title: UVB 3

city: Paris

first: Min

last: ZHAO

state: France

address: 15 rue de l'Ecole de Médecine

institute: INSERM U1138, Centre de Recherche des Cordelier, University Paris Descartes

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used to align reads on reference genome rd6 using standard options.
Quantification was performed with genecode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools
Assembly: rn7
Supplementary files format and content: tab-delimited text file includes raw counts for each  sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each  sample

source_name: meibomian gland

extract_protocol:
Total RNA was isolated from tissues using the RNeasy Mini Kit inluding DNase I treatment (Qiagen). 1µg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The upper eyelids of 3-month female Sprague-Dawley rats were shaved and exposed to UVB irradiation for 5 min (300mJ/cm2) per day for 5 days. Eyelids were then removed and meibomian glands were dissected and snap frozen.

value: meibomian gland

value: wild-type

value: UVB


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample06

status: Public on Dec 31 2025

type: SRA

city: Bordeaux

first: Charlotte

last: Madore

address: 146 rue Leo Saignat

department: Alimentation Humaine

country: France

institute: INRAE

description:
Library name: PFC_MIA_PLX_M_06
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_06

library_source: transcriptomic

data_processing:
R sfotware and Rstudio were used;
Reads were trimmed using Trimmomatic package followed by feature count generation (Rsubread).
Reads were mapped to the mouse reference transcriptome GRCm39, v27 using STAR (v2.6.1d)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: prefrontal cortex

extract_protocol:
RNA was extracted using the miRNeasy Micro kit (Qiagen). 200ng of total RNA was used to construct RNA libraries.
RNA libraries were prepared using the Illumina Stranded mRNA Ligation Sample Prep kit following manufacturer's protocol.

tag: csf1r inhibitor

value: Plexxikon

tag: tissue

value: prefrontal cortex

tag: Sex

value: Male

tag: treatment

value: Maternal Immune Activation


title: BiTS-6_R1

city: New York

first: Jun

last: Wang

state: NY

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

description: Library name: BiTS-2, OTI, 48h

data_processing:
The DEGs between groups were analyzed using the R package DESeq2 (version v1.42.1) with the cutoff as |log2FoldChange|>1 and p-value <0.05.
The Gene Ontology (GO) enrichment analysis was performed to analyze the functions of DEGs by R clusterProfiler (version v4.6.2). The analyses were based on the GO resource (http://www.geneontology. org), p < 0.05 was considered statistically significant enrichment.
Assembly: mm10
Supplementary files format and content: Text file with raw counts for each sample

source_name: splenocytes

extract_protocol:
RNA was extracted from cells using an RNA extraction kit (Qiagen) after 48 hours of stimulation.
Libraries were constructed at Azenta LifeSciences

value: splenocytes

tag: cell type

value: naive primary CD8 T cells

tag: genotype

value: OT-I

value: SIINFEKL


title: BiTS-3

description: Library name: BiTS-1, OTI, 48h


title: UVB 2

organism: Rattus norvegicus


title: DSP-1001660002550-B-F08_R6_C7

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

institute: Yale University

description: Library name: DSP-1001660002550-B-F08

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: Lung Cancer

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: Lung Cancer

value: immunotherapy

tag: batch


title: DSP-1001660002550-B-F09_R6_C7

description: Library name: DSP-1001660002550-B-F09


title: iso-1_R1

description: Library name: Iso-1, OTI, 48h


title: DSP-1001660002550-B-G02_R6_C8

description: Library name: DSP-1001660002550-B-G02


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample05

description:
Library name: PFC_MIA_PLX_M_05
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_05


title: YUMM52-in-NSG-CD18KO-rep3

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

data_processing:
Reads were aligned to the Mus musculus genome version mm10 ucsc-201112, using STAR v2.6.1d
Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon v1.6.0
TPM measurements were transformed to counts per gene estimated using tximport.
Assembly: mm10 ucsc-201112
Supplementary files format and content: TPM counts per gene, csv file.

source_name: tumor

extract_protocol:
Total RNA was extracted from frozen tissue samples using the RNeasy Plus mini kit (Qiagen, Hilden, Germany).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s recommendations.

value: tumor

tag: cell line

tag: strain

value: NOD/SCID IL-2Rg(-/-) KO

value: beta2 integrin KO


title: mut-2_R1

description: Library name: Mut-1, OTI, 48h


title: Control 4

value: no treatment


title: DSP-1001660002550-B-F07_R6_C6

description: Library name: DSP-1001660002550-B-F07


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample04

description:
Library name: PFC_MIA_PLX_M_04
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_04


title: YUMM52-in-NSG-CD18KO-rep2


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample03

description:
Library name: PFC_MIA_PLX_M_03
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_03


title: Control 3

value: meibomian gland


title: YUMM52-in-NSG-CD18KO-rep1


title: Control 2

value: wild-type


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample02

description:
Library name: PFC_MIA_PLX_M_02
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_02


title: DSP-1001660002550-B-F05_R6_C6

description: Library name: DSP-1001660002550-B-F05


title: YUMM52-in-NSG-Cas9-control-rep4

value: control


title: UVB 1

value: UVB


title: PreFrontal Cortex, MIA, Plexxikon-treated, Male, Sample01

description:
Library name: PFC_MIA_PLX_M_01
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_M_01

value: Plexxikon

value: prefrontal cortex


title: Control 1


title: DSP-1001660002550-B-F04_R6_C6

description: Library name: DSP-1001660002550-B-F04


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample06

description:
Library name: PFC_MIA_PLX_F_06
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_06

value: Female

value: Maternal Immune Activation


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample05

description:
Library name: PFC_MIA_PLX_F_05
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_05


title: DSP-1001660002550-B-F03_R6_C5

description: Library name: DSP-1001660002550-B-F03


title: COL-0, wild type, repB

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
RNA-seq data were aligned to the TAIR10 (EnsemblePlants, release 58) genome sequence with corresponding gtf file using STAR (v 2.7.11a) to obtain read count per gene.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count per gene, one file per sample

organism: Arabidopsis thaliana

source_name: 7 day-old seedlings

extract_protocol:
RNA was extracted from 7 day-old seedlings grown on half strength MS10 medium using the Sigma-Aldrich Plant Total RNA Kit (STRN50) and the On-Column DNase I Digestion Set (DNASE10-1SET). Tissue was ground in liquid nitrogen before incubation in lysis solution containing 2-mercaptoethanol at 65°C for 3 min. Debris was removed by centrifugation and column filtration and RNA was captured onto a binding column using the supplied binding solution. DNA was removed by wash solutions and DNase treatment on the column. Purified RNA was eluted using RNAase free water.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant Sample Preparation kit (RS-122-2401). Ribosomal RNA (rRNA) was removed and purified RNA was quality checked using a TapeStation 2200 (Agilent Technology) with High Sensitivity RNA ScreenTape (5067-5579). mRNA was fragmented into 120-200 bp sequences with a median size of 150 bp, and used as template to synthesize first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. Newly synthesized cDNA had a single adenine base added with ligation of adaptors, before being purified and amplified by PCR to make the final library. Library quality control was carried out again using a TapeStation with D1000 ScreenTape (catalog number 5067-5582).

value: 7 day-old seedlings

value: COL-0 wild type


title: YUMM52-in-NSG-Cas9-control-rep3


title: YUMM52-in-NSG-Cas9-control-rep1


title: YUMM52-in-NSG-Cas9-control-rep2


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample04

description:
Library name: PFC_MIA_PLX_F_04
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_04


title: DSP-1001660002550-B-F02_R6_C5

description: Library name: DSP-1001660002550-B-F02


title: COL-0, wild type, repC

growth_protocol: RNA was extracted from 7 day-old seedlings grown on half strength MS10 medium


title: DSP-1001660002550-B-F01_R6_C5

description: Library name: DSP-1001660002550-B-F01


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample03

description:
Library name: PFC_MIA_PLX_F_03
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_03


title: COL-0, wild type, repA


title: DSP-1001660002550-B-E12_R6_C5

description: Library name: DSP-1001660002550-B-E12


title: YUMM52-in-ICAM1ko-CD18KO-rep2

value: ICAM-1tm1Jcgr KO C57BL/6


title: YUMM52-in-ICAM1ko-CD18KO-rep1


title: COL-0, PLS overexpressor, repB

value: COL-0 PLS overexpressor


title: DSP-1001660002550-B-F06_R6_C6

description: Library name: DSP-1001660002550-B-F06

value: Lung Cancer

value: immunotherapy


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample01

description:
Library name: PFC_MIA_PLX_F_01
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_01


title: COL-0, PLS overexpressor, repA


title: DSP-1001660002550-B-E10_R6_C4

description: Library name: DSP-1001660002550-B-E10


title: YUMM52-in-ICAM1ko-Cas9-control-rep3

value: tumor


title: PreFrontal Cortex, MIA, Control, Male, Sample06

description:
Library name: PFC_MIA_CTRL_M_06
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_M_06

value: Control

value: Male


title: C24, wild type, repC

value: C24 wild type


title: YUMM52-in-ICAM1ko-Cas9-control-rep2


title: C24, wild type, repB


title: PreFrontal Cortex, MIA, Control, Male, Sample05

description:
Library name: PFC_MIA_CTRL_M_05
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_M_05


title: PreFrontal Cortex, MIA, Control, Male, Sample04

description:
Library name: PFC_MIA_CTRL_M_04
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_M_04


title: YUMM52-in-ICAM1ko-Cas9-control-rep1


title: DSP-1001660002550-B-E07_R6_C3

description: Library name: DSP-1001660002550-B-E07


title: C24, wild type, repA


title: DSP-1001660002550-B-E08_R6_C4

description: Library name: DSP-1001660002550-B-E08


title: COL-0, PLS overexpressor, repC


title: C24, pls mutant, repC

value: C24 pls mutant


title: PreFrontal Cortex, MIA, Control, Male, Sample02

description:
Library name: PFC_MIA_CTRL_M_02
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_M_02


title: PreFrontal Cortex, MIA, Plexxikon-treated, Female, Sample02

description:
Library name: PFC_MIA_PLX_F_02
Column name in normalized_counts_all_samples.txt: PFC_MIA_PLX_F_02


title: DSP-1001660002550-B-E11_R6_C4

description: Library name: DSP-1001660002550-B-E11


title: PreFrontal Cortex, MIA, Control, Male, Sample03

description:
Library name: PFC_MIA_CTRL_M_03
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_M_03


