title: MIAPaCa2_KRASG12R_RN118_untreated_4d_3

description: MIAPaCa2 KRASG12R RN118 untreated 4d

value: MIA PaCa-2

value: untreated

value: 4 days


title: F_292_CBP_TNF

status: Public on Jul 04 2023

type: SRA

city: Bern

first: Kerstin

last: Klein

state: Bern

address: Murtenstrasse 28

department: Department of Rheumatology and Immunology

country: Switzerland

institute: University Hospital Bern

library_source: transcriptomic

data_processing:
quality control was conducted using FASTQC
reads were cleaned using Trimmomatic
Reads were mapped to the human reference genome (hg 19) using STAR
Counts per gene were assessed using Feature Counts
Assembly: hg19

molecule: total RNA

organism: Homo sapiens

source_name: RA synovial tissue (finger)

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen), including Dnase digest.
Librariesfor RNAseq were generated using the Illumina TruSeq Stranded total RNA Sample Preparation Kit.

tag: tissue

value: RA synovial tissue (finger)

tag: cell line

tag: cell type

value: synovial fibroblast

tag: genotype

tag: treatment

value: TNF


title: MIAPaCa2_KRASG12R_RN118_doxycycline_4d_3

city: Vienna

first: Alexandra

last: Popa

state: Austria

address: Doktor-Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim

description: MIAPaCa2 KRASG12R RN118 doxycycline 4d

data_processing:
Base-calling was performed using the Real-Time Analysis (RTA)
Mapping of raw reads was performed with STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences.
Quantification of read counts to transcript annotations was implemented using RSEM(v1.3.0) and featureCounts (v1.5.1).
Normalization of read counts and differential analysis was implemented with the limma and voom R packages.
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text files include normalized count values for all samples.

source_name: MIA PaCa-2 cell line

growth_protocol: PC-9 cells were cultured in McCoy’s 5A medium (Thermo Fisher), supplemented with 10% FBS and 1 x GlutaMAX (Thermo Fisher). MIA PaCa-2 (ATCC: CRL-1420) cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
2x106 Dox-treated and untreated control cells were harvested, washed with PBS, lysed, treated with DNAse I (QIAGEN) and total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Next generation sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: Engineered MIA PaCa-2 and PC-9 cells were cultured in the presence of 1 µg/ml Dox to induce expression of the ARTi shRNA. Samples were taken at the indicated timepoints (d4, d8)

tag: construct

value: doxycycline

tag: timepoint

tag: target


title: CAST-seq on sample treated with two RNPs  [UNC-u3d4-2]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
u3d4 replicate 2
UNC-u3d4_U3_OVL2_FINAL.xlsx
UNC-u3d4_D4_OVL2_FINAL.xlsx

library_source: genomic

data_processing:
library strategy: CAST-seq
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: mm10
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq pipeline with first gRNA. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq pipeline with second gRNA. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

molecule: genomic DNA

organism: Mus musculus

source_name: HSPCs from bone marrow

growth_protocol: Cells were cultured at 37°C and 5% CO2. Lineage-negative (Lin-) HSCs (Miltenyi Biotec, 130-090-858) from femur and tibia-derived BM were stimulated for 3h in StemSpan SFEM II medium (StemCell Technologies) supplemented with L-glutamine (20 mM, Gibco), mSCF, mTPO and hIGF2 (20 ng/ml each) plus hIGF2 and mIL-3 (10 ng/ml each, Peprotech) before nucleofection followed by 20h of culture without mIL-3 prior to harvest for CAST-Seq.

extract_protocol:
Genomic DNA was isolated from cells using theNucleoSpin Tissue Mini kit for DNA from cells and tissue (Macherey-Nagel) according to the manufacturer’s instructions.
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 200-350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interes (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR were purified using the QIAquick® PCR purification kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) on where it was performed on a Illumina HiSeq4000 device collecting 2x150 bp paired-end reads.

treatment_protocol: Lineage-negative (Lin-) HSCs (Miltenyi Biotec, 130-090-858) from femur and tibia-derived BM were stimulated for 3h in StemSpan SFEM II medium (StemCell Technologies) supplemented with L-glutamine (20 mM, Gibco), mSCF, mTPO and hIGF2 (20 ng/ml each) plus hIGF2 and mIL-3 (10 ng/ml each, Peprotech) before nucleofection (Lonza 4D nucleofector, P4 kit, program CA137) with two times 3µg Cas9 (IDT) complexed at a 1:3 molar ratio with sgRNAs (BioLegio). After approximately 20h of culture cells were harvested and their genomic DNA subjected to CAST-Seq.

value: HSPCs

tag: sample type

value: CAST-seq derived amplicons from gDNA

value: Jinx; C57BL/6J-Unc13dJinx/Mmucd

value: Cas9+sgRNAs u3 and d4-treated


title: CAST-seq on sample treated with two RNPs  [UNC-u3d4-1]

description:
u3d4 replicate 1
UNC-u3d4_U3_OVL2_FINAL.xlsx
UNC-u3d4_D4_OVL2_FINAL.xlsx


title: FBC_Wildtype_Pax5, rep1

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

institute: Technical University of Munich, TUM University Hospital

library_source: other

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Hashtag-derived oligonucleotide (HTO)

extract_protocol:
Extract and clean hind legs of the mouse with scalpel and place in mortar. Crush bones with 2 ml FACS buffer (PBS, 2% FCS, 2mM EDTA) and transfer the liquid to a 100 µm filter (blue) on a 15 ml falcon tube with a 22G needle and 3ml syringe. Repeat 2 more times (3 x 2ml in total) and grind remaining liquid through the filter with pipette tip and tap the filter onto the tube to collect remaining drops. Centrifuge 5 min, 400g, 4°C. Discard supernatant and remove remaining liquid by taping the tube onto a tissue. Resuspend the pellet in 500 µl ACK-Lysing buffer; 5 min incubation on ice. Centrifuge 5 min, 400g, 4°C. Resuspend in 1 ml FACS Buffer and transfer to a 30 µm filter (green); repeat with additional 1 ml  (for maximum transfer efficiency hold pipette tip from the first transfer and re-use for the second transfer). Tap and push through the liquid with the pipette tip and fill up to 10 ml. Count cells (1:1 Dilution).
The 5' gene expression and VDJ (BCR) libraries were prepared following manufacturer instructions (10x Genomics). cDNA qualities were assessed using Bioanalyzer. Libraries were index barcoded and sequenced using NovaSeq 6000 S2 runs.
10x Chromium 5' kit for CITE-seq and VDJ-seq

value: bone marrow

value: preleukemic population (pre-BII = B220+IgM/D-CD25+)

tag: disease

value: healthy

tag: library type

value: HTO

tag: hto

tag: run description

value: run 1:preleukemic population from 2 mice (1 WT mouse, 1 Pax5+/- mouse) using 2 different hashtags identifying each mouse


title: mRNA_Wildtype_Pax5, rep1

description: data processed using Cell Ranger version 3.1.0

library_source: transcriptomic single cell

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv

molecule: polyA RNA

source_name: polyA RNA

value: mRNA


title: F_292_CTRL_TNF


title: CAST-seq on sample treated with two RNPs  [UNC-u1d4-2]

description:
u1d1 replicate 2
UNC-u1d4_U1_OVL2_FINAL.xlsx
UNC-u1d4_D4_OVL2_FINAL.xlsx

value: Cas9+sgRNAs u1 and d4-treated


title: F_379_p300

value: unstimulated


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_4d_3

description: MIAPaCa2 KRASG12R RN118RN287 batch untreated 4d

value: MIA PaCa-2

value: untreated

value: 4 days


title: F_292_p300

value: RA synovial tissue (finger)

value: synovial fibroblast


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_4d_3

description: MIAPaCa2 KRASG12R RN118RN287 batch doxycycline 4d

value: doxycycline


title: CAST-seq on sample treated with two RNPs  [UNC-u1d4-1]

description:
u1d1 replicate 1
UNC-u1d4_U1_OVL2_FINAL.xlsx
UNC-u1d4_D4_OVL2_FINAL.xlsx

value: HSPCs

value: CAST-seq derived amplicons from gDNA


title: F_292_CBP


title: s6_6209

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/) was used to perform a basic quality control of the resulting sequencing data.
Fragments were aligned to the mouse reference genome GRCm39 with support of the Ensembl 104 splice sites using the aligner gsnap (2020-12-16).
Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: bfx1656_processed.xlsx: raw counts (results from featureCounts)

source_name: bone marrow

extract_protocol:
Extract and clean hind legs of the mouse with scalpel and place in mortar. Crush bones with 2 ml FACS buffer (PBS, 2% FCS, 2mM EDTA) and transfer the liquid to a 100 µm filter (blue) on a 15 ml falcon tube with a 22G needle and 3ml syringe. Repeat 2 more times (3 x 2ml in total) and grind remaining liquid through the filter with pipette tip and tap the filter onto the tube to collect remaining drops. Centrifuge 5 min, 400g, 4°C. Discard supernatant and remove remaining liquid by taping the tube onto a tissue. Resuspend the pellet in 500 µl ACK-Lysing buffer; 5 min incubation on ice. Centrifuge 5 min, 400g, 4°C. Resuspend in 1 ml FACS Buffer and transfer to a 30 µm filter (green); repeat with additional 1 ml  (for maximum transfer efficiency hold pipette tip from the first transfer and re-use for the second transfer). Tap and push through the liquid with the pipette tip and fill up to 10 ml. Count cells (1:1 Dilution).
mRNA was isolated from on average 30 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation NEB Next Adapter for Illumina of the NEB Next Multiplex Oligos for Illumina Kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was done during the following PCR enrichment (16 cycles) using amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode with an average of 40 million fragments per library.

value: WT

tag: Sex

value: female

tag: age

value: 10 weeks


title: Non-treated control CAST-seq sample for samples treated Cas9 nucleases [UNC-UT2]

description:
used as non-treated control for u3d4
UNC-u3d4_U3_OVL2_FINAL.xlsx
UNC-u3d4_D4_OVL2_FINAL.xlsx

value: Jinx; C57BL/6J-Unc13dJinx/Mmucd

value: non-treated


title: s5_6208

value: bone marrow


title: Non-treated control CAST-seq sample for samples treated Cas9 nucleases [UNC-UT1]

description:
used as non-treated control for u1d4
UNC-u1d4_U1_OVL2_FINAL.xlsx
UNC-u1d4_D4_OVL2_FINAL.xlsx


