title: 145_49_CTRL (reanalysis)

tag: disease

tag: subject

tag: surface density


title: 293FT, RNAseq, Cas13b, R3

status: Public on Oct 09 2023

type: SRA

city: Shenyang

first: Teng

last: Fei

state: Liaoning

address: 195 Chuangxin Rd. Life Sciences Building A426. Hunnan District.

department: College of Life and Health Sciences

country: China

institute: Northeastern University, China

library_source: transcriptomic

data_processing:
The RNA-seq reads were aligned against the hg38 human reference genome using HISAT2.
Count table generated by htseq-count using gencode.v38.basic.annotation.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each gene

molecule: total RNA

organism: Homo sapiens

source_name: human embryonal kidney cells

growth_protocol: 293FT cells were regularly tested negative for mycoplasma contamination and maintained in DMEM (SEVEN Biotech) supplemented with 10% fetal bovine serum (ExCell) and 1% penicillin–streptomycin (Solarbio). Cells were passaged every 2-4 days to maintain exponential growth and were kept in a humidity-controlled incubator at 37°C with 5% CO2.

extract_protocol: Total RNA from cells is isolated using The Invitrogen Life Technologies TRIzol Reagent (Total RNA Isolation Reagent)

treatment_protocol: Plasmid expressing Cas9 or Cas13 protein were  transfected into 293FT cells using Lipofectamine™ 2000 Transfection Reagent.

tag: tissue

value: kidney

tag: cell line

tag: transfection

tag: time

value: Day 3 after transient transfection


title: E14 TKO cells, Day1, batch1 replicate 40 (SMARTseq2_EpiLC)

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

library_source: transcriptomic single cell

data_processing:
Paired-end reads were trimmed with trim Galore (v0.6.5) in order to remove adapter sequences and Ns nucleotides from both side of the read.
Cleaned reads were aligned onto a concatenated genome (the Mouse reference genome mm10 + fasta file with the ERCC spike-in sequences) with STAR (v2.7.5a) reporting random alignment with at most 6 % of mismatches. ERCCs, genes and TE families-based quantification was performed with featureCounts (v1.5.1) using a concatenated file with repeatMasker, ERCC spike-in and Gencode vM25 annotations. Filtering of cells was performed with the following criteria: cells with less than 7500 genes with at least one read and cells with more than 2% of mitochondrial reads or more than 10% of ribosomal reads were filtered out.
Assembly: GRCm38/mm10
Supplementary files format and content: Text file with quantification per gene

organism: Mus musculus

growth_protocol: ESCs were grown for at least two weeks on fibronectin-coated plates (1/60 dilution in PBS) in 2i+VitC medium (N2B27 (50% Neurobasal medium and 50% DMEM/F12 (Gibco) complemented with 2mM L-glutamine, 0.1mM β-Mercaptoethanol, N2 supplement (Gibco) and B27 serum-free supplement (Gibco)), complemented with 1000U/ml LIF, 2i (3μM Gsk3 inhibitor and 1μM of MEK inhibitor), and vitamin C 100µg/ml final (Sigma)) and passed with accutase (GIBCO) every 2-3 days.

extract_protocol:
Single cells were index-sorted individually by FACS (SONY SH800) into wells of a 96-well PCR plate containing 2.3 µl of lysis buffer (200U/µL SUPERase-IN (LifeTechnologies), 10% Triton X100, RNAse free H2O). scRNA-seq SMARTseq2 was performed as previously described (Picelli et al., 2014).
The Illumina Nextera XT DNA kit was used to prepare libraries that were sequenced on the Illumina HiSeq 4000 (paired-end 50bp). Samples from all cell lines were included in each sequencing lane, to control for technical lane effects

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x106 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 0, 1, 2, and 4 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

tag: cell type

value: Embryonic stem cells (murine)

tag: genotype

value: WT

tag: treatment

value: EpiLC differentiation


title: WI-38 cells, multi-fraction, 110mGy, input, rep1

city: Chalk River

first: Richard

middle: B.

last: Richardson

state: Ontario

address: 286 Plant Rd

department: Radiobiology and Health

country: Canada

institute: Canadian Nuclear Laboratories

library_source: genomic

data_processing:
Quality control was conducted using FastQ Screen (v0.4.1) and FastQC (v0.11.9).
Trimming was performed using TrimGalore (v0.6.6) with parameters: --clip_R1 1; --clip_R2 1; --three_prime_clip_R1 1; - three_prime_clip_R2 1; --trim-n; --length 50; -q 20 and --stringency 5. Quality of trimmed filtered reads was revaluated using FastQC (v0.11.9).
Alignment to the human reference genome GRCh38 was conducted using BWA (v0.7.17) in the paired-end mode of the BWA-MEM algorithm with the default parameter settings.
Mapped read files (*.sam) were converted to sorted BAM files by SAMtools (v1.11). Unmapped reads were filtered out using SAMtools (v1.11).
Bioconductor package MEDIPS (v1.40.0) was used to identify differentially methylated regions (DMRs) between controls and irradiated cells for both regimens with ws=50 bp; shift=0 and uniq=1.
Differential coverage was calculated using the edgeR function in MEDIPS with minRowSum=5 and quantile normalization. P-values were adjusted for multiple testing using the FDR method. Statistically significant methylation coverage results were selected using the criteria of FDR<0.05.
Genomic annotation was carried out using HOMER (v4.11). Neighboring significant regions located within the same chromosome, and with the same annotation and Gene ID, were merged using an in-house Python script.
Assembly: GRCh38
Supplementary files format and content: Bam files include only mapped sorted reads for each sample
Supplementary files format and content: RData files include differential coverage results using the edgeR function (mr.edgeR). When available, it also includes specific data extracted from the "mr.edgeR" file as follows:  differential coverage results with unadjusted P value<0.05 (mr.edgeR.sna), differential coverage results with FDR<0.1 (mr.edgeR.s0.1), differential coverage results with FDR<0.05 (mr.edgeR.s), differential coverage results with FDR<0.05 of hyperDMRs (mr.edgeR.s.gain), differential coverage results with FDR<0.05of hypoDMRs (mr.edgeR.s.lost)

molecule: genomic DNA

growth_protocol: WI-38 cells were maintained in EMEM medium supplemented with 10% fetal bovine serum (FBS), 50 U/mL Penicillin, 50 µg/mL Streptomycin, and 2 mM L-Glutamine in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with minor modifications.
Cell pellets were resuspended in PBS and treated with proteinase K and RNase A. The DNA-loaded spin columns were washed three times with buffer AW2. DNA was then eluted in Tris-EDTA (TE) buffer (low EDTA, pH 8.0) after 5 m at RT. DNA samples displayed A260/A280 ratios in the range of 1.8 to 2.0 and A260/A230 ratios higher than 2.1.
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 μg of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer’s guidelines. Immunoprecipitation with a 5mC antibody was conducted using a Diagenode MagMeDIP kit as described in the manufacturer’s protocol with starting volume of 15 µL. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturer’s instructions.
The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 7 cycles for the Input and 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.

treatment_protocol:
Cells were irradiated to seven doses of americium-241 α-sources ranging from 2.0 to 2,200 mGy using two exposure regimens, a single-fraction where the total dose was given at once, and a multi-fraction method, where the total dose was equally distributed over 14 consecutive days.
Cells in both exposure regimens were trypsinized and collected after the last irradiation following 1 h incubation at 37 °C in a 5% CO2 humidified atmosphere. Collected cells were immediately flash-frozen in liquid nitrogen and subsequently stored at -80 °C.

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

tag: dose (mgy)

tag: radiation regimen

value: multi-fraction

tag: total number_of_fractions

tag: antibody


title: 145_27_CTRL (reanalysis)

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

country: USA

institute: Yale School of Medicine

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5.
After quality control for adapter contamination and trimming, fastq files were mapped on human genome (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1.
Assembly: hg38
Supplementary files format and content: Matrix table with FPKM gene counts for every gene and every sample.

source_name: Lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen) from each core according to the manufacturer protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station.
20 ng RNA input was used for library preparation by AmpliSeq Transcriptome Human Gene Expression kit. The cDNA was then amplified and barcoded using the Ion Xpress RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485). The Ion Chip Kit v2 BC (Life Technologies 4484270) was then loaded using the Ion Chef System (Life Technologies 4484177) with the Ion PI IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI IC 200 Kit.

treatment_protocol: Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor. The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 4 cores were randomly selected per lung.

value: Lung

value: Control (donor)

tag: tissue percentage

tag: terminal bronchioles/ ml

tag: smoking ever

value: no

tag: age transplant

tag: gender

value: Male


title: E14 WT cells, Day1, batch1 replicate 40 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas13b, R2


title: WI-38 cells, multi-fraction, 23mGy, input, rep4


title: WI-38 cells, multi-fraction, 110mGy, input, rep4


title: 247_149_CTRL

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5.
After quality control for adapter contamination and trimming, fastq files were mapped on human genome (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1.
Assembly: hg38
Supplementary files format and content: TissueCoreProject_fpkm.txt: Matrix table with FPKM gene counts for every gene and every sample.

tag: disease

tag: subject

tag: surface density


title: WI-38 cells, multi-fraction, 23mGy, input, rep3

tag: cell line


title: WI-38 cells, multi-fraction, 220mGy, input, rep1


title: 293FT, RNAseq, Cas13b, R1

tag: tissue

tag: transfection

tag: time


title: E14 TKO cells, Day1, batch1 replicate 39 (SMARTseq2_EpiLC)

tag: cell type

tag: genotype

tag: treatment


title: 247_147_CTRL


title: WI-38 cells, multi-fraction, 23mGy, input, rep2

tag: dose (mgy)

tag: radiation regimen

tag: total number_of_fractions


title: WI-38 cells, multi-fraction, 23mGy, input, rep1

tag: antibody


title: 293FT, RNAseq, dCas13a, HR, R2


title: 247_115_CTRL

tag: smoking ever


title: E14 WT cells, Day1, batch1 replicate 38 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, dCas13a, HR, R3


title: E14 TKO cells, Day1, batch1 replicate 38 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 37 (SMARTseq2_EpiLC)


title: 247_2_CTRL

tag: age transplant


title: 293FT, RNAseq, dCas13a, R, R3


title: 244_117_CTRL

tag: gender


title: 145_110_CTRL (reanalysis)

tag: disease

tag: tissue percentage

tag: terminal bronchioles/ ml


title: WI-38 cells, multi-fraction, 11mGy, input, rep3

tag: cell line


title: 244_93_CTRL

tag: tissue

tag: subject

tag: surface density


title: WI-38 cells, multi-fraction, 11mGy, input, rep2

tag: cell type


title: E14 TKO cells, Day1, batch1 replicate 36 (SMARTseq2_EpiLC)

tag: genotype

tag: time


title: 293FT, RNAseq, dCas13a, R, R2

tag: transfection


title: E14 WT cells, Day1, batch1 replicate 39 (SMARTseq2_EpiLC)

tag: treatment


title: 293FT, RNAseq, dCas13a, R, R1


title: E14 WT cells, Day1, batch1 replicate 37 (SMARTseq2_EpiLC)


title: 244_70_CTRL


title: WI-38 cells, multi-fraction, 11mGy, input, rep1

tag: dose (mgy)

tag: radiation regimen

tag: total number_of_fractions


title: E14 WT cells, Day1, batch1 replicate 36 (SMARTseq2_EpiLC)


title: 225_88_COPD

value: COPD

tag: smoking ever

value: yes

tag: age transplant


title: 293FT, RNAseq, dCas13a, H, R3


title: WI-38 cells, multi-fraction, 2mGy, input, rep4

tag: antibody


title: 293FT, RNAseq, dCas13a, H, R2


title: WI-38 cells, multi-fraction, 11mGy, input, rep4


title: 225_79_COPD

tag: disease

tag: gender


title: E14 WT cells, Day1, batch1 replicate 35 (SMARTseq2_EpiLC)

