title: OA Meniscus single cell RNAseq, Donor6

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

institute: The Scripps Research Institute

description: 10X Genomics

data_processing:
Cell Ranger's mkfastq was used to demultiplex raw BCL files into paired-end gzip-compressed FASTQ files. Cell Ranger's count was used to align reads to the human reference genome (GRCh38) and generate a counts matrix for each gene for each cell.
Assembly: GRCh38
Supplementary files format and content: Tab-separated feature and barcode files and matrix files

source_name: Whole mensicus

extract_protocol:
All human tissues were obtained with approval by the Scripps Human Subjects Committee. Normal human knee joints were obtained from Lifesharing, San Diego from donors without history of joint injury or disease. OA tissues were obtained from donors undergoing total knee arthroplasty. Cartilage samples were minced with a #21 Feather disposable scalpel, and then digested in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 1% Anti-Anti and 2% collagenase type II with 100 rpm shaking at 37°C for 2 hours.  Cells were passed through a 100 µm filter followed by passage through a 40 µm filter. Filtered cells were spun down at 1200 rpm for 5 minutes at room temperature. The supernatant was removed, and the remaining cell pellet was resuspended in PBS supplemented with 5% CS and 5 mM EDTA. Resuspended single cells were then treated with DNase I for 15 minutes at room temperature. Single cells were then spun down at 1200 rpm for 5 minutes at room temperature. The supernatant was removed, and the remaining cell pellet was resuspended in PBS supplemented with 0.04% BSA. Whole meniscus was minced with a #21 Feather disposable scalpel, and then digested in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 1% Anti-Anti and 1% collagenase type II with 100 rpm shaking at 37°C for 30 minutes.  Cells were passed through a 100 µm filter followed by passage through a 40 µm filter. Filtered cells were spun down at 1200 rpm for 5 minutes at room temperature. Cells were then resuspended in DMEM supplemented in 10% CS, 1% Anti-Anti and 1% PSG and stored at 37°C. The digestion, spin down and filtration steps were repeated for 1 hour and then 2 hours, for a total of 3.5 hours of digestion. The stored cells were combined and then spun down at 1200 rpm for 5 minutes at room temperature. The supernatant was removed, and the remaining cell pellet was resuspended in PBS supplemented with 5% CS and 5 mM EDTA. Single cells were then spun down at 1200 rpm for 5 minutes at room temperature. The supernatant was removed, and the remaining cell pellet was resuspended in PBS supplemented with 0.04% BSA. For both tissues, the Invitrogen Countess II FL automated cell counter was used to quantify single cells and determine cell viability. Live cells were determined by trypan blue staining. If >70% cell viability was confirmed, the single cell suspension was diluted to a concentration of 1x106 cells/mL and cells were then loaded onto a Chromium Next GEM chip G (10X Genomics).
Single cell RNAseq was performed using the 10X Genomics Chromium technology. Briefly, cells were partitioned into droplets using the Chromium Controller with the Next GEM Single Cell 3’ Reagent Kit v3.1 using dual indexing. Next, cells were lysed and the polyadenylated transcripts reverse transcribed to generate barcoded cDNA following the recommended 10X Genomics protocol. The quality of both the cDNA and the final libraries were assessed using the Agilent Bioanalyzer 2100 following the guidance provided by the 10X Genomics user guide.

value: Whole mensicus

tag: disease state

value: OA

tag: patient id

value: M


title: V_2_0_B

status: Public on Apr 18 2023

type: SRA

city: Wageningen

first: Annemarie

last: Castricum

state: Gelderland

address: Droevendaalsesteeg 4

department: Bioscience

country: Netherlands

institute: Wageningen university and research

library_source: transcriptomic

data_processing:
Mapping and quantification were done using RSEM and Bowtie2 as a mapper
Differential expression analysis was done in R using DESeq2, performing the nbinomWaldTest and only focusing on genes with a maximum 0.01 padj value
Assembly: V1_clustered_reference.fasta -> Reference sequences used for mapping the reads were constructed using Trinity de novo assembly of all read pairs of V1 using default settings. Reference sequences used for mapping the reads were constructed using Trinity de novo   assembly of all read pairs of V1 using default settings.
Supplementary files format and content: csv file with per sample read counts

molecule: total RNA

organism: Chrysanthemum x morifolium

source_name: Inflorescence (flower bud)

growth_protocol: Plants were grown under greenhouse conditions

extract_protocol:
flower buds were sampled, put in liquid nitrogen and RNA was isolated using CTAB/LiCl
Illumina TruSeq® Stranded mRNA sample preparation kit for low-input with an imput of 2,5 µg RNA per sample. Elution 2 for three minutes instead of eight and enrichment PCR for 13 cycles instead of 15.

treatment_protocol: Diameter sizes per stage: stage 0, 0.5–2   mm; stage 1, 2-3 mm; stage 2, 3–5 mm; stage 3, 5–6 mm; stage 4, 7–10 mm; and stage 5, 10–  25 mm

tag: tissue

value: Inflorescence (flower bud)

tag: genotype

tag: treatment

value: stage 0


title: OA Meniscus single cell RNAseq, Donor5

city: La Jolla

state: CA

department: CCBB

country: USA

description: 10X Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

tag: age

tag: Sex

value: F


title: panc1, si-NC1

city: Chongqing

first: Fuming

last: Xie

address: Yuzhong District Yixueyuan Road 1#

country: China

institute: Chongqing Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Seqtk(https://github.com/lh3/seqtk).
Trimmed sequence reads were mapped to GRCh38 using Hisat2 (version:2.0.4).
Read count extraction and normalization were performed using Stringtie (version:1.3.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Pancreatic duct cell

growth_protocol: PANC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cells using an Ultrapure RNA kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: PANC-1 cells were transfected with siRNA of METTL16 and control siRNA.

value: Pancreatic duct cell

tag: cell line

tag: cell type

value: pancreatic adenocarcinoma cells

tag: transfection

value: WT


title: V_2_0_A


title: Usf2 shRNA 2 treated, PWK 1, unirradiated control

city: Novato

first: Taekyu

last: Kang

address: 8001 Redwood Blvd

institute: Buck Institute

description:
P4.U4.CONT
Usf2KD_allTPM.txt

data_processing:
Reads were mapped to their corresponding genomes via tophat v2.1.1
Reads were filtered for only those that mapped uniquely via samtools v1.3.1
Gene counts were generated using HTSeq v0.11.2
TPM counts were generated using custom R scripts.
Assembly: GRCm38.96, SPRET_EiJ_v1.96
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: Tail

growth_protocol: All cells were cultured in DMEM with 10% FBS and 1% pen-strep in a 3% O2 and 10% CO2 humidified incubator at 37˚C.

extract_protocol:
RNA was extracted from cells using TriZol and chloroform extraction, then cleaned and treated with DNase on RNeasy columns.
Libraries were constructed in the corresponding sequencing facilities.

treatment_protocol: All senescent samples were treated with 15 Gy of ionizing radiation in a X-RAD 320 X-Ray Biological Irradiator. Senescent samples were collected 10 days or 20 days after IR treatment. 6HR samples were collected 6 hours after IR treatment.  All shRNA treated samples were infected with shRNA containing lentiviral particles with 4 µg/mL of polybrene at an MOI of 5. Cells were then cultured with 2 µg/mL of polybrene in complete medium for 10 days to select for infected cells.

value: Tail

value: Primary fibroblast

value: Usf2 knockdown


title: OA Meniscus single cell RNAseq, Donor4

description: 10X Genomics


title: OA Meniscus single cell RNAseq, Donor3

description: 10X Genomics


title: M_1_3_B

data_processing:
Mapping and quantification were done using RSEM and Bowtie2 as a mapper
Differential expression analysis was done in R using DESeq2 with normalised data, performing the nbinomWaldTest and only focusing on genes with a maximum 0.01 padj value
Assembly: V1_clustered_reference.fasta -> Reference sequences used for mapping the reads were constructed using Trinity de novo assembly of all read pairs of V1 using default settings. Reference sequences used for mapping the reads were constructed using Trinity de novo   assembly of all read pairs of V1 using default settings.
Supplementary files format and content: xlsx file with per sample read counts

treatment_protocol: Diameter sizes per stage; stage 0, 0.5–2 mm; stage 1, 2-3 mm; stage 2, 4–5.5  mm; stage 3, 6–8 mm; stage 4, 9–13 mm; and stage 5, 15–25 mm

value: stage 3


title: Usf2 shRNA 1 treated, PWK 2, unirradiated control

description:
P1.U5.CONT
Usf2KD_allTPM.txt


title: OA Meniscus single cell RNAseq, Donor2

description: 10X Genomics


title: PWK 3, senescent

description:
P5_sen_TPM
PWK_STF_SEN_TPM.txt

value: ionizing radiation, 15 Gy


title: Usf2 shRNA 1 treated, PWK 1, unirradiated control

description:
P1.U4.CONT
Usf2KD_allTPM.txt


title: M_1_3_A


title: PWK 3, unirradiated control

description:
P5_cont_TPM
PWK_STF_SEN_TPM.txt


title: WT rep1

city: Beijing

first: Lijun

last: Wang

state: Beijing Shi

address: Shuangqing Road 30#

department: Department of Basic Medical Science

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
High quality reads in each sample were mapped to the reference genome using Bowtie2.
RSEM computes maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
TPM method is used to calculated expression level.
We identified differentially expressed genes by using the DESeq2 package.
Genome_build: K. pneumoniae ATCC43816 (CP009208)  as reference genome
Supplementary_files_format_and_content: An excel file include TPM, counts, fold change, P values for each Sample.

organism: Klebsiella pneumoniae ATCC 43816

source_name: bacteria culture

extract_protocol:
Total RNA was extracted from culture grown on BAP overnight using RNAprep pure Cell / Bacteria Kit according the manufacturer’s instructions (Tiangen Biotech, China) and further purified with a RNeasy Mini Kit (QIAGEN, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wide type

tag: medium

value: Columbia blood plate

tag: temperature

tag: condition

value: 5 percent CO2


title: M_1_2_C

value: stage 2


title: OA Meniscus single cell RNAseq, Donor1

description: 10X Genomics

value: Whole mensicus

value: OA


title: PWK 2, senescent

description:
P4_sen_TPM
PWK_STF_SEN_TPM.txt


title: Normal Meniscus single cell RNAseq, Donor7

description: 10X Genomics

value: Normal


title: M_1_2_B

value: Inflorescence (flower bud)


title: panc1, si-NC2


title: Normal Meniscus single cell RNAseq, Donor6

description: 10X Genomics

value: M


title: PWK 2, unirradiated control

description:
P4_cont_TPM
PWK_STF_SEN_TPM.txt


title: bro1-ABA-02Hours-3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

data_processing:
Quality filtering and adapter trimming with BBDUK 2 v. 37.02 (parameters: trimq=20, maq=10, k=23 mink=11, hdist=1, tbo, tpe, minlength=100, removeifeitherbad=t)
rRNA mapping reads were discarded by mapping with Bowtie 2 v. 2.3.5.1 against A. thaliana ribosomal RNAs
Expression values were calculated with RSEM v1.2.30 (strand-specific data)
Supplementary files format and content: Provided are files with tab-separated values exactly as output by RSEM; they contain particular gene names and their expression values (raw and normalized ones)

organism: Arabidopsis thaliana

source_name: two weeks old seedlings

growth_protocol: Seeds of WT Arabidopsis thaliana, Columbia ecotype (Col-0), as well as bro1-1 mutant were used in this study. After two days of stratification at 4°C, the plants were grown in Half Murashige and Skoog Basal Medium supplemented with sucrose.

