title: 7dpw_batch1_aged_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-2
aged_v3_batch1_matrix.mtx.gz
aged_v3_batch1_barcodes.tsv.gz
aged_v3_batch1_features.tsv.gz
7dpw_batch1_aged_v3_possorted_genome_bam.bam

value: Aged

value: Wound at 7dpw


title: Con_IEL

status: Public on Aug 02 2022

type: SRA

city: Shanghai

first: haohao

last: zhang

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Fastp v0.20.0 was used to remove adapter and low-quality reads.
Align paired-end reads using Bowtie2 version 2.3.4.3 with options: --end-to-end –sensitive.
Peak calling was performed using SEACR software.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated and scores represent the degree of enrichment.

molecule: genomic DNA

organism: Mus musculus

source_name: small intestinal TCRβ+CD8αα+ IELs

extract_protocol:
Small intestinal TCRαβ+CD8αα+IELs (CD45+TCRβ+TCRγδ-CD4-CD8α+CD8β-) were sorted from wild type C57BL/6 mice and subject to CUT&Tag assay. Anti-H3K27Me3 was used as the primary antibody to guide the proteinA/G-Tn5 transposome-mediated target DNA fragmentation. DNA fragments were purified for library preparation.
CUT&Tag library was constructed using HyperactiveTM In-Situ ChIP Library Prep Kit (TD901, Vazyme, China) and sequenced using PE150 on an illumina Nova6000 sequencing platform.

tag: tissue

value: small intestine

tag: cell type

value: primary TCRBeta+CD8alphaalpha+ IELs

tag: age

value: 4 weeks

tag: strain

tag: antibody

value: anti-H3K27Me3 (Millipore  07-449)


title: Sample8.Roe deer.204529320094_R02C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Roe deer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

organism: Capreolus capreolus

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: confidenceinageestimate

tag: Sex

value: Female


title: Sample7.Roe deer.204529320094_R01C02


title: T4_Tx_1

city: Taoyuan

first: Nian Kang

last: Sun

address: No.261, Wenhua 1st Rd.Guishan Dist

department: Division of Biomedical Sciences

country: Taiwan

institute: Chang Gung University of Science and Technology

library_source: transcriptomic

data_processing:
1. Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
2. TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
3. Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
4. Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for each samples

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian carcinoma

growth_protocol: SKOV3 cells were stably transfected with TLR4 expressing vector using blasticidin selection. Cells were maintained under standard cell culture conditions  (37ºC; 5% CO2) in DMEM/F12 nutrient medium (Life Technologies).

extract_protocol:
RNA were prepared with TRIzol Reagent (Thermo Fisher Scientific) according to the manufacturer's instruction. Purified RNA was qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA).
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: Cells were seeded at the day before treatment and treated with taxol (2 nM) alone or combined with curcumin (20 uM) for 24 hours.

tag: cell line

value: Ovarian carcinoma cell line

tag: genotype/variation

tag: treatment

value: taxol


title: uw_batch2_young_v3

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

description:
chromium kit version Cell barcode suffix for aggr file:
-3
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
uw_batch2_young_v3_possorted_genome_bam.bam

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 3.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across the libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

molecule: polyA RNA

source_name: Mouse back skin

growth_protocol: All mice were purchased from Jax

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 or v3 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

value: dorsal skin

value: Young

tag: wound timepoint

value: Unwounded skin

tag: chromium kit version


title: MCS_Tx_2

value: Mock


title: APP-PS1_blood, C87

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

data_processing:
Quality control of raw sequencing data was conducted using FastQC tool (Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were then mapped to the genome (Mus musculus genome GRCm38) using bowtie2 (version 2.2.2, (Langmead and Salzberg, 2012)). Reads that overlap with genes were then counted using HTSEQ tool (version 0.11.2, (Anders et al., 2015), -m intersection-nonempty -s no -i gene_id -t exon).
Expression values of protein coding genes were first normalized and differential expression analysis between the different groups was conducted using Deseq2 (Love et al., 2014)
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_raw_counts.csv (file with HT-seq count output for all samples)

source_name: blood

growth_protocol: Female and male APP Swedish PS1 dE9 mice expressing a chimeric mouse/human mutant amyloid precursor protein (Mo/HuAPP695swe) and a mutant human presenilin 1 (PS1-dE9) both directed to CNS neurons under the prion protein promoter were used (available by Jackson Laboratory, http://www.jax.org/strain/005864). Mice were housed at the Paracelsus Medical University Salzburg in groups under standard conditions at a temperature of 22°C and a 12 h light/dark cycle with ad libitum access to standard food and water. Animal care, handling, genotyping and experiment were approved by local ethical committees (BMWFW-66.019/0011-WF/V/3b/2016). Animal breeding was done under special pathogen free (SPF) conditions and mice were transferred to non-SPF conditions a few days before the use in the experiment.

extract_protocol:
Brain: Brain samples were split in two hemispheres and both hemispheres per mouse were prepared. In short, each brain hemisphere (including brainstem and cerebellum) was mechanically chopped with a razor blade and homogenized in 2 mL ice cold HBSS with 15 mM HEPES (all from Thermofisher), 0.5% glucose (Sigma) and RNAsin (1:250, Promega) using a glass homogenizer. Cells were passed through a 100 µm cell strainer and rinsed two times with 2 mL ice cold HBSS (with 15 mM HEPES and 0.5% glucose). Cell suspensions were centrifuged at 340 g for 7 min. at 4°C. Myelin was removed by resuspending the cell pellet in 30% percoll (Sigma) solution and centrifuged at 950 g for 20 min. at 4°C. Supernatant was carefully removed and pellets containing cells of interest were diluted in HBSS followed by centrifugation at 300 g for 10 min at 4°C. Pellets were resuspended in PBS containing fixable viability dye eFlour780 (1:2000, eBioscience #65-0865) for 3-10 min. at RT and transferred to round-bottom polystyrene tubes (Corning). After centrifugation for 5 min. at 300 g, cell pellets were dissolved in FACS buffer (PBS with 2% BSA and 2 mM EDTA) containing Rat Anti-Mouse CD16/CD32 Fc-Block (1:100, BD Biosciences, #553141) for 5 min. at RT. Primary fluorescent-labeled antibodies were added and antibody incubation was performed for 45 min. at 4°C in the dark. Samples were washed in FACS buffer two times and centrifuged at 400 g for 5 min. Finally, cell pellets were resuspended in 800 µL FACS buffer with RNAsin (1:250, Promega #N2115) and filtered with a 30 µm cell strainer.  Blood:  Blood samples were incubated for 7-10 minutes with 1x RBC lysis buffer (eBiosciences, #00-4300) for lysis of red blood cells. Reaction was stopped with FACS buffer and samples were centrifuged for 5 min. at 500 g. Supernatant was removed and cell pellets resuspended in PBS containing fixable viability dye eFlour780 (1:2000, eBioscience #65-0865) for 3-10 min at RT. Samples were centrifuged for 5 min. at 500 g and supernatant was removed. Afterwards cell pellets were dissolved in FACS buffer containing Rat Anti-Mouse CD16/CD32 Fc-Block (1:100, BD Biosciences, #553141) for 5 min. Primary fluorescent-labeled antibodies were directly added to the samples and samples were incubated for 30 minutes at RT in the dark. Samples were washed with FACS buffer and filtered through a 30 µm cell strainer. After final centrifugation for 5 minutes at 500 g, cell pellets were dissolved in 800 µL FACS buffer with RNAsin (1:250, Promega #N2115). Samples were placed on 4 °C until they were analysed by flow cytometry. Following primary antibodies were used: CD3-PE (17A2) (1:100, BD Biosciences #555275), CD8a FITC (1:100, eBioscience #11-0081). Single stains and isotype controls were performed with PBMCs for compensation and verification of the signals. The following isotype control antibodies were used: PE IgG2b kappa (1:100, BDBiosciences #553989), FITC IgG2a kappa (1:100, eBioscience 11-4321-80). Single, living CD3 and CD8 double positive cells were gated (see, Figure 1D) and sorted from brain and blood samples via flow cytometry-based cell sorting (FACS sort) using the BD FACS Aria cell sorter (BD Biosciences) with BD FACS Diva software (8.0.1, BD Biosciences). In general about 104 CD3+/CD8+ T-cells were sorted from total brains or blood samples directly in RNA later (Sigma) and stored at -80°C. Sort purity was analyzed with sorted samples for every experiment day using LSR Fortessa flow cytometer (BD Biosciences). Sorted samples had a purity of about 97-100 %. RNeasy Micro Kit (Qiagen) was used to isolate the RNA from the sorted CD8+ T-cells. Isolation procedure was performed according to the manufacturer’s instructions using an elution volume of 14 µl. The elution step was carried out twice to increase the yield.
The mRNAseq was performed by Qiagen using QIAseq UPX 3’ Transcriptome analysis according to the companies protocols.
3’ Transcriptome analysis

value: blood

tag: disease state

value: AD animal model

value: female

value: CD8+ T cells


title: Sample5.Roe deer.204529320094_R05C01


title: Sample6.Roe deer.204529320094_R06C01


title: CUS Mus hippocampus 3

city: Nanjing

first: Rongrong

last: Huang

state: Jiangsu

address: 87 Dingjiaqiao

institute: Southeast University

data_processing:
Mainstream softwares (CIRCexplorer and Mapsplice) were used to identify circRNA transcripts through site recognition and analyze the splicing of circRNA forming from exon or intron. If the species of the sample exists in circBase, all identified circRNA will be compared with known circRNA, and the number and proportion of known circRNA in sequencing results will be counted.
The expression of known circRNA and new circRNA in each sample was counted and normalized by TPM.The gene expression pattern of the sample can be examined as a whole by TPM density distribution.Similarity between samples can be preliminarily inferred from the overall gene expression pattern.
According to the read count value of circRNA in each sample, the differential expression of circRNA among samples was analyzed. DESeq or DEGseq software could be used according to whether there were biological duplicates.The differences of circRNA can better reflect the reasons for the formation of biological phenotypes.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for circRNA by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: CUS Mus hippocampus

growth_protocol: Adult male C57BL/6J mice (24.0–26.0 g, 8–10 weeks old) were purchased from the Model Animal Research Center of Nanjing University (Nanjing, China) and randomly assigned to experimental groups. All animals were housed under a constant temperature and humidity and a 12-h light/12-h dark cycle, with the lights turned on at 7:00 AM. Food and water were available ad libitum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: CUS used in this study followed the procedure previously validated in mice.The stressors included (1) food deprivation for 24 h, (2) water deprivation for 24 h, (3) overnight illumination, (4) absence of sawdust in cage for 24 h, (5) moistened sawdust with water for 24 h, (6) forced swimming at 8℃ for 5 min, (7) tail nipping (1 cm from the tip of the tail), (8) physical restraint for 6 h, and (9) 45° cage-tilt along the vertical axis for 3 h.Mice were exposed to various randomly scheduled, low-intensity social and environmental stressors 2-3 times a day for 4 weeks.