title: C24, pls mutant, repA


title: YUMM52-in-ICAM1ko-Cas9-control-rep4

value: control


title: YUMM52-in-C57BL6WT-CD18KO-rep2

value: beta2 integrin KO


title: DSP-1001660002550-B-E05_R6_C3

description: Library name: DSP-1001660002550-B-E05


title: C24, pls mutant, repB


title: PreFrontal Cortex, MIA, Control, Female, Sample06

description:
Library name: PFC_MIA_CTRL_F_06
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_06


title: YUMM52-in-C57BL6WT-Cas9-control-rep4


title: DSP-1001660002550-B-E04_R6_C3

description: Library name: DSP-1001660002550-B-E04


title: YUMM52-in-C57BL6WT-CD18KO-rep1


title: DSP-1001660002550-B-E09_R6_C4

description: Library name: DSP-1001660002550-B-E09


title: DSP-1001660002550-B-E03_R6_C2

description: Library name: DSP-1001660002550-B-E03


title: 50mg/kg dose of retrorsine intraperitoneal injection sample 3

city: Guiyang

first: Qing

last: Rao

address: Natural Products Research Center of Guizhou Province

country: China

description: Library name: 50mg-3

data_processing:
HISAT2（http://ccb.jhu.edu/software/hisat2/index.shtml )
Assembly: Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
Supplementary files format and content: mRNA file include FPKM values for each sample

source_name: liver

extract_protocol:
RNA was harvested  using Rneasy mini plus kit (Qiagen), 1.5 ug of totol RNA was used for the construction of sequencing libraries.
Enrich mRNA with polyA structure in total RNA using Oligo (dT) magnetic beads, and use ion disruption to break the RNA into fragments of approximately 300 bp in length. Using RNA as a template, the first strand of cDNA was synthesized using 6-base random primers and reverse transcriptase, and the second strand of cDNA was synthesized using the first strand of cDNA as a template. PCR amplification was used for library fragment enrichment, followed by library selection based on fragment size, with a library size of 450bp. Then, the library was inspected using Agilent 2100 Bioanalyzer, and the total concentration and effective concentration of the library were detected. Then, based on the effective concentration of the library and the required amount of data, the library containing different Index sequences (each sample is added with a different Index, and the off machine data of each sample is distinguished based on the Index) is mixed proportionally. The mixed library was uniformly diluted to 2nM and subjected to alkaline denaturation to form a single stranded library.

value: liver

value: WT


title: PreFrontal Cortex, MIA, Control, Female, Sample05

description:
Library name: PFC_MIA_CTRL_F_05
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_05

value: prefrontal cortex

value: Female


title: YUMM52-in-C57BL6WT-Cas9-control-rep3


title: YUMM52-in-C57BL6WT-CD18KO-rep3


title: DSP-1001660002550-B-E06_R6_C3

description: Library name: DSP-1001660002550-B-E06


title: DSP-1001660002550-B-E02_R6_C2

description: Library name: DSP-1001660002550-B-E02


title: 50mg/kg dose of retrorsine intraperitoneal injection sample 2

institute: Natural Products Research Center of Guizhou Province

description: Library name: 50mg-2


title: PreFrontal Cortex, MIA, Control, Female, Sample04

description:
Library name: PFC_MIA_CTRL_F_04
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_04

value: Maternal Immune Activation


title: YUMM52-in-C57BL6WT-Cas9-control-rep2


title: PreFrontal Cortex, MIA, Control, Female, Sample03

description:
Library name: PFC_MIA_CTRL_F_03
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_03


title: 50mg/kg dose of retrorsine intraperitoneal injection sample 1

description: Library name: 50mg-1


title: DSP-1001660002550-B-D12_R6_C2

description: Library name: DSP-1001660002550-B-D12


title: YUMM52-in-C57BL6WT-Cas9-control-rep1


title: 25mg/kg dose of retrorsine intraperitoneal injection sample 3

description: Library name: 25mg-3


title: PreFrontal Cortex, MIA, Control, Female, Sample07

description:
Library name: PFC_MIA_CTRL_F_07
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_07


title: tx CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 08

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

data_processing:
Adapter trimming using Cutadapt (v2.10)
Alignment and read counting with STAR aligner (v2.7.5; default settings)
Library size normalization in R v4.1.0 with DESeq2 v1.4
Assembly: GRCm38
Supplementary files format and content: TSV-formatted table with raw gene counts for every gene and every sample

source_name: CD8+ OT-I cells

growth_protocol: CD8+ OT-I T cells were co-cultured with SIINFEKL-pulsed BMDCs in the presence of DMSO (ctrl) or 2µM RGX-104.

extract_protocol:
CD8+ OT-I T cells were purified by FACS and RNA was isolated using the Total RNA Isolation kit (Norgen).
Illumina Truseq

treatment_protocol: DMSO versus 2µM RGX-104.

value: CD8+ OT-I cells

value: OT-I


title: 25mg/kg dose of retrorsine intraperitoneal injection sample 2

description: Library name: 25mg-2


title: PreFrontal Cortex, MIA, Control, Female, Sample02

description:
Library name: PFC_MIA_CTRL_F_02
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_02


title: tx CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 07


title: PreFrontal Cortex, MIA, Control, Female, Sample01

description:
Library name: PFC_MIA_CTRL_F_01
Column name in normalized_counts_all_samples.txt: PFC_MIA_CTRL_F_01


title: DSP-1001660002550-B-D11_R6_C1

description: Library name: DSP-1001660002550-B-D11


title: 25mg/kg dose of retrorsine intraperitoneal injection sample 1

description: Library name: 25mg-1


title: DSP-1001660002550-B-D10_R6_C1

description: Library name: DSP-1001660002550-B-D10


title: tx CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 06


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample06

description:
Library name: HPC_Sal_PLX_M_06
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_06

source_name: hippocampus

value: Plexxikon

value: hippocampus

value: Saline injection


title: NaCl  intraperitoneal injection sample 3

description: Library name: NaCl-3

value: NaCl  intraperitoneal injection sample 3


title: DSP-1001660002550-B-D09_R6_C1

description: Library name: DSP-1001660002550-B-D09

value: Lung Cancer

value: immunotherapy


title: tx CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 05


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample05

description:
Library name: HPC_Sal_PLX_M_05
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_05

value: Male


title: ctrl CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 04


title: DSP-1001660002550-B-E01_R6_C2

description: Library name: DSP-1001660002550-B-E01


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample04

description:
Library name: HPC_Sal_PLX_M_04
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_04


title: DSP-1001660002550-B-D08_R5_C8

description: Library name: DSP-1001660002550-B-D08


title: DSP-1001660002550-B-D07_R5_C8

description: Library name: DSP-1001660002550-B-D07


title: DSP-1001660002550-B-D06_R5_C8

description: Library name: DSP-1001660002550-B-D06


title: DWYG-H,rep 2

city: Wuhan

first: Yu

last: Zhou

address: No. 16, West Huangjiahu Road, Hongshan District

institute: Hubei University of Chinese Medicine

description: Library name: Sample8

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Invitrogen Ambion RNA extract kit. 2μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  SMART-Seq mRNA LP (Takara) following manufacturer's protocols.


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample02

description:
Library name: HPC_Sal_PLX_M_02
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_02


title: NaCl  intraperitoneal injection sample 1

description: Library name: NaCl-1

value: NaCl  intraperitoneal injection sample 1


title: DWYG-H,rep 1

description: Library name: Sample7


title: ctrl CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 03

value: control


title: ctrl CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 01


title: DSP-1001660002550-B-D05_R5_C8

description: Library name: DSP-1001660002550-B-D05


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample01

description:
Library name: HPC_Sal_PLX_M_01
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_01


title: DSP-1001660002550-B-D04_R5_C7

description: Library name: DSP-1001660002550-B-D04


title: DWYG-M,rep 2

description: Library name: Sample6


title: NaCl  intraperitoneal injection sample 2

description: Library name: NaCl-2

value: NaCl  intraperitoneal injection sample 2


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample06

description:
Library name: HPC_Sal_PLX_F_06
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_06


title: DSP-1001660002550-B-D03_R5_C7

description: Library name: DSP-1001660002550-B-D03


title: SAM24380136_VG_KO_4

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed and aligned to the mouse reference transcriptome (GRCm38) via the 10x software Cellranger (v3.1.0) using default parameters to generate the raw feature and barcodes matrices. CellBender (v0.2.0) was used to remove ambient RNA effects from raw_featur e_bc_matrix matrices for each sample using the remove-background function with the following parameters: epochs=200, fpr=0.01, total-droplets-included=30000, a nd expected-cells=number of cells called by CellRanger. Biological replicates were merged and analyzed using Seurat (v3.1.1) following the standard workflow. B riefly, cells with less than 500 UMIs or mitochondria RNA content greater than 25% were filtered.
Assembly: GRCh38
Supplementary files format and content: H5

source_name: vagal ganglia

extract_protocol:
Due to the low number of nodose neurons we pooled VG from 3 mice for nuclei isolation per analyzed sample (4 samples total). Harvested VG were incubated in 0.5 mL Lysis buffer (10 mM NaCl; 10 mM Tris pH 7.5; 3 mM MgCl2; 0.2 U/mL RNase inhibitor) for 5 min on ice. VG were then careful ly homogenized using a dounce homogenizer and spun at 300 g for 5 minutes. Supernatant was discarded and the pellet was resuspended in 0.5 mL PBS+ 3% BSA+ 0.2 U/mL RNase inhibitor containing 5 uL RNase free DNaseI and incubated at RT for 2 minutes. The solution containing nuclei was gently triturated, pelleted and re suspended in PBS+ 3% BSA+ 0.2 U/mL RNase inhibitor. Isolated nuclei were injected into Chromium for GEM generation and subsequent library construction (V3 of t he Chromium 3’ EXP reagent kit; 10x Genomics). cDNA of the first RT reaction as well as the final library was QC’ed via High Sensitivity DNA chip bioanalyzer ( Agilent).
10x Genomics 3' v3 chemistry

value: vagal ganglia

value: Tmc3 knockout


title: DWYG-M,rep 1

description: Library name: Sample5

value: liver


title: DEN+CCl4,rep 2

description: Library name: Sample4


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample05

description:
Library name: HPC_Sal_PLX_F_05
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_05

value: Female


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample04

description:
Library name: HPC_Sal_PLX_F_04
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_04


title: DSP-1001660002550-B-D02_R5_C7

description: Library name: DSP-1001660002550-B-D02


title: SAM24380134_VG_KO_2

description: 10x Genomics


title: DEN+CCl4,rep 1

description: Library name: Sample3


title: DSP-1001660002550-B-D01_R5_C7

description: Library name: DSP-1001660002550-B-D01


title: SAM24380133_VG_KO_1

description: 10x Genomics


title: ctrl CD8+ OT-I T cells after crosspresentation by LXR-/- BMDCs, sample 02


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample03

description:
Library name: HPC_Sal_PLX_F_03
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_03


title: control,rep 2

description: Library name: Sample2


title: DSP-1001660002550-B-C12_R5_C6

description: Library name: DSP-1001660002550-B-C12


title: SAM24380132_VG_WT_4

description: 10x Genomics

value: wildtype


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample02

description:
Library name: HPC_Sal_PLX_F_02
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_02


title: control,rep 1

description: Library name: Sample1


title: DSP-1001660002550-B-C11_R5_C6

description: Library name: DSP-1001660002550-B-C11


title: Hippocampus, Saline, Plexxikon-treated, Female, Sample01

description:
Library name: HPC_Sal_PLX_F_01
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_F_01