extract_protocol:
For each condition (mock and ABA treated), three independent biological replicates were used and total RNA was extracted using RNAeasy kit (Qiagen) according to the manufacturer’s protocol and ABA application was confirmed by the amplification of ABA related marker mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were grown weeks for two weeks, then treated with ABA (100 µM) for 2 and hours.

tag: ecotype

value: Columbia

value: Salk Line Mutant bro1-1

value: two weeks

value: seedlings


title: bro1-ABA-04Hours-2


title: bro1-ABA-04Hours-3


title: M_1_2_A


title: M_1_3_C


title: PWK 1, senescent

description:
P3_sen_TPM
PWK_STF_SEN_TPM.txt

value: Tail

value: Primary fibroblast

value: WT


title: bro1-ABA-02Hours-1


title: bro1-ABA-04Hours-1


title: Normal Meniscus single cell RNAseq, Donor5

description: 10X Genomics


title: M_1_1_C

value: stage 1


title: Normal Meniscus single cell RNAseq, Donor4

description: 10X Genomics


title: PWK 1, unirradiated control

description:
P3_cont_TPM
PWK_STF_SEN_TPM.txt


title: bro1-Mock-2


title: M_1_1_B


title: epidermal cells, I3C, Papain (D771T115)

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Assembly: mm10
Supplementary files format and content: Count matrix (raw counts) was obtained using DESeq2.

source_name: epidermal cells

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.
Sequencing was performed in 3 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end) with an average depth of 40 millions of clusters per sample.

treatment_protocol: Mice were fed with a synthetic diet (SYNTH) enriched or not in Indole-3-carbinol (I3C). Papain or vehicle (PBS) was injected in the footpad.

value: epidermal cells

tag: diet

value: Papain


title: bro1-Mock-1


title: epidermal cells, SYNTH, Papain (D771T104)

value: SYNTH


title: M_1_1_A


title: M_1_0_C

value: stage 0


title: Normal Meniscus single cell RNAseq, Donor2

description: 10X Genomics

value: Whole mensicus


title: Normal Meniscus single cell RNAseq, Donor3

description: 10X Genomics


title: bro1-ABA-02Hours-2


title: epidermal cells, SYNTH, PBS (D771T103)

value: PBS


title: WT-ABA-04Hours-3

value: Wild Type


title: WT-ABA-04Hours-2


title: Normal Meniscus (avascular) single cell RNAseq, Donor1

description: 10X Genomics

source_name: Avascular mensicus

value: Avascular mensicus

value: Normal

value: F


title: WT-ABA-04Hours-1

value: Columbia


title: epidermal cells, I3C, Papain (D771T106)


title: V_1_3_C

value: Inflorescence (flower bud)

value: stage 3


title: epidermal cells, I3C, Papain (D771T114)


title: epidermal cells, SYNTH, Papain (D771T105)


title: OA Cartilage single cell RNAseq, Donor6

description: 10X Genomics

source_name: Cartilage

value: Cartilage

value: OA

value: M


title: WT-ABA-02Hours-3

value: two weeks

value: seedlings


title: OA Cartilage single cell RNAseq, Donor5

description: 10X Genomics


title: bro1-Mock-3

value: Salk Line Mutant bro1-1


title: Normal Meniscus (vascular) single cell RNAseq, Donor1

description: 10X Genomics

source_name: Vascular mensicus

value: Vascular mensicus


title: V_1_3_B


title: WT-ABA-02Hours-2


title: epidermal cells, SYNTH, PBS (D771T102)

value: epidermal cells

value: SYNTH


title: OA Cartilage single cell RNAseq, Donor4

description: 10X Genomics


title: OA Cartilage single cell RNAseq, Donor3

description: 10X Genomics


title: V_1_2_C

value: stage 2


title: WT-ABA-02Hours-1

value: Wild Type


title: epidermal cells, I3C, PBS (D771T110)

value: PBS


title: M_1_0_B

value: stage 0


title: M_1_0_A


title: OA Cartilage single cell RNAseq, Donor2

description: 10X Genomics

value: F


title: 10H_M_67

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: strain

value: male


title: epidermal cells, I3C, PBS (D771T109)


title: WT-Mock-2

value: Columbia


title: OA Cartilage single cell RNAseq, Donor1

description: 10X Genomics

tag: disease state


title: WT-Mock-1


title: V_1_2_A

value: Inflorescence (flower bud)


title: V_1_1_C

value: stage 1


title: Normal Cartilage single cell RNAseq, Donor6

description: 10X Genomics

value: Cartilage

value: Normal

tag: patient id


title: V_1_2_B

tag: tissue


title: Normal Cartilage single cell RNAseq, Donor5

description: 10X Genomics

value: M


title: V_1_1_B

tag: genotype


title: epidermal cells, SYNTH, PBS (D771T101)

tag: treatment


title: V_1_3_A

value: stage 3


title: epidermal cells, I3C, PBS (D771T111)


title: STF 3, unirradiated control

description:
S4_cont_TPM
PWK_STF_SEN_TPM.txt

organism: Mus spretus

value: Tail

value: Primary fibroblast

value: WT


title: epidermal cells, SYNTH, PBS (D771T100)

value: epidermal cells

value: SYNTH


title: Normal Cartilage single cell RNAseq, Donor4

description: 10X Genomics

tag: age


title: epidermal cells, I3C, PBS (D771T108)


title: STF 2, senescent

description:
S2_sen_TPM
PWK_STF_SEN_TPM.txt

value: ionizing radiation, 15 Gy


title: WT-Mock-3

value: Wild Type

value: two weeks

value: seedlings


title: V_1_1_A


title: V_1_0_C

value: stage 0


title: STF 2, unirradiated control

description:
S2_cont_TPM
PWK_STF_SEN_TPM.txt


title: Normal Cartilage single cell RNAseq, Donor3

description: 10X Genomics

tag: Sex


title: epidermal cells, SYNTH, Papain (D771T112)

value: Papain


title: Normal Cartilage single cell RNAseq, Donor2

description: 10X Genomics


title: G_TJ_out_4

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description: Group housed rat after tamoxifen and Jaeumganghwa-tang treatment

data_processing:
All raw data passed FastQC quality check. Adapter trimming was firstly performed on raw data using cutadapt (v2.9)
The reference genome was downloaded from Ensembl (Rattus norvegicus release 99), and the reference genome index was built using STAR (v2.7.9a)
Paired-end trimmed reads alignment and raw read count calculation were both conducted using RSEM (v1.3.1)
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include expected-count values for each sample

organism: Rattus norvegicus

source_name: tumor-free mammary gland

growth_protocol: A total of 80 Sprague Dawley rats were obtained from Envigo and arrived at 6 weeks of age to Georgetown University animal facility located at the Department of Comparative Medicine. Rats were housed in groups of 3 per cage. All rats received semi-purified AIN93G diet. The animals were housed in a temperature- and humidity-controlled room with a 12-hour light-dark cycle

extract_protocol:
RNA from tumor-free mammary gland was extracted using Qiagen RNeasy Mini Kit (Qiagen, MD) according to the manufacturer’s instructions. RNA concentration and purity were analyzed by Nanodrop 1000 spectrophotometer
Paired-end, dual-indexed libraries for RNAseq were constructed from 500ng total RNA using the TruSeq Stranded Total RNA Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: ER+ mammary tumors were induced by administration of 10 mg of 7,12-dimethylbenz[a]anthracene (DMBA, Sigma) diluted in 1 mL of peanut oil by gavage when rats were 50-days of age.  Tumor development was checked weekly and when a first tumor become palpable per an animal, rats were divided into two groups: those kept on group-housed (3 animals per cage, n=40), or those housed singly (social isolation, n=40). When the first tumor per animal reached a size of ~11mm in diameter, group-housed and socially isolated rats were divided into 2 additional groups. At this point forward, the experiment contained four groups: group-housed treated with tamoxifen (n=19), group-housed treated with tamoxifen+JGT (n=17), socially isolated treated with tamoxifen (n=17) and socially isolated treated with tamoxifen+JGT (n=18).

value: tumor-free mammary gland

value: TAM+JGT


title: STF 3, senescent

description:
S4_sen_TPM
PWK_STF_SEN_TPM.txt


title: V_1_0_B

value: Inflorescence (flower bud)


title: STF 1, senescent

description:
S1_sen_TPM
PWK_STF_SEN_TPM.txt


title: Normal Cartilage single cell RNAseq, Donor1

description: 10X Genomics

value: Cartilage

value: Normal

value: F


title: STF 1, unirradiated control

description:
S1_cont_TPM
PWK_STF_SEN_TPM.txt

value: Tail


title: V_1_0_A


title: 2638P

status: Public on Apr 17 2023

city: Boulder

first: Julie

last: Sadino

state: CO

address: 1945 Colorado Ave

department: MCDB

institute: University of Colorado Boulder

data_processing:
Quality control and trimming adapters using FastQC (0.11.8) and Trimmomatic-Src (0.38) with TruSeq3-SE adapters
Read alignment using HiSat2 (2.1.0) with default options
Individual runs were merged into a single sample using SAMtools (1.9)
Reads were counted using Htseq (0.11.2) using default options
Genes with fewer than 10 read counts were filtered for downstream analysis
Ensemble IDs were converted to prairie vole gene IDs using BioMart
Genome_build: Microtus_ochrogaster.MicOch1.0.95.gtf
Supplementary_files_format_and_content: pseudocount files

molecule: polyA RNA

organism: Microtus ochrogaster

source_name: Nucleus accumbens

extract_protocol:
Fresh nucleus accumbens tissue was hand dissected, homogenized, and purified as described in Heiman et al., 2014.
Library preparation for sequencing was done using the KAPA mRNA HyperPrep kit with polyA enrichment according to the manufacturer’s instructions for a 100-200 bp insert size and using 1.5 uM TruSeq3-SE adapters.

treatment_protocol: Samples were part of 1 of 8 groups (detailed above) prior to collecting fresh tissue.

tag: pairing type

value: opposite-sex

tag: social condition

value: Paired

tag: timepoint

value: 4 weeks

tag: vtrap sample?

value: yes

tag: input or pulldown?

