 5'


title: WT PDAC Tumor 5

value: WT


title: Max floxed male PGC_E12.5 with no Cre

description:
Reference sample for Max gene-floxed male PGCs at E12.5 with CreERT2 transgene
12.5M

source_name: Max gene-floxed male PGCs at E12.5 with no CreERT2

value: no CreERT2


title: rhTCR BOB11585_2

description:
BOB11585_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ovCHA110, scTCR-seq

description: ovCHA110_TCR_filtered_contig_annotations.csv

value: Y


title: rhTCR BOB11759_4

description:
BOB11759_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Tumor 4


title: rhTCR BOB11940_4

description:
BOB11940_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ovCHA107, scTCR-seq

description: ovCHA107_TCR_filtered_contig_annotations.csv

source_name: Lymph node, paraaortic

value: Lymph node, paraaortic

value: Metastatic

value: Recurrent


title: rhTCR BOB11575_2

description:
BOB11575_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB11390_2

description:
BOB11390_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Tumor 3

value: Tumor

value: KPC derived Tcelllow PDAC


title: ovCHA070, scTCR-seq

description: ovCHA070_TCR_filtered_contig_annotations.csv

source_name: Omentum

value: Omentum


title: Max floxed female PGC_E12.5 with Oct4-CreERT2

source_name: Max gene-floxed female PGCs at E12.5 with CreERT2 transgene

value: Female


title: WT PDAC Tumor 2


title: rhTCR BOB11644_4

description:
BOB11644_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB11512_5

description:
BOB11512_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB11228_2

description:
BOB11228_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Max floxed female PGC_E12.5 with no Cre

description:
Reference sample for Max gene-floxed female PGCs at E12.5 with CreERT2 transgene
12.5F

source_name: Max gene-floxed female PGCs at E12.5 with no CreERT2


title: ovCHA066, scTCR-seq

description: ovCHA066_TCR_filtered_contig_annotations.csv

value: Fallopian tube

value: Primary

value: N


title: rhTCR BOB11213_2

description:
BOB11213_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Tumor 1


title: rhTCR BOB11745_3

description:
BOB11745_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ovCHA039, scTCR-seq

description: ovCHA039_TCR_filtered_contig_annotations.csv

source_name: Fallopian tube

value: Single Cell TCR


title: rhTCR BOB11149_3

description:
BOB11149_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Liver 6

description: 25451_Alb-Cre+/+ STAT3f/f_PDAC_Liver

source_name: Liver

extract_protocol:
Mouse livers were stored in TRIzol (Thermofisher) at -80°C from necropsy until extraction. Samples were then thawed on ice and equilibrated to room temperature before RNA was isolated using an RNeasy Mini kit (Qiagen) following the manufacturer’s protocol.
Libraries were prepared using a Quantseq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen)

value: Liver

value: Alb-Cre+/+ STAT3f/f


title: rhTCR BOB11198_2

description:
BOB11198_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

value: blood


title: rhTCR BOB11125_2

description:
BOB11125_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Liver 5

description: 25450_Alb-Cre+/+ STAT3f/f_PDAC_Liver


title: ovCHA034, scTCR-seq

description: ovCHA034_TCR_filtered_contig_annotations.csv

value: Ovary


title: rhTCR BOB11117_2

description:
BOB11117_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB11031_5

description:
BOB11031_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10954_5

description:
BOB10954_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10921_2

description:
BOB10921_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10864_2

description:
BOB10864_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Liver 4

description: 25449_Alb-Cre+/+ STAT3f/f_PDAC_Liver


title: AlbCre;Stat3f/f PDAC Liver 2

description: 25447_Alb-Cre+/+ STAT3f/f_PDAC_Liver


title: ovCHA017, scTCR-seq

description: ovCHA017_TCR_filtered_contig_annotations.csv


title: rhTCR BOB10852_2

description:
BOB10852_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: ovCHA004, scTCR-seq

description: ovCHA004_TCR_filtered_contig_annotations.csv


title: AlbCre;Stat3f/f PDAC Liver 1

description: 25444_Alb-Cre+/+ STAT3f/f_PDAC_Liver


title: ovCHA018, scTCR-seq

description: ovCHA018_TCR_filtered_contig_annotations.csv


title: offspring of obese dam PVH5

first: Laura

last: Dearden

address: Addenbrookes Hospital

department: Institute of metabolic science

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw reads were mapped to the mouse genome through bowtie v1.2.3. Reads per Kilobase of transcript per Million mapped reads were produced from RNA Sequencing raw output and statistically analysed through likelihood ratio test using edgeR version 3.36.0.
Assembly: GRCm38
Supplementary files format and content: excel sheet of cpm

source_name: PVH of hypothalamus

extract_protocol:
miRNesy micro kit from Qiagen
TruSeq®Small RNA Library Preparation kit (Illumina, Cambridge, UK)

value: PVH of hypothalamus

value: wild type C57bl6J


title: rhTCR BOB10587_2

description:
BOB10587_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB1070WB_1

description:
BOB1070WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: AlbCre;Stat3f/f PDAC Liver 3

description: 25448_Alb-Cre+/+ STAT3f/f_PDAC_Liver


title: rhTCR BOB10582_3

description:
BOB10582_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of obese dam PVH4


title: rhTCR BOB10576_2

description:
BOB10576_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10546_3

description:
BOB10546_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Liver 6

value: WT


title: offspring of obese dam PVH3


title: offspring of obese dam PVH2


title: WT PDAC Liver 5


title: rhTCR BOB10426_2

description:
BOB10426_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10991_5

description:
BOB10991_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10358_3

description:
BOB10358_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10356_2

description:
BOB10356_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Liver 4


title: rhTCR BOB10267_5

description:
BOB10267_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of lean dam PVH6


title: rhTCR BOB10274_2

description:
BOB10274_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT PDAC Liver 3


title: offspring of obese dam PVH1


title: WT PDAC Liver 2


title: rhTCR BOB10208_1

description:
BOB10208_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10198_2

description:
BOB10198_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of lean dam PVH3


