title: FiTAc-seq for H3K27ac of ES5090L WT_1+2


title: XPC054_p9_v2

status: Public on Sep 12 2022

type: SRA

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

library_source: transcriptomic

data_processing:
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Pair end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio)
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text file (.csv) include RAW counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: mesanchymal stem cell derivated from hIPSc

growth_protocol: The hIPSc were differentiated into MSC, cultivated in KO DMEM supplemented 15% FBS, 10ng Beta FGF, 1mM ascobic acid 2-P, 1X glutamax, 1X NEAA, 50 µM Beta mercaptoethanol

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay.  (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: cell type

tag: disease state

value: HGPS-l (Hutchinson-Gilford progeria syndrome like)

tag: batch

value: II


title: FiTAc-seq for H3K27ac of ES5090L WT_6

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse SCLC tumor

extract_protocol:
FiTAc-seq has been previously described, briefly, ten 1mm mice tumor tissue cores were used for ChIP profiling. Samples were treated with xylene to remove paraffin and then rehydrated with 100% ethanol for 10 min, 70% ethanol for 10 min, and water for another 10 min. Hydrated tissues were resuspended in 200ul of 1% SDS lysis buffer with 4ul of 50× EDTA-free protease inhibitor cocktail (PIC) and 1ul of 1 M sodium butyrate, then incubated overnight at 65°C with constant agitation at 1,000 r.p.m. The homogenized tissues were sonicated with Bioruptor for 12 cycles of 30 second on and 30 second off at 4°C. The soluble chromatins were subject to ChIP assay as described above. Library preparation and sequencing were done as described above.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

tag: tissue

value: formalin-fixed, paraffin-embedded (FFPE) tissues

tag: genotype

value: Rb1fl/flTrp53fl/fl (RP)

tag: antibody

value: acetyl-histone H3K27  (Abcam, ab4729)


title: FiTAc-seq for H3K27ac of ES5090L WT_4


title: XPC054_p9

value: mesanchymal stem cell derivated from hIPSc


title: FiTAc-seq for H3K27ac of ES5090L WT_3


title: PBMC, during exercise, 80% VO2max replicate 3

city: Tucson

first: Tiffany

middle: Marie

last: Zuniga

state: AZ

address: 1501 N Campbell Ave.

department: School of Nutritional Health and Wellness

institute: University of Arizona

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FastQ files were converted into expression matrices using the “cellranger count” function provided by Cell Ranger 6.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from 6mL of ACD whole blood collected at rest,  80% VO2max, and +1hr post exercise by density gradient centrifugation (Cytiva Ficoll-PaqueTM, Fisher Scientific, Hampton, NH) and cryopreserved for later analysis. Isolated PBMCs from blood collected at rest, 80%, and +1H were then resuspended in a PBS/RNAlater solution and delivered to the University of Arizona Genetics Core for single cell RNA sequencing (scRNAseq) analysis using the 10x Genomics platform.
Targeted Gene Expression libraries generated from Chromium Single Cell 5’ Gene Expression and Chromium Single Cell V(D)J libraries comprised standard Illumina paired-end constructs which begin with P5 and end with P7. The gene expression libraries were quantified, normalized, pooled, and sequenced on an Illumina NextSeq500 sequencer.

value: Blood

value: PBMCs

tag: treatment

value: 80% VO2max


title: PBMC, pre, replicate 2

description: 10x Genomics

value: Pre


title: X1972_p8

value: HGPS (Hutchinson-Gilford progeria syndrome)


title: PBMC, 1hour recovery, replicate 1

description: 10x Genomics

value: 1 hour recovery


title: X_OM2_p8

value: Atypical Progeria syndrome


title: XhFF15_p8

value: CT young


title: PBMC, pre, replicate 1

description: 10x Genomics


title: 2018A99

value: I


title: 2018A98


title: 2018A97


title: PBMC, 1hour recovery, replicate 2

description: 10x Genomics


title: FiTAc-seq for H3K27ac of ES2606L WT_1


title: X_10742_L_p8

value: CT aged


title: 2018A95


title: 2018A94


title: 2018A93


title: 2018A103


title: FiTAc-seq for H3K27ac of ES5090L WT_7


title: PBMC, during exercise, 80% VO2max replicate 2

description: 10x Genomics


title: PBMC, pre, replicate 3

description: 10x Genomics


title: PBMC, during exercise, 80% VO2max replicate 1

description: 10x Genomics


title: 2018A102


title: 2018A100


title: 2018A83R

source_name: hIPSc

value: hIPSc


title: ips_1972_p120


title: ips_10742_L_p34


title: 2018A96


title: ips_hFF15_p59


title: 2018A81R


title: 2018A82R

value: HGPS-l (Hutchinson-Gilford progeria syndrome like)


title: SOX1 gRNA 3 NCI-H187 cells

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95
Transcript abundance was estimated using kallisto (v0.45.0)
Genome_build: GRCh38.95
Supplementary_files_format_and_content: Text files

source_name: small cell lung cancer

growth_protocol: NCI-H187 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.

value: cell line

tag: crispr-cas9 vector

tag: grna vector

value: pLenti-GFP-SOX1 sRNA3


title: ips_OM2_p37

value: II


title: 2018A79R


title: 2018A76R


title: NKX2-1 gRNA 3 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA3


title: 2018A77R


title: 2018A78R


title: SOX1 gRNA 2 NCI-H187 cells

value: pLenti-GFP-SOX1 sRNA2


title: SOX1 gRNA 1 NCI-H187 cells

value: pLenti-GFP-SOX1 sRNA1


title: 2018A80R


title: PB, KO, 3

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
rawCounts.csv
normalizedCounts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCm38 whole genome using Hisat2 v2.2.1
Read summarization was performed by the program featureCounts v2.0.1 as part of the SubRead package using the NCBI Mus musculus Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.32.1 in R
Assembly: GRCm38
Supplementary files format and content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary files format and content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

molecule: polyA RNA

source_name: Peripheral Blood

growth_protocol: in vivo

extract_protocol:
Peripheral blood was isolated from LysM or K2KO mice. Density gradient cetrifugation was performed and neutrophil purity was confirmed using flow cytometry. RNA was isolated using the RNeasy micro kit (Qiagen). RNA quantity and quality were assessed using NanoDrop (ThermoFisher) and Fragment Analyzer (Agilent).
RNA libraries were prepared for sequencing using the SMART-Seq v4 for CDNA and the Nextera XT kit for library creation on a NextSeq 550 instrument in a Paired-End 75 bp configuration.

tag: strain

value: Peripheral Blood

value: Neutrophil

tag: age

value: 8 weeks


title: 2018A75R


title: NKX2-1 gRNA 2 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA2


title: NKX2-1 gRNA 1 NCI-H187 cells

value: pLenti-GFP-NKX2-1 sRNA1


title: PB, KO, 4

description:
rawCounts.csv
normalizedCounts.csv


title: 2018A74R


title: PB, KO, 2

description:
rawCounts.csv
normalizedCounts.csv


title: PB, Cre, 4

description:
rawCounts.csv
normalizedCounts.csv

value: LysM


title: non-target gRNA 2 NCI-H187 cells

value: pLenti-GFP-NT sRNA2


title: non-target gRNA 1 NCI-H187 cells

value: pLenti-GFP-NT sRNA1


title: ips_PC054_p59

value: HGPS-l


title: PB, Cre, 2

description:
rawCounts.csv
normalizedCounts.csv


title: Parental H187 cells


title: SOX1 ChIP for H209

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig

source_name: Small cell lung cancer

growth_protocol: NCI-H345 was maintained in HITES medium (serum free) with 1% P/S. NCI-H1436 was maintained in HITES medium with 5% FBS and 1% P/S, the others Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin,

extract_protocol:
For SOX1, NKX2-1 and H3K27ac ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: Cell line


title: SOX1 ChIP for DMS 79


title: LTBR_AIR_vs_HEK-mLight3_3

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description: LTBR AIR vs HEK-mLight

data_processing:
Demultiplexing was performed with bcl2fastq v2.20.0.422 (Illumina)
Quality control and read mapping to the mouse reference genome (GRCm38, gencode,release23) was performed using an adapted version of the SnakePipes analysis pipeline (v1.2.2 including rDNA removal)
Inside the snakePipes Pipeline mapping was performed using STAR  with default values and gene counts were created by featrureCounts.
Quality control of the count matrix and DE-Gene calling was performed with DESeq2. Gene counts were imported and prefiltered with edgeR:filterByExpr and the fdr was set to 0.05. GO-Analysis was performed with genes UP-regulated with a log2FC>1 and fdr<0.05 using goseq. GESA analysis was performed using fgsea. Plots were created with ggplot2 and EnhancedVolcano
Genome_build: GRCm38, gencode,release2

source_name: regulatory T-cell

growth_protocol: murine regulatory T-cells were cultured with anti-CD3/CD28 stimulation and IL2 for 2 days,then transduced with MSCV retroviral vector containing ORFS for anti-CD19 CAR as control or DR3,LTBR or TNFR2 AIR.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit and RNA was eluted in 14 µL RNAse-free water. RNA quality was assessed using the Tapestation system 4200 and High-Sensitivity RNA screentape (Agilent).
7 µl of the RNA was used for generating RNA-seq libraries using the SMART-seq Stranded Kit from Takara.
Indexed libraries were pooled in an equimolar ratio and sequenced on an Illumina NextSeq 550 machine with NextSeq 500/550 High Output Kit v2.5 (75 cycles).

