title: MRTX1133-E7553

city: Göttingen

first: Adi

last: Mackay

address: Robert-Koch-Straße 40

department: Pathology

institute: University Medical Center Göttingen

description: Library name: MRTX1133-E7553

data_processing:
Raw base call (BCL) files were converted to FASTQ format and processed using bcl2fastq (version 2.20.0.422). The Illumina BaseSpace DRAGEN Single Cell RNA Pipeline (version 4.4.4) on the BaseSpace Cloud platform. The DRAGEN single-cell pipeline performed read alignment, barcode processing, UMI counting, and gene quantification. Cell barcodes and UMIs were automatically extracted and filtered according to DRAGEN single-cell quality control criteria by using “Ratio” method to create maximum number of cells with expected noise which calculated by estimation the count threshold as max(Te, Tm). Tm is 10% of the count seen in the cell at the 10th percentile of the expected cells (defined as 10000). Te is 50% of the count seen in the least abundant expected cell. The rest of the parameters were kept to their default values.
Assembly: Mus musculus mm39 (based on GENCODE )
Supplementary files format and content: Xxx.barcodes.tsv.gz: text file with cellular barcodes of the sample.
Supplementary files format and content: xxx.features.tsv.gz: text file with the genes quantified in the sample.
Supplementary files format and content: xxx.matrix.mtx.gz: text file containing the counts matrix.

source_name: Pancreas

extract_protocol:
Single cells were isolated from mouse tumors using the Tumor Dissociation Kit mouse (130-096-730, Miltenyi Biotec) with the 37C_m_TDK_2 program  followed by DNase A (200U/mL, E1010, Zymo Research) treatment.
Single cell suspensions were counted and stained prior to library prep starting with 17K cells (vitality 60 to 78%). Library preparation was conducted according to the PIPseq™ T2 3′ Single Cell RNA Kit v4.0.

value: Pancreas

value: KPC

value: Cell Line


title: Vehicle-E7540

status: Public on Dec 18 2025

type: SRA

country: Germany

description: Library name: Vehicle-E7540

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Carrier


title: PalboMRTX1133-E7549

description: Library name: PalboMRTX1133-E7549

value: Palbociclib+ MRTX-1133


title: Palbociclib-E7535

description: Library name: Palbociclib-E7535

value: Palbociclib


title: sPalbociclib-E7530

description: Library name: sPalbociclib-E7530


title: Vehicle-E7528

description: Library name: Vehicle-E7528


title: MRTX1133-E7550

description: Library name: MRTX1133-E7550


title: TM+ Rep4, bioChIP

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

country: USA

institute: University of Texas at Austin

description: Library name: TM+ Rep4, bioChIP

library_source: genomic

data_processing:
ChIP-seq samples were adapter-trimmed by TrimGalore v0.6.10 (https://github.com/FelixKrueger/TrimGalore), aligned by Bowtie v2.5.1 (Langmead & Salzberg, 2012), then processed with Samtools v1.20 (Danecek et al, 2021) and Picard MarkDuplicates v3.0.0 (http://broadinstitute.github.io/picard).
Peak calling was performed using Macs3 v3.0.1 (Zhang et al, 2008), and the heatmap was generated using DeepTools v3.5.5 (Ramírez et al, 2016).
Assembly: mm10
Supplementary files format and content: bigWig (except for input samples)

molecule: genomic DNA

source_name: embryonic stem cells

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The bioChIP protocol was conducted as previously described (Kim et al, 2009). Genomic DNA was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602).
Library preparation was performed using the NEBNext® Ultra™ DNA Library Prep Kit (NEB, 7103L)

treatment_protocol: bioChIP-seq was performed on PREB- and PREBΔTM-OE ES cells treated with 0.5 µg/mL doxycycline for 24 hours.

value: embryonic stem cells


title: Astro-TE_NN.male.9mo

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: sample 5
read length: 151

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Hisat3n.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: brain

tag: Sex

value: male


title: TM- Rep4, INPUT

description: Library name: TM- Rep4, INPUT


title: AB378_4

city: nanjing

first: Jiaquan

last: Lin

address: Hankou road

country: China

institute: nanjing university

description:
Library name: AB378_4
FPKM.AB378_4

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: primary microglia

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: primary microglia

value: Microglia

value: WT

value: A β oligomers+miR-378a-3p mimics


title: TM- Rep4, bioChIP

description: Library name: TM- Rep4, bioChIP


title: TM+ Rep3, INPUT

description: Library name: TM+ Rep3, INPUT


title: TM- Rep3, INPUT

description: Library name: TM- Rep3, INPUT


title: TM+ Rep3, bioChIP

description: Library name: TM+ Rep3, bioChIP


title: TM+ Rep2, bioChIP

description: Library name: TM+ Rep2, bioChIP


title: TM- Rep2, INPUT

description: Library name: TM- Rep2, INPUT


title: TM- Rep2, bioChIP

description: Library name: TM- Rep2, bioChIP


title: TM+ Rep2, INPUT

description: Library name: TM+ Rep2, INPUT


title: TM+ Rep1, INPUT

description: Library name: TM+ Rep1, INPUT


title: PalboMRTX1133-E7555

description: Library name: PalboMRTX1133-E7555


title: TM+ Rep1, bioChIP

description: Library name: TM+ Rep1, bioChIP


title: TM- Rep3, bioChIP

description: Library name: TM- Rep3, bioChIP


title: TM- Rep1, bioChIP

description: Library name: TM- Rep1, bioChIP


title: EC_cells_EB_4

city: San Francisco

first: Holly

middle: A

last: Ingraham

address: 1550 4th Street Rock Hall 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

description: Library name: ECcells_EB_Repeat_4

data_processing:
Raw RNA-seq reads were processed using the Galaxy server. The reads were aligned to the mm10 reference genome using RNA STAR  (Dobin et al., 2012) in a unstranded manner. The resulting BAM files were subsequently used as input for featureCounts (Liao et al., 2013) to quantify reads mapped reads. Raw counts from different datasets were then imported into the DESeq2 pipeline (Love et al., 2014) to identify differentially expressed genes and generate normalized counts using default thresholds.
Assembly: mm10
Supplementary files format and content: xlsx file contains normalzied counts

source_name: colon

extract_protocol:
RNA was harvested using TRIzol LS
Ultra-low input RNA sequencing library was prepared by using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: colon

value: Female

value: EC-cells

value: ECFLTG

value: estradiol benzoate

tag: age

tag: status

value: Ovariectomized

tag: strain


title: EC_cells_EB_3

description: Library name: ECcells_EB_Repeat_3


title: TM- Rep1, INPUT

description: Library name: TM- Rep1, INPUT


title: EC_cells_EB_2

description: Library name: ECcells_EB_Repeat_2


title: EC_cells_EB_1

description: Library name: ECccells_EB_Repeat_1


title: L_cells_EB_3

description: Library name: Lcells_EB_Repeat_3

value: L-cells


title: L_cells_EB_2

description: Library name: Lcells_EB_Repeat_2


title: L_cells_Veh_1

description: Library name: Lcells_Veh_Repeat_1

value: sesame oil


title: EC-Tfeb_Tg_DOX_04

city: Columbus

first: Wa

last: Du

state: OH

address: 460 West 12th Avenue, Biomedical Research Tower, Rm 360A

department: Department of Surgery, Division of Vascular Diseases and Surgery

institute: The Ohio State University

description:
Library name: EC-Tfeb_Tg_DOX_04
10x Genomics

data_processing:
Batch1: The raw FASTQ files were processed using STAR (version 2.7.10b). STARsolo was used for read alignment to the reference genome [mm10]. Key STARsolo Parameters: Cell barcode length: 16 bp. UMI length: 12 bp. Barcode whitelist: 10X Genomics whitelist.
Batch2: Sequencing data were demultiplexed and processed using Cell Ranger (v9.0) on an Ubuntu 22.04 system. A mouse whole transcriptome reference (GRCh38) was used for alignment and quantification. The Cell Ranger multi pipeline was used to assign cells to individual samples based on CMO barcodes and to generate per-sample gene expression matrices. Output files included filtered expression matrices, quality control reports, and cell/sample assignment data. Results were reviewed using the web-based summaries and further analyzed in downstream bioinformatics pipelines.
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values fiiles and matrix files

