title: alligator hindlimb bud st13 H3K27ac input rep1

description: PE150 sequencing


title: atac_HDP2_Day7_WT_rep1

status: Public on Apr 04 2025

type: SRA

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

country: USA

institute: Boston Childrens Hospital

library_source: genomic

data_processing:
CUT&RUN analysis and normalization: We used CUT&RUNTools (Zhu et al) to process BCL11A, NF-Y and MTA2 CUT&RUN experiments from raw fastq reads. This process included reads trimming, alignment to the reference genome (hg19), BAM file duplicate marking, and fragment filtering based on fragment size. Next, we performed background-based data normalization on the group of experiments to be normalized together. For experiment in each group, we pooled all the BAM files and performed MACS2 peak calling to get initial set of peaks. Peak-flanking regions were obtained and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor was called on the matrix of peak-flanking region reads over all reads to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file based on fragments of 120bp or less. A normalized bigwig file was used for visualization. ATAC-seq analysis and normalization: ATAC-Seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150 bp instead of <120 bp setting for TF CUT&RUN. For ATAC-Seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN. RNA-seq and DE analysis: We aligned raw cDNA reads, quantified exonic expression, and finally gene abundances using the HISAT pipeline. Afterward with gene expression count matrix, we proceeded with differential expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: NarrowPeak - narrow peak calls from MACS2
Supplementary files format and content: .txt - gene counts for RNAseq
Supplementary files format and content: .de_files.txt - differentially expressed genes for RNAseq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: ATACseq: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF. CUT&RUN: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF. RNASeq: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with Penicillin-Streptomycin solution (2%), SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10-6 M), and doxycycline (1 ug/mL). Erythroid differentiation was carried out by replacing the medium to EDM-II: Iscove’s modified Dulbecco’s medium (IMDM, Corning, 15-016-CV) supplemented with Penicillin-Streptomycin solution (2%), L-Glutamine (1%), holo-human transferrin (330 ug/mL), recombinant human insulin solution (10 ug/mL), heparin (2 IU/mL), inactivated human plasma (5%), EPO (3 IU/mL), SCF (100 ng/mL), doxycycline (1 ug/mL). Cells were cultured in EDM-II for 4 days, followed by 3 more days in medium without SCF.

extract_protocol:
ATAC-seq: ATAC-seq was performed with the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit, as previously described (Buenrostro et al., 2015). 50,000 cells were collected and washed once with cold PBS. Cells were then permeabilized with 50 μL ice-cold lysis buffer containing10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-360 for 10 minutes. The transposition reaction was carried out at 37°C for 90 minutes in 50 μL volume containing 25 μL TD Buffer and 2.5 μL TDE1 Tagment DNA Enzyme. Immediately following transposition incubation, DNA was purified with the MinElute PCR Purification Kit (Qiagen).  CUT&RUN was performed as previously described (Liu et al., 2021). Briefly, 1x106 cells were freshly collected for each sample. Cells were washed once with cold PBS and processed according to the following steps: (1) 800 μL of NE buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol and protease inhibitor (Roche)) was added to the pellet for nuclear isolation. Nuclei were pelleted at 600g for 3 min and resuspended in 200 μL of NE buffer. (2) 30 μL of BioMagPlus Concanavalin A bead slurry was washed twice and resuspended in 100 μL of binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2). Beads were then added to the nuclear suspension. The mixture was thoroughly mixed on a rocker for 10 min at RT to allow binding of nuclei to the beads. The nuclei were pelleted with a magnet stand and blocked with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA and protease inhibitor (Roche)) supplemented with 2 mM EDTA for 5 min on ice. (4) After washing once with wash buffer, nuclei were resuspended in 200 μL of wash buffer containing 1 μg of antibody and incubated overnight at 4°C. (5) The next day, nuclei were washed twice on a magnet stand with wash buffer and incubated with 1:1000 Protein A-micrococcal nuclease fusion protein (pA-MNase) in 200 μL of wash buffer for 1 hr at 4°C. The nuclei were then washed twice with wash buffer to remove unbound pA-MNase. (6) Nuclei were resuspended in 150 μL of wash buffer and chilled on a metal block at 0°C in a water-ice mixture. 3 μL of 100 mM CaCl2 was added to the nuclei to activate pA-MNase with incubation at 0°C for 60 min. (7) The reaction was stopped by the addition of 150 μL of 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A and 40 μg/mL glycogen). The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit fluorometry and bioanalyzer quality control. The antibodies used for CUT&RUN were BCL11A (Sigma, ZRB1518), NF-YA (Abcam, ab139402) and MTA2 (Abcam, ab8106). RNA: Total RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen).
ATACseq: Transposed DNA fragments were amplified using NEBNext® Ultra™ II Q5 Master Mix and PCR reaction was carried out as follows: 72°C for 5 min; 98°C for 30 s; 8 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The resulting libraries were purified using the QIAquick PCR Purification Kit (Qiagen), quantified with Qubit fluorometer and TapeStation, and then sequenced using the NextSeq 500 platform. Paired-end sequencing was performed with read length of 42 bp and index of 8 bp. CUT&RUN: Library preparation of CUT&RUN was performed using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, as previously described (Liu et al., 2021). Briefly, 6 ng of DNA was used as input. End preparation was performed at 20 °C for 30 min and then 50 °C for 60 min. 0.6 pmol adapter was added and ligated to end-preparation products at 20 °C for 15 min. USER enzyme was then added to cleave the uracil in the loop at 37°C for 15 min. 1.7x volume of AMPure XP beads was used to purify the ligation product for efficient recovery of short fragments. To amplify the library, the ligation product was mixed with 2x NEBNext® Ultra™ II Q5 Master Mix, universal primer and index primers. PCR reaction was carried out as follows: 98°C for 30 s; 12 cycles of 98°C for 10 s and 65°C for 10 s; and a final extension at 65°C for 5 min. The PCR product was subjected to double-size selection, first with 0.8x and then with 1.2x AMPure XP beads. The purified library was quantified by Qubit fluorometer and TapeStation. Libraries were pooled in equimolar ratios and sequenced using the NextSeq500 platform. Paired-end sequencing was performed with read length of 42 bp and index of 6 bp. RNAseq: RNA sequencing libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) from 200 ng of purified total RNA. The finished dsDNA libraries were quantified by Qubit fluorometer, TapeStation, and RT-qPCR using the KAPA Library Quantification Kit (Roche). Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq500 with single-end 75bp reads.
ATACseq and CUT&RUN: read length 42
RNAseq: read length 75

tag: cell line

tag: cell type

value: erythroid

tag: genotype

value: WT

tag: time

value: Day 7

tag: antibody

tag: replicate

tag: batch


title: atac_HDP2_Day7_delN_rep3

value: delN


title: alligator hindlimb bud st13 H3K27ac ChIP rep1

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

department: Genetics

institute: University of Georgia

description:
PE150 sequencing
am_HL_st13_H3K27ac_naive_overlap.narrowPeak.gz
am_HL_st13_H3K27ac_pooled.bw

data_processing:
Libraries were sequenced by the Georgia Genomics and Bioinformatics Core (SE75) or by Genewiz (PE150). The GGBC provided pre-trimmed reads, while Genewiz reads were subsequently trimmed using cutadapt using the settings -O 1, -m 25
RNA-seq reads were aligned to mm10 using STAR (v. 2.7.3a). Transcripts were counted using HTSeq (v. 0.13.5). Differential gene expression was determined using DESeq2 (Galaxy v. 2.11.40.6).
ChIP-seq data were processed using the AQUAS Transcription Factor and Histone ChIP-seq pipeline. We used the pipeline's default bwa aligner to align mouse reads to mm10 (UCSC), chick to galGal6 (UCSC), alligator to allMis0.2/allMis1 (UCSC), turtle to CAS_Tse_1.0 NCBI RefSeq), and lizard to AnoSag2.0 (local genome build). Fragment size was set to 175 (-speak_spp 175, -extsize_macs2 175).
SPP was used to call IDR peaks using the default cutoff (0.05) in ISL1 ChIP-seq experiments performed in duplicate, while MACS2 peaks were used from individual experiments and from H3K27ac datasets. In H3K27ac datasets, the naive overlap peaks were used, while MACS2 peaks from ISL1 ChIP-seq in alligator, turtle, and lizard were filtered using a q-value cutoff of 0.01 and fold-enrichment cutoff of 4. bigWig files were generated using MACS2 and represent fold-enrichment values of ChIP vs control samples.
Mouse forelimb ISL1 ChIP-seq IDR peaks were used as a negative control to filter false-positive peaks from ISL1 peak sets, generating "FL_filtered" files
Assembly: varied by species (see above)
Supplementary files format and content: DESeq2 tabular files, SPP or MACS2 peak files, and MACS2 bigWig files

organism: Alligator mississippiensis

source_name: hindlimb bud

extract_protocol:
For RNA-seq, genital tubercle samples were placed in RNA-Later, which was then removed before freezing samples at -80C. For hindlimb field samples, both sides from each embryo were placed directly into mirVana Lysis/Binding buffer and frozen. RNA was extracted using the mirVana miRNA isolation kit. For ChIP-seq, tissues form multiple embryos were sonified using a probe sonifier followed by a bath sonifier. Lysates were then incubated with the antibody with a portion kept as input DNA.
RNA-seq libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina); ChIP-seq libraries were constructed using the NEBNext Ultra II Library Prep Kit

tag: developmental stage

tag: chip antibody

value: H3K27ac (Millipore or Cosmo Bio, CMA309)


title: atac_HDP2_Day7_delN_rep2


title: chick hindlimb bud HH18-20 ISL1 input rep1

description: SE75 sequencing

organism: Gallus gallus

tag: strain


title: KO1

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Column KO1 within counts file

library_source: transcriptomic

data_processing:
Data Formatting: bcltofastq-2.19.1
Data Cleaning: fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification: subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Assembly: m38 + Gencode-M27 Annotation
Supplementary files format and content: raw gene counts

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Rneasy Plus Micro Kit (Qiagen, Valencia, CA)
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the llumina NextSeq 550 (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample.