treatment_protocol: regulatory T-cells were rested without TCR stimulation for 24 h and afterwards coculturd with wildtype HEK cells or HEK cells expressing corresponding TNF family ligands. After 18 hour of coculture Tregs were stained and sorted via flow cytometry for CD4+CD25+CD90.1+ (Nr4a1+LAP+)

value: regulatory T-cell

tag: phenotype

tag: Sex

value: pooled male and female

tag: treatments

value: LTBR AIR vs HEK-mLight


title: SOX1 ChIP for H345


title: CD19_CAR_vs_HEK-mLight3_2

description: CD19 CAR vs HEK-mLight

value: CD19 CAR vs HEK-mLight


title: NKX2-1 ChIP for H345

value: NKX2-1 (Bethyl Laboratories, A300-BL4000)


title: NKX2-1 ChIP for COR-L88


title: NKX2-1 ChIP for H2087

source_name: Lung adenocarcinoma


title: LTBR_AIR_vs_HEK-mLight2_3

description: LTBR AIR vs HEK-mLight


title: PB, Cre, 1

description:
rawCounts.csv
normalizedCounts.csv


title: LTBR_AIR_vs_HEKcontrol2_1

description: LTBR AIR vs HEKwt

value: LTBR AIR vs HEKwt


title: LTBR_AIR_vs_HEKcontrol3_1

description: LTBR AIR vs HEKwt


title: NKX2-1 ChIP for H209


title: CD19_CAR_vs_HEK-mLight2_2

description: CD19 CAR vs HEK-mLight


title: PB, Cre, 3

description:
rawCounts.csv
normalizedCounts.csv


title: LTBR_AIR_vs_HEKcontrol1_1

description: LTBR AIR vs HEKwt


title: LTBR_AIR_vs_HEK-mLight1_3

description: LTBR AIR vs HEK-mLight


title: ChIP input for H196

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS
wig file was depth normalized and converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig

extract_protocol:
For H3K27ac, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.


title: TNFR2_AIR_mTNF6_3

description: TNFR2 AIR vs HEK-mTNF

value: sorted CD4+CD25+CD90.1+Nr4a1+LAP+

value: TNFR2 AIR vs HEK-mTNF


title: ChIP input for HCC33


title: ChIP input for H1963


title: ChIP input for H841


title: CD19_CAR_vs_HEK-mLight1_2

description: CD19 CAR vs HEK-mLight


title: CD19_CAR_mTNF6_2

description: CD19 CAR vs HEK-mTNF

value: sorted CD4+CD25+CD90.1+

value: CD19 CAR vs HEK-mTNF


title: ChIP input for H2171


title: ChIP input for SHP-77


title: TNFR2_AIR_control6_1

description: TNFR2 AIR vs HEKwt

value: TNFR2 AIR vs HEKwt


title: NKX2-1 ChIP for DMS 79


title: TNFR2_AIR_mTNF5_3

description: TNFR2 AIR vs HEK-mTNF


title: ChIP input for DMS 79


title: CD19_CAR_mTNF5_2

description: CD19 CAR vs HEK-mTNF


title: ChIP input for H187


title: ChIP input for H209


title: TNFR2_AIR_mTNF4_3

description: TNFR2 AIR vs HEK-mTNF


title: TNFR2_AIR_control4_1

description: TNFR2 AIR vs HEKwt


title: DR3_AIR_mTLA3_3

description: DR3 AIR vs HEK-mTL1A

value: DR3 AIR vs HEK-mTL1A


title: ChIP input for COR-L88


title: ChIP input for H2081_2


title: ChIP input for H1436_2


title: TNFR2_AIR_control5_1

description: TNFR2 AIR vs HEKwt


title: ChIP input for H2081_1


title: ChIP input for H82


title: ChIP input for H69


title: CD19_CAR_mTLA3_2

description: CD19 CAR vs HEK-mTL1A

value: CD19 CAR vs HEK-mTL1A


title: ChIP input for H1436_1


title: DR3_AIR_mTLA1_3

description: DR3 AIR vs HEK-mTL1A


title: CD19_CAR_mTLA2_2

description: CD19 CAR vs HEK-mTL1A


title: ChIP input for H526


title: DR3_AIR_control2_1

description: DR3 AIR vs HEKwt

value: DR3 AIR vs HEKwt


title: DR3_AIR_mTLA2_3

description: DR3 AIR vs HEK-mTL1A


title: H3K27ac ChIP for H69

value: acetyl-histone H3K27  (Abcam, ab4729)


title: CD19_CAR_mTLA1_2

description: CD19 CAR vs HEK-mTL1A


title: H3K27ac ChIP for H526


title: DR3_AIR_control1_1

description: DR3 AIR vs HEKwt


title: ChIP input for H345


title: CD19_CAR_CD3CD283_3_CD19_CAR_vsantiCD3_CD28beads

description: CD19 CAR vs antiCD3 CD28beads

value: CD19 CAR vs antiCD3 CD28beads


title: H3K27ac ChIP for H82

value: Cell line


title: CD19_CAR_mTNF4_2

description: CD19 CAR vs HEK-mTNF

value: regulatory T-cell


title: H3K27ac ChIP for H2081_2


title: H3K27ac ChIP for H2081_1


title: CD19_CAR_control3_2_CD19_CAR_vsPhoenix

description: CD19 CAR vs HEK

value: pooled male and female

value: CD19 CAR vs HEK


title: DR3_AIR_control3_1

description: DR3 AIR vs HEKwt


title: CD19_CAR_control2_2_CD19_CAR_vsPhoenix

description: CD19 CAR vs HEK


title: H3K27ac ChIP for H1436_2


title: CD19_CAR_CD3CD282_3_CD19_CAR_vsantiCD3_CD28beads

description: CD19 CAR vs antiCD3 CD28beads


title: H3K27ac ChIP for H841


title: H3K27ac ChIP for H1436_1


title: CD19_CAR_CD3CD281_3_CD19_CAR_vsantiCD3_CD28beads

description: CD19 CAR vs antiCD3 CD28beads


title: H3K27ac ChIP for H1963


title: CD19_CAR_light1_1_CD19_CAR_vsPhoenixlight

description: CD19 CAR vs HEK-mLight

value: CD19 CAR vs HEK-mLight


title: H3K27ac ChIP for H2171


title: H3K27ac ChIP for H187


title: H3K27ac ChIP for DMS 79


title: WT [Oxford Nanopore]

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

data_processing:
Read quality assessment, base calling and adapter trimming was carried out with the Guppy software (version 3.2.6)
Nanofilt (version 2.7.1) was then used to remove low quality reads (Q-value < 7) and short-length reads (<50 bp)
The clean reads were subsequently corrected using Fclmr2 (version 0.1.2)
Minimap2 (version 2.17-r941)  was used to map the clean reads to the A. thaliana genome
Alignment ratio of clean reads to the reference genes was calculated using Samtools (version 1.10)
To identify m6A sites, the Tombo software de novo model together with MINES was used for calculation
Methylkit software was then used to analyze differential methylation sites (DML)
Logistic regression test was used to detect differential methylation sites.
Assembly: Minimap2 (version 2.17-r941)  was used to map the clean reads to the A. thaliana genome
Supplementary files format and content: Expression: PNG, PDF, XLS files. Boxplot, Correlation, Density, PCA
Supplementary files format and content: DE: PNG, PDF, XLS files. Boxplot, Barplot, Volcano, MA, Heatmap, Correlation
Supplementary files format and content: Methylation: M5C and M6A. PNG, PDF, XLS files. Boxplot, Density, Barplot, Dotplot, MA, Volcano
Supplementary files format and content: PolyA length: PDF, PNG, XLS files. Violin, Dotplot.
Supplementary files format and content: Structure: Novel transcripts, AS, Fusion, lncRNA, APA. PDF, PNG, XLS, FA, DPSI files.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seedlings grown until 14 days old on MS media in long day conditions

extract_protocol:
Extraction was done using the kit Spectrum Plant Total RNA Kit from Sigma (STRN250-1KT)
Prepared by CD genomics byt annealing dT adapters, reverse transcription and ligation of a motor adapter (Oxford Nanopore DRS protocol - SQK-RNA002, Oxford Nanopore Technologies)
Nanoport Direct RNA sequencing

value: Seedlings

value: wildtype

value: 14 days on MS

tag: ecotype


title: fio1-1 [Oxford Nanopore]


title: fio1-2 [Oxford Nanopore]

description: When samples were submitted for sequencing our mutant fio1-2 was named as such. Before publishing more fio mutants had been described and therefore our mutant was in the end named fio1-5, which is then the correct genotype.


