title: H3.1_cleavable_HIR_KO_2_I_myc


title: RR 7

status: Public on May 24 2023

type: SRA

city: Tromsø

first: Wei

last: Meng

address: MH bygget

department: Faculty of Health Sciences

country: Norway

institute: University of Tromsø

library_source: transcriptomic

data_processing: DESeq2 log normalization+1

molecule: total RNA

organism: Homo sapiens

source_name: mucosal biopsy

extract_protocol:
Total RNA was isolated using the Allprep DNA/ RNA Mini Kit from Qiagen(catalogue number 80204)
Whole transcriptome libraries of UC remission samples were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (catalogue number RS-122–2203).

tag: remission status

value: Relapsed

tag: remission duration

tag: tissue

value: mucosal biopsy


title: RR 9


title: RR 6


title: RBG25062_WT

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were mapped simultaneously to the Mus musculus genome (mm10) and the 92 ERCC sequences using STAR. FeatureCounts was used to count the number of reads mapped to each gene. Quality control was applied to exclude dead and dying cells as well as poor quality cells (using the parameters fGenes:Total > 12%, mit:mappedToGene < 20%, nNuclearReads > 150K, ercc:mapped < 20%). Data was pre-processed using the in-house pre-processing tool smqpp in Python analysed using Scanpy (1.7.1). Cells were normalised using the DESeq2 method and logged.
Assembly: mm10
Supplementary files format and content: a h5ad file that contains raw counts, metadata for each cell and gene annoataion information.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
To harvest mouse bone marrow cells, spine, femurs, tibiae and pelvic bones were crushed with a pestle and mortar in 3 mL PBS + 2% FBS. Further 3 mL PBS + 2% FCS were used to wash the bones and the resulting cell suspension was filtered through a 0.75 uM filter. Cells were pelleted and resuspended in 3 mL PBS + 2% FBS. Red cell lysis was performed using cold ammonium chloride (StemCell Technologies cat. no 07800). PBS 2% FCS was added to dilute the red cell lysis buffer during subsequent centrifugation at 4 oC.   For lineage depletion, EasySep™ Mouse Hematopoietic Progenitor Cell Enrichment Kit from StemCell Technologies (cat no. 19816A) was used according to the manufacturer’s instructions but avoiding the use of rat serum. Samples were transferred into 5 ml polystyrene (352058) FACS tubes and incubated with 10 µl/ml EasySep mouse hematopoietic progenitor cell isolation cocktail labelled with biotin. 40 µl/ml of EasySep™ Streptavidin RapidSpheres were added and allowed to bind on ice for 10 minutes. The samples were subsequently diluted to 2.5 ml using PBS + 2% FBS and placed in the EasyStep magnet (StemCell Technologies cat no. 18000) for 3 minutes at room temperature. After incubation, samples were transferred into new tubes, spun down, and resuspended in 100 ul PBS + 2% FCS.   For antibody staining, a master mix was prepared as indicated in table 2 and cell suspensions were incubated on ice, in the dark for 30 minutes. After staining, cells were washed, pelleted, and resuspended in 100 ul PBS + 2% FCS. Were necessary, streptavidin conjugated antibody was added in a second step. Samples were pelleted and resuspended to a final volume of 500 ul PBS + 2% FCS. We used single colour, unstained, and full panel controls that were made using pooled BM cells from all mice before lineage depletion.
Primary single cells (LSK cells – Lin-Sca1+ckit+) were FACS index sorted into lysis buffer (0.2% Triton X-100 (Sigma), RNase inhibitor (SUPERase, Thermofisher), and nuclease-free water (Thermo Fisher)). scRNA sequencing was performed according to the Smart-Seq2 protocol.
Libraries were prepared using the Illumina nextera XT DNA preparation kit and sequenced on the Illumina Hi-Seq 2500.

tag: cell type

value: Bone marrow

tag: genotype

value: WT


title: RR 12

value: Non-relapsed


title: H3.1_cleavable_HIR_KO_2_I_HA

city: Rehovot

first: Yonatan

last: Stelzer

state: Israel

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300
Assembly: mm10
Supplementary files format and content: bw

molecule: genomic DNA

source_name: mESC

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Crosslinked pellet was re-suspended in 20ul of cell lysis buffer (50mM Tris pH8.0, 150mM NaCl, 1%TritonX-100, 0.1%sodium deoxycholate, 5 mM CaCl2, EDTA-free protease inhibitor cocktail and incubated on ice for 15 minutes. Cells were centrifuged at 3000RPM for 10 minutes at 4°C. The supernatant was discarded, and pellet was re-suspended in 10ul of lysis buffer supplemented with 17.5 units of micrococcal nuclease (Worthington MNase, LS004798) and chilled on ice for 10 minutes. Samples were incubated at 37°C for 15 minutes. To stop reaction, 20mM EDTA was added and samples were vortexed and placed on ice for 30 minutes. Cell lysate was then centrifuged at max speed (20,000xg) for 10 minutes at 4°C and supernatant moved to a separate tube. Reaction volume was increased to 180ul with RIPA buffer (10mM Tris pH8.0, 140mM NaCl, 1mM EDTA, 0.1%SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail), and reaction was then split into two separate wells of 96-well LoBind Eppendorf plate. ~5ug of anti-HA (12CA5) and anti-myc (9E10) antibodies was added to the separate wells and incubated at 4°C for 2 hours with rotations. Both antibody stocks were the supernatant of the respective hybridoma cell cultures grown in miniPERM bioreactors in-house by the Weizmann Institute Core Facility Antibody Unit. All subsequent steps were carried out as described in (Gutin et al., 2018).
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: chip antibody

value: HA

value: mESC

tag: sensor type

value: cleavable H3.1

value: HIRA KO


title: RBG25061_WT


title: RR 5


title: RBG25060_WT


title: 185 – PN6

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin Biopsy

tag: serum ige (kiu/l)

tag: diagnosis

value: Prurigo Nodularis


title: 157 – PN5


title: H3.1_cleavable_HIR_KO_1_II_myc

value: myc


title: 155 – PN4


title: 154 – PN3


title: RR 3


title: RBG25059_WT


title: RR 4


title: RBG25058_WT


title: WB2 – PN2


title: H3.1_cleavable_HIR_KO_1_II_HA


title: RR 2


title: H3.1_cleavable_HIR_KO_1_I_myc


title: H3.1_cleavable_HIR_KO_1_I_HA


title: 132 – PN1


title: RR 1


title: RBG25057_DKO

value: Aldh2 & Fancd2 double knock-outs


title: RBG25056_DKO


title: H3.1_cleavable_II_myc


title: 96 – AP

value: Atopic Prurigo


title: HepG2_sh3_3

city: Nanjing

first: Anliang

last: Xia

address: 321 Zhongshan Road

institute: Nanjing University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: HepG2 cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HepG2 cells

value: HCC-derived cells

value: LINC01977 knockdown

tag: treatment

value: treated with shLINC01977 lentivirus for 72 hours


title: RBG25054_WT


title: H3.1_cleavable_I_myc


title: HepG2_sh3_2


title: HepG2_sh3_1


title: HepG2_shNC3

value: Control

value: treated with shNC lentivirus for 72 hours


title: H3.1_NC_I_myc

value: non-cleavable H3.1

value: WT


title: HepG2_shNC2


title: RBG25051_WT

value: Bone marrow


title: HepG2_shNC1


title: H2B_cleavable_II_myc

value: mESC

value: cleavable H2B


title: RBG25050_WT


title: H3.1_NC_I_HA

value: HA


title: RBG25049_WT


title: human CD8 T cells, BATF3, day 10 [BATF3-D3]

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

country: USA

institute: Duke University

description:
BATF3-D3
pSM65-IL-2-D3

data_processing:
Consistent quality validation using FastQC v0.11.2 (Babraham Institute).
Raw reads were trimmed to remove adapters and bases with average quality score (Q; Phred33) of 20 using a 4-bp sliding window (SlidingWindow:4:20) with Trimmomatic v0.32 (Bolger et al., 2014).
Trimmed reads were aligned to the primary assembly of the GRCh38 human reference genome using STAR v2.4.1a removing alignments containing noncanonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical).
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using featureCounts (v1.4.6-p4) with default settings.
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (single table) including TPM values and ENSEMBL IDs for all samples and genes in Gencode v22.

source_name: CD8 T cells

growth_protocol: CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicillin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).

extract_protocol:
RNA was harvested using Norgen's Total RNA Purification Kit.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences.

treatment_protocol:
Cells were activated with a 3:1 ratio of CD3/CD28 dynabeads to cells. 24 hours post-activation, cells were transduced with lentivirus encoding for either BATF3 or GFP.
T cells were maintained at a concentration of 1-2e6 per mL for 10 days before RNA-sequencing.

value: CD8 T cells

value: BATF3 overexpression

value: CD3/CD28 dynabead activation

tag: time point

value: day 10

tag: donor


title: human CD8 T cells, BATF3, day 10 [BATF3-D2]

description:
BATF3-D2
pSM65-IL-2-D2


title: H2B_cleavable_II_HA


title: Pancreas-Input DNA

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
Rubioseq pipeline was used to carry out the analysis:
Alignment performed using BWA aligner
Duplicates marked and removed using Picard
Normalization performed with MACS2
Peak-calling using MACS2 with --nomodel --extsize 200 --gsize mm
Genome_build: mm10
Supplementary_files_format_and_content: peak

source_name: Pancreas

extract_protocol:
Lysates were clarified from sonicated pancreas and NFIC-DNA complexes were isolated with antibody.
Libraries were prepared from purified DNA using "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7645), as per the manufacturer’s instructions. Briefly, DNA samples were processed through subsequent enzymatic treatments for fragmentation (5 min), end-repair, dA-tailing, and ligation to adapters Adapter-ligated libraries were amplified by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size was 350 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.