source_name: Heart

extract_protocol:
Mouse hearts were minced and placed into a 15-ml conical tube containing DMEM with Collagenase I (450 U/ml), DNase I (60 U/ml), and hyaluronidase (60 U/ml). The mixture was then incubated at 37 ℃ for 30 minutes with agitation. Digestion was stopped by adding DMEM with 2% FBS, followed by passing the mixture through a cell strainer (40-mm) into a 50-ml conical tube. The filtrate was then centrifuged at 300g for 5 minutes at 4 ℃. After discarding the supernatant, the cell pellet was resuspended in 1 ml ACK lysing buffer and incubated at room temperature for 5 minutes. Subsequently, 9 ml DMEM was added, and the cell viability (~80%) was assessed.
Batch1: Chromium Next GEM Chip G Single cell 3’ Reagent V3.1 kit from 10× genomics, with 10,000 cells loaded into a Chip G for GEM generation. Reverse transcription, barcoding, complementary DNA amplification, and purification for library preparation were performed according to the Chromium 3’ V3.1 protocol. Batch2: Library preparation was carried out using the Chromium X platform and the Fixed RNA Profiling 3’ v3.1 chemistry, following the manufacturer’s standard protocol.

value: Heart

value: mixed single cells

value: Endothelial TFEB transgenic

value: Doxorubicin

tag: batch


title: Ligation.Tnc.cKO

city: Shanghai

first: Guangzheng

last: Shi

state: Shanghai

address: No. 197 Ruijin 2nd Road, Huangpu District, Shanghai

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

description:
Library name: Sample1
single cell RNA sequencing

data_processing:
1. Genome Alignment Cell Ranger (http://support.10xgenomics.com/single-cell/software/overview/welcome) uses an aligner called STAR (https://github.com/alexdobin/STAR), which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that are confidently mapped to the transcriptome are used for UMI countin 2.Calling Cell Barcodes Cell Ranger takes as input the expected number of recovered cells, N. Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. 3.Depth normalization When combining data from multiple libraries, we recommend equalizing the read depth between libraries before merging, to reduce the batch effect introduced by sequencing. Subsample reads from higher-depth libraries until they all have an equal number of total reads per cell.
Assembly: mm10
Supplementary files format and content: Seurat was use to perform QC, analysis, and exploration of scRNA-seq data.

source_name: carotid arteries

extract_protocol:
Euthanized mice were perfused with PBS. Carotid arteries were extracted and placed on ice in DMEM containing 10% fetal bovine serum. To get single-cell suspensions, arteries were washed three times with PBS, cut into fine pieces, and digested for 30 minutes at 37 °C with reciprocal shaking in a mixed digesting solution containing collagenase I (1mg/ml). Single cells were resuspended in DMEM with 10% FBS. At the completion of the digestion process, all digested cells from a single sample were pooled together. Cells were collected after being filtered through a 40um cell strainer and centrifuged for 8 minutes at 500g speed at 4 °C. Subsequently, cell pellet was suspended in HBSS for further experiments.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A_x005f_x0002_tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: carotid arteries


title: L_cells_Veh_2

description: Library name: Lcells_Veh_Repeat_2


title: EC-Tfeb_Tg_DOX_02

description:
Library name: EC-Tfeb_Tg_DOX_02
10x Genomics


title: EC-Tfeb_Tg_DOX_01

description:
Library name: EC-Tfeb_Tg_DOX_01
10x Genomics


title: WT_DOX_02

description:
Library name: WT_DOX_02
10x Genomics

value: Wild type


title: WT_DOX_03

description:
Library name: WT_DOX_03
10x Genomics


title: EC-Tfeb_Tg_vehicle_02

description:
Library name: EC-Tfeb_Tg_vehicle_02
10x Genomics

value: Vehicle


title: EC-Tfeb Tg_vehicle_05

description:
Library name: EC-Tfeb_Tg_vehicle_05
10x Genomics


title: EC-Tfeb_Tg_vehicle_03

description:
Library name: EC-Tfeb_Tg_vehicle_03
10x Genomics


title: EC-Tfeb_Tg_vehicle_04

description:
Library name: EC-Tfeb_Tg_vehicle_04
10x Genomics


title: WT_vehicle_04

description:
Library name: WT_vehicle_04
10x Genomics


title: WT_DOX_01

description:
Library name: WT_DOX_01
10x Genomics


title: EC-Tfeb_Tg_vehicle_01

description:
Library name: EC-Tfeb_Tg_vehicle_01
10x Genomics


title: WT_vehicle_03

description:
Library name: WT_vehicle_03
10x Genomics


title: WT_vehicle_01

description:
Library name: WT_vehicle_01
10x Genomics


title: MIC_DGhh_8325

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

description: Library name: Sample 8

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic (Bolger et al., 2014). The resulting reads were aligned to the GRCm38 assembly of the mouse reference genome, using STAR (Dobin et al., 2012). Read counts were obtained using HTSeq (Anders et al 2015) with parameters -m intersection-nonempty -stranded=reverse.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file contains the read counts matrix, with genes as rows and samples as columns.

source_name: Mammary tumor

growth_protocol: ESR1-Y541S or ESR1-D542G mutations were knocked into the inducible polyoma middle T-driven transgenic mouse model of mammary tumorigenesis (MIC model). Mice were induced on doxycycline water and primary mammary tumors harvested at endpoint.

extract_protocol:
Flash-frozen pieces of tumors were crushed in liquid nitrogen. Total RNA was isolated using FavorPrep™ Tissue Total RNA Mini Kit (Cat Number FATRK 001) according to manufacturer’s protocol. RNA quantity was determined using NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.).
RNA library preparation for RNA-seq was done by Genome Quebec with the polyA Enriched RNA Library Preparation.

