title: d4PGCLC_ATAC_2

data_processing:
ATAC-seq data processing including public data was performed as previously described (Buenrostro et al., 2013) with minor modifications. First, adaptor sequences were trimmed from the reads using trim galore!.
These reads were aligned using Bowtie2 v2.3.4.1 to GRCm38p3 with the “--very-sensitive -X 2000” option.
The properly mapped reads with the flag (99, 147, 83 or 163) were extracted by awk, and mitochondrial reads were excluded.
Duplicated reads were removed using MarkDuplicates command of Picard Tools v2.18.23.
These de-duplicated reads were then filtered for high quality (MAPQ≧30).
The reads whose insert size was less than 100 bp were extracted as nucleosome free region (NFR) reads.
Bed files for downstream analysis were generated by the bamtobed command of BEDTools v2.29.2 with the “-bedpe” option.
Peak calling was performed using MACS v2.1.1 with the “--nomodel --shift -100 --extsize 200 --keep-dup all” option after shifting NFR reads with the offset by +4bp in the + strand and by -5bp in the - strand.
Then, confident peak sets in each cell type were obtained by IDR method (https://www.encodeproject.org/software/idr/) using two replicates.
Genome_build: mm10
Supplementary_files_format_and_content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” option of deepTools v3.5.0. The blacklist regions (https://www.encodeproject.org/files/ENCFF999QPV/)  were excluded.
Supplementary_files_format_and_content: bed files contain peaks defined by MACS2 followed by IDR method.

extract_protocol:
ATAC-seq experiment was performed as described previously (Corces et al., 2017; Buenrostro et al., 2013) with minor modifications. We used FACs-sorted viable cells for mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs, d4 mPGCLCs, and d4c7 mPGCLCs, and FACS-sorted AAG-positive cells for GSCs and GSCLCs. 50,000 cells were permeabilized in cold lysis buffer 1 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin (Promega)) for 3 min followed by addition of 1 ml of cold lysis buffer 2 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20). Nuclei were centrifuged and resuspended with a 50 ul of transposase reaction mixture (25 ul of 2xTD buffer (Illumina, 20034197), 2.5 ul of Transposase (Illumina, 20034197), 16.5 ul of PBS, 0.5 ul of Digitonin, 0.5 ul of Tween-20, 5 ul of DDW). After incubation at 37°C for 30 min, the tagged DNA was purified using the Minelute PCR purification kit (QIAGEN).
The purified DNA was amplified 8 cycles by a PCR reaction (NEB, M0541S) followed by size selection using AMPure XP beads (Corning) to remove primer dimers.

value: DBA/2 x C57BL/6


title: BL28

status: Public on Jun 15 2022

type: SRA

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

country: USA

institute: Houston Methodist Hospital

library_source: genomic

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg19  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for all sample with raw reads count summarised to genebody region.

molecule: genomic DNA

organism: Homo sapiens

source_name: Acute Myeloid Leukemia_Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).

tag: diagnosis

value: Acute Myeloid Leukemia

tag: training/validation group in diagnostic model

value: Training

tag: training/validation group in survival analysis

value: Test

tag: age

tag: gender

value: male

tag: vital status (0

value: censored; 1:event):1

tag: survival (months)


title: d4PGCLC_ATAC_1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

organism: Mus musculus

growth_protocol: The BDF1-2-1 mouse mESCs bearing Blimp1-mVenus and Stella-ECFP (BVSC) transgenes (Ohta et al., 2021) were cultured as described previously (Hayashi et al., 2011). Briefly, mESCs were maintained in N2B27 medium supplemented with PD0325901 (0.4 uM) (Stemgent), CHIR99021 (3 uM) (Bio Vision), and leukemia inhibitory factor (LIF) (1000 U/ml) (Merck Millipore) on a 12-well plate coated with poly-L-ornithine (0.01%) (Sigma) and laminin (10 ng/ml) (BD Bioscience). In this study, all cells were cultured at 37°C under an atmosphere of 5% CO2 in air. Induction of EpiLCs and PGCLCs was performed as described previously (Hayashi et al., 2011) with minor modifications. Briefly, the EpiLCs were induced by plating 8 x 104 mESCs on a well of 12-well plate coated with human plasma fibronectin (16.7 mg/ml) (Merck Millipore) in N2B27 medium containing activin A (20 ng/ml) (Peprotech), bFGF (12 ng/ml) (Invitrogen), and KSR (1%) (Gibco). PGCLCs were induced from d2 EpiLCs (2 days after induction) under a floating condition in wells of a low-cell-binding U-bottom 96-well plate in GMEM medium (Thermo Fisher Scientific) containing 15% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific) and 2mM L-glutamin (Thermo Fisher Scientific) supplemented with BMP4 (500 ng/ml) (RSD), LIF (1000 U/ml) (Merck Millipore), SCF (100 ng/ml) (RSD), EGF (50 ng/ml) (RSD). The expansion culture of PGCLCs was performed as previously described (Ohta et al., 2021). Briefly, following incubation in TrypLE™ Express (Gibco) for 10 min, the aggregates of d4 mPGCLCs (PGCLCs induced for 4 days) were dissociated into single cells by rigorous pipetting. Subsequently, BV-positive cells were sorted with a FACSAriaIII cell sorter. Purified d4 mPGCLCs were cultured on m220-5 cells as the feeder cells in GMEM (Gibco) containing 10% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 2.5% FBS (Hyclone), SCF (100 ng/ml) (RSD), 10 uM forskolin (Sigma), 10 uM rolipram (abcam), 5 uM CsA (Sigma). Half of the culture medium was changed every two days. GSCs and GSCLCs bearing Acro/Act-EGFP (AAG) transgenes (Ishikura et al., 2016) were cultured as described previously (Ishikura et al., 2016). Briefly, cells were cultured in Stempro-34 SFM supplemented with Stempro Supplement (Gibco), with 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 1% FBS (Hyclone), 1xMEM vitamin solution (Thermo Fisher Scientific), 5.0mg/ml AlbMAXI (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 1x Insulin-Transferrin-Selenium (ITS-G) (Gibco), 10 ng/ml bFGF (Invitrogen), 20 ng/ml GDNF Rat Recombinant (RSD), 20 ng/ml EGF (RSD), and 1000 U/ml LIF (Merck Millipore) in a well of 6-well plate on mouse embryonic fibroblast cells (MEFs) as feeder cells. Half of the medium was replaced every two or three days.

tag: cell type

tag: genotype

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

tag: strain


title: d2PGCLC_ATAC_2


title: L14

value: female

value: censored; 1:event):0


title: L22


title: d2PGCLC_ATAC_1


title: ESC_Input_3

data_processing:
Single-end reads were processed using Trim-Galore v0.4.1/cutadapt v1.9.1 to remove adaptor sequence.
The truncated reads were then aligned to (GRCm38p3) using Bowtie2 v2.3.4.1 with the “-very-sensitive” option.
The reads aligned to chromosome 1 to 19, X, Y were transformed to BAM format by SAMtools v1.7. BED files were obtained from the BAM files using the bamtobed command of BEDTools v2.29.2.
Genome_build: mm10
Supplementary_files_format_and_content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” or bamcompare for IP/Input command with the “--pseudocount 1 -bs 1000” option of deepTools v3.5.0. In both cases, the blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary_files_format_and_content: bed files describe peaks or domains files detected by macs2 or epic2, respectively

source_name: ESC

extract_protocol:
The ChIP-seq library preparation was performed as previously described (Lee et al., 2006) with minor modifications. We used harvested mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs and d4c7 mPGCLCs samples, and FACS-sorted AAG-positive cells for GSCs and GSCLCs samples. Briefly, the harvested cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific)/PBS for 10 min at RT and quenched with 125 mM glycine. Crosslinked cells were lysed consecutively using LB1 (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% Triton-100, protease inhibitors (Roche, 11873580001)), LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease inhibitors), and LB3 (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors) and then sonicated by picoruptor to achieve a mean DNA fragment size of around 200-400 bp. Sonicated chromatin was incubated with  Dynabeads M-280 Sheep anti Mouse IgG beads (Thermo Fisher Scientific) or Dynabeads ProteinA beads (Thermo Fisher Scientific) for 35 min at 4°C for preclear. Precleared chromatin was then incubated with antibody that was preincubated with the appropriate Dynabeads in 0.5% BSA (Gibco) in PBS as follows: chromatin equivalent of 5 x 105 cells with anti-H3K4me1 (rabbit monoclonal, CST, D1A9, 5 μl),  anti-H3K9me2 (mouse monoclonal, MBL, MABI0317, 5 μl), anti-H3K27me3 (mouse monoclonal, MBL, MABI0323, 5 μl); 1 x 106 cells with anti-H3K4me3 (mouse monoclonal, MBL, MABI0304, 5 μl), anti-H3K9me3 (mouse monoclonal, MBL, MABI0318, 5 μl), anti-H3K36me2 (rabbit monoclonal, CST, C75H12, 5 μl), anti-H2AK119ub1 (rabbit monoclonal, D27C4, 10 μl), anti-H3K36me3 (rabbit polyclonal, Active Motif, 61101, 2 μl); 1.5 x 106 cells with anti-H3K27ac (mouse monoclonal, MBL, MABI0309, 5 μl); 2 x 106 cells with anti-CTCF (rabbit monoclonal, CST, D31H2, 5 μl), anti-Laminb1 (rabbit polyclonal, Proteintech, 12987-1-AP, 10 μl); 3 x 106 cells with anti-Setdb1 (rabbit ployclonal, Proteintech, 11231-1-AP, 10 μl); 4 x 106 cells with anti-Ring1b (rabbit monoclonal, CST, D22F2, 10 μl); and 4.5 x 106 cells with anti-Rad21 (rabbit monoclonal, ab992, 5 μl). After incubation for 6 h at 4°C, the beads were washed 4 times in wash buffer 1 (20 mM Tris-HCl pH8.0, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 0.1% SDS), 2 times in wash buffer 2 (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.1% SDS), and 2 times in wash buffer 3 (10 mM Tris-HCl  pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% Na-Deoxycolate, 1% NP-40). Then, the washed beads were eluted in 10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 1% SDS, and crosslinks were reversed overnight at 65°C. Input samples were treated in a similar manner. The following day, IP and Input samples were incubated with RNaseA (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific). IP or Input DNA was purified using QIA quick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA) following the manufacturer’s guidelines. An adaptor kit (Fastgene, FG-NGSAD24) was used for the sample indexes. The average size and concentration of libraries were analyzed using LabChIP GX (PerkinElmer) and KAPA library Quantification kit (KAPA), respectively.

