title: CaP_Week6_Rep3

value: Cap Scaffold at 6 weeks


title: Het 3-4 e

status: Public on Jul 02 2024

type: SRA

city: Cambridge

first: Matthew

middle: D

last: Shoulders

state: MA

address: 77 Massachusetts Avenue

department: Chemistry

country: USA

institute: Massachusetts Institute of Technology

description:
p.Gly1170Ser heterozygous substitution in COL2A12
Het_3-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

library_source: transcriptomic

data_processing:
Base calling was performed using the Illumina Offline Base Caller, Illumina RTA v. 2.11.3.
Forward reads containing barcode information (Read 1) were extracted and split into well barcode and unique molecular identifier (UMI) sequences and added to the header of the corresponding reverse read (Read 2), which was then treated as a single-end read.
Reads were aligned against hg19 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
For mapping and quantitation, reads were scored against GRCh38/ENSEMBL 101 annotation using Salmon v.1.3 with flags quant -p 8 -l ISR –validateMappings. The resulting quant.sf files were imported into the R statistical environment using the tximport library (tximport function, option “salmon”), and gene-level counts and transcript per-milllion (TPM) estimates were calculated for all genes.
Assembly: GRCh38/ENSEMBL 101
Supplementary files format and content: Raw counts per sample (merged salmon quant.sf output).
Supplementary files format and content: log2Tpm values per sample (merged salmon quant.sf output).

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC-derived cartilage

growth_protocol: iPSCs were grown on Matrigel (Corning) coated plates in Essential 8 medium. Differentiation to chondrocytes was carried out as descirbed by Lamandé et al. (PNAS, 2023)

extract_protocol:
Individual chondronoids were snap frozen and pulverized. Each of the three independent differentiations was considered a biological replicate. Chondronoids from the same differentiation are indicated as such (-1,-2 etc.). The pulverized tissue was resuspended in TRIzol, and extracted by chloroform according to manufacturer's protocol. The aqueous phase was collected and RNA was purified using Direct-zol RNA Microprep kit (Zymo Research) according to manufacturer's protocol.
High throughput three prime digital gene expression (HT-3'DGE) was adapted from the Soumillon et al. protocol (Soumillon et al. BioRxiv https://www.biorxiv.org/content/10.1101/003236v1) to perform reverse-transcription reactions using a dedicated RT primer containing sample and unique molecular identifier (UMI) sequences, to generate four subpools of 24 samples each. After second strand synthesis, Illumina adapters were added using the Nextera Flex tagmentation protocol substituting the normal P500 primer with an ad-hoc primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500 in high-output paired-end mode (20/57 nt reads).

tag: tissue

value: iPSC-derived cartilage

tag: cell type

value: iPSC-derived chondrocyte

tag: Sex

value: female

tag: genotype

value: Gly1170Ser heterozygote

tag: time point

value: EARLY (day 34)

tag: technical replicate

tag: biological replicate

tag: replicate

tag: included


title: MOLT4_H3K4me3

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files
Supplementary files format and content: bigWig files

molecule: genomic DNA

growth_protocol: MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end Cut&Run-Seq sequencing

treatment_protocol: The cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina Novaseq at GENEWIZ Azenta Life Sciences Co. Ltd.

tag: cell line

value: T-ALL

tag: antibody

value: MOLT4_H3K4me3 (Epicypher)


title: Old, 5, spatial transcriptomics

city: Philadelphia

first: Yicheng

last: Wu

state: Pennsylvania

address: 415 Curie Boulevard

department: Neuroscience

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Raw data was processed using the Cell Ranger (v6) and Space Ranger (v2) softwares.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Whole brain

extract_protocol:
For scRNA-seq, freshly collected brain cells from dentate gyrus of C57Bl6/JRj mice were dissociated using Neural Tissue Dissociation Kit (P) and Myelin Removal Beads II (Miltenyi Biotec).  For spatial transcriptomics, mouse brains were collected and embedded in OCT.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, spatial gene expression protocol, 10x Genomics).

value: Brain cells

value: Whole brain

tag: strain

tag: age

value: 16-21 month old


title: MOLT4_H3K4me3_Input

value: IgG


title: CaP_Week6_Rep1

city: Rochester

first: Hani

middle: A

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

data_processing:
Data Formatting bcl2fastq version 2.20.0
Data Cleaning FastP version 0.23.1 with parameters --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r
Genome Alignment STAR_2.7.9a with parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx
Read Quantification subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Assembly: Rnor_6.0 GCA_000001895.4
Supplementary files format and content: tab-delimited text file of gene counts

organism: Rattus norvegicus

source_name: Repair bone tissue

extract_protocol:
For the bone marrow, tissue dissociation was achieved with red blood cell lysis buffer, followed by enzymatic digestion using Type IV collagenase, dispase, and DNase. Bone tissue was mechanically disrupted into fine pieces and further digested with Type I collagenase. Cells released from the marrow and bone were pooled and submitted to the GRC for mRNA extraction.
mRNA libraries for RNA-Seq were prepared using the Illumina mRNA prep kit following manufacturers protocols

value: Repair bone tissue

value: WT

tag: treatment


title: Old, 4, spatial transcriptomics

description: 10x Genomics


title: Het 3-2 e

description:
p.Gly1170Ser heterozygous substitution in COL2A10
Het_3-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Het 3-1 e

description:
p.Gly1170Ser heterozygous substitution in COL2A9
Het_3-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: TALL1-15_ATAC

data_processing:
ATAC-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ATAC-seq reads were remove duplicate with Picard MarkDuplicates package. Multiple mapping reads were removed using samtools view -q 10
ATAC-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-5, keep-dup=all, --SPMR were used to normalized the bedGraph output.The signal has been floored to 0.1 after bdgcmp subtract function.
Assembly: hg19
Supplementary files format and content: narrowPeak files of ATAC-seq
Supplementary files format and content: bigWig files of ATAC-seq

source_name: T-ALL cells

growth_protocol: T-ALL cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the ATAC-seq samples and sequencing of paired-end 150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end ATAC-Seq sequencing

treatment_protocol: The cells are incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

tag: atac antibody

value: ATAC


title: Old, 2, spatial transcriptomics

description: 10x Genomics


title: CaP_Week2_Rep3

value: Cap Scaffold at 2 weeks


title: Old, 3, spatial transcriptomics

description: 10x Genomics


title: Old, 1, spatial transcriptomics

description: 10x Genomics


title: Hom 1-2 e

description:
p.Gly1170Ser homozygous substitution in COL2A14
Hom_1-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: Gly1170Ser homozygote


title: CaP_Week2_Rep2


title: MOLT4-12_ATAC


title: Middle-age, 4, spatial transcriptomics

description: 10x Genomics

value: 9-11 month old


title: HBP-ALL-4_ATAC

value: HBP-ALL


title: Het 2-4 e

description:
p.Gly1170Ser heterozygous substitution in COL2A8
Het_2-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte


title: CaP_Week2_Rep1


title: KOPTK-7_ATAC


title: Middle-age, 3, spatial transcriptomics

description: 10x Genomics


title: Het 2-3 e

description:
p.Gly1170Ser heterozygous substitution in COL2A7
Het_2-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: female

value: Gly1170Ser heterozygote


title: DND-2_ATAC


title: Het 2-2 e

description:
p.Gly1170Ser heterozygous substitution in COL2A6
Het_2-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: EARLY (day 34)


title: CaP_Week6_Rep2

value: Cap Scaffold at 6 weeks


title: Normal, Male#2 [S51_CMB140]

city: PALO ALTO

first: Soochi

last: Kim

state: California

address: Bldg 101 Rm 141, Miranda

institute: Stanford University

data_processing:
Raw reads were pre-processed to remove adapter, poly-N, low-quality reads.
Aligned to the human reference genome using Hisat2 (v2.0.5).
Count reads were generated using featureCounts v1.5.0-p3.
Assembly: hg38
Supplementary files format and content: tab-delimited xlsx file include gene count for each Sample

source_name: vastus lateralis muscle

extract_protocol:
Total RNA were isolated using the AllPrep Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared by Novogene Corporation

value: vastus lateralis muscle

tag: disease state

value: Normal

value: Male

tag: time

value: Fresh frozen


title: Middle-age, 2, spatial transcriptomics

description: 10x Genomics

value: Brain cells

tag: tissue

value: Whole brain


title: Het 3-3 e

description:
p.Gly1170Ser heterozygous substitution in COL2A11
Het_3-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: cell type


title: Normal, Male#1 [S50_UK24]

tag: Sex


title: CCRF-1_ATAC

value: CCRF-CEM

value: ATAC


title: Het 2-1 e

description:
p.Gly1170Ser heterozygous substitution in COL2A5
Het_2-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: genotype


title: Middle-age, 1, spatial transcriptomics

description: 10x Genomics


title: Sarcopenia, Male#2 [S49_UK08]

value: Sarcopenia


title: Het 1-4 e

description:
p.Gly1170Ser heterozygous substitution in COL2A4
Het_1-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: time point


title: Sarcopenia, Male#1 [S48_UK17]


title: MOLT4_ACBI-3H1_ATAC

growth_protocol: DND-41 and MOLT-4 were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep with 100nM ACBI-1 or DMSO.