value: Mammary tumor

value: MIC ESR1-D542G


title: MIC_YShh_8722

description: Library name: Sample 6

value: MIC ESR1-Y541S


title: WT_vehicle_02

description:
Library name: WT_vehicle_02
10x Genomics


title: MIC_DGhh_5594

description: Library name: Sample 7


title: L_cells_EB_1

description: Library name: Lcells_EB_Repeat_1

value: colon

value: Female


title: MIC_DGhh_8525

description: Library name: Sample 9


title: EC_cells_Veh_2

description: Library name: ECcells_Veh_Repeat_2

value: EC-cells

value: ECFLTG


title: EC-Tfeb Tg_DOX_05

description:
Library name: EC-Tfeb_Tg_DOX_05
10x Genomics


title: EC-Tfeb_Tg_DOX_03

description:
Library name: EC-Tfeb_Tg_DOX_03
10x Genomics


title: MIC_WT_8029

description: Library name: Sample 2

value: MIC WT


title: MIC_YShh_8326

description: Library name: Sample 4


title: MIC_WT_9469

description: Library name: Sample 3


title: MIC_YShh_8687

description: Library name: Sample 5


title: EC_cells_Veh_1

description: Library name: ECcells_Veh_Repeat_1

value: Ovariectomized


title: Thymus, LAR, Mouse 4

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

institute: Saarland University

description: Library name: Thymus-LAR_2_2-Mouse_4-Pool_3

data_processing:
The obtained reads were mapped to the mm10 reference genome using cellranger (version 5.0.0, 10X Genomics). Ambient cell free mRNA contamination of each sample was removed using SoupX (version 1.5.2). Samples with more than 10% estimated contamination were removed. Raw gene counts were loaded into Seurat (version 4.0.3) for further processing. Cells with less than 200 or more than 2500 features, as well as cells with more than 50% mitochondrial RNA were removed. Samples with less than 50 cells were removed from the dataset. Finally, doublets were removed using DoubletFinder (version 2.0.3).
Assembly: mm10 2020 A
Supplementary files format and content: barcode.tsv:Barcode file containing the valid cell barcodes (output of cellranger pipeline)
Supplementary files format and content: features.tsv:file containing the feature names (output of cellranger pipeline)
Supplementary files format and content: matrix.mtx:Matrix file containing the gene counts for each cell barcode (output of cellranger pipeline)

source_name: Thymus

growth_protocol: Rodent Research Reference Mission 1 (RRR-1) / Rodent Research-8 (RR-8) consisted of 40 BALB/cAnNTac females (8 used for this study) termed Flight which were sent on 12/5/2018 to the International Space Station (ISS), and a control group of 40 mice remained on Earth, termed Habitat Ground Control (HC). Furthermore, two age groups were used, younger (∼3 months) and older (∼8 months). Flight mice were housed at double density on launch and again during the return to earth. HC mice were housed to match, as closely as possible, conditions experienced by Flight mice. This included double density housing in identical Mouse Habitat Units and Transporters as used by NASA during launch for Flight mice, and matched temperature, humidity, and carbon dioxide levels (elevated on the ISS compared to Earth) based on actual flight environmental monitoring. HC mice were shipped to Scripps Institute just prior to the return of the Flight mice so that all mice could be dissected together in matching conditions (+/- 1 day). The mice from the Flight group were returned alive to Earth on 1/14/2019 after 39.5 days on the ISS and collected 2-4 days after splashdown following functional assays at Scripps Research Institute. In this study, fresh organ samples were obtained and immediately processed from 8 live mice that arrived at Stanford University from Scripps Research Institute on 1/16/2019. Two mice each from the following groups were included: Flight 3mo, Flight 8mo, HC 3mo, HC 8mo. All four Flight mice were dissected on 1/16/2019 to minimize time spent outside of microgravity, and all four HC mice dissected on 1/17/2019. All mice were adapted to NASA Nutrient Food Bars, four weeks prior to launch, and bars were exchanged weekly. Mice had ad libitum access to both food and water.

extract_protocol:
Peripheral blood samples (0.5 – 1 mL) were collected by cardiac puncture into K2/EDTA-coated syringes and MiniCollect tubes (Greiner Bio-One) immediately after mice were euthanized by CO2 inhalation and cervical dislocation. Red blood cells were depleted with Histopaque-1119 (SigmaAldrich RNBF0417). The cell suspension was then pelleted (300 x g, 4o C, 5 min), filtered through a 70 μm strainer, and resuspended in FACS buffer (2% sterile FBS in PBS) with 100 U/mL DNase I (Worthington LS006344) prior to loading cells on a 10x chromium chip.  Murine eyes were collected carefully using forceps in cold PBS. The whole eyes from each donor were weighed. Subsequently, each of the eyes was dissected under a dissecting microscope to segregate the extraocular muscles, retina, cornea, lens and optic nerve tissue components. Each of these tissues for each donor were digested separately for single cell preparation and pooled together as eye cell suspension. The optic nerves and retina were digested for 15 mins in papain and subsequently resuspended in HBSS solution for mechanical dissociation of single cells by pipetting. The corneal tissue was incubated in Dispase II for an hour with shaking followed by 10 mins of 0.25% trypsin digestion. The corneal cells were then mechanically dissociated using pipetting and resuspended in PBS (with 1% FBS). The lens tissue was processed in 0.02% EDTA for 10 mins and mechanically resuspended into single cells by pipetting. The extraocular muscles were treated with 1mg/ml collagenase for 45mins with pipetting every 15 mins for single cell suspension. All the pooled cells were finally resuspended in 1% FBS containing PBS at a concentration of 106 cells/ml for subsequent processing on 10X.  Femurs, hip bones and vertebral columns were dissected and cleaned of soft tissue. Bones were then processed as previously described (https://doi.org:10.1016/j.cell.2014.12.002, https://doi.org:10.1038/nprot.2018.041). Briefly, bones were crushed using mortar and pestle and subsequently digested in M199 (cat#11150067, Thermo Fisher Scientific) with 2.2 mg ml-1 collagenase II buffer (cat#C6885, Sigma-Aldrich) at 37 °C for 60 min under constant agitation. Dissociated cells were strained through a 100-μm nylon filter, washed in staining medium (10% fetal bovine serum (FBS) in PBS) and pelleted at 200g at 4°C. The cell pellet was resuspended in staining medium and red blood cells were depleted via ACK lysis for 3 min. After an additional wash step cells were pelleted at 200g at 4°C. The single cell suspension was then prepared for fluorescence activated cell sorting (FACS) by staining them with fluorochrome-conjugated antibodies (Thermo Fisher Scientific) against CD45 (cat#15-0451; 1:200), TER119 (cat#15-5921; 1:200), CD51 (cat#12-0512; 1:50), Tie2 (cat#14-5987; 1:20), CD31 (cat#11-0311;1:200), Th1.1 (cat#47-0900; 1:100), Thy1.2 (47-0902; 1:100), 6c3 (cat#17-5891; 1:100), CD105 (cat#13-1051; 1:50) and streptavidin–PE–Cy7 conjugate (cat#25-4317-82; 1:100). Target populations were sorted on a FACS Aria II Instrument (BD BioSciences) using a 70-μm nozzle in the Shared FACS Facility in the Lokey Stem Cell Institute (Stanford). 16 Gating of cell populations was guided by appropriate isotype and fluorescence-minus- one controls. Propidium iodide staining was used to separate dead cells. Cells were sorted into staining medium and directly processed for 10X Genomics scRNA-seq.  All other tissues were processed as previously described (https://doi.org:10.1038/s41586-020-2496-1).
Single cells were captured in droplet emulsions using the GemCode Single-Cell Instrument (10x Genomics) and scRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3’ Gel Bead and Library v3 Kit. Cells were loaded in each channel with a target output of up to 5,000 cells per sample, though fewer cells were captured for small sample types. All reactions were performed in the Biorad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated on a Fragment Analyzer using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Library preparation was performed one organ type at a time, in sets of 8 samples. Within each organ set, cDNA was normalized and 13-20 PCR cycles run depending on cDNA amount. The average fragment length of 10x cDNA libraries was quantitated on a Fragment Analyzer (AATI), and by qPCR with the Kapa Library Quantification kit for Illumina. Each library was diluted to 4nM, and equal volumes were pooled for each NovaSeq sequencing run. Pools were sequenced with 100 cycle run kits with 28 bases for Read 1, 8 bases for Index 1, and 91 bases for Read 2 (Illumina 20012862). A PhiX control library was spiked in at 0.2 to 1%. Libraries were sequenced on the NovaSeq 6000 Sequencing System (Illumina).