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_untreated_4d_3

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 untreated 4d


title: F_292_CTRL


title: MIAPaCa2_KRASG12R_RN118_untreated_8d_3

description: MIAPaCa2 KRASG12R RN118 untreated 8d

value: 8 days


title: s4_6207


title: BCR_Wildtype_Pax5, rep1

data_processing:
scRNA- data was aligned with Cell Ranger (version 3 or version 6) to mouse reference (mm10) from 10x Genomics with default parameters.
Donor (and singlet/doublet) assignment by hashtag signals.
The VDJ-data for BCR were separately processed using Cell Ranger (version 3 or version 6) by alignment to VDJ-reference (mm10) with default parameters.
Assembly: mm10
Supplementary files format and content: CITE-seq: barcodes.tsv.gz: barcode annotation (raw and filtered); features.tsv.gz: feature annotation (raw and filtered): 10x Cell Ranger feature list; matrix.mtx.gz: count matrix (raw and filtered): 10x Cell Ranger raw UMI count matrix
Supplementary files format and content: VDJ-seq: all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: VDJ-seq

source_name: B cell receptor

value: preleukemic population (pre-BII = B220+IgM/D-CD25+)

value: healthy

value: BCR

value: run 1:preleukemic population from 2 mice (1 WT mouse, 1 Pax5+/- mouse) using 2 different hashtags identifying each mouse


title: HemSC-EVs-Transcriptome

city: Shanghai

first: Enhao

last: Lu

address: 826 Zhangheng Road

country: China

institute: Fudan University

data_processing:
miRNA-seq:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer.
Firstly, Q30 was used to perform quality control.  The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA.  The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
RNA-seq:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality trimmed reads were used to analyse circRNAs and LncRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4).   edgeR software (v3.16.5) was used to normalized the data
LncRNA: The high quality reads were aligned to the reference genome with hisat2 software (v2.0.4).   Then, HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization
Assembly: hg19
Supplementary files format and content: Raw count and normalized count of miRNAs
Supplementary files format and content: Raw count and normalized count of CircRNAs
Supplementary files format and content: Raw count and normalized count of LncRNAs

source_name: infantile hemangioma

extract_protocol:
miRNA-seq: Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNA-seq: The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions.
RNA-seq: Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA-seq: Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

value: infantile hemangioma

value: Hemangioma stem cells (HemSC)


title: mCTCF, Input, 24h Starved, Liver, Rep3

city: Odense M

first: Babukrishna

last: Maniyadath

address: Campusvej 1

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality control of sequencing reads was performed using FastQC
Reads were aligned to the reference genome (mm10) obtained from the UCSC genome browser using BWA software v.0.7.5a
Samples were filtered for regions blacklisted by the ENCODE project
PCR duplicates and multimapping reads were removed using Samtools
Alignment coordinates were converted to BED format using BEDTools v.2.17 and Peak calling was performed using MACS2
Biological triplicates of MACS2 called CTCF peaks and mm10 aligned files (bam) in Ad-lib fed and 24 hrs starved samples were combined using Samtools merge and mergePeaks (Homer) using parameter -d given, respectively.
Bigwig files were generated using bamCompare (normalized with input) on Galaxy.
Assembly: mm10
Supplementary files format and content: bigWig, BED (except for Input sample)

source_name: Liver

growth_protocol: 3–4-month-old male C57BL6NCrl mice housed under standard condition of 12 hrs of light/dark cycle were used the experiment.

extract_protocol:
Mice were euthanised by cervicval dislocation and whole livers were isolated and were either snap-frozen in liquid nitrogen.
Library preparation was performed on chromatin immunoprecipitated and input DNA using the MicroPLEX v2 protocol

treatment_protocol: For the feed-fast paradigm, mice had either ad-libitum excess to normal chow diet or were starved for 24 hrs and the tissue collection time corresponds to: Ad-lib fed tissue harvested at ZT16, 24 hrs starved group- fasted for 24 hrs and tissue harvested at ZT13.

tag: strain

value: M

value: Liver

tag: collection time_in_zt

tag: diet

value: Normal Chow

value: 24 hour Starved

tag: chip antibody


title: s2_6201

tag: tissue


title: mCTCF, Input, 24h Starved, Liver, Rep2

tag: genotype

value: WT


title: visceral adipose tissue 6 [8V]

city: Daejeon

first: Ju Hee

last: Lee

address: Munhwa-ro 266

country: South Korea

institute: Chungnam National University

description:
8V_Read_Count
processed data_GEO.txt

data_processing:
The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, #5067-5582).
Indexed libraries were then submitted to Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.
After removing the low-quality and adapter sequences using Trimmomatic, the reads were aligned with Homo sapiens (GRCh38) using HISAT (ver. 2.1.0)
Two types of indices were used for alignment (a global, whole-genome index and tens of thousands of small local indices), which were downloaded from the UCSC table browser (http://genome.ucsc.edu).
StringTie v2.1.3b was used to assemble the transcript, and it provided the relative abundance estimates as fragments per kilobase of exon per million fragments mapped (FPKM) values of the transcript or gene.
Assembly: GRCh38
Supplementary files format and content: read count for each Sample

source_name: omental adipose tissue

extract_protocol:
RNA was isolated using TRIzolTM Reagent (15596018, Life Technologies, Thermo Fisher Scientific). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).

value: omental adipose tissue

value: male


title: visceral adipose tissue 5 [7V]

description:
7V_Read_Count
processed data_GEO.txt


title: MIAPaCa2_KRASG12R_RN118RN287_batch_untreated_8d_3

description: MIAPaCa2 KRASG12R RN118RN287 batch untreated 8d

tag: cell line

value: MIA PaCa-2

tag: treatment

value: untreated


title: mCTCF, Input, 24h Starved, Liver, Rep1


title: MIAPaCa2_KRASG12R_RN118RN287_batch_doxycycline_8d_3

description: MIAPaCa2 KRASG12R RN118RN287 batch doxycycline 8d

tag: construct

value: doxycycline

tag: timepoint


title: s1_6200

value: bone marrow

value: female

value: 10 weeks


title: Heart, Myocardial infarction, 28days, rep3

first: Peng

last: Yu

state: Shanghai

address: 2205 Songhu Road, Yangpu District,Shanghai, China

data_processing:
Raw reads were trimmed adaptor sequences and removed low-quality reads using TrimGalore with default settings
Trimmed reads were aligned to the mm10 reference genome by STAR with default settings
Read count extraction were performed using FeatureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

extract_protocol:
RNA was harvested using TRIzol Reagent (ThermoFisher) according to the manufacturer's instructions . 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA hyperPrep Kit following manufacturer's protocols.

value: Heart

value: MI

tag: time

value: 28 days after MI


title: Heart, Myocardial infarction, 28days, rep2


title: mCTCF, Input, Ad-Lib Fed, Liver, Rep2

value: ad-libitum fed


title: visceral adipose tissue 3 [4V]

description:
4V_Read_Count
processed data_GEO.txt


title: mCTCF, Input, Ad-Lib Fed, Liver, Rep3

value: M


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_4d_3

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 doxycycline 4d

value: 4 days

tag: target


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_untreated_8d_3

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 untreated 8d

value: 8 days


title: MIAPaCa2_KRASG12R_RN118RN287_Cl16_doxycycline_8d_3

description: MIAPaCa2 KRASG12R RN118RN287 Cl16 doxycycline 8d


title: Heart, Myocardial infarction, 7days, rep3

value: 7 days after MI


title: visceral adipose tissue 4 [5V]

description:
5V_Read_Count
processed data_GEO.txt


title: s3_6205

value: WT


title: mCTCF, Input, Ad-Lib Fed, Liver, Rep1

value: Liver

value: Normal Chow


title: PC9_EGFR_RN76_untreated_4d_1

description: PC9 EGFR RN76 untreated 4d

source_name: PC-9 cell line

value: EGFR


title: MIAPaCa2_KRASG12R_RN118_doxycycline_8d_3

description: MIAPaCa2 KRASG12R RN118 doxycycline 8d

value: MIA PaCa-2


title: Heart, Myocardial infarction, 28days, rep1


title: subcutaneoua adipose tissue 6 [8S]

description:
8S_Read_Count
processed data_GEO.txt

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: male


title: mCTCF, IP, 24h Starved, Liver, Rep3

value: 24 hour Starved

value: Diagenode antibody, C15410210, lot A2359-00234D


title: visceral adipose tissue 1 [1V]

description:
1V_Read_Count
processed data_GEO.txt

value: omental adipose tissue


title: Heart, Myocardial infarction, 7days, rep2

value: Heart

value: MI


title: PC9_EGFR_RN108RN76_untreated_4d_1

description: PC9 EGFR RN108RN76 untreated 4d

value: untreated


title: PC9_EGFR_RN76_doxycycline_4d_1

description: PC9 EGFR RN76 doxycycline 4d

value: doxycycline


title: Heart, Myocardial infarction, 7days, rep1


title: mCTCF, IP, 24h Starved, Liver, Rep1

value: M


title: subcutaneoua adipose tissue 5 [7S]

description:
7S_Read_Count
processed data_GEO.txt


title: subcutaneoua adipose tissue 4 [5S]

description:
5S_Read_Count
processed data_GEO.txt


title: PC9_EGFR_RN108RN76_doxycycline_4d_1

description: PC9 EGFR RN108RN76 doxycycline 4d

value: 4 days


title: visceral adipose tissue 2 [3V]

description:
3V_Read_Count
processed data_GEO.txt


title: Heart, Sham, rep3

value: Sham


title: subcutaneoua adipose tissue 3 [4S]

description:
4S_Read_Count
processed data_GEO.txt


title: PC9_EGFR_RN108RN76_untreated_8d_1

description: PC9 EGFR RN108RN76 untreated 8d

value: 8 days


title: Heart, Sham, rep2


title: mCTCF, IP, Ad-Lib Fed, Liver, Rep3

value: Liver

value: WT

value: ad-libitum fed


title: mCTCF, IP, Ad-Lib Fed, Liver, Rep2

value: Normal Chow


title: PC9_EGFR_RN76_doxycycline_8d_1

description: PC9 EGFR RN76 doxycycline 8d

value: EGFR


title: subcutaneoua adipose tissue 2 [3S]

