title: Cal33-sgMED12-2-D5-rep1

description: raw counts

value: human head and neck squamous cell carcinoma cell line


title: open_chor_08h_ck29Fl_s520

status: Public on Dec 20 2023

type: SRA

city: Boston

first: Debora

last: Nickla

state: MA

address: 424 Beacon St

department: Dept. of Biosciences and Disease

country: USA

institute: New England College of Optometry

library_source: transcriptomic

data_processing:
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample

molecule: total RNA

organism: Gallus gallus

source_name: choroid

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
Illumina TruSeq stranded kit using roughly equal amounts of RNA (between 100 and 300ng)

treatment_protocol: chick eyes were goggled (occl) or open

tag: tissue

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: F


title: Trn_S-Med_S16

city: Bilthoven

first: Jelena

last: Cvetkovic

address: Antonie van Leewenhoeklaan 9

department: Centre for Infectious Disease Control

country: Netherlands

institute: RIVM

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
RNAseq reads were aligned to the Homo sapiens reference genome (GRCh38) and transcript abundance was quantified using kallisto (version 0.46.1).
Assembly: GRCh38
Supplementary files format and content: Raw_counts_all_samples.txt

organism: Homo sapiens

source_name: human monocyte

growth_protocol: Human monocytes were purified from buffy coats from healthy donors. Briefly, peripheral blood mononuclear cells (PBMC) were isolated using a Lymphoprep (Nycomed, Zurich, Switzerland) gradient.  Monocytes were isolated by negative magnetic sorting from PBMC using a MojoSort™ Human CD14+Monocytes kit (BioLegend, San Diego, CA) according to the manufacturer’s instructions. Purity of isolated monocytes was determined using anti-CD14-PE (BD Biosciences) FACS-staining. Data was acquired using the FACS Canto II (BD Biosciences) and analyzed using FlowJo software (Tree Star). CD14+ cell purity of 90% or more was obtained for each donor.

extract_protocol:
The total RNA was purified from the lysates using miRNeasy Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. The RNA quality with RNA integrity number (RIN) was checked by Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit. The RIN of all RNA samples were >8 indicating high RNA integrity. Also, the concentration of RNA was measured by the Quantus™ Fluorometer (Promega Corporation, USA) using Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific, MA, USA).
500 ng of total RNA from each samples was used to construct the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s instructions. In short, the mRNA molecules were purified from total RNA using poly-T oligo attached magnetic beads, fragmented and converted into first strand cDNA using reverse transcriptase and random hexamers in the presence of Actinomycin D. Next, to create strand specificity, dTTP was replaced with dUTP in the second-strand cDNA synthesis and then dsDNA was subjected to adenylation 3’ ends. Indexing unique dual adapters were ligated to both ends of the double-stranded cDNA and PCR was performed to enrich DNA fragments with sequencing adapters. After library amplification, the quality of DNA libraries was checked on QIAxcel Advanced System (Qiagen, Germany) and library concentration was determined by qPCR using KAPA Library Quantification Kit (Roche, Basel, Switzerland). The libraries were normalized to 4 nM, pooled at equimolar concentrations and sequenced on a NextSeq500 (Illumina, NY, USA). More than 15 million reads were obtained and analyzed for each samples. FASTQ files coming from Ilumina platform were merged and quality controls were performed with FASTQC tools.

treatment_protocol: To evaluate the effects of inactivated (i)SARS-CoV-2 training on monocyte gene expression, human monocytes were cultured in 6-well plate (1×106 cells/well) exposed to iSARS-CoV-2 at multiplicity of infection (MOI:1) or left in medium only as untrained control. After 24 hours incubation, cells were washed and allowed to rest for 5 days with a medium refreshing step on day 3. On day 6, before or 3h after LPS (10 ng/ml) stimulation, the cells were lyzed in QIAzol (Qiagen) and stored at -80°C for subsequent RNA isolation.

tag: cell type

value: human monocyte

tag: genotype

tag: treatment

value: trained monocytes with iSARS-CoV-2without LPS stimulation on day 6


title: O23.Input

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

country: China

institute: Chinese Academy of Science

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) and Drosophila melanogaster genome (dmel-all-chromosome-r6.36) using STAR (v2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Homo sapiens (Ensembl: GRCh38.94) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively.
Assembly: GRCh38 and dmel-all-chromosome-r6.36
Supplementary files format and content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

molecule: polyA RNA

source_name: Peripheral mononuclear blood cell

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108). NAD-RNAs were captured following method detailed in ONE-seq manuscript (https://doi.org/10.1093/nar/gkac1136). Briefly, total RNAs were subjected to one-step chemo-enzymatic biotinylation, followed by streptavidin capture and the NudC-catalyzed elution, to specifically recover NAD-capped RNAs for epitranscriptomic profiling.
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)
RNA-Seq; 150bp paired-end

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

value: Input

tag: age

value: 61 years

tag: gender

value: Male


title: occl_chor_12h_ck31Fr_s602

value: occl

value: right


title: open_chor_08h_ck28Ml_s516

value: M


title: occl_chor_08h_ck28Mr_s514


title: Unt-Med_S13

value: untrained monocytes in medium only


title: Trn_S-Med_S14

value: trained monocytes with iSARS-CoV-2 without LPS stimulation on day 6


title: Trn_S-LPS_S15

value: iSARS-CoV-2-trained monocytes stimulated with LPS on day 6


title: Trn_S-Med_S26


title: open_chor_08h_ck30Ml_s524

value: choroid

value: open


title: O22.Input

value: Validation

value: 63 years


title: occl_chor_08h_ck30Mr_s522


title: O23.Enrich

value: Enrich


title: Trn_S-LPS_S11

value: human monocyte


title: open_chor_08h_ck27Ml_s512

value: left


title: O22.Enrich

value: Peripheral mononuclear blood cell

value: Old


title: Trn_S-Med_S10

value: trained monocytes with iSARS-CoV-2 without without LPS stimulation on day 6


title: occl_chor_08h_ck27Mr_s510


title: Trn-S-Med_S8


title: O21.Input

value: Discovery

value: Input

value: 56 years

value: Male


title: open_chor_08h_ck26Ml_s508

value: M


title: O21.Enrich


title: O20.Input

value: Female


title: Unt-Med_S6

value: untrained monocytes in medium only


title: Trn_S-LPS_S4

value: iSARS-CoV-2-trained monocytes stimulated with LPS on day 6


title: Trn_S-Med_S3

value: trained monocytes with iSARS-CoV-2 without LPS stimulation on day 6


title: occl_chor_08h_ck26Mr_s506

value: choroid

value: occl

value: right


title: Unt-LPS_S2

value: human monocyte

value: untrained monocytes stimulated with LPS on day 6


title: open_chor_08h_ck25Ml_s504

value: open

value: left


title: O19.Input

value: Peripheral mononuclear blood cell

value: Old


title: occl_chor_20h_ck24Fr_s422

value: F


title: Trn_S-Med_S7


title: occl_chor_08h_ck25Mr_s502


title: MG63, 1g, rep3

city: Liege

first: Nancy

last: Garbacki

address: avenue Hippocrate 13

country: Belgium

institute: University of Liege

description:
Biol rep 07-03
X07.03_R1

data_processing:
NF-Core RNAseq pipeline (trimming + mapping + QCs), options : --clip_r1 1 --clip_r2 1 --three_prime_clip_r1 1 --three_prime_clip_r2 1 --trim_nextseq 10 --aligner star_salmon
DESeq2 : downstream analysis (normalization + DE) from raw counts
Assembly: hg38
Supplementary files format and content: MG63_µg_vs_1g.xlsx file includes Ensembl gene ID, gene symbol, log2 fold change, pvalue, padj, base mean counts, each samples counts

growth_protocol: Cells were transported to the ISS as frozen cultures (-80°C) inserted in culture chambers units. Cryopreservation medium was made of 1:1 dilution of DMEM (containing antibiotics, 10% fetal bovine serum, 25 mM HEPES and 30 mM N-acetyl-L-cysteine) and Lonza cryoprotective medium (containing 15%DMSO). On the ISS, culture chambers were thawed and the cryopreservative medium was replaced by DMEM culture medium containing 10% fetal bovine serum.

extract_protocol:
RNA was harvested using High Pure RNA Isolation Kit (Roche) as per the manufacturer's instructions. The quantity, the quality and the integrity of RNA was assessed using Agilent 2100 Bioanalyzer (Agilent).
Total RNA was purified, fragmented and a double-stranded cDNA library was synthesized using the SMARTer Stranded RNA-Seq Kit (Takara) following manufacturer's protocols.

treatment_protocol: All cell cultures were allowed to recover from freezing for 38 h at 37°C in centrifuges running at 1 g in the Biolab incubator. For control cultures, the centrifuge continued to run for an additional 34 h, while for µg cultures, the centrifuge was turned off. Cells were 'fixed' in RNAlater and stored at -20°C until RNA extraction.