treatment_protocol: Treated mice were transplanted BCR-ABL and NUP98-HOXA9 primary leukemia cells

tag: tissue

value: Spleen

value: leukemia

value: SLC6A6 KO


title: atac_HDP2_Day7_delN_rep1


title: atac_HDP2_Day7_WT_rep3


title: chick hindlimb bud HH18-20 ISL1 ChIP rep2

description:
SE75 sequencing
gg_HL_HH18-20_ISL1_IDR.narrowPeak.gz
gg_HL_HH18-20_ISL1_IDR_mouse_FL_filtered.bed
gg_HL_HH18-20_ISL1_pooled.bw


title: chick hindlimb bud HH18-20 ISL1 ChIP rep1


title: LN-GEL-3-1

city: Beijing

first: Cuifeng

last: Li

address: Qinghua Yuan Street

country: China

institute: Tsinghua University

description: Library name: sample9-1

data_processing:
Fragment Analyzer 1.0.2.9 was used to quality library size, with fragments primarily distributed between 300-700 bps. The sequencing libraries were quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Sequencing was conducted using Paired-end PE150 method based on Illumina Novaseq sequencing platform. Raw reads obtained from RNA-seq experiments underwent quality control (QC) using FastQC, a tool for assessing quality distributions across entire reads. Low-quality bases and adapter sequences were removed during pre-processing. The stripped sequences were then aligned to the mouse reference genome (mm19) using Tophat (version 2.0.3). Cufflinks (v 2.2.1) was used to normalize and verify expression level between two samples, employing default parameters.
Assembly: GrCm39
Supplementary files format and content: All_FPKM.txt
Supplementary files format and content: FPKM_DEG_Summary.txt
Supplementary files format and content: readCount.txt

molecule: total RNA

source_name: LN

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA samples were assessed using an Agilent 2200 TapeStation (Agilent Technologies) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific).
RNA-seq libraries were prepared with KAPA Hyper Prep Kits following manufacturer’s protocol (Illumina, KK8504).

value: LN


title: LN-GEL-2-1

description: Library name: sample8-1


title: lizard hemiphallus st7-9 ISL1 input rep2

description: SE75 sequencing

organism: Anolis sagrei

source_name: hemiphallus (fine dissection)


title: alligator forelimb bud st13 H3K27ac input rep1

description: PE150 sequencing

source_name: forelimb bud


title: atac_HDP2_Day7_BCL11A_KO_rep3

value: BCL11A KO


title: alligator forelimb bud st13 H3K27ac input rep2

description: PE150 sequencing


title: lizard hemiphallus st7-9 ISL1 input rep1

description: SE75 sequencing

source_name: hemiphallus and cloacal region


title: atac_HDP2_Day7_BCL11A_KO_rep1


title: alligator forelimb bud st13 H3K27ac ChIP rep2

description:
PE150 sequencing
am_FL_st13_H3K27ac_naive_overlap.narrowPeak.gz
am_FL_st13_H3K27ac_pooled.bw


title: lizard hemiphallus st7-9 ISL1 ChIP rep2

description:
SE75 sequencing
as_HP_st7-9_ISL1_ChIP_R2_qval0.01_4fold.narrowPeak
as_HP_st7-9_ISL1_ChIP_R2.bw


title: alligator forelimb bud st13 H3K27ac ChIP rep1


title: alligator hindlimb bud st13 H3K27ac ChIP rep2


title: atac_HDP2_Day4_WT_rep2

value: Day 4


title: LN-GEL-1-1

description: Library name: sample7-1


title: atac_HDP2_Day4_WT_rep1


title: LN-AL-1-1

description: Library name: sample4-1


title: LN-AL-3-1

description: Library name: sample6-1


title: alligator genital tubercle st15-16 H3K27ac ChIP rep2

description:
PE150 sequencing
am_GT_st15-16_H3K27ac_naive_overlap.narrowPeak.gz
am_GT_st15-16_H3K27ac_pooled.bw

source_name: genital tubercle


title: alligator genital tubercle st15-16 input

description: PE150 sequencing


title: LN-PBS-3-1

description: Library name: sample3-1


title: atac_HDP2_Day7_BCL11A_KO_rep2


title: atac_HDP2_Day4_BCL11A_KO_rep2


title: nhr-180(cmh19) bio rep 3

city: Worcester

first: Rui

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

description: Library name: NHR-180m_3

data_processing:
RNASeq analysis was performed with OneStopRNAseq
Paired-end reads were aligned to mouse genome PRJNA13758.WS286, with star_2.5.3a
annotated with PRJNA13758.WS286.canonical_geneset
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2
TPM was calculated based on the gene length and count reported by featureCounts
Assembly: c_elegans.PRJNA13758.WS286.genomic_softmasked.fa
Supplementary files format and content: Excel, count and TPM

organism: Caenorhabditis elegans

source_name: All

growth_protocol: Worms were grown on HT115 E. coli bacteria and harvested at the L4 stage.

extract_protocol:
Trizol Reagent whole worm RNA extraction.
P_Stranded Library&Seq(PE100)

value: All


title: MVC_2

city: Wuhan

first: Xueyan

last: Zhang

address: 湖北省武汉市武昌区水果湖街道

institute: wuhan institute of virology

description:
Library name: Sample4
MVC.ac4C.site.xls

data_processing:
library strategy: RedaC:T-seq
Use Fastp (version 0.23.2) software for data quality control
Sequence reads were trimmed for adaptor sequence/low-quality sequence using by fastp (version 0.23.1)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR(version 2.7.6a) with default parameters.
The featureCounts（version 1.5.1）was used for reads distribution statistic
Assembly: accession no. FJ214110
Supplementary files format and content: MVC.ac4C.site.anno.xls

organism: Canis lupus familiaris

source_name: canine

growth_protocol: WRD cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)at 37 ℃ in a 5% CO2 environment

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent following the manufacturer's recommended protocol.Polyadenylated RNA enrichment was conducted using VAHTS mRNA Capture Beads from the total RNA
RNA libraries for RNA-seq were prepared using components of the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan,China)

treatment_protocol: WRD cells infected with MVC for 48 hours

value: canine

value: WRD

value: walter reed canine

value: canine cells

tag: treatment

value: MVC infected


title: LN-PBS-1-1

description: Library name: sample1-1


title: LN-PBS-2-1

description: Library name: sample2-1


title: alligator genital tubercle st15-16 H3K27ac ChIP rep1


title: atac_HDP2_Day4_BCL11A_KO_rep1

value: erythroid


title: wildtype bio rep 3

description: Library name: N2_3

value: wildtype


title: MVC_1

address: 湖北省武汉市武昌区水果湖街道

description:
Library name: Sample3
MVC.ac4C.site.xls


title: atac_HDP2_Day4_delN_rep2


title: wildtype bio rep 2

description: Library name: N2_2


title: LN-AL-2-1

description: Library name: sample5-1


title: Endosperm WT 4

city: Lyon

first: Nicolas

last: Doll

address: 46 allée d'Italie

department: RDP

country: France

institute: ENS de Lyon

data_processing:
The illumina adapter were trimmed of the reads with Trimmomatic v0.39 (PMID: 24695404) with leading and trailing cutoff at 3 and minlen at 35.
Assembly: Alignment was done with HISAT2 (PMID: 31375807) against the KSU A188 1.0 reference genome (PMID: 34108023). Annotations from the B73 GRAMENE 4.0 reference genome were mapped to the KSU A188 genome using Liftoff (PMID: 33320174)
Supplementary files format and content: Tab-delimited text file includes raw feature counts for all samples

organism: Zea mays

source_name: EAS Endosperm

extract_protocol:
Total RNAs were extracted in a two-step protocol. A trizol purification according to published protocol was performed (PMID: 17897408) and followed by a second purification using a ReliaPrep RNA tissue kit from Promega, which included a step of on-column DNAse treatment
Pair-end librairies were performed and sequencing with an Element Bio AVITI instrument following these parameters: AVITI 300 cycles Cloudbreak sequencing kit paired-end reads (151-10-10-151), 0.5%Phix. A total of 348.432M passing filter (PF) read pairs was obtained

value: EAS Endosperm

value: WT


title: atac_HDP2_Day4_delN_rep1

value: delN


title: lizard hemiphallus st7-9 ISL1 ChIP rep1

description:
SE75 sequencing
as_HP_st7-9_ISL1_IDR.narrowPeak.gz
as_HP_st7-9_ISL1_ChIP_pooled.bw


title: Endosperm WT 3


title: atac_HDP2_Day0_delN_rep2

value: Day 0


title: MVC_Input_2

address: 湖北省武汉市武昌区水果湖街道

description:
Library name: Sample2
MVC.ac4c.raw.txt


title: atfs-1(null)_nhr-180(cmh19) bio rep 3

description: Library name: ATFS-1_NHR-180_3


title: wildtype bio rep 1

description: Library name: N2_1


title: nhr-180(cmh19) bio rep 2

description: Library name: NHR-180m_2


title: atfs-1(null)_nhr-180(cmh19) bio rep 2

description: Library name: ATFS-1_NHR-180_2


title: MVC_Input_1

address: 湖北省武汉市武昌区水果湖街道

description:
Library name: Sample1
MVC.ac4c.raw.txt


title: acRIP_2

address: 湖北省武汉市武昌区水果湖街道

description: Library name: Sample4

data_processing:
*library strategy: acRIP-seq
Use Fastp (version 0.23.2) software for data quality control
Sequence reads were trimmed for adaptor sequence/low-quality sequence using by Trimmomatic (version 0.36)
Trimmed sequence reads were mapped to FJ214110 using STAR(version 2.7.6a) with default parameters.
The ac4C peaks were annotated using exomePeak（Version 3.8）
Assembly: accession no. FJ214110
Supplementary files format and content: acRIP.depth.xls; Input.depth.xls

source_name: WRD

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）. DNA digestion was carried out after RNA extraction by DNaseI. Anti-ac4C antibodies was used to pull down modified RNA .
RNA libraries for RNA-seq were prepared using components of the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan,China)

value: walter reed canine cells


title: atfs-1(null)_nhr-180(cmh19) bio rep 1

description: Library name: ATFS-1_NHR-180_1


title: Endosperm WT 1


title: atac_HDP2_Day0_delN_rep1


title: Endosperm MT 4

value: KIL1 KIL2 knockout


title: atac_HDP2_Day0_BCL11A_KO_rep2


title: atac_HDP2_Day0_WT_rep2


title: Endosperm MT 2


title: atfs-1(null) bio rep 3

description: Library name: ATFS-1_3


title: acRIP_1

address: 湖北省武汉市武昌区水果湖街道

description: Library name: Sample3


title: Input_1

address: 湖北省武汉市武昌区水果湖街道

description: Library name: Sample1


title: atac_HDP2_Day0_BCL11A_KO_rep1


title: atfs-1(null) bio rep 1

description: Library name: ATFS-1_1


title: LPY-3

status: Public on Apr 03 2025

first: Xinyue

address: No. 95 Luoyu Road, Luonan Street, Hongshan District, Wuhan

institute: The Affiliated Hospital of Wuhan Sports University

description:
Library name: sample9
LPY3_tpm

data_processing:
Raw Data Quality Control: Assess the quality of sequencing data, including base quality scores, read length, adapter contamination, etc. Sequence Alignment: Map the sequencing reads to a reference genome or transcriptome database to identify known genes and transcripts. Transcript Assembly: Assemble the reads that do not align to the reference database to identify novel transcripts and gene structures. Gene Expression Analysis: Calculate gene expression levels and perform differential expression analysis to compare gene expression differences between different samples or conditions. Functional Annotation: Annotate genes and transcripts for their functions, including gene function, pathway analysis, etc.
Assembly: Using known gene structure information, the sequencing data is compared to the reference genome and new transcripts are identified.
Supplementary files format and content: DESeq2 file: Format: text format to store the differential expression analysis results. Contents: Gene name, differential expression multiple, statistical significance and other information.