value: ESC

tag: controlled by


title: 3B-10

value: Train


title: Rep2-EV-pRXEG1:RXEG1synΔ90-95/Δ786-792ΔCT-1

city: Nanjing

first: Yan

last: Wang

address: No.1 Weigang Road

department: Plant Pathology

country: China

institute: Nanjing Agricultural University

library_source: transcriptomic

data_processing:
Removing reads containing sequencing adapter;  Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; Removing reads whose unknown base ('N' base) ratio is more than 5%
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) . After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs),
Assembly: Nicotiana benthamiana draft genome sequence v1.0.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Nicotiana benthamiana

source_name: 12-day-old seedlings

extract_protocol:
RNA was harvested using E.Z.N.A.® Total RNA extraction Kit (Omega). 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit(3.0) following manufacturer's protocols.

value: rxeg1 knockout mutant

tag: tissue

value: 12-day-old seedlings

tag: treatment

value: mock

tag: time

value: 3 h


title: 3B-46


title: Rep2-EV-pRXEG1:RXEG1synΔ90-95/Q786AK791AΔCT-1


title: Rep2-XEG1-pRXEG1:RXEG1synΔ90-95/Q786AK791AΔCT-1

value: XEG1 protein


title: 3B-33


title: 3B-26

value: censored; 1:event):NA


title: Rep2-EV-pRXEG1:RXEG1synΔCT-2


title: BL31


title: BL11


title: Rep2-XEG1-pRXEG1:RXEG1synΔCT-1


title: L21


title: 3B-2


title: Rep2-EV-pRXEG1:RXEG1synΔCT-1


title: Rep2-XEG1-pRXEG1:RXEG1synΔ90-95/Δ786-792ΔCT-1


title: Rep2-XEG1-sobir1/sobir1-like

value: sobir1/sobir1-like knock out mutant


title: Rep2-EV-sobir1/sobir1-like


title: BL75

value: Acute Myeloid Leukemia


title: Rep2-XEG1-pRXEG1:RXEG1synΔCT-2


title: Rep2-XEG1-rxeg1


title: 3B-50

value: Training


title: Rep2-EV-rxeg1


title: L32

value: Test


title: BL18

value: male


title: Rep2-XEG1-WT

value: wild type


title: L29

value: censored; 1:event):1


title: Colorectal tissue_17hr_65°C_rep2

type: RNA

city: Chang Sha

first: Shan

last: Zeng

address: 87 Xiangya Road, Changsha city, Hunan Province, China

institute: Xiangya Hospital, Central South University

description: Gene expression after 17hr，65°C

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 1 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

source_name: Colorectal tissue，17hr，65°C

label_protocol: The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

treatment_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA.

value: Colorectal tissue

tag: Sex


title: Colorectal cancer tissue_17hr_65°C_rep1

description: Gene expression after 17hr，65°C

source_name: Colorectal cancer tissue，17hr，65°C

value: Colorectal cancer tissue


title: 3B-15


title: M10.1_Combo

city: Barcelona

first: Roger

last: Esteban-Fabró

state: Barcelona

address: Rosselló, 149-153

country: Spain

institute: IDIBAPS

description: Gene expresion data from fresh-frozen tumour

hyb_protocol: Total mRNA was prepared for hybridization following the manufacturer’s protocols. Samples were hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix) also following the manufacturer protocols.

scan_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations from the Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232).

data_processing: Mouse expression data were retrieved, quality checked and processed through RMA using the R package affy (v.1.62.0). After quality filtering, probe-gene correlates were identified with the R package htmg430pmprobe (v.2.18.0).

label: Biotin

source_name: Murine HCC subcutaneous tumour

label_protocol: Double-stranded cDNAs were synthesized from total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

growth_protocol: 5 million Hepa1-6 cells suspended in Matrigel (50% v/v) were implanted into the right flank of male 5-week old C57BL/6 mice.

extract_protocol: Total RNA was extracted from FF samples using QIAGEN RNeasy Mini Kit and quantified using Nanodrop. 50 ng of total RNA was submitted for whole-genome expression profiling using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

treatment_protocol: When tumours reached 200-300mm3, animals were randomly assigned to receive a) Placebo: Hamster IgG 10 mg/kg i.p. every 3 days for a total of 5 doses; b) Cabozantinib: 30 mg/kg p.o. daily until the end of the study; c) Anti-PD1: Hamster anti-murine PD1 mAb J43 (BioXCell) i.p. at 10 mg/kg every 3 days for a total of 5 doses; or d) Combination of cabozantinib with anti-PD1. Animals were culled at day 14 and tumours were extracted for the transcriptomic assessment.

tag: disease state

value: HCC

value: Subcutaneous tumour


title: Rep2-EV-WT


title: Colorectal cancer tissue_17hr_65°C_rep3

description: Gene expression after 17hr，65°C


title: M4.3_Combo


title: Colorectal tissue_17hr_65°C_rep3

description: Gene expression after 17hr，65°C


title: Colorectal tissue_17hr_65°C_rep1

description: Gene expression after 17hr，65°C


title: Colorectal cancer tissue_17hr_65°C_rep2

description: Gene expression after 17hr，65°C


title: Rep1-XEG1-pRXEG1:RXEG1synΔ90-95/Δ786-792ΔCT-1

value: rxeg1 knockout mutant


title: M19.1_Combo


title: M18.1_Combo


title: M18.4_Cabo

value: Cabozantinib


title: M11.2_Cabo


title: Rep1-EV-pRXEG1:RXEG1synΔ90-95/Δ786-792ΔCT-1

value: 12-day-old seedlings

value: mock


title: M15.1_Cabo


title: L7


title: M17.4_AntiPD1


title: M11.1_Cabo


title: M3.1_Cabo


title: M12.4_AntiPD1


title: M17.1_Placebo

value: Placebo


title: Rep1-XEG1-pRXEG1:RXEG1synΔ90-95/Q786AK791AΔCT-1

value: XEG1 protein

value: 3 h


title: M12.1_Placebo


title: M14.4_Placebo


title: L20

value: Acute Myeloid Leukemia

value: female

value: censored; 1:event):NA


title: M16.1_Anti_PD1


title: Rep1-EV-pRXEG1:RXEG1synΔ90-95/Q786AK791AΔCT-1


title: M5.1_Placebo


title: BL3

value: Training

value: Train

value: male

value: censored; 1:event):0


title: BL115

value: censored; 1:event):1


title: Rep1-EV-pRXEG1:RXEG1synΔCT-2


title: 3B-12


title: Liver_HCC_Nontumor_Adjacent_99

description: Gene expresion data from fresh-frozen non-tumour adjacent tissue

hyb_protocol: Total mRNA was prepared for hybridization using the GeneChip 3’ IVT Pico Kit assay (Thermo Fisher) following the manufacturer’s protocols. Samples were hybridized to the Human Genome U219 Array (Affymetrix) also following the manufacturer protocols.

data_processing: Affymetrix CEL files that passed the quality control were normalized using the ExpressionFileCreator module from GenePattern using the Robust Multi-array Average algorithm with background correction. Subsequently, the dataset was collapsed using the relative CHIP platform and choosing the maximum expression value for the set.

source_name: Non-tumour adjacent liver tissue

extract_protocol: Total RNA was extracted from FF samples using QIAGEN RNeasy Mini Kit and quantified using Nanodrop. 50 ng of total RNA was submitted for whole-genome expression profiling using the Affymetrix Human Genome U219 Array Plate.

treatment_protocol: Fresh frozen samples were obtained through macrodissection of the surgical specimens after resection of HCC tumours in previously untreated patients.

value: HCC

value: Non-tumour adjacent (liver)


title: BL9


title: Rep1-XEG1-pRXEG1:RXEG1synΔCT-1

value: rxeg1 knockout mutant


title: 3B-31


title: Rep1-XEG1-pRXEG1:RXEG1synΔCT-2


title: Rep1-EV-pRXEG1:RXEG1synΔCT-1


title: Rep1-XEG1-sobir1/sobir1-like

value: sobir1/sobir1-like knock out mutant


title: BL59

value: Test


title: Liver_HCC_Nontumor_Adjacent_9


title: BL95


title: Liver_HCC_Nontumor_Adjacent_93


title: Rep1-EV-sobir1/sobir1-like

value: 12-day-old seedlings

value: mock


title: Liver_HCC_Nontumor_Adjacent_94


title: Liver_HCC_Nontumor_Adjacent_96


title: Liver_HCC_Nontumor_Adjacent_95


title: Liver_HCC_Nontumor_Adjacent_84


title: Liver_HCC_Nontumor_Adjacent_86


title: L37


title: Rep1-XEG1-rxeg1

value: XEG1 protein


title: Liver_HCC_Nontumor_Adjacent_8


title: Rep1-EV-rxeg1

value: 3 h


title: Liver_HCC_Nontumor_Adjacent_72


title: Liver_HCC_Nontumor_Adjacent_63


title: L34

value: Acute Myeloid Leukemia


title: Liver_HCC_Nontumor_Adjacent_70


title: Liver_HCC_Nontumor_Adjacent_81


title: Liver_HCC_Nontumor_Adjacent_7


title: Liver_HCC_Nontumor_Adjacent_64


title: Liver_HCC_Nontumor_Adjacent_75


title: Liver_HCC_Nontumor_Adjacent_6


title: Liver_HCC_Nontumor_Adjacent_68


title: L30


title: BL33


title: Rep1-EV-WT

value: wild type


title: G8-12: pEGFP-N1-injected at 12hpf

state: Jiangsu

address: No.12, Xuefu Road

institute: Qingshun Zhao

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: GRCz10
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: In the 1-cell stage of zebrafish embryos, 8ng/μL pEGFP-N1 was injected, and the embryos of the injected group and the non-injected group were collected when the embryos developed to 1hpf, 6hpf and 12hpf. Add 1mL TRIzol (Invitrogen, USA), store at -80℃

value: TU

tag: developmental stage

value: embryo


title: Liver_HCC_Nontumor_Adjacent_58


title: Liver_HCC_Nontumor_Adjacent_59


title: L24

tag: diagnosis

value: Training

value: censored; 1:event):NA


title: Rep1-XEG1-WT


title: Liver_HCC_Nontumor_Adjacent_62


title: G8-1: pEGFP-N1-injected at 1hpf


title: BL89

value: Control

tag: training/validation group in diagnostic model

value: female


title: L5

tag: training/validation group in survival analysis

value: male


title: C6: un-injected at 6pf


title: BL91

tag: age


title: C12: un-injected at 12hpf


title: G8-6: pEGFP-N1-injected at 6pf


title: Liver_HCC_Nontumor_Adjacent_51

value: HCC

value: Non-tumour adjacent (liver)


title: Liver_HCC_Nontumor_Adjacent_53


title: Liver_HCC_Nontumor_Adjacent_5


title: Liver_HCC_Nontumor_Adjacent_52


title: Liver_HCC_Nontumor_Adjacent_54


title: BL99

tag: gender


title: BL86

tag: vital status (0


title: Liver_HCC_Nontumor_Adjacent_48


title: Liver_HCC_Nontumor_Adjacent_44


title: BL79

tag: survival (months)