description:
3S_Read_Count
processed data_GEO.txt

value: subcutaneous adipose tissue

value: male


title: mCTCF, IP, Ad-Lib Fed, Liver, Rep1

value: Diagenode antibody, C15410210, lot A2359-00234D


title: mCTCF, IP, 24h Starved, Liver, Rep2

value: 24 hour Starved


title: PC9_EGFR_RN76_untreated_8d_1

description: PC9 EGFR RN76 untreated 8d


title: PC9_EGFR_RN108RN76_doxycycline_8d_1

description: PC9 EGFR RN108RN76 doxycycline 8d


title: Human_brain2

city: Blacksburg

first: Chang

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

data_processing:
Barcode extraction and raw read demultiplexing based on barcodes: Sequencing reads were demultiplexed based on i5/i7 indexes and split into different samples. Sequences ranging from the 25th base to the 39th base in Read 2 (from 5’ to 3’) were barcodes while the first 24 bases (TAAGTAGAAGATGGTATATGAGAT) were constant in Read 2. For each sample, a barcode whitelist was identified using umi_tools whitelist with the following settings: --stdin the read2 file, --error-correct-threshold=1, --extract-method=regex --bc-pattern='(?P<discard_1>TAAGTAGAAGATGGTATATGAGAT){s<=4}(?P<cell_1>.{15})(?P<umi_1>.{0})', --set-cell-number=5000, --log2stderr. Sequencing reads with a barcode within the barcode whitelist were extracted and had the barcode inserted in the header line, using umi_tools extract with the following settings: --stdin the R2 file,  --extract-method=regex, --bc-pattern='(?P<discard_1>TAAGTAGAAGATGGTATATGAGAT){s<=4}(?P<cell_1>.{15})(?P<umi_1>.{0})', --error-correct-cell 1, --read2-in the R1 file, --filter-cell-barcode. Extracted sequencing R1 and R2 reads were trimmed by Tim Galore! with the following settings: --paired, --clip_R1 15, --clip_R2 40. Trimmed reads were demultiplexed into individual files based on the barcodes (i.e., reads with the same barcode were written into the same file) using idemp. Subsequently, alignment to the hg19/mm10 reference genome was performed with Bismark (bowtie2) using the default parameter settings for R2 reads and –pbat for R1 reads.     Quality control and construction of allc file for each single cell  We filtered out barcodes with lower mapping efficiency and lower number of raw reads based on the bismark report. Then we performed a sort on R1 and R2 reads using samtools sort before combining R1 and R2 together into one file for each single cell using bamtools merge. Subsequently, we used picard to get rid of duplicated reads in each singe cell. We used methyKit to call the methylation states for each cytosine in the unique reads. We finally constructed the allc file for each singe cell. The format of this allc file can be found here (https://github.com/yupenghe/methylpy).     Construction of feature matrix and clustering  We used the allc file to calculate the CG methylation rate for the three cell line data (or the CH methylation rate for the mouse/human brain data) over 1 Mbp (100 kbp for the mouse/human brain data) bins across the whole genome for each cell using a customized script (bin_allc_files.py). We combined the methylation rate data from each singe cell to a feature matrix. We then normalized the matrix by dividing by the global mCH in that cell. We carried out PCA to reduce the dimensions of the normalized matrix and used the top 50 principal components for Louvain clustering using a customized script. Finally, we projected the clustering results using UMAP.
Assembly: hg19, mm10
Supplementary files format and content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

source_name: Human brain 2

growth_protocol: GM12878 cells were purchased from Coriell Institute and propagated in RPMI 1640 (ATCC, 30-2001) containing 15% fetal bovine serum (Life Technologies Corporation, 16000044), 100 U/mL Penicillin-Streptomycin (contains 100 units/mL of penicillin and 100 µg/mL of streptomycin, Gibco from Thermo Fisher Scientific, 15140122) at 37 °C in a humidified incubator containing 5% CO2. GM12878 cells were sub-cultured every two days. HEK293 cells and MCF7 cells purchased from ATCC were cultured in DMEM (high glucose, Life Technologies Corporation, 11965084) containing 15% fetal bovine serum, 100 U/mL Penicillin-Streptomycin at 37 °C in a humidified incubator containing 5% CO2. HEK293 cells and MCF7 cells were sub-cultured when reaching ~80% confluency.

extract_protocol:
10-week-old male mice were sacrificed by compressed CO2 followed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice and stored at -80°C. To collect prefrontal cortex (PFC) samples, mouse brains were sectioned coronally at Bregma 2.5 and 0.5 with a razor blade in dissection media (20 mM Sucrose, 28 mM D-Glucose, 0.42 mM NaHCO3 in HBSS). The dissected brain tissues were stored at -80 °C until use. Human brains were obtained during autopsies performed at the Basque Institute of Legal  Medicine, Bilbao, Spain. The brain tissue for the human brain 1 (HB1) sample belonged to a 41-year-old Caucasian female and the brain tissue for the human brain 2 (HB2) sample belonged to a 74-year-old Caucasian female with a postmortem interval (PMI) of 22 h. To isolate nuclei, the PFC was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl, and 0.1% Triton X-100 with freshly added 50 μl of PIC, 5 μl of 100 mM PMSF and 5 μl of 1M DTT). The tissue was thawed and homogenized by slowly douncing on ice with a loose pestle A (Kimble, 7-ml size) for 15 times, and with a pestle B for 25 times. We filtered the homogenate with a 40-μm nylon mesh cell strainer (Fisher Scientific, 22-363-547) and then centrifuged the sample at 1,000 g for 10 min at 4 °C. We then removed the supernatant and resuspended the pellet in 500 μl ice-cold nuclei extraction buffer.     The suspension was mixed with 750 μl of 50% iodixanol solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 20 mM Tris-HCl (pH 7.8)) and centrifuged at 5,000 g for 15 min at 4 °C. After centrifugation, we followed the s3_WGS protocol1 to perform nuclei fixation and nucleosome depletion. Briefly, the nuclei pellet was resuspended in 5 ml of NIB:HEPES buffer (10 mM HEPES-KOH (pH 7.2), 10 mM NaCl, 3mM MgCl2, 0.1 % Igepal, 0.1 % Tween-20) in a 15 ml centrifuge tube (Corning, 430791). We incubated the mixture at room temperature for 10 min on a rotator (speed: 50 rpm, Argos Technologies RotoFlex) after adding 246 μl of 16 % formaldehyde (Thermo Fisher Scientific, 28908) to the suspension. The mixture was centrifuged at 500 g for 5 min at 4 °C to form nuclei pellet and the supernatant was then removed. 1 mL of NIB:Tris (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1 % Igepal, 0.1 % Tween-20) was then added to resuspend and wash the nuclei pellet to quench the fixation. The nuclei were pelleted by centrifuging at 500 g for 5 min at 4 °C and resuspended in 200 μl 1X NEBuffer 2.1 (50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 100 µg/ml BSA; NEB, B7202) in a 1.5 ml tube. The suspension was centrifuged at 500 g for 5 min at 4 °C to pellet nuclei which were then resuspended in 760 μl of 1X NEBuffer 2.1. We added 40 μl of 1 % SDS to the nuclei suspension and incubated the mixture at 37 °C for 20 min on a Multi-Therm shaker (Benchmark Scientific, H5000-HC) with a shaking speed of 300 rpm. After SDS treatment, the mixture was centrifuged at 500 g for 5 min at 4 °C. The pellet was resuspended in 1 ml of ATAC-RSB buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 with freshly added 10 μl of 10% Tween-20). The suspension was pipetted up and down several times and then centrifuged at 500 g for 5 min at 4 °C. Finally, the nuclei were resuspended in 100 μl of ATAC-RSB buffer with freshly added 1 μl of 10% Tween-20. We measured the concentration of the nuclei using a hematocytometer and diluted the nuclei concentration to 5 million/ml using the ATAC-RSB buffer.
Library preparation follows Drop-BS protocol. We first completed single-cell lysis, genomic DNA fragmentation, DNA barcoding and bisulfite conversion in droplets. Then we used random priming to add the second adapter to DNA. Finally, we utilized indexing PCR to amplify DNA to obtain sequencing library.

value: Human brain 2

value: 74 years old

tag: cell type

value: Human prefrontal cortex neurons and glia


title: HSAL_2, Day7

city: Hangzhou

first: Qiang

last: Liu

state: Zhejiang

address: Xihu District, Yuhangtang road 866

department: College of Environmental & Resource Science

institute: Zhejiang University

data_processing:
The reference genome and gene model annotation files were downloaded from the genome website（https://plants.ensembl.org/)
The clean reads were aligned to the Oryza sativa L. Nipponbare genome assembly (version 4) using Tophat (v2.0.9)
The gene expression level was calculated using the FPKM (fragments per kilobase of transcript per million mapped reads) by the Python package HTSeq with default settings.
The DESeq2 R (1.10.1) package54 was used to evaluate differential gene expression between two groups.
Assembly: Oryza sativa L. Nipponbare genome assembly (version 4) at https://plants.ensembl.org/
Supplementary files format and content: The gene expression level was calculated using the FPKM (fragments per kilobase of transcript per million mapped reads).

organism: Oryza sativa

source_name: root tip

growth_protocol: Rice seedlings were cultivated in the water for 7 days.

extract_protocol:
We extracted the total RNA of the root tips with the TRIzol reagent (Invitrogen) by following the manufacturer's instructions.
The total RNA was subject to library preparation with Truseq stranded mRNA sequencing kit (Illumina Inc.)

treatment_protocol: The root tips (around 5 mm) of rice seedlings (28 root tips as a group) with or without HSAL treatment for 12 h.