tag: stress

value: chronic unpredictable stress (CUS)

value: brain

tag: tissue region

value: hippocampus


title: CUS Mus hippocampus 2


title: MCS_Tx_1


title: APP-PS1_brain, C75

source_name: brain

value: male


title: APP-PS1_blood, C63


title: FL500

type: RNA

city: Cuernavaca

first: Daniela

last: Morales Sanchez

state: Morelos

address: Av. Universidad 2000

department: Instituto de Biotecnologia

country: Mexico

institute: Universidad Nacional Autonoma de MExico

description: Test

data_processing:
The web-based software package automatically provide the delta Ct.
Target gene data were normalized using the normalization factor calculated based on the expression of the 2 most stable reference genes (housekeeping genes). All calculations were performed using geNorm (Vandesompele et al., 2002).
Fold Change worksheet reports test/control (i.e., FL5/CL) ratios.

label: SYBR Green

organism: Nannochloropsis gaditana

source_name: Algal cell (eukaryotic)

growth_protocol: Cultivation for all flashing light experiments were performed using batch cultivation for 13 days in tissue culture flasks (Falcon Scientific, Seaton Delaval, UK) with a total working volume of 250 mL (light path: 3.7 cm). Humidified and filtered air (0.2 m, Acrodisc ® PTFE filter, Pall Corporation, USA) enriched in CO2 was supplied to each cultivation unit at a flow rate of 160 mL min-1 using a rotameter (Omega, Manchester, UK) for controlling CO2 supply and mixing.

extract_protocol: Total cell RNA was extracted from cultures of N. gaditana at a concentration of 1x106 cells/mL using the E.Z.N.A® total DNA/RNA isolation kit (Omega Bio-tek, Inc., USA). The samples of N. gaditana under different flashing lights conditions were centrifuged at 2000xg, 4 C for 5 min, the supernatant was discarded, and the pellet was stored at -80 C for at least 24 hours. After this time, 700 µL of the lysis buffer from the E.Z.N.A® total DNA/RNA isolation kit was added to the sample and then the cells were disrupted using a bead mill (Bertin technologies, Precellys Evolution, France) using a mixture of 0.1 mm glass beads and 1.4 mm ceramic beads. Samples were centrifuged at 10000xg, 4 C for 10 min. The supernatant was used for RNA isolation according to manufacturer’s protocol.

treatment_protocol: The flashing light conditions applied were: continuous light (CL) and flashing light (FL) with a duty cycle of 0.05 with frequencies of 5 (FL5), 50 (FL50), and 500 (FL500) Hz (more detailed in Lima et al. 2021). The time-averaged light intensity was Ia= 300 µmol s-1 m-2 under all conditions, which corresponded to an instantaneous flash intensity of Il = 6000 µmol s-1 m-2. The flashes were set using PWM-OCX (RMCybernetics Ltd, Alsager, UK) pulse width modulators (PWMs) powered by a bench power supply EA-PS 2084-05B (EA Elektro-Automatik). The pulse signal was provided by a TG4001 (TTi, Huntingdon, UK) function generator or directly by the PWMs. For continuous light control, and the LEDs were connected directly to the power supply units. The LEDs were regulated to adjust Ia to 300 µmol s 1 m 2 and compensate switching and working losses at the LEDs and PWMs. The supplied light intensity (i.e., photosynthetically active radiation) was measured for one minute at the same position as the flasks (SPQA 5234 connected to a data logger LI-1500, Li-Cor, Lincoln, NE, USA) and averaged over time.

tag: light condition

value: Cells cultivated at 500 hz flashing light


title: Sample4.Roe deer.204529320094_R04C01

value: Male


title: APP-PS1_brain, C51


title: CUS Mus hippocampus 1


title: Sample3.Roe deer.204529320094_R03C01

value: Female


title: APP-PS1_blood, C39


title: Control Mus hippocampus 3

source_name: Control Mus hippocampus

value: Control


title: APP-PS1_brain, C4


title: Control Mus hippocampus 2


title: APP-PS1_brain, C27


title: Sample1.Roe deer.204529320094_R01C01


title: Control Mus hippocampus 1


title: FL50

description: Test

value: Cells cultivated at 50 hz flashing light


title: FL5

description: Test

value: Cells cultivated at 5 hz flashing light


title: HFL, palbo, sort-all, rep4

status: Public on Aug 01 2022

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description:
HFL_palbo_sort-all_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); sort-all = FACS control.

data_processing:
read alignment, RNA-seq data:  STAR-2.5.3a
bigWig file generation:  custom code
Assembly: hg38 + dm6
Supplementary files format and content: The files are bigWig, but their content is a bedGraph file; bedGraph of read coverage, normalized to RPM.

organism:
Drosophila melanogaster
Homo sapiens

source_name: HFL, palbo, sort-all

extract_protocol:
RNA was extracted using Direct-zolTM RNA Microprep Kit (Zymo Research)
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). The NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing (Novogene)

tag: human cell type

value: Human lung fibroblasts (HLF)

tag: cell status

tag: sorted cells

value: sort-all = FACS control.

tag: fly spike-in

value: S2 cells


title: CL

description: Control

tag: strain

value: Cells cultivated at continuous light


title: HFL, palbo, sort-all, rep1

description:
HFL_palbo_sort-all_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); sort-all = FACS control.


title: 2yr_MN_ATAC_rep1

city: Piscataway

first: Tulsi

last: Patel

state: New Jersey

address: 683 Hoes Lane West

department: Neuroscience and Cell Biology

institute: Rutgers University

data_processing:
RNA: Reads were trimmed for adaptors and low-quality positions using Trimgalore (Cutadapt v0.6.2)88. Reads were aligned to the mouse genome (mm10) and gene-level counts were quantified using RSEM (v1.3.0)89 rsem-calculate-expression using default parameters and STAR (v2.5.2b) for alignment.
ATAC: Reads were trimmed for adaptors and low-quality positions using Trimgalore (Cutadapt v0.6.2)88. Reads were aligned to the mouse genome (mm10) with bwa mem (v0.7.1.7)91 with default parameters. Duplicates were removed with samtools (v1.7.2)92 markdup and properly paired mapped reads were filtered. Accessible regions were called using MACS2 (v2.2.7.1)93 with the parameters -f BAMPE -g mm -p 0.01 --shift -36 --extsize 73 --nomodel --keep-dup all --call-summits. Accessible regions that overlapped genome blacklist regions were excluded from downstream analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq RSEM gene level outputs with expected counts, TPM, FPKM
Supplementary files format and content: ATAC-seq bed files containing called peaks

source_name: mouse spinal cords

growth_protocol: Motor neurons were differenitiated using standard protocols (Wichterle and Peljto, 2008), dissociated, and co-cultured with primary astrocytes derived from mouse cortex at P2 for 28 days in the presence of neurotrophic factors.

extract_protocol:
Nuclei were extracted using an optimized version of the INTACT protocol (Mo et al., 2016)
ATAC-seq libraries were build as described (Buenrostro et al., 2015) and RNA-seq libraries were built with Clontech SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian with ZAPr ribosomal depletion

treatment_protocol: For testing role of activity, cells were treated with TTX (1uM) for the entire 28 day co-culture

value: C57BL/6- Chat-Cre;SUN1-GFP-3xMYC

tag: age

tag: tissue/cell type

value: mouse spinal cords

tag: molecule subtype

value: Tn5 Tagemented DNA


title: HFL, palbo, bin4, rep1

description:
HFL_palbo_bin4_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 4 = extra large cells.

source_name: HFL, palbo, bin4

value: bin 4 = extra large cells.


title: HFL, palbo, bin4, rep3

description:
HFL_palbo_bin4_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 4 = extra large cells.


title: HFL, palbo, bin4, rep2

description:
HFL_palbo_bin4_rep2
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 4 = extra large cells.


title: HFL, palbo, pre-sort, rep3

description:
HFL_palbo_pre-sort_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); pre-sort = input population before FACS.

source_name: HFL, palbo, pre-sort


title: HFL, palbo, pre-sort, rep2

description:
HFL_palbo_pre-sort_rep2
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); pre-sort = input population before FACS.


title: HFL, palbo, pre-sort, rep4

description:
HFL_palbo_pre-sort_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); pre-sort = input population before FACS.


title: HFL, palbo, bin3, rep3

description:
HFL_palbo_bin3_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 3 = large cells.

source_name: HFL, palbo, bin3

value: bin 3 = large cells.


title: HFL, palbo, pre-sort, rep1

description:
HFL_palbo_pre-sort_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); pre-sort = input population before FACS.


title: HFL, palbo, bin3, rep4

description:
HFL_palbo_bin3_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 3 = large cells.


title: HFL, palbo, bin4, rep4

description:
HFL_palbo_bin4_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 4 = extra large cells.


title: HFL, palbo, bin3, rep1

description:
HFL_palbo_bin3_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 3 = large cells.


title: HFL, palbo, bin2, rep4

description:
HFL_palbo_bin2_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 2 =  small cells.

source_name: HFL, palbo, bin2

value: bin 2 =  small cells.


title: Sample2.Roe deer.204529320094_R02C01

tag: confidenceinageestimate

tag: Sex


title: HFL, palbo, bin2, rep2

description:
HFL_palbo_bin2_rep2
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 2 =  small cells.


title: HFL, palbo, bin2, rep3

description:
HFL_palbo_bin2_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 2 =  small cells.


title: HFL, palbo, bin2, rep1

description:
HFL_palbo_bin2_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 2 =  small cells.


title: HFL, palbo, sort-all, rep3

description:
HFL_palbo_sort-all_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); sort-all = FACS control.


title: HFL, palbo, bin1, rep3

description:
HFL_palbo_bin1_rep3
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 1 = extra small cells.

source_name: HFL, palbo, bin1

value: bin 1 = extra small cells.


title: HFL, palbo, bin1, rep4

description:
HFL_palbo_bin1_rep4
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 1 = extra small cells.


title: HFL, palbo, bin1, rep2

description:
HFL_palbo_bin1_rep2
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 1 = extra small cells.