title: C1: un-injected at 1hpf


title: GZ35_dorsal skin

city: Berkeley

first: Diana

last: Aguilar Gomez

state: CA

address: 4th floor VLSB, University of California Berkeley

department: Center for Computational Biology

institute: University of California Berkeley

data_processing:
Illumina Casava1.7 (or Casava 2.19)  software used for basecalling.
DESeq2
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample
RSEM for expression quantification
Supplementary_files_format_and_content: Readcount_FPKM.txt
GZvsHSK.Differential_analysis_results.txt:  differential expression results DESeq2
Annotation_Summary.txt:  annotation using different databases

organism: Phrynocephalus versicolor

source_name: dorsal skin

extract_protocol:
Flash tissue frozen on liquid nitrogen, then transferred to dry ice for shipment. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

tag: location

value: Guazhou County, Gansu, China

value: dorsal skin

tag: phenotype

value: non-melanic population GZ


title: Liver_HCC_Nontumor_Adjacent_50


title: Liver_HCC_Nontumor_Adjacent_47


title: Liver_HCC_Nontumor_Adjacent_45


title: Liver_HCC_Nontumor_Adjacent_43


title: Liver_HCC_Nontumor_Adjacent_41


title: Liver_HCC_Nontumor_Adjacent_42


title: Liver_HCC_Nontumor_Adjacent_49


title: Liver_HCC_Nontumor_Adjacent_4


title: GZ40_dorsal skin


title: BL77

value: Test


title: Liver_HCC_Nontumor_Adjacent_36


title: BL69


title: BL68


title: HSK02_dorsal skin

value: Heishankou, Guazhou County, Gansu, China

value: melanic population HSK


title: BL55


title: HSK07_dorsal skin


title: BL78


title: Liver_HCC_Nontumor_Adjacent_40


title: Liver_HCC_Nontumor_Adjacent_33


title: HSK19_dorsal skin


title: Liver_HCC_Nontumor_Adjacent_34


title: BL5


title: Liver_HCC_Nontumor_Adjacent_3


title: Liver_HCC_Nontumor_Adjacent_30


title: Liver_HCC_Nontumor_Adjacent_29


title: Liver_HCC_Nontumor_Adjacent_38


title: Liver_HCC_Nontumor_Adjacent_25


title: Liver_HCC_Nontumor_Adjacent_31


title: Liver_HCC_Nontumor_Adjacent_32


title: TER2-T30

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Raw sequence reads were mapped against the Escherichia coli str. K-12 substr. MG1655, complete genome MTCC 1302 (NCBI GenBank accession number NC_000913) using Segemehl with mapping accuracy set at 100%
Number of reads mapped to each genes was calculated using custom Perl script.
Reads were normalized using VOOM transformation (Log2 normalized read counts) from Limma R package
Differential bene expression was calculated using Limma package
Genome_build: NC_000913
Supplementary_files_format_and_content: Tab-delimited text file includes VOOM transformaed log2 normalized read counts for each samples.

organism: Escherichia coli K-12

source_name: Bacterial cell

extract_protocol:
RNeasy Mini Kit (Qiagen, USA)
Illumina RNA-seq library preparation protocol

tag: strain

value: MTCC 1302

tag: growth stage

value: Mid-log phase

value: L-Ag NPs treatment- 30 min. at 37 °C


title: GZ42_dorsal skin

description: Raw data:  R1 available at SRA.  R2 mate is not available.

tag: tissue


title: BT-549 (TQ- / control)

city: Luzhou

first: Md. Asaduzzaman

last: Khan

state: Sichuan

address: 3-319, Zhongshan road

department: The research center for preclinical medicine

institute: Southwest Medical University

data_processing:
raw data QC with FastQC
reads filtered and mapped to the mm9 genome assembly using Bowtie2 which default parameters.
peaks were called using MACS2 version 2.2.4 with default parameters.
call genes with 2K bandwidth at two side of  each peak with R codes.
genes annotation was performed using ANNOVAR (June 8 2017)
Genome_build: mm9
Supplementary_files_format_and_content: fastq
Supplementary_files_format_and_content: peak

source_name: Breast cancer cells

growth_protocol: BT-549 cells were cultured in DMEM media (Gibco, Thermo Fisher ScientificTM) supplemented with 10-15% fetal bovine serum (FBS) in cell culture dishes or flasks.

extract_protocol:
DNA Lysates were clarified from sonicated nuclei and Anti-MBD1 could precipitate specific genomic region, which are methylated.
Libraries were prepared according to Life's instructions accompanying the DNA Sample Kit (Ion AmpliSeq Library Kit 2.0). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Life primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Ion Torrent S5 following the manufacturer's protocols.

treatment_protocol: BT-549 cells were treated with thymoquinone for 6 h and chromatin immune-precipitation (ChIP) was performed using anti- MBD1 antibody (Abcam, USA).

tag: cell type

value: Triple negative breast cancer

tag: chip antibody

value: anti- MBD1 (#ab2846, Abcam, USA)

tag: treatment

value: thymoquinone untreated (DMSO treated)


title: BL45

value: Control

value: female

value: censored; 1:event):NA


title: BL43

value: male


title: BL38


title: Liver_HCC_Nontumor_Adjacent_19

tag: disease state

value: HCC

value: Non-tumour adjacent (liver)


title: Liver_HCC_Nontumor_Adjacent_23


title: Liver_HCC_Nontumor_Adjacent_12


title: TER2-T05

value: L-Ag NPs treatment- 5 min. at 37 °C


title: BL8

value: Training


title: BL20

value: Test


title: CER2-T30

value: No treatment- 30 min. at 37 °C


title: TER1-T30


title: Liver_HCC_Nontumor_Adjacent_20


title: Liver_HCC_Nontumor_Adjacent_13


title: Liver_HCC_Tumor_99

description: Gene expresion data from fresh-frozen HCC tumour

source_name: HCC tumour tissue

value: Tumour (liver)


title: Liver_HCC_Nontumor_Adjacent_14


title: Liver_HCC_Nontumor_Adjacent_28


title: Liver_HCC_Nontumor_Adjacent_18


title: BT-549 (TQ+)

value: thymoquinone treated


title: Liver_HCC_Nontumor_Adjacent_10


title: BL100


title: Liver_HCC_Tumor_94


title: CER2-T05

value: MTCC 1302

value: Mid-log phase

value: No treatment- 5 min. at 37 °C


title: Liver_HCC_Tumor_96


title: Liver_HCC_Tumor_93


title: CER1-T30


title: CER1-T05


title: BL97


title: BL53


title: Liver_HCC_Tumor_81


title: BL47


title: Liver_HCC_Tumor_84


title: Liver_HCC_Nontumor_Adjacent_35


title: TER1-T05


title: BL87


title: Liver_HCC_Tumor_95


title: InVitro_36.5dpc_3

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads from each individual sample were aligned to the rn6 release of the rat genome with STAR (version 2.5.2a). Briefly, STAR program was first run for each fastq file, using the RefSeq transcript annotation (GTF format) of rat genome (release rn6) downloaded in November 2017. Exon junction outputs were then added to a splice junction set. STAR was next run a second time complemented by the splice junction dataset to produce a final alignment file (BAM format) for each sample.
Principal component analysis (PCA) was performed based on the gene abundance values with the FactoMineR package to graphically evaluate the distribution of sequenced samples
The statistical filtration of the genes showing a differential expression (DE) across experimental samples was performed using AMEN. Genes were selected if abundance levels exceeded 0.5 RPKM in at least one experimental condition (median value of sample duplicates).
We compared 14.5 dpp testicular tissue samples to D6, D16, D22 and D28 cultured tissue conditions and selected 1,490 genes yielding at least one-fold change greater or equal to 2.0 (median values of sample duplicates).
A Linear Models for Microarray Data (LIMMA) statistical test was used to identify 1,240 genes with significant abundance variations across samples (F-value adjusted with the FDR method: P ≤ 0.05) (Smyth, 2004).
Finally, we intersected the three sets of DEGs to select 600 genes showing significant differential abundances in all three comparisons.
Genome_build: rn6
Supplementary_files_format_and_content: genes.FPKM.txt (log2-transformed normalized expression matrix)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: testis

growth_protocol: Tissues were cultured using the gas-liquid interphase method. Rat prepubertal testicles at 8.5 dpp were cut into 6 fragments and cultured onto agarose gels in 6-well plates. The day before the beginning of each culture, agarose gels were soaked completely in basal medium (αMEM + 0.01% gentamicin) and kept overnight in the incubator. Tissues were maintained under 5% CO2-95% air at 34°C for 16, 22 or 28 days. The culture medium was composed of αMEM supplemented with 10% Knock-out serum replacement, 10-6 M retinol and 3.4 mM vitamin E. The medium was prepared and replaced every 3-4 days.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit according to the manufacturer’s instructions and stored at -20°C until use. Genomic DNA was removed by incubation with Turbo Dnase.
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit, according to the manufacturer's instructions. Briefly, following purification with poly(T)-oligo attached magnetic beads, mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 seconds at 98°C; [10 seconds at 98°C, 30 seconds at 60°C, 30 seconds at 72°C] X 12 cycles; 5 minutes at 72°C) to create the cDNA library. The excess of PCR primers was further removed by purification using AMPure XP beads and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Libraries were then single-read sequenced with a length of 50 bp on an Illumina Hiseq4000 sequencer. Image analysis and base calling were carried out using RTA v.2.7.7 and bcl2fastq v.2.17.1.14.