tag: cell line

value: Osteosarcoma

tag: time

value: 34 ± 1 hours

value: 1 g centrifugation


title: O20.Enrich

value: Discovery

value: Enrich

value: 63 years

value: Female


title: MG63, µg, rep6

description:
Biol rep 08-03
X08.03_R1

value: microgravity


title: MG63, µg, rep4

description:
Biol rep 08-01
X08.01_R1


title: TA4301_NSCLC_CTA | 047 | PanCK neg

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx COVID19 Immune Response Atlas v1 Platform file & GeoMx_COVID19_v1.0.pkc file
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Initial: uncollapsed probe counts, QC: collapsed probe counts, Norm: RUV normalised data
Library strategy: GeoMx Seq

source_name: NSCLC

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: MG63, µg, rep5

description:
Biol rep 08-02
X08.02_R1

tag: cell type

tag: treatment


title: MG63, 1g, rep1

description:
Biol rep 07-01
X07.01_R1


title: MG63, 1g, rep2

description:
Biol rep 07-02
X07.02_R1


title: O18.Input

tag: age group

tag: group

value: Validation

tag: assay

value: Input

value: 56 years

value: Male


title: TA4301_NSCLC_CTA | 047 | PanCK pos

description:
NA
NA

tag: tissue

value: PanCK pos

tag: qcflags

value: Low Nuclei Count

tag: qc fail

value: Fail


title: open_chor_20h_ck23Ml_s420

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: M


title: O19.Enrich

value: Peripheral mononuclear blood cell

value: Old

value: Discovery

value: Enrich

tag: age

tag: gender

value: Female


title: Unt-LPS_S9

value: human monocyte

tag: genotype

value: untrained monocytes stimulated with LPS on day 6


title: TA4301_NSCLC_CTA | 046 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: open_chor_20h_ck22Fl_s416

tag: tissue

tag: eye treatment

tag: timept

value: F


title: occl_chor_20h_ck23Mr_s418

value: choroid

value: occl

tag: chickid

tag: eye

value: right

tag: Sex


title: TA4301_NSCLC_CTA | 045 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment


title: O18.Enrich

tag: cell type

tag: age group

tag: group

value: Validation

tag: assay

tag: age

value: 56 years

tag: gender

value: Male


title: TA4301_NSCLC_CTA | 046 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

tag: segment

value: PanCK pos

tag: area

tag: aoinucleicount

tag: patient id

tag: response

tag: followup


title: O17.Input

value: Peripheral mononuclear blood cell

value: Old

value: Discovery

value: Input

value: 58 years


title: TA4301_NSCLC_CTA | 044 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

tag: status

tag: plate coord

tag: initial data_file


title: open_chor_20h_ck20Fl_s408

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex


title: TA4301_NSCLC_CTA | 044 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

value: Non-responder

value: Deceased


title: TA4301_NSCLC_CTA | 045 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi


title: occl_chor_20h_ck21Mr_s410

value: choroid

value: occl

value: M


title: O16.Input

tag: cell type

tag: age group

tag: group

tag: assay

tag: age

value: 59 years

tag: gender


title: O17.Enrich

value: Enrich

value: Female


title: TA4301_NSCLC_CTA | 043 | PanCK neg

description:
NA
NA

tag: tissue

tag: segment

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: aoinucleicount

tag: patient id

tag: response

tag: followup

value: Alive


title: O16.Enrich

value: Peripheral mononuclear blood cell

value: Old

value: Discovery

value: Male


title: TA4301_NSCLC_CTA | 042 | PanCK pos

description:
NA
NA

value: NSCLC

tag: treatment

value: Immunotherapy

value: PanCK pos

value: Low Nuclei Count

tag: status

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 041 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

value: Responder


title: TA4301_NSCLC_CTA | 042 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: Non-responder


title: occl_chor_20h_ck20Fr_s406

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: F


title: open_chor_20h_ck19Fl_s404

tag: tissue

value: open

value: left


title: TA4301_NSCLC_CTA | 041 | PanCK neg

description:
NA
NA

tag: segment

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count

tag: qc fail

value: Fail

value: Alive


title: TA4301_NSCLC_CTA | 043 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: area

tag: aoinucleicount

tag: patient id


title: occl_chor_20h_ck22Fr_s414


title: TA4301_NSCLC_CTA | 039 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: response

tag: followup


title: TA4301_NSCLC_CTA | 040 | PanCK neg

description:
NA
NA

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

value: LB16 948 TL B

tag: status

tag: plate coord

tag: initial data_file


title: O15.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Validation

tag: assay

value: Enrich

tag: age

value: 64 years

tag: gender

value: Female


title: TA4301_NSCLC_CTA | 040 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK pos

value: Responder


title: O15.Input

value: Input


title: occl_chor_20h_ck19Fr_s402

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: F


title: TA4301_NSCLC_CTA | 039 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Alive


title: open_chor_16h_ck18Ml_s324

value: open

value: left

value: M


title: O14.Input

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

tag: age

value: 64 years

value: Male


title: TA4301_NSCLC_CTA | 037 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: Responder

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 038 | PanCK neg

description:
NA
NA

tag: treatment

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

tag: qc fail

value: Fail

value: Deceased


title: TA4301_NSCLC_CTA | 036 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id


title: occl_chor_16h_ck17Mr_s318

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex


title: TA4301_NSCLC_CTA | 037 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK pos

tag: response

tag: followup

tag: status

value: Alive


title: open_chor_16h_ck17Ml_s320

tag: tissue

value: open

value: left

value: M


title: TA4301_NSCLC_CTA | 035 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

tag: segment

value: Non-responder

tag: plate coord


title: TA4301_NSCLC_CTA | 038 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: initial data_file


title: occl_chor_16h_ck16Fr_s314

value: F


title: occl_chor_16h_ck18Mr_s322


title: TA4301_NSCLC_CTA | 035 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

tag: area


title: open_chor_16h_ck15Ml_s312


title: TA4301_NSCLC_CTA | 034 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: Immunotherapy

tag: aoinucleicount


title: O13.Input

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

value: Input

tag: age

value: 67 years

tag: gender

value: Male


title: O12.Input

value: Validation

value: 65 years

value: Female


title: O13.Enrich

value: Enrich


title: O11.Input


title: O14.Enrich

value: 64 years


title: O12.Enrich


title: TA4301_NSCLC_CTA | 036 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK pos

tag: patient id

tag: response

value: Responder

value: Alive


title: TA4301_NSCLC_CTA | 032 | PanCK neg

description:
NA
NA

value: PanCK neg

tag: qcflags

value: Low Sequencing Saturation

tag: qc fail

value: Fail

value: Non-responder

tag: followup

tag: status


title: TA4301_NSCLC_CTA | 033 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: LB18 159 TL B

tag: plate coord


title: O11.Enrich

value: Peripheral mononuclear blood cell

value: Old

value: Discovery


title: occl_chor_16h_ck15Mr_s310

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: M


title: TA4301_NSCLC_CTA | 032 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

value: PanCK pos

tag: area

tag: aoinucleicount

tag: initial data_file


title: open_chor_16h_ck14Ml_s308

value: open

value: left


title: O9.Input

tag: cell type

tag: age group

tag: group

tag: assay

value: Input

tag: age

value: 60 years

tag: gender

value: Male


title: TA4301_NSCLC_CTA | 031 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: roi

tag: segment

value: PanCK neg

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased


title: occl_chor_16h_ck14Mr_s306

tag: eye treatment

tag: timept

tag: chickid

tag: eye

tag: Sex


title: TA4301_NSCLC_CTA | 030 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

tag: treatment

value: Immunotherapy

tag: area

tag: aoinucleicount

value: Alive

tag: plate coord

tag: initial data_file


title: O9.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

tag: gender


title: open_chor_16h_ck13Fl_s304

tag: tissue

value: choroid

value: F


title: TA4301_NSCLC_CTA | 034 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

tag: segment

value: PanCK pos

tag: patient id

tag: response

tag: followup

tag: status


title: TA4301_NSCLC_CTA | 030 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: area


title: TA4301_NSCLC_CTA | 029 | PanCK neg

description:
NA
NA

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

tag: aoinucleicount

value: Responder

tag: plate coord


title: O8.Input

tag: cell type

tag: age group

tag: group

value: Input

value: 54 years

value: Male


title: TA4301_NSCLC_CTA | 033 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: LB18 159 TL B

tag: initial data_file


title: occl_chor_16h_ck13Fr_s302

tag: tissue

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex


title: TA4301_NSCLC_CTA | 029 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

tag: patient id

tag: response

tag: followup

tag: status

value: Alive


title: O8.Enrich

value: Peripheral mononuclear blood cell

value: Old

value: Discovery

tag: assay

tag: age

tag: gender


title: TA4301_NSCLC_CTA | 027 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

value: PanCK neg

tag: area

tag: aoinucleicount

value: LB11 551 TL C

value: Deceased

tag: plate coord


title: O7.Input

tag: cell type

tag: age group

tag: group

value: 62 years

value: Female


title: open_chor_04h_ck12Fl_s224

tag: tissue

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: F


title: occl_chor_04h_ck12Fr_s222

value: occl


title: TA4301_NSCLC_CTA | 027 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

tag: segment

value: PanCK pos

tag: patient id

tag: response

value: Responder

tag: followup

tag: status

tag: initial data_file


title: TA4301_NSCLC_CTA | 028 | PanCK neg

description:
NA
NA

value: NSCLC

tag: treatment

value: Immunotherapy

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: aoinucleicount

value: LB15 746  TL A

value: Non-responder

tag: plate coord


title: TA4301_NSCLC_CTA | 028 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: Alive


title: TA4301_NSCLC_CTA | 026 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK neg

value: Deceased


title: TA4301_NSCLC_CTA | 031 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv


title: TA4301_NSCLC_CTA | 026 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv


title: open_chor_04h_ck11Fl_s220

tag: eye treatment

tag: timept

tag: chickid


title: O6.Input

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

value: Input

tag: age

value: 55 years

tag: gender

value: Female


title: occl_chor_04h_ck11Fr_s218

value: choroid

value: occl

tag: eye

value: right

tag: Sex

value: F


title: TA4301_NSCLC_CTA | 025 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

tag: treatment

value: Immunotherapy

tag: roi

tag: segment

value: PanCK pos

tag: patient id

tag: response

tag: followup

tag: status

tag: initial data_file


title: TA4301_NSCLC_CTA | 025 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: area

tag: aoinucleicount

value: Non-responder

tag: plate coord


title: TA4301_NSCLC_CTA | 024 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: Responder

value: Alive


title: open_chor_04h_ck10Fl_s216

tag: eye treatment

value: open

tag: timept

tag: chickid

value: left


title: O6.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

tag: assay

value: Enrich

tag: age

tag: gender


title: O5.Input

value: Discovery

value: Input

value: 55 years


title: O7.Enrich

value: 62 years

value: Female


title: O5.Enrich


title: TA4301_NSCLC_CTA | 024 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: roi

tag: segment

value: PanCK neg

tag: patient id

tag: response


title: O4.Input

value: 67 years

value: Male


title: TA4301_NSCLC_CTA | 022 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

value: PanCK pos

tag: area

tag: followup

tag: status

value: Deceased

tag: initial data_file


title: TA4301_NSCLC_CTA | 023 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: aoinucleicount

value: Non-responder

tag: plate coord


title: TA4301_NSCLC_CTA | 021 | PanCK neg

description:
NA
NA

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

value: Alive


title: open_chor_04h_ck9Ml_s212

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: M


title: TA4301_NSCLC_CTA | 022 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: roi

tag: segment


title: TA4301_NSCLC_CTA | 023 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: patient id

tag: response


title: occl_chor_04h_ck9Mr_s210

value: occl

value: right


title: TA4301_NSCLC_CTA | 020 | PanCK neg

description:
NA
NA

value: PanCK neg

value: Low Surface Area

tag: area

tag: followup

tag: status


title: O4.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

value: 67 years

tag: gender

value: Male


title: TA4301_NSCLC_CTA | 021 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

value: PanCK pos

tag: aoinucleicount

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 020 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: roi

value: Non-responder

value: Alive


title: TA4301_NSCLC_CTA | 019 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: segment

value: Responder


title: open_chor_04h_ck8Ml_s208

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: M


title: occl_chor_04h_ck8Mr_s206

value: occl

value: right


title: occl_chor_04h_ck10Fr_s214

value: F


title: O3.Input

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Old

value: Discovery

value: Input

value: 57 years


title: TA4301_NSCLC_CTA | 019 | PanCK pos

description:
NA
NA

value: NSCLC

value: Immunotherapy

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: patient id

tag: response

tag: followup

tag: status


title: MC3T3-E1_vehicle-treatment_input

city: changsha

first: Jian xi

last: Zhu

state: -- Select state --

address: XiangYa hospital

department: Department of Orthopaedics

institute: Xiangya Hospital, Central South University

library_source: genomic

data_processing:
Image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8.0)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Mouse genome (UCSC MM10) using BOWTIE software (V2.1.0)
MACS v1.4.2 (Model-based Analysis of ChIP-seq) software was used to detect the peak from ChIP-seq data. We run MACS with mapped reads. An EXCEL/BED format file containing the ChIP-enriched regions was generated for each comparison/sample
Assembly: mm10
Supplementary files format and content: BED, EXCEL

molecule: genomic DNA

organism: Mus musculus

growth_protocol: MEMα, 10% fetal bovine serum, Penicillin/Streptomycin (1%). Cells were cultured at 37C at 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

treatment_protocol: treated with PTH (1μg/mL) or PBS solution for 24 hours

tag: cell line

value: preosteoblast

tag: chip antibody

tag: treatment

value: treated with vehicle for 24 hours


title: MC3T3-E1_vehicle-treatment_PTH1R

value: PTH1R (santa cruz, #SC-12722)


title: TA4301_NSCLC_CTA | 018 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: roi

tag: segment

value: PanCK neg

tag: aoinucleicount

value: Non-responder

value: Deceased

tag: plate coord

tag: initial data_file


title: O3.Enrich

tag: cell type

tag: age group

tag: group

tag: assay

value: Enrich

tag: age

tag: gender

value: Male


title: TA4301_NSCLC_CTA | 018 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK pos

tag: area

tag: patient id

tag: response

tag: followup


title: O2.Enrich

value: Peripheral mononuclear blood cell

value: Old

value: 63 years

value: Female


title: MC3T3-E1_PTH-treatment_input

tag: cell line

tag: chip antibody

tag: treatment

value: treated with PTH for 24 hours


title: O2.Input

value: Discovery

value: Input


title: O1.Input

value: 65 years


title: MC3T3-E1_PTH-treatment_THR

value: preosteoblast

value: THR (Thermo Scientific, #MA1-215)


title: TA4301_NSCLC_CTA | 017 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: Responder

tag: status

value: Alive


title: AB

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street

institute: Yale University

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing and gene counting were made using the Cell Ranger software (v3)
Supplementary files format and content: mm10
Supplementary files format and content: Tab seperated barcodes, matrix, and features files

source_name: decidua

extract_protocol:
The uterine tissues were finely minced and subjected to enzymatic digestion to obtain single cell suspensions.
Libraries were created with Single Cell 3′ Library kit V2 according to the manufacturer’s protocol

value: decidua

tag: genotype

value: wildtype


title: O1.Enrich

tag: cell type

tag: age group

value: Enrich


title: EvoETRs 8 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

data_processing:
Reads quality was controlled with Fastqc v0.11.9, while low-quality reads and the adapters were removed using Trim Galore v0.6.6. with the following parameters: --quality 20, --length 25, --paired, --clip_R2 5
Remaining reads were analyzed using the Bismark read mapper Methylation caller tool v0.23.0
In detail, reads were aligned to both the converted and unconverted genomes (GRCm38) using bismark v0.23.0 with default parameters. Duplicates were then removed using the deduplicate_bismark script and the methylation status was obtained using bismark_methylation_extractor script
The methylation calls were processed using the R/Bioconductor package MethylKit v1.16.1
Imported data were filtered using the filterByCoverage function (low count filter equal to 1 and high percentile equal to 99.9) and normalized using the normalizeCoverage function
Information from the different samples was merged using the unite function considering the positions covered in all the 3 replicates per condition
The percentage of methylation was calculated with the percMethylation function and the correlation among the samples was determined applying the cor function (default Pearson method)
Differential methylation analysis was performed using the R/Bioconductor packages bsseq v 1.26.0 and DSS v 2.44.0
The DMLtest function was used for the normalization step and the differential analysis with the following parameters: smoothing = TRUE and smoothing.span = 500. Then, the callDML function was applied to determine the differential methylated loci (DML) setting as thresholds delta = 0.4 and p.threshold = 1e-3. The differentially methylated regions (DMR) were defined applying the callDRM function with the same thresholds
The DMR identified were annotated using the annotatePeakInBatch function from the R/Bioconductor package ChIPpeakAnno v 3.24.2 using the Gencode v M25 annotation and the following parameters: PeakLocForDistance = "middle", FeatureLocForDistance = "TSS", output = "both" and multiple = TRUE
Assembly: GRCm38
Supplementary files format and content: Bismark coverage

source_name: Liver

extract_protocol:
Genomic DNA extraction by Maxwell® 16 Cell LEV DNA Purification Kit and following provider indications
DNA was sheared using Covaris LE220 Focused-ultrasonicator for an average 350 bp size
NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing and adaptor ligation of EM-seq adaptor. The ligated samples were cleaned up according to the manufacturer’s instructions with NEBNext Sample Purification Beads

value: Liver

value: Hepa 1-6

value: Hepatocyte

value: EvoETRs 8 against Pcsk9


title: MC3T3-E1_PTH-treatment_PTH1R

value: PTH1R (santa cruz, #SC-12722)

value: treated with PTH for 24 hours


title: TA4301_NSCLC_CTA | 017 | PanCK neg

description:
NA
NA

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

tag: aoinucleicount

tag: plate coord

tag: initial data_file


title: EvoETRs 8 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: occl_chor_00h_ck5Fr_s118

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: F


title: M22.Input

value: Peripheral mononuclear blood cell

value: Middle

tag: group

value: Discovery

tag: assay

value: Input

tag: age

value: 40 years

tag: gender

value: Male


title: M22.Enrich

value: Enrich


title: occl_chor_00h_ck6Mr_s122

tag: tissue

value: M


title: open_chor_00h_ck6Ml_s124

value: open

value: left


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: Liver

tag: cell line

value: Hepa 1-6

tag: cell type

value: Hepatocyte

tag: genotype

tag: treatment

value: Mock


title: M21.Input

tag: age group

value: 43 years


title: open_chor_00h_ck4Ml_s116

value: choroid


title: occl_chor_04h_ck7Mr_s202

value: occl

value: right


title: M21.Enrich

value: Peripheral mononuclear blood cell

value: Middle


title: TA4301_NSCLC_CTA | 016 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK pos

