title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 2, Amplicon 3, with TP expressed

city: Chapel Hill

first: Breanne

middle: Marie

last: Hatfield

state: North Carolina

address: 125 South Rd, CB#3290 Kenan Labs

department: Chemistry

institute: UNC - Chapel Hill

description:
Library name: 3UTR_DMSminus_Rep2_primer3_withTP
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR with the MS2 (TP) protein co- expressed

data_processing:
Paired-end sequencing reads from modified samples were combined with FLASH (v1.2.11) and trimmed with umi_tools (v1.1.2) using -extract options to produce combined and trimmed (combinied_trimmed) processed files.
combined and trimmed processed files were de-duplicated as exact sequence matches were removed to overcome PCR artifacts with dedupe.sh (Bushnell and Rood, 2020) to produce combined, trimmed, and deduped (combined_trimmed_deduped) processed files.
ShapeMapper (v2.1.5) was used to align and calculate per nucleotide reactivities using --output-parsed and --amplicon options. Raw sequencing reads were analyzed twice using ShapeMapper, once with all three amplicons aligned to the full mRNA sequence to provide unified per-nucleotide reactivities, and once with each amplicon aligned to its own sub-sequence for PAIR analysis to produce profile.txt processed files.
PairMapper (from RingMapper v1.1) was used to (i) calculate PAIRs with ShapeMapper data from each amplicon aligned to its own sub-sequence and (ii) re-normalize per nucleotide DMS reactivities from unified ShapeMapper normalized reactivities to produce pairmap.txt and .bp processed files.
Per amplicon PAIRs were combined. In the overlapping regions, the intersection of PAIRs from each amplicon were used to produce combined-pairmap-txt and combined.bp files
Partition and ProbabilityPlot [from RNAStructure v6.2, (49)] were used to predict pairing probabilities using DMS reactivities (normalized per nucleotide) and PAIRs and produced combined.dp processed files.
Fold (from RNAStructure) was used to calculate a minimum free energy structure of each mRNA to produce .ct processed files
Assembly: mRNA with TH in 5'-UTR: GTCAGATCACTAGAAGCTTTATTGCGGTAGTTTATCACAGTTTCTAGGCGATCGCTCGAGAAAACATGAGGATCACCCATGTCTGCAGGTCGACTCTAGAAATAAATTGCTAACGCAGTCAGTGGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACCATGGTCTTCACACTCGAAGATTTCGTTGGGGACTGGCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTTTGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGGTGAAAATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCAAATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTAAGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGACTATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAACAGGGACCCTGTGGAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCTCCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCGAATTCTCACGGCTTTCCGCCTGAGGTTGAAGAGCAAGCCGCCGATACATTGCCTATGTCCTGCGCACAAGAAAGCGGTATGGACCGGCACCCAGCCGCTTGTGCTTCAGCTCGCATCAACGTCTAAGGCCGCGACTCTAGAGTCGCTCGAGGGCTGGTACCGTTGCTAGCACGAGCGGCCGCTTACCGGCCGGCCGCTTCGAGCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAAC
Assembly: mRNA with TH in CDS1: GTCAGATCACTAGAAGCTTTATTGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGTGGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACCATGGTCTTCACACTCGAAGATTTCGTTGGGGACTGGCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTTTGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGTACATGAGGATCACCCATGTGGTGAAAATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCAAATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTAAGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGACTATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAACAGGGACCCTGTGGAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCTCCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCGAATTCTCACGGCTTTCCGCCTGAGGTTGAAGAGCAAGCCGCCGATACATTGCCTATGTCCTGCGCACAAGAAAGCGGTATGGACCGGCACCCAGCCGCTTGTGCTTCAGCTCGCATCAACGTCTAAGGCCGCGACTCTAGAGTCGCTCGAGGGCTGGTACCGTTGCTAGCACGAGCGGCCGCTTACCGGCCGGCCGCTTCGAGCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAAC
Assembly: mRNA with TH in CDS2: GTCAGATCACTAGAAGCTTTATTGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGTGGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACCATGGTCTTCACACTCGAAGATTTCGTTGGGGACTGGCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTTTGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGGTGAAAATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCAAATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTAAGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGACTATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAACAGGGACCCTGTGGGTACATGAGGATCACCCATGTAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCTCCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCGAATTCTCACGGCTTTCCGCCTGAGGTTGAAGAGCAAGCCGCCGATACATTGCCTATGTCCTGCGCACAAGAAAGCGGTATGGACCGGCACCCAGCCGCTTGTGCTTCAGCTCGCATCAACGTCTAAGGCCGCGACTCTAGAGTCGCTCGAGGGCTGGTACCGTTGCTAGCACGAGCGGCCGCTTACCGGCCGGCCGCTTCGAGCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAAC
Assembly: mRNA with TH in 3'-UTR: GTCAGATCACTAGAAGCTTTATTGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGTGGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACCATGGTCTTCACACTCGAAGATTTCGTTGGGGACTGGCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTTTGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGGTGAAAATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCAAATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTAAGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGACTATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAACAGGGACCCTGTGGAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCTCCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCGAATTCTCACGGCTTTCCGCCTGAGGTTGAAGAGCAAGCCGCCGATACATTGCCTATGTCCTGCGCACAAGAAAGCGGTATGGACCGGCACCCAGCCGCTTGTGCTTCAGCTCGCATCAACGTCTAAGGCCGCGACTCTAGAGTCGTTCTAGGCGATCGCTCGAGAAAACATGAGGATCACCCATGTCTGCAGGTCGACTCTAGAAACGCTTCGAGCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAAC
Assembly: mRNA with no TH: GTCAGATCACTAGAAGCTTTATTGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGTGGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACCATGGTCTTCACACTCGAAGATTTCGTTGGGGACTGGCGACAGACAGCCGGCTACAACCTGGACCAAGTCCTTGAACAGGGAGGTGTGTCCAGTTTGTTTCAGAATCTCGGGGTGTCCGTAACTCCGATCCAAAGGATTGTCCTGAGCGGTGAAAATGGGCTGAAGATCGACATCCATGTCATCATCCCGTATGAAGGTCTGAGCGGCGACCAAATGGGCCAGATCGAAAAAATTTTTAAGGTGGTGTACCCTGTGGATGATCATCACTTTAAGGTGATCCTGCACTATGGCACACTGGTAATCGACGGGGTTACGCCGAACATGATCGACTATTTCGGACGGCCGTATGAAGGCATCGCCGTGTTCGACGGCAAAAAGATCACTGTAACAGGGACCCTGTGGAACGGCAACAAAATTATCGACGAGCGCCTGATCAACCCCGACGGCTCCCTGCTGTTCCGAGTAACCATCAACGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCGAATTCTCACGGCTTTCCGCCTGAGGTTGAAGAGCAAGCCGCCGATACATTGCCTATGTCCTGCGCACAAGAAAGCGGTATGGACCGGCACCCAGCCGCTTGTGCTTCAGCTCGCATCAACGTCTAAGGCCGCGACTCTAGAGTCGCTCGAGGGCTGGTACCGTTGCTAGCACGAGCGGCCGCTTACCGGCCGGCCGCTTCGAGCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAAC
Supplementary files format and content: any processed file ending in profile.txt is a comma seperated processed containing DMS reactivities for each nucleotide
Supplementary files format and content: any processed file ending in pairmap.txt is a comma seperated processed filed containing pairmapper filtered correlations
Supplementary files format and content: any processed file ending in .bp is a comma seperated processed filed containing base-pairing bonuses for PAIR-MaP structure modeling in RNAstructure
Supplementary files format and content: any processed file ending in .dp is a comma seperated processed filed containing nucleotide partitions from Probability Plot
Supplementary files format and content: any processed file ending in .ct is a comma seperated processed filed containing the minimum free energy structure from Fold
Library strategy: DMS-MaP

