title: J1 WT cells, D3 (WGBS_EpiLCD3)

data_processing:
The first eight base pairs of the reads were trimmed using FASTX-Toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Adapter sequences were removed with Cutadapt v1.3 and reads shorter than 16 bp were discarded.
Cleaned sequences were aligned onto the Mouse reference genome (mm10) using Bismark v0.12.5 with Bowtie2-2.1.0 and default parameters. Only reads mapping uniquely on the genome were conserved. Methylation calls were extracted after duplicate removal. Only CG dinucleotides covered by a minimum of 5 reads were conserved.
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig

extract_protocol:
50ng of bisulfite-converted genomic DNA using the EpiGnome/Truseq DNA Methylation Kit (Illumina) following the manufacturer instructions.
Sequencing was performed in 100pb paired-end reads at a 30X coverage using the Illumina HiSeq2000 platform.

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x106 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 3 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

value: Day 3


title: n2o2_12_s2

status: Public on Oct 09 2023

type: SRA

city: Ithaca

first: Hao

last: Wu

state: NY

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

country: USA

institute: Cornell University

library_source: transcriptomic

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

molecule: total RNA

organism: Zea mays

source_name: Endosperm

growth_protocol: Field grown plants were self-pollinated

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

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

tag: strain

tag: genotype

tag: age

value: 12 DAP


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

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

library_source: transcriptomic single cell

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

organism: Mus musculus

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

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

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

tag: cell line

tag: cell type

value: Embryonic stem cells (murine)

value: WT

tag: treatment

value: EpiLC differentiation

tag: time


title: n2o2_12_s1


title: E14 TKO cells, Day0, batch1 replicate 16 (SMARTseq2_EpiLC)


title: ET assay 5, replicate C

city: Toronto

first: Nicholas

last: Stepankiw

state: ON

address: 160 College St. Room 1350

country: Canada

institute: University of Toronto

description:
Transient transfection
Transient transfection assay 5

data_processing:
Sequencing reads had constant sequences clipped and were trimmed to 45 bp.  Sequencing reads were mapped to hg38 genome using HISAT2 version 2.2.1. Reads were filtered to have maping quality scores > 20.
Mapped uniquely aligning reads were assigned genomic exon termini positisions based on the maximum MaxEntScan score within 3 bp of the mapped read termini. Exon counts are the sum of reads assigned identical exon termini.
Assembly: hg38
Supplementary files format and content: bed file of exon-trapping found exon coordinates
Supplementary files format and content: tab-delminited text file containing exon-trapping cound exons and read counts

organism: Homo sapiens

extract_protocol:
HEK293 RNA was extracted using Trizol. PolyA RNA was selected using Invitrogen Poly(A)Purist.
Custom, RNA was reverse transcribe into cDNA using Invitrogen SSIV. Two rounds of PCR primers target constant flanking sequence of reporter assay transcript and incorporate sequences for sequencing by Illumina  sequencer platforms.
Other: exon-trapping. Reverse transcription of reporter gene containing query DNA sequence and PCR targeting sequenc flanking the reporter query DNA sequence.

treatment_protocol: Exon trapping reporter plasmids were transiently transfected using Promega Viafect. Growth media was replaced at 24 hours.


title: E14 TKO cells, 96H, biological replicate 3 (BulkRNAseq_PGCLC)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v0.6.2 (parameter Adapter: auto, Min quality: 20, Min length :10)
Trimmed sequence reads were mapped to GrCM38/mm10 using Kallisto (kallisto quant -i  Mus_musculus.GRCm38.cdna.all.index -o  -t 4 )
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include estimated counts and tpm for each Sample

extract_protocol:
RNA extraction was performed on cell pellets using standard Trizol (Life Technologies)-chloroform protocol. RNA pellet was treated with DNase before clean up with RNeasy Mini kit (QIAGEN).
RNA-seq libraries were prepared from a minimum of 10ng of DNase-treated total RNAs SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian

treatment_protocol: After 40h, 48h ou 96h of EpiLC differentiation, cells were resuspended in PGCLC basic medium: GMEM (GIBCO), KSR 15% (GIBCO), Non-Essential Amino Acid (GIBCO), Sodium Pyruvate 1mM (GIBCO), L-Glutamine 2mM (GIBCO), Penicillin-Streptomycin 100U/ml (GIBCO), β-Mercaptoethanol 0.5mM (GIBCO). Then EpiLCs were distributed into ultra-low adhesive U-bottom 96-well plates at a density of 2.5x103 cells/well in 100μl of PGCLC medium complemented with cytokines for PGCLC induction (PGCLC basic medium, 0.5 µg/ml BMP4 (R&D system), 0.5 µg/ml BMP8 (R&D system), 0.1 µg/ml stem cell factor (SCF, R&D system), 50 ng/ml epidermal growth factor (EGF, R&D system), 1000 u/ml mouse LIF). After 4 days of culture, embryoid bodies were harvested and dissociated with 10mM EDTA in PBS+3%FBS for subsequent FACS analyses.

value: TKO

value: PGCLC differentiation

value: 96H EpiLC


title: ET assay 5, replicate E


title: ET assay 5, replicate D


title: E14 TKO cells, 96H, biological replicate 2 (BulkRNAseq_PGCLC)


title: E14 WT cells, Day0, batch1 replicate 16 (SMARTseq2_EpiLC)


title: n2o2_8_s4

value: 8 DAP


title: n2o2_16_s1

value: 16 DAP


title: ET assay 5, replicate B


title: E14 TKO cells, 96H, biological replicate 1 (BulkRNAseq_PGCLC)


title: E14 TKO cells, Day0, batch1 replicate 15 (SMARTseq2_EpiLC)


title: ET assay 5, replicate A


title: ET assay 4, replicate D

description:
Transient transfection
Transient transfection assay 4


title: n2o2_8_s2


title: E14 TKO cells, 48H, biological replicate 3 (BulkRNAseq_PGCLC)

value: 48H EpiLC


title: E14 WT cells, Day0, batch1 replicate 15 (SMARTseq2_EpiLC)


title: E14 TKO cells, 48H, biological replicate 2 (BulkRNAseq_PGCLC)


title: n2o2_12_s3


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

library_source: genomic

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

molecule: genomic DNA

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

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

tag: chip antibody

value: H3K27ac (Active motif 39133)


title: E14 TKO cells, Day0, batch1 replicate 14 (SMARTseq2_EpiLC)


title: n2o2_8_s1


title: E14 TKO cells, 48H, biological replicate 1 (BulkRNAseq_PGCLC)


title: n1o2_16_s4


title: ET assay 4, replicate B


title: E14 TKO cells, Day0, batch1 replicate 13 (SMARTseq2_EpiLC)


title: E14 TKO cells, 40H, biological replicate 3 (BulkRNAseq_PGCLC)

value: 40H EpiLC


title: ET assay 3, replicate E

description:
Transient transfection
Transient transfection assay 3


title: E14 TKO cells, 40H, biological replicate 2 (BulkRNAseq_PGCLC)


title: ET assay 4, replicate A


title: n1o2_16_s2


title: ET assay 3, replicate D


title: E14 TKO cells, Day0, batch1 replicate 12 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 13 (SMARTseq2_EpiLC)


title: n1o2_16_s3


title: n1o2_16_s1


title: E14 TKO cells, 40H, biological replicate 1 (BulkRNAseq_PGCLC)


title: E14 WT cells, 40H, biological replicate 3 (BulkRNAseq_PGCLC)


title: n2o2_8_s3


title: ET assay 4, replicate C


title: n1o2_12_s4


title: E14 WT cells, Day0, batch1 replicate 12 (SMARTseq2_EpiLC)


title: E14 WT cells, 40H, biological replicate 2 (BulkRNAseq_PGCLC)


title: n1o2_12_s3


title: ET assay 3, replicate B


title: ET assay 3, replicate C


title: E14 TKO cells, Day0, batch1 replicate 11 (SMARTseq2_EpiLC)


title: E14 WT cells, 40H, biological replicate 1 (BulkRNAseq_PGCLC)


title: ET assay 3, replicate A


title: E14 WT cells, Day0, batch1 replicate 14 (SMARTseq2_EpiLC)


title: E14 TKO cells, D8, biological replicate 2 (BulkRNAseq_NPC)

growth_protocol: ESCs were cultured on 0.1% gelatin-coated plates with serum-LIF medium (Glasgow medium (Sigma), 2mM L-glutamine (Gibco), 0.1mM MEM non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 15% Fetal Bovine Serum (FBS), 0.1mM β-Mercaptoethanol and 1000 U/ml leukemia inhibitory factor (LIF, Chemicon)). ESCs were cultured in feeder-free conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
RNA extraction was performed on cell pellets using standard Trizol (Life Technologies)-chloroform protocol. RNA pellet was treated with DNase before clean up with RNeasy Mini kit (QIAGEN).
RNA-seq libraries were prepared from a minimum of 200 ng of DNase-treated total RNAs with the TRuSeq Stranded mRNA protocol (Illumina)

treatment_protocol: ESCs were split with accutase onto laminin-coated 6-well/plates (Sigma, 10μg/ml in PBS) at a density of 0.75x104 cells/well in plain N2B27 medium (50% Neurobasal medium and 50% DMEM/F12 (Gibco) complemented with 2mM L-glutamine, 0.1mM β-Mercaptoethanol, N2 supplement (Gibco) and B27 serum-free supplement (Gibco)). Cells were harvested at D0, D2, D4, D6 and D8 of NPC differentiation.