value: Thymus

value: BALB/cAnNTac

value: female

value: spaceflight

value: Pool 3


title: Thymus, LAR, Mouse 3

description: Library name: Thymus-LAR_2_2-Mouse_3-Pool_3


title: Thymus, LAR, Mouse 1

description: Library name: Thymus-LAR_2_2-Mouse_1-Pool_3


title: WT_DOX_04

description:
Library name: WT_DOX_04
10x Genomics

value: Heart

value: mixed single cells

value: Doxorubicin


title: Thymus, HC, Mouse 3

description: Library name: Thymus-HC_1_5-Mouse_3-Pool_3

value: control


title: Thymus, HC, Mouse 1

description: Library name: Thymus-HC_1_5-Mouse_1-Pool_3


title: Spleen, LAR, Mouse 4

description: Library name: Spleen-LAR_1_5-Mouse_4-Pool_1

source_name: Spleen

value: Spleen

value: Pool 1


title: Spleen, LAR, Mouse 3

description: Library name: Spleen-LAR_1_5-Mouse_3-Pool_1


title: Spleen, LAR, Mouse 2

description: Library name: Spleen-LAR_1_5-Mouse_2-Pool_1


title: Spleen, HC, Mouse 4

description: Library name: Spleen-HC_1_6-Mouse_4-Pool_1


title: Spleen, LAR, Mouse 1

description: Library name: Spleen-LAR_1_5-Mouse_1-Pool_4

value: Pool 4


title: Spleen, HC, Mouse 3

description: Library name: Spleen-HC_1_6-Mouse_3-Pool_1


title: Spleen, HC, Mouse 2

description: Library name: Spleen-HC_1_6-Mouse_2-Pool_1


title: Skin, LAR, Mouse 2

description: Library name: Skin-LAR_2_1-Mouse_2-Pool_1

source_name: Skin

value: Skin


title: MIC_WT_7056

description: Library name: Sample 1

value: Mammary tumor


title: Skin, LAR, Mouse 3

description: Library name: Skin-LAR_2_1-Mouse_3-Pool_1


title: Skin, HC, Mouse 4

description: Library name: Skin-HC_1_3-Mouse_4-Pool_1


title: Skin, LAR, Mouse 1

description: Library name: Skin-LAR_2_1-Mouse_1-Pool_1


title: Spleen, HC, Mouse 1

description: Library name: Spleen-HC_1_6-Mouse_1-Pool_1


title: Skin, LAR, Mouse 4

description: Library name: Skin-LAR_2_1-Mouse_4-Pool_1


title: Skin, HC, Mouse 3

description: Library name: Skin-HC_1_3-Mouse_3-Pool_1


title: Skin, HC, Mouse 2

description: Library name: Skin-HC_1_3-Mouse_2-Pool_1


title: Thymus, LAR, Mouse 2

description: Library name: Thymus-LAR_2_2-Mouse_2-Pool_3


title: Skin, HC, Mouse 1

description: Library name: Skin-HC_1_3-Mouse_1-Pool_1


title: Skeletal Stem Cells, LAR, Mouse 3

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_3-Pool_3


title: Skeletal Stem Cells, LAR, Mouse 4

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_4-Pool_3


title: Thymus, HC, Mouse 4

description: Library name: Thymus-HC_1_5-Mouse_4-Pool_3


title: Skeletal Stem Cells, LAR, Mouse 1

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_1-Pool_3


title: Skeletal Stem Cells, HC, Mouse 2

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_2-Pool_3


title: Skeletal Stem Cells, HC, Mouse 3

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_3-Pool_3


title: Skeletal Stem Cells, HC, Mouse 4

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_4-Pool_3


title: Skeletal Stem Cells, HC, Mouse 1

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_1-Pool_3


title: SCAT, LAR, Mouse 4

description: Library name: SCAT-LAR_2_5-Mouse_4-Pool_1

source_name: SCAT

value: SCAT


title: Thymus, HC, Mouse 2

description: Library name: Thymus-HC_1_5-Mouse_2-Pool_3


title: SCAT, LAR, Mouse 2

description: Library name: SCAT-LAR_2_5-Mouse_2-Pool_1


title: SCAT, LAR, Mouse 3

description: Library name: SCAT-LAR_2_5-Mouse_3-Pool_1


title: SCAT, LAR, Mouse 1

description: Library name: SCAT-LAR_2_5-Mouse_1-Pool_1


title: SCAT, HC, Mouse 3

description: Library name: SCAT-HC_2_2-Mouse_3-Pool_1


title: SCAT, HC, Mouse 2

description: Library name: SCAT-HC_2_2-Mouse_2-Pool_1


title: SCAT, HC, Mouse 1

description: Library name: SCAT-HC_2_2-Mouse_1-Pool_1


title: Pancreas, LAR, Mouse 2

description: Library name: Pancreas-LAR_1_3-Mouse_2-Pool_2

value: Pancreas

value: Pool 2


title: Pancreas, LAR, Mouse 4

description: Library name: Pancreas-LAR_1_3-Mouse_4-Pool_2


title: Pancreas, LAR, Mouse 3

description: Library name: Pancreas-LAR_1_3-Mouse_3-Pool_2


title: Pancreas, LAR, Mouse 1

description: Library name: Pancreas-LAR_1_3-Mouse_1-Pool_2


title: Pancreas, HC, Mouse 3

description: Library name: Pancreas-HC_1_5-Mouse_3-Pool_2


title: Pancreas, HC, Mouse 2

description: Library name: Pancreas-HC_1_5-Mouse_2-Pool_2


title: Skeletal Stem Cells, LAR, Mouse 2

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_2-Pool_3


title: Pancreas, HC, Mouse 4

description: Library name: Pancreas-HC_1_5-Mouse_4-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 4

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_4-Pool_2


title: Pancreas, HC, Mouse 1

description: Library name: Pancreas-HC_1_5-Mouse_1-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 3

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_3-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 1

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_1-Pool_2


title: Non, myeloid Forebrain, HC, Mouse 4

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_4-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 3

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_3-Pool_3


title: Non, myeloid Forebrain, LAR, Mouse 2

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_2-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 4

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_4-Pool_3


title: Non, myeloid Forebrain, HC, Mouse 3

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_3-Pool_2


title: Non, myeloid Forebrain, HC, Mouse 1

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_1-Pool_2


title: SCAT, HC, Mouse 4

description: Library name: SCAT-HC_2_2-Mouse_4-Pool_1


title: Non, myeloid Forebrain, HC, Mouse 2

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_2-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 2

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_2-Pool_3


title: Non, myeloid Cerebellum, LAR, Mouse 1

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_1-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 4

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_4-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 3

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_3-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 2

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_2-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 2

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_2-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 4

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_4-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 1

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_1-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 3

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_3-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 1