value: root tip

value: Apical meristem cells

value: hydroponic with 0.05% HSAL

value: Day 7


title: subcutaneoua adipose tissue 1 [1S]

description:
1S_Read_Count
processed data_GEO.txt


title: HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep3

first: Florian

last: Andersch

address: Campus-Vienna-Biocenter 1

institute: Institute of Molecular Pathology

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.TRA.3

data_processing:
For human Quant-seq (3’ mRNA-Seq) data, the six nucleotide long 5’ UMIs were attached to each read name with umi-tools (v1.0.0) (Smith et al., 2017), before trimming away the UMIs plus the next four nucleotides (UMI spacer), as well as 3’ adapters (stringency of 3) and bases with low quality (threshold of 25), using cutadapt (v1.18) (MARIN, 2011) and its wrapper tool trimgalore (v0.6.2).
Read quality control was performed with FastQC (v0.11.8) (Andrews, 2010).
The remaining reads were sample-wise aligned to the human (GRCh38.p13; GCA_000001405.28) reference genome.
Mapping and subsequent filtering of 3’ UTR mapped reads was performed with slamdunk (v0.4.3) (Neumann et al., 2019). 3’ UTR regions were assembled as described previously (Muhar et al., 2018).
Aligned and filtered reads were deduplicated with umi-tools (v1.0.0) (Smith et al., 2017), based on the mapping coordinate and the UMI attached to the read name, prior to quantifying read abundances within 3’ UTR regions using featureCounts (v2.0.1) (Liao et al., 2014).
Differential expression analysis was performed with DESeq2 (v1.30.1) (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample

source_name: Connective tissue

growth_protocol: RKO (ATCC: CRL-2577) were cultured in RPMI 1640, supplemented with 10% FBS (Sigma-Aldrich), 4mM L-glutamine (Thermo Fisher), 1mM sodium pyruvate (Sigma-Aldrich), and penicillin/streptomycin (100 U ml−1/100 μg ml−1, Sigma-Aldrich). HT-1080 (ATCC: CCL-121) were cultivated in DMEM (Thermo Fisher) with 10% FBS, 4mM L-glutamine, 1mM sodium pyruvate, and penicillin/streptomycin (100 U ml−1/100 μg ml−1). All cell lines were maintained at 37°C with 5% CO2, routinely tested for mycoplasma contamination and authenticated by short tandem repeat analysis.

extract_protocol:
Total RNA was isolated using in-house magnetic beads kit and King Fisher Duo Prime Purification System (Thermo Fisher).
QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) HT for Illumina, UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen)
3'-end mRNA-seq
Illumina NovaSeq 6000 S4 PE150

treatment_protocol: RKO and HT-1080 human cell lines transduced with ARTi.6570, ARTi.6634, ARTi.6786 artificial short-hairpin RNA constructs or with empty vector control (+/- trametinib treatment) in biological triplicates.

value: Connective tissue

value: empty vector + 960nM trametinib for 24 hrs


title: HSAL_3, Day7

value: WT


title: in vitro-derived Treg, oxPAPC-treated, Replicate 3

city: Nashville

first: Amy

last: Major

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

data_processing:
Paired-End 150bp sequencing on Illumina NovaSeq6000
50M reads per sample
Sequence alignment used STAR software v2.7.8a
Mapped reads were assigned to gene features and quantified using featureCounts v2.0.2
Normalization and differential expression were performed using DESeq2 v1.30.1
Assembly: mouse GENCODE GRCm38.p6
Supplementary files format and content: comma-separated values file includes read counts for each sample and normalized abundance measurements for each group
Supplementary files format and content: information on line above

source_name: Spleen

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen).
Libraries were prepared using 200-500ng of total RNA using NEBNext Poly(A) selection kit

value: Spleen

value: Primary Cell Culture

value: Treg

value: oxPAPC


title: in vitro-derived Treg, oxPAPC-treated, Replicate 4


title: PC9_EGFR_RN76_untreated_4d_2

description: PC9 EGFR RN76 untreated 4d

value: untreated

value: 4 days

value: EGFR


title: HSAL_1, Day7


title: in vitro-derived Treg, Control, Replicate 4

value: Control


title: PC9_EGFR_RN76_doxycycline_4d_2

description: PC9 EGFR RN76 doxycycline 4d

value: doxycycline


title: HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.TRA.2


title: in vitro-derived Treg, Control, Replicate 3


title: HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.TRA.1


title: Control_3, Day7

value: hydroponic with water


title: Heart, Sham, rep1

value: Heart

value: Sham


title: Control_2, Day7

value: root tip

value: Apical meristem cells


title: in vitro-derived Treg, oxPAPC-treated, Replicate 2


title: PC9_EGFR_RN108RN76_untreated_4d_2

description: PC9 EGFR RN108RN76 untreated 4d


title: HT1080 cell line, empty vector, rep3

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.3

value: Connective tissue

value: empty vector


title: in vitro-derived Treg, Control, Replicate 2


title: rtel1-3, RNA-seq, rep2

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

country: France

institute: CNRS

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with default parameters.
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.2b (Dobin et al 2013) retaining multi-mapped reads mapping up to 10 positions. Subsequent read counting was performed with featureCounts version 2.0.0 (Liao, Smyth, and Shi 2014) on the TAIR10 TE and PCG annotations. Normalization and differential analyses were done using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) with default parameters. Only loci with Benjamini-Hochberg adjusted p-values < 0.05 and with a log2-fold change ≥ 0.585 or ≤ − 0.585 were considered differentially expressed.
BS-seq datasets : data analysis was done using the Methylpy analysis pipeline v1.4.6 (Schultz et al. 2015). Reads were filtered to remove PCR duplicates using Picard v2.23.3 and mapped to TAIR10 using Bowtie2 v2.4.1 (Langmead and Salzberg 2012). Only cytosines with a minimum coverage of 6 reads were retained.
ATAC-seq datasets : Reads were mapped to the Arabidopsis TAIR10 reference genome using STAR version 2.7.2b (--outFilterMultimapNmax 1 --outFilterMatchNmin 10 --alignIntronMax 10000, all other parameters default).Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite v2.23.3.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq: bigWig format files with methylation levels for CG, CHG and CHH methylation. Only positions with 6+ coverage were used to generate the bigWig files. RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins. ATAC-seq: bigWig format files with normailzed read densities (Reads Per Genomic Content) calculated in 1 bp bins.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
Total RNA was extracted from 16-day-old seedlings using RNAzol (Sigma)
TruSeq Stranded mRNA library prep kit (Illumina), sequenced on HiSeq 4000 (Illumina)

treatment_protocol: no treatment

tag: developmental stage

value: 16-day-old seedlings

value: seedling


title: PC9_EGFR_RN76_untreated_8d_2

description: PC9 EGFR RN76 untreated 8d

value: 8 days


title: Control_1, Day7

value: WT

value: Day 7


title: in vitro-derived Treg, Control, Replicate 1

value: Spleen

value: Primary Cell Culture

value: Treg


title: HT1080 cell line, empty vector, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.1


title: PC9_EGFR_RN76_doxycycline_8d_2

description: PC9 EGFR RN76 doxycycline 8d

value: EGFR


title: rtel1-3, RNA-seq, rep1


title: rtel1-1, RNA-seq, rep2


title: rtel1-1, RNA-seq, rep1


title: PC9_EGFR_RN76_untreated_4d_3

description: PC9 EGFR RN76 untreated 4d

value: untreated

value: 4 days


title: NPRC-/-ApoE-/- 1

city: Jinan

first: Cheng

last: cheng

address: Qilu Hospital, Shandong University, No.107, Wen Hua Xi Road, Jinan, Shandong, 250012, P.R. China

institute: Qilu Hospital of Shandong University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V96
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: aorta

growth_protocol: the entire aortas isolated from ApoE-/- and NPRC-/-ApoE-/- mice

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before the tissue collection,mice were fed with the western diet

value: aorta

value: Apoe-/-

value: Western diet


title: NPRC-/-ApoE-/- 2


title: HT1080 cell line, REN.713 shRNA, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.REN713.2

value: REN.713 shRNA


title: L5, RNA-seq, rep2


title: PC9_EGFR_RN108RN76_doxycycline_8d_2

description: PC9 EGFR RN108RN76 doxycycline 8d

value: doxycycline


title: HT1080 cell line, empty vector, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.empty.2

value: Connective tissue

value: empty vector


title: PC9_EGFR_RN76_doxycycline_4d_3

description: PC9 EGFR RN76 doxycycline 4d


title: NPRC-/-ApoE-/- 3

value: Nprc-/-Apoe-/-


title: PC9_EGFR_RN108RN76_doxycycline_4d_2

description: PC9 EGFR RN108RN76 doxycycline 4d


title: HT1080 cell line, ARTi.6786 shRNA, rep3

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6786.3

value: ARTi.6786 shRNA


title: ApoE-/- 5


title: L5, RNA-seq, rep1

value: 16-day-old seedlings

value: seedling


title: HT1080 cell line, ARTi.6786 shRNA, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6786.2


title: ApoE-/- 4


title: PC9_EGFR_RN108RN76_untreated_4d_3

description: PC9 EGFR RN108RN76 untreated 4d


title: HT1080 cell line, REN.713 shRNA, rep3

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.REN713.3


title: GMD-78

city: Zurich

first: Stefan

last: Grob

address: Zollikerstrasse 107

department: Institute of Plant Biology

institute: University of Zurich

data_processing:
data filtering sRNA: custom python script to remove ribosomic reads
alignment sRNA: bowtie, version 7.3.0, parameters:-v 2 --best -p 24 -m 1000
binning sRNA: HiCdat
alignment mRNA: hisat2, version 7.2.0, parameters: -p 20 --max-intronlen 10000
mapping mRNA alignments to features: featureCounts, version 1.6, parameters:-T 24 -p -M --fraction -O --fraction -C
alignment mC: bismark, parameters: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
extract methylation levels: methylkit, parameters: save.context = c("CpG","CHH","CHG"), read.context = "none", nolap = TRUE,mincov = 10, minqual = 20, phred64 = FALSE
Genome_build: TAIR10
Supplementary_files_format_and_content: Final processed files are tab-separated bed-like files

source_name: Col-SylA

growth_protocol: Seedlings were grown in the growth chamber under long-day conditions: 15 hours of light at 25°C and 60% of humidity and 10 hours of night at 21°C and 75% of humidity.

extract_protocol:
Trizol
http://www.fasteris.com

treatment_protocol: Three to five one week old plantlets were transferred in a 24 wells plate with 500μL of liquid Ms ½. The plate was then return to the growth chamber and place under agitation. Seedlings were allowed to recover for 24h. After recovery, the seedlings were treated with Syringolin A (SylA) at a final concentration of 20μM during 24h. Syringolin A stock solution (10mM in water) was stored at-20°C. After 24h hours, seedlings were collected and immediately frozen in liquid nitrogen and use for subsequent extraction.