title: MOLT4_ACBI-3H2_ATAC


title: Het 1-2 e

description:
p.Gly1170Ser heterozygous substitution in COL2A2
Het_1-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: technical replicate


title: Normal, Female#2 [S47_CMB125]

value: Female


title: Het 1-3 e

description:
p.Gly1170Ser heterozygous substitution in COL2A3
Het_1-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

tag: biological replicate


title: Young, 3, spatial transcriptomics

description: 10x Genomics

value: 3 month old


title: MOLT4_DMSO-3H2_ATAC


title: Normal, Female#1 [S46_CMB47]


title: Het 1-1 e

description:
p.Gly1170Ser heterozygous substitution in COL2A1
Het_1-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

tag: replicate


title: Young, 1, spatial transcriptomics

description: 10x Genomics


title: MOLT4_DMSO-3H1_ATAC


title: WT 3-4 e

description:
wild-type control
WT_3-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived chondrocyte

value: Wild-type

tag: included


title: Old, 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data was processed using the Cell Ranger (v6) and Space Ranger (v2) softwares.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dentate gyrus

value: Dentate gyrus

value: 16-21 month old


title: Sarcopenia, Female#1 [S44_CMB2]


title: Old, 1, scRNAseq

description: 10x Genomics


title: Microgravity, Donor#2, SW033291, Day 7 [S40_9DF]

source_name: primary myoblast

value: primary myoblast

value: Day 7

value: Migrogravity + SW033291


title: DND41_ACBI-3H1_ATAC

tag: cell line


title: WT 3-3 e

description:
wild-type control
WT_3-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: female

value: EARLY (day 34)


title: Young, 4, spatial transcriptomics

description: 10x Genomics

value: Brain cells


title: DND41_ACBI-3H2_ATAC


title: DND41_DMSO-3H2_ATAC


title: Middle-age, scRNAseq

description: 10x Genomics

value: 9-11 month old


title: WT 3-1 e

description:
wild-type control
WT_3-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: DND41_DMSO-3H1_ATAC


title: Young, 2, spatial transcriptomics

description: 10x Genomics

value: Whole brain


title: Young, scRNAseq

description: 10x Genomics


title: WT 2-4 e

description:
wild-type control
WT_2-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: Microgravity, Donor#2, IGF1, Day 7 [S33_8DF]

value: Normal

value: Microgravity + IGF1


title: Microgravity, Donor#1, IGF1, Day 7 [S32_8CF]


title: WT 2-3 e

description:
wild-type control
WT_2-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: MOLT4_ACBI-24H2_ATAC

value: ATAC


title: WT_spleen_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter using the auto detection mode and the following parameters: --clip_r1 3 --three_prime_clip_r2 3.
Then reads were mapped to the mouse Ensembl GRCm38 transcriptome index using salmon (v.1.3.0).
Gene-level normalization and differential gene expression analysis were performed with Bioconductor (Gentleman et al., 2004; Huber et al., 2015) package DESeq2 v.1.28 (Love et al., 2014) using the R environment v.4.0 (R Core Team, 2015).
The Wald test was used for significance testing and the resulting false discovery rate (FDR) p-values were adjusted for multiple comparisons using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) and genes were considered differentially expressed (DEGs) only at FDR < 0.05
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: spleen

extract_protocol:
Total RNA was isolated with the Single Cell RNA Purification Kit (Norgen) following the manufacturer’s protocol.
RNA-Seq library for mRNA sequencing was prepared with SMARTer Stranded Total RNA-Seq kit - Pico Input Mammalian. All extracted RNA samples were quality controlled for integrity with a 2100 Bioanalyzer system (Agilent Technologies) and were sequenced on a NovaSeq 6000 System (Illumina)

value: spleen

value: CD4+ YFP+ Treg

value: Foxp3YFPCre/+ Tfrc+/+


title: floxed_spleen_rep3

value: Foxp3YFPCre/+ Tfrcfl/fl


title: Sarcopenia, Female#2 [S45_CMB138]

value: vastus lateralis muscle

value: Sarcopenia

value: Female

value: Fresh frozen


title: Gravity, Donor#2, Day 7 [S7_4DG]

value: primary myoblast

value: Day 7

value: In gravity


title: MOLT4_DMSO-24H2_ATAC


title: MOLT4_ACBI-24H1_ATAC


title: WT 2-2 e

description:
wild-type control
WT_2-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte

value: female

value: Wild-type

value: EARLY (day 34)


title: floxed_spleen_rep2


title: WT 3-2 e

description:
wild-type control
WT_3-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: WT 2-1 e

description:
wild-type control
WT_2-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: MOLT4_DMSO-24H1_ATAC

value: ATAC


title: Microgravity, Donor#2, Day 7 [S4_4DF]

value: Normal

value: Microgravity


title: Microgravity, Donor#1, SW033291, Day 7 [S39_9CF]

value: Migrogravity + SW033291


title: WT 1-4 e

description:
wild-type control
WT_1-4_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: DND41_ACBI-24H2_ATAC


title: WT_spleen_rep2

value: spleen

value: CD4+ YFP+ Treg

value: Foxp3YFPCre/+ Tfrc+/+


title: Microgravity, Donor#1, Day 7 [S3_4CF]


title: floxed_spleen_rep1

value: Foxp3YFPCre/+ Tfrcfl/fl


title: DND41_DMSO-24H2_ATAC


title: WT 1-3 e

description:
wild-type control
WT_1-3_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: RNA-seq-WT-MM-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
RNA-seq in WT strain after MM induction
RNA-seq.bed

data_processing:
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
For Ribo-seq library, the raw reads was mapped to the  Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). The reads was counts by bedtools
The DMS-seq library was analysised through Structure-seq2 pipeline.
Assembly: Pseudomonas sringae 1448A (NC_005773.3)
Supplementary files format and content: React files for all DMS-seq results
Supplementary files format and content: Raw count bed fiels

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

extract_protocol:
The RNA was extracted by using the RNA isolater total RNA extraction reagent (Vazyme, #R401)
For DMS-seq library, the cDNA was synthesis by reversed transcription. ssDNA was ligated to cDNA by circligase ssDNA ligase. The DNA library was constructed by PCR.

value: WT

value: MM condition


title: WT 1-2 e

description:
wild-type control
WT_1-2_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz


title: DND41_ACBI-24H1_ATAC


title: WT_spleen_rep1


title: RNA-seq-WT-MM-1

source_name: Pseudomonas savastanoi pv. phaseolicola 1448A


title: RNA-seq-WT-KB-2

description:
RNA-seq in WT strain in KB condition
RNA-seq.bed

value: Pseudomonas savastanoi pv. phaseolicola 1448A

value: KB condition


title: Patient P9 Primary Tumor, T cell receptors, Biopsy

city: New York

first: Alexander

last: Tsankov

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomics

institute: Icahn School of Medicine at Mount SInai

data_processing:
Pair-ended FASTQ files were mapped to the GRCh38 human transcriptome using the count function in Cell Ranger
The count matrices obtained were normalized, log-transformed and scaled using the Seurat version 3 package in R
Cells with < 400 genes, < 1000 unique molecular identifier (UMI) counts or > 25% mitochondrial gene expression detected were removed from downstream analyses
Assembly: GRCh38
Supplementary files format and content: cell-filtered count matrices, TCR contig info
Library strategy: TCR-seq

source_name: Primary Tumor Biopsy

extract_protocol:
Tumor samples were transported in RPMI stored at 4°C, rinsed with PBS, minced and incubated in a rotation shaker for 40 minutes at 37°C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Dead cells were removed using an EasySep Dead Cell Removal (Annexin V) Kit. Cell suspensions were sorted into CD45+ and CD45- cells using the EasySep™ Human CD45 Depletion Kit per kit instructions.
PBMCs from the blood samples were isolated within 3 hours of collection via Ficoll density gradient centrifugation for 10 min at 1200g room temperature. The supernatant was then spun down at 500g for 10 min at 4 degrees C and the pellet resuspended to a concentration of 10x10^6 cells/ml cold Human Serum AB (GemCell HAB and HAB + 20% DMSO in 1:1 ratio). The resulting PBMCs were stored in 2ml Cryogenic vials in liquid nitrogen. Previously frozen PBMCs were thawed, washed 2X in RPMI 2% FCS, treated with ACK lysis buffer (Lonza) to remove RBCs and briefly incubated with DAPI. 300,000 cells were then sorted on a DAPI negative gate. Cells were then stained for 30 minutes at room temperature with a panel of 138 Total-Seq-C antibodies (Biolegend, Stoeckius et al 2017) and washed 3x using the HT1000 laminar wash system (Curiox). Cells were then counted using the Cellaca MX High-throughput Automated Cell Counter as described in the manufacturer’s protocol (Nexcelom), pooled and loaded on the 10x Chromium Next GEM Chip K Kit using a superloading strategy mixing cells from the same sample across lanes.
For tumor samples, 10x libraries were constructed using the 10x supplied protocol and sequenced at the Mount Sinai Genomics Core Facility.
For PBMCs in the blood samples, libraries were prepared according to manufacturer’s protocol (10x Genomics).
scRNA-seq, CITE-seq (blood only), TCR-seq

value: Primary Tumor Biopsy

tag: tumor stage

value: II

tag: molecule type

value: T cell receptor


title: WT 1-1 e

description:
wild-type control
WT_1-1_e
Gene_expression_counts.txt.gz
Gene_expression_log2TPMs.txt.gz

value: iPSC-derived cartilage

value: iPSC-derived chondrocyte

value: female

value: Wild-type


title: Gravity, Donor#1, Day 7 [S6_4CG]

value: primary myoblast

value: Normal

value: Day 7

value: In gravity


title: DND41_DMSO-24H1_ATAC

value: ATAC


title: Lacrimal Gland, replicate 5, scRNAseq

city: Zhengzhou

first: Zhijie

last: Li

state: Henan

address: Weiwu Road No. 7

country: China

institute: Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software (version 7.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Lacrimal Gland