value: Wistar Han

value: testis

value: post natal day 8.5

tag: time

value: 28 days (Culture)

tag: group


title: Liver_HCC_Tumor_75


title: Liver_HCC_Tumor_86


title: Liver_HCC_Tumor_9


title: InVitro_36.5dpc_1


title: BL108

tag: diagnosis

value: Control

tag: training/validation group in diagnostic model

value: female

value: censored; 1:event):NA


title: Liver_HCC_Tumor_70

value: HCC


title: BL52

tag: training/validation group in survival analysis

tag: age


title: Liver_HCC_Tumor_68


title: InVitro_36.5dpc_2


title: Liver_HCC_Tumor_72


title: InVitro_30.5dpc_2

value: 22 days (Culture)


title: Liver_HCC_Tumor_8


title: Liver_HCC_Tumor_7


title: Liver_HCC_Tumor_63


title: BL72

value: Training

tag: gender

tag: vital status (0


title: Liver_HCC_Tumor_6


title: BL37

tag: survival (months)


title: InVitro_30.5dpc_1


title: Liver_HCC_Tumor_64


title: Liver_HCC_Tumor_59


title: Liver_HCC_Tumor_58


title: BL41

value: male


title: InVitro_24.5dpc_2

value: 16 days (Culture)


title: InVitro_30.5dpc_3


title: Liver_HCC_Tumor_54

value: Tumour (liver)


title: BL12


title: BL40


title: Liver_HCC_Tumor_62


title: Liver_HCC_Tumor_50


title: InVitro_24.5dpc_3


title: Liver_HCC_Tumor_52


title: BL50


title: Liver_HCC_Tumor_53


title: BL82


title: InVitro_14.5dpc_3

value: 6 days (Culture)


title: InVitro_14.5dpc_2


title: Liver_HCC_Tumor_51


title: Liver_HCC_Tumor_48


title: BL64


title: NU-DUL-1

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

data_processing:
RNA sequencing reads from each cell line were aligned to the hg19 reference using the STAR aligner (v2.5.2a), which also generated per-gene counts with HTSeq.
To compare the expression of the Ca2+ channel genes between different pathological groups, RNA sequencing counts from all samples were analyzed in R (v3.6.1) using the DESeq2 package (v1.26.0).
Counts from all cell lines were read into a merged DESeqDataSet object, and lowly expressed genes (1 or fewer counts across all samples) were removed. The count data were then normalized using a variance-stabilizing transformation (vst function). Pairwise t-tests were used to compare normalized counts of the Ca2+ channel genes between each combination of pathologies. For specific comparisons of interest, differential expression was also performed between pathological pairs (DESeq function), and the results for the Ca2+ channel genes (p value, adjusted p value (q value), and log2 fold change) were assessed.
Genome_build: hg19
Supplementary_files_format_and_content: DESEQeq output files (normalized abundance measurements): differential expression between (1) ABC-DLBCL vs GCB-DLBCL cell lines, (2) cHL vs other B-cell lymphoma cell lines, (3) PMBCL vs other B-cell lymphoma cell lines
Supplementary_files_format_and_content: Normalized abundance measurements (normalized with the DESeq2 variance stabilizing transformation)

source_name: Cell line

extract_protocol: RNA sequencing data were generated using standard Illumina protocols at the British Columbia Cancer Research Centre from 44 lymphoma cell lines representing multiple pathologies. These datasets were generated at multiple timepoints.

tag: pathology

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)

tag: read length


title: Liver_HCC_Tumor_5


title: WSU-DLCL2

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: InVitro_14.5dpc_1

tag: strain


title: InVitro_24.5dpc_1

tag: tissue


title: SU-DHL-6


title: OCI-Ly7


title: Liver_HCC_Tumor_49


title: BL98


title: Liver_HCC_Tumor_44


title: OCI-Ly10


title: InVivo_53.5dpc_3

value: post natal day 53.5

value: No culture


title: BL34


title: L-428

value: Classical Hodgkin Lymphoma


title: InVivo_53.5dpc_2

value: Wistar Han

value: testis


title: InVivo_53.5dpc_1


title: BL88

value: Control


title: Liver_HCC_Tumor_47


title: NU-DHL-1


title: BL16

value: female


title: Liver_HCC_Tumor_43


title: Liver_HCC_Tumor_45


title: Karpas422


title: KM-H2


title: Karpas-1106P

value: Primary Mediastinal B-cell Lymphoma


title: InVivo_36.5dpc_3

value: post natal day 36.5


title: Liver_HCC_Tumor_42

value: HCC


title: Liver_HCC_Tumor_41


title: BL60

value: Training

value: censored; 1:event):NA


title: InVivo_36.5dpc_1


title: InVivo_30.5dpc_3

value: post natal day 30.5


title: InVivo_36.5dpc_2


title: DEV

value: Nodular lymphocyte-predominant Hodgkin lymphoma


title: DOHH-2


title: BL61

value: male


title: BL65


title: BL21


title: Liver_HCC_Tumor_40

value: Tumour (liver)


title: InVivo_30.5dpc_2


title: InVivo_30.5dpc_1


title: BL39


title: BL44


title: BL90


title: DB

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: activated B cells, KO2-ANTI

city: Shenzhen

first: Yuxing

address: No. 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Bcl2fastq (v2.17.1.14) were used for basecalling.
Sequence reads were filtrated using Cutadapt (V1.9.1)
Clean reads were mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1).
Gene expression level was calculated using Htseq software (V0.6.1)
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKMs for every gene and every sample

source_name: Anti-CD40 and anti-IgM activated B cells

growth_protocol: B cells were cultured 36 hours at the concentration of 2 million cells per ml in DMEM medium  supplemented with 10% FBS, 1% penicillin/streptomycin, 1% non-essential amino acids, 1 μg/ml anti-CD40 and 10 μg/ml anti-IgM  at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

value: spleen

tag: cell type

tag: genotype

value: Adar1 cKO


title: Liver_HCC_Tumor_4


title: 20ER_Experiment1

city: San Diego

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

description:
targeted mRNA
~500 amplified mRNA targets

data_processing:
Bcl2fastq (Illumina) was used to demultiplex sequencing libraries using plate barcodes and assort reads by well barcodes prior to sequence alignment using Bowtie2 (v2.2.9) to a custom genome consisting of the amplicon regions for the specifically targeted genes used in the experiment based on the murine genome GRCm38.p6, version R97 (Ensembl). HTseq was used for read and UMI reduced tabulation.
Quality control discarded wells that contained fewer than 125UMI counts and fewer than 25 unique genes and removed genes that were not expressed in at least 10 different cells. A secondary filter included naïve B cells wells containing 2 of 3 genes (Cd79a, Cd79b, Ptprc) and PC wells containing 2 of 3 genes (Prdm1, Irf4, Xbp1)
Assembly: GRCm38.p6
Supplementary files format and content: Processed data files consist of a cell x gene matrix of raw UMI counts combined with surface phenotype fluorescence and metadata headers

source_name: SP

extract_protocol:
Single-cell suspensions were made from the spleen. Processing of cells and flow cytometry staining were performed on ice. Briefly, cells were lysed (ACK red cell lysis buffer, Gibco), passed through a 70μm cell strainer (Fisher Scientific), washed, and resuspended in ice cold phenol red-free DMEM (Gibco) with 2% (vol/vol) Fetal Calf Serum FACS buffer at 4 x 108 cells/mL. For surface staining, cells were incubated for 5 mins with 2% (vol/vol) normal mouse and normal rat serum (Jackson ImmunoResearch Laboratories), prior to staining with a 2X master mix containing fluorophore-labeled antibodies at pre-titrated concentrations in Brilliant Violet Staining Buffer (BD Biosciences), and added to suspended cells at a final staining concentration of 2 x 108 cells/mL for 30-45 min. Cells were washed and resuspended in FACS buffer before flow cytometry analysis and sorting
Library preparation was carried out using a custom scRNA-seq strategy described in detail in (Shuparksi et al., 2021 STAR Protocols). In brief, Single cells were sorted into 384 well plates with each well containing the necessary reagents for reverse transcription (RT). Including polyA targeting oligoDT primers with unique molecular identifiers and cell barcodes. Negative control wells without sorted cells were included to enable assessment of potential contamination. Following the completion of the sort an RT reaction was performed (42˚C for 50 mins then 80˚C for 10 mins) and wells from the same plate were pooled into a single PCR tube. To remove excess oligoDT primer, cDNA libraries were treated with ExoSAP-IT Express according to manufacturer’s instructions (Affymetrix). Libraries were then volume reduced via a 0.8x ratio of AMpure XP SPRIselect magnetic beads (BeckmandCoulter). Ensuring separation between plates to preserve barcode fidelity, two nested PCR reactions were performed utilizing external and internal mixed primer sets targeting ~500 gene transcript species of interest. A final PCR reaction was carried out to allow for the ligation of adapter sequences enabling Illumina flow cell binding. Final cDNA libraries containing the amplified targeted mRNA species were quantified using a Qubit 4 Fluorometer (Invitrogen Technologies) and 2100 BioAnalyzer (Agilent). Multiplexed plates were then sequenced on an Illumina NextSeq 500 (Read 1: 19 cycles; Index Read 1: 6 cycles; Read 2: 67 cycles)
Targeted plate based scRNA-seq

treatment_protocol: For NP specific experiments, subcutaneous injection of NP-KLH base of tail, with tissue harvest 5 or 14 days post immunization.

value: C57BL/6 Blimp1 YFP

tag: treatment

value: Steady state analysis of splenic PCs


title: activated B cells, KO1-ANTI

value: Anti-CD40 and anti-IgM activated B cells


title: InVivo_24.5dpc_2

value: Wistar Han

value: testis

value: post natal day 24.5

value: No culture


title: 20IX_Experiment2

data_processing:
library strategy: Targeted plate based scRNA-seq
Bcl2fastq (Illumina) was used to demultiplex sequencing libraries using plate barcodes and assort reads by well barcodes prior to sequence alignment using Bowtie2 (v2.2.9) to a custom genome consisting of the amplicon regions for the specifically targeted genes used in the experiment based on the murine genome GRCm38.p6, version R97 (Ensembl). HTseq was used for read and UMI reduced tabulation.
Quality control discarded wells that contained fewer than 125UMI counts and fewer than 25 unique genes and removed genes that were not expressed in at least 10 different cells. A secondary filter included naïve B cells wells containing 2 of 3 genes (Cd79a, Cd79b, Ptprc) and PC wells containing 2 of 3 genes (Prdm1, Irf4, Xbp1)
Assembly: GRCm38.p6
Supplementary files format and content: Processed data files consist of a cell x gene matrix of raw UMI counts combined with surface phenotype fluorescence and metadata headers

extract_protocol:
Single-cell suspensions were made from the spleen. Processing of cells and flow cytometry staining were performed on ice. Briefly, cells were lysed (ACK red cell lysis buffer, Gibco), passed through a 70μm cell strainer (Fisher Scientific), washed, and resuspended in ice cold phenol red-free DMEM (Gibco) with 2% (vol/vol) Fetal Calf Serum FACS buffer at 4 x 108 cells/mL. For surface staining, cells were incubated for 5 mins with 2% (vol/vol) normal mouse and normal rat serum (Jackson ImmunoResearch Laboratories), prior to staining with a 2X master mix containing fluorophore-labeled antibodies at pre-titrated concentrations in Brilliant Violet Staining Buffer (BD Biosciences), and added to suspended cells at a final staining concentration of 2 x 108 cells/mL for 30-45 min. Cells were washed and resuspended in FACS buffer before flow cytometry analysis and sorting
Library preparation was carried out using a custom scRNA-seq strategy described in detail in (Shuparksi et al., 2021 STAR Protocols). In brief, Single cells were sorted into 384 well plates with each well containing the necessary reagents for reverse transcription (RT). Including polyA targeting oligoDT primers with unique molecular identifiers and cell barcodes. Negative control wells without sorted cells were included to enable assessment of potential contamination. Following the completion of the sort an RT reaction was performed (42˚C for 50 mins then 80˚C for 10 mins) and wells from the same plate were pooled into a single PCR tube. To remove excess oligoDT primer, cDNA libraries were treated with ExoSAP-IT Express according to manufacturer’s instructions (Affymetrix). Libraries were then volume reduced via a 0.8x ratio of AMpure XP SPRIselect magnetic beads (BeckmandCoulter). Ensuring separation between plates to preserve barcode fidelity, two nested PCR reactions were performed utilizing external and internal mixed primer sets targeting ~500 gene transcript species of interest. A final PCR reaction was carried out to allow for the ligation of adapter sequences enabling Illumina flow cell binding. Final cDNA libraries containing the amplified targeted mRNA species were quantified using a Qubit 4 Fluorometer (Invitrogen Technologies) and 2100 BioAnalyzer (Agilent). Multiplexed plates were then sequenced on an Illumina NextSeq 500 (Read 1: 19 cycles; Index Read 1: 6 cycles; Read 2: 67 cycles)

tag: molecule subtype

value: targeted mRNA; ~500 amplified mRNA targets


title: InVivo_24.5dpc_1

tag: time


title: activated B cells, WT1-ANTI

value: wild type


title: InVivo_24.5dpc_3

tag: group


title: 20JA_Experiment1

source_name: LN

value: Immunization with NP-KLH in MPL adjuvant

tag: time point

value: Analysis at day 14 post-immunization.


