title: genomic_DNAmethylation_M0085_vc

city: Boston

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridised to the Illumina Infinium  MethylationEPIC Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an HiSCAN with standard recommended Illumina scanner settings.

data_processing:
See original publication
Beta values with dasen + noob normalization, filtered for quality probes.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: V-NORM and V-SSRI samples: 1.5-2 cm3 samples of chorionic villi were taken from each of four distinct cotyledons (sites) from below the surface of the fetal-facing side of the placental disc. The samples were washed thoroughly to remove blood, and any thick vessels were removed. Samples were frozen at -20°C until use. DNA was then extracted from all four cotyledon samples using a salting-out DNA extraction procedure, and extracted DNA from the four sites was pooled in equimolar proportions to provide a representative sample of each placenta. The second sampling process involved the QF-2011 placentas, which were processed in Brisbane, Australia within 60 minutes of delivery, and eight sites (1 cm3 each) representing different cotyledons were sampled across the fetal-facing side of each placenta. These samples were snap frozen in liquid nitrogen and subsequently shipped frozen to Montreal, Canada. Samples were pooled and ground while snap frozen over liquid nitrogen. DNA was extracted using a commercial kit  from pooled samples in Montreal, before shipping to Vancouver on dry ice for DNAme processing.

tag: cohort

tag: batch

value: NIH Batch 1

tag: sentrix

value: FALSE

value: Male

value: European/Caucasian

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc


title: genomic_DNAmethylation_QF0151_vc_R1

status: Public on Aug 08 2023

type: genomic

state: MA

country: USA

molecule: genomic DNA

organism: Homo sapiens

tag: Sex

value: Female


title: breast, 2-2

type: SRA

city: shanghai

first: zhangjingnan

middle: zhangjinnan

last: zhangjinnan

address: cailunroad 1200

country: China

institute: Shanghai University of Traditional Chinese medicine

library_source: transcriptomic

data_processing:
To be updated.
Assembly: mm10
Supplementary files format and content: The FPKM of gene in samples.

molecule: total RNA

organism: Mus musculus

source_name: breast

growth_protocol: Mice were supplied with standard laboratory diet and water ad libitum at a temperature 22±1 °C with a 12 h light–dark cycle (6:00–18:00) and 65±5% humidity. All mice were received humane care in compliance with the institutional animal care guidelines approved by the Experimental Animal Ethical Committee, Shanghai University of Traditional Chinese Medicine.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
1) RNA product after fragmentation mRNA enrichment (or rRNA removal) treatment.
2) Reverse transcription to generate first-strand cDNA:
3) Synthesis of double-stranded cDNA by dUTP addition:
4) End repair of double-stranded cDNA by each polymerase:
5) Ligase ligation of Illumina-specific connectors.
(6) PCR amplification and purification to obtain the final RNA sequencing library.
The constructed libraries were quality checked by Agilent 2100 Bioanalyzer (library concentration, fragment size 400-600bp, presence of splice, etc.) and final quantification of the libraries was performed by 9PCR method. The libraries were mixed according to the quantification results and the final sequencing data volume required to enter the sequencing process.

treatment_protocol: Six balb/c male mice were randomly divided into 2 groups: (1) vehicle control (n=3) and (2) 1 mg/kg ITSN (n=3), where mice were given ITSN orally (1 mg/kg/day, administered intragastrically).

tag: tissue

value: breast

tag: strain

value: Balb/c

tag: treatment

value: ITSN


title: genomic_DNAmethylation_M0028_vc


title: genomic_DNAmethylation_QF0350_vc_R1


title: genomic_DNAmethylation_QF0240_vc


title: Mouse #7651, replicate 1

city: Irvine

first: Scott

last: Atwood

state: CA

address: 4238 McGaugh Hall

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

description:
LT-1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files, and the CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices, against the mouse genome GRCm38/mm10. For downstream analysis, the Seurat (v4.3.0) R package (Hao et al., 2021) was used to combine the 4 cell libraries and a merged Seurat object was generated. Genes detected in <3 cells were removed. Low-quality cells were further filtered on the basis of total UMI counts per cell (>900 and <80,000), number of detected genes (>200 and <7,000) and mitochondrial genes fraction (<15%). Applying these filters resulted in a final data-set of 1,066 single cell transcriptomes.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Dorsal skin

extract_protocol:
Label-on PPARG;YFP male mouse #7651 was euthanized at 8 weeks of age, and dorsal skin was shaved and removed. Epidermal cells were obtained by overnight trypsinization (0.25% trypsin, Invitrogen). Single cells were resuspended in 2% BSA/HBSS, stained with DAPI to exclude dead cells, and sorted using a SH800 cell sorter (Sony). 60,000 YFP+ cells were sorted for single cell analysis into 2% BSA/HBSS buffer, at a ratio of 3:1 FSC/BSC-high:FSC/BSC-low, where “high” cells represented the largest ~10% of cells by FSC/BSC.
Single cell suspensions were subjected to counting on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 300 cells/μL. Single nuclei 3’ Gene Expression LT libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ LT Kit v3.1). In brief, suspensions were loaded onto the 10x chip along with reverse transcription (RT) master mix and appropriate gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned up and the cDNA is amplified. cDNA was subjected to enzymatic fragmentation and size selection to optimize the cDNA size prior to final library construction following the manufacturer’s protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Four LT reactions were run in parallel (LT1-4) from the same animal.

tag: cell type

value: Sebaceous gland

value: Dorsal skin

value: PPARG;YFP label-on

tag: age

value: 8 weeks


title: breast, 2-1


title: breast, 1-3

value: DMSO


title: genomic_DNAmethylation_QF0232_vc


title: breast, 1-2


title: genomic_DNAmethylation_QF0302_vc


title: breast, 1-1


title: Treated-3

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
Spliced Transcripts Alignment to Reference (STAR, version 2.7.10a)
FASTQ files were generated using bcl2fastq2 software
Sequence reads from each sample were mapped to mouse genome (GRCm39) using Spliced Transcripts Alignment to Reference (STAR, version 2.7.10a) with the default parameters.
Number of reads per gene were counted while mapping with --quantMode GeneCounts option.
Normalized gene counts were generated using R package DESeq2 (version 1.36.0).
Assembly: GRCm39
Supplementary files format and content: comma-separated values files include normalized number reads per gene for each sample

source_name: bone cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of RNA libraries.
RNA libraries for sequencing were constructed using KAPA Stranded mRNA-Seq Kit (Roche) following manufacturer's protocols.

value: bone cells

value: Dexamethasone Treated


title: Kidney cortex biopsy_baboon_female_14012

city: Winston Salem

first: Laura

middle: A

last: Cox

state: NC

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

data_processing:
Female and male transcripts were processed together in Partek Flow with an average read length of 93.58± 1.52 (minimum=25) and an average Phred score of 36.46 ± 0.54 (minimum=30).
Reads were aligned to the olive baboon genome (papAnu2.0; March 2012) with 57,005 transcripts represented by an average of 11,161,874 ± 3,684,392 total reads and 5.80 ± 1.88% coverage and 16.23 ± 2.71 depth.
Transcripts were excluded where the sum was less than or equal to 5 among all samples and normalized using TMM with a +1 offset to eliminate zeros for downstream analyses.
The full transcript list generated in Partek Flow was imported into Partek Genomics Suite for principal component analysis (PCA) (Partek®, Inc).
Transcripts were filtered for expression values totaling <17 among all samples and filtered based on coefficient of variation for values equal to 0 prior to sex-specific WGCNA.
The R package WGCNA was run as a Pearson’s correlation with default settings as described by Langfelder and Horvath34.
Genome_build: papAnu2.0
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from male samples.
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from female samples.

organism: Papio hamadryas

source_name: Kidney cortex biopsy

growth_protocol: Animals were maintained on a low salt chow diet their whole life leading up to the study.

extract_protocol:
RNA was isolated from kidney biopsy samples using the Direct-zol RNA Miniprep Plus Kit (Zymo Research). Tissue was homogenized in 600 μL of TRI reagent (Zymo Research) using a BeadBeater for 3 x 30 sec with RNA purification according to the Direct-zol RNA Miniprep Plus Kit instructions. RNA was quantified by Qubit RNA BR Assay Kit (Invitrogen) and RIN was determined by with an RNA ScreenTape Kit on the Tapestation 2200 (Agilent).
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Roche). Libraries were quantified by Qubit dsDNA Assay Kit (Invitrogen) and quality was determined by with a DNA ScreenTape Kit on the Tapestation 2200 (Agilent).

tag: animal id

tag: sample name

tag: diet

value: low salt control chow

value: female

tag: colony

value: Southwest national primate research center

tag: collection

value: Ultrasound guided biopsy into liquid nitrogen

tag: surgery anesthetic

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

value: Kidney cortex biopsy


title: genomic_DNAmethylation_QF0130_vc

tag: cohort

tag: batch

value: NIH Batch 1

tag: sentrix

value: FALSE

value: Female

value: European/Caucasian

tag: syncytiotrophoblast

tag: cytotrophoblast


title: Treated-2


title: female infected with Citrobacter rodentium

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Illumina’s bcl2fastq software was used for demultiplexing index 1 i7 for each of the four samples.
The fastq files were aligned to the mm10 mouse genome using the Cell Ranger (7.0.0) pipeline, including intronic reads.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: large intestine lamina propria

extract_protocol:
After perfusion, large intestines were harvested and minced before transferring to conical tubes. The minced pieces were resuspended in 10ml of complete RPMI-1640 containing 1% P/S, 20mM HEPES, 0.05 mg/ml Liberase TL (Roche), 0.05% DNaseI (Roche) and shaken at 200 rpm for 30 min at 37°C in 50-ml Falcon tubes. The tissue suspension was collected and passed through a 70 mm cell strainer and the cells were pelleted by centrifugation at 1500 rpm. The cells were then resuspended and purified by 47% Percoll and centrifuged at 1500 rpm for 10 min. The pellet were collected, washed and resuspended in complete RPMI media. CD45+ immune cells were then enriched for by Miltenyi Beads.
Library was performed according to the manufacter’s instructions (SC RNA3’ V3.1, 10X Genomics) GEMS were generated, poly-A RNA in every GEM was retrotranscripted to cDNA, cleaned up with Dynabeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect for library constrution. A sample index (i7) was added to each of the four samples during library construction.

value: large intestine lamina propria

value: 2-3 months

tag: Sex

value: F

value: immune cells

tag: genotype

value: infected with 5.0 x 109 CFU of Citrobacter Rodentium strain DBS100


title: Treated-1

tag: strain

value: bone cells


title: genomic_DNAmethylation_M0078_vc

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc


title: genomic_DNAmethylation_M0035_vc

value: Male


title: Kidney cortex biopsy_baboon_female_13988

tag: animal id

tag: sample name

value: low salt control chow

tag: age

tag: tissue


title: Ctrl-3

tag: cell type

tag: treatment

value: Control


title: Ctrl-1


title: OE_ZS_5_S36

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

data_processing:
fastq files were aligned to ensembl mouse reference genome mm10 using HISAT2 (Version 2.1.0).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using DESEQ2 (Version 2.11.40.6) followed by normalizaton with RUVrseq estimation of variation (Version 1.24.0)
Differentially expressed genes (10% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Assembly: mm10 mouse genome
Supplementary files format and content: Featurecounts output raw counts data, filtered to remove low counts (<10) in all samples.