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Lacrimal Gland

tag: strain

tag: age

value: Male


title: Natural Cycle-LH9 [EMB038]

city: Newark

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Demultiplexing (picardtools v2.17.1)
Trimming (trimgalore v0.3.7)
Alignment (STAR v2.5.1b)
Feature calling (HTSeq v 0.12.3)
Differential gene expression (DESeq2 v1.22.1)
Assembly: HG38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

source_name: Endometrial Biopsy

extract_protocol:
Total RNA was extracted and purified with the RNeasy Plus Mini Kit (Qiagen). 500 ng total RNA was sent to Albert Einstein College of Medicine for mRNA enrichement and library construction.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom secondstrand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the secondstrand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the doublestranded cDNA library is completed through size selection and PCR enrichment

tag: group

tag: race

value: Black

tag: bmi

tag: gravida

tag: para

tag: estradiol

tag: progesterone


title: Lacrimal Gland, replicate 4, scRNAseq

description: 10x Genomics

tag: tissue

tag: Sex


title: Lacrimal Gland, replicate 3, scRNAseq

description: 10x Genomics


title: RNA-seq-WT-KB-1

tag: cell type

value: Pseudomonas savastanoi pv. phaseolicola 1448A

tag: genotype

value: WT

tag: treatment


title: Ribo-seq-WT-MM-2

description:
Ribo-seq in WT strain after MM induction
Ribo-seq.bed

data_processing:
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
For Ribo-seq library, the raw reads was mapped to the  Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). The reads was counts by bedtools
The DMS-seq library was analysised through Structure-seq2 pipeline.
Assembly: Pseudomonas sringae 1448A (NC_005773.3)
Supplementary files format and content: React files for all DMS-seq results
Supplementary files format and content: Raw count bed fiels
Library strategy: Ribo-seq

value: MM condition


title: Patient P6 Primary Tumor, T cell receptors, Biopsy

value: Primary Tumor Biopsy

value: IIIB


title: Natural Cycle-LH2 [EMB035]


title: Natural Cycle-LH2 [EMB037]


title: Lacrimal Gland, replicate 2, scRNAseq

description: 10x Genomics


title: Ovarian Stimulation Cycle-hCG2 [EMB034]

value: White


title: Patient P2 Primary Tumor, gene expression, Biopsy, pos

data_processing:
Pair-ended FASTQ files were mapped to the GRCh38 human transcriptome using the count function in Cell Ranger
The count matrices obtained were normalized, log-transformed and scaled using the Seurat version 3 package in R
Cells with < 400 genes, < 1000 unique molecular identifier (UMI) counts or > 25% mitochondrial gene expression detected were removed from downstream analyses
Assembly: GRCh38
Supplementary files format and content: cell-filtered count matrices, TCR contig info

value: mRNA


title: Ribo-seq-WT-MM-1


title: Lacrimal Gland, replicate 1, scRNAseq

description: 10x Genomics


title: Patient P2 Primary Tumor, gene expression, Biopsy, neg


title: Patient P9 Primary Tumor, gene expression, Biopsy

value: II


title: Ovarian Stimulation Cycle-hCG9 [EMB030]


title: Ribo-seq-WT-KB-1

description:
Ribo-seq in WT strain in KB condition
Ribo-seq.bed

value: KB condition


title: Natural Cycle-LH2 [EMB029]


title: Patient P6 Primary Tumor, gene expression, Biopsy


title: DMS-seq-hfq-plus-2

description:
DMS-seq in △hfq/p-EV strain after MM induction; DMS treatment group
DMS-seq-hfq-2.react

data_processing:
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
For Ribo-seq library, the raw reads was mapped to the  Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). The reads was counts by bedtools
The DMS-seq library was analysised through Structure-seq2 pipeline.
Assembly: Pseudomonas sringae 1448A (NC_005773.3)
Supplementary files format and content: React files for all DMS-seq results
Supplementary files format and content: Raw count bed fiels
Library strategy: DMS-seq

value: deltahfq/p-EV

value: MM condition DMS-treatment


title: Ovarian Stimulation Cycle-hCG2 [EMB003]


title: Negative Control_miRNA_3

type: RNA

city: Suita

first: Masahito

last: Shimojo

address: 1-6 Yamadaoka

country: Japan

institute: Osaka University

description: Gene expression after 48hr in 22Rv1 transfected with Negative Control

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software Ver. 12.1.1.1 (Agilent) using default parameters (protocol miRNA_1200_Jun14 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 22Rv1 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Version 3.1 December 2015 (Agilent) according to the manufacturer's instructions, followed by Micro Bio-Spin.  Dye incorporation and cRNA yield were checked with the NanoDrop One Spectrophotometer (Thermo Fisher Scientific, MA, USA).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: transfected with Negative Control


title: Patient P2 Primary Tumor, T cell receptors, Biopsy, pos

tag: tumor stage

value: T cell receptor


title: Lacrimal Gland, replicate 6, scRNAseq

description: 10x Genomics


title: No Treatment_miRNA_3

description: Gene expression after 48hr in 22Rv1 without ASO

value: without ASO


title: AmNA7168_miRNA_3

description: Gene expression after 48hr in 22Rv1 transfected with AmNA7168

value: transfected with AmNA7168


title: DMS-seq-hfq-plus-1

description:
DMS-seq in △hfq/p-EV strain after MM induction; DMS treatment group
DMS-seq-hfq-1.react


title: Ovarian Stimulation Cycle-hCG2 [EMB002]

value: Asian


title: DMS-seq-hfq-minus-2

description:
DMS-seq in △hfq/p-EV strain after MM induction; control group
DMS-seq-hfq-2.react

value: MM condition control


title: Blood, T cell receptors_1

source_name: Blood

value: Blood

tag: hashtags

value: GTCAACTCTTTAGCG (HASH1) = P1, AGTAAGTTCAGCGTA (HASH4) = P4, CTCCTCTGCAATTAC (HASH8) = P8, CAGTAGTCACGGTCA (HASH9) = P3, ATTGACCCGCGTTAG (HASH10) = P5

tag: molecule type


title: AmNA[+23/+44]_miRNA_3

description: Gene expression after 48hr in 22Rv1 transfected with AmNA[+23/+44]

value: transfected with AmNA[+23/+44]


title: Blood, protein features_2

library_source: other

data_processing:
Pair-ended FASTQ files were mapped to the GRCh38 human transcriptome using the count function in Cell Ranger
The count matrices obtained were normalized, log-transformed and scaled using the Seurat version 3 package in R
Cells with < 400 genes, < 1000 unique molecular identifier (UMI) counts or > 25% mitochondrial gene expression detected were removed from downstream analyses
Assembly: GRCh38
Supplementary files format and content: cell-filtered count matrices, TCR contig info
Library strategy: CITE-seq

molecule: protein

value: surface protein


title: DMS-seq-hfq-minus-1

description:
DMS-seq in △hfq/p-EV strain after MM induction; control group
DMS-seq-hfq-1.react

value: Pseudomonas savastanoi pv. phaseolicola 1448A


title: Blood, protein features_1

value: IIIB


title: DMS-seq-hfq-25-minus-2

description:
DMS-seq in △hfq/p-Y25D strain after MM induction; control group
DMS-seq-hfq-25-2.react


title: AmNA[+21/+40]_miRNA_3

description: Gene expression after 48hr in 22Rv1 transfected with AmNA[+21/+40]

value: transfected with AmNA[+21/+40]


title: No Treatment_miRNA_2


title: Ribo-seq-WT-KB-2

value: WT


title: DMS-seq-hfq-25-plus-2

description:
DMS-seq in △hfq/p-Y25D strain after MM induction; DMS treatment group
DMS-seq-hfq-25-2.react


title: DMS-seq-hfq-25-minus-1

description:
DMS-seq in △hfq/p-Y25D strain after MM induction; control group
DMS-seq-hfq-25-1.react


title: DMS-seq-hfq-25-plus-1

description:
DMS-seq in △hfq/p-Y25D strain after MM induction; DMS treatment group
DMS-seq-hfq-25-1.react


title: Ovarian Stimulation Cycle-hCG2 [E025]

tag: age


title: AmNA[+23/+44]_miRNA_2


title: AmNA[+21/+40]_miRNA_2


title: Ovarian Stimulation Cycle-hCG2 [E026]

tag: group

value: White


title: DMS-MM-treat-2

description:
DMS-seq in WT strain after MM induction; DMS treatment group
WT-MM_2.react


title: Natural Cycle-LH9 [E019]

tag: race

value: Black


title: Patient P7 Primary Tumor, gene expression, Biopsy

value: Primary Tumor Biopsy

value: IA

value: mRNA


title: Blood, gene expression_2


title: Blood, gene expression_1


title: Natural Cycle-LH9 [E022]

tag: bmi


title: AmNA7168_miRNA_2


title: Blood, T cell receptors_2

value: T cell receptor


title: Negative Control_miRNA_2

value: transfected with Negative Control


title: DMS-MM-con-2

description:
DMS-seq in WT strain after MM induction; control group
WT-MM_2.react


title: Natural Cycle-LH2 [E020]

tag: gravida


title: Ovarian Stimulation Cycle-hCG9 [E016]

tag: para


title: Natural Cycle-LH2 [E027]

tag: estradiol


title: Natural Cycle-LH2 [E028]

tag: progesterone


title: DMS-MM-con-1

description:
DMS-seq in WT strain after MM induction; control group
WT-MM_1.react


title: Fisetin_Input_3

city: hangzhou province

first: chaojie

last: huang

state: zhejiang

address: shangtang road No158, Hangzhou city, zhejiang province china

institute: Zhejiang provincial people’s Hospital

description: Fisetin_inputVScon_differential_expression.txt

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: GRCh38（hg38）
Supplementary_files_format_and_content: text files include FPKM values and annotation for each Sample
Supplementary_files_format_and_content: text files include peak  information for each group

source_name: PANC-1 cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Fisetin Input


title: DMS-MM-treat-1

description:
DMS-seq in WT strain after MM induction; DMS treatment group
WT-MM_1.react

value: MM condition DMS-treatment


title: Ovarian Stimulation Cycle-hCG9 [E017]


title: Fisetin_Input_2


title: AmNA[+23/+44]_miRNA_1


title: Fisetin_Input_1


title: con_Input_1

value: con Input


title: No Treatment_miRNA_1

value: without ASO


title: Fisetin_IP_3

description: FisetinVScon_diffPeak_Gene_differential_expression

value: Fisetin IP


title: MDCC-MSB1 cells, CIAV-infected, A3 (RNA-seq)

city: 广州

first: Mengyue

last: Dong

address: 广东省广州市天河区五山483号

department: College Of Animal Science Of South China Agricultural University

institute: South China Agricultural University

data_processing:
After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperature.  Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP..  An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.  Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.  Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.  After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;  8cycles 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 library was 300 bp (±50 bp).
Assembly: GRCg7b
Supplementary files format and content: excel, expression profiles

organism: Gallus gallus

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.  Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA).