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord


title: TA4301_NSCLC_CTA | 015 | PanCK neg

description:
NA
NA

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

tag: qc fail

value: Fail

value: Responder

value: Alive

tag: initial data_file


title: open_chor_00h_ck3Ml_s112

tag: tissue

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: M


title: TA4301_NSCLC_CTA | 015 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: roi

tag: segment


title: open_chor_00h_ck5Fl_s120

value: choroid

value: F


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

value: Liver

tag: cell line

value: Hepa 1-6

tag: cell type

value: Hepatocyte

tag: genotype

value: Mock


title: Mock treated Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: M20.Input

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Input

tag: age

value: 40 years

tag: gender

value: Female


title: TA4301_NSCLC_CTA | 014 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

value: NSCLC

value: Immunotherapy

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 016 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

tag: roi

tag: segment


title: M20.Enrich

tag: cell type

tag: age group

value: Enrich


title: TA4301_NSCLC_CTA | 014 | PanCK pos

description:
NA
NA

value: PanCK pos

tag: qcflags

value: Low Sequencing Saturation

tag: qc fail

value: Fail


title: M19.Enrich

tag: group

tag: assay

tag: age

value: 43 years

tag: gender

value: Male


title: TA4301_NSCLC_CTA | 013 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: area

tag: aoinucleicount

tag: patient id


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

tag: genotype

value: Cas9 against Pcsk9


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

tag: treatment


title: open_chor_00h_ck1Fl_s104

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex

value: F


title: open_chor_00h_ck2Ml_s108

value: M


title: Cas9 against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

tag: cell type


title: M19.Input

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

value: Input


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: dCas9-ETRs against Pcsk9


title: M18.Input

tag: assay

tag: age

value: 42 years

value: Female


title: occl_chor_00h_ck3Mr_s110

tag: tissue

value: occl

value: right


title: TA4301_NSCLC_CTA | 012 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

tag: area

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 013 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: treatment

value: PanCK pos

tag: aoinucleicount

tag: patient id


title: open_chor_04h_ck7Ml_s204

value: choroid

tag: eye treatment

value: open

tag: timept

tag: chickid

tag: eye

value: left

tag: Sex


title: occl_chor_00h_ck1Fr_s102

tag: tissue

value: F


title: M18.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

tag: gender


title: TA4301_NSCLC_CTA | 012 | PanCK pos

description:
NA
NA

tag: roi

tag: segment

tag: qcflags

value: Low Sequencing Saturation

tag: qc fail

value: Fail

tag: area

tag: response

tag: followup

tag: status

tag: plate coord


title: M17.Input

value: Input

value: 42 years

value: Female


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

tag: genotype

tag: treatment

value: dCas9-ETRs against Pcsk9


title: TA4301_NSCLC_CTA | 011 | PanCK neg

description:
NA
NA

tag: tissue

value: NSCLC

value: Immunotherapy

value: PanCK neg

tag: aoinucleicount

tag: patient id

value: Non-responder

value: Deceased

tag: initial data_file


title: RyR2 CKO Tconv, with stimulation, repeat 2

city: Calgary

first: Shuang

last: Geng

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

data_processing:
Basecalls were performed with bcl2fastq.
Reads were trimmed with Trimmomatic v0.36, reads quality >30, discarding reads trimed <36nt.
Reads were aligned to gemone with Bowtie2.
Peaks were called out with MACS2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Splenocyte

extract_protocol:
Cells were fixed, quenched and lysed to release chromatin DNA
Tn5-based TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55°C.

value: Splenocyte

tag: cell type

value: primary T cell

value: CD4+CD25- Tconv

value: CD4-Cre X RyR2fl/fl


title: RyR2 CKO Tconv, with stimulation, repeat 1


title: TA4301_NSCLC_CTA | 011 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

value: PanCK pos


title: M17.Enrich

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

tag: gender


title: occl_chor_00h_ck2Mr_s106

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: M


title: RyR2 CKO Tconv, without stimulation, repeat 2

tag: genotype

tag: treatment

value: No


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

tag: tissue

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

value: untargeted ZFP-ETRs


title: M16.Input

value: Input

value: 48 years

value: Male


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1


title: M16.Enrich


title: TA4301_NSCLC_CTA | 010 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: segment

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: M15.Input

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

tag: age

value: 40 years

tag: gender

value: Female


title: RyR2 CKO Treg, with stimulation, repeat 2

tag: tissue

value: Splenocyte

value: primary T cell

value: CD4+CD25+ Treg

tag: genotype

value: CD4-Cre X RyR2fl/fl

tag: treatment


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

value: ZFP-ETRs against Pcsk9


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2


title: RyR2 CKO Treg, with stimulation, repeat 1


title: TA4301_NSCLC_CTA | 009 | PanCK neg

description:
NA
NA

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

tag: qcflags

value: Low Nuclei Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: aoinucleicount

value: Responder

value: Alive


title: RyR2 CKO Treg, without stimulation, repeat 2

value: No


title: dCas9-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 2

value: dCas9-ETRs against Pcsk9


title: TA4301_NSCLC_CTA | 009 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK pos

tag: patient id

tag: response

tag: followup

tag: status

tag: plate coord

tag: initial data_file


title: M15.Enrich

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

value: 40 years

tag: gender

value: Female


title: untargetd ZFP-ETRs treated Hepa 1-6 Pcsk9tdTomato cells, replicate 3

tag: tissue

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

tag: genotype

tag: treatment

value: untargeted ZFP-ETRs


title: RyR2 CKO Treg, without stimulation, repeat 1

value: Splenocyte

value: primary T cell

value: CD4+CD25+ Treg

value: CD4-Cre X RyR2fl/fl


title: TA4301_NSCLC_CTA | 008 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

tag: area

tag: aoinucleicount

value: Responder

value: Alive


title: M14.Input

value: Peripheral mononuclear blood cell

value: Middle

value: Discovery

value: Input

value: 46 years


title: HD3 and IPEX 3, stim, ADT

city: Stanford

first: Jason

last: Nideffer

state: CA

address: 240 Pasteur Drive

department: Medicine

institute: Stanford University

description:
Hashtag 2 = HD3; Hashtag 1 = IPEX3
S6_GEX_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
Raw .fastq files were processed usuing Cell Ranger Count v7.1.0, and reads were aligned to a the human genome GRCh38 (2020-A).
Data cleaning and preliminary analyses were performed using Seurat to generate the supplementary data files provided.
Assembly: GRCh38 (2020-A)
Supplementary files format and content: Cell Ranger Output Files: filtered feature-barcode matrices (including ADT data) and filtered TCR annotations

molecule: protein

source_name: Blood

extract_protocol:
Single cell suspensions were loaded onto a Chromium Controller to generate GEMs.
GEX, TCR, and ADT libraries were generated following 10x Genomics' protocol (CG000330 Rev D)

treatment_protocol: PBMC samples were thawed from 3 IPEX and 3 HD. CD4+ T were isolated using CD4+ T Cell Isolation Kit, human (Miltenyi Biotech). Samples were split into "unstimulated" and "stimulated" fractions. The "stimulated" fraction was incubated with Dynabeads™ Human T-Activator CD3/CD28 at a ratio of 1:1 for 6 hours. The "unstimulated" fraction was processed immediately.

tag: condition

value: mixed sample (HD3 and IPEX 3)

value: Blood

value: CD4+ T cells

tag: library type

value: ADT + HTO

value: CD3/CD28 Stimulation


title: M14.Enrich

value: Enrich

value: Female


title: RyR2 CKO Tconv, without stimulation, repeat 1

value: Splenocyte

value: primary T cell

value: CD4+CD25- Tconv

value: CD4-Cre X RyR2fl/fl

value: No


title: M13.Input

value: Peripheral mononuclear blood cell

value: 41 years


title: TA4301_NSCLC_CTA | 010 | PanCK pos

description:
NA
NA

value: NSCLC

value: Immunotherapy

value: PanCK pos

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count

tag: qc fail

value: Fail

tag: patient id

tag: response

value: Non-responder

tag: followup

tag: status

value: Deceased

tag: plate coord

tag: initial data_file


title: HD2 and IPEX 2, stim, ADT

description:
Hashtag 2 = HD2; Hashtag 1 = IPEX2
S5_GEX_filtered_feature_bc_matrix.h5

value: mixed sample (HD2 and IPEX 2)

tag: tissue

value: Blood

tag: cell type

value: CD4+ T cells

value: ADT + HTO

value: CD3/CD28 Stimulation


title: WT Tconv, with stimulation, repeat 1

value: Splenocyte

value: primary T cell

value: CD4+CD25- Tconv

tag: genotype

value: WT

tag: treatment


title: HD1 and IPEX 1, stim, ADT

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S4_GEX_filtered_feature_bc_matrix.h5

value: mixed sample (HD1 and IPEX 1)


title: M13.Enrich

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

value: 41 years

tag: gender

value: Female


title: WT Tconv, without stimulation, repeat 2

value: No


title: WT Tconv, with stimulation, repeat 2


title: WT Tconv, without stimulation, repeat 1


title: ZFP-ETRs against Pcsk9 treated Hepa 1-6 Pcsk9tdTomato cells, replicate 1

value: Liver

tag: cell line

value: Hepa 1-6

value: Hepatocyte

value: ZFP-ETRs against Pcsk9


title: M12.Input

value: Input

value: 48 years

value: Male


title: M12.Enrich


title: HD1 and IPEX 1, unstim, ADT

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S1_GEX_filtered_feature_bc_matrix.h5