value: Pulldown


title: 2639P

value: Separated


title: 2617P


title: 2662P


title: 2669P


title: 2612P


title: 2656P


title: 2658P


title: epidermal cells, I3C, Papain (D771T113)

tag: cell type

value: epidermal cells


title: 2615P


title: 2611P


title: 2604P


title: 2665P

value: same-sex


title: 2601P


title: 2647P


title: 2599P


title: 2594P


title: 2660P


title: 2664

value: Input


title: 2658


title: 2664P


title: 2659P


title: 2639


title: 2669


title: 2612


title: 2617


title: epidermal cells, SYNTH, Papain (D771T107)

value: SYNTH

value: Papain


title: 2659


title: 2656


title: 2601


title: 2647


title: 2611


title: 2599


title: 2660


title: 2604


title: 2638


title: 2984

value: no


title: 2615


title: 2594


title: 2977


title: 2959


title: 2973


title: 2954


title: 2913

value: 48 hours


title: 2662


title: 2910


title: 2909


title: 2906


title: 2801


title: 2898


title: 2758


title: 2737


title: 2762


title: 2644


title: 2736


title: 2665


title: 2644P


title: 2728


title: 2945


title: 2939


title: 2921


title: 2780


title: 2750


title: 2723


title: 2920


title: 2919


title: 2766


title: 2756


title: 2911


title: 2917


title: primary cultured astrocytes OASIS deficient 1

city: Hiroshima

first: Atsushi

last: Saito

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

country: Japan

institute: Hiroshima University

data_processing:
DRAGEN Bio-IT Platform v3.5.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using DRAGEN Bio-IT Platform.
Trimmed sequence reads were mapped to GRCm38 using DRAGEN Bio-IT Platform.
Read count extraction and normalization were performed using DRAGEN Bio-IT Platform.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Supplementary files format and content: excel files include RPKM values for each Sample

source_name: primary cultured astrocytes

growth_protocol: Primary cultured mouse astrocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using ISOGEN (Qiagen). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit following manufacturer's protocols.

treatment_protocol: DNA damage was induced by pretreatment of 5-day post confluent cells with 1ug/ml doxorubicin (Wako) for 1 h. Cells were maintained in each culture medium for 24 h after replacing the medium three times.

tag: cell line

value: primary cultured astrocytes

value: glial cells

value: OASIS deficient

value: non-treatment


title: primary cultured astrocytes OASIS deficient 2

value: DNA damage by the treatment with doxorubicin


title: primary cultured astrocytes OASIS wild type 2

value: OASIS wild type


title: Liver Female 19mo DR 64ID

city: South San Francisco

first: Oliver

last: Hahn

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Liver

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: Liver

value: Female

tag: age (months)

tag: experiment group

value: Dietary Intervention

value: DR

tag: library strategy

value: Unstranded mRNA-seq

tag: mouse id_number


title: Liver Female 19mo AL 66ID

tag: strain

value: AL


title: Liver Female 19mo AL 63ID

tag: tissue


title: Liver Female 19mo AL 69ID


title: Liver Female 19mo AL 68ID


title: Liver Female 19mo DR 65ID


title: Liver Female 19mo DR 61ID


title: Liver Female 19mo DR 67ID


title: Visual cortex Male 19mo YMP 81ID

source_name: Visual cortex

value: Visual cortex

value: Male

value: Young Plasma Injection

value: YMP


title: Visual cortex Male 19mo YMP 77ID


title: Visual cortex Male 19mo PBS 84ID

value: PBS


title: Visual cortex Male 19mo YMP 73ID


title: 2887

value: same-sex

value: Paired

value: 48 hours

value: no

value: Input


title: Thalamus Male 19mo PBS 80ID

source_name: Thalamus

value: Thalamus


title: Thalamus Male 19mo YMP 77ID


title: Thalamus Male 19mo PBS 84ID


title: primary cultured astrocytes OASIS wild type 1

value: primary cultured astrocytes

value: glial cells

tag: genotype

value: OASIS wild type

value: non-treatment


title: Thalamus Male 19mo PBS 76ID

tag: treatment

value: Unstranded mRNA-seq


title: Thalamus Male 19mo YMP 73ID


title: Thalamus Male 19mo PBS 72ID


title: Thalamus Male 19mo YMP 81ID


title: Liver Female 19mo DR 62ID

value: Liver

value: Female

value: Dietary Intervention

value: DR


title: SVZ Male 19mo PBS 80ID

source_name: SVZ

value: SVZ

value: Male

value: Young Plasma Injection


title: SVZ Male 19mo YMP 81ID

value: YMP


title: Visual cortex Male 19mo PBS 80ID

value: Visual cortex

value: PBS


title: SVZ Male 19mo YMP 77ID


title: Pons Male 19mo PBS 76ID

source_name: Pons

value: Pons


title: Pons Male 19mo PBS 84ID


title: SVZ Male 19mo PBS 72ID


title: Visual cortex Male 19mo PBS 76ID


title: SVZ Male 19mo PBS 76ID


title: Pons Male 19mo YMP 73ID


title: Pons Male 19mo PBS 80ID


title: Pons Male 19mo YMP 77ID


title: Pons Male 19mo YMP 81ID


title: Choroid plexus Male 19mo YMP 81ID

source_name: Choroid plexus

value: Choroid plexus


title: Choroid plexus Male 19mo PBS 84ID


title: Choroid plexus Male 19mo PBS 80ID


title: Choroid plexus Male 19mo YMP 73ID


title: Choroid plexus Male 19mo YMP 77ID


title: Olfactory bulb Male 19mo PBS 80ID

source_name: Olfactory bulb

value: Olfactory bulb


title: Choroid plexus Male 19mo PBS 72ID


title: Olfactory bulb Male 19mo PBS 84ID


title: Olfactory bulb Male 19mo YMP 77ID


title: Medulla Male 19mo YMP 81ID

source_name: Medulla

value: Medulla


title: Medulla Male 19mo PBS 84ID


title: Olfactory bulb Male 19mo YMP 73ID


title: Olfactory bulb Male 19mo PBS 72ID


title: SVZ Male 19mo YMP 73ID


title: Medulla Male 19mo PBS 80ID


title: Medulla Male 19mo YMP 77ID


title: Medulla Male 19mo PBS 76ID


title: Hypothalamus Male 19mo PBS 84ID

source_name: Hypothalamus

value: Hypothalamus


title: Hypothalamus Male 19mo YMP 81ID


title: Hypothalamus Male 19mo YMP 77ID


title: Hippocampus (anterior) Male 19mo PBS 84ID

source_name: Hippocampus (anterior)

value: Hippocampus (anterior)


title: Hypothalamus Male 19mo YMP 73ID

value: Unstranded mRNA-seq


title: Medulla Male 19mo PBS 72ID


title: Medulla Male 19mo YMP 73ID


title: Hippocampus (anterior) Male 19mo PBS 80ID


title: Choroid plexus Male 19mo PBS 76ID


title: Hypothalamus Male 19mo PBS 80ID


title: Olfactory bulb Male 19mo YMP 81ID


title: Hippocampus (anterior) Male 19mo PBS 76ID


title: Hippocampus (anterior) Male 19mo YMP 73ID


title: Hippocampus (anterior) Male 19mo YMP 81ID


title: Hypothalamus Male 19mo PBS 72ID


title: Hippocampus (anterior) Male 19mo PBS 72ID


title: Hippocampus (posterior) Male 19mo PBS 84ID

source_name: Hippocampus (posterior)

value: Hippocampus (posterior)


