title: Retinal Detachment, Day 1 Sample 12

city: Ann Arbor

middle: F

last: Abcouwer

state: MI

address: 1000 Wall Street

department: Ophthalmology and Visual Sciences

institute: University of Michigan

data_processing:
The adapter trimming was performed usingfastq-mcfprogram (v1.05) andcutadapt(v2.5).
Contamination removal was performed usingBowtie2(v2.5.1)
The paired-end reads were aligned to the reference Mouse genome downloaded from Ensembl database (genome-build GRCm38.p6)
Alignment was performed usingSTAR(2.7.3a). The raw read counts were estimated using HTSeq (v0.11.2).
Differential expression analysis was performed using DESeq2 (R Bioconductor package)
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file containing raw and DEseq2 normalized counts for each Sample

source_name: Eye

extract_protocol:
After removing the retina the remaining posterior eyecup was quickly washed in PBS buffer and then immediately transferred into a 1.5 mL microcentrifuge tube containing 300 µL of RNAprotect® Cell Reagent
RPE RNA pellets were dissolved in RLT Buffer (Qiagen) and total RNA was obtained using the column-based RNA purification kit, RNeasy Plus Micro (Qiagen)
TruSeq stranded mRNA kit (Illumina) was used for library generation

treatment_protocol: Retinal detachments - A sclerotomy was created approximately 1 mm posterior to the limbus using a 30-gauge needle. Subsequently, 1% sodium hyaluronate was carefully injected into the subretinal space until approximately 50% of the retina became detached from the RPE.

value: Eye

tag: strain

value: RPE

tag: Sex

value: Male

value: 1 day retinal detachment


title: Retinal Detachment, Day 7 Sample 13

status: Public on Apr 03 2024

type: SRA

first: Steven

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: treatment

value: 7 day retinal detachment


title: 5M_CO_3_ATAC

city: New York

first: James

last: Nicholson

address: 413 East 69th Street

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices for downstream preprocessing and analysis using the Seurat v4.0 R package
For quality control, cells with fewer than 750 genes detected or greater than 10% mitochondrial gene expression were removed
Raw Multiome sequencing data were converted to fastq format and subsequently aligned to the GRCh38 genome using “cellranger-arc mkfastq” and “cellranger-arc count” (10X Genomics, v2.0.0).
Assembly: GRCh38 human reference genome
Supplementary files format and content: Cellranger output series matrix files for scRNAseq; filtered_feature_bc_matrix.h5 & atac_fragments.tsv.gz for paired scRNA/ATACseq

molecule: genomic DNA

organism: Homo sapiens

source_name: Cerebral Organoid

growth_protocol: Cerebral Organoids and GSCs lines were generated and maintained as previosuly described (Linklous et al. 2019, Cell Reports)

extract_protocol:
COs were dissociated into single-cell suspensions using the Papain Dissociation System following manufacturers instructions (Worthington Biochemical, LK003150). Cells were filtered through a 40um strainer and resuspended on ice-cold PBS/2%BSA. For GLICO samples, GFP-positive/DAPInegative spGSCs were sorted by FACS (Becton-Dickinson Aria II) and collected on PBS/2%BSA for Single-cell ATAC-/ RNA-sequencing.
Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237)

value: Cerebral Organoid

tag: cell line

tag: time


title: Retinal Detachment, Day 7 Sample 15


title: 5M_CO_2_ATAC


title: Retinal Detachment, Day 7 Sample 16


title: Retinal Detachment, Day 7 Sample 17


title: Retinal Detachment, Day 1 Sample 11


title: 5M_CO_3_GEX


title: Retinal Detachment, Day 7 Sample 18


title: Retinal Detachment, Day 1 Sample 9


title: Retinal Detachment, Day 1 Sample 10


title: Retinal Detachment, Day 7 Sample 14


title: Retinal Detachment, Day 1 Sample 8


title: 9M_CO_2_GEX


title: 7M_CO_HPX_2


title: 12M_CO_2_GEX


title: 5M_CO_2_GEX


title: Retinal Detachment, Day 1 Sample 7


title: 7M_CO_HPX_1


title: Naïve B6 Sample 6

value: Naïve


title: Naïve B6 Sample 5


title: 7M_CO_cntrl_2


title: 9M_CO_3_GEX


title: 7M_CO_cntrl_1


title: Naïve B6 Sample 4


title: 12M_CO_3


title: Naïve B6 Sample 3


title: Naïve B6 Sample 2


title: RT, Replicate 2, scRNAseq

city: Chongqing

first: Yongzhong

last: Wu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Radiation Oncology Center

country: China

institute: Chongqing University Cancer Hospital

description: SeekOne Kit

library_source: transcriptomic single cell

data_processing:
We used the Seekone Tools pipeline to process the cleaned reads and generated the transcript expression matrix. Firstly, the cell barcodes and UMI sequences were extracted based on the defined pattern about the localization of the barcode, linker and UMI within a read. The barcode was corrected with whitelist. The corrected barcode , together with UMI, were put in the header of their corresponding reads. Secondly, the reads were mapped to the reference genomes using STAR 2.5.1b (Dobin, Davis et al. 2012). Then, the reads with barcode and UMI information were assigned to transcriptome using featureCounts of package Subread 1.6.4 (Liao, Smyth et al. 2014) with the default parameters except “-s 1 –fracOverlap 0.5”. Finally, similar to the raw_feature_bc_matrix results of Cell Ranger(Zheng, Terry et al. 2017), the raw UMI count matrix according to barcodes and transcripts was generated.
Assembly: GRCm39(mm39)
Supplementary files format and content: Tab-separated value files and matrix files

source_name: LLC tumor

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Multi-tissue dissociation kit 2(Miltenyi Biotec, Cat#: 130-110-203) from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
Library was performed according to manufacture's instruction ( SeekOne® MM Single Cell 3’ library preparation kit). Briefly, appropriate number of cells were loaded into the flow channel of SeekOne® MM chip which had 170,000 microwells and allowed to settle in microwells by gravity. After removing the unsettled cells, sufficient Cell Barcoded Magnetic Beads (CBBs) were pipetted into flow channel and also allowed to settle in microwells with the help of a magnetic field. Next excess CBBs were rinsed out and cells in MM chip were lysed to release RNA which was captured by the CBB in the same microwell. Then all CBBs were collected and reverse transcription were performed at 37℃for 30 minutes to lable cDNA with cell barcode on the beads. Further exonuclease I treatment were performed to remove unused primer on CBBs. Subsequently, barcoded cDNA on the CBBs was hybridized with random primer which had reads 2 SeqPrimer sequence on the 5’ end and could extend to form the second strand DNA with cell barcode on the 3’ end. The resulting second strand DNA were denatured off the CBBs, purified and amplified in PCR reaction. The amplified cDNA product was then cleaned to remove unwanted fragment and added to full length sequencing adapter and sample index by indexed PCR. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length.

treatment_protocol: Once tumors reached an average volume of 100mm3, radiation was given on day 7-9 post-tumor cell injection with total dose 24Gy in 3 fractions (8Gy each fraction).

value: LLC tumor

value: LLC

tag: age

value: 6-8 weeks old

value: Radiation


title: 4M_CO_3


title: M24-3

city: Beijing

first: Quan

last: Rui

state: Haidian District

address: 10 Tianxiu Road

department: Department of Nutrition and Health

institute: China Agricultural University

data_processing:
Sequencing was performed on the NovaSeq 6000 platform with PE150 read length. The data generated from the Illumina platform were used for bioinformatics analysis
The raw data in fastq format were processed using a Perl script to remove adapter sequences and filter out low-quality reads (reads with more than 60% bases with a quality score of less than or equal to 25) and reads with more than 5% N (ambiguous base) content, resulting in clean reads suitable for subsequent analysis.
The clean reads were aligned to the reference genome using HISAT2 software, generating mapped reads suitable for subsequent analysis.
FeatureCounts was used to calculate the number of reads mapped to each gene, and the FPKM values for each gene were calculated based on gene length.
Differential expression analysis of genes between groups was performed using DESeq2, with a default threshold for selecting differentially expressed genes set as |log2FC| > 1 and Padj < 0.05.
Assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was extracted using pre-chilled TRNzol reagent (TIANGEN, DP424), followed by the manufacturer's protocol. RNA concentration was determined using the Nanodrop ND-2000 (Thermo Scientific, USA). RNA integrity was checked by Agilent Bioanalyzer 4150 (AgilentTechnologies, CA, USA). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following manufacturer's protocols.

treatment_protocol: we extracted primary cells from lung tissues of naturally aged C57/6J mice at 3 months and 24 months of age. Subsequently, flow cytometry was employed to sort CD45- CD31- CD326+ MHCII+ cells, which represent AT2 cells.

value: lung

value: primary cell

tag: genotype

value: WT

value: natural aging


title: Human Sperm 16

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

country: Germany

institute: Helmholtz Zentrum München

description: Human sperm (BMI 20.3)

data_processing:
After preliminary quality check, single read sequences were analyzed with sports 1.1. The adapter sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) was trimmed with Cutadapt built in the pipeline and sequences with the length of 15-45 nucleotides were further processed. Using human genome version hg19 and allowed mismatch number set to 2, sports 1.1 mapped reads to small RNA subtypes. After joining sequences from all samples into a common count matrix, filter was applied to exclude sequences with no reads  in more than 80 % of samples. Samples were analyzed based on BMI variation. Sequence-based differential expression analysis (DEA) was performed using DESeq2 addressing BMI as a continuous variable.
hg19
Table files for annotation information for every unique sequence and reads number of each major smallrna biotype for every samples.

source_name: Sperm

extract_protocol:
Human Spermatozoa were purified by centrifuging through a 50% gradient of Puresperm (Nidacon International AB). Total RNA was extracted from spermatozoa with trizol-chloroform phase separation method followed by precipitation and wash steps with 100% and 70% ethanol. RNA purity, integrity and quality was examined by Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
Sequencing libraries were prepared using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA) with 100-120 ng RNA as a total input.