tag: cell line


title: WI-38 cells, multi-fraction, 2mGy, input, rep3


title: WI-38 cells, multi-fraction, 2mGy, input, rep2


title: 293FT, RNAseq, dCas13a, H, R1

tag: tissue


title: E14 TKO cells, Day1, batch1 replicate 35 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas13a, DR, R3


title: 225_45_COPD

tag: subject


title: WI-38 cells, multi-fraction, 2mGy, input, rep1


title: E14 WT cells, Day1, batch1 replicate 34 (SMARTseq2_EpiLC)


title: 225_39_COPD

tag: surface density


title: 223_28_COPD


title: 293FT, RNAseq, Cas13a, R3


title: E14 TKO cells, Day1, batch1 replicate 33 (SMARTseq2_EpiLC)

tag: cell type


title: E14 TKO cells, Day1, batch1 replicate 34 (SMARTseq2_EpiLC)

tag: genotype


title: 293FT, RNAseq, Cas13a, DR, R1

tag: time


title: 293FT, RNAseq, Cas13a, DR, R2

tag: transfection


title: WI-38 cells, multi-fraction, 0mGy, input, rep2

tag: treatment

value: Sham


title: WI-38 cells, multi-fraction, 0mGy, input, rep4

tag: dose (mgy)


title: WI-38 cells, multi-fraction, 0mGy, input, rep3

tag: radiation regimen


title: 223_60_COPD


title: E14 WT cells, Day1, batch1 replicate 33 (SMARTseq2_EpiLC)


title: 223_13_COPD


title: 221_125_CTRL


title: 293FT, RNAseq, dCas13a, HR, R1


title: 293FT, RNAseq, Cas13a, R1


title: E14 TKO cells, Day1, batch1 replicate 32 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas9, R3

value: pLenti-CRISPR v2


title: 293FT, RNAseq, Cas13a, R2


title: E14 WT cells, Day1, batch1 replicate 31 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 2200mGy, input, rep3

value: single-fraction

tag: total number_of_fractions


title: 221_3_CTRL

tag: smoking ever


title: E14 WT cells, Day1, batch1 replicate 32 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 0mGy, input, rep1


title: WI-38 cells, single-fraction, 2200mGy, input, rep4


title: 221_67_CTRL

tag: age transplant


title: E14 TKO cells, Day1, batch1 replicate 31 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 2200mGy, input, rep2

tag: antibody


title: E14 TKO cells, Day1, batch1 replicate 30 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas9, R1

value: kidney


title: 293FT, RNAseq, Vector, R3

value: pLenti-backbone

value: Day 3 after transient transfection


title: WI-38 cells, single-fraction, 2200mGy, input, rep1


title: 211_99_CTRL

tag: disease


title: 221_147_CTRL

tag: gender


title: E14 TKO cells, Day1, batch1 replicate 29 (SMARTseq2_EpiLC)

tag: cell line

value: Embryonic stem cells (murine)

value: WT


title: WI-38 cells, single-fraction, 1100mGy, input, rep4

value: Human fibroblast from 3-month-old female lung tissue


title: 211_92_CTRL

tag: tissue


title: WI-38 cells, single-fraction, 1100mGy, input, rep3

value: alpha-irradiation


title: E14 WT cells, Day1, batch1 replicate 29 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: 211_68_CTRL

value: Lung

tag: subject


title: 293FT, RNAseq, Vector, R1


title: 293FT, RNAseq, Cas9, R2


title: E14 TKO cells, Day1, batch1 replicate 28 (SMARTseq2_EpiLC)


title: 211_44_CTRL

value: Control (donor)

tag: surface density


title: 210_122_COPD

value: Female


title: WI-38 cells, single-fraction, 1100mGy, input, rep1

tag: cell type


title: Pupae replicate 3

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Kallisto (PMID  27043002) was used for pseudoalignment of reads to a reference combining the Ensembl 74 annotation and additional lincRNAs from modENCODE (Young et al. PMID  22403033, Brown et al. PMID 24670639). We then used sleuth (Pimentel et al. PMID 28581496) for differential expression analysis
Assembly: dm3
Supplementary files format and content: kallisto output

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Imaginal leg disc

growth_protocol: Standard culturing lab condition

extract_protocol:
Total RNA was isolated from embryos with Trizol (Ambion). 100 ng of total RNA was used for the construction of polyA sequencing libraries. The quality of RNA was evaluated on Fragment Analyser.
mRNA libraries (polyA) for RNA-seq were prepared using NEBNext® Ultra™ II mRNA-Seq (strand specific) following manufacturer's protocols.

value: Imaginal leg disc

tag: genotype


title: 210_19_COPD

value: COPD


title: E14 WT cells, Day1, batch1 replicate 28 (SMARTseq2_EpiLC)

tag: time


title: Pupae replicate 2


title: Pupae replicate 1


title: E14 WT cells, Day1, batch1 replicate 30 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 27 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 220mGy, input, rep3


title: E14 WT cells, Day1, batch1 replicate 27 (SMARTseq2_EpiLC)


title: 210_6_COPD

value: yes


title: 293FT, RNAseq, Vector, R2

tag: transfection


title: WI-38 cells, single-fraction, 220mGy, input, rep2

tag: treatment


title: E14 TKO cells, Day1, batch1 replicate 26 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 1100mGy, input, rep2

tag: dose (mgy)


title: 200_77_COPD

value: Male


title: Larvae replicate 2


title: WI-38 cells, single-fraction, 220mGy, input, rep1

tag: radiation regimen


title: 155_64_CTRL

value: no


title: Larvae replicate 3


title: 155_87_CTRL


title: Larvae replicate 1


title: 155_47_CTRL


title: E14 WT cells, Day1, batch1 replicate 25 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 110mGy, input, rep4

value: single-fraction

tag: total number_of_fractions


title: E14 WT cells, Day1, batch1 replicate 26 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 220mGy, input, rep4


title: E14 TKO cells, Day1, batch1 replicate 25 (SMARTseq2_EpiLC)


title: WT_3

city: Graz

first: Tommaso

last: Sconocchia

address: Auenbruggerplatz 38

department: Hematology

country: Austria

institute: Medical University of Graz

data_processing:
Base calling was performed on-instrument using the Illumina Real-Time Analysis Software (RTA, 2.7.7).
NGS reads were mapped to the human reference genome hg38 using STAR and the Ensembl transcript annotation version e100 (April 2020).
Aligned NGS reads were counted with the GenomicAlignments (1.26.0) package via the summarizeOverlaps function in Union mode.
Differential expression analysis was performed with the DESeq2 (1.30.0) package on the basis of read counts from independent biological triplicates.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Cord blood-derived CD34+ HSPCs were expanded for 3 days in SFEM II media (Stemcell Technologies, Vancouver, BC, Canada) supplemented with 100 ng/ml of SCF, FLT3L, TPO, IL-6, 750 nM of SR1 and 35 nM of UM171 (HSPC retention media) prior to CRISPR modification.

extract_protocol:
Total RNA was isolated using the Monarch Total RNA Miniprep Kit (NEB, Ipswich, MA, USA).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) according to manufacturer's recommendations.

treatment_protocol: BRAFV600E mutation was introduced by utilizing a CRISPR/Cas9 and AAV6-mediated knock-in strategy. The modified cells were purified 48h after editing by FACS and cultured additionally for 2 days in HSPC retention media prior to RNA isolation.

value: Umbilical cord blood

value: Hematopoietic stem and progenitor cells

value: BRAF WT


title: WI-38 cells, single-fraction, 110mGy, input, rep3


title: E14 TKO cells, Day1, batch1 replicate 24 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: RNP_3

value: BRAF +/+


title: WI-38 cells, single-fraction, 110mGy, input, rep2

value: Human fibroblast from 3-month-old female lung tissue


title: 75_106_COPD

tag: smoking ever


title: WI-38 cells, single-fraction, 110mGy, input, rep1

value: alpha-irradiation


title: V600E_2


title: E14 WT cells, Day1, batch1 replicate 24 (SMARTseq2_EpiLC)

value: WT

value: EpiLC differentiation


title: 75_81_COPD

value: Lung

tag: age transplant


title: WI-38 cells, single-fraction, 23mGy, input, rep4

tag: antibody


title: WT_2


title: 75_68_COPD

tag: disease

value: Female


title: E14 TKO cells, Day1, batch1 replicate 23 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch1 replicate 23 (SMARTseq2_EpiLC)


title: RNP_2


title: V600E_3


title: V600E_1


title: E14 TKO cells, Day1, batch1 replicate 22 (SMARTseq2_EpiLC)


title: 155_21_CTRL

value: Control (donor)

tag: gender


title: 75_55_COPD

value: COPD


title: 72_108_COPD

value: yes


title: E14 WT cells, Day1, batch1 replicate 22 (SMARTseq2_EpiLC)

tag: cell line


title: 72_68_COPD

tag: tissue


title: WI-38 cells, single-fraction, 23mGy, input, rep1


title: WI-38 cells, single-fraction, 11mGy, input, rep4


title: WT_1


title: E14 TKO cells, Day1, batch1 replicate 21 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 11mGy, input, rep3


title: RNP_1


title: 72_28_COPD

tag: subject


title: FoxP3 pulldown_nucleosome rep2

city: Boston

first: Wenxiang

last: Zhang

state: Massachusetts

address: 300 Longwood Ave

institute: Boston Childrens Hospital

data_processing:
Fastq files were trimmed with Trimmomatic, aligned to UCSC mm10 genome with Bowtie2, converted to bam file, sorted and indexed by samtools (version 1.9) for downstream analysis.
Macs2 (version 2.1.1) was used for peak calling (p value=0.01 or 0.05).
Devo motif analysis used MEME-ChIP (https://meme-suite.org/meme/doc/meme-chip.html).
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: Pulldown-seq

growth_protocol: EL4 cells were cultured in DMEM (High glucose, L-glutamine, Pyruvate) supplemented with 10% fetal bovine serum, ranging from 1X105 to 1X106 cells/mL.

extract_protocol:
Mouse EL4 cells were lysed using a hypotonic buffer (20mM Bis-Tris pH 7.5, 0.05% NP-40, 1.5mM MgCl2, 10mM KCL, 5mM EDTA, 1Xmammalian protease inhibitor) and the nuclear fraction was isolated by spinning down at 4˚ and 2,500 RPM for 10 mins. The isolated nuclear fraction was then digested with Micrococcal Nuclease (Thermo Scientific, #88216) for 1 hour at 4℃ to fragment the chromatin into individual nucleosomes.
The libraries were made by NEBNext® Ultra™ II DNA Library Prep Kit (Illumina) according to the manufacturer’s instructions and submitted to Novogene for NGS with PE150.