title: InVivo_14.5dpc_3_outlier

value: post natal day 14.5


title: 20IC_Experiment1


title: InVivo_14.5dpc_2


title: Liver_HCC_Tumor_35

tag: disease state

value: HCC


title: PADP6 iron unchelated, PA_RP01

city: Singapore

first: Casandra

last: Tan

address: 60 Nanyang Drive

country: Singapore

institute: SCELSE

description:
PADP6 total RNA
PA_RP01
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt

data_processing:
Raw reads were quality and adapter trimmed using bbduk from BBMap tools (Version 39.79).
Trimmed reads were then mapped using bwa-mem of BWA (Version 0.7.17-r1188) with options “-T 20 -k 13” against E. faecalis OG1RF (NCBI accession: CP002621) or P. aeruginosa PAO1 (NCBI accession: NC_002516) reference genomes.
Reads mapped to predicted open reading frames were quantified using htseq-count of HTSeq (Version 0.12.4) with option “-m intersection-strict”.
Ribosomal sequences were filtered out from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Genome_build: E. faecalis OG1RF (NCBI accession: CP002621) and P. aeruginosa PAO1 (NCBI accession: NC_002516).
Supplementary_files_format_and_content: toOG1RF.txt, toPAO1.txt (Text files containing raw counts of sequencing reads for each sample mapped to E. faecalis OG1RF or P. aeruginosa PADP6.)
Supplementary_files_format_and_content: *VS*.txt (Normalized counts using edgeR for every comparison made. )
Supplementary_files_format_and_content: *conditions.txt (Sample metadata csv file used in DGE analysis in edgeR.)

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PADP6 macrocolonies on TSBG agar (single-species)

growth_protocol: Single-species (E. faecalis OG1RF, E. faecalis ∆ldh1 or P. aeruginosa PADP6) and mixed-species (PADP6+OG1RF or PADP6+∆ldh1) macrocolonies grown in TSBG agar (TSB supplemented with 10 mM glucose) at 37ᵒC for 48 hours.

extract_protocol:
Macrocolonies were first scraped into RNAprotect™ Bacteria Reagent and bacteria pellets were then subjected to total RNA extraction using RNeasy® mini kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme and further supplemented with 20 µL proteinase K. Followed by incubation at 37 °C for 1 h, and subsequent extraction steps was performed according to manufacturer’s protocol. Extracted RNA samples were treated with DNase (TURBO DNA-free™ kit, Invitrogen, USA) and purified using Monarch® RNA cleanup kit.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.

treatment_protocol: Macrocolonies were grown in TSBG agar with or without 2 mM 2,2’ bipyridyl.

tag: genotype mapped

tag: growth protocol

value: iron replete

tag: condition

value: single

tag: e. faecalis strain

value: noEF


title: PADP6 iron unchelated, PA_RP04

description:
PADP6 total RNA
PA_RP04
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt


title: Liver_HCC_Tumor_38

value: Tumour (liver)


title: 20CR_Experiment1


title: activated B cells, WT2-ANTI

value: spleen


title: Liver_HCC_Tumor_36


title: Liver_HCC_Tumor_31


title: InVivo_14.5dpc_1

tag: age


title: Liver_HCC_Tumor_33


title: Liver_HCC_Tumor_32


title: InVivo_8.5dpc_3

value: post natal day 8.5


title: 20FD_Experiment1

value: Analysis at day 5 and 14 post-immunization.


title: Liver_HCC_Tumor_30


title: Liver_HCC_Tumor_3


title: Liver_HCC_Tumor_34


title: PADP6 iron chelated, PA_DP12

description:
PADP6 total RNA
PA_DP12
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt

source_name: P. aeruginosa PADP6 macrocolonies on iron chelated TSBG agar (single-species)

value: iron deplete


title: PADP6 iron unchelated, PA_RP06

description:
PADP6 total RNA
PA_RP06
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt


title: InVivo_8.5dpc_2

value: Wistar Han

value: testis


title: PADP6 iron chelated, PA_DP08

description:
PADP6 total RNA
PA_DP08
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt


title: PADP6 iron chelated, PA_DP09

description:
PADP6 total RNA
PA_DP09
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, ToPAO1conditions.txt, toOG1RF.txt


title: InVivo_8.5dpc_1

value: No culture


title: GSCLC_Rad21_1

source_name: GSCLC

value: GSCLC

tag: chip antibody

tag: controlled by

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: Liver_HCC_Tumor_29


title: GSCLC_Rad21_2

tag: strain


title: Liver_HCC_Tumor_28

tag: tissue


title: Input RPO21-FLAG in thiolutin

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

data_processing:
Sequenced single-end 65-bp reads were mapped to the yeast genome using Bowtie2 version 2.4.1 with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary_files_format_and_content: BigWig files (100-bp bin) were generated by DROMPAplus version 1.8.2 with "--nofilter" option. The total read number of ChIP samples was normalized based on the corresponding qPCR data (see the manuscript for detail).

organism: Saccharomyces cerevisiae

source_name: thiolutin

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described, with the following details and modifications (Katou, Y., Kaneshiro, K., Aburatani, H. & Shirahige, K. Genomic approach for the understanding of dynamic aspect of chromosome behavior. Methods Enzymol 409, 389-410 (2006).). One hundred ml of cell culture (at an OD of 1.0) was crosslinked with 1 % formaldehyde for 30 minutes at room temperature, followed by incubation at 4°C overnight. Chromatin was sheared to a size of 300-500 base pairs by sonication (Bandelin Sonopuls HD 2070.2) and IP reactions, with anti-FLAG antibody (Sigma, F1804) conjugated to Dynabeads Protein A (Invitrogen, 10002D), were allowed to proceed overnight at 4°C. After completing the immunoprecipitation and reversing crosslinks as in 5, the DNA clean-up step was modified as follows. One hundred μl TE containing 10 μg RNase A (VWR, A3832) was added to IP and input fractions and the reactions were incubated for 1 hour at 37°C. Then, 2 μl of 50 mg ml-1 Proteinase K (Sigma, 000000003115879001) was added and the reactions were incubated for 2 hours at 37°C. Lastly, the DNA was purified using Qiagen PCR Purification kit according to standard instructions.
DNA from ChIP and input fractions was further sheared to an average size of approximately 150 bp by sonication (Covaris M220). Samples were then prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacture's protocol.

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

tag: target protein

value: Input

tag: antibody

value: G2/M-arrest, thiolutin


title: GSCLC_CTCF_1

tag: cell type

value: CTCF

tag: genotype


title: GSCLC_CTCF_2


title: 20CI_Experiment1

tag: treatment

value: Immunization with NP-KLH in MPL adjuvant

value: Analysis at day 5 post-immunization.

tag: molecule subtype

value: targeted mRNA; ~500 amplified mRNA targets


title: KTFAKWT4_VEH

city: La Jolla

first: Duygu

last: Ozmadenci

address: Moores Cancer Center 3855 Health Sciences Drive

department: OBGYN

institute: UC San Diego

description: Total mRNA was isolated from 2 million cells

hyb_protocol: Performed according to Nanostring service.

data_processing: Data is analysed using Nsolver platform and Log2 normalized to housekeeping genes  Hdac3, Sdha, Oaz1, Sf3a3, G6pdx, Hprt, Abcf1, Tubb5, Eif2b4, Rpl19, Polr1b.

source_name: peritoneal ascites

growth_protocol: 5 million  tumor cells were intraperitoneally injected into mice and were recovered 21 days later.

extract_protocol: Total mRNA from 2 million ascites cells were isolated using invitrogen RNA extraction kit.

treatment_protocol: For FAK inhibitor or Vehicle treatments, mice were gavaged 100mg/kg twice a day,

tag: tissue type

value: ovarian cancer

value: KTFAKKD

tag: agent

value: vehicle


title: GSCLC_K9me3_2

description:
GSCLC_K9me3_pool_log2ratio_1000.bw
GSCLC_K9me3_pool.bed

data_processing:
Single-end reads were processed using Trim-Galore v0.4.1/cutadapt v1.9.1 to remove adaptor sequence.
The truncated reads were then aligned to (GRCm38p3) using Bowtie2 v2.3.4.1 with the “-very-sensitive” option.
The reads aligned to chromosome 1 to 19, X, Y were transformed to BAM format by SAMtools v1.7. BED files were obtained from the BAM files using the bamtobed command of BEDTools v2.29.2.
Genome_build: mm10
Supplementary_files_format_and_content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” or bamcompare for IP/Input command with the “--pseudocount 1 -bs 1000” option of deepTools v3.5.0. In both cases, the blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary_files_format_and_content: bed files describe peaks or domains files detected by macs2 or epic2, respectively