value: Wild-type Col-0

value: SylA treatment


title: HT1080 cell line, ARTi.6786 shRNA, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6786.1


title: PC9_EGFR_RN108RN76_doxycycline_4d_3

description: PC9 EGFR RN108RN76 doxycycline 4d

data_processing:
Base-calling was performed using the Real-Time Analysis (RTA)
Mapping of raw reads was performed with STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences.
Quantification of read counts to transcript annotations was implemented using RSEM(v1.3.0) and featureCounts (v1.5.1).
Normalization of read counts and differential analysis was implemented with the limma and voom R packages.
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text files include normalized count values for all samples.


title: PC9_EGFR_RN108RN76_untreated_8d_2

description: PC9 EGFR RN108RN76 untreated 8d

value: 8 days


title: GMD-77

source_name: Col-crt

value: control


title: HT1080 cell line, ARTi.6634 shRNA, rep3

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6634.3

value: ARTi.6634 shRNA


title: PC9_EGFR_RN76_untreated_8d_3

description: PC9 EGFR RN76 untreated 8d

value: untreated

value: EGFR


title: ApoE-/- 2

value: aorta

value: Apoe-/-


title: HT1080 cell line, REN.713 shRNA, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.REN713.1

value: REN.713 shRNA


title: SP3

extract_protocol:
DNeasy Plant Mini Kit
PE150, WGBS library
https://en.novogene.com/


title: HT1080 cell line, ARTi.6634 shRNA, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6634.2


title: PC9_EGFR_RN76_doxycycline_8d_3

description: PC9 EGFR RN76 doxycycline 8d

value: doxycycline


title: HT1080 cell line, ARTi.6634 shRNA, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6634.1

value: Connective tissue


title: PC9_EGFR_RN108RN76_untreated_8d_3

description: PC9 EGFR RN108RN76 untreated 8d


title: ApoE-/- 1

value: Western diet


title: in vitro-derived Treg, oxPAPC-treated, Replicate 1

value: Spleen

value: Primary Cell Culture

value: Treg

value: oxPAPC


title: SP2

extract_protocol:
QIAzol Lysis Reagent
PE150, PolyA enriched library
https://en.novogene.com/

value: seedling

value: Wild-type Col-0


title: SM3


title: HT1080 cell line, ARTi.6570 shRNA, rep3

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6570.3

value: ARTi.6570 shRNA


title: HT1080 cell line, ARTi.6570 shRNA, rep2

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6570.2


title: SP1

value: SylA treatment


title: 6C_RNP_Jinx_LCMV

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

description: splenocytes, RNP treated Jinx in Jinx HSC chimera after LCMV infection

data_processing:
Sequences were processed with Molecular Identifier Groups-Based Error Correction (MIGEC) program v1.2.9
The steps performed included: which included demultiplexing, UMI clustering, filtering, V(D)J junction and CDR3 region extraction, and clonotype assembly
The final CDR3 sequences were obtained by the FilterCdrBlastResults which filter for hot-spot PCR and NGS errors.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with CDR3 sequences
Library strategy: TCR-seq

source_name: spleen

extract_protocol:
Total RNA was extracted from splenocytes or CD8+ T cells (Qiagen, 74106), reverse transcribed (500ng), and uracil-DNA glycosylase-treated (NEB). TCR sequences were amplified in PCR I (2 μl cDNA) and II (3 μl PCR I) using two TCR specific Primers for the 3'region and UMI SmartN oligos and bardode primers for the 5'region (IDT, Table S7).
After agarose gel separation, 400-800 bp long PCR II fragments were barcoded with Illumina NEBNext Multiplex Oligos in PCR III (NEB, E7645L). The R2 fastq files start with an 8 bp barcode + 19bp adapter + 16bp Unique Molecular Identifier (UMI).

value: spleen

value: splenocytes

value: Jinx

value: HSC transplantation of RNP treated cells, LCMV infection

tag: barcode umi_r2


title: SM2

value: control


title: 6A_RNP_Jinx_LCMV


title: 6B_RNP_Jinx_LCMV


title: PC9_EGFR_RN108RN76_doxycycline_8d_3

description: PC9 EGFR RN108RN76 doxycycline 8d

extract_protocol:
2x106 Dox-treated and untreated control cells were harvested, washed with PBS, lysed, treated with DNAse I (QIAGEN) and total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Next generation sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

value: 8 days

value: EGFR


title: HT1080 cell line, ARTi.6570 shRNA, rep1

description:
QuantSeq
HT1080_normalized_counts.tsv
HT1080.ARTi.6570.1

value: Connective tissue


title: 5C_WT_WT_LCMV

description: splenocytes, wt in wt HSC chimera after LCMV infection

value: BL/6 wt

value: HSC transplantation, LCMV infection


title: ApoE-/- 3

value: aorta

value: Apoe-/-

value: Western diet


title: 5B_WT_WT_LCMV


title: RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.TRA.3

source_name: Large intestine

value: Large intestine

value: RKO

value: empty vector + 130nM trametinib for 24 hrs


title: SM1

value: seedling

value: Wild-type Col-0


title: RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep2

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.TRA.2


title: 5A_WT_WT_LCMV

value: spleen

value: splenocytes


title: 4C_WT_LCMV

description: splenocytes, wt mice after LCMV infection

value: LCMV infection


title: RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.TRA.1


title: RKO cell line, empty vector, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.3

value: empty vector


title: 4B_WT_LCMV


title: 4A_WT_LCMV


title: RKO cell line, empty vector, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.1


title: RKO cell line, empty vector, rep2

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.empty.2


title: 3B_WT

description: CD8 T cells, wt mice

value: CD8 T cells

value: UT


title: 3C_WT

description: CD8 T cells, wt mice


title: RKO cell line, REN.713 shRNA, rep2

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.REN713.2

value: REN.713 shRNA


title: FdC2 RNAi line 8 individual 4

type: RNA

city: London

first: Guy

last: Hanke

address: Mile End

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description:
254534110001_1_4
gene expression in FdC2 RNAi line 11

hyb_protocol: performed by Oaklabs Scientific

scan_protocol: performed by Oaklabs Scientific

data_processing:
Data validated by M vs A analysis, principle component analysis and  heirarchical clustering. Sample RNAi line 8, individual 3 excluded from furtehr analysis on the basis of heirarchical clustering
normalized signal intensity. Data were normalised by removal of signals from control probes, taking the mean of signals from replicate probes and then the mean of signals from all probes of a target gene

source_name: FdC2 RNAi line 8 individual 4

label_protocol: performed by Oaklabs Scientific

growth_protocol: 12 h light 12 h dark, 150 umol photons m2 s-1

extract_protocol: Qiagen Plant Rneasy

treatment_protocol: none, sampled 2 h into light

value: total leaf

value: 4 weeks


title: FdC2 RNAi line 8 individual 6

description:
254534110001_2_1
gene expression in FdC2 RNAi line 13

source_name: FdC2 RNAi line 8 individual 6


title: 3A_WT

description: CD8 T cells, wt mice

value: BL/6 wt


title: FdC2 RNAi line 8 individual 5

description:
254534110001_2_2
gene expression in FdC2 RNAi line 12

source_name: FdC2 RNAi line 8 individual 5


title: genomic DNA from Liver from ST_OldHet5

type: genomic

city: Boston

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

description: Short-term old heterochronic parabiosis

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: For mammalian microarray analysis, raw methylation data were first normalized and beta values were calculated using the SeSAMe R package.

label: Cy3 and Cy5

source_name: Liver from ST_OldHet5

label_protocol: Standard Illumina protocol

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol: DNA was isolated from whole blood using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis.

tag: age (years)

tag: mouse strain

value: C57BL/6 WT

tag: Sex

value: Female

tag: mouse id

value: Liver


title: FdC2 RNAi line 8 individual 1

description:
254534110002_1_3
gene expression in FdC2 RNAi line 8

source_name: FdC2 RNAi line 8 individual 1

tag: age


title: RKO cell line, REN.713 shRNA, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.REN713.1

value: Large intestine

value: RKO


title: 2C_P14_WT_LCMV

description: splenocytes, P14 wt mice after LCMV infection

value: P14 wt

value: adoptive T cell transfer, LCMV infection


title: genomic DNA from Liver from ST_OldIso2

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso2


title: RKO cell line, REN.713 shRNA, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.REN713.3


title: FdC2 RNAi line 8 individual 2

description:
254534110002_1_4
gene expression in FdC2 RNAi line 9

source_name: FdC2 RNAi line 8 individual 2


title: FdC2 RNAi line 8 individual 3

description:
254534110002_1_2
gene expression in FdC2 RNAi line 10

source_name: FdC2 RNAi line 8 individual 3


title: 2B_P14_WT_LCMV

value: spleen


title: FdC2 RNAi line 1 individual 4

description:
254534110002_1_1
gene expression in FdC2 RNAi line 1

source_name: FdC2 RNAi line 1 individual 4


title: genomic DNA from Liver from ST_OldHet3

description: Short-term old heterochronic parabiosis

source_name: Liver from ST_OldHet3


title: genomic DNA from Liver from ST_OldHet2

description: Short-term old heterochronic parabiosis

source_name: Liver from ST_OldHet2


title: FdC2 RNAi line 1 individual 1

description:
254534110002_2_2
gene expression in FdC2 RNAi line 1

source_name: FdC2 RNAi line 1 individual 1


title: FdC2 RNAi line 1 individual 3

description:
254534110001_1_3
gene expression in FdC2 RNAi line 1

source_name: FdC2 RNAi line 1 individual 3


title: genomic DNA from Liver from ST_OldIso5

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso5


title: RKO cell line, ARTi.6786 shRNA, rep2

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6786.2

value: ARTi.6786 shRNA


title: genomic DNA from Liver from ST_OldIso3

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso3


title: 2A_P14_WT_LCMV

source_name: spleen

value: splenocytes


title: RKO cell line, ARTi.6786 shRNA, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6786.1

source_name: Large intestine


title: RKO cell line, ARTi.6634 shRNA, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6634.3

value: ARTi.6634 shRNA


title: 1C_P14_WT

description: CD8 T cells, P14 wt mice

value: CD8 T cells


title: 1B_P14_WT

description: CD8 T cells, P14 wt mice

value: UT


title: genomic DNA from Liver from ST_YoungIso3

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso3


title: genomic DNA from Liver from ST_YoungIso5

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso5


title: RKO cell line, ARTi.6786 shRNA, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6786.3


title: FdC2 RNAi line 1 individual 2

description:
254534110001_2_3
gene expression in FdC2 RNAi line 1

source_name: FdC2 RNAi line 1 individual 2


title: genomic DNA from Liver from ST_YoungIso4

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso4


title: Wt- individual 6

description:
254534110001_1_1
gene expression in Wt Arabidopsis

source_name: Wt- individual 6


title: 1A_P14_WT

description: CD8 T cells, P14 wt mice


title: Wt- individual 5

description:
254534110001_1_2
gene expression in Wt Arabidopsis

source_name: Wt- individual 5


title: RKO cell line, ARTi.6634 shRNA, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6634.1


title: RKO cell line, ARTi.6570 shRNA, rep3

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6570.3

value: ARTi.6570 shRNA


title: Human_mouse_species_mixing

description: The species mixing data set is for quality control of the method.  No processed data are available for this sample.