title: E14 TKO cells, Day1, batch1 replicate 20 (SMARTseq2_EpiLC)


title: FoxP3 pulldown_nucleosome rep1


title: WI-38 cells, single-fraction, 23mGy, input, rep3


title: WI-38 cells, single-fraction, 11mGy, input, rep2


title: 72_7_COPD

tag: surface density


title: WI-38 cells, single-fraction, 23mGy, input, rep2

tag: cell type


title: E14 WT cells, Day1, batch1 replicate 20 (SMARTseq2_EpiLC)

tag: genotype


title: 70_140_COPD

value: Male


title: WI-38 cells, single-fraction, 2mGy, input, rep4


title: E14 TKO cells, Day1, batch1 replicate 19 (SMARTseq2_EpiLC)

tag: time


title: MBP pulldown_nucleosome rep2


title: WI-38 cells, single-fraction, 11mGy, input, rep1


title: 70_92_COPD


title: WI-38 cells, single-fraction, 2mGy, input, rep3


title: E14 WT cells, Day1, batch1 replicate 19 (SMARTseq2_EpiLC)


title: 70_43_COPD


title: WI-38 cells, single-fraction, 2mGy, input, rep2


title: WI-38 cells, single-fraction, 2mGy, input, rep1


title: E14 TKO cells, Day1, batch1 replicate 18 (SMARTseq2_EpiLC)


title: Input_nucleosome rep2


title: 68_112_COPD


title: Input_nucleosome rep1


title: AAA_RNAseq rep4

data_processing:
Raw sequence files were subjected to pre-processing using Trimmomatic v.0.36 to remove Illumina adaptor sequences and low-quality bases. Trimmed reads were then aligned to the mouse genome (UCSC mm10) using bowtie2/2.3.4.3.
For gene read counting, HTseq-count (v. 0.12.4) was employed. Normalization of gene counts and differential analysis were carried out using DESeq2 (v. 5).
The creation of heatmaps was accomplished using Pheatmap.
Assembly: mm10
Supplementary files format and content: .csv

source_name: CD4+T cell

growth_protocol: Naive CD4+ T cells were isolated by using Naive CD4+ T Cell Isolation Kit (Miltenyi Biotec, Cat#130-104-453) according to the manufacturer’s instructions and maintained in complete RPMI medium (10% FBS heat-inactivated, 2mM L-Glutamine, 1mM Sodium Pyruvate, 100μM NEAA, 5mM HEPES, 0.05mM 2-ME).

extract_protocol:
mRNA-seq was conducted using CD4+ T cells. Activated CD4+ T cells that had been transduced with wild-type or mutant FoxP3 were sorted based on Thy1.1 reporter expression. For each sample, 1X106 cells were sorted and subjected to total RNA extraction using TRIzol reagent and Direct-zol RNA Miniprep Kits.
Quality control and the construction of mRNA-seq libraries were undertaken by Novogene Co. Ltd.. The NEB Next Ultra II kit and the non-directional mRNA approach with the polyA pipeline were used. The libraries were subsequently sequenced using the Illumina NovaSeq 6000 instrument, generating paired-end reads with a length of 2X150 bp, resulting in ~30 M reads per sample.

value: CD4+T cell

value: AAA


title: E14 WT cells, Day1, batch1 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch1 replicate 18 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 0mGy, input, rep4

value: Sham

value: single-fraction


title: E14 TKO cells, Day1, batch1 replicate 17 (SMARTseq2_EpiLC)


title: AAA_RNAseq rep3


title: 68_80_COPD


title: AAA_RNAseq rep2


title: MBP pulldown_nucleosome rep1


title: 68_61_COPD


title: 70_136_COPD


title: WI-38 cells, single-fraction, 0mGy, input, rep2


title: 56_46_COPD


title: AAA_RNAseq rep1


title: E14 WT cells, Day1, batch1 replicate 16 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 0mGy, input, rep1


title: V408M_RNAseq rep4


title: 68_118_COPD


title: E14 TKO cells, Day1, batch1 replicate 15 (SMARTseq2_EpiLC)


title: V408M_RNAseq rep3


title: 56_4_COPD


title: WI-38 cells, multi-fraction, 2200mGy, 5mC, rep3

value: multi-fraction

value: anti-5mC (33D3 clone - Diagenode #C15200081)


title: E14 WT cells, Day1, batch1 replicate 15 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: 56_2_COPD


title: WI-38 cells, multi-fraction, 2200mGy, 5mC, rep4

value: Human fibroblast from 3-month-old female lung tissue


title: V408M_RNAseq rep2


title: WI-38 cells, multi-fraction, 2200mGy, 5mC, rep2

value: alpha-irradiation


title: WI-38 cells, single-fraction, 0mGy, input, rep3


title: E14 WT cells, Day1, batch1 replicate 17 (SMARTseq2_EpiLC)

value: WT


title: V408M_RNAseq rep1


title: 39_140_COPD


title: E14 WT cells, Day1, batch1 replicate 14 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: WI-38 cells, multi-fraction, 1100mGy, 5mC, rep4


title: E14 TKO cells, Day1, batch1 replicate 13 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 16 (SMARTseq2_EpiLC)


title: 39_113_COPD

value: Lung


title: V396E_RNAseq rep3


title: 39_63_COPD

value: Female


title: V396E_RNAseq rep4


title: 56_25_COPD


title: WI-38 cells, multi-fraction, 1100mGy, 5mC, rep3


title: E14 WT cells, Day1, batch1 replicate 13 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 1100mGy, 5mC, rep2


title: 39_9_COPD


title: V396E_RNAseq rep1


title: 19_79_COPD


title: E14 TKO cells, Day1, batch1 replicate 12 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 1100mGy, 5mC, rep1


title: E14 TKO cells, Day1, batch1 replicate 14 (SMARTseq2_EpiLC)


title: V396E_RNAseq rep2


title: E14 WT cells, Day1, batch1 replicate 12 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 220mGy, 5mC, rep4


title: 19_62_COPD


title: R356E_RNAseq rep4


title: E14 TKO cells, Day1, batch1 replicate 11 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 2200mGy, 5mC, rep1


title: R356E_RNAseq rep3


title: 19_7_COPD


title: R356E_RNAseq rep2


title: WI-38 cells, multi-fraction, 220mGy, 5mC, rep3


title: E14 WT cells, Day1, batch1 replicate 11 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 220mGy, 5mC, rep2


title: E14 TKO cells, Day1, batch1 replicate 10 (SMARTseq2_EpiLC)


title: R356E_RNAseq rep1


title: 19_5_COPD


title: FoxP3_RNAseq rep4

value: FoxP3 overexpressed


title: E14 WT cells, Day1, batch1 replicate 10 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 9 (SMARTseq2_EpiLC)


title: FoxP3_RNAseq rep3


title: WI-38 cells, multi-fraction, 110mGy, 5mC, rep4


title: S5, biol rep 2, Treg, scRNAseq

city: Philadelphia

first: Emma

middle: L

last: Lewis

state: PA

address: 3400 Spruce Street

department: Obstetrics and Gynecology

institute: University of Pennsylvania

data_processing:
Transcriptomic matrices were created with 10X Genomics' Cell Ranger Single Cell Software Suite 3.1.0 (http://10xgenomics.com/). Raw base call files from the HiSeq2500 sequencer were demultiplexed with the Cell Ranger *mkfastq* pipeline into library-specific FASTQ files.
All library-related FASTQ file were subsequently transformed into count matrices with Cell Ranger's *count* pipeline. This pipeline aligned reads to mouse reference mm10-3.0.0 (Ensembl 93) before barcodes were used for filtering and corrective purposes.
Assembly: mm10-3.0.0 (Ensembl 93)
Supplementary files format and content: tab-separated values and matrix files

source_name: E15 pregnant uterus

growth_protocol: Timed matings of CBA females with DBA/2 males

extract_protocol:
Uterine tissue was minced and suspended in digest solution (HBSS + 10% FBS + 1mg/ml Collagenase IV) in a 37°C water bath for 30 minutes. Digested tissue was passed through 40mm cell strainers. Red blood cells were removed with ACK lysing buffer and incubation at room temberature for 10 minutes, rinsed with HBSS. CD11b+ cells were enriched using CD11b+ microbeads follwoing the manufacturer's protocol (Miltenyi Biotec). Cells were stained with Live/Dead Fixable Aqua for 30 minutes. Cells were then stained with the following extracellular antibody mix, all diluted 1:400 in FACS buffer (PBS + 2% FBS + 20mM EDTA):  anti-CD45-SB702 (eBioscience); anti-CD11b-PE, anti-CD3e-APC-Cy7, and anti-CD19-APC.Cy7 (BioLegend) for 30 minutes. Cells were sorted on a BD FACS Aria, collecting live, singlet, CD45+, CD11b+ cells in 50% FBS + 50% PBS. Cells were resuspending in 1000 cells/1ml sterile PBS for library preparation.
10X Genomics Single Cell 3' version3 was used and manufacturer's protocol was followed. Briefly, cDNA was created from uterine myeloid cells using Chromium single cell 3' v3 gel beads and RT mix, which use a primer containing the illumina R1 primer, UMI, 10X barcode and poly(dT) sequence.  Dynabeads MyOne Silane were used to purify cDNA from GEM/RT mix. cDNA was amplified by PCR followed by SPRI enzyme fragmentation for ideal sizing. P5, P7, a sample index and R2 primers were then added via adaptor ligation to create a gene expression library with paired-end constructs begining and ending with P5 and P7.

treatment_protocol: At E2, females received either 2x105 Tregs (in 100ml sterile PBS) or 100ml sterile PBS by retroorbital injection (N = 3 mice/treatment group). At E15, uteri were harvested from the pregnant mice and processed into a single cell suspension.

value: E15 pregnant uterus

tag: mouse strain

value: CBA

value: live CD45+ CD11b+

value: Treg Adoptive transfer


title: S6, biol rep 3, Treg, scRNAseq

tag: treatment


title: WI-38 cells, multi-fraction, 110mGy, 5mC, rep3

tag: dose (mgy)


title: E14 WT cells, Day1, batch1 replicate 9 (SMARTseq2_EpiLC)


title: S4, biol rep 1, Treg, scRNAseq


title: S3, biol rep 3, PBS, scRNAseq

value: PBS


title: E14 TKO cells, Day1, batch1 replicate 8 (SMARTseq2_EpiLC)


title: FoxP3_RNAseq rep1

value: CD4+T cell


title: WI-38 cells, multi-fraction, 110mGy, 5mC, rep2

tag: radiation regimen


title: E14 WT cells, Day1, batch1 replicate 8 (SMARTseq2_EpiLC)


title: S2, biol rep 2, PBS, scRNAseq


title: EV_RNAseq rep4


title: WI-38 cells, multi-fraction, 23mGy, 5mC, rep4

tag: total number_of_fractions


title: WI-38 cells, multi-fraction, 220mGy, 5mC, rep1


title: E14 TKO cells, Day1, batch1 replicate 7 (SMARTseq2_EpiLC)


title: EV_RNAseq rep3


title: S1, biol rep 1 PBS, scRNAseq


title: N3ko_UV_2

city: Zürich

first: Selina

last: Gurri

address: Otto-Stern-Weg 7

department: Institute of Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic
Sequence alignment of the resulting high-quality reads to the Mouse reference genome (build GRCm38 with the gene annotations downloaded on 2014-02-25 from Ensembl) and quantification of gene level expression was carried out using RSEM
Differential expression was computed using the generalized linear model implemented in the Bioconductor package DESeq2. Genes showing altered expression   with adjusted (Benjamini and Hochberg method) p-value < 0.05 were considered differentially expressed.
Assembly: GRCm38
Supplementary files format and content: Matrix file with normalized counts and FPKM

source_name: skin

extract_protocol:
The epidermis was isolated as described previously (Siegenthaler et al., 2018) and the RNA extracted with Trizol followed by purification with the RNeasy Mini Kit, including on-column DNase treatment according to the manufacturer’s instructions.
Library preparation was performed with Illumina’s TruSeq mRNA stranded kit with 700ng totalRNA as input amount.

value: skin

value: keratinocytes

value: ko

value: UV irradiation


title: E14 WT cells, Day1, batch1 replicate 7 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: WI-38 cells, multi-fraction, 23mGy, 5mC, rep3