extract_protocol:
The ChIP-seq library preparation was performed as previously described (Lee et al., 2006) with minor modifications. We used harvested mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs and d4c7 mPGCLCs samples, and FACS-sorted AAG-positive cells for GSCs and GSCLCs samples. Briefly, the harvested cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific)/PBS for 10 min at RT and quenched with 125 mM glycine. Crosslinked cells were lysed consecutively using LB1 (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% Triton-100, protease inhibitors (Roche, 11873580001)), LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease inhibitors), and LB3 (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors) and then sonicated by picoruptor to achieve a mean DNA fragment size of around 200-400 bp. Sonicated chromatin was incubated with  Dynabeads M-280 Sheep anti Mouse IgG beads (Thermo Fisher Scientific) or Dynabeads ProteinA beads (Thermo Fisher Scientific) for 35 min at 4°C for preclear. Precleared chromatin was then incubated with antibody that was preincubated with the appropriate Dynabeads in 0.5% BSA (Gibco) in PBS as follows: chromatin equivalent of 5 x 105 cells with anti-H3K4me1 (rabbit monoclonal, CST, D1A9, 5 μl),  anti-H3K9me2 (mouse monoclonal, MBL, MABI0317, 5 μl), anti-H3K27me3 (mouse monoclonal, MBL, MABI0323, 5 μl); 1 x 106 cells with anti-H3K4me3 (mouse monoclonal, MBL, MABI0304, 5 μl), anti-H3K9me3 (mouse monoclonal, MBL, MABI0318, 5 μl), anti-H3K36me2 (rabbit monoclonal, CST, C75H12, 5 μl), anti-H2AK119ub1 (rabbit monoclonal, D27C4, 10 μl), anti-H3K36me3 (rabbit polyclonal, Active Motif, 61101, 2 μl); 1.5 x 106 cells with anti-H3K27ac (mouse monoclonal, MBL, MABI0309, 5 μl); 2 x 106 cells with anti-CTCF (rabbit monoclonal, CST, D31H2, 5 μl), anti-Laminb1 (rabbit polyclonal, Proteintech, 12987-1-AP, 10 μl); 3 x 106 cells with anti-Setdb1 (rabbit ployclonal, Proteintech, 11231-1-AP, 10 μl); 4 x 106 cells with anti-Ring1b (rabbit monoclonal, CST, D22F2, 10 μl); and 4.5 x 106 cells with anti-Rad21 (rabbit monoclonal, ab992, 5 μl). After incubation for 6 h at 4°C, the beads were washed 4 times in wash buffer 1 (20 mM Tris-HCl pH8.0, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 0.1% SDS), 2 times in wash buffer 2 (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.1% SDS), and 2 times in wash buffer 3 (10 mM Tris-HCl  pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% Na-Deoxycolate, 1% NP-40). Then, the washed beads were eluted in 10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 1% SDS, and crosslinks were reversed overnight at 65°C. Input samples were treated in a similar manner. The following day, IP and Input samples were incubated with RNaseA (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific). IP or Input DNA was purified using QIA quick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA) following the manufacturer’s guidelines. An adaptor kit (Fastgene, FG-NGSAD24) was used for the sample indexes. The average size and concentration of libraries were analyzed using LabChIP GX (PerkinElmer) and KAPA library Quantification kit (KAPA), respectively.


title: RPO21-FLAG in thiolutin

value: anti-FLAG (Sigma, F1804)


title: KTFAKKD5


title: Liver_HCC_Tumor_23

tag: disease state

value: HCC

value: Tumour (liver)


title: KTFAKWT9_VEH


title: Input RPO21-FLAG in DMSO

source_name: DMSO WT

value: G2/M-arrest, DMSO


title: KTFAKWT3_VEH


title: GSCLC_K4me3_2


title: RPO21-FLAG in DMSO


title: Liver_HCC_Tumor_20


title: Liver_HCC_Tumor_19


title: Liver_HCC_Tumor_18


title: KTFAKKD4


title: Input Scc1-FLAG in thiolutin G2M

source_name: thiolutin G2M


title: Liver_HCC_Tumor_25


title: Liver_HCC_Tumor_14


title: Scc1-FLAG in thiolutin G2M


title: GSCLC_Input_2


title: GSCLC_K4me3_1


title: Liver_HCC_Tumor_13


title: KTFAKKD3


title: GSCLC_Input_1


title: KTFAKWT6_FAKi

value: KTFAKWT

value: FAKi VS4716


title: GSCLC_K9me3_1

value: GSCLC


title: Liver_HCC_Tumor_10


title: Input Scc1-FLAG in thiolutin

value: HU-arrest, thiolutin


title: Input Scc1-FLAG in HU

source_name: HU WT

value: Input

value: HU-arrest


title: Scc1-FLAG in DMSO G2M

source_name: DMSO G2M


title: GSC_CTCF_1

source_name: GSC

value: GSC

value: CTCF

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: Scc1-FLAG in HU


title: KTFAKWT3


title: WT_H3K9me2_1

city: Memphis

first: Mario

last: Halic

state: Tennessee

address: 262 Danny Thomas Place

department: Structural Biology

institute: St. Jude Children’s Research Hospital

data_processing:
Sequencing reads obtained in the poly(A) RNA sequencing (pA RNA), Pol II ChIP, nascent RNA sequencing (Pol II RIP) and total RNA sequencing experiments were mapped to the S. pombe reference genome (PomBase, release 2018) using splice-aware alignment tool STAR version 2.7.3a (Dobin et al., 2013).  Alignment of RIP-seq and RNA-seq data was performed with STAR default parameters. Unspliced alignments of ChIP-seq data was enforced through parameters ‘--alignIntronMax 1’ and ‘--alignEndsType EndToEnd’. Reads mapping to ribosomal RNA have been removed from further analysis.
Genomic read counts were obtained using a custom script that extended basic htseq-count functionality with ‘--mode intersection-strict’ option. Additionally, for RNA assays pA RNA, Pol II RIP and total RNA, we used the ‘--stranded yes’ option to disambiguate which strand reads originated from. In short, reads mapping uniquely to protein-coding genes and reads that map less than 16 times were counted and normalized by gene length and sequencing depth (TPM, Transcripts Per Million). We chose 16 (dg/dh have in 12-13 copies) as multi-mapping threshold for heterochromatic genes to eliminate low-complexity reads without discarding reads originating from heterochromatic regions. In the read counting, we did not distinguish between individual gene copies but used one representative copy to collect all reads stemming from any one copy.
Assembly: PomBase, release 2018
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Schizosaccharomyces pombe

source_name: wt

growth_protocol: Cells were grown in rich YES medium.

extract_protocol:
50 ml yeast cultures with an OD600 of 1.2 were cross-linked with 1% formaldehyde (Roth) for 15 min at room temperature. The reaction was quenched with 125 mM glycine for 5 min. The frozen pellet was resuspended in 500 µl lysis buffer (250 mM KCl, 1x Triton-X, 0.1% SDS, 0.1% Na-Desoxycholate, 50 mM HEPES pH 7.5, 2 mM EDTA, 2 mM EGTA, 5 mM MgCl2, 0.1% Nonidet P-40, 20% Glycerol) with 1 mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche). Lysis was performed with 0.25-0.5 mm glass beads (Roth) and the BioSpec FastPrep-24 bead beater (MP-Biomedicals), 8 cycles at 6.5 m/s for 30s and 3 min on ice. DNA was sheared by sonication (Bioruptor, Diagenode) 35 times for 30 s with a 30 s break. Cell debris was removed by centrifugation at 13 000 x g for 15 min. The crude lysate was normalized based on the RNA and Protein concentration (Nanodrop, Thermo Scientific) and incubated with 1.2 µg immobilized (Dynabeads Protein A, Thermo Scientific) antibody against Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam) for at least 2 h at 4°C. The resin with immunoprecipitates was washed five times with each 1 ml of lysis buffer and eluted with 150 µl of elution buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 15 min. Cross-linking was reversed at 95°C for 15 min and subsequent RNase A (Thermo Scientific) digest for 30 min followed by Proteinase K (Roche) digest for at least 2 h at 37°C. DNA was recovered by phenol-chloroform-isoamylalcohol (25:24:1, Roth) extraction with subsequent ethanol precipitation.
For sequencing, a ChIP-seq library was made using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB).

tag: strain number

value: wt

tag: target molecule

value: H3K9me2 bound DNA

tag: ip antibody

value: H3K9me2, Abcam AB1220


title: KTFAKWT4_FAKi

value: ovarian cancer


title: 638_H3K9me2_1


title: Input Scc1-FLAG in DMSO

value: HU-arrest, DMSO


title: SNU-449 cells, siFOXS1#2_TGFb_R3_72h

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

description: SNU449 transfected with siFOXS1#2 TGFb treated Replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20101102). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded. Normalization was based on the 75th percentile shift.

source_name: SNU449 transfected with siFOXS1#2, TGFb-treated

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions.

growth_protocol: SNU-449 cells (ATCC® CRL-2234, grade II-III/IV)  were grown in a MEM medium (Sigma, M2279) supplemented with 100U/ml penicillin, 100μg/ml streptomycin (Gibco, 15070-063), 2mM L-Gluta and 10% fetal bovine serum (HyClone). Cultures were performed at 37°C in a 5% CO2 atmosphere. Overnight serum starvation was performed before each treatment.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were treated with 1ng/mL recombinant human TGFβ1 (R&D system, Minneapolis, USA) versus BSA control for 72hrs. FOXS1 loss of function was performed by using two different small interfering RNAs (siRNA) purchased from Ambion: siFOXS1#1 (s5256, 5’-AAUCGGCCCAUGAUGUAGCgg-3’) and siFOXS1#2 (s107325, 5’-CAUGCAAAAAUUCAGUGCCgg-3’). FAM-labeled negative control siRNA No.1 (Ambion AM4620) was used as control (siNC). Cells were transfected at 70% confluency with 50nM siRNA using lipofectamine RNAiMAX reagent and Opti-MEM medium according to manufacturer’s instructions (Invitrogen). Experiments were performed in triplicates.

tag: cell line

value: TGFb Treated

tag: sirna

value: FOXS1 silencing


title: GSC_K9me3_1

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University, Graduate school of medicine

description:
GSC_K9me3_pool_log2ratio_1000.bw
GSC_K9me3_pool.bed

tag: chip antibody

tag: controlled by


title: SNU-449 cells, siFOXS1#2_TGFb_R1_72h

description: SNU449 transfected with siFOXS1#2 TGFb treated Replicate 1


title: Input Scc1-FLAG in DMSO G2M

tag: strain

value: G2/M-arrest, DMSO


title: Scc1-FLAG in thiolutin

tag: target protein

value: anti-FLAG (Sigma, F1804)


title: GSC_Rad21_1


title: Scc1-FLAG in DMSO

tag: antibody


title: GSC_Rad21_2

tag: cell type


title: GSC_CTCF_2

tag: genotype


title: KTFAKWT2

value: KTFAKWT


title: Liver_HCC_Tumor_12

source_name: HCC tumour tissue

value: HCC

tag: tissue

value: Tumour (liver)