title: H3K27ac ChIP for H345


title: H3K27ac ChIP for H209


title: CD19_CAR_light3_1_CD19_CAR_vsPhoenixlight

description: CD19 CAR vs HEK-mLight


title: H3K27ac ChIP for COR-L88


title: CD19_CAR_light2_1_CD19_CAR_vsPhoenixlight

description: CD19 CAR vs HEK-mLight


title: H3K27ac ChIP for H196


title: Zebrafish GFP #3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description:
Zeb-GFP3
single index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome danrer11 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ATAC-seq peak calling was performed on the Tn5- corrected single-base insertions using the following parameters --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all –qvalue 0.01.
Genome_build: danrer11
Supplementary files format and content: macs narrowpeaks

organism: Danio rerio

source_name: embryonic brain

extract_protocol:
ATAC-seq was performed using a previously described protocol 3. Briefly, 50000 of cells for each experimental replicated were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, Sigma aldrich) to perform crude nuclei isolation. Trasposition reaction was then performed using Tn5 transposase (Illumina).  After transposition, DNA was purified using Zymo DNA Clean & Concentrator kit (cat. D4013) and amplified by PCR (NebNext ultra II polymerase, cat. M0544S). After 5 cycles the reaction was stopped, the necessary amount of cycles needed for the final amplification were calculated with qPCR. After amplification libraires were purified using Ampure XPbeads selection fragments between 100-1000 bp. Subsequently samples were sequenced paired-end on NovaSeq6000 by GeneWiz.
NexTera

value: embryonic brain

value: SET WT


title: Zebrafish GFP #1

description:
Zeb-GFP1
single index library


title: H3K27ac ChIP for HCC33


title: WT1

city: East Lansing

first: Jonathan

last: Hardy

state: Michigan

address: 775 Woodlot Drive

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Used Galaxy web platform
Sequencing adopter and low qualitiy bases were trimmed using Trimmomatic
Processed reads were mapped to the mouse reference genome using HISAT2
Gene expression of mapped reads were measured using featureCounts
DESeq2 was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: excel file includes read counts for each sample

source_name: Extracellular vesicles from infected trophoblast stem cells

extract_protocol:
Total RNA was extracted using Trizol Reagent method (Thermo Fisher Scientific)
Illumina Nextera XT library was used for sequencing library preparation

tag: cell line

value: Trophoblast stem cells

tag: rna population

value: Extracellular vesicle RNA

tag: condition

value: Infected

value: Listeria monocytogenes


title: WT2


title: CD19_CAR_control1_2_CD19_CAR_vsPhoenix

description: CD19 CAR vs HEK

tag: cell type

value: sorted CD4+CD25+CD90.1+


title: UI3

source_name: Extracellular vesicles from uninfected trophoblast stem cells

value: Uninfected

value: Phosphate buffered saline


title: Zebrafish GFP #2

description:
Zeb-GFP2
single index library


title: Zebrafish SETV5 #3

description:
Zeb-ATAC3
single index library

value: SET overexp.


title: H3K27ac ChIP for SHP-77

value: Cell line

value: acetyl-histone H3K27  (Abcam, ab4729)


title: WT3


title: UI2


title: Zebrafish SETV5 #2

description:
Zeb-ATAC2
single index library


title: UI1


title: Control 1

type: RNA

city: Tel Aviv

first: Nour

last: Ershaid

state: Israel

address: Postal code 2373,

country: Israel

institute: Tel Aviv University

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
Per each sample, 250ng of total RNA was hybridized to biotinylated capture probe and reporter probe with unique target gene specific fluorochromes present in the NanoString nCounter mouse inflammation v2 panel as per the manufacturer's protocol. Hybridized complexes in solution were immobilized onto catridges for digital count analysis.
Post hybridization, digital count analysis was performed by nCounter instrument. Raw data counts were obtained for further analysis. NanoString?s data analysis application software, nSolver version 4.0 was utilized for the analysis of raw data counts.

label: not provided

source_name: Lung fibroblasts at early-metastatic stage

label_protocol: standard protocol

extract_protocol: Mice in early-stage metastasis experiments were euthanized 24h after the second dose of chemotherapy or vehicle.  Single cell suspensions were stained with cell type-specific antibodies. FACS Sorting was performed using BD FACSAria III to isolate lung fibroblasts (CD45-CD31-EpCAM-PDGFRα+); RNA from sorted cells was isolated using the EZ-RNAII Kit (20-410-100, Biological Industries). RNA samples were analyzed with NanoDrop 2000c Spectrophotometer. Expression profiling of 248 inflammatory genes was analyzed by the nCounter Nanostring Mouse Inflammation v2 assay (NanoString Technologies)

value: Early-stage metastatic lungs

tag: treatment/time point

value: vehicle


title: Control 3

tag: tissue


title: Dox 3

value: 24h after the second dose of chemotherapy


title: Control 2


title: Dox 1


title: Dox 2


title: ECRi_-6hAPF_Wing_FAIRE_Rep1

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

description:
faire_deseq_WT_Leg_v_WT_SG.csv
faire_deseq_WT_Wing_v_EcRi_Wing.csv
faire_deseq_WT_Wing_v_WT_Leg.csv
faire_deseq_WT_Wing_v_WT_SG.csv
EcRi_-6hAPF_Wing_FAIRE_Merge_dm6_trim_q5_dupsRemoved_peaks.narrowPeak
EcRi_-6hAPF_Wing_FAIRE_Merge_dm6_trim_q5_dupsRemoved_rpgcNorm_zNorm.bw

data_processing:
fastq files from technical replicates were concatenated together
Adapter sequences were removed using bbmap (v38.75) using parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Trimmed sequences were aligned to the dm6 reference genome using bowtie2 (v2.3.4.1) using paramaters --phred33 --seed123
Aligned bam files were filtered to only include reads with MAPQ > 5 using samtools (v1.9)
PCR duplicates were removed using picard (v2.2.4)
For paired-end samples, fragments between 150-700bp were split into a separate sam file using a custom awk script
For paired-end samples, 150-700bp fragments were converted to bed files using the furthest start and end coordinates of each fragment
bed files from biological replicates were merged
bigwig files were generated from merged bed files using bedtools (v2.26) genomecov with parameters -bga
z-score normalized bigwigs were generated using a custom R script using R (v3.5.2)
peaks were called on merged replicates using MACS2 (v2.1.2) using parameters  --nomodel --seed 123 -g 137547960 --extsize 125
A union peak set was generated in R
Rsubread was used to assign reads to features using parameters:  strandSpecific = 0, allowMultiOverlap = T
DESeq2 was used to identify differentially-bound regions using parameters: lfcShrink = T, type = 'ashr'
Assembly: dm6
Supplementary files format and content: narrowpeak peaks from peaks called on merged replicates
Supplementary files format and content: z-score normalized bigwigs from merged replicates
Supplementary files format and content: comma-delimted tables with DESeq2 results

organism: Drosophila melanogaster

source_name: wing

growth_protocol: Animals were raised at 25C. For –30hAPF, embryos on apple juice plates were cleared of any larvae, four hours later any animals that had hatched were transferred to vials, and animals dissected 72hrs later. For the -6hAPF time point, wandering (3LW) larvae were used. For the +6hAPF time point, animals were staged at the white, pre-pupae stage.

extract_protocol:
A minimum of 40 SG, wings, or legs were individually dissected in 1xPBS
The Takara Thruplex DNAseq kit with unique dual-indexes was used following manufacturer's instructions

value: wing

tag: developmental stage

value: female

tag: genotype

value: yw/yw; Vg-GAL4, UAS-Flp, Tub>>CD2>>GAL4; UAS-GFP / UAS-EcR-RNAi[104]


title: Zebrafish SETV5 #1

description:
Zeb-ATAC1
single index library

value: embryonic brain


title: WT_-6hAPF_Leg_FAIRE_Rep2

description:
faire_deseq_WT_Leg_v_WT_SG.csv
faire_deseq_WT_Wing_v_EcRi_Wing.csv
faire_deseq_WT_Wing_v_WT_Leg.csv
faire_deseq_WT_Wing_v_WT_SG.csv
WT_-6hAPF_Leg_FAIRE_Merge_dm6_trim_q5_dupsRemoved_peaks.narrowPeak
WT_-6hAPF_Leg_FAIRE_Merge_dm6_trim_q5_dupsRemoved_rpgcNorm_zNorm.bw

source_name: leg

value: leg


title: VCaP-LMNB1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

description:
VCaP-LaminB1_rNorm_HMM.txt.gz
VCaP-LaminB1_log2FE_rNorm.bed

data_processing:
The fastq reads from both the LaminB1 ChIP and input files were first processed separately for adapter and quality trimming using the BBDuk. Following that, the reads were aligned to the reference genome hg19 using STAR aligner. Finally, log2 ratio of the Lamin B1 ChIP reads over input were calculated in a genome-wide fashion and a hidden markov model was used to call lamina associated domains from that data using the HMMt R package (https://github.com/gui11aume/HMMt).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include genome-wide lamina-associated domains at 40 kb resolution for each sample. Here AD indicates lamina association and iAD means not lamina associated.
.bed files

source_name: Bone metastatic prostate cancer

growth_protocol: LNCaP and VCaP cells growing under continuous culture conditions in T75 flasks were allowed to reach 90% confluency. LNCaP cells were grown in RPMI (Gibco; 11835030) supplemented with 4.5 g/liter glucose, 2.383 g/liter HEPES, 0.11 g/liter sodium pyruvate and 10% FBS (Corning; 35–010-CV). VCaP cells were cultured in DMEM F12: Ham 1:1 (Gibco; 11–320-033) with 10% FBS.