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

value: multi-fraction

value: anti-5mC (33D3 clone - Diagenode #C15200081)


title: WI-38 cells, multi-fraction, 23mGy, 5mC, rep2


title: E14 TKO cells, Day1, batch1 replicate 6 (SMARTseq2_EpiLC)

value: WT

value: EpiLC differentiation


title: EV_RNAseq rep2


title: N3ko_UV_6


title: N3ko_UV_4


title: FoxP3_RNAseq rep2

value: FoxP3 overexpressed


title: AAA_ChIP rep2

data_processing:
Fastq files were trimmed with Trimmomatic, aligned to UCSC mm10 genome with Bowtie2, converted to bam file, sorted and indexed by samtools (version 1.9) for downstream analysis.
Macs2 (version 2.1.1) was used for peak calling (p value=0.01 or 0.05).
Devo motif analysis used MEME-ChIP (https://meme-suite.org/meme/doc/meme-chip.html).
FIMO was used to identify TnG repeat-containing vs non-TnG repeat-containing peaks
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
Activated CD4+ T cells that had been transduced with wild-type or mutant FoxP3 were sorted based on Thy1.1 reporter expression. For each sample (5X106 cells), cross-linking was achieved with 1% formaldehyde for 10 minutes. Subsequently, the cells were lysed on ice using RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, 140 mM NaCl, and 1X proteinase inhibitor). Chromatin fragmentation was achieved using an AFA Focused-ultrasonicator (Covaris M220) for 30 minutes (5% duty cycle, 140W max power, 200 cycle/burst), resulting in DNA fragments ranging from 100 to 200 bp. The sheared material underwent a 10-minute centrifugation at 13,000 rpm at 4°C to clear the solution. The cleared material was then subjected to immunoprecipitation overnight with HA-tag antibody (Cell Signaling, #3724) at 4°C, and Protein G beads (Active motif, #53014) were added for an additional 2 hours. The beads were sequentially washed with various buffers: RIPA Wash Buffer (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X100, 1mM EDTA, 10mM TrisHCl pH 8.0, 150mM NaCl), RIPA 500 Wash Buffer (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X100, 1mM EDTA, 10mM TrisHCl pH 8.0, 500mM NaCl), LiCl wash buffer (10mM TrisHCl, pH 8.0, 250mM LiCl, 0.5% Triton X100, 0.5% Sodium Deoxycholate), and Tris buffer (10mM TrisHCl, pH 8.5). The chromatin was eluted from the beads using Elution buffer (1X TE, pH 8.0, 0.1% SDS, 150mM NaCl, 5 mM DTT). After elution, the DNA was treated with 1 µg DNase-free RNase (Roche) for 30 minutes at 37°C, followed by treatment with Proteinase K (Roche) for at least 4 hours at 63°C to reverse the crosslinks. The reverse-crosslinked DNA was then purified using SPRI beads (Beckman, #B23318).
Library preparations steps, including end repair, A-base addition, adaptor-ligation, and PCR amplification, were carried out to prepare the ChIP-seq library for each sample. The libraries were made by NEBNext® Ultra™ II DNA Library Prep Kit (Illumina) according to the manufacturer’s instructions and submitted to Novogene for NGS with PE150.

value: AAA

value: HA-tag


title: WI-38 cells, multi-fraction, 11mGy, 5mC, rep4


title: EV_RNAseq rep1


title: WI-38 cells, multi-fraction, 110mGy, 5mC, rep1


title: AAA_ChIP rep1


title: E14 WT cells, Day1, batch1 replicate 6 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 5 (SMARTseq2_EpiLC)


title: N3wt_UV_1

value: wt


title: V408M_ChIP rep2


title: E14 WT cells, Day1, batch1 replicate 5 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 11mGy, 5mC, rep3


title: WI-38 cells, multi-fraction, 11mGy, 5mC, rep2


title: E14 TKO cells, Day1, batch1 replicate 4 (SMARTseq2_EpiLC)


title: N3ko_noUV_6

value: mock


title: WI-38 cells, multi-fraction, 11mGy, 5mC, rep1


title: E14 WT cells, Day1, batch1 replicate 4 (SMARTseq2_EpiLC)


title: V408M_ChIP rep1

value: CD4+T cell


title: N3ko_noUV_3

value: skin


title: V396E_ChIP rep2


title: WI-38 cells, multi-fraction, 2mGy, 5mC, rep4


title: WI-38 cells, multi-fraction, 23mGy, 5mC, rep1


title: E14 TKO cells, Day1, batch1 replicate 3 (SMARTseq2_EpiLC)


title: N3ko_noUV_2

value: keratinocytes


title: V396E_ChIP rep1


title: WI-38 cells, multi-fraction, 2mGy, 5mC, rep3


title: N3wt_UV_3


title: E14 WT cells, Day1, batch1 replicate 3 (SMARTseq2_EpiLC)


title: R356E_ChIP rep2


title: N3wt_noUV_5


title: E14 TKO cells, Day1, batch1 replicate 2 (SMARTseq2_EpiLC)


title: R356E_ChIP rep1


title: N3wt_noUV_4


title: N3wt_UV_5


title: WI-38 cells, multi-fraction, 2mGy, 5mC, rep2


title: N3wt_noUV_1


title: FoxP3_ChIP rep2


title: WI-38 cells, multi-fraction, 0mGy, 5mC, rep4

value: Sham


title: WI-38 cells, multi-fraction, 2mGy, 5mC, rep1


title: E14 TKO cells, Day1, batch1 replicate 1 (SMARTseq2_EpiLC)


title: PlasmidPool-for-Cas13d-TwoVector

description: Pcr product from plasmid pool

library_source: other

data_processing:
Read count table generated by MAGeCK 0.5.9.4
MAGeCK count command was used to collect read count from the fastq file
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

molecule: other

organism: synthetic construct

source_name: Plasmid pool

growth_protocol: A375 cells were regularly tested negative for mycoplasma contamination and maintained in DMEM (SEVEN Biotech) supplemented with 10% fetal bovine serum (ExCell) and 1% penicillin–streptomycin (Solarbio). Cells were passaged every 2-4 days to maintain exponential growth and were kept in a humidity-controlled incubator at 37°C with 5% CO2. Protein-coding gene and lncRNA-targeting plasmid libraries under lentiviral backbone were firstly transfected along with pCMV8.74 and pMD2.G packaging plasmids into 293FT cells using Lipofectamine™ 2000 Transfection Reagent to generate crRNA-expressing lentivirus. Harvest virus-containing media at 72 hours post-transfection, and spin down the media at 1000 g for 5 min to remove the floating cells and cell debris. Carefully collect the virus supernatant, aliquot and store them at -80°C for further use. Test the virus titer and MOI (multiplicity of infection) before proceeding to the screen.

extract_protocol:
The regions encompassing the sgRNAs were firstly PCR-amplified for around 20-23 cycles . The second round of PCR were employed to attach the illumina adaptors and index for around 10-12 cycles. These PCR products were gel purified and pooled for high-throughput sequencing to identify sgRNA abundance on illumina PE150 sequencing platform (Novogene, China).
The pooled synthesized oligos (Synbio Technologies, China) were PCR amplified and then cloned into pLentiGuideDR-puro vector (for expressing Cas13b/d crRNA) via BsmBI site by Gibson Assembly. The ligated Gibson Assembly mix was transformed into self-prepared electrocompetent Stable E. coli cells by electro-transformation to reach the efficiency with at least 100X coverage representation of each clone in the designed library. The transformed bacteria were cultured directly in liquid LB medium for 16~20 hours at temperature 30°C to minimize the recombination events in E. coli. The library plasmids were then extracted with EndoFree Maxi Plasmid Kit (TIANGEN, Cat no. 4992194).
Ensembl gene and lncRNA annotations (version: GRCh38) are used to extract the sequences of corresponding genes or lncRNAs. For genes (or lncRNAs) with multiple transcripts, the transcripts that have the corresponding RefSeq ID are used. We first enumerate all possible guides (22bp for Cas13d and 30bp for Cas13b) that span the entire transcript, then remove guides that (1) map to more than one location in the human genome and transcriptome (allowing up to 1 mismatch) or (2) contains BsmBI digestion sites (“CGTCTC” or “GAGACG”). The remaining guides are randomly selected if they hit the greatest number of transcripts (“common” guides) within the same gene/lncRNA. If all the guides that hit the greatest number of transcripts are selected, the remaining guides that hit the second greatest number of transcripts will be randomly selected, and so on. For essential and non-essential genes, 35 guides are designed per gene. For other genes or lncRNAs, 15 guides are designed per gene or lncRNA.

treatment_protocol: Cas13b/d-expressing A375 cells were firstly generated by lentiviral infection of Cas13b/d (pLentiCas13b/d-NES-blast) and then amplified to a number around 3x10^7. Then, these cells were infected with Cas13b/d crRNA-expressing lentiviral CRISPR library with MOI ~0.3. Two days later, select the infected cells with puromycin (1 µg/mL) for three days to get rid of any non-infected cells before changing back to normal media. At least ~300x coverage of cells were collected as Day 5 sample and stored at -80°C for later genomic DNA isolation. The rest of cells were continually cultured until Day 33 before harvesting as the end point sample.

tag: sample type

value: PlasmidPool

tag: infection


title: FoxP3_ChIP rep1

tag: antibody


title: E14 WT cells, Day1, batch1 replicate 1 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: WI-38 cells, multi-fraction, 0mGy, 5mC, rep3

value: Human fibroblast from 3-month-old female lung tissue


title: WI-38 cells, multi-fraction, 0mGy, 5mC, rep2


title: EV_ChIP rep1

value: Empty vector


title: PlasmidPool-for-Cas13d-OneVector

description: Pcr product from plasmid pool


title: WI-38 cells, multi-fraction, 0mGy, 5mC, rep1

value: multi-fraction


title: E14 WT cells, Day0, batch1 replicate 48 (SMARTseq2_EpiLC)


title: Infected-BMDM Rep3

city: CORDOBA

first: JUAN

middle: NAHUEL

last: QUIROZ

state: CORDOBA

address: HAYA DE LA TORRE Y MEDINA ALLENDE S/N

department: CLINICAL BIOCHEMISTRY

country: Argentina

institute: CIBICI

data_processing:
Rna-seq reads were aligned with BWA Aln (v 0.7.10) against the mm10 transcriptome.
All reads containing bases with quality lower than Q10 were filtered out. Reads which are aligned must have no more than one mismatch, no more than 20As in a row (poly A tail) and not be aligned to more than 20 different positions in the transcriptome.
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1.
Uniquely mapped read counts were normalized using TMM normalization and CPM.
Differential genes expression was accessed using Limma (v3.34.1) with p<0.05.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes CPM normalized counts for each sample

source_name: Bone marrow

extract_protocol:
Bone marrow macrophages (BMDM) from C57BL/6 mice were cultured for 24h with Trypanosoma cruzi (Tulahuen Strain, TcVI). Cell to parasite ratio was set to 1:3. Then, 2x106 BMDM were pelleted, lysed, and RNA was harvested according to the Qiagen RNeasy Mini Kit protocol. Only Samples that passed the purity cutoff (Abs 260/Abs 280 = 1,7-2) were selected for downstream processing.
Libraries were processed by the Broad Institute's Broad Technology Labs and the Broad Genomics Platform. Libraries were prepared according to the 3’ Digital Gene Expression (3' DGE) protocol (Soumillon et al., 2014). RNA was sequenced at the Broad Technology Services using the High-throughput eukaryote 3' DGE library.