value: NPC differentiation

value: Day 8


title: n1o2_12_s2


title: n1o2_12_s1


title: E14 WT cells, Day0, batch1 replicate 11 (SMARTseq2_EpiLC)


title: ET assay 2, replicate D

description:
Transient transfection
Transient transfection assay 2


title: E14 TKO cells, D8, biological replicate 1 (BulkRNAseq_NPC)


title: E14 TKO cells, Day0, batch1 replicate 10 (SMARTseq2_EpiLC)


title: ET assay 2, replicate C


title: ET assay 2, replicate B


title: n1o2_8_s3


title: E14 TKO cells, D6, biological replicate 1 (BulkRNAseq_NPC)

value: Day 6


title: E14 WT cells, Day0, batch1 replicate 10 (SMARTseq2_EpiLC)


title: n1o2_8_s2


title: ET assay 2, replicate A


title: E14 TKO cells, Day0, batch1 replicate 9 (SMARTseq2_EpiLC)


title: ET assay 1, replicate E

description:
Transient transfection
Transient transfection assay 1


title: E14 WT cells, Day0, batch1 replicate 9 (SMARTseq2_EpiLC)


title: E14 TKO cells, D4, biological replicate 2 (BulkRNAseq_NPC)

value: Day 4


title: E14 TKO cells, D4, biological replicate 1 (BulkRNAseq_NPC)


title: E14 TKO cells, D2, biological replicate 2 (BulkRNAseq_NPC)

value: Day 2


title: E14 WT cells, Day0, batch1 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch1 replicate 8 (SMARTseq2_EpiLC)


title: ET assay 1, replicate D


title: ET assay 1, replicate C


title: o2_16_s4


title: o2_16_s3


title: E14 TKO cells, Day0, batch1 replicate 7 (SMARTseq2_EpiLC)


title: n1o2_8_s4


title: E14 WT cells, Day0, batch1 replicate 7 (SMARTseq2_EpiLC)


title: ET assay 1, replicate B


title: E14 TKO cells, D0, biological replicate 2 (BulkRNAseq_NPC)

value: Day 0


title: E14 TKO cells, D6, biological replicate 2 (BulkRNAseq_NPC)

value: Embryonic stem cells (murine)


title: ET assay 1, replicate A


title: o2_16_s1


title: E14 TKO cells, Day0, batch1 replicate 6 (SMARTseq2_EpiLC)

value: WT


title: o2_12_s4

value: 12 DAP


title: E14 TKO cells, D0, biological replicate 1 (BulkRNAseq_NPC)

value: TKO


title: 293FT, RIPseq, Cas13d, FLAG, RIP

city: Shenyang

first: Teng

last: Fei

state: Liaoning

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

department: College of Life and Health Sciences

country: China

institute: Northeastern University, China

description: Binding RNA

data_processing:
The RIP-seq reads were aligned against the hg38 human reference genome using HISAT2.
Since the RIP-seq data is strand-specific, the peaks were called (RIP vs input) and identified for “+” and “–” strands separately using MACS2, with false-discovery rate (FDR) ≤ 0.01 and arbitrary extension size of 150 bp.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include peak called for each Sample

source_name: human embryonal kidney cells

growth_protocol: HEK293FT  cells were regularly tested negative for mycoplasma contamination and maintained in DMEM (SEVEN Biotech) supplemented with 10% fetal bovine serum (ExCell) and 1% penicillin–streptomycin (Solarbio). Cells were passaged every 2-4 days to maintain exponential growth and were kept in a humidity-controlled incubator at 37°C with 5% CO2.

extract_protocol:
After 3 days transfection, cells were harvested by cross-linking with 0.3% formaldehyde for 10 min at room temperature and lysing with RIPA lysis buffer (50 mM Tris (pH 7.6), 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate, protease inhibitor and RNase inhibitor) for 10 min on ice before sonication.
The supernatant was collected and incubated with IgG and FLAG antibodies at 4 °C overnight. After washing with RIPA buffer (50 mM Tris (pH 7.6), 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate), RNA was eluted from the beads with elution buffer (0.1 M NaHCO3 and 1% SDS, addition with proteinase K and RNase inhibitor) at room temperature for 10 min with gently vortex. The eluted material was then de-cross-linked at 65 °C for 45–60 min and treated with RNase inhibitor and proteinase K. Afterwards, RNA was purified using TRIzol LS reagent (Life Technologies) and treated with DNase I to remove any residual DNA. RIP RNA was used for library preparation.

treatment_protocol: HEK293FT cells were plated in 15 cm plates and transfected at > 50% confluency with 25 µg of indicated plasmids using NeofectTM DNA transfection reagent according to the manufacturer’s protocol.

tag: tissue

value: kidney

tag: transfection

value: Day 3 after transient transfection

tag: rip antibody

value: FLAG （Invitrogen #MA1-91878）


title: n1o2_8_s1

value: 8 DAP


title: E14 WT cells, D8, biological replicate 2 (BulkRNAseq_NPC)


title: o2_12_s3


title: E14 WT cells, Day0, batch1 replicate 6 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: 293FT, RIPseq, Cas13d, FLAG, input

description: Binding RNA


title: E14 TKO cells, Day0, batch1 replicate 5 (SMARTseq2_EpiLC)


title: E14 WT cells, D8, biological replicate 1 (BulkRNAseq_NPC)


title: E14 WT cells, D6, biological replicate 2 (BulkRNAseq_NPC)


title: E14 WT cells, Day0, batch1 replicate 5 (SMARTseq2_EpiLC)


title: o2_12_s2


title: 293FT, RIPseq, Cas13b, crNT, FLAG, RIP

description: Binding RNA


title: o2_12_s1


title: E14 TKO cells, D2, biological replicate 1 (BulkRNAseq_NPC)


title: o2_16_s2

value: 16 DAP


title: 293FT, RIPseq, Cas13b, FLAG, RIP

description: Binding RNA


title: E14 TKO cells, Day0, batch1 replicate 4 (SMARTseq2_EpiLC)


title: 293FT, RIPseq, Cas13b, crNT, FLAG, input

description: Binding RNA


title: o2_8_s4


title: 293FT, RIPseq, Cas13b, FLAG, input

description: Binding RNA


title: E14 WT cells, Day0, batch1 replicate 4 (SMARTseq2_EpiLC)


title: E14 WT cells, D4, biological replicate 1 (BulkRNAseq_NPC)


title: E14 WT cells, D4, biological replicate 2 (BulkRNAseq_NPC)


title: o2_8_s3


title: E14 WT cells, D2, biological replicate 2 (BulkRNAseq_NPC)


title: o2_8_s2


title: E14 WT cells, Day0, batch1 replicate 3 (SMARTseq2_EpiLC)


title: E14 WT cells, D6, biological replicate 1 (BulkRNAseq_NPC)


title: o2_8_s1


title: E14 TKO cells, Day0, batch1 replicate 2 (SMARTseq2_EpiLC)


title: E14 WT cells, D2, biological replicate 1 (BulkRNAseq_NPC)


title: n2_16_s4


title: E14 WT cells, D0, biological replicate 2 (BulkRNAseq_NPC)


title: E14 WT cells, Day0, batch1 replicate 2 (SMARTseq2_EpiLC)


title: n2_16_s3


title: E14 WT cells, D0, biological replicate 1 (BulkRNAseq_NPC)


title: n2_16_s2


title: E14 TKO cells, Day0, batch1 replicate 1 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch1 replicate 1 (SMARTseq2_EpiLC)


title: 293FT, RIPseq, Vector, FLAG, RIP

description: Binding RNA

value: pLenti-backbone


title: 293FT, RIPseq, Cas9, FLAG, input

description: Binding RNA

value: pLenti-CRISPR v2


title: 293FT, RIPseq, Cas13a, FLAG, input

description: Binding RNA


title: 293FT, RIPseq, Cas9, FLAG, RIP

description: Binding RNA


title: 293FT, RIPseq, Cas13a, FLAG, RIP

description: Binding RNA


title: E14 TKO cells, D7, biological replicate 2 (BulkRNAseq_EpiLC)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Atropos (github.com/jdidion/atropos)
Trimmed sequence reads were mapped to GrCM38/mm10 using Kallisto (kallisto quant -i  Mus_musculus.GRCm38.cdna.all.index -o  -t 4 )
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include estimated counts and tpm for each Sample

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x106 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 0,  2, 4, and 7 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

value: Day 7


title: n2_16_s1


title: 293FT, RIPseq, Vector, FLAG, input

description: Binding RNA


title: E14 TKO cells, Day0, batch1 replicate 3 (SMARTseq2_EpiLC)


title: Breast Cancer, Xenium In Situ Spatial Gene Expression

type: RNA

city: Pleasanton

first: Stephen

middle: Richardson

last: Williams

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

hyb_protocol: The Xenium samples underwent 15 rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section. Decoding of transcripts was performed using a Xenium codebook ? a collection of codewords that were assigned to genes in the gene panel. In order to assign mRNAs to cells, the spatial boundaries of cells were defined by nuclear expansion. Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/assay/xenium-in-situ-gene-expression-probe-hybridization-ligation-amplification. Xenium was run on a prototype instrument.

scan_protocol: Xenium In Situ Analyzer

data_processing: Data processed using Xenium Ranger software

label: Xenium Human Probe Set

source_name: 5 µm section Breast Cancer

label_protocol: Xenium Human Probe Set

extract_protocol: Two replicate 5 μm sections were taken each for Xenium. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy.  A 5 μm section was also taken from Sample #2 for Xenium.

tag: disease state

value: Breast Cancer


title: n2_12_s4


title: 293FT, RIPseq, Vector, IgG, RIP

description: Binding RNA

value: IgG （Santa Cruz #sc-2025）


title: E14 TKO cells, D4, biological replicate 2 (BulkRNAseq_EpiLC)

value: Day 4


title: n2_12_s3


title: 293FT, RIPseq, Vector, IgG, input

description: Binding RNA


title: n2_12_s2


title: E14 TKO cells, D2, biological replicate 2 (BulkRNAseq_EpiLC)

value: Day 2


title: n2_12_s1


title: UBQ10::mCitrine-IMA1,-Fe+flg22 root, rep3

city: La Jolla

first: Ling

last: Zhang

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were trimmed for adaptors and masked for low-quality sequence
RNA-Seq read were mapped to A. thaliana reference genome (TAIR10) using STAR 2.7.0a
Differentially expressed genes were detected by edgeR (version 3.36.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes CPM values for all Samples
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
The root total RNA was isolated from around 15 roots (as a pool for one biological replicate) by using SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, Cat. STRN250).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Root

value: No Fe and flg22


title: A375-Cas13bnls-13bTwoVector-Day33-R2

description: Pcr product from genomic DNA of cell line

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

source_name: melanoma cells

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

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

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

value: skin

tag: infection

value: Lentivirus Pool for Cas13b_TwoVector

value: Day 33


title: UBQ10::mCitrine-IMA1,-Fe+flg22 root, rep2


title: E14 TKO cells, D2, biological replicate 1 (BulkRNAseq_EpiLC)

value: Embryonic stem cells (murine)

value: TKO


title: A375-Cas13bnls-13bTwoVector-Day33-R1


title: n2_8_s4

value: 8 DAP


title: A375-Cas13bnls-13bTwoVector-Day5-R2

value: Day 5


title: UBQ10::mCitrine-IMA1,-Fe+flg22 root, rep1


title: UBQ10::mCitrine-IMA1,-Fe root, rep3

description: IMA1ox _noFe_3

value: No Fe


title: n2_8_s3


title: A375-Cas13bnls-13bTwoVector-Day5-R1


title: E14 TKO cells, D7, biological replicate 1 (BulkRNAseq_EpiLC)