title: Mouse-rat chimera testis

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

library_source: transcriptomic single cell

data_processing:
CellRanger v6 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.2.1 used for quality control + normalization + dimensionality reduction + clustering
Monocle3 used for pseudotime trajectory analysis
Assembly: GRCm38.p6_Rnor_6.0
Supplementary files format and content: Filtered count matrices from Cell Ranger

organism:
Mus musculus
Rattus norvegicus

source_name: Mus musculus/Rattus norvegicus Chimera

extract_protocol:
Chromium Single Cell 3’ Reagents kits v3.1 user guide RevD
Single Cell 3’ v3.1 chemistry

tag: cell type

value: Testicular cells, Spermatids, Spermatocytes

tag: host

value: goGermline


title: PFOA

first: Wu

last: Bing

address: No.163 Xianlin Avenue

department: School of the Environment

institute: Nanjing university

description: barcodes end in '-2'

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW:  4:10) (2) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3) Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa:  2: 30: 7) (4) Drop reads below the 26 bases long (5) Discard those reads that can not form paired
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean reads.
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting.
Cell Ranger takes as input the expected number of recovered cells, N (see -- expect-cells). Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group (library) and, if the reference contains multiple genomes, for each genome.
Genome_build: Danio_rerio_Ensemble_91
Supplementary_files_format_and_content: gene-barcode expression matrix

organism: Danio rerio

source_name: embryos

extract_protocol:
The zebrafish embryos were digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument(10x Genomics, USA) to generate single cell Gel bead in Emulsion (GEMs).
ScRNA-seq libraries were prepared using the GemCode Single-Cell 3’ Gel Bead, Chip and Library Kits (10x Genomics, USA) as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq X Ten.

treatment_protocol: Exposure solutions were prepared by adding 25μg/L PFOA.  After 30hpf exposure, zebrafish embryos were collected and prepared single cell suspensions.

tag: tissue

value: zebrafish embryos single cell suspension

value: 30 hpf

tag: exposed pollutants

value: 25u/L PFOA


title: Cardiac Leukocytes, Control BMT, TAC, scRNAseq

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

description: 10x Genomics

data_processing:
Illumina FASTQ Generation
CellRanger v5.0.0 Alignment
CellRanger v5.0.0 Standard Filtering of Quality Cells
Assembly: mm10
Supplementary files format and content: Processed data are standard outputs by CellRanger v5.0.0: Barcodes, Genes, and Matrix files

source_name: Heart

extract_protocol:
Hearts were flushed with 15 ml of cold PBS from apex and excised. Right ventricles were removed, and left ventricles were minced and digested in collagenase I (450 U/ml), collagenase XI (125 U/ml), hyaluronidase (450 U/ml), and DNase I (60 U/ml) (Sigma-Aldrich, Cat. #C0130, C7657, H3506, and D4513, respectively) at 900 rpm at 37°C for 30 minutes using ThermoMixer® C (Eppendorf). Hearts were subsequently homogenized through a FisherbrandTM Cell Strainers. After dead cell staining with Live/Dead Fixable Aqua Dead Cell Stain Kit (Invitrogen, Cat. #L34957), single cell suspension of heart tissue was incubated with fluorochrome-conjugated antibodies for 20 minutes at room temperature. Viable BMT-derived cardiac immune (DAPI-CD45+RFP+) cells were FACS-isolated (n = 3 per condition, pooled samples after FACS).
Single cell suspensions of ~8,000 cells per sample were then used to generate single cell RNA sequencing libraries (Chromium Single Cell v3.1 3’ Reagent Kit, 10x Genomics), and nucleotide reads were generated by paired-end next-generation sequencing (P2 2x100 Sequencing Kit, NextSeq 2000 Sequencer, Illumina). Library preparation and sequencing was performed according to validated standard operating procedures established by the University of Virginia Genome Analysis and Technology Core, RRID: SCR_018883.

value: Heart

value: Cardiac Leukocytes

tag: genotype

value: Control

tag: treatment

value: TAC


title: Cardiac Leukocytes, LOY BMT, TAC, scRNAseq

description: 10x Genomics

value: LOY


title: B6_5m_cereb_tsection_K9me3_rep1

city: Baltimore

first: Joseph

last: Tran

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

description: ChIP DNA

data_processing:
DNA was aligned using bowtie v2.3.2
DNA reads were counted into 10kb or 100kb windows using bedtools v2.26.0 coverage, and calculated as a log2(StrepD/input). The data was covnerted to a z-score and these z-score values were averaged for the indicated samples.
Hidden Markov Model (HMM) was called using depmixS4 v1.4-0 in RStudio v0.98.953 (R v3.5.1). Note we used a three state model
HMM calls were intersected between replicates to generate a consensus bed file for downstream analysis.
Assembly: hg19 and mm10
Supplementary files format and content: bedgraph files of the cTSA-seq or H3K9me3 ChIP-seq data at either 20kb or 100kb resolution.

source_name: Cerebellum

growth_protocol: K562 cells were grown in T25/T75 flasks with IMDM + 15% FBS. Mice were housed @12h/12h light/dark cycle and fed ad libitum. Mice were anesthsized, perfused with saline, and then paraformaldehyde. The brain was removed and post-fixed for 16-24h at 4 C. Brains were saturated in a 30% sucrose solution and embedded in O.C.T. freezing media for cryosectioning.

extract_protocol:
Cultured cells were permeabilized with PBS +0.25% Triton X-100 and stained for Lamin B1, and then a secondary HRP antibody. THe TSA reaction was performed according the kit [Biotin-XX-Tyramide Superboost kit (Invitrogen, #2005939)]. The cells were digested with Proteinase K in RIPA buffer overnight. DNA was extracted using phenol/chloroform/isoamy alcohol. Pure DNA was sonicated with a Misonix sonicator and biotinylation of DNA was monitored by dot blot onto positively charged nylon membranes. Streptavidin pulldown was done in a manner similar Chen, et al., 2018 and we used the modified protocol for washes. For tissue sections, cells/nuclei were isolated by brief sonication and collagenase type 2 digestion. The TSA reaction was done as described for cultured cells. Chromatin fragmentationn was done using a combination of sonication and MNase digestion in RIPA buffer and Streptavidin pulldown was done for 1 hour at room temperature.
Rubicon Genomics (Takara) ThruPlex 48 kit.

treatment_protocol: Cells were fixed with 4% PFA for 10 minutes at room temperature and neutralized with glycine.

value: Cerebellum

tag: cell line

tag: developmental stage

value: 5 months

tag: source

value: Tissue sections


title: CK

description: barcodes end in '-1'


title: B6_5m_cereb_tsection_inputforChIPseq_rep2

description: input DNA


title: B6_5m_cereb_tsection_K9me3_rep2

description: ChIP DNA


title: HFL, palbo, bin3, rep2

description:
HFL_palbo_bin3_rep2
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 3 = large cells.

tag: human cell type

value: Human lung fibroblasts (HLF)

tag: cell status

tag: sorted cells

value: S2 cells


title: B6_P0.5_cereb_tsection_StrePD_rep1

description: Streptavidin pulldown DNA

value: Postnatal day 0.5


title: B6_P0.5_cereb_tsection_input_rep2

description: input DNA


title: B6_P0.5_cereb_tsection_input_rep1

description: input DNA


title: B6_5m_cereb_tsection_StrePD_rep2

description: Streptavidin pulldown DNA


title: B6_5m_cereb_tsection_inputforChIPseq_rep1

description: input DNA


title: B6_5m_cereb_tsection_input_rep2

description: input DNA


title: B6_P0.5_cereb_tsection_StrePD_rep2

description: Streptavidin pulldown DNA


title: B6_5m_cereb_tsection_StrePD_rep1

description: Streptavidin pulldown DNA


title: B6_5m_cereb_tsection_input_rep1

description: input DNA


title: Isolated subclone NT2, biological replicate 4 [NT2_4]

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria St

department: Cancer Ecosystems Program

country: Australia

institute: Garvan Institute of Medical Research

description: High Output V2.5 300 cycle kit

data_processing:
Trimmed with FASTQC, mapped wit STAR Aligner, RSM to count over gene models and DEG defned with EdgeR
Assembly: mm10 (GRCm38.p4)
Supplementary files format and content: Samples IE1_3 and IE2_1 are intentionally missing from the all_counts.tsv file. These samples were identified as outliers after RNAseq and were removed from all downstream analyses.

source_name: cell line

extract_protocol:
QIAGEN Rneasy Mini Kit, according to manufacturers instructions
KAPA RNA HyperPrep Kit with RiboErase

value: cell line

value: cancer epithlial cell

tag: strain

value: Balb/c

tag: clone

value: non target clone 2


title: Isolated subclone NT1, biological replicate 2 [NT1_2]

description: High Output V2.5 300 cycle kit

value: non target clone 1


title: Isolated subclone NT2, biological replicate 2 [NT2_2]

description: High Output V2.5 300 cycle kit


title: Isolated subclone NT2, biological replicate 3 [NT2_3]

description: High Output V2.5 300 cycle kit


title: Isolated subclone NT1, biological replicate 3 [NT1_3]

description: High Output V2.5 300 cycle kit


title: Isolated subclone NT1, biological replicate 4 [NT1_4]

description: High Output V2.5 300 cycle kit


title: HLF, palbo, bin1, rep1

description:
HLF_palbo_bin1_rep1
Human lung fibroblasts (HLF) arrested in G1 with Palbociclib (Palbo; Cdk4/6 inhibitor); bin 1 = extra small cells.

source_name: HLF, palbo, bin1

value: bin 1 = extra small cells.