value: Bone marrow

value: Immune cell

value: Tc-infection


title: E14 TKO cells, Day0, batch1 replicate 47 (SMARTseq2_EpiLC)

value: WT

value: EpiLC differentiation


title: Infected-BMDM Rep4


title: Male Control 8

city: Edinburgh

first: Emily

last: Osterweil

state: Scotland

address: Hugh Robson Building, 15 George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Filtering and QC were performed by the sequencing facility
RNA-seq reads were aligned to the GRCm39 genome assembly using STAR version 2.7.1a
Assembly: GRCm39
Supplementary files format and content: count files were generating using feature counts

extract_protocol:
V1 tissue was collected and snap frozen from mice that were briefly anesthetized (isoflurane) and decapitated. Tissue was homogenized using a bead mill (Bead Mill 24, Fisher Scientific) and RNA was isolated using an RNeasy kit (Qiagen) according to manufacturer’s instructions
Handled by Oxford Genomic Centre that used a PolyA sequencing strategy

treatment_protocol: Mice (7-9 weeks of age) either had ad libitum access to food (RM1 expanded pellets; DBM Scotland UK) or were food restricted for 2-3 weeks to 85% of their baseline bodyweight prior to experimentation. Briefly, for food restriction, one ration of food was given 4-8 hours prior to the end of the dark cycle, with the amount of food progressively reduced to achieve target weight. 1-2 hour prior to experimentation, all animals had ad libitum access to food until sated

tag: strain

tag: Sex

value: Male

tag: developmental stage

value: adult


title: Infected-BMDM Rep2

tag: tissue


title: Male Control 7


title: WI-38 cells, single-fraction, 2200mGy, 5mC, rep4

tag: cell line

value: alpha-irradiation

value: single-fraction

value: anti-5mC (33D3 clone - Diagenode #C15200081)


title: E14 WT cells, Day1, batch1 replicate 2 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 2200mGy, 5mC, rep3


title: Male Control 6


title: E14 WT cells, Day0, batch1 replicate 47 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 2200mGy, 5mC, rep1


title: WI-38 cells, single-fraction, 2200mGy, 5mC, rep2


title: E14 TKO cells, Day0, batch1 replicate 46 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 46 (SMARTseq2_EpiLC)


title: Infected-BMDM Rep1


title: Non-infected BMDM, Rep4


title: EV_ChIP rep2

value: CD4+T cell

value: HA-tag


title: E14 TKO cells, Day0, batch1 replicate 48 (SMARTseq2_EpiLC)


title: Male Food Deprived 4

value: Food restriction


title: Non-infected BMDM, Rep3


title: E14 TKO cells, Day0, batch1 replicate 45 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: Male Food Deprived 3


title: WI-38 cells, single-fraction, 1100mGy, 5mC, rep3

value: Human fibroblast from 3-month-old female lung tissue


title: Non-infected BMDM, Rep2


title: WI-38 cells, single-fraction, 1100mGy, 5mC, rep4


title: E14 WT cells, Day0, batch1 replicate 45 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 1100mGy, 5mC, rep2


title: E14 TKO cells, Day0, batch1 replicate 44 (SMARTseq2_EpiLC)


title: Non-infected BMDM, Rep1


title: Chipseq_CD8_Input_2

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description: Chipmentation

data_processing:
ChIP-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ChIP-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1. Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Assembly: mm10
Supplementary files format and content: bw

source_name: Spleen

extract_protocol:
CD8 T cells were isolated from spleen for ChIP-Seq analysis.
ChIP-Seq was performed according to the published chipmentation protocol (Schmidl, C., Rendeiro, A. F., Sheffield, N. C., & Bock, C. (2015).http://doi.org/10.1038/nmeth.3542).

value: Spleen

value: ex vivo

value: CD8 T cells


title: E14 WT cells, Day0, batch1 replicate 44 (SMARTseq2_EpiLC)


title: Male Food Deprived 1


title: Male Control 5


title: Male Food Deprived 2


title: Female Control 8

value: Female


title: E14 TKO cells, Day0, batch1 replicate 43 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 1100mGy, 5mC, rep1


title: WI-38 cells, single-fraction, 220mGy, 5mC, rep4


title: Female Control 7


title: Chipseq_CD8_FOXP1_2

description: Chipmentation


title: Chipseq_CD8_Input_1

description: Chipmentation


title: WI-38 cells, single-fraction, 220mGy, 5mC, rep3


title: E14 WT cells, Day0, batch1 replicate 43 (SMARTseq2_EpiLC)


title: Chipseq_CD8_FOXP1_1

description: Chipmentation


title: E14 TKO cells, Day0, batch1 replicate 42 (SMARTseq2_EpiLC)


title: Female Control 5


title: Female Control 6


title: Chipseq_CD8_KLF2_2

description: Chipmentation


title: WI-38 cells, single-fraction, 220mGy, 5mC, rep1


title: WI-38 cells, single-fraction, 220mGy, 5mC, rep2


title: E14 WT cells, Day0, batch1 replicate 42 (SMARTseq2_EpiLC)


title: Chipseq_CD8_KLF2_1

description: Chipmentation


title: Female Food Deprived 4


title: WI-38 cells, single-fraction, 110mGy, 5mC, rep4


title: E14 TKO cells, Day0, batch1 replicate 41 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 110mGy, 5mC, rep3


title: E14 WT cells, Day0, batch1 replicate 41 (SMARTseq2_EpiLC)


title: Female Food Deprived 3


title: Endosperm, WT, rep1

city: Ithaca

first: Hao

last: Wu

state: NY

address: 236 Tower Rd, Plant Science Building Room #236

institute: Cornell University

data_processing:
The raw read quality control was performed via FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by the adapter trimming via Trimmomatic (v0.32)
The trimmed reads were mapped to B73 RefGen_v4 (AGPv4) via Bowtie2 (v 2.4.2)
The mapped reads in the output files were sorted, assembled and filtered by SAMtools (v1.9) using default parameters
Peak calling was performed via MACS2
Assembly: B73 RefGen_v4 (AGPv4)
Supplementary files format and content: bigWig (.bw)

organism: Zea mays

source_name: Endosperm

extract_protocol:
Frozen 16 DAP endosperms (0.2g) of nkd1, 2 and o2 single, double and triple mutants, as well as the wild type counterpart (two biological replicates each) were collected and ground in liquid nitrogen. Add 2mL of pre-chilled lysis buffer (15mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5mM 2-ME, 0.2% TritonX-100) to resuspend the ground powder. Then the resuspension was filtered three times through miracloth. The crude nuclei were stained with 4,6-Diamidino-2-phenylindole (DAPI, from Millipore Sigma, St. Louis, MO) (4uL DAPI per ~500uL filtered resuspension), and at least 50,000 triploid nuclei (3C) were sorted for ATAC-Seq library construction.
The library was constructed using the Active Motif ATAC-Seq Kit following the manufacturer’s manual. The library was sequenced using NovaSeq 6000 SP flow cell sequencing platform at 2X50 bp paired-end in 50 million bp depth.

value: Endosperm

value: Endosperm cells

value: nuclear extraction and sorting


title: Endosperm, WT, rep2

value: WT


title: E14 TKO cells, Day0, batch1 replicate 40 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: WI-38 cells, single-fraction, 110mGy, 5mC, rep2

value: alpha-irradiation


title: Female Food Deprived 2

value: adult


title: WI-38 cells, single-fraction, 110mGy, 5mC, rep1

value: single-fraction

value: anti-5mC (33D3 clone - Diagenode #C15200081)


title: Female Food Deprived 1


title: Endosperm, o2, rep2


title: Endosperm, o2, rep1


title: FoxP3-pulldown rep2

data_processing:
Fastq files were trimmed with Trimmomatic, aligned to UCSC mm10 genome with Bowtie2, converted to bam file, sorted and indexed by samtools (version 1.9) for downstream analysis.
Macs2 (version 2.1.1.20160309) was used for peak calling (p value=0.01 or 0.05).
Devo motif analysis used MEME-ChIP (https://meme-suite.org/meme/doc/meme-chip.html).
Assembly: mm10
Supplementary files format and content: bam
Supplementary files format and content: narrowPeak
Library strategy: Pulldown-seq

extract_protocol:
Mouse EL4 genomic DNA was isolated by QIAGEN Blood & Cell Culture DNA Kit (QIAGEN, #13343). The purified genomic DNA was then fragmented to 100~200bp by using DNase I (ZYMO RESEARCH, #E1010) in the digestion buffer (50 mM NaCl, 20 mM Tris-Cl PH 7.5, 1.5 mM MgCl2) (for 200μL system, 50μg genomic DNA was treated with 8μL DNase I for 3~4mins to get 100~200 DNA fragments). The digested genomic DNA from 100~200bp was purified by QIAquick Nucleotide Removal Kit (QIAGEN, #28306) and used as input for the pulldown-seq.
Purified MBP-tag or MBP-mFoxP3ΔN protein was incubated with input DNA fragments in incubation buffer (20 mM Tirs, pH 7.5, 100 mM NaCl, 1.5 mM MgCl2) for 20 mins at room temperature and then subjected to MBP pulldown by using Amylose Resin (New England Biolabs). After proteinase K (New England Biolabs) treatment, the final DNAs were recovered by QIAquick Nucleotide Removal kit (QIAGEN) and used for library preparation. The libraries were made by NEBNext® Ultra™ II DNA Library Prep Kit (Illumina) according to the manufacturer’s instructions and submitted to Novogene for NGS with PE150.


title: E14 TKO cells, Day0, batch1 replicate 39 (SMARTseq2_EpiLC)

data_processing:
Paired-end reads were trimmed with trim Galore (v0.6.5) in order to remove adapter sequences and Ns nucleotides from both side of the read.
Cleaned reads were aligned onto a concatenated genome (the Mouse reference genome mm10 + fasta file with the ERCC spike-in sequences) with STAR (v2.7.5a) reporting random alignment with at most 6 % of mismatches. ERCCs, genes and TE families-based quantification was performed with featureCounts (v1.5.1) using a concatenated file with repeatMasker, ERCC spike-in and Gencode vM25 annotations. Filtering of cells was performed with the following criteria: cells with less than 7500 genes with at least one read and cells with more than 2% of mitochondrial reads or more than 10% of ribosomal reads were filtered out.
Assembly: GRCm38/mm10
Supplementary files format and content: Text file with quantification per gene


title: WI-38 cells, single-fraction, 23mGy, 5mC, rep4

data_processing:
Quality control was conducted using FastQ Screen (v0.4.1) and FastQC (v0.11.9).
Trimming was performed using TrimGalore (v0.6.6) with parameters: --clip_R1 1; --clip_R2 1; --three_prime_clip_R1 1; - three_prime_clip_R2 1; --trim-n; --length 50; -q 20 and --stringency 5. Quality of trimmed filtered reads was revaluated using FastQC (v0.11.9).
Alignment to the human reference genome GRCh38 was conducted using BWA (v0.7.17) in the paired-end mode of the BWA-MEM algorithm with the default parameter settings.
Mapped read files (*.sam) were converted to sorted BAM files by SAMtools (v1.11). Unmapped reads were filtered out using SAMtools (v1.11).
Bioconductor package MEDIPS (v1.40.0) was used to identify differentially methylated regions (DMRs) between controls and irradiated cells for both regimens with ws=50 bp; shift=0 and uniq=1.
Differential coverage was calculated using the edgeR function in MEDIPS with minRowSum=5 and quantile normalization. P-values were adjusted for multiple testing using the FDR method. Statistically significant methylation coverage results were selected using the criteria of FDR<0.05.
Genomic annotation was carried out using HOMER (v4.11). Neighboring significant regions located within the same chromosome, and with the same annotation and Gene ID, were merged using an in-house Python script.
Assembly: GRCh38
Supplementary files format and content: Bam files include only mapped sorted reads for each sample
Supplementary files format and content: RData files include differential coverage results using the edgeR function (mr.edgeR). When available, it also includes specific data extracted from the "mr.edgeR" file as follows:  differential coverage results with unadjusted P value<0.05 (mr.edgeR.sna), differential coverage results with FDR<0.1 (mr.edgeR.s0.1), differential coverage results with FDR<0.05 (mr.edgeR.s), differential coverage results with FDR<0.05 of hyperDMRs (mr.edgeR.s.gain), differential coverage results with FDR<0.05of hypoDMRs (mr.edgeR.s.lost)


title: E14 WT cells, Day0, batch1 replicate 39 (SMARTseq2_EpiLC)