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre+ mouse4

city: Shanghai

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

description: Library name: Sample 8

library_source: genomic

data_processing:
RRBS reads were mapped to the reference mouse genome (mm10) by Bismark (version 0.16.3). DSS V2.30.1 in R was used to detect DMLs. Differentially methylated loci (DMLs) were analyzed based on a Bayesian approach and were summarized as follows: two groups were modeled according to the Bayesian stratification model, and the Wald test was applied to each locus to obtain a p-value for each CpG site. A methylation region was defined as a differently methylated regions (DMR) when it met the following three criteria: 1) the length of this region was at least 50 bp; 2) the region contained no less than three CpG sites; and 3) the proportion of DMLs in this region was no less than 50%. When a DMR showed no less than 50% overlap with one element of the gene, it was defined as a differentially methylated gene (DMG).
Assembly: Mouse mm10
Supplementary files format and content: bedgraph.gz

molecule: genomic DNA

source_name: pancreatic islet

extract_protocol:
Adult mouse pancreatic islets were isolated by collagenase IV (2 mg/ml; Worthington) digestion, separated by density gradient centrifugation, and handpicked under a stereomicroscope. Islets were cultured in a standard RPMI medium supplemented with 10% FBS. After isolation and extraction, each tube contained 200-300 islets; they were digested with 0.25% Trypsin-EDTA, at 37 ℃ for 2 min. Digestion was stopped using RPMI 1640 containing 10% fetal bovine serum (FBS), blowing evenly. It was centrifuged at 1360 rpm for 5 min at 4 ℃. Genomic DNA was isolated from pancreatic islets by AllPrep DNA/RNA Micro Kit.
Briefly, sufficient genomic DNA was digested using the methylation-insensitive restriction enzyme MspI (New England Biolabs, Beverly, MA, USA). The ends of each restriction fragment were filled in and adenosine was added at the 3′-end. Methylated paired-end Illumina adapters were ligated to the ends of the DNA fragments using T4 DNA ligase, and fragments sized 100-200 bp were purified by agarose gel extraction. The purified fragments were treated with sodium bisulfite and then amplified by PCR. The final PCR products were sequenced on HiSeq 2500 (Illumina Inc., San Diego, CA, USA).

value: pancreatic islet

value: male

tag: age

value: 8 weeks


title: SAM24380130_VG_WT_2

description: 10x Genomics


title: DSP-1001660002550-B-C10_R5_C6

description: Library name: DSP-1001660002550-B-C10


title: Hippocampus, Saline, Control, Male, Sample06

description:
Library name: HPC_Sal_CTRL_M_06
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_06

value: Control

value: hippocampus


title: SAM24380131_VG_WT_3

description: 10x Genomics


title: SAM24380135_VG_KO_3

description: 10x Genomics


title: DSP-1001660002550-B-C09_R5_C6

description: Library name: DSP-1001660002550-B-C09


title: SAM24380129_VG_WT_1

description: 10x Genomics


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre+ mouse2

description: Library name: Sample 6


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre+ mouse3

description: Library name: Sample 7


title: Hippocampus, Saline, Control, Male, Sample05

description:
Library name: HPC_Sal_CTRL_M_05
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_05

value: Saline injection


title: DSP-1001660002550-B-C08_R5_C5

description: Library name: DSP-1001660002550-B-C08

value: Lung Cancer


title: Hippocampus, Saline, Control, Male, Sample04

description:
Library name: HPC_Sal_CTRL_M_04
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_04


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre+ mouse1

description: Library name: Sample 5


title: Hippocampus, Saline, Plexxikon-treated, Male, Sample03

description:
Library name: HPC_Sal_PLX_M_03
Column name in normalized_counts_all_samples.txt: HPC_Sal_PLX_M_03

value: Plexxikon


title: DSP-1001660002550-B-C07_R5_C5

description: Library name: DSP-1001660002550-B-C07

value: immunotherapy


title: ko_Nodose_rep4

description:
Name: SAM24343540
genotype: ko
tissue: Nodose

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality and ribosomal RNA contamination. The remaining reads were then aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool (Wu and Nacu, 2010). Alignments were produced using the following GSNAP parameters: ‘-M 2 n 10 -B 2 -i 1 N 1 w 200000 -E 1 –pairmax-rna = 200000 –clip-overlap’. These steps, and the downstream processing of the resulting alignments to obtain read counts and normalized Reads Per Kilobase Million (nRPKMs) per gene (over all exons of RefSeq gene models), are implemented in the Bioconductor package, HTSeqGenie (v 3.12.0) (Pau and Reeder, 2014). Only uniquely mapped reads were used for further analysis.
Genome_build: GRCh38

source_name: ko, SAM24343540, Nodose

extract_protocol: Low input bulk RNAseq was performed using VG and thoracic DRG from individual animals (n=5). VG and DRG were transferred into an 1.5ml tube containing one Tungsten Carbide bead (3mm, Qiagen, #69997) and 1 mL of Qiazol lysis reagent (Qiagen, #79306) and homogenized for 2 x 3 minutes, at a frequency of 28/s @ 4°C (Tissue Lyser II, Qiagen). After this step the samples were adjusted to RT for 5 minutes and processed using the RNeasy Lipid Tissue Mini Kit (Qiagen) as described in the user manual. After elution of the RNA in 12 μl RNase free water, the RNA concentration was determined via Nanodrop and up to 100 ng was used as an input material for library preparation using the Clontech Ultra Low kit (Clontech).

value: TMC3 KO

value: Nodose

tag: sample


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre- mouse4

description: Library name: Sample 4


title: ko_Nodose_rep3

description:
Name: SAM24343539
genotype: ko
tissue: Nodose

source_name: ko, SAM24343539, Nodose


title: DSP-1001660002550-B-C06_R5_C5

description: Library name: DSP-1001660002550-B-C06


title: Hippocampus, Saline, Control, Male, Sample02

description:
Library name: HPC_Sal_CTRL_M_02
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_02

value: Male


title: Hippocampus, Saline, Control, Male, Sample03

description:
Library name: HPC_Sal_CTRL_M_03
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_03


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre- mouse3

description: Library name: Sample 3


title: DSP-1001660002550-B-C05_R5_C5

description: Library name: DSP-1001660002550-B-C05


title: Hippocampus, Saline, Control, Male, Sample01

description:
Library name: HPC_Sal_CTRL_M_01
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_M_01


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre- mouse2

description: Library name: Sample 2


title: DSP-1001660002550-B-C04_R5_C4

description: Library name: DSP-1001660002550-B-C04


title: ko_Nodose_rep1

description:
Name: SAM24343537
genotype: ko
tissue: Nodose

source_name: ko, SAM24343537, Nodose


title: Hippocampus, Saline, Control, Female, Sample06

description:
Library name: HPC_Sal_CTRL_F_06
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_06


title: ko_Nodose_rep2

description:
Name: SAM24343538
genotype: ko
tissue: Nodose

source_name: ko, SAM24343538, Nodose


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre- mouse1

description: Library name: Sample 1


title: DSP-1001660002550-B-C03_R5_C4

description: Library name: DSP-1001660002550-B-C03


title: wt_Nodose_rep5

description:
Name: SAM24343536
genotype: wt
tissue: Nodose

source_name: wt, SAM24343536, Nodose

value: wt


title: DSP-1001660002550-B-C02_R5_C4

description: Library name: DSP-1001660002550-B-C02


title: wt_Nodose_rep4

description:
Name: SAM24343535
genotype: wt
tissue: Nodose

source_name: wt, SAM24343535, Nodose


title: Hippocampus, Saline, Control, Female, Sample04

description:
Library name: HPC_Sal_CTRL_F_04
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_04


title: ko_Nodose_rep5

description:
Name: SAM24343541
genotype: ko
tissue: Nodose

source_name: ko, SAM24343541, Nodose


title: wt_Nodose_rep3

description:
Name: SAM24343534
genotype: wt
tissue: Nodose

source_name: wt, SAM24343534, Nodose


title: DSP-1001660002550-B-C01_R5_C4

description: Library name: DSP-1001660002550-B-C01


title: mouse intestine organoid, RNase5 knockdown, rep3

city: HangZhou

first: xin

last: xu

state: Zhejiang

address: No. 866, Tang Road, Yuhang District, Zhejiang University, Zijingang Campus, School of Medicine.