molecule: polyA RNA

source_name: Bulk orbitofronal cortex tissue

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

value: Bulk orbitofronal cortex tissue

value: adult

tag: gender

value: male

tag: virus

tag: stress condition

value: acute stress


title: genomic_DNAmethylation_QF0344_vc

tag: cohort

tag: batch

value: NIH Batch 1

tag: sentrix

tag: syncytiotrophoblast

tag: cytotrophoblast


title: genomic_DNAmethylation_QF0291_vc

value: FALSE

tag: Sex

tag: stromal

tag: endothelial


title: OE_ZS_4_S28


title: OE_ZS_3_S20


title: genomic_DNAmethylation_M0109_vc_R1

tag: hofbauer

tag: nrbc


title: OE_ZS_2_S12

tag: age


title: genomic_DNAmethylation_M0204_vc

value: Female


title: OE_ZC_6_S50

tag: tissue

value: control


title: genomic_DNAmethylation_M0067_vc

value: European/Caucasian


title: genomic_DNAmethylation_M0205_vc


title: genomic_DNAmethylation_QF0148_vc_R2

value: TRUE


title: genomic_DNAmethylation_M0050_vc


title: genomic_DNAmethylation_QF0161_vc


title: genomic_DNAmethylation_M0208_vc


title: genomic_DNAmethylation_QF0137_vc_R1


title: OE_ZC_5_S34


title: genomic_DNAmethylation_M0076_vc


title: OE_GS_6_S40


title: OE_ZC_4_S26


title: OE_ZS_7_S43


title: OE_ZC_3_S18


title: genomic_DNAmethylation_QF0197_vc


title: OE_GS_5_S35


title: Ctrl-2

tag: strain

tag: cell type


title: OE_ZC_1_S2

tag: gender


title: genomic_DNAmethylation_QF0252_vc


title: OE_GS_7_S41

tag: virus


title: OE_GS_4_S27

tag: stress condition


title: genomic_DNAmethylation_M0002_vc

tag: cohort


title: genomic_DNAmethylation_M0109_vc_R2

tag: batch


title: genomic_DNAmethylation_M0033_vc

tag: sentrix


title: OE_GC_4_S25


title: OE_GS_2_S11


title: genomic_DNAmethylation_QF0191_vc

tag: syncytiotrophoblast


title: genomic_DNAmethylation_QF0139_vc

tag: cytotrophoblast


title: OE_GC_5_S33


title: genomic_DNAmethylation_QF0222_vc

tag: Sex


title: genomic_DNAmethylation_QF0235_vc

tag: stromal


title: OE_ZS_6_S42


title: genomic_DNAmethylation_M0029_vc

tag: endothelial


title: OE_GC_3_S17


title: genomic_DNAmethylation_QF0371_vc_R2

tag: hofbauer


title: OE_GC_1_S1


title: KD_ZS_5_S39

value: chronic stress


title: OE_GS_3_S19


title: genomic_DNAmethylation_QF0283_vc

tag: nrbc


title: OE_GC_2_S9

tag: age


title: genomic_DNAmethylation_M0101_vc


title: KD_ZS_4_S32

tag: tissue


title: KD_ZS_8_S49


title: OE_GS_1_S3


title: genomic_DNAmethylation_QF0362_vc


title: KD_ZS_2_S16


title: KD_ZS_7_S48


title: genomic_DNAmethylation_QF0311_vc


title: KD_ZS_1_S8


title: genomic_DNAmethylation_QF0316_vc


title: KD_ZC_5_S37


title: genomic_DNAmethylation_M0112_vc


title: KD_ZS_6_S47


title: KD_ZS_3_S24


title: genomic_DNAmethylation_QF0323_vc


title: KD_ZC_4_S30


title: genomic_DNAmethylation_M0015_vc


title: genomic_DNAmethylation_QF0188_vc


title: KD_ZC_2_S14


title: genomic_DNAmethylation_QF0371_vc_R1


title: genomic_DNAmethylation_QF0151_vc_R2


title: KD_GS_8_S46


title: genomic_DNAmethylation_QF0180_vc_R2


title: genomic_DNAmethylation_TO-27_vc

value: V-SSRI

value: East Asian


title: KD_GS_7_S45


title: genomic_DNAmethylation_QF0148_vc_R1


title: genomic_DNAmethylation_TO-81_vc

value: Black


title: KD_GS_5_S38


title: KD_GS_3_S23


title: genomic_DNAmethylation_TO-23_vc


title: genomic_DNAmethylation_M0206_vc

value: Male


title: genomic_DNAmethylation_QF0314_vc


title: KD_GS_2_S15


title: genomic_DNAmethylation_TO-60_vc


title: KD_GS_6_S44


title: KD_GS_1_S7


title: KD_GS_4_S31


title: KD_ZC_3_S22


title: genomic_DNAmethylation_TO-34_vc


title: genomic_DNAmethylation_TO-41_vc


title: genomic_DNAmethylation_QF0315_vc


title: KD_GC_3_S21


title: genomic_DNAmethylation_TO-12_vc


title: genomic_DNAmethylation_TO-28_vc


title: genomic_DNAmethylation_TO-54_vc


title: genomic_DNAmethylation_TO-48_vc


title: genomic_DNAmethylation_TO-79_vc


title: KD_GC_4_S29


title: genomic_DNAmethylation_TO-35_vc


title: genomic_DNAmethylation_TO-56_vc


title: genomic_DNAmethylation_TO-43_vc

value: Other(including mixed)


title: KD_GC_2_S13


title: genomic_DNAmethylation_TO-69_vc


title: KD_GC_1_S5


title: OE_N_Z7_S16

data_processing:
fastq files were aligned to ensembl mouse reference genome mm10 using HISAT2 (Version 2.1.0).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using DESEQ2 (Version 2.11.40.6) followed by normalizaton with RUVrseq estimation of variation (Version 1.24.0)
Differentially expressed genes (10% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Supplementary files format and content: mm10 mouse genome
Supplementary files format and content: Featurecounts output raw counts data, filtered to remove low counts (<10) in all samples.

source_name: OFC

value: OFC

value: Neuron


title: genomic_DNAmethylation_PM77_vc_R3

value: V-NORM

value: Unknown


title: OE_N_G7_S15

value: male

value: adult


title: genomic_DNAmethylation_TO-65_vc

value: NIH Batch 1

value: FALSE


title: OE_N_G6_S13


title: OE_N_Z5_S8


title: OE_A_Z6_S10

value: Astrocyte


title: OE_N_Z2_S6


title: OE_N_G8_S19


title: genomic_DNAmethylation_TO-61_vc


title: OE_N_G5_S7


title: genomic_DNAmethylation_TO-80_vc


title: genomic_DNAmethylation_TO-38_vc

value: European/Caucasian


title: OE_A_G8_S17


title: OE_A_G6_S9


title: OE_N_Z6_S14


title: genomic_DNAmethylation_TO-64_vc


title: OE_A_G5_S3


title: genomic_DNAmethylation_TO-50_vc

value: Female


title: OE_A_G1_S1


title: genomic_DNAmethylation_TO-22_vc


title: genomic_DNAmethylation_TO-25_vc


title: OE__A_Z2_S2


title: genomic_DNAmethylation_TO-30_vc


title: OE_A_Z7_S12


title: genomic_DNAmethylation_TO-53_vc


title: genomic_DNAmethylation_TO-51_vc


title: genomic_DNAmethylation_TO-58_vc


title: KD_N_ZS2_S28


title: OE_A_Z5_S4


title: KD_N_ZS1_S26


title: KD_N_ZS4_S36


title: KD_N_ZS3_S34


title: genomic_DNAmethylation_M0062_vc


title: genomic_DNAmethylation_M0105_vc


title: genomic_DNAmethylation_QF0154_vc


title: KD_N_ZC4_S48


title: genomic_DNAmethylation_QF0322_vc


title: genomic_DNAmethylation_QF0159_vc


title: genomic_DNAmethylation_TO-33_vc


title: genomic_DNAmethylation_TO-14_vc


title: KD_N_GS3_S33


title: genomic_DNAmethylation_TO-37_vc


title: KD_N_GS2_S27


title: KD_N_GS1_S25


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep4

type: RNA

city: Houston

first: Raisa

last: Reyes-Castro

state: Texas

address: 6767 Bertner Ave

department: Genetics

institute: UT Health MD Anderson Cancer Center

description: miRNAs were assayed using Ncounter Nanostring mouse miRNAs v1.5

hyb_protocol: Hybridization was performed following nCounter Nanostring miRNA (NS_M_MIR_V1.5) protocol in where miRNA reporter codeset, hybridization buffer and miRNA capture probe set was added to each sample.

scan_protocol: Nanostring nCounter instrunent

data_processing: Results were analyzed in nCounter Analysis Software v4.0. Statistical analysis was performed using two-tailed t-test and Benjamin-Yekutieli for false discovery rate.

label: miRNA reported and capture probes

source_name: primary lung tumor

label_protocol: nCounter Nanostring mouse miRNA (NS_M_MIR_V1.5) assay with capture probes which are complementary to miRNAs sequence

growth_protocol: 30 to 37 weeks old mice from both genotypes were euthanized following IACUC protocol

extract_protocol: Lungs were removed from  mouse. Then tumors were  identified and collected under the dissecting microscope. 50ug of tumors were homogenized in 1 mL of Trizol (Ambion, #15596018). Total RNA was purified following miRNeasy Mini Kit (Qiagen, #217004).  100ng of total RNA was used for nCounter Nanostring miRNA (NS_M_MIR_V1.5) assay.

treatment_protocol: No treatment. This are genetically modified mouse models that carry oncogenic Kras G12D (Kras LA1/+); and phosphomimetic Dicer1 wherein serines at positions 1712 and 1836 were replaced to aspartic acid in a oncogenic Kras G12D background (KrasLA1/+;Dicer1S2D/+)

value: female

tag: age in weeks

tag: strain

value: lung tumor

tag: genotype


title: KD_N_ZC5_S56

tag: cell type

tag: virus


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep5

tag: gender


title: KD_N_ZC1_S40


title: Mouse Lung tumor_KrasLA1_rep2


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep2


title: genomic_DNAmethylation_QF0299_vc

tag: cohort

tag: batch


title: Adult glioma patient 5

city: Utrecht

first: Carlo

last: Vermeulen

state: Nederland

address: Universiteitsweg 100

country: Netherlands

institute: UMC Utrecht

description: This sample corresponds to case nr 24 in table 1.

library_source: genomic

data_processing:
Megalodon V2.5.0
Guppy V5
Rerio res_dna_r941_min_modbases_5mC_CpG_v001.cfg
binarization at cutoff 0.5 log likelihood ratio
Assembly: CHM13_v2.0
Supplementary files format and content: BED file containing methylation calls per illumina 450K array probe site (ie, GPL13534 system probes).

source_name: Glioma tissue

extract_protocol:
DNA is extracted from a tumor sample using an adapted QiaAmp mini (Qiagen) protocol. Ideally, a tumor sample of roughly 5x5x5mm is used as input material. 180uL ATL buffer is added to the sample and the sample is briefly ground using a pestle, then 200uL buffer AL and 20uL Proteinase K are added and the sample is moved to a 70C heat-block. Once heated the sample is ground with a pestle every minute to improve Proteinase K accessibility. When the sample contains no more solid tissue, or after five minutes of incubation and grinding, the sample is added to a Qiashredder column (Qiagen ID: 79656), not including any solid matter if still present. Shredder column is centrifuged at 20,000g for 1 minute. 200uL of 96% ethanol is added to the eluate and the eluate is moved to a qiaAmp column and centrifuged for 1 minute at 6,000g. The column is washed with 500uL AW1, centrifuged at 6,000g for 1 minute, then with 500uL AW2 at 12,000g for 1.5 minutes. Remaining ethanol is removed in a fresh elution column, centrifuged at 12,000g for 10 seconds. Sample is eluted with 25 uL of MilliQ water. Samples are quantified using a Nanodrop spectrophotometer (Thermo Fisher).
Library was constructed using the SQK-RBK004 protocol
Shallow Whole genome sequencing

tag: individual

value: Adult glioma patient 5

value: Glioma tissue


title: KD_N_ZC3_S46


title: Adult glioma patient 3

description: This sample corresponds to case nr 12 in table 1.