title: MBP-pulldown rep2


title: WI-38 cells, single-fraction, 23mGy, 5mC, rep2


title: E14 TKO cells, Day0, batch1 replicate 38 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 23mGy, 5mC, rep3


title: E14 WT cells, Day0, batch1 replicate 40 (SMARTseq2_EpiLC)


title: WI-38 cells, single-fraction, 23mGy, 5mC, rep1


title: Endosperm, nkd2, rep2


title: MBP-pulldown rep1


title: Endosperm, nkd2o2, rep1


title: Input rep2


title: Input rep1


title: E14 TKO cells, Day0, batch1 replicate 37 (SMARTseq2_EpiLC)


title: Endosperm, nkd1o2, rep2


title: WI-38 cells, single-fraction, 11mGy, 5mC, rep3


title: E14 WT cells, Day0, batch1 replicate 37 (SMARTseq2_EpiLC)


title: Endosperm, nkd2o2, rep2


title: FoxP3-pulldown rep1


title: AP-1-3week

city: Beijing

first: Yongting

last: luo

state: Beijing

address: No.10 Tianxiu Road

institute: Beijing Advanced Innovation Center for Food Nutrition and Human Health

data_processing:
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer.
First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed.
After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).
DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).
The sequencing library was then sequenced on a Hiseq platform (Illumina).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: aorta

extract_protocol:
To recapitulate possible changes in transcriptome profile, aortas from BAPN-induced mice treated without or with coQ10, TPA, or T-5224 were subjected to RNA isolation using the Trizol Reagent (Invitrogen Life Technologies). The concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: For induction of aortic dissection, forty-eight C57BL/6J mice were randomly divided into 4 groups and were fed with BAPN solution (1 g/kg/day, n = 36) or distilled water (control, n = 12). Mice fed with BAPN solution were given the AP-1 inhibitor T-5224 (5 mg/kg/day) or coQ10 (10 mg/kg/day) by daily gavage from day 7 or 14 to killing on day 28 (n = 12 for each group). For TPA treatment, mice fed with BAPN solution were intraperitoneally administrated with the AP-1 activator TPA (50 ng/g/day) from day 1 to killing on day 28 (n = 12 for each group).

value: aorta

value: vascular cell


title: Endosperm, nkd1o2, rep1


title: WI-38 cells, single-fraction, 11mGy, 5mC, rep2


title: E14 TKO cells, Day0, batch1 replicate 36 (SMARTseq2_EpiLC)

extract_protocol:
Single cells were index-sorted individually by FACS (SONY SH800) into wells of a 96-well PCR plate containing 2.3 µl of lysis buffer (200U/µL SUPERase-IN (LifeTechnologies), 10% Triton X100, RNAse free H2O). scRNA-seq SMARTseq2 was performed as previously described (Picelli et al., 2014).
The Illumina Nextera XT DNA kit was used to prepare libraries that were sequenced on the Illumina HiSeq 4000 (paired-end 50bp). Samples from all cell lines were included in each sequencing lane, to control for technical lane effects

value: Embryonic stem cells (murine)


title: Endosperm, nkd1nkd2o2, rep2


title: WI-38 cells, single-fraction, 11mGy, 5mC, rep1

extract_protocol:
Total DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with minor modifications.
Cell pellets were resuspended in PBS and treated with proteinase K and RNase A. The DNA-loaded spin columns were washed three times with buffer AW2. DNA was then eluted in Tris-EDTA (TE) buffer (low EDTA, pH 8.0) after 5 m at RT. DNA samples displayed A260/A280 ratios in the range of 1.8 to 2.0 and A260/A230 ratios higher than 2.1.
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 μg of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer’s guidelines. Immunoprecipitation with a 5mC antibody was conducted using a Diagenode MagMeDIP kit as described in the manufacturer’s protocol with starting volume of 15 µL. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturer’s instructions.
The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 7 cycles for the Input and 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.

value: Human fibroblast from 3-month-old female lung tissue


title: Endosperm, nkd1nkd2o2, rep1


title: TPA-2


title: WI-38 cells, single-fraction, 2mGy, 5mC, rep4


title: E14 WT cells, Day0, batch1 replicate 36 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 35 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 38 (SMARTseq2_EpiLC)


title: TPA-1


title: Endosperm, nkd1nkd2, rep2


title: WI-38 cells, single-fraction, 2mGy, 5mC, rep3


title: E14 WT cells, Day0, batch1 replicate 35 (SMARTseq2_EpiLC)


title: co110


title: Endosperm, nkd2, rep1


title: WI-38 cells, single-fraction, 11mGy, 5mC, rep4


title: Endosperm, nkd1nkd2, rep1


title: WI-38 cells, single-fraction, 2mGy, 5mC, rep2


title: E14 TKO cells, Day0, batch1 replicate 34 (SMARTseq2_EpiLC)


title: Endosperm, nkd1, rep2


title: WI-38 cells, single-fraction, 2mGy, 5mC, rep1


title: E14 WT cells, Day0, batch1 replicate 34 (SMARTseq2_EpiLC)


title: BAPN-1

value: BAPN


title: Endosperm, nkd1, rep1


title: WI-38 cells, single-fraction, 0mGy, 5mC, rep4

value: Sham


title: NKD2

description: 150 bp PE

data_processing:
DAP-seq reads were trimmed using trimmomatic with the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Trimmed reads were mapped to the maize reference genome using bowtie2.3.3
Mapped reads were filtered for reads containing > MAPQ30 using samtools
Peaks were called using GEM v2.5 with default thresholds
Assembly: B73 RefGen_v3
Supplementary files format and content: narrowPeak
Library strategy: DAP-Seq

source_name: 14-d old seedlings

extract_protocol:
DNA was extracted from maize B73 14-day old seedlings. Five grams of tissue was ground in liquid nitrogen and the genomic DNA was extracted in a phenol/chloroform/IAA extract cocktail. The DNA pellet was resuspended and diluted in EB (10mM Tris-HCl pH 8.5).
The EB diluted DNA was sheared to 200bp fragments using a Covaris S2 sonicator. DNA was purified using AmpureXP beads with a 2:1 bead to DNA ratio, and then end-repaired using an End-It kit (Lucigen) according to the manufacturer’s recommendations. Samples were cleaned using a Qiaquick PCR purification kit (Qiagen), A-tailed using Klenow (3’ to 5’ exo-), cleaned with Qiaquick and ligated overnight with a truncated Illumina Y-adapter. Final libraries were purified using AMPureXP beads with a 1:1 bead to DNA ratio and eluted in 30ul of EB. DNA concentration was determined using the Qubit HS kit.

value: 14-d old seedlings

tag: cultivar

value: Plant seedling cells


title: E14 TKO cells, Day0, batch1 replicate 33 (SMARTseq2_EpiLC)

tag: cell type


title: normal-2


title: AP-1-2week


title: E14 WT cells, Day0, batch1 replicate 33 (SMARTseq2_EpiLC)

tag: genotype


title: NKD1

description: 150 bp PE


title: normal-1


title: n1n2o2_16_s3

data_processing:
The raw reads were mapped to maize reference genome (B73 RefGen_v4, AGPv4) by HISAT2 (v2.1.0)
The output SAM files were converted to BAM files and were sorted by SAMtools (v1.9)
Mapped transcripts in sorted BAM files were assembled and normalized with StringTie (v1.3.6) using maize genome annotation file Zea_mays.B73_RefGen_v4.43.gtf downloaded from Gramene
Readcounts were calculated by HTSeq (v0.11.1)
Genome_build: B73 RefGen_v4, AGPv4
Supplementary_files_format_and_content: Tab Separated Values (TSV) files (HTSeq output file) with gene read count for each sample

growth_protocol: Field grown plants were self-pollinated

extract_protocol:
Dissected samples were immediately frozen in liquid N2 and ground to fine powder. The total mRNA was extracted using conventional SDS/phenol extraction and LiCl/ethanol precipitation protocol
Library was prepared with a TruSeq RNA Library Prep Kit (Illumina) and 150-base paired end sequencing using NovaSeq 6000 with the S4 cell platform

treatment_protocol: Endosperms were dissected at 8, 12 and 16 DAP

tag: age

value: 16 DAP


title: scRNAseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Klf2KO

description: 10x Genomics

data_processing:
ScRNAseq: Fastq files of gene expression were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Multiome: Cell versus gene matrix of UMI counts for gene expression assay and cell versus fragment matrix for ATAC assay were generated from fastq files aligned to mm10 using cellranger-arc (v 2.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CAR T cells isolated from spleen, bone marrow or tumor were sorted for scRNA-Seq or multiome anallysis.
We used Chromium Next GEM Single Cell 5' Kit (10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol. We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq and scATAC-Seq libraries according to the manufacturer’s protocol.

value: Spleen

value: ex vivo

value: CAR T cells


title: scATACseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Klf2KO

description: 10x Genomics


title: E14 TKO cells, Day0, batch1 replicate 32 (SMARTseq2_EpiLC)

value: WT

value: EpiLC differentiation

tag: time


title: n1n2o2_16_s4


title: WI-38 cells, single-fraction, 0mGy, 5mC, rep1

tag: treatment


title: E14 WT cells, Day0, batch1 replicate 32 (SMARTseq2_EpiLC)


title: BAPN-2


title: scATACseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Foxp1KO

description: 10x Genomics


title: D886T241_tumor_Tex_patient5

city: Paris

first: Sebastian

last: Amigorena

institute: Institut Curie

description: Bulk RNAseq

data_processing:
Fastq files were aligned to hg19 human reference genome using STAR (v2.7.1a)
Genes and TEs expression were quantified using featureCounts from subread suite tools (v1.6.4)
Raw counts were imported an processed in R (v4.2.1)
TPM and FPKM counts were calculated using R package scuttle (1.8.4)
Differentially expressed features were identified using DESeq2 R package (v1.36.0)
Assembly: hg19
Supplementary files format and content: tab-delimited text files including gene raw counts values for each sample
Supplementary files format and content: tab-delimited text files including individual TE counts values for each sample
Supplementary files format and content: tab-delimited text files including TE subfamily counts values for each sample