title: Hippocampus (posterior) Male 19mo YMP 81ID


title: Olfactory bulb Male 19mo PBS 76ID


title: Hippocampus (posterior) Male 19mo YMP 77ID


title: Hippocampus (posterior) Male 19mo YMP 73ID


title: Hippocampus (posterior) Male 19mo PBS 76ID


title: Entorhinal cortex Male 19mo PBS 84ID

source_name: Entorhinal cortex

value: Entorhinal cortex


title: Entorhinal cortex Male 19mo YMP 81ID


title: Entorhinal cortex Male 19mo PBS 80ID


title: Entorhinal cortex Male 19mo YMP 77ID


title: Entorhinal cortex Male 19mo PBS 76ID


title: Hippocampus (anterior) Male 19mo YMP 77ID


title: Caudate putamen Male 19mo PBS 84ID

source_name: Caudate putamen

value: Caudate putamen


title: Entorhinal cortex Male 19mo YMP 73ID


title: Caudate putamen Male 19mo PBS 80ID


title: Entorhinal cortex Male 19mo PBS 72ID


title: Caudate putamen Male 19mo YMP 77ID


title: Motor cortex Male 19mo PBS 84ID

source_name: Motor cortex

value: Motor cortex


title: Caudate putamen Male 19mo PBS 76ID


title: Caudate putamen Male 19mo YMP 73ID


title: Motor cortex Male 19mo YMP 81ID


title: Caudate putamen Male 19mo YMP 81ID


title: Caudate putamen Male 19mo PBS 72ID


title: Hippocampus (posterior) Male 19mo PBS 80ID


title: Motor cortex Male 19mo PBS 76ID


title: Motor cortex Male 19mo PBS 80ID


title: Motor cortex Male 19mo PBS 72ID


title: Cerebellum Male 19mo PBS 84ID

source_name: Cerebellum

value: Cerebellum


title: Cerebellum Male 19mo YMP 81ID

value: Male


title: Motor cortex Male 19mo YMP 77ID

value: Young Plasma Injection


title: Motor cortex Male 19mo YMP 73ID

value: YMP


title: Cerebellum Male 19mo PBS 80ID


title: Cerebellum Male 19mo YMP 77ID


title: Corpus callosum Male 19mo PBS 84ID

source_name: Corpus callosum

value: Corpus callosum


title: Corpus callosum Male 19mo YMP 81ID


title: Corpus callosum Male 19mo PBS 80ID

value: PBS


title: Corpus callosum Male 19mo YMP 77ID


title: Cerebellum Male 19mo YMP 73ID


title: Corpus callosum Male 19mo PBS 76ID


title: Visual cortex Female 19mo aDR 67ID

value: Visual cortex

value: Female

value: Dietary Intervention

value: aDR


title: Visual cortex Female 19mo AL 69ID

value: AL


title: Visual cortex Female 19mo AL 66ID


title: Visual cortex Female 19mo AL 63ID


title: Visual cortex Female 19mo aDR 65ID


title: Visual cortex Female 19mo AL 68ID


title: Visual cortex Female 19mo aDR 64ID


title: Visual cortex Female 19mo aDR 62ID


title: Visual cortex Female 19mo aDR 61ID


title: Thalamus Female 19mo AL 68ID

value: Thalamus


title: Thalamus Female 19mo AL 66ID

value: Unstranded mRNA-seq


title: Thalamus Female 19mo aDR 65ID


title: Thalamus Female 19mo aDR 67ID


title: Thalamus Female 19mo aDR 64ID


title: Cerebellum Male 19mo PBS 72ID


title: Thalamus Female 19mo AL 69ID


title: Thalamus Female 19mo AL 63ID


title: Thalamus Female 19mo aDR 62ID


title: Thalamus Female 19mo aDR 61ID


title: SVZ Female 19mo AL 69ID

value: SVZ


title: SVZ Female 19mo AL 68ID


title: SVZ Female 19mo aDR 67ID


title: SVZ Female 19mo aDR 64ID


title: SVZ Female 19mo aDR 65ID


title: SVZ Female 19mo AL 66ID


title: SVZ Female 19mo AL 63ID


title: SVZ Female 19mo aDR 61ID


title: SVZ Female 19mo aDR 62ID


title: Pons Female 19mo AL 69ID

value: Pons


title: Pons Female 19mo AL 68ID


title: Pons Female 19mo aDR 67ID


title: Pons Female 19mo aDR 65ID


title: Pons Female 19mo AL 66ID


title: Pons Female 19mo AL 63ID


title: Pons Female 19mo aDR 64ID


title: Pons Female 19mo aDR 61ID


title: Choroid plexus Female 19mo AL 68ID

value: Choroid plexus


title: Choroid plexus Female 19mo AL 69ID


title: Choroid plexus Female 19mo aDR 67ID


title: Choroid plexus Female 19mo AL 63ID


title: Olfactory bulb Female 19mo AL 68ID

value: Olfactory bulb


title: Choroid plexus Female 19mo aDR 61ID


title: Olfactory bulb Female 19mo AL 69ID


title: Choroid plexus Female 19mo aDR 64ID


title: Choroid plexus Female 19mo aDR 62ID


title: Choroid plexus Female 19mo AL 66ID


title: Choroid plexus Female 19mo aDR 65ID


title: Olfactory bulb Female 19mo AL 63ID


title: Olfactory bulb Female 19mo aDR 64ID


title: Olfactory bulb Female 19mo aDR 67ID


title: Medulla Female 19mo AL 68ID

value: Medulla


title: Olfactory bulb Female 19mo aDR 65ID


title: Olfactory bulb Female 19mo AL 66ID


title: Medulla Female 19mo AL 69ID


title: Olfactory bulb Female 19mo aDR 62ID


title: Olfactory bulb Female 19mo aDR 61ID


title: Medulla Female 19mo aDR 67ID


title: Pons Female 19mo aDR 62ID


title: Medulla Female 19mo aDR 65ID


title: Medulla Female 19mo AL 66ID


title: Medulla Female 19mo AL 63ID


title: Medulla Female 19mo aDR 64ID


title: Medulla Female 19mo aDR 61ID


title: Medulla Female 19mo aDR 62ID


title: Hypothalamus Female 19mo aDR 67ID

value: Hypothalamus


title: Hypothalamus Female 19mo AL 68ID


title: Hypothalamus Female 19mo aDR 65ID


title: Hypothalamus Female 19mo aDR 62ID


title: Hypothalamus Female 19mo AL 63ID


title: Hypothalamus Female 19mo AL 66ID


title: Hippocampus (anterior) Female 19mo AL 69ID

value: Hippocampus (anterior)


title: Hippocampus (anterior) Female 19mo AL 66ID


title: Hippocampus (anterior) Female 19mo aDR 65ID


title: Hippocampus (anterior) Female 19mo aDR 67ID


title: Hippocampus (anterior) Female 19mo aDR 64ID


title: Hippocampus (anterior) Female 19mo AL 68ID


title: Hippocampus (anterior) Female 19mo aDR 61ID


title: Hippocampus (posterior) Female 19mo AL 68ID

value: Hippocampus (posterior)


title: Hippocampus (posterior) Female 19mo aDR 67ID


title: Hippocampus (anterior) Female 19mo aDR 62ID


title: Hippocampus (posterior) Female 19mo AL 66ID


title: Hippocampus (posterior) Female 19mo AL 69ID


title: Hippocampus (posterior) Female 19mo aDR 65ID


title: Hippocampus (posterior) Female 19mo aDR 64ID


title: Hippocampus (posterior) Female 19mo AL 63ID


title: Hypothalamus Female 19mo AL 69ID


title: Hippocampus (posterior) Female 19mo aDR 61ID


title: Entorhinal cortex Female 19mo aDR 67ID

value: Entorhinal cortex


title: Entorhinal cortex Female 19mo AL 66ID


title: Hypothalamus Female 19mo aDR 64ID


title: Entorhinal cortex Female 19mo aDR 65ID


title: Entorhinal cortex Female 19mo AL 63ID


title: SVZ Male 19mo PBS 84ID

value: Male

value: Young Plasma Injection

value: PBS


title: Entorhinal cortex Female 19mo aDR 64ID

value: Female

value: Dietary Intervention


title: Entorhinal cortex Female 19mo aDR 62ID

value: aDR


title: Hippocampus (anterior) Female 19mo AL 63ID

value: AL


title: Caudate putamen Female 19mo AL 69ID

value: Caudate putamen

value: Unstranded mRNA-seq


title: Caudate putamen Female 19mo AL 68ID


title: Caudate putamen Female 19mo aDR 67ID


title: Caudate putamen Female 19mo AL 63ID


title: Caudate putamen Female 19mo aDR 62ID


title: Caudate putamen Female 19mo aDR 64ID


title: Caudate putamen Female 19mo aDR 65ID


title: Motor cortex Female 19mo AL 69ID

value: Motor cortex


title: Motor cortex Female 19mo aDR 65ID


title: Motor cortex Female 19mo AL 66ID


title: Motor cortex Female 19mo aDR 64ID


title: Entorhinal cortex Female 19mo AL 69ID


title: Hippocampus (posterior) Female 19mo aDR 62ID


title: Motor cortex Female 19mo AL 63ID


title: Motor cortex Female 19mo aDR 62ID


title: Cerebellum Female 19mo AL 69ID

value: Cerebellum


title: Cerebellum Female 19mo AL 68ID


title: Cerebellum Female 19mo aDR 67ID


title: Entorhinal cortex Female 19mo aDR 61ID


title: Cerebellum Female 19mo aDR 64ID


title: Cerebellum Female 19mo aDR 65ID


title: Cerebellum Female 19mo aDR 61ID


title: Cerebellum Female 19mo AL 66ID


title: Caudate putamen Female 19mo AL 66ID


title: Cerebellum Female 19mo AL 63ID


title: Caudate putamen Female 19mo aDR 61ID


title: Corpus callosum Female 19mo AL 69ID

value: Corpus callosum


title: Motor cortex Female 19mo aDR 67ID


title: Corpus callosum Female 19mo aDR 67ID


title: Corpus callosum Female 19mo aDR 65ID


title: Motor cortex Female 19mo AL 68ID


title: Corpus callosum Female 19mo AL 63ID


title: Corpus callosum Female 19mo aDR 62ID


title: Corpus callosum Female 19mo aDR 61ID


title: Corpus callosum Female 19mo AL 66ID


title: Motor cortex Female 19mo aDR 61ID


title: Long-term DR;  Hippocampus Sample 3 24 mo

description:
10x Genomics
DR_3

data_processing:
Raw reads were processed using the CellRanger software (v4.0.0) provided by 10x Genomics and counting reads mapping to introns.  The number of nuclei for each sample was determined using the cellranger count command.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Single-nuclei preparation and sequencing was performed as previously described (Hahn et al., 2020) with the following modifications: Nuclei from whole hippocampus were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice. Samples were placed into 2 ml cold EZ lysis buffer in a 2 ml glass dounce tissue grinder (Sigma, D8938) and homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15 ml tube on ice. The tissue grinder was rinsed with 2 ml fresh lysis buffer and transferred to the tube holding the homogenate for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant removed and pellet resuspended with 4 ml EZ lysis buffer, and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. Pellet was resuspended in 400 ul PBS containing 1% BSA (Thermo Fisher, BP9700100), 0.2 ul Hoechst dye (Thermo Fisher, H3570) , and 2 ul recombinant RNase inhibitor (Takara, 2313B). Isolated nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology). 50k single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with PBS, UltraPure BSA (Thermo Fisher, AM2618), and RNase inhibitor (Takara, 2313B). Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40 ul suspended nuclei. Nuclei were counted using a hemocytometer (Sigma, Z359629-1EA) and assessed for concentration and quality.
Reagents of the Chromium Single Cell 3’ GEM & Gel Bead Kit v3.0 (10X Genomics,) were thawed and prepared according to the manufacturer’s protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3’ Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility.
10X Nuc-seq, v3.0 chemistry

value: Hippocampus

tag: diet

value: Long-term dietary restriction

tag: age

value: 24 months


title: Long-term DR;  Hippocampus Sample 4 24 mo

description:
10x Genomics
DR_4

tag: Sex


title: AL;  Hippocampus Sample 2 5 mo

description:
10x Genomics
ALY_2

value: Ad libitum

value: 5 months


title: AL;  Hippocampus Sample 3 5 mo

description:
10x Genomics
ALY_3


title: Long-term DR;  Hippocampus Sample 1 24 mo

description:
10x Genomics
DR_1


title: Long-term DR;  Hippocampus Sample 2 24 mo

description:
10x Genomics
DR_2


title: AL;  Hippocampus Sample 1 5 mo

description:
10x Genomics
ALY_1


title: AL;  Hippocampus Sample 4 24 mo

description:
10x Genomics
ALO_4


title: Acute DR;  Hippocampus Sample 2 24 mo

description:
10x Genomics
aDR_2

value: Acute dietary restriction


title: Acute DR;  Hippocampus Sample 3 24 mo

description:
10x Genomics
aDR_3


title: AL;  Hippocampus Sample 1 24 mo

description:
10x Genomics
ALO_1


title: AL;  Hippocampus Sample 2 24 mo

description:
10x Genomics
ALO_2


title: Cerebellum Female 19mo aDR 62ID


title: Ko6mAb

city: Singapore

first: Pazhanichamy

last: Kalailingam

address: 60 Nanyang Drive

country: Singapore

institute: NTU

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9. 1, phred cutoff: 20, error rate: 0. 1, adapter overlap: 1bp, min. length: 75, proportion of N: 0. 1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0. 1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0. 1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6. 1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted
Assembly: mm10
Supplementary files format and content: Excel (.xlsx) files include FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using Trizol method.
1 ug of total RNA was used for the construction of sequencing libraries. 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Novaseq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: 1mg/kg/week of mAb IP injection  to KO mice

value: lung

value: mAB (1mg/kg)


title: Ko4mAb


title: WT1

value: PBS


title: WT2


title: WT3


title: WGBS Control CD11b+ Biol. Rep. 2, NovaSeq 6000

first: Isaac

middle: F.