extract_protocol:
Cell pellets were lysed and chromatin fragmented using a Covaris M220 Sonicator, and the Covaris truChIP Chromatin shearing kit (Covaris; 520154). Briefly, cell pellets were thawed on ice and resuspended in 1 ml of 1X lysis buffer, supplemented with protease inhibitors. Samples were incubated on ice for 10 minutes, with gentle vortexing every 2 min. Nuclei were collected by centrifugation at 1700 g for 5 min (at 4 degrees C). The nuclei pellet was then resuspended in 1 ml of 1X wash buffer (supplemented with protease inhibitors), and collected by centrifugation as before. Samples were then washed twice, using centrifugation as before, with 1 ml of complete shearing buffer. Pellets were resuspended in 1 ml of fresh shearing buffer and transferred into a cold 1 ml AFA tube (Covaris). Sonication conditions were as follows: PIP 75, duty factor 10%, CBP 200, 4 degrees C, 12 minutes.  To verify sonication, aliquots of time-zero and sonicated samples were treated with RNase A (30 min at 37 degrees C) and reverse crosslinked overnight with proteinase K via incubation at 65 degrees C. After reverse crosslinking, DNA was purified using QIAquick PCR Purification Kit (Qiagen;. 28104), according to the manufacturer’s instructions. Shearing efficiency was verified via agarose gel electrophoresis. Chromatin immunoprecipitation was done using the MAGnify Chromatin immunoprecipitation system (Life Technologies, 49-2024), according to the manufacturer’s protocol, diluting the sheared chromatin at a 1:3 ratio in the kit’s dilution buffer and using three reactions per sample. Three micrograms of rabbit polyclonal antibody against Lamin B1 were used, per reaction (Abcam; ab16048). After pulldown and purification, DNA fragments were sonicated for a second time, using the following parameters in a Covaris M220 sonicator: 130 microliter AFA tube, 10 o C, PIP 50%, duty factor 20%, CPB 200, for 45 seconds.
ChIP-seq libraries were constructed by Azenta/Genewiz using the Illumina TruSeq library preparation approach and paired end 150 bp sequencing was performed

treatment_protocol: After media removal, the cell monolayer was washed once with HBSS, which was promptly removed by aspiration. Cells were fixed in-situ by incubation in 1% formaldehyde (37% formaldehyde diluted in HBSS) for 10 minutes, under gentle shaking. Crosslinking was quenched by adding glycine to a final concentration of 0.14 M (MP biomedicals ICN19482591), followed by a 5 min incubation at room temperature, with shaking. Flasks were then cooled down on ice for 15 min, after which the formaldehyde solution was aspirated from the plate and substituted with 10 ml of ice-cold HBSS, supplemented with 1X Halt Protease Inhibitor cocktail (Thermo PI78438). Cells were then collected by centrifugation and snap frozen in liquid nitrogen.

value: VCaP

value: Bone metastatic prostate cancer

tag: chip antibody

value: Lamin B1


title: LNCaP-Input

description:
LNCaP-LaminB1_rNorm_HMM.txt.gz
LNCaP-LaminB1_log2FE_rNorm.bed

source_name: Prostate adenocarcinoma

value: LNCaP

value: Prostate adenocarcinoma


title: VCaP-Input


title: LNCaP-LMNB1


title: WT_-6hAPF_Leg_FAIRE_Rep1


title: WT_-6hAPF_Wing_FAIRE_Rep2

description:
faire_deseq_WT_Leg_v_WT_SG.csv
faire_deseq_WT_Wing_v_EcRi_Wing.csv
faire_deseq_WT_Wing_v_WT_Leg.csv
faire_deseq_WT_Wing_v_WT_SG.csv
WT_-6hAPF_Wing_FAIRE_Merge_dm6_trim_q5_dupsRemoved_peaks.narrowPeak
WT_-6hAPF_Wing_FAIRE_Merge_dm6_trim_q5_dupsRemoved_rpgcNorm_zNorm.bw


title: WT_-6hAPF_Wing_FAIRE_Rep1


title: Control Adeno-K5-Cre

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

data_processing:
10x Cell Ranger (cellranger) mkfastq command is used to generate fastq files from Illumina® sequencer's base call files (BCLs)
10x Cell Ranger ATAC (cellranger) count command is used with default parameters for alignment and generating count matrices of the scRNA data
Filtered peak barcode matrices are used for further analysis in Seurat R package.
Genome_build: mm10
Supplementary_files_format_and_content: TSV, H5. (Count matrix, features matrix, barcode matrix)

source_name: mammary epithelial cells (basal enriched)

extract_protocol:
Two mammary glands were disected and pooled per mouse. Glands were digested in 2x gentle collagenase/hyaluronidase for 2 hours, then treated with ammonium chloride and triturated for 2 minutes in pre-warmed trypsin followed by dispase. Cells were then sorted for GFP+ infected cells and immediately processed
Libraries were constructed according to 10x Genomics protocol

treatment_protocol: Mice were administered the treatment virus 2 weeks prior to tissue harvest

tag: sample type


title: PEM-seq_HEK293T_PlmCas12e_KLHL29

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

country: China

institute: Peking University

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file
Library strategy: PEM-seq

source_name: cell line

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

value: cell line

value: Human embryonic kidney

value: WT

tag: treatment

value: plasmid transfection


title: PEM-seq_HEK293T_control_KLHL29

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_KLHL29

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI_KLHL29

description: The cells were transfected with gRNA-CasMINI plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: PEM-seq_HEK293T_LbCas12a_KLHL29

description: The cells were transfected with gRNA-LbCas12a plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_KLHL29

description: The cells were transfected with gRNA-SpCas9 plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PEM-seq_HEK293T_control_P2RX5-TAX1BP3


title: PEM-seq_HEK293T_AsCas12a_KLHL29

description: The cells were transfected with gRNA-AsCas12a plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12f1_KLHL29

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: Pik3caHR Kdm6aKO Adeno-K5-Cre


title: Pik3caHR Kdm6aKO Adeno-Cre

source_name: mammary epithelial cells

value: Adeno-Cre


title: Pik3caHR Adeno-K5-Cre

value: LSL-Cas9-EGFP; LSL-Pik3caH1047R


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: ECRi_-6hAPF_Wing_FAIRE_Rep2


title: PEM-seq_HEK293T_Un1Cas12f1_KLHL29

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: Control Adeno-Cre


title: PEM-seq_HEK293T_CasMINI-ge4.1_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: Pik3caHR Kdm6afl/fl Ad-K5-Cre - Rep3

description: CombinedCounts.csv

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0)
Raw reads obtained from bam files using featureCounts and mm10 annotation file from ensembl (Mus_musculus.GRCm38.94.gtf)
DESeq2 package in R was used to determine differentially expressed genes between samples
Genome_build: mm10
Supplementary_files_format_and_content: txt, count files

source_name: mammary tumor

extract_protocol:
Tumors were dissected and incubated with 10% collagenase in DMEM/F12 for 45 minutes followed by 10 minutes of digestion in trypsin-EDTA. GFP+,DAPI- cells sorted by flow cytometry prior to RNA extraction by Zymo RNA mini-prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Mixed C57BL/6 x FVB/N

value: Adenoviral Krt5-Cre

tag: mouseline


title: Pik3caHR Kdm6aKO

data_processing:
10x Cell Ranger ATAC (cellranger-atac) mkfastq command is used to generate fastq files from Illumina® sequencer's base call files (BCLs)
10x Cell Ranger ATAC (cellranger-atac) count command is used with default parameters for alignment and generating count matrices of the scATAC data
Filtered peak barcode matrices are used for further analysis in Seurat R package.
Genome_build: mm10
Supplementary_files_format_and_content: H5: (Count matrix, features matrix, barcode matrix)

extract_protocol:
Two mammary glands were disected and pooled per mouse. Glands were digested in 2x gentle collagenase/hyaluronidase for 2 hours, then treated with ammonium chloride and triturated for 2 minutes in pre-warmed trypsin followed by dispase. Cells were then sorted for GFP+ infected cells and immediately processed
Libraries were constructed according to 10x Genomics protocol
snATAC-sec

treatment_protocol: Mice were administered adeno-Cre virus 2 weeks prior to tissue harvest


title: PEM-seq_HEK293T_AsCas12f1_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI-ge4.1_KLHL29

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting KLHL29 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: Pik3caHR Ad-K5-Cre - Rep2

description: CombinedCounts.csv

value: LSL-Pik3caH1047R; LSL-Cas9-EGFP


title: Pik3caHR Ad-K5-Cre - Rep3

description: CombinedCounts.csv


title: Control


title: Pik3caHR


title: PEM-seq_HEK293T_AsCas12a_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-AsCas12a plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: Pik3caHR Adeno-Cre


title: PEM-seq_HEK293T_Un1Cas12f1_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: sgTrp53 - Rep4

description: CombinedCounts.csv

value: F1 C57BL/6 x FVB/N

value: Lentiviral Cre-sgTrp53


title: Pik3caHR Ad-K5-Cre - Rep1

description: CombinedCounts.csv


title: PEM-seq_HEK293T_LbCas12a_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-LbCas12a plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-SpCas9 plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: sgApc - Rep2

description: CombinedCounts.csv

value: Lentiviral Cre-sgApc


title: sgApc - Rep3

description: CombinedCounts.csv


title: sgSetd2 - Rep2

description: CombinedCounts.csv

value: Lentiviral Cre-sgSetd2


title: sgTrp53 - Rep1

description: CombinedCounts.csv


title: PEM-seq_HEK293T_control_FGF18

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: sgApc - Rep4

description: CombinedCounts.csv


title: sgTrp53 - Rep2

description: CombinedCounts.csv


title: PEM-seq_HEK293T_CasMINI_P2RX5-TAX1BP3

description: The cells were transfected with gRNA-CasMINI plasmid targeting P2RX5-TAX1BP3 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_FGF18