source_name: Peripheral brain tissue

value: Adult glioma patient 3

value: Peripheral brain tissue


title: genomic_DNAmethylation_M0072_vc

tag: sentrix

value: Male

tag: syncytiotrophoblast

tag: cytotrophoblast


title: Adult glioma patient 2

description: This sample corresponds to case nr 10 in table 1.

value: Adult glioma patient 2


title: Mouse Lung tumor_KrasLA1_rep4


title: genomic_DNAmethylation_QF0123_vc

tag: Sex

tag: stromal

tag: endothelial


title: KD_-N_ZS5_S54

value: OFC

value: Neuron

tag: age


title: genomic_DNAmethylation_QF0239_vc

tag: hofbauer

tag: nrbc


title: KD_A_ZS5_S50

tag: tissue

value: male


title: CD4_HIVdelta6_Vehicle_tPol2_CUTRUN_Rep3

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Reads were filtered for adapter contamination using Cutadapt96 and filtered such that at least 90% of bases of each read had a quality score>20.
Duplicated sequences were then capped at a maximum of five occurrences
Reads were aligned to a custom reference genome that concatenated GRCh38 (hg38) with the HIV-dreGFP/Thy1.2 sequence and E. coli K12 sequence each added as additional pseudo-chromosomes. Alignment was performed using STAR version 2.7.3a retaining only primary alignments. Reads overlapping regions of the genome deemed problematic by ENCODE were excluded
Regions of significant enrichment were identified using MACS2 with a threshold of q < 0.1, and H3K27me3 data were run in “broad” mode. A union set of peaks called for all samples and conditions was then assembled using BEDtools. Regions exhibiting significant changes in abundance between vorinostat and vehicle-control conditions were detected using CSAW wherein the tested windows were restricted to those overlapping the union peak set, and significance was reported if p < 0.01
Assembly: hg38-HIVp379d6-eColi_K12
Supplementary files format and content: bigWig files have been normalized to the total number of aligned reads, and eColi reads have been removed

growth_protocol: Healthy donor T cells were infected with HIV-dreGFP/Thy1.2 and isolated based on Thy1.2 surface expression. Infected cells were cultured for 21d, during which cells exhibited progressive decline in viral gene expression as latency is established. Latently infected cells were then re-stimulated with anti-CD3/anti-CD28 dynabeads to increase cell numbers and then allowed to return to latency

extract_protocol:
3x105 CD4 T cells per antibody condition were harvested, washed, and coupled to Concanavalin A-coated beads for 30 min at 4o C with mixing. Cells were incubated overnight in Digitonin-containing (0.01%) antibody buffer with the indicated antibodies at the following concentrations: IgG 1:50, H3K4me3 1:50, H3K27ac 1:100, H3K27me3 1:17, H3K9ac 1:17, H3K9me3 1:80, RNA pol2 1:17, RNApol2 P-S2 1:50. After incubation, cells were washed twice in cell permeabilization buffer (buffer CP, 0.01% Digitonin) and incubated with pAG-MNase for 15 min at room temperature. Cells were washed twice in buffer CP before CaCl2 was added for a 2h cutting reaction at 4oC with rotation. Stop buffer containing EDTA, RNase A, and E. coli spike-in DNA was added to halt the reaction during a 37° 10-min incubation step. Supernatants were collected and added to DNA binding buffer for subsequent DNA isolation by spin columns. Supernatant DNA yields were eluted from columns in 12μL of Tris-HCl elution buffer and quantified by Qubit High-Sensitivity dsDNA assay.
CUT&RUN Next-Generation Sequencing (NGS) library preparation was performed using NEBNext Ultra II DNA library preparation kits (New England Biolabs). DNA end repair and A-tailing was performed followed by adapter ligation to NEBNext hairpin adaptors and linearization of NEBNext adaptors with USER enzyme. Adaptor ligated libraries were amplified with sample-specific barcoded dual-index primers with PCR conditions optimized for amplification of short fragments: 14 cycles 15s at 98°C and 10s at 60°C. Libraries were quantified and examined by Qubit dsDNA assay (ThermoFisher) and capillary electrophoresis (Agilent Tapestation).
OTHER: CUT&RUN

treatment_protocol: As the reactivated cells returned to a resting state, cells were treated in triplicate with or without vorinostat (335nM) for 21d

tag: treatment

value: Vehicle

tag: replicate

tag: antibody

tag: method

value: CUT&RUN


title: KD_N_GC5_S55

tag: cell type

tag: virus

value: adult


title: KD_N_GC3_S45


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep3

tag: gender

tag: age in weeks

tag: strain

tag: genotype


title: genomic_DNAmethylation_M0056_vc

tag: cohort

tag: batch

value: NIH Batch 1

tag: sentrix

value: FALSE

tag: Sex

value: Other(including mixed)

tag: syncytiotrophoblast

tag: cytotrophoblast


title: Mouse Lung tumor_KrasLA1_rep3

tag: tissue


title: genomic_DNAmethylation_M0017_vc

value: Female

value: European/Caucasian

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc


title: KD_A_ZS4_S32

tag: cell type

value: Astrocyte

tag: age


title: genomic_DNAmethylation_M0202_vc


title: KD_N_GC4_S47

tag: virus


title: genomic_DNAmethylation_QF0307_vc


title: CD4_HIVdelta6_Vehicle_IgG_CUTRUN_Rep2

tag: treatment

tag: replicate

tag: antibody

value: IgG

tag: method


title: Mouse Lung tumor_KrasLA1_rep1

tag: gender

tag: age in weeks

tag: strain

value: lung tumor

tag: genotype


title: KD_N_GC2_S39

tag: Sex


title: KD_N_GS5_S53

tag: tissue


title: genomic_DNAmethylation_M0051_vc

tag: cohort

tag: batch

tag: sentrix

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal


title: Adult glioma patient 1

description: This sample corresponds to case nr 6 in table 1.

tag: individual

value: Adult glioma patient 1

value: Glioma tissue


title: CD4_HIVdelta6_Vehicle_IgG_CUTRUN_Rep1

tag: treatment


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep1


title: CD4_HIVdelta6_Vehicle_H3K9me3_CUTRUN_Rep3

tag: replicate


title: genomic_DNAmethylation_QF0360_vc

tag: endothelial

tag: hofbauer

tag: nrbc


title: KD_A_ZS2_S24

tag: cell type

tag: virus

tag: age


title: KD_A_ZC5_S52

tag: Sex


title: genomic_DNAmethylation_M0079_vc


title: genomic_DNAmethylation_QF0199_vc


title: Adult glioma patient 4

description: This sample corresponds to case nr 17 in table 1.

value: Adult glioma patient 4

tag: tissue


title: CD4_HIVdelta6_Vehicle_tPol2_CUTRUN_Rep2

tag: antibody

tag: method


title: CD4_HIVdelta6_Vehicle_tPol2_CUTRUN_Rep1


title: CD4_HIVdelta6_Vehicle_Pol2s2_CUTRUN_Rep3


title: genomic_DNAmethylation_M0053_vc

tag: cohort

tag: batch

tag: sentrix


title: KD_A_ZC4_S44

value: OFC


title: CD4_HIVdelta6_Vehicle_Pol2s2_CUTRUN_Rep2


title: CD4_HIVdelta6_Vehicle_Pol2s2_CUTRUN_Rep1


title: CD4_HIVdelta6_Vehicle_H3K4me3_CUTRUN_Rep1


title: KD_A_ZC1_S38


title: KD_A_ZS3_S30


title: genomic_DNAmethylation_QF0306_vc

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal


title: KD_A_ZS1_S22


title: CD4_HIVdelta6_Vehicle_H3K27me3_CUTRUN_Rep2

tag: treatment

tag: replicate


title: CD4_HIVdelta6_Vehicle_H3K9me3_CUTRUN_Rep1


title: CD4_HIVdelta6_Vehicle_H3K9me3_CUTRUN_Rep2


title: CD4_HIVdelta6_Vehicle_H3K27ac_CUTRUN_Rep2


title: genomic_DNAmethylation_QF0153_vc

value: Male

tag: endothelial

tag: hofbauer


title: CD4_HIVdelta6_Vehicle_H3K27ac_CUTRUN_Rep1


title: CD4_HIVdelta6_SAHA_tPol2_CUTRUN_Rep3

value: SAHA


title: CD4_HIVdelta6_Vehicle_H3K9ac_CUTRUN_Rep3

value: Vehicle


title: genomic_DNAmethylation_PM77_vc_R2

value: V-NORM

value: TRUE

value: Unknown

tag: nrbc


title: genomic_DNAmethylation_QF0280_vc

value: NIH Batch 1

value: FALSE

value: East Asian


title: CD4_HIVdelta6_Vehicle_H3K9ac_CUTRUN_Rep2

value: CUT&RUN


title: CD4_HIVdelta6_Vehicle_H3K9ac_CUTRUN_Rep1


title: CD4_HIVdelta6_Vehicle_H3K4me3_CUTRUN_Rep3


title: CD4_HIVdelta6_Vehicle_H3K4me3_CUTRUN_Rep2


title: CD4_HIVdelta6_SAHA_Pol2s2_CUTRUN_Rep2


title: genomic_DNAmethylation_QF0350_vc_R2

value: European/Caucasian


title: KD_A_GS5_S49

tag: cell type

value: Astrocyte

tag: virus

value: male

value: adult


title: CD4_HIVdelta6_Vehicle_H3K27me3_CUTRUN_Rep1


title: KD_A_GS3_S29

tag: Sex

tag: age


title: genomic_DNAmethylation_QF0178_vc


title: KD_A_GS2_S23

tag: tissue


title: genomic_DNAmethylation_M0003_vc

value: Female


title: KD_A_GC3_S41


title: KD_A_ZC3_S42


title: CD4_HIVdelta6_SAHA_Pol2s2_CUTRUN_Rep3

tag: antibody

tag: method


title: CD4_HIVdelta6_SAHA_IgG_CUTRUN_Rep1

value: IgG


title: KD_A_GC2_S37

value: OFC


title: CD4_HIVdelta6_SAHA_H3K9ac_CUTRUN_Rep3


title: CD4_HIVdelta6_Vehicle_H3K27me3_CUTRUN_Rep3


title: CD4_HIVdelta6_SAHA_tPol2_CUTRUN_Rep2


title: CD4_HIVdelta6_SAHA_H3K9ac_CUTRUN_Rep2


title: CD4_HIVdelta6_SAHA_tPol2_CUTRUN_Rep1


title: genomic_DNAmethylation_QF0128_vc

tag: cohort

tag: batch

value: Black


title: KD_A_GS1_S21


title: genomic_DNAmethylation_M0102_vc

tag: sentrix

value: Male

tag: syncytiotrophoblast


title: CD4_HIVdelta6_SAHA_H3K9me3_CUTRUN_Rep1

value: SAHA


title: CD4_HIVdelta6_SAHA_Pol2s2_CUTRUN_Rep1


title: KD_A_GC5_S51


title: WT-HU, 2 replicates, scRNA-seq

city: CAMBRIDGE

first: Mona

last: Shehata

state: Cambridgeshire

address: Cambridge Biomedical Campus, Hills Road

department: Department of Oncology

country: United Kingdom

institute: Early Cancer Institute

description: 10x Genomics

data_processing:
Cell Ranger 6.0.2 (http://10xgenomics.com) was used to process Chromium scRNA-seq output and generate the count table. Samples were demultiplexed using barcode assignment and unique molecular identifier (UMI) quantification. FASTQ reads were aligned to the mouse reference genome refdata-cell ranger-mm10-3.0.0. Seurat (V4.0) in R (V4.1.3) was used to carry out all analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary gland

extract_protocol:
Organoids were dissociated into single cell suspension using TrypLE at 30°C for 10-15mins with mechanical pipetting every 5 minutes. Cells washed with media + 10%FBS to inactivate the TrypLE, then filtered and resuspended in ice-cold HBSSwo (Mg2+/Ca2+ free) supplemented with 0.04% w/v BSA.
Library preparation was performed according to instruction in the 10× Chromium single-cell kit version 3.