organism: Rattus norvegicus

source_name: gastric mucosa

extract_protocol:
Tissue Grinding and Lysis: Tissue is ground and added to Trizol reagent. It is then incubated at room temperature for 10 minutes to allow for lysis. Phase Separation: Chloroform is added, and the mixture is vigorously shaken and centrifuged to separate the aqueous and organic phases. RNA Extraction: The aqueous phase is collected and an equal volume of phenol:chloroform is added. The mixture is centrifuged again to separate the phases. Additional Phenol:Chloroform Extraction: The aqueous phase is collected again and an equal volume of chloroform is added. The mixture is centrifuged once more to separate the phases. RNA Precipitation: The aqueous phase is collected and an equal volume of isopropanol is added. The mixture is incubated at -20°C for 1 hour and then centrifuged to precipitate RNA. Washing and Drying: The supernatant is removed, and 75% ethanol is added to wash the pellet. The mixture is centrifuged, and the supernatant is removed. Repeat Washing: Step 6 is repeated to wash the pellet again. Drying: The pellet is briefly centrifuged to remove any remaining ethanol and then dried under vacuum. RNA Resuspension: RNase-Free water is added to dissolve the RNA, and the solution is stored at -80°C.
mRNA Isolation and Fragmentation: mRNA is isolated using magnetic beads with Oligo (dT) sequences. It is then fragmented and primers are added. First Strand cDNA Synthesis: The fragmented mRNA is reverse transcribed into cDNA using random primers and a reverse transcriptase enzyme. Second Strand cDNA Synthesis: The first strand cDNA is used as a template to synthesize the second strand, resulting in double-stranded cDNA. End Preparation: The ends of the double-stranded cDNA are repaired and prepared for adapter ligation. Adapter Ligation: Adapters are ligated to the ends of the cDNA molecules. Purification: The ligation products are purified using magnetic beads. PCR Amplification: The purified cDNA library is amplified using PCR with index primers to add barcodes for sample identification. Final Purification: The amplified library is purified using magnetic beads to remove any remaining impurities. Library Quality Control: The final library is assessed for size distribution and concentration using a bioanalyzer or other suitable method.

value: gastric mucosa

value: Wistar

value: received intragastric administration of Jiawei Lianpu Yin treatment based on the gastritis model


title: atac_HDP2_Day0_WT_rep1


title: atfs-1(null) bio rep 2

description: Library name: ATFS-1_2

value: All


title: Endosperm MT 1


title: MCM, scRNAseq

city: Osaka

first: Yasunori

last: Shintani

address: 6-1, Kishibe-shinmachi, Suita

department: Molecular Pharmacology

country: Japan

institute: National Cerebral and Cardiovascular Center

description:
Library name: Sample5
10X Genomics

data_processing:
Raw FASTQ files and histological images were processed using 10X Genomics Space Ranger software (version 2.0.1).
Assembly: GRch38-2020-A (human)
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Tissues were obtained during assist device implantation and were formalin-fixed then paraffin-embedded (FFPE). RNA quality was performed on FFPE tissue sections (10 μm) using Total RNA Pico assay (Agilent technologies) which were then processed according to the 10X Genomics Visium CytAssist manufacturer’s instructions. Briefly, sections were mounted on a glass slide under RNase-free conditions and libraries were prepared with Visium Human Transcriptome Probe Set v2.0. Sequencing was performed using DNBseq-G400RS (MGI Tech Co.). Raw FASTQ files and histological images were processed using 10X Genomics Space Ranger software (version 2.0.1). Alignment was performed using the GRch38-2020-A reference genome.
libraries were prepared with 10X Genomics Visium Human Transcriptome Probe Set v2.0.

value: Heart

tag: Sex

value: Female


title: Endosperm WT 2


title: LPY-2

description:
Library name: sample8
LPY2_tpm


title: Model-3

description:
Library name: sample6
Model3_tpm

value: gastritis was induced in rats using Helicobacter pylori infection


title: Model-2

description:
Library name: sample5
Model2_tpm


title: LPY-1

description:
Library name: sample7
LPY1_tpm


title: Control-3

description:
Library name: sample3
Control3_tpm

value: no intervention


title: Model-1

description:
Library name: sample4
Model1_tpm


title: Control-2

description:
Library name: sample2
Control2_tpm


title: Input_2

address: 湖北省武汉市武昌区水果湖街道

description: Library name: Sample2

value: WRD

value: MVC infected


title: Endosperm MT 3


title: 231, ArA, rep3

first: Xiaohui

address: Bayi Road, Wuchang District

institute: Wuhan University

description: Library name: Sample 6

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: 231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 40 μM of ArA and subsequently cultured for 24h with the non-treated cells serving as control.

value: Breast cancer cells

value: 40 μM of ArA


title: Control-1

description:
Library name: sample1
Control1_tpm


title: 231, NC, rep2

description: Library name: Sample 2

value: control


title: 231, ArA, rep1

description: Library name: Sample 4


title: 231, NC, rep3

description: Library name: Sample 3


title: 231, ArA, rep2

description: Library name: Sample 5


title: Control,infected,day2,SMA

city: Chapel Hill

first: Victor

last: Garcia

state: North Carolina

address: 120 Mason Farm Rd CB #7042

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL SMA 1 | Full ROI

data_processing:
Raw data were processed in GeoMx DSP.  Reads were transformed into counts, and then filtered for QC and biologic probe QC. Then were put through Q3 normalization.
ROI with low read counts were dropped from analysis
Data were exported into R for statistical analysis using the zoom package.
Assembly: GRCh38.p13, GRCm38.p6 M25, NC_045512
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Library strategy: Spatial Transcriptomics

source_name: lung

growth_protocol: See https://pubmed.ncbi.nlm.nih.gov/31451733/ for mice rearing procedure.

extract_protocol:
Probe capture on GeoMx
Probe captured RNAseq (GeoMx-NGS Readout Library Preparation)

treatment_protocol: Viruses were directly injected into the human lung tissue of.LOM mice and lung tissue collected either 2, 6, or 14 days post-exposure for virus titer determination and/or analysis by histology, electron microscopy, or RNA-seq

value: lung

value: LOM

value: SARS-CoV-2 infected


title: 231, NC, rep1

description: Library name: Sample 1


title: Inter.2,infected,day2,-,Segment1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL Inter 2 | Segment 1


title: Inter.1,infected,day2,-,Segment1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL Inter 1 | Segment 1


title: Foam,infected,day2,nonSMA

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL Foam 1 | Full ROI


title: Control,infected,day2,SMA,E836LHL3

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL 3 | Full ROI


title: Foam,infected,day2,-,E836LHL4

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL Foam 4 | Full ROI


title: Pre_scTCR_P049

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

library_source: transcriptomic single cell

data_processing:
The RNA-seq and paired Total-seq reads were aligned to the GRCh38 reference genome, which was modified with the CAR transgene sequence used in axicabtagene ciloleucel, and quantified using the cellranger count (10x Genomics, version 6.0.0). The filtered gene/feature-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. We obtained a total of 32,741 cells from 13 samples with on average 97,036 reads per cell and a median of 1979 genes per cell.
The TCR-seq reads from each sample were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10x Genomics, version 6.0.0). The results were then aggregated using the cellranger aggr function, with the source patient (donor) and timepoint (origin) of each sample supplied in the metadata to guide the clonotype assignment. The resultant clonotype and filtered contig annotation data were used for downstream analyses. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions for paired productive TCRα and TCRβ chains. TCR clonality overlap and tracing analyses were carried out using the immunarch package (version 0.6.7).
Assembly: GRCh38
Supplementary files format and content: final merged raw count matrices of scRNA and Totalseq
Supplementary files format and content: final R object of combined scTCR data

source_name: PBMC

extract_protocol:
Cryopreserved patient biospecimens were thawed in warm RPMI+10% FBS and washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Next, Fc receptors were blocked by incubation with Human TruStain FcX (BioLegend, 422301) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-anti-CD3E (clone SK7), CITE-seq antibodies, and Alexa Fluor 647-labeled antigen-tetramers at 3 nM final concentration for CAR-detection. Subsequently, cells were incubated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) diluted 1:1000 in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media. Infusion products were partitioned and analyzed directly. Peripheral blood mononuclear cells were subject to fluorescence-activated cell sorting before single-cell partitioning and analysis.
T cells were partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). From the resulting barcoded nucleic acids, TCR-seq libraries were prepared via the Chromium Single-Cell Human TCR Amplification Kit (10x Genomics, 1000252). Sequencing libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via a high-sensitivity D5000 screentape (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq-6000).

tag: disease state

value: Diffuse Large B-Cell Lymphoma

value: Blood PBMCs

tag: molecule type

value: TCR mRNA


title: Inter.3,infected,day6,-,Segment.1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Inter 3 | Segment 1


title: Control,infected,day2,SMA,E836LHL2

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL 2 | Full ROI


title: Inter.2,infected,day6,-,Segment.1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Inter 2 | Segment 1


title: Post_scTCR_049-d90-CART


title: Inter.1,infected,day6,-,Segment.1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Inter 1 | Segment 1


title: Foam,infected,day2,-,E836LHL3

description: E836 LHL_E130 LHL Bond 2I8A_1 | E836 LHL Foam 3 | Full ROI


title: Pre_scTCR_P034


title: Foam.3,infected,day6,-,E130LHL

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Foam 3 | Full ROI


title: Pre_scTCR_P033


title: Post_scTCR_049-d28-CART


title: Post_scTCR_049-d12-CART


title: Foam.1,infected,day6,-

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Foam 1 | Full ROI


title: Control,infected,day6,SMA,LHL.3

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL 3 | Full ROI


title: Post_scTCR_034-d08-CART


title: Post_scTCR_034-d21-CART


title: Post_scTCR_033-d28-CART


title: Control,infected,day6,SMA,LHL.1

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL 1 | Full ROI


title: Post_scTCR_033-d21-CART


title: Inter.3,uninfected,naive,-,Segment.1

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Inter 3 | Segment 1

value: uninfected


title: Post_scTCR_033-d10-CART


title: Pre_TotalSeq_P049

value: ADT (feature barcode)


title: Inter.2,uninfected,naive,-,Segment.1

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Inter 2 | Segment 1


title: Inter.1,uninfected,naive,-,Segment1

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Inter 1 | Segment 1


title: Foam.2,uninfected,naive,nonSMA

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Foam 2 | Full ROI


title: Pre_scRNA_P049

value: mRNA


title: Foam.3,uninfected,naive,nonSMA

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Foam 3 | Full ROI


title: Post_scTCR_049-d21-CART


title: Control,infected,day2,SMA.2

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL SMA 2 | Full ROI


title: Pre_scRNA_P033


title: Foam.003,uninfected,naive,nonSMA

description: E828 LHL_E133 LHL Bond 2I89_1 | E828 LHL Foam 003 | Full ROI


title: Control,infected,day2,SMA.1

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL SMA 1 | Full ROI


title: Foam.2,infected,day6,-

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL Foam 2 | Full ROI


title: Pre_scRNA_P034


title: single cell G4 CUT&Tag mixed cell line

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Library name: scG4CnT_mESC_3T3