tag: condition

value: Blood

value: CD4+ T cells

tag: library type

value: ADT + HTO

value: No Stimulation


title: HD2 and IPEX 2, unstim, ADT

description:
Hashtag 2 = HD2; Hashtag 1 = IPEX2
S2_GEX_filtered_feature_bc_matrix.h5

value: mixed sample (HD2 and IPEX 2)


title: HD3 and IPEX 3, unstim, ADT

description:
Hashtag 2 = HD3; Hashtag 1 = IPEX3
S3_GEX_filtered_feature_bc_matrix.h5

value: mixed sample (HD3 and IPEX 3)


title: TA4301_NSCLC_CTA | 006 | PanCK neg

description:
NA
NA

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

value: Deceased


title: TA4301_NSCLC_CTA | 007 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: tissue

tag: treatment

value: PanCK pos

value: Responder

tag: followup

tag: status

value: Alive

tag: plate coord

tag: initial data_file


title: TA4301_NSCLC_CTA | 005 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv


title: TA4301_NSCLC_CTA | 007 | PanCK neg

description:
NA
NA

value: Low Nuclei Count


title: WT Treg, with stimulation, repeat 2

value: Splenocyte

tag: cell type

value: primary T cell

value: CD4+CD25+ Treg

tag: genotype

value: WT


title: TA4301_NSCLC_CTA | 008 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv


title: TA4301_NSCLC_CTA | 006 | PanCK pos

description:
NA
NA

value: Low Sequencing Saturation


title: HD3 and IPEX 3, stim, TCR

description:
Hashtag 2 = HD3; Hashtag 1 = IPEX3
S6_TCR_filtered_contig_annotations.csv

data_processing:
Raw .fastq files were processed usuing Cell Ranger Count v7.1.0, and reads were aligned to a the human genome GRCh38 (2020-A).
Data cleaning and preliminary analyses were performed using Seurat to generate the supplementary data files provided.
Assembly: GRCh38 (2020-A)
Supplementary files format and content: Cell Ranger Output Files: filtered feature-barcode matrices (including ADT data) and filtered TCR annotations
Library strategy: scTCR-seq

tag: condition

value: mixed sample (HD3 and IPEX 3)

value: Blood

value: CD4+ T cells

tag: library type

value: VDJ (TCR)

value: CD3/CD28 Stimulation


title: WT Treg, without stimulation, repeat 2

value: No


title: TA4301_NSCLC_CTA | 005 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: Non-responder


title: WT Treg, with stimulation, repeat 1


title: HD2 and IPEX 2, stim, TCR

description:
Hashtag 2 = HD2; Hashtag 1 = IPEX2
S5_TCR_filtered_contig_annotations.csv

value: mixed sample (HD2 and IPEX 2)


title: M11.Enrich

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

value: 45 years

tag: gender

value: Male


title: M10.Input

value: Input


title: HD1 and IPEX 1, stim, TCR

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S4_TCR_filtered_contig_annotations.csv

value: mixed sample (HD1 and IPEX 1)

tag: tissue


title: WT Treg, without stimulation, repeat 1

value: Splenocyte

value: primary T cell

value: CD4+CD25+ Treg

value: WT

tag: treatment


title: TA4301_NSCLC_CTA | 004 | PanCK neg

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK neg

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Responder

tag: followup

value: Alive


title: M10.Enrich

tag: cell type


title: TA4301_NSCLC_CTA | 004 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

value: PanCK pos

tag: status

tag: plate coord

tag: initial data_file


title: M9.Input

value: Peripheral mononuclear blood cell

value: Middle

value: 46 years

value: Female


title: M11.Input

value: Discovery

value: 45 years

value: Male


title: sch9, DSB, Stationary 8day, biol rep2

first: Xin

last: Wang

address: 300 Longwood Ave,

institute: Boston children's hospital

description:
The library has the forward index: CAC and reverse index: CAT. A total of  40720 colony number was in this library.
Stationary sch9 8 day rep1

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Reference: Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Reference: Methods of Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

source_name: No

growth_protocol: For amplicon sequencing analysis in normal conditions, cells were grown in YEPD (1% yeast extract, 2% peptone, 2% dextrose) o/n to saturation. Cells were washed twice in YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) media and inoculated in 10 ml of YEP-Raffinose and grown overnight. Once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For all analyses in stationary phase cells, we followed a previously established protocol for yeast growth (Hu et al., 2013). Yeasts were initially streaked out on YEPD plates and individual colonies were inoculated in 3 ml SC media (1.72g/L yeast nitrogen base without amino acids (USBiological, cat# Y2030), 2g/L amino acid mix (Bufferad, cat#S0051), 0.5% ammonium sulfate, 2% dextrose) and incubated overnight at 30 °C. The culture was diluted into fresh 50 mL SC media in 250 mL flasks to an OD600 of 0.1. Logarithmic growth phase control cells were plated when the culture reached 1x107 cells/ml. Cells were incubated on a shaker for 24 hrs (day 1), 3 days, 8 days, 16 days or as specified in individual experiments and plated on YEPGal plates for HO induction. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. Populations of old yeast mother cells were isolated as previously described (Tsuchiyama et al., 2013) with the following modifications. 3x10e8 yeast cells from a fresh log-phase culture in YEPD were treated with 3 mg of Sulfo-NHS-LC-Biotin (Thermo Scientific) and were used to seed a 1L culture in YEP-Raffinose. Seeded cultures were incubated with shaking at 30 °C for 15 hours to age biotin-labeled cells. The aged biotin-labeled cells were isolated using 1 mL Dynabeads Biotin Binder (Thermo Scientific). Three rounds of aging and sorting were conducted to obtain old mother cells with an average replicative age of around 20. Control young cells were obtained from last sorting and wash.

extract_protocol:
All colonies from YEP-Galactose plates were collected, pooled together and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl.
The construction of the sequencing library was adapted from Illumina’s amplicon sequencing protocol #15044223 Rev. B. Two rounds of PCR were performed to construct the sequencing library. For each sample, 3.2 μl genomic DNA, 0.5 μl 10 μM primers and 12.5 μl KAPA HiFi HotStart ReadyMix (Roche, 7958927001) was used for the first round of PCR for a total volume of 25 μl. The forward primers are 66-mers that contain (5’ to 3’): 33 bases Illumina adapter sequence, 3 bases unique home index, and 30 bases targeting the Mata locus which is located 11 bp upstream the HO cleavage site. The reverse primers are 66-mers that contain (5’ to 3’): 34 bases Illumina adapter sequence, 3 bases unique home index, and 29 bases targeting the MATa locus which is located 18 bp downstream the HO cleavage site. The following conditions were used for the first round of PCR: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 18μl PCR product was purified with 20μl AMPure XP beads (Beckman Coulter, A63880) and eluted with 52.5 μl 10 mM Tris pH 8.5. For the second round of PCR, 5 μl purified PCR product, 5 μl Nextera XT V2 Index (Illumina, FC-131-2001) primer N7xx, 5 μl index primer S5xx, and 25 μl KAPA HiFi HotStart ReadyMix were used. The total volume of PCR is 50 μl. The following conditions were used for PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 40 μl PCR product was purified with 48 μl AMPure XP beads and eluted with 27.5 μl 10 mM Tris pH 8.5. The DNA concentration of each sample was determined with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850) and the average size of the DNA was determined with TapeStation. The DNA was diluted to 4 nM using 10 mM Tris pH 8.5. An equal amount of DNA was pooled from ~20 samples into the library. The pooled library and PhiX library (Illumina, FC‐110‐3001) were denatured with 0.2 M NaOH separately and diluted with pre-chilled HT1 to 12 pM. 540μl pooled library and 60 μl PhiX were mixed, incubated at 96 °C for 2 min and immediately placed in an ice-water bath for 5 min.
The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003) for amplicon sequencing.

treatment_protocol: For growing cells once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For stationary phase cells, cells were plated after 1,2,3,8,16 days of incubation in SC media on YEPGalactose plates. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. For aged cells and control young cells, they were plated on YPE-Gal plates.

value: No

tag: cell line

value: mutant isogenic to JKM139

tag: genotype

value: sch9::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary pol4 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: TA4301_NSCLC_CTA | 003 | Geometric Segment

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

tag: roi

tag: segment

value: Geometric Segment

value: Non-responder


title: M9.Enrich

tag: age group

tag: group

tag: assay

value: Enrich

tag: age


title: HD2 and IPEX 2, unstim, TCR

description:
Hashtag 2 = HD2; Hashtag 1 = IPEX2
S2_TCR_filtered_contig_annotations.csv

tag: condition

value: mixed sample (HD2 and IPEX 2)

tag: tissue

value: Blood

value: CD4+ T cells

tag: library type

value: VDJ (TCR)

tag: treatment

value: No Stimulation


title: TA4301_NSCLC_CTA | 002 | PanCK neg

description:
NA
NA

value: NSCLC

value: Immunotherapy

value: PanCK neg

tag: qcflags

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

tag: qc fail

value: Fail

tag: area

tag: aoinucleicount

tag: patient id

tag: response

tag: followup

value: Deceased


title: M8.Input

tag: cell type

value: Peripheral mononuclear blood cell

value: Middle

value: Discovery

value: Input

value: 47 years

tag: gender

value: Male


title: lig4, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: TGC and reverse index: GCA. A total of  4440 colony number was in this library.
Stationary lig4 8 day rep2

value: No

tag: cell line

value: mutant isogenic to JKM139

tag: genotype

value: lig4::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary lig4 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: HD1 and IPEX 1, unstim, TCR