last: López-Moyado

address: 9420 Athena Cir

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

data_processing:
For WGBS analysis, we employed BSMAP (v2.9) (Xi and Li, 2009) to align paired-end reads from bisulfite-treated samples to the mm10 mouse reference genome allowing 4 mismatches. Reads mapping to multiple locations in the reference genome with the same mapping score were removed as well as the 5' ends bearing quality lower than 20 (mapping parameters: -n 1 -v 4 -w 2 -r 0 -q 20 -R -p 8). Duplicate reads caused by PCR amplification were removed by BSeQC (v1.0.3) (Lin et al., 2013) using default parameters. An effective genome size of 1.87e9 (as suggested in BSeQC for Mus musculus genome) was employed to calculate maximum coverage at the same genomic location. In addition, BSeQC was employed for removing DNA methylation artifacts introduced by end repair during adaptor ligation. For paired-end sequencing, overlapping segments of two mates of a pair were reduced to only one copy to avoid considering the same region twice during the DNA methylation quantification. To estimate CpG DNA methylation, we employed the methratio.py tool included in BSMAP (v2.9) (Xi and Li, 2009), merging DNA methylation at each CpG di-nucleotide (combining CpG methylation ratios on both DNA strands).
Assembly: mm10
Supplementary files format and content: Methylation summary matrices were generated using the methratio.py tool included in BSMAP (v2.9), and summarize the ratio of bisulfite-unconverted to total cytosines (C_count/[C_count+CT_count]).

source_name: Bone marrow

growth_protocol: To delete TET genes, total bone marrow cells from Control (Rosa26-LSL-YFP) or Tet1/2/3 f/f Rosa26-LSL-YFP 6-8-week-old mice were lentivirally infected with a Cre vector. These cells were transferred into lethally irradiated CD45.1+ mice with 2 x 10^6 helper bone marrow cells from CD45.1+ mice.

extract_protocol:
CD11b+ cells were isolated by flow cytometry and DNA was isolated using the PureLink genomic DNA mini kit (Life technologies).
DNA was fragmented to an average size of 200 bp using the Adaptive Focused Acoustics Covaris E220 instrument. Before bisulfite treatment, fully unmethylated λ (lambda) DNA (Promega) was spiked into the mouse genomic DNA at a ratio of 1:200. DNA library was prepared by NEBNext® DNA Library Prep Master Mix Set for Illumina (New England BioLabs). Methylated adapters (NeBNext Multiplex Oligos for Illumina, New England BioLabs) were used to determine the bisulfite conversion efficacy. DNA was bisulfite-treated using the MethylCode Bisulfite Conversion Kit (Life Technologies). After the bisulfite conversion the purified DNA was amplified for 4 cycles (low amplification) using Kapa HiFi Uracil+ (Kapa Biosystems). Two independent WGBS samples per genotype were evaluated.

value: Bone marrow

value: Lentivirally transduced with Cre


title: Ko3


title: Ko1


title: Het1


title: Het2


title: Het3


title: WGBS TetTKO CD11b+ Biol. Rep. 1, NovaSeq 6000

value: Tet1/2/3 f/f Rosa26-YFPLSL


title: WGBS TetTKO CD11b+ Biol. Rep. 2, NovaSeq 6000


title: WGBS Control CD11b+ Biol. Rep. 1, NovaSeq 6000


title: Total RNA-seq Control CD11b+ Biol. Rep. 1, NovaSeq 6000

description: WT_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable

data_processing:
For total RNA-seq analysis, quality and adapter trimming was performed on raw RNA-seq reads using TrimGalore! 431 v0.4.5 with default parameters, retaining reads with minimal length of 25 bp. Ribosomal RNA reads were filtered out using Tagdust2. Resulting reads were aligned to mouse genome mm10 using STAR v2.5.3a (Dobin et al., 2013). Bioconductor libraries rtracklayer and GenomicAlignments were used to generate a table of counts from gene annotations. The DESeq2 package v1.30.0 was used to normalize the raw counts and identify differentially expressed genes (greater than 2-fold change with adjusted p-value < 0.05).
Assembly: mm10
Supplementary files format and content: Table of raw counts of genes

growth_protocol: To delete TET genes, total bone marrow cells from Control (Rosa26-LSL-YFP), Tet2/3 f/f Rosa26-LSL-YFP, or Tet1/2/3 f/f Rosa26-LSL-YFP 6-8-week-old mice were lentivirally infected with a Cre vector. These cells were transferred into lethally irradiated CD45.1+ mice with 2 x 10^6 helper bone marrow cells from CD45.1+ mice.

extract_protocol: 10 million cells were sorted and then whole RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Ribo-zero RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) with minor modifications. The starting RNA was 800 ng. Ribosomal RNAs were depleted using magnetic beads. Next, RNA was fragmented, and cDNA was synthesized using Superscript II (Invitrogen). After A-tailing and adaptor ligation, libraries were generated by amplifying the cDNA for 10 cycles.


title: Total RNA-seq TetTKO CD11b+ Biol. Rep. 1, NovaSeq 6000

description: TKO_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: Total RNA-seq TetTKO CD11b+ Biol. Rep. 2, NovaSeq 6000

description: TKO_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: Acute DR;  Hippocampus Sample 1 24 mo

description:
10x Genomics
aDR_1

value: Female


title: Ko2mAb


title: Ko2


title: Total RNA-seq Tet2/3 DKO CD11b+ Biol. Rep. 2, NovaSeq 6000

description: DKO_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable

value: Tet2/3 f/f Rosa26-YFPLSL


title: RNA-seq Control CD11b+ Biol. Rep. 1

data_processing:
For RNA-seq analysis, quality and adapter trimming was performed on raw RNA-seq reads using TrimGalore! 431 v0.4.5 with default parameters, retaining reads with minimal length of 25 bp. Resulting reads were aligned to mouse genome mm10 using STAR v2.5.3a (Dobin et al., 2013). Bioconductor libraries rtracklayer and GenomicAlignments were used to generate a table of counts from gene annotations. The DESeq2 package v1.30.0 was used to normalize the raw counts and identify differentially expressed genes (greater than 2-fold change with adjusted p-value < 0.05).
Assembly: mm10
Supplementary files format and content: Table of raw counts of genes

extract_protocol: RNA sequencing with Smart-seq2: CD11b+ cells were sorted from Tet iTKO or control mice, and total RNA was isolated by RNeasy micro Kit (QIAGEN), and the integrity of the RNA was accessed with TapeStation RNA analysis ScreenTape or BioAnalyzer RNA Pico Kit (Agilent). Ten nanograms of RNA was reverse-transcribed using oligo-dT30 VN primer in the presence of Template Switching Oligo (TSO) with SuperScript II reverse transcriptase. cDNA was preamplified with IS PCR primers, and PCR products were cleaned up with Ampure XP beads. One nanogram of the PCR product was used to generate library using Nextera XT Library Prep Kit (Illumina), and tagmentated DNA was amplified for a 12-cycle PCR and purified with Ampure XP beads.

treatment_protocol: To delete floxed alleles using the Cre-ERT2 recombinase, tamoxifen (Sigma) was solubilized at 10 mg ml−1 in corn oil (Sigma) and delivered into mice by intraperitoneal injection of 2 mg tamoxifen per mouse every day for 5 consecutive days. The day of the last tamoxifen injection was designated Day 0.

value: Tamoxifen intraperitoneal injection


title: RNA-seq Tet iTKO CD11b+ Biol. Rep. 2

value: Tet1/2/3 f/f CreERT2


title: RNA-seq Control CD11b+ Biol. Rep. 2


title: Hi-C Tet iTKO CD11b+ Biol. Rep. 1

data_processing:
Reads corresponding to each extreme of a fragment were trimmed after the MboI restriction site using HOMER (Heinz et al., 2010) homerTools trim and independently mapped employing BWA-aln (v0.7.13) (single-end mode)(Li and Durbin, 2010). Reads were filtered out if they had a MAPQ score of less than 30, and only reads that were at least 25 bp were considered for the rest of the analysis. Only reads falling within the autosomes were considered for the analysis (no sex chromosomes included). Hi-C analysis was performed using HOMER (Heinz et al., 2010) and its Hi-C data analysis suite. Independently mapped reads were paired using the makeTagDirectory command, allowing only 1 tag per bp (- tbp. Reads were filtered to remove uninformative reads (contiguous genomic fragments, selfligation, re-ligation, and reads originating from regions of unusually high tag density) and also filtered based on the distance tor restriction sites (-genome mm10 -removePEbg -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000. To perform the principal component analysis (PCA) of Hi-C data (A/B compartment identification), we used the tool runHiCpca.pl on the normalized interaction matrix, with the options -res 50000 -superRes 100000 -genome mm10.
Assembly: mm10
Supplementary files format and content: BedGraph file containing Hi-C PC1 values, related to A/B compartment analysis.

extract_protocol: For Hi-C library preparation, between 10^5 and 1.5x1^6 cells were fixed in PBS containing 1% Formaldehyde, then quenched with 125mM glycine and washed twice with an excess of PBS. Cells were then resuspended in lysis buffer containing 0.5% SDS and lysed at 62°C for 7 minutes. This step also allows to remove proteins that were not fixed to the chromatin. SDS was further quenched with 1% Triton-X-100 at 37°C for 15 minutes. Next, permeabilized nuclei were subsequently digested with 100 Units MboI (NEB) at 37°C for 2 hours. After subsequent washing and inactivation of enzymes, the restriction sites were further filled in with Biotin-14-dATP and klenow polymerase at room temperature for 40 minutes. Samples were transferred into a ligation solution containing 600 units of T4 DNA ligase. Proximity ligation was stopped by addition of 2-fold molar excess of EDTA, and samples were de-crosslinked at 65°C overnight. DNA was further purified by proteinase K digestion and phenol/chloroform extraction. 400-800 ng of DNA was sonicated to an average of 300bp fragments length and was used for subsequent library preparation that includes (1) blunting of DNA, (2) A-tailing, (3) ligation of sequencing adapters, and (4) amplification of library.