title: rhTCR BOB10187_5

description:
BOB10187_5
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT Ctrl Liver 6


title: offspring of lean dam PVH4


title: WT PDAC Liver 1


title: WT Ctrl Liver 5


title: rhTCR BOB10159_3

description:
BOB10159_3
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10455_2

description:
BOB10455_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB0855WB_1

description:
BOB0855WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of lean dam PVH2


title: rhTCR BOB0637WB_1

description:
BOB0637WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT Ctrl Liver 4


title: rhTCR BOB0468WB_1

description:
BOB0468WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of lean dam PVH 1


title: rhTCR BOB0464WB_1

description:
BOB0464WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB10236_2

description:
BOB10236_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of obese dam ARC 5

source_name: ARC of hypothalamus

value: ARC of hypothalamus


title: offspring of lean dam PVH5


title: rhTCR BOB0431WB_1

description:
BOB0431WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB0463WB_1

description:
BOB0463WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB0380_2

description:
BOB0380_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB0987WB_1

description:
BOB0987WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of obese dam ARC 4


title: rhTCR BOB10216_4

description:
BOB10216_4
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR 2422

description:
2422
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR BOB0263_1_2

description:
BOB0263_1_2
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Tcell high 5

data_processing:
FASTQ files were uploaded to the BaseSpace Suite (Illumina) and aligned using its RNA-Seq Alignment application (version 2.0.2), in which STAR was selected to align sequences with maximum mismatches set to 14 as recommended by Lexogen.
Differentially expressed genes were determined using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: csv sheet with DeSeq2 normalized counts

value: KPC derived Tcellhigh PDAC


title: rhTCR 854

description:
854
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT Ctrl Liver 1


title: rhTCR BOB0174_1

description:
BOB0174_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of obese dam ARC 3


title: rhTCR 835

description:
835
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: offspring of obese dam ARC 2


title: offspring of obese dam ARC 1


title: Tcell high 4


title: rhTCR 834

description:
834
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Tcell high 6


title: rhTCR 799

description:
799
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: WT Ctrl Liver 3


title: rhTCR BOB0519WB_1

description:
BOB0519WB_1
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR 756

description:
756
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Offspring of lean dam ARC 6


title: WT Ctrl Liver 2


title: Offspring of lean dam ARC 5


title: Tcell high 2


title: Offspring of lean dam ARC 4


title: rhTCR 671

description:
671
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Tcell high 1


title: Offspring of lean dam ARC 3


title: rhTCR 607

description:
607
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR 652

description:
652
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Offspring of lean dam ARC 2


title: rhTCR 590

description:
590
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: rhTCR 603

description:
603
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: Tcell low 4


title: SW1353_DMSO_3

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

country: Spain

institute: Health Research Institute of Asturias (ISPA)

data_processing:
The generated libraries were normalized and combined in equimolecular concentrations for optimal generation of DNA clusters.
Pair-end sequencing (2x100 pb) of the libraries were performed on the NovaSeq 6000  (Illumina Inc.) with a read quality of 90%>Q30
All sequencing data files were evaluated using the fastQC software (v.0.11.9) for quality control
Adapters and poor quality paired-end reads were removed using fasp (v.0.20.1)
Preprocessed reads were pseudo-aligned to the GRCh38 human genome
Preprocessed reads were quantified at the transcript-level using the mapping-based mode of the Salmon package (v.1.3.0)
Analyses of gene expression data were performed using R statistical software (v.4.0.2)
Transcript-level information was summarized at the gene-level for both exploratory and differential analyses using the tximport package (v.1.16.1)
The matrix of raw counts was rlog (regularized logarithm) transformed according to the DESeq2 package (v.1.28.1)
Non-expressed genes (< 2 counts across all conditions) were discarded
Differential gene expression analyses were performed using the negative binomial generalized linear model fitting implemented in DESeq2
Assembly: GRCh38 human genome
Supplementary files format and content: .xlsx file include matrix of counts

source_name: chondrosarcoma cell line

growth_protocol: L2975 and SW1353 chondrosarcoma cell line were growth in high glucose DMEM suplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNA was extracted using EurX Universal RNA purification Kit (EurX). > 1 ug of total RNA (concentration >50 ng/ul) was used for the construction of sequencing libraries
Stranded library for RNA-seq was generated with TrueSeq mRNA Library Prep (Illumina Inc.) following manufacturer´s protocols

treatment_protocol: L2975 and SW1353 chondrosarcoma cell line was treated with 20 uM of enasidenib and DMSO (control) for 48 h

value: chondrosarcoma cell line

value: chondrosarcoma cells

value: IDH2 mutant

value: DMSO

tag: time


title: SW1353_ENASIDENIB_2

value: ENASIDENIB 20 uM


title: Tcell high 3


title: SW1353_ENASIDENIB_3


title: Tcell low 1

value: KPC derived Tcelllow PDAC


title: Tcell low 3


title: Tcell low 2


title: Whole brain, 24m, rep 2

city: Göttingen

first: Nisha

last: Hemandhar Kumar

address: Humboldtallee 23

department: Institute for Neuro and Sensory Physiology

institute: University Medical Center Goettingen

data_processing:
RNA-seq reads were aligned to the GRCm39.103 genome assembly using hisat2 v2.1.0
Assembly: GRCm39.103

source_name: Whole brain

extract_protocol:
RNA was extracted from a total of 8 biological samples, corresponding to 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males). Raw data were procured in HiSeq4000 sequencing
NEBNext Ultra II directional polyA+

value: Whole brain

value: Male

tag: age

value: 24 months


title: L2975_ENASIDENIB_2

tag: tissue


title: SW1353_DMSO_2

tag: treatment


title: SW1353_DMSO_1

tag: cell line


title: rhTCR 748

description:
748
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR


title: L2975_DMSO_2

tag: cell type


title: L2975_ENASIDENIB_3

tag: genotype


title: G4 liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description:
liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4