library_source: genomic single cell

data_processing:
Libraries were sequenced on an Illumina Nextseq 2000
Single Cell Fastq files were processed using cellranger-ATAC v2.2.0.Reads were aligned to the mm10 genome reference. Processing of Cell Ranger ATAC H5 files and the subsequent single-cell analysis workflow were done in R using packages Seurat (v5.0.3) and Signac.Reduction of dimensionality was done using package Signac's LSI and UMAP. Bulk CUT&Tag FASTQ files were processed through the nf-core/atacseq pipeline (v1.2.1). Essentially, reads were aligned to the mm10 reference genome with BWA (v0.7.17-r1188), deduplicated with Picard (v2.23.1), peaks were called with MACS2 (v2.2.7.1).
Cluster-specific peaks were retrieved by Signac’s CallPeaks function using a simple MACS2 (71) peak calling (with the default parameters of CallPeaks) and with group.by = “seurat_clusters” to call peaks on each cluster separately.
Generating bam files from each Seurat cluster was performed by the filterbarcodes function of the package called sinto.The retrieved bam files were converted to RPGC normalized bigwig files by bamCoverage of deepTools (v3.5.4).
For bulk CUT&Tag deepTools (21) 3.5.2 bamCoverage was used to produce bigWig files using RPGC (1x Genome Coverage) normalization.
Assembly: mm10
Supplementary files format and content: bigWig,peak,Rds files

growth_protocol: Mouse embryonic stem cells were cultured feeder-free in 0.1% gelatin-coated flasks (Sigma, G1890) under standard conditions (5% CO2, 90% humidity, 37°C) in KnockOut DMEM (LifeTechnologies, 10829018), 2 mM alanyl-glutamine (Sigma, G8541), 0.1 mM non-essential amino acids (Sigma, M7145), 15% fetal bovine serum (FBS) (Sigma, F7524), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), 1 μM PD0325901 (PZ0162-25MG) and 3 μM CHIR99021 (SML1046-25MG). NIH-3T3 cells were cultured in DMEM (Gibco, 31966047) supplemented with 10% fetal bovine serum (FBS; Gibco, 26140079) and 1× penicillin/streptomycin (Sigma, P4333). Brain was dissociated using Miltenyi neural tissue dissociation kit P (130-092-628), cleared with Debris removal solution (130-109-398), filtered through 50 um strainer and FACS sorted for GFP+/GFP- on FACS Aria III or FACS Aria Fusion

extract_protocol:
Nuclei were extracted using NP-40 / Digitonin buffer. Bulk G-quadruplex CUT&Tag experiments were performed as in Lyu et al. (33), but without Concanavaline A beads to better maintain the integrity of the nuclei. All the centrifugation steps in the protocol were performed at 600g or 1700rpm at 4℃ with swing bucket centrifuge. 200,000 cells were harvested by centrifugation, resuspended in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine) and pelleted again, incubated in 200ul of antibody binding buffer (wash buffer with 2 mM EDTA, 0.01% NP-40, 0.05% digitonin and 1% BSA) containing 2ug of BG4 antibody (Addgene #55756) with rotation overnight at 4℃. The next day, cells were washed with 200ul of dig-wash buffer (wash buffer with 0.01% NP-40, 0.05% digitonin and 1% BSA) three times by centrifugation at 600g or 1700rpm for 4min with swing bucket centrifuge. After washing, cells were incubated with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) for one hour at room temperature with rotation. Cells were washed with 200ul of dig-wash buffer to remove unbound anti-FLAG antibodies. Anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in a dig-wash buffer for one hour at room temperature, followed by washing with 200ul of dig-wash buffer three times. After antibody incubation, cells were incubated with 1:200 dilution of assembled pA-Tn5 in 200ul of dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% NP-40, 0.05% digitonin and 1% BSA) for 1h at room temperature. After pA-Tn5 binding, cells were washed with 200ul of dig-300 buffer three times. Afterwards, pA-Tn5 bound cells were incubated in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1h without shaking. After tagmentation, genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013). To generate the G4 library, purified genomic DNA was amplified with the universal i5 primer and barcoded i7 primer using NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced on an Illumina Nextseq 2000 instrument. For single-cell CUT&Tag, antibody and Tn5 incubation steps were performed as above. After tagmentation, the cells were centrifuged for 3 min at 300g and resuspended in 15–25 μl of 1× PBS + 1% BSA and processed using 10x Chromium Single Cell ATAC-Seq kit. Tagmented nuclei were processed using the 10x scATAC-seq kit according to manufactureres instructions skipping Step 1 "Transposition" and continuing from Step 2.0 "Generation and barcoding". Final library amplification was performed according to the Chromium Single Cell ATAC Library kit manual sequenced on an Illumina Nextseq 2000 instrument.
For bulk CUT&Tag, purified genomic DNA was amplified with the universal i5 primer and barcoded i7 primer using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter) and sequenced on an Illumina Nextseq 2000 instrument (illumina). For single cell CUT&Tag, After tagmentation, the sample was centrifuged for 3 min at 300g and resuspended in 15–25 μl of 1× PBS + 1% BSA and processed using 10x Chromium Single Cell ATAC-Seq kit. Final library amplification was performed according to the Chromium Single Cell ATAC Library kit manual.

treatment_protocol: There was no treatment

value: embryonic stem cell, mouse embryonic fibroblasts

value: WT

value: No treatment


title: Control,infected,day2,SMA.3

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL SMA 3 | Full ROI


title: single cell G4 CUT&Tag mouse brain unsorted

description: Library name: scG4CnT_unsorted

source_name: mouse brain

value: mouse brain


title: Inter.3,infected,day2,-

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL Inter 3 | Segment 1


title: Pre_TotalSeq_P034


title: Inter.2,infected,day2,-

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL Inter 2 | Segment 1


title: Control,infected,day6,SMA,LHL.2

description: E836 LHL_E130 LHL Bond 2I8A_1 | E130 LHL 2 | Full ROI


title: bulk G4 CUT&Tag 3T3 rep2

description: Library name: bulk_G4CnT_3T3_rep2

data_processing:
Libraries were sequenced on an Illumina Nextseq 2000
Single Cell Fastq files were processed using cellranger-ATAC v2.2.0.Reads were aligned to the mm10 genome reference. Processing of Cell Ranger ATAC H5 files and the subsequent single-cell analysis workflow were done in R using packages Seurat (v5.0.3) and Signac.Reduction of dimensionality was done using package Signac's LSI and UMAP. Bulk CUT&Tag FASTQ files were processed through the nf-core/atacseq pipeline (v1.2.1). Essentially, reads were aligned to the mm10 reference genome with BWA (v0.7.17-r1188), deduplicated with Picard (v2.23.1), peaks were called with MACS2 (v2.2.7.1).
Cluster-specific peaks were retrieved by Signac’s CallPeaks function using a simple MACS2 (71) peak calling (with the default parameters of CallPeaks) and with group.by = “seurat_clusters” to call peaks on each cluster separately.
Generating bam files from each Seurat cluster was performed by the filterbarcodes function of the package called sinto.The retrieved bam files were converted to RPGC normalized bigwig files by bamCoverage of deepTools (v3.5.4).
For bulk CUT&Tag deepTools (21) 3.5.2 bamCoverage was used to produce bigWig files using RPGC (1x Genome Coverage) normalization.
Assembly: mm10
Supplementary files format and content: bigWig,peak,Rds files
Library strategy: CUT&Tag

value: mouse embryonic fibroblasts


title: single cell G4 CUT&Tag mouse brain GFP positive

description: Library name: scG4CnT_GFP_positive


title: Foam.1,infected,day2,nonSMA

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL Foam 1 | Full ROI


title: Pre_TotalSeq_P033


title: bulk G4 CUT&Tag mESC rep1

description: Library name: bulk_G4CnT_mESC_rep1

value: embryonic stem cell


title: Foam.2,infected,day2,-

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL Foam 2 | Full ROI


title: bulk G4 CUT&Tag 3T3 rep1

description: Library name: bulk_G4CnT_3T3_rep1


title: Inter.1,infected,day2,-

description: E828 LHL_E133 LHL Bond 2I89_1 | E133 LHL Inter 1 | Segment 1


title: Th17, IgG, rep1, CUT&RUN

city: South San Francisco,

first: Saiyu

last: Hang

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Basecalling was performed using bcl2fastq v2.20.0 from NextSeq2000 output
CUT&RUN reads were trimmed using Trim Galore v.0.6.6
CUT&RUN reads were aligned to mm10 using Bowtie2 followed by duplicate removal and subsequent peak calling with SEACR
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
Nuclei were prepared from  in-vitro-differentiated Th17 cells using  nuclear extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1x Roche cOmplete™, Mini, EDTA-free Protease Inhibitor)
CUT&RUN libraries were prepared using Epicypher's CUTANA™ ChIC/CUT&RUN Kit (#141-048) and NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645S) indexed using NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB #E6440S).

tag: cut&run antibody

value: IgG (EpiCypher #13-0042)


title: Inter.4,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL Inter 4 | Interstitial Segment


title: Control,uninfected,naive,SMA.3

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL SMA 3 | Full ROI


title: Inter.3,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL Inter 3 | Interstitial Segment


title: Control,uninfected,naive,SMA.4

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL SMA4 | Full ROI


title: Th17, H2Bub1, rep3, CUT&RUN


title: Th17, H3K4me3, rep1, CUT&RUN

value: H3K4me3 (EpiCypher #13-0041)


title: Inter.2,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL Inter 2 possible | Interstitial Segment

value: lung


title: Foam.3,uninfected,naive,SMA

description: E734 UHL_E835 LHL Bond 2I88_1 | E835 LHL Foam 3 | Full ROI

value: LOM


title: Th17, H2Bub1, rep2, CUT&RUN


title: Inter.1,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E734 UHL Inter 1 | Interstitial Segment


title: Th17, H2Bub1, rep1, CUT&RUN


title: Foam.3,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E734 UHL Foam 3 | Full ROI


title: Th17, RTF1, rep1, CUT&RUN

value: RTF1 (Bethyl #A300-179A-T)


title: Th17, RTF1, rep2, CUT&RUN


title: Foam.2,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E734 UHL Foam 2 | Full ROI


title: Foam.1,uninfected,naive,-

description: E734 UHL_E835 LHL Bond 2I88_1 | E734 UHL Foam 1 | Full ROI


title: bulk G4 CUT&Tag mESC rep2

description: Library name: bulk_G4CnT_mESC_rep2


title: Inter.4,infected,day6,-,E741UHL

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Inter 4 | Segment 1

value: SARS-CoV-2 infected


title: IMR32, NCA, RNA-seq, rep3

city: Gent

first: Louis

last: Delhaye

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

description:
Library name: NCA_IMR32_rep3
IMR32_NCA_3
Normalized_count_matrix_IMR32_RNA.txt

data_processing:
Reads were quality controlled using FastQC (v0.11.8) and trimmed with cutadapt (v1.18) to remove any low quality bases and Illumina adapter sequences.
Trimmed reads were aligned using STAR (v2.6.0) to the human hg19 reference genome assembly (GRCh37)
Read quantification was performed with HTSeq (v0.6.1)
Count data was imported in R, and differential analysis was performed with DESeq2 (v1.42.0) with the ASO treatment as the only design variable (design = ASO).
Assembly: hg19
Supplementary files format and content: Normalized_count_matrix_IMR32_RNA.txt contains DESeq2-normalized counts per gene for NESPR-targeting and NC ASO RNA-sequencing experiments in IMR32.
Supplementary files format and content: Normalized_count_matrix_NGP_RNA.txt contains DESeq2-normalized counts per gene for NESPR-targeting and NC ASO RNA-sequencing experiments in NGP.
Supplementary files format and content: Normalized_count_matrix_SK-N-BE2c_RNA.txt contains DESeq2-normalized counts per gene for NESPR-targeting and NC ASO RNA-sequencing experiments in SK-N-BE(2)c.