value: Pancreas

tag: strain

value: Mixed


title: RBG25055_DKO

value: Aldh2 & Fancd2 double knock-outs


title: H2B_cleavable_I_myc

value: myc


title: human CD8 T cells, BATF3, day 10 [BATF3-D1]

description:
BATF3-D1
pSM65-IL-2-D1


title: H3.1_cleavable_II_HA

value: cleavable H3.1


title: H2B_cleavable_I_HA


title: Pancreas-NFIC_rep2

value: NFIC (Bethyl ,A303-123A)


title: shPRMT6-2

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Typically, base call quality diminishes toward the end of a read. This is characteristic to first- and second-generation sequencing technologies (Sanger, Illumina, SOLiD, 454)
SOAPnuke, a filtering software independently developed by BGI, is used for filtering.
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts or in FPKM (fragments per thousand nucleotides per million mapped reads).
Assembly: hg19_ucsc
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell

growth_protocol: MDA-MB-231 cells were cultured in a humidified incubator equilibrated with 5% CO2 at 37 °C. The media (Dulbecco Modified Eagle Medium (DMEM)) was supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected and drug screende in MDA-MB-231 cells with shSCR or shPRMT6.


title: shPRMT6-3


title: shPRMT6-1


title: Pancreas-NFIC_rep3


title: H3.1_cleavable_I_HA


title: RBG25052_WT


title: human CD8 T cells, GFP control, day 10 [GFP-D3]

description:
GFP-D3
pSM7-IL-2-D3

value: GFP control


title: Pancreas-NFIC_rep1


title: shSCR-3


title: human CD8 T cells, GFP control, day 10 [GFP-D2]

description:
GFP-D2
pSM7-IL-2-D2


title: shSCR-2


title: H2B_NC_I_myc

data_processing:
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
Assembly: mm10
Supplementary files format and content: bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300

value: non-cleavable H2B


title: human CD8 T cells, GFP control, day 10 [GFP-D1]

description:
GFP-D1
pSM7-IL-2-D1


title: shSCR-1


title: TF CRISPRa screen donor 3, day 10

description:
CRISPRa_D3
polyA mRNA and gRNA
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: *.tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; MatrixMarket files are compatible with most single-cell RNA-seq software.

molecule: polyA RNA

extract_protocol:
Transduced T cells were sorted, counted, and resuspended at 1000 cells/uL. 33,300 cells were loaded into the 10x Chromium X for a targeted recovery of 20,000 cells per donor per treatment.
Libraries were constructed according to manufacturer instructions (single cell 5’ HT v2 protocol, 10x Genomics).

treatment_protocol:
CD8+CCR7+ T cells were activated with a 3:1 ratio of CD3/CD28 dynabeads to cells. 24 hours post-activation, cells were transduced with CRISPRa or CRISPRi TF gRNA lentivirus.
T cells were maintained at a concentration of 1-2e6 per mL for 10 days before scRNA-seq.

tag: grna library

value: CRISPRa TF


title: CT26 Phf8 KO2, INPUT

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

institute: East China Normal University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for INPUT and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: colorectal cancer

value: Phf8 knockout


title: Scrambled Antagomir, Day 8, sc3

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George st

department: Genetics/Internal Medicine

institute: Yale University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDUK
Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR
Read count extraction was performed using HTSEQ
Differential gene expression was performed using Deseq2
Assembly: GRCz10 /GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: CD34+CD43- hPSC-derived cells

extract_protocol:
RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and ~10ng were used to prepare libraries.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3′ mRNA-Seq kit following manufacturer's protocols.

value: CD34+CD43- hPSC-derived cells

value: endothelial cells

value: WT

value: scramble antagomir

tag: time

value: Day 8


title: TF CRISPRa screen donor 2, day 10

description:
CRISPRa_D2
polyA mRNA and gRNA
10x Genomics

value: CD8 T cells

value: day 10


title: PUB23

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
RNA seq analysis was performed using Nextpresso analysis pipeline. Graña, Osvaldo & Rubio-Camarillo, M & Fdez-Riverola, F & Pisano, David & Glez-Peña, Daniel. (2018). Nextpresso: Next Generation Sequencing Expression Analysis Pipeline. Current Bioinformatics. 13. 583-591. 10.2174/1574893612666170810153850.
Genome_build: mm10
Supplementary_files_format_and_content: HOMER.rawCount.txt : raw count matrix text file.
Supplementary_files_format_and_content: HOMER.rawTPM.txt : annotated normalized counts text file.
Supplementary_files_format_and_content: NFICwt.vs.NFICko.scatter.txt : differential expression analysis DESeq2 text file.

extract_protocol:
Total pancreatic RNA was isolated using guanidine thiocyanate, followed by acid phenol-chloroform extraction. 1µg of total RNA samples, each containing an equal amount of ERCC ExFold RNA Spike-In Mix 1 (Ambion 4456739), was used as provided by the user. Average sample RNA Integrity Number was 8.4 (range 7.8 - 9.2) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nfic_KO -/- (KO)

tag: age

value: 8-10 week-old mice


title: H2B_NC_I_HA

value: HA

value: mESC


title: Scrambled Antagomir, Day 8, sc2


title: CT26 con2, INPUT

value: control


title: PUB49

value: Nfic_KO +/+ (WT)


title: TF CRISPRa screen donor 1, day 10

description:
CRISPRa_D1
polyA mRNA and gRNA
10x Genomics


title: CT26 con1, INPUT


title: Scrambled Antagomir, Day 8, sc1


title: PUB48


title: CT26 Phf8 KO2, PHF8

value: anti-PHF8 (ab280887, abcam)


title: TF CRISPRi screen donor 3, day 10

description:
CRISPRi_D3
polyA mRNA and gRNA
10x Genomics

value: CRISPRi TF


title: miRNA 128  Antagomir, Day 8, miR2

value: miR-128 antagomiR


title: TF CRISPRi screen donor 2, day 10

description:
CRISPRi_D2
polyA mRNA and gRNA
10x Genomics


title: miRNA 128  Antagomir, Day 8, miR3


title: CT26 Phf8 KO1, PHF8

value: colorectal cancer

value: Phf8 knockout


title: PUB22


title: PUB33


title: TF CRISPRi screen donor 1, day 10

description:
CRISPRi_D1
polyA mRNA and gRNA
10x Genomics


title: miRNA 128  Antagomir, Day 8, miR1

value: CD34+CD43- hPSC-derived cells

value: endothelial cells


title: CT26 con2, PHF8


title: PUB38


title: PUB24


title: mtDNAwide_CoII_2plasmid_with HHR_pairID_46_repeat2 [Z9]

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38)
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Assembly: GRChm38
Supplementary files format and content: xlsx file with off target %, on target % and average coverage

source_name: NIH-3T3 cells

growth_protocol: Cells were cultured at 37 °C under 5 % (vol/vol) CO2 in complete Dulbecco's Modified Eagle Medium (DMEM) (4.5 g/L glucose 2 mM glutamine, 110 mg/ml sodium pyruvate), supplemented with 10% calf bovine serum with iron, 5% penicillin/streptomycin (all from Gibco) and 50 µg/ml uridine (Sigma, cn. U3750). The Atp6 animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse ear biopsies was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT

treatment_protocol: NIH/3T3 mouse cells plated in 6-well tissue culture plates at a confluency of 70% were transfected with 3200 ng of each monomer (L and H - see pairID), or 6400 ng of plasmid DNA when using Tandem architectures in a single plasmid (L + H), with 16 µl of FuGENE-HD (Promega), following manufacturer´s guidelines.

tag: ddcbe pair id used

tag: days after transfection

tag: target

value: mtDNA


title: CT26 Phf8 KO1, INPUT

tag: cell type


title: mtDNAwide_Cytb_2plasmid_with HHR_pairID_42_repeat2 [Z8]


title: CT26 con1, PHF8

tag: genotype


title: RCC4 cells, shMIRE_2

city: Hefei

first: Bingyan

last: Li

state: Anhui

address: Huangshan Road Shushan District

institute: University of Science and Technology of China

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: RCC4 cell line was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Sigma) supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: RCC4 cells were infected with shctrl or shMIRE lentiviruses.

value: epithelial cells

value: MIRE knockdown

value: shMIRE

value: Day 3


title: RCC4 cells, shMIRE_1


title: ANM_127

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description:
whole transcriptome sequencing
P127

data_processing:
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads were filtered from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads.
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 on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Then coding potential analysis was performed with CNCI, CPC, Pfam-sca, and phyloCSF, Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were candidate set of lncRNAs. Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cancer and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US) immediately following the manufacturer’s instructions.