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e_FGF18

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: sgApc - Rep1

description: CombinedCounts.csv


title: sgSetd2 - Rep1

description: CombinedCounts.csv


title: sgKmt2c - Rep3

description: CombinedCounts.csv

value: Lentiviral Cre-sgKmt2c


title: sgKmt2c - Rep2

description: CombinedCounts.csv


title: sgKdm6a - Rep2

description: CombinedCounts.csv

value: Lentiviral Cre-sgKdm6a


title: sgAsxl2 - Rep2

description: CombinedCounts.csv

value: Lentiviral Cre-sgAsxl2


title: sgKmt2c - Rep1

description: CombinedCounts.csv


title: PEM-seq_HEK293T_Un1Cas12f1_FGF18

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: sgAsxl2 - Rep1

description: CombinedCounts.csv


title: sgKdm6a - Rep1

description: CombinedCounts.csv


title: PEM-seq_HEK293T_CasMINI-ge4.1_FGF18

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12f1_FGF18

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: sgNT - Rep2

description: CombinedCounts.csv

value: Lentiviral Cre-sgNon-targetting


title: PEM-seq_HEK293T_AsCas12a_FGF18

description: The cells were transfected with gRNA-AsCas12a plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.

value: cell line


title: sgTrp53 - Rep3

description: CombinedCounts.csv


title: cohort III 848

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_4

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0)
Raw reads obtained from bam files using featureCounts and mm10 annotation file from ensembl (Mus_musculus.GRCm38.94.gtf)
DESeq2 package in R was used to determine differentially expressed genes between samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited raw read counts
tab-delimited DESEQ2 results: Healthy Brain Tissue (Ctrl) vs Type II Low Grade glioma Tumor Tissue

source_name: Type II Low Grade glioma Tumor Tissue

extract_protocol:
Mouse brains were harvested and embedded into paraffin, 10x 10 micron thick saggital paraffin sections were generated and tumor/tissue was scraped off the slide and RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Type II Low Grade glioma Tumor Tissue


title: 6239#2820

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_6

source_name: Healthy brain tissue

value: Healthy brain tissue

value: NestinCreERT2; Cas9 fl/+


title: CII-477

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_3


title: sgNT - Rep1

description: CombinedCounts.csv

value: Lentiviral Cre-sgNonTargetting


title: 6239#2818

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_5


title: PEM-seq_HEK293T_LbCas12a_FGF18

description: The cells were transfected with gRNA-LbCas12a plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.

value: Human embryonic kidney

value: WT

value: plasmid transfection


title: PEM-seq_HEK293T_CasMINI_FGF18

description: The cells were transfected with gRNA-CasMINI plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_LNX1

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_FGF18

description: The cells were transfected with gRNA-SpCas9 plasmid targeting FGF18 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: cohort I 205

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_1


title: PEM-seq_HEK293T_control_LNX1

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e_LNX1

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI-ge4.1_LNX1

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_Un1Cas12f1_LNX1

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12f1_LNX1

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: cohort I 206

description:
F_rawCounts.txt, DESEQ2Res_sLFC.txt
Sample_2


title: PEM-seq_HEK293T_AsCas12a_LNX1

description: The cells were transfected with gRNA-AsCas12a plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_LNX1

description: The cells were transfected with gRNA-SpCas9 plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI_LNX1

description: The cells were transfected with gRNA-CasMINI plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_CLIC4

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_LbCas12a_LNX1

description: The cells were transfected with gRNA-LbCas12a plasmid targeting LNX1 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: C10

city: Kalyani

first: SAMANWOY

last: MUKHOPADHYAY

state: West Bengal, INDIA

country: India

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

description:
C10
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normexp background correction using negative control probes and quantile normalization using negative and positive control probes, was performed using function ‘neqc’ of the package ‘limma’ in R.

label: Biotin

source_name: Subject C10, Healthy

label_protocol: Illumina TotalPrep RNA Amplification Kit was used to convert the total RNA to biotinylated cRNA for hybridisation to microarray chip.

extract_protocol: PAXgene Blood RNA isolation Kit from Qiagen, Hilden, Germany (cat. no. 762164) was used to isolate the RNA from the whole blood according to manufacturer’s instructions. Spectroscopy was done in Nanodrop-2000 (ND-2000, from Thermo Fisher Scientific, Waltham, Massachusetts, USA) for checking RNA quality and concentration. Agilent Bioanalyzer RNA nano kit (Agilent RNA 6000 Nano) was used for checking RNA quality.

value: Whole blood

tag: age

value: M

tag: diagnosis

value: Healthy

tag: time of sample collection

value: 0 hr

tag: outcome

value: Survived


title: C17

description:
C17
Replicate 1

source_name: Subject C17, Healthy

tag: Sex


title: C21

description:
C21
Replicate 1

source_name: Suject C21, Healthy


title: ctrl_sm

description:
9553976077_L
Replicate 1

source_name: Subject C1, Healthy


title: 90D1

description:
9553976077_A
Replicate 1

source_name: Subject 90, Severe Sepsis, Day 1

value: Severe Sepsis


title: C9

description:
C9
Replicate 1

source_name: Subject C9, Healthy

value: F


title: PEM-seq_HEK293T_control_CLIC4

tag: cell line


title: C8

description:
C8
Replicate 1

source_name: Subject C8, Healthy


title: C7

description:
C7
Replicate 1

source_name: Subject C7, Healthy


title: C20

description:
C20
Replicate 1

source_name: Subject C20, Healthy


title: PEM-seq_HEK293T_PlmCas12e_CLIC4

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: C12

description:
C12
Replicate 1

source_name: Subject C12, Healthy


title: PEM-seq_HEK293T_AsCas12f1_CLIC4

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: 14D2

description:
9553976072_I
Replicate 1

source_name: Subject 14, Severe Sepsis, Day 2

value: 24 hrs


title: PEM-seq_HEK293T_CasMINI-ge4.1_CLIC4

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: 70D2

description:
9553976077_D
Replicate 1

source_name: Subject 70, Septic Shock, Day 2

value: Septic Shock


title: PEM-seq_HEK293T_AsCas12a_CLIC4

description: The cells were transfected with gRNA-AsCas12a plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.

source_name: cell line

value: cell line


title: C18

description:
C18
Replicate 1

source_name: Subject C18, Healthy


title: PEM-seq_HEK293T_Un1Cas12f1_CLIC4

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI_CLIC4

description: The cells were transfected with gRNA-CasMINI plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: C11

description:
C11
Replicate 1

source_name: Subject C11, Healthy


title: 90D2

description:
9553976077_B
Replicate 1

source_name: Subject 90, Severe Sepsis, Day 2


title: 55D1

description:
9553976072_F
Replicate 1

source_name: Subject 55, Severe Sepsis,Day 1


title: 66D1

description:
9553976072_E
Replicate 1

source_name: Subject 66, Day 1


title: 70D1

description:
9553976077_C
Replicate 1

source_name: Subject 70, Septic Shock, Day 1


title: PEM-seq_HEK293T_SpCas9_CLIC4

description: The cells were transfected with gRNA-SpCas9 plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PEM-seq_HEK293T_LbCas12a_CLIC4

description: The cells were transfected with gRNA-LbCas12a plasmid targeting CLIC4 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: 14D1

description:
9553976072_H
Replicate 1

source_name: Subject 14, Severe Sepsis, Day 1


title: C4

description:
C4
Replicate 1

source_name: Subject C4, Healthy


title: 62D2

description:
9553976091_J
Replicate 1

source_name: Subject 62, Severe Sepsis,Day 2


title: 54D2

description:
9553976072_A
Replicate 1

source_name: Subject 54, Septic Shock, Day 2

value: Died


title: 56D1

description:
9553976072_B
Replicate 1

source_name: Subject 56, Septic Shock, Day 1


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_INFg

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting INFg locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: 55D2

description:
9553976072_G
Replicate 1

source_name: Subject 55, Severe Sepsis,Day 2


title: 63D1

description:
9553976091_K
Replicate 1

source_name: Subject 63, Severe Sepsis, Day 1


title: 59D2

description:
9553976072_C
Replicate 1

source_name: Subject 59, Severe Sepsis, Day 2


title: 60D2

description:
9553976091_F
Replicate 1

source_name: Subject 60, Severe Sepsis, Day 2


title: 60D1

description:
9553976091_E
Replicate 1

source_name: Subject 60, Severe Sepsis, Day 1


title: 61D1

description:
9553976091_G
Replicate 1

source_name: Subject 61, Severe Sepsis, Day 1


title: 61D2

description:
9553976091_H
Replicate 1

source_name: Subject 61, Severe Sepsis, Day 2


title: 58D1

description:
9553976091_C
Replicate 1

source_name: Subject 58, Sepsis, Day 1

value: Sepsis


title: 62D1

description:
9553976091_I
Replicate 1

source_name: Subject 62, Severe Sepsis,Day 1


title: 57D2

description:
9553976091_B
Replicate 1

source_name: Subject 57, Sepsis, Day 2


title: 63D2

description:
9553976091_L
Replicate 1

source_name: Subject 63, Severe Sepsis, Day 2


title: PEM-seq_HEK293T_PlmCas12e_INFg

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.