growth_protocol: SK-N-BE(2)c, NGP, IMR32, and SH-SY5Y cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 2 mM glutamine, and 30 U/mL Penicillin-Streptomycin. Cell cultures were maintained under 60-70% confluency and passaged twice a week. Cells lines were confirmed mycoplasma-free on a regular basis by a mycoplasma colorimetric detection assay on medium of 48 h-confluent cultures. STR genotyping was performed to validate cell line authenticity. Cells were cultured in designated incubators at 37°C with a humidified atmosphere containing 5% CO2.

extract_protocol:
Attached cells were washes once with PBS, trypsinized, and collected by centrifugation. After two more PBS washes, pellets were redissolved in 700 uL QIAzol, incubated for 15 min at room temperature, snap-frozen, and stored at -80°C until further processing. Samples were unthawed at room temperature and 140 uL 100% chloroform was added. After vigorous mixing and centrifugation at 12 000 x g for 15 min at 4°C, the upper aqueous phase was collected to which 600 uL 100% EtOH was added. RNA from the mixture was isolated with the miRNeasy Micro kit following the manufacturer’s instructions including a Dnase I digestion to remove contaminating DNA. RNA concentrations were measured by nanodrop. RNA was stored at -80°C. cDNA synthesis was performed with the iScript Advanced cDNA synthesis Kit according to the manufacturer’s instructions with maximal shared RNA input across samples up to a maximum of 500 ng RNA template. cDNA was stored at -20°C.
Total RNA libraries were prepared from 8 uL purified RNA using the SMARTer Stranded Total RNA-seq Kit v3 – Pico Input Mammalian following the manufacturer’s instructions or TruSeq Stranded mRNA Library Prep Kit LT. RNA was fragmented at 94°C for 4 min prior to first strand cDNA synthesis. Library amplification was performed with 12 PCR cycles. Library size analysis was performed by running the libraries on a fragment analyzer. Library quantification was performed by RT-qPCR with the KAPA Library Quantification kit and libraries were pooled equimolarly. The final pool was quantified by Qubit. 675 pM of PicoV3-prepped libraries was loaded on a NextSeq 2000 instrument (NextSeq 2000 P2 v3, 2X 50 cycles, paired-end sequencing) with 2% PhiX or 2 pM of TruSeq-prepped libraries was loaded on a NextSeq 500 instrument (NextSeq 500/550 High-Output kit, 75 cycles, single-end sequencing) with 1% PhiX.

treatment_protocol: Cells were transfected with 100 nM ASO using lipofectamine 2000 according to the manufacturer’s instructions.

value: Neuroblastoma cell line

value: NCA

value: Antisense oligonucleotide


title: IMR32, NCA, RNA-seq, rep4

description:
Library name: NCA_IMR32_rep4
IMR32_NCA_4
Normalized_count_matrix_IMR32_RNA.txt


title: IMR32, NCA, RNA-seq, rep2

description:
Library name: NCA_IMR32_rep2
IMR32_NCA_2
Normalized_count_matrix_IMR32_RNA.txt


title: Foam.7,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Foam 7 | Full ROI


title: IMR32, ASO2, RNA-seq, rep4

description:
Library name: ASO2_IMR32_rep4
IMR32_LNA2_4
Normalized_count_matrix_IMR32_RNA.txt


title: IMR32, NCA, RNA-seq, rep1

description:
Library name: NCA_IMR32_rep1
IMR32_NCA_1
Normalized_count_matrix_IMR32_RNA.txt


title: Inter.3,infected,day6,-E731UHL

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Inter 3 | Segment 1


title: Foam.6,infected,day6,nonSMA

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Foam 6 | Full ROI


title: IMR32, ASO2, RNA-seq, rep3

description:
Library name: ASO2_IMR32_rep3
IMR32_LNA2_3
Normalized_count_matrix_IMR32_RNA.txt


title: Foam.4,infected,day6,nonSMA

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Foam 4 | Full ROI


title: Foam.5,infected,day6,nonSMA

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Foam 5 | Full ROI


title: IMR32, ASO2, RNA-seq, rep1

description:
Library name: ASO2_IMR32_rep1
IMR32_LNA2_1
Normalized_count_matrix_IMR32_RNA.txt


title: IMR32, ASO1, RNA-seq, rep4

description:
Library name: ASO1_IMR32_rep4
IMR32_LNA1_4
Normalized_count_matrix_IMR32_RNA.txt


title: IMR32, ASO2, RNA-seq, rep2

description:
Library name: ASO2_IMR32_rep2
IMR32_LNA2_2
Normalized_count_matrix_IMR32_RNA.txt


title: Th17, RTF1, rep3, CUT&RUN


title: Foam.3,infected,day6,-,E371UHL

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL Foam 3 | Full ROI


title: Control,infected,day6,SMA,E731UHL1

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL 1 | Full ROI


title: Control,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL 2 | Full ROI


title: Control.3,infected,day6,SMA

description: E434 LHL_E731 UHL Bond 2I8B_1 | E731 UHL 3 | Full ROI


title: Inter.4,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Inter 4 | Segment 1


title: IMR32, ASO1, RNA-seq, rep1

description:
Library name: ASO1_IMR32_rep1
IMR32_LNA1_1
Normalized_count_matrix_IMR32_RNA.txt


title: GATA1_KO_D2

first: Alexis

last: Caulier

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

description: demultiplexed with BCL Convert

library_source: other

data_processing:
Sequencing reads were trimmed to 41bp, and only those with an average quality >20 were retained. Adapters were removed using cutadapt 1.14 and 3’ bases with low quality. An initial alignment step of R1 reads was performed to the control Drosophila genome spike-in using Bowtie 1.2.2. Unmapped reads were then aligned to the hg38 genome, sorted, and converted to bedGraph format.
Assembly: GRCh38
Supplementary files format and content: .txt
Supplementary files format and content: .bw
Library strategy: PRO-seq

molecule: other

source_name: erythroid cells

growth_protocol: Erythroid media

extract_protocol:
Cells were permeabilized and subjected to nuclear run on with biotinylated NTPs. RNA was isolated, fragmented and nascent RNA enriched for library construction. All steps were performed as described in Mimoso CA, Goldman SR. Current Protocols 2023;3:e961.
PRO-seq libraries were constructed as described in Mimoso CA, Goldman SR. Current Protocols 2023;3:e961.

value: erythroid cells


title: IMR32, ASO1, RNA-seq, rep3

description:
Library name: ASO1_IMR32_rep3
IMR32_LNA1_3
Normalized_count_matrix_IMR32_RNA.txt


title: Inter.3,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Inter 3 | Segment 1


title: GATA1_KO_D1

description: demultiplexed with BCL Convert


title: AAVS1_D2

description: demultiplexed with BCL Convert


title: Inter.1,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Inter 1 | Segment 1


title: AAVS1_D1

description: demultiplexed with BCL Convert


title: Inter.2,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Inter 2 | Segment 1


title: Foam.4,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Foam 4 | Full ROI


title: P7F1_IgG_Rep2

city: Badalona

first: Gerard

last: Martinez-Cebrian

state: Barcelona

address: Edifici Josep carreras, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Institut Josep carreras

data_processing:
For Cut&Run raw reads were aligned with bowtie2 v2.3.5.1 to the human genome (hg38 assembly). Next, we removed unmapped and duplicate reads with MarkDuplicates from Picard v2.18.11 and called peaks using MACS2 v2.1.1 (the --broad option was used for H3K4me1). BigWig files were obtained using deeptools v3.2.1 and bedtools v2.26.0.
Assembly: hg38
Supplementary files format and content: bigwigs and MACS2 narrow/broadPeak files
Library strategy: Cut&Run

source_name: induced pluripotent stem cell muscle progenitor

growth_protocol: Human iPS cells expressing PAX7 (muscle progenitors)(Wu et al., 2016) were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% penicillin/streptomycin (Corning), 50 μg/ml L-ascorbic acid (Sigma), 4.5mM 1-thioglycerol (Sigma), and 10 ng/ml recombinant human basic-FGF (Peprotech). These muscle progenitors were infected using lentiviral doxycycline-inducible or constitutive (EF1α promoter) constructs driving expression of a cDNA encoding the exact PAX7-FOXO1 or PAX3-FOXO1 fusion protein found in ARMS tumors. PAX7 transgene expression was induced by adding Dox (Sigma-Aldrich, final concentration 1 μg/ml), and then maintained throughout the protocol by replacing the medium (including dox) with 10 ng/ml human basic-FGF (Preprotech) every 2 days.

extract_protocol:
Cut&Run was performed for two technical replicates per condition, from 0.25 x 106 cells using the Cell Signaling Cut&Run kit (#86652) according to the manufacturer's instructions. We used 2 mg of antibody or Normal Rabbit IgG as background control with overnight incubation at 4°C. Protein A/G coupled MNase was incubated with antibodies to digest proximal DNA. The fragmented DNA was extracted and purified using DNA spin columns (Cell signaling #14209).
The enriched DNA from Cut&Run was used to construct  sequencing libraries with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7103) and sequenced (2 x 50bp paired end) in an Illumina NextSeq 2000 machine.

treatment_protocol: For cultures without Dox, cells were harvested at day 3 following Dox removal for analysis.

tag: c&r antibody

value: normal IgG


title: Foam.3,infected,day6,-

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Foam 3 | Full ROI


title: P7F1_IgG_Rep1

value: induced pluripotent stem cell muscle progenitor


title: Control,infected,day6,SMA,.3

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL 3 | Full ROI


title: P3F1_IgG_Rep2


title: P3F1_IgG_Rep1


title: Control,infected,day6,-,.2

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL 2 | Full ROI


title: IMR32, ASO1, RNA-seq, rep2

description:
Library name: ASO1_IMR32_rep2
IMR32_LNA1_2
Normalized_count_matrix_IMR32_RNA.txt

tag: cell line


title: Control,infected,day6,SMA.1

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL 1 | Full ROI


title: P7F1_Flag_Rep2

tag: cell type

value: Flag


title: Control_IgG_Rep1

tag: genotype

value: WT


title: Tumor, RT, rep2

source_name: Xenograft tumor

growth_protocol: Xenograft models were established by injecting subcutaneously 5 × 105 WT MDA-MB-231 cells with an equal volume of Matrigel on left flank of NOD/SCID/IL2Rγ-null (NSG) mice. All mice were housed in a specific pathogen-free (SPF)  environment under a 12 h light/dark cycle at a relative humidity of 50-60% and room temperature of 22.2 ± 1.1°C, and allowed free access to food and water.