value: EpiLC differentiation


title: A375wt-13bTwoVector-Day33-R2


title: E14 TKO cells, D0, biological replicate 2 (BulkRNAseq_EpiLC)

value: Day 0


title: n2_8_s2


title: E14 TKO cells, D0, biological replicate 1 (BulkRNAseq_EpiLC)


title: UBQ10::mCitrine-IMA1,-Fe root, rep2

description: IMA1ox _noFe_2


title: E14 WT cells, D7, biological replicate 1 (BulkRNAseq_EpiLC)

value: WT

value: Day 7


title: A375wt-13bTwoVector-Day33-R1


title: E14 TKO cells, D4, biological replicate 1 (BulkRNAseq_EpiLC)


title: A375wt-13bTwoVector-Day5-R2


title: UBQ10::mCitrine-IMA1,+Fe+flg22 root, rep3

description: IMA1ox _Fe_flg22_3

value: Plus Fe and flg22


title: n1_16_s3

value: 16 DAP


title: E14 WT cells, D4, biological replicate 2 (BulkRNAseq_EpiLC)

value: Day 4


title: E14 WT cells, D4, biological replicate 1 (BulkRNAseq_EpiLC)


title: UBQ10::mCitrine-IMA1,+Fe+flg22 root, rep2

description: IMA1ox _Fe_flg22_2

value: Root


title: A375wt-13bTwoVector-Day5-R1


title: n1_16_s2


title: UBQ10::mCitrine-IMA1,+Fe+flg22 root, rep1

description: IMA1ox _Fe_flg22_1


title: A375-Cas13dnls-13dTwoVector-Day33-R2

value: Lentivirus Pool for Cas13d_TwoVector


title: E14 WT cells, D2, biological replicate 2 (BulkRNAseq_EpiLC)

value: Day 2


title: E14 WT cells, D7, biological replicate 2 (BulkRNAseq_EpiLC)


title: n1_16_s1


title: A375-Cas13dnls-13dTwoVector-Day33-R1

value: skin


title: E14 WT cells, D2, biological replicate 1 (BulkRNAseq_EpiLC)


title: UBQ10::mCitrine-IMA1,-Fe root, rep1

description: IMA1ox _noFe_1


title: UBQ10::mCitrine-IMA1,+Fe root, rep2

description: IMA1ox _Fe_2

value: Plus Fe


title: n2_8_s1


title: E14 WT cells, D0, biological replicate 2 (BulkRNAseq_EpiLC)

value: Embryonic stem cells (murine)


title: n1_12_s3

value: 12 DAP


title: n1_12_s4


title: UBQ10::mCitrine-IMA1,+Fe root, rep1

description: IMA1ox _Fe_1


title: A375-Cas13dnls-13dTwoVector-Day5-R1


title: A375-Cas13dnls-13dTwoVector-Day5-R2


title: n1_16_s4


title: E14 WT cells, D0, biological replicate 1 (BulkRNAseq_EpiLC)


title: A375wt-13dTwoVector-Day33-R2

value: Day 33


title: fls2,-Fe+flg22 root, rep3

value: No Fe and flg22


title: n1_12_s2


title: n1_12_s1


title: fls2,-Fe+flg22 root, rep2


title: E14 TKO cells, D4, biological replicate 1 (ATAC_EpiLC)

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

extract_protocol:
The ATAC protocol was optimized from Fursova et al., 2021. First, 1x10^7 ESCs were mixed with 2.5x10^6 Drosophila S2 cells, and resuspended and incubated in 1ml Lysis Buffer (50mM KCl, 10mM MgSO4.7H20, 5mM HEPES, 0.05% NP40) for 5 min at RT. After a spin at 4°C 1500g for 5 min, the supernatant was discarded and nuclei pellet was resuspended in ice-cold RS Buffer (10mM NaCl, 10mM Tris-HCl, 3mM MgCl2). Nuclei were counted using Beckman Coulter ViCell XR cyto-counter, to ensure nuclei integrity. Tagmentation was performed on 50 000 nuclei per sample, with TDE1 Tn5 transposase (Nextera), at 37°C for 30 min. The reaction was stopped by the addition of PB Buffer and tagmented DNA was eluted using minElute columns from Reaction clean-up Qiagen Kit. We used 50ng of tagmented genomic DNA isolated from the same nuclei preparation to control for Tn5 transposition bias.
Library preparation was made according to the manufacturer’s instructions (Accel NGS 2S DNA library kit, Swift Biosciences). For library amplification, 12 PCR cycles were applied as followed: 98°C for 10 sec, 60°C for 15 sec and 68°C for one minute. Library size and quantification was assessed on Agilent 4200 Tapestation. C

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x10^6 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 0, 2, and 4 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

tag: tn5 transposase

value: TDE1 Tn5 transposase (Nextera)

value: TKO


title: A375wt-13dTwoVector-Day5-R2

value: Day 5


title: fls2,-Fe+flg22 root, rep1


title: n1_8_s4

value: 8 DAP


title: E14 TKO cells, D2, biological replicate 2 (ATAC_EpiLC)


title: UBQ10::mCitrine-IMA1,+Fe root, rep3

description: IMA1ox _Fe_3


title: n1_8_s3


title: fls2,-Fe root, rep3

description: fls2 _noFe_3

value: No Fe


title: A375wt-13dTwoVector-Day5-R1


title: fls2,-Fe root, rep2

description: fls2 _noFe_2


title: fls2,-Fe root, rep1

description: fls2 _noFe_1


title: WT_16_s4


title: E14 TKO cells, D2, biological replicate 1 (ATAC_EpiLC)


title: A375-Cas13d-OneVector-Day33-R2

value: Lentivirus Pool for Cas13d OneVector


title: fls2,+Fe+flg22 root, rep3

value: Plus Fe and flg22


title: A375-Cas13d-OneVector-Day5-R1


title: n1_8_s2


title: E14 TKO cells, D0, biological replicate 2 (ATAC_EpiLC)


title: n1_8_s1


title: WT_16_s2

value: 16 DAP


title: E14 TKO cells, D4, biological replicate 2 (ATAC_EpiLC)


title: fls2,+Fe+flg22 root, rep2

value: Root


title: A375-Cas13d-OneVector-Day33-R1


title: A375-Cas13d-OneVector-Day5-R2


title: E14 TKO cells, D0, biological replicate 1 (ATAC_EpiLC)


title: WT_16_s3


title: A375wt-13dTwoVector-Day33-R1

value: Lentivirus Pool for Cas13d_TwoVector


title: E14 WT cells, D4, biological replicate 1 (ATAC_EpiLC)

value: WT


title: E14 WT cells, D2, biological replicate 1 (ATAC_EpiLC)


title: Total RNA from patient HDF with K181N mutation- Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Basic QC and mapping were performed using snakePipes v.2.5.1
Reads were trimmed using cutadapt and aligned to the hg38 or mm10 genome assembly using STAR.
Counts for individual genes were obtained using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 LFC output in tsv format

source_name: Human Derived Fibroblasts

growth_protocol: Both MEFs and HDFs were cultured in High Glucose DMEM supplemented with GlutaMax, 10 % FBS and penicillin-streptomycin at 37 °C and 5 % CO2.

extract_protocol:
Total RNA was collected using Trizol and purified using Zymo Research DirectZol RNA Mini Prep Kit.
Libraries were prepared according to the instructions of Illumina's Stranded RNA with RiboZero Plus kit.

treatment_protocol: For glucose/galactose adaption experiment in primary MEFs, cells were cultured in no-glucose growth medium supplemented with either 25 mM glucose or galactose for 2 weeks followed by 4-OHT treatment for additional 4 days.

value: Untreated

value: KAT8 Syndrome Patient


title: E14 WT cells, D4, biological replicate 2 (ATAC_EpiLC)

value: Embryonic stem cells (murine)


title: fls2,+Fe+flg22 root, rep1


title: fls2,+Fe root, rep1

value: Plus Fe


title: Total RNA from patient HDF with K181N mutation- Rep1


title: WT_16_s1


title: WT,-Fe+flg22 root, rep3

value: WT (Col-0)


title: E14 WT cells, D0, biological replicate 1 (ATAC_EpiLC)


title: Total RNA from patient HDF with K181N mutation- Rep3


title: Total RNA from patient HDF with K181N mutation- Rep4


title: fls2,+Fe root, rep3


title: WT,-Fe+flg22 root, rep2

value: No Fe and flg22


title: scRNAseq_Multiome_B16_CAR_T_D7_Tumor

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description: 10x Genomics

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

source_name: Tumor

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

value: Tumor

value: ex vivo

value: CAR T cells


title: fls2,+Fe root, rep2


title: E14 WT cells, D0, biological replicate 2 (ATAC_EpiLC)

value: TDE1 Tn5 transposase (Nextera)


title: WT_8_s4

value: 8 DAP


title: WT_12_s4

value: 12 DAP


title: Total RNA from patient HDF with A165V mutation- Rep3


title: Total RNA from patient HDF with A165V mutation- Rep2


title: Total RNA from patient HDF with A165V mutation- Rep4


title: scATACseq_Multiome_B16_CAR_T_D7_Tumor

description: 10x Genomics


title: Total RNA from patient HDF with A165V mutation- Rep1


title: WT,-Fe root, rep3

value: No Fe


title: WT_12_s1


title: E14 WT cells, D2, biological replicate 2 (ATAC_EpiLC)


title: scRNAseq_B16_CAR_T_D21_Spleen

description: 10x Genomics

source_name: Spleen

value: Spleen


title: WT_12_s2


title: WT,-Fe+flg22 root, rep1

value: Root


title: WT_12_s3


title: scRNAseq_B16_CAR_T_D21_Tumor

description: 10x Genomics


title: WT_8_s2


title: Total RNA from patient HDF with  R99Q mutation- Rep4


title: WT_8_s1


title: Total RNA from patient HDF with  R99Q mutation- Rep3


title: WT,-Fe root, rep2


title: scRNAseq_B16_CAR_T_D7_Tumor

description: 10x Genomics


title: scRNAseq_B16_CAR_T_D7_Spleen

description: 10x Genomics


title: Total RNA from patient HDF with  R99Q mutation- Rep2


title: WT,+Fe+flg22 root, rep3

value: Plus Fe and flg22


title: WT,-Fe root, rep1


title: WT_8_s3


title: scRNAseq_Multiome_E2APBX1_CAR_T_D7_Spleen

description: 10x Genomics

value: WT


title: Total RNA from patient HDF with R99Q mutation- Rep1

value: Untreated


title: Total RNA from healthy HDF- Rep4

value: Wild-type

value: Healthy


title: WT,+Fe+flg22 root, rep1


title: WT,+Fe+flg22 root, rep2


title: WT,+Fe root, rep3

value: Plus Fe


title: Total RNA from healthy HDF- Rep3


title: WT,+Fe root, rep2

value: WT (Col-0)


title: Total RNA from healthy HDF- Rep2


title: scRNAseq_E2APBX1_CAR_T_D7_BoneMarrow

description: 10x Genomics

source_name: Bone Marrow

value: Bone Marrow


title: scRNAseq_E2APBX1_CAR_T_D21_Spleen

description: 10x Genomics


title: Normal_blood_rep1

city: Guangzhou

first: Weixin

last: Guo

state: Guangdong

address: No. 106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

description:
N1
circRNA expression of normal male blood

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 22.5 μL containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 22.5 μL of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression (8*60k) for 17 hours at 65 ℃ 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 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent ONA Microarray Scanner (G2505C) using one color scan setting for 4×l80k array slides (Scan Area 61×21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintatined.