source_name: cell line


title: PEM-seq_HEK293T_Un1Cas12f1_INFg

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_control_INFg

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: PEM-seq_HEK293T_CasMINI-ge4.1_INFg

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: 57D1

description:
9553976091_A
Replicate 1

source_name: Subject 57, Sepsis, Day 1


title: PEM-seq_HEK293T_AsCas12f1_INFg

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: 42D1

description:
9553976020_G
Replicate 1

source_name: Subject 42, Severe Sepsis, Day 1


title: 34D2

description:
9553976020_F
Replicate 1

source_name: Subject 34, Septic Shock, Day 2


title: 58D2

description:
9553976091_D
Replicate 1

source_name: Subject 58, Sepsis, Day 2


title: 65D1

description:
9553976072_D
Replicate 1

source_name: Subject 65, Day 1


title: 42D2

description:
9553976020_H
Replicate 1

source_name: Subject 42, Severe Sepsis, Day 2


title: 32D2

description:
9553976020_D
Replicate 1
sample also analyzed on Affymetrix array

source_name: Subject 32, Severe Sepsis, Day 2


title: 34D1

description:
9553976020_E
Replicate 1

source_name: Subject 34, Septic Shock, Day 1


title: PEM-seq_HEK293T_AsCas12a_INFg

description: The cells were transfected with gRNA-AsCas12a plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: 31D1

description:
9553976020_A
Replicate 1

source_name: Subject 31, Severe Sepsis, Day 1


title: 19D2

description:
9553976015_J
Replicate 1

source_name: Subject 19, Septic Shock,Day 2


title: PEM-seq_HEK293T_CasMINI_INFg

description: The cells were transfected with gRNA-CasMINI plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: 19D1

description:
9553976015_I
Replicate 1

source_name: Subject 19, Septic Shock,Day 1


title: 32D1

description:
9553976020_C
Replicate 1
sample also analyzed on Affymetrix array

source_name: Subject 32, Severe Sepsis, Day 1


title: 21D2

description:
9553976015_K
Replicate 1

source_name: Subject 21, Septic Shock, Day 2


title: 31D2

description:
9553976020_B
Replicate 1

source_name: Subject 31, Severe Sepsis, Day 2


title: 10D1

description:
9553976015_G
Replicate 1

source_name: Subject 10, Severe Sepsis, Day 1


title: PEM-seq_HEK293T_SpCas9_INFg

description: The cells were transfected with gRNA-SpCas9 plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: 8D2

description:
9553976015_F
Replicate 1

source_name: Subject 8, Severe Sepsis, Day 2


title: PEM-seq_HEK293T_LbCas12a_INFg

description: The cells were transfected with gRNA-LbCas12a plasmid targeting INFg locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.

source_name: cell line


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_HBB

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting HBB locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_control_HBB


title: PEM-seq_HEK293T_PlmCas12e_HBB

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: PEM-seq_HEK293T_Un1Cas12f1_HBB

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: 8D1

description:
9553976015_E
Replicate 1

source_name: Subject 8, Severe Sepsis, Day 1


title: PEM-seq_HEK293T_CasMINI-ge4.1_HBB

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12a_HBB

description: The cells were transfected with gRNA-AsCas12a plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: 6D1

description:
9553976015_C
Replicate 1

source_name: Subject 6, Septic Shock, Day 1


title: PEM-seq_HEK293T_CasMINI_HBB

description: The cells were transfected with gRNA-CasMINI plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12f1_HBB

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: 5D2

description:
9553976015_B
Replicate 1

source_name: Subject 5, Septic Shock, Day 2


title: 1D1

description:
9553976020_I
Replicate 1

source_name: Subject 1, Severe Sepsis,Day 1


title: 6D2

description:
9553976015_D
Replicate 1

source_name: Subject 6, Septic Shock, Day 2


title: PEM-seq_HEK293T_SpCas9_HBB

description: The cells were transfected with gRNA-SpCas9 plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: 1D2

description:
9553976020_J
Replicate 1

source_name: Subject 1, Severe Sepsis,Day 2


title: 5D1

description:
9553976015_A
Replicate 1

source_name: Subject 5, Septic Shock, Day 1


title: PEM-seq_HEK293T_LbCas12a_HBB

description: The cells were transfected with gRNA-LbCas12a plasmid targeting HBB locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_NUDT16

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_control_NUDT16

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e_NUDT16

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #29_205624860127_R05C01_Cancer Untrained_Post_Participant 12

type: genomic

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing: Partek Genomic Suite V7 (Using MethylationEPIC_v-1-0_B4 manifest file)

label: Cy3 and Cy5

source_name: DNA from Vastus Lateralis Muscle_ Sample No.29_205624860127_R05C01_Cancer Untrained_Post_Participant 12

label_protocol: Labels (Sample number_Beadchip Barcode_Beadchip position_Group_Time point_Participant number)

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with  manufacturers guidelines. The DNA was then bisulfite converted using the EZ DNA Methylation Kit, Zymo Research, CA, United States, as per manufacturer’s instructions.

tag: gender

value: Female

value: Skeletal Muscle_Vastus Lateralis


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #20_205624860053_R04C01_Healthy Aged-matched Trained_Post_Participant 13

source_name: DNA from Vastus Lateralis Muscle_ Sample No.20_205624860053_R04C01_Healthy Aged-matched Trained_Post_Participant 13


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #32_205624860127_R08C01_Cancer Untrained_Post_Participant 11

source_name: DNA from Vastus Lateralis Muscle_ Sample No.32_205624860127_R08C01_Cancer Untrained_Post_Participant 11


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #26_205624860127_R02C01_Cancer Untrained_Post_Participant 10

source_name: DNA from Vastus Lateralis Muscle_ Sample No.26_205624860127_R02C01_Cancer Untrained_Post_Participant 10


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #28_205624860127_R04C01_Cancer Trained_Pre_Participant 14

source_name: DNA from Vastus Lateralis Muscle_ Sample No.28_205624860127_R04C01_Cancer Trained_Pre_Participant 14


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #27_205624860127_R03C01_Healthy Aged-matched Trained_Pre_Participant 15

source_name: DNA from Vastus Lateralis Muscle_ Sample No.27_205624860127_R03C01_Healthy Aged-matched Trained_Pre_Participant 15


title: PEM-seq_HEK293T_Un1Cas12f1_NUDT16

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.

tag: cell type

value: Human embryonic kidney


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #18_205624860053_R02C01_Cancer Trained_Post_Participant 4

source_name: DNA from Vastus Lateralis Muscle_ Sample No.18_205624860053_R02C01_Cancer Trained_Post_Participant 4


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #16_205624860016_R08C01_Cancer Trained_Post_Participant 16

source_name: DNA from Vastus Lateralis Muscle_ Sample No.16_205624860016_R08C01_Cancer Trained_Post_Participant 16


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #23_205624860053_R07C01_Cancer Trained_Post_Participant 14

source_name: DNA from Vastus Lateralis Muscle_ Sample No.23_205624860053_R07C01_Cancer Trained_Post_Participant 14


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #24_205624860053_R08C01_Healthy Aged-matched Trained_Post_Participant 9

source_name: DNA from Vastus Lateralis Muscle_ Sample No.24_205624860053_R08C01_Healthy Aged-matched Trained_Post_Participant 9


title: PEM-seq_HEK293T_AsCas12f1_NUDT16

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.

source_name: cell line

value: WT


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #14_205624860016_R06C01_Cancer Untrained_Pre_Participant 11

source_name: DNA from Vastus Lateralis Muscle_ Sample No.14_205624860016_R06C01_Cancer Untrained_Pre_Participant 11


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #30_205624860127_R06C01_Cancer Trained_Pre_Participant 16

source_name: DNA from Vastus Lateralis Muscle_ Sample No.30_205624860127_R06C01_Cancer Trained_Pre_Participant 16


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #31_205624860127_R07C01_Healthy Aged-matched Trained_Post_Participant 15

source_name: DNA from Vastus Lateralis Muscle_ Sample No.31_205624860127_R07C01_Healthy Aged-matched Trained_Post_Participant 15


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #19_205624860053_R03C01_Cancer Untrained_Pre_Participant 6

source_name: DNA from Vastus Lateralis Muscle_ Sample No.19_205624860053_R03C01_Cancer Untrained_Pre_Participant 6


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #13_205624860016_R05C01_Cancer Untrained_Pre_Participant 10

description: Note: This sample was removed from downstream differential methylation analysis

source_name: DNA from Vastus Lateralis Muscle_ Sample No.13_205624860016_R05C01_Cancer Untrained_Pre_Participant 10


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #17_205624860053_R01C01_Cancer Untrained_Post_Participant 3

source_name: DNA from Vastus Lateralis Muscle_ Sample No.17_205624860053_R01C01_Cancer Untrained_Post_Participant 3


title: PEM-seq_HEK293T_AsCas12a_NUDT16

description: The cells were transfected with gRNA-AsCas12a plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.