institute: Zhejiang university

description:
Library name: KO-3
Table6_tiRNA results.xlsx

data_processing:
For tiRNA analysis, reads were annotated using MINTmap software on GitHub and further processed using the R package BioData. To identify differentially expressed tiRNAs in crypts from WT and RNase5-/- mice, each fragment sequence was grouped according to tRNA isoacceptor, origin and length according to MINTmap annotation. The statistical significance of differences was conveniently estimated by Student’s t test. tiRNAs with fold changes ≥1.5 and P values ≤0.05 were selected as the significantly differentially expressed tiRNAs.
Assembly: GRCm38-mm10
Supplementary files format and content: the processed data file was a xlsx file. It contains the RPM of each tiRNA and log2FC, pvalue also in it

source_name: intestine

extract_protocol:
the crypt lysates were triturated by passing them through a 26-G needle ten times, and nuclei and debris were removed by centrifugation at 18,928 × g for 10 min. The supernatant was lysed using Trizol, and the RNA was isolated.Total RNA was diluted in Novex TBE-Urea sample buffer, heated to 65°C for 5 min and cooled briefly to room temperature prior to loading. A 15% polyacrylamide TBE-urea gel was prerun for 30 min, and samples were electrophoresed to the bottom of the gel at 100 V in 0.5× TBE running buffer. Following electrophoresis, the gel was equilibrated in 0.5× TBE for 5 min and stained with SYBR Gold solution diluted in 20 mL of 0.5× TBE buffer for 20 min with agitation, according to the manufacturer’s instruction. Gels were imaged on a Gel Doc XR System (Bio-Rad) using UV illumination.
Small RNAs with 10-50 nt fragment sizes were isolated by size excision on a 15% polyacrylamide TBE-urea gel. Before library preparation, the following treatments were carried out: 3′-aminoacyl (charged) deacylation to 3′-OH and 3′-cP (2′,3′-cyclic phosphate) removal to 3′-OH for 3′ adaptor ligation, 5′-OH (hydroxyl group) phosphorylation to 5′-P for 5′-adaptor ligation, and m1A and m3C demethylation for efficient reverse transcription. The small RNA library was prepared with the NEBNext Small RNA Library Prep Set for Illumina. The libraries were qualified and absolutely quantified using an Agilent BioAnalyzer 2100. For standard small RNA sequencing on an Illumina HiSeq 2500 instrument, the sequencing type was a 50-bp single read.

value: intestine

value: organoid

value: RNase5 knockdown


title: Hippocampus, Saline, Control, Female, Sample03

description:
Library name: HPC_Sal_CTRL_F_03
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_03

value: Female


title: Hippocampus, Saline, Control, Female, Sample02

description:
Library name: HPC_Sal_CTRL_F_02
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_02


title: DSP-1001660002550-B-B12_R5_C3

description: Library name: DSP-1001660002550-B-B12

source_name: Lung Cancer


title: wt_Nodose_rep2

description:
Name: SAM24343533
genotype: wt
tissue: Nodose

source_name: wt, SAM24343533, Nodose


title: mouse intestine organoid, RNase5 knockdown, rep1

description:
Library name: KO-1
Table6_tiRNA results.xlsx


title: DSP-1001660002550-B-B11_R5_C3

description: Library name: DSP-1001660002550-B-B11


title: Hippocampus, Saline, Control, Female, Sample01

description:
Library name: HPC_Sal_CTRL_F_01
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_01


title: wt_Nodose_rep1

description:
Name: SAM24343532
genotype: wt
tissue: Nodose

source_name: wt, SAM24343532, Nodose


title: mouse intestine organoid, control, rep3

description:
Library name: WT-3
Table6_tiRNA results.xlsx

value: WT


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample06

description:
Library name: HPC_MIA_PLX_M_06
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_06

value: Maternal Immune Activation


title: mouse intestine organoid, control, rep2

description:
Library name: WT-2
Table6_tiRNA results.xlsx


title: DSP-1001660002550-B-B09_R5_C3

description: Library name: DSP-1001660002550-B-B09


title: ko_Lumbar_rep4

description:
Name: SAM24343530
genotype: ko
tissue: Lumbar

source_name: ko, SAM24343530, Lumbar

value: Lumbar


title: Hippocampus, Saline, Control, Female, Sample05

description:
Library name: HPC_Sal_CTRL_F_05
Column name in normalized_counts_all_samples.txt: HPC_Sal_CTRL_F_05

value: Control


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample05

description:
Library name: HPC_MIA_PLX_M_05
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_05

value: hippocampus


title: DSP-1001660002550-B-B08_R5_C2

description: Library name: DSP-1001660002550-B-B08


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample04

description:
Library name: HPC_MIA_PLX_M_04
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_04


title: mouse intestine organoid, control, rep1

description:
Library name: WT-1
Table6_tiRNA results.xlsx


title: HSD_10

city: Bonn

first: Clivia

last: Lisowski

address: Venusberg-Campus 1

institute: Universität Bonn

data_processing:
FASTQ files were aligned to the mm10 mouse reference genome with StarAligner. Further computational 3' mRNA-seq analysis was performed with the Bioconductor/R computing environment (voom method_ limma package )
Assembly: FASTQ files were aligned to the mm10 mouse reference genome with StarAligner.
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: melanoma

extract_protocol:
RNA was isolated with Macherey-Nagel Nucleo Spin RNA, LOT 1708/001
RNA libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (Lexogen) according to the manufacturer's protocol.
Standard 3´RNA sequencing (50cycles)

value: melanoma

value: HSD


title: HSD_9


title: ko_Lumbar_rep3

description:
Name: SAM24343529
genotype: ko
tissue: Lumbar

source_name: ko, SAM24343529, Lumbar


title: DSP-1001660002550-B-B07_R5_C2

description: Library name: DSP-1001660002550-B-B07

value: Lung Cancer


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample03

description:
Library name: HPC_MIA_PLX_M_03
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_03

source_name: hippocampus

value: Plexxikon


title: HSD_8


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample02

description:
Library name: HPC_MIA_PLX_M_02
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_02


title: mouse intestine organoid, RNase5 knockdown, rep2

description:
Library name: KO-2
Table6_tiRNA results.xlsx


title: HSD_7


title: ko_Lumbar_rep1

description:
Name: SAM24343527
genotype: ko
tissue: Lumbar

source_name: ko, SAM24343527, Lumbar

value: TMC3 KO


title: DSP-1001660002550-B-B05_R5_C2

description: Library name: DSP-1001660002550-B-B05

value: immunotherapy


title: wt_Lumbar_rep5

description:
Name: SAM24343526
genotype: wt
tissue: Lumbar

source_name: wt, SAM24343526, Lumbar


title: DSP-1001660002550-B-B06_R5_C2

description: Library name: DSP-1001660002550-B-B06


title: Hippocampus, MIA, Plexxikon-treated, Male, Sample01

description:
Library name: HPC_MIA_PLX_M_01
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_M_01

value: Male


title: DSP-1001660002550-B-B10_R5_C3

description: Library name: DSP-1001660002550-B-B10


title: ko_Lumbar_rep5

description:
Name: SAM24343531
genotype: ko
tissue: Lumbar

source_name: ko, SAM24343531, Lumbar


title: DSP-1001660002550-B-B04_R5_C1

description: Library name: DSP-1001660002550-B-B04


title: HSD_6


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample06

description:
Library name: HPC_MIA_PLX_F_06
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_06


title: wt_Lumbar_rep4

description:
Name: SAM24343525
genotype: wt
tissue: Lumbar

source_name: wt, SAM24343525, Lumbar

value: wt


title: ko_Lumbar_rep2

description:
Name: SAM24343528
genotype: ko
tissue: Lumbar

source_name: ko, SAM24343528, Lumbar


title: DSP-1001660002550-B-B03_R5_C1

description: Library name: DSP-1001660002550-B-B03


title: NSD_5

value: NSD


title: wt_Lumbar_rep3

description:
Name: SAM24343524
genotype: wt
tissue: Lumbar

source_name: wt, SAM24343524, Lumbar


title: DSP-1001660002550-B-B02_R5_C1

description: Library name: DSP-1001660002550-B-B02


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample05

description:
Library name: HPC_MIA_PLX_F_05
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_05


title: wt_Lumbar_rep2

description:
Name: SAM24343523
genotype: wt
tissue: Lumbar

source_name: wt, SAM24343523, Lumbar


title: NSD_4


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample04

description:
Library name: HPC_MIA_PLX_F_04
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_04


title: NSD_3


title: wt_Lumbar_rep1

description:
Name: SAM24343522
genotype: wt
tissue: Lumbar

source_name: wt, SAM24343522, Lumbar


title: DSP-1001660002550-B-B01_R5_C1

description: Library name: DSP-1001660002550-B-B01


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample03

description:
Library name: HPC_MIA_PLX_F_03
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_03


title: DSP-1001660002550-B-A12_R4_C8

description: Library name: DSP-1001660002550-B-A12


title: ko_Thoracic_rep5

description:
Name: SAM24343521
genotype: ko
tissue: Thoracic

source_name: ko, SAM24343521, Thoracic

value: Thoracic


title: NSD_2


title: NSD_1


title: DSP-1001660002550-B-A11_R4_C8

description: Library name: DSP-1001660002550-B-A11


title: ko_Thoracic_rep4

description:
Name: SAM24343520
genotype: ko
tissue: Thoracic

source_name: ko, SAM24343520, Thoracic


title: DSP-1001660002550-B-A10_R4_C8

description: Library name: DSP-1001660002550-B-A10

source_name: Lung Cancer


title: L929 cells HT-DNA+AOA+Asp-3

first: YH

last: Liao

address: Dongan road 131

institute: Fudan university

data_processing:
CLC Genomics Work bench v11.0.1
Assembly: Majorbio
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Mus musculus

growth_protocol: L929 cells were grown in DMEM (Meilunbio) containing 10% FBS (Gibco), penicillin (100 U/ml) and streptomycin (100 g/ml). All cells were maintained at 37 °C and 5% CO2 and were tested for mycoplasma. Cells were seeded in 6-well plate and HT-DNA was transfected into cells using Lipofectamine 2000 (Thermo Fisher) at a concentration of 0.5/μg ml.