value: Sperm


title: Human Sperm 17

description: Human sperm (BMI 23.5)


title: Human Sperm 18

description: Human sperm (BMI 25.4)


title: M24-2


title: 8M_CO_3


title: Human Sperm 14

description: Human sperm (BMI 31.7)


title: M24-1


title: RT, Replicate 3, scRNAseq

description: SeekOne Kit


title: M3-3


title: NT, Control, scRNAseq

description: SeekOne Kit

value: Mock


title: Human Sperm 13

description: Human sperm (BMI 20.8)


title: Human Sperm 12

description: Human sperm (BMI 21.9)


title: Human Sperm 15

description: Human sperm (BMI 21.8)


title: M3-2


title: Human Sperm 11

description: Human sperm (BMI 21)


title: Human Sperm 10

description: Human sperm (BMI 22.7)


title: M3-1


title: Sample 19_Bulk Lung IFNARKO IL1R1KO.Inf rep4

city: Chicago

first: Shabaana

last: Khader

state: Illinois

address: 920 East 58th Street

institute: The University of Chicago

data_processing:
RNA-seq data were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software (GTAC MGI)
The read count data of each gene were generated using featureCounts from Rsubread package
Assembly: mm10
Supplementary files format and content: tab-delimited text file contain raw read counts

source_name: Lung

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen).Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases

value: Lung

value: IFNAR-/- IL1R1-/-

tag: infected strain

value: DS Mtb HN878 st. 6

tag: timepoint

value: 14 days post infection


title: Human Sperm 9

description: Human sperm (BMI 25.4)


title: Sample 18_Bulk Lung IFNARKO IL1R1KO.Inf rep3


title: RT, Replicate 1, scRNAseq

description: SeekOne Kit


title: Human Sperm 19

description: Human sperm (BMI 26.6)


title: Sample 16_Bulk Lung IFNARKO IL1R1KO.Inf rep1


title: Human Sperm 8

description: Human sperm (BMI 21)


title: Human Sperm 7

description: Human sperm (BMI 19.7)


title: Human Sperm 6

description: Human sperm (BMI 22.5)


title: Sample 14_Bulk Lung IL1R1KO.Inf rep4


title: Sample 12_Bulk Lung IL1R1KO.Inf rep2


title: Human Sperm 5

description: Human sperm (BMI 25.7)


title: Human Sperm 3

description: Human sperm (BMI 26)


title: Human Sperm 2

description: Human sperm (BMI 30.8)


title: Human Sperm 1

description: Human sperm (BMI 19.8)


title: Sample 13_Bulk Lung IL1R1KO.Inf rep3


title: 137536

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

data_processing:
STAR alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: read count

source_name: Skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

value: Skin

value: Fibroblasts

tag: patient

value: TNF-A

tag: disease state

value: Control


title: Sample 9_Bulk Lung IFNARKO.Inf rep4

value: IFNAR-/-


title: 137538

value: IFNG


title: Sample 6_Bulk Lung IFNARKO.Inf rep1


title: 137537

value: IFNA


title: 137529

value: NoStim


title: 137535

value: TGF-B


title: Sample 5_Bulk Lung B6.Inf rep5

value: wt


title: Sample 17_Bulk Lung IFNARKO IL1R1KO.Inf rep2


title: Sample 3_Bulk Lung B6.Inf rep3


title: 137525


title: 137526


title: Sample 4_Bulk Lung B6.Inf rep4


title: Sample 1_Bulk Lung B6.Inf rep1


title: Human Sperm 4

description: Human sperm (BMI 25.7)


title: 137524


title: Sample 8_Bulk Lung IFNARKO.Inf rep3


title: Sample 15_Bulk Lung IL1R1KO.Inf rep5


title: Sample 7_Bulk Lung IFNARKO.Inf rep2


title: 137517


title: Sample 11_Bulk Lung IL1R1KO.Inf rep1


title: Sample 21_Bulk Lung IFNARKO IL1R1KO rep4

value: DR Mtb H445Y HN14 st. 2

value: 17 days post infection


title: Sample 20_Bulk Lung IFNARKO IL1R1KO rep3

value: 16 days post infection


title: 997-CD-9


title: 997-CD-7


title: 997-CD-46


title: Sample 18_Bulk Lung IFNARKO IL1R1KO rep1

value: Lung


title: Sample 17_Bulk Lung IL1R1KO rep6


title: 997-CD-45


title: 997-CD-44


title: Sample 2_Bulk Lung B6.Inf rep2


title: Sample 13_Bulk Lung IL1R1KO rep3


title: Sample 14_Bulk Lung IL1R1KO rep4


title: 137523


title: 997-CD-8


title: Sample 19_Bulk Lung IFNARKO IL1R1KO rep2

value: IFNAR-/- IL1R1-/-

value: 15 days post infection


title: Sample 12_Bulk Lung IL1R1KO rep2

value: 14 days post infection


title: 997-CD-37

value: Skin


title: Sample 10_Bulk Lung IFNARKO rep5


title: Sample 15_Bulk Lung IL1R1KO rep5


title: 997-CD-34

value: Fibroblasts


title: Sample 8_Bulk Lung IFNARKO rep3


title: 997-CD-31


title: 997-CD-43


title: 997-CD-33


title: 997-CD-32

value: TNF-A


title: Sample 7_Bulk Lung IFNARKO rep2


title: Sample 6_Bulk Lung IFNARKO rep1


title: Sample 9_Bulk Lung IFNARKO rep4


title: Sample 5_Bulk Lung B6 rep5


title: 997-CD-22

value: Control


title: Sample 3_Bulk Lung B6 rep3


title: 997-CD-25


title: 8992-RP-0012

city: Frederick

first: Himanshu

last: Goel

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Homo sapiens (108) transcriptome downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Assembly: Homo sapiens (version 108)
Supplementary files format and content: tab-delimited text files, including abundance measurements

source_name: Liver

extract_protocol:
Total RNA was isolated from all human liver samples obtained from Sekisui XenoTech.These RNA samples were submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for quantity and quality check before sequencing.
VUMC successfully identified and purchased from a supplier, Sekisui XenoTech, these 5 collections (lots) of pooled plateable cryopreserved human hepatocytes with 3 lots composed of cells derived from 10 different donors per lot and 2 lots derived from 5 different donors per lot. Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: in vitro hepatocytes

value: Liver

tag: duration

tag: dose

value: High (12 mM Thioacetamide)


title: Sample 4_Bulk Lung B6 rep4


title: Sample 11_Bulk Lung IL1R1KO rep1


title: 997-CD-1

value: NoStim


title: 997-CD-21

value: IFNA


title: Sample 2_Bulk Lung B6 rep2

value: wt


title: 997-CD-13


title: 997-CD-19

value: TGF-B


title: Skin-KO

city: Durham

first: Jennifer

middle: Yunyan

last: Zhang

state: NC

address: 3 Genome Ct, rm4130

department: Dermatology

institute: Duke University

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of Skin-WT  and Skin-KO Tumor , using 10X Cellranger v6.1.2 with default parameters.
Assembly: Mm10-2020-A
Supplementary files format and content: Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary files format and content: Barcode sequences that correspond to column indices in matrix.mtx.
Supplementary files format and content: Gene names that correspond to row indices in matrix.mtx.

source_name: Skin-KO

growth_protocol: 8-weeks old mice

extract_protocol: Skin samples were cut into 1-2 mm pieces, digested by Liberase TM (Roche; Cat# 05401119001) for 30 minutes in a 37C incubator, followed by further digestion with 0.05% Trypsin at 37 C for 10 minutes and red blood cell lysis.

treatment_protocol: Mice received 4-hydroxytamoxifen (1mg/mL; 40uL per treatment) or 100% Ethanol (40uL per treatment) topically dropwise onto a section of dorsal skin.

value: UBE2N-KO skin cells

value: 1 mg/ml 4-hydroxytamoxifen in 100% Ethanol applied every 48 hours for a total of 4 treatments

value: 8 weeks

tag: sample collection

value: 15 days after 1st 4-OHT treatment


title: 997-CD-10

value: IFNG


title: Skin-WT

source_name: Skin-WT

value: WT skin cells

value: 100% Ethanol applied every 48 hours for a total of 4 treatments

value: 15 days after 1st vehicle treatment


title: 796-CD-8

value: Skin

value: Fibroblasts

value: TNF-A


title: 997-CD-20

value: Control


title: L19

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

data_processing:
Illumina bcl2fastq was used for conversion into Fastq files.
Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.7.2) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools  (1.7) (Li et al. 2009).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
Raw reads and Fragments Per Kilobase per Million mapped reads (RPKM) were calculated using HOMER (v4.11) (Heinz et al. 2010)
Assembly: mm10
Supplementary files format and content: bigWig and tab-delimited text files include raw read counts and FPKM values for each Sample.

molecule: polyA RNA

growth_protocol: Male C57BL/6J (10 weeks old) were purchased from SLC (Hamamatsu, Japan). Mice was housed separately in individual cages (170 × 350 × 145 mm) with a 120-mm diameter running wheel (SANKO, Osaka, Japan) in light-shield mouse housing boxes (1800 × 360 × 520 mm) at the room temperature of 25.0 ± 1.5 ºC with food and water available ad libitum. The light intensity was set at approximately 200 lx within the cages. The mice were entrained to a 12:12-h light-dark cycle with an 8:00–20:00 light period for 2 weeks and then housed in the constant darkness (DD) for 2 weeks.

extract_protocol:
Mouse livers were homogenized in TRIzol reagent (Thermo Fischer Scientific). Total RNA was extracted using RNeasy column (QIAGEN) according to the manufacturer’s instructions.
Poly(A)-enriched stranded RNA sequencing was carried out using TruSeq stranded mRNA kit by Macrogen Japan on Illumina NovaSeq 6000 with 101-bp paired-end reads.

treatment_protocol: After DD condition, mice were returned to normal light condition (8:00 to 20:00) and then divided into two groups of light-schedule conditions: LD-condition (light–dark condition with an 8:00–20:00 light period, n=19) and ADV-condition (8-h phase advance once every 4 days, n=23). Tissue sampling was done from 9:30 to 18:00 in 47 weeks after chronic jet lag condition when ADV mice were in the same light-dark cycle as LD mice with an 8:00–20:00 light period.