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption


title: ANM_126

description:
whole transcriptome sequencing
P126


title: RCC4 cells, shControl_2

value: WT

value: shControl


title: mtDNAwide_Nd3_2plasmid_with HHR_pairID_32_repeat2 [Z7]


title: RCC4 cells, shControl_1


title: ATAC_CT26_IFNPhf8 KO_2

description: CT26 sgPhf8 treated with IFNγ, replicate2

data_processing:
All sequencing data were mapped onto the mm10 mouse genome assembly using bowtie2 (–very-sensitive). Low quality mapped  reads were removed using samtools (view –q 35) and only unique reads mapping to a single genomic location and strand were  kept.
We removed mitochondrial sequences using ‘grep –v ‘chrM’. Biological replicates were merged, and peaks were called using  dfilter  (with the settings: -bs = 100 –ks = 60 –refine)
BigWig files were produced using genomeCoverageBed from bedtools (scale = 107/ < each_sample’s_total_unique_reads > ) and then bedGraphToBigWig. Gene ontology and gene expression  measures were called by first collecting all TSSs within 10 kb of an ATAC-seq peak.  bedtools (scale = 107/ < each_sample’s_total_unique_reads > ) and then bedGraphToBigWig. Gene ontology and gene expression  measures were called by first collecting all TSSs within 10 kb of an ATAC-seq peak.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Control or Phf8 KO CT26 cells treated with or without 20 ng/mL IFN-γ for 24 hours were dissociated and 50,000 cells were washed twice in cold PBS at 4°C.
ATAC-seq libraries were prepared using the N248, Illumina Nextera Kit (Novoprotein, shanghai, China).  Cells were resuspended in 50 μL cell lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40) and incubated on ice for 5 min. Samples were then washed with 950 μL cold wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40, 0.1% Tween 20). Samples were centrifuged at 500 g for 5 min at 4°C and supernatant were removed. The transposase reaction was carried out by titurating in 50 μL per sample in TD Buffer (10 mM Tris-HCl, pH 8, 5 mM Magnesium Chloride) with 4 μL Transposase (N248, Illumina Nextera Kit, Novoprotein, shanghai, China), and incubated at 37°C for 30 min, and 10 μL of 100 mM EDTA was added. Then, samples were incubated at 55°C for 5 min and transferred to ice. Samples and DNA recovered using Tagment DNA extract beads (N245, Illumina Nextera Kit, Novoprotein). Libraries were generated by PCR in 50 μL reaction (35 μL sample, 10 μL 5 x AmpliMix, 2.5 μL of each custom Illumina primers at 10 μM). The PCR reaction followed 72 °C for 3 min, 98°C for 30 s, followed by 9 cycles of 98°C for 15 s, 60°C for 15 s, 72°C for 8 s, followed by 72°C for 2 min. DNA was recovered using DNA clean beads (N240, Illumina Nextera Kit, Novoprotein).

value: Phf8 knockdown

value: 20 ng/mL IFN-γ for 24 hours


title: ANM_125

description:
whole transcriptome sequencing
P125


title: ATAC_CT26_IFNPhf8 KO_1

description: CT26 sgPhf8 treated with IFNγ, replicate1


title: ANM_124

description:
whole transcriptome sequencing
P124


title: cro_11_BL_core_34

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

data_processing:
Final libraries were sequenced on a NovaSeq6000 S1 flowcell (illumina) as 50 paired-end reads
Raw bcl files were demultiplexed into fastq.gz files using bcl2fastq v2.20.0.422
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v 0.22.0 (--complexity_threshold 10 -Q -f 3 -F 3)
Trimmed sequence reads were mapped to GRCh38 STAR v2.7.10a with the default parameters for paired-end data
Read counts for each sample were produced with STAR v2.7.10a --quantMode GeneCounts option using the GRCh38.p13_rel40/gencode.v40.annotation.gtf gtf file. The column correspondent to Unstranded libraries was used for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts (unstranded) values for each sample

growth_protocol: After thawing, PBMCs were cultured in complete RPMI 1640 supplemented with 8% human serum. Short-term T cell lines were generated by PBMCs stimulation with 15-mer HBV peptides or HLA-A2-restricted peptides (1μM) in humidified atmosphere with 5% CO2 at 37C for 10 days

extract_protocol:
RNA was harvested using reagents provided in the SMART-Seq HT PLUS kit (Takara-Bio, Japan)
RNA libraries for RNA-seq were prepared using SMART-Seq HT PLUS kit (Takara-Bio, Japan) following manufacturer's protocols.

treatment_protocol: T cells were cultured in the presence/absence of b-Nicotinamide mononucleotide (NMN, 10, 100, 500 μM, Sigma). The CD38 inhibitor was tested at a concentration of 1 or 5 nM.

value: CD8 T cells

tag: disease state

value: chronic HBV infection

tag: sorted by

value: HBV-specific (core 18-27) HLA-A* 0201Dextramers

value: Untreated

value: ex vivo baseline

tag: patient

value: H


title: ATAC_CT26_IFNcon_2

description: CT26 cells treated with IFNγ , replicate2

tag: cell line

value: colorectal cancer

tag: treatment


title: ANM_123

description:
whole transcriptome sequencing
P123


title: ATAC_CT26_IFNcon_1

description: CT26 cells treated with IFNγ , replicate1


title: ATAC_CT26_Phf8 KO_2

description: CT26 sgPhf8, replicate2


title: ANM_122

description:
whole transcriptome sequencing
P122


title: cro_8_BL_pol_92

value: HBV-specific (pol 455-463) HLA-A* 0201Dextramers

value: G


title: mtDNAwide_CoII_2plasmid_with HHR_pairID_46_repeat1 [Z4]

value: mtDNA


title: ANM_121

description:
whole transcriptome sequencing
P121


title: mtDNAwide_Atp6_2plasmid_with HHR_pairID_50_repeat1 [Z5]


title: mtDNAwide_Cytb_2plasmid_with HHR_pairID_42_repeat1 [Z3]


title: ATAC_CT26_Phf8 KO_1

description: CT26 sgPhf8, replicate1


title: Atp6_mouse_CVBC3.1f_F1 [Z21]

source_name: Ear biopsy

value: around 3 weeks of age


title: cro_8_BL_core_90


title: ANM_120

description:
whole transcriptome sequencing
P120


title: Atp6_mouse_CVBC3.1e_F1 [Z20]


title: cro_7_BL_pol_263

value: F


title: ANM_119

description:
whole transcriptome sequencing
P119

value: Not Applicable


title: mtDNAwide_WT_2plasmid_with HHR_pairID__repeat2 [Z6]

value: empty


title: mtDNAwide_Nd3_2plasmid_with HHR_pairID_32_repeat1 [Z2]


title: cro_7_BL_core_260


title: Atp6_mouse_CVBC3.1d_F1 [Z19]


title: ANM_118

description:
whole transcriptome sequencing
P118


title: cro_6_BL_pol_202

value: E


title: CT26 Phf8 KO2_ input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: CT26 Phf8 knockout cell

tag: chip antibody


title: CT26 Phf8 KO1_ input


title: cro_10_BL_core_240


title: Atp6_mouse_CVBC3.1c_F1 [Z18]


title: ANM_116

description:
whole transcriptome sequencing
P116


title: CT26 con2_input

value: CT26 cells


title: Atp6_mouse_CVBC3.1b_F1 [Z17]


title: ANM_117

description:
whole transcriptome sequencing
P117


title: CT26 Phf8 KO2_H4K20me1

value: anti-H4K20me1 (ab177188, abcam)


title: cro_3_BL_pol_72

value: CD8 T cells

value: chronic HBV infection

value: C


title: Atp6_mouse_CVBC3.1a_F1 [Z16]


title: mtDNAwide_Atp6_2plasmid_with HHR_pairID_50_repeat3 [Z15]


title: cro_4_BL_core_220

value: HBV-specific (core 18-27) HLA-A* 0201Dextramers

value: Untreated

value: ex vivo baseline

value: D


title: cro_3_BL_core_70


title: cro_6_BL_core_200


title: CT26 con1_input

value: colorectal cancer


title: ANM_115

description:
whole transcriptome sequencing
P115


title: ATAC_CT26_con_1

description: CT26 cells, replicate1

value: WT


title: ANM_114

description:
whole transcriptome sequencing
P114


title: mtDNAwide_CoII_2plasmid_with HHR_pairID_46_repeat3 [Z14]

value: mtDNA


title: ATAC_CT26_con_2

description: CT26 cells, replicate2


title: cro_2_BL_pol_172

value: HBV-specific (pol 455-463) HLA-A* 0201Dextramers

value: B


title: ANM_112

description:
whole transcriptome sequencing
P112

value: Not Applicable


title: mtDNAwide_Cytb_2plasmid_with HHR_pairID_42_repeat3 [Z13]


title: cro_2_BL_core_170


title: ANM_111

description:
whole transcriptome sequencing
P111


title: CT26 con2_H4K20me1


title: CT26 con1_H4K20me1


title: ANM_110

description:
whole transcriptome sequencing
P110


title: mtDNAwide_Nd3_2plasmid_with HHR_pairID_32_repeat3 [Z12]


title: cro_1_BL_pol_52

value: A


title: CT26 Phf8 KO2_H3K27me2

value: CT26 Phf8 knockout cell

value: anti-H3K27me2 (ab24684, abcam)


title: mtDNAwide_WT_2plasmid_with HHR_pairID__repeat3 [Z11]

value: empty


title: CTRL_ACU_4_pol_332

value: CD8 T cells

value: resolved HBV infection

value: N


title: ANM_105

description:
whole transcriptome sequencing
P105


title: ANM_107

description:
whole transcriptome sequencing
P107


title: CTRL_ACU_3_pol_322

value: M


title: ANM_113

description:
whole transcriptome sequencing
P113


title: ANM_109

description:
whole transcriptome sequencing
P109


title: CT26 Phf8 KO1_H3K27me2


title: CT26 con2_H3K27me2

value: CT26 cells


title: CTRL_ACU_4_core_330

value: HBV-specific (core 18-27) HLA-A* 0201Dextramers

value: Untreated

value: ex vivo baseline


title: CT26 Phf8 KO1_H4K20me1

value: colorectal cancer

value: anti-H4K20me1 (ab177188, abcam)


title: ANM_108

description:
whole transcriptome sequencing
P108


title: ANM_106

description:
whole transcriptome sequencing
P106


title: CTRL_ACU_3_core_320


title: mtDNAwide_Atp6_2plasmid_with HHR_pairID_50_repeat2 [Z10]

value: mtDNA


title: CT26 Phf8 KO2_H3K9me3


title: Screening_COII_pairID_46 [B9]


title: Screening_COI_pairID_44 [B8]