tag: fly spike-in


title: Isolated subclone IE2, biological replicate 4 [IE2_4]

description: High Output V2.5 300 cycle kit

value: immune invasive clone 2


title: Isolated subclone IE2, biological replicate 2 [IE2_2]

description: High Output V2.5 300 cycle kit


title: Isolated subclone NT1, biological replicate 1 [NT1_1]

description: High Output V2.5 300 cycle kit


title: Isolated subclone NT2, biological replicate 1 [NT2_1]

description: High Output V2.5 300 cycle kit


title: Isolated subclone IE2, biological replicate 3 [IE2_3]

description: High Output V2.5 300 cycle kit


title: Isolated subclone IE1, biological replicate 4 [IE1_4]

description: High Output V2.5 300 cycle kit

value: immune invasive clone 1


title: Isolated subclone IE1, biological replicate 2 [IE1_2]

description: High Output V2.5 300 cycle kit


title: Isolated subclone IE1, biological replicate 3 [IE1_3]

description: High Output V2.5 300 cycle kit


title: 4t1 bulk, biological replicate 3 [4T1_3]

description: High Output V2.5 300 cycle kit

value: parental


title: Isolated subclone IE2, biological replicate 1 [IE2_1]

description: High Output V2.5 300 cycle kit


title: 4t1 bulk, biological replicate 4 [4T1_4]

description: High Output V2.5 300 cycle kit


title: 4t1 bulk, biological replicate 1 [4T1_1]

description: High Output V2.5 300 cycle kit


title: 4t1 bulk, biological replicate 2 [4T1_2]

description: High Output V2.5 300 cycle kit


title: Isolated subclone IE1, biological replicate 1 [IE1_1]

description: High Output V2.5 300 cycle kit


title: 7763 NSG Lung [SJ030-48767783]

description: target barcode amplified gDNA

data_processing:
Barcode counting using algorithm provided with barcode library (https://www.addgene.org/pooled-library/clontracer/)
Assembly: mm10 (GRCm38.p4)

source_name: lung

extract_protocol: phenol chloroform gDNA extraction

value: lung

value: cancer

value: immunocompromised


title: 22310BC primary tumour [SJ044-48758832]

description: target barcode amplified gDNA

value: WT


title: SJ42 Cell pellet [SJ041-48762825]

description: target barcode amplified gDNA


title: 7759 NSG Lung [SJ029-48763799]

description: target barcode amplified gDNA


title: 7756 NSG Lung [SJ028-48758819]

description: target barcode amplified gDNA


title: SJ41 Cell pellet [SJ040-48764795]

description: target barcode amplified gDNA


title: 7752 NSG LUNG [SJ026-48760822]

description: target barcode amplified gDNA


title: 7755 NSG Lung [SJ027-48763797]

description: target barcode amplified gDNA


title: 7759 NSG primary tumour [SJ014-48769781]

description: target barcode amplified gDNA

source_name: primary tumour

value: primary tumour


title: 7763 NSG primary tumour [SJ015-48761812]

description: target barcode amplified gDNA


title: 22311BC Lungs [SJ024-48767787]

description: target barcode amplified gDNA


title: 22285BC Lungs [SJ021-48762823]

description: target barcode amplified gDNA


title: 22313BC Lungs [SJ025-48771781]

description: target barcode amplified gDNA


title: 7756NSG primary tumour [SJ013-48761811]

description: target barcode amplified gDNA


title: 7752NSG primary tumour [SJ011-48760820]

description: target barcode amplified gDNA


title: 7755NSG primary tumour [SJ012-48765807]

description: target barcode amplified gDNA


title: 22285BC primary tumour [SJ006-48765805]

description: target barcode amplified gDNA


title: 22311BC primary tumour [SJ009-48770789]

description: target barcode amplified gDNA


title: 24354 primary tumour [SJ51-29]

description: target barcode amplified gDNA

value: Immunocompromised


title: 24354 lung [SJ51-30]

description: target barcode amplified gDNA


title: 29638Nude Lungs [SJ045-48767789]

description: target barcode amplified gDNA


title: 22286BC primary tumour [SJ007-48774754]

description: target barcode amplified gDNA


title: 24332 lung [SJ51-26]

description: target barcode amplified gDNA


title: 24353 lung [SJ51-28]

description: target barcode amplified gDNA


title: 22313BC primary tumour [SJ010-48769780]

description: target barcode amplified gDNA


title: 24332 primary tumour [SJ51-25]

description: target barcode amplified gDNA


title: 24353 primary tumour [SJ51-27]

description: target barcode amplified gDNA


title: 4T1 BC Cell pellet  [SJ042-48758831]

description: target barcode amplified gDNA


title: 22310BC Lungs [SJ023-48770794]

description: target barcode amplified gDNA


title: 24329 primary tumour [SJ51-21]

description: target barcode amplified gDNA


title: 24329 lung [SJ51-22]

description: target barcode amplified gDNA


title: 22286BC Lungs [SJ022-48763805]

description: target barcode amplified gDNA


title: 29451 lung [SJ51-20]

description: target barcode amplified gDNA


title: 29451 primary tumour [SJ51-19]

description: target barcode amplified gDNA


title: 29444 lung [SJ51-14]

description: target barcode amplified gDNA


title: 29444 primary tumour [SJ51-13]

description: target barcode amplified gDNA


title: 29448 primary tumour [SJ51-15]

description: target barcode amplified gDNA


title: 29450 primary tumour [SJ51-17]

description: target barcode amplified gDNA


title: 29441 lung [SJ51-12]

description: target barcode amplified gDNA


title: 29441 primary tumour [SJ51-11]

description: target barcode amplified gDNA


title: Cell pellet 3 [SJ49 4T1 BC 5000A]

description: target barcode amplified gDNA

source_name: Cell pellet

value: Cell pellet


title: Cell pellet 2 [4T1 BC 5000B]

description: target barcode amplified gDNA


title: Cell pellet 1 [ 4T1 BC 5000A]

description: target barcode amplified gDNA


title: 23823 primary tumour [SJ41-8]

description: target barcode amplified gDNA


title: 23858 Liver met 2 [SJ41-29]

description: target barcode amplified gDNA

source_name: Liver metastasis

value: Liver metastasis


title: 23858 Liver met 3 [SJ41-30]

description: target barcode amplified gDNA


title: 23855 Liver met 2 [SJ41-26]

description: target barcode amplified gDNA


title: 26854 lungs immunotherapy treated [SJ41-24]

description: target barcode amplified gDNA


title: 24330 lung [SJ51-24]

description: target barcode amplified gDNA


title: 23855 Liver met 1 [SJ41-25]

description: target barcode amplified gDNA


title: 26853 lungs immunotherapy treated [SJ41-23]

description: target barcode amplified gDNA


title: 23858 Liver met 1 [SJ41-28]

description: target barcode amplified gDNA


title: 26833 lungs control treated [SJ41-22]

description: target barcode amplified gDNA

value: control IgG


title: 26822 lungs control treated [SJ41-19]

description: target barcode amplified gDNA


title: 26819 lungs control treated [SJ41-18]

description: target barcode amplified gDNA


title: 26827 lungs control treated [SJ41-21]

description: target barcode amplified gDNA


title: 26813 lungs control treated [SJ41-17]

description: target barcode amplified gDNA


title: 24330 primary tumour [SJ51-23]

description: target barcode amplified gDNA


title: 29450 lung [SJ51-18]

description: target barcode amplified gDNA


title: 29448 lung [SJ51-16]

description: target barcode amplified gDNA


title: 26823 lungs control treated [SJ41-20]

description: target barcode amplified gDNA


title: 23812 Lungs control treated [SJ41-16]

description: target barcode amplified gDNA


title: 23854 primary tumour [SJ41-12]

description: target barcode amplified gDNA


title: 23853 primary tumour [SJ41-11]

description: target barcode amplified gDNA


title: 23809 Lungs immunotherapy treated [SJ41-13]

description: target barcode amplified gDNA


title: 23810 Lungs immunotherapy treated [SJ41-14]

description: target barcode amplified gDNA


title: 23822 primary tumour [SJ41-7]

description: target barcode amplified gDNA


title: 23827 primary tumour [SJ41-9]

description: target barcode amplified gDNA


title: 23819 primary tumour [SJ41-6]

description: target barcode amplified gDNA


title: 23813 primary tumour [SJ41-5]

description: target barcode amplified gDNA


title: 23810 primary tumour [SJ41-2]

description: target barcode amplified gDNA


title: 23811 primary tumour [SJ41-3]

description: target barcode amplified gDNA


title: Cell pellet  [SJ59-24]

description: target barcode amplified gDNA

source_name: cell pellet

value: cell pellet


title: SJ59 LUNG 36540 [SJ59-21]

description: target barcode amplified gDNA


title: SJ59 LUNG 36545 [SJ59-22]

description: target barcode amplified gDNA

value: Control IgG


title: SJ59 LUNG 36549 [SJ59-23]

description: target barcode amplified gDNA


title: 23809 primary tumour immunotherapy treated [SJ41-1]

description: target barcode amplified gDNA


title: SJ59 LUNG 36539 [SJ59-20]

description: target barcode amplified gDNA


title: 23855 Liver met 3 [SJ41-27]

description: target barcode amplified gDNA


title: SJ59 LUNG 36536 [SJ59-18]

description: target barcode amplified gDNA


title: SJ59 LUNG 36537 [SJ59-19]

description: target barcode amplified gDNA


title: SJ59 LUNG 36523 [SJ59-13]

description: target barcode amplified gDNA


title: SJ59 LUNG 36534 [SJ59-16]

description: target barcode amplified gDNA


title: SJ59 LUNG 36535 [SJ59-17]

description: target barcode amplified gDNA


title: SJ59 LUNG 36524 [SJ59-14]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36545 [SJ59-11]

description: target barcode amplified gDNA


title: SJ59 LUNG 36533 [SJ59-15]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36536 [SJ59-6]

description: target barcode amplified gDNA


title: 23833 primary tumour [SJ41-10]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36549 [SJ59-12]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36537 [SJ59-7]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36540 [SJ59-10]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36539 [SJ59-9]

description: target barcode amplified gDNA


title: 23812 primary tumour [SJ41-4]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36534 [SJ59-4]

description: target barcode amplified gDNA


title: Cell pellet [LB11-4-CP]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36523 [SJ59-1]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-63]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-61]

description: target barcode amplified gDNA


title: 23811 Lungs immunotherapy treated [SJ41-15]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-23-B]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-26]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-04-B]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-31]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-00]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-05]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-27]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-22-B]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36535 [SJ59-5]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36533 [SJ59-3]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-14]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-04]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-22]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-18]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-12]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-02]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-23]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-10]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-13]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-99]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-62]

description: target barcode amplified gDNA


title: lung anti-asialo-GM1 treated [LB11-4-97]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-96]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-98]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-95]

description: target barcode amplified gDNA


title: lung anti-CD8 treated [LB11-4-80]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-78]

description: target barcode amplified gDNA


title: SJ59 primary tumour 36524 [SJ59-2]

description: target barcode amplified gDNA


title: lung control IgG treated [LB11-4-01]

description: target barcode amplified gDNA


title: Dendrobium nobile protocorm

first: Chen

last: Jishuang

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

description:
miRNA_novel_miRdeep2.xls
miRNA.expr.xls
Dnp

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then detected miRNA using miRDeep2 v2_0_0_8; mapper.pl with parameters -d -c -i -j -l 18 -m,miRDeep2.pl with default parameter
miRNA expression were calcuated using quantifier.pl from miRDeep2 v2_0_0_8 with parameters, then differential analysis using R package Ballgown
Genome_build: GCF_001605985.1
Supplementary_files_format_and_content: miRNA_novel_miRdeep2.xls (miRdeep2 analysis output), miRNA.expr.xls (abundance measurements)