value: Liver

value: male

value: Wild-type

value: LD


title: L18


title: 796-CD-9

value: IFNA


title: 796-CD-7

value: TGF-B


title: L17


title: L14


title: 796-CD-43


title: 796-CD-45


title: L15


title: L13


title: 796-CD-44


title: L12


title: 796-CD-46


title: 796-CD-34


title: L11


title: 796-CD-37

value: NoStim


title: 796-CD-33


title: 796-CD-32


title: Sample 1_Bulk Lung B6 rep1

value: Lung

value: wt

value: DR Mtb H445Y HN14 st. 2

value: 14 days post infection


title: 796-CD-31


title: L09


title: L10


title: L07


title: 796-CD-25


title: 796-CD-22

value: IFNG


title: L06


title: L05


title: 796-CD-21


title: L04


title: 796-CD-20


title: 796-CD-1


title: L02


title: 796-CD-19


title: L03


title: L01


title: 796-CD-13


title: 796-CD-10


title: A22

value: ADV


title: L08


title: A23


title: 739-CD-9

value: Skin


title: A21


title: A20


title: 739-CD-8

value: Fibroblasts


title: 739-CD-43


title: 739-CD-44

value: TNF-A


title: A18


title: A16


title: A19


title: A17


title: 739-CD-45

value: Control


title: 739-CD-37


title: A13

value: Liver


title: 739-CD-33


title: A14

value: male


title: 739-CD-34


title: A12

value: Wild-type


title: A15


title: A11


title: A10


title: 739-CD-31


title: 739-CD-46


title: 739-CD-7


title: 739-CD-22


title: A09


title: 739-CD-32


title: 739-CD-21


title: 739-CD-20


title: A06


title: A07


title: A05


title: 739-CD-10


title: A04


title: 739-CD-19


title: 739-CD-1


title: A03


title: A01


title: 739-CD-13


title: 3070-CD-7

value: Lupus


title: A02


title: 3070-CD-32


title: 3070-CD-33

value: IFNA


title: 3070-CD-34


title: hippocampus,CORT,Bio rep 5

city: Shanghai

first: Guanhao

last: Wang

address: Siping Road

institute: Tongji University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < WT1,WT2,WT3,CORT1,CORT2,CORT3> samples of homo sapiens was sequenced run with Illumina Novaseq TM 6000 sequence platform.
The raw paire-end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. Transcript abundances were quantified using RSEM software tool.
Assembly: Mus_musculus GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared with 1μg of total RNA using TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA).

value: brain

value: cortisone


title: hippocampus,CORT,Bio rep 4


title: 739-CD-25

value: NoStim


title: hippocampus,CORT,Bio rep 3


title: 3070-CD-31

value: TGF-B


title: A08


title: 3070-CD-25


title: hippocampus,veh,Bio rep 3

value: vehicle


title: hippocampus,veh,Bio rep 2


title: 3070-CD-1


title: 3070-CD-13


title: hippocampus,veh,Bio rep 1


title: HFD-130

data_processing:
Data quality was assessed with MultiQC (version 1.11). Paired-end RNA-seq reads were processed with trim_galore (version 0.6.6) to remove Nextera adaptors. Reads were subsequently mapped to the mouse genome (GRCm38),  using STAR (version  2.7.10a). We then used featurecounts to calculate counts for the total transcripts. Differential expression analysis was performed using DESeq2 package. Uniquely mapped reads were extracted from the BAM files using samtools. These files were used to estimate mtDNA heteroplasmy using MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) a R package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: Early 2-cell embryo

extract_protocol:
Early 2 cell embryo have been procsessed according to the SMARTseq2 protocol
Single early 2-cell embryos from the HFD and LFD groups were collected for RNA sequencing. A cDNA library was generated according to the Smart-seq2 protocol (Picelli et al., 2014) without any modifications.

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: HFD-127


title: 3070-CD-10

value: Skin

value: IFNG


title: HFD-128


title: HFD-123


title: 2902-CD-13

value: Fibroblasts


title: HFD-126


title: 2876-CD-9


title: HFD-119


title: 2902-CD-19


title: 2876-CD-8

value: TNF-A


title: HFD-104


title: 2876-CD-1


title: 2876-CD-7


title: HFD-101


title: HFD-102


title: HFD-103


title: 2738-CD-9

value: Psoriasis


title: 2738-CD-7


title: HFD-100


title: 2738-CD-16


title: HFD-99


title: HFD-98


title: 2738-CD-1


title: 2738-CD-10


title: FP5 0.005ng 2

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description:
replicate 2
VAN6259-32

data_processing:
Fastq files were mapped using STAR mapping software
Readcounts were assigned using FeatureCounts
Assembly: hg38
Supplementary files format and content: readcounts_raw

source_name: colon

extract_protocol:
Qiagen RNeasy kit
Ilumina stranded polyA

value: colon

value: Organoid


title: 2902-CD-22

value: Lupus


title: FP5 0ng 2

description:
replicate 2
VAN6259-31


title: HFD-97


title: 2736-CD-9

value: IFNA


title: CJ R505C 0.005ng 2

description:
replicate 2
VAN6259-28


title: 2736-CD-7


title: HFD-118


title: CJ R505C 0ng 2

description:
replicate 2
VAN6259-27


title: FP5 0.005ng 1

description:
replicate 1
VAN6259-30


title: 2876-CD-10


title: CJ R505C 0.005ng 1

description:
replicate 1
VAN6259-26


title: 2736-CD-1


title: CJ R505C 0ng 1

description:
replicate 1
VAN6259-25


title: CJ wt 0.005ng 2

description:
replicate 2
VAN6259-24

value: wt


title: HFD-83


title: HFD-73


title: 2736-CD-14


title: CJ wt 0ng 2

description:
replicate 2
VAN6259-23


title: CJ wt 0ng 1

description:
replicate 1
VAN6259-21


title: CJ wt 0.005ng 1

description:
replicate 1
VAN6259-22


title: HFD-72


title: 2696-CD-9


title: HFD-70


title: 2696-CD-8


title: A. fumigatus Af293 peptone DFP and H2O2 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A. fumigatus Af293 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
FeatureCounts 2.0.0, (Liao et al. 2014) was used to generate read counts and RPKM values.
Assembly: A_fumigatus_Af293_version_s03-m05-r17_chromosomes.fasta.gz (from from http://www.aspergillusgenome.org/download/sequence/A_fumigatus_Af293/current); A_fumigatus_Af293_version_s03-m05-r17_features_with_chromosome_sequences.gff.gz (from http://www.aspergillusgenome.org/download/gff/A_fumigatus_Af293)
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: Barratt’s minimal broth (100 mL in 500 mL Erlenmeyer flask) supplemented with 5 g/L yeast extract and inoculated with 1x108 conidia was incubated in a rotary shaker at 37 °C, 220 rpm (approx. 3.7 Hz) for 17 h.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.
RNA-seq (single read, 75 bp)

treatment_protocol: Mycelia from 4 × 100 mL of these exponential growth phase cultures were transferred into 12 × 100 mL fresh minimal broth containing 1.52 g/L KH2PO4, 0.52 g/L MgSO4 4H2O and 0.52 g/L KCl (pH 6.5) and 20 g/L glucose, 4 g/L casein peptone (glucose + peptone cultures) as carbon/energy source. These cultures were supplemented with either 0.1 v/v% Barratt’s trace element solution (“iron supplemented” cultures) or 0.1 v/v% iron free Barratt’s trace element solution and 1 mM deferiprone (“DFP treated” or “iron limited” cultures) as iron chelator. Cultures were incubated for 8 h at 37 °C and 220 rpm, then some of them were treated with 75 mM H2O2 and samples were taken for RNA isolation 1 h after oxidative stress treatment. The whole experiment was repeated with minimal broth containing only 4 g/L casein peptone (“peptone”) (instead of 20 g/L glucose and 4 g/L casein peptone).

value: mycelium

value: Af293 reference strain

value: peptone DFP and H2O2


title: HFD-68


title: FP5 0ng 1

description:
replicate 1
VAN6259-29


title: HFD-91


title: 2696-CD-7

value: TGF-B


title: HFD-67

value: Early 2-cell embryo


title: A. fumigatus Af293 peptone DFP 3

value: peptone DFP


title: A. fumigatus Af293 peptone DFP 2


title: A. fumigatus Af293 peptone DFP and H2O2 1


title: A. fumigatus Af293 peptone DFP and H2O2 2


title: HFD-66

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: 2696-CD-10

value: Skin

value: IFNG


title: A. fumigatus Af293 peptone H2O2 2

value: peptone H2O2


title: 2696-CD-1

value: Fibroblasts

value: NoStim

value: Psoriasis


title: A. fumigatus Af293 peptone H2O2 1


title: A. fumigatus Af293 peptone untreated 2

value: peptone untreated


title: HFD-62


title: 2695-CD-8

value: TNF-A


title: A. fumigatus Af293 peptone untreated 1


title: 2695-CD-7


title: A. fumigatus Af293 glucose+peptone DFP and H2O2 2

value: glucose+peptone DFP and H2O2


title: HFD-61


title: A. fumigatus Af293 peptone H2O2 3

value: mycelium


title: HFD-60


title: A. fumigatus Af293 glucose+peptone DFP and H2O2 1

value: Af293 reference strain


title: 2695-CD-10


title: A. fumigatus Af293 peptone DFP 1


title: A. fumigatus Af293 glucose+peptone DFP 2

value: glucose+peptone DFP


title: HFD-65


title: 2694-CD-9

value: IFNA


title: A. fumigatus Af293 glucose+peptone DFP 1


title: HFD-58

value: Early 2-cell embryo


title: HFD-57


title: 2694-CD-8


title: HFD-21


title: A. fumigatus Af293 glucose+peptone H2O2 3

value: glucose+peptone H2O2


title: A. fumigatus Af293 peptone untreated 3


title: 2695-CD-9


title: A. fumigatus Af293 glucose+peptone H2O2 1


title: A. fumigatus Af293 glucose+peptone H2O2 2


title: HFD-12

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: 2694-CD-7

value: TGF-B


title: A. fumigatus Af293 glucose+peptone untreated 3

value: glucose+peptone untreated


title: 2694-CD-13

value: Skin


title: A. fumigatus Af293 glucose+peptone untreated 1


title: A. fumigatus Af293 glucose+peptone untreated 2


title: HFD-1

value: High Fat Diet


title: 2694-CD-10

value: Fibroblasts

value: IFNG


title: LoowFD-82

value: Low Fat Diet


title: A. fumigatus Af293 glucose+peptone DFP 3


title: IBA group, Subject 4

city: New Haven

first: Viktor

last: Feketa

state: Connecticut

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University School of Medicine

data_processing:
Raw sequencing reads were processed using 10X CellRanger v.6.1.2 (10X Genomics, Pleasanton, CA).
Custom genome reference for thirteen-lined ground squirrel (Ictidomys tridecemlineatus) was built based on the reference genome sequence and annotation obtained from the Ensembl project (www.ensembl.org (6) Release 101; all files accessed on 11/20/2020)
The gene annotation was filtered to include only protein-coding genes using cellranger mkgtf. 10X CellRanger was used to obtain transcript read counts for each cell barcode, filtered for cell barcodes called as cells based on the default parameters.
Read count matrix was further processed using R 4.2.1, RStudio 2022.02.3, and Seurat 4.1.1 (7). Non-descriptive ground squirrel gene symbols (i.e. those starting with “ENSSTOG…”) were replaced with gene symbols of mouse homolog genes, using the homolog conversion table from Ensembl. Initial set of cells/barcodes was further filtered to include only those with >= 500 features/cells, >= UMIs/cells, and <= 10% of mitochondrial genes (defined as those with gene symbol starting with “MT-“). This resulted in ~11,000-20,000 cells/sample included in the dataset for further analysis, with the sequencing depth of ~70-100k reads/cell.
Read counts were processed according to the standard Seurat analysis workflow, including normalization, identification of variable features, scaling, PCA, clustering and visualization using UMAP plots. Graphs report normalized gene expression values.
Assembly: SpeTri2.0 (GCA_000236235.1)
Supplementary files format and content: Each processed file for each sample is a tar.gz package of the "filtered_feature_bc_matrix" folder from the output of the 10X cellranger count run. Each folder contains the feature-barcode matrix in the MEX format, containing the number of UMIs associated with every feature (rows) and barcode (columns), and gzipped .tsv files with feature and barcode sequences.