extract_protocol:
RNA was harvested using TRIzol.
Following manufacture's protocal

value: Mus musculus

value: Mouse fibroblast

value: HT-DNA+AOA+Asp


title: ko_Thoracic_rep3

description:
Name: SAM24343519
genotype: ko
tissue: Thoracic

source_name: ko, SAM24343519, Thoracic


title: L929 cells HT-DNA+AOA+Asp-2

value: WT


title: Hippocampus, MIA, Control, Male, Sample06

description:
Library name: HPC_MIA_CTRL_M_06
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_M_06

value: Maternal Immune Activation


title: ko_Thoracic_rep2

description:
Name: SAM24343518
genotype: ko
tissue: Thoracic

source_name: ko, SAM24343518, Thoracic


title: L929 cells HT-DNA+AOA+Asp-1


title: DSP-1001660002550-B-A09_R4_C8

description: Library name: DSP-1001660002550-B-A09


title: DSP-1001660002550-B-A08_R4_C7

description: Library name: DSP-1001660002550-B-A08


title: Hippocampus, MIA, Control, Male, Sample04

description:
Library name: HPC_MIA_CTRL_M_04
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_M_04

value: Control


title: ko_Thoracic_rep1

description:
Name: SAM24343517
genotype: ko
tissue: Thoracic

source_name: ko, SAM24343517, Thoracic


title: DSP-1001660002550-B-A07_R4_C7

description: Library name: DSP-1001660002550-B-A07


title: Hippocampus, MIA, Control, Male, Sample03

description:
Library name: HPC_MIA_CTRL_M_03
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_M_03

value: hippocampus


title: L929 cells HT-DNA+AOA-2

value: HT-DNA+AOA


title: Hippocampus, MIA, Control, Male, Sample02

description:
Library name: HPC_MIA_CTRL_M_02
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_M_02


title: L929 cells HT-DNA+AOA-1


title: wt_Thoracic_rep3

description:
Name: SAM24343514
genotype: wt
tissue: Thoracic

source_name: wt, SAM24343514, Thoracic


title: DSP-1001660002550-B-A06_R4_C7

description: Library name: DSP-1001660002550-B-A06


title: Hippocampus, MIA, Control, Female, Sample07

description:
Library name: HPC_MIA_CTRL_F_07
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_07

source_name: hippocampus

value: Female


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample01

description:
Library name: HPC_MIA_PLX_F_01
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_01


title: L929 cells HT-DNA-3

value: HT-DNA


title: wt_Thoracic_rep4

description:
Name: SAM24343515
genotype: wt
tissue: Thoracic

source_name: wt, SAM24343515, Thoracic


title: DSP-1001660002550-B-A04_R4_C6

description: Library name: DSP-1001660002550-B-A04

value: Lung Cancer


title: wt_Thoracic_rep2

description:
Name: SAM24343513
genotype: wt
tissue: Thoracic

source_name: wt, SAM24343513, Thoracic


title: Hippocampus, MIA, Control, Male, Sample05

description:
Library name: HPC_MIA_CTRL_M_05
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_M_05


title: L929 cells HT-DNA-1


title: wt_Thoracic_rep1

description:
Name: SAM24343512
genotype: wt
tissue: Thoracic

source_name: wt, SAM24343512, Thoracic


title: DSP-1001660002550-B-A02_R4_C6

description: Library name: DSP-1001660002550-B-A02


title: Hippocampus, MIA, Control, Female, Sample05

description:
Library name: HPC_MIA_CTRL_F_05
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_05


title: 120h_FGF4

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, which deconvolved reads to their cell of origin using the UMI tags, aligned these to the mm10 transcriptome using STAR (v.2.5.1b) and reported cell-specific gene expression count estimates.
All subsequent analyses were performed in R v.3.6.1 using the Seurat (v3) package.
GRCm38 - release 89
CellRanger output: Unfiltered feature-barcode matrix (matrix.mtx.gz)  in the Market Exchange Format (MEX) for sparse matrices.
Assembly: CellRanger output: features.tsv.gz; tab-delimited information of the row indices for the matrix.mtx.gz file
Supplementary files format and content: CellRanger output: barcodes.tsv.gz; tab-delimited information of barcodes (column indices of matrix.mtx.gz)

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were initially grown in 2i LIF media

extract_protocol:
Gastruloids wrere washed twice in PBS (5 min at 1000 RPM) and dissociated to single cells by incubation with TrypLE Express (Gibco) for 10 min at 37C, with pipetting at 5min. Cells were washed with PBS (5 min at 1000 RPM) and passed through 70µm cell strainers and re-suspended in 1% BSA in PBS.
Single cell suspensions were assessed for cell number and viability using an EVE automated cell counter (NanoEnTech) with trypan blue staining.  Approximately 10,000 cells were processed for single cell mRNA-Seq using the 10x Chromium 3’ mRNA-Seq kit version 3.1 according to the manufacturer’s instructions.  Sequencing was carried out on the HiSeq 4000 (Illumina) with a read configuration conforming to the required sequencing parameters for single indexed 10x 3’ mRNA-Seq libraries.
10X_3prime_mRNA

treatment_protocol: Mouse embryonic stem cells grown in 2i LIF media were harvested and re-suspended in N2B27media containing FGF2 (100ng/ml) or FGF4 (100ng/ml). 300 cells were plated in 40ul volume per well of low-adherence round-bottom 96-well plate and incubated at 37 °C for 48h and subsequently stimulated for 24h with 150ul of 3uM CHIR in N2B27. Thereafter media was replaced with N2B27 every 24h. Samples were collected at 0h, 48h, 60h, 72 and 120h.

value: Embryonic stem cells

tag: time


title: Hippocampus, MIA, Control, Female, Sample06

description:
Library name: HPC_MIA_CTRL_F_06
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_06


title: DSP-1001660002550-B-A03_R4_C6

description: Library name: DSP-1001660002550-B-A03

value: immunotherapy


title: L929 cells HT-DNA+AOA-3


title: wt_Thoracic_rep5

description:
Name: SAM24343516
genotype: wt
tissue: Thoracic

source_name: wt, SAM24343516, Thoracic


title: Hippocampus, MIA, Control, Female, Sample04

description:
Library name: HPC_MIA_CTRL_F_04
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_04


title: L929 cells AOA+Asp-3

value: AOA+Asp


title: 120h_FGF2


title: DSP-1001660002549-A-H12_R4_C5

description: Library name: DSP-1001660002549-A-H12


title: Hippocampus, MIA, Control, Female, Sample03

description:
Library name: HPC_MIA_CTRL_F_03
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_03


title: DSP-1001660002549-A-H11_R4_C5

description: Library name: DSP-1001660002549-A-H11


title: L929 cells AOA+Asp-2


title: DSP-1001660002550-B-A05_R4_C7

description: Library name: DSP-1001660002550-B-A05


title: Hippocampus, MIA, Plexxikon-treated, Female, Sample02

description:
Library name: HPC_MIA_PLX_F_02
Column name in normalized_counts_all_samples.txt: HPC_MIA_PLX_F_02

value: Plexxikon


title: 72h_FGF4


title: Hippocampus, MIA, Control, Female, Sample02

description:
Library name: HPC_MIA_CTRL_F_02
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_02


title: L929 cells AOA+Asp-1


title: Hippocampus, MIA, Control, Female, Sample01

description:
Library name: HPC_MIA_CTRL_F_01
Column name in normalized_counts_all_samples.txt: HPC_MIA_CTRL_F_01


title: DSP-1001660002549-A-H10_R4_C5

description: Library name: DSP-1001660002549-A-H10


title: 72h_FGF2


title: L929 cells AOA-3

value: AOA


title: L929 cells HT-DNA-2


title: DSP-1001660002549-A-H09_R4_C5

description: Library name: DSP-1001660002549-A-H09


title: L929 cells AOA-2


title: 60h_FGF4


title: DSP-1001660002549-A-H08_R4_C4

description: Library name: DSP-1001660002549-A-H08


title: 60h_FGF2


title: L929 cells AOA-1


title: IL-36γ armored CAR T treatment-1

city: Buffalo

first: Jianmin

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: EXP6-D6-5
10x Genomics

data_processing:
Raw sequencing data, mapping results (BAM files), and quantification matrices were generated using Cell Ranger software (10x genomics) with mouse mm10 genome and GENCODE annotation database. Filtered gene-barcode matrices, containing barcodes with Unique Molecular Identifier (UMI) counts that passed the cell detection algorithm were used for further analysis.
Assembly: mm10
Supplementary files format and content: Tab seperated value and matrix files

source_name: Tumor

extract_protocol:
Tumors were dissociated using the Mouse Tumor Dissociation Kit and a gentleMACS™ Octo Dissociator with Heaters. The resulting cell suspensions were filtered through 70-μm strainers and stained with anti-CD45 antibodies and the LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit.
Amplified cDNA is separated into full-length and Feature Barcode fractions using SPRISelect beads (Beckman Coulter).  The full-length amplified cDNA was used to generate libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  Feature barcode derived cDNA was PCR amplified to incorporate Illumina adapter sequences and unique sample indexes.  The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies) and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina.  They were then pooled, denatured, and diluted to 300 pM with 1% PhiX control library added.  The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: Tumor

value: N2N1G cell

value: SCLC

value: IL-36γ armored CAR T


title: DSP-1001660002549-A-H07_R4_C4

description: Library name: DSP-1001660002549-A-H07


title: L929 cells mock-3

value: Mus musculus

value: Mouse fibroblast

value: WT

value: DMSO


title: 48h_FGF4


title: IL-18 armored CAR T treatment-1

description:
Library name: EXP6-D8-3
10x Genomics

value: IL-18 armored CART


title: 48h_FGF2


title: DSP-1001660002549-A-H06_R4_C4

description: Library name: DSP-1001660002549-A-H06


title: L929 cells mock-2


title: 0h_none


title: L929 cells mock-1


title: unarmored CAR T treatment-2

description:
Library name: EXP6-D-2
10x Genomics

value: unarmored CAR T


title: DSP-1001660002549-A-H04_R4_C3

description: Library name: DSP-1001660002549-A-H04


title: Gastroluid_60h_CHIR_input replicate 3

data_processing:
Samples were sequenced on an Illumina HiSeq4000 generating 76bp single ended read with about 40-50 million reads per sample.  ChIP-seq reads were processed using the nf-core/chipseq pipeline (https://nf-co.re/chipseq) version 1.1.0 aligning reads against the mouse genome (GRCm38).
The nf-core/chipseq pipeline was run with the parameter --narrowpeak and –min_reps_consensus 2
Assembly: GRCm38
Supplementary files format and content: bed file of consensus peaks called using MACS
Supplementary files format and content: Tab-delimited file with annotation of consensus peaks

extract_protocol:
Mouse embryonic stem cells grown in 2i LIF media were harvested and re-suspended in N2B27media containing FGF2 (100ng/ml). 300 cells were plated in 40ul volume per well of low-adherence round-bottom 96-well plate and incubated at 37 °C for 48h and subsequently stimulated with 150ul of 3uM CHIR in N2B27. Samples were collected at 48h and 60h as well as 0h untreated control.
DNA fragment distribution was assessed via High Sensitivity D1000 ScreenTape on the TapeStaton (Agilent) and quantity assessed using the QuantiFluor dsDNA System (Promega) measured on the GloMax system (Promega).  DNA was normalised to 0.1 ng and converted into Illumina compatible libraries using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) according to manufacturer’s instructions.  Sequencing was performed on the HiSeq 4000 (Illumina) using single ended reads of at least 75 bp.

treatment_protocol: Mouse ES cells were routinely grown in 2iLIF before gastruloid formation


title: DSP-1001660013460-E-H11

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: FFPE GeoMx DSP profiling

data_processing:
Geomx sequencing data was analyzed with the standR (version 1.5.3), edge R (version 3.40.2), and limma (version 3.54.2) packages.
Assembly: mm10
Supplementary files format and content: .dcc files
Library strategy: GEOMx Spatial Transcriptomics

source_name: Spleen

extract_protocol:
Formalin-fixed paraffin embedded (FFPE) spleen tissue from two cohorts of WT mice was used to construct a tissue-micro array (TMA)
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep user guide (MAN-10153-01).