title: ANM_104

description:
whole transcriptome sequencing
P104


title: CTRL_ACU_2_pol_312

value: HBV-specific (pol 455-463) HLA-A* 0201Dextramers

value: L


title: CTRL_ACU_2_core_310


title: CT26 con1_H3K9me3


title: cro_1_BL_core_50

value: chronic HBV infection

value: A


title: mtDNAwide_WT_2plasmid_with HHR_pairID__repeat1 [Z1]


title: CT26 con2_H3K9me3


title: Screening_COI_pairID_43 [B7]


title: Screening_CYTB_pairID_42 [B6]


title: ANM_103

description:
whole transcriptome sequencing
P103

value: Not Applicable


title: Screening_ATP8_pairID_52 [C2]


title: CT26 con1_H3K27me2

value: anti-H3K27me2 (ab24684, abcam)


title: CT26 Phf8 KO1_H3K9me2

value: CT26 Phf8 knockout cell

value: anti-H3K9me2 (ab176882, abcam)


title: CT26 con2_H3K9me2


title: ANM_98

description:
whole transcriptome sequencing
P98


title: CTRL_ACU_1_core_300

value: CD8 T cells

value: resolved HBV infection

value: I


title: Screening_ND5_pairID_38 [B5]


title: CT26 Phf8 KO2_H3K9me2


title: Screening_ATP6_pairID_49 [B11]


title: A549 cells, shRALY_1

first: Kailiang

last: Zhao

address: Huangshan Road, Shushan district

growth_protocol: A549 cell line was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Sigma) supplemented with 10% FBS and antibiotics.

treatment_protocol: A549 cells were infected with shctrl or shRALY lentiviruses.

value: Alveolar basal epithelial cells

value: RALY knockdown

value: lentivirus infection

value: Day 2


title: ANM_102

description:
whole transcriptome sequencing
P102


title: Screening_ND4_pairID_33 [B2]


title: Screening_ND3_pairID_32 [B1]


title: CT26 con1_H3K9me2

value: colorectal cancer

value: CT26 cells


title: Screening_ATP6_pairID_50 [B12]

value: mtDNA


title: ANM_100

description:
whole transcriptome sequencing
P100


title: ANM_99

description:
whole transcriptome sequencing
P99


title: ANM_101

description:
whole transcriptome sequencing
P101


title: CT26 Phf8 KO1_H3K9me1

value: anti-H3K9me1 (ab9045, abcam)


title: CT26 Phf8 KO1_H3K9me3


title: CT26 Phf8 KO2_H3K9me1


title: donor2_Mock_1

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova

data_processing:
Read quality was verified using FastQC (v. 0.11.9). Raw reads were trimmed for adapters and low-quality tails (quality < Q20) with BBDuk (v. 38.92); moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp after trimming were removed.
Reads were subsequently aligned to the human reference genome (hg38) using STAR (v. 2.7.9a). Raw gene counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.6.4) and the GENCODE 38 basic gene annotation for hg38 reference genome.
Gene counts were normalized to counts per million mapped reads (CPM) using the edgeR R package (v. 3.34.1); only genes with a CPM greater than 1 in at least 2 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: CPM obtained using edgeR

source_name: erythroblasts (day 13) derived from SCD CD34+ HSPCs

growth_protocol: terminal erythroid differentiation day 13

extract_protocol:
RNA was harvested using Quick-RNA MicroPrep kit (Zymo Research). 35ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ovation Universal RNA-Seq System (NUGEN)

value: SCD (SS)

value: mock-transduced


title: ANM_97

description:
whole transcriptome sequencing
P97

value: Not Applicable


title: CT26 con2_H3K9me1


title: Screening_COIII_pairID_47 [B10]


title: ANM_96

description:
whole transcriptome sequencing
P96


title: CTRL_ACU_1_pol_302

value: HBV-specific (pol 455-463) HLA-A* 0201Dextramers

value: Untreated

value: ex vivo baseline


title: donor2_AS3_2

data_processing:
Read quality was verified using FastQC (v. 0.11.9). Raw reads were trimmed for adapters and low-quality tails (quality < Q20) with BBDuk (v. 38.92); moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp after trimming were removed.
Reads were subsequently aligned to the human reference genome (hg38) using STAR (v. 2.7.9a). Raw gene counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.6.4) and the GENCODE 38 basic gene annotation for hg38 reference genome.
Gene counts were normalized to counts per million mapped reads (CPM) using the edgeR R package (v. 3.34.1); only genes with a CPM greater than 1 in at least 2 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: CPM obtained using edgeR; the expression values of transgenes and vector-derived short RNAs can be inspected in the uploaded gene expression matrices looking for "transgene_AS3", " transgene_AS3m", and " immature_miR7m", respectively.

value: erythroblasts (day 13) derived from SCD CD34+ HSPCs

value: transduced with BetaAS3-LV


title: Screening_ND1_pairID_28 [A9]


title: A549 cells, shRALY_2


title: A549 cells, shControl_2

value: WT


title: A549 cells, shControl_1

value: Alveolar basal epithelial cells


title: Screening_ND1_pairID_27 [A8]


title: CT26 con1_H3K9me1


title: donor2_AS3_1


title: ANM_94

description:
whole transcriptome sequencing
P94


title: Screening_ND3_pairID_31 [A12]


title: donor2_AS3m_miRnt_2

value: transduced with BetaAS3m/miRnt-LV


title: donor2_AS3m_miRnt_1


title: ANM_93

description:
whole transcriptome sequencing
P93


title: Anti-PD1 antibody treatment GEX2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

source_name: Tumor

growth_protocol: 8-week-old WT mice were used

extract_protocol:
CD45- tumour cells, macrophages (CD45+CD64+), CD45+  non-macrophage immune cells (CD45+CD64-), and dendritic cells (CD45+CD64-CD11c+MHC-II+) were sorted from tumour tissues
Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)

treatment_protocol: Wild-type mice were challenged with MC38 colon adenocarcinoma cells, and treated with PBS or glutamine daily starting from day 5. Anti-PD-1 antibody or rat IgG2b isotype control was injected intraperitoneally three times on day 7, 10 and 13.

value: Sorted CD45- tumour cells, macrophages (CD45+CD64+), CD45+ non-macrophage immune cells (CD45+CD64-), and dendritic cells (CD45+CD64-CD11c+MHC-II+) in the tumour tissues

tag: strain

tag: agent

value: Anti-PD1 antibody


title: Glutamine and anti-PD1 antibody treatment GEX1

value: Glutamine and anti-PD1 antibody


title: Screening_ND2_pairID_30 [A11]


title: Glutamine and anti-PD1 antibody treatment GEX2


title: Screening_WT_pairID_empty1 [A1]

value: empty


title: Anti-PD1 antibody treatment GEX1


title: Screening_ND2_pairID_29 [A10]

value: mtDNA


title: donor2_AS3m_miRHBB_1

value: transduced with BetaAS3m/miR7m-LV


title: ANM_91

description:
whole transcriptome sequencing
P91


title: ANM_90

description:
whole transcriptome sequencing
P90


title: ANM_92

description:
whole transcriptome sequencing
P92


title: donor1_Mock_1

value: SCD (SS)


title: Glutamine treatment GEX2

value: Glutamine


title: ANM_89

description:
whole transcriptome sequencing
P89

value: Not Applicable


title: mtDNAwide_CoII_T2A_Stable_with HHR_pairID_46 [5F5]


title: donor1_AS3_1


title: ANM_88

description:
whole transcriptome sequencing
P88


title: Glutamine treatment GEX1


title: mtDNAwide_Cytb_T2A_Stable_with HHR_pairID_42 [5F4]


title: ANM_95

description:
whole transcriptome sequencing
P95


title: donor2_AS3m_miRHBB_2


title: ANM_87

description:
whole transcriptome sequencing
P87


title: PBS treatment GEX1

value: PBS


title: PBS treatment GEX2


title: Flcn KO GEX2

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq

growth_protocol: 8-week-old WT mice and Flcn∆DC KO mice were used

extract_protocol:
Tumor tissues were digested and CD45+  and dendritic cells (CD45+CD64-CD11c+MHC-II+) were sorted from tumour tissues on day 15
Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)

treatment_protocol: Mice were challenged with MC38 cells

value: FlcndeltaDC KO


title: ANM_85

description:
whole transcriptome sequencing
P85


title: mtDNAwide_Atp6_T2A_Stable_with HHR_pairID_50 [5F6]


title: Gastrocnemius 87F

city: San Francisco

first: Emilie

last: Barruet

state: California

address: 513 Parnassus Av

institute: UCSF

data_processing:
Sequencing reads were processed with Cell Ranger version 2.0.1. using the human reference transcriptome GRCh38.
Genome_build: GRCh18
Supplementary_files_format_and_content: filtered_gene_bc_matrices (barcodes.tsv, genes.tsv, matrix.mtx)

extract_protocol:
Freshly harvested human muscle was  stored in DMEM with 30% FBS at 4°C overnight. Muscle was digested, erythrocytes were lysed, and hematopoietic and endothelial cells were depleted with magnetic column depletion. Viable cells were depleted for CD31, CD34, and CD45 expressing cells. Cells that remained after depletion were sorted for CXCR4+/CD29+/CD56+ and collected for single cell rna sequencing (Garcia et al., 2018; Garcia et al., 2017). To capture individual cells, we utilized the Chromium Single Cell 3' Reagent Version 3 Kit from 10X Genomics (Zheng et al., 2017).
Libraries were prepared with the Chromium Single Cell 3' Reagent Version 3 Kit.

value: muscle stem cell

value: untreated

tag: subject status

value: healthy donor

tag: subject gender

value: female

tag: subject age


title: ANM_84

description:
whole transcriptome sequencing
P84


title: mtDNAwide_Nd3_T2A_Stable_with HHR_pairID_32 [5F3]

tag: ddcbe pair id used

tag: days after transfection

tag: target


title: ANM_83

description:
whole transcriptome sequencing
P83

tag: tumor stage


title: mtDNAwide_CoII_T2A_Stable_without HHR_pairID_46 [5F11]


title: Wild type GEX2

tag: cell type

tag: genotype

value: Wild type


title: Wild type GEX1


title: Vastus Lateralis 73M

value: male


title: Vastus Lateralis 66M


title: Vastus Lateralis 83M


title: mtDNAwide_Atp6_T2A_Stable_without HHR_pairID_50 [5F2]


title: ANM_82

description:
whole transcriptome sequencing
P82

tag: tobacco smoking

tag: alcohol consumption


title: mtDNAwide_Atp6_T2A_Stable_without HHR_pairID_50 [5D8]


title: cDC1_Flcn_KO 4

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM38_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

source_name: Spleen

growth_protocol: Spleens were digested, and denritic cells were enriched with anti-CD11c MicroBeads prior to sorting. Splenic cDC1 (CD11c+CD8α+CD24+TCRβ−CD49b−B220−) were sorted from naïve WT and Flcn∆DC mice.