data_processing:
Fastp was used for trimming and quality control
Reads were aligned with STAR to the GRCh38.p13 human reference genome (Gencode 42 release)
UMI_tools were used for deduplication
FeatureCounts were used to build a gene count matrix for the deduplicated and non-deduplicated data
Assembly: GRCh38.p13
Supplementary files format and content: FeatureCounts output files, before (*pre_deduplication.txt) and after deduplication (*post_deduplication.txt)

source_name: liver

extract_protocol:
Human Liver total RNA was bought from Thermofisher Scientific
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Unique Dual Index UMI Adapters RNA Set1

value: liver


title: Whole brain, 24m, rep 4


title: rhTCR 688

description:
688
Bulk RNA from peripheral blood of the breast cancer diagnosed patients
rhTCR

value: blood


title: SW1353_ENASIDENIB_1


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Whole brain, 24m, rep 3


title: L2975_ENASIDENIB_1


title: G4 liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: L2975_DMSO_1


title: Whole brain, 24m, rep 1


title: G4 liver, mRNA derived cDNA, 500ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Whole brain, 6m, rep 4

value: 6 months


title: Whole brain, 6m, rep 3


title: Offspring of lean dam ARC 1


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles


title: G4 liver, mRNA derived cDNA, 500ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 11 PCR cycles


title: Whole brain, 6m, rep 2


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles


title: G4 liver, mRNA derived cDNA, 500ng input, 7 PCR cycles

description:
liver, mRNA derived cDNA, 500ng input, 7 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 7 PCR cycles


title: Whole brain, 6m, rep 1


title: L2975_DMSO_3


title: G4 liver, mRNA derived cDNA, 250ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 8 PCR cycles

description:
liver, mRNA derived cDNA, 250ng input, 8 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Orai1KI_2

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1 with annotations from Ensembl version 96 and “union" mode. Only non-ambiguously assigned reads have been retained for further analyses.
Assembly: mm10
Supplementary files format and content: TSV file containing raw counts for each sample

molecule: polyA RNA

source_name: Complete tibialis anterior muscle

extract_protocol:
Muscle RNA was extracted from tibialis anterior using TRI Reagent (Molecular Research Center, Cincinnati, USA) following the manufacturer’s instructions.
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina X TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Complete tibialis anterior muscle


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 9 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 9 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 125ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, KIKI_3


title: TA muscle, WT1


title: G4 liver, mRNA derived cDNA, 250ng input, 10 PCR cycles


title: TA muscle, KIKI_2


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 11 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 125ng input, 13 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 9 PCR cycles


title: TA muscle, KIKI_4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 12 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 250ng input, 8 PCR cycles


title: G4 liver, mRNA derived cDNA, 62ng input, 14 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Stim1KI_8


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 31ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 62ng input, 12 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, KIKI_1


title: G4 liver, mRNA derived cDNA, 125ng input, 9 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 12 PCR cycles

description:
liver, mRNA derived cDNA, 15ng input, 12 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Stim1KI_7


title: G4 liver, mRNA derived cDNA, 62ng input, 10 PCR cycles

description:
liver, mRNA derived cDNA, 62ng input, 10 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 125ng input, 11 PCR cycles


title: TA muscle, Stim1KI_6


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 31ng input, 15 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 10 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Stim1KI_5


title: TA muscle, Orai1KI_4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: LI_m369_TCR

description: adaptive T cell transfer in Rag2 KO, Tnaive T cells were injected 18 days prior to Tregs which were in vitro expanded (group 2) , TCR

source_name: large intestine

value: large intestine


title: G4 liver, mRNA derived cDNA, 31ng input, 11 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 31ng input, 13 PCR cycles


title: G4 liver, mRNA derived cDNA, 15ng input, 16 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: LI_m368_TCR

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs from the same Treg culture as in m369 were (group 2), TCR


title: TA muscle, Orai1KI_1


title: G4 liver, mRNA derived cDNA, 15ng input, 14 PCR cycles


title: TA muscle, WT_7

value: WT


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 20 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 20 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 15ng input, 12 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, WT_6


title: LI_m367_TCR

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs from the same Treg culture as in m367 were (group 1), TCR


title: G4 liver, mRNA derived cDNA, 7ng input, 17 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 21 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 21 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Orai1KI_3


title: G4 liver, mRNA derived cDNA, 7ng input, 15 PCR cycles


title: LI_m369_GEX

description: adaptive T cell transfer in Rag2 KO, Tnaive T cells were injected 18 days prior to Tregs which were in vitro expanded (group 2) , GEX


title: TA muscle, KIKO_4


title: LI_m366_TCR

description: adaptive T cell transfer in Rag2 KO, Tnaive T cells were injected 18 days prior to Tregs which were in vitro expanded (group 1) , TCR


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: G4 liver, mRNA derived cDNA, 4ng input, 18 PCR cycles


title: Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: LI_m366_GEX

description: adaptive T cell transfer in Rag2 KO, Tnaive T cells were injected 18 days prior to Tregs which were in vitro expanded (group 1) , GEX


title: LI_m367_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs from the same Treg culture as in m367 were (group 1), GEX


title: D4, KO, AMLN (NASH) liver

city: lexington

first: Shuxia

last: Wang

state: KY

address: 900 S. Limestone street, Wethington Bldg. Room 583

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

data_processing:
sequence reads were trimmed for adaptor sequence or low quality sequence (using FASTQ software)
Trimed sequence reads were mapped to mm1o ( HISAT2 software)
Read counts extarct, nomalization, and quntification were done (DEseq2 software)
Assembly: mm10
Supplementary files format and content: raw counts and RPKM values

extract_protocol:
RNA from liver was extracted by using Rneasy mini kit (Qiagen). 2ug of total RNA was sent to company for constructing of sequencing library.
RNA libraries for RNA-seq were prepared by the company (Novogene).