value: Spleen

value: Young


title: IL-36γ armored CAR T treatment-2

description:
Library name: EXP6-D6-6
10x Genomics


title: Gastroluid_60h_CHIR_input replicate 2

value: Embryonic stem cells


title: DSP-1001660002549-A-H03_R4_C3

description: Library name: DSP-1001660002549-A-H03

value: Lung Cancer

value: immunotherapy


title: Mouse liver treated with indole sample G14

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: Library name: G14

data_processing:
Adapters were trimmed using Novogene’s bioinformatics pipeline and  alignment were performed using HISAT2 and Mouse genome GRCm38 Ensembl version 102.
Uniquely mapped reads were taken forward for gene-level counts and differential gene expression analysis using DESeq2
Assembly: GRCm38
Supplementary files format and content: Raw count table in tab-delimited format

molecule: polyA RNA

source_name: Liver

extract_protocol:
RNA was purified by using the RNeasy® Plus Mini kit (Qiagen, Hildon, Germany) according to the manufacturer’s instructions.
Strand-specific mRNA (polyA) libraries were constructed at Novogene UK Ltd

treatment_protocol: Mice received an oral gavage of 20mg/kg indole or vehicle control (water) twice daily for seven consecutive days

value: Liver

value: TALLYHO

value: indole


title: DSP-1001660013460-E-H03

description: FFPE GeoMx DSP profiling


title: Gastroluid_60h_CHIR_input replicate 1


title: Gastroluid_60h_CHIR replicate 3


title: DSP-1001660002549-A-H01_R4_C3

description: Library name: DSP-1001660002549-A-H01

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads


title: DSP-1001660013460-E-H10

description: FFPE GeoMx DSP profiling


title: Mouse liver treated with indole sample G12

description: Library name: G12


title: IL-18 armored CAR T treatment-2

description:
Library name: EXP6-D8-4
10x Genomics

value: Tumor

value: N2N1G cell


title: DSP-1001660002549-A-G12_R4_C2

description: Library name: DSP-1001660002549-A-G12


title: DSP-1001660013460-E-H02

description: FFPE GeoMx DSP profiling


title: Mouse liver treated with water sample G11

description: Library name: G11

value: water


title: Gastroluid_60h_CHIR replicate 1


title: DSP-1001660002549-A-G11_R4_C2

description: Library name: DSP-1001660002549-A-G11


title: DSP-1001660002549-A-H05_R4_C4

description: Library name: DSP-1001660002549-A-H05


title: Gastroluid_60h_CHIR replicate 2


title: DSP-1001660013460-E-G11

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-G10_R4_C2

description: Library name: DSP-1001660002549-A-G10


title: Mouse liver treated with water sample G13

description: Library name: G13


title: Mouse liver treated with water sample G9

description: Library name: G9


title: DSP-1001660002549-A-G09_R4_C2

description: Library name: DSP-1001660002549-A-G09


title: DSP-1001660002549-A-H02_R4_C3

description: Library name: DSP-1001660002549-A-H02


title: DSP-1001660002549-A-G08_R4_C1

description: Library name: DSP-1001660002549-A-G08


title: Gastroluid_48h_input replicate 2


title: unarmored CAR T treatment-1

description:
Library name: EXP6-D-1
10x Genomics

value: SCLC


title: Gastroluid_48h_input replicate 3


title: DSP-1001660013460-E-G09

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-G10

description: FFPE GeoMx DSP profiling


title: Gastroluid_48h_input replicate 1


title: DSP-1001660002549-A-G07_R4_C1

description: Library name: DSP-1001660002549-A-G07


title: DSP-1001660013460-E-H01

description: FFPE GeoMx DSP profiling


title: Mouse liver treated with indole sample G8

description: Library name: G8


title: Mouse liver treated with indole sample G7

description: Library name: G7


title: Gastroluid_48h replicate 3


title: DSP-1001660013460-E-G08

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-G06_R4_C1

description: Library name: DSP-1001660002549-A-G06


title: Mouse liver treated with water sample G10

description: Library name: G10


title: DSP-1001660013460-E-G12

description: FFPE GeoMx DSP profiling


title: Gastroluid_48h replicate 2


title: Mouse liver treated with indole sample G5

description: Library name: G5


title: DSP-1001660013460-E-G07

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-G05_R4_C1

description: Library name: DSP-1001660002549-A-G05


title: Mouse liver treated with water sample G4

description: Library name: G4


title: Gastroluid_48h replicate 1


title: DSP-1001660013460-E-G06

description: FFPE GeoMx DSP profiling


title: Mouse liver treated with indole sample G3

description: Library name: G3


title: 2iLIF_0h_input replicate 3


title: DSP-1001660002549-A-G04_R3_C8

description: Library name: DSP-1001660002549-A-G04


title: DSP-1001660013460-E-G05

description: FFPE GeoMx DSP profiling


title: 2iLIF_0h_input replicate 2


title: DSP-1001660002549-A-G03_R3_C8

description: Library name: DSP-1001660002549-A-G03


title: DSP-1001660002549-A-G02_R3_C8

description: Library name: DSP-1001660002549-A-G02


title: Mouse liver treated with indole sample G2

description: Library name: G2


title: DSP-1001660013460-E-G02

description: FFPE GeoMx DSP profiling


title: Mouse liver treated with water sample G1

description: Library name: G1


title: uPA-SCID mouse, TAF treated

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences

description: Library name: SAM007170_LIB007613

data_processing:
Illumina Fastq files were aligned to 10x Visium human transcriptome probe set v2.0_GRCh38-2020-A using Spaceranger-3.0.1
Count data were merged in R using the Seurat package and normalized using SCTransform
Cell-type estimation was performed using RCTD from spacexr version 2.2.1
Assembly: hg38
Supplementary files format and content: compressed Seurat R data objects
Library strategy: Spatial Transcriptomics

extract_protocol:
10X Visium FFPE Kit
FFPE sections of 5µm thickness were prepared using a Leica RM2255 microtome and placed on Superfrost Plus glass slides (Epredia, Cat#22-042-941), as per guidance outlined in 10X Genomics Visium CytAssist Tissue preparation guide (CG000518). Slides were subjected to H&E staining as outlined in guidance provided by 10X Genomics (CG000518). Following H&E staining, slides were imaged using Aperio AT2 DX scanner (Leica Biosystems, Cat#23AT2100) at 40X magnification. Following imaging, coverslips were removed, and tissues were decrosslinked. Library construction was conducted as described in 10X Genomics, CG000495. Post library construction QC was performed on the 2100 Bioanalyzer Instrument (Agilent) with the High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626). Library concentrations were measured using the Qubit dsDNA High Sensitive Assay Kit (Invitrogen, Cat#Q32854). Sequencing was performed on the Illumina NovaSeq6000, following the guidance outlined in the 10X Genomics Visium CytAssist Spatial Gene Expression User Guide (CG000495). Sequencing was performed to meet a targeted sequencing depth of 50,000 read pairs per tissue-covered spot.


title: 2iLIF 0h replicate 2

value: 2iLIF 0h


title: Mouse liver treated with water sample G6

description: Library name: G6


title: DSP-1001660013460-E-G03

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-F12_R3_C7

description: Library name: DSP-1001660002549-A-F12


title: 2iLIF 0h replicate 3


title: DSP-1001660013460-E-G01

description: FFPE GeoMx DSP profiling

value: Old


title: 2iLIF 0h replicate 1


title: DSP-1001660002549-A-F11_R3_C7

description: Library name: DSP-1001660002549-A-F11


title: DSP-1001660013460-E-F12

description: FFPE GeoMx DSP profiling


title: DNT cells from EGR2fl/fl Cre+/- B6/lpr mice, rep2

city: Blacksburg

first: Zhuang

state: VA

address: 1739 Autumn Splendor Way

institute: VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY

description: Library name: DNT-EK2

data_processing:
Remove reads containing N > 10% and Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Further data processed by Seurat percentage of mitochondrial genes, nCount and nFeature RNA in R.
Assembly: GRCM39
Supplementary files format and content: RDS files were uploaded, each contains the processed data file of DNT cells samples.

source_name: spleen

extract_protocol:
Splenocytes from B6/lpr mice were prepared following a standard lab protocol. DNT cells were isolated by flow sorting of CD3+CD4-CD8- cells.
Libraries are prepared following Parse Biosciences protocol.

value: spleen

value: EGR2fl/fl Cre+/- (EK)


title: DSP-1001660002549-A-F10_R3_C7

first: Thazin

address: 310 Cedar Street

institute: Yale University

description: Library name: DSP-1001660002549-A-F10


title: DSP-1001660013460-E-G04

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-F09_R3_C7

description: Library name: DSP-1001660002549-A-F09


title: DNT cells from EGR2fl/fl Cre+/- B6/lpr mice, rep1

description: Library name: DNT-EK1


title: 2iLIF_0h_input replicate 1


title: DSP-1001660002549-A-F08_R3_C6

description: Library name: DSP-1001660002549-A-F08


title: DSP-1001660002549-A-G01_R3_C8

description: Library name: DSP-1001660002549-A-G01


title: DSP-1001660013460-E-F10

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-F09

description: FFPE GeoMx DSP profiling


title: DNT cells from EGR2fl/fl Cre-/- B6/lpr mice, rep1

description: Library name: DNT-EF1

value: EGR2fl/fl Cre-/- (EF)


title: DSP-1001660002549-A-F07_R3_C6

description: Library name: DSP-1001660002549-A-F07


title: DSP-1001660013460-E-F08

description: FFPE GeoMx DSP profiling

value: Spleen


title: DSP-1001660002549-A-F06_R3_C6

description: Library name: DSP-1001660002549-A-F06


title: Brain (hippocampus)

first: Kimberle

last: Shen

address: 1 Dna way

description:
Library name: Brain (hippocampus)
10X Genomics

data_processing: FASTQ files from 10X libraries were processed using Cell Ranger (10x Genomics) for alignment to the mouse reference genome (GRCm38). Filtered count matrices were analysed using the Seurat package (version 5.3.0) in R (version 4.3.1).