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

treatment_protocol: No treatment

value: splenic cDC8

value: naive FlcndeltaDC


title: mtDNAwide_CoII_T2A_Stable_without HHR_pairID_46 [5D7]


title: donor1_AS3m_miRnt_1

value: erythroblasts (day 13) derived from SCD CD34+ HSPCs

value: transduced with BetaAS3m/miRnt-LV


title: Rectus Abdominis 59F


title: ANM_86

description:
whole transcriptome sequencing
P86


title: cDC1_Flcn_KO 3

value: splenic cDC7


title: donor1_AS3m_miRHBB_1

value: transduced with BetaAS3m/miR7m-LV


title: Vastus Lateralis 57F


title: mtDNAwide_Cytb_T2A_Stable_without HHR_pairID_42 [5D6]

value: mtDNA


title: cDC1_Flcn_KO 2

value: splenic cDC6


title: ANM_80

description:
whole transcriptome sequencing
P80

value: Not Applicable


title: mtDNAwide_Nd3_T2A_Stable_without HHR_pairID_32 [5D5]


title: Flcn KO GEX1

value: Sorted CD45- tumour cells, macrophages (CD45+CD64+), CD45+ non-macrophage immune cells (CD45+CD64-), and dendritic cells (CD45+CD64-CD11c+MHC-II+) in the tumour tissues


title: Rectus Abdominis 56F


title: mtDNAwide_Nd3_T2A_Stable_with HHR_pairID_32 [5D9]


title: ANM_79

description:
whole transcriptome sequencing
P79


title: cDC1_Flcn_KO 1

value: splenic cDC5


title: mtDNAwide_WT_T2A_Stable_without HHR_pairID_ [5D4]

value: empty


title: cDC1_WT 3

value: splenic cDC3

value: naive WT


title: cDC1_WT 4

value: splenic cDC4


title: Atp6_mouse_CVBC6.1f_F3 [5D3]

value: around 3 weeks of age


title: Pectoralis Major 40F

value: muscle stem cell

value: untreated

value: healthy donor

value: female


title: Atp6_mouse_CVBC6.1e_F3 [5D2]


title: Vastus Lateralis 55M

value: male


title: cDC1_WT 2

value: splenic cDC2


title: ANM_78

description:
whole transcriptome sequencing
P78


title: LSCC_127

description:
whole transcriptome sequencing
C127

source_name: LSCC tissue

value: No


title: Vastus Lateralis 52M


title: LSCC_126

description:
whole transcriptome sequencing
C126

value: Yes


title: mtDNAwide_Atp6_T2A_Stable_with HHR_pairID_50 [5D12]

value: mtDNA


title: Pectoralis Major 21F


title: LSCC_125

description:
whole transcriptome sequencing
C125


title: cDC1_WT 1

value: splenic cDC1


title: mtDNAwide_CoII_T2A_Stable_with HHR_pairID_46 [5D11]


title: ANM_81

description:
whole transcriptome sequencing
P81

value: Not Applicable


title: LSCC_124

description:
whole transcriptome sequencing
C124


title: mtDNAwide_Atp8_pairID_51_repeat3 [i715_i505]


title: Vastus Lateralis 20M


title: mtDNAwide_CoI_pairID_69_repeat3 [i715_i504]


title: K562.DNTTOE-Lib8-Rep2

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake university

description:
Hlib3-S2.DNTTOER3
DSB_Repair_Map.xlsx

data_processing:
Library strategy: Amplicon Sequencing
Reads adapter were removed by cutadapt, then the reads were mapped to the library using bowtie2.  oligo with synthesis error in the  gRNA region were removed.
The repairing pattern was classified according to the sequecing reads and the library design.
Genome_build: custermized oligo library
Supplementary_files_format_and_content: excel

growth_protocol: HEK293T cell was grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% penicillin/streptomycin (Gibco #15140-122). K562 and Jurkat cells were grown in RPMI 1640 (SIGMA #R8758) with 10% FBS (Gemini #900-108) and 1% penicillin/streptomycin. H1 cells were cultured on Matrigel (Corning)-coated plates with mTeSR medium (StemCell Technologies). Medium was changed daily. Cells were passaged every 3–4 days using ReLeSR (StemCell Technologies). K562 and Jurkat cells were harvested at day-3.5 post-transduction and H1 cells were collected at day-5.

extract_protocol:
Genomic DNA (gDNA) was isolated using DNeasy Blood & Tissue Kits according to the manufacturer’s protocol (Qiagen).
The region that was integrated with genomic DNA including both the gRNA, target sequence, and barcode was PCR amplified from genomic DNA for HTS. Primers for HTS were used to specifically amplify all of the gDNA using 25 µl NEBNext Ultra II Q5 Master Mix (New England Biolabs), 17 µl of gDNA (~2.5ug), 2.5 µl of primer mix at a final concentration of 250 nM, and 5.5 µl water. For each gDNA sample, PCR reactions were in the range from 30 to 60.

treatment_protocol: For screening in Jurkat-Cas9 and K562-cas9 cell line using “ON” and “OFF” library, 15 million cells were resuspended with 6ml RPMI in the presence of 8 µg/ml polybrene, and we transferred 1ml cell suspension into each well of 6-well plate. Predetermined volume of virus in the same 6-well format was added into each well to achieve a MOI of 5. After centrifugation at 600g for 2h at 32°C, 2ml pre-warmed RPMI with 15% FBS and 8 µg/ml polybrene was immediately added into each well of 6-well plate. For screening in H1-Cas9 cell line using “ON” and “OFF” library, the same number of cells should be plated on each matrigel-coated T175 flask 48 hours prior to transduction. When the monolayer cell density reaches to the optimal 50%-60% confluency, a T175 flask of cells were dissociated for cell counting (~20 million cells/T175). Calculated volume of virus was added into each T175 to achieve a MOI of 2 with 20ml mTeSR medium in the presence of 6 µg/ml polybrene. Cells were selected with puromycin (2.5-3 µg/ml) for 2d (Jurkat-cas9 and K562-cas9) or 3.5d (H1-cas9) at 36h post-transfection to remove uninfected cells. Cells were harvested at day 3.5 after transduction (day 5 for H1)

tag: celi type

value: K562-Cas9 cell


title: Atp6_mouse_CVBC6.1d_F3 [5D1]


title: mtDNAwide_Cytb_T2A_Stable_with HHR_pairID_42 [5D10]


title: LSCC_123

description:
whole transcriptome sequencing
C123


title: mtDNAwide_Nd4l_pairID_61_repeat3 [i715_i503]


title: Atp6_mouse_CVBC5.1f_F2 [5C9]


title: LSCC_122

description:
whole transcriptome sequencing
C122


title: K562.DNTTOE-Lib8-Rep1

description:
Hlib3-S.DNTTOER3
DSB_Repair_Map.xlsx


title: mtDNAwide_Nd1_pairID_28_repeat3 [i715_i502]


title: LSCC_121

description:
whole transcriptome sequencing
C121


title: Jurkat.DNTTKO-Lib3-Rep2

description:
Hlib3-S2.DNTTKOR1
DSB_Repair_Map.xlsx

value: Jurkat-Cas9 cell


title: Atp6_mouse_CVBC5.1e_F2 [5C8]


title: Jurkat.DNTTKO-Lib3-Rep1

description:
Hlib3-S.DNTTKOR1
DSB_Repair_Map.xlsx


title: mtDNAwide_CoIII_pairID_47_repeat2 [i714_i504]


title: Atp6_mouse_CVBC5.1c_F2 [5C6]


title: mtDNAwide_Nd6_pairID_66_repeat2 [i714_i503]


title: Atp6_mouse_CVBC5.1b_F2 [5C5]


title: LSCC_118

description:
whole transcriptome sequencing
C118


title: K562-Mismatch_Lib2-Rep1

description:
Hlibmis2-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Atp6_mouse_CVBC5.1a_F2 [5C4]


title: Jurkat-Mismatch_Lib2-Rep1

description:
Hlibmis2-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: LSCC_117

description:
whole transcriptome sequencing
C117


title: mtDNAwide_Atp6_T2A_with HHR_pairID_50_repeat3 [5C3]


title: LSCC_120

description:
whole transcriptome sequencing
C120


title: mtDNAwide_CoIII_pairID_47_repeat1 [i712_i504]


title: mtDNAwide_Atp6_T2A_with HHR_pairID_50_repeat2 [5C2]


title: LSCC_116

description:
whole transcriptome sequencing
C116


title: LSCC_115

description:
whole transcriptome sequencing
C115


title: mtDNAwide_Nd6_pairID_66_repeat1 [i712_i503]