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_1-Pool_3


title: Non, meyloid Hippocampus, HC, Mouse 3

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_3-Pool_3


title: Myeloid Hippocampus, LAR, Mouse 3

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_3-Pool_2


title: Myeloid Hippocampus, LAR, Mouse 4

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_4-Pool_2


title: Myeloid Hippocampus, HC, Mouse 2

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_2-Pool_2


title: Non, meyloid Hippocampus, HC, Mouse 1

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_1-Pool_3


title: Myeloid Hippocampus, LAR, Mouse 1

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_1-Pool_2


title: Myeloid Hippocampus, HC, Mouse 1

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_1-Pool_2


title: Non, meyloid Hippocampus, HC, Mouse 4

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_4-Pool_3


title: Myeloid Hippocampus, HC, Mouse 3

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_3-Pool_2


title: Non, meyloid Hippocampus, HC, Mouse 2

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_2-Pool_3


title: Myeloid Forebrain, LAR, Mouse 2

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_2-Pool_1


title: Myeloid Forebrain, LAR, Mouse 4

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_4-Pool_1


title: Myeloid Forebrain, HC, Mouse 2

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_2-Pool_1


title: Myeloid Hippocampus, LAR, Mouse 2

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_2-Pool_2


title: Myeloid Forebrain, HC, Mouse 1

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_1-Pool_1


title: Myeloid Forebrain, LAR, Mouse 3

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_3-Pool_1


title: Myeloid Hippocampus, HC, Mouse 4

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_4-Pool_2


title: Myeloid Cerebellum, LAR, Mouse 4

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_4-Pool_1


title: Myeloid Forebrain, HC, Mouse 3

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_3-Pool_1


title: Myeloid Cerebellum, LAR, Mouse 3

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_3-Pool_1


title: Myeloid Cerebellum, LAR, Mouse 1

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_1-Pool_1


title: Myeloid Forebrain, LAR, Mouse 1

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_1-Pool_1


title: Myeloid Cerebellum, HC, Mouse 4

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_4-Pool_1


title: Myeloid Cerebellum, HC, Mouse 3

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_3-Pool_1


title: MAT, LAR, Mouse 4

description: Library name: MAT-LAR_2_6-Mouse_4-Pool_3

source_name: MAT

value: MAT


title: MAT, LAR, Mouse 1

description: Library name: MAT-LAR_2_6-Mouse_1-Pool_3

value: BALB/cAnNTac


title: MAT, HC, Mouse 4

description: Library name: MAT-HC_2_3-Mouse_4-Pool_3

value: female


title: MAT, LAR, Mouse 2

description: Library name: MAT-LAR_2_6-Mouse_2-Pool_3

value: spaceflight


title: Myeloid Forebrain, HC, Mouse 4

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_4-Pool_1


title: MAT, HC, Mouse 3

description: Library name: MAT-HC_2_3-Mouse_3-Pool_3

value: Pool 3


title: MAT, HC, Mouse 2

description: Library name: MAT-HC_2_3-Mouse_2-Pool_3


title: Marrow, LAR, Mouse 3

description: Library name: Marrow-LAR_2_4-Mouse_3-Pool_3

source_name: Marrow

value: Marrow


title: MAT, HC, Mouse 1

description: Library name: MAT-HC_2_3-Mouse_1-Pool_3


title: Marrow, LAR, Mouse 2

description: Library name: Marrow-LAR_2_4-Mouse_2-Pool_3


title: Marrow, LAR, Mouse 4

description: Library name: Marrow-LAR_2_4-Mouse_4-Pool_3


title: Marrow, HC, Mouse 3

description: Library name: Marrow-HC_1_8-Mouse_3-Pool_3


title: Marrow, LAR, Mouse 1

description: Library name: Marrow-LAR_2_4-Mouse_1-Pool_3


title: Marrow, HC, Mouse 1

description: Library name: Marrow-HC_1_8-Mouse_1-Pool_3


title: Mammary, LAR, Mouse 3

description: Library name: Mammary-LAR_1_6-Mouse_3-Pool_2

source_name: Mammary

value: Mammary


title: Mammary, LAR, Mouse 2

description: Library name: Mammary-LAR_1_6-Mouse_2-Pool_2


title: Mammary, LAR, Mouse 4

description: Library name: Mammary-LAR_1_6-Mouse_4-Pool_2


title: Myeloid Cerebellum, LAR, Mouse 2

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_2-Pool_1


title: Mammary, HC, Mouse 4

description: Library name: Mammary-HC_1_7-Mouse_4-Pool_2


title: Mammary, LAR, Mouse 1

description: Library name: Mammary-LAR_1_6-Mouse_1-Pool_2


title: Mammary, HC, Mouse 2

description: Library name: Mammary-HC_1_7-Mouse_2-Pool_2


title: Lung, LAR, Mouse 3

description: Library name: Lung-LAR_1_4-Mouse_3-Pool_2

source_name: Lung

value: Lung


title: Myeloid Cerebellum, HC, Mouse 2

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_2-Pool_1

value: control


title: MAT, LAR, Mouse 3

description: Library name: MAT-LAR_2_6-Mouse_3-Pool_3


title: Lung, LAR, Mouse 2

description: Library name: Lung-LAR_1_4-Mouse_2-Pool_2


title: Lung, LAR, Mouse 1

description: Library name: Lung-LAR_1_4-Mouse_1-Pool_2


title: Lung, HC, Mouse 4

description: Library name: Lung-HC_1_4-Mouse_4-Pool_2


title: Marrow, HC, Mouse 2

description: Library name: Marrow-HC_1_8-Mouse_2-Pool_3


title: Lung, HC, Mouse 3

description: Library name: Lung-HC_1_4-Mouse_3-Pool_2


title: Lung, HC, Mouse 2

description: Library name: Lung-HC_1_4-Mouse_2-Pool_2


title: Lung, HC, Mouse 1

description: Library name: Lung-HC_1_4-Mouse_1-Pool_2


title: Liver, LAR, Mouse 3

description: Library name: Liver-LAR_1_4-Mouse_3-Pool_2

source_name: Liver

value: Liver


title: Liver, LAR, Mouse 2

description: Library name: Liver-LAR_1_4-Mouse_2-Pool_2


title: Liver, HC, Mouse 4

description: Library name: Liver-HC_1_9-Mouse_4-Pool_2


title: Liver, LAR, Mouse 1

description: Library name: Liver-LAR_1_4-Mouse_1-Pool_2


title: Liver, HC, Mouse 2

description: Library name: Liver-HC_1_9-Mouse_2-Pool_2


title: Liver, HC, Mouse 3

description: Library name: Liver-HC_1_9-Mouse_3-Pool_2


title: Limb Muscle, LAR, Mouse 4

description: Library name: Limb_Muscle-LAR_2_6-Mouse_4-Pool_2


title: Mammary, HC, Mouse 3

description: Library name: Mammary-HC_1_7-Mouse_3-Pool_2


title: Liver, HC, Mouse 1

description: Library name: Liver-HC_1_9-Mouse_1-Pool_2


title: Limb Muscle, LAR, Mouse 3

description: Library name: Limb_Muscle-LAR_2_6-Mouse_3-Pool_2


title: Limb Muscle, LAR, Mouse 1

description: Library name: Limb_Muscle-LAR_2_6-Mouse_1-Pool_2


title: Limb Muscle, HC, Mouse 4

description: Library name: Limb_Muscle-HC_2_1-Mouse_4-Pool_2


title: LAR, LAR, Mouse 3

description: Library name: Large_Intestine-LAR_2_7-Mouse_3-Pool_1

value: Pool 1


title: Limb Muscle, HC, Mouse 3

description: Library name: Limb_Muscle-HC_2_1-Mouse_3-Pool_2