title: RNA-seq Tet iTKO CD11b+ Biol. Rep. 1


title: Hi-C Control CD11b+ Biol. Rep. 2


title: Hi-C Control CD11b+ Biol. Rep. 1


title: 10G_M_3030

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: male


title: 10G_M_3029


title: 10G_M_3027


title: 10G_M_3028


title: Total RNA-seq Tet2/3 DKO CD11b+ Biol. Rep. 1, NovaSeq 6000

description: DKO_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: 10G_M_3021


title: 10G_M_3022


title: 10G_M_3023


title: 10G_M_3024


title: 10G_M_3020


title: Total RNA-seq Control CD11b+ Biol. Rep. 2, NovaSeq 6000

description: WT_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: 10G_M_3026


title: 10G_M_3025


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title: 10G_M_3011


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title: 10G_M_3012


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title: 10G_M_3003


title: 10G_M_3002


title: 10G_M_3007


title: Hi-C Tet iTKO CD11b+ Biol. Rep. 2


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title: 10G_M_2372


title: 10G_M_2368


title: 10G_M_2365


title: 10G_M_2339


title: 10G_M_2336


title: 10G_M_2363


title: 10G_M_2337


title: 10G_M_2340


title: 10G_M_2335


title: 10G_M_2354


title: 10G_M_2351


title: 10G_M_2346


title: 10G_M_2332


title: 10G_M_2330


title: 10G_M_2334


title: 10G_M_2349


title: 10G_M_2329


title: 10G_M_2331


title: 10G_M_2333


title: 10G_M_2327


title: 10G_M_2326


title: 10G_M_2323


title: 10G_M_2324


title: 10G_M_2325


title: 10G_M_2341


title: 10G_M_2321


title: 10G_M_2320


title: 10G_M_2316


title: 10G_M_2318


title: 10G_M_2317


title: 10G_M_2314


title: 10G_M_2313


title: 10G_M_2312


title: 10G_M_2311


title: 10G_M_2310


title: 10G_M_2309


title: 10G_M_2322


title: 10G_M_2308


title: 10G_M_2305


title: 10G_M_2304


title: 10G_M_2307


title: 10G_M_2306


title: 10G_M_2300


title: 10G_M_2297


title: 10G_M_2296


title: 10G_M_2291


title: 10G_M_2292


title: 10G_M_2303


title: 10G_M_2301


title: 10G_M_2289


title: 10G_M_2288


title: 10G_M_2294


title: 10G_M_2286


title: 10G_M_2287


title: 10G_M_2299


title: 10G_M_2285


title: 10G_M_2302


title: 10G_M_2284


title: 10G_M_2282


title: 10G_M_2319


title: 10G_M_2348


title: 10G_M_2280


title: 10G_M_2315


title: 10G_M_2295


title: 10G_M_2279


title: 10G_M_2278


title: 10G_M_2276


title: 10G_M_2290


title: 10G_M_2274


title: 10G_M_2271


title: 10G_M_2270


title: 10G_M_2269


title: 10G_M_2273


title: 10G_M_2272


title: 10G_M_2268


title: 10G_M_2267


title: 10G_M_2283


title: 10G_M_2266


title: 10G_M_2263


title: 10G_M_2258


title: 10G_M_2261


title: 10G_M_2260


title: 10G_M_2265


title: 10G_M_2255


title: 10G_M_2259


title: 10G_M_2257


title: 10G_M_2254


title: 10G_M_2253


title: 10G_M_2250


title: 10G_M_2252


title: 10G_M_2249


title: 10G_M_2251


title: 10G_M_2275


title: 10G_M_2248


title: 10G_M_2247


title: 10G_M_2243


title: 10G_M_2242


title: 10G_M_2241


title: 10G_M_2237


title: 10G_M_2239


title: 10G_M_2240


title: 10G_M_2238


title: 10G_M_2236


title: 10G_M_2234


title: 10G_M_2256


title: 10G_M_2233


title: 10G_M_2235


title: 10G_M_2231


title: 10G_M_2232


title: 10G_M_2230


title: 10G_M_2224


title: 10G_M_2244


title: 10G_M_2229


title: 10G_M_2218


title: 10G_M_2221


title: 10G_M_2226


title: 10G_M_2225


title: 10G_M_2215


title: 10G_M_2227


title: 10G_M_2222


title: 10G_M_2223


title: 10G_M_2217


title: 10G_M_2220


title: 10G_M_2216


title: 10G_M_2214


title: 10G_M_2213


title: 10G_M_2219


title: 10G_M_2208


title: 10G_M_2210


title: 10G_M_2209


title: 10G_M_2211


title: 10G_M_2207


title: 10G_M_2200


title: 10G_M_2203


title: 10G_M_2205


title: 10G_M_2206


title: 10G_M_2201


title: 10G_M_2196


title: 10G_M_2198


title: 10G_M_2199


title: 10G_M_2195


title: 10G_M_2186


title: 10G_M_2187


title: 10G_M_2188


title: 10G_M_2190


title: 10G_M_2189


title: 10G_M_2212


title: 10G_M_2183


title: 10G_M_2185


title: 10G_M_2180


title: 10G_M_2179


title: 10G_M_2174


title: 10G_M_2193


title: 10G_M_2177


title: 10G_M_2173


title: 10G_M_2172


title: 10G_M_2192


title: 10G_M_2178


title: 10G_M_2181


title: 10G_M_2169


title: 10G_M_2194


title: 10G_M_2167


title: 10G_M_2168


title: 10G_M_2163


title: 10G_M_2166


title: 10G_M_2164


title: 10G_M_2162


title: 10G_M_2182


title: 10G_M_2159


title: 10G_M_2161


title: 10G_M_2158


title: 10G_M_2156


title: 10G_M_2157


title: 10G_M_2155


title: 10G_M_2175


title: 10G_M_2154


title: 10G_M_2149


title: 10G_M_2152


title: 10G_M_2148


title: 10G_M_2150


title: 10G_M_2147


title: 10G_M_2171


title: 10G_M_2145


title: 10G_M_2143


title: 10G_M_2142


title: 10G_M_2146


title: 10G_M_2144


title: 10G_M_2170


title: 10G_M_2139


title: 10G_M_2141


title: 10G_M_2138


title: 10G_M_2140


title: 10G_M_2137


title: 10G_M_2135


title: 10G_M_2134


title: 10G_M_2136


title: 10G_M_2153


title: 10G_M_2133


title: 10G_M_2129


title: 10G_M_2131


title: 10G_M_2127


title: 10G_M_2125


title: 10G_M_2128


title: 10G_M_2122


title: 10G_M_2123


title: 10G_M_2120


title: 10G_M_2121


title: 10G_M_2119


title: 10G_M_2118


title: 1658286TN90Controlleaf

city: Neuchâtel

first: Kacper

middle: Piotr

last: Kaminski

address: Rue Fleury 5

country: Switzerland

institute: Philip Morris International

description: PMT1 leaf sample bio rep 8

data_processing:
The generated sequencing data were demultiplexed by Illumina BaseSpace® Clarity LIMS (© Illumina, Inc.) and subsequently imported to Qiagen CLC Genomics Workbench version 11.0.1 (CLC bio, a QIAGEN Company). Transcriptome reads were mapped to updated version the N. tabacum reference genome [49] using the ‘RNA-Seq Analysis’ 2.16 tool with similarity of 0.95 (S=0.95) and fraction length of 0.95 (L=0.95) as mapping criteria. The mismatch, insertion, and deletion costs were set to 2, 3, and 3, respectively.
Global alignment was not performed, and paired distances were detected automatically. The maximum number of read hits was set to 10, and paired reads were counted as 2. RPKM values were retrieved for each gene in the reference genome, including for those without transcript models. A fusion gene table was not created.
For each sample principal component analysis (PCA) was performed with the CLC ‘PCA for RNA-Seq’ tool. Gene expression analysis was performed with the ‘Empirical Analysis of DGE’ tool, where RPKM values for each gene were retrieved and compared by empirical analysis of DGE, which employs the ‘exact test’ developed by Robinson and Smyth [50] that was incorporated into the EdgeR Bioconductor package [51]. Genes with pairwise comparison p-values ≤0.05 and an absolute fold change ≥2 were regarded as significantly different.
Assembly: Transcriptome reads were mapped to updated version the N. tabacum reference genome by Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV: The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 2014, 5:3833.
Supplementary files format and content: Sample-specific mapping statistics are provided in Supporting Table 1.xlsx
Supplementary files format and content: A total of 2075 genes with statistically different expression were present in at least one of these comparisons and their expression for each samples is presented in Supporting Table 2.xlsx

organism: Nicotiana tabacum

source_name: root

extract_protocol:
With use of liquid nitrogen, tobacco samples were grinded to fine powder in mortars, and 200-mg samples were taken for RNA extraction. RNA extraction was performed by RNeasy® Plant Mini Kit (© QIAGEN N.V., Venlo, the Netherlands).
Subsequenlt sequencing library preparation was performed (no fragmentation) by TruSeq® Stranded Total RNA Gold (© Illumina, Inc., San Diego, CA, USA).