value: KO-AMLN

value: 32 weeks of AMLN diet

tag: strain background


title: TA muscle, WT_8


title: G4 liver, mRNA derived cDNA, 4ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: D3, KO, AMLN (NASH) liver


title: TA muscle, KIKO_3


title: TA muscle, KIKO_2


title: LI_m368_GEX

description: adaptive T cell co transfer (Tregs and Tnaive) in Rag2 KO, Tregs from the same Treg culture as in m369 were (group 2), GEX


title: ABE9_rep3_HEK293T

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
The raw data were processed by fastp v0.23.4 with adapter trimming, low quality bases trimming (-q 20, -r, -W 10, -c), low complexity filtering and length filtering (-l 75).
The clean data were aligned to the reference genome hg38 by using hisat2 v2.2.1. samtools v1.18 was used to sort and index mapping results.
The sorted mapping results were marked duplicates and recalibrated base quality using MarkDuplicates, BaseRecalibrator and ApplyBQSR in GATK toolkit v4.2.5.0.
The variants were detected using HaplotypeCaller.
The SNP variants were further filtered to retain SNP variants with base-quality score >25, mapping quality score >20, Fisher strand values <30.0, qual by depth values >2.0 and sequencing depth >20. The depth for a given off-target edit should be at least 10x and these edits were required to have at least 99% of reads supporting the reference allele in the wild-type samples.
Assembly: hg38
Supplementary files format and content: ABE_offTarget_DP10_ALT_1pct_2cnt_mutated_sites_overview
Supplementary files format and content: Off-Target mutated sites

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle medium (Gibco) supplemented with 10% fetal bovine serum (Gemini) and 1% penicillin–streptomycin (Gibco) in an incubator (37 °C, 5% CO2).

extract_protocol:
Total RNA is extracted utilizing the Trizol method
Total RNA is extracted utilizing the Trizol method, subsequently assessed for purity using NanoDrop One, and its integrity is evaluated with Agilent 2100.Following this, mRNA enrichment and purification from eukaryotic total RNA are executed with the VAHTS mRNA Capture Beads kit (Vazyme), and RNA is fragmented through ion interruption to attain insert sizes ranging from 250 to 450 bp. cDNA first-strand synthesis is conducted using fragmented RNA as a template, succeeded by second-strand cDNA synthesis employing the first-strand cDNA as a template, and subsequent ds cDNA end repair and dA-tailing. Following the ligation of universal adapters, bead-based purification is utilized, and fragment selection is executed for sizes ranging between 250 and 350 bp. PCR amplification is conducted, incorporating primer double-end indexes, and the products undergo bead-based purification to yield the complete library. Second-generation sequencing technology, leveraging the Illumina NovaSeq 6000 sequencing platform, is employed for paired-end (PE) sequencing of the library.

value: Human embryonic kidney


title: G4 liver, mRNA derived cDNA, 4ng input, 14 PCR cycles

description:
liver, mRNA derived cDNA, 4ng input, 14 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: ABE9_rep2_HEK293T


title: TA muscle, KIKO_1


title: D2, KO, AMLN (NASH) liver


title: G4 liver, mRNA derived cDNA, 2ng input, 19 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 19 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: ABE9_rep1_HEK293T


title: D1, KO, AMLN (NASH) liver


title: TA muscle, Stim1KI_4


title: G4 liver, mRNA derived cDNA, 7ng input, 13 PCR cycles

description:
liver, mRNA derived cDNA, 7ng input, 13 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: ABE8e_rep3_HEK293T


title: G4 liver, mRNA derived cDNA, 2ng input, 17 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 17 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: C3, KO, LF liver

value: KO-LF

value: 32 weeks of LF diet


title: ABE8e_rep2_HEK293T


title: C4, KO, LF liver


title: G4 liver, mRNA derived cDNA, 2ng input, 15 PCR cycles

description:
liver, mRNA derived cDNA, 2ng input, 15 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Stim1KI_1


title: G4 liver, mRNA derived cDNA, 1ng input, 20 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 20 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: ABE8e_rep1_HEK293T


title: TadA-AI-15.8-In_rep3_HEK293T


title: C2, KO, LF liver


title: G4 liver, mRNA derived cDNA, 1ng input, 16 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 16 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TadA-AI-15.8-In_rep2_HEK293T


title: C1, KO, LF liver


title: TA muscle, Orai1KO_4


title: TA muscle, WT_5


title: G4 liver, mRNA derived cDNA, 1ng input, 18 PCR cycles

description:
liver, mRNA derived cDNA, 1ng input, 18 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TadA-AI-15.8-In_rep1_HEK293T


title: TA muscle, Orai1KO_2


title: TA muscle, Stim1KI_3


title: B3, WT, AMLN (NASH) liver

value: WT-AMLN


title: G4 liver, mRNA derived cDNA, 0ng input, 21 PCR cycles

description:
liver, mRNA derived cDNA, 0ng input, 21 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4


title: TA muscle, Orai1KO_3


title: B4, WT, AMLN (NASH) liver


title: G4 liver, mRNA derived cDNA, 0ng input, 19 PCR cycles


title: G4 liver, mRNA derived cDNA, 0ng input, 17 PCR cycles


title: TA muscle, Stim1KI_2


title: TadA-AI-15.8_rep2_HEK293T


title: B2, WT, AMLN (NASH) liver


title: TadA-AI-15.8_rep3_HEK293T


title: TA muscle, Orai1KO_1


title: TA muscle, WT4


title: TadA-AI-15.8_rep1_HEK293T


title: WT_R2 (RNA-seq)

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Assembly: hg38
Supplementary files format and content: Counts tables contain the raw counts quantified by Salmon and DESeq2.

value: undifferentiated pleomorphic sarcoma cell line


title: NC_rep3_HEK293T

value: NC


title: WT_R3 (RNA-seq)


title: TA muscle, WT3


title: A3, WT, LF liver

value: WT-LF


title: TA muscle, WT2


title: WT_R1 (RNA-seq)


title: A2, WT, LF liver

value: Male


title: NC_rep1_HEK293T


title: sg1_clone6_R3 (RNA-seq)

value: Atrx knockout


title: SeMet_rep4

city: Chicago

first: Robert

last: Sargis

state: IL

address: 835 S Wolcott st

institute: University of Illinois at Chicago

data_processing:
fastq files were aligned to the mouse reference genome mm10 using STAR software
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
The gene expression level was calculated using fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Differential expression analysis was performed using DEGSeq R package. Genes with an adjusted P value (using q value) < 0.05 were considered as differentially expressed (DEG).
Genome_build: mouse reference genome mm10
Supplementary_files_format_and_content: xls files include gene fpkm of all samples

growth_protocol: 4x10^4 MIN6-K8 cells/well were plated in 24 well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina Inc, according to the manufacturer’s instructions.