organism:
Homo sapiens
Mus musculus

source_name: GM12878/Mouse brain

extract_protocol:
10-week-old male mice were sacrificed by compressed CO2 followed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice and stored at -80°C. To collect prefrontal cortex (PFC) samples, mouse brains were sectioned coronally at Bregma 2.5 and 0.5 with a razor blade in dissection media (20 mM Sucrose, 28 mM D-Glucose, 0.42 mM NaHCO3 in HBSS). The dissected brain tissues were stored at -80 °C until use. Human brains were obtained during autopsies performed at the Basque Institute of Legal  Medicine, Bilbao, Spain. The frozen PFC tissue belonged to a 41-year-old female with a PMI of 22 h. To isolate nuclei, the PFC was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl, and 0.1% Triton X-100 with freshly added 50 μl of PIC, 5 μl of 100 mM PMSF and 5 μl of 1M DTT). The tissue was thawed and homogenized by slowly douncing on ice with a loose pestle A (Kimble, 7-ml size) for 15 times, and with a pestle B for 25 times. We filtered the homogenate with a 40-μm nylon mesh cell strainer (Fisher Scientific, 22-363-547) and then centrifuged the sample at 1,000 g for 10 min at 4 °C. We then removed the supernatant and resuspended the pellet in 500 μl ice-cold nuclei extraction buffer.     The suspension was mixed with 750 μl of 50% iodixanol solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 20 mM Tris-HCl (pH 7.8)) and centrifuged at 5,000 g for 15 min at 4 °C. After centrifugation, we followed the s3_WGS protocol1 to perform nuclei fixation and nucleosome depletion. Briefly, the nuclei pellet was resuspended in 5 ml of NIB:HEPES buffer (10 mM HEPES-KOH (pH 7.2), 10 mM NaCl, 3mM MgCl2, 0.1 % Igepal, 0.1 % Tween-20) in a 15 ml centrifuge tube (Corning, 430791). We incubated the mixture at room temperature for 10 min on a rotator (speed: 50 rpm, Argos Technologies RotoFlex) after adding 246 μl of 16 % formaldehyde (Thermo Fisher Scientific, 28908) to the suspension. The mixture was centrifuged at 500 g for 5 min at 4 °C to form nuclei pellet and the supernatant was then removed. 1 mL of NIB:Tris (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1 % Igepal, 0.1 % Tween-20) was then added to resuspend and wash the nuclei pellet to quench the fixation. The nuclei were pelleted by centrifuging at 500 g for 5 min at 4 °C and resuspended in 200 μl 1X NEBuffer 2.1 (50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 100 µg/ml BSA; NEB, B7202) in a 1.5 ml tube. The suspension was centrifuged at 500 g for 5 min at 4 °C to pellet nuclei which were then resuspended in 760 μl of 1X NEBuffer 2.1. We added 40 μl of 1 % SDS to the nuclei suspension and incubated the mixture at 37 °C for 20 min on a Multi-Therm shaker (Benchmark Scientific, H5000-HC) with a shaking speed of 300 rpm. After SDS treatment, the mixture was centrifuged at 500 g for 5 min at 4 °C. The pellet was resuspended in 1 ml of ATAC-RSB buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 with freshly added 10 μl of 10% Tween-20). The suspension was pipetted up and down several times and then centrifuged at 500 g for 5 min at 4 °C. Finally, the nuclei were resuspended in 100 μl of ATAC-RSB buffer with freshly added 1 μl of 10% Tween-20. We measured the concentration of the nuclei using a hematocytometer and diluted the nuclei concentration to 5 million/ml using the ATAC-RSB buffer.
Library preparation follows Drop-BS protocol. We first completed single-cell lysis, genomic DNA fragmentation, DNA barcoding and bisulfite conversion in droplets. Then we used random priming to add the second adapter to DNA. Finally, we utilized indexing PCR to amplify DNA to obtain sequencing library.

value: GM12878/Mouse brain

value: N.A./10 weeks old

value: Human  B-Lymphocyte/Mouse prefrontal cortex neurons and glia


title: Wt- individual 3

description:
254534110001_2_4
gene expression in Wt Arabidopsis

source_name: Wt- individual 3

value: total leaf

value: 4 weeks


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-3

city: shanghai

first: Xiaohui

last: Yuan

state: shanghai

address: 83 fenyang road

institute: Eye & ENT Hospital of Fudan University

data_processing:
Raw data of  fastq format were firstly processed using Trimmomatic
The clean reads were mapped to the human genome using HISAT2
FPKM value of each gene was calculated using cufflinks
The read counts of each gene were obtained by HTSeq-count
DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest.  Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and annotations

source_name: LSCC cell

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded  mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s  instructions.

value: laryngeal cancer

value: F. nucleatum-treated


title: genomic DNA from Liver from ST_YoungIso7

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso7

value: C57BL/6 WT

value: Female

value: Liver


title: genomic DNA from Liver from ST_YoungIso6

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso6


title: genomic DNA from Liver from ST_OldHet6

description: Short-term old heterochronic parabiosis

source_name: Liver from ST_OldHet6


title: RKO cell line, ARTi.6634 shRNA, rep2

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6634.2

value: Large intestine

value: RKO


title: iPS11_pSin_p53IDH1R132H_2

city: Magdeburg

first: Ulf

last: Kahlert

address: Leipziger Str 44

institute: Otto-vo-Guericke University

description: IDH1-R132H over-expression

data_processing:
Data analyses on fastq files were conducted with Partek Flow.
The reads of all probes were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2)
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner and unaligned reads were further processed using Bowtie 2 v2.2.5 aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: txt

source_name: human foreskin

extract_protocol:
Total RNA was extracted from snap-frozen cell pellets using the NucleoSpin RNA extraction kit (Macherey-Nagel, Germany) with DNaseI treatment according to manufactures protocol
Library preparation was performed according to the manufacturer’s protocol using the VAHTS™ Stranded mRNA-Seq Library Prep Kit for Illumina® V2 (Vazyme, China)

tag: gender

value: male

value: induced pluripotent cell line

tag: disease state

value: glioblastoma


title: genomic DNA from Liver from ST_OldIso6

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso6

tag: tissue


title: genomic DNA from Liver from ST_OldHet4

description: Short-term old heterochronic parabiosis

source_name: Liver from ST_OldHet4


title: Wt- individual 4

description:
254534110002_2_3
gene expression in Wt Arabidopsis

source_name: Wt- individual 4


title: iPS11_pSin_p53IDH1R132H_3

description: IDH1-R132H over-expression


title: iPS11_pSin_p53IDH1R132H_1

description: IDH1-R132H over-expression


title: Wt- individual 2

description:
254534110002_2_4
gene expression in Wt Arabidopsis

source_name: Wt- individual 2


title: genomic DNA from Liver from ST_OldIso4

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso4


title: genomic DNA from Liver from ST_YoungIso2

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso2


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-1

tag: cell line


title: AMC-HN-8 cells, F. nucleatum-treated, replicate-2

tag: treatment


title: RKO cell line, ARTi.6570 shRNA, rep1

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6570.1

source_name: Large intestine


title: AMC-HN-8 cells, control, replicate-3

value: control


title: Mouse_brain

source_name: Mouse brain

value: Mouse brain

value: 10 weeks old

value: Mouse prefrontal cortex neurons and glia


title: ATAC-seq of HFF

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across all genes). The deeptools tool is used for this analysis.
Reads distributions (from bigwig) across peaks are presented as an average plot (average of reads signals across all peaks). The deeptools tool is used for this analysis.
Peaks were annotated by the function of annotatePeak of ChIPseeker.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: HFF

extract_protocol:
1. Nucleus extraction: Cell samples refer to ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide to lyse cells and obtain nuclei; Frozen tissue samples refer to An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues The method in extracts nuclei.
2. Transposition reaction: 40,000 nuclei were taken into Tn5 enzyme (Illumina) for transposition reaction, and the DNA fragments after transposition were recovered with MinElute PCR Purification Kit (Qiagen).
3. Library construction: PCR amplification was performed with 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). The amplified products were recovered with MinElute PCR Purification Kit (Qiagen).