source_name: Blood, normal

label_protocol: Cyanlne-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color low RNA Input Linear Ampllfieation PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Blosystem p/n AM1556) following the manufacturer's Instructions.

treatment_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). 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). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

tag: group

value: control group

value: Blood

tag: gender

value: male


title: Cases_blood_rep3

description:
C3
circRNA expression after infected sepsis male blood

source_name: Blood, cases

value: sepsis group


title: Total RNA from healthy HDF- Rep1


title: scRNAseq_E2APBX1_CAR_T_D7_Spleen

description: 10x Genomics

value: ex vivo

value: CAR T cells


title: Normal_blood_rep3

description:
N3
circRNA expression of normal male blood


title: Cases_blood_rep2

description:
C2
circRNA expression after infected sepsis male blood


title: Cases_blood_rep1

description:
C1
circRNA expression after infected sepsis male blood


title: WT,+Fe root, rep1


title: scATACseq_Multiome_E2APBX1_CAR_T_D7_Spleen

description: 10x Genomics


title: dease6

status: Public on Oct 08 2023

city: Shenzhen

first: Li

last: Yudi

address: No. 1098 Xueyuan Avenue, 518060 Shenzhen, Guangdong, China.

institute: Shenzhen Hospital, Southern Medical University

description: Biological replicate 5 of 5，Peripheral blood mononuclear cells from patients with Cervical artery dissection

data_processing:
Trimmomatictools(V0.36)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below15
drop reads which are less than 35% of initiation read length. Then reads quality was inspected using thefastq.gzC software then output statistical result
CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to humanreference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat
CIRI2 detectsthe paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment withBWA-MEM and combines with systematic filtering steps to remove potential false positives.CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs. If a circRNA can be detected by both methods, it will be consided as an identified circRNA
The DEseq/DESeq2/edgeR/DEGseq package in Bioconductor was used to determine differently expressed circRNAs
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes circName, Strand, Junction_reads for each sample

source_name: Peripheral blood

growth_protocol: Venous blood samples (10 mL) were collected from patients with Cervical artery dissection (CeAD) and healthy controls

extract_protocol:
Total RNA was isolated from PBMCs using the Magzol Reagent (Magen, China), as per manufacturer’s protocol. The quantity and integrity of the RNA was assessed using the K5500 micro-spectrophotometer (Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA), respectively. Briefly, rRNAs were removed from the total RNA using the QIAseq FastSelect-rRNA HMR Kit (QIAGEN, Germany). The RNA was then treated with RNase R (Epicenter, USA) and fragmented to approximately 200 bp
the purified RNA fragments were subjected to first strand and second strand cDNA synthesis, followed by adaptor ligation and enrichment with a low cycle according to manufacturer’s instructions for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The library products were evaluated using the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA), and further sequenced using an Illumina (Illumina, USA), through the paired-end 150 bp approach, at Ribobio Co. Ltd. (Ribobio, China).

treatment_protocol: Peripheral blood mononuclear cells ( PBMCs) were extracted as previously described(Deng, Pan et al. 2017)

value: Peripheral blood

value: human

value: mononuclear cells


title: con5

description: Biological replicate 5 of 5，Peripheral blood mononuclear cells from normal patients

value: patients with no Cervical artery dissection


title: dease4

description: Biological replicate 3 of 5，Peripheral blood mononuclear cells from patients with Cervical artery dissection


title: scRNAseq_E2APBX1_CAR_T_D21_BoneMarrow

description: 10x Genomics

value: WT


title: dease1

description: Biological replicate 1 of 5，Peripheral blood mononuclear cells from patients with Cervical artery dissection


title: dease3

description: Biological replicate 2 of 5，Peripheral blood mononuclear cells from patients with Cervical artery dissection


title: con4

description: Biological replicate 4 of 5，Peripheral blood mononuclear cells from normal patients


title: Normal_blood_rep2

description:
N2
circRNA expression of normal male blood


title: con3

description: Biological replicate 3 of 5，Peripheral blood mononuclear cells from normal patients


title: con2

description: Biological replicate  2 of 5，Peripheral blood mononuclear cells from normal patients


title: con1

description: Biological replicate 1 of 5，Peripheral blood mononuclear cells from normal patients


title: SC-WT3_S15

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description:
sample name:
Sample 71

data_processing:
All analysis was performed on Partek Flow Genomic Analysis Software
Reads were aligned to the Mus musculus genome (mm10) using STAR – 2.7.3a
Alignments were quantified using Partek E/M
Quantified alignments were normalized with TPM (transcripts per million), followed by and quantile normalization including all samples
Assembly: Mus musculus genome (mm10)
Supplementary files format and content: Tab-separated values matrix file containing raw read counts (counts.txt) and normalized read counts (normalized.txt) are provided

source_name: Spinal Cord

extract_protocol:
RNA was then extracted using the Qiagen miRNeasy Mini Kit. RNA quality and quantity were assessed with the RNA 6000 Nano kit on the Agilent 2100 Bioanalyzer.
For forebrain heart, muscle and striatum, sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep kit, using 1 microgram total RNA as input. For cerebellum and spinal cord, sequencing libraries were prepared using the Illumina Stranded mRNA Library Prep kit Ligation, using 500 nanograms Total RNA as input. Library size was assessed with the DNA 1000 Kit on the Agilent 2100 Bioanalyzer.

treatment_protocol: Tissue was disputed in QIAzol lysis reagent, using the Qiagen TissueRuptor.

value: Spinal Cord

tag: age (months)


title: SC-WT2_S14

description:
sample name:
Sample 70


title: SC-KI1_S9

description:
sample name:
Sample 65

value: KI


title: SC-WT1_S13

description:
sample name:
Sample 69


title: SC-WT4_S16

description:
sample name:
Sample 72


title: dease5

description: Biological replicate 4 of 5，Peripheral blood mononuclear cells from patients with Cervical artery dissection


title: SC-KI4_S12

description:
sample name:
Sample 68


title: SC-KI3_S11

description:
sample name:
Sample 67


title: SC-KI2_S10

description:
sample name:
Sample 66


title: M-KI1_S9

description:
sample name:
Sample 57

source_name: Muscle

value: Muscle


title: M-WT4_S16

description:
sample name:
Sample 64


title: H-KI1_S1

description:
sample name:
Sample 49

source_name: Forebrain

value: Forebrain


title: M-WT3_S15

description:
sample name:
Sample 63


title: M-WT2_S14

description:
sample name:
Sample 62


title: M-WT1_S13

description:
sample name:
Sample 61


title: M-KI4_S12

description:
sample name:
Sample 60


title: B-KI2_S2

description:
sample name:
Sample 42


title: M-KI3_S11

description:
sample name:
Sample 59


title: 30mo-SC-WT5_S13

description:
sample name:
Sample 37


title: M-KI2_S10

description:
sample name:
Sample 58


title: H-WT4_S8

description:
sample name:
Sample 56


title: H-KI4_S4

description:
sample name:
Sample 52


title: H-WT1_S5

description:
sample name:
Sample 53


title: H-KI2_S2

description:
sample name:
Sample 50


title: H-KI3_S3

description:
sample name:
Sample 51


title: B-WT4_S8

description:
sample name:
Sample 48


title: B-WT3_S7

description:
sample name:
Sample 47


title: B-WT2_S6

description:
sample name:
Sample 46


title: 30mo-SC-KI4_S10

description:
sample name:
Sample 34


title: 30mo-SC-KI1_S7

description:
sample name:
Sample 31


title: B-WT1_S5

description:
sample name:
Sample 45


title: B-KI4_S4

description:
sample name:
Sample 44


title: 30mo-M-WT3_S4

description:
sample name:
Sample 28


title: B-KI3_S3

description:
sample name:
Sample 43


title: 30mo-M-WT1_S2

description:
sample name:
Sample 26


title: 30mo-M-WT2_S3

description:
sample name:
Sample 27


title: B-KI1_S1

description:
sample name:
Sample 41


title: 30mo-M-KI4_S13

description:
sample name:
Sample 24


title: 30mo_SC_WT3_S13

description:
sample name:
Sample 40


title: 30mo_SC_WT2_S12

description:
sample name:
Sample 39


title: H-WT3_S7

description:
sample name:
Sample 55


title: 30mo_SC_WT1_S11

description:
sample name:
Sample 38


title: 30mo-SC-WT4_S12

description:
sample name:
Sample 36


title: 30mo_H_WT3_S3

description:
sample name:
Sample 18

source_name: Heart

value: Heart


title: H-WT2_S6

description:
sample name:
Sample 54


title: 30mo-SC-KI5_S11

description:
sample name:
Sample 35


title: 30mo_H_KI5_S10

description:
sample name:
Sample 15


title: 30mo-SC-KI3_S9

description:
sample name:
Sample 33


title: 30mo-M-WT5_S6

description:
sample name:
Sample 30


title: 30mo-SC-KI2_S8

description:
sample name:
Sample 32


title: 30mo_H_KI3_S8

description:
sample name:
Sample 13


title: 30mo_H_KI1_S6

description:
sample name:
Sample 11


title: 30mo-M-KI5_S14

description:
sample name:
Sample 25


title: 30mo-M-WT4_S5

description:
sample name:
Sample 29


title: 30mo-Ce-WT5_S10

description:
sample name:
Sample 10

source_name: Cerebellum

value: Cerebellum


title: 30mo-Ce-WT4_S9

description:
sample name:
Sample 9


title: 30mo-M-KI3_S12

description:
sample name:
Sample 23


title: 30mo-M-KI2_S11

description:
sample name:
Sample 22


title: 30mo-M-KI1_S1

description:
sample name:
Sample 21


title: 30mo_H_WT5_S5

description:
sample name:
Sample 20


title: 30mo-Ce-KI4_S4

description:
sample name:
Sample 4


title: 30mo-Ce-KI2_S2

description:
sample name:
Sample 2


title: 30mo-Ce-KI5_S5

description:
sample name:
Sample 5


title: 30mo_H_WT4_S4

description:
sample name:
Sample 19


title: 30mo_H_WT2_S2

description:
sample name:
Sample 17


title: 30mo-Ce-KI1_S1

description:
sample name:
Sample 1


title: P16 Zeb1-CKO ATAC 1

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institute of Biological Sciences