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S1_TCR_filtered_contig_annotations.csv

value: mixed sample (HD1 and IPEX 1)

value: Blood

value: CD4+ T cells

value: VDJ (TCR)

value: No Stimulation


title: TA4301_NSCLC_CTA | 001 | PanCK neg

description:
NA
NA

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK neg

value: Low Nuclei Count,Low Negative Probe Count,Low Surface Area

value: Fail

value: Responder

tag: status

value: Alive

tag: plate coord

tag: initial data_file


title: lig4, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: TCC and reverse index: CTT. A total of  5760 colony number was in this library.
Stationary lig4 8 day rep1

tag: tissue

tag: treatment


title: M8.Enrich

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

value: Discovery

tag: assay

value: Enrich

tag: age

value: 47 years

value: Male


title: TA4301_NSCLC_CTA | 002 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: PanCK pos

tag: area

tag: aoinucleicount

tag: patient id

tag: response

value: Non-responder

value: Deceased


title: HD3 and IPEX 3, stim, GEX

tag: condition

value: mixed sample (HD3 and IPEX 3)

value: Blood

tag: cell type

value: CD4+ T cells

tag: library type

value: mRNA

value: CD3/CD28 Stimulation


title: HD2 and IPEX 2, stim, GEX

value: mixed sample (HD2 and IPEX 2)


title: rad51, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: CAG and reverse index: GAG. A total of  16000 colony number was in this library.
Stationary rad51 8 day rep2

value: No

tag: cell line

value: mutant isogenic to JKM139

tag: genotype

value: rad51::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary rad51 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: HD3 and IPEX 3, unstim, TCR

description:
Hashtag 2 = HD3; Hashtag 1 = IPEX3
S3_TCR_filtered_contig_annotations.csv

value: VDJ (TCR)

value: No Stimulation


title: M7.Enrich

value: Peripheral mononuclear blood cell

value: Middle

value: Discovery

value: Enrich

value: 48 years

tag: gender


title: rad51, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: CTC and reverse index: GGT. A total of  20720 colony number was in this library.
Stationary rad51 8 day rep1


title: pol4, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: TTC and reverse index: GTC. A total of  20880 colony number was in this library.
Stationary pol4 8 day rep1

value: pol4::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary pol4 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: L Pleural Fluid

city: Pittsburgh

first: Kai

last: Ding

state: PA

address: 204 Craft Ave

institute: University of Pittsburgh

data_processing:
Reads alignment to GRCh38 Ensembl v82 : Salmon v0.8
Gene level expression estimate: tximport
Data normalization: log2 transformed trimmed mean of M-values normalized count per million
Assembly: GRCh38 Ensembl v82
Supplementary files format and content: WCRC25.log2.tmmNorm.cpm.txt: Tab-delimited text file includes genes as rows, samples as columns.

source_name: Fluid

growth_protocol: WCRC25 is cultured in DMEM + 10% FBS.

extract_protocol:
AllPrep DNA/RNA FFPE Kit (Qiagen #80234).
Illumina’s TruSeq RNA Access Library kit.
Libraries were sequenced at 40-50 million reads per sample on the Illumina NextSeq 500 platform with High Output flow cell (2 x 75, stranded, paired-end reads).

tag: disease

value: Breast cancer (invasive lobular carcinoma)

value: Fluid

value: mixed cell types


title: HD3 and IPEX 3, unstim, GEX

value: mixed sample (HD3 and IPEX 3)

tag: tissue

value: Blood

value: CD4+ T cells

value: mRNA


title: pol32, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: ACG and reverse index: GTG. A total of  6500 colony number was in this library.
Stationary pol32 8 day rep2

value: No

value: mutant isogenic to JKM139

value: pol32::natMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

tag: treatment

value: Stationary pol32 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: pol32, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: AAG and reverse index: CGT. A total of  6520 colony number was in this library.
Stationary pol32 8 day rep1


title: M6.Enrich

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

value: 49 years

value: Female


title: HD2 and IPEX 2, unstim, GEX

value: mixed sample (HD2 and IPEX 2)

value: No Stimulation


title: nuc1-ND, DSB, Stationary 8day, biol rep4

description:
The library has the forward index: AGG and reverse index: GGA. A total of  36816 colony number was in this library.
Stationary nuc1-ND 8 day rep4

value: nuc1-H138A DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1-ND 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: HD1 and IPEX 1, unstim, GEX

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S1_GEX_filtered_feature_bc_matrix.h5

value: mixed sample (HD1 and IPEX 1)


title: FR999_GBM_PVM_Men_7 [FR999_GBM_PVM_Men_7]

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

description: reference_mapped_celseq2_ctrl_cd206_gate_no_lowq_cells.H5Seurat

data_processing:
Celseq2: Fastq files were aligned using STAR v2.7.10a with default parameters. 10X: Non-multiplexed files were run with Cellranger v7.1.0 count functionality, multiplexed and fixed RNA profiling samples were run using the Cellranger v7.1.0. multi functionality.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
The number of observed UMIs was converted into transcript counts using Seurat v4 Hao et al, Cell 2021 10.1016/j.cell.2021.04.048
GENCODE human genome release 33
Assembly: Celseq2: matrix files as output by StarSolo, with up to 192 cells per sample. 10X h5 files with counts information and, where available CITE-Seq and multiplexing information

source_name: Bain or brain tumor

extract_protocol: Single-cell RNA sequencing using 10x and Cel-Seq2 was conducted on cell suspensions and after nuclei extraction from fresh frozen sections or formalin-fixed formalin embedded tissues. A part of the single cell analyses was multilexed and analyzed using CITE-Seq.

value: Bain or brain tumor

value: CD45-CD206-positive cells

tag: developmental stage

value: postnatal


title: UN Pleural Fluid

value: Breast cancer (invasive lobular carcinoma)

value: Fluid

value: mixed cell types


title: M7.Input

tag: group

value: Discovery

tag: assay

value: Input

value: 48 years

value: Male


title: M5.Enrich

value: Peripheral mononuclear blood cell

value: Middle

value: Enrich

tag: age

value: 41 years


title: TA4301_NSCLC_CTA | 001 | PanCK pos

description:
4301_CTA_QC.csv
4301_CTA_norm.csv

value: NSCLC

value: Immunotherapy

tag: roi

tag: segment

value: PanCK pos

tag: area

tag: aoinucleicount

value: Responder

tag: followup

tag: status

value: Alive

tag: plate coord

tag: initial data_file


title: HD1 and IPEX 1, stim, GEX

description:
Hashtag 2 = HD1; Hashtag 1 = IPEX1
S4_GEX_filtered_feature_bc_matrix.h5

tag: condition

value: mixed sample (HD1 and IPEX 1)

value: Blood

tag: cell type

value: CD4+ T cells

tag: library type

value: mRNA

value: CD3/CD28 Stimulation


title: M4.Input

value: Discovery

value: Input

tag: gender


title: Chest Skin Metastasis 1

description: 34 1A

source_name: Tumor

tag: disease

value: Breast cancer (invasive lobular carcinoma)

tag: tissue

value: Tumor

value: mixed cell types


title: FR960_DM_1_2 [FR960_DM_1_2]

value: Bain or brain tumor

value: CD45-CD206-positive cells

tag: developmental stage

value: postnatal


title: WCRC25 DMEM

description: Cell Line DMEM

tag: cell line

value: cancer epithelial


title: FR999_GBM_Men_4 [FR999_GBM_Men_4]


title: M6.Input

value: Peripheral mononuclear blood cell

tag: age group

value: Middle

tag: group

tag: assay

tag: age

value: 49 years

value: Female


title: M4.Enrich

value: Enrich

value: 41 years

value: Male


title: nuc1-ND, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: AAG and reverse index: CGT. A total of  24552 colony number was in this library.
Stationary nuc1-ND 8 day rep2

value: No

value: mutant isogenic to JKM139

tag: genotype

value: nuc1-H138A DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

tag: treatment

value: Stationary nuc1-ND 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: FR960_DM_1_1 [FR960_DM_1_1]


title: L Axilla LN Metastasis

value: Breast cancer (invasive lobular carcinoma)

value: Tumor


title: nuc1, DSB, Stationary 16day, biol rep4

description:
The library has the forward index: TTG and reverse index: CTG. A total of  38400 colony number was in this library.
Stationary nuc1 16 day rep4