organism: Ictidomys tridecemlineatus

source_name: Arcuate nucleus of hypothalamus/Median eminence

growth_protocol: All experimental procedures were performed in compliance with the Institutional Animal Care and Use Committee of Yale University (protocol 2021-11497). Thirteen-lined ground squirrels (Ictidomys tridecemlineatus; age 0.5 – 3 years) of both sexes were single housed in temperature- and humidity-controlled facilities at Yale University. All squirrels were implanted with an interscapular temperature transponder (IPTT-300, BMDS).

extract_protocol:
Primary neurons were isolated from the arcuate nucleus of hypothalamus and median eminence following a published protocol (Vazirani et al. 2013 JOVE) with modification (n = 3). Animals were euthanized by isoflurane inhalation overdose followed by cardiac perfusion with brain perfusion solution (containing in mM: 196 sucrose, 2.5 KCl, 28 NaHCO3, 1.25 NaH2PO4, 7 Glucose, 1 Sodium Ascorbate, 0.5 CaCl2, 7 MgCl2, 3 Sodium Pyruvate, oxygenated with 95% O2/5% CO2, osmolarity adjusted to 300 mOsm with sucrose, pH adjusted to 7.4). The brain was dissected and slices were cut on a vibratome (Leica, VT1200). A brain slice containing the ARC and ME were identified by the presence of the third ventricle and separation of the optic chiasm. Three successive 600-µm slices containing the ARC were collected. The area around the third ventricle was microdissected from the brain slices using a micro-scalpel (Fine Science Tools, 10055-12). Tissue was digested in Hibernate A medium (custom formulation with 2.5 mM glucose and osmolarity adjusted to 280 mOsm, BrainBits) supplemented with 1 mM lactic acid (Sigma, L1750), 0.5 mM GlutaMAX (ThermoFisher, 35050061) and 2% B27 minus insulin (ThermoFisher, A1895601) containing 20 U/ml papain (Worthington Biochemical Corporation, LS003124) in a shaking water bath at 34°C for 30 min and dissociated by mechanical trituration through the tips of glass Pasteur pipettes with decreasing diameter (0.9 mm, 0.7 mm, 0.5 mm, 0.3 mm). Cell suspension was centrifuged over 8% bovine serum albumin (Sigma, A9418-5G) layer. Supernatant was removed leaving ~50 µl of suspension. Cell suspension was resuspended in 950 µl of Hibernate A medium (same formulation as above) and centrifuged at 300 rcf for 5 min. Supernatant was removed, leaving ~50 µl of cell suspension, which was gently mixed with a glass pipette and stored on ice. A 10 µl aliquot of cell suspension was mixed with 10 µl of Trypan Blue stain, loaded into a hemocytometer, and used to assess cell concentration and viability.
Cell suspension was processed according to the 10X Genomics library preparation protocol at the Center for Genome Analysis/Keck Biotechnology Resource Laboratory at Yale University. Single cell suspension in RT Master Mix was loaded on the Single Cell G Chip and partitioned with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). The volume of cell suspension for loading was calculated based on cell concentration to capture 10,000 cells. Upon dissolution of the Gel Beads in a GEM, the primers were released and mixed with cell lysate and Master Mix. Incubation of the GEMs produced barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) was added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Sequencing libraries were sequenced on an Illumina NovaSeq instrument with 150 bp reads according to the manufacturer's instructions at the depth of ~1.1-1.4 billion reads/sample.

treatment_protocol: During the active season (May – August), squirrels were kept at 20°C under a 12 hour:12 hour light:dark cycle at 40 – 60% humidity and maintained on a diet of dog food (IAMS) supplemented with sunflower seeds, superworms, and fresh vegetables (celery and carrots) with ad libitum access to water.  During hibernation (September – April), hypothermic squirrels (body temperature ~20 °C) were moved to 4°C at 40 – 60% humidity under constant darkness, without access to food or water. In this study, “active” squirrels were those with a constant core body temperature (CBT) of 37°C during the active season. “IBA” squirrels were those who had undergone at least one bout of hypothermic torpor during the hibernation season, but had achieved a CBT of > 32°C for ≥ 60 minutes, or ≥ 20 minutes for the central thyroid hormone experiments.

value: WT

tag: group

value: Inter-bout arousal (IBA)


title: IBA group, Subject 1A

value: Arcuate nucleus of hypothalamus/Median eminence


title: Active group, Subject 3

value: Active


title: 2528-CD-20

value: TNF-A

value: Lupus


title: Active group, Subject 2


title: 2528-CD-13

value: NoStim


title: LoowFD-74

value: Early 2-cell embryo


title: LoowFD-73


title: 2463-CD-22


title: LoowFD-62


title: Active group, Subject 1


title: LoowFD-60


title: 2463-CD-20


title: 2463-CD-21

value: IFNA


title: IBA group, Subject 3


title: LoowFD-61

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: LoowFD-57


title: 2463-CD-19

value: TGF-B


title: LoowFD-55


title: 2389-CD-7


title: 2389-CD-9


title: LoowFD-51


title: Caco2 cell line, Reverse (Withdrawal treatment), Replicate 3

type: RNA

city: Chapel Hill

first: Yanguang

last: Cao

state: North Carolina

address: 301 Pharmacy Ln

institute: UNC Chapel Hill

description: Caco2, Reverse (Withdrawal treatment) cells, replicate 3

hyb_protocol: Processed cDNA was then hybridized to the Human HT Clariom S 24-peg plate arrays, washed, stained.

scan_protocol: Scanned by the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

label: biotin

label_protocol: Briefly, the GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA (250 ng). Then the cDNA was fragmented and labeled with the kit and was used to prepare a hybridization cocktail with the GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Thermo Fisher).

growth_protocol: LIM1215 cells were cultured in RPMI 1640 medium with L-glutamine, supplemented with 10% FBS, 1 μg/ml hydrocortisone, 1 μg/ml human insulin, 100 U/mL penicillin-streptomycin. SW48 cells were cultured in complete medium: RPMI 1640 medium with L-glutamine, supplemented with 10% FBS and 100U/mL penicillin-streptomycin. Caco-2 cells were cultured with Eagle's MEM, supplemented with 20% FBS and 100 U/mL penicillin-streptomycin.

extract_protocol: RNA was then isolated from cell pellets using RNeasy Plus Mini Kit (QIAGEN) following the instructions.

treatment_protocol: Parental human CRC cell lines cultured from single clone were seeded overnight in 10 cm dish at 1000000 cells per dish. The following day, 1000000 NK-CD16 cells with 1 μg/ml cetuximab (anti-EGFR) were added for ADCC challenge.

value: Human colorectal cancer cell

value: Reverse (Withdrawal treatment)


title: Caco2 cell line, Resistant, Replicate 3

description: Caco2 resistant cells, replicate 3

data_processing: GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

value: Resistant


title: Caco2 cell line, Reverse (Withdrawal treatment), Replicate 2

description: Caco2, Reverse (Withdrawal treatment) cells, replicate 2


title: 2389-CD-1

value: Skin

value: Fibroblasts


title: LoowFD-49

value: Low Fat Diet


title: Caco2 cell line, Reverse (Withdrawal treatment), Replicate 1

description: Caco2, Reverse (Withdrawal treatment) cells, replicate 1


title: Caco2 cell line, Resistant, Replicate 2

description: Caco2 resistant cells, replicate 2


title: Caco2 cell line, Parental, Replicate 3

description: Caco2 parental cells, replicate 3

value: Parental


title: Caco2 cell line, Parental, Replicate 1

description: Caco2 parental cells, replicate 1


title: Caco2 cell line, Resistant, Replicate 1

description: Caco2 resistant cells, replicate 1


title: SW48 cell line, Reverse (Withdrawal treatment), Replicate 3

description: SW48, Reverse (Withdrawal treatment) cells, replicate 3


title: SW48 cell line, Reverse (Withdrawal treatment), Replicate 2

description: SW48, Reverse (Withdrawal treatment) cells, replicate 2


title: 2389-CD-10

value: IFNG


title: LoowFD-47


title: SW48 cell line, Resistant, Replicate 3

description: SW48 resistant cells, replicate 3


title: LoowFD-46


title: 2336-CD-8


title: SW48 cell line, Reverse (Withdrawal treatment), Replicate 1

description: SW48, Reverse (Withdrawal treatment) cells, replicate 1


title: LoowFD-44


title: 2336-CD-1


title: 2336-CD-13


title: LoowFD-41


title: SW48 cell line, Parental, Replicate 3

description: SW48 parental cells, replicate 3


title: LoowFD-40


title: Caco2 cell line, Parental, Replicate 2

description: Caco2 parental cells, replicate 2


title: SW48 cell line, Parental, Replicate 2

description: SW48 parental cells, replicate 2


title: LIM1215 cell line, Reverse (Withdrawal treatment), Replicate 3

description: Lim1215, Reverse (Withdrawal treatment) cells, replicate 3


title: 2235-CD-9


title: SW48 cell line, Resistant, Replicate 1

description: SW48 resistant cells, replicate 1


title: LoowFD-37


title: 2235-CD-8


title: LoowFD-36


title: 2235-CD-1


title: 2336-CD-10


title: 2235-CD-16


title: U2OS cells, VEGFA site 2 replicate 2

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

data_processing:
Instructions as in the TTISS-seq manuscript (https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30143-X)
- Open in a web browser the site http://BrowserGenome.org - Click the “Map deep sequencing data” tab
- Under point 2 click “Browse” to choose the human genome file “hg38.2bit” on your hard drive (download from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit) - Under point 3 click “Browse” to choose all un-compressed FASTQ files to be analyzed - Under point 4, enter the filter values 0 bp, TTATCCTCCTCGCCCTTGCTCACAAC - Under point 5 enter forward mapping start = 26 bp - Under point 6 enter forward mapping length = 25 bp - Under point 7 enter reverse mapping length = 15 bp - Under point 8 enter max forward/reverse span = 1000 bp
- Click “Start mapping,” which takes about one hour per ten million reads - When all data has been processed, click “Save all” on bottom right to save mapping data files - Click on the “Process” tab, then “Remove single read noise” and “Enforce antisense-overlap reads” for basic noise reduction and off-target site identification - Click “Export peak list” to save a list of detected cleavage sites, which can be opened in a text or spreadsheet editor for further analysis
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: tab separated file with genome position, local sequence, number of double-strand breaks

source_name: derived from sarcoma of the tibia

extract_protocol:
gDNA was extracted with DNeasy® Blood & Tissue kit
Library prep was performerd as described in the TTISS-seq manuscript: https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30143-X
TTISS-seq