treatment_protocol: MIN6-K8 cells were either left untreated, or treated with 40 μM SeMet for 6 days.

tag: background strain

value: mouse Insulinoma Cell Line

value: wild-type

value: 40 μM SeMet treated for 6 d


title: NC_rep2_HEK293T


title: SeMet_rep3


title: SeMet_rep2


title: Embryo brain, ND, replicate 4

city: Singapore

first: Long

middle: Nam

address: 28 Medical Drive

department: Biochemistry

country: Singapore

institute: Singapore

description:
EBN4
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastp software
In this step, clean data (clean reads) were obtained by removing readscontaining adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene
Assembly: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Supplementary files format and content: file.txt excel files contain differential analysis data with FPKM and gene count

source_name: brain

extract_protocol:
RNAs were extracted using the RNeasy Mini Plus kit from Qiagen; about 8ug was used to send to Novogene company for RNA-sequencing service
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads; The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size  distribution  detection.  Quantified  libraries  will  be  pooled  and  sequenced  on  Illumina platforms, according to effective library concentration and data amount.

value: brain

value: embryo

value: normal chow diet for pregnant mother


title: HSPCs, barcode-derived cDNA

city: San Francisco

first: Catherine

last: Smith

state: California

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description: Mission Bio Tapestri

data_processing:
FASTQ files from single-cell RNAseq were processed via the Fluent Cloud Platform. This analysis platform trims adapter sequences, demultiplexes sequencing data into single cells matched against a list of known barcodes, maps reads against the GRCh38.p13 reference transcriptome, and separates putative cells from background.
Genes were filtered if detected in <3 cells and cells were filtered based on having low-complexity libraries (feature count < 200) or high mitochondrial content (>15%).
Downstream bioinformatics analysis, including scaling and log-normalization of single-cell transcriptional data and centered-log ratio normalization of single-cell protein expression data, was performed using Seurat 4.3.0. Across all samples, data integration was performed using reciprocal principal component analysis (RPCA).
Assembly: hg38
Supplementary files format and content: matrix files (.mtx)
Supplementary files format and content: tab-separated values files (.tsv)

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
We performed SC RNAseq on a sample form a healthy bone marrow donor using a pre-templated instant partitions (PIP) sequencing platform.
Briefly, cryopreserved cells were thawed, normalized combined in a 1:10 ratio with barcoded PIPs, which were then vortexed and centrifuged into emulsifications. Emulsions were thermocycled, broken, mixed, washed, and pelleted. Reverse transcription was performed, and cDNA synthesis completed. After whole transcriptome amplification, PIPs were column filtered and purified with Ampure XP. Libraries were generated from WTA amplified material using the Nextera XT DNA Library Preparation Kit with a custom primer (PIPs_P5library) and standard Nextera P7 indexing primers (N70x). Libraries were pooled and sequenced using an Illumina NextSeq 2000.

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: sg1_clone6_R1 (RNA-seq)


title: SeMet_rep1


title: sg1_clone6_R2 (RNA-seq)


title: A1, WT, LF liver

value: liver


title: B1, WT, AMLN (NASH) liver

value: 32 weeks of AMLN diet


title: sg1_clone4_R3 (RNA-seq)


title: A4, WT, LF liver

value: 32 weeks of LF diet


title: Embryo brain, ND, replicate 2

description:
EBN2
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt


title: CD8_O2R33

city: Waltham

first: Susan

middle: Dina

last: Ghiassian

address: 500 Totten Pond Rd, 6th Floor

institute: Scipher Medicine

description: female CD patient; aged 26 years

data_processing:
Sequence reads were aligned to GRCh38 using STAR alignment software.
Gene expression was calculated (in fragments per kilobase of transcript per million mapped reads) using the RSEM software package.
Assembly: hg38
Supplementary files format and content: Comma-delimited text file includes FPKM values for each sample.

source_name: colon

growth_protocol: Biopsy tissues were cultured in triplicate in 12-well plates containing a modified Connaught Medical Research Laboratory (CMRL)–based cell-culture media at 37 °C, 5% CO2.

extract_protocol:
RNA was extracted by proprietary process by REPROCELL. Briefly, tissue lysates were treated with Proteinase K. NA was eluted with an elution solution of concentration ≥20 ng/μL. The lysates were then centrifuged, ethanol was added to the supernatant, and the solutions were loaded onto spin-columns. DNase digestion was performed on column to remove any traces of DNA and RNA.
RNA libraries for 150bp paired-end sequencing were prepared by an mRNA library prep kit for sequencing by an Illumina Novaseq 6000.

treatment_protocol: Culture plates were incubated in media with either test compounds (10 uM) or vehicle. Tissues were treated with Staphylococcus enterotoxin B (List Biological Laboratories, Campbell, CA) to stimulate inflammatory cytokine secretion.