source_name: Tumor infiltrated CD8+ T cells

extract_protocol:
Tumor tissue and  normal adjacent (juxta) tissue  samples were obtained from early stage, untreated patients with NSCLC. Tumor tissue samples were obtained from surgical specimens, after macroscopical examination of the tissue by a pathologist. Tissue samples were stored in C02-independent medium (Invitrogen) with 5% human serum and transferred within 1-hour post-surgery to the research institute. For each specimen, a fragment was formalin-fixed, and paraffin embedded for histology and immunohistochemistry. Tumor tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25µg/ml, Sigma-Aldrich). Tissue fragments were gently triturated with a 20 ml syringe plunger on a 40 µm cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco), until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g.  Tumor-infiltrating lymphocytes were isolated using Ficoll-Paque PLUS solution (Sigma-Aldrich). After tissue digestion, cells are resuspended in C02-independent medium and layered onto Ficoll-Paque PLUS solution. Subsequently cells were centrifuged for 20 minutes at room temperature at 800g without breaks. After centrifugation tumor-infiltrating lymphocytes were carefully transferred to a new tube and washed with 1X PBS with 1% FBS and 2mM EDTA (Gibco). CD3+ T cells were isolated using the Pan T cell Isolation Kit (Miltenyi), that leads to approximately 80% purity.  CD3+ T cells were resuspended 1X PBS with 1% FBS and 2mM EDTA (Gibco). Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer/ trypan blue.   For isolation of the distinct CD8+ T cell subsets, upon TILs isolation, cells were washed and resuspended in 100ul staining buffer containing antibodies. After 20 minutes incubation at 4oC, cells were washed twice and resuspended in 200ul of 1X Phosphate Buffered Saline (PBS) buffer with 1mM EDTA and 1% fetal bovine serum. Cell sorting was performed using MoFlo ASTRIOS cell sorter from Beckman Coulter Life Sciences. Cells were stained with a combination of surface markers, using a set of monoclonal antibodies from the following:  CD3-AF532 (1:50, clone UCHT1, #2067979, Thermofischer Scientific), CD8-BV510 (1:50, clone 2ST8SH7, #9259590, BD Biosciences), PD1-BV421 (1:40, clone EH12.2H7, #B268454, Biolegend), KLRG1-PE-Cy7 (1:40, clone SA231A2 ,#B256810, Biolegend), TIM3-BV786 (1:40, clone 7D3, #9259393, BD Biosciences), CD39-APC (1:50, clone eBioA1, 2#2071264, Thermofischer Scientific). Cells were gated on single cells based on the FSC-A/FSC-H and SSC-A/ SSC-H scatters, live cells (Zombie NIR negative), CD3+, CD8+ cells and afterwards on the population of interest, on the basis of the expression of the protein markers: KLRG1, CD103, PD1, TIM3 and CD39.   Upon sorting of the CD8+ subsets, cells were centrifuged at 300g for 3 minutes, resuspended in 350ul of TCL buffer (QIAGEN) with 1% b-mercaptoethanol inside a 1.5ml eppendorf tube and rapidly stored at -80oC. Within a period of a maximum 7 days, cells were thawed and prepared for RNA isolation. Norgen single cell RNA purification kit was used for RNA extraction. Residual genomic DNA was removed using the RNase free DNase set (Qiagen). RNA quantity and quality was measured by Agilent RNA 6000 Pico kit (Agilent Technologies). Samples with high quality RNA (RIN>7) were further selected. On average the samples had between 500pg-1ng of total RNA. To synthesize and amplify cDNA from those samples, the SMART-Seq v4 Ultra Low Input RNA kit (TaKaRa) was used, according to manufacturer’s instructions. cDNA quantity and quality were measured by High Sensitivity DNA kit (Agilent Technologies). 9ng of amplified cDNA was used for library synthesis, using the KAPA HyperPlus library preparation kit (Roche) according to manufacturer’s instructions. Sequencing libraries were quantified with the LabChip® GX Touch™ nucleic acid analyzer and libraries were sequenced on a HiSeq4000 sequencer (Illumina).    Tumor tissue samples were obtained from surgical specimens, after macroscopical examination of the tissue by a pathologist. Tissue samples were stored in C02-independent medium (Invitrogen) with 5% human serum and transferred within 1-hour post-surgery to the research institute. For each specimen, a fragment was formalin-fixed, and paraffin embedded for histology and immunohistochemistry.    Tissue dissociation  Tumor tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25µg/ml, Sigma-Aldrich).    The tissue pieces were gently triturated with a 20 ml syringe plunger on a 40 µm cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco), until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g.      Tumor- infiltrating lymphocytes isolation  Tumor-infiltrating lymphocytes were isolated using Ficoll-Paque PLUS solution (Sigma-Aldrich). After tissue digestion, cells are resuspended in C02-independent medium and layered onto Ficoll-Paque PLUS solution. Subsequently cells were centrifuged for 20 minutes at room temperature at 800g without breaks. After centrifugation tumor-infiltrating lymphocytes were carefully transferred to a new tube and washed with 1X PBS with 1% FBS and 2mM EDTA (Gibco).    CD3+ T cell isolation and purification  CD3+ T cells were isolated using the Pan T cell Isolation Kit (Miltenyi), that leads to approximately 80% purity.  CD3+ T cells were resuspended 1X PBS with 1% FBS and 2mM EDTA (Gibco). Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer/ trypan blue.     CD8+ T cell sorting  For isolation of the distinct CD8+ T cell subsets, upon TILs isolation, cells were washed and resuspended in 100ul staining buffer containing antibodies. After 20 minutes incubation at 4oC, cells were washed twice and resuspended in 200ul of 1X Phosphate Buffered Saline (PBS) buffer with 1mM EDTA and 1% fetal bovine serum. Cell sorting was performed using MoFlo ASTRIOS cell sorter from Beckman Coulter Life Sciences. Cells were stained with a combination of surface markers, using a set of monoclonal antibodies from the following:  CD3-AF532 (1:50, clone UCHT1, #2067979, Thermofischer Scientific), CD8-BV510 (1:50, clone 2ST8SH7, #9259590, BD Biosciences), PD1-BV421 (1:40, clone EH12.2H7, #B268454, Biolegend), KLRG1-PE-Cy7 (1:40, clone SA231A2 ,#B256810, Biolegend), TIM3-BV786 (1:40, clone 7D3, #9259393, BD Biosciences), CD39-APC (1:50, clone eBioA1, 2#2071264, Thermofischer Scientific). Cells were gated on single cells based on the FSC-A/FSC-H and SSC-A/ SSC-H scatters, live cells (Zombie NIR negative), CD3+, CD8+ cells and afterwards on the population of interest, on the basis of the expression of the protein markers: KLRG1, CD103, PD1, TIM3 and CD39.     Samples preparation for RNAseq  Upon sorting of the CD8+ subsets, cells were centrifuged at 300g for 3 minutes, resuspended in 350ul of TCL buffer (QIAGEN) with 1% b-mercaptoethanol inside a 1.5ml eppendorf tube and rapidly stored at -80oC.    Within a period of a maximum 7 days, cells were thawed and prepared for RNA isolation. Norgen single cell RNA purification kit was used for RNA extraction. Residual genomic DNA was removed using the RNase free DNase set (Qiagen). RNA quantity and quality was measured by Agilent RNA 6000 Pico kit (Agilent Technologies). Samples with high quality RNA (RIN>7) were further selected. On average the samples had between 500pg-1ng of total RNA. To synthesize and amplify cDNA from those samples, the SMART-Seq v4 Ultra Low Input RNA kit (TaKaRa) was used, according to manufacturer’s instructions. cDNA quantity and quality were measured by High Sensitivity DNA kit (Agilent Technologies). 9ng of amplified cDNA was used for library synthesis, using the KAPA HyperPlus library preparation kit (Roche) according to manufacturer’s instructions. Sequencing libraries were quantified with the LabChip® GX Touch™ nucleic acid analyzer and libraries were sequenced on a HiSeq4000 sequencer (Illumina).  Study design  The overall objective of this study was to characterize the diversity and ontogeny of CD8+ T cells in untreated lung tumors. This was accomplished by performing bulk RNAseq and flow cytometry analysis on CD8+ T cell subsets isolated from tumor tissue, normal adjacent to tumor tissue, and blood samples from patients undergoing surgical resection for early-stage lung cancer. All samples were collected from the Institute Mutualist Montsouris, under a dedicated protocol for lung cancer specimens approved by the French Ethics and Informatics Commission (EUdract 2017-A03081-52). All patients in this study provided written informed consent for sample collection and data analysis. Cohort size was selected to assess interpatient variability in subpopulation levels.    Human samples  Tumor tissue, normal adjacent (juxta) tissue and blood samples were obtained from early stage, untreated patients with NSCLC.  All patients enrolled in this study patients in this study provided written informed consent for sample collection and data analyses.    Tumor tissue samples were obtained from surgical specimens, after macroscopical examination of the tissue by a pathologist. Tissue samples were stored in C02-independent medium (Invitrogen) with 5% human serum and transferred within 1-hour post-surgery to the research institute. For each specimen, a fragment was formalin-fixed, and paraffin embedded for histology and immunohistochemistry.    Tissue dissociation  Tumor tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25µg/ml, Sigma-Aldrich).    The tissue pieces were gently triturated with a 20 ml syringe plunger on a 40 µm cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco), until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g.      Tumor- infiltrating lymphocytes isolation  Tumor-infiltrating lymphocytes were isolated using Ficoll-Paque PLUS solution (Sigma-Aldrich). After tissue digestion, cells are resuspended in C02-independent medium and layered onto Ficoll-Paque PLUS solution. Subsequently cells were centrifuged for 20 minutes at room temperature at 800g without breaks. After centrifugation tumor-infiltrating lymphocytes were carefully transferred to a new tube and washed with 1X PBS with 1% FBS and 2mM EDTA (Gibco).    CD3+ T cell isolation and purification  CD3+ T cells were isolated using the Pan T cell Isolation Kit (Miltenyi), that leads to approximately 80% purity.  CD3+ T cells were resuspended 1X PBS with 1% FBS and 2mM EDTA (Gibco). Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer/ trypan blue.     CD8+ T cell sorting  For isolation of the distinct CD8+ T cell subsets, upon TILs isolation, cells were washed and resuspended in 100ul staining buffer containing antibodies. After 20 minutes incubation at 4oC, cells were washed twice and resuspended in 200ul of 1X Phosphate Buffered Saline (PBS) buffer with 1mM EDTA and 1% fetal bovine serum. Cell sorting was performed using MoFlo ASTRIOS cell sorter from Beckman Coulter Life Sciences. Cells were stained with a combination of surface markers, using a set of monoclonal antibodies from the following:  CD3-AF532 (1:50, clone UCHT1, #2067979, Thermofischer Scientific), CD8-BV510 (1:50, clone 2ST8SH7, #9259590, BD Biosciences), PD1-BV421 (1:40, clone EH12.2H7, #B268454, Biolegend), KLRG1-PE-Cy7 (1:40, clone SA231A2 ,#B256810, Biolegend), TIM3-BV786 (1:40, clone 7D3, #9259393, BD Biosciences), CD39-APC (1:50, clone eBioA1, 2#2071264, Thermofischer Scientific). Cells were gated on single cells based on the FSC-A/FSC-H and SSC-A/ SSC-H scatters, live cells (Zombie NIR negative), CD3+, CD8+ cells and afterwards on the population of interest, on the basis of the expression of the protein markers: KLRG1, CD103, PD1, TIM3 and CD39.     Samples preparation for RNAseq  Upon sorting of the CD8+ subsets, cells were centrifuged at 300g for 3 minutes, resuspended in 350ul of TCL buffer (QIAGEN) with 1% b-mercaptoethanol inside a 1.5ml eppendorf tube and rapidly stored at -80oC.    Within a period of a maximum 7 days, cells were thawed and prepared for RNA isolation. Norgen single cell RNA purification kit was used for RNA extraction. Residual genomic DNA was removed using the RNase free DNase set (Qiagen). RNA quantity and quality was measured by Agilent RNA 6000 Pico kit (Agilent Technologies). Samples with high quality RNA (RIN>7) were further selected. On average the samples had between 500pg-1ng of total RNA. To synthesize and amplify cDNA from those samples, the SMART-Seq v4 Ultra Low Input RNA kit (TaKaRa) was used, according to manufacturer’s instructions. cDNA quantity and quality were measured by High Sensitivity DNA kit (Agilent Technologies). 9ng of amplified cDNA was used for library synthesis, using the KAPA HyperPlus library preparation kit (Roche) according to manufacturer’s instructions. Sequencing libraries were quantified with the LabChip® GX Touch™ nucleic acid analyzer and libraries were sequenced on a HiSeq4000 sequencer (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols (NovaSeq 6000)

value: Tumor

tag: donor

value: Tex

tag: subgroup


title: E14 TKO cells, Day0, batch1 replicate 31 (SMARTseq2_EpiLC)


title: n1n2o2_16_s2


title: WI-38 cells, single-fraction, 0mGy, 5mC, rep3

tag: dose (mgy)

tag: radiation regimen

value: single-fraction

tag: total number_of_fractions

value: anti-5mC (33D3 clone - Diagenode #C15200081)


title: n1n2o2_16_s1


title: scRNAseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Foxp1KO

description: 10x Genomics


title: D886T237_tumor_TpexRes_patient4

description: Bulk RNAseq

value: Tpex

value: TPresident


title: scATACseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Ctrl

description: 10x Genomics


title: E14 TKO cells, Day0, batch1 replicate 30 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: E14 WT cells, Day0, batch1 replicate 30 (SMARTseq2_EpiLC)