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 16 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: M3.Input

value: Discovery

value: Input

value: 50 years


title: Peritoneum Metastasis 2

value: mixed cell types


title: M5.Input

value: Peripheral mononuclear blood cell

value: Middle


title: nuc1-ND, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: ACG and reverse index: GTG. A total of  38256 colony number was in this library.
Stationary nuc1-ND 8 day rep3


title: Peritoneal Fluid

value: Fluid


title: nuc1, DSB, Stationary 16day, biol rep3

description:
The library has the forward index: TAG and reverse index: GTA. A total of  18240 colony number was in this library.
Stationary nuc1 16 day rep3


title: FR742_Men_2_4 [FR742_Men_2_4]

value: Bain or brain tumor

value: CD45-CD206-positive cells

value: postnatal


title: Chest Skin Metastasis 2

description: 34 2A


title: M3.Enrich

value: Enrich

value: Female


title: FR742_Men_1_3 [FR742_Men_1_3]


title: Peritoneum Metastasis 1


title: nuc1-ND, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: ATC and reverse index: CAG. A total of  26376 colony number was in this library.
Stationary nuc1-ND 8 day rep1

value: No

value: mutant isogenic to JKM139

value: nuc1-H138A DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1-ND 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: M2.Input

value: Validation

value: Male


title: Stomach Metastasis

value: Breast cancer (invasive lobular carcinoma)

value: Tumor


title: FR685_Men_1 [FR685_Men_1]


title: M2.Enrich

value: 50 years


title: nuc1, DSB, Stationary 16day, biol rep1

description:
The library has the forward index: CAG and reverse index: GAG. A total of  31776 colony number was in this library.
Stationary nuc1 16 day rep1

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 16 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: L Breast Masectomy 1

description: 28 1P

value: mixed cell types


title: L Breast Mastectomy 2

description: 28 1E


title: M1.Input

value: Peripheral mononuclear blood cell

value: Middle

value: Input

value: 42 years


title: nuc1, DSB, Stationary 8day, biol rep6

description:
The library has the forward index: TAC and reverse index: CGA. A total of  36768 colony number was in this library.
Stationary nuc1 8 day rep6

value: Stationary nuc1 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: M1.Enrich

value: Enrich


title: FR648_Men_3 [FR648_Men_3]

value: Bain or brain tumor

value: CD45-CD206-positive cells

value: postnatal


title: FR648_GM_PVM_6 [FR648_GM_PVM_6]


title: nuc1, DSB, Stationary 8day, biol rep4

description:
The library has the forward index: TTC and reverse index: GTC. A total of  22128 colony number was in this library.
Stationary nuc1 8 day rep4

value: No

value: mutant isogenic to JKM139


title: L Breast Biopsy 2

value: Breast cancer (invasive lobular carcinoma)


title: nuc1, DSB, Stationary 8day, biol rep5

description:
The library has the forward index: TGG and reverse index: CCT. A total of  24096 colony number was in this library.
Stationary nuc1 8 day rep5


title: FR648_GM_WM_PVM_9 [FR648_GM_WM_PVM_9]


title: FR648_CP_4 [FR648_CP_4]


title: nuc1, DSB, Stationary 16day, biol rep2

description:
The library has the forward index: TCC and reverse index: CTT. A total of  25056 colony number was in this library.
Stationary nuc1 16 day rep2


title: L Breast Biopsy 1

description: 25 2A

value: Tumor


title: nuc1, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: TAC and reverse index: CGA. A total of  15696 colony number was in this library.
Stationary nuc1 8 day rep3


title: Y24.Input

value: Young

value: Discovery

value: 26 years

value: Female


title: Y24.Enrich

value: Peripheral mononuclear blood cell


title: R Breast Masectomy

description: 28 5E

value: mixed cell types


title: occl_chor_00h_ck4Mr_s114

value: choroid

tag: eye treatment

value: occl

tag: timept

tag: chickid

tag: eye

value: right

tag: Sex

value: M


title: Y23.Input

tag: cell type

value: Input

value: Male


title: nuc1, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: CTC and reverse index: GGT. A total of  14064 colony number was in this library.
Stationary nuc1 8 day rep2

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y23.Enrich

value: Enrich

tag: gender


title: FR645_DM_8 [FR645_DM_8]

value: Bain or brain tumor

value: CD45-CD206-positive cells

value: postnatal


title: R Breast Biopsy

description: 25 1A

tag: disease

value: Breast cancer (invasive lobular carcinoma)

value: Tumor


title: nuc1, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: ATC and reverse index: CAG. A total of  27408 colony number was in this library.
Stationary nuc1 8 day rep1

tag: tissue

value: No

value: mutant isogenic to JKM139


title: nuc1, DSB, Stationary 3day, biol rep5

description:
The library has the forward index: AGG and reverse index: GGA. A total of  23088 colony number was in this library.
Stationary nuc1 3 day rep5

value: Stationary nuc1 3 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: FR541_GM_WM_PVM_5 [FR541_GM_WM_PVM_5]

tag: developmental stage


title: FR541_Men_2 [FR541_Men_2]


title: Y22.Input

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: 27 years

value: Female


title: nuc1, DSB, Stationary 3day, biol rep4

description:
The library has the forward index: TCG and reverse index: GAT. A total of  21360 colony number was in this library.
Stationary nuc1 3 day rep4

tag: cell line


title: Palatal shelves from GD12 embryos, V3

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

data_processing:
An average of 31.5 million paired-end reads  were sequenced per sample. An initial check of quality was assessed for each pair-mate using FastQC. After reads were assessed for quality, paired-end reads were trimmed for adapter contamination using trim_galore run with default parameters. Trimmed and filtered reads were aligned to the Mus musculus genome (mm10) using RSEM v1.3.1 which utilized STAR v2.7.0. An average of 27.3 million reads passed quality filtering through STAR, and an average of 23.4 million reads (85.6%) were successfully aligned for each sample. Gene expression was calculated using RSEM which employed a forward probability of 0.0, followed by differential expression analysis using DESeq2 [Love (2014) Genome Biology]. To account for multiple comparisons and to reduce false positives, a false discovery rate (FDR) of 0.05 was employed in the determination of differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts, TPMs, FPKMs per sample

source_name: Vehicle control for AzadC

extract_protocol:
Palatal shelves from GD12 embryos were microdissected under a stereomicroscope, snap-frozen in liquid nitrogen, and then stored at −80 °C. Embryos were genotyped, and palatal shelves from two embryos of the same genotype were pooled for RNA extraction. Three RNA samples (from six embryos) for each group were used for subsequent sequencing. No more than three embryos of the same genotype were used from a single litter, and embryos from at least three litters were included for each genotype. RNA was isolated using the Illustra RNAspin kit (GE) using the manufacturer recommendations with on-column DNase I digestion. RNA was eluted in 30 μL of water, and RNA concentration was quantified using a Qubit fluorometer (ThermoFisher Scientific).
Approximately 100 ng of total RNA  from three pooled RNA samples (from six embryos) for each group was used for sequence library construction following instructions of the NuGen mRNA sample prep kit (cat# 0348).

value: Embryonic palatal shelves

value: WT

value: 5-aza-2'-deoxycytidine vehicle control


title: Palatal shelves from GD12 embryos, V2


title: Y22.Enrich

tag: age group

value: Enrich


title: Palatal shelves from GD12 embryos, V1


title: nuc1, DSB, Stationary 3day, biol rep3

description:
The library has the forward index: TGC and reverse index: GCA. A total of  22800 colony number was in this library.
Stationary nuc1 3 day rep3

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: Y21.Input

tag: group

value: Input

value: Male


title: FR240_Men_1_3 [FR240_Men_1_3]

description: reference_mapped_celseq2_ctrl_cd206_gate_no_lowq_cells.H5Seurat

value: Bain or brain tumor

value: CD45-CD206-positive cells

value: postnatal


title: FR240_Men_2_4 [FR240_Men_2_4]


title: CP_5 [CP_5]

value: CD45-positive cells


title: nuc1, DSB, Stationary 3day, biol rep2

description:
The library has the forward index: CTG and reverse index: CCA. A total of  22560 colony number was in this library.
Stationary nuc1 3 day rep2

value: No

value: mutant isogenic to JKM139

value: Stationary nuc1 3 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: nuc1, DSB, Stationary 3day, biol rep1

description:
The library has the forward index: CAC and reverse index: CAT. A total of  19104 colony number was in this library.
Stationary nuc1 3 day rep1


title: Y21.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

tag: assay


title: Palatal shelves from GD12 embryos, K1

source_name: conditional KO animal

value: Embryonic palatal shelves

value: DNMT1 KO

value: untreated


title: Y20.Enrich

value: Enrich

tag: age

value: 23 years

value: Female


title: Y19.Input

value: Input

value: 27 years

value: Male


title: Y20.Input


title: Palatal shelves from GD12 embryos, K2

tag: genotype


title: WT, DSB, Stationary 16day, biol rep7

description:
The library has the forward index: ATG and reverse index: GCT. A total of  4152 colony number was in this library.
Stationary WT 16 day rep7

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

tag: treatment

value: Stationary WT 16 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y19.Enrich


title: Palatal shelves from GD12 embryos, C2

source_name: Control animal

value: WT


title: Patient 2, scRNAseq from skin and blood

city: Vienna

first: Johanna

last: Strobl

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: 10x Genomics single cell RNA-seq using cell hashing technique for blood and skin cell distinction