value: root

value: non GMO

value: topped


title: 1658288TN90Controlleaf

description: PMT1 leaf sample bio rep 10

source_name: leaf

value: leaf


title: 1658286TN90Controlroot

description: PMT1 root sample bio rep 8


title: 1658288TN90Controlroot

description: PMT1 root sample bio rep 10


title: 1658284TN90Controlroot

description: PMT1 root sample bio rep 6


title: 1658283TN90Controlleaf

description: PMT1 leaf sample bio rep 5

value: untopped


title: 1658284TN90Controlleaf

description: PMT1 leaf sample bio rep 6


title: 1658287TN90Controlroot

description: PMT1 root sample bio rep 9


title: 1658282TN90Controlleaf

description: PMT1 leaf sample bio rep 4


title: 1658285TN90Controlroot

description: PMT1 root sample bio rep 7


title: 1658280TN90Controlleaf

description: PMT1 leaf sample bio rep 2


title: 1658278PMT3root

description: PMT3 root sample bio rep 10

value: PMT RNAi suppresion


title: 1658282TN90Controlroot

description: PMT1 root sample bio rep 4


title: 1658281TN90Controlroot

description: PMT1 root sample bio rep 3


title: 1658285TN90Controlleaf

description: PMT1 leaf sample bio rep 7


title: 1658283TN90Controlroot

description: PMT1 root sample bio rep 5


title: 1658277PMT3root

description: PMT3 root sample bio rep 9


title: 1658279TN90Controlroot

description: PMT1 root sample bio rep 1


title: 1658281TN90Controlleaf

description: PMT1 leaf sample bio rep 3


title: 10G_M_2126


title: 1658279TN90Controlleaf

description: PMT1 leaf sample bio rep 1


title: 1658277PMT3leaf

description: PMT3 leaf sample bio rep 9


title: 1658280TN90Controlroot

description: PMT1 root sample bio rep 2


title: 1658276PMT3root

description: PMT3 root sample bio rep 8


title: 1658276PMT3leaf

description: PMT3 leaf sample bio rep 8


title: 1658275PMT3root

description: PMT3 root sample bio rep 7


title: 1658278PMT3leaf

description: PMT3 leaf sample bio rep 10


title: 1658274PMT3root

description: PMT3 root sample bio rep 6


title: 1658275PMT3leaf

description: PMT3 leaf sample bio rep 7


title: 1658274PMT3leaf

description: PMT3 leaf sample bio rep 6


title: 1658273PMT3leaf

description: PMT3 leaf sample bio rep 5


title: 1658271PMT3root

description: PMT3 root sample bio rep 3


title: 1658272PMT3root

description: PMT3 root sample bio rep 4


title: 1658271PMT3leaf

description: PMT3 leaf sample bio rep 3


title: 1658273PMT3root

description: PMT3 root sample bio rep 5


title: 1658269PMT3root

description: PMT3 root sample bio rep 1


title: 1658270PMT3leaf

description: PMT3 leaf sample bio rep 2


title: 1658269PMT3leaf

description: PMT3 leaf sample bio rep 1


title: 1658268PMT2leaf

description: PMT2 leaf sample bio rep 10


title: 1658268PMT2root

description: PMT2 root sample bio rep 10


title: 1658267PMT2root

description: PMT2 root sample bio rep 9


title: 1658267PMT2leaf

description: PMT2 leaf sample bio rep 9


title: 1658266PMT2leaf

description: PMT2 leaf sample bio rep 8


title: 1658265PMT2root

description: PMT2 root sample bio rep 7


title: 1658264PMT2root

description: PMT2 root sample bio rep 6


title: 1658262PMT2root

description: PMT2 root sample bio rep 4


title: 1658265PMT2leaf

description: PMT2 leaf sample bio rep 7


title: 1658266PMT2root

description: PMT2 root sample bio rep 8


title: 1658263PMT2root

description: PMT2 root sample bio rep 5


title: 1658263PMT2leaf

description: PMT2 leaf sample bio rep 5


title: 1658264PMT2leaf

description: PMT2 leaf sample bio rep 6


title: 1658260PMT2root

description: PMT2 root sample bio rep 2


title: 1658261PMT2leaf

description: PMT2 leaf sample bio rep 3


title: 1658261PMT2root

description: PMT2 root sample bio rep 3


title: 1658260PMT2leaf2

description: PMT2 leaf sample bio rep 2_2


title: 1658260PMT2leaf1

description: PMT2 leaf sample bio rep 2_1


title: 1658259PMT2root

description: PMT2 root sample bio rep 1


title: 1658258PMT1root

description: PMT1 root sample bio rep 10


title: 1658272PMT3leaf

description: PMT3 leaf sample bio rep 4


title: 1658258PMT1leaf

description: PMT1 leaf sample bio rep 10


title: 1658256PMT1root

description: PMT1 root sample bio rep 8


title: 1658257PMT1leaf

description: PMT1 leaf sample bio rep 9


title: 1658257PMT1root

description: PMT1 root sample bio rep 9


title: 1658255PMT1leaf

description: PMT1 leaf sample bio rep 7


title: 1658256PMT1leaf

description: PMT1 leaf sample bio rep 8


title: 1658254PMT1root

description: PMT1 root sample bio rep 6


title: 1658255PMT1root

description: PMT1 root sample bio rep 7


title: 1658254PMT1leaf

description: PMT1 leaf sample bio rep 6


title: 1658253PMT1leaf

description: PMT1 leaf sample bio rep 5


title: 1658251PMT1root

description: PMT1 root sample bio rep 3


title: 1658252PMT1leaf

description: PMT1 leaf sample bio rep 4


title: 1658252PMT1root

description: PMT1 root sample bio rep 4


title: 1658251PMT1leaf

description: PMT1 leaf sample bio rep 3


title: 1658250PMT1root

description: PMT1 root sample bio rep 2


title: 1658249PMT1leaf

description: PMT1 leaf sample bio rep 1


title: 1658259PMT2leaf

description: PMT2 leaf sample bio rep 1


title: Mhc2_hi_192

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 1000 genes), potential dead cells (>10% mitochondrial gene percentage) and contaminating Prox1- cells were removed for EC datasets. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural Cd206_hi cells and Mhc2_hi cells

source_name: mouse dura mhc2_hi cell

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted dural Cd206_hi cells and Mhc2_hi cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: dura mater