value: Chicken lymphoma cell

tag: infection

value: CIAV


title: MDCC-MSB1 cells, CIAV-uninfected, B1 (RNA-seq)

address: 广东省广州市天河区五山483号

value: uninfected


title: AmNA7168_miRNA_1

value: transfected with AmNA7168


title: MDCC-MSB1 cells, CIAV-uninfected, B3 (miRNA-seq)

address: 广东省广州市天河区五山483号

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCg7b
Supplementary files format and content: excel, expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: con_Input_3


title: MDCC-MSB1 cells, CIAV-infected, A2 (RNA-seq)

address: 广东省广州市天河区五山483号


title: MDCC-MSB1 cells, CIAV-uninfected, B2 (miRNA-seq)

address: 广东省广州市天河区五山483号


title: Fisetin_IP_1


title: Natural Cycle-LH9 [E013]


title: DMS-KB-treat-1

description:
DMS-seq in WT strain after KB induction; DMS treatment group
WT-KB_1.react

value: Pseudomonas savastanoi pv. phaseolicola 1448A

value: WT

value: KB condition DMS-treatment


title: DMS-KB-treat-2

description:
DMS-seq in WT strain after KB induction; DMS treatment group
WT-KB_2.react


title: con_Input_2


title: MDCC-MSB1 cells, CIAV-infected, A1 (RNA-seq)

address: 广东省广州市天河区五山483号


title: AmNA[+21/+40]_miRNA_1

value: transfected with AmNA[+21/+40]


title: DMS-hrpL-treat-1

description:
DMS-seq in △hrpL strain after MM induction; DMS treatment group
hrpL-MM_1.react

value: deltahrpL

value: MM Induction DMS-treatment


title: Natural Cycle-LH9 [E006]

value: White


title: con_IP_3

value: con IP


title: con_IP_2


title: DMS-KB-con-2

description:
DMS-seq in WT strain after KB induction; control group
WT-KB_2.react

value: KB condition control


title: MDCC-MSB1 cells, CIAV-infected, A2 (miRNA-seq)

address: 广东省广州市天河区五山483号


title: Negative Control_miRNA_1

description: Gene expression after 48hr in 22Rv1 transfected with Negative Control

value: transfected with Negative Control


title: DMS-KB-con-1

description:
DMS-seq in WT strain after KB induction; control group
WT-KB_1.react


title: Fisetin_IP_2


title: con_IP_1


title: DMS-hrpL-con-1

description:
DMS-seq in △hrpL strain after MM induction; control group
hrpL-MM_1.react

value: MM Induction control


title: DMS-hrpL-treat-2

description:
DMS-seq in △hrpL strain after MM induction; DMS treatment group
hrpL-MM_2.react


title: Ovarian Stimulation Cycle-hCG9 [E015]


title: MDCC-MSB1 cells, CIAV-uninfected, B1 (miRNA-seq)

address: 广东省广州市天河区五山483号


title: DMS-hrpL-con-2

description:
DMS-seq in △hrpL strain after MM induction; control group
hrpL-MM_2.react


title: MDCC-MSB1 cells, CIAV-uninfected, B3 (RNA-seq)

address: 广东省广州市天河区五山483号


title: B18

status: Public on Jul 01 2024

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters and the first 12 base pairs of each read were trimmed using BBDuk and reads <50bp post-trimming were discarded. Reads were aligned and quantified using STAR (2.6.0a) against the Ensembl mouse transcriptome (mg38.p6 genome (release 96)).
Assembly: Ensembl mouse transcriptome (GRCm38.p6, release 96)
Supplementary files format and content: Text file containing gene counts

source_name: placenta

extract_protocol:
The RNA from each of the 30 individual placentas was isolated using a Qiagen RNeasy mini kit following the manufacturer’s instructions. Next, a reverse transcriptase reaction was performed using the Qiagen Quantitect RT kit according to manufacturer’s instructions (Qiagen, Hilden, Germany).
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan, Männedorf, Switzerland) with an input of 200ng of total RNA to generate RNA-Seq libraries.

tag: strain

tag: tissue

value: placenta

value: mixed

tag: miscarriage

value: No

tag: rin

value: Control


title: B26

tag: cell type

value: Yes

tag: treatment


title: B22


title: B13


title: MDCC-MSB1 cells, CIAV-infected, A3 (miRNA-seq)

address: 广东省广州市天河区五山483号

tag: cell line

value: Chicken lymphoma cell

value: CIAV


title: B5


title: B7


title: B151


title: B11


title: MDCC-MSB1 cells, CIAV-uninfected, B2 (RNA-seq)

address: 广东省广州市天河区五山483号

value: uninfected


title: MDCC-MSB1 cells, CIAV-infected, A1 (miRNA-seq)

address: 广东省广州市天河区五山483号


title: A3

value: RT


title: B1


title: B23


title: B24


title: B32


title: B17


title: A50


title: B6


title: A112


title: A118


title: A90


title: A92


title: B4


title: A99


title: A48


title: A38


title: A79


title: A33


title: A75


title: A9


title: A102


title: S38 at embryonic day 12.5, snRNA-seq

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description:
10X Genomics
E12.5_all_genes.csv
E12.5_cell_metadata.csv
E12.5_DGE.mtx

data_processing:
The demultiplexing, barcoded processing, gene couting and aggregation wre made using the Parse Bioscience Pipeline (v1.0.6)
Assembly: mm10
Supplementary files format and content: DGE.mtx is a sparse matrix with cell-gene counts. Each row corresponds to a cell and each column corresponds to a gene (see "genes.csv" file for names/gene-id of each column)
Supplementary files format and content: all_genes.csv file contains the gene name, gene id, and genome for each column in DGE.mtx.
Supplementary files format and content: cell_metadata.csv file contains information about each cell including the cell barcode, species, sample, well in each round of barcoding. and number of transcript/genes detected

molecule: nuclear RNA

source_name: placentas/decidual tissue

extract_protocol:
Nuclei were isolated following a protocol detailed by Rousselle et al. (3) for human kidney biopsies, which we modified to suit mouse placental and decidual samples. Each sample was minced into roughly 1 mm pieces and returned to their original centrifuge tubes. A 7 mm micro stir-bar was placed in each tube, along with 1 ml lysis buffer that was composed of 1× PBS pH, 7.4 10 mM Tris–HCL pH 7.5,0.0125% Triton X-100, 1 mM dithiothreitol, and 0.2 U/mL RNAse inhibitor (Promega, cat. no. PRN2611), and 1.5 l DNAse I, RNase free (1U/l, Thermo Fisher Scientific, cat. no. AM2222). The samples were then placed on ice on a magnetic stir plate and stirred at ~350 RPM for 10 min. The contents were allowed to settle, and the supernatant solution removed by gentle suction with a P1000 pipette. The homogenate was passed through a 100 m filter into a 15 ml collection tube and the filter washed with 6 ml nuclear wash and resuspension buffer (1x PBS, pH 7.4, 2 % bovine serum albumin [Sigma-Aldrich, cat. no. A9418-50G], and 0.2U/ml RNAse inhibitor). The process was repeated twice on the original tissue samples, and the three preparations combined, re-centrifuged, resuspended, and filtered through a 100 m filter. The pelleted nuclei were resuspended in 0.2 ml of ice-cold buffer and pipetted 50 times to minimize nuclear aggregation. Next, the isolated nuclei samples were transferred to a 1.5 mL microcentrifuge tube and were purified with Optiprep as detailed in Martelotto’s protocol (4), which is recommended by Parse Biosciences.
Isolated nuclei were fixed with Evercode™ Nuclei Fixation v2.  Nuclei barcoding, cDNA synthesis, and library preparation were performed with the Parse Evercode™ WT v2 kit.
Final library sequencing
The size and purity of the final library was determined with the Fragment Analyzer (Agilent Technologies, Inc.), quantified with the Qubit dsDNA HS Assay kit (Invitrogen), and diluted according to Illumina’s standard sequencing protocol. Libraries were pooled and run on an Illumina NovaSeq 6000 sequencer by using a paired end 100 bp read format on a S4 flow cell to generate ~100 million paired reads per sample.
snRNA-seq

value: placentas/decidual tissue

value: embryonic day 12.5


title: S39 at embryonic day 12.5, snRNA-seq


title: S7 at embryonic day 9.5, snRNA-seq

description:
10X Genomics
E9.5_all_genes.csv
E9.5_cell_metadata.csv
E9.5_DGE.mtx

value: embryonic day 9.5


title: S6 at embryonic day 9.5, snRNA-seq


title: Iso

city: South San Francisco

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

description: paired single cell RNA

data_processing:
Raw fastq files were aligned to the Mouse GRCm38 reference genome using CellRanger (10x Genomics, v6.1)
Subsequent quality control, normalization, dimensional reduction, and clustering was performed in Seurat v4.0. Clusters were annotated using canonical gene and protein markers.
Assembly: GRCm38
Supplementary files format and content: metadata.csv contains meta information of all samples with cells in rows and labels in columns. For each sample, the CellRanger output filtered matrix files including  barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.