title: LSCC_119

description:
whole transcriptome sequencing
C119


title: mtDNAwide_Nd3_pairID_32_repeat1 [i712_i502]


title: Atp6_mouse_CVBC6.1c_F3 [5C12]


title: mtDNAwide_Nd3_pairID_32_repeat2 [i714_i502]


title: K562-Mismatch_Lib2-Rep2

description:
Hlibmis2-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_CoII_pairID_46_repeat3 [i711_i504]


title: H1-Mismatch_Lib2-Rep2

description:
Hlibmis2-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx

value: H1-Cas9 cell


title: H1-Mismatch_Lib2-Rep1

description:
Hlibmis2-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: LSCC_113

description:
whole transcriptome sequencing
C113


title: Atp6_mouse_CVBC6.1b_F3 [5C11]


title: Jurkat-Mismatch_Lib2-Rep2

description:
Hlibmis2-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Atp6_mouse_CVBC6.1a_F3 [5C10]


title: H1-Mismatch_Lib1-Rep1

description:
Hlibmis1-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Nd2_pairID_29_repeat3 [i711_i502]


title: mtDNAwide_Nd5_pairID_64_repeat3 [i711_i503]


title: mtDNAwide_Atp6_T2A_with HHR_pairID_50_repeat1 [5C1]


title: Jurkat-Mismatch_Lib1-Rep1

description:
Hlibmis1-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_CoII_pairID_46_repeat2 [i710_i504]


title: mtDNAwide_Cytb_T2A_with HHR_pairID_42_repeat3 [5B9]


title: LSCC_111

description:
whole transcriptome sequencing
C111


title: mtDNAwide_Nd5_pairID_64_repeat2 [i710_i503]


title: LSCC_110

description:
whole transcriptome sequencing
C110


title: H1-Mismatch_Lib1-Rep2

description:
Hlibmis1-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Cytb_T2A_with HHR_pairID_42_repeat2 [5B8]


title: K562-Mismatch_Lib1-Rep2

description:
Hlibmis1-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Cytb_T2A_with HHR_pairID_42_repeat1 [5B7]


title: Jurkat-Mismatch_Lib1-Rep2

description:
Hlibmis1-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_CoII_pairID_46_repeat1 [i709_i504]


title: LSCC_114

description:
whole transcriptome sequencing
C114


title: mtDNAwide_Nd2_pairID_29_repeat2 [i710_i502]


title: mtDNAwide_Nd3_T2A_with HHR_pairID_32_repeat3 [5B6]


title: LSCC_108

description:
whole transcriptome sequencing
C108


title: LSCC_109

description:
whole transcriptome sequencing
C109


title: LSCC_106

description:
whole transcriptome sequencing
C106


title: LSCC_107

description:
whole transcriptome sequencing
C107


title: mtDNAwide_Nd5_pairID_64_repeat1 [i709_i503]


title: K562-Lib8-Rep1

description:
Hlib9-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Nd3_T2A_with HHR_pairID_32_repeat1 [5B4]


title: mtDNAwide_Nd3_T2A_with HHR_pairID_32_repeat2 [5B5]


title: K562-Mismatch_Lib1-Rep1

description:
Hlibmis1-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: LSCC_105

description:
whole transcriptome sequencing
C105


title: LSCC_112

description:
whole transcriptome sequencing
C112


title: mtDNAwide_CoIII_pairID_47_repeat3 [i708_i504]


title: Jurkat-Lib8-Rep1

description:
Hlib9-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Atp6_T2A_without HHR_pairID_50_repeat3 [5B3]


title: mtDNAwide_Nd2_pairID_29_repeat1 [i709_i502]


title: H1-Lib8-Rep2

description:
Hlib9-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Nd6_pairID_66_repeat3 [i708_i503]


title: mtDNAwide_Atp6_T2A_without HHR_pairID_50_repeat2 [5B2]


title: K562-Lib8-Rep2

description:
Hlib9-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: LSCC_103

description:
whole transcriptome sequencing
C103


title: mtDNAwide_Nd3_pairID_32_repeat3 [i708_i502]


title: mtDNAwide_CoII_T2A_with HHR_pairID_46_repeat3 [5B12]


title: LSCC_104

description:
whole transcriptome sequencing
C104


title: H1-Lib7-Rep1

description:
Hlib8-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_CoII_T2A_with HHR_pairID_46_repeat2 [5B11]


title: LSCC_102

description:
whole transcriptome sequencing
C102


title: LSCC_101

description:
whole transcriptome sequencing
C101


title: mtDNAwide_Atp8_pairID_51_repeat2 [i707_i505]


title: H1-Lib8-Rep1

description:
Hlib9-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_CoII_T2A_with HHR_pairID_46_repeat1 [5B10]


title: K562-Lib7-Rep1

description:
Hlib8-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Atp6_T2A_without HHR_pairID_50_repeat1 [5B1]


title: LSCC_100

description:
whole transcriptome sequencing
C100


title: mtDNAwide_Nd1_pairID_28_repeat2 [i707_i502]


title: mtDNAwide_Cytb_T2A_without HHR_pairID_42_repeat3 [5A9]


title: H1-Lib7-Rep2

description:
Hlib8-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Nd4l_pairID_61_repeat2 [i707_i503]


title: mtDNAwide_Atp8_pairID_51_repeat1 [i706_i505]


title: LSCC_99

description:
whole transcriptome sequencing
C99


title: mtDNAwide_Cytb_T2A_without HHR_pairID_42_repeat2 [5A8]


title: LSCC_98

description:
whole transcriptome sequencing
C98


title: K562-Lib7-Rep2

description:
Hlib8-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_CoI_pairID_69_repeat1 [i706_i504]


title: LSCC_97

description:
whole transcriptome sequencing
C97


title: mtDNAwide_Cytb_T2A_without HHR_pairID_42_repeat1 [5A7]


title: Jurkat-Lib7-Rep2

description:
Hlib8-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: LSCC_96

description:
whole transcriptome sequencing
C96


title: mtDNAwide_Nd4l_pairID_61_repeat1 [i706_i503]


title: H1-Lib6-Rep1

description:
Hlib7-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Jurkat-Lib8-Rep2

description:
Hlib9-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: mtDNAwide_CoI_pairID_69_repeat2 [i707_i504]


title: LSCC_95

description:
whole transcriptome sequencing
C95


title: mtDNAwide_Nd1_pairID_28_repeat1 [i706_i502]


title: Jurkat-Lib7-Rep1

description:
Hlib8-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Nd3_T2A_without HHR_pairID_32_repeat2 [5A5]


title: mtDNAwide_Atp6_pairID_50_repeat3 [i704_i505]


title: mtDNAwide_Nd3_T2A_without HHR_pairID_32_repeat1 [5A4]


title: Jurkat-Lib6-Rep1

description:
Hlib7-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: LSCC_94

description:
whole transcriptome sequencing
C94


title: LSCC_93

description:
whole transcriptome sequencing
C93


title: mtDNAwide_Cytb_pairID_42_repeat3 [i704_i504]


title: mtDNAwide_WT_T2A_without HHR_pairID__repeat3 [5A3]

value: empty


title: LSCC_92

description:
whole transcriptome sequencing
C92


title: mtDNAwide_Nd4_pairID_60_repeat3 [i704_i503]


title: K562-Lib6-Rep1

description:
Hlib7-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_WT_T2A_without HHR_pairID__repeat2 [5A2]


title: LSCC_91

description:
whole transcriptome sequencing
C91


title: mtDNAwide_WT_pairID_ empty_repeat3 [i704_i502]


title: mtDNAwide_CoII_T2A_without HHR_pairID_46_repeat3 [5A12]


title: H1-Lib6-Rep2

description:
Hlib7-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mtDNAwide_Atp6_pairID_50_repeat2 [i703_i505]


title: LSCC_90

description:
whole transcriptome sequencing
C90


title: mtDNAwide_Nd3_T2A_without HHR_pairID_32_repeat3 [5A6]


title: mtDNAwide_CoII_T2A_without HHR_pairID_46_repeat2 [5A11]


title: H1-Lib5-Rep1

description:
Hlib6-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: LSCC_89

description:
whole transcriptome sequencing
C89


title: mtDNAwide_Cytb_pairID_42_repeat2 [i703_i504]


title: LSCC_88

description:
whole transcriptome sequencing
C88


title: Jurkat-Lib6-Rep2

description:
Hlib7-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Nd4_pairID_60_repeat2 [i703_i503]


title: mtDNAwide_CoII_T2A_without HHR_pairID_46_repeat1 [5A10]


title: K562-Lib5-Rep1

description:
Hlib6-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_WT_T2A_without HHR_pairID__repeat1 [5A1]


title: LSCC_87

description:
whole transcriptome sequencing
C87


title: Jurkat-Lib5-Rep1

description:
Hlib6-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: LSCC_86

description:
whole transcriptome sequencing
C86


title: Screening_ND5_pairID_64 [3I2]


title: K562-Lib6-Rep2

description:
Hlib7-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: H1-Lib5-Rep2

description:
Hlib6-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Screening_ND4L_pairID_62 [3I1]


title: mtDNAwide_Atp6_pairID_50_repeat1 [i702_i505]


title: LSCC_85

description:
whole transcriptome sequencing
C85


title: K562-Lib5-Rep2

description:
Hlib6-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Jurkat-Lib5-Rep2

description:
Hlib6-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: Screening_ND5_pairID_63 [3H9]


title: LSCC_84

description:
whole transcriptome sequencing
C84


title: Screening_ND4L_pairID_61 [3H8]


title: H1-Lib4-Rep1

description:
Hlib5-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: LSCC_83

description:
whole transcriptome sequencing
C83


title: mtDNAwide_WT_pairID_empty_repeat1 [i702_i502]


title: Screening_ND4_pairID_60 [3H7]


title: LSCC_82

description:
whole transcriptome sequencing
C82


title: CH-4-2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

description: IP, sample3

data_processing:
Library strategy: MeRIPSeq
Basecalls performed using CASAVA version 1.4
Adapter sequences and reads with phred <30 were removed using the TrimGalore wrapper for Cutadapt and FastQC
Reads were aligned to the reference chicken genome (Gallus_gallus, GRCg6a) using STAR (v2.5.3a)
Genome_build: Gallus gallus (GRCg6a)
Supplementary_files_format_and_content: Bedgraph files were generated using Bedtools genomecov

organism: Gallus gallus

source_name: Embryo stage HH27

growth_protocol: Fertile  chicken eggs (Gallus gallus; Henry Stewart, UK) were incubated and the chicken embryos were collected after 5.5 days at Hamburger and Hamilton stage 27 (HH 27) (44). The samples were snap frozen in liquid nitrogen and stored at –80°C until further use

extract_protocol:
Total RNA was prepared from cells and tissues using Trizol reagent (Invitrogen). The poly(A) RNA was prepared using two rounds of oligo(dT) magnetic beads purification (New England Biolabs).
Libraries were prepared using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina).