value: Mammary gland

tag: cell line

value: organoid

value: mammary epithelial cells

tag: genotype

value: Wildtype

value: HU


title: WT, 2 replicates, scRNA-seq

description: 10x Genomics

tag: treatment

value: Untreated


title: CD4_HIVdelta6_SAHA_H3K27me3_CUTRUN_Rep1

tag: replicate

value: CUT&RUN


title: CD4_HIVdelta6_SAHA_IgG_CUTRUN_Rep3


title: KD_A_GC4_S43


title: genomic_DNAmethylation_QF0347_vc

value: NIH Batch 1

value: FALSE

value: European/Caucasian

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer


title: CD4_HIVdelta6_SAHA_IgG_CUTRUN_Rep2


title: CD4_HIVdelta6_SAHA_H3K27ac_CUTRUN_Rep3


title: CD4_HIVdelta6_SAHA_H3K9me3_CUTRUN_Rep3


title: genomic_DNAmethylation_M0075_vc

tag: Sex

tag: nrbc


title: CD4_HIVdelta6_SAHA_H3K27ac_CUTRUN_Rep2


title: CD4_HIVdelta6_SAHA_H3K9me3_CUTRUN_Rep2


title: genomic_DNAmethylation_QF0140_vc


title: CD4_HIVdelta6_SAHA_H3K9ac_CUTRUN_Rep1


title: B2-HU, 2 replicates, scRNA-seq

description: 10x Genomics

tag: tissue

tag: cell type


title: genomic_DNAmethylation_M0034_vc


title: CD4_HIVdelta6_SAHA_H3K4me3_CUTRUN_Rep3

tag: antibody

tag: method


title: genomic_DNAmethylation_QF0297_vc_R2

tag: cohort

tag: batch

value: TRUE


title: Microglia cx3-tgfb1 KO mouse 4

city: Cincinnati

first: Yu

last: Luo

state: Ohio

address: 231 Albert Sabin Way

institute: University of Cincinnati

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: brain

growth_protocol: N/A sorted cells from in vivo tissue

extract_protocol:
enzymatic isolation (with inhibitors), FACS into Lysis buffer
Qubit quantification (ThermoFisher, Waltham, MA), individually indexed libraries were proportionally pooled and sequenced using NextSeq 2000 Sequencer (Illumina, San Diego, CA) under the sequencing setting of PE 2x61 bp to generate about 60M reads

treatment_protocol: 5x Tamoxifen 180mg/kg oral gavage

value: brain

value: Microglia

value: KO

tag: strain background


title: B2, 2 replicates, scRNA-seq

description: 10x Genomics

tag: cell line


title: genomic_DNAmethylation_QF0180_vc_R1

tag: sentrix

tag: syncytiotrophoblast


title: Microglia Cx3 Control mouse 4

tag: genotype

value: WT


title: genomic_DNAmethylation_M0063_vc

value: Male

tag: cytotrophoblast


title: Astrocyte cx3-tgfb1 KO mouse 3

value: Astrocytes


title: CD4_HIVdelta6_SAHA_H3K4me3_CUTRUN_Rep1

tag: treatment

value: SAHA

tag: replicate


title: CD4_HIVdelta6_SAHA_H3K4me3_CUTRUN_Rep2


title: Astrocyte Cx3 Control mouse 4


title: CD4_HIVdelta6_SAHA_H3K27me3_CUTRUN_Rep3


title: Microglia cx3-tgfb1 KO mouse 3


title: CD4_HIVdelta6_SAHA_H3K27me3_CUTRUN_Rep2


title: Microglia cx3-tgfb1 KO mouse 2


title: genomic_DNAmethylation_QF0198_vc

value: Female

tag: stromal

tag: endothelial

tag: hofbauer


title: genomic_DNAmethylation_M0070_vc

tag: Sex

tag: nrbc


title: ITK-SYK+ CD4+ T cells PD1 KO DMSO replicate 2

city: Munich

first: Tim

last: Wartewig

address: Einsteinstrasse 25

department: Clinical Chemistry

country: Germany

institute: TUM

data_processing:
Cutadapt (v3.1) was used to remove adapter sequences. Reads were aligned to the mm9 genome using Bowtie2.
Duplicates were marked with MarkDuplicates (Picard, v2.24.0) and removed with Samtools (v1.11). To filter properly mapped reads, we used Samtools with the following options: exclude multi-mapped reads (MAPQ < 30) and reads with flag 1796 or 1804.
Samtools with option “-f 2” was used to filter properly paired reads. Adjustment using the Tn5 shift was performed with alignmentSieve (deepTools (v3.3.2)).
Next, we filtered for nucleosome-free reads (0-100 bp). Visual inspection after filtering was performed using the bamPEFragmentSize function from deepTools (v3.3.2).
Next, we used MACS2 (v2.2.7.1) to call ATAC-seq peaks with the following parameters: –nomodel –nolambda –keep-dup auto -call-summits. chromVAR (v1.14.0) was used to calculate motif scores.
Assembly: mm9
Supplementary files format and content: tab-delimited text file include counts values for each Sample

source_name: primary cells

growth_protocol: ITK-SYKCD4-creERT2 or ITK-SYKCD4-creERT2;Pdcd1-/- mice received a single dose of 2 mg tamoxifen. Five days after injection, single-cell suspensions were generated from the spleens and 50,000 eGFP+ FACS-sorted cells were used for the transposase reaction.

extract_protocol: The transposase reaction was performed as previously described (M.R. Corces et al. Nat Methods 2017).

treatment_protocol:
For the ATAC-seq experiments involving inhibitor incubation, single-cell suspensions were generated from spleens of acutely induced ITK-SYKCD4-creERT2, or ITK-SYKCD4-creERT2;Pdcd1-/- mice.
Next, the cells were incubated in vitro for three hours in presence of 5 μM ACLY inhibitor BMS-303141 or DMSO. Finally, ITK-SYK expressing eGFP+ cells were FACS-sorted and immediately processed for ATAC-seq.

value: primary cells

tag: cell type

value: ITK-SYK+ CD4+ T cells

value: PD1 KO

value: DMSO

tag: time

value: Day 5 post TAM


title: R3_Spatial_31dpi

first: Barry

last: Stripp

address: 8700 Beverly Blvd

department: Lung Institute

institute: Cedars Sinai Medical Center

description: 10x genomics Visium, transcriptome: refdata-gex-mm10-2020-A

data_processing:
align with cellranger
Assembly: refdata-gex-mm10-2020-A
Library strategy: spatial transcriptome

source_name: spatial RNAseq: 31 days post infection with PR8

extract_protocol:
10x genomics chromium 3' V2, V3.1 single cell RNAseq kit and Visium spatial RNAseq
follow 10x genomics instruction

tag: tissue

value: lung

value: bulk


title: ITK-SYK+ CD4+ T cells PD1 KO BMS replicate 1


title: genomic_DNAmethylation_M0210_vc

tag: cohort

tag: batch

value: NIH Batch 1

value: FALSE

value: European/Caucasian


title: ITK-SYK+ CD4+ T cells PD1 KO BMS replicate 2

tag: cell line


title: Astrocyte Cx3 Control mouse 5

value: brain

tag: strain background


title: genomic_DNAmethylation_QF0304_vc

tag: sentrix

tag: syncytiotrophoblast


title: Microglia Cx3 Control mouse 5

value: Microglia

tag: genotype


title: Astrocyte cx3-tgfb1 KO mouse 4

value: KO


title: ITK-SYK+ CD4+ T cells PD1 WT BMS replicate 1

value: PD1 WT

tag: treatment


title: genomic_DNAmethylation_QF0189_vc

value: Male

tag: cytotrophoblast


title: ITK-SYK+ CD4+ T cells PD1 KO DMSO replicate 1


title: ITK-SYK+ CD4+ T cells PD1 WT BMS replicate 2


title: genomic_DNAmethylation_QF0332_vc

tag: stromal


title: ITK-SYK+ CD4+ T cells PD1 WT DMSO replicate 2


title: Astrocyte Cx3 Control mouse 2

value: Astrocytes

value: WT


title: Astrocyte  Cx3 Control mouse 3


title: Microglia Cx3 Control mouse 2


title: genomic_DNAmethylation_M0087_vc

value: Female

tag: endothelial


title: Astrocyte cx3-tgfb1 KO mouse 2


title: Microglia cx3-tgfb1 KO mouse 1


title: Astrocyte cx3-tgfb1 KO mouse 1


title: ITK-SYK+ CD4+ T cells PD1 WT DMSO replicate 1

value: primary cells

value: ITK-SYK+ CD4+ T cells


title: genomic_DNAmethylation_QF0343_vc

tag: hofbauer


title: genomic_DNAmethylation_QF0137_vc_R2

value: TRUE

tag: Sex


title: Astrocyte Cx3 Control mouse 1


title: Microglia Cx3 Control mouse 1


title: ZS.invivo.ICB.3

city: Philadelphia

first: Ben

middle: Z

last: Stanger

state: PA

address: 421 Curie Blvd

institute: Perelman School of Medicine

data_processing:
Illumina bcl2fastq was used to convert bcl to fastq files
Sequencing reads were aligned to the mouse (GRCm39) reference and quantified using salmon (v2.5.1) with default settings.
differential analysis performed with DESeq2
Assembly: GRCm39

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 10% glutamine, and 150 µg/mL gentamicin at 37°C, 5% CO2, 21% O2, and 100% humidity.

extract_protocol:
RNA was prepared from cultured tumor cells or sorted cells using the or RNeasy Mini Kit (Qiagen) according to manufacturer's protocol,
Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. Libraries were constructed by Novogene (Beijing, China)

treatment_protocol: cells were co-cultured with OT-1 cells if indicated

value: pancreatic cancer cells

value: YFP+; Zeb1/Snail overexpression

value: immunotherapy-treated


title: EV.invivo.ICB.3

value: YFP+


title: genomic_DNAmethylation_M0071_vc

value: NIH Batch 1

value: FALSE

tag: nrbc


title: genomic_DNAmethylation_M0068_vc

value: European/Caucasian


title: EV.invivo.ICB.2

tag: cell type


title: ZS.invivo.ICB.2


title: ITK-SYK+ CD4+ T cells PD1 KO ex vivo replicate 2

value: PD1 KO

value: ex vivo

tag: time

value: Day 5 post TAM


title: Astrocyte Cx3 Control mouse 3

tag: tissue

value: brain


title: ZS.invivo.ICB.1


title: ITK-SYK+ CD4+ T cells PD1 KO ex vivo replicate 1


title: ZS.invivo.2


title: ITK-SYK+ CD4+ T cells PD1 WT ex vivo replicate 2

value: PD1 WT


title: EV.invivo.ICB.1


title: EV.invivo.2


title: ZS.invivo.1


title: genomic_DNAmethylation_QF0146_vc

tag: cohort


title: escape.invivo.ICB.3


title: genomic_DNAmethylation_M0065_vc

tag: batch


title: genomic_DNAmethylation_QF0167_vc

value: Male


title: EV.invivo.1


title: ITK-SYK+ CD4+ T cells PD1 WT ex vivo replicate 1

tag: cell line

value: Day 5 post  TAM


title: parental.invivo.ICB.3


title: escape.invivo.ICB.1


title: 12mo_HSC_MHCII_hi_rep3

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

institute: Army Medical University

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 was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus GRCm38.
The mapped reads of each sample were then assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All the transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: All mice used were randomized, background-matched. All mice used were housed in individually ventilated specific pathogen-free (SPF) conditions and fed with autoclaved water and food.