value: Dural macrophage

tag: cell sorting

value: FACS sorted

tag: sorted cell type

tag: infection

value: LCMV


title: Mhc2_hi_191

tag: cell type


title: Mhc2_hi_190


title: Mhc2_hi_187


title: Mhc2_hi_185


title: Mhc2_hi_189


title: 1658250PMT1leaf

description: PMT1 leaf sample bio rep 2


title: Mhc2_hi_186


title: Mhc2_hi_184


title: Mhc2_hi_188


title: Mhc2_hi_183


title: Mhc2_hi_181


title: Mhc2_hi_180


title: Mhc2_hi_178


title: Mhc2_hi_179


title: 1658253PMT1root

description: PMT1 root sample bio rep 5


title: Mhc2_hi_175


title: Mhc2_hi_182


title: Mhc2_hi_177


title: Mhc2_hi_174


title: 1658249PMT1root

description: PMT1 root sample bio rep 1


title: Mhc2_hi_172


title: Mhc2_hi_171


title: Mhc2_hi_170


title: Mhc2_hi_169


title: Mhc2_hi_167


title: Mhc2_hi_164


title: Mhc2_hi_166


title: Mhc2_hi_165


title: Mhc2_hi_162


title: Mhc2_hi_160


title: Mhc2_hi_176


title: Mhc2_hi_159


title: Mhc2_hi_163


title: Mhc2_hi_154


title: Mhc2_hi_155


title: Mhc2_hi_153


title: Mhc2_hi_173


title: Mhc2_hi_148


title: Mhc2_hi_150


title: Mhc2_hi_151


title: Mhc2_hi_147


title: Mhc2_hi_146


title: Mhc2_hi_168


title: Mhc2_hi_145


title: Mhc2_hi_143


title: Mhc2_hi_144


title: Mhc2_hi_142


title: Mhc2_hi_141


title: Mhc2_hi_158


title: Mhc2_hi_161


title: Mhc2_hi_157


title: Mhc2_hi_140


title: Mhc2_hi_156


title: Mhc2_hi_138


title: Mhc2_hi_139


title: Mhc2_hi_152


title: Mhc2_hi_134


title: Mhc2_hi_136


title: Mhc2_hi_131


title: Mhc2_hi_149


title: Mhc2_hi_130


title: Mhc2_hi_135


title: Mhc2_hi_137


title: Mhc2_hi_133


title: Mhc2_hi_129


title: Mhc2_hi_132


title: Mhc2_hi_127


title: Mhc2_hi_123


title: Mhc2_hi_128


title: Mhc2_hi_122


title: Mhc2_hi_121


title: Mhc2_hi_126


title: Mhc2_hi_125


title: Mhc2_hi_120


title: Mhc2_hi_118


title: Mhc2_hi_119


title: Mhc2_hi_117


title: Mhc2_hi_116


title: Mhc2_hi_115


title: Mhc2_hi_113


title: Mhc2_hi_114


title: Mhc2_hi_112


title: Mhc2_hi_109


title: Mhc2_hi_108


title: Mhc2_hi_111


title: Mhc2_hi_110


title: Mhc2_hi_103


title: Mhc2_hi_104


title: Mhc2_hi_101


title: Mhc2_hi_105


title: Mhc2_hi_124


title: Mhc2_hi_97


title: Mhc2_hi_96


title: Mhc2_hi_98


title: Mhc2_hi_94


title: Mhc2_hi_99


title: Mhc2_hi_95


title: Mhc2_hi_93


title: Mhc2_hi_92


title: Mhc2_hi_89


title: Mhc2_hi_88


title: Mhc2_hi_90


title: Mhc2_hi_87


title: Mhc2_hi_85


title: Mhc2_hi_107


title: Mhc2_hi_86


title: Mhc2_hi_83


title: Mhc2_hi_106


title: Mhc2_hi_102


title: Mhc2_hi_82


title: Mhc2_hi_79


title: Mhc2_hi_84


title: Mhc2_hi_77


title: Mhc2_hi_75


title: Mhc2_hi_76


title: Mhc2_hi_100


title: Mhc2_hi_74


title: Mhc2_hi_73


title: Mhc2_hi_71


title: Mhc2_hi_91


title: Mhc2_hi_80


title: Mhc2_hi_72


title: Mhc2_hi_81


title: Mhc2_hi_67


title: Mhc2_hi_70


title: Mhc2_hi_69


title: Mhc2_hi_68


title: Mhc2_hi_66


title: Mhc2_hi_63


title: Mhc2_hi_64


title: Mhc2_hi_62


title: Mhc2_hi_61


title: Mhc2_hi_59


title: Mhc2_hi_58


title: Mhc2_hi_57


title: Mhc2_hi_56


title: Mhc2_hi_78


title: Mhc2_hi_55


title: Mhc2_hi_60


title: Mhc2_hi_51


title: Mhc2_hi_49


title: Mhc2_hi_50


title: Mhc2_hi_48


title: Mhc2_hi_53


title: Mhc2_hi_46


title: Mhc2_hi_47


title: Mhc2_hi_44


title: Mhc2_hi_45


title: Mhc2_hi_65


title: Mhc2_hi_41


title: Mhc2_hi_38


title: Mhc2_hi_39


title: Mhc2_hi_43


title: Mhc2_hi_37


title: Mhc2_hi_40


title: Mhc2_hi_34


title: Mhc2_hi_42


title: Mhc2_hi_36


title: Mhc2_hi_35


title: Mhc2_hi_29


title: Mhc2_hi_52


title: Mhc2_hi_54


title: Mhc2_hi_26


title: Mhc2_hi_33


title: Mhc2_hi_30


title: Mhc2_hi_25


title: Mhc2_hi_31


title: Mhc2_hi_28


title: Mhc2_hi_27


title: Mhc2_hi_32


title: Mhc2_hi_24


title: Mhc2_hi_22


title: Mhc2_hi_21


title: Mhc2_hi_20


title: Mhc2_hi_19


title: Mhc2_hi_18


title: Mhc2_hi_16


title: Mhc2_hi_17


title: Mhc2_hi_14


title: Mhc2_hi_15


title: Mhc2_hi_13


title: Mhc2_hi_12


title: Mhc2_hi_10


title: Mhc2_hi_9


title: Mhc2_hi_11


title: Mhc2_hi_8


title: Mhc2_hi_23


title: Mhc2_hi_5


title: Cd206_hi_188

source_name: mouse dural cd206_hi cell


title: Cd206_hi_189


title: Mhc2_hi_4


title: Mhc2_hi_1


title: Mhc2_hi_2


title: Mhc2_hi_3


title: Cd206_hi_192


title: Cd206_hi_191


title: Cd206_hi_190


title: Cd206_hi_185


title: Cd206_hi_187


title: Cd206_hi_184


title: Cd206_hi_186


title: Cd206_hi_181


title: Cd206_hi_180


title: Cd206_hi_179


title: Mhc2_hi_7


title: Cd206_hi_178


title: Cd206_hi_175


title: Cd206_hi_177


title: Mhc2_hi_6


title: Cd206_hi_174


title: Cd206_hi_173


title: Cd206_hi_170


title: Cd206_hi_171


title: Cd206_hi_164


title: Cd206_hi_169


title: Cd206_hi_166


title: Cd206_hi_183


title: Cd206_hi_156


title: Cd206_hi_159


title: Cd206_hi_155


title: Cd206_hi_162


title: Cd206_hi_165


title: Cd206_hi_168


title: Cd206_hi_163


title: Cd206_hi_182


title: Cd206_hi_161


title: Cd206_hi_157


title: Cd206_hi_160


title: Cd206_hi_158


title: Cd206_hi_167


title: Cd206_hi_154


title: Cd206_hi_153


title: Cd206_hi_152


title: Cd206_hi_172


title: Cd206_hi_176


title: Cd206_hi_151


title: Cd206_hi_150


title: Cd206_hi_149


title: Cd206_hi_148


title: Cd206_hi_147


title: Cd206_hi_146


title: Cd206_hi_145


title: Cd206_hi_144


title: Cd206_hi_143


title: Cd206_hi_141


title: Cd206_hi_142


title: Cd206_hi_138


title: Cd206_hi_139


title: Cd206_hi_137


title: Cd206_hi_131


title: Cd206_hi_132


title: Cd206_hi_133


title: Cd206_hi_140


title: Cd206_hi_134


title: Cd206_hi_128


title: Cd206_hi_127


title: Cd206_hi_129


title: Cd206_hi_136


title: Cd206_hi_130


title: Cd206_hi_125


title: Cd206_hi_124


title: Cd206_hi_126


title: Cd206_hi_118


title: Cd206_hi_120


title: Cd206_hi_117


title: Cd206_hi_121


title: Cd206_hi_122


title: Cd206_hi_119


title: Cd206_hi_123


title: Cd206_hi_116


title: Cd206_hi_115


title: Cd206_hi_135


title: Cd206_hi_114


title: Cd206_hi_112


title: Cd206_hi_113


title: Cd206_hi_110


title: Cd206_hi_111


title: Cd206_hi_106


title: Cd206_hi_103


title: Cd206_hi_109


title: Cd206_hi_107


title: Cd206_hi_104


title: Cd206_hi_108


title: Cd206_hi_99


title: Cd206_hi_105


title: Cd206_hi_97


title: Cd206_hi_100


title: Cd206_hi_95


title: Cd206_hi_98


title: Cd206_hi_93


title: Cd206_hi_94


title: Cd206_hi_102


title: Cd206_hi_91


title: Cd206_hi_101


title: Cd206_hi_89


title: Cd206_hi_96


title: Cd206_hi_92


title: Cd206_hi_90


title: Cd206_hi_87


title: Cd206_hi_88


title: Cd206_hi_86


title: Cd206_hi_85


title: Cd206_hi_84


title: Cd206_hi_82


title: Cd206_hi_81


title: Cd206_hi_80


title: Cd206_hi_79


title: Cd206_hi_75


title: Cd206_hi_77


title: Cd206_hi_78


title: Cd206_hi_76


title: Cd206_hi_73


title: Cd206_hi_68


title: Cd206_hi_71


title: Cd206_hi_69


title: Cd206_hi_70


title: Cd206_hi_61


title: Cd206_hi_67


title: Cd206_hi_64


title: Cd206_hi_65


title: Cd206_hi_66


title: Cd206_hi_72


title: Cd206_hi_63


title: Cd206_hi_57


title: Cd206_hi_58


title: Cd206_hi_56


title: Cd206_hi_59


title: Cd206_hi_83


title: Cd206_hi_55


title: Cd206_hi_54


title: Cd206_hi_53


title: Cd206_hi_74


title: Cd206_hi_52


title: Cd206_hi_51


title: Cd206_hi_62


title: Cd206_hi_60


title: Cd206_hi_49


title: Cd206_hi_50


title: Cd206_hi_48


title: Cd206_hi_47


title: Cd206_hi_46


title: Cd206_hi_45


title: Cd206_hi_44


title: Cd206_hi_42


title: Cd206_hi_41


title: Cd206_hi_34


title: Cd206_hi_37


title: Cd206_hi_40


title: Cd206_hi_35


title: Cd206_hi_31


title: Cd206_hi_30


title: Cd206_hi_29


title: Cd206_hi_36


title: Cd206_hi_28


title: Cd206_hi_43


title: Cd206_hi_26


title: Cd206_hi_25


title: Cd206_hi_33


title: Cd206_hi_24


title: Cd206_hi_23


title: Cd206_hi_22


title: Cd206_hi_21


title: Cd206_hi_19


title: Cd206_hi_20


title: Cd206_hi_18


title: Cd206_hi_39


title: Cd206_hi_15


title: Cd206_hi_38


title: Cd206_hi_32


title: Cd206_hi_13


title: Cd206_hi_9


title: Cd206_hi_11


title: Cd206_hi_7


title: Cd206_hi_5


title: Cd206_hi_6


title: Cd206_hi_8


title: Cd206_hi_27


title: Cd206_hi_3


title: Cd206_hi_2


title: Cd206_hi_1


title: Cd206_hi_4


title: Cd206_hi_17


title: Cd206_hi_16


title: 14d_rep2

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Hi-C sequencing data were 150bp paired-end reads. Paired-end reads were fully mapped to the mouse reference genome (mm10) using bowtie v.1.1.1(ref.9) with parameters: -m 1 -k 1.
We filtered out any reads that were not fully mapped to the genome and truncated the reads by DpnII restriction site
Truncated reads that were longer than 20bp were mapped back to the genome.
Using 4-cutter restriction enzyme DpnII, size selecting for 300–500 bp used in Hi-C experiment, we filtered out the proximal ligation that the distance between 2 reads < 500bp in a read pair. The duplication removal step was to discard the read pairs which were aligned to the same genome position.
We divided the linear genome into 40kb bins and counted the contacts between each bin pair of all samples. We kept the bins with more than 10 PETs in prossessed data file.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated matrix

source_name: mouse tail fibroblast overexpressed Foxa3, Gata4 and Hnf1a

growth_protocol: To induce ihep cells, 5x10^5 mouse tail fibroblast were seeded in dishes and overexpressed Foxa3, Gata4 and Hnf1a by lentivirus. Culture medium was replaced to blocks medium after 48hour.

extract_protocol:
DNA was cut with restriction enzyme DpnII (NEB), and the end of the restriction fragment was labeled with biotin-14-dATP (Life Technologies). Then, the biotinylated products were used for proximity ligation. After the reversed cross-linking of the ligated biotinylated DNA, it was purified and cut into about 400bp fragments by ultrasonic treatment (Covaris S220). The ligation products with biotin-labeled ligaments were isolated by using MyOne streptavidin anti-biotin protein C1 Dynabeads (Life Technologies) and followed by Illumina double-ended sequenced ligation.
Biotinylated fragments were pulled down with streptavidin beads and amplified using 11-12 PCR cycles to enrich for physically interacting sites.

treatment_protocol: Five million cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature to immobilize the nucleus.

value: fibroblast undergoing iHep induction

tag: overexpression

value: Foxa3, Gata4 and Hnf1a

tag: time point


title: Cd206_hi_14


title: 2d_rep1


title: 4d_rep2


title: 4d_rep1


title: 14d_rep1


title: 2d_rep2


title: 0d_rep2

source_name: mouse tail fibroblast

value: fibroblast


title: 6d_rep1


title: Cd206_hi_12


title: Cd206_hi_10


title: CTCF_14d

data_processing:
CutAdapt v.1.16 was used to remove adaptor sequences from reads of rawdata.
Reads were mapped to the mouse reference genome (mm10) using bowtie v.1.1.1.
Peaks were called using macs v.1.3.7.1.
Quantile normalized to remove the bias across the samples by using haystack_bio v.0.5.5.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated for visulization data in igv.

extract_protocol:
Sonicate the chromatin in nuclear extracts to fragments by ultrasonication (Covaris S220). Primary antibodies were used for immunoprecipitation in sonication supernatant by incubation at 4℃ overnight. Protein G Dynabeads (Life Technologies, 10004D) were used for pulling down antibody-chromatin complex followed by washing and eluting. Foxa3:5 micrograms for ChIP, from Santa Cruz, cat id sc-5361. Gata4:5 micrograms for ChIP, from Santa Cruz, cat id sc-1237. Hnf1a:5 micrograms for ChIP, from Santa Cruz, cat id sc-6547. CTCF:5 micrograms for ChIP, from Active Motif, cat id 61312. H3K27ac:5 micrograms for ChIP, from Abcam, cat id ab4729. H3K27me3:5 micrograms for ChIP, from CST, cat id 9733.
MinElute PCR purification kit (Qiagen) was used for ChIP fragments collection. NEBNext Ultra DNA Library Prep Kit was used for ChIP-seq library preparation.

treatment_protocol: Cell were collected by cell scraper and washed by PBS once.

tag: chip antibody

value: CTCF


title: CTCF_6d


title: CTCF_4d


title: CTCF_2d


title: 0d_rep1


title: CTCF_0d


title: Hnf1a_2d


title: ATAC_6d_1

extract_protocol:
Nuclei isolated from 50,000 counted cells were used for transposition reaction with Tn5 transposase (Vazyme Biotech).
10 PCR cycles were performed for library setup for each reaction mix using high-fidelity 2x PCR Master Mix (New England Biolabs) using primers with unique barcodes (Vazyme Biotech).


title: ATAC_6d_2


title: ATAC_4d_2


title: ATAC_14d_2


title: ATAC_14d_1


title: ATAC_2d_2


title: ATAC_4d_1


title: 6d_rep2


title: ATAC_0d_2


title: ATAC_0d_1


title: 10G_M_2117


title: 10G_M_2116


title: 10G_M_2115


title: 10G_M_2114


title: 10G_M_2113


title: 10G_M_2112


title: 10G_M_2110


title: 10G_M_2107


title: 10G_M_2102


title: 10G_M_2103


title: 10G_M_2099


title: 10G_M_2100


title: 10G_M_2095


title: 10G_M_2094


title: ATAC_2d_1


title: 10G_M_2089


title: 10G_M_2088


title: 10G_M_2086


title: 10G_M_2092


title: 10G_M_2083


title: 10G_M_2087


title: 10G_M_2084


title: 10G_M_2091


title: 10G_M_2090


title: 10G_M_2082


title: 10G_M_2081


title: 10G_M_2080


title: 10G_M_2106


title: 10G_M_2105


title: 10G_M_2079


title: 10G_M_2078


title: 10G_M_2077


title: 10G_M_2076


title: 10G_M_2072


title: 10G_M_2075


title: 10G_M_2073


title: 10G_M_2101


title: 10G_M_2071


title: 10G_M_2069


title: 10G_M_2068


title: 10G_M_2064


title: 10G_M_2067


title: 10G_M_2062


title: 10G_M_2063


title: 10G_M_2085


title: 10G_M_2061


title: 10G_M_2060


title: 10G_M_2059


title: 10G_M_2058


title: 10G_M_2057


title: 10G_M_2052


title: 10G_M_2054


title: 10G_M_2053


title: 10G_M_2051


title: 10G_M_2056


title: 10G_M_2050


title: 10G_M_2047


title: 10G_M_2049


title: 10G_M_2045


title: 10G_M_2044


title: 10G_M_2048


title: 10G_M_2042


title: 10G_M_2043


title: 10G_M_2039


title: 10G_M_2066


title: 10G_M_2037


title: 10G_M_2035


title: 10G_M_2038


title: 10G_M_2036


title: 10G_M_2032


title: 10G_M_2031


title: 10G_M_2028


title: 10G_M_2027


title: 10G_M_2030


title: 10G_M_2055


title: 10G_M_2029


title: 10G_M_2026


title: 10G_M_2025