tag: developmental stage

tag: tissue

value: embryo

tag: merip antibody

value: IP, anti-m6A antibody Epimark (NEB)


title: Screening_ND2_pairID_56 [3H6]


title: Screening_ATP8_pairID_51 [3H5]


title: LSCC_81

description:
whole transcriptome sequencing
C81


title: mtDNAwide_WT_pairID_ empty_repeat2 [i703_i502]


title: Jurkat-Lib4-Rep1

description:
Hlib5-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: H1-Lib4-Rep2

description:
Hlib5-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: CH-4-1

description: input, sample3

value: input


title: LSCC_80

description:
whole transcriptome sequencing
C80


title: CH-3-1

description: input, sample2


title: CH-3-2

description: IP, sample2


title: LSCC_79

description:
whole transcriptome sequencing
C79


title: Jurkat-Lib4-Rep2

description:
Hlib5-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: Screening_ND6_pairID_14 [3H4]


title: mtDNAwide_Nd4_pairID_60_repeat1 [i702_i503]


title: LSCC_78

description:
whole transcriptome sequencing
C78


title: CH-2-2

description: IP, sample1


title: Screening_ND6_pairID_13 [3H3]


title: K562-Lib4-Rep2

description:
Hlib5-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Screening_ND4L_pairID_10 [3H2]


title: K562-Lib3-Rep1

description:
Hlib4-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Screening_ND2_pairID_55 [3H11]


title: K562-Lib4-Rep1

description:
Hlib5-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Screening_ND1_pairID_54 [3H10]


title: Jurkat-Lib3-Rep1

description:
Hlib4-S.R1
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: Atp6_mouse_CVBC2.1f_F0 [2G9]

value: around 3 weeks of age


title: Atp6_mouse_CVBC2.1e_F0 [2G8]


title: H1-Lib3-Rep2

description:
Hlib4-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: K562-Lib3-Rep2

description:
Hlib4-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: mtDNAwide_Cytb_pairID_42_repeat1 [i702_i504]


title: H1-Lib3-Rep1

description:
Hlib4-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: mouse bone GFP+(hi) - rep3

city: stanford

first: Hui

last: Zhu

address: 1651 Page Mill Road

institute: Stanford Universtiy

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFP+ rep3

data_processing:
For RNA-seq, paired end sequencing reads (100bp) were generated and aligned to mouse reference sequence NCBI Build 37/mm9 with the STAR (v2.4.2a) algorithm.
For RNA-seq, normalization of RefSeq annotated genes, expression level and differential expression analysis were performed using the Bioconductor package DESeq2 in R (Version 3.2.2)
Genes with False Discovery Rate (FDR) <0.05 were defined as differentially expressed genes.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

source_name: GFP + (hi) freshly sorted from mouse long bone

extract_protocol:
RNA was extracted by using PureLink® RNA Mini Kit. Poly-A mRNA was purified using Dynabeads® mRNA Purification Kit according to the manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: osteoblast


title: DEPR

city: Suzhou

first: Yihang

last: Shen

state: Jiangsu

address: 2666 Ludang Road

institute: Suzhou Ninth People's Hospital

description: chronic stress stimulation

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: Rnor 6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: Hippocampus

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

treatment_protocol: Hippocampus was freshly isolated, and washed by cold RPMI 1640 medium with 0.04% BSA for twice, then cut into small pieces about 0.5 mm3 in size, then digested into single cell using Neural Tissue Dissociation Kit (Cat. No. 130-092-628, Miltenyi Biotec, Bergisch Gladbach, North Rhine-Westphalia, Germany). Single-cell suspension was filtrated by BD FALCON 40 μm cell filter (BD, Franklin Lakes, NJ, USA), then centrifuged 300 g at 4 °C for 5 min. The supernatant was mixed by 500 μL medium and 500 μL red cell lysate (Cat. No. 130-094-183, Miltenyi Biotec) at 4 °C for 10 min, then centrifuged and washed twice, and finally resuspended by 100 μL medium. Cell concentration and viability was evaluated using Luna-IITM Automated Cell Counter (Logos Biosystems, Anyang-si, Gyeonggi-do, South Korea).

value: Hippocampus

value: Wild type


title: MD

description: chronic stress stimulation


title: MCAO

description: Unilateral middle cerebral artery occlusion


title: Atp6_mouse_CVBC2.1d_F0 [2G7]


title: Jurkat-Lib3-Rep2

description:
Hlib4-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: CH-2-1

description: input, sample1


title: mouse bone GFP+(hi) - rep1

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFP+ rep1

source_name: GFP+ (hi) freshly sorted from mouse long bone


title: Atp6_mouse_CVBC2.1c_F0 [2G6]


title: 19_9_18_NPC75_KC4 [JMCT24]

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed using cutadapt version 1.10 (Kechin et al., 2017) in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). Reads in Fastq format were mapped onto the mm10 assembly of the Mus musculus genome using STAR version 2.5.3a (Dobin et al., 2013).  Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1 (Anders et al., 2015), with annotations from Ensembl version 94 and “union” mode. Read counts were normalized across samples with the median-of-ratios method (Anders and Huber, 2010), suitable for inter-sample comparison. Gene expression profiles were compared using the Bioconductor package DESeq2 version 1.16.1 (Love et al., 2014).  P-values were adjusted for multiple correction testing using the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
Assembly: mm10

source_name: Liver cells are isolated via FACS. Purity and specificity assessed by qPCR and IF. RNA extracted on column. All RIN are >6. RNA amount is >50ng

growth_protocol: Mice were fed adlibitum with a chow diet

extract_protocol:
RNA was extracted using the Macherey-Nagel™ Mini kit Nucleospin™ (Dutscher, # 872061) or Qiagen micro kit, depending on abundance of cell preparations, following the manufacturer’s instructions. RNA concentration and purity were assessed using a Nanodrop One device (ThermoFisher Scientific) or a Qubit fluorometer (ThermoFisher Scientific) and a Qubit RNA hs assay kit (ThermoFisher Scientific), while RNA integrity was analyzed on a Bionanalyzer 2100 (Agilent). RNA preparations with RIN<6.0 were discarded.
Total RNA-Seq libraries were generated from 38 to 100ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
RNA preparations were first depleted from unwanted, abundant transcripts using Ribo-Zero Plus rRNA depletion kit (Illumina, # 20040526). cDNA synthesis, 3’end adenylation, adapter ligation and PCR amplification were performed using the TruSeq Stranded total RNA sample preparation kit (Illumina). DNAs were sequenced using a Hiseq4000 sequencer with 50b single reads. Sequencing depth was 75 million reads on average.

value: Kupffer cells (KCs)

value: liver

tag: strain

tag: Sex

value: male


title: Atp6_mouse_CVBC2.1a_F0 [2G4]

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38)
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Assembly: GRChm38
Supplementary files format and content: xlsx file with off target %, on target % and average coverage

value: mtDNA


title: H1-Lib2-Rep1

description:
Hlib3-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Jurkat-Lib2-Rep1

description:
Hlib3-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: K562-Lib2-Rep1

description:
Hlib3-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: 19_9_18_NPC75_KC3 [JMCT23]


title: Atp6_mouse_CVBC1.1f_F0 [2G3]


title: mouse bone GFP+(hi) - rep2

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFP+ rep2

value: GFP + (hi) freshly sorted from mouse long bone


title: H1-Lib2-Rep2

description:
Hlib3-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: K562-Lib2-Rep2

description:
Hlib3-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Atp6_mouse_CVBC2.1h_F0 [2G11]


title: NC

description: Negative control


title: 19_9_18_HSC3 [JMCT17]

value: hepatic stellate cells (HSCs)


title: 19_9_18_NPC75_KC1 [JMCT21]


title: Atp6_mouse_CVBC2.1b_F0 [2G5]


title: Atp6_mouse_CVBC1.1e_F0 [2G2]


title: Atp6_mouse_CVBC2.1g_F0 [2G10]


title: Jurkat-Lib2-Rep2

description:
Hlib3-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: 19_9_18_HSC2 [JMCT18]


title: H1-Lib1-Rep1

description:
Hlib2-S.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx


title: Atp6_mouse_CVBC1.1d_F0 [2G1]


title: K562-Lib1-Rep1

description:
Hlib2-S.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx

value: K562-Cas9 cell


title: 19_9_18_LSEC4 [JMCT16]

value: liver sinuisoidal endothelial cells (LSECs)


title: 19_9_18_HSC4 [JMCT20]


title: Liver_ZT21_replicate 1

type: RNA

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

hyb_protocol: Following fragmentation, 2,3 microgrammes of ssDNA were hybridized for 16 hr at 45C on Mogen2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36, then probeset values were grouped and averaged using gene symbols
MoGene-2_0-st.pgf and MoGene-2_0.clf
MoGene-2_0-st-v1.na36.mm10.probeset.csv

label: biotin

source_name: Liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: 13 week old C56bl/6J male mice were ad libitum feed with chow diet.