value: plasmid transfection


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #25_205624860127_R01C01_Healthy Aged-matched Trained_Pre_Participant 13

source_name: DNA from Vastus Lateralis Muscle_ Sample No.25_205624860127_R01C01_Healthy Aged-matched Trained_Pre_Participant 13


title: PEM-seq_HEK293T_CasMINI-ge4.1_NUDT16

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI_NUDT16

description: The cells were transfected with gRNA-CasMINI plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #15_205624860016_R07C01_Cancer Untrained_Pre_Participant 12

source_name: DNA from Vastus Lateralis Muscle_ Sample No.15_205624860016_R07C01_Cancer Untrained_Pre_Participant 12


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #21_205624860053_R05C01_Healthy Aged-matched Trained_Pre_Participant 5

source_name: DNA from Vastus Lateralis Muscle_ Sample No.21_205624860053_R05C01_Healthy Aged-matched Trained_Pre_Participant 5


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #7_205624860002_R07C01_Cancer_Untrained_Post_Participant 6

source_name: DNA from Vastus Lateralis Muscle_ Sample No.7_205624860002_R07C01_Cancer_Untrained_Post_Participant 6


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #12_205624860016_R04C01_Healthy Aged-matched Trained_Pre_Participant 9

source_name: DNA from Vastus Lateralis Muscle_ Sample No.12_205624860016_R04C01_Healthy Aged-matched Trained_Pre_Participant 9


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #22_205624860053_R06C01_Cancer Trained_Pre_Participant 2

source_name: DNA from Vastus Lateralis Muscle_ Sample No.22_205624860053_R06C01_Cancer Trained_Pre_Participant 2


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #10_205624860016_R02C01_Cancer Trained_Pre_Participant 8

source_name: DNA from Vastus Lateralis Muscle_ Sample No.10_205624860016_R02C01_Cancer Trained_Pre_Participant 8


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #8_205624860002_R08C01_Healthy Aged-matched Trained_Pre_Participant 7

source_name: DNA from Vastus Lateralis Muscle_ Sample No.8_205624860002_R08C01_Healthy Aged-matched Trained_Pre_Participant 7


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #11_205624860016_R03C01_Cancer Trained_Post_Participant 8

source_name: DNA from Vastus Lateralis Muscle_ Sample No.11_205624860016_R03C01_Cancer Trained_Post_Participant 8


title: PEM-seq_HEK293T_LbCas12a_NUDT16

description: The cells were transfected with gRNA-LbCas12a plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_NLRC4

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_NUDT16

description: The cells were transfected with gRNA-SpCas9 plasmid targeting NUDT16 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: PEM-seq_HEK293T_PlmCas12e_NLRC4

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.


title: Normalized cardiomycyte, FoxO1+Mst1-DN

city: Stanford

first: Siavash

last: Moghadami

state: CA

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

institute: Stanford University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of 2 housekeeping genes and 3 RNAs as internal controls. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_controls)
normalized data file includes: normalized signal (against housekeeping genes)

label: SYBR Green

source_name: cardiomycytes, tranduced with FoxO1+Mst1-DN

label_protocol: The expression profile of 91 FoxO1-related genes was determined using a 96-well format custom mouse FoxO1 signalling pathway RT2 Profiler PCR array (No. CLAR23789, QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

extract_protocol: miRNeasy Kits (QIAGEN) was used to purify mRNAs

treatment_protocol: cardiomyocytes transduced with LacZ, Mst1, FoxO1, FoxO1+Mst1, or FoxO1+DN-Mst1 genes

value: cardiomyocyte


title: Normallized cardiomycyte, FoxO1+Mst1

description: Test

source_name: cardiomycytes, tranduced with FoxO1+Mst1


title: cardiomycyte, FoxO1+Mst1-DN, (rep1)

description: Test


title: cardiomycyte, FoxO1+Mst1, (rep1)

description: Test


title: cardiomycyte, FoxO1+Mst1-DN, (rep2)

description: Test


title: cardiomycyte, FoxO1+Mst1, (rep3)

description: Test


title: cardiomycyte, FoxO1+Mst1, (rep2)

description: Test


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #5_205624860002_R05C01_Cancer Trained_Pre_Participant 4

source_name: DNA from Vastus Lateralis Muscle_ Sample No.5_205624860002_R05C01_Cancer Trained_Pre_Participant 4


title: cardiomycyte, FoxO1+Mst1-DN, (rep3)

description: Test


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #4_205624860002_R04C01_Cancer Untrained_Pre_Participant 3

source_name: DNA from Vastus Lateralis Muscle_ Sample No.4_205624860002_R04C01_Cancer Untrained_Pre_Participant 3


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #6_205624860002_R06C01_Healthy Aged-matched Trained_Post_Participant 5

source_name: DNA from Vastus Lateralis Muscle_ Sample No.6_205624860002_R06C01_Healthy Aged-matched Trained_Post_Participant 5


title: Normalized cardiomycyte, Mst1

description: Test

source_name: cardiomycytes, tranduced with Mst1


title: PEM-seq_HEK293T_Un1Cas12f1_NLRC4

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.

source_name: cell line


title: cardiomycyte, Mst1, (rep2)

description: Test


title: Normalized cardiomycyte, FoxO1

description: Test

source_name: cardiomycytes, tranduced with FoxO1


title: cardiomycyte, FoxO1, (rep3)

description: Test


title: cardiomycyte, FoxO1, (rep2)

description: Test


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #9_205624860016_R01C01_Healthy Aged-matched Trained_Post_Participant 7

source_name: DNA from Vastus Lateralis Muscle_ Sample No.9_205624860016_R01C01_Healthy Aged-matched Trained_Post_Participant 7


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #3_205624860002_R03C01_Healthy Aged-matched Trained_Pre_Participant 1

source_name: DNA from Vastus Lateralis Muscle_ Sample No.3_205624860002_R03C01_Healthy Aged-matched Trained_Pre_Participant 1


title: PEM-seq_HEK293T_CasMINI_NLRC4

description: The cells were transfected with gRNA-CasMINI plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: Normalized cardiomycyte, LacZ, (rep3)

description: Control

source_name: cardiomycytes, tranduced with LacZ


title: cardiomycyte, Mst1, (rep1)

description: Test


title: cardiomycyte, FoxO1, (rep1)

description: Test


title: PEM-seq_HEK293T_CasMINI-ge4.1_NLRC4

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12f1_NLRC4

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_SpCas9_NLRC4

description: The cells were transfected with gRNA-SpCas9 plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: cardiomycyte, LacZ, (rep3)

description: Control


title: cardiomycyte, LacZ, (rep2)

description: Control


title: JP10

hyb_protocol: According to Diagenode protocol

scan_protocol: According to Diagenode protocol

data_processing: Raw IDAT files were processed using R package ChAMP. Probes with missing values are removed, samples with more than 10% of probes with a detection p-value of greater than 0.01, probes with a detection p-value of greater than 0.01 in at least one sample and probes for which 5% of samples have a bead count less than 3 are filtered out.  Probes targeting CpG sites that are near SNPs, belong to X/Y chromosomes, or align with multiple locations are filtered out

label: biotin

source_name: Mesenchymal stem cells

label_protocol: According to Diagenode protocol

extract_protocol: macherey nagel nucleospin tissue kit

tag: disease

value: APS (Atypical progria syndrome)

tag: sentrix id

tag: sentrix position


title: PEM-seq_HEK293T_LbCas12a_NLRC4

description: The cells were transfected with gRNA-LbCas12a plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.

tag: tissue

tag: genotype


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_COL8A1

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.


title: OE1882

city: wuhan

first: yao

last: teng

state: hubei

address: tongji medical school

institute: wuhan union hosipital

data_processing:
fastx_toolkit (version: 0.0.13.2)
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with 100% sequence identity  were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human blood

growth_protocol: Human CD4+T cells were maintained in XVIVO medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using miRneasy Mini kit (Qiagen). 1.0ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
LINC01882 overexpression lentiviral vector and empty vector containing green fluorescence protein (GFP) were transfected into CD3/CD28 activated CD4+T cells
Three days later, the CD4+T cells were sorted for GFP positive cells using Flow Sorter for microRNA sequencing.

value: CD4+T cell

value: human blood

value: adipogenic differentiation

tag: time

value: Day 3


title: NC_T

tag: treatment


title: cardiomycyte, LacZ, (rep1)

description: Control


title: NPCs SETV5 no Doxy #2

description:
NPC-SETV5-2
single index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ATAC-seq peak calling was performed on the Tn5- corrected single-base insertions using the following parameters --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all –qvalue 0.01.
Genome_build: hg38
Supplementary files format and content: macs narrowpeaks

source_name: NPCs

value: NPCs

value: SET WT


title: PEM-seq_HEK293T_control_COL8A1

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: NPCs SETV5 Doxy #1

description:
NPC-SETV5-1-Doxy
single index library

value: SET overexp.


title: NPCs SETV5 Doxy #2

description:
NPC-SETV5-2-Doxy
single index library


title: PEM-seq_HEK293T_PlmCas12e_COL8A1

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.