organism: Dendrobium nobile

source_name: Dendrobium nobile protocorm

growth_protocol: The original plants of Dendrobium species were collected from Chishui City, Guizhou Province, China. The capsules were washed thoroughly under running tap for 30 minutes. Then treated with 75% ethanol for 30 seconds, and washed three times with sterile water. After this, the capsules were dipped in 0.1% mercuric chloride for 10 minutes and washed six times with sterile water. Finally, the sterilized capsules were excised longitudinally with a sterile surgical blade and around 1g of seeds was inoculated on improved 1/2 Murashige and Skoog (MS) medium, which was supplemented with potato juice (potato 30g/L, the juice was boiled for 20 min), 3% (w/v) sucrose, 0.2 mg/L NAA and 0.6% (w/v) agar, pH 5.8. After germinating to protocorms, the protocorms were transferred to proliferation media: 1/2 MS+ potato 30 g/L+ 3% (w/v) sucrose+ 0.3% (w/v) powder milk+ 1.5 mg/L 6-BA + 0.5 mg/L NAA and 0.6% (w/v) agar, pH 5.8. The protocorms were kept in a greenhouse. The temperature is 23 ± 1℃, the light/dark cycle is 12/12 h and relative humidity is 60-70%. Protocorms were collected after culturing for 30 days

extract_protocol:
Total small RNA was extracted by QIAGEN miRNeasy Mini Kit (QIAGEN, USA) according to the manufacturer’s instructions. RNA concentration and purity were measured on a NanoDrop ND-2000 UV-Vis Spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity was confirmed by denaturing agarose gel electrophoresis
Small RNA sequencing libraries were prepared using TruSeq Small RNA Sample Prep Kit (Illumina, USA). Briefly, the RNA fragments were firstly ligated to 5'- and 3’-adapters using T4 RNA Ligase, and reverse-transcribed with miScriptII RT-Kit (Qiagen, Germany). The resultant cDNA fragments were electrophoresed on a 4% agarose gel. Bands between 140 and 160 bp were excised and extracted by MinElute Gel Extraction Kit (Qiagen, Germany)

value: protocorm

value: culturing for 30 days


title: lung anti-asialo-GM1 treated [LB11-4-60]

description: target barcode amplified gDNA


title: lung Nk depleted [SJ66-LUNG-44562]

description: target barcode amplified gDNA

value: anti-asialo GM1


title: lung anti-asialo-GM1 treated [LB11-4-56]

description: target barcode amplified gDNA


title: lung control [SJ66-LUNG-44557]

description: target barcode amplified gDNA


title: lung control [SJ66-LUNG-44552]

description: target barcode amplified gDNA


title: Dendrobium. nobile leaf

description:
miRNA_novel_miRdeep2.xls
miRNA.expr.xls
Dnl

source_name: Dendrobium. nobile leaf

value: leaf

value: about 4 years old


title: Cell pellet [SJ66-cell-pellet]

description: target barcode amplified gDNA


title: lung Nk depleted [SJ66-LUNG-44563]

description: target barcode amplified gDNA


title: lung CD8 depleted [SJ66-LUNG-44551]

description: target barcode amplified gDNA


title: lung CD8 depleted [SJ66-LUNG-44550]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-79]

description: target barcode amplified gDNA


title: lung CD8 depleted [SJ66-LUNG-44549]

description: target barcode amplified gDNA


title: lung anti-asialo-GM1 treated [LB11-4-71]

description: target barcode amplified gDNA


title: lung CD8 depleted [SJ66-LUNG-44547]

description: target barcode amplified gDNA


title: LFR-43

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: T-LOH pattern of LFR-43

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. White and red colonies were mapped using Agilent platforms with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromosome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of LFR-43

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (JSC24-2) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25-1 cells were cultured on YPD plates containing 0.6 g/L furfural and single white and red colonies were picked up randomly for chromosome IV microarray.

tag: type

value: Red colony

source_name: cell culture of JSC24-2


title: LFR-44

description: T-LOH pattern of LFR-44

source_name: cell culture of LFR-44


title: lung Nk depleted [SJ66-LUNG-44545]

description: target barcode amplified gDNA

value: lung


title: LFR-39

description: T-LOH pattern of LFR-39

source_name: cell culture of LFR-39


title: LFR-42

description: T-LOH pattern of LFR-42

source_name: cell culture of LFR-42


title: LFR-41

description: T-LOH pattern of LFR-41

source_name: cell culture of LFR-41


title: LFR-40

description: T-LOH pattern of LFR-40

source_name: cell culture of LFR-40


title: lung Nk depleted [SJ66-LUNG-44544]

description: target barcode amplified gDNA

value: cancer


title: LFR-36

description: T-LOH pattern of LFR-36

source_name: cell culture of LFR-36


title: LFR-35

description: T-LOH pattern of LFR-35

source_name: cell culture of LFR-35


title: LFR-37

description: T-LOH pattern of LFR-37

source_name: cell culture of LFR-37


title: lung CD8 depleted [SJ66-LUNG-44534]

description: target barcode amplified gDNA

source_name: lung


title: lung control [SJ66-LUNG-44535]

description: target barcode amplified gDNA


title: lung anti-CD4 treated [LB11-4-02-B]

description: target barcode amplified gDNA


title: LFR-38

description: T-LOH pattern of LFR-38

source_name: cell culture of LFR-38


title: primary tumour Nk depleted [SJ66-PT-44564]

description: target barcode amplified gDNA

source_name: primary tumour


title: LFR-32

description: T-LOH pattern of LFR-32

source_name: cell culture of LFR-32


title: lung CD8 depleted [SJ66-LUNG-44548]

description: target barcode amplified gDNA


title: primary tumour Nk depleted [SJ66-PT-44563]

description: target barcode amplified gDNA


title: LFR-34

description: T-LOH pattern of LFR-34

source_name: cell culture of LFR-34


title: LFR-33

description: T-LOH pattern of LFR-33

source_name: cell culture of LFR-33


title: LFR-28

description: T-LOH pattern of LFR-28

source_name: cell culture of LFR-28


title: LFR-30

description: T-LOH pattern of LFR-30

source_name: cell culture of LFR-30


title: lung control [SJ66-LUNG-44536]

description: target barcode amplified gDNA


title: LFR-27

description: T-LOH pattern of LFR-27

source_name: cell culture of LFR-27

source_name: cell culture of JSC24-2


title: LFR-29

description: T-LOH pattern of LFR-29

source_name: cell culture of LFR-29


title: primary tumour Nk depleted [SJ66-PT-44562]

description: target barcode amplified gDNA


title: primary tumour CD8 depleted [SJ66-PT-44551]

description: target barcode amplified gDNA


title: primary tumour control [SJ66-PT-44552]

description: target barcode amplified gDNA


title: LFR-25

description: T-LOH pattern of LFR-25

source_name: cell culture of LFR-25


title: primary tumour control [SJ66-PT-44557]

description: target barcode amplified gDNA


title: primary tumour CD8 depleted [SJ66-PT-44547]

description: target barcode amplified gDNA


title: primary tumour CD8 depleted [SJ66-PT-44549]

description: target barcode amplified gDNA


title: LFR-31

description: T-LOH pattern of LFR-31

source_name: cell culture of LFR-31


title: LFR-24

description: T-LOH pattern of LFR-24

source_name: cell culture of LFR-24


title: primary tumour CD8 depleted [SJ66-PT-44550]

description: target barcode amplified gDNA


title: primary tumour Nk depleted [SJ66-PT-44544]

description: target barcode amplified gDNA


title: LFR-15

description: T-LOH pattern of LFR-15

source_name: cell culture of LFR-15


title: LFR-19

description: T-LOH pattern of LFR-19

source_name: cell culture of LFR-19


title: LFR-17

description: T-LOH pattern of LFR-17

source_name: cell culture of LFR-17


title: LFR-11

description: T-LOH pattern of LFR-11

source_name: cell culture of LFR-11


title: LFR-21

description: T-LOH pattern of LFR-21

source_name: cell culture of LFR-21


title: LFR-20

description: T-LOH pattern of LFR-20

source_name: cell culture of LFR-20


title: primary tumour control [SJ66-PT-44536]

description: target barcode amplified gDNA

source_name: primary tumour


title: LFR-16

description: T-LOH pattern of LFR-16

source_name: cell culture of LFR-16


title: primary tumour control [SJ66-PT-44535]

description: target barcode amplified gDNA


title: primary tumour CD8 depleted [SJ66-PT-44534]

description: target barcode amplified gDNA


title: Cell pellet [LB5-4_SJ19]

description: target barcode amplified gDNA

value: NSG


title: NSG primary tumour biol rep 6 [LB5-4_SJ18]

description: target barcode amplified gDNA


title: LFR-8

description: T-LOH pattern of LFR-8

source_name: cell culture of LFR-8


title: LFR-5

description: T-LOH pattern of LFR-5

source_name: cell culture of LFR-5


title: primary tumour CD8 depleted [SJ66-PT-44548]

description: target barcode amplified gDNA

value: WT


title: LFR-7

description: T-LOH pattern of LFR-7

source_name: cell culture of LFR-7


title: primary tumour Nk depleted [SJ66-PT-44545]

description: target barcode amplified gDNA

value: primary tumour


title: NSG primary tumour biol rep 4 [LB5-4_SJ16]

description: target barcode amplified gDNA


title: NSG primary tumour biol rep 3 [LB5-4_SJ15]

description: target barcode amplified gDNA


title: NSG primary tumour biol rep 2 [LB5-4_SJ14]

description: target barcode amplified gDNA


title: NSG primary tumour biol rep 5 [LB5-4_SJ17]

description: target barcode amplified gDNA


title: LFR-1

description: T-LOH pattern of LFR-1

source_name: cell culture of LFR-1


title: LFR-4

description: T-LOH pattern of LFR-4

source_name: cell culture of LFR-4

source_name: cell culture of JSC24-2


title: LFW-251

description: T-LOH pattern of LFW-251

source_name: cell culture of LFW-251

value: White colony


title: LFW-260

description: T-LOH pattern of LFW-260

source_name: cell culture of LFW-260


title: LFW-248

description: T-LOH pattern of LFW-248

source_name: cell culture of LFW-248


title: WT IT treated primary tumour biol rep 5 [LB5-4_12]

description: target barcode amplified gDNA

value: immunotherapy


title: WT IT treated primary tumour biol rep 4 [LB5-4_11]