extract_protocol:
MHCII-hi and MHCII-lo HSCs were sorted from the BM of WT mice at 12 mo.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: Hematopoietic stem cell

value: WT

tag: cell subtype

tag: age

value: 12 months


title: escape.invivo.ICB.2

value: pancreatic cancer cells


title: ITK-SYK+ CD4+ T cells PD1 KO ex vivo replicate 3

value: primary cells

value: ITK-SYK+ CD4+ T cells


title: genomic_DNAmethylation_QF0317_vc

data_processing:
See original publication
Beta values with dasen + noob normalization, filtered for quality probes.

value: NIH Batch 1

tag: sentrix

value: Female

tag: syncytiotrophoblast


title: ITK-SYK+ CD4+ T cells PD1 WT ex vivo replicate 3

tag: genotype

tag: treatment


title: parental.invivo.ICB.1

value: YFP+

value: immunotherapy-treated


title: escape.invivo.2


title: 12mo_HSC_MHCII_hi_rep1


title: parental.invivo.ICB.2


title: genomic_DNAmethylation_QF0170_vc

value: FALSE

value: European/Caucasian

tag: cytotrophoblast

tag: stromal


title: parental.invivo.1


title: genomic_DNAmethylation_TO-29_vc

value: V-SSRI

tag: endothelial

tag: hofbauer


title: escape.Irf6OE.OT1.1

value: Irf6 overexpression

value: OT1 co-culture


title: genomic_DNAmethylation_M0207_vc

tag: Sex

value: Male

tag: nrbc


title: escape.EV.OT1.2

tag: cell type

value: wildtype


title: genomic_DNAmethylation_QF0290_vc


title: escape.invivo.1


title: 12mo_HSC_MHCII_lo_rep2

tag: tissue

value: Bone marrow

value: Hematopoietic stem cell


title: escape.Irf6OE.OT1.2


title: parental.invivo.2


title: IR_HSC_MHCII_hi_rep3

extract_protocol:
MHCII-hi and MHCII-lo HSCs were sorted from the BM of WT mice with IR.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: WT

value: MHCII-hi

tag: agent

value: 5 Gy total body irradiation


title: 12mo_HSC_MHCII_lo_rep1

value: 12 months


title: genomic_DNAmethylation_QF0297_vc_R1

extract_protocol: V-NORM and V-SSRI samples: 1.5-2 cm3 samples of chorionic villi were taken from each of four distinct cotyledons (sites) from below the surface of the fetal-facing side of the placental disc. The samples were washed thoroughly to remove blood, and any thick vessels were removed. Samples were frozen at -20°C until use. DNA was then extracted from all four cotyledon samples using a salting-out DNA extraction procedure, and extracted DNA from the four sites was pooled in equimolar proportions to provide a representative sample of each placenta. The second sampling process involved the QF-2011 placentas, which were processed in Brisbane, Australia within 60 minutes of delivery, and eight sites (1 cm3 each) representing different cotyledons were sampled across the fetal-facing side of each placenta. These samples were snap frozen in liquid nitrogen and subsequently shipped frozen to Montreal, Canada. Samples were pooled and ground while snap frozen over liquid nitrogen. DNA was extracted using a commercial kit  from pooled samples in Montreal, before shipping to Vancouver on dry ice for DNAme processing.

tag: cohort

tag: batch

value: NIH Batch 1


title: IR_HSC_MHCII_hi_rep1

tag: cell subtype


title: escape.EV.steadystate.1

value: pancreatic cancer cells


title: genomic_DNAmethylation_QF0327_vc


title: 12mo_HSC_MHCII_hi_rep2

tag: age


title: genomic_DNAmethylation_TO-16_vc

tag: sentrix

value: Female


title: IR_HSC_MHCII_lo_rep3

value: MHCII-lo


title: parental.ZS.steadystate.2

value: Zeb1/Snail overexpression


title: escape.Irf6OE.steadystate.2


title: IR_HSC_MHCII_hi_rep2


title: escape.Irf6OE.steadystate.1


title: parental.EV.steadystate.2


title: parental.EV.steadystate.1


title: IR_HSC_MHCII_lo_rep2


title: 12mo_HSC_MHCII_lo_rep3


title: genomic_DNAmethylation_TO-45_vc

value: FALSE

value: European/Caucasian

tag: syncytiotrophoblast


title: Y2_cerebellum_RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina sequencing reads (~46 million paired-end reads per sample) were de-multiplexed using bcl2fastq/2.20.0.
Reads were trimmed to remove adapter sequences using trimmomatic/0.39. The quality of the resulting FASTQs was assessed using FASTQC/0.11.9 and reads were aligned to the GRCm38/mm10 genome assembly using STAR/2.7.5b.
BAM files were sorted and indexed using samtools/1.10, and duplicates were removed using picard/2.20.8. The BAM files were then filtered to retain alignments with a minimum mapping quality of 10 using samtools/1.10.
The bamCoverage function in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. Input reads were subtracted from 5hmC using the bigwigCompare function.
The featureCounts function of the Rsubread R package/2.6.4 was used to estimate counts for all genes.
Assembly: mm10
Supplementary files format and content: count files were generated using the featureCounts function in the Rsubread R package/2.6.4.
Supplementary files format and content: bigWig files were generated using the bamCoverage function in deepTools/3.5/0; scores represent the coverage on the genome location.

source_name: cerebellum

extract_protocol:
RNA was isolated from frozen tissue by homogenization in Trizol followed by isopropanol precipitation, and  further purified using RNeasy columns (Qiagen). An on-column DNase I digestion was performed during the purification step to remove genomic DNA. The RNA amount and integrity were confirmed using the Qubit RNA HS Assay Kit and RNA IQ Assay (Thermo Fisher) respectively.
Total RNA (~700 ng) was used to make RNA-seq libraries following the Zymo-Seq Ribo-free Total RNA Library Kit (Zymo Research) instructions with dual indexing. Library quality and quantity was confirmed using a high-sensitivity Agilent BioAnalyzer DNA chip. Equimolar amounts of each library were combined, and the pooled library was further quantified using NEBNext Library Quant Kit (New England Biolabs) and Qubit HS DNA kit (Thermo Fisher).

treatment_protocol: Old as treated group

tag: strain

value: male

value: 19 weeks

value: cerebellum


title: genomic_DNAmethylation_TO-19_vc

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

value: V-SSRI

value: Male

value: East Asian


title: escape.EV.OT1.1

tag: genotype

value: wildtype

tag: treatment

value: OT1 co-culture


title: escape.EV.steadystate.2


title: genomic_DNAmethylation_TO-77_vc

value: Other(including mixed)

tag: cytotrophoblast

tag: stromal


title: genomic_DNAmethylation_TO-67_vc

tag: endothelial

tag: hofbauer


title: parental.ZS.steadystate.1


title: genomic_DNAmethylation_TO-44_vc

tag: Sex

tag: nrbc


title: Y4_cerebellum_RNA

value: female

value: 22 weeks

tag: tissue


title: Y3_cerebellum_RNA


title: O3_cerebellum_RNA

value: 83 weeks


title: O2_cerebellum_RNA


title: genomic_DNAmethylation_TO-83_vc

value: NIH Batch 1


title: Ctrl_HSC_MHCII_hi_rep3

extract_protocol:
MHCII-hi and MHCII-lo HSCs  were sorted from the BM of WT mice at 5 mo.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
RNA libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

tag: cell type

value: Hematopoietic stem cell

value: MHCII-hi

value: WT


title: Ctrl_HSC_MHCII_lo_rep2

value: MHCII-lo


title: Y1_cerebellum_RNA

value: male

value: 19 weeks


title: O4_cerebellum_RNA

value: 102 weeks

value: cerebellum


title: genomic_DNAmethylation_TO-73_vc

tag: cohort

value: V-SSRI

value: FALSE

value: Male

value: European/Caucasian


title: genomic_DNAmethylation_TO-49_vc

tag: batch

value: Female


title: Ctrl_HSC_MHCII_hi_rep2

tag: cell subtype


title: Ctrl_HSC_MHCII_hi_rep1


title: O1_cerebellum_RNA

tag: age

value: 93 weeks


title: genomic_DNAmethylation_TO-32_vc

tag: sentrix

value: Other(including mixed)


title: O4_cerebellum_Input

data_processing:
library strategy: hMeDIP-seq
Illumina sequencing reads (~31 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned to the GRCm38/mm10 genome assembly using bowtie/2-2.4.2 with parameters “--end-to-end --no-mixed --no-discordant --very-sensitive -I 10 -X 700”.
Sam output files were then filtered to keep reads with a minimum mapping quality of 10 using samtools/1.9. sambamba/0.7.1 was used to keep uniquely mapping reads with parameters “-F "[XS] == null and not unmapped and not duplicate"”. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis using bedtools/2.30.0.
The bamCoverage function in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. Input reads were subtracted from 5hmC samples using bigWigCompare function.
Peaks were called using macs/2.2.7.1 with parameters “-f BAMPE -g 1.87e9 -B --broad -q 0.001 --broad-cutoff 0.001” using input as control and 5hmC as treatment sample.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using the bamCoverage function in deepTools/3.5/0; Scores represent the coverage on the genome location.

extract_protocol:
Genomic DNA was isolated from ~25 mg of frozen tissue using the Quick-DNA Miniprep Pus Kit (Zymo Research) following the manufacturer's protocol with an overnight proteinase K digestion. The amount and quality of extracted DNA was assessed by NanoDrop One (Thermo Fisher). The hMeDIP assay was performed using the MagMeDIP-seq Package (Diagenode, C02010040) with an antibody against 5hmC (Diagenode, C15200200-50). 1.2 µg of genomic DNA was sonicated into ~200 bp fragments using the S220 focused ultrasonicator (Covaris). To maximize IP yield, we processed the samples in duplicates and then pool before performing IPure purification. Prior to immunoprecipitation, samples were spiked with hydroxymethylated (Diagenode, C02040018) and unmethylated DNA controls.
Immunoprecipitated and 10% input DNA was used to prepare libraries according to the MagMeDIP-seq Package protocol except libraries were dual indexed using the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Biolabs) followed by PCR amplification. The quantity and quality of individual libraries were verified on a BioAnalyzer DNA 1000 (Agilent) then pooled into equimolar amounts. The quantity of the pooled library was assessed using the NEBNext Library Quant Kit (New England Biolabs) and Qubit HS DNA kit (Thermo Fisher).