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files., Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Assembly: hg38
Supplementary files format and content: Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

source_name: Skin and peripheral blood

extract_protocol:
Human skin tissue was digested for 2h in Collagenase and DNAse passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Peripheral blood mononuclear cells were isolated from the blood using Ficoll gradients.
Single-Cell 5’ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s instructions

tag: disease state

value: human acute Graft-versus host disease (GVHD)

value: Skin and peripheral blood

value: Skin cells, peripheral blood leukocytes

value: naive


title: Palatal shelves from GD12 embryos, C3

value: Embryonic palatal shelves


title: WT, DSB, Stationary 16day, biol rep6

description:
The library has the forward index: AAG and reverse index: CGT. A total of  192 colony number was in this library.
Stationary WT 16 day rep6

value: No


title: Patient 1, scRNAseq from skin and blood


title: Palatal shelves from GD12 embryos, C1

value: untreated


title: WT, DSB, Stationary 16day, biol rep5

description:
The library has the forward index: TTG and reverse index: CTG. A total of  270000 colony number was in this library.
Stationary WT 16 day rep5


title: Palatal shelves from GD12 embryos, A3

source_name: AzadC treated animal


title: WT, DSB, Stationary 16day, biol rep4

description:
The library has the forward index: TGG and reverse index: CCT. A total of  270000 colony number was in this library.
Stationary WT 16 day rep4


title: Y18.Input

value: Peripheral mononuclear blood cell

value: Young

value: Validation


title: Y18.Enrich

value: Enrich


title: nexn-/-, biological replicate 2

city: Ulm

first: Janessa

last: Hofeichner

address: Albert-Einstein-Allee 23

department: Internal Medicine II

institute: Uniklinik Ulm

data_processing:
Raw sequencing data is screened for reads originating from rRNA using RiboDetector (eurofins genomics, INVIEW transcriptome)
High quality sequence reads are aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference), run through Sentieon framework, along with the known gene models. (eurofins genomics, INVIEW transcriptome)
Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM tool. (eurofins genomics, INVIEW transcriptome)
Assembly: GRCz11
Supplementary files format and content: Sample-wise, gene wise read counts, TPM value and FPKM value

organism: Danio rerio

source_name: whole organism

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit. 1,25 µg total RNA was used for library preparation.
INVIEW transcriptome, done by eurofins Genomics

value: whole organism

value: nexn knockout


title: WT, DSB, Stationary 16day, biol rep3

description:
The library has the forward index: CTC and reverse index: GGT. A total of  7480 colony number was in this library.
Stationary WT 16 day rep3

value: S. cerevisiae haploid strain


title: Palatal shelves from GD12 embryos, K3

value: DNMT1 KO


title: nexn-/-, biological replicate 1


title: Y17.Input

value: Discovery

value: Input

value: 25 years

value: Male


title: WT, DSB, Stationary 16day, biol rep2

description:
The library has the forward index: AAG and reverse index: CGT. A total of  2820 colony number was in this library.
Stationary WT 16 day rep2

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary WT 16 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Palatal shelves from GD12 embryos, A1

value: Embryonic palatal shelves

value: WT


title: WT, DSB, Stationary 16day, biol rep1

description:
The library has the forward index: TGC and reverse index: GCA. A total of  66480 colony number was in this library.
Stationary WT 16 day rep1

value: No


title: Palatal shelves from GD12 embryos, A2


title: nexn+/+, biological replicate 2


title: nexn+/+, biological replicate 1


title: WT, DSB, Stationary 8day, biol rep10

description:
The library has the forward index: AGC and reverse index: CTA. A total of  18000 colony number was in this library.
Stationary WT 8 day rep10

value: Stationary WT 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: WT, DSB, Stationary 8day, biol rep9

description:
The library has the forward index: CAC and reverse index: CAT. A total of  19776 colony number was in this library.
Stationary WT 8 day rep9


title: OPC, Day3, siPdgfra, rep.1

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company

data_processing:
OmicSoft ArrayStudio (v11, QIAGEN)
Sequence reads were mapped to mm10 and counted by RNA-seq pipeline workflow in OmicSoft ArrayStudio
Differentially expressed genes were identified by DESeq(V2) one way method in OmicSoft Studio function
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include statistics values for each comparison

source_name: primary oligodendrocyte precursor cells

growth_protocol: Mouse primary oligodendrocyte precursor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 80 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit for NeoPrep followingthe manufacturer's protocol.

tag: strain

value: primary oligodendrocyte precursor cells

value: Pdgfra knockdown

tag: time


title: Y16.Enrich

source_name: Peripheral mononuclear blood cell

value: Peripheral mononuclear blood cell

value: Young

value: Enrich


title: OPC, Day3, siPdgfra, rep.2


title: NC-3

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

description:
BD
RX20221125-13

data_processing:
the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
Unique molecular identifier (UMI) count matrix of 2 SAP and 3 JZL184and 3 CON samples were retrieved form the raw sequence data. The R package Seurat were used to convert the UMI count matrix into a Seurat object (Butler et al. 2018) (version 4.0.4). The low-quality cells with UMI numbers <1000, and detected genes < 500 and over 15% mitochondrial-derived UMI counts were removed. Genes that were detected in less than 5 cells were removed. The filtered UMI count matrix of each sample were used for downstream analyses.
After quality control, log normalization were performed to the UMI count matrix. FindIntegration Anchors function of Seurat were conducted to create potential Anchors through top 2000 variable genes.
IntegrateData function was perofored to integrate data of different samples. Based on the integrated data matrix, dimensionality reduction was achieved by performing the principal omponent analysis (PCA)
top 50 PCs were selected for downstream analysis based on the plots by performing Elbowplot function in Seurat. FindClusters function in Seurat were performed to identify the main cell clusters with default resolution parameter (res = 0.6)
Supplementary files format and content: tab-delimited text files and  matrix files

organism: Rattus norvegicus

source_name: ileal tissue

extract_protocol:
Newly collected fresh ileal tissue were washed in ice-cold RPMI1640，cut into small pieces (<1 mm) with the sterile scissors on ice. The tissues were dissociated using Collagenase Ⅱ (Sigma, V900892-100MG), Trypsin (Hyclone, SH30042.01) and DNase I (Sigma, DN25-1G). The obtained single-cell solution was sieved through a 70 μM cell strainer (Corning). Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio, R1010)
Single-cell cDNA libraries were generated as described in detail (Single cell 3’ whole transcriptome amplification protocol, BD Rhapsody) using successfully prepared single-cell suspensions. In brief, freshly single-cell suspensions were washed three times, and counted and subsequently loaded onto a cartridge, lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell capture beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent extension using the WTA extension primers, purified, and then purified using SPRIselect magnetic beads (Beckman Coulter). Quantity of PCR products was determined by Qubit 4.0 with Qubit dsDNA HS Assay (Q32854)

value: ileal tissue

tag: strain background

value: Sprague-Dawley (SD)

value: male

value: healthy

value: vehicle (CON)


title: OPC, Day3, siSbp2l, rep.2

value: Secisbp2l knockdown


title: WT, DSB, Stationary 8day, biol rep7

city: Boston

description:
The library has the forward index: AGC and reverse index: CTA. A total of  23328 colony number was in this library.
Stationary WT 8 day rep7

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: Y15.Input

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) and Drosophila melanogaster genome (dmel-all-chromosome-r6.36) using STAR (v2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Homo sapiens (Ensembl: GRCh38.94) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively.
Assembly: GRCh38 and dmel-all-chromosome-r6.36
Supplementary files format and content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

value: Discovery

value: Input

value: 26 years

value: Female


title: NC-2

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description:
BD
RX20221125-12

tag: Sex


title: OPC, Day3, NC siRNA#2, rep.2

value: primary oligodendrocyte precursor cells

value: WT


title: WT, DSB, Stationary 8day, biol rep6

description:
The library has the forward index: AGG and reverse index: GGA. A total of  19824 colony number was in this library.
Stationary WT 8 day rep6

value: No

tag: cell type

value: Stationary WT 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y15.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: Enrich

tag: gender


title: OPC, Day3, siSbp2l, rep.1


title: NC-1

description:
BD
RX20221125-11

value: ileal tissue

value: Sprague-Dawley (SD)

value: male


title: Y14.Input

value: 30 years


title: OPC, Day3, NC siRNA#2, rep.1


title: Y14.Enrich


title: MAGL-2

description:
BD
RX20221125-9

value: severe acute pancreatitis (SAP) model

value: monoacylglycerol lipase (MAGL) inhibitor (JZL184)


title: OPC, Day3, NC siRNA#1, rep.2


title: WT, DSB, Stationary 8day, biol rep4

description:
The library has the forward index: AGC and reverse index: CTA. A total of  24960 colony number was in this library.
Stationary WT 8 day rep4

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: WT, DSB, Stationary 8day, biol rep5

description:
The library has the forward index: ATC and reverse index: CAG. A total of  20064 colony number was in this library.
Stationary WT 8 day rep5


title: Y17.Enrich

value: Discovery

value: 25 years

value: Male


title: OPC, Day3, NC siRNA#1, rep.1

value: primary oligodendrocyte precursor cells

value: WT


title: Y13.Input

value: Input

value: 24 years


title: Y16.Input

value: Peripheral mononuclear blood cell

value: Young


title: MAGL-1

description:
BD
RX20221125-8

value: ileal tissue


title: WT, DSB, Stationary 8day, biol rep8

description:
The library has the forward index: ATC and reverse index: CAG. A total of  18912 colony number was in this library.
Stationary WT 8 day rep8

value: No

value: Stationary WT 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: SAP-3

description:
BD
RX20221125-7

value: Sprague-Dawley (SD)

value: male

value: vehicle


title: OPC, Day3, mock, rep.2


title: WT, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: ATC and reverse index: CAG. A total of  20920 colony number was in this library.
Stationary WT 8 day rep2

value: S. cerevisiae haploid strain