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: WT

value: digested with VEGFA site 2 sgRNA


title: U2OS cells, VEGFA site 2 replicate 1


title: LoowFD-34


title: 2235-CD-10

value: Lupus


title: U2OS cells, non-target library replicate 2

value: undigested


title: LoowFD-33

value: Early 2-cell embryo


title: 2175-CD-8

value: TNF-A


title: k562wt_stag_2

data_processing:
CRISPResso version 2.2.12 called with Pooled mode and the following parameters: --min_reads_to_use_region 100 --skip_failed –ignore_substitutions
Supplementary files format and content: tab-separated file with the number of occurrences of aligned sequences for each amplicon. Fields represent: Aligned_Sequence, Reference_Sequence, Unedited, n_deleted, n_inserted, n_mutated, #Reads, %Reads

source_name: human immortalised myelogenous leukemia cell line

extract_protocol:
gDNA was extracted using the Qiagen Dneasy Blood & Tissue kit
The region containing the gRNA sequence and 79nt portion of the allele was amplified using the Fwd_pool and Rev_pool primers (Supplementary Table 12) with the NEBNext® Ultra™ II Q5® Master Mix (New England Biosciences #M0544) with the following program: 98oC for 60s, 24 loops of 98oC for 10s and 72oC for 30s, followed by a final extension at 72oC for 2 minutes. The PCR product was purified using 0.9x volumes of DNA AMPure XP beads (Beckman Coulter A63987) and eluted in nuclease-free water. The entire product of clean-up was used for a second PCR round with indexed primers (Supplementary Table 12) with the following conditions: 98oC for 60s, 13 loops of 98oC for 10s, 67oC for 10s and 72oC for 20s, followed by a final extension at 72oC for 2 minutes. The indexed libraries were pooled and the band corresponding to the amplicon size (464 base pairs) was excised from a 2% agarose gel, purified and sequenced in paired-end mode (2x150bp) in a NextSeq2000 sequencer with 40% PhiX spike-in
Amplicon-seq

value: For lentiviral packaging of gRNA-target libraries, the blunt or staggered library was independently co-transfected with the two packaging plasmids and the supernatants were pooled and concentrated 50-100-fold. Packaging and transduction were performed. Briefly, we produced the viruses by co-transfection of 293T cells with each of the four library pools and two helper plasmids, psPAx2 and pMD2.g encoding the VSV-G envelope and the lentiviral gag-pol genes, respectively. We harvested the lentiviral vector-containing supernatant twice, at ~42 and 66 hours post-transfection and concentrated it by using Lenti-X-concentrator (Takara, 631232).


title: LoowFD-35

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: LoowFD-32


title: 2175-CD-7

value: TGF-B


title: SW48 cell line, Parental, Replicate 1

description: SW48 parental cells, replicate 1

value: Human colorectal cancer cell


title: LoowFD-30


title: k562wt_blunt_2

value: human immortalised myelogenous leukemia cell line


title: k562wt_blunt_1


title: 2175-CD-17

value: Skin

value: Fibroblasts

value: IFNA


title: U2OS cells, non-target library replicate 1


title: LoowFD-29

value: Low Fat Diet


title: k562cas9_stag_1


title: 2175-CD-13

value: NoStim


title: k562cas9_blunt_2


title: LoowFD-26


title: k562wt_stag_1


title: k562cas9_blunt_1


title: 2154-CD-21

value: Control


title: helawt_stag_2

source_name: derived from cervical cancer cells

value: derived from cervical cancer cells

value: HeLa

value: WT


title: helawt_stag_1


title: 2154-CD-19


title: k562cas9_stag_2


title: helawt_blunt_2


title: HFD-79

value: High Fat Diet


title: LIM1215 cell line, Reverse (Withdrawal treatment), Replicate 1

description: Lim1215, Reverse (Withdrawal treatment) cells, replicate 1

value: Reverse (Withdrawal treatment)


title: A. fumigatus Af293 glucose+peptone DFP and H2O2 3

value: mycelium

value: Af293 reference strain

value: glucose+peptone DFP and H2O2


title: 2154-CD-13


title: helawt_blunt_1

value: For lentiviral packaging of gRNA-target libraries, the blunt or staggered library was independently co-transfected with the two packaging plasmids and the supernatants were pooled and concentrated 50-100-fold. Packaging and transduction were performed. Briefly, we produced the viruses by co-transfection of 293T cells with each of the four library pools and two helper plasmids, psPAx2 and pMD2.g encoding the VSV-G envelope and the lentiviral gag-pol genes, respectively. We harvested the lentiviral vector-containing supernatant twice, at ~42 and 66 hours post-transfection and concentrated it by using Lenti-X-concentrator (Takara, 631232).


title: helacas9_stag_2


title: HFD-78

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: HFD-77


title: helacas9_stag_1


title: 212-CD-8

value: Skin

value: TNF-A


title: HFD-80


title: helacas9_blunt_1


title: 2154-CD-10

value: Fibroblasts

value: IFNG


title: helacas9_blunt_2


title: RPL32P3_2

description: In-vitro digested with RPL32P3 gRNA and Cas12

data_processing:
NGSpipe2go Breaktag pipeline (https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/master/pipelines/breaktag)
Reads without breaktag adaptor were filtered out
Reads with breaktag adaptor were mapped using BWA v0.7.15 with “bwa mem” on genome assembly hg38 and filtered out reads with mapping quality below 60
Deduplication of mapped reads based on unique molecular identifiers (UMIs)
Mapped read ends are summed up and reported in BED format
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: Breaktag signal as a proxy of double strand breaks counts, a a standard 6-columns BED containing the “chromosome | start | end | name | breaktag_signal | strand”

source_name: derived from human embryonic kidney cells

extract_protocol:
gDNA was extracted with DNeasy® Blood & Tissue kit
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O. Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip
BreakTag

value: Human Embryonic Kidney

value: digested with RPL32P3 gRNA and Cas12


title: SW48 cell line, Resistant, Replicate 2

description: SW48 resistant cells, replicate 2

value: Human colorectal cancer cell

value: Resistant


title: RPL32P3_1

value: derived from human embryonic kidney cells

value: WT


title: LIM1215 cell line, Reverse (Withdrawal treatment), Replicate 2

description: Lim1215, Reverse (Withdrawal treatment) cells, replicate 2

value: Reverse (Withdrawal treatment)


title: 212-CD-7

value: TGF-B

value: Control


title: NT_2

description: undigested

value: undigested


title: HFD-74

value: High Fat Diet


title: HFD-76

value: Early 2-cell embryo


title: 212-CD-49

value: IFNA


title: EMX_2

description: In-vitro digested with EMX gRNA and Cas12

value: digested with EMX gRNA and Cas12


title: NT_1

description: undigested


title: LIM1215 cell line, Resistant, Replicate 1

description: Lim1215 resistant cells, replicate 1


title: LIM1215 cell line, Resistant, Replicate 3

description: Lim1215 resistant cells, replicate 3


title: EMX_1


title: LIM1215 cell line, Resistant, Replicate 2

description: Lim1215 resistant cells, replicate 2


title: HFD-64

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: DNMT1_2

description: In-vitro digested with DNMT1 gRNA and Cas12

value: digested with DNMT1 gRNA and Cas12


title: LIM1215 cell line, Parental, Replicate 2

description: Lim1215 parental cells, replicate 2

value: Parental


title: 212-CD-46

value: Skin

value: Fibroblasts

value: IFNG


title: 212-CD-45


title: CCR5_2

description: In-vitro digested with CCR5 gRNA and Cas12

value: Human Embryonic Kidney

value: digested with CCR5 gRNA and Cas12


title: DNMT1_1

value: derived from human embryonic kidney cells

value: WT


title: HFD-63


title: LIM1215 cell line, Parental, Replicate 3

description: Lim1215 parental cells, replicate 3

value: Human colorectal cancer cell


title: CLO-R50-6

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the SST-RMA algorism using a Transcriptome analyses console (Affymetrix) software.

source_name: exposure group

label_protocol: The total RNA (250 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmentated and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Imidiately after the rotarod test, brains were dissected under the anesthesia.

extract_protocol: Total RNA was extracted from brain tissue using a NucleoSpin®  RNA plus isolation kit (MACHEREY-NAGEL, GmbH).  The quality of total RNA was analyzed using a Bioanalyzer 2100 (Agilent Technologies, Inc.). The RNA samples with RIN (RNA integrity number) values > 7.0 were considered acceptable.

treatment_protocol: Mice were orally administrated 50 mg/kg/day of CLO or vehicle for 4 days of rotarod test.