title: Limb Muscle, HC, Mouse 2

description: Library name: Limb_Muscle-HC_2_1-Mouse_2-Pool_2


title: Limb Muscle, HC, Mouse 1

description: Library name: Limb_Muscle-HC_2_1-Mouse_1-Pool_2


title: LAR, LAR, Mouse 4

description: Library name: Large_Intestine-LAR_2_7-Mouse_4-Pool_1


title: LAR, LAR, Mouse 2

description: Library name: Large_Intestine-LAR_2_7-Mouse_2-Pool_1


title: LAR, LAR, Mouse 1

description: Library name: Large_Intestine-LAR_2_7-Mouse_1-Pool_1


title: LAR, HC, Mouse 1

description: Library name: Large_Intestine-HC_1_7-Mouse_1-Pool_1


title: LAR, HC, Mouse 4

description: Library name: Large_Intestine-HC_1_7-Mouse_4-Pool_1


title: Kidney, LAR, Mouse 4

description: Library name: Kidney-LAR_1_5-Mouse_4-Pool_1

source_name: Kidney

value: Kidney


title: Liver, LAR, Mouse 4

description: Library name: Liver-LAR_1_4-Mouse_4-Pool_2


title: Kidney, LAR, Mouse 3

description: Library name: Kidney-LAR_1_5-Mouse_3-Pool_1


title: Kidney, LAR, Mouse 1

description: Library name: Kidney-LAR_1_5-Mouse_1-Pool_4

value: Pool 4


title: Kidney, HC, Mouse 4

description: Library name: Kidney-HC_1_6-Mouse_4-Pool_1


title: Kidney, LAR, Mouse 2

description: Library name: Kidney-LAR_1_5-Mouse_2-Pool_4


title: Kidney, HC, Mouse 3

description: Library name: Kidney-HC_1_6-Mouse_3-Pool_1


title: Kidney, HC, Mouse 1

description: Library name: Kidney-HC_1_6-Mouse_1-Pool_1


title: Limb Muscle, LAR, Mouse 2

description: Library name: Limb_Muscle-LAR_2_6-Mouse_2-Pool_2


title: Kidney, HC, Mouse 2

description: Library name: Kidney-HC_1_6-Mouse_2-Pool_1


title: Mammary, HC, Mouse 1

description: Library name: Mammary-HC_1_7-Mouse_1-Pool_2


title: Heart Ventricles, LAR, Mouse 3

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_3-Pool_3


title: Heart Ventricles, LAR, Mouse 4

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_4-Pool_3


title: Heart Ventricles, LAR, Mouse 1

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_1-Pool_3


title: Heart Ventricles, HC, Mouse 4

description: Library name: Heart_Ventricles-HC_1_2-Mouse_4-Pool_3


title: Heart Ventricles, LAR, Mouse 2

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_2-Pool_3


title: Heart Ventricles, HC, Mouse 1

description: Library name: Heart_Ventricles-HC_1_2-Mouse_1-Pool_3


title: Heart Ventricles, HC, Mouse 2

description: Library name: Heart_Ventricles-HC_1_2-Mouse_2-Pool_3


title: LAR, HC, Mouse 3

description: Library name: Large_Intestine-HC_1_7-Mouse_3-Pool_1


title: Heart Atria, LAR, Mouse 3

description: Library name: Heart_Atria-LAR_1_2-Mouse_3-Pool_3


title: LAR, HC, Mouse 2

description: Library name: Large_Intestine-HC_1_7-Mouse_2-Pool_1


title: Heart Atria, HC, Mouse 3

description: Library name: Heart_Atria-HC_1_2-Mouse_3-Pool_3


title: Heart Atria, LAR, Mouse 1

description: Library name: Heart_Atria-LAR_1_2-Mouse_1-Pool_3


title: Heart Atria, HC, Mouse 4

description: Library name: Heart_Atria-HC_1_2-Mouse_4-Pool_3


title: Heart Atria, LAR, Mouse 4

description: Library name: Heart_Atria-LAR_1_2-Mouse_4-Pool_3


title: Heart Atria, LAR, Mouse 2

description: Library name: Heart_Atria-LAR_1_2-Mouse_2-Pool_3


title: Heart Atria, HC, Mouse 2

description: Library name: Heart_Atria-HC_1_2-Mouse_2-Pool_3


title: Heart Atria, HC, Mouse 1

description: Library name: Heart_Atria-HC_1_2-Mouse_1-Pool_3


title: GAT, LAR, Mouse 3

description: Library name: GAT-LAR_2_3-Mouse_3-Pool_1

source_name: GAT

value: GAT


title: GAT, LAR, Mouse 4

description: Library name: GAT-LAR_2_3-Mouse_4-Pool_1


title: GAT, LAR, Mouse 1

description: Library name: GAT-LAR_2_3-Mouse_1-Pool_1


title: GAT, HC, Mouse 2

description: Library name: GAT-HC_2_1-Mouse_2-Pool_1


title: GAT, HC, Mouse 4

description: Library name: GAT-HC_2_1-Mouse_4-Pool_1


title: GAT, LAR, Mouse 2

description: Library name: GAT-LAR_2_3-Mouse_2-Pool_1


title: GAT, HC, Mouse 1

description: Library name: GAT-HC_2_1-Mouse_1-Pool_1


title: Heart Ventricles, HC, Mouse 3

description: Library name: Heart_Ventricles-HC_1_2-Mouse_3-Pool_3


title: Eye, LAR, Mouse 1

description: Library name: Eye-LAR_2_7-Mouse_1-Pool_2

source_name: Eye

value: Eye


title: Eye, LAR, Mouse 3

description: Library name: Eye-LAR_2_7-Mouse_3-Pool_2


title: Eye, LAR, Mouse 2

description: Library name: Eye-LAR_2_7-Mouse_2-Pool_2


title: GAT, HC, Mouse 3

description: Library name: GAT-HC_2_1-Mouse_3-Pool_1


title: Eye, LAR, Mouse 4

description: Library name: Eye-LAR_2_7-Mouse_4-Pool_2


title: Eye, HC, Mouse 4

description: Library name: Eye-HC_1_9-Mouse_4-Pool_2


title: Diaphragm, LAR, Mouse 4

description: Library name: Diaphragm-LAR_2_5-Mouse_4-Pool_1

source_name: Diaphragm

value: Diaphragm


title: Eye, HC, Mouse 2

description: Library name: Eye-HC_1_9-Mouse_2-Pool_2

value: Pool 2


title: Diaphragm, LAR, Mouse 2

description: Library name: Diaphragm-LAR_2_5-Mouse_2-Pool_1


title: Eye, HC, Mouse 3

description: Library name: Eye-HC_1_9-Mouse_3-Pool_2


title: Eye, HC, Mouse 1

description: Library name: Eye-HC_1_9-Mouse_1-Pool_2


title: Diaphragm, LAR, Mouse 3

description: Library name: Diaphragm-LAR_2_5-Mouse_3-Pool_1


title: Diaphragm, HC, Mouse 1

description: Library name: Diaphragm-HC_2_2-Mouse_1-Pool_4


title: Diaphragm, HC, Mouse 4

description: Library name: Diaphragm-HC_2_2_-Mouse_4-Pool_1


title: Diaphragm, LAR, Mouse 1

description: Library name: Diaphragm-LAR_2_5-Mouse_1-Pool_1


title: Diaphragm, HC, Mouse 3

description: Library name: Diaphragm-HC_2_2_-Mouse_3-Pool_1


title: Diaphragm, HC, Mouse 2

description: Library name: Diaphragm-HC_2_2_-Mouse_2-Pool_1


title: Bone, LAR, Mouse 3

description: Library name: Bone-LAR_2_8-Mouse_3-Pool_3

source_name: Bone

value: Bone


title: Bone, HC, Mouse 3

description: Library name: Bone-HC_3_6-Mouse_3-Pool_3

value: BALB/cAnNTac


title: Bone, LAR, Mouse 1

description: Library name: Bone-LAR_2_8-Mouse_1-Pool_3

value: female


title: Bone, LAR, Mouse 2

description: Library name: Bone-LAR_2_8-Mouse_2-Pool_3

value: spaceflight


title: Bone, HC, Mouse 4

description: Library name: Bone-HC_3_6-Mouse_4-Pool_3

value: Pool 3


title: Bone, HC, Mouse 2

description: Library name: Bone-HC_3_6-Mouse_2-Pool_3


title: Blood, LAR, Mouse 2

description: Library name: Blood-LAR_2_4-Mouse_2-Pool_3

source_name: Blood

value: Blood


title: Blood, HC, Mouse 4

description: Library name: Blood-HC_1_8-Mouse_4-Pool_3


title: Bone, HC, Mouse 1

description: Library name: Bone-HC_3_6-Mouse_1-Pool_3


title: Blood, HC, Mouse 2

description: Library name: Blood-HC_1_8-Mouse_2-Pool_3


title: BAT, LAR, Mouse 2

description: Library name: BAT-LAR_2_3-Mouse_2-Pool_1

source_name: BAT

value: BAT


title: Blood, HC, Mouse 1

description: Library name: Blood-HC_1_8-Mouse_1-Pool_3


title: Blood, HC, Mouse 3