source_name: brain

extract_protocol:
Dissociation of brain tissue was done following manufacturer’s instructions with the Neural Dissociation Kit (Miltenyi Biotec).
Libraries from dissociated single cells were generated using Chromium Next GEM Single Cell 3’ Reagent Kits v3.2 (Dual Index) (10X Genomics). Cell numbers were counted by FACS and 8,000 cells per mouse were pooled after hashing, with a total of 32,000 cells used to generate libraries. Libraries were generated according to the manufacturer’s instructions (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for Cell Surface Protein). Feature barcoding was incorporated as BioLegend TotalSeq antibodies were used for cell hashing, where hashtag oligonucleotide (HTO) barcodes were added. Final libraries had a fragment length of 400–450 bp, and were sequenced on an Illumina NovaSeq 6000 using paired-end 150 bp (PE150) reads.

value: brain

value: WT and KO

value: Basal and LPS


title: uPA-SCID mouse, vehicle treated

description: Library name: SAM009166_LIB009656


title: mouse skin, HdR3, imiquimod treatment day1

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

country: Japan

institute: Kyoto University

description: Library name: HdR3

data_processing:
Sequenced reads were quantified using Genomon (version .2.63, genomon: http://genomon.hgc.jp/exome/index.html) against the Mus musculus transcriptome (GRCm38).
Assembly: GRCm38
Supplementary files format and content: The comma-separated CSV file contains the raw counts for each sample.

source_name: Skin

extract_protocol:
Total RNA was isolated from the ear skin with TRIzol reagent (Invitrogen, Grand Island, NY) and RNeasy mini kits (Qiagen, Hilden, Germany.
RNA-sequencing libraries were generated using NEBNext Ultra II RNA Library kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions and sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA).

treatment_protocol: Mice ears were treated topically with 10 mg of an IMQ-containing cream (5%; Beselna; Mochida Pharmaceutical, Tokyo, Japan).

value: Skin

value: HdR

value: Imiqimod day1


title: DSP-1001660013460-E-F07

description: FFPE GeoMx DSP profiling

value: Young


title: leaf_Col-0_6d-Amb_D

first: Sheng Yang

last: He

address: 124 Science Drive

institute: Duke University

description: Library name: leaf_Col-0_6d-Amb_D_S93_

data_processing:
The pool was loaded onto two (2) lanes of an Illumina flow cell and sequencing was performed in a PAIRED end read format using a NovaSeq v1.5, 100 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. A summary of the run output is attached below. Basic QC information about  sequence data is provided by FastQC reports. Reads were mapped with TAIR genome using STAR and DEseq2 was used to identifiy  differntially expressed genes.
Assembly: TAIR v10
Supplementary files format and content: A CSV file contain Read counts.

source_name: Leaf blade

growth_protocol: Arabidopsis  plants were grown in mix soil (1:1:1 SureMix perlite:vermiculite:perilite) in air-circulating growth chambers at 60% relative humidity, a temperature range of 20 °C to 22 °C, and light intensity of 100 µmol m-2 s-1 with a 12-hour light, 12-hour dark photoperiod for 4-4.5 weeks.

extract_protocol:
Total RNA was extracted using QIAGEN  RNeasy Plant mini kit.
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina RNA UD Indexes, following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Arabidopsis plants were placed under 60% or 100% relative humidity at the setuo temperature range of 20 °C to 22 °C, and light intensity of 100 µmol m-2 s-1 with a 12-hour light, 12-hour dark photoperiod.

value: Leaf blade

value: high humidity


title: leaf_fer-4_6d-HH_C

description: Library name: leaf_fer-4_6d-HH_C_S92_


title: leaf_Col-0_6d-HH_D

description: Library name: leaf_Col-0_6d-HH_D_S94_


title: leaf_fer-4_6d-Amb_D

description: Library name: leaf_fer-4_6d-Amb_D_S95_


title: leaf_fer-4_6d-Amb_C

description: Library name: leaf_fer-4_6d-Amb_C_S91_


title: DSP-1001660002549-A-F05_R3_C6

city: New Haven

last: Aung

description: Library name: DSP-1001660002549-A-F05

source_name: Lung Cancer

value: Lung Cancer

value: immunotherapy


title: mouse skin, HdR2, imiquimod treatment day1

description: Library name: HdR2


title: DSP-1001660013460-E-F06

description: FFPE GeoMx DSP profiling


title: leaf_Col-0_6d-HH_C

description: Library name: leaf_Col-0_6d-HH_C_S90_


title: leaf_fer-4_6d-HH_D

description: Library name: leaf_fer-4_6d-HH_D_S96_


title: DSP-1001660002549-A-F04_R3_C5

description: Library name: DSP-1001660002549-A-F04


title: DSP-1001660013460-E-F11

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-F05

description: FFPE GeoMx DSP profiling


title: mouse skin, WT3, imiquimod treatment day1

description: Library name: WT3

value: WT


title: DNT cells from EGR2fl/fl Cre-/- B6/lpr mice, rep2

last: Wang

description: Library name: DNT-EF2


title: leaf_Col-0_6d-Amb_C

description: Library name: leaf_Col-0_6d-Amb_C_S89_


title: DSP-1001660013460-E-F04

description: FFPE GeoMx DSP profiling

value: Old


title: Pet_fer-4_6d-HH_D

description: Library name: Pet_fer-4_6d-HH_D_S88

source_name: Petiole

value: Petiole


title: mouse skin, WT2, imiquimod treatment day1

description: Library name: WT2


title: DSP-1001660002549-A-F02_R3_C5

description: Library name: DSP-1001660002549-A-F02


title: Pet_fer-4_6d-Amb_D

description: Library name: Pet_fer-4_6d-Amb_D_S87


title: DSP-1001660013460-E-F03

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-F01_R3_C5

description: Library name: DSP-1001660002549-A-F01


title: DSP-1001660002549-A-E12_R3_C4

description: Library name: DSP-1001660002549-A-E12


title: Pet_Col-0_6d-HH_D

description: Library name: Pet_Col-0_6d-HH_D_S86


title: mouse skin, WT1, imiquimod treatment day1

description: Library name: WT1


title: DSP-1001660013460-E-F02

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-E11_R3_C4

description: Library name: DSP-1001660002549-A-E11


title: Pen-2_CKO3

city: nanjing

first: Jinxing

last: Hou

state: china

address: Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road

department: Department of Orthopedic Surgery

description: Library name: Sample6

data_processing:
RNA-sequencing was performed on the Illumina NovaSeq 6000 platform, generating > 55 million reads per sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Cortex

growth_protocol: Control and Pen-2 cKO mice at P8

extract_protocol:
Total RNA was extracted from the cerebral cortex of Control and Pen-2 cKO mice at P8 using the MagBeads Total RNA Extraction Kit (Cat# T02-096) following the manufacturer’s instructions.
Libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Cat# NR604-02, Vazyme, China) according to the manufacturer’s instructions.

value: Cortex

value: Pen-2 F/F; hGFAP-Cre


title: DSP-1001660013460-E-F01

description: FFPE GeoMx DSP profiling

value: Spleen


title: Pet_Col-0_6d-Amb_D

city: Durham

description: Library name: Pet_Col-0_6d-Amb_D_S85


title: DSP-1001660013460-E-E12

description: FFPE GeoMx DSP profiling


title: Pet_fer-4_6d-HH_C

description: Library name: Pet_fer-4_6d-HH_C_S84


title: DSP-1001660002549-A-E10_R3_C4

description: Library name: DSP-1001660002549-A-E10


title: Pen-2_CKO2

institute: The Affiliated Hospital of Nanjing University Medical School

description: Library name: Sample5


title: mouse skin, HdR1, imiquimod treatment day1

description: Library name: HdR1


title: Pen-2_CKO1

description: Library name: Sample4


title: Pet_fer-4_6d-Amb_C

description: Library name: Pet_fer-4_6d-Amb_C_S83


title: Control3

description: Library name: Sample3

value: Pen-2 F/F


title: DSP-1001660002549-A-E09_R3_C4

description: Library name: DSP-1001660002549-A-E09


title: DSP-1001660002549-A-F03_R3_C5

description: Library name: DSP-1001660002549-A-F03


title: DSP-1001660013460-E-E10

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-E08_R3_C3

description: Library name: DSP-1001660002549-A-E08


title: Pet_Col-0_6d-HH_C

description: Library name: Pet_Col-0_6d-HH_C_S82


title: Control2

description: Library name: Sample2


title: DSP-1001660013460-E-E09

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-E07_R3_C3

description: Library name: DSP-1001660002549-A-E07


title: Pet_Col-0_6d-Amb_C

description: Library name: Pet_Col-0_6d-Amb_C_S81


title: DSP-1001660002549-A-E06_R3_C3

description: Library name: DSP-1001660002549-A-E06


title: DSP-1001660013460-E-E08

description: FFPE GeoMx DSP profiling


title: Control1

description: Library name: Sample1


title: DSP-1001660002549-A-E05_R3_C3

description: Library name: DSP-1001660002549-A-E05


title: DSP-1001660013460-E-E07

description: FFPE GeoMx DSP profiling


title: leaf_fer-4_6d-HH_B

description: Library name: leaf_fer-4_6d-HH_B_S72_


title: Tet2 P53 bone marrow ZO45

city: New York

first: Alan

last: Shih

address: 1 Gustave L Levy Place

institute: Icahn School  of Medicine at Mount Sinai

description:
Library name: ZO45
mm_IMPACT

data_processing:
The data processing pipeline for detecting variants in Illumina HiSeq data is as follows. First the FASTQ files are processed to remove any adapter sequences at the end of the reads using cutadapt (v1.6). The files are then mapped using the BWA mapper  (bwa mem v0.7.12 ). After mapping the SAM files are sorted and read group tags are added using the PICARD tools. After sorting in coordinate order the BAM’s are processed with PICARD MarkDuplicates. The marked BAM files are then processed using the GATK toolkit (v 3.2) according the best practices for tumor normal pairs. They are first realigned using ABRA (v 0.92) and then the base quality values are recalibrated with the BaseQRecalibrator. Somatic variants are then called in the processed BAMs using muTect (v1.1.7) for SNV and the Haplotype caller from GATK with a custom post-processing script to call somatic indels. The full pipeline is available here https://github.com/soccin/BIC-variants_pipeline and the post processing code is at https://github.com/soccin/Postprocess-Mouse.
Assembly: GRCm38
Supplementary files format and content: MAF containing somatic mutations

source_name: Bone marrow

extract_protocol:
Genomic DNA was extracted using Qiagen Blood and Tissue Kit and Puregene Kits.
After PicoGreen quantification, 100 ng of mouse genomic DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR. After sample barcoding, 90-220 ng of each library were pooled and captured by hybridization with the mm_IMPACT (Nimblegen) (Integrated Mutation Profiling of Actionable Cancer Targets) assay, which captures all protein-coding exons and select introns of 578 cancer-related genes. Capture pools were sequenced on the HiSeq 4000 or NovaSeq 6000, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 Reagent Kit (Illumina), respectively, for PE100 reads. Following these criteria, the average coverage was 361X for tumor samples and 191X for normals.