description:
primary retina EC
Zeb1-cko_P16_rep1

data_processing:
Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘ILLUMINACLIP:NexteraPE-PE:1:13:6:1:True SLIDINGWINDOW:10:10 MINLEN:15’.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 10 -b’.
Broad peak calling to determine enriched ATAC regions was performed on individual sample replicates as well as pooled replicates using MACS2 v2.1.1 (Zhang et al., 2008) with parameters ‘--nomodel --shift -100 --extsize 200 –broad’. Peaks in blacklisted regions (ENCODE Project Consortium, 2012) were filtered using the bedtools v2.26.0 (Quinlan, Hall, 2010) intersect command.
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak files of preaks called by MACS2 indicating open chromatin

source_name: Retina

growth_protocol: Endothelila cell were FACS isolated from mouse retina

extract_protocol:
Following a 10min centrifugation at 4°C, nucleic extracts were resuspended in transposition buffer for 30 min at 37°C.
Transposed DNA was amplified by PCR with Nextera primers (Buenrostro, 2013) to generate Dual-indexed libraries. Library quality control was carried out using the Bioanalyzer High-Sensitivity DNA analysis kit. Libraries were sequenced on the Illumina Nova-seq 6000 platform.

treatment_protocol: 2000 FACS isolated retinal endothelial cells were collected and suspended in ice-cold PBS. Cells were pelleted and resuspended in lysis buffer

value: Retina

value: Zeb1 knockdown

tag: strain

value: endothelial cells

value: FACS isolated EC


title: P16 Zeb1-CKO ATAC 2

description:
primary retina EC
Zeb1-cko_P16_rep2

tag: genotype


title: 30mo_H_KI4_S9

description:
sample name:
Sample 14


title: P16 Control EC ATAC 2

description:
primary retina EC
Control_P16_Rep2

value: control


title: 30mo_H_KI2_S7

description:
sample name:
Sample 12


title: 30mo-Ce-WT1_S6

description:
sample name:
Sample 6


title: P16 Control EC 2

description: primary retina EC

data_processing:
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters 'SLIDINGWINDOW:10:20 MINLEN:30'.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated table of genes with their corresponding FPKM values as output by Ballgown

extract_protocol:
Total RNA pellets were dissolved in lysis solution and used as a template for low-cell number RNA-seq.
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 150).

treatment_protocol: 100 FACS isolated retinal endothelial cells were collected. Samples were lysed in inguanidine isotheiocyanate solutionand.


title: P16 Control EC 1

description: primary retina EC


title: 30mo-Ce-WT3_S8

description:
sample name:
Sample 8


title: AtTPax7_SMC1

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

institute: IRCM

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Reads from multiple biological replicates were merged (if applicable).
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools/3.5.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept for library preparation.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Corticotrope


title: 30mo-Ce-KI3_S3

description:
sample name:
Sample 3


title: AtTERPax7_Pax7_Tam30d

source_name: Cell line

value: Cell line

value: Tam 30 days


title: 30mo-Ce-WT2_S7

description:
sample name:
Sample 7


title: H6_136_SU22_O

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

data_processing:
Bcl2fastq2 v2.18 (Illumina) was used to extract the data and generate FASTQ files for each sample by using unique barcode combinations from the Nextera preparation. Raw paired-end FASTQ reads were then aligned to GENCODE v25 reference transcripts (GRCh38.p7) with Salmon v0.7.2 using the --seq-bias flag and otherwise default parameters. Salmon results were merged into a single gene-level TPM matrix using the R package, tximport v1.4.0. Low quality cells, identified as cells expressing <1,000 detectable genes, were excluded from further analysis. Using Seurat, clusters were identified by running ‘FindClusters’ on the first 10 principal components of the data with the resolution parameter set to 0.6. Cell labels for known epithelial subpopulations were assigned according to the expression of previously described marker genes (KRT14high, MYLKhigh = basal; MMP7high, RARRES1high = luminal progenitor; MUC1high, AREGhigh = mature luminal; FAPhigh, PDGFRAhigh = fibroblast; CDH5high, EMCNhigh, PECAM1high = endothelial cell, CD3high, CD4high = CD4 T cell, CD3high, CD8high = CD8 T cell, CD19high = B cell, CD14high = macrophages).
Genome_build: GENCODE v25 (GRCh38.p7)
Supplementary_files_format_and_content: Tab-delimited text files include (1) Transcripts per million (TPM) values for each single cell (2) Metadata for each single cell

extract_protocol:
Tumor biopsies from human breast cancer patients (n = 18) were obtained from the primary site (n =16), lymph nodes (n = 1; paired primary), or brain metastasis (n = 2) during surgical resection of breast tumors at Stanford Hospital and City of Hope National Medical Center. Samples were mechanically dissociated into < 1-2 mm3 pieces with a razor blade and then digested at 37 oC with 1500 U collagenase and 500 U hyaluronidase in Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM Glutamax (Invitrogen), and an antibiotic/antimycotic mix containing 120 μg/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin-B (PSA) for 4-6 hrs with hourly pipetting for 5 min. After digestion, cells were treated with ACK lysis buffer to deplete red blood cells and then incubated with 10 U dispase to further dissociate the tissue into single cells and 1000 U DNase I to prevent cell clumping. Cells were filtered through a 70 μm nylon mesh and washed with staining buffer containing 2% fetal bovine serum (FBS) and PSA in Hank’s Balanced Salt Solution (HBBS). Single cell suspensions of fresh breast tissue were then stained with fluorescent antibodies to prepare for FACS. To reduce nonspecific antibody binding, single cells were blocked with 10 μg/mL rat IgG on ice for 10 minutes. Cells were then stained, in the dark, on ice for 30 minutes. FACS was performed with a 130 μm nozzle on a BD FACSAria II with BD FACSDiva software. Side scatter and forward scatter profiles (area and width) were used to eliminate debris and cell doublets. Dead cells were eliminated by excluding 4’,6-diamidino-2-phenylindole (DAPI) positive cells. Breast epithelial cells were enriched by negative gating of lineage cells expressing CD45, CD31, CD3, CD16, or CD64. Human breast basal cells were then gated as CD49fhighEPCAMmed-low, luminal progenitors as CD49fhighEPCAMhigh, mature luminal cells as CD49flowEPCAMhigh, and cancer-associated fibroblasts (CAFs) and endothelial cells (ECs) as CD49f–EpCAM–. Although ECs are generally CD31+, the chemical digestion for tumor isolation cleaves surface CD31, so these cells are detected on flow cytometry as CD31–. CAFs and ECs were then distinguished based on transcriptional expression of FAP and PDGFRA in CAFs and CDH5, EMCN, and PECAM1 in ECs. Hematopoietic populations were sorted separately based on surface expression of CD45 followed by CD14+ for macrophages, CD3+CD4+ for CD4 T cells, CD3+CD8+ for CD8 T cells, and CD19+ for B cells.
cDNA libraries were constructed using a modified Smart-seq2 protocol and machine-automated pipeline by the Stanford Functional Genomic Facility (SFGF), as described previously (PMIDs: 24385147, 30241615, and 31974247). Notably, 21 to 27 cycles of PCR amplification were required to obtain cDNA amounts within range of the recommended concentrations (0.05 – 0.32 ng/μL) for downstream tagmentation. Wells with over-amplified cDNA were diluted. Libraries were prepared using the Nextera XT DNA Library Prep (Illumina) kit and sequenced on a NextSeq 500 (Illumina) to obtain 2x76 or 2x151 bp paired-end reads.

value: Other

value: Primary

value: Endothelial cell


title: H5_183_SU196_O

value: Fibroblast


title: H4_136_SU22_O


title: 30mo_H_WT1_S1

description:
sample name:
Sample 16

value: WT


title: G9_144_SU193_N

value: Normal

value: Basal


title: P16 Control EC ATAC 1

description:
primary retina EC
Control_P16_Rep1


title: G9_136_SU22_O


title: G9_145_SU193_N


title: G9_045_SU11_T

value: Tumor


title: G8_184_SU196_O

value: Macrophages


title: P16 Zeb1-CKO 1

description: primary retina EC


title: P16 Zeb1-CKO 2

description: primary retina EC


title: G8_145_SU193_N


title: MIA PaCa-2 cells, sgGFP

city: Pittsburgh

first: Wen

last: Xie

state: Pennsylvania

address: 10068 Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
Assembly: hg38
Supplementary files format and content: DEG_sgTPST2 vs sgGFP.csv includes gene expression and differential expression details.