description: target barcode amplified gDNA


title: WT IT treated mammary gland biol rep 3 [LB5-4_10]

description: target barcode amplified gDNA


title: LFW-234

description: T-LOH pattern of LFW-234

source_name: cell culture of LFW-234


title: LFW-221

description: T-LOH pattern of LFW-221

source_name: cell culture of LFW-221


title: LFW-215

description: T-LOH pattern of LFW-215

source_name: cell culture of LFW-215


title: WT Control treated primary tumour biol rep 2 [LB5-4_8]

description: target barcode amplified gDNA

value: control


title: WT Control treated primary tumour biol rep 1 [LB5-4_7]

description: target barcode amplified gDNA


title: WT Control treated primary tumour biol rep 3 [LB5-4_9]

description: target barcode amplified gDNA


title: LFW-210

description: T-LOH pattern of LFW-210

source_name: cell culture of LFW-210


title: LFW-194

description: T-LOH pattern of LFW-194

source_name: cell culture of LFW-194


title: LFW-191

description: T-LOH pattern of LFW-191

source_name: cell culture of LFW-191


title: WT IT treated primary tumour biol rep 1 [LB5-4_5]

description: target barcode amplified gDNA

source_name: primary tumour


title: WT Control treated primary tumour biol rep 3 [LB5-4_3]

description: target barcode amplified gDNA


title: LFR-2

description: T-LOH pattern of LFR-2

source_name: cell culture of LFR-2


title: LFW-199

description: T-LOH pattern of LFW-199

source_name: cell culture of LFW-199


title: WT Control treated primary tumour biol rep 2 [LB5-4_2]

description: target barcode amplified gDNA


title: NSG primary tumour biol rep 1 [LB5-4_SJ13]

description: target barcode amplified gDNA


title: LFW-186

description: T-LOH pattern of LFW-186

source_name: cell culture of LFW-186


title: LFW-171

description: T-LOH pattern of LFW-171

source_name: cell culture of LFW-171


title: LFW-183

description: T-LOH pattern of LFW-183

source_name: cell culture of LFW-183


title: WT Control treated primary tumour biol rep 1 [LB5-4_1]

description: target barcode amplified gDNA


title: LFW-169

description: T-LOH pattern of LFW-169

source_name: cell culture of LFW-169


title: LFW-160

description: T-LOH pattern of LFW-160

source_name: cell culture of LFW-160

source_name: cell culture of JSC24-2


title: LFW-245

description: T-LOH pattern of LFW-245

source_name: cell culture of LFW-245


title: C2Cnuc_ctrl1

city: New York

first: David

middle: William

last: McKellar

state: NY

address: 101 6th Ave

institute: New York Genome Center

description: Single-nucleus RNA-sequencing (Chromium v3, 10x Genomics) of C2C12 myoblasts

data_processing:
3' polyA trimming with cutadapt v3.4
3' polyG trimming and 5' TSO trimming (CCCATGTACTCTGCGTTGATACCACTGCTT) with cutadapt v3.4
Alignment and quantitation with STAR v2.7.10a; used GRCm39 reference with GENCODE M28 annotations
Pseudoalignment with  kallisto v0.48.0 and quantitation with bustools v0.41.0; used GRCm39 reference with GENCODE M28 annotations
Assembly: GRCm39 (GENCODE M28 annotaitons)
Supplementary files format and content: Count matrices were uploaded in matrix market (.mtx) with the spot barcodes and feature names in separate tab-delimited .txt files (count matrices from the Reovirus-appended reference have "REO" in the filename)
Supplementary files format and content: Stitched and shading-corrected H&E images are uploaded as .tif files
Supplementary files format and content: Tissue section coordinates are uploaded as .json files, manually selected using the Loupe Browser software from 10x Genomics

extract_protocol: Single-nucleus RNA-sequencing with Chromium v3 (10x Genomics) with or without in situ polyadenylation (yeast poly(A) polymerase)


title: LFW-162

description: T-LOH pattern of LFW-162

source_name: cell culture of LFW-162


title: LFW-174

description: T-LOH pattern of LFW-174

source_name: cell culture of LFW-174


title: C2Cnuc_yPAP1

description: Single-nucleus RNA-sequencing (Chromium v3, 10x Genomics) of C2C12 myoblasts after in situ polyadenylation of RNAs with yeast poly(A) polymerase


title: LFW-155

description: T-LOH pattern of LFW-155

source_name: cell culture of LFW-155


title: KPC_2_PD1_CTLA4_3

city: Cambridge

first: Peter

middle: P

last: Du

state: MA

address: 415 Main St

institute: Broad Institute

data_processing:
Cellranger v3.0.0 mkfastq command to demultiplex fastq files
Cellranger v3.0.0 count command to generate raw and filtered count matrices
Assembly: mm10
Supplementary files format and content: filtered count matrix h5 file
Supplementary files format and content: raw count matrix h5 file

source_name: pancreatic cancer

growth_protocol: 2e6 KPC tumor cells were injected subcutaneously into the flanks of WT C57BL6/J mice

extract_protocol:
Tumors were dissected 12 days post tumor challenge. Immune cells were isolated using a Lympholyte-M gradient followed by CD45+ MACS positive selection. Single-cell suspensions were run through a 10X Chromium Controller to obtain droplets.
Single cell libraries were generated using 10X Genomics 3' chemistry kits per the manufacturer's instructions

treatment_protocol: Mice in the treatment group were treated with 100ug of aPD-1 and 100ug of aCTLA-4 antibody on days 6 and 9 post tumor challenge

value: pancreatic cancer

value: CD45+ immune cells


title: KPC_2_PD1_CTLA4_1


title: KPC_2_PD1_CTLA4_4


title: KPC_2_PD1_CTLA4_2


title: KPC_2_NoTx_2


title: LFW-140

description: T-LOH pattern of LFW-140

source_name: cell culture of LFW-140


title: KPC_2_NoTx_1


title: LFW-143

description: T-LOH pattern of LFW-143

source_name: cell culture of LFW-143


title: KPC_2_NoTx_4


title: KPC_2_NoTx_3


title: LFW-113

description: T-LOH pattern of LFW-113

source_name: cell culture of LFW-113


title: LFW-116

description: T-LOH pattern of LFW-116

source_name: cell culture of LFW-116


title: LFW-102

description: T-LOH pattern of LFW-102

source_name: cell culture of LFW-102


title: LFW-94

description: T-LOH pattern of LFW-94

source_name: cell culture of LFW-94


title: LFW-96

description: T-LOH pattern of LFW-96

source_name: cell culture of LFW-96


title: LFW-106

description: T-LOH pattern of LFW-106

source_name: cell culture of LFW-106


title: YUMMER1.7_NS_rep1

data_processing:
Trimmomatic v0.36 with the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:37
Pseudo-alignment to the mm10 reference transcriptome using Kallisto and a 31 k-mer index constructed from GRCm38
Abundances were converted into estimated counts using tximport
Assembly: mm10
Supplementary files format and content: tab-delimited estimated counts

source_name: melanoma

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kits following the manufacturer's instructions
RNA libraries were constructed using NEB RNA Ultra II Directional kits following the manufacturer's instructions

treatment_protocol: Cells were stimulated with 100ng/mL IFNg or 1000 activity units/mL of IFNb for 48h

value: melanoma

value: cancer cell line

value: no stimulation


title: YUMMER1.7_IFNg_rep2

value: IFNg


title: YUMMER1.7_IFNg_rep3


title: YUMMER1.7_NS_rep3


title: LFW-93

description: T-LOH pattern of LFW-93

source_name: cell culture of LFW-93


title: LFW-80

description: T-LOH pattern of LFW-80

source_name: cell culture of LFW-80


title: YUMMER1.7_IFNg_rep1


title: YUMMER1.7_IFNb_rep2

value: IFNb


title: YUMMER1.7_NS_rep2


title: LFW-57

description: T-LOH pattern of LFW-57

source_name: cell culture of LFW-57

source_name: cell culture of JSC24-2


title: LFW-47

description: T-LOH pattern of LFW-47

source_name: cell culture of LFW-47


title: YUMMER1.7_IFNb_rep1


title: LFW-37

description: T-LOH pattern of LFW-37

source_name: cell culture of LFW-37


title: LFW-64

description: T-LOH pattern of LFW-64

source_name: cell culture of LFW-64


title: Renca_NS_rep3

source_name: renal cancer

value: renal cancer

value: Renca

value: BALB/c


title: Renca_NS_rep2


title: YUMMER1.7_IFNb_rep3


title: LFW-28

description: T-LOH pattern of LFW-28

source_name: cell culture of LFW-28


title: LFW-32

description: T-LOH pattern of LFW-32

source_name: cell culture of LFW-32


title: LFW-69

description: T-LOH pattern of LFW-69

source_name: cell culture of LFW-69


title: Renca_IFNg_rep3


title: Renca_IFNg_rep2


title: Renca_IFNb_rep3


title: Renca_IFNb_rep2


title: LFW-23

description: T-LOH pattern of LFW-23

source_name: cell culture of LFW-23


title: LFW-18

description: T-LOH pattern of LFW-18

source_name: cell culture of LFW-18


title: Renca_IFNg_rep1


title: LFW-27

description: T-LOH pattern of LFW-27

source_name: cell culture of LFW-27


title: LFW-15

description: T-LOH pattern of LFW-15

source_name: cell culture of LFW-15


title: LFW-13

description: T-LOH pattern of LFW-13

source_name: cell culture of LFW-13


title: Panc02.3_NS_rep2

source_name: pancreatic cancer


title: Panc02.3_NS_rep1


title: WT IT treated primary tumour biol rep 2 [LB5-4_6]

description: target barcode amplified gDNA

source_name: primary tumour

value: cancer


title: Panc02.3_IFNg_rep3


title: LFW-17

description: T-LOH pattern of LFW-17

source_name: cell culture of LFW-17


title: LFW-14

description: T-LOH pattern of LFW-14

source_name: cell culture of LFW-14


title: Panc02.3_IFNg_rep1


title: Renca_IFNb_rep1


title: LFW-12

description: T-LOH pattern of LFW-12

source_name: cell culture of LFW-12

source_name: cell culture of JSC24-2


title: Panc02.3_IFNb_rep2


title: LFW-11

description: T-LOH pattern of LFW-11

source_name: cell culture of LFW-11


title: Panc02.3_IFNg_rep2


title: Panc02.3_IFNb_rep3


title: MC38.7_NS_rep3

source_name: colorectal cancer

value: colorectal cancer


title: Panc02.3_NS_rep3


title: LFW-8

description: T-LOH pattern of LFW-8

source_name: cell culture of LFW-8


title: MC38.7_NS_rep2


title: MC38.7_NS_rep1


title: LFW-4

description: T-LOH pattern of LFW-4

source_name: cell culture of LFW-4


title: LFW-2

description: T-LOH pattern of LFW-2

source_name: cell culture of LFW-2


title: LFW-3

description: T-LOH pattern of LFW-3

source_name: cell culture of LFW-3


title: genomic DNA from maternal facing placenta tissue  [S0386]

city: Singapore

first: Jonathan

middle: Yinhao

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
R/Rstudio
Average Beta
The filtered and normalized (preprocessNoob) average Beta values are provided in the EPIC850k-GUSTO-Placenta-BetaNoob-708655Probes-Geo.txt.