value: Bone marrow

value: hematopoietic

value: Tet2-Trp53 dKO


title: Tet2 P53 bone marrow PGP5

description:
Library name: PGP5_SPL
mm_IMPACT


title: leaf_fer-4_6d-Amb_B

description: Library name: leaf_fer-4_6d-Amb_B_S71_


title: DSP-1001660013460-E-E06

description: FFPE GeoMx DSP profiling


title: leaf_Col-0_6d-HH_B

description: Library name: leaf_Col-0_6d-HH_B_S70_


title: DSP-1001660013460-E-E05

description: FFPE GeoMx DSP profiling


title: Tet2 P53 bone marrow 1321

description:
Library name: BMT1321_Lin_neg
mm_IMPACT

source_name: Bone Marrow

value: Bone Marrow


title: DSP-1001660002549-A-E04_R3_C1

description: Library name: DSP-1001660002549-A-E04


title: DSP-1001660002549-A-E03_R3_C1

description: Library name: DSP-1001660002549-A-E03


title: WT normal control

description:
Library name: MOUSEPOOLEDNORMAL
mm_IMPACT

value: POOL


title: DSP-1001660013460-E-E11

description: FFPE GeoMx DSP profiling

value: Young


title: leaf_Col-0_6d-Amb_B

description: Library name: leaf_Col-0_6d-Amb_B_S69_

value: Leaf blade


title: DSP-1001660013460-E-E04

description: FFPE GeoMx DSP profiling


title: Tet2 P53 tail control BF42

description:
Library name: BF42_tail_control
mm_IMPACT

source_name: Skin & Muscle

value: Skin & Muscle

value: epithelial, muscle


title: leaf_fer-4_6d-HH_A

description: Library name: leaf_fer-4_6d-HH_A_S68_

value: high humidity


title: DSP-1001660013460-E-E03

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-E01_R3_C1

description: Library name: DSP-1001660002549-A-E01

value: Lung Cancer

value: immunotherapy


title: DSP-1001660002549-A-E02_R3_C1

description: Library name: DSP-1001660002549-A-E02


title: leaf_fer-4_6d-Amb_A

description: Library name: leaf_fer-4_6d-Amb_A_S67_


title: Tet2 P53 bone marrow BF42

description:
Library name: BF42_BM
mm_IMPACT


title: DSP-1001660013460-E-E02

description: FFPE GeoMx DSP profiling


title: leaf_Col-0_6d-HH_A

description: Library name: leaf_Col-0_6d-HH_A_S66_


title: DSP-1001660002549-A-D12_R2_C8

description: Library name: DSP-1001660002549-A-D12


title: Tet2 P53 bone marrow AY78

description:
Library name: AY78_BM
mm_IMPACT


title: DSP-1001660013460-E-E01

description: FFPE GeoMx DSP profiling


title: leaf_Col-0_6d-Amb_A

description: Library name: leaf_Col-0_6d-Amb_A_S65_


title: Tet2 P53 spleen AC48

description:
Library name: AC48_SPL
mm_IMPACT


title: Pet_fer-4_6d-HH_B

description: Library name: Pet_fer-4_6d-HH_B_S64

value: Petiole


title: DSP-1001660013460-E-D12

description: FFPE GeoMx DSP profiling


title: Tet2 P53 bone marrow AC47

description:
Library name: AC47
mm_IMPACT


title: DSP-1001660002549-A-D09_R2_C8

description: Library name: DSP-1001660002549-A-D09


title: P53 bone marrow 1266-9987

description:
Library name: 1266_9987
mm_IMPACT

value: Trp53 KO


title: Pet_fer-4_6d-Amb_B

description: Library name: Pet_fer-4_6d-Amb_B_S63


title: Pet_Col-0_6d-HH_B

description: Library name: Pet_Col-0_6d-HH_B_S62


title: Tet2 P53 bone marrow 1266-635

description:
Library name: 1266_635
mm_IMPACT


title: DSP-1001660013460-E-D10

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-D09

description: FFPE GeoMx DSP profiling

value: Old


title: DSP-1001660013460-E-D11

description: FFPE GeoMx DSP profiling

value: Spleen


title: Pet_Col-0_6d-Amb_B

description: Library name: Pet_Col-0_6d-Amb_B_S61


title: DSP-1001660002549-A-D07_R2_C7

description: Library name: DSP-1001660002549-A-D07


title: DSP-1001660002549-A-D06_R2_C7

description: Library name: DSP-1001660002549-A-D06


title: DSP-1001660013460-E-D07

description: FFPE GeoMx DSP profiling


title: Pet_fer-4_6d-Amb_A

description: Library name: Pet_fer-4_6d-Amb_A_S59


title: DSP-1001660002549-A-D05_R2_C7

description: Library name: DSP-1001660002549-A-D05


title: Brain, 24 Months, Rep 10

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

description:
Library name: sample_24M_N10_B
24M.N10

data_processing:
RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim from both end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Comma separated matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

source_name: Brain

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.

value: Brain

value: 24 Months

value: Prep 3


title: Pet_fer-4_6d-HH_A

description: Library name: Pet_fer-4_6d-HH_A_S60


title: DSP-1001660013460-E-D08

description: FFPE GeoMx DSP profiling


title: Brain, 3 Months, Rep 14

description:
Library name: sample_3M_N14_B
3M.N14

value: 3 Months


title: DSP-1001660002549-A-D04_R2_C6

description: Library name: DSP-1001660002549-A-D04


title: Liver, 24 Months, Rep 10

description:
Library name: sample_24M_N10_L
24M.N10

value: Liver


title: DSP-1001660002549-A-D11_R2_C8

description: Library name: DSP-1001660002549-A-D11


title: Pet_Col-0_6d-HH_A

description: Library name: Pet_Col-0_6d-HH_A_S58


title: Liver, 3 Months, Rep 14

description:
Library name: sample_3M_N14_L
3M.N14


title: DSP-1001660002549-A-D10_R2_C8

description: Library name: DSP-1001660002549-A-D10


title: DSP-1001660002549-A-D03_R2_C6

description: Library name: DSP-1001660002549-A-D03


title: Brain, 28 Months, Rep 16

description:
Library name: sample_28M_N16_B
28M.N16

value: 28 Months


title: Pet_Col-0_6d-Amb_A

description: Library name: Pet_Col-0_6d-Amb_A_S57


title: DSP-1001660013460-E-D04

description: FFPE GeoMx DSP profiling

value: Young


title: leaf_fer-4_24h_D

description: Library name: leaf_fer-4_24h_D_S56_

value: Leaf blade


title: DSP-1001660002549-A-D01_R2_C6

description: Library name: DSP-1001660002549-A-D01


title: DSP-1001660013460-E-C07

description: FFPE GeoMx DSP profiling


title: leaf_fer-4_60m_D

description: Library name: leaf_fer-4_60m_D_S55_


title: Brain, 24 Months, Rep 16

description:
Library name: sample_24M_N16_B
24M.N16


title: DSP-1001660002549-A-C12_R2_C5

description: Library name: DSP-1001660002549-A-C12


title: DSP-1001660002549-A-D02_R2_C6

description: Library name: DSP-1001660002549-A-D02


title: DSP-1001660013460-E-C06

description: FFPE GeoMx DSP profiling


title: leaf_fer-4_15m_D

description: Library name: leaf_fer-4_15m_D_S54_


title: Liver, 24 Months, Rep 16

description:
Library name: sample_24M_N16_L
24M.N16


title: DSP-1001660013460-E-D06

description: FFPE GeoMx DSP profiling


title: leaf_fer-4_0m_D

description: Library name: leaf_fer-4_0m_D_S53_


title: DSP-1001660013460-E-C05

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-C04

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-C11_R2_C5

description: Library name: DSP-1001660002549-A-C11


title: DSP-1001660002549-A-C10_R2_C5

description: Library name: DSP-1001660002549-A-C10


title: Brain, 3 Months, Rep 8

description:
Library name: sample_3M_N8_B
3M.N8


title: DSP-1001660013460-E-C03

description: FFPE GeoMx DSP profiling


title: leaf_Col-0_24h_D

description: Library name: leaf_Col-0_24h_D_S52_


title: leaf_Col-0_60m_D

description: Library name: leaf_Col-0_60m_D_S51_


title: DSP-1001660002549-A-C09_R2_C5

description: Library name: DSP-1001660002549-A-C09


title: Brain, 15 Months, Rep 9

description:
Library name: sample_15M_N9_B
15M.N9

value: 15 Months


title: DSP-1001660013460-E-C02

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-C08_R2_C4

description: Library name: DSP-1001660002549-A-C08


title: DSP-1001660013460-E-D05

description: FFPE GeoMx DSP profiling


title: Liver, 28 Months, Rep 16

description:
Library name: sample_28M_N16_L
28M.N16


title: leaf_Col-0_15m_D

description: Library name: leaf_Col-0_15m_D_S50_


title: Liver, 15 Months, Rep 9

description:
Library name: sample_15M_N9_L
15M.N9


title: DSP-1001660002549-A-C07_R2_C4

description: Library name: DSP-1001660002549-A-C07


title: leaf_Col-0_0m_D

description: Library name: leaf_Col-0_0m_D_S49_


title: DSP-1001660013460-E-C01

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-B12

description: FFPE GeoMx DSP profiling


title: leaf_fer-4_24h_C

description: Library name: leaf_fer-4_24h_C_S48_


title: Liver, 28 Months, Rep 3

description:
Library name: sample_28M_N3_L
28M.N3


title: Brain, 28 Months, Rep 3

description:
Library name: sample_28M_N3_B
28M.N3


title: DSP-1001660013460-E-B11

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-C05_R2_C3

description: Library name: DSP-1001660002549-A-C05


title: Liver, 3 Months, Rep 8

description:
Library name: sample_3M_N8_L
3M.N8


title: Brain, 24 Months, Rep 9

description:
Library name: sample_24M_N9_B
24M.N9


title: DSP-1001660013460-E-B10

description: FFPE GeoMx DSP profiling