source_name: MIA PaCa-2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: MIA PaCa-2

value: Pancreatic cancer cells


title: H2_136_SU22_O


title: MIA PaCa-2 cells, sgTPST2

value: TPST2 KD


title: G7_139_SU22_O


title: H5_136_SU22_O


title: G9_184_SU196_O


title: G6_145_SU193_N


title: G6_139_SU22_O


title: G8_144_SU193_N


title: G8_045_SU11_T


title: G8_012_COH87_O

value: Brain metastasis


title: G6_184_SU196_O


title: G6_144_SU193_N


title: G5_184_SU196_O


title: G6_136_SU22_O


title: G5_144_SU193_N


title: G5_145_SU193_N


title: G5_139_SU22_O


title: G5_045_SU11_T


title: G5_020_SU20_O


title: G4_145_SU193_N


title: G4_184_SU196_O


title: G4_144_SU193_N


title: G6_009_SU20_O


title: G7_145_SU193_N


title: G6_047_SU11_T


title: G6_045_SU11_T


title: G4_039_SU9_O


title: G4_139_SU22_O


title: G7_144_SU193_N


title: G4_045_SU11_T


title: G7_045_SU11_T


title: G3_144_SU193_N


title: G3_184_SU196_O


title: G2_136_SU22_O


title: G3_145_SU193_N


title: G12_184_SU196_O


title: G12_145_SU193_N


title: G3_045_SU11_T


title: G3_056_SU8_T

value: Lymph node metastasis


title: G2_144_SU193_N


title: G2_139_SU22_O


title: G12_144_SU193_N


title: G12_136_SU22_O


title: G11_145_SU193_N


title: G11_139_SU22_O


title: G10_139_SU22_O


title: G10_184_SU196_O


title: G10_045_SU11_T


title: G10_042_SU9_O


title: G11_184_SU196_O


title: G1_045_SU11_T


title: G11_144_SU193_N


title: G2_145_SU193_N


title: G11_042_SU9_O


title: G10_145_SU193_N


title: G10_144_SU193_N


title: G1_145_SU193_N


title: G1_183_SU196_O

value: CD8+ T cell


title: F9_066_SU42_T


title: F9_042_SU9_O


title: F9_037_SU17_O


title: F8_143_SU193_N


title: G1_144_SU193_N


title: F7_184_SU196_O


title: F9_184_SU196_O


title: G1_184_SU196_O


title: F9_139_SU22_O


title: G1_143_SU193_N


title: F8_145_SU193_N


title: F7_136_SU22_O


title: F5_184_SU196_O


title: F6_042_SU9_O


title: F5_145_SU193_N


title: F8_184_SU196_O


title: F8_139_SU22_O


title: F6_045_SU11_T


title: F7_139_SU22_O


title: F6_144_SU193_N


title: F6_184_SU196_O


title: F5_037_SU17_O


title: F6_145_SU193_N


title: F6_139_SU22_O


title: F7_045_SU11_T


title: F4_184_SU196_O


title: F8_136_SU22_O


title: F7_145_SU193_N


title: F4_144_SU193_N


title: F4_012_COH87_O


title: F3_184_SU196_O


title: F6_136_SU22_O


title: F3_139_SU22_O


title: F5_144_SU193_N


title: F2_145_SU193_N


title: F3_045_SU11_T


title: F5_136_SU22_T


title: F8_144_SU193_N


title: F4_136_SU22_O


title: F12_145_SU193_N


title: F12_184_SU196_O


title: F3_144_SU193_N


title: F11_045_SU11_T


title: F11_037_SU17_O


title: F11_012_COH87_T


title: F10_145_SU193_N


title: F10_184_SU196_O


title: F2_012_COH87_O


title: F2_042_SU9_O


title: F12_136_SU22_O


title: F2_139_SU22_O


title: F1_136_SU22_O


title: F2_144_SU193_N


title: F1_045_SU11_T


title: E9_145_SU193_N


title: F12_045_SU11_T


title: F11_144_SU193_N


title: F11_184_SU196_O


title: E9_066_SU42_T


title: E9_056_SU8_T


title: F1_184_SU196_O


title: E9_045_SU11_T


title: E9_037_SU17_O


title: F1_145_SU193_N


title: F1_144_SU193_N


title: F11_042_SU9_O


title: E9_144_SU193_N


title: F12_144_SU193_N


title: E8_136_SU22_O


title: E8_184_SU196_O

value: CD4+ T cell


title: E9_039_SU9_O


title: E9_136_SU22_O


title: E8_144_SU193_N


title: F10_045_SU11_T


title: E7_183_SU196_O


title: E7_145_SU193_N


title: E7_144_SU193_N


title: E7_184_SU196_O


title: E6_145_SU193_N


title: E8_045_SU11_T


title: E8_145_SU193_N


title: E7_045_SU11_T


title: E6_184_SU196_O


title: E6_042_SU9_O


title: E6_141_COH68_T


title: E5_145_SU193_N


title: E5_144_SU193_N


title: E6_045_SU11_T


title: E5_184_SU196_O


title: E4_144_SU193_N


title: E4_145_SU193_N


title: E4_184_SU196_O


title: E4_045_SU11_T


title: E3_183_SU196_O


title: E6_046_SU11_T


title: E3_139_SU22_O


title: E4_136_SU22_O


title: E3_045_SU11_T


title: E3_184_SU196_O


title: E3_037_SU17_O


title: E3_145_SU193_N


title: E7_136_SU22_O


title: E6_144_SU193_N


title: E2_136_SU22_O


title: E2_045_SU11_T


title: E2_184_SU196_O


title: E2_144_SU193_N


title: E12_184_SU196_O


title: E12_139_SU22_O


title: E5_045_SU11_T


title: E12_037_SU17_O


title: E11_144_SU193_N


title: E11_145_SU193_N


title: E11_184_SU196_O


title: E12_045_SU11_T


title: E11_045_SU11_T


title: E11_136_SU22_O


title: E10_184_SU196_O


title: E2_145_SU193_N


title: E1_184_SU196_O


title: E10_112_COH84_T


title: E10_045_SU11_T


title: D9_144_SU193_N


title: D9_184_SU196_O


title: E1_144_SU193_N


title: D9_139_SU22_O


title: D9_045_SU11_T


title: E2_139_SU22_T


title: E1_050_SU8_T


title: D9_145_SU193_N


title: D8_145_SU193_N


title: E12_145_SU193_N


title: D8_144_SU193_N


title: D8_184_SU196_O


title: D8_136_SU22_O


title: D8_045_SU11_T


title: D7_136_SU22_O


title: D8_050_SU8_T


title: D7_045_SU11_T


title: D6_184_SU196_O


title: E1_045_SU11_T


title: E1_145_SU193_N


title: D6_045_SU11_T


title: D6_145_SU193_N


title: D5_145_SU193_N


title: D5_184_SU196_O


title: D5_144_SU193_N


title: D5_139_SU22_O


title: D4_136_SU22_O


title: D4_045_SU11_T


title: D3_142_SU193_N


title: D4_184_SU196_O


title: D3_184_SU196_O


title: D4_145_SU193_N


title: D4_144_SU193_N


title: D3_145_SU193_N


title: D2_184_SU196_O


title: D3_045_SU11_T


title: D3_139_SU22_O


title: D3_042_SU9_O


title: D7_145_SU193_N


title: D7_184_SU196_O


title: D2_045_SU11_T


title: D2_144_SU193_N


title: D12_184_SU196_O


title: D12_139_SU22_O


title: D12_136_SU22_O


title: D12_045_SU11_T


title: D5_042_SU9_O


title: D11_184_SU196_O


title: D11_145_SU193_N


title: D11_136_SU22_O


title: D11_144_SU193_N


title: D11_045_SU11_T


title: D10_184_SU196_O


title: D10_145_SU193_N


title: D10_142_SU193_N


title: D10_139_SU22_O


title: D10_144_SU193_O


title: D1_045_SU11_T


title: D10_136_SU22_T


title: C9_144_SU193_N


title: C9_141_COH68_T


title: C9_136_SU22_T


title: D1_145_SU193_N


title: D10_045_SU11_T


title: C9_045_SU11_T


title: C8_184_SU196_O


title: C9_184_SU196_O


title: C9_139_SU22_O


title: C8_066_SU42_T


title: SKBR3_HR cuttag input

city: Nanjing

first: Nignjun

last: Duan

address: 300 Guangzhou Road

institute: JSPH

data_processing:
DNA-seq reads were aligned to hg38 build of the human genome using Bowtie2 (v2.2.5).
Aligned reads were filtered and sorted by Samtools (v1.14) and Bedtools (v2.30.0).
SEACR (v1.3) was applied for peak calling.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: bed file includes peak information of each sample
Library strategy: Cut & Tag

extract_protocol:
Cell were harvested by ConA conjugated magnetic beads and permeabilized by Digitonin.
DNA library was prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following manufacturer's protocol.

value: Breast; Mammary gland, epithelial

value: trastuzumab


title: SKBR3 cuttag input


title: C8_045_SU11_T

value: Primary


title: C8_042_SU9_O

value: Other

value: Endothelial cell


title: SKBR3 H3K27ac cuttag rep2


title: C7_184_SU196_O


title: SKBR3 H3K27ac cuttag rep1


title: SKBR3_HR H3K4me3 cuttag rep2


title: SKBR3_HR H3K4me3 cuttag rep1


title: C7_145_SU193_N


title: D1_144_SU193_N


title: C8_039_SU9_O


title: C9_145_SU193_N


title: C7_144_SU193_N


title: SKBR3 H3K4me3 cuttag rep1


title: C7_066_SU42_T


title: C7_136_SU22_O


title: SKBR3 H3K4me3 cuttag rep2


title: C7_042_SU9_O


title: C7_045_SU11_T


title: SKBR3_HR H3K27me3 cuttag rep1


title: SKBR3_HR H3K27ac cuttag rep1


title: SKBR3_HR H3K27me3 cuttag rep2


title: SKBR3 H3K27me3 cuttag rep1


title: SKBR3_HR_rep3

data_processing:
RNA-seq reads were aligned to the hg38 build of the human genome reference using STAR 2.4.2a.
The GENCODE v19 annotation was used for the STAR alignment and all other quantifications.
Gene level read count values were calculated using RNA-SeQC v1.1.8.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.