description: Library name: Blood-HC_1_8-Mouse_3-Pool_3


title: BAT, LAR, Mouse 1

description: Library name: BAT-LAR_2_3-Mouse_1-Pool_1


title: Blood, LAR, Mouse 1

description: Library name: Blood-LAR_2_4-Mouse_1-Pool_3


title: BAT, LAR, Mouse 4

description: Library name: BAT-LAR_2_3-Mouse_4-Pool_1


title: BAT, HC, Mouse 4

description: Library name: BAT-HC_2_3-Mouse_4-Pool_1


title: Aorta, LAR, Mouse 1

description: Library name: Aorta-LAR_2_2-Mouse_1-Pool_2

source_name: Aorta

value: Aorta


title: Aorta, LAR, Mouse 2

description: Library name: Aorta-LAR_2_2-Mouse_2-Pool_2


title: Aorta, LAR, Mouse 3

description: Library name: Aorta-LAR_2_2-Mouse_3-Pool_2


title: BAT, LAR, Mouse 3

description: Library name: BAT-LAR_2_3-Mouse_3-Pool_1


title: BAT, HC, Mouse 2

description: Library name: BAT-HC_2_3-Mouse_2-Pool_1

value: control


title: Bone, LAR, Mouse 4

description: Library name: Bone-LAR_2_8-Mouse_4-Pool_3


title: Aorta, LAR, Mouse 4

description: Library name: Aorta-LAR_2_2-Mouse_4-Pool_2


title: BAT, HC, Mouse 1

description: Library name: BAT-HC_2_3-Mouse_1-Pool_1


title: BAT, HC, Mouse 3

description: Library name: BAT-HC_2_3-Mouse_3-Pool_1


title: Aorta, HC, Mouse 3

description: Library name: Aorta-HC_1_4-Mouse_3-Pool_2


title: SynCRE_E4_10M_4

first: Ayushi

last: Agrawal

address: 1650 Owens St

institute: Gladstone Institutes

description: 10x Genomics single nucleus RNA sequencing

data_processing:
Demultiplexed fastq files were aligned to a custom reference genome built from mm10 2020-A that includes introns, using the Cellranger v6.1.1 counts function with default parameters, as described in the Cellranger documentation. UMI counts were also determined using the Cellranger counts function. UMI counts were also determined using the Cellranger counts function, and aggregation of these counts was performed using the Cellranger aggr function.
Assembly: The Homo sapiens APOE are genes of interest for this study. Custom mouse reference genome was made using these genes of interest , the reference mouse genome sequence (GRCm38) from Ensembl (release 98) and the mouse gene annotation file from GENCODE (release M23), similar to those used in 10x Genomics Cell Ranger mouse reference package mm10 2020-A.
Supplementary files format and content: feature-barcode matrix in the Hierarchical Data Format (HDF5 or H5) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

molecule: nuclear RNA

source_name: hippocampus

growth_protocol: Human LoxP-floxed APOE knock-in (fE) mice with conditional deletion of the human APOE gene were generated as previously described. Briefly, homozygous fE3 and fE4 mice were crossbred with Synapsin 1-Cre transgenic mice [B6.Cg-Tg(Syn1-Cre)671Jxm/J] (The Jackson Laboratory #003966) to generate fE4 and fE3 mice with no Cre or Syn1-Cre. For generation of the fE/Syn1-Cre line, only female Syn1-Cre mice were used for breeding purposes because germline recombination has been reported to occur in the progeny of male Syn1-Cre mice. All mice were on a pure C57BL/6 genetic background and were housed in a pathogen-free barrier facility on a 12 h light cycle at 19-23ºC and 30-70% humidity. Animals were identified by ear punch under brief isoflurane anesthesia and genotyped by polymerase chain reaction (PCR) of a tail clipping. All animals otherwise received no procedures except those reported in this study. For all studies, both male and female mice were used. All animal experiments were conducted in accordance with the guidelines and regulation of the National Institutes of Health, the University of California, and the Gladstone Institutes under the protocol AN176773.

extract_protocol:
The mouse hippocampus was dissected on ice and placed into a pre-chilled 2 mL Dounce with 1 mL of cold 1X Homogenization Buffer (1X HB) (250 mM Sucrose, 25 mM KCL, 5 mM MgCl2, 20 mM Tricine-KOH pH7.8, 1 mM DTT, 0.5 mM Sermidine, 0.15 mM Sermine, 0.3% NP40, 0.2 units/µL RNase inhibitor, ~0.07 tablets/sample Protease inhibitor). Dounce with “A” loose pestle (~10 strokes) and then with “B” tight pestle (~15 strokes). The homogenate was filtered using a 70 µM Flowmi strainer (Eppendorf) and transferred to a pre-chilled 2 mL LoBind tube (Fischer Scientific). Nuclei were pelleted by spinning for 5 min at 4°C at 350 RCF. The supernatant was removed and the nuclei were resuspended in 400 µL 1X HB. Next, 400 µL of 50% Iodixanol solution was added to the nuclei and then slowly layered with 600 µL of 30% Iodixanol solution under the 25% mixture, then layered with 600 µL of 40% Iodixanol solution under the 30% mixture. The nuclei were then spun for 20 min at 4°C at 3,000g in a pre-chilled swinging bucket centrifuge. 200 µL of the nuclei band at the 30%-40% interface was collected and transferred to a fresh tube. Then, 800 µL of 2.5% BSA in PBS plus 0.2 units/µL of RNase inhibitor was added to the nuclei and then were spun for 10 min at 500 RCF at 4C. The nuclei were resuspended with 2% BSA in PBS plus 0.2 units/µL RNase inhibitor to reach ~500 nuclei/µL. The nuclei were then filtered with a 40 µM Flowmi stainer. The nuclei were counted and then ~13,000 nuclei per sample were loaded onto 10x Genomics Next GEM chip G. The snRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.
The snRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.
10X Single-nucleus RNAseq

value: hippocampus


title: SynCRE_E3_5M_4


title: Aorta, HC, Mouse 4

description: Library name: Aorta-HC_1_4-Mouse_4-Pool_2


title: Aorta, HC, Mouse 2

description: Library name: Aorta-HC_1_4-Mouse_2-Pool_2


title: SynCRE_E3_10M_4


title: Aorta, HC, Mouse 1

description: Library name: Aorta-HC_1_4-Mouse_1-Pool_4


title: SynCRE_E4_5M_3


title: Blood, LAR, Mouse 4

description: Library name: Blood-LAR_2_4-Mouse_4-Pool_3


title: SynCRE_E4_5M_4


title: SynCRE_E3_10M_3


title: SynCRE_E4_10M_3


title: SynCRE_E3_10M_2


title: SynCRE_E3_5M_2


title: SynCRE_E4_10M_1


title: SynCRE_E3_5M_1


title: 48dox-RPL22-NTrep1

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Bulk RNA-seq

data_processing:
Reads were aligned with STARv2.7.6a
Assembly: mm10
Supplementary files format and content: tsv files contain edits-per-read (EPR) for each gene

source_name: primary cortical neurons

growth_protocol: Cortices were dissected from E18 C57BL/6J embryos in Leibovitz's L-15 Medium (Life Technologies) and incubated in TrypLE Express (Life Technologies) at 37°C for 4 min. Neurons were mechanically dissociated and plated on poly-D-lysine hydrobromide-coated 6-well plates (600,000 cells/well). Neurons were maintained in a humidified environment at 37°C and 5% CO2 in Neurobasal medium (Life Technologies) supplemented with B27 Plus Supplement (Life Technologies) and GlutaMAX (Life Technologies). At day in vitro (DIV) 3 Floxuridine was added to the medium to limit growth of dividing cells.