value: female

tag: antibody


title: genomic_DNAmethylation_TO-66_vc

value: NIH Batch 1

tag: syncytiotrophoblast


title: O3_cerebellum_Input

tag: strain

value: 83 weeks


title: Treg_IR_rep3

extract_protocol:
Tregs were sorted from the BM of control or IR mice.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: regulatory T cell

tag: genotype

tag: treatment

value: three months post irradiation (IR)


title: Ctrl_HSC_MHCII_lo_rep3

value: Hematopoietic stem cell

value: MHCII-lo

value: WT


title: O2_cerebellum_Input

value: cerebellum


title: IR_HSC_MHCII_lo_rep1

tag: agent

value: 5 Gy total body irradiation


title: Y1_cerebellum_Input

value: male

value: 19 weeks


title: Y4_cerebellum_5hmC

value: 22 weeks


title: Ctrl_HSC_MHCII_lo_rep1


title: genomic_DNAmethylation_TO-52_vc

value: V-SSRI

value: FALSE

value: Male

value: European/Caucasian

tag: cytotrophoblast

tag: stromal

tag: endothelial


title: genomic_DNAmethylation_TO-40_vc

value: NIH Batch 1

tag: Sex

value: Female

tag: hofbauer

tag: nrbc


title: Y3_cerebellum_Input

value: female

tag: tissue


title: O1_cerebellum_Input

value: 93 weeks


title: Treg_IR_rep2

value: Bone marrow

tag: cell type

value: regulatory T cell

value: three months post irradiation (IR)


title: genomic_DNAmethylation_TO-17_vc

tag: cohort

tag: batch


title: Treg_Ctrl_rep3

value: WT

value: control


title: genomic_DNAmethylation_TO-63_vc

tag: sentrix

value: Unknown


title: Y3_cerebellum_5hmC

tag: age

value: cerebellum

tag: antibody


title: O3_cerebellum_5hmC

tag: strain

value: male

value: 83 weeks


title: O2_cerebellum_5hmC


title: Y4_cerebellum_Input

value: 22 weeks


title: HSC_IR_rep2

extract_protocol:
HSCs were sorted from the BM of control or IR mice.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Hematopoietic stem cell

tag: genotype

value: ionizing radiation


title: genomic_DNAmethylation_TO-55_vc

value: V-SSRI

value: FALSE

value: Male

value: European/Caucasian

tag: syncytiotrophoblast


title: Treg_IR_rep1

tag: treatment


title: Y2_cerebellum_Input

value: 19 weeks


title: Y1_cerebellum_5hmC


title: genomic_DNAmethylation_TO-26_vc

value: NIH Batch 1

value: East Asian

tag: cytotrophoblast


title: O4_cerebellum_5hmC

value: female

value: 102 weeks


title: HSC_Ctrl_rep2

value: Bone marrow

value: WT

tag: agent

value: control


title: Treg_Ctrl_rep2

value: regulatory T cell


title: genomic_DNAmethylation_TO-57_vc

value: Female

tag: stromal

tag: endothelial


title: genomic_DNAmethylation_TO-75_vc

tag: Sex

tag: hofbauer


title: O1_cerebellum_5hmC

value: male

value: 93 weeks

tag: tissue

value: cerebellum


title: genomic_DNAmethylation_TO-62_vc

value: V-SSRI

tag: nrbc


title: BMMs, no treatment, donor C3 [NT_C3]

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed using Dragen BCLConvert (v3.7.4).
RNA-seq analysis was performed in R (v4.1.0). The scPipe package (v1.14.0) was employed to process and de-multiplex the data. A combined multiplexed FASTQ file was created from the R1 and R2 FASTQ files, by trimming the sample index and UMI sequences and storing them in the read header, using the sc_trim_barcode function (with bs2 = 0, bl2 = 8, us = 8, ul = 10).
Additionally, the original multiplexed R1 and R2 FASTQ files were de-multiplexed using cutadapt v2.10 (with error rate 0 and action none).
Read alignment was performed on the combined multiplexed FASTQ file using the RSubread package (v2.6.1). An index was built using the Ensembl Mus musculus GRCm39 primary assembly genome file and alignment was performed with default settings. Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm39 v104 GFF3 genome annotation file.
The resulting BAM file was de-multiplexed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function.
UMI gene counts were processed using the edgeR package (v3.34.0). Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method.
Differential gene expression analyses were performed using the edgeR and limma (v3.48.3) packages, with the voomLmFit, contrasts.fit and treat functions.
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with UMI gene counts for every gene and every sample

source_name: Bone marrow-derived macrophages

growth_protocol: Primary bone marrow derived macrophages (BMDMs) from 3 Trex1-mutant mice were extracted and differentiated for 6 days in complete DMEM supplemented with L929 conditioned medium (20%) - as per Ferrand and Gantier, Methods Mol. Biol., 1390, 79–90

extract_protocol:
Total RNA was purified from cell lysates with the ISOLATE II RNA Mini Kit (Bioline)
Libraries were generated using an in-house multiplex RNA-seq method (MHTP, Medical Genomics Facility; as per Grubman et al., 2021, Nature Communications, 12(1):3015). Libraries were prepared using 10 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 and P7 sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilised a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) used the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Paired-end sequencing (R1 19 bp; R2 72 bp) was performed on a NextSeq 2000 (Illumina) P2 run.

treatment_protocol: The cells were then plated and treated overnight with fresh L929 medium (20%) with or without 1.25uM idronoxil (IDX).

tag: strain background

value: NT

tag: donor


title: genomic_DNAmethylation_TO-59_vc

tag: cohort

tag: batch

tag: sentrix

value: FALSE

value: Male


title: genomic_DNAmethylation_TO-76_vc

value: European/Caucasian


title: HSC_IR_rep3

tag: cell type

value: Hematopoietic stem cell

value: ionizing radiation


title: Treg_Ctrl_rep1

tag: genotype


title: HSC_IR_rep1


title: HSC_Ctrl_rep3


title: genomic_DNAmethylation_TO-46_vc

value: NIH Batch 1

tag: syncytiotrophoblast


title: Y2_cerebellum_5hmC

tag: strain

tag: age

value: 19 weeks

tag: antibody


title: genomic_DNAmethylation_TO-18_vc

value: Other(including mixed)

tag: cytotrophoblast

tag: stromal


title: genomic_DNAmethylation_TO-47_vc

tag: Sex

tag: endothelial


title: genomic_DNAmethylation_TO-15_vc

tag: hofbauer


title: HSC_Ctrl_rep1

tag: tissue

value: Bone marrow

value: WT

tag: agent


title: R3_IL22ra1_KO_21dpi

description: 10x genomics chromium 3' V3.1, transcriptome: mm10-3.0.0

data_processing:
align with cellranger
Assembly: refdata-gex-mm10-2020-A, refdata-cellranger-mm10-1.2.0, mm10-3.0.0

source_name: IL22ra1 KO 21 days post infection with PR8

value: lung

value: epithelium

tag: treatment


title: R3_Spatial

data_processing:
align with cellranger
Assembly: refdata-gex-mm10-2020-A, refdata-cellranger-mm10-1.2.0, mm10-3.0.0
Library strategy: spatial transcriptome

source_name: spatial RNAseq: 14 days post infection with PR8

value: bulk


title: genomic_DNAmethylation_TO-13_vc

tag: cohort

tag: nrbc


title: BMMs, IDX treatment, donor C3 [IDX_C3]

tag: strain background

value: IDX

tag: donor


title: BMMs, no treatment, donor C2 [NT_C2]


title: R3_IL22ra1_WT_21dpi

source_name: Wt 21 days post infection with PR8

tag: cell type

tag: genotype


title: BMMs, no treatment, donor C1 [NT_C1]


title: genomic_DNAmethylation_TO-36_vc

tag: batch

tag: sentrix

value: Female

value: East Asian

tag: syncytiotrophoblast


title: R2_epi_240dpi

description: 10x genomics chromium 3' V2, transcriptome: refdata-cellranger-mm10-1.2.0

source_name: 240 days post infection with PR8


title: genomic_DNAmethylation_TO-68_vc

value: V-SSRI

tag: cytotrophoblast


title: BMMs, IDX treatment, donor C1 [IDX_C1]


title: R2_epi_21dpi

source_name: 21 days post infection with PR8


title: R2_epi_9dpi_11dpi_14dpi HTO

source_name: 9, 11, 14 days post infection with PR8


title: genomic_DNAmethylation_TO-24_vc

value: FALSE

tag: stromal


title: cow, pair-fed, rep3

city: Ithaca

first: Guangsheng

last: Li

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

data_processing:
The adaptor removal and quality control of the raw sequencing reads were carried out using fastp (v0.23.2) . Reads with a percentage of low-quality base (quality score < 20) > 40% were removed. Reads with length < 30 bp or with too much Ns (> 5%) were also removed in this study. The cow reference genome (ARS-UCD 1.2) was downloaded from the UCSC database, and the alignment of clean reads were performed with STAR (v2.7.9a)  allowing no more than 3 mismatches. The raw read counts for each gene were extracted using featureCounts (v2.0.3).
Assembly: ARS-UCD 1.2
Supplementary files format and content: tab-delimited text files include raw read count for each Sample

organism: Bos taurus

source_name: liver

extract_protocol:
Total RNA was isolated from each sample using TRIzol reagent (Invitrogen, Carlsbad, CA), Phasemaker Tubes (Invitrogen), and RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions with minor modifications. Specifically, tissue samples were homogenized in TRIzol and lysates were transferred to Phasemaker Tubes with chloroform for 20 min rotation at 4°C. The aqueous phase was then transferred to the gDNA elimination column for 1 min rotation at room temperature. The eluted RNA was washed with cold 70% ethanol, transferred to the RNeasy mini spin column, and washed with buffer RPE and RW1 (RNeasy Mini Kit). Finally, RNAs were eluted in RNAse-free water and concentrations were determined by a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA).
RNA quality was evaluated on Bioanalyzer 2100 (Agilent) and only samples passed the QC were proceed with the downstream process. Next, mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after a series of subsequent steps, including end pair, A-tailing, adapter ligation, size selection, amplification, and purification. Finally, the library was checked with Qubit and real-time PCR for qualification and evaluated on a bioanalyzer for fragment size distribution. Quantified libraries were pooled and sequenced on Illumina platforms in paired-end mode (2x150bp).

value: liver

value: pair-fed


title: cow, pair-fed, rep2


title: cow, Heat stress, rep1

value: Heat stress


title: BMMs, IDX treatment, donor C2 [IDX_C2]


title: cow, thermoneutrality, rep2

value: thermoneutrality


title: Organoid mixing species experiment, replicate 1, fragment BC

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

library_source: other

data_processing:
deMULTIplex (v1.0.2)
Assembly: GRCh38 v2020-A genecode, GRCm38 vM25, GFP 3'UTR
Supplementary files format and content: 3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Supplementary files format and content: UMI count matrix for MULTI-seq barcodes per cell; column "Barcode" contains the allocated MULTI-seq BC (.txt format)
Supplementary files format and content: Cell barcodes in first column and total UMI counts in second column (.txt format)

molecule: other

organism:
Homo sapiens
Mus musculus

source_name: Colon organoids

extract_protocol:
in-vitro digestion
MULTI-seq cell hashing

value: Colon cancer organoid cells

value: Colon organoids

tag: disease state

value: colon cancer


title: R2_epi_9dpi_11dpi_14dpi cDNA


title: genomic_DNAmethylation_TO-82_vc

city: Boston

value: NIH Batch 1

tag: Sex

value: Male

value: European/Caucasian

tag: endothelial


title: R2_epi_naive_3dpi_5dpi_7dpi HTO

source_name: Naïve intralobar, 3, 5, 7 days post infection with PR8

tag: tissue

value: lung

value: epithelium

value: WT


title: cow, pair-fed, rep1


title: R2_epi_17dpi

source_name: 17 days post infection with PR8


title: genomic_DNAmethylation_TO-31_vc

value: Female

tag: hofbauer


title: cow, Heat stress, rep3

tag: treatment


title: cow, thermoneutrality, rep3


title: genomic_DNAmethylation_TO-42_vc

tag: cohort

value: East Asian


title: cow, Heat stress, rep2


title: Organoid mixing species experiment, replicate 1, WTA

data_processing:
zUMIs (v. 2.9.4)
Assembly: GRCh38 v2020-A genecode, GRCm38 vM25, GFP 3'UTR
Supplementary files format and content: 3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Supplementary files format and content: UMI count matrix for MULTI-seq barcodes per cell; column "Barcode" contains the allocated MULTI-seq BC (.txt format)
Supplementary files format and content: Cell barcodes in first column and total UMI counts in second column (.txt format)