treatment_protocol: Upon reaching approximately 800 mm3, tumors were locally irradiated with a single dose of 10 Gy using a clinical linear accelerator (Varian Medical Systems). Radiation was delivered at a dose rate of 6 Gy/min with 6 MV X-rays. Mice were sacrificed 3 days post-IR with the non-irradiated tumors serving as control.

value: Xenograft tumor

value: Breast cancer cells

value: irradiation of X-rays


title: P7F1_Flag_Rep1


title: Tumor, RT, rep1


title: P3F1_Flag_Rep1


title: Tg_R3

city: La Jolla

first: R

middle: Luke

last: Wiseman

state: California

address: 10550 N Torrey Pines Rd, Mb110 Receiving Department

institute: The Scripps Research Institute

description:
Library name: Sample 43
Column name in HEK293_IRE1_activators_raw counts_all samples, Tg_R3

data_processing:
Alignment of reads was performed using DNAstar Lasergene SeqManPro
Aligned reads were imported into ArrayStar 12.2 with QSeq (DNAStar Inc.) to quantify gene expression levels.
Differential expression analysis and statistical significance calculations between different conditions were assessed using DEseq2 v. 1.42.1 in R
Assembly: HEK293 reads were aligned to the human genome GRCh38 assembly. Reads generated from mouse kidney and liver samples were aligned to the mouse genome GRCm39 assembly.
Supplementary files format and content: csv files contain raw counts for each sample

growth_protocol: Male C57BL/6J mice, aged 8-10 weeks, were obtained from the rodent breeding colonies at Scripps Research and were housed under a 12-h light/dark cycle with ad libitum access to food and water. HEK 293 cells were cultured in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning Cellgro) supplemented with 10% fetal bovine serum (FBS) (Omega Scientific), 2 mM L-glutamine (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco) and under typical tissue culture conditions (37°C, 5% CO2).

extract_protocol:
For mouse tissue experiments, 4-5 biological replicates were studied for each treatment condition. Total RNA from liver or kidney was isolated using Zymo Research Direct-zol RNA Miniprep kits following the manufacturer’s instructions after homogenization in TRIzol reagent. For HEK293 cells, 3 biological replicates were studied for each treatment condition.Total RNA from HEK293 cells were isolated using QuickRNA mini kit (Zymo) according to the manufacturer′s instructions. Whole transcriptome RNA sequencing was conducted by BGI Americas on the BGI Proprietary platform.
libraries were constructed at BGI

treatment_protocol: For in vivo study, IXA62 was prepared in a formulation of 10% DMSO, 30% Kolliphor EL:ethanol (2:1 ratio), and 60% saline at a concentration of 10 mg/mL. mice were weighted and administered IXA62 (50 mpk) or vehicle by IP injection once daily in the morning for 7 days, and sacrificed 4 h after the final injection. For HEK 293 cells, DMSO, 10 uM compounds, including IXA21(Life chemicals, Cat #F2574-0132), IXA62 (Enamine, Cat #T5347952), IXA76 (ChemDiv, Cat #1486-0766), IXA502 (ChemDiv, Cat #K898-0862), IXA554 (Life chemicasl,Cat #F2506-1107), IXA624 (Life chemicals, Cat# F5772-8755) or 0.5 uM Thapsigargin (Tg) (Fisher, Cat # 50-464-295) were treated for 6 h.

value: 0.5 uM Tg


title: P7F1_H3K27ac_Rep2


title: P7F1_H3K27ac_Rep1


title: Tg_R1

description:
Library name: Sample 41
Column name in HEK293_IRE1_activators_raw counts_all samples, Tg_R1


title: Tumor, CT, rep3

value: control


title: IXA624_R3

description:
Library name: Sample 40
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA624_R3

value: 10 uM IXA624


title: Tumor, CT, rep2


title: P3F1_H3K27ac_Rep2


title: P3F1_H3K27ac_Rep1


title: Foam.1,infected,day6,nonSMA

description: E434 LHL_E731 UHL Bond 2I8B_1 | E434 LHL Foam 1 | Full ROI

value: lung

value: LOM


title: Control_H3K27ac_Rep2


title: IXA624_R2

description:
Library name: Sample 39
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA624_R2


title: P7F1_H3K4me3_Rep2


title: Control_H3K27ac_Rep1


title: Tumor, CT, rep1


title: IXA624_R1

description:
Library name: Sample 38
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA624_R1


title: 231, RT, rep3

treatment_protocol: Cells were irradiated with 20Gy of X-rays and subsequently cultured for 24h with the non-treated cells serving as control.


title: Control_IgG_Rep2


title: P7F1_H3K4me3_Rep1


title: Tumor, RT, rep3


title: Tg_R2

description:
Library name: Sample 42
Column name in HEK293_IRE1_activators_raw counts_all samples, Tg_R2


title: P3F1_Flag_Rep2


title: P3F1_H3K4me3_Rep2


title: IXA554_R3

description:
Library name: Sample 37
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA554_R3

value: 10 uM IXA554


title: 231, RT, rep2


title: Control_H3K4me3_Rep2


title: IXA554_R2

description:
Library name: Sample 36
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA554_R2


title: P3F1_H3K4me3_Rep1


title: Control_H3K4me3_Rep1


title: 231, RT, rep1


title: P7F1_H3K4me1_Rep2


title: 231, CT, rep3


title: P7F1_H3K4me1_Rep1


title: IXA554_R1

description:
Library name: Sample 35
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA554_R1


title: P3F1_H3K4me1_Rep2


title: P3F1_H3K4me1_Rep1


title: 231, CT, rep2


title: IXA502_R3

description:
Library name: Sample 34
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA502_R3

value: 10 uM IXA502


title: Control_H3K4me1_Rep2


title: IXA502_R2

description:
Library name: Sample 33
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA502_R2


title: Control_H3K4me1_Rep1


title: 231, CT, rep1


title: IXA502_R1

description:
Library name: Sample 32
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA502_R1


title: Conditioned Medium treated Replicate 2

city: Palermo

first: Veronica

last: Veschi

address: Via del Vespro, 131

country: Italy

institute: University of Palermo

data_processing:
STAR v 2.7.0.f
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt
Trimmed sequence reads were mapped to hg38 using STAR
Read count were performed using RSEM
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: colon

extract_protocol:
The RNA was extracted using the Qiagen RNeasy mini kit including the optional DNase clean-up step. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: colon

value: cancer stem cell freshly isolated from human patient #14

value: conditioned media 3


title: IXA76_R3

description:
Library name: Sample 31
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA76_R3

value: 10 uM IXA76


title: Untreated Replicate 1


title: IXA76_R1

description:
Library name: Sample 29
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA76_R1


title: Conditioned Medium treated Replicate 1


title: IXA62_R3

description:
Library name: Sample 28
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA62_R3

value: 10 uM IXA62


title: FgPH-1-FgDDT-GFP_IP2

city: Hefei

first: zhao

middle: xiao

last: zhen

address: Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China

institute: Anhui Agricultural University

description: ChIP-Seq of Fusarium graminearum PH-1:FgDDT-GFP_IP

data_processing: For ChIP-seq analysis, the raw sequencing reads were controlled quality-checked using SOAPnuke (v2.1.7) (Chen et al., 2018b), and then were aligned to the reference genome of F. graminearum strain PH-1 by Bowtie2 (version 2.4.5) with default parameters (Langmead and Salzberg, 2012). RPKM (reads per kilobase per million mapped reads) were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a control (Fidel et al., 2014).

organism: Fusarium graminearum PH-1

source_name: Fusarium graminearum ΔFgDDT::FgDDT-GFP

extract_protocol: ChIP technique was performed as described previously. (Gu et al., 2022). First, the mycelia were fixed with 1% formaldehyde, and were lysed. Second, Chromatin was sheared into 500bp fragments by sonication. Third, the selective immunoprecipitation of protein–DNA complexes were obtained by utilizing anti-GFP antibody (ab290, Abcam, Cambridge, UK) and their conjugated protein A agarose beads (sc-2003, Santa Cruz, CA). Finally, the cross-linked protein–DNA complexes were reversed, and the immunoprecipitated DNA was extracted by phenol/chloroform method. Half of the extracted DNA was then subjected to high-throughput sequencing on the IlluminaHiseq4000 platform by BGI (Shenzhen, China).

value: Mycelium

tag: infection

value: NO

value: Day 2 of fresh mycelium


title: IXA76_R2

description:
Library name: Sample 30
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA76_R2


title: donor heart store in HTK+CAN for 10h, MR

first: IENG LAM

last: LEI

state: MN

address: 321 3rd Street SW

institute: Mayo Clinic

data_processing:
For snRNA-seq, the count matrix were generated by Cellranger v7.
For Cut&Run seq, the reads were trimmed using Trimmomatic, and then aligned to GRCh38 using bowite2 with --dovetail option. The bigwig signal track of MR vs IgG were coverted using bam files with bamcompare. The peaks were called using MACS3.
Assembly: GRCH38
Supplementary files format and content: count matrix file for single cell RNA-seq
Supplementary files format and content: bigwig file and narrowPeak file for cut&run seq.
Library strategy: Cut&run

source_name: left ventricle

extract_protocol:
The cut&run assay was performed using Epicypher cut&run kit following the manufacturer's protocol
The library was prepared using NEB ultraII DNA library kit. The snRNA-seq libraries were prepared using 10x Chromium fixed RNA profiling protocol.

value: left ventricle

value: store in HTK+CAN for 10h


title: FgPH-1_input

description: ChIP-Seq of Fusarium graminearum PH-1:PH-1_Input

source_name: Fusarium graminearum PH-1

value: WT


title: donor heart snRNA-seq

data_processing:
For snRNA-seq, the count matrix were generated by Cellranger v7.
For Cut&Run seq, the reads were trimmed using Trimmomatic, and then aligned to GRCh38 using bowite2 with --dovetail option. The bigwig signal track of MR vs IgG were coverted using bam files with bamcompare. The peaks were called using MACS3.
Assembly: GRCH38
Supplementary files format and content: count matrix file for single cell RNA-seq
Supplementary files format and content: bigwig file and narrowPeak file for cut&run seq.