value: HFF

value: human foreskin fibroblast

tag: genotype

value: WT


title: ATAC-seq of KOE6E7SiHa

value: cervical cancer cells


title: RKO cell line, ARTi.6570 shRNA, rep2

city: Vienna

description:
QuantSeq
RKO_normalized_counts.tsv
RKO.ARTi.6570.2

value: ARTi.6570 shRNA


title: genomic DNA from Liver from ST_OldHet1

description: Short-term old heterochronic parabiosis

source_name: Liver from ST_OldHet1

value: C57BL/6 WT


title: AMC-HN-8 cells, control, replicate-2

value: laryngeal cancer


title: iPS11_pSin_p53_IDH1wt_2

description: IDH1 wild type over-expression


title: AMC-HN-8 cells, control, replicate-1


title: iPS11_pSin_p53_IDH1wt_1

description: IDH1 wild type over-expression


title: ATAC-seq of H8

value: Immortalized human cervical epithelial cells


title: Wt- individual 1

description:
254534110002_2_1
gene expression in Wt Arabidopsis

source_name: Wt- individual 1

value: total leaf

value: 4 weeks


title: genomic DNA from Liver from ST_OldIso1

description: Short-term old isochronic parabiosis

source_name: Liver from ST_OldIso1

value: Female

value: Liver


title: genomic DNA from Liver from ST_YoungIso1

description: Short-term young isochronic parabiosis

source_name: Liver from ST_YoungIso1


title: iPS11_pSin_p53_IDH1wt_3

description: IDH1 wild type over-expression

value: male

value: induced pluripotent cell line

value: glioblastoma


title: ATAC-seq of SiHa

source_name: SiHa

value: SiHa


title: Human_brain

source_name: Human brain

value: Human brain

value: 41 years old

value: Human prefrontal cortex neurons and glia


title: iPS11_pSin_EGFRv3p53R175h_3

description: EGFRvIII + TP53-R275H over-expression


title: Three_cell_lines_mixing

value: Human  B-Lymphocyte/Human embryonic kidney/Human breast cancer


title: iPS11_pSin_EGFRv3p53R175h_2

description: EGFRvIII + TP53-R275H over-expression


title: MCF7

value: Human breast cancer


title: genomic DNA from Liver from OldHetRec4

description: Old heterochronic recovery

source_name: Liver from OldHetRec4


title: HEK293

value: Human embryonic kidney


title: iPS11_pSin_EGFRv3_1

description: EGFRvIII over-expression

source_name: human foreskin


title: GM12878

value: Human  B-Lymphocyte


title: genomic DNA from Liver from OldHetRec2

description: Old heterochronic recovery

source_name: Liver from OldHetRec2

value: C57BL/6 WT


title: 5_ECFC_D3_CD34Low

city: Paris-cedex 10

first: Antonio

middle: José

last: Alberdi

state: Ile-de-France

address: 1, Av Claude Vellefaux

department: Institut de REcherche Saint Louis

institute: Université Paris Cité

hyb_protocol: GeneChip® WT Kit Affymetrix

scan_protocol: GeneChip® WT Kit Affymetrix

data_processing: Trancriptome Analysis Console Affymetrix

label: biotin

source_name: umbilical cord blood

label_protocol: GeneChip® WT Kit Affymetrix

growth_protocol: Peripheral Blood Mononuclear Cells (PBMC) were isolated by centrifugation on Lymphocyte Separation Medium (Eurobio Scientific), and were plated in 6 well culture dishes (Falcon, Corning, USA) coated with collagen I (Collagen Type I Solution from rat tail, Sigma-Aldrich, USA) at a density of 1x105  cells/cm2 , in EGM2-mv culture medium (Lonza, USA). The medium was renewed twice a week, until the appearance of adherent cell colonies.

extract_protocol: RNeasy Plus Mini Kit (Qiagen, Germany)

tag: cell marker

value: endothelial colony-forming cell

tag: cell population


title: genomic DNA from Liver from OldHetRec3

description: Old heterochronic recovery

source_name: Liver from OldHetRec3


title: genomic DNA from Liver from OldHetRec5

description: Old heterochronic recovery

source_name: Liver from OldHetRec5


title: iPS11_pSin_p53R175H_3

description: TP53-R275H over-expression


title: 3_ECFC_D2_CD34Low


title: iPS11_pSin_p53R175H_2

description: TP53-R275H over-expression


title: 2_ECFC_D1_CD34High


title: CFs, IRX2_3

city: Wuhan

first: Zhen-Guo

last: Ma

state: Hubei

address: No.238 Jiefang Road

institute: Renmin Hospital fo Wuhan University

data_processing:
After cluster generation with TruSeq PE Cluster Kit v3-cBot-HS (Illumina), the library preparations were sequenced on an Illumina HiSeq platform, and paired-end reads were generated
The high-quality clean data were aligned to a mouse genome (mm10) with HISAT2
Low-quality reads were removed with FASTX-Toolkit
Differentially expressed gene (DEG) analysis between the two groups was conducted with the DESeq2 R package
RNA-seq and subsequent analyses were performed by Novogene (Beijing, China).
Assembly: mm10
Supplementary files format and content: gene_count.txt, gene_fpkm.txt

source_name: Heart

extract_protocol:
Total RNA was extracted with TriZol, and RNA degradation and potential contamination were determined with 1% agarose gels.
Library construction was performed with a NEBNext® UltraTM RNA Library Prep Kit Illumina® (NEB, USA) with 3 µg RNA per sample following the manufacturer’s recommendations. Library quality was evaluated with an Agilent Bioanalyzer 2100 system. After cluster generation with TruSeq PE Cluster Kit v3-cBot-HS (Illumina), the library preparations were sequenced on an Illumina HiSeq platform, and paired-end reads were generated.

value: Heart

value: Mouse cardiac fibroblast

value: IRX2 knockdown

value: Ang II treatment


title: genomic DNA from Liver from OldHet5

description: Old heterochronic parabiosis

source_name: Liver from OldHet5

value: Female

value: Liver


title: genomic DNA from Liver from OldHet4

description: Old heterochronic parabiosis

source_name: Liver from OldHet4


title: rtel1-3-k27m3-2

data_processing:
For all libraries: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with default parameters.
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.2b (Dobin et al 2013) retaining multi-mapped reads mapping up to 10 positions. Subsequent read counting was performed with featureCounts version 2.0.0 (Liao, Smyth, and Shi 2014) on the TAIR10 TE and PCG annotations. Normalization and differential analyses were done using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) with default parameters. Only loci with Benjamini-Hochberg adjusted p-values < 0.05 and with a log2-fold change ≥ 1 or ≤ − 1 were considered differentially expressed.
Assembly: TAIR10 (Araport11 annotation)
Supplementary files format and content: RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins. ChIP-seq: bigWig format files with normailzed read densities (Reads Per Genomic Content) calculated in 1 bp bins.

source_name: 14-day-old seedlings

growth_protocol: Plants were grown on soil in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol: none provided

value: 14-day-old seedlings

tag: antibody

value: anti-H3K27me3 (C15410069, Diagenode)


title: rtel1-3-k27m3-1


title: 1_ECFC_D1_CD34High

tag: cell type


title: iPS11_pSin_EGFRv3_3

description: EGFRvIII over-expression

value: male

value: induced pluripotent cell line

value: glioblastoma


title: L5_k27m3-2


title: CFs, IRX2_2


title: CFs, IRX2_1


title: iPS11_pSin_EGFRv3_2

description: EGFRvIII over-expression


title: iPS11_pSin_Gli1_3

description: Gli1 over-expression

value: meduloblastoma


title: 4_ECFC_D3_CD34High


title: iPS11_pSin_Gli1_2

description: Gli1 over-expression


title: genomic DNA from Liver from OldHet3

description: Old heterochronic parabiosis

source_name: Liver from OldHet3


title: iPS11_pSin_Cmyc_3

description: cMyc over-expression


title: CFs, GFP_3

value: WT


title: rtel1-3-MMC-r2

treatment_protocol: Plants were grown on Murashige and Skoog medium supplemented with 2.5mg/l mitomycin C (M0503; Sigma-Aldrich)  in long-day conditions (16h light, 8h dark) at 23°C

value: 2.5 mg/l mitomycin C (M0503; Sigma-Aldrich)


title: genomic DNA from Liver from OldHetRec1

description: Old heterochronic recovery

source_name: Liver from OldHetRec1


title: genomic DNA from Liver from OldHet1

description: Old heterochronic parabiosis

source_name: Liver from OldHet1


title: genomic DNA from Liver from OldHet2

description: Old heterochronic parabiosis

source_name: Liver from OldHet2


title: iPS11_pSin_Cmyc_2

description: cMyc over-expression


title: CFs, GFP_2


title: 6_ECFC_D4_CD34Low


title: genomic DNA from Liver from OldIsoRec5

description: Old isochronic recovery

source_name: Liver from OldIsoRec5


title: iPS11_pSin_Blank_3

description: pSin-empty vector

value: blank


title: CFs, GFP_1


title: genomic DNA from Liver from OldIsoRec4

description: Old isochronic recovery

source_name: Liver from OldIsoRec4

value: C57BL/6 WT


title: rtel1-3-NT-r2

extract_protocol: Total RNA was extracted from 14-day-old seedlings using NucleoSpin RNA Plus kit (MACHEREY-NAGEL)


title: iPS11_pSin_Blank_2

description: pSin-empty vector


title: iPS11_wt_3

description: wild type

value: wild type


title: L5-MMC-r2


title: lung MHCIIlow, CI, rep1

city: Chengdu

first: Teng

address: No.17 People's South Road

institute: sichuan university

data_processing:
Before applying any data filtering criteria, RNA-Seq reads were adapter trimmed using Trim Galore (v0.6.7) for removing low-quality data, and FastQC (v0.11.9) software was used to assess data quality.
Reads were mapped to the mouse reference genome (mm10) using HISAT2 software (v2.2.1).
The mapped reads were assembled into transcripts or genes by featureCounts (v2.0.2) software and genome annotation (mm10.gtf).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mapped reads for each Sample

source_name: Lung

extract_protocol:
For RNA extraction, a 1% agarose gel was used to detect RNA degradation and contamination.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530L) and index codes were added to the attribute sequences of each sample and sequenced using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, PE-401-3001) on the cBot Cluster Generation System to cluster the index-coded samples.

value: Lung

value: cells

value: primary cells

value: tumor-bearing


title: lung MHCIIlow, CI, rep3


title: lung MHCIIhi, CTRL, rep3


title: L5-MMC-r1


title: iPS11_wt_2

description: wild type


title: iPS11_pSin_EGFRvIII_p53R175H_1

description: EGFRvIII + TP53-R275H over-expression


title: rtel1-3-MMC-r1


title: L5-NT-r2


title: L5-NT-r1


title: lung MHCIIhi, CTRL, rep2


title: rtel1mom1_RNA_setB_rep2

extract_protocol: Total RNA was extracted from 16-day-old seedlings using RNAzol (EUROMEDEX)

value: rtel1-3 mom1-2


title: iPS11_pSin_p53R175H_1

description: TP53-R275H over-expression


title: blood MHCIIhi, rep3

source_name: Blood

value: Blood

tag: neutrophils

value: MHCIIhi


title: lung MHCIIhi, CTRL, rep1


title: iPS11_pSin_cMyc_1

description: cMyc over-expression

source_name: human foreskin


title: rtel1mom1_RNA_setB_rep1

value: 14-day-old seedlings


title: blood MHCIIhi, rep2


title: iPS11_pSin_Blank_1

description: pSin-empty vector

value: male


title: Fusion mitosis biorep 3

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

country: Japan

institute: Waseda Institute for Advanced Study

data_processing:
basecalling with bcl2fastq v2.20.0
alignment using BWA 0.7.17
processing using Juicer 1.5.6
Genome_build: Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Juicer inter_30.hic file

organism: Schizosaccharomyces pombe

source_name: Fusion mitosis_cell culture

growth_protocol: Cells were grown in EMM supplemented with glutamate. Then, cells were transfered to Rich YE5s media and incubated for 4 hours at 25 ºC.