value: 50 mg/kg/day of CLO for 4 days

value: male

value: 10 weeks

value: cerebellum

tag: strain


title: CLO-R50-7

tag: Sex


title: Ctrl-R0-7

source_name: control group

value: vehicle for 4 days

tag: tissue


title: CCR5_1

tag: cell type


title: 212-CD-44

tag: treatment

value: TNF-A

value: Control


title: HepG2 cells, LZ3, undigested

source_name: derived from liver cancer

value: derived from liver cancer

tag: cell line

value: human liver cancer cell line

value: undigested


title: LIM1215 cell line, Parental, Replicate 1

description: Lim1215 parental cells, replicate 1

value: Parental


title: HFD-56

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: HFD-71


title: HFD-55


title: HepG2 cells, LZ3, Pool of sgRNAs no. nine

value: digested with pool one of sgRNAs complexed with LZ3cas9- HiPlex1 library


title: 212-CD-34

value: Skin

value: Fibroblasts

value: IFNG


title: HFD-54


title: HepG2 cells, LZ3, Pool of sgRNAs no. seven

value: WT


title: HepG2 cells, LZ3, Pool of sgRNAs no. eight


title: 212-CD-43

value: TGF-B


title: HepG2 cells, LZ3, Pool of sgRNAs no. six


title: HFD-53


title: HepG2 cells, LZ3, Pool of sgRNAs no. five


title: HFD-52


title: HepG2 cells, LZ3, Pool of sgRNAs no. four


title: 212-CD-32


title: HepG2 cells, LZ3, Pool of sgRNAs no. three


title: HFD-51


title: HepG2 cells, LZ3, Pool of sgRNAs no. one


title: 212-CD-31


title: HFD-50


title: 2nd run BT30_VEGFAsite1_POOLVEGFAsite1

data_processing:
Raw reads were trimmed using cutadapt with the folloring parameters: -a AGATCGGAAGAGC -a GAAGATCGGAAGAGC -a AACGAGATCGGAAGAGC -a GCGATAGATCGGAAGAGC -A AGATCGGAAGAGC -A CTAGATCGGAAGAGC -A CAAGAGATCGGAAGAGC -A CAATGAAGATCGGAAGAGC
Trimmed reads were mapped with BWA mem version 0.7.17 to the Hsapiens GRCh38 primary assembly as a reference genome (downloaded from UCSC as of Mar 14 2016)
Abra2 2.23 was used to recalibrate indels
Indels where called using Abra2’s Cadabra with a paired normal-tumor approach using the non-targeted libraries as normals.
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: tab-separated file showing the number of modifications for positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the number of reads with insertions (row 2), insertions_left (row 3), deletions (row 4), substitutions (row 5) and the sum of all modifications (row 6). Additionally, the last row shows the number of reads aligned.

extract_protocol:
DNA was extracted using the DNEasy Blood & Tissue kit
AmpliSeq (Illumina) primer pairs panel was designed for off-targets nominated with either/or: BreakTag and TTISS-seq. Library prep was performed using the AmpliSeq™ Library PLUS (Illumina 20019101) following the manufacturer's instruction

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with sgRNA targeting REF alelle


title: 2nd run BT30_NT_POOLVEGFAsite2


title: HepG2 cells, LZ3, Pool of sgRNAs no. two


title: 212-CD-22

value: Control


title: 212-CD-21

value: IFNA


title: 2nd run BT30_FANCF_POOLFANCF


title: HFD-48


title: 212-CD-25

value: NoStim


title: 212-CD-33


title: 2nd run BT23_VEGFAsite2_POOLVEGFAsite2


title: HepG2 cells, LZ3, Pool of sgRNAs no. ten

value: derived from liver cancer

value: human liver cancer cell line


title: 2nd run BT30_NT_POOLFANCF

value: undigested


title: 2nd run BT23_NT_POOLVEGFAsite2


title: 2nd run BT23_VEGFAsite1_POOLVEGFAsite1


title: HFD-47

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: 212-CD-1


title: 212-CD-20

value: TNF-A


title: 212-CD-19

value: Skin


title: 2nd run BT23_FANCF_POOLFANCF


title: 2nd run BT30_VEGFAsite2_POOLVEGFAsite2


title: 2nd run BT23_NT_POOLFANCF


title: Ctrl-R0-9

value: vehicle for 4 days

value: male

value: 10 weeks

value: cerebellum


title: 2nd run BT23_NT_POOLVEGFAsite1

value: derived from sarcoma of the tibia

value: WT


title: HFD-44

value: High Fat Diet


title: BT30_VEGFAsite2_POOLVEGFAsite2

data_processing:
Raw reads were trimmed using cutadapt with the folloring parameters: -a AGATCGGAAGAGC -a GAAGATCGGAAGAGC -a AACGAGATCGGAAGAGC -a GCGATAGATCGGAAGAGC -A AGATCGGAAGAGC -A CTAGATCGGAAGAGC -A CAAGAGATCGGAAGAGC -A CAATGAAGATCGGAAGAGC
Trimmed reads were mapped with BWA mem version 0.7.17 to the Hsapiens GRCh38 primary assembly as a reference genome (downloaded from UCSC as of Mar 14 2016)
Abra2 2.23 was used to recalibrate indels
Indels where called using Abra2’s Cadabra with a paired normal-tumor approach using the non-targeted libraries as normals.
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: indels called in VCF format

extract_protocol:
DNA was extracted using the DNEasy Blood & Tissue kit
AmpliSeq (Illumina) primer pairs panel was designed for off-targets nominated with either/or: BreakTag and TTISS-seq. Library prep was performed using the AmpliSeq™ Library PLUS (Illumina 20019101) following the manufacturer's instruction
Amplicon-seq

value: sarcoma of the tibia

value: digested with sgRNA targeting REF alelle


title: 212-CD-13

value: Fibroblasts

value: NoStim

value: Control


title: 2nd run BT30_NT_POOLVEGFAsite1

value: undigested


title: BT30_VEGFAsite1_POOLVEGFAsite1


title: HFD-43

value: Early 2-cell embryo


title: BT30_NT_POOLVEGFAsite2


title: BT30_NT_POOLVEGFAsite1


title: 212-CD-10

value: IFNG


title: BT30_NT_POOLFANCF


title: 2123-CD-9

value: IFNA

value: Lupus


title: HFD-46

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: BT23_VEGFAsite2_POOLVEGFAsite2


title: 2123-CD-7

value: Skin

value: TGF-B


title: BT30_FANCF_POOLFANCF


title: BT23_NT_POOLVEGFAsite2


title: HFD-41


title: BT23_VEGFAsite1_POOLVEGFAsite1


title: HFD-40


title: 2123-CD-10


title: 2123-CD-8

value: TNF-A


title: P18_ref_8

data_processing:
CRISPResso version 2.2.12 called with following parameters: --amplicon_min_alignment_score 50 --quantification_window_size 10 --quantification_window_center -3 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --ignore_substitutions --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: TAR of tab-separated files showing the number of modifications for positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the number of reads with insertions (row 2), insertions_left (row 3), deletions (row 4), substitutions (row 5) and the sum of all modifications (row 6). Additionally, the last row shows the number of reads aligned.

source_name: Blood

extract_protocol:
The gDNA of lymphoblastoid cells nucleofected with RNPs was extracted 3 days after CRISPR delivery using the Qiagen Blood and Tissue Kit (Qiagen 69506) according to the manufacturer’s instructions.
Approximately 100ng of gDNA from each sample was used for locus amplification using the primers listed in Supplementary Table 8. Amplicon libraries were generated as described elsewhere 65 with the following modifications: a first round of amplification using the NEBNext UltraII Q5 Master Mix (M0544) was performed with 33 cycles. The amplified DNA was purified using a 1× volume of DNA AMPure XP beads (Beckman Coulter A63987) and the entire purified product was used for a second round of PCR with primers containing p5 and p7 sequences for Illumina sequencing (Supplementary Table 8). Amplicons were pooled and sequenced in a MiniSeq sequencer with the MiniSeq Mid Output Kit (Illumina FC-420-1004) in single-read mode and 150 cycles.
Amplicon-seq

value: Blood

value: B-Lymphocyte

value: Nucleofection of Cas9 and gRNA targeting the REF or ALT alelle


title: BT23_NT_POOLVEGFAsite1

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: WT


title: P18_ref_9


title: BT23_FANCF_POOLFANCF

value: digested with sgRNA targeting REF alelle


title: P18_ref_7


title: HFD-36

value: High Fat Diet


title: 2122-CD-9

data_processing:
STAR alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: read count

source_name: Skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

value: Fibroblasts


title: HFD-37

value: Early 2-cell embryo


title: P18_ref_5


title: 2122-CD-8


title: HFD-42


title: P18_ref_4


title: HFD-45


title: HFD-39


title: HFD-38


title: 2122-CD-7


title: P18_ref_3


title: P18_ref_1


title: P18_ref_6


title: LoowFD-95

value: Low Fat Diet


title: LoowFD-94


title: LoowFD-96


title: 2122-CD-1

value: NoStim


title: 2122-CD-10

value: IFNG

value: Lupus


title: P18_ref_12


title: P18_ref_11


title: 2121-CD-9

value: Skin

value: IFNA


title: P18_ref_10


title: 2121-CD-8

value: TNF-A


title: P18_alt_9

value: Blood


title: P18_alt_7

value: B-Lymphocyte


title: LoowFD-93

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: LoowFD-92


title: P18_alt_6

value: Nucleofection of Cas9 and gRNA targeting the REF or ALT alelle


title: P18_alt_8


title: 2121-CD-7

value: TGF-B


title: P18_alt_5

value: WT


title: 2121-CD-1


title: HFD-35


title: LoowFD-91


title: P18_alt_4


title: LoowFD-90


title: P18_alt_2


title: P18_alt_3


title: 2121-CD-15


title: LoowFD-87


title: 2099-CD-8


title: P17_ref_5


title: P17_ref_6


title: P18_alt_11


title: P17_ref_3


title: P18_alt_1


title: P18_ref_2


title: LoowFD-85


title: 2099-CD-9


title: P18_alt_12


title: P17_ref_2


title: 2099-CD-1


title: LoowFD-86


title: 2099-CD-7


title: LoowFD-84


title: BT23_NT_POOLFANCF

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: undigested


title: P17_alt_6


title: LoowFD-88

value: Early 2-cell embryo


title: 2099-CD-10

value: Fibroblasts


title: P17_alt_5


title: P17_alt_4


title: LoowFD-81

value: Low Fat Diet


title: 2098-CD-1

value: NoStim


title: P17_alt_3


title: P17_ref_4


title: P17_alt_2


title: P17_alt_1


title: LoowFD-80


title: LoowFD-79


title: EVs from aneuploid cleavage stage embryos, biol rep 3 [A3]