title: IXA62_R1

description:
Library name: Sample 26
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA62_R1


title: SK-N-BE(2)c, NCA_ATAC, rep2

description:
Library name: NCA_SK-N-BE2c_ATAC_rep2
NCA_2

data_processing:
Sequencing quality was verified with FastQC Read counts per called overlapping peak were used as input for DESeq2 differential analysis, similar as described above (design =  ASO).
Reads were trimmed with NGMerge
Alignment to the hg38 human genome assembly (GRCh38) was performed with Bowtie2 (v2.2.6)
Duplicate reads were removed with SAMTools
MACS2 (v2.1.2) was used for peak calling. Peaks with an adjusted P-value less or equal than 5% were considered significant, and significant peaks with a 50% overlap across samples were merged into a single matrix.
Reads were counted with the SummarizeOverlaps function from the GenomicAlignments (v1.38.0) R package with the overlap matrix and corresponding BAM files per replicate and condition as input.
Read counts per called overlapping peak were used as input for DESeq2 (v1.42.0) differential analysis (design =  ASO)
Assembly: hg38
Supplementary files format and content: ATAC_SKNBE2C_counts.csv contains DESeq2-normalized counts per peak for NESPR-targeting and NC ASO ATAC-sequencing experiments in SK-N-BE(2)c.

extract_protocol:
25 0000 SK-N-BE(2)c cells were seeded, and next day transfected with ASO2, ASO10, or NCA. Forty-eight hours post transfection cells washed once with PBS, pelleted, and genomic DNA was extracted from 90% of the pellet. Genomic DNA was tagmented by Tn5 transposase and DNA libraries were generated as described previously by Roels et al. 2020 (Nat Immunol, 21, 1280-1292).
Libraries were quantified by RT-qPCR with the KAPA Library Quantification kit and were pooled equimolarly. 1.9 pM of the final pool and 1% PhiX were loaded, and paired-end sequencing was performed on a NextSeq 500 instrument (NextSeq 500/550 High-Output kit, 150 cycles) with a 150 bp read length.

value: Neuroblastoma cell line

value: NCA

value: Antisense oligonucleotide


title: FgPH-1-FgDDT-GFP_IP1


title: donor heart store in HTK+CAN for 10h, IgG


title: SK-N-BE(2)c, ASO10_ATAC, rep3

description:
Library name: ASO10_SK-N-BE2c_ATAC_rep3
ASO10_3


title: Untreated Replicate 2


title: IXA62_R2

description:
Library name: Sample 27
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA62_R2


title: IXA21_R3

description:
Library name: Sample 25
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA21_R3

value: 10 uM IXA21


title: SK-N-BE(2)c, ASO10_ATAC, rep2

description:
Library name: ASO10_SK-N-BE2c_ATAC_rep2
ASO10_2


title: SK-N-BE(2)c, ASO10_ATAC, rep1

description:
Library name: ASO10_SK-N-BE2c_ATAC_rep1
ASO10_1


title: SK-N-BE(2)c, ASO2_ATAC, rep3

description:
Library name: ASO2_SK-N-BE2c_ATAC_rep3
ASO2_3


title: donor heart store in HTK+CAN baseline, IgG

value: store in HTK+CAN baseline


title: IXA21_R1

description:
Library name: Sample 23
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA21_R1


title: SK-N-BE(2)c, ASO2_ATAC, rep2

description:
Library name: ASO2_SK-N-BE2c_ATAC_rep2
ASO2_2


title: donor heart store in HTK for 10h, MR

value: store in HTK for 10h


title: SK-N-BE(2)c, ASO2_ATAC, rep1

description:
Library name: ASO2_SK-N-BE2c_ATAC_rep1
ASO2_1


title: SK-N-BE(2)c, NCA, RNA-seq, rep3

description:
Library name: NCA_SK-N-BE2c_rep3
SKN_NCA2_3
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: DMSO_R3

description:
Library name: Sample 22
Column name in HEK293_IRE1_activators_raw counts_all samples, DMSO_R3

value: DMSO


title: DMSO_R2

description:
Library name: Sample 21
Column name in HEK293_IRE1_activators_raw counts_all samples, DMSO_R2


title: SK-N-BE(2)c, NCA, RNA-seq, rep2

description:
Library name: NCA_SK-N-BE2c_rep2
SKN_NCA2_2
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: SK-N-BE(2)c, NCA_ATAC, rep3

description:
Library name: NCA_SK-N-BE2c_ATAC_rep3
NCA_3


title: SK-N-BE(2)c, NCA_ATAC, rep1

description:
Library name: NCA_SK-N-BE2c_ATAC_rep1
NCA_1


title: SK-N-BE(2)c, NCA, RNA-seq, rep1

description:
Library name: NCA_SK-N-BE2c_rep1
SKN_NCA_1
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: DMSO_R1

description:
Library name: Sample 20
Column name in HEK293_IRE1_activators_raw counts_all samples, DMSO_R1


title: SK-N-BE(2)c, ASO10, RNA-seq, rep1

description:
Library name: ASO10_SK-N-BE2c_rep1
SKN_LNA10_1
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: SK-N-BE(2)c, ASO10, RNA-seq, rep2

description:
Library name: ASO10_SK-N-BE2c_rep2
SKN_LNA10_2
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: SK-N-BE(2)c, ASO2, RNA-seq, rep3

description:
Library name: ASO2_SK-N-BE2c_rep3
SKN_LNA2_3
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: donor heart store in HTK baseline, MR

value: store in HTK baseline


title: D1R2_B

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

description:
Library name: D1R2_B
Isolated transgenes from Round 2 of tTA VLVs without selection, to identify transgene substitutions in ADAR/ADARB1 double KO cells

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGCTAGATTAGATAAAAGTAAAGTGATTAACagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgcgtacagccgcgcgcgtacgaaaaacaattacgggtctaccatcgagggcctgctcgatctcccggacgacgacgcccccgaagaggcggggctggcggctccgcgcctgtcctttctccccgcgggacacacgcgcagactgtcgacggcccccccgaccgatgtcagcctgggggacgagctccacttagacggcgaggacgtggcgatggcgcatgccgacgcgctagacgatttcgatctggacatgttgggggacggggattccccgggtccgggatttaccccccacgactccgccccctacggcgctctggatatggccgacttcgagtttgagcagatgtttaccgatgcccttggaattgacgagtacggtgggtag
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.

organism: Semliki Forest virus

extract_protocol:
Total RNA from VLV supernatant extracted. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Samples were sequenced with Australian Genomics Research Facility using their ‘Amplicon’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.


title: donor heart store in HTK+CAN baseline, MR


title: donor heart store in HTK baseline, IgG


title: SK-N-BE(2)c, ASO2, RNA-seq, rep2

description:
Library name: ASO2_SK-N-BE2c_rep2
SKN_LNA2_2
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: IXA21_R2

description:
Library name: Sample 24
Column name in HEK293_IRE1_activators_raw counts_all samples, IXA21_R2


title: CSF-3 scRNA-seq

city: Nanjing

first: xuhui

last: Ge

address: Hanzhong Road

institute: Nanjing medical university

description: 10x Genomics

data_processing:
I. Tissue digestion-single cell suspension preparation, II. Microarray on board-water-in-oil system construction, III. Purification and amplification-cDNA library construction, IV. Interrupted tailing and amplification-INDEX library construction, V. Library quality control, VI. IIIumina novaseq 6000 sequencing.
High-throughput sequencing produces raw data in fastq format, and to ensure the quality of the sequencing, the quality of the downstream raw data is assessed using FastQC software.10 CellRanger, the official software of Genomics, is used to perform data quality statistics on the raw data and compare it with the reference genome.
Doublets were removed using R package scDblFinder.Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
Assembly: hg38
Supplementary files format and content: CSF1_matrix.mtx,CSF1_barcodes.tsv,CSF_features.tsv.gz
Supplementary files format and content: CSF2_matrix.mtx,CSF2_barcodes.tsv,CSF_features.tsv.gz
Supplementary files format and content: CSF3_matrix.mtx,CSF3_barcodes.tsv,CSF_features.tsv.gz

source_name: CSF

extract_protocol:
Freshly collected CSF from SCI patients were centrifuged at 1000 r.p.m. for 5 min, cells were then washed with ice-cold PBS and erythrocytes in CSF were lysed using Red Blood Cell Lysis Buffer for 5 min on ice. Remaining cells were subjected to MACS for live singlets using Dead Cell Removal Microbeads. Afterwards, cells were respended in PBS with 1% BSA before scRNA.
Libraries were performed according to the manufacter's protocol (Chromium Next GEM Single Cell 5' Kit v2, 10x Genomics). Briefly, CSF cells were respended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA in every single GEM was retrotranscripted into cDNA. The pooled barcoded cDNA was then cleaned up with Dynabeads CLeanup Mix, amplified by PCR and the appropriated sized fragments were selected with SPPIselect reagent for subsequent library construction.

value: CSF

value: CSF cells

value: immune cells


title: D1R2_A

description:
Library name: D1R2_A
Isolated transgenes from Round 2 of tTA VLVs without selection, to identify transgene substitutions in ADAR/ADARB1 double KO cells


title: CSF-2 scRNA-seq

description: 10x Genomics


title: SK-N-BE(2)c, ASO2, RNA-seq, rep1

description:
Library name: ASO2_SK-N-BE2c_rep1
SKN_LNA2_1
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: D5R2_B

description:
Library name: D5R2_B
Isolated transgenes from tTA VLVs, to identify pre-existing mutations in ADAR/ADARB1 double KO cells


title: NGP, NCA, RNA-seq, rep3

description:
Library name: NCA_NGP_rep3
NGP_NCA2_3
Normalized_count_matrix_NGP_RNA.txt

source_name: NGP

value: NGP


title: NGP, NCA, RNA-seq, rep2

description:
Library name: NCA_NGP_rep2
NGP_NCA2_2
Normalized_count_matrix_NGP_RNA.txt


title: CSF-1 scRNA-seq

description: 10x Genomics


title: donor heart store in HTK for 10h, IgG

city: Rochester


title: D5R2_A

description:
Library name: D5R2_A
Isolated transgenes from tTA VLVs, to identify pre-existing mutations in ADAR/ADARB1 double KO cells


title: NGP, ASO10, RNA-seq, rep3

description:
Library name: ASO10_NGP_rep3
NGP_LNA10_3
Normalized_count_matrix_NGP_RNA.txt


title: SK-N-BE(2)c, ASO10, RNA-seq, rep3

description:
Library name: ASO10_SK-N-BE2c_rep3
SKN_LNA10_3
Normalized_count_matrix_SK-N-BE2c_RNA.txt


title: NGP, ASO10, RNA-seq, rep2

description:
Library name: ASO10_NGP_rep2
NGP_LNA10_2
Normalized_count_matrix_NGP_RNA.txt


title: CSF-3 TCR-seq

description: 10x Genomics

data_processing:
I. Tissue digestion-single cell suspension preparation, II. Microarray on board-water-in-oil system construction, III. Purification and amplification-cDNA library construction, IV. Interrupted tailing and amplification-INDEX library construction, V. Library quality control, VI. IIIumina novaseq 6000 sequencing.
High-throughput sequencing produces raw data in fastq format, and to ensure the quality of the sequencing, the quality of the downstream raw data is assessed using FastQC software.10 CellRanger, the official software of Genomics, is used to perform data quality statistics on the raw data and compare it with the reference genome.
Doublets were removed using R package scDblFinder.Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
TCR analysis were performed using scRepertoire with clonotypes being called strictly by the combination of the CDR3 nucleotide sequences and genes.
Assembly: hg38
Supplementary files format and content: CSF1_clonotypes.csv,CSF1_filtered_contig_annotations.csv
Supplementary files format and content: CSF2_clonotypes.csv,CSF2_filtered_contig_annotations.csv
Supplementary files format and content: CSF3_clonotypes.csv,CSF3_filtered_contig_annotations.csv
Library strategy: TCR-seq

extract_protocol:
Freshly collected CSF from SCI patients were centrifuged at 1000 r.p.m. for 5 min, cells were then washed with ice-cold PBS and erythrocytes in CSF were lysed using Red Blood Cell Lysis Buffer for 5 min on ice. Remaining cells were subjected to MACS for live singlets using Dead Cell Removal Microbeads. Afterwards, cells were respended in PBS with 1% BSA before TCRseq.
Libraries were performed according to the manufacter's protocol (Chromium Next GEM Single Cell 5' Kit v2, 10x Genomics). Briefly, CSF cells were respended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA in every single GEM was retrotranscripted into cDNA. The pooled barcoded cDNA was then cleaned up with Dynabeads CLeanup Mix, amplified by PCR and the appropriated sized fragments were selected with SPPIselect reagent for subsequent library construction.