extract_protocol:
Crosslinked chromatin was digested by DpnII. The sticky ends were filled in by Biotin-14-dATP and the other dNTPs. Proximal ligation was performed, followed by DNA recovery by Biotin-Streptavidin interaction.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.

treatment_protocol: Cells were crosslinked with 0.5 % formaldehyde for 30 minutes at 25 ºC.

tag: strain

tag: cell cycle

value: mitosis arrested cells

tag: restriction enzyme

value: DpnII

tag: biological replicate


title: genomic DNA from Liver from OldIso3

description: Old isochronic parabiosis

source_name: Liver from OldIso3

tag: age (years)

tag: mouse strain

tag: Sex

value: Female

tag: mouse id

value: Liver


title: genomic DNA from Liver from OldIso5

description: Old isochronic parabiosis

source_name: Liver from OldIso5

tag: tissue


title: genomic DNA from Liver from OldIsoRec2

description: Old isochronic recovery

source_name: Liver from OldIsoRec2


title: genomic DNA from Liver from OldIso2

description: Old isochronic parabiosis

source_name: Liver from OldIso2


title: genomic DNA from Liver from OldIsoRec1

description: Old isochronic recovery

source_name: Liver from OldIsoRec1


title: blood MHCIIhi, rep1

tag: cell line

value: WT


title: iPS11_wt_1

description: wild type

tag: gender

value: induced pluripotent cell line

tag: disease state


title: genomic DNA from Liver from OldIsoRec3

description: Old isochronic recovery

source_name: Liver from OldIsoRec3

value: C57BL/6 WT


title: genomic DNA from Liver from OldIso4

description: Old isochronic parabiosis

source_name: Liver from OldIso4


title: Fusion mitosis biorep 2


title: Fusion mitosis biorep 1


title: genomic DNA from Liver from OldIso1

description: Old isochronic parabiosis

source_name: Liver from OldIso1


title: mom1_RNA_setB_rep1

source_name: 14-day-old seedlings

tag: genotype


title: lung MHCIIlow, rep3

value: MHCIIlow

tag: treatment


title: Fusion interphase biorep 3

source_name: Fusion interphase_cell culture

value: interphase arrested cells


title: iPS11_pSin_Gli1_1

description: Gli1 over-expression

value: meduloblastoma


title: lung MHCIIlow, rep2

value: Lung

value: cells

value: primary cells


title: rtel1_RNA_setB_rep2


title: Fusion interphase biorep 2


title: mom1_RNA_setB_rep2


title: rtel1_RNA_setB_rep1


title: C. elegans, 5-Ph-IAA D1, rep4

city: Nanjing

first: Xiao

last: Zang

address: 12 Xuefu Rd, Pukou

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
Reads were aligned to the C.elegans genome (version Wbcel235) using TopHat2 with parameters -r 30 -G -p 8 --microexon-search --library-type fr-unstranded.
Raw counts of sequencing reads were generated by using the python script HTSeq.
Differential expression and dataset normalization were performed using the Bioconductor package DESeq2.
Assembly: Wbcel235
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms are fed on NGM plates with OP50 till L4, extracted on D1.

extract_protocol:
RNA samples were extracted by  Trizol reagent (Takara#9108Q) and Direct-zol RNA MiniPrep Kit (Zymo#R2052). 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme #NR605-01).

treatment_protocol: L4 worms are treated with etoh or 5-Ph-IAA for 24 hours.

value: whole worm

value: neuronal DAF-15 AID worm


title: C. elegans, etoh D1, rep4

value: etoh


title: Fusion interphase biorep 1


title: C. elegans, 5-Ph-IAA D1, rep3


title: L5_RNA_setB_rep2

value: 14-day-old seedlings


title: lung MHCIIhi, rep3

value: MHCIIhi

value: tumor-bearing


title: rtel1-3, BS-seq, rep2

source_name: seedlings

extract_protocol:
DNA was extracted from 16-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Bisulfite conversion, library preparation and sequencing were performed at the Beijing Genomics Institute (Hong Kong). Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were sequenced PE 100 bp on HiSeq X Ten (Illumina)

tag: developmental stage

value: 16-day-old seedlings

value: seedling


title: C. elegans, etoh D1, rep3


title: lung MHCIIhi, rep2

tag: cell type

value: WT


title: C. elegans, 5-Ph-IAA D1, rep2


title: rtel1-3, BS-seq, rep1


title: L5_RNA_setB_rep1


title: C. elegans, etoh D1, rep2


title: lung MHCIIhi, rep1

tag: neutrophils


title: YPD_18°C replicate 3

city: Palaiseau

first: Nicolas

last: Lapalu

address: 22 place de l'agronomie

department: SPE

institute: INRAE

description: all_transcripts_counts_filter.sort.ggb.gff.gz

data_processing:
Iso-Seq raw data were processed with the Iso-Seq V3.2 pipeline from PacBio providing polished Circular Consensus Sequences (CCS). CCS were then mapped to the Z. tritici IPO323 genome with Gmap (2019-01- 31) and unmapped, low mapping quality (≤0) or multi-mapped CCS were filtered out.
RNA-Seq data were cleaned and trimmed with Trimomatic (v 0.36). The cleaned sequences were then mapped to Z.tritici IPO323 genome using STAR (v 2.5.1b, --alignIntronMin 4 --alignIntronMax 5000 -- alignMatesGapMax 5000). Wig files of uniquely mapped reads were converted in BigWig files with wigToBigWig (v4). StringTie (v2.1.1) were then used to assemble the mapped RNA-Seq reads into transcripts with different parameters depending of the depth sequencing of libraries and type (-m 150 --rf --g 0 -f 0.1 -a 10 -j 2 or -j 4). Trinity script inchworm_transcript_splitter.pl (version 2.8.5) was used to split the transcripts with non-uniform coverage based on the jaccard clip method. Clipped transcripts were extracted with home-made script and clustered with Stringtie and associated bam files to obtain TPM counts. All libraries were concatenated into one gff file without merge to avoid loss of information by fusion of small transcripts into larger ones due to the large number of genes in Z.tritici with overlapping UTRs.
The CupCake package (v10.0.0, https://github.com/Magdoll/cDNA_Cupcake) filtered the isoforms, removing the less expressed and degraded ones using the following tools: collapse_isoforms_by_sam.py, get_abundance_post_collapse.py, filter_by_count.py, filter_away_subset.py. Readthrough transcripts were removed using the previous annotation (MPI, JGI, CURTIN, RRES) with BEDTools intersect with an overlap 100% full CDS (-F 1.0) and same strand (-s)) of at least 2 CDS. Mitochondrial transcripts were filtered out as well. Then, all libraries were processed with chain_samples.py from CupCake and clustered for stringent selection. Splicing junctions obtained by STAR (SJ.out.tab files) from Illumina RNA-Seq libraries were used to filter out isoform transcripts with unsupported junctions. Finally, long-read transcripts fully spanning Transposable Element were removed with BEDTools, giving the final set of transcript evidence.
Assembly: Z.tritici IPO323
Supplementary files format and content: gff format file with isoforms from Iso-Seq data
Supplementary files format and content: gff format file with all transcripts assembles from RNA-Seq data

organism: Zymoseptoria tritici

source_name: mycelium

growth_protocol: The reference isolate of Z. tritici IPO323 was stored at -80°C as a yeast-like cell suspension (10e7-8 cells/mL in 30% glycerol). Z. tritici was grown at 18°C in the dark on Yeast extract Peptone Dextrose (YPD) agar, Potato Dextrose Broth (PDB). For RNA production, Z. tritici IPO323 isolate (4 days old yeast-like cells diluted to 10-5 cells/mL final) was cultivated in 75 mL agitated liquid cultures (500 mL Erlen flasks, 150 rpm) at 18°C in the dark for 4 days. Different media were used including Glucose-NO3 synthetic medium defined as MM-Zt (E. Marchegiani et al, 2015). MM-Zt was modified by replacing glucose (10 g/L) by different carbon sources (Xylose, Mannitol, Galactose, Sucrose at 10 g/L)). Histone Deacetylase inhibitors such as trichostatin (TSA, Sigma ref, 1 microM final) and SAHA (SAHA, Sigma ref, 1 mM final) were added to MM-Zt. The composition of complex media (YPD, PDB, AE) was already described (G. Scalliet et al, 2012). Cultures of IPO323 in YPD and PDB were performed at 18°C and 25°C, while AE cultures were performed only at 18°C. A total of 14 culture conditions were used for RNA production. All cultures for RNA-Seq were performed in triplicates.

extract_protocol:
Cultures were centrifuged at 3000 rpm for 10 minutes and mycelium pellet washed with water was frozen with liquid nitrogen. Frozen mycelium was lyophilized and kept at -80°C until extraction. RNAs were extracted using Quiagen Plant RNAeasy Kit according to manufacturer protocol (Ref. 74904, Quiagen France SAS, Courtaboeuf, France).
PacBio Iso-Seq libraries preparation and sequencing was performed by the INRAE platform Gentyane (http://gentyane.clermont.inrae.fr). SMARTer PCR cDNA Synthesis Kit (ref 634926, Clontech, Mountain View, CA, USA) was used for polyA primed first cDNA strand synthesis followed by optimized PCR amplification and library preparation using SMRTbell Template Prep Kit (ref 101-357-000, Pacific Bioscience, Menlo Park, CA, USA) according to manufacturer protocols. The cDNA libraries were prepared without size selection and bar-coded for multiplexing. Sequencing was performed on a PacBio SEQUEL (version 1). Illumina RNA-seq single stranded libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490, New England BioLabs, Ipswich, Massachusetts, USA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765, New England BioLabs, Ipswich, Massachusetts, USA). Custom 8 bp barcode was added to each library during the preparation process. Sample were pooled and cleaned with magnetic beads included in the library preparation kit. The pool was run on a lane of Illumina HiSeqX (Illumina, San Diego, California, USA) using a 150-cycle paired end run

value: mycelium

tag: strain

tag: growth media

value: YPD


title: YPD_18°C replicate 2


title: C. elegans, 5-Ph-IAA D1, rep1