source_name: Human Embrionic Kidney

growth_protocol: HEK293 cells (ATCC, CRL 1573) were cultured in Dulbecco′s Modified Eagle Medium with 10% fetal bovine serum, 100 µg/ml streptomycin, and 100 U/ml penicillin (complete DMEM) at 5% CO2 and 37 C. Cells were passaged twice and grown to ~80% confluency before each experiment. For biological replicates, experiments were performed on distinct cell populations. For all plasmid transfections, HEK293 cells were plated at a concentration of 100,000 cells per mL. Plasmids were transfected into cells 24 hours after plating using Fugene 6 (Promega; 6X ratio, 0.6 μL Fugene 6:100 ng DNA). Plasmid concentrations were quantified with a fluorometer (Qubit 2.0). Experiments were performed as either two (target mRNA and firefly control plasmids) or three plasmid transfections (target mRNA, firefly control, and effector-TP fusion plasmids). For each target mRNA, 10 mL of HEK293 cells (1,000,000 cells) were plated in a 10-cm dish and transfected (two-plasmid transfection) with 700 ng of target mRNA plasmid, 1000 ng of firefly control plasmid, and 3300 ng of carrier DNA (Promega) or (three-plasmid transfection) with 700 ng of target mRNA plasmid, 1000 ng of firefly control plasmid, 1000 ng of TP plasmid and 2300 ng of carrier DNA (Promega).

extract_protocol:
RNA was extracted (TRIzol reagent, 1 mL; Invitrogen), and residual DNA removed (TURBO DNase, 2 units; Thermo Fisher; 30 min at 37 C).
MaP reverse transcription was performed as described (Siegfriefd et al. Nat. 2014) with 1 µg of total cellular RNA. For all target mRNAs, except the mRNA with the TH in the 3′-UTR, reactions were performed with three primers (DMS-RT-1, DMS-RT-2, and DMS-RT-3) to generate amplicons 1, 2 and 3, respectively, covering the entire transcript. For the mRNA with the TH in the 3′-UTR, a sequence-specific primer (DMS-RT-2(3′-UTR)) was used. Products of reverse transcription were purified (G-50 microspin columns; Cytiva). Sequencing libraries were generated using a two-step PCR approach (Smola et al. Nat. Prot. 2015). In brief, 5 μL of reverse transcription reaction products for amplicons 1, 2, and 3 were amplified [98 C for 30 s, 10 cycles of (98 C for 10 s, 65 C for 30 s, and 72 C for 30 s), and 72 C for 2 min] with primer pairs DMS-F1 and DMS-R1, DMS-F2 and DMS-R2 (or DMS-R2(3′-UTR) for the mRNA with the TH in the 3′-UTR), DMS-F3 and DMS-R3, respectively. Products were purified (magnetic beads, 0.8x ratio, Omega Bio-tek), eluted in water, and 10 μL aliquots were used for the second step of PCR [98 C for 30 s, 20 cycles of (98 C for 10 s, 68 C for 30 s, and 72 C for 30 s), and 72 C for 2 min]. Products were purified (magnetic beads, 0.8x ratio, Omega Bio-tek), eluted in water, and libraries were sequenced [Illumina Miseq; 2 x 300 (v3 chemistry) paired-end sequencing].

treatment_protocol: Transfected cells were washed twice in 1x PBS 36-48 hours after transfection. Cells were trypsinized and pelleted at 250 rcf. The supernatant was removed, and cells were resuspended in 900 μL of complete DMEM supplemented with 200 mM Bicine (pH 8). In-cell DMS treatment was performed as described by adding 450 μL of buffered cells to 50 μL 1.7 M DMS in ethanol or 50 μL of ethanol (vehicle control) for 6 minutes at 37 C. Reactions were quenched with 500 μL of 20% beta-mercaptoethanol (chilled) and placed on ice for 4 minutes. Cells were pelleted at 250 rcf.

value: Human Embrionic Kidney

value: adherent epithelial cell


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 2, Amplicon 3, with TP expressed

status: Public on Dec 11 2024

type: SRA

country: USA

description:
Library name: 3UTR_DMSplus_Rep2_primer3_withTP
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR with the MS2 (TP) protein co- expressed

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: dimethyl sulfate


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 2, Amplicon 1, with TP expressed

description:
Library name: CDS1_DMSplus_Rep2_primer1_withTP
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1) with the MS2 (TP) protein co-expressed


title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 1, Amplicon 3, with TP expressed

description:
Library name: 3UTR_DMSminus_Rep1_primer3_withTP
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR with the MS2 (TP) protein co- expressed


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 2, Amplicon 1, with TP expressed

description:
Library name: CDS1_DMSminus_Rep2_primer1_withTP
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1) with the MS2 (TP) protein co-expressed


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 1, Amplicon 3, with TP expressed

description:
Library name: 3UTR_