title: 510_H3K9me2_1


title: Input Scc1-FLAG WT rep2

source_name: WT

value: Input

tag: treatment

value: G2/M-arrest, auxin, doxycycline


title: GSC_K4me3_1

value: GSC


title: SNU-449 cells, siFOXS1#2_TGFb_R2_72h

description: SNU449 transfected with siFOXS1#2 TGFb treated Replicate 2


title: GSC_K9me3_2


title: KTFAKWT1

tag: tissue type


title: SNU-449 cells, siFOXS1#2_BSA_R1_72h

description: SNU449 transfected with siFOXS1#2 BSA treated Replicate 1

source_name: SNU449 transfected with siFOXS1#2, BSA-treated

value: BSA Control


title: SNU-449 cells, siFOXS1#2_BSA_R3_72h

description: SNU449 transfected with siFOXS1#2 BSA treated Replicate 3


title: SNU-449 cells, siFOXS1#1_TGFb_R1_72h

description: SNU449 transfected with siFOXS1#1 TGFb treated Replicate 1

source_name: SNU449 transfected with siFOXS1#1, TGFb-treated


title: SNU-449 cells, siFOXS1#1_TGFb_R2_72h

description: SNU449 transfected with siFOXS1#1 TGFb treated Replicate 2


title: SNU-449 cells, siFOXS1#1_BSA_R3_72h

description: SNU449 transfected with siFOXS1#1 BSA treated Replicate 3

source_name: SNU449 transfected with siFOXS1#1, BSA-treated


title: HDMYZ

source_name: Cell line

tag: pathology

value: Classical Hodgkin Lymphoma

tag: read length


title: 530_H3K9me2_1

tag: strain number


title: Scc1-FLAG WT rep1


title: 504_H3K9me2_1

tag: target molecule


title: Farage

value: Primary Mediastinal B-cell Lymphoma


title: 301_H3K9me2_1

value: H3K9me2 bound DNA

tag: ip antibody


title: GSC_K4me3_2

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: 491_H3K9me2_1

value: H3K9me2, Abcam AB1220


title: Input Scc1-FLAG


title: d4c7PGCLC_CTCF_2

value: CTCF

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: SNU-449 cells, siFOXS1#1_TGFb_R3_72h

description: SNU449 transfected with siFOXS1#1 TGFb treated Replicate 3

tag: cell line

value: TGFb Treated

value: FOXS1 silencing


title: GSC_Input_1


title: SNU-449 cells, siFOXS1#2_BSA_R2_72h

description: SNU449 transfected with siFOXS1#2 BSA treated Replicate 2

tag: sirna


title: d4c7PGCLC_Rad21_1

tag: chip antibody


title: GSC_Input_2

tag: controlled by


title: Scc1-FLAG WT rep2

tag: strain

value: anti-FLAG (Sigma, F1804)


title: 324_H3K9me2_1


title: d4c7PGCLC_Rad21_2


title: WT_S2-ChIP-INPUT_1

value: wt

value: genomic DNA


title: SNU-449 cells, siNC_TGFb_R3_72h

description: SNU449 transfected with siNC TGFb treated Replicate 3

source_name: SNU449 transfected with siNC, TGFb-treated

value: siNC

value: control


title: 302_H3K9me2_1


title: d4c7PGCLC_CTCF_1


title: SNU-449 cells, siFOXS1#1_BSA_R2_72h

description: SNU449 transfected with siFOXS1#1 BSA treated Replicate 2


title: SNU-449 cells, siFOXS1#1_BSA_R1_72h

description: SNU449 transfected with siFOXS1#1 BSA treated Replicate 1


title: 80_S2-ChIP-INPUT_1


title: d4c7PGCLC_K9me3_2

description:
d4c7PGCLC_K9me3_pool_log2ratio_1000.bw
d4c7PGCLC_K9me3_pool.bed


title: 638_S2-ChIP-INPUT_1


title: d4c7PGCLC_K9me3_1


title: d4c7PGCLC_K4me3_2


title: 530_S2-ChIP-INPUT_1


title: SNU-449 cells, siNC_TGFb_R1_72h

description: SNU449 transfected with siNC TGFb treated Replicate 1


title: 544_S2-ChIP-OIN_1


title: SNU-449 cells, siNC_TGFb_R2_72h

description: SNU449 transfected with siNC TGFb treated Replicate 2


title: d4c7PGCLC_K4me3_1


title: 510_S2-ChIP-INPUT_1


title: RA-exposed HT Stage embryos (E9.25), 3 pooled embryos, scRNAseq

city: New York City

first: Nicole

last: Dubois

state: NY

address: 1470 Madison Avenue, 8th Floor, Room 301

institute: Icahn School of Medicine of Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Alignment was also performed against a custom EGFP reference to identify Foxa2-lineage traced cells.  Downstreamclustering and  differential expression analysis was done in Seurat to generate .rds objects included with this data.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, as well as Seurat R objects as .rds files

source_name: subdissected heart tube and surrounding area

extract_protocol:
Foxa2Cre;mTmG embryos were dissected at E8.25, E8.75 and E9.25. The cardiac region was sub-dissected at each stage, including the surrounding endoderm, head folds, and pharyngeal structures. Embryos were dissected in cold PBS with 0.1% BSA and kept on ice until dissociation. Three stage matched litter-mates were incubated separately in 200 ul of 0.25% Trypsin-EDTA in a 37C water bath for 5 minutes or until the tissue dissociated completely, vortexing once halfway. Trypsin solution was quenched with 1ml DMEM with 10% FBS, centrifuged at 300g for 5 minutes, and resuspended in 50 ul PBS with 0.1% BSA for single-cell RNA sequencing preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ 3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For samples labeled "RA", pregnant dams were injected with 3.25 mg/kg retinoic acid at E7.25. These embryos were collected and processed in the same manner as control samples included in the study.

value: Embryonic cardiac region

value: Foxa2Cre;mTmG +/+

tag: age


title: crwn1/4_3h_rep3

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

description: SAMPLE 35

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 10.7.3

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 100 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp WT Labeling Kit (Agilent).

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown on MGRL, 1.5% gellan gum medium for two weeks.

extract_protocol: Total RNA was extracted from whole roots of zeocin treated plants using PureLink® Plant RNA Reagent (Thermo Fisher Scientific).

treatment_protocol: Two-weeks-old plants were transferred to container containing half strength of MGRL solution without sucrose. After 3 hours acclimation to hydroponic condition, seedlings were transferred to different containers containing half strength of MGRL with 10 μM zeocin. The whole roots were harvested after the treatment with zeocin for 0, 1 hour, 3 hours and subsequently subjected to total RNA extraction and microarray analysis.

tag: genotype/variation

value: whole roots

value: 3h zeocin treatment


title: 504_S2-ChIP-INPUT_1


title: crwn1/4_3h_rep4

description: SAMPLE 36


title: crwn1/4_3h_rep1

description: SAMPLE 33


title: crwn1/4_3h_rep2

description: SAMPLE 34


title: RA-exposed PHT Stage embryos (E8.75), 3 pooled embryos, scRNAseq

description: 10x Genomics

source_name: subdissected primitive heart tube and surrounding area

tag: cell type


title: 491_S2-ChIP-INPUT_1

tag: genotype


title: RA-exposed CC Stage embryos (E8.25), 3 pooled embryos, scRNAseq

description: 10x Genomics

source_name: subdissected cardiac crescent and surrounding area

tag: tissue


title: cap-h2-2_3h_rep4

description: SAMPLE 32

tag: treatment


title: SNU-449 cells, siNC_BSA_R1_72h

description: SNU449 transfected with siNC BSA treated Replicate 1

source_name: SNU449 transfected with siNC, BSA-treated

value: BSA Control


title: SNU-449 cells, siNC_BSA_R2_72h

description: SNU449 transfected with siNC BSA treated Replicate 2


title: EpiLC_Rad21_2

city: Kyoto

first: Yukihiro

last: Yabuta

source_name: EpiLC

value: EpiLC


title: d4c7PGCLC_Input_1


title: E8.75, PHT Stage, 3 pooled embryos, scRNAseq

description: 10x Genomics

value: subdissected primitive heart tube and surrounding area


title: cap-h2-2_3h_rep3

description: SAMPLE 31


title: 324_S2-ChIP-INPUT_1


title: EpiLC_Rad21_1


title: 302_S2-ChIP-INPUT_1


title: EpiLC_CTCF_2


title: 301_S2-ChIP-INPUT_1


title: cap-h2-2_3h_rep2

description: SAMPLE 30


title: cap-h2-2_3h_rep1

description: SAMPLE 29


title: d4c7PGCLC_Input_2


title: E8.25, CC Stage, 3 pooled embryos, scRNAseq

description: 10x Genomics

value: subdissected cardiac crescent and surrounding area


title: SNU-449 cells, siNC_BSA_R3_72h

description: SNU449 transfected with siNC BSA treated Replicate 3


title: E9.25, HT Stage, 3 pooled embryos, scRNAseq

description: 10x Genomics

value: subdissected heart tube and surrounding area


title: EpiLC_CTCF_1

value: CTCF

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: Col-0_3h_rep4

description: SAMPLE 28


title: Col-0_3h_rep3

description: SAMPLE 27


title: EpiLC_K9me3_1

description:
EpiLC_K9me3_pool_log2ratio_1000.bw
EpiLC_K9me3_pool.bed


title: Col-0_3h_rep2

description: SAMPLE 26


title: 1022_S2-ChIP-INPUT_1


title: TIL-rep3-gRNA2gRNA3 [mTcell.CP.TA3.G23]

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

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

department: School of Life Sciences

institute: Westlake university

data_processing:
Adapter were removed by cutadpt, and then reads were aligned to the predesigned oligo library using bowtie2.
gRNA counts were counted and normlized using total sequencing reads.
Assembly: predesinged olilgo library
Supplementary files format and content: EXCEL

source_name: sgRNA lib inserted in genome of murine T cells

growth_protocol: After ex vivo stimulation for 24h, CD8+T cells were transduced with lentivirus in the presence of polybrene at 8μg/ml during spinfection at 2,000g for 2h at 32oC. At 48h after transduction, T cells were collected for transduction efficiency test via flow cytometry and adoptive transfer.

extract_protocol:
Genomic DNA extraction was performed using TIANamp Genomic DNA kit (TIANGEN) and finally resuspended into 50μl nuclease free water. The DNA concentration was maesured via Q-bit. The SR sgRNA library readout was produced using direct PCR, whereas the TIL sgRNA library readout was produced using two-step PCR.
Two regions in the 4-sgRNA tandem cassette were amplified in step-1 PCR using primers specific to the library vector. Region-1 contained sgRNA#1 and sgRNA#2 spacers, Region-2 contained gRNA#2 and sgRNA#3 spacers. Any sequence in the two regions was unique, which could be the indicator for the 4-sgRNA combination. PCR (400~800ng DNA input per reaction, 2~4 reactions per sample) was performed using Ultra II Q5 Master Mix (NEB) with thermocycling parameters as 98oC for 30 sec,  cycles of  (98oC for 10 sec, 60oC for 30 sec, 72oC for 20 sec), 72oC for 2 min. Then, the PCR product was enriched into nuclease free water after size selection via AMPureXP beads. In step-2 PCR and direct PCR, all genomic DNA or step-1 PCR products were amplified with thermocycling parameters as 98oC for 30 sec, cycles of (98oC for 10 sec, 64oC for 30 sec, 72oC for 20 sec), 72oC for 2 min. Then, the redundant adaptor primers were depleted via AMPureXP beads. All PCR cycles were determined by Q-PCR prior to scale-up.