title: NGP, ASO2, RNA-seq, rep3

description:
Library name: ASO2_NGP_rep3
NGP_LNA2_3
Normalized_count_matrix_NGP_RNA.txt


title: CSF-2 TCR-seq

description: 10x Genomics


title: B1R2_A

description:
Library name: B1R2_A
Isolated transgenes from Round 2 of tTA VLVs without selection, to identify transgene substitutions in ADARB1 KO cells


title: B1R2_B

description:
Library name: B1R2_B
Isolated transgenes from Round 2 of tTA VLVs without selection, to identify transgene substitutions in ADARB1 KO cells


title: NGP, ASO10, RNA-seq, rep1

description:
Library name: ASO10_NGP_rep1
NGP_LNA10_1
Normalized_count_matrix_NGP_RNA.txt


title: CSF-1 TCR-seq

description: 10x Genomics


title: NGP, ASO2, RNA-seq, rep1

description:
Library name: ASO2_NGP_rep1
NGP_LNA2_1
Normalized_count_matrix_NGP_RNA.txt


title: NGP, ASO2, RNA-seq, rep2

description:
Library name: ASO2_NGP_rep2
NGP_LNA2_2
Normalized_count_matrix_NGP_RNA.txt


title: P7F1_HiC_Rep2

data_processing:
For HiC, raw sequencing reads were processed using juicer v1.4 with genome assembly hg38 and ARIMA’s restriction sites. Technical replicates for each cell line were merged after alignment within the juicer pipeline. For pCHiC, raw sequencing reads were processed using ARIMA’s pipeline for promoter capture experiments (Arima-CHiC-v1.4). Briefly, we used the HiCUP pipeline from the Babraham Institute to map with bowtie2 each pair of the ligated fragments to the human genome (hg38 assembly). Next, BAM files were converted into CHiCAGO input files and processed with CHiCAGO to obtain interaction confidence scores for each cell line.
Assembly: hg38
Supplementary files format and content: interaction bed files and hic files

extract_protocol:
For HiC and pCHiC, we used a commercial kit from Arima Genomics (A510008). Briefly, 106 cells were cross-linked with formaldehyde and extracted following the manufacturer’s instructions. 4 mg of DNA per condition were digested and ligated, and biotin was incorporated to select successfully ligated fragments. Ligated DNA was sonicated with a Diagenode Bioruptor for 20 min, 30 seconds ON/OFF, at 4°C to obtain ~400 bp DNA fragments. Biotinylated DNA was purified using streptavidin beads.
HiC and pcHiC libraries were constructed using the library preparation protocol in ARIMA’s HiC kit. A fraction of the HiC library was used for sequencing in an Illumina NovaSeq 6000 for 300 cycles pair-end at a depth of ~200M reads per sample. Next, the remainder of the HiC library was used for promoter capture using ARIMA’s custom panel of human promoters (~84,000 probes for ~26,000 promoters). After promoter capture, the pcHiC libraries were amplified following the manufacturer’s instructions and sequenced with Illumina NovaSeq 6000 (300 bp, paired-end) at a depth of ~200M reads per sample.

value: induced pluripotent stem cell muscle progenitor


title: B5R2_A

description:
Library name: B5R2_A
Isolated transgenes from tTA VLVs, to identify pre-existing mutations in ADARB1 KO cells


title: SK-N-BE(2)c, NCA, VP1

description: Library name: NCA_SK-N-BE2c_VP1

data_processing:
Sequencing libraries were demultiplexed based on the presence of the viewpoint-specific reading primer sequence preceding the captured DNA sequence.
After removal of the reading primer prefixes, captured sequences were mapped to the hg19 human reference genome assembly (GRCh37) with Bowtie2 (v2.2.6).
Mapped reads on the cis-chromosome were binned per DpnII restriction fragment.
Finally, 4C coverage profiles were obtained by per fragment normalization to reads per million (RPM) on the cis-chromosome and smoothing the normalized coverage use the rollmean function of the zoo (v1.8.12) R package with a window size of 21 fragments.
Assembly: hg19
Supplementary files format and content: be2c_phox2b_aso.bedgraph contain 4C-seq interaction profiles in bedgraph format for the PHOX2B VP.
Supplementary files format and content: be2c_nespr_aso.bedgraph contain 4C-seq interaction profiles in bedgraph format for the NESPR VP.
Supplementary files format and content: be2c_phox2b_ntc.bedgraph contain 4C-seq interaction profiles in bedgraph format for the PHOX2B VP.
Supplementary files format and content: be2c_nespr_ntc.bedgraph contain 4C-seq interaction profiles in bedgraph format for the NESPR VP.
Library strategy: 4C-Seq

extract_protocol:
The 4C templates were prepared as described previously van de Werken et al. 2012 (Methods Enymol, 513, 89-112). In brief, 10 x 106 SH-SY5Y or SK-N-BE(2)c cells were seeded per template. The day after seeding or 48 hours after ASO transfection cells were detached by trypsinization, and cross-linked with 2% formaldehyde for 10 min at room temperature. Cell lysates were digested with 400 U DpnII, and proximal DNA fragments were ligated with 50 U T4 DNA ligase. Ligated DNA circles were de-crosslinked overnight using proteinase K and purified with NucleoMag P-Beads to obtain an intermediate 3C template. 3C templates were digested with 50 U Csp6I and religated as described before, resulting in 4C templates.
Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify interacting genomic regions relative to the viewpoint. For each viewpoint, 16 PCR reactions, with 200 ng 4C template as input, were pooled. Resulting 4C-sequencing libraries were purified using QIAquick PCR Purification kit. 4C-sequencing libraries were pooled, and 1.6 pM with 1% PhiX was loaded on an NextSeq 500 instrument (NextSeq 500/550 High-Output kit, 75 cycles) for single-end sequencing.


title: P7F1_HiC_Rep1


title: SK-N-BE(2)c, NCA, VP2

description: Library name: NCA_SK-N-BE2c_VP2


title: B5R2_B

description:
Library name: B5R2_B
Isolated transgenes from tTA VLVs, to identify pre-existing mutations in ADARB1 KO cells


title: SK-N-BE(2)c, ASO2, VP2

description: Library name: ASO2_SK-N-BE2c_VP2


title: NGP, NCA, RNA-seq, rep1

description:
Library name: NCA_NGP_rep1
NGP_NCA_1
Normalized_count_matrix_NGP_RNA.txt


title: A5R2

description:
Library name: A5R2
Isolated transgenes from tTA VLVs, to identify pre-existing mutations in ADAR KO cells


title: P3F1_HiC_Rep2


title: OVCAR8 Adipo CC rep2

first: Daniela

middle: Elena

last: Matei

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Assembly: GRCh38
Supplementary files format and content: counts

source_name: Ovarian Primary Tumor

growth_protocol: OVCAR5 Cells were cultured in RPMI 1640 (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), and 1X GlutaMAX (Gibco), OVCAR8 cells were grown in DMEM (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), both cell lines were growth in a humidify atmosphere, 5% and 37°C.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen) according to the manufacturer’s instructions and quantified using a NanoDrop 3300 Fluorospectrometer.
The RNA-sequencing (RNA-seq) libraries were prepared from 1 μg of total RNA of OVCAR5, and OVCAR8 mono- or co-culture. Libraries were generated using the NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs, Inc.). Library preparation was performed accoding to manufacter's protocol.

treatment_protocol: OVCAR8 and OVCAR5 cells were co-cultured on with mature viseral adipocytes for 3 days and then FACS separated.

value: Ovarian Primary Tumor

value: High grade serous ovarian cancer

value: transfected with RFP

value: Adipocyte Co-culture


title: OVCAR8 Adipo CC rep1


title: A1R2

description:
Library name: A1R2
Isolated transgenes from Round 2 of tTA VLVs without selection, to identify transgene substitutions in ADAR KO cells


title: OVCAR8 Adipo CC rep3


title: OVCAR8 Control rep2

value: Control


title: OVCAR8 Control rep3


title: Control_HiC_Rep2

value: WT


title: P3F1_HiC_Rep1


title: Liver_IXA62-4

description:
Library name: Sample 18
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_4_liver

source_name: liver

value: liver

value: 50 mpk IXA62


title: OVCAR8 Control rep1


title: Control_HiC_Rep1


title: Liver_IXA62-3

description:
Library name: Sample 17
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_3_liver


title: OVCAR5 Adipo CC rep2

source_name: ascites

value: ascites

value: transfected with GFP


title: OVCAR5 Adipo CC rep3


title: Liver_IXA62-2

description:
Library name: Sample 16
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_2_liver


title: SK-N-BE(2)c, ASO2, VP1

description: Library name: ASO2_SK-N-BE2c_VP1

value: Neuroblastoma cell line

value: Antisense oligonucleotide


title: OVCAR5 Control rep3


title: P7F1_pcHiC_Rep1

data_processing:
For HiC, raw sequencing reads were processed using juicer v1.4 with genome assembly hg38 and ARIMA’s restriction sites. Technical replicates for each cell line were merged after alignment within the juicer pipeline. For pCHiC, raw sequencing reads were processed using ARIMA’s pipeline for promoter capture experiments (Arima-CHiC-v1.4). Briefly, we used the HiCUP pipeline from the Babraham Institute to map with bowtie2 each pair of the ligated fragments to the human genome (hg38 assembly). Next, BAM files were converted into CHiCAGO input files and processed with CHiCAGO to obtain interaction confidence scores for each cell line.
Assembly: hg38
Supplementary files format and content: interaction bed files and hic files
Library strategy: pcHi-C


title: Liver_IXA62-1

description:
Library name: Sample 15
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_1_liver