value: colon

tag: age (years)

value: Female

tag: ethnicity

value: Unknown (not stated)

tag: blood pressure

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

tag: drinking

tag: major reason_for_surgery

value: Extended (RT) Hemicolectomy

tag: medical history

value: Crohns. Psoriasis

tag: acute medication

tag: chronic medication

value: budesonide, cocodamol, ferrous sulphate, fucidin, ibuprofen, paracetemol, sertraline, ustekinumab


title: UC4_O2R41

description: male UC patient; aged 34 years

tag: tissue

tag: Sex

value: Male

value: White

value: BACK SURGERY                   bone was fused to his back at age 6 "      PR COLONOSCOPY FLX DX W/COLLJ SPEC WHEN PFRMD      N/A      2021 "      PR SIGMOIDOSCOPY FLX WITH WITH BAND LIGATION(S)      N/A      2021 Abdominal CT 2021:radiology impression:Active IBD related inflammation involving a long segment of colon from the splenic flexure through the rectum. Subjectively, the degree of inflammation has worsened from 2021 Abdominal CT 2021:radiology impression:Findings of active colitis, moderately improved extending from the distal transverse colon to the rectum when compared to 2021 examination in this patient with history of ulcerative colitis.  Colonoscopy 2021:Pancolitis ulcerative colitis. Inflammation was found from the anus to the ascending colon. This was severe. Biopsied.  /2021:Severe (Mayo Score 3) pancolitis ulcerative colitis;Biopsies were taken with a cold forceps for histology in the right colon, transverse colon, left colon, and rectum.  Pathology 2021:diagnosis:COLON, RANDOM, BIOPSY:SEVERELY ACTIVE CHRONIC COLITIS (CRYPT ABSCESSES AND CRYPTITIS) AND FOCAL EROSION

value: Blood clotting disorder (CMS/HCC)       "      Chronic diarrhea      may "      Irritable bowel syndrome       "      Scoliosis       "      Ulcerative colitis (CMS/HCC)      2021                               5 month history of bloody diarrhea consistent with active ulcerative colitis. He first started experiencing occasional episodes of diarrhea in 2016 and was diagnosed with colitis after a colonoscopy at an outside facility. Since2016, he reports having occasional episodes of diarrhea, often triggered by consumption of fried foods. These episodes increased in frequency and severity up until 2021. In 2021, he was hospitalized at --- due to bloody diarrhea and was diagnosed with ulcerative colitis. --- has also since been hospitalized multiple times at --- since 2021, including 2-3 ED visits and at least 2 inpatient stays. He has been on a low-fiber diet since his hospitalization in 2021 as well as a weight loss of about 70 lbs since then

value: Remicade, prednisone

tag: treatment


title: sg1_clone4_R2 (RNA-seq)

tag: cell line

tag: cell type

value: undifferentiated pleomorphic sarcoma cell line

tag: genotype

value: Atrx knockout


title: Control_rep4

tag: background strain

value: mouse Insulinoma Cell Line

value: wild-type

value: untreated


title: CD7_O2R49

description: female CD patient; aged 30 years

tag: age (years)

tag: ethnicity

tag: blood pressure

value: No

value: Past

value: Significant history of stricturing ileocolonic Crohn's disease with perianal involvement. Diagnosed (age):2016 (25).  Status post total colectomy with end ileostomy due to steroid and Remicade refractory disease while inpatient. It was recommended to resume Remicade as she had only received 2 infusions before her surgery. Current therapy:Remicade since 2019. Past therapy:prednisone. No family GI history. Prior medical history:CXrohn's, colitis, depression, supraventricular tachycardia, anxiety, ovarian cyst

value: Current medication list which includes the following prescription(s):acetaminophen (TYLENOL), chlorhexidine (HIBICLENS), clindamycin (CLEOCIN T), hydrocortisone (ANUSOL-HC), hyoscyamine (LEVSIN), infliximab (REMICADE), ondansetron (ZOFRAN), and promethazine hcl (PHENERGAN


title: sg1_clone4_R1 (RNA-seq)


title: Embryo brain, ND, replicate 1

description:
EBN1
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

value: brain

tag: developmental stage

value: embryo

value: normal chow diet for pregnant mother


title: Embryo brain, ND, replicate 3

description:
EBN3
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt


title: UC3_O2R81

description: female UC patient; 39 years

value: colon

value: Female

value: Unknown (not stated)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

value: post colectomy in summer 2021 and now active rectosigmoid pouch inflammation

value: past medical history of Colitis. Past history of Venous thromboembolism and Iron Deficiency

value: Currently on Eliquis


title: Control_rep2


title: Embryo brain, CDD, replicate 4

description:
EBC4
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

value: choline deficient diet for pregnant mother


title: WT_k9me3_R3 (Cut&Run)

data_processing:
Cut and run reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software.
Assembly: hg38
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: bed files generated by SEACR
Library strategy: CUT&RUN

extract_protocol:
Cells were collected by trypsin. Washed by PBS and followed the protocol from EpiCypher.
Libraries were generated using NEBNext Ultra II kits.

value: undifferentiated pleomorphic sarcoma cell line

value: WT

tag: chip antibody


title: Control_rep3

value: mouse Insulinoma Cell Line

value: wild-type

value: untreated


title: Hippocampus, ISC9_S10

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were aligned to the rat reference genome (rn6) using HISAT2 (Kim et al., 2019).
MACS was utilized to assess sites of chromatin accessibility in ATAC-seq samples
diffReps (Shen et al., 2013) was run on the processed samples to find differential sites for the comparisons to the IS control group (ID, IDch, or ISch vs IS).
The atacseq.txt and chipseq.txt files are the annotation peak lists obtained from MACS software. The fold change for each peak is computed as the ratio of the read count in the peak to the maximum of the local and global lambda values.
Local Lambda: MACS2 computes a local lambda value for each peak, which is a measure of the local background noise around the peak.
Global Lambda: MACS2 also computes a global lambda value, which is a measure of the background noise across the entire genome.
Assembly: rn6
Supplementary files format and content: tab-delimited text peaks file

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Hippocampi were bisected, flash-frozen in liquid nitrogen, and stored at -80°C. For ATAC-seq, nuclei were isolated from tissue using iodixanol gradient and DNA was transposed with Tn5 transposase followed by MinElute Reaction Cleanup kit purification. DNA was quantified using the PicoGreen dsDNA Assay Kit.
ATAC-seq library preparation was performed in accordance with the ATAC-seq protocol as described by Buenrostro et al. (2015). Libraries were assessed for quality using electrophoresis on an Agilent Bioanalyzer (Agilent) and size-selected for 200~800 bp fragments.