source_name: Heart

extract_protocol:
Single cells were isolated according to 10x Genomics protocol from mouse heart
Collected cells were processed using the using the single Cell 3’ Kit v 3.1 (10x Genomics PN: 1000268) and libraries were sequenced on a NovaSeq 6000 S4 flow cell.

value: Heart

value: Ang II/PE infusion, Isotype control treated


title: A55


title: Sham

description: paired single cell RNA

value: no Ang II/PE infusion, Isotype control treated


title: Young mice, control2

city: Fuzhou

first: Xiaochun

last: Zheng

state: Fujian

address: Dong street

department: Anesthessia

institute: Fujian Provincial Hospital

description: Control

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hippocampus

extract_protocol:
RNA was harvested usina Rneasy mini plus kit (Qiagen) 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Se1 library Prep Kit following manufacturer's protocols

value: Hippocampus


title: Young mice, control3

description: Control


title: Young mice, lidocaine2

description: lidocaine injections

value: lidocaine injections


title: Iso_plus

description: paired single cell RNA

extract_protocol:
Single cells were isolated according to 10x Genomics protocol from mouse heart and sorted with following gating stratigy: Pdpn+, singlets, Cd45-/Cd31-, Pdpn+/PDgfra+, and Fap vs Pdgfra gate was used to look at Fap+ fibroblasts.
Collected cells were processed using the using the single Cell 3’ Kit v 3.1 (10x Genomics PN: 1000268) and libraries were sequenced on a NovaSeq 6000 S4 flow cell.


title: Young mice, lidocaine1

description: lidocaine injections


title: IL1_plus

description: paired single cell RNA

value: Ang II/PE infusion, anti-IL-1β mAb treated


title: Iso_neg

description: paired single cell RNA


title: pump_het

description: paired single cell RNA

extract_protocol:
Single cells were isolated of from mouse hearts with saline or Ang II/PE infused pumps at day 28 according to 10x Genomics protocol
Collected cells were processed using the using the single Cell 3’ Kit v 3.1 (10x Genomics PN: 1000268) and libraries were sequenced on a NovaSeq 6000 S4 flow cell.

value: angpe


title: 55

city: hangzhou

first: Jiawei

last: Zhang

address: NO.2318, Yuhangtang Rd, Yuhang District, 311121, Hangzhou, Zhejiang, P.R.China

institute: Hangzhou Normal university

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: Ensembl_v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: The organisms were kept at minus 80 degrees.

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.

treatment_protocol: Me1 hepatocyte-specific knockout mice and wild-type littermates were fed for 16 weeks with high-fat diet.

value: Liver

tag: genotype

value: Me1 Alb/Alb

value: fed for 16 weeks with high-fat diet


title: 64


title: pump_sal

description: paired single cell RNA

value: saline


title: 44


title: 62

value: Me1 flox/flox


title: 54


title: 30


title: 21


title: 9633_6(4)10_zQ175WT_nTB-Estop_STR_snRNAseq

city: Princeton

first: Jeff

last: Aaronson

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description: 10x Genomics

data_processing:
The raw fastq files were aligned using CellRanger v6.1.2 .
Assembly: mm10-2020A
Supplementary files format and content: raw and filtered feature bc matrices in h5 format

source_name: Corpus Striatum

extract_protocol:
Isolation of nuclei was performed following 10x Genomics recommendations on sample preparation for Single Cell RNA-seq (10X genomics protocol: CG000124). In brief, frozen tissue samples were homogenized using 5 strokes of pestle A and B in a 2 mL Dounce homogenizer (Kimble) in 1 mL lysis buffer (10 mM Tris-HCL pH 7,4, 10 mM NaCl, 3 mM MgCl2, 0,1 % IGEPAL, 0,2 U/µl RNase inhibitor, 1 % BSA, 1 mM DTT). Samples were strained using a 100 µm strainer (PluriSelect). Nuclei were collected by centrifugation (500 rcf, 5 min, 4°C) and washed with 1 mL wash buffer (10 mM Tris-HCL pH 7,4, 10 mM NaCl, 3 mM MgCl2, 0,5 U/µl RNase inhibitor, 1 % BSA, 1 mM DTT).  Density gradient centrifugation was performed to purify the nuclei from sample specific contaminants and debris. Briefly, nuclei in 300 µl wash buffer were underlaid with 1 mL gradient buffer (30 % w/v OptiPrep, 10 mM Tris-HCL pH 7,4, 10 mM NaCl, 3 mM MgCl2, 0,2 U/µl RNase inhibitor, 1 % BSA, 1 mM DTT) and pelleted at 8000 rcf, 10 min, 4°C.  Two additional washing steps with 1 mL wash buffer (500 rcf, 5 min, 4°C) were performed to further purify the nuclei. Nuclei were strained using a 40 µm Flowmi tip strainer.
Isolated nuclei were counted using Luna FX7 (Logos Biosystems) automated cell counter with AO/PI to adapt the volume of the nuclei suspension targeting 10.000 nuclei for each sample. The nuclei suspension was subjected to the 10x Genomics Single Cell 3’ Reagent Kit v3.1 workflow and library preparation was performed according to the manufacturers’ instructions (10X genomics protocol: CG000315). cDNA and library quality were assessed using Qubit and BioAnalyzer technology. The final libraries were pooled in an equimolar ratio and submitted to CeGaT (Tübingen) for sequencing using Illumina NovaSeq6000 S4 platform targeting at least 20.000 reads per nucleus.

treatment_protocol: Two month old zQ175DN and WT littermate mice were injected bilaterally with active ZFP AAV(nZFP) or inactive control AAVs (DBD or EStop) into each striatal hemisphere respectively,  and striatal tissue (left and right hemisphere) was collected at six months (four months of treatment) or eight months (six months of treatment). Six month old zQ175KI and WT mice were injected bilaterally with active ZFP AAV (nZFP) or inactive control AAVs (DBD or EStop) into each striatal hemisphere respectively and striatal  tissue (left and right hemisphere) was collected at eight months (two months of treatment), ten months (four months of treatment), or 12 months (six months of treatment).

value: Corpus Striatum

value: wild type

tag: animal id

tag: Sex

value: female

tag: age

value: 10 months

value: nTB-Estop

tag: treatment location

value: Left Hemisphere

tag: age at_treatment

value: 6 months

tag: treatment age_group

tag: sample group_label

tag: sequencing provider_id

tag: batch group

tag: qc status

value: not OK


title: 9713_6(4)10_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics

tag: tissue

value: zQ175 het


title: IL1_neg

description: paired single cell RNA

value: Heart

tag: strain

value: no Ang II/PE infusion, anti-IL-1β mAb treated


title: Il1

description: paired single cell RNA

value: Ang II/PE infusion, anti-IL-1β mAb treated


title: Young mice, lidocaine3

description: lidocaine injections

value: Hippocampus

value: lidocaine injections


title: 5368_6(6)12_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: 12 months


title: 22

value: Liver

value: Me1 Alb/Alb

value: fed for 16 weeks with high-fat diet


title: 619_2(6)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: Corpus Striatum

value: wild type

value: male

value: 8 months

value: Right Hemisphere

value: 2 months


title: Young mice, control1

description: Control


title: 63

value: Me1 flox/flox


title: 2725_2(4)6_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: zQ175 het

value: 6 months

value: nZFP-DBD

value: 2 months-6 months

value: OK


title: 5356_6(6)12_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: female


title: 608_2(4)6_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 9633_6(4)10_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: 10 months


title: 9665_6(4)10_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: nTB-Estop

value: Left Hemisphere

value: not OK


title: 5312_6(6)12_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: Corpus Striatum

value: 12 months


title: 617_2(6)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: wild type


title: 9715_6(4)10_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1123_6(2)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: 8 months


title: 1113_6(2)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: male

value: Right Hemisphere


title: 38

value: Liver

value: Me1 Alb/Alb

value: fed for 16 weeks with high-fat diet


title: 5343_6(6)12_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: zQ175 het

value: 6 months


title: 5368_6(6)12_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: OK


title: 2734_2(4)6_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: female

value: 2 months

value: 2 months-6 months


title: 9670_6(4)10_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: 10 months

value: nTB-Estop


title: 9671_6(4)10_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: Corpus Striatum


title: 9684_6(4)10_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: nZFP-DBD


title: 2735_2(4)6_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: wild type


title: 1105_6(2)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: 8 months


title: 1102_6(2)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 1158_6(2)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1115_6(2)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 625_2(6)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5335_6(6)12_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics

value: 12 months


title: 5346_6(6)12_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: male

value: Right Hemisphere


title: 5308_6(6)12_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 629_2(6)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 9665_6(4)10_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1114_6(2)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 2727_2(4)6_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 9713_6(4)10_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2719_2(4)6_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 642_2(6)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5330_6(6)12_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 5357_6(6)12_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 1101_6(2)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 8257_2(6)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 3760_6(4)10_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 5345_6(6)12_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2721_2(4)6_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2702_2(4)6_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 798_6(2)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 637_2(6)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5324_6(6)12_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 647_2(6)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 618_2(6)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 626_2(6)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 9667_6(4)10_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 2733_2(4)6_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 0 1124_6(2)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 8355_2(6)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 9609_6(4)10_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 9690_6(4)10_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2749_2(4)6_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1107_6(2)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 628_2(6)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 1128_6(2)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 9677_6(4)10_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 2730_2(4)6_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5348_6(6)12_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2738_2(4)6_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 5335_6(6)12_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics

value: Left Hemisphere


title: 9670_6(4)10_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5356_6(6)12_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1158_6(2)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 2719_2(4)6_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5330_6(6)12_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 642_2(6)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1114_6(2)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 8257_2(6)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 9671_6(4)10_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2727_2(4)6_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5346_6(6)12_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 3760_6(4)10_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 1115_6(2)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2702_2(4)6_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1107_6(2)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 9667_6(4)10_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 618_2(6)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5324_6(6)12_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5345_6(6)12_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 0 1124_6(2)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 9609_6(4)10_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 637_2(6)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2749_2(4)6_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5348_6(6)12_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 798_6(2)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1123_6(2)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2738_2(4)6_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 1101_6(2)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 1128_6(2)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 617_2(6)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 626_2(6)8_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5357_6(6)12_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2721_2(4)6_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 8355_2(6)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 2733_2(4)6_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 9690_6(4)10_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 619_2(6)8_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 2730_2(4)6_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 5343_6(6)12_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 5312_6(6)12_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 9684_6(4)10_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 9715_6(4)10_zQ175het_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 628_2(6)8_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 608_2(4)6_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 625_2(6)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 1102_6(2)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 647_2(6)8_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2734_2(4)6_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 1105_6(2)8_zQ175WT_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 629_2(6)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 1113_6(2)8_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: 2735_2(4)6_zQ175WT_nTB-Estop_STR_snRNAseq

description: 10x Genomics


title: 2725_2(4)6_zQ175het_nZFP-30645_STR_snRNAseq

description: 10x Genomics


title: 9677_6(4)10_zQ175het_nZFP-DBD_STR_snRNAseq

description: 10x Genomics


title: zQ175_nZFP_6M_12M_STR_R2

data_processing:
Sequencing was done on Illumina NovaSeq 6000, 2x150 bp configuration; ~50 M PE reads per sample
Custom genome and gene annotation were created to include transgenic sequences for EGFP, WPRE, nZFP  viral components as well as Htt1a transcript. GRCm38 genome fasta and GRCm38 version 76 gtf were used as a base for the custom genome and annotation.
Pre-alignment QC metrics such as read coverage, percent of un-mapped reads and GC contents were computed in Omicsoft
Omicsoft aligner was used to map the reads to the custom genome and RSEM software from Omicsoft was used to quantify gene and transcript expression
Adapter and quality trimming were performed in Omicsoft using the following settings: Trimming , Mode=TrimByQuality, ReadTrimQuality=2; AverageQualityCutoff=10, EnablePolyRateCutoff=True, PolyRateCutoff=80 FilterSource IlluminaAdapters,Human.rRNA,Human.tRNA,Ercc
Assembly: GRCm38HD.EGFP_WPRE_ZFPs_tdTomatoStiff custom genome assembly and GRCm38.76.Htt1a_EGFP_WPRE_ZFPs_tdTomatoStiff custom gene annotation
Supplementary files format and content: Tab-delimited files containing RSEM counts and FPKM values for genes and transcripts.

extract_protocol:
RNA was extracted with Qiagen RNeasy Microkit
Libraries were prepared with according Illumina RNA with PolyA selection protocol (NEB Next Ultra RNA Library Preparation Kit)

treatment_protocol: Two month old zQ175DN and WT littermate mice were injected bilaterally with active ZFP AAV(nZFP) or inactive control AAVs (DBD or EStop) into each striatal hemisphere respectively,  and striatal tissue (left and right hemisphere) was collected at six months (four months of treatment) or eight months (six months of treatment) and frozen. Six month old zQ175KI and WT mice were injected bilaterally with active ZFP AAV (nZFP) or inactive control AAVs (DBD or EStop) into each striatal hemisphere respectively and striatal  tissue (left and right hemisphere) was collected at eight months (two months of treatment), ten months (four months of treatment), or 12 months (six months of treatment) and frozen.