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.32)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts. Only reads mapped to exons were considered in the counting procedure for stromal cell samples (samples 1-28), while all the reads mapped somewhere on the transcripts or on the gene bodies were considered in the counting procedure for EVs samples (D3_35a, D3_35b, D3_35x and E1-5, A1-4 respectively).
Genomic features were annotated according to the Gencode basic annotations (Gencode version 28 for samples D3_35a, D3_35b, D3_35x; Gencode version 31 for all the other samples A1-4, E1-5, 1-28)
Assembly: UCSC hg38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Extracellular vesicles

extract_protocol:
EVs samples (D3_35a, D3_35b, D3_35x, E1-5, A1-4) were lysed directly using lysis buffer from the library preparation kit, RNA extraction from ESCs and dESCs untreated or treated with EVs (sample 1-28) was performed using the RNeasy Plus Micro kit (Qiagen)
cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan) for Evs samples (D3_35a, D3_35b, D3_35x, E1-5, A1-4), and using the Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, CA) for ESCs and dESCs untreated or treated sampes (samples 1-28)

tag: sample source

value: Embryo spent media

value: Extracellular vesicles

value: aneuploid

value: Culture media from n=35 cleavage stage embryos


title: 2085-CD-7

city: Ann Arbor

institute: University of Michigan

value: Skin

value: Lupus


title: LoowFD-78

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: EVs from euploid cleavage stage embryos, biol rep 5 [E5]

value: euploid


title: EVs from aneuploid cleavage stage embryos, biol rep 2 [A2]


title: P17_ref_1

value: Blood

value: B-Lymphocyte

value: Nucleofection of Cas9 and gRNA targeting the REF or ALT alelle


title: EVs from aneuploid cleavage stage embryos, biol rep 4 [A4]


title: 2085-CD-8

value: TNF-A


title: EVs from euploid cleavage stage embryos, biol rep 4 [E4]


title: EVs from euploid cleavage stage embryos , biol rep 3 [E3]


title: 2085-CD-10

value: IFNG


title: LoowFD-77

value: Early 2-cell embryo


title: LoowFD-83


title: EVs from euploid cleavage stage embryos, biol rep 2 [E2]


title: EVs from aneuploid cleavage stage embryos, biol rep 1 [A1]


title: 2085-CD-9

value: Fibroblasts

value: IFNA


title: 2084-CD-9


title: 2085-CD-1

value: NoStim


title: EVs from undiagnosed cleavage stage embryos, biol rep 2 [D3_35b]

value: Embryo spent media


title: LoowFD-72

value: Low Fat Diet


title: EVs from undiagnosed cleavage stage embryos, biol rep 3 [D3_35x]

value: Extracellular vesicles


title: EVs from euploid cleavage stage embryos, biol rep 1 [E1]

value: Culture media from n=35 cleavage stage embryos


title: LoowFD-71


title: S_AJ_ALT_pos18

data_processing:
CRISPResso version 2.2.12 called with following parameters: --amplicon_min_alignment_score 50 --quantification_window_size 10 --quantification_window_center -3 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --ignore_substitutions --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0
Supplementary files format and content: tab-separated file showing the number of modifications for positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the number of reads with insertions (row 2), insertions_left (row 3), deletions (row 4), substitutions (row 5) and the sum of all modifications (row 6). Additionally, the last row shows the number of reads aligned.
Library strategy: BreakTag

extract_protocol:
gDNA was obtained from Coriell
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O. Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip

value: WT

value: digested with sgRNA targeting ALT alelle


title: 2084-CD-8

value: Skin

value: Lupus


title: EVs from undiagnosed cleavage stage embryos, biol rep 1 [D3_35a]


title: 2084-CD-1


title: S_CH_REF_pos18

value: Blood

value: digested with sgRNA targeting REF alelle


title: S_CH_REF_pos17

value: B-Lymphocyte


title: M_AJ_ALT_pos17


title: LoowFD-69

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: 2070-CD-9


title: HEK293 cells, Pool of sgRNAs no. ten

data_processing:
library strategy: BreakTag
NGSpipe2go Breaktag pipeline (https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/master/pipelines/breaktag)
Reads without breaktag adaptor were filtered out
Reads with breaktag adaptor were mapped using BWA v0.7.15 with “bwa mem” on genome assembly hg38 and filtered out reads with mapping quality below 60
Deduplication of mapped reads based on unique molecular identifiers (UMIs)
Mapped read ends are summed up and reported in BED format
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: Breaktag signal as a proxy of double strand breaks counts, a a standard 6-columns BED containing the “chromosome | start | end | name | breaktag_signal | strand”

extract_protocol:
gDNA was extracted with DNeasy® Blood & Tissue kit
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O.  Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip

value: derived from sarcoma of the tibia

value: mmortalized human embryonic kidney cells

value: digested with pool ten sgRNAs - HiPlex3 library


title: 2070-CD-8

value: Fibroblasts

value: TNF-A


title: LoowFD-68

value: Early 2-cell embryo


title: HEK293 cells, Pool of sgRNAs no. nine

value: digested with pool nine sgRNAs - HiPlex3 library


title: LoowFD-76

value: Low Fat Diet


title: HEK293 cells, Pool of sgRNAs no. eight

value: digested with pool eight sgRNAs - HiPlex3 library


title: LoowFD-67


title: HEK293 cells, Pool of sgRNAs no. six

value: WT

value: digested with pool six sgRNAs - HiPlex3 library


title: HEK293 cells, Pool of sgRNAs no. seven

value: digested with pool seven sgRNAs - HiPlex3 library


title: 2070-CD-10

value: Skin

value: IFNG

value: Lupus


title: HEK293 cells, Pool of sgRNAs no. five

value: digested with pool five sgRNAs - HiPlex3 library


title: HFD-129

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: 2069-CD-9

value: IFNA

value: Control


title: HEK293 cells, Pool of sgRNAs no. three

value: derived from sarcoma of the tibia

value: mmortalized human embryonic kidney cells

value: digested with pool three sgRNAs - HiPlex3 library


title: LoowFD-70

value: Early 2-cell embryo


title: 2069-CD-7

value: Fibroblasts

value: TGF-B


title: HEK293 cells, Pool of sgRNAs no. two

value: WT

value: digested with pool two sgRNAs - HiPlex3 library


title: HEK293 cells, Pool of sgRNAs no. four

value: digested with pool four sgRNAs - HiPlex3 library


title: HFD-124


title: HFD-125


title: S_CH_REF_pos18

extract_protocol:
gDNA was obtained from Coriell
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O.  Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip

value: Blood

value: B-Lymphocyte

value: digested with HiPlex pool targeting REF alelle

tag: biomaterial provider


title: 2069-CD-1

value: Skin

value: NoStim


title: HFD-122

extract_protocol:
Early 2 cell embryo have been procsessed according to the SMARTseq2 protocol
Single early 2-cell embryos from the HFD and LFD groups were collected for RNA sequencing. A cDNA library was generated according to the Smart-seq2 protocol (Picelli et al., 2014) without any modifications.

tag: genotype

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: S_CH_REF_pos17


title: HFD-121


title: 2069-CD-10

value: IFNG

value: Control


title: HFD-120


title: S_AJ_REF_pos18


title: 1795-CD-8

value: TNF-A


title: 1795-CD-9

value: IFNA


title: S_AJ_REF_pos17


title: S_CH_ALT_pos18

value: digested with HiPlex pool targeting ALT alelle


title: S_CH_NT

value: undigested


title: S_CH_ALT_pos17


title: S_AJ_NT


title: HFD-115

value: Early 2-cell embryo


title: S_AJ_ALT_pos18

value: WT


title: 1795-CD-7

value: Fibroblasts

value: TGF-B


title: S_AJ_ALT_pos17

value: Blood


title: HFD-114


title: HFD-96


title: M_UM_REF_pos17

value: B-Lymphocyte


title: 1795-CD-30

value: Lupus


title: M_UM_ALT_pos18


title: P18_alt_10

value: Nucleofection of Cas9 and gRNA targeting the REF or ALT alelle


title: M_UM_REF_pos18

value: digested with HiPlex pool targeting REF alelle


title: 2070-CD-7

value: Skin


title: HFD-95

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: M_CH_REF_pos17


title: HFD-94


title: 1795-CD-27

value: IFNG

value: Control


title: 1795-CD-22


title: M_AJ_REF_pos18


title: HFD-93


title: M_UM_ALT_pos17


title: M_CH_ALT_pos17


title: M_AJ_ALT_pos18


title: 1774-CD-20

value: IFNA


title: 1795-CD-31


title: HFD-87


title: F_CH_REF_pos18


title: M_CH_ALT_pos18

value: digested with HiPlex pool targeting ALT alelle


title: 2123-CD-1

value: NoStim


title: M_AJ_ALT_pos17


title: HFD-85

value: Early 2-cell embryo


title: M_CH_REF_pos18

value: WT


title: F_CH_ALT_pos18


title: F_CH_REF_pos17


title: F_CH_ALT_pos17


title: HFD-84


title: 1774-CD-19

value: Fibroblasts

value: TNF-A


title: HFD-92


title: HEK293 cells, Pool of sgRNAs no. one

value: derived from sarcoma of the tibia

value: mmortalized human embryonic kidney cells

value: digested with pool one sgRNAs - HiPlex3 library


title: 1795-CD-20

value: Lupus


title: 1774-CD-10


title: M_AJ_REF_pos17

value: Blood

value: B-Lymphocyte

value: digested with HiPlex pool targeting REF alelle


title: F_AJ_REF_pos18


title: 1746-CD-9

value: Skin

value: PSLE


title: HFD-81

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: HFD-82


title: HepG2 cells, undigested

value: human liver cancer cell line

value: undigested


title: 1746-CD-17

value: IFNG


title: HepG2 cells, Pool of sgRNAs no. ten

value: WT

value: digested with pool ten of sgRNAs - HiPlex1 library


title: HFD-49

value: Early 2-cell embryo


title: F_AJ_ALT_pos17

value: digested with HiPlex pool targeting ALT alelle


title: HFD-33


title: HepG2 cells, Pool of sgRNAs no. eight

value: derived from sarcoma of the tibia

value: digested with pool eight gDNA


title: 1746-CD-13

value: Fibroblasts

value: NoStim


title: HepG2 cells, Pool of sgRNAs no. seven

value: digested with pool seven of sgRNAs - HiPlex1 library


title: HepG2 cells, Pool of sgRNAs no. nine

value: digested with pool nine of sgRNAs - HiPlex1 library


title: HepG2 cells, Pool of sgRNAs no. six

value: digested with pool six of sgRNAs - HiPlex1 library


title: HFD-29


title: HepG2 cells, Pool of sgRNAs no. five

value: digested with pool five of sgRNAs - HiPlex1 library


title: F_AJ_REF_pos17

value: Blood

value: B-Lymphocyte

value: digested with HiPlex pool targeting REF alelle


title: HepG2 cells, Pool of sgRNAs no. four

value: human liver cancer cell line

value: digested with pool four of sgRNAs - HiPlex1 library


title: F_AJ_ALT_pos18

value: WT


title: HFD-28

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: 1735-CD-1

value: Skin

value: Lupus


title: HFD-27

value: Early 2-cell embryo


title: HepG2 cells, Pool of sgRNAs no. two

value: derived from sarcoma of the tibia

value: digested with pool two of gRNAs - HiPlex1 library


title: HepG2 cells, Pool of sgRNAs no. three

value: digested with pool three of sgRNAs - HiPlex1 library


title: 1735-CD-14

value: Fibroblasts

value: IFNA


title: HepG2 cells, Pool of sgRNAs no. one

value: digested with pool one of sgRNAs - HiPlex1 library


title: HFD-23


title: PCCF_Sniper_pool9Chk

description: in vitro digested with Pool9 of HiPlex1 library

value: sarcoma of the tibia

value: digested with Sniper and Pool9 of HiPlex1 library sgRNA


title: 1774-CD-18

value: TGF-B


title: PPCF_LZ3_pool9Chk

value: digested with LZ3 and Pool9 of HiPlex1 library sgRNA


title: HFD-24


title: 1735-CD-13

value: TNF-A


title: 1712-CD-8

value: Control


title: 1735-CD-7


title: HFD-15

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: PCCF_evoCas9_pool9Chk

value: WT

value: digested with evoCas9 and Pool9 of HiPlex1 library sgRNA


title: IDT_HiFICas9_pool9Chk

value: digested with HiFICas9 and Pool9 of HiPlex1 library sgRNA


title: 1735-CD-15

value: Skin

value: IFNG

value: Lupus


title: HFD-14

value: Early 2-cell embryo

value: High Fat Diet


title: 1712-CD-7

value: Fibroblasts


title: 1712-CD-1

value: NoStim


title: PCCF_spCas9_pool9Chk

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with spCas9 and Pool9 of HiPlex1 library sgRNA