extract_protocol:
in-vitro digestion
BD Rhapsody: WTA kit


title: genomic_DNAmethylation_PM77_vc_R1

value: V-NORM

value: TRUE

value: Unknown

tag: nrbc


title: cow,thermoneutrality, rep1

value: liver


title: Y3_liver_LongRead_RNA

data_processing:
Nanopore direct RNA sequencing data were basecalled using Guppy (v6.1.2).
Reads were subsequently mapped to mouse genome mm10 using minimap2 (version 2.24) with parameters -a -x splice -k 12 -u b --secondary=no. Basecalled reads were also separately aligned against the mouse transcriptome (Ensembl version 92) using -a -x map-ont -k 12 -u f --secondary=no.
FLAIR (v1.7.0) was used to identify and quantify novel transcripts.
DESeq2 and DRIMSeq were used for differential expression and differential isoform usage calculations respectively. Poly(A) tail lengths were extracted from sequenced reads using the nanopolish polya package.
To identify transcripts with systematic whole-molecule or poly(A) length changes across experimental conditions, we employed in-house scripts that use linear mixed models to compare replicates using the library as a random effect (https://github.com/maragkakislab/nanoplen).
Assembly: mm10
Supplementary files format and content: Count txt files generated using FLAIR/v1.7.0

extract_protocol:
RNA integrity was assessed using QubitTM RNA IQ assay kit (ThermoFisher, Q33221) before library preparation. Libraries were constructed using 25-50 µg of total RNA  using the direct RNA sequencing kit (Oxford Nanopore Technologies) as previously described with modifications (Ibrahim et al. 2021, PMID: 34428294). After selection of poly(A) RNAs using Oligo d(T)25 Magnetic Beads (New England Biolabs), 15 pmoles of REL5 adapter (/5Bio/rArArUrGrArUrArCrGrGrCrGrArCrCrArCrCrGrArGrArUrCrUrArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU) was ligated to the 5′ ends of poly(A)-purified RNAs using T4 RNA ligase 1 (New England Biolabs) for 3 hours at 37°C.
REL-ligated poly(A) RNA (750 ng) was used for library preparation according to manufacturer’s protocol (Oxford Nanopore Technologies). Final libraries were quantified using Qubit 1X dsDNA High Sensitivity (HS) assay kit (Thermo Fisher) and sequenced on a MinION device using R9.4.1 flow cells (Oxford Nanopore Technologies).

tag: strain

value: female

tag: age

value: 80 weeks


title: R2_epi_naive_3dpi_5dpi_7dpi cDNA

tag: cell type


title: Y4_liver_LongRead_RNA


title: Y2_liver_LongRead_RNA

value: male


title: R2_epi_Trachea_120dpi cDNA

source_name: Naïve trachea & Wt 120 days post infection with PR8

tag: genotype


title: genomic_DNAmethylation_PM374_vc

tag: batch

value: NIH Batch 2

value: FALSE


title: genomic_DNAmethylation_PM366_vc_R2

tag: sentrix


title: R2_epi_Trachea_120dpi HTO


title: R1_immune_Naive

description: 10x genomics chromium 3' V2, transcriptome: refdata-gex-mm10-2020-A

source_name: Naive intralobar immune

value: immune

value: Naïve


title: Y1_liver_LongRead_RNA


title: O3_liver_LongRead_RNA

value: 12 weeks


title: O2_liver_LongRead_RNA


title: O4_liver_LongRead_RNA


title: genomic_DNAmethylation_PM366_vc_R1

tag: syncytiotrophoblast


title: O1_liver_LongRead_RNA


title: R1_immune_21dpi

value: lung


title: genomic_DNAmethylation_PM375_vc

value: Mixed

tag: cytotrophoblast


title: REST ChIP-seq - WT_rep4

first: Jae Joon

last: Choi

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: REST ChIP-seq: WT mouse cortex, age 11 months, 4 female cortices were pooled (replicate 4)

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR (v2.7.0a) (--alignIntronMax 1 --alignEndsType EndToEnd).
Duplicate reads were marked using Picard tool (MarkDuplicates)
Peak locations were determined using MACS algorithm44 (v2.1.0) (--nomodel) and normalized fold enrichment tracks were generated by using the callpeak function with --SPMR, then passing the bedgraph outputs into the bdgcmp function with the setting -m FE.
Assembly: mm10
Supplementary files format and content: Bedgraph files were converted into bigWig and visualized using Integrated Genome Viewer (IGV, v2.4).  Peaks were filtered for fold enrichment more than 5, q-value less than 0.01 and ENCODE blacklist of known false ChIP-Seq peaks were removed.
Supplementary files format and content: Differential binding sites was identified using Diffbind (default settings) and peaks were annotated using ChIPseeker.

source_name: Mouse cortex

growth_protocol: Age 11 months

extract_protocol:
The frozen tissue was sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, the tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (25 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against the C-terminal region of REST (generous gift from Gail Mandel, Vollum Institute). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: mouse cortex, bulk tissue

value: 11 months

tag: chip antibody

value: REST C-terminal antibody, gift from Dr. Gail Mandel, Vollum Institute, Oregon Health & Science University. References:Ballas, N., Grunseich, C., Lu, D.D., Speh, J.C. & Mandel, G. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121, 645-657 (2005).  McGann, J.C. et al. The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus. J Neurosci 41, 6582-6595 (2021).

value: Wildtype


title: REST ChIP-seq - WT_rep3

description: REST ChIP-seq: WT mouse cortex, age 11 months, 4 female cortices were pooled (replicate 3)

tag: disease state


title: REST ChIP-seq - 3xTg_rep4

description: REST ChIP-seq: 3xTg mouse cortex, age 11 months, 4 female cortices were pooled (replicate 4)

tag: Sex

value: Alzheimer's Disease


title: R1_immune_17dpi

value: WT


title: genomic_DNAmethylation_PM77_vc

value: V-NORM

value: Male

value: Unknown

tag: stromal

tag: endothelial


title: genomic_DNAmethylation_PM381_vc

value: European/Caucasian

tag: hofbauer


title: REST ChIP-seq - 3xTg_rep3

description: REST ChIP-seq: 3xTg mouse cortex, age 11 months, 4 female cortices were pooled (replicate 3)

value: female

tag: tissue


title: R1_immune_120dpi

source_name: 120 days post infection with PR8

tag: treatment


title: scRNA-seq CSP library

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

data_processing:
Detailed description of analytical packages in linked publication
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: spleen (Totalseq C1), mesenteric LN (Totalseq C2),inguinal LN (Totalseq C3), skin (Totalseq C4)

extract_protocol:
Detailed description of tissue digestion and sorting available in linked publication
Target cells from spleen (12,500 CD3+CD4+CD25+ Treg cells, TotalSeqC1), mesenteric (10,000 CD3+CD4+CD25+ Treg cells, TotalSeqC2), inguinal lymph nodes (7,500 CD3+CD4+CD25+ Treg cells, TotalSeqC3) and skin (10,000 CD3+ T cells, TotalSeqC4) have all been sorted in a single 1.5 mL Eppendorf tube containing 350 μL MACS buffer, and the sample collection tube was cooled to 4°C. It is important to process the sample quickly after sorting to decrease the number of dying cells, which would again increase the count for mitochondrial DNA in the sequencing data. Therefore, shortly after sorting, cells are pelleted by centrifugation (5 min, 300 xg, 4°C). Supernatant is removed and the sample is supplemented with master mix and beads to a final volume of 70 μL, loaded on a 10X Chromium Next GEM Chip K (10X Genomics #1000287) and processed on the 10X Chromium Controller (10X Genomics #120212), followed by cDNA amplification using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10X Genomics #1000263) and 5’ Feature Barcode Kit (10X Genomics #1000256).
V(D)J amplification was done from cDNA by using the Chromium Single Cell Mouse TCR Amplification Kit (10X Genomics #1000254) and GEX, CSP and VDJ library preparation according to the Library Construction protocol (10X Genomics #1000190).

value: CD4 T cells

tag: library type

value: Cell surface protein library


title: young.veh.3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline. The analyzed DeSeq2 results were uploaded on the web-based application called iPathway Guide and significantly upregulated and downregulated genes and pathways were identified. The log2fold change threshold was >0.6 and the p-value threshold was <0.05 was applied.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: macrophages

growth_protocol: Male C57BL/6 young (age 2 months) mice or old (18 months) mice were i.p. injected with 200 µg of ZymA (or ZymA, Sigma, Cat #Z4250) per mouse. After 72 hours, peritoneal cells were harvested by lavage and cultured overnight in complete DMEM containing L-cell media. The following day, unattached cells were washed by PBS and young or old peritoneal macrophages were treated with either vehicle (PBS) or 10nM RvD2 for 6 hours.

extract_protocol:
mRNA was extracted from macrophages with a Qiagen Rneasy Mini kit (Cat #74106) according to the manufacturer's instructions
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

value: Peritoneal Cells

value: macrophages

value: young (age 2 months)

value: male

tag: strain


title: scRNA-seq VDJ library

value: spleen (Totalseq C1), mesenteric LN (Totalseq C2),inguinal LN (Totalseq C3), skin (Totalseq C4)

value: T-cell receptor library


title: genomic_DNAmethylation_PM359_vc

tag: cohort

value: NIH Batch 2

value: FALSE

value: East Asian

tag: nrbc


title: R1_immune_14dpi

city: Los Angeles

source_name: 14 days post infection with PR8

extract_protocol:
10x genomics chromium 3' V2, V3.1 single cell RNAseq kit and Visium spatial RNAseq
follow 10x genomics instruction

value: lung

tag: cell type

value: immune

tag: genotype

value: WT


title: scRNA-seq GEX library

value: Wildtype

value: Gene expression library


title: genomic_DNAmethylation_PM372_vc

value: V-NORM

tag: batch

tag: sentrix

value: Male

value: European/Caucasian


title: young.veh.1

value: Peritoneal Cells

tag: age


title: old.veh.3

value: macrophages

value: old (18 months)


title: old.veh.1

value: male


title: old.veh.2


title: genomic_DNAmethylation_PM367_vc

value: Female

tag: syncytiotrophoblast

tag: cytotrophoblast


title: genomic_DNAmethylation_PM373_vc

tag: Sex

value: Mixed


title: R1_immune_7dpi

source_name: 7 days post infection with PR8


title: R1_immune_5dpi

source_name: 5 days post infection with PR8


title: Stomach, WT, rep3

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern

description:
small RNA
WT_vs_ZSWIM8KO_Stomach.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Stomach.csv

data_processing:
The raw reads were trimmed using CutAdapt
Reads with base quality less than 20 were dropped
mthe miRNA sequences were downloaded from miRBase v22
Each read was assigned to an miRNA according to the first 18 nt
TMM normalization and differential expresssion analysis performed using edgeR
For each miRNA, proportion of reads with each observed length was calculated
The minimum length of the normal range of a miRNA was set with a proportion greater than 14.5% (Lmin)
The maximum length of the normal range of a miRNA was set with a proportion greater than 14.5% (Lmax)
Reads with lengths in between Lmin and Lmax were assigned to "normal" miRNA
Reads with lengths less than Lmin were assigned to "trimmed" miRNA, and reads with length greater than Lmax were assigned to "tailed" miRNA
Assembly: mm10
Supplementary files format and content: Table of the edgeR analysis of these RNA-seq data
Supplementary files format and content: Table of the analysis of "tailed" and "trimmed" miRNAs

source_name: Stomach

growth_protocol: Zswim8 heterozygous mice were crossed and tissues were harvested from resulting pups at E18.5

extract_protocol:
RNA was isolated using the miRNeasy Mini kit (Qiagen) for small RNA seq
Library construction was perfomred following AQ-seq protocol [PMID: 35104843]

value: Stomach

tag: developmental stage


title: genomic_DNAmethylation_PM369_vc

value: NIH Batch 2

value: FALSE

tag: stromal

tag: endothelial


title: Skin, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Skin.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Skin.csv

source_name: Skin

tag: tissue

value: Skin


title: Liver, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Liver.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Liver.csv

source_name: Liver

value: Liver


title: Intestines, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Intestines.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Intestines.csv