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

value: ISC

tag: offspring age


title: CD5_O2R57

description: female CD patient; aged 57 years

tag: tissue

tag: Sex

value: White

tag: drinking

value: Yes, <14 units/week, 1 can beer/week

tag: major reason_for_surgery

tag: medical history

value: HTN, HLD, anemia, fatty liver, kidney stones, hydronephrosis with renal and ureteral calculcus obstruction, obesity, depression, anxiety, arthritis, GERD, anemia, essential hypertension, depression, spinal stenosis Crohn's disease.  An overlap syndrome of Crohn's disease with lupus/scleroderma.  Diagnosed (age) 1987 (age 25). BMI 36.96 kg/m² .  Montreal Classification:CD:A2 17-40 L3 ileocolonic B2 stricturing.  Has frequent Crohn's flares.

tag: acute medication

value: Is still on Stelara injections.  Budesonide was switched to prednisone.  Has been on prednisone for the past month and is currently taking 10 mg daily.  Was advised to stop Stelara and taper prednisone off 2 weeks before her surgery.  The patient has a current medication list which includes the following prescription(s):acetaminophen, aspirin-acetaminophen-caffeine, budesonide, calcium citrate-vitamin d, cyclobenzaprine, cyclosporin, dicyclomine, DISABILITY PLACARD, duloxetine, folic acid, hydrocortisone, mesalamine, mesalamine, omeprazole, oxycodone, prednisone, prednisone, pregabalin, prenatal vit-fe fumarate-fa, sertraline, sulfasalazine, ustekinumab, cholecalciferol, and zinc.

tag: chronic medication

tag: treatment


title: WT_k9me3_R2 (Cut&Run)

tag: cell line

tag: cell type

tag: genotype


title: Embryo brain, CDD, replicate 2

last: Nguyen

description:
EBC2
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

value: brain

tag: developmental stage

value: embryo


title: CD4_O2R73

description: female CD patient; aged 55 years

value: colon

tag: age (years)

value: Female

tag: ethnicity

tag: blood pressure

value: Unknown (not stated)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

value: No

value: ectovaginal fistula s/p loop ileostomy in 2017 with later repair with flap complicated by pelvic fluid collection noted in July 2020. Patient was noted to have an additional fistula with active disease during EUA on 12/20. Here for completion proctocolectomy

value: hx of fistulizing Crohn's disease and rectovaginal fistula. She  has a past medical history of Anemia (09/2017), Crohn disease, Crohn's colitis, with fistula, Essential hypertension, benign, Hyperlipidemia, Ileostomy in place, OSA (obstructive sleep apnea), and Renal disease

value: She continues on therapy with Remicade. She declined adding AZA when she had undetectable drug levels and drug antibodies in the fall.She eclined adding Imuran.She was agreeable to increasing dose of infusion and has remained on 10 mg/kg every8weeks. Had drug levels repeated which showed improved in drug level to 5.1 and antibodies reduced from 10.0 to 6.1.


title: WT_k9me3_R1 (Cut&Run)

value: undifferentiated pleomorphic sarcoma cell line

value: WT

tag: chip antibody


title: Hippocampus, ISC8_S9

tag: tissue

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

tag: offspring age


title: WT_k27ac_R3 (Cut&Run)

tag: cell line

value: H3K27Ac (Active motif,39133)


title: UC2_O2R89

description: male UC patient; aged 56 years

tag: Sex

value: Male

value: White

tag: drinking

tag: major reason_for_surgery

value: none listed

tag: medical history

value: history of Ulcerative colitis diagnosed in 1980's and colon cancer.  UC for >30yrs. Has not had regular f/u w GI for several years.  No current therapy/medications.  Started w weight loss (<10 pounds) and had colonoscopy. Pancolitis, anus to hepatic inflammation. Lesion in sigmoid colon bx'd & tattooed. Adenocarcinoma

tag: acute medication

value: He has not responded to IV steroids. Started infliximab on fall of 2021, appears to have experienced improvement initially, now symptoms worsening. Started on prednisone 30mg daily on early 2022.

tag: chronic medication

tag: treatment


title: Embryo brain, CDD, replicate 1

description:
EBC1
WT_CDDvsWT_ND_deg.txt
WT_CDDvsWT_ND_deg_all.txt
WT_CDDvsWT_ND_deg_up.txt
WT_CDDvsWT_ND_deg_down.txt

value: brain

tag: developmental stage

value: embryo

tag: cell type

tag: genotype

value: wild-type

value: choline deficient diet for pregnant mother


title: Hippocampus, ISC11_S12

value: ISC


title: Whole brain, 24m, rep 4 [Illumina]

data_processing:
Trimming for adapters using trimgalore v0.4.11
RNA-seq reads were aligned to the GRCm39.103 genome assembly using hisat2 v2.1.0
Assembly: GRCm39.103

extract_protocol:
RNA was extracted from a total of 8 biological samples, corresponding to 4 young-adult samples (6-month, brain hemisphere, from 4 males), 4 aged (24-month, brain hemisphere, from 4 males). Raw data were procured inNovoSeq 6000 sequencing
NEBNext Ultra II directional polyA+

value: Whole brain

tag: age

value: 24 months


title: CD2_O2R25

description: male CD patient; aged 29 years

tag: tissue

value: colon

tag: age (years)

tag: ethnicity

value: Unknown (not stated)

tag: blood pressure

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

value: Yes

value: Right Hemicolectomy

value: Crohns


title: CD3_O2R65

description: male CD patient; aged 55 years

tag: Sex

value: Male

value: No

tag: drinking

value: Yes, <14 units/week, couple times a month

tag: major reason_for_surgery

value: crohn's disease. Symptoms since his 30s (always had abdominal cramping, diarrhea issues) but was diagnosed at age 47 when he presented w bloody diarrhea.  Montreal Classification:CD:A3 >40 L1 ileal B2 stricturing.

value: Current therapy:Infliximab.  Past therapy:Prednisone x 6months.  Current Outpatient Medications:•  Cholecalciferol (Vitamin D) •  inFLIXimab 100 MG Recon Soln, •  iron polysaccharides (Ferrex 150) 150 MG capsule.