title: HFD-5


title: IDT_spcas9_pool9Chk

value: digested with spcas9 and Pool9 of HiPlex1 library sgRNA


title: 1712-CD-10


title: IDT_spcas9_NT

value: digested with spcas9 and no target sgRNA


title: HFD-4


title: PCCF_Sniper_NT

value: digested with Sniper and no target sgRNA


title: PPCF_LZ3_NT

value: digested with LZ3 and no target sgRNA


title: PCCF__xCas9_pool9Chk

value: WT

value: digested with xCas9 and Pool9 of HiPlex1 library sgRNA


title: HFD-3

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: PCCF_HypaCas9_NT

value: digested with HypaCas9 and no target sgRNA


title: 1681-CD-9

value: Skin

value: IFNA


title: LoowFD-104

value: Early 2-cell embryo

value: Low Fat Diet


title: PCCF_HypaCas9_pool9Chk

value: digested with HypaCas9 and Pool9 of HiPlex1 library sgRNA


title: 1681-CD-7

value: Fibroblasts

value: TGF-B

value: Lupus


title: LoowFD-103


title: IDT_HiFICas9_NT

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with HiFICas9 and no target sgRNA


title: PCCF_spCas9_NT

value: digested with spCas9 and no target sgRNA


title: 1681-CD-1

value: NoStim


title: LoowFD-102


title: 1681-CD-10

value: IFNG


title: DA neurons, Parkin_B554_P1

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

data_processing:
Reads were mapped to the mm10 mouse genome merged with eGFP and ERCC spike-in sequences using STAR v2.3.0 with default settings and filtered for uniquely mapping reads.
Read counts and RPKM per gene were computed using rpkmforgenes.py with default settings and Ensembl release 75 gene annotations with addition of the EGFP reporter sequence.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file containing number of mapped reads per gene for all samples.
Supplementary files format and content: A tab-delimited text file containing RPKM per gene for all samples.

source_name: midbrain

extract_protocol:
FACS
smart-seq2

treatment_protocol: Tamoxifen injection

value: midbrain

value: DA neurons

value: Parkin loxP/loxP; +/DatCreERT2

tag: facs population

value: mitoYFP-positive

value: Tamoxifen injection

tag: mouse id

tag: technical replicate

tag: time point

value: 40 weeks after tamoxifen injection

tag: sequencing year


title: mixed cells, Parkin_B554_N3

value: mixed cells

value: mitoYFP-negative


title: DA neurons, Parkin_B554_P2


title: DA neurons, Parkin_B554_P3


title: LoowFD-101

data_processing:
Data quality was assessed with MultiQC (version 1.11). Paired-end RNA-seq reads were processed with trim_galore (version 0.6.6) to remove Nextera adaptors. Reads were subsequently mapped to the mouse genome (GRCm38),  using STAR (version  2.7.10a). We then used featurecounts to calculate counts for the total transcripts. Differential expression analysis was performed using DESeq2 package. Uniquely mapped reads were extracted from the BAM files using samtools. These files were used to estimate mtDNA heteroplasmy using MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) a R package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each sample

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: PCCF__xCas9_NT

value: derived from sarcoma of the tibia

value: WT

value: digested with xCas9 and no target sgRNA


title: mixed cells, Parkin_B554_N2


title: 1544-CD-9

value: Skin

value: Fibroblasts

tag: patient

value: IFNA

tag: disease state

value: Control


title: DA neurons, Parkin_B549_P5

value: midbrain

value: DA neurons


title: DA neurons, Parkin_B549_P4

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-positive


title: LoowFD-100


title: 1544-CD-8

value: TNF-A


title: 1681-CD-8

value: Lupus


title: PCCF_evoCas9_NT

value: sarcoma of the tibia

value: digested with evoCas9 and no target sgRNA


title: DA neurons, Parkin_B549_P3

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection


title: LoowFD-99

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: DA neurons, Parkin_B549_P2


title: DA neurons, Parkin_B549_P1


title: LoowFD-97


title: 1544-CD-7

value: Skin

value: TGF-B


title: 1544-CD-13

value: Fibroblasts

value: NoStim


title: DA neurons, Parkin_2142_P2

value: midbrain

value: 5 weeks after tamoxifen injection


title: LoowFD-24


title: DA neurons, Parkin_2142_P3

value: DA neurons

value: Parkin loxP/loxP; +/DatCreERT2


title: DA neurons, Parkin_2142_P1

value: mitoYFP-positive


title: D103, miRNA-seq

city: Hangzhou

first: Jiahui

last: Liu

state: Zhejiang

address: 3333 Binsheng Rd

institute: Children's Hospital, Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match were further analyzed and annotated based on the reference genome. HISAT2 soft were used to map with reference genome.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: Rnor_6.0
Supplementary files format and content: TXT files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: proliferative zone of the acetabular cartilage

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Library preparation for mRNA sequencing: A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library preparation for miRNA sequencing: A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR(NEB, USA) folloing manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: DDH

tag: time

value: ten days after birth


title: LoowFD-23


title: 1544-CD-10

value: IFNG

value: Control


title: DA neurons, Parkin_2141_P4

value: Tamoxifen injection


title: LoowFD-21

value: Early 2-cell embryo


title: 1525-CD-8

value: TNF-A


title: D102, miRNA-seq

value: proliferative zone of the acetabular cartilage


title: mixed cells, Parkin_B554_N1

value: mixed cells

value: mitoYFP-negative

value: 40 weeks after tamoxifen injection


title: DA neurons, Parkin_2141_P2


title: N103, miRNA-seq

value: control


title: D101, miRNA-seq


title: 1525-CD-7

value: Skin

value: Fibroblasts

value: TGF-B


title: DA neurons, Parkin_2141_P1

value: midbrain

value: DA neurons

value: Parkin loxP/loxP; +/DatCreERT2

value: 5 weeks after tamoxifen injection


title: LoowFD-17

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: N102, miRNA-seq

value: ten days after birth


title: mixed cells, Parkin_2141_N3

value: Tamoxifen injection


title: 1525-CD-1

value: NoStim

value: Control


title: 1525-CD-10

value: IFNG


title: N101, miRNA-seq

value: proliferative zone of the acetabular cartilage


title: 1513-CD-9

value: IFNA


title: mixed cells, Parkin_2141_N2

value: mixed cells

value: mitoYFP-negative


title: 1513-CD-8

value: Skin

value: Fibroblasts

value: TNF-A


title: LoowFD-14

value: Early 2-cell embryo


title: LoowFD-16


title: LoowFD-15


title: 1525-CD-9


title: DA neurons, Parkin_2141_P3

value: midbrain

value: DA neurons

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-positive


title: LoowFD-19

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: 1513-CD-7

value: TGF-B


title: D53, miRNA-seq

value: DDH

value: five days after birth


title: D51, miRNA-seq

value: proliferative zone of the acetabular cartilage


title: DA neurons, Parkin_2083_P4

value: Tamoxifen injection

value: 5 weeks after tamoxifen injection


title: DA neurons, Parkin_2083_P5


title: 1513-CD-1

value: NoStim

value: Control


title: N53, miRNA-seq

value: control


title: LoowFD-11


title: LoowFD-12


title: DA neurons, Parkin_2083_P3


title: LoowFD-10


title: DA neurons, Parkin_2083_P2


title: 1377-CD-9

value: Skin

value: Fibroblasts

value: IFNA

value: PSLE


title: mixed cells, Parkin_2141_N1

value: midbrain

value: mixed cells

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-negative


title: LoowFD-9

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: N51, miRNA-seq

value: proliferative zone of the acetabular cartilage

value: five days after birth


title: D103, RNA-seq

value: DDH

value: ten days after birth


title: 1377-CD-8

value: TNF-A


title: D52, miRNA-seq


title: LoowFD-13


title: D102, RNA-seq


title: 1377-CD-7

value: TGF-B


title: LoowFD-6


title: LoowFD-7


title: DA neurons, Parkin_1659_P5

value: DA neurons

value: mitoYFP-positive

value: Tamoxifen injection

value: 5 weeks after tamoxifen injection


title: DA neurons, Parkin_1659_P4

value: midbrain


title: 1377-CD-49

value: Skin

value: Fibroblasts

value: IFNG

value: Lupus


title: D101, RNA-seq


title: DA neurons, Parkin_1659_P3

value: Parkin loxP/loxP; +/DatCreERT2


title: 1513-CD-10

value: Control


title: 1377-CD-46


title: LoowFD-3

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: N103, RNA-seq

value: proliferative zone of the acetabular cartilage

value: control

value: ten days after birth


title: N102, RNA-seq


title: LoowFD-5


title: DA neurons, Parkin_1659_P2

value: DA neurons


title: DA neurons, Parkin_1659_P1

value: mitoYFP-positive


title: LoowFD-2


title: DA neurons, Parkin_2083_P1

value: Tamoxifen injection


title: 1377-CD-45

value: IFNA


title: 1377-CD-44

value: TNF-A


title: N101, RNA-seq


title: HFD-113

value: High Fat Diet


title: 1377-CD-43

value: Skin

value: Fibroblasts

value: TGF-B


title: mixed cells, Parkin_1659_N5

value: midbrain

value: mixed cells

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-negative

value: 5 weeks after tamoxifen injection


title: mixed cells, Parkin_1659_N4