source_name: Intestines

value: Intestines

value: WT


title: Lung, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Lung.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Lung.csv

source_name: Lung

value: Lung


title: R1_epi_Naive

source_name: Naive intralobar epithelium

value: lung

value: epithelium

tag: treatment

value: Naïve


title: Kidneys, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Kidneys.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Kidneys.csv

source_name: Kidneys

value: Kidneys


title: genomic_DNAmethylation_PM370_vc

value: V-NORM

value: East Asian

tag: hofbauer


title: R1_immune_11dpi

source_name: 11 days post infection with PR8

value: immune


title: R1_immune_3dpi

source_name: 3 days post infection with PR8


title: Heart, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Heart.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Heart.csv

source_name: Heart

value: Heart

tag: strain


title: R1_epi_21dpi

source_name: 21 days post infection with PR8


title: young.veh.2

value: Peritoneal Cells

value: macrophages

value: young (age 2 months)

value: male


title: genomic_DNAmethylation_PM379_vc

tag: cohort

value: NIH Batch 2

value: FALSE

value: Female


title: Brain, WT, rep3

description:
small RNA
WT_vs_ZSWIM8KO_Brain.csv
WT_vs_ZSWIM8KO_Tailed_Trimmed_Brain.csv

source_name: Brain

value: Brain

value: WT


title: Stomach, WT, rep2

value: Stomach


title: genomic_DNAmethylation_PM139_vc

value: TRUE

value: Male

tag: nrbc


title: genomic_DNAmethylation_PM371_vc

value: European/Caucasian


title: R1_epi_17dpi

source_name: 17 days post infection with PR8

value: lung

tag: cell type

value: epithelium


title: R1_immune_9dpi

source_name: 9 days post infection with PR8

value: immune

tag: genotype


title: Skin, WT, rep2

value: Skin


title: Lung, WT, rep2

value: Lung


title: genomic_DNAmethylation_PM362_vc

value: V-NORM

tag: batch

value: Mixed


title: Kidneys, WT, rep2

value: Kidneys


title: R1_epi_11dpi


title: genomic_DNAmethylation_PM365_vc

value: NIH Batch 2

tag: sentrix


title: Intestines, WT, rep2

value: Intestines


title: Heart, WT, rep2

value: Heart


title: genomic_DNAmethylation_PM378_vc

value: FALSE


title: Stomach, Zswim8-/-, rep3


title: Brain, WT, rep2

value: Brain

value: WT


title: Skin, Zswim8-/-, rep3


title: genomic_DNAmethylation_PM368_vc


title: Liver, Zswim8-/-, rep3

value: Liver


title: genomic_DNAmethylation_PM364_vc

value: Male

value: East Asian


title: R1_epi_5dpi

value: lung


title: R1_epi_3dpi

value: epithelium


title: Intestines, Zswim8-/-, rep3


title: genomic_DNAmethylation_PM219_vc

value: NIH Batch 3


title: genomic_DNAmethylation_PM376_vc

value: Female


title: Brain, Zswim8-/-, rep3


title: Stomach, Zswim8-/-, rep2

value: Stomach


title: Heart, Zswim8-/-, rep3


title: R1_epi_7dpi


title: Skin, Zswim8-/-, rep2

value: Skin


title: CMe-vct-567

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

institute: Guangzhou Laboratory

data_processing:
Sequencing quality of raw sequencing data was evaluated by fastp (Chen et al., 2018).
Reads were mapped to the mm10 genome assemblies by HISAT2 (Pertea et al., 2016) using default settings. Mapping ratio was calculated based on the number of mapped reads and total reads for each sample.
All mapped reads were processed by StringTie (Pertea et al., 2016) to quantify gene expression levels (measured by FPKM, Fragment Per Kilobase per Million mapped reads respectively) using default parameters.
Assembly: mm10/GRCm38.91
Supplementary files format and content: tab-delimited text files include log10(FPKM+1) values for each samples

source_name: Mes

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

value: Mes

value: mvct

value: Embryonic day 14.5


title: CMe-vco-567

value: mvco


title: R1_epi_14dpi

source_name: 14 days post infection with PR8


title: Liver, WT, rep2


title: genomic_DNAmethylation_PM354_vc

extract_protocol: V-NORM and V-SSRI samples: 1.5-2 cm3 samples of chorionic villi were taken from each of four distinct cotyledons (sites) from below the surface of the fetal-facing side of the placental disc. The samples were washed thoroughly to remove blood, and any thick vessels were removed. Samples were frozen at -20°C until use. DNA was then extracted from all four cotyledon samples using a salting-out DNA extraction procedure, and extracted DNA from the four sites was pooled in equimolar proportions to provide a representative sample of each placenta. The second sampling process involved the QF-2011 placentas, which were processed in Brisbane, Australia within 60 minutes of delivery, and eight sites (1 cm3 each) representing different cotyledons were sampled across the fetal-facing side of each placenta. These samples were snap frozen in liquid nitrogen and subsequently shipped frozen to Montreal, Canada. Samples were pooled and ground while snap frozen over liquid nitrogen. DNA was extracted using a commercial kit  from pooled samples in Montreal, before shipping to Vancouver on dry ice for DNAme processing.

value: V-NORM


title: Lung, Zswim8-/-, rep2

value: Lung


title: CMe-vo-567

value: mvo


title: genomic_DNAmethylation_PM167_vc

value: FALSE

value: European/Caucasian


title: R1_epi_9dpi

value: WT


title: Lung, Zswim8-/-, rep3


title: Liver, Zswim8-/-, rep2

value: Liver


title: Kidneys, Zswim8-/-, rep3

value: Kidneys


title: Intestines, Zswim8-/-, rep2

value: Intestines


title: genomic_DNAmethylation_PM357_vc

value: NIH Batch 3

value: Male


title: Heart, Zswim8-/-, rep2

value: Heart


title: genomic_DNAmethylation_M0201_vcN


title: CMe-dco-567

value: mdco


title: Brain, Zswim8-/-, rep2

value: Brain


title: CMe-vt-567

value: Mes

value: mvt


title: CMe-dct-567

value: mdct

value: Embryonic day 14.5


title: Stomach, WT, rep1

value: Stomach


title: genomic_DNAmethylation_QF0136_vcN

value: Female


title: Skin, WT, rep1

value: Skin


title: genomic_DNAmethylation_PM180_vc

value: V-NORM

value: FALSE

value: European/Caucasian


title: CMe-do-567

value: mdo


title: Liver, WT, rep1

value: Liver

value: WT


title: CMe-dt-567

value: mdt


title: genomic_DNAmethylation_QF0194_vcN

value: NIH Batch 3


title: Intestines, WT, rep1

value: Intestines


title: Heart, WT, rep1

value: Heart


title: genomic_DNAmethylation_PM77_vc_R

value: TRUE

value: Male

value: Unknown


title: CR-vco-567

source_name: RPE

value: RPE

value: vco

value: Embryonic day 14.5


title: Brain, WT, rep1

value: Brain


title: Kidneys, Zswim8-/-, rep2

value: Kidneys


title: Stomach, Zswim8-/-, rep1

source_name: Stomach

value: Stomach


title: CR-vct-567

value: vct


title: genomic_DNAmethylation_QF0230_vcN

value: FALSE

value: Female

value: European/Caucasian


title: Skin, Zswim8-/-, rep1

source_name: Skin

value: Skin


title: Lung, Zswim8-/-, rep1

value: Lung


title: CR-vo-567

value: vo


title: genomic_DNAmethylation_PM352_vc

value: V-NORM

value: NIH Batch 3


title: Liver, Zswim8-/-, rep1

source_name: Liver

value: Liver


title: Lung, WT, rep1

value: WT


title: Kidneys, Zswim8-/-, rep1


title: genomic_DNAmethylation_QF0365_vcN

value: Male


title: Intestines, Zswim8-/-, rep1

source_name: Intestines

value: Intestines


title: CR-dco-567

value: RPE

value: dco

value: Embryonic day 14.5


title: CR-vt-567

value: vt


title: Heart, Zswim8-/-, rep1

value: Heart


title: Brain, Zswim8-/-, rep1

value: Brain


title: WT sham microglia 2

city: Pittsburgh

first: Yejie

last: Shi

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

data_processing:
Genome alignment to GRCm38 using HISAT2 in Chipster v3.15
Counting reads using HTSeq in Chipster v3.15
Assembly: GRCm38
Supplementary files format and content: tsv files include read counts for each sample

source_name: brain

extract_protocol:
Single-cell suspensions were prepared from mouse brains 3 days after stroke or sham operation. Mice were transcardially perfused with sterile 0.9% NaCl. The ipsilesional brain hemisphere was harvested, and cell suspensions were prepared using the Neural Tissue Dissociation Kit and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Suspensions were passed through a 70 μm cell strainer, and fractionated on a 30% and 70% Percoll gradient at 500 g for 30 min. Mononuclear cells at the interface were collected. Isolated mononuclear cells were washed, resuspended at 1×10^6 per mL, and stained with fluorophore-conjugated antibodies and the appropriate isotype controls. Fluorescence-activated cell sorting was performed using the FACS Aria I sorter and FACS Diva software (BD Biosciences). Microglia were gated as CD11c–Ly6G–CD11b+CD45low and sorted for bulk RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: microglia


title: Kidneys, WT, rep1

value: Kidneys


title: TSA treated Min6 cells_rep_3

city: Lille

first: Frederik

last: Oger

address: Faculté de Médecine - Pôle Recherche - 2eme etage - 1 place de Verdun

country: France

institute: Université de Lille

description: RNA polyA

data_processing:
The demultiplexing of sequence data (from BCL files generated by Illumina sequencing systems to standard FASTQ file formats) was performed using bcl2fastq Conversion Software (Illumina; version 2.19.1).
Trimming of residuals adapters and low-quality reads was performed using Cutadapt software (version 1.7.1).
Sequence reads from FASTQ files were mapped to the mouse genome (mm10) or human genome (Hg38) using STAR Aligner (version 2.5.2b). On average, 38M reads were generated per sample, and 93.5 % +/- 0.9% of them were accurately mapped.
The counting of the different genes and isoforms was performed using RSEM (version 1.3). Finally, differential expression was performed using DESeq2 package
Assembly: mm10 (mouse) and Hg38 (human)
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

source_name: Min6 cells

growth_protocol: Min6 cells (Addexbio, C0018008) were cultured in DMEM high Glucose glutaMAX medium (Gibco, 31966-021) supplemented with 15 % SVF, 0.1 % β-mercaptoethanol and antibiotics (penicillin/streptomycin).

extract_protocol:
Total RNA was extracted from EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets using RNeasy Plus mini kit (Qiagen, 74136) according to the manufacturer’s instructions. Total RNA sample concentrations were determined using a Nanodrop spectrophotometer (Implen). RNA quality was verified using RNA 6000 nanochips (Agilent, 5067-1511) on the Agilent 2100 bioanalyzer (Agilent, G2939A). 500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation
500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation with the TrueSeq Stranded mRNA library Prep (Illumina, 20020594) and sequenced in paired end 2x75 on the NextSeq device.
Libraries were prepared with the TruSeq Stranded mRNA library Prep (Illumina, #20020594) and sequenced on the Illumina NextSeq500 system using a paired-end 2×75 bp protocol.

treatment_protocol: EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets were treated either with DMSO (0.1%) or TSA (0.5µM) for 16h.

value: Mouse beta cell model - Min6


title: CR-dct-567

value: dct


title: CR-do-567

value: do


title: TSA treated Min6 cells_rep_2

description: RNA polyA


title: genomic_DNAmethylation_QF0150_vcN

data_processing:
See original publication
Beta values with dasen + noob normalization, filtered for quality probes.

value: NIH Batch 3

value: FALSE

value: Female

value: European/Caucasian