extract_protocol: Total RNA was extracted using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions.

tag: time point

tag: replicate


title: Atp6_mouse_CVBC1.1c_F0 [2F12]

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse ear biopsies was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT


title: Jurkat-Lib1-Rep1

description:
Hlib2-S.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx

value: Jurkat-Cas9 cell


title: Atp6_mouse_CVBC1.1b_F0 [2F11]


title: 19_9_18_LSEC3 [JMCT15]


title: Liver_ZT18_replicate 2


title: H1-Lib1-Rep2

description:
Hlib2-S2.R7
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx

value: H1-Cas9 cell


title: Atp6_mouse_CVBC1.1a_F0 [2F10]


title: Liver_ZT21_replicate 3


title: Liver_ZT18_replicate 3


title: Liver_ZT0_replicate 3


title: Liver_ZT18_replicate 1


title: 19_9_18_LSEC2 [JMCT14]


title: K562-Lib1-Rep2

description:
Hlib2-S2.R3
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
K562_integrated_DSB_repair_category.xlsx


title: Liver_ZT21_replicate 2


title: Liver_ZT15_replicate 3


title: Jurkat-Lib1-Rep2

description:
Hlib2-S2.R2
OnTarget-OffTarget.xlsx
DSB_Repair_Map.xlsx
Jurkat_integrated_DSB_repair_category.xlsx


title: 19_9_18_CH4 [JMCT12]

value: cholangiocytes (CHs)


title: Screening_COI_pairID_69 [2D9]


title: Liver_ZT12_replicate 3


title: Screening_CYTB_pairID_68 [2D8]


title: 19_9_18_CH1 [JMCT9]


title: 19_9_18_CH3 [JMCT11]


title: Screening_CYTB_pairID_67 [2D7]


title: 19_9_18_Heps3 [JMCT7]

value: hepatocytes (HCs)


title: Screening_ND6_pairID_65 [2D5]


title: 19_9_18_Heps2 [JMCT6]


title: siBtg2-3

city: Cincinnati

first: Katherine

middle: E

last: Yutzey

state: Ohio

address: 3333 Burnet Ave

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were trimmed to remove adapter and low quality sequences using FastQC, Trim Galore, and Cutadapt.
Trimmed reads were aligned to the reference rat genome version rn5 with the program STAR.
Aligned reads were stripped of duplicate reads with the program sambamba.
Read counting was done with the program featureCounts from the Rsubread package. Raw counts were normalized as transcripts per million (TPM).
Assembly: rn5
Supplementary files format and content: tab separated file with raw read counts for all samples
Supplementary files format and content: tab separated file with TPM for all samples

source_name: Neonatal rat ventricular myocyte culture

growth_protocol: Primary neonatal rat cardiomyocytes were isolated from hearts of newborn rats. Following separation of fibroblasts, cardiomyocyte-enriched media with ~3 million cells were plated on 6-well plates. Cells were grown in 1X Medium-199 with Earle’s salts, L-glutamine, 15% bovine growth serum, and 2X penicillin/streptomycin for ~40 hours to obtain 70 to 80% confluency.

extract_protocol:
At 48 hours post-siRNA transfection, cardiomyocyte culture wells were washed in sterile PBS and flash-frozen for RNA isolation. Total RNA was isolated following NucleoSpin RNA Isolation Kit protocol (Macherey-Nagel, Germany).
RNA that passed quality control by the Agilent 2100 Bioanalyzer was amplified using Ovation RNA-Seq System v2. DNA libraries were generated using Nextera XT DNA Library Preparation Kit. Samples were then subjected to paired-end sequencing on Illumina HiSeq 2500 system to a depth of 35-40 million mapped reads.

treatment_protocol: Transfection cocktails were freshly prepared in Opti-MEM media with Lipofectamine 3000 (Thermo Fisher Scientific, USA). Commercially-available rat siBtg1 and siBtg2, with siScramble as control (Thermo Fisher Scientific, USA) were utilized for single- and double- knockdowns by siRNA. Four treatment groups were as follows: 20nM siScramble (Scramble control), 10nM siBtg1 with 10nM siBtg2 (Btg1/Btg2 double knockdown), 10nM siScramble with 10nM siBtg1 (Btg1 single knockdown), and 10nM siScramble with 10nM siBtg2 (Btg2 single knockdown). Cells were incubated at 37°C for 48 hours.

value: Sprague-Dawley

value: Heart ventricles

value: Wildtype

tag: age

value: Newborn (P0)

tag: treatment

value: Btg2 siRNA


title: siBtg2-1


title: siBtg2-2


title: Screening_COII_pairID_72 [2D12]

tag: ddcbe pair id used

tag: days after transfection


title: siBtg1-3

value: Btg1 siRNA


title: 19_9_18_Heps1 [JMCT5]

value: liver


title: Liver_ZT12_replicate 1


title: sperm_traditional-treated rep5

city: Riverside

first: Changcheng

last: Zhou

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

description:
15-50 nt RNA
RNAs were sequenced with standard protocols.

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: sperm

growth_protocol: 8 week old WT male mice were exposed to DCHP for 4 weeks by oral gavage

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: small RNA-seq processed with PANDORA-seq were treated wih AlkB and PNK4

value: sperm

value: wild type

value: DCHP oral gavage

tag: time

value: 4 weeks


title: Liver_ZT15_replicate 2


title: Liver_ZT12_replicate 2


title: Screening_COII_pairID_71 [2D11]

tag: target

value: mtDNA


title: siBtg1-1

tag: genotype


title: Screening_ND6_pairID_66 [2D6]


title: Liver_ZT15_replicate 1


title: siBtg12-3

value: Btg1+Btg2 siRNA


title: Screening_COI_pairID_70 [2D10]


title: sperm_traditional-treated rep4


title: sperm_traditional-control rep5


title: siBtg12-2


title: sperm_traditional-control rep4


title: siBtg1-2


title: siBtg12-1


title: Screening_WT_pairID_empty2 [2C4]

value: empty


title: sperm_traditional-treated rep3


title: siScr-3

value: Scramble siRNA


title: sperm_traditional-control rep3


title: Liver_ZT6_replicate 2


title: Liver_ZT9_replicate 2


title: Liver_ZT9_replicate 1


title: Screening_ND4_pairID_59 [2C11]


title: Liver_ZT9_replicate 3


title: siScr-2


title: Liver_ZT3_replicate 2


title: Liver_ZT6_replicate 1


title: Screening_ND3_pairID_57 [2C9]


title: Screening_ND1_pairID_53 [2C5]


title: Screening_ND3_pairID_58 [2C10]


title: siScr-1


title: sperm_traditional-control rep2


title: sperm_traditional-treated rep2


title: Liver_ZT6_replicate 3


title: sperm_traditional-treated rep1


title: Liver_ZT3_replicate 1


title: Liver_ZT0_replicate 2


title: Screening_CYTB_pairID_41 [2B4]


title: Liver_ZT3_replicate 3


title: Liver_ZT0_replicate 1


title: m5.4

city: Houston

first: Swathi

last: Arur

state: Texas

address: 6767 Bertner Ave,

department: Genetics

institute: MD Anderson Cancer Center

data_processing:
Trimmed adaptor reads and low quality (Q > 30) base pairs using Cutadapt v1.18
Quality check with FastQC v0.11.5
Read mapping was performed using STAR Alignmer v2.4.0 to the C. elegans reference genome WS259
Mapping results were summarized to counts with featureCount v1.5.3
Differential Expression analysis performed on features with > 2 reads in at least 8 of 12 oocytes using DESeq2 v1.32.0
Assembly: C. elegans WS259
Supplementary files format and content: comma separated file including the counts for each mapped feature per oocyte position, per biological replicate
Supplementary files format and content: comma separated file with DESeq results between the -1 and -5 oocyte
Supplementary files format and content: comma separated file with DESeq results between the -1 and -3 oocyte
Supplementary files format and content: comma separated file with DESeq results between the -3 and -5 oocyte

organism: Caenorhabditis elegans

source_name: Oocyte

extract_protocol:
Freshly collected C. elegans oocytes were lysed in 5.25 µl of lysis buffer with 2 U/µl of RNase inhibitor (Takara Bio) and then promptly frozen at -80 °C.
Libraries were prepared using SMART-seq v4 3’ DE Kit (Takara Bio) following the manufacturer’s manual

tag: cell type

value: Oocyte

tag: position

value: Adult


title: sperm_traditional-control rep1


title: sperm_PANDORAseq-treated rep5

description:
15-50 nt RNA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: m5.3


title: m5.2


title: Screening_ND5_pairID_37 [2B2]

first: Lindsey

last: Van Haute

address: Hills Road


title: Screening_COIII_pairID_48 [2B11]


title: sperm_PANDORAseq-treated rep4


title: m5.1


title: Screening_ND4_pairID_34 [2B1]


title: sperm_PANDORAseq-control rep4


title: Screening_ND4L_pairID_9 [2A2]


title: m3.4


title: m3.3


title: Screening_ATP8_pairID_78 [2E6]


title: sperm_PANDORAseq-treated rep3


title: sperm_PANDORAseq-control rep3


title: Screening_ATP8_pairID_77 [2E5]


title: sperm_PANDORAseq-treated rep2


title: Screening_ATP6_pairID_76 [2E4]