label: Cy5 and Cy3

source_name: maternal facing side placenta tissue

extract_protocol: Frozen sections of placenta are chipped and crushed in liquid nitrogen on aluminum foil-lined mortar and pestle. Mortar and pestle are washed with 70% ethanol and foil changed between each sample. For each sample: In a 1.5 ml tube, we measured out 75mg (+/- 10%) of crushed placenta tissue and added 500 ul ATL & 30 ul PK. We then incubate them overnight in a thermomixer(shaking incubator). The total lysate was then transferred into the Qiasymphony SP and the DNA was extracted using Qiagen DNA Midi kit (Cat: 937255). DNA was quantified using Qubit Flex and quality was assessed using Nanodrop

tag: gender

value: Male

tag: sample type

value: maternal facing side placenta

tag: group

tag: ethnicity

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0385]

value: Female

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0389]

value: ART


title: genomic DNA from maternal facing placenta tissue  [S0391]


title: genomic DNA from maternal facing placenta tissue  [S0387]


title: MC38.7_IFNg_rep3

tag: tissue

tag: cell type


title: MC38.7_IFNg_rep2

tag: genotype

tag: treatment


title: LFW-7

description: T-LOH pattern of LFW-7

source_name: cell culture of LFW-7

value: White colony


title: genomic DNA from maternal facing placenta tissue  [S0380]


title: LFW-1

description: T-LOH pattern of LFW-1

source_name: cell culture of LFW-1


title: MC38.7_IFNg_rep1

tag: cell line


title: MC38.7_IFNb_rep3


title: genomic DNA from maternal facing placenta tissue  [S0378]


title: genomic DNA from maternal facing placenta tissue  [S0379]

value: malay


title: Panc02.3_IFNb_rep1

value: pancreatic cancer

value: cancer cell line


title: MC38.7_IFNb_rep2


title: genomic DNA from maternal facing placenta tissue  [S0377]


title: MC38.7_IFNb_rep1


title: genomic DNA from maternal facing placenta tissue  [S0373]


title: LFW-10

description: T-LOH pattern of LFW-10

source_name: cell culture of LFW-10


title: LFW-16

description: T-LOH pattern of LFW-16

source_name: cell culture of LFW-16


title: genomic DNA from maternal facing placenta tissue  [S0372]


title: LLC_NS_rep3

source_name: lung cancer

value: lung cancer

value: LLC

value: no stimulation


title: genomic DNA from maternal facing placenta tissue  [S0369]


title: LLC_NS_rep2


title: LLC_IFNg_rep3

value: IFNg


title: LLC_NS_rep1


title: genomic DNA from maternal facing placenta tissue  [S0366]


title: LLC_IFNg_rep1


title: genomic DNA from maternal facing placenta tissue  [S0361]


title: KPC.2_NS_rep3

source_name: pancreatic cancer


title: LLC_IFNb_rep1

value: IFNb


title: LLC_IFNb_rep3


title: LLC_IFNb_rep2


title: KPC.2_NS_rep1


title: genomic DNA from maternal facing placenta tissue  [S0355]


title: KPC.2_IFNg_rep3


title: genomic DNA from maternal facing placenta tissue  [S0352]


title: KPC.2_NS_rep2


title: genomic DNA from maternal facing placenta tissue  [S0351]


title: genomic DNA from maternal facing placenta tissue  [S0360]


title: genomic DNA from maternal facing placenta tissue  [S0344]


title: KPC.2_IFNg_rep2


title: genomic DNA from maternal facing placenta tissue  [S0339]


title: genomic DNA from maternal facing placenta tissue  [S0337]


title: genomic DNA from maternal facing placenta tissue  [S0340]


title: KPC.2_IFNb_rep3


title: genomic DNA from maternal facing placenta tissue  [S0368]


title: KPC.2_IFNg_rep1


title: genomic DNA from maternal facing placenta tissue  [S0332]


title: KPC.2_IFNb_rep2


title: KPC.2_IFNb_rep1


title: genomic DNA from maternal facing placenta tissue  [S0331]


title: genomic DNA from maternal facing placenta tissue  [S0364]


title: CT26.2_NS_rep3

value: BALB/c


title: genomic DNA from maternal facing placenta tissue  [S0354]


title: CT26.2_NS_rep2

value: colorectal cancer


title: genomic DNA from maternal facing placenta tissue  [S0330]

value: Male


title: CT26.2_NS_rep1


title: genomic DNA from maternal facing placenta tissue  [S0328]

value: maternal facing side placenta


title: CT26.2_IFNg_rep3


title: genomic DNA from maternal facing placenta tissue  [S0322]

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0321]


title: CT26.2_IFNg_rep2


title: genomic DNA from maternal facing placenta tissue  [S0327]


title: CT26.2_IFNb_rep3


title: genomic DNA from maternal facing placenta tissue  [S0324]


title: CT26.2_IFNg_rep1


title: genomic DNA from maternal facing placenta tissue  [S0319]

value: Female


title: CT26.2_IFNb_rep2


title: CT26.2_IFNb_rep1


title: genomic DNA from maternal facing placenta tissue  [S0315]


title: genomic DNA from maternal facing placenta tissue  [S0317]


title: B16.1_NS_rep1

source_name: melanoma

value: melanoma


title: B16.1_NS_rep2


title: B16.1_NS_rep3


title: genomic DNA from maternal facing placenta tissue  [S0318]

value: ART


title: B16.1_IFNg_rep3


title: genomic DNA from maternal facing placenta tissue  [S0312]


title: genomic DNA from maternal facing placenta tissue  [S0308]


title: B16.1_IFNg_rep1


title: genomic DNA from maternal facing placenta tissue  [S0307]

value: indian


title: B16.1_IFNb_rep3


title: B16.1_IFNg_rep2


title: genomic DNA from maternal facing placenta tissue  [S0329]


title: genomic DNA from maternal facing placenta tissue  [S0306]

value: malay


title: B16.1_IFNb_rep2


title: genomic DNA from maternal facing placenta tissue  [S0305]


title: B16.1_IFNb_rep1


title: genomic DNA from maternal facing placenta tissue  [S0301]


title: genomic DNA from maternal facing placenta tissue  [S0300]


title: genomic DNA from maternal facing placenta tissue  [S0297]


title: genomic DNA from maternal facing placenta tissue  [S0295]


title: Set3_11_1

city: Cologne

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

description:
data from three samples of different organoid pools, grown in early (passage 4) and late (passage 11) passages.
passageOrganoids_4vs11_countmatrix.txt

data_processing:
Fastq files were processed with zUMIs (version 2.9.5) using its miniconda environment (Parekh et al. 2018) with STAR index 2.7 (Dobin et al. 2013), samtools (version 1.9) (Li et al. 2009) and “featureCounts” from Rsubread (version 1.32.4) (Liao et al. 2013). Reads were mapped to Mus musculus (mm10) with Ensembl annotation version GRCm38.93.
Libraries were  down-sampled  within  zUMIs,  depending  on  library  size  variability: Single organoid libraries were down sampled to 4-12 million reads and the suspension-dome data to 3-6 million reads. Passage 4 vs 11 orgsnoids bulk RNA-seq data was not downsampled.
Downstream computational analysis was conducted in R (version 3.6.3). The count matrix was normalized and filtered with edgeR (version 3.28.1) (Robinson et al. 2010) using “filterByExpr” with min.count = 3. For differential gene expression analysis, the limma-voom approached by limma (version 3.42.2) (Ritchie et al. 2015) was used with a pipeline including linear model fit (lmFit) and p-value adjustment for multiple testing (“topTableF” with adjust.method = ‘BH’, “decideTests” with method = ‘global’).
Assembly: mm10
Supplementary files format and content: countmatrix

source_name: organoids

growth_protocol: Organoids were maintained as 30 μl Matrigel domes in a 37 °C incubator at 5% CO2 and 20% O2. The medium was changed every 2 days and cultures passaged every 5-7 days with mechanical dissociation of the Matrigel. Organoids  cultured  in  a  dilute  suspension  culture were maintained in a 10% Matrigel mixture. The cultures were maintained on an orbital shaker at 80 r.p.m. in a 37 °C incubator, 5% CO2, 20%  O2.  Every  3-4  days,  the  organoids  were  passaged  by  mechanical  breakdown  of  the Matrigel.

extract_protocol:
The  mRNA  was  extracted  with  the  Dynabeads  mRNA  DIRECT  Kit  by  Fisher  Scientific (#61011)  with  a  few  modifications  and  self-made  buffers.  For  each  sample  (i.e., single organoid) 10 μl of resuspended beads were transferred to a 2 ml DNA low-binding tube and supernatant was discarded with the help of a magnet stand. Beads were resuspended in 50 μl room temperature Lysis/Binding Buffer. With a volume of 150 μl room temperature Lysis/Binding Buffer, each organoid was transferred to a 1.5 ml low-  binding tube already containing the equivalent amount of buffer. The content was pipetted up and  down  5  times  to  allow  lysis.  The  following  steps  were  performed  according  to  the manufacturer’s instructions.
Equal amounts of mRNA per sample were used for cDNA synthesis with Maxima H Minus reverse transcriptase  (Thermo  Fisher  Scientific).  During  reverse  transcription,  unique  barcodes including  unique  molecular  identifiers  (UMI)  were  attached  to  each  sample.  After  cDNA synthesis, all samples were pooled and processed in one single tube. After purification and ExoI treatment, cDNA was PCR-amplified for 12 cycles and subsequently purified. cDNA was tagmented in 10 technical replicates of 1 ng cDNA each   using the Nextera XT Kit (Illumina), according to the manufacturer's instructions.