title: SKBR3_HR H3K27ac cuttag rep2


title: C6_145_SU193_N


title: C6_184_SU196_O


title: SKBR3 H3K27me3 cuttag rep2


title: C6_144_SU193_N


title: SKBR3_HR_rep1


title: SKBR3_HR_rep2


title: C6_042_SU9_O


title: C6_045_SU11_T


title: C5_145_SU193_N


title: C5_144_SU193_N


title: C5_139_SU22_O


title: C5_004_SU2_O


title: C5_049_SU8_N


title: C5_045_SU11_T


title: A549-ACE2_infected_total_3

first: Nolwenn

last: Jouvenet

address: 25 rue du Dr Roux

institute: Institut Pasteur

description: presence of Spike protein

data_processing:
Paired-end (2x150) reads adapters were trimmed with TrimGalore v0.6.4 with options --stringency 5 --trim-n -q 20 --length 20 --paired –retain_unpaired
Mapping with STAR  v2.7.3a with default parameterrs, to a reference containing human genome (hg38), SARS-CoV-2 (NC045512.2), and bam files were then filtered using SAMtools v1.10 to retained reads flagged as primary alignment, and with mapping quality > 30 (option -q 30 -F 0x100 -F 0x800)
Gene counts were obtained using featureCounts v2.0.0, with options -O -M --fraction -s 2 -p, using a merged annotation of gencode v32, SARS-CoV-2 (NC045512.2) & newly annotated transcripts.
Gene count were normalized using estimateSizeFactorsForMatrix from DESeq2 package (R v3.6.2).
Assembly: hg38
Assembly: NC045512.2
Supplementary files format and content: raw_counts.tsv, tab delimited file of raw gene count for each replicate

growth_protocol: A549-ACE2 and African green monkey Vero E6 cells (ATCC CRL-1586) were cultured in high-glucose DMEM media (Gibco), supplemented with 10% fetal bovine serum (FBS; Sigma) and 1% penicillin-streptomycin (P/S; Gibco). Cells were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
At 24 h post infection, cells were detached with trypsin, fixed in 4% PFA for 30 min on ice and stained for spike protein as described above for flow cytometry, with RNasin added to FACS buffer (1:100 dilution) just before use to prevent RNA degradation. Infected cell samples were resuspended in PBS 2%, 25 mM Hepes, 5 mM EDTA (sorting buffer) and sorted at 4°C on a FACSAria Fusion4L Sorter into infected (presence of S protein expression) and bystander (absence of viral protein expression) cell populations. Cells were collected in FBS-coated tubes containing buffer with RNasin to minimize RNA degradation. After sorting, cells were pelleted at 500g for 5 min at 4°C and RNA was extracted with the RecoverAll Total Nucleic Acid Isolation Kit starting at the protease digestion step. Digestion was performed for 15 min at 50°C and 15 min at 80°C in the presence of RNasin. Extraction was performed according to manufacturer’s instructions and the addition of RNAsin to all buffers just before use until final elution of RNA in DNAse-free water. Residual DNA was further digested using DNAse I (Invitrogen AM1906). RNAs were sorted at -80°C until further analysis.
The libraries were prepared using the Illumina Stranded mRNA Prep Ligation Reference Guide, using 500-1000ng of total RNA.

treatment_protocol: Viral stocks were produced by amplification on Vero E6 cells, for 72 h in DMEM 2% FBS. The cleared supernatant was stored at 80°C and titrated on Vero E6 cells by using standard plaque assays to measure plaque-forming units per ml (PFU/ml). A549-ACE2 cells were seeded the day prior to infection. A549-ACE2 were infected at MOI of 1 in DMEM without FBS or mock infected. After 2 h, DMEM with 5% FBS was added to the cells. Infections were done in two independent repeats with three technical replicates each.

value: human alveolar basal epithelial cells

value: SARS-CoV-2 infection at MOI 1 during 24 h


title: A549-ACE2_infected_total_5

description: absence of Spike protein


title: A549-ACE2_infected_total_6

description: absence of Spike protein


title: A549-ACE2_infected_total_4

description: absence of Spike protein


title: C4_184_SU196_O


title: C4_145_SU193_N

value: Normal

value: Basal


title: C5_042_SU9_O


title: A549-ACE2_infected_total_1

description: presence of Spike protein


title: A549-ACE2_bystander_total_6

description: absence of Spike protein


title: C4_139_SU22_O


title: A549-ACE2_bystander_total_4

description: absence of Spike protein


title: A549-ACE2_infected_total_2

description: presence of Spike protein


title: A549-ACE2_bystander_total_5

description: absence of Spike protein


title: C4_144_SU193_N


title: A549-ACE2_bystander_total_1

description: absence of Spike protein


title: C4_136_SU22_O


title: A549-ACE2_bystander_total_2

description: absence of Spike protein


title: C4_045_SU11_T

value: Tumor


title: C4_111_COH75_T


title: A549-ACE2_bystander_total_3

description: absence of Spike protein


title: C4_042_SU9_O


title: C3_184_SU196_O


title: A549-ACE2_mock_total_5

description: mock infected

value: mock


title: A549-ACE2_mock_total_4

description: mock infected


title: A549-ACE2_mock_total_3

description: mock infected


title: C3_144_SU193_N


title: A549-ACE2_mock_total_6

description: mock infected


title: C3_139_SU22_O


title: A549-ACE2_mock_total_1

description: mock infected


title: A549-ACE2_mock_total_2

description: mock infected


title: A549-ACE2_infected_total_cov_depleted_6

description: absence of Spike protein

data_processing:
Paired-end (2x150) reads adapters were trimmed with TrimGalore v0.6.4 with options --stringency 5 --trim-n -q 20 --length 20 --paired –retain_unpaired
Mapping with STAR  v2.7.3a with default parameterrs, to a reference containing human genome (hg38), SARS-CoV-2 (NC045512.2) and ERCC sequences, and bam files were then filtered using SAMtools v1.10 to retained reads flagged as primary alignment, and with mapping quality > 30 (option -q 30 -F 0x100 -F 0x800)
Gene counts were obtained using featureCounts v2.0.0, with options -O -M --fraction -s 2 -p, using a merged annotation of gencode v32, SARS-CoV-2 (NC045512.2), newly annotated transcripts and ERCC transcripts.
Gene count were normalized using estimateSizeFactorsForMatrix from DESeq2 package (R v3.6.2).
Assembly: hg38
Assembly: NC045512.2
Supplementary files format and content: raw_counts.tsv, tab delimited file of raw gene count for each replicate

extract_protocol:
At 24 h post infection, cells were detached with trypsin, fixed in 4% PFA for 30 min on ice and stained for spike protein as described above for flow cytometry, with RNasin added to FACS buffer (1:100 dilution) just before use to prevent RNA degradation. Infected cell samples were resuspended in PBS 2%, 25 mM Hepes, 5 mM EDTA (sorting buffer) and sorted at 4°C on a FACSAria Fusion4L Sorter into infected (presence of S protein expression) and bystander (absence of viral protein expression) cell populations. Cells were collected in FBS-coated tubes containing buffer with RNasin to minimize RNA degradation. After sorting, cells were pelleted at 500g for 5 min at 4°C and RNA was extracted with the RecoverAll Total Nucleic Acid Isolation Kit starting at the protease digestion step. Digestion was performed for 15 min at 50°C and 15 min at 80°C in the presence of RNasin. Extraction was performed according to manufacturer’s instructions and the addition of RNAsin to all buffers just before use until final elution of RNA in DNAse-free water. Residual DNA was further digested using DNAse I (Invitrogen AM1906). RNAs were sorted at -80°C until further analysis.
500-1000 ng of total RNA were depleted of SARS-CoV-2 RNA using custom designed probes. The probes were synthesized using the NC_045512.2 Wuhan-Hu-1 complete genome reference. The design was made by Illumina and is composed of 459 probes, separated into two pools synthetized by IDT. For the SARS-CoV-2 depletion, we mixed both pools and used 1µl of this mix per sample, replacing the Ribozero+ probes at the ribodepletion reaction step of the Illumina Stranded Total RNA prep ligation protocol. The SARS-CoV-2 depleted RNA samples were normalized to 300ng and ERCC Spike was added as recommended by the protocol ERCC RNA Spike-In Control mixes User Guide. The libraries were prepared using the Illumina Stranded mRNA Prep Ligation Reference Guide.


title: C3_045_SU11_T


title: C3_113_COH84_T


title: C2_184_SU196_O


title: A549-ACE2_infected_total_cov_depleted_5

description: absence of Spike protein


title: A549-ACE2_infected_total_cov_depleted_4

description: absence of Spike protein


title: C2_144_SU193_N


title: C2_145_SU193_N


title: C2_142_SU193_N


title: C2_143_SU193_N


title: A549-ACE2_infected_total_cov_depleted_1

description: presence of Spike protein


title: C2_139_SU22_O


title: A549-ACE2_bystander_total_cov_depleted_6

description: absence of Spike protein


title: C3_145_SU193_N


title: A549-ACE2_bystander_total_cov_depleted_5

description: absence of Spike protein


title: A549-ACE2_bystander_total_cov_depleted_4

description: absence of Spike protein


title: C2_042_SU9_O


title: A549-ACE2_bystander_total_cov_depleted_2

description: absence of Spike protein


title: C12_145_SU193_N


title: C12_184_SU196_O


title: A549-ACE2_bystander_total_cov_depleted_3

description: absence of Spike protein


title: C12_144_SU193_N


title: A549-ACE2_bystander_total_cov_depleted_1

description: absence of Spike protein


title: C3_012_COH87_O


title: A549-ACE2_mock_total_cov_depleted_6

description: mock infected


title: C11_145_SU193_N


title: A549-ACE2_mock_total_cov_depleted_4

description: mock infected


title: A549-ACE2_infected_total_cov_depleted_3

description: presence of Spike protein


title: A549-ACE2_mock_total_cov_depleted_5

description: mock infected


title: A549-ACE2_infected_total_cov_depleted_2

description: presence of Spike protein


title: C12_139_SU22_O


title: C11_144_SU193_N


title: C11_045_SU11_T


title: A549-ACE2_mock_total_cov_depleted_3

description: mock infected


title: A549-ACE2_mock_total_cov_depleted_1

description: mock infected


title: A549-ACE2_mock_total_cov_depleted_2

description: mock infected


title: C10_184_SU196_O


title: A549-ACE2_infected_3

description: presence of Spike protein

data_processing:
Paired-end (2x150) reads adapters were trimmed with TrimGalore v0.6.4 with options --stringency 5 --trim-n -q 20 --length 20 --paired –retain_unpaired
Mapping with STAR  v2.7.3a with default parameterrs, to a reference containing human genome (hg38), SARS-CoV-2 (NC045512.2) and ERCC sequences, and bam files were then filtered using SAMtools v1.10 to retained reads flagged as primary alignment, and with mapping quality > 30 (option -q 30 -F 0x100 -F 0x800)
Transcript assembly was done with Scallop v0.10.5 on each library, and the resulting annotations were merged using cuffmerge v1.0.0, with gencode annotation (v32) as reference (-g option). BEDtools v2.29.2 was used to retain only intergenic and antisens transcripts regarding reference annotation.
Gene counts were obtained using featureCounts v2.0.0, with options -O -M --fraction -s 2 -p, using a merged annotation of gencode v32, SARS-CoV-2 (NC045512.2), newly annotated transcripts and ERCC transcripts.
Gene count were normalized using estimateSizeFactorsForMatrix from DESeq2 package (R v3.6.2).
Assembly: hg38
Assembly: NC045512.2
Supplementary files format and content: normalized_counts.tsv, tab delimited file of normalized gene count for each replicate

molecule: polyA RNA

treatment_protocol: Viral stocks were produced by amplification on Vero E6 cells, for 72 h in DMEM 2% FBS. The cleared supernatant was stored at 80°C and titrated on Vero E6 cells by using standard plaque assays to measure plaque-forming units per ml (PFU/ml). A549-ACE2 cells were seeded the day prior to infection. A549-ACE2 were infected at MOI of 1 in DMEM without FBS or mock infected. After 2 h, DMEM with 5% FBS was added to the cells. Infections were done in one biological sample with three technical replicates.