title: D886T233_tumor_TpexCirc_patient3

description: Bulk RNAseq

value: TPcirculating


title: D886T234_tumor_TpexRes_patient3

description: Bulk RNAseq


title: n1n2o2_12_s4

value: 12 DAP


title: n1n2o2_12_s3


title: scRNAseq_Multiome_E2APBX1_CAR_T_D7_Spleen_Ctrl

description: 10x Genomics


title: WI-38 cells, single-fraction, 0mGy, 5mC, rep2

value: Human fibroblast from 3-month-old female lung tissue

value: Sham

tag: antibody


title: E14 TKO cells, Day0, batch1 replicate 29 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 29 (SMARTseq2_EpiLC)


title: n1n2o2_12_s1

tag: strain


title: E14 TKO cells, Day0, batch1 replicate 28 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 31 (SMARTseq2_EpiLC)


title: E14 TKO cells, D4, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)

data_processing:
Paired-end reads were trimmed with trim Galore (v0.4.4) in order to remove adapter sequences and Ns nucleotides from both side of the read
Cleaned reads were aligned onto the Mouse reference genome mm10 with bowtie2 (v2.2.9) in end-to-end and very sensitive mode. Duplicated reads were removed using Picard (v2.6.0).
Bigwig files for UCSC genome browser and heatmaps were created with deepTools (v2.5.3).
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

extract_protocol:
The Cut&Run protocol was optimized from Skene and Henikoff, 2017. Concanavalin A beads (Polysciences) were activated in 1ml of Binding Buffer (20mM HEPES-KOH, 10mM KCl, 1mM CaCl2, 10mM MnCl2). Between 200 000 and 300 000 cells were aliquoted in 1ml of Wash Buffer (20mM HEPES-KOH, 150mM NaCl, 0.5mM Spermidine (Sigma) and 1X Complete EDTA-free (Roche) protease inhibitor cocktail) and 20µL of activated beads were added to the cells, followed by 5 min incubation at RT on a rotating wheel. Cells were collected on a magnetic rack; the supernatant was replaced by 400µL of primary antibody diluted to 1:200 in Wash Buffer complemented with 2mM EDTA and 0.02% Digitonin (Millipore). Cells were incubated for one hour at RT. Samples were then washed twice in Dig-Wash Buffer (Wash Buffer + 0.02% Digitonin) for 15 min at RT and incubated with 1:400 home-made pA-MNase in Dig-Wash for 15 min at RT. After two more washes, cells were resuspended in 150µl of Dig-Wash and cooled-down for five min at 0°C. For targeted digestion, CaCl2 was added to the cells to a final concentration of 2mM followed by 30 min incubation on ice. The reaction was stopped by adding 150µl of 2X STOP Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 100ng/ml RNase1, 250ng/ml glycogen) and incubating the samples at 37°C for 20 min before centrifugation at 4°C 16000g for 5 min. Samples were placed on a magnetic rack and supernatant was recovered in a low binding eppendorf tube. Following addition of 0.1% SDS and 0.17mg/ml Proteinase K, samples were incubated at 70°C for 30 min. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% Ethanol incubation at -20°C for at least 20 min. The DNA pellet was washed in 85% ethanol, spun down and air-dried before being resuspended in 25µl of 1mM Tris-HCl pH8.0.
Library preparation was made according to the manufacturer’s instructions (Accel NGS 2S DNA library kit, Swift Biosciences). For library amplification, 12 PCR cycles were applied as followed: 98°C for 10 sec, 60°C for 15 sec and 68°C for one minute. Library size and quantification was assessed on Agilent 4200 Tapestation. C

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x106 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 0, 2, and 4 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

tag: chip antibody

value: TKO


title: D886T230_tumor_TpexCirc_patient1

description: Bulk RNAseq


title: E14 TKO cells, D2, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: D886T227_tumor_TpexRes_patient2

description: Bulk RNAseq


title: E14 TKO cells, D4, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: n1n2o2_8_s4

value: 8 DAP


title: E14 WT cells, Day0, batch1 replicate 28 (SMARTseq2_EpiLC)


title: E14 TKO cells, D2, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)


title: n1n2o2_8_s3


title: n1n2o2_8_s2


title: E14 TKO cells, Day0, batch1 replicate 27 (SMARTseq2_EpiLC)


title: D886T232_tumor_Tex_patient3

description: Bulk RNAseq


title: E14 TKO cells, D0, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 27 (SMARTseq2_EpiLC)


title: D886T226_tumor_TpexCirc_patient2

description: Bulk RNAseq


title: RescueNRF3_DOX3

data_processing:
Raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.20.0)
Sequence pseudo alignment of the resulting high-quality reads to the human reference genome (build GRCh38.p13) and quantification of gene level expression (gene model definition from GENCODE release 37) was carried out using Kallisto (Version 0.46.1)
To identify differentially expressed genes, we used the glm approach implemented in the software package DESeq2 (R version: 4.2.0, DESeq2 version: 1.36.0)
Assembly: GRCh38.p13
Supplementary files format and content: Matrix file with normailzed counts and FPKM

extract_protocol:
Total cellular RNA was isolated from SCC13 cells using a Total RNA Mini Kit (IBI Scientific, Dubuque, IO; IB47303) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocol.

value: skin

value: epithelial cancer cells

value: DOX


title: E14 TKO cells, D0, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)

value: EpiLC differentiation


title: n1n2o2_8_s1


title: D886T219_tumor_Tex_patient1

description: Bulk RNAseq

value: Tumor


title: E14 TKO cells, Day0, batch1 replicate 26 (SMARTseq2_EpiLC)

value: WT


title: E14 TKO cells, D4, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)

value: H3K27ac (Active motif 39133)


title: n1n2o2_12_s2


title: n1n2_16_s4

value: 16 DAP


title: E14 TKO cells, D4, biological replicate 1, H3K27ac (CUT&RUN_EpiLC)


title: RescueNRF3_DOX1


title: n1n2_16_s2


title: RescueNRF3_DMSO3

value: DMSO


title: E14 TKO cells, D2, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)


title: D886T225_tumor_Tex_patient2

description: Bulk RNAseq

value: Tex


title: E14 WT cells, Day0, batch1 replicate 26 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: E14 TKO cells, Day0, batch1 replicate 24 (SMARTseq2_EpiLC)


title: RescueNRF3_DMSO2


title: n1n2_12_s4


title: n1n2_16_s3


title: RescueNRF3_DOX2


title: E14 TKO cells, Day0, batch1 replicate 23 (SMARTseq2_EpiLC)


title: SiHa-IP

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

data_processing:
Clustered libraries were loaded onto reagem cartridge and ftxwarded to sequencing nm on Illumina Hiseq 6000 system
The sequence data obtained by Illumina HiSeq sequencing and filtering will be used for the following analysis: Quality control with FastQC (v0.11.7);
high quality data with adapter sequences and low quality parts removed (ClHmmomatic V0.32) are compared to the reference genome (H1SAT2 v2.L0);
use exomePeak (v2.13.2) to determine the peaks of each sample and the differentially methylated peaks of each comparison, and annotate the obtained peaks
according to the annotation information of the Ensembl database; count the regions of each transcript Whether there are peaks in each sample;   finally perform a motif analysis on the obtained peaks
Assembly: GRCh38/hg38
Supplementary files format and content: Differential gene expression was calculated by DEGseq R packages. The RIP targets were defined as genes with fragments per kilobase,

source_name: cervical  cancer cells

extract_protocol:
The purity and coDceniration of total RNA samples were detennined with NanoDrop ND-1000. Results were provided m Sample QC report.
RNA-seq libraries of YTHDF3 antibody enriched mRNAs and input mRNAs were prepared using KAPA Stranded mRNA-seq Kit (Illumina). And finally, the completed libraries were qualified by Agilent 2100 Bioanalyzer.
The rip-seq  of SiHa and KOSiHa cells

value: cervical  cancer cells


title: RescueNRF3_DMSO1


title: E14 TKO cells, D0, biological replicate 1, H3K27ac (CUT&RUN_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 25 (SMARTseq2_EpiLC)


title: n1n2_16_s1


title: E14 TKO cells, D2, biological replicate 1, H3K27ac (CUT&RUN_EpiLC)


title: SiHa-input_L1_2


title: E14 WT cells, D4, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: n1n2_12_s2

value: 12 DAP


title: E14 TKO cells, D0, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)


title: E14 WT cells, D4, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 23 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 25 (SMARTseq2_EpiLC)


title: n1n2_12_s1


title: KOY3SiHa-IP_L3_2


title: n1n2_8_s4


title: E14 TKO cells, Day0, batch1 replicate 22 (SMARTseq2_EpiLC)


title: E14 WT cells, D2, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: KOY3SiHa-input_L2_2


title: E14 WT cells, Day0, batch1 replicate 22 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, D2, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)


title: n1n2_12_s3


title: n1n2_8_s3


title: E14 TKO cells, Day0, batch1 replicate 21 (SMARTseq2_EpiLC)


title: SiHa-IP-R1-biorep.1

data_processing:
Clustered libraries were loaded onto reagem cartridge and ftxwarded to sequencing nm on Illumina Hiseq 6000 system
The sequence data obtained by Illumina HiSeq sequencing and filtering will be used for the following analysis: Quality control with FastQC (v0.11.7);
high quality data with adapter sequences and low quality parts removed (ClHmmomatic V0.32) are compared to the reference genome (H1SAT2 v2.L0);
use exomePeak (v2.13.2) to determine the peaks of each sample and the differentially methylated peaks of each comparison, and annotate the obtained peaks
according to the annotation information of the Ensembl database; count the regions of each transcript Whether there are peaks in each sample;   finally perform a motif analysis on the obtained peaks
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include fold  enrichment for each Sample

extract_protocol:
The purity and coDceniration of total RNA samples were detennined with NanoDrop ND-1000. Results were provided m Sample QC report.
RNA-seq libraries of ac4c antibody enriched mRNAs and input mRNAs were prepared using KAPA Stranded mRNA-seq Kit (Illumina). And finally, the completed libraries were qualified by Agilent 2100 Bioanalyzer.
The ac-seq  of SiHa and KONAT10SiHa cells


title: n1n2_8_s1


title: SiHa-Input-R1-biorep.2


title: E14 WT cells, D0, biological replicate 1, H3K27me3 (CUT&RUN_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 20 (SMARTseq2_EpiLC)


title: SiHa-Input-R1-biorep.1


title: n1n2_8_s2


title: E14 WT cells, Day0, batch1 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 20 (SMARTseq2_EpiLC)


title: n2o2_16_s4


title: E14 WT cells, D4, biological replicate 1, H3K27ac (CUT&RUN_EpiLC)


title: n2o2_16_s3


title: E14 WT cells, D4, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 19 (SMARTseq2_EpiLC)


title: KONAT10SiHa-IP-R1-biorep.2


title: E14 WT cells, D2, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)


title: n2o2_16_s2


title: E14 WT cells, Day0, batch1 replicate 19 (SMARTseq2_EpiLC)


title: KONAT10SiHa-IP-R1-biorep.1


title: E14 WT cells, D2, biological replicate 1, H3K27ac (CUT&RUN_EpiLC)


title: KONAT10SiHa-Input-R1-biorep.2


title: SiHa-IP-R1-biorep.2


title: E14 WT cells, D0, biological replicate 2, H3K27me3 (CUT&RUN_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 18 (SMARTseq2_EpiLC)


title: n2o2_12_s4


title: KONAT10SiHa-Input-R1-biorep.1


title: E14 WT cells, Day0, batch1 replicate 18 (SMARTseq2_EpiLC)


title: E14 WT cells, D0, biological replicate 2, H3K27ac (CUT&RUN_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 17 (SMARTseq2_EpiLC)