title: Hippocampus, ISC10_S11

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

tag: offspring age


title: Hippocampus, IS2_S2

value: IS


title: WT_k27ac_R2 (Cut&Run)

tag: cell line

tag: cell type

value: undifferentiated pleomorphic sarcoma cell line

tag: genotype

value: WT

tag: chip antibody

value: H3K27Ac (Active motif,39133)


title: WT_k27ac_R1 (Cut&Run)


title: CD1_O2R1

description: female CD patient; aged 34 years

source_name: ileum

tag: tissue

value: ileum

tag: age (years)

value: Female

tag: ethnicity

value: Past

value: Ileocaecal resection and end ileostomy

tag: medical history

value: Crohn's, primary sclerosing cholangitis (PSC), anaemia

tag: acute medication

tag: chronic medication

value: Adalimumab, colesevelam, fexofenadine, folic acid, hydroxocobalmin, hyoscine butylbromide, paracetamol

tag: treatment


title: Whole brain, 24m, rep 2 [Illumina]

value: Whole brain

tag: Sex

value: Male

tag: age

value: 24 months


title: Control_rep1

tag: background strain

value: mouse Insulinoma Cell Line

value: wild-type

value: untreated


title: WT_IgG_R2 (Cut&Run)

value: IgG (diagenode,C15410206)


title: Whole brain, 24m, rep 1 [Illumina]


title: UC1_O2R9

description: male UC patient; aged 56 years

value: colon

value: Asian

tag: blood pressure

value: Unknown (not stated)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking

value: No

tag: drinking

tag: major reason_for_surgery

value: Ulcertaive colitis diagnosed 1991

value: azathioprine (50mg x3), mesalazine (400mg x2), Ferras sulphate 200mg


title: Hippocampus, IS1_S1

tag: tissue

value: Brain

tag: tissue region

value: Hippocampus

tag: group

tag: maternal treatment

value: IS

tag: offspring age


title: Hippocampus, IS14_S4


title: WT_IgG_R1 (Cut&Run)

tag: cell line

tag: cell type

value: undifferentiated pleomorphic sarcoma cell line

tag: genotype

value: WT

tag: chip antibody


title: Hippocampus, IS13_S3


title: Whole brain, 6m, rep 3 [Illumina]

value: Whole brain

tag: Sex

value: Male

tag: age

value: 6 months


title: WT_H3_3_R3 (Cut&Run)


title: Whole brain, 6m, rep 2 [Illumina]


title: WT_H3_3_R2 (Cut&Run)


title: Hippocampus, IDC9_S14

value: IDC


title: WT_IgG_R3 (Cut&Run)


title: M-L07

city: qingdao

first: xuechao

last: liu

address: jiangsuroad

institute: Affiliated Hospital of Qingdao University

description: HiSeq X Ten

data_processing:
Quality control
Cell type identification and clustering analysis were conducted using the Seurat program (v.3.0.1), an R package for scRNA-seq analysis.
The UMI count tables of each cellular barcode were loaded into R with the read.table function.
Assembly: mm10
Supplementary files format and content: expression matrix file using RNA raw count

source_name: gastrointestinal stromal tumors

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS (HyClone) were prepared.
The scRNA-seq libraries were constructed using the GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies), according to the manufacturer's protocol

value: gastrointestinal stromal tumors

value: Spindle cell

value: KIT exon 11 and exon 18

tag: treatment

value: First-line


title: Whole brain, 6m, rep 1  [Illumina]


title: WT_H3_3_R1 (Cut&Run)

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University


title: P-C07

description: HiSeq X Ten


title: Hippocampus, IDC8_S13


title: TC32 siNEG CUT&Tag

first: Rebecca

last: Kaufman

address: 3400 Civic Center Blvd

department: Center for Childhood Cancer Research

institute: Children's Hospital of Philadelphia

data_processing:
Reads were trimmed using TrimGalore-0.6.6
Reads were aligned to hg38 geneome using Bowtie2 version 2.4.5.  Mapped read pairs with a quality score above 2 were retained
Peaks were called using MACS2 v 2.2.9.1 with the significance cut-off q-value <= 0.05
bigwig files were generated using bedGraphToBigWig. narrowPeak files were generated with MACS2
Assembly: hg38
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Active motif cut and tag protocol with SPRI bead clean up
14 cycle PCR amplification, SPRI bead clean up, 20 more PCR cycles

value: Ewing Sarcoma

value: siNEG


title: TC32 siEWS-FLI CUT&Tag

value: siEWS-FLI


title: Hippocampus, IDC11_S16


title: clone6_k9me3_R3 (Cut&Run)

value: Atrx knockout


title: P-G06

description: HiSeq X Ten

value: PDGFRA exon 18 (D842V)

value: No


title: Hippocampus, IDC10_S15

value: Brain

value: Hippocampus


title: SAA-/- Pooled Tumor 2, scRNAseq

first: Jesse

last: Lee

address: South Pavilion, Room 8-326

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Data was demultiplexed and aligned using the Cell Ranger pipeline (10x Genomics, v.6.1.2).
Datasets were processed using Seurat (v.4.3.0) in R (v.4.2.2) and filtered to include cells with a minimum of 200 genes and genes expressed in greater than 3 cells.
Assembly: mm10
Supplementary files format and content: feature count matrix exported as csv sheet with raw counts per UMI

source_name: Tumor

extract_protocol:
Tumors from Saa+/+ and Saa-/- mice were processed and pooled for scRNAseq (n=4 mice pooled to n=2 per condition). Following tumor digestion, live cells were isolated using a dead cell removal kit (Miltenyi Biotec #130-090-101) according to manufacturer’s instructions.
Single cell libraries were generated using the 10x Genomics Chromium Single Cell 3’ GEM Kit per manufacturer’s instructions

value: Tumor

value: KPC derived Tcelllow PDAC


title: P-G05

description: HiSeq X Ten

value: KIT exon 11


title: Hippocampus, ID9_S5

value: ID