value: cell line


title: IPSCs SETV5 no Doxy #2

description:
IPSCs-SETV5-2
single index library

source_name: iPSCs

value: iPSCs


title: IPSCs SETV5 no Doxy #1

description:
IPSCs-SETV5-1
single index library


title: JP9

first: Frederique

last: Magdinier

institute: Aix-Marseille Université - Marseille Medical Genetics


title: PEM-seq_HEK293T_AsCas12a_NLRC4

description: The cells were transfected with gRNA-AsCas12a plasmid targeting NLRC4 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: JP3

value: CT aged


title: IPSCs SETV5 Doxy #1

description:
IPSC-SETV5-1-Doxy
single index library


title: IPSCs SETV5 Doxy #2

description:
IPSC-SETV5-2-Doxy
single index library


title: PEM-seq_HEK293T_AsCas12f1_COL8A1

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_Un1Cas12f1_COL8A1

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI-ge4.1_COL8A1

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: NPCs D868N RNA #6

description:
NPC_MUT6
dual index library

data_processing:
FASTQ reads were quality checked and adaptor trimmed with FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). High-quality trimmed reads were mapped to the hg38 reference genome with the STAR aligner90 (v2.7.9.a) using the latest GENCODE main annotation file91. Differential gene expression was calculated with DESeq292 (v1.32)
Genome_build: hg38
Supplementary files format and content: STAR gene counts

extract_protocol:
RNA was extracted using the TRI Reagent isolation system (Sigma-Aldrich) according to the manufacturer’s instructions.
TruSeq

value: SETBP1 D868N


title: NPCs D868D RNA #4

description:
NPC_WT4
dual index library

value: SETBP1 D868D


title: Neurons D868D RNA #3

description:
WT3
dual index library

source_name: NPC-derived Neurons

value: NPC-derived Neurons


title: NPCs SETV5 no Doxy #1

description:
NPC-SETV5-1
single index library


title: JP7

value: HGPS-l (huntington gilford progeria syndrome like)


title: Neurons D868D RNA #1

description:
WT1
dual index library


title: PEM-seq_HEK293T_AsCas12a_COL8A1

description: The cells were transfected with gRNA-AsCas12a plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.

value: Human embryonic kidney

value: WT

value: plasmid transfection


title: Neurons D868N RNA #3

description:
D868N3
dual index library


title: PEM-seq_HEK293T_CasMINI_COL8A1

description: The cells were transfected with gRNA-CasMINI plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: Neurons D868N RNA #2

description:
D868N2
dual index library


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #2_205624860002_R02C01_Cancer Trained_Post_Participant 2

source_name: DNA from Vastus Lateralis Muscle_ Sample No.2_205624860002_R02C01_Cancer Trained_Post_Participant 2

value: Female

value: Skeletal Muscle_Vastus Lateralis


title: cardiomycyte, Mst1, (rep3)

description: Test

value: cardiomyocyte


title: JP5

value: HGPS (huntington gilford progeria syndrome)


title: Healthy volunteer 1, TCR3

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

institute: University Freiburg Medical Center

description: 10x Genomics

data_processing:
BCL-files were demultiplexed into samples using bcl2fastq 2.20.0.422
scRNA: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.0.1 software with method count
VDJ: The demultiplexing, barcoded processing, V(D)J sequences and annotations were made using the Cell Ranger v6.0.1 software with method vdj
Assembly: mRNA: cellranger gex-GRCh38-2020-A
Assembly: VDJ: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: mRNA: h5 of countmatrix
Supplementary files format and content: VDJ: csv table of cell annotations
Library strategy: scTCR seq

source_name: peripheral blood

growth_protocol: 12 day in vitro expansion

extract_protocol:
Sorted T cells were washed and counted according to the 10x Genomics Cell Preparation Guide. Shortly, cells were washed three times in 1 ml 1X PBS 0.04% BSA respectively using wide-bore pipette tips for low-shear mixing and centrifuged at 300 rcf for 5 min. After final centrifugation step, cells were resuspended in 50 µl 1X PBS 0.04% BSA and cell numbers were obtained by using a Neubauer chamber. T cells were adjusted to a final stock concentration of 100 cells/µl and 1000 cells were loaded to the Chromium Next GEM Chip for each sample.
Library construction was performed according to the manufacture's protocol (single cell 5' v2 (dual index) + human TCR amplification). To generate gel beads-in-emulsion (GEMs), T cells were loaded to Chromium Next GEM Chip K together with master mix, gel beads and partitioning oil. After GEM generation, poly-A RNA was retrotranscripted to cDNA and Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode were included. For final library construction, pooled cDNA was cleaned up with Silane DynaBeads, further amplified by PCR and size-restricted by using SPRIselect reagent. To generate TCR libraries, a part of the amplified cDNA was used for V(D)J amplification followed by SPRIselect cleanup steps. During final libarary construction and V(D)J amplification, Illumina R2 primer, paired-end constructs and induvidual sample indeces were included.
scRNA-seq and TCR seq

treatment_protocol: in vitro priming followed by single cell sort of peptide-specific CD8+ T cells

tag: individual

value: Healthy volunteer 1

value: female

tag: disease state

value: healthy donor

value: peripheral blood

tag: library type

value: VDJ (TCR)

value: CD8+ T cells


title: JP8

city: Marseille

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone


title: Healthy volunteer 2, MRNA4

description: 10x Genomics

data_processing:
BCL-files were demultiplexed into samples using bcl2fastq 2.20.0.422
scRNA: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.0.1 software with method count
VDJ: The demultiplexing, barcoded processing, V(D)J sequences and annotations were made using the Cell Ranger v6.0.1 software with method vdj
Assembly: mRNA: cellranger gex-GRCh38-2020-A
Assembly: VDJ: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: mRNA: h5 of countmatrix
Supplementary files format and content: VDJ: csv table of cell annotations

value: Healthy volunteer 2

value: male

value: mRNA

value: in vitro priming followed by single cell sort of peptide-specific CD8+ T cells


title: Healthy volunteer 2, TCR4

description: 10x Genomics


title: JP1

value: CT young


title: JP2


title: Neurons D868N RNA #1

description:
D868N1
dual index library

value: NPC-derived Neurons

value: SETBP1 D868N


title: PEM-seq_HEK293T_SpCas9_COL8A1

description: The cells were transfected with gRNA-SpCas9 plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.

value: cell line

value: Human embryonic kidney

value: WT

value: plasmid transfection


title: NPCs D868N ChIP Input

description:
NPCD868N_Chip_Input
dual index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ChIP-seq narrow peaks (H3K27ac), the following parameters were used -f  BAMPE --nomodel --qvalue 0.01 --keep-dup all --call-summits using Input for each condition as control sample.
Genome_build: hg38
Supplementary files format and content: macs narrowpeak

extract_protocol:
To perform ChIP experiment 200000 cells for each experimental replicate were used. Cells were cross-linked in 1% formaldehyde for 10’ minutes at room temperature.  Cells were lysed in ChIP-lysis Buffer (10mM Tris-HCl 8.0,1% SDS, 5 mM EDTA). Sonication was performed using a Diagenode Bioruptor Pico sonicator (65 cycles, 30” ON-30” OFF, each cycle). Input were collected before precipitation. Samples (two technical replicates for each ChIP) were then incubated overnight at 4° using primary antibodies for H3K27ac, H3K27me3, H3K9me3 and SET in iC buffer from iDeal ChIP‐seq kit for Histones (Diagenode, cod. C01010051).   The next day, incubation with magnetic beads was performed on a rotator wheel for 3 hours at 4°. Beads were subsequently washed using iW1, iW2,iW3 and IW4 buffer (Diagenode). ChIP-DNA was then eluted, decrosslinked for 30’ at 37° and 4 hours at 65° and purified using.  After quantification 5 ng of DNA were used to build libraries using NebNext-UltraII kit (NEB, cod.). Samples were sequenced paired-end NovaSeq6000 by GeneWiz.
TruSeq

value: NPCs


title: Genomic DNA from Skeletal Muscle Biopsy_Sample #1_205624860002_R01C01_Healthy Aged-matched Trained_Post_Participant 1

source_name: DNA from Vastus Lateralis Muscle_ Sample No.1_205624860002_R01C01_Healthy Aged-matched Trained_Post_Participant 1

value: Female

value: Skeletal Muscle_Vastus Lateralis


title: PEM-seq_HEK293T_control_NLRC4


title: Neurons D868D RNA #2

description:
WT2
dual index library

value: SETBP1 D868D


title: Healthy volunteer 1, MRNA3

description: 10x Genomics

value: Healthy volunteer 1

value: female

value: healthy donor

value: peripheral blood


title: Patient 1, TCR2

description: 10x Genomics

value: Patient 1

value: FL-HCC

value: VDJ (TCR)

value: CD4+ T cells

value: 12 day in vitro expansion


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_VEGFA-2

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.

value: cell line


title: JP4

value: CT aged


title: Patient 1, MRNA2

description: 10x Genomics

value: mRNA


title: PEM-seq_HEK293T_control_VEGFA-2

value: Human embryonic kidney

value: WT

value: plasmid transfection


title: NPCs D868N ChIP H3K27ac #1

description:
NPCD868N_Chip_H3K27ac_1
dual index library

value: NPCs

value: SETBP1 D868N


title: NPCs D868D ChIP Input

description:
NPCD868D_Chip_Input
dual index library

value: SETBP1 D868D


title: NPCs D868N ChIP SET #1

description:
NPCD868N_Chip_SET_1
dual index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ChIP-seq narrow peaks (H3K27ac), the following parameters were used -f  BAMPE --nomodel --qvalue 0.01 --keep-dup all --call-summits using Input for each condition as control sample.
Genome_build: hg38
Supplementary files format and content: macs broadpeak