treatment_protocol: At d12 after tumor cell inoculation, 1E7 CD8+ T cells with screening library transduction (5% ~10% mKate2+ cells in total cells) were adoptively transferred into each recipient via i.v. injection. Meanwhile, 2~3E6 CD8+ T cells with screening library transduction were frozen as starting reference (SR). At d7 after injection, tumor was collected and cut into small fragments. After consecutively mashing through 100μm and 40μm filters, RBCs in the cell suspension were lysed. Then, the tumor infiltrating CD8+T cells were enriched by density gradient centrifugation via Lymphprep (StenCell). Cells at the interface were carefully collected and washed by PBS. Then, the cells were re-suspended into PBS and stained with anti-mouse CD8a for 30 mins on ice. Finally, CD8+mKate2+ TILs were sorted via FACS. A total of 20,000-40,000 CD8+mKate2+ TIL could be collected per tumor.  TIL from 3-4 recipient mice were mixed together and pelleted with carrier cells (Raji cell) at 1:50 (CD8+ T cells: carrier cells) for genomic DNA extraction.

value: murine T cells

value: Tumor infiltraing T cells with genomic insertion delivered via  lentivirus tranduction

tag: molecule type

value: genomic inserted sgRNA amplicon


title: WT_total-RNA_3

value: wt

value: total RNA


title: TIL-rep3-gRNA1gRNA2 [mTcell.CP.TA3.G12]


title: EpiLC_K4me3_2


title: WT_total-RNA_2


title: TIL-rep2-gRNA2gRNA3 [mTcell.CP.TA1.G23]


title: EpiLC_K4me3_1


title: LSK, CLP, scRNAseq

city: Manhasset

first: Yong-Rui

last: Zou

address: 350 Community Drive

department: The Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Bone marrow cells were harvested from femurs and tibias collected from 3 mice at 12 weeks after sham or CLP surgery, and were resuspended in FACS buffer (PBS supplemented with 2 mM EDTA and 0.5% BSA). Lineage marker-negative cells were first enriched from bone marrow cells using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies), and then stained with antibodies specific for lineage markers [B220 (clone RA3-6B2), CD19 (clone 1D3), TCR (clone H57-597), CD3 (clone 17A2), CD4 (clone GK1.5), CD8 (clone 53-6.7), CD11c (clone N418), CD11b (clone M1/70), Gr1 (clone RB6-8C5), Ly6C (clone AL-21), F4/80 (clone BM8), TER119 (clone TER-119), NK1.1 (clone PK136)], c-Kit (clone 2B8) and Sca1 (clone D7). FACS sorting was performed on a FACSAria II instrument (BD Biosciences). LSK cells were washed and resuspended in PBS supplemented with 0.04% w/v BSA.
Single cell partitioning and cDNA library construction were done using Chromium Single Cell 3’ Kit v3 per manufacturer’s instruction (10X Genomics).

value: Bone marrow

value: LSK cells

value: CLP surgery


title: EpiLC_Input_2


title: 1168_S2-ChIP-OIN_1

value: genomic DNA


title: LSK, sham, scRNAseq

description: 10x Genomics

value: sham surgery


title: Col-0_3h_rep1

description: SAMPLE 25

value: whole roots

value: 3h zeocin treatment


title: EpiLC_K9me3_2

value: EpiLC


title: crwn1/4_1h_rep4

description: SAMPLE 24

value: 1h zeocin treatment


title: TIL-rep2-gRNA1gRNA2 [mTcell.CP.TA1.G12]


title: 80_total-RNA_2


title: 80_total-RNA_1


title: TIL-rep1-gRNA2gRNA3 [mTcell.CP.T1.G23]


title: EpiLC_Input_1


title: 638_total-RNA_2


title: crwn1/4_1h_rep3

description: SAMPLE 23


title: TIL-rep1-gRNA1gRNA2 [mTcell.CP.T1.G12]


title: crwn1/4_1h_rep2

description: SAMPLE 22


title: SR-rep3-gRNA2gRNA3 [mTcell.CP.SR3.G23]

value: T cells with sgRNA lib genomic insertion delivered via  lentivirus tranduction


title: 638_total-RNA_1


title: crwn1/4_1h_rep1

description: SAMPLE 21


title: 510_total-RNA_2


title: SR-rep3-gRNA1gRNA2 [mTcell.CP.SR3.G12]


title: ESC_CTCF_2

source_name: ESC

value: ESC

value: CTCF


title: SR-rep2-gRNA2gRNA3 [mTcell.CP.SR2.G23]

value: murine T cells


title: cap-h2-2_1h_rep4

description: SAMPLE 20


title: cap-h2-2_1h_rep3

description: SAMPLE 19


title: cap-h2-2_1h_rep1

description: SAMPLE 17


title: ESC_CTCF_1

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: cap-h2-2_1h_rep2

description: SAMPLE 18


title: ESC_K9me3_2

description:
ESC_K9me3_pool_log2ratio_1000.bw
ESC_K9me3_pool.bed


title: SR-rep2-gRNA1gRNA2 [mTcell.CP.SR2.G12]

value: genomic inserted sgRNA amplicon


title: 510_total-RNA_1


title: SR-rep1-gRNA2gRNA3 [mTcell.CP.SR.G23]


title: WT_S2-RIP_2

source_name: wt

value: wt

value: RNA-PolII bound RNA

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: ESC_Rad21_2


title: ESC_K9me3_1


title: WT_S2-RIP_1


title: SR-rep1-gRNA1gRNA2 [mTcell.CP.SR.G12]


title: ESC_Rad21_1


title: 80_S2-RIP_3


title: 80_S2-RIP_2


title: 80_S2-RIP_1


title: ESC_K4me3_1


title: Col-0_1h_rep2

description: SAMPLE 14


title: Col-0_1h_rep1

description: SAMPLE 13


title: mfs_male_tdt_pos

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

description: Sequenced on two lanes (6 total raw files)

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded
Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

source_name: Aortic tissue

extract_protocol:
The aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided midway between the aortic valve and the takeoff of the brachiocephalic artery . Aortas were transferred to a separate dish and rinsed in HBSS. Specimens were combined into groups with age and genotype-matched animals as biologic replicates. The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to seperate fluorescent (tdTomato+) SHF lineage-traced cells and lineage negative cells.. Samples were then processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generate from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

tag: fbn1 genotype

tag: lineage

value: Nkx2-5-Cre traced (SHF)

tag: Sex

value: Male

value: Aorta


title: 638_S2-RIP_2

tag: strain number

tag: target molecule


title: mfs_male_tdt_neg

value: Non lineage-traced


title: Col-0_1h_rep3

description: SAMPLE 15

value: whole roots


title: Col-0_1h_rep4

description: SAMPLE 16


title: crwn1/4_0h_rep4

description: SAMPLE 12

value: 0h zeocin treatment


title: 591_S2-RIP_1

tag: ip antibody


title: mfs_female_tdt_pos

value: Female


title: ESC_K4me3_2


title: mfs_female_tdt_neg


title: wt_male_tdt_pos

value: Control


title: ESC_Input_1


title: 638_S2-RIP_1


title: GSC_netcage_2

description: nascent RNA

data_processing:
Library strategy: NET-CAGE
Sequences were first trimmed using fastp v0.21.0
Then trimmed reads were aligned using STAR 2.7.6a using default options.
Uniquely-mapped reads were converted to coverage bigWig tracks with G-bias correction using CAGEr v1.32.0 using default options.
Tag clusters were identified using CAGEfightR v1.7.6 with pooledCutoff = 0.1 and mergeDist = 20 for unidirectional clusters as well as balanceThreshold = 0.8 for bidirectional clusters.
These clusters were subsequently filtered to require at least 1 sample demonstrating expression level exceeding 1 TPM. Unidirectional clusters (putative promoters) were removed if they overlapped bidirectional clusters (putative enhancers), and the two region sets were subsequently combined to identify coordinately regulation enhancer-promoter co-transcription across stages. In particular, this Kendall correlation analysis of finding co-transcribed enhancer clusters within 1mb of expressed promoter clusters with TPM as the expression unit.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are coverage tracks generated by CAGEr v1.32.0 using default options.

source_name: GSC

extract_protocol:
NET-CAGE library preparation was performed as described previously (Hirabayashi et al., 2019) with minor modifications. For extraction of nascent RNA, cells were firstly lysed with 1400 μl Buffer A, which is Nuclei EZ Lysis Buffer (Sigma) supplemented with 25 μM α-amanitin (Wako), 1× cOmplete Protease Inhibitor Cocktail (Roche, 4693116001) and SUPERase•IN RNase Inhibitor (20 units; Thermo Fisher Scientific), was incubated on ice for 10 min and centrifuged at 800 g for 5 min at 4°C followed by wash once with the same buffer. Washed pellets were resuspended in 200μl Buffer B, containing 1% NP-40, 20 mM HEPES pH7.5, 300 mM NaCl, 2 M urea, 0.2 mM EDTA, 1 mM dithiothreitol (DTT) (Promega), 25 μM α-amanitin, 1× cOmplete Protease Inhibitor Cocktail and SUPERase•IN RNase Inhibitor (20 units), and incubated for 10 min on ice. The suspension was centrifuged at 3000g for 2 min at 4°C. After removing the supernatant, the nuclear insoluble fraction was washed once with 100 μl Buffer B. DNase I solution (50 μl) containing DNase I (10 units; Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and SUPERase•IN RNase Inhibitor (20 units) was added to the pellets. The samples were incubated for 30 min at 37°C while being pipetted up and down several times every 10 min. QIAzol (700 μl) was then added and the solution was thoroughly mixed. RNA was extracted with an miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. On-column DNase I digestion was carried out with an RNase-free DNase set (QIAGEN). RNA was eluted in 30 μl RNase-free water, and its quality and quantity were measured with Qubit RNA HS assay kit (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent). cDNA was synthesized from 200 ng nascent RNA.
CAGE libraries were generated according to the no amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) protocol (Murata et al., 2014) with PCR amplifications (Takara, R060A).

value: GSC

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: crwn1/4_0h_rep3

description: SAMPLE 11


title: wt_male_tdt_neg


title: GSCLC_netcage_1

description: nascent RNA

source_name: GSCLC

value: GSCLC


title: cap-h2-2_0h_rep4

description: SAMPLE 8


title: crwn1/4_0h_rep2

description: SAMPLE 10


title: wt_female_tdt_pos


title: GSCLC_netcage_2

description: nascent RNA


title: ESC_Input_2

value: ESC


title: GSC_netcage_1

description: nascent RNA


title: 544_S2-RIP_1


title: crwn1/4_0h_rep1

description: SAMPLE 9