value: nZFP

tag: sample group

tag: sample id


title: zQ175_nZFP_6M_12M_STR_R8

value: zQ175 het

tag: treatment


title: zQ175_nZFP_6M_12M_STR_R3

value: 6 months


title: zQ175_nZFP_6M_12M_STR_R4


title: zQ175_nZFP_6M_12M_STR_R5


title: zQ175_nZFP_6M_12M_STR_R6


title: zQ175_nZFP_6M_12M_STR_R7


title: WT_nZFP_6M_12M_STR_R8


title: WT_nZFP_6M_12M_STR_R6


title: 5308_6(6)12_zQ175WT_nZFP-DBD_STR_snRNAseq

description: 10x Genomics

value: OK


title: WT_nZFP_6M_12M_STR_R4


title: zQ175_nZFP_6M_12M_STR_R1


title: WT_nZFP_6M_12M_STR_R5


title: WT_nZFP_6M_12M_STR_R3

value: female


title: WT_Estop_6M_12M_STR_R6

value: Estop


title: WT_nZFP_6M_12M_STR_R1


title: WT_nZFP_6M_12M_STR_R2


title: WT_Estop_6M_12M_STR_R5


title: WT_Estop_6M_12M_STR_R1


title: WT_Estop_6M_12M_STR_R2


title: WT_DBD_6M_12M_STR_R5

value: DBD


title: WT_DBD_6M_12M_STR_R8


title: WT_DBD_6M_12M_STR_R7


title: WT_DBD_6M_12M_STR_R6


title: WT_DBD_6M_12M_STR_R3


title: WT_DBD_6M_12M_STR_R2


title: zQ175_Estop_6M_12M_STR_R8


title: zQ175_Estop_6M_12M_STR_R5


title: WT_nZFP_6M_12M_STR_R7


title: zQ175_Estop_6M_12M_STR_R7


title: WT_Estop_6M_12M_STR_R8


title: zQ175_Estop_6M_12M_STR_R4


title: zQ175_Estop_6M_12M_STR_R6


title: WT_DBD_6M_12M_STR_R1


title: zQ175_Estop_6M_12M_STR_R3


title: zQ175_DBD_6M_12M_STR_R8


title: WT_Estop_6M_12M_STR_R3


title: zQ175_Estop_6M_12M_STR_R2


title: zQ175_Estop_6M_12M_STR_R1


title: WT_Estop_6M_12M_STR_R4


title: zQ175_DBD_6M_12M_STR_R6


title: zQ175_DBD_6M_12M_STR_R5


title: zQ175_DBD_6M_12M_STR_R4


title: zQ175_DBD_6M_12M_STR_R1


title: zQ175_DBD_6M_12M_STR_R3


title: zQ175_DBD_6M_12M_STR_R2


title: zQ175_nZFP_2M_8M_STR_R8

value: 2 months


title: zQ175_nZFP_2M_8M_STR_R6


title: zQ175_nZFP_2M_8M_STR_R7


title: zQ175_nZFP_2M_8M_STR_R5


title: zQ175_nZFP_2M_8M_STR_R3


title: zQ175_nZFP_2M_8M_STR_R1


title: WT_nZFP_2M_8M_STR_R8


title: WT_nZFP_2M_8M_STR_R7


title: WT_nZFP_2M_8M_STR_R4


title: WT_nZFP_2M_8M_STR_R3


title: WT_nZFP_2M_8M_STR_R5


title: WT_nZFP_2M_8M_STR_R2


title: WT_nZFP_2M_8M_STR_R6


title: zQ175_Estop_2M_8M_STR_R8


title: zQ175_Estop_2M_8M_STR_R4


title: zQ175_Estop_2M_8M_STR_R6


title: zQ175_Estop_2M_8M_STR_R3


title: zQ175_Estop_2M_8M_STR_R7


title: zQ175_Estop_2M_8M_STR_R5


title: zQ175_Estop_2M_8M_STR_R2


title: zQ175_nZFP_2M_8M_STR_R4


title: zQ175_nZFP_2M_8M_STR_R2


title: zQ175_DBD_2M_8M_STR_R8


title: zQ175_DBD_2M_8M_STR_R6


title: zQ175_DBD_2M_8M_STR_R7


title: zQ175_DBD_2M_8M_STR_R4


title: zQ175_Estop_2M_8M_STR_R1


title: zQ175_DBD_2M_8M_STR_R2


title: zQ175_DBD_2M_8M_STR_R5


title: WT_Estop_2M_8M_STR_R6


title: zQ175_DBD_2M_8M_STR_R1


title: WT_Estop_2M_8M_STR_R5


title: WT_Estop_2M_8M_STR_R4


title: WT_Estop_2M_8M_STR_R3


title: WT_nZFP_2M_8M_STR_R1


title: WT_DBD_2M_8M_STR_R6


title: WT_Estop_2M_8M_STR_R2


title: WT_Estop_2M_8M_STR_R1


title: WT_DBD_2M_8M_STR_R7


title: WT_DBD_2M_8M_STR_R8


title: WT_DBD_2M_8M_STR_R5


title: WT_DBD_2M_8M_STR_R2


title: WT_DBD_2M_8M_STR_R4


title: zQ175_DBD_6M_12M_STR_R7


title: WT_DBD_2M_8M_STR_R3


title: WT_DBD_2M_8M_STR_R1


title: zQ175_nZFP_6M_10M_STR_R6

value: 10 months


title: zQ175_nZFP_6M_10M_STR_R4

value: Corpus Striatum


title: zQ175_nZFP_6M_10M_STR_R8


title: WT_nZFP_6M_10M_STR_R7


title: WT_nZFP_6M_10M_STR_R8


title: zQ175_nZFP_6M_10M_STR_R3


title: zQ175_DBD_2M_8M_STR_R3


title: zQ175_nZFP_6M_10M_STR_R1


title: WT_nZFP_6M_10M_STR_R5


title: WT_nZFP_6M_10M_STR_R6


title: WT_nZFP_6M_10M_STR_R3


title: WT_nZFP_6M_10M_STR_R1


title: WT_nZFP_6M_10M_STR_R2


title: WT_Estop_6M_10M_STR_R6


title: WT_Estop_6M_10M_STR_R7


title: WT_Estop_6M_10M_STR_R2


title: WT_Estop_6M_10M_STR_R4


title: WT_Estop_6M_10M_STR_R3


title: WT_Estop_6M_10M_STR_R1


title: WT_nZFP_6M_10M_STR_R4


title: zQ175_nZFP_6M_10M_STR_R2


title: WT_DBD_6M_10M_STR_R8


title: WT_DBD_6M_10M_STR_R4


title: WT_DBD_6M_10M_STR_R5


title: WT_DBD_6M_10M_STR_R7


title: WT_DBD_6M_10M_STR_R2


title: WT_DBD_6M_10M_STR_R1


title: WT_DBD_6M_10M_STR_R6


title: zQ175_Estop_6M_10M_STR_R6


title: zQ175_Estop_6M_10M_STR_R8


title: zQ175_Estop_6M_10M_STR_R3


title: zQ175_Estop_6M_10M_STR_R5


title: zQ175_Estop_6M_10M_STR_R7


title: WT_Estop_6M_10M_STR_R5


title: zQ175_DBD_6M_10M_STR_R6


title: zQ175_DBD_6M_10M_STR_R8


title: zQ175_Estop_6M_10M_STR_R1


title: zQ175_Estop_6M_10M_STR_R4


title: zQ175_DBD_6M_10M_STR_R7


title: zQ175_DBD_6M_10M_STR_R5


title: zQ175_Estop_6M_10M_STR_R2


title: zQ175_DBD_6M_10M_STR_R2


title: zQ175_DBD_6M_10M_STR_R3


title: zQ175_DBD_6M_10M_STR_R1


title: WT_DBD_6M_10M_STR_R3


title: zQ175_nZFP_2M_6M_STR_R8


title: zQ175_nZFP_2M_6M_STR_R7


title: zQ175_nZFP_2M_6M_STR_R6


title: zQ175_nZFP_2M_6M_STR_R4


title: zQ175_nZFP_2M_6M_STR_R3


title: WT_nZFP_2M_6M_STR_R7


title: zQ175_nZFP_2M_6M_STR_R1


title: zQ175_nZFP_2M_6M_STR_R2


title: WT_nZFP_2M_6M_STR_R8


title: zQ175_nZFP_2M_6M_STR_R5


title: WT_nZFP_2M_6M_STR_R6


title: WT_nZFP_2M_6M_STR_R5


title: WT_nZFP_2M_6M_STR_R3


title: WT_nZFP_2M_6M_STR_R4


title: WT_nZFP_2M_6M_STR_R2


title: WT_nZFP_2M_6M_STR_R1


title: zQ175_Estop_2M_6M_STR_R8


title: zQ175_DBD_6M_10M_STR_R4


title: zQ175_Estop_2M_6M_STR_R7


title: zQ175_Estop_2M_6M_STR_R6


title: zQ175_Estop_2M_6M_STR_R5


title: zQ175_Estop_2M_6M_STR_R3


title: zQ175_Estop_2M_6M_STR_R4


title: zQ175_Estop_2M_6M_STR_R2


title: zQ175_DBD_2M_6M_STR_R6


title: zQ175_DBD_2M_6M_STR_R7


title: zQ175_Estop_2M_6M_STR_R1


title: zQ175_DBD_2M_6M_STR_R3


title: zQ175_DBD_2M_6M_STR_R5


title: zQ175_DBD_2M_6M_STR_R4


title: zQ175_DBD_2M_6M_STR_R2


title: WT_Estop_2M_6M_STR_R4


title: WT_Estop_2M_6M_STR_R5


title: zQ175_DBD_2M_6M_STR_R1


title: WT_Estop_2M_6M_STR_R3


title: WT_Estop_2M_6M_STR_R6


title: WT_Estop_2M_6M_STR_R2


title: WT_DBD_2M_6M_STR_R7


title: WT_DBD_2M_6M_STR_R8


title: WT_DBD_2M_6M_STR_R4


title: WT_DBD_2M_6M_STR_R5


title: WT_DBD_2M_6M_STR_R3


title: zQ175_nZFP_6M_8M_STR_R7


title: WT_DBD_2M_6M_STR_R1


title: zQ175_nZFP_6M_8M_STR_R6


title: zQ175_nZFP_6M_8M_STR_R8


title: WT_Estop_6M_10M_STR_R8


title: zQ175_nZFP_6M_8M_STR_R4


title: WT_DBD_2M_6M_STR_R2


title: WT_Estop_2M_6M_STR_R7


title: zQ175_nZFP_6M_8M_STR_R3


title: zQ175_nZFP_6M_8M_STR_R1


title: WT_nZFP_6M_8M_STR_R6


title: WT_Estop_2M_6M_STR_R1


title: WT_nZFP_6M_8M_STR_R5


title: WT_nZFP_6M_8M_STR_R4


title: WT_DBD_2M_6M_STR_R6


title: WT_nZFP_6M_8M_STR_R2


title: WT_Estop_6M_8M_STR_R6


title: zQ175_nZFP_6M_8M_STR_R5


title: WT_nZFP_6M_8M_STR_R3


title: WT_Estop_6M_8M_STR_R5


title: WT_Estop_6M_8M_STR_R7


title: WT_Estop_6M_8M_STR_R2


title: WT_nZFP_6M_8M_STR_R1


title: WT_Estop_6M_8M_STR_R4


title: zQ175_nZFP_6M_8M_STR_R2


title: WT_DBD_6M_8M_STR_R6


title: WT_DBD_6M_8M_STR_R7


title: WT_DBD_6M_8M_STR_R5


title: WT_nZFP_6M_8M_STR_R7


title: WT_nZFP_6M_8M_STR_R8


title: WT_DBD_6M_8M_STR_R2


title: WT_Estop_6M_8M_STR_R1


title: WT_DBD_6M_8M_STR_R4


title: WT_DBD_6M_8M_STR_R1


title: zQ175_Estop_6M_8M_STR_R7


title: WT_Estop_6M_8M_STR_R8


title: zQ175_Estop_6M_8M_STR_R6


title: zQ175_Estop_6M_8M_STR_R8


title: zQ175_Estop_6M_8M_STR_R5


title: WT_DBD_6M_8M_STR_R3


title: zQ175_Estop_6M_8M_STR_R4


title: zQ175_Estop_6M_8M_STR_R2


title: zQ175_Estop_6M_8M_STR_R3


title: WT_Estop_6M_8M_STR_R3


title: zQ175_Estop_6M_8M_STR_R1


title: zQ175_DBD_6M_8M_STR_R7


title: WT_DBD_6M_8M_STR_R8


title: zQ175_DBD_6M_8M_STR_R8


title: JM833-T1

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ files were analyzed for read and base quality using FastQC (Version: 0.11.9). Files that passed QC were analyzed for gene expression
Briefly, reads were aligned using STAR (Version: 2.7.10b) with default parameters to themm39 (GRCm39)reference genomeand gene expression was determined from mapped reads counted using RSEM (Version: 1.3.3)using the GENCODE (vM34) annotation ofMus musculusgenes.
Assembly: mm39 (GRCm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: Mouse mammary tumor

growth_protocol: Trp53R172H/-, Trp53R245W/-, and Trp53-/- mice were generated via mammary gland injection of adenovirus containing Cre-recombinase (Ad-Cre). Recombination in the mammary gland results in excision of WT Trp53 cDNA sequences from the endogenous locus, resulting in mammary ductal epithelial cell-specific mutant p53 expression of Trp53R172H or Trp53R245W and biallelic loss of Trp53 (referred to as MaPR172H, MaPR245W, or MaP- from hereon)

extract_protocol:
A portion of mouse mammary tumor was homogenized using Trizol and Qiagen RNeasy Kits to isolate total RNA using a modified extraction protocol.
Bulk RNA libraries were generated and  constructed following standard Illumina protocols for RNA sequencing  on an Illumina HiSeq4000 (MaPR172H/- tumors) or Illumina NovaSeq 6000 (MaPR245W/- and MaP-/- tumors) by the the MD Anderson Cancer Center ATGC  Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.
Stranded mRNA-Seq

treatment_protocol: MaPR172H/-, MaPR245W/-, and MaP-/- mice were sacrificed upon mammary tumor burden. Portions of mammary tumors and matched metastases were flash frozen for downstream genomic analysis.