title: C11_042_SU9_O


title: C10_053_SU21_O


title: C10_045_SU11_T


title: A549-ACE2_infected_2

description: presence of Spike protein


title: A549-ACE2_infected_1

description: presence of Spike protein


title: A549-ACE2_bystander_3

description: absence of Spike protein


title: A549-ACE2_bystander_1

description: absence of Spike protein


title: A549-ACE2_bystander_2

description: absence of Spike protein


title: C1_145_SU193_N


title: A549-ACE2_mock_3


title: C11_184_SU196_O


title: C1_143_SU193_N


title: A549-ACE2_mock_2


title: C1_045_SU11_T


title: C1_026_SU8_N


title: A549-ACE2_mock_1


title: A549-ACE2_TNFa_induced_p65

description: treated with TNF-alpha for 3h

data_processing:
Adaptors were trimmed with Trim Galore v.0.6.4 using default parameters for paired-end data.
Reads were aligned on human genome (hg38) using Bowtie2 (v2.4.1, with default parameters) and only properly mapped reads with a mapping quality >=30 were kept.
Peaks were detected using macs2 (v2.2.7.1), with the option –keep-dup all, using IgG as control.
IP – IgG coverage was computed with macs2 subtract command and UCSC bedGraphToBigWig (v2.8) tool
Assembly: hg38
Supplementary files format and content: A549-ACE2_TNFa_induced_p65_peaks.bed, bed format file containing the coordinates of p65 peaks
Supplementary files format and content: A549-ACE2_TNFa_induced_p65.bw, bigWig file containing read coverage (IP-IgG)

extract_protocol:
Cells were pelleted after scraping and resuspended in wash buffer (HEPES 20mM, NaCl 150mM, Spermidine 0.5mM) at 107 cells/ml. At room temperature, per sample, 10 μl of Concanavalin A beads slurry washed in bead activation buffer (HEPES 20mM, KCl 10mM, CaCl2 1mM, MnCl2 1mM) was added per 106 cells in the total volume of 1 ml of wash buffer and incubated for 10 min with rotation at 15–20 rpm. Antibodies against H3K27ac (Millipore, MABE647) were diluted 50 times, p65 (Cell Signaling, D14E12)  diluted 100 times and IgG (Invitrogen, 31235) 500 times in the buffer (wash buffer with 0.1% digitonin, 2 mM EDTA) and 50 μl of diluted antibody was added to the cells fixed on beads and incubated for 1h. Afterward, the beads were washed twice with 250 µl of digitonin buffer (wash buffer with 0.1% digitonin),  resuspended in 52 µl digitonin buffer containing 35ng of  pAG-MNase (produced at Institut Curie platform) , and incubated 10 min with agitation. Beads were washed twice in 250 µl of ice-cold digitonin buffer, resuspended in 100 µl of ice-cold digitonin buffer, kept on ice for 5 min before adding 2 µl of 100 mM CaCl₂ and incubating for 30 min on ice. The reaction was stopped by addition of 100 µl of stop buffer (NaCl 340mM, EDTA 20mM, EGTA 4mM, RNase A 50 μg/mL, glycogen 50 μg/mL and 0.1% digitonin) and incubated for 10 min at 37°C.
Bead suspension was centrifuged at 16k rcf at 4°C for 5 min and beads were recovered for DNA fragments purification with NEB Monarch PCR & DNA purification kit, following the protocol enriching for short DNA fragments.

treatment_protocol: Cells were stimulated with 10 ng/µL Poly(I:C) (HMW, #vac-pic Invivogen) using Lipofectamine 3000 Reagent (Thermo Fisher Scientific) according to manufacturer’s protocol, during 3h.

value: TNF-alpha

tag: antibody

value: p65 (Cell Signaling, D14E12)


title: A549-ACE2_TNFa_induced_IgG

description: Non treated

tag: cell line

value: IgG (Invitrogen, 31235)


title: B9_145_SU193_N


title: C10_144_SU193_N


title: C1_136_SU22_O


title: hDC-untreated2

first: Zhu

last: Xiaofeng

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

data_processing:
Data were analyzed using STAR software (STAR_2.6.1a) for sequence aligning with default parameters, RSEM software (v1.2.28) for gene quantification.
Data were analyzed using STAR software (STAR_2.6.1a) for sequence aligning with default parameters, RSEM software (v1.2.28) for gene quantification.
Finally, gene expression profile was generated by Python (version 3.6.7).
Assembly: hg38
Supplementary files format and content: excel table files include read counts for each Sample

source_name: primary culture cell

extract_protocol:
RNA was extracted from DCs using the AllPrep DNA/RNA/miRNA Universal Kit
RNA-seq libraries were prepared using the TruSeq RNA Access Library Prep Kit.Total RNA was quantified using the Quant-iTTM RiboGreen® RNA Assay Kit.Each sample was transferred into a library preparation that was an automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation Kit.

tag: cell type

value: Dendritic cells

value: primary culture cell

value: antigen-presenting cells

value: WT

value: untreated


title: B9_139_SU22_O

value: Primary


title: B9_136_SU22_O

value: Other


title: hDC-untreated3

tag: treatment


title: C1_144_SU193_N


title: B9_050_SU8_T


title: hDC-liposone2

value: liposome


title: hDC-liposone3


title: hDC-liposone1


title: hDC-linearRNA3

value: linearRNA


title: B9_045_SU11_T


title: hDC-linearRNA2


title: B9_064_SU42_O

value: Brain metastasis

value: Endothelial cell


title: B8_183_SU196_O

value: Fibroblast


title: C1_139_SU22_O


title: hDC-linearRNA1


title: B8_184_SU196_O

value: CD8+ T cell


title: B8_144_SU193_N

value: Normal

value: Basal


title: circ-RNA-Seq P9-T

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome.  CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
If a circRNA can be detected by both methods, it will be considered as an identified circRNA. The DEseq/DESeq2/edgeR/DEGseq package in Bioconductor was used to determine differently expressed circRNA.
Supplementary files format and content: excel table files include read counts for each Sample

source_name: tumor

extract_protocol:
Total RNA was extracted from cells or tissues with TRIzol reagent according to the manufacturer’s instruction.
The total RNA  of the samples were extracted and treated with RNase (R), and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection. Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.

value: tumor

tag: diagnosis

value: breast cancer

tag: Sex

value: female

tag: age

tag: tumor stage

value: II


title: hDC-circRNA1

value: Dendritic cells

value: primary culture cell

value: antigen-presenting cells

value: circRNA


title: hDC-untreated1-1

value: WT

value: untreated


title: B8_139_SU22_O

tag: tissue

value: Other

value: Primary


title: B9_144_SU193_N


title: hDC-circRNA2


title: hDC-circRNA3


title: B8_145_SU193_N


title: B8_042_SU9_O

value: Endothelial cell


title: B7_184_SU196_O


title: circ-RNA-Seq P8-T


title: B7_183_SU196_O

value: Fibroblast


title: circ-RNA-Seq P9-N

source_name: normal

value: normal


title: circ-RNA-Seq P8-N


title: B8_039_SU9_O


title: B7_145_SU193_N

value: Normal


title: circ-RNA-Seq P10-N


title: circ-RNA-Seq P7-T


title: circ-RNA-Seq P10-T


title: B7_066_SU42_T

value: Tumor

value: Brain metastasis

value: Basal


title: circ-RNA-Seq P7-N

value: breast cancer

value: female


title: circ-RNA-Seq P12-T

value: tumor

value: II


title: B6_145_SU193_N


title: circ-RNA-Seq P12-N


title: B6_139_SU22_O


title: B6_136_SU22_T


title: circ-RNA-Seq P11-T


title: circ-RNA-Seq P11-N


title: B6_045_SU11_T


title: Ribo-Seq P9_T_1

data_processing:
Clean sequences were obtained from raw data using Cutadapt (v1.15) to remove adapter and low-quality sequences with an N-base ratio of more than 5 %, and Bowtie (v1.3.0) to remove rRNA sequences.
The clean reads were then compared to the reference genome using STAR55,56 (v2.7.1a) with the following parameters: --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd.
The python scripts were used to count the reads covered by the UTR and lncRNA regions as quantitative results.
Assembly: hg19
Supplementary files format and content: excel table files include read counts for each Sample

extract_protocol:
Fresh tumor samples and the paired adjacent normal tissue were collected and treated with specific lysis buffer with cycloheximide. Concentration of the lysate was measured by the NanoDrop™ 2000 Spectrophotometer. Then the lysate was treated with unspecific endoribonuclease RNase I to digest RNA other than ribosome protected fragments (RPFs) and monosomes were isolated by size-exclusion chromatography with MicroSpin S-400 HR columns.
The RNA samples were then treated with rRNA depletion kit to eliminate as much rRNA contamination as possible. Subsequently, the relatively short (20~38 nt) RPFs were purified using PAGE and the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR.


title: B5_145_SU193_N


title: B6_042_SU9_O


title: Ribo-Seq P9_N_1


title: Ribo-Seq P8_T_1


title: Ribo-Seq P8_N_1


title: B5_144_SU193_N


title: B7_144_SU193_N


title: B5_142_SU193_N


title: Ribo-Seq P7_N_1


title: B5_012_COH87_O


title: Ribo-Seq P7_T_1


title: Ribo-Seq P4_T_1


title: Ribo-Seq P4_N_1


title: B4_145_SU193_N


title: B4_045_SU11_T


title: Ribo-Seq P2_N_1


title: Ribo-Seq P2_T_1


title: B7_045_SU11_T


title: B4_184_SU196_O

value: CD8+ T cell


title: Ribo-Seq P10_T_1


title: B3_184_SU196_O


title: Ribo-Seq P10_N_1


title: B5_184_SU196_O