extract_protocol:
RNA isolation was performed using Direct-zol RNA microprep kit (Zymo #R2062) and RNA quality was measured via RNA ScreenTape Analysis (Agilent) before proceeding to library prep.
Illumina TruSeq Stranded mRNA kit (Illumina #20020595) was used for library preps.

treatment_protocol: DIV 6 neurons were infected with 1x1013 viral genomes/ml of inducible Ribo-STAMP AAV virions. Ribo-STAMP expression was induced with 1µg/ml Doxycycline for 48 h prior collection at DIV14.

value: primary cortical neurons

value: WT

value: 48h dox, AAV-RPL22-STAMP


title: 48dox-RPL22-NTrep3

description: Bulk RNA-seq


title: 48dox-RPL10-NTrep3

description: Bulk RNA-seq

value: 48h dox, AAV-RPL10A-STAMP


title: 48dox-RPL22-NTrep2

description: Bulk RNA-seq


title: SynCRE_E3_10M_1


title: 48dox-RPL10-NTrep1

description: Bulk RNA-seq


title: 48dox-RPL10-NTrep2

description: Bulk RNA-seq


title: brain, WT_1007MDA5 R3

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: WT_1007MDA5 R3

data_processing:
Illumina adapter sequences and low-quality reads were filtered using the tool Trimmomatic
reads were aligned to the mouse reference genome mm10 by STAR aligner
RNA alterations were called by BCFtools
Assembly: mm10
Supplementary files format and content: TAB for reads per genes

source_name: brain

extract_protocol:
The whole brains of the WT and AdarG1007R/G1007R;Ifih1-/- mice at two weeks of age were used for RNA isolation. Three RNA samples of each genotype were used for RNA-seq studies. 100ng total RNA of each mouse was used for the RNA library preparation.
RNA libraries were generated using theKAPA RNA HyperPrep Kit with the removal of ribosome RNAs by RiboErase (Kapa Biosystems) according to the manufacturer’s protocol.

value: brain


title: brain, WT_1007MDA5 R2

description: WT_1007MDA5 R2


title: brain, WT_1007 R3

description: WT_1007 R3

data_processing:
Illumina adapter sequences and low-quality reads were filtered using the tool Trimmomatic
reads were aligned to the mouse reference genome mm10 by STAR aligner
RNA alterations were called by BCFtools
Assembly: mm10
Supplementary files format and content: TAB for reads per genes, TXT for the variant calling by BCFtools


title: brain, WT_1007MDA5 R1

description: WT_1007MDA5 R1


title: brain, WT_1007 R1

description: WT_1007 R1


title: brain, WT_WT R3

description: WT_WT R3


title: Total-RNA-2

description: Bulk RNA-seq

data_processing:
reads were mapped using STARv2.7.6a
counts were compiled with subread featureCounts
Assembly: mm10
Supplementary files format and content: .txt files with featurecounts counts per gene

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and complexes were immunoprecipitated with protein-specific antibody from Bethyl Laboratories
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

value: no treatment


title: brain, WT_WT R2

description: WT_WT R2


title: Total-RNA-1

description: Bulk RNA-seq


title: brain, WT_WT R1

description: WT_WT R1


title: SynCRE_E4_5M_2


title: SynCRE_E3_5M_3


title: SynCRE_E4_10M_2


title: RPS2-eCLIP-IP-2

description: Bulk RNA-seq

value: rRNA depletion


title: SynCRE_E4_5M_1


title: RPS2-eCLIP-IP-1

description: Bulk RNA-seq


title: 48dox-RPS2-B60rep3

description: Bulk RNA-seq

data_processing:
STARv
Assembly: mm10
Supplementary files format and content: .tsv files containing edit per read (EPR) data per gene per sample

treatment_protocol: DIV 6 neurons were infected with 1x1013 viral genomes/ml of inducible Ribo-STAMP AAV virions. Ribo-STAMP expression was induced with 1µg/ml Doxycycline for 48 h prior collection at DIV14. BDNF (100 ng/ml) was applied 15 min and 60 min prior to collection.

value: 48h dox, BDNF 60'


title: 48dox-RPS2-B60rep2

description: Bulk RNA-seq


title: 48dox-RPS2-B60rep1

description: Bulk RNA-seq


title: 48dox-RPS2-NTrep3

description: Bulk RNA-seq

value: 48h dox, non-treated


title: 48dox-RPS2-B15rep3

description: Bulk RNA-seq

value: 48h dox, BDNF 15'


title: 48dox-RPS2-NTrep1

description: Bulk RNA-seq


title: 48dox-RPS2-B15rep1

description: Bulk RNA-seq


title: 48dox-RPS2-B15rep2

description: Bulk RNA-seq


title: 48dox-RPS2-NTrep2

description: Bulk RNA-seq


title: brain, WT_1007 R2

description: WT_1007 R2


title: colon, cKO_DSS, rep4

city: Beijing

first: Meng

middle: zhen

last: Li

address: 2 West Yuanmingyuan Road

department: College of biological science

institute: China Agricultural University

data_processing:
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Supplementary files format and content: mm10

source_name: colon

extract_protocol:
TrIZOL
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.

value: colon

value: colonic epithelial cells

value: Rictor Flox; Villin-Cre

value: DSS


title: colon, cKO_DSS, rep3


title: colon, WT_DSS, rep4

value: Villin-Cre


title: colon, cKO_DSS, rep1


title: colon, WT_DSS, rep1


title: colon, WT_DSS, rep3


title: colon, cKO, rep4

value: no


title: colon, WT_DSS, rep2


title: colon, cKO, rep2


title: colon, cKO, rep1


title: colon, cKO, rep3


title: Blood, LAR, Mouse 3

description: Library name: Blood-LAR_2_4-Mouse_3-Pool_3

value: Blood

value: BALB/cAnNTac

value: female

value: spaceflight

value: Pool 3


title: colon, WT, rep4


title: colon, WT, rep3


title: colon, WT, rep2


title: colon, WT, rep1


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-P11

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: 9 months

tag: brain region

value: DHC

tag: gender

value: M


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-P12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-P23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-P24


title: colon, cKO_DSS, rep2


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-O12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-N24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-O11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-O23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-N12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-M24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-N11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-M23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-M11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-M12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-L12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-L23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-K23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-K11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-J23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-K12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-O24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-J12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-J11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-I24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-N23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-I12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-I23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-I11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-H11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-H23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-G24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-H12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-G23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-H24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-L24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-G12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-F23


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-G11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-F12


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-K24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-L11


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-J24


title: AMB_200218_9mo_8E_9H_8J_9J_2_P4-6-P12-E24


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