value: liver organoid

tag: age

value: 3-4 months old


title: Set3_11_2


title: genomic DNA from maternal facing placenta tissue  [S0311]


title: Set4_11_1


title: genomic DNA from maternal facing placenta tissue  [S0294]


title: genomic DNA from maternal facing placenta tissue  [S0289]


title: genomic DNA from maternal facing placenta tissue  [S0290]


title: genomic DNA from maternal facing placenta tissue  [S0287]


title: Set1_11_2


title: Set4_4_2


title: Set4_4_1


title: Set1_11_1


title: genomic DNA from maternal facing placenta tissue  [S0285]


title: Set1_4_2


title: genomic DNA from maternal facing placenta tissue  [S0283]


title: Set1_4_1


title: Set3_4_1


title: genomic DNA from maternal facing placenta tissue  [S0284]


title: Batch SB1

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Batch
Supplementary files format and content: single cell expression matrix; Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: concatenated raw counts

growth_protocol: Cells were cultured previously in 2i/LIF containing CHI 99021 (Chiron), PD03 and LIF, and then in RACL as described in Anderson et al., 2017.

extract_protocol:
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

value: in vitro PrE differentiation


title: genomic DNA from maternal facing placenta tissue  [S0279]


title: genomic DNA from maternal facing placenta tissue  [S0273]


title: Pregnancy plasticity scATACseq

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

data_processing:
For scRNA-seq, sequencing data were aligned to the genome and processed according to a previously published pipeline (https://github.com/indrops/indrops). Briefly, this pipeline was used to build a custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1, after filtering the annotation gtf file ((gencode.v17.annotation.gtf filtered for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN"). Unique molecular identifiers (UMIs) were used to link sequence reads back to individual captured molecules. All steps of the pipeline were run using default parameters unless explicitly stated.
Nuclei for scATAC-seq were processed using standard 10X Genomics pipelines.
Assembly: mm10
Supplementary files format and content: counts for scRNA-seq, peak matrix for ATAC-seq

source_name: Hippocampus

extract_protocol:
Frozen tissue was thawed in 500 uL Buffer HB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, 1mM DTT). The tissue was transferred to a 2 mL dounce. 500ul 5% IGEPAL CA-630 (Sigma) and 1 mL HB were added to the tissue and the tissue was homogenized with a tight pestle 10-15 times. The sample was transferred to a 15 mL tube and total solution brought to 9 mL with HB. In a Corex tube (Fisher Scientific), 1 mL 30% iodixanol layered on top of 1 mL 40% iodixanol. The 9 mL sample was layered on top of the iodixanol cushion. The sample was spun at 10,000 xg for 18 minutes. 1 mL of sample at the 30-40% iodixanol interface was collected for subsequent nuclei processing.
Nuclei were processed for scRNA-seq using the Indrops platform and for scATAC-seq using 10X Genomics standard protocols.

value: Hippocampus

value: multiplexed sample:(E18) pregnant female,  8 week old virgin female and P21 post-partum female


title: Batch SB2


title: Set4_11_2


title: Mm_E12_5_MS252_165

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: cDNAs amiplified from 1 ng total RNA extracted from cells using 3'-RNA-seq technology

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCm38.p6, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

source_name: Germ cells from E12.5 fetal testis (Vasa+)

extract_protocol:
The cells were lysed and the total RNAs were purified using a NucleoSpin RNA XS (Takara Bio, #U0902A) according to the manufacturer’s instructions.  1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs.
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

tag: developmental stage

tag: Sex

tag: celltype

value: Germ cells


title: genomic DNA from maternal facing placenta tissue  [S0271]

last: Huang


title: Pregnancy plasticity scRNAseq


title: genomic DNA from maternal facing placenta tissue  [S0275]


title: genomic DNA from maternal facing placenta tissue  [S0268]


title: genomic DNA from maternal facing placenta tissue  [S0278]


title: genomic DNA from maternal facing placenta tissue  [S0270]


title: genomic DNA from maternal facing placenta tissue  [S0269]


title: Set3_4_2

tag: strain


title: genomic DNA from maternal facing placenta tissue  [S0264]


title: Mm_E11_5_MS252_186

source_name: Germ cells from E11.5 fetal testis (Stella+Vasa+)

value: Dppa3-EGFPTg/0; mvh(Ddx4)-RFPTg/0


title: genomic DNA from maternal facing placenta tissue  [S0286]


title: Mm_E11_5_MS252_185


title: Mm_P1_MS173_146

source_name: Somatic cells from P1 fetal ovary (Vasa-)

value: Gonadal somatic cells


title: genomic DNA from maternal facing placenta tissue  [S0265]


title: Mm_E11_5_MS252_183

source_name: Germ cells from E11.5 fetal testis (Stella+Vasa-)


title: Mm_E11_5_MS252_184


title: genomic DNA from maternal facing placenta tissue  [S0257]


title: genomic DNA from maternal facing placenta tissue  [S0260]


title: Mm_P1_MS173_145


title: genomic DNA from maternal facing placenta tissue  [S0262]


title: genomic DNA from maternal facing placenta tissue  [S0277]


title: Mm_P0_MS173_144

source_name: Somatic cells from P0 fetal ovary (Vasa-)


title: Mm_P0_MS173_143


title: Mm_E18_5_MS173_141

source_name: Somatic cells from E18.5 fetal ovary (Vasa-)


title: Mm_E17_5_MS173_140

source_name: Somatic cells from E17.5 fetal ovary (Vasa-)


title: Mm_E11_5_MS252_182


title: genomic DNA from maternal facing placenta tissue  [S0256]

source_name: maternal facing side placenta tissue


title: Mm_E16_5_MS173_137

source_name: Somatic cells from E16.5 fetal ovary (Vasa-)


title: genomic DNA from maternal facing placenta tissue  [S0246]


title: genomic DNA from maternal facing placenta tissue  [S0245]


title: Mm_E15_5_MS173_136

source_name: Somatic cells from E15.5 fetal ovary (Vasa-)


title: genomic DNA from maternal facing placenta tissue  [S0242]


title: genomic DNA from maternal facing placenta tissue  [S0243]


title: Mm_E15_5_MS173_135


title: genomic DNA from maternal facing placenta tissue  [S0239]


title: Mm_E14_5_MS173_134

source_name: Somatic cells from E14.5 fetal ovary (Vasa-)


title: genomic DNA from maternal facing placenta tissue  [S0241]


title: Mm_P1_MS173_133

source_name: Germ cells from P1 fetal ovary (Vasa+)


title: Mm_P1_MS173_132


title: genomic DNA from maternal facing placenta tissue  [S0263]


title: genomic DNA from maternal facing placenta tissue  [S0237]


title: Mm_E18_5_MS173_142


title: genomic DNA from maternal facing placenta tissue  [S0230]


title: genomic DNA from maternal facing placenta tissue  [S0228]


title: Mm_E18_5_MS173_129

source_name: Germ cells from E18.5 fetal ovary (Vasa+)


title: Mm_P0_MS173_131

source_name: Germ cells from P0 fetal ovary (Vasa+)


title: Mm_P0_MS173_130


title: genomic DNA from maternal facing placenta tissue  [S0248]


title: Mm_E17_5_MS173_139


title: Mm_E18_5_MS173_128


title: genomic DNA from maternal facing placenta tissue  [S0225]


title: genomic DNA from maternal facing placenta tissue  [S0240]


title: Mm_E17_5_MS173_127

source_name: Germ cells from E17.5 fetal ovary (Vasa+)


title: genomic DNA from maternal facing placenta tissue  [S0218]


title: genomic DNA from maternal facing placenta tissue  [S0224]


title: genomic DNA from maternal facing placenta tissue  [S0219]


title: Mm_E12_5_MS252_167

source_name: Germ cells from E12.5 fetal ovary (Vasa+)


title: Mm_E16_5_MS173_124

source_name: Germ cells from E16.5 fetal ovary (Vasa+)


title: Mm_E17_5_MS173_126


title: genomic DNA from maternal facing placenta tissue  [S0250]


title: genomic DNA from maternal facing placenta tissue  [S0212]


title: genomic DNA from maternal facing placenta tissue  [S0217]


title: genomic DNA from maternal facing placenta tissue  [S0211]


title: Mm_E11_5_MS252_191

source_name: Germ cells from E11.5 fetal ovary (Stella+Vasa+)


title: Mm_E11_5_MS252_192


title: genomic DNA from maternal facing placenta tissue  [S0208]


title: Mm_E11_5_MS252_190


title: genomic DNA from maternal facing placenta tissue  [S0236]


title: genomic DNA from maternal facing placenta tissue  [S0203]


title: genomic DNA from maternal facing placenta tissue  [S0207]


title: Mm_E11_5_MS252_188

source_name: Germ cells from E11.5 fetal ovary (Stella+Vasa-)


title: genomic DNA from maternal facing placenta tissue  [S0206]


title: genomic DNA from maternal facing placenta tissue  [S0220]


title: Mm_E16_5_MS173_125


title: Mm_E11_5_MS252_187


title: genomic DNA from maternal facing placenta tissue  [S0196]


title: genomic DNA from maternal facing placenta tissue  [S0194]


title: male WT rep5 [MUP22]

first: Adhideb

last: Ghosh

data_processing:
Trim Galore v0.6.4 used for read trimming
Bismark v0.22.3 used for read mapping and methylation site extraction
EdgeR v3.32.1 used for DMR analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Compressed methylation coverage report

source_name: male WT_liver

extract_protocol:
At twelve weeks of age mice were sacrificed by cardiac puncture and liver samples were taken and snap frozen. Genomic DNA was extracted using the All Prep DNA/RNA Extraction Kit (QIAGEN).
The gDNA was digested with  MspI (Tango Buffer.Thermo Scientific), followed by nucleotide end-repair and A-tailing (Klenow Fragment exo- with dCTPs, dGTPs, and dATPs in Tango Buffer, Thermo Scientific) and heat inactivation.  EM-seq Adaptors (NEB E7165A, New England Biolaps) were ligated to the A-tailed DNA fragments using T4 DNA ligase (HC; Thermo Scientific). Bisulfite conversion was performed using ZYMO EZ-96 DNA Methylation-DirectTM MagPrep Kit.  Bisulfite converted libraries were amplified  Kapa (Uracil+ 2x MasterMix ;Roche) and purified (0.8x SPRIselect; Agencourt, Beckman Coulter).

value: male

value: WT


title: female KO rep5 [MUP23]

source_name: female KO_liver

value: female

value: KO


title: genomic DNA from maternal facing placenta tissue  [S0192]

value: Female

value: maternal facing side placenta

value: chinese


title: genomic DNA from maternal facing placenta tissue  [S0200]

value: Male

value: indian


title: genomic DNA from maternal facing placenta tissue  [S0193]