value: Mouse mammary tumor

value: MaP-/-


title: JM833-T2


title: JM779-T1


title: JM663-T2


title: JM663-T1


title: zQ175_DBD_6M_8M_STR_R2

value: 8 months


title: zQ175_DBD_6M_8M_STR_R1


title: zQ175_DBD_6M_8M_STR_R5


title: zQ175_DBD_6M_8M_STR_R6


title: JM836-T1


title: JM1133


title: JM1564

value: MaPR245W/-; Rosa26LSL-TdTomato/+


title: JM1233


title: JM1126


title: WT, replicate 3

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 2215-B Garland Ave, 1075 MRB4

institute: Vanderbilt University Medical Center

data_processing:
Raw data is aligned to mouse mm39 ref genome using PIPseeker
Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Vega et al., 2023), resulting in the processed data table.
Assembly: mm39
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: Duodenum (small intestine)

extract_protocol:
Mouse tissues were incubated in a chelating buffer composed of 20mM HEPES and 3mM EDTA in DPBS for 1.25hrs. Tissue was then transferred to 10ml of PBS and shook vigorously for 2-3 minutes to liberate crypts, which were then passed through a 70µm filter and washed by centrifugation at 300g for 5 minutes and resuspension in PBS.  Isolated crypts were pelleted and resuspended in a solution of cold active protease (5 mg/ml Protease from Bacillus licheniformis and 2.5 mg/mL Dnase in PBS) and incubated for 25 minutes at 4°C. Following this, the tissues were gently pipetted 10-20 times to obtain single cells and passed through a 70µm filter into a clean tube. Isolated cells werepelleted by centrifugation at 700g for 5 min and washed in PBS containing 0.02% BSA. Cells were further washed 2 additional times and encapsulated using reagents and consumables in the PIPseq T2 kit (targeting capture of ~2,00 cells) version 4.5 from Fluent Biosciences.
Library prep was performed using reagtents provided in the PIPseq T2 V4.5 kit from Fluent Biosciences. Cells are co-encapsulated in droplets with beads using an emulsifying oil and controlled vortexing. Cellular RNA is then captured through hybridization to poly dT sequences on barcoded beads. Droplets are then broken, and beads are washed and incubated with reverse transcriptase to generate barcoded cDNA. Beads are once again washed and then incubated in a PCR "Whole transcriptome amplification" reaction to amplify barcoded transcripts. PCR products are then purified and prepared for sequencing through fragmentation, A-Tailing, and ligation to add sequencing adapters, before undergoing a final PCR amplification to add dual Illumina indexes.
scRNA-seq with PIPseq library version V4.5

value: Duodenum (small intestine)

value: Mtgr1+/+ (WT)


title: Mtgr1 null, replicate 2

value: Mtgr1-/- (null)


title: Mtgr1 null, replicate 1


title: WT, replicate 2


title: RM0014


title: WT, replicate 1


title: Mdm2 KD-H3K27me3

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
The raw data underwent quality filtering using Trimmomatic to obtain clean data.
These clean data were then aligned to the mm10 genome using Bowtie2. For the identification of peaks, we utilized MACS2. sequenced (RPKM) values.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CuT&Tag

source_name: embryo

growth_protocol: The cell lines were maintained on feeder cells using a basic serum/LIF medium.

extract_protocol:
CUT&Tag assay was conducted using the NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, N259)
The libraries were amplified and subjected to sequencing using the Illumina platform

value: embryo

tag: cell line

value: mESCs

tag: cell type

value: mouse embryonic stem cells

tag: chip antibody

value: Mdm2 KD


title: WT_Estop_2M_8M_STR_R7

tag: genotype

value: wild type

tag: Sex

value: male

value: Left Hemisphere


title: WT-H3K27me3

value: WT


title: Mdm2-KD-3

data_processing:
To analyze the data, clean reads were mapped to the Mus musculus genome using HISAT2.
Read counts were quantified using HTSeq-count (v0.6.0) and then normalized to obtain the Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) values.
Assembly: mm10
Supplementary files format and content: FPKM values

extract_protocol:
Total RNA was purified using magnetic beads (TIANGEN Biotech) with Oligo (dT) to selectively isolate mRNA
RNA-seq libraries were subsequently constructed and assessed using a combination of TIANGEN Biotech and the Agilent 2100 BioAnalyzer.

value: Mdm2 knockdown


title: Mdm2-KD-1


title: WT-3


title: zQ175_DBD_6M_8M_STR_R4

value: Corpus Striatum

value: zQ175 het

value: female

tag: age

value: DBD

tag: treatment location

value: 6 months


title: Mdm2 OE-H3K27me3

value: Mdm2 OE


title: Mdm2-KD-2


title: zQ175_DBD_6M_8M_STR_R3

value: 8 months

tag: age at_treatment

tag: treatment age_group


title: WT-2


title: OCT4-mESCs-1


title: OCT4-mESCs-3


title: WT-1


title: MERVL-2CLCs-3


title: MERVL-2CLCs-2


title: OCT4-mESCs-2


title: MERVL-2CLCs-1


title: OFer4 Old with CDA-HFD diet and Ferrostatin-1 treatment

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mice genome reference combining the GRCm38.  STAR v2.7.5 was used to align reads to reference genome.  Gene count was quantified by featureCounts v2.0.1.
Assembly: GRCm38
Supplementary files format and content: DK_featurecount_rawcount.txt: Reads mapped to mice GRCm38, featurecount was used to count reads per gene per sample, tab-delimited txt file

source_name: Old mice with CDA-HFD diet and Fer1 treatment

growth_protocol: Young and old mice were fed with a chow diet or CDA-HFD diet for 6 weeks. Old mice were intraperitoneally injected with Fer1 or its vehicle every other day during the last 8 days of feeding .

extract_protocol:
Total RNA was extracted using an RNAeasy kit (Qiagen) and dissolved in RNase-free water. RNA samples were sequenced by Novogene Corporation. In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer

treatment_protocol: all mice were fed with CDA-HFD diet for 6 week, for Ofer group, mice were intraperitoneally injected with Fer1 every other day during last 8 days of feeding.

value: whole liver

value: Old

tag: diet

value: CDA-HFD diet


title: Female microglia, Sham, Day 3

first: Wei

last: Yang

state: United States

address: 300 Duke Street

description:
10X Genomics
F_Sham

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of all 4 samples , using 10X Cellranger v7.1.0 with default parameters.
Assembly: mm10-2020-A custome ref with ZsGreen seq added
Supplementary files format and content: raw read counts in gene-barcode matrix

source_name: brain

extract_protocol:
Mice were intubated, anesthesized with isoflurane and transcardially perfused. Brains were immediately harvested and only the ipsilateral hemisphere was proccessed. Brain tissue was dissociated by mechanical dissociation, filtered (70 um). A percoll gradient  were used to isolate enriched microglial cells yield (pellet) after centrifugation . Samples were resuspended in FASC buffer (RPMI1640, 2% FBS, and 2 mM EDTA). Four samples per condition were combined at this step. Next, live ZsGreen+ cells were sorted using fluorescence-activated cell sorting (BD FACSAria II) and immediately after sequenced (Novaseq 6000).
10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) was used to generate single-cell gel beads with reverse transcription (RT) reagents in emulsions (GEMs). After GEM-RT was performed, the single-strand cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). The cDNA was then amplified and purified. Indexed sequencing libraries were constructed using the Chromium Single-Cell 3’ v3.1 Library Kit following the manufacture’s instruction. The barcoded sequencing libraries were quantified and loaded on a Novaseq 6000 (Illumina, San Diego, CA, USA) for sequencing.

treatment_protocol: pMCAO was performed by permanent ligation of the right middle cerebral artery. Body temperature was monitored during the entire surgical process. Sham mice underwent similar surgical procedure without ligation of the middle cerebral artery.

value: brain

value: Female

value: microglial cells

value: Sham surgery


title: OFer3 Old with CDA-HFD diet and Ferrostatin-1 treatment


title: Male microglia, Sham, Day 3

description:
10X Genomics
M_Sham

value: Male


title: WT_rep1_RNA

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

data_processing:
The fastq files were processed with Cellranger-arc v2.0.2 pipeline to make gene expression matrices.
The filtered matrix files (barcodes.tsv.gz/features.tsv.gz/matrix.mtx.gz) have been compressed into a tar file for each sample.
Assembly: mm10
Supplementary files format and content: Cellranger filtered matrices, ATAC fragment files, and h5 files

source_name: FACS-sorted microglia

growth_protocol: In vivo microglia from each brain were non-enzymatically isolated.

extract_protocol:
Microglia were FACS-sorted, immediately lysed according to the standard 10x procedures (ref. CG000365).
Isolated nuclei were then subjected to the libraries as the protocols that 10x Genomics provides (ref. CG000338).
single nuclei RNA-Seq and ATAC-seq

value: male

value: FACS-sorted microglia

value: WT

value: Tamoxifen for 5 days


title: WT_rep2_ATAC

library_source: genomic single cell


title: IRF8cKO_rep1_ATAC


title: OFer2 Old with CDA-HFD diet and Ferrostatin-1 treatment


title: O3 Old with CDA-HFD diet

source_name: Old mice with CDA-HFD diet

value: No


title: Female microglia, pMCAO, Day 3

description:
10X Genomics
F_Stroke

value: pMCAO


title: O4 Old with CDA-HFD diet


title: IRF8cKO_rep1_RNA


title: WT_rep1_ATAC


title: O1 Old with CDA-HFD diet


title: O2 Old with CDA-HFD diet


title: Y4 Young with CDA-HFD diet

source_name: Young mice with CDA-HFD diet

value: Young


title: OFer1 Old with CDA-HFD diet and Ferrostatin-1 treatment


title: Y3 Young with CDA-HFD diet


title: IRF8cKO_rep2_ATAC


title: Y1 Young with CDA-HFD diet


title: Male microglia, pMCAO, Day 3

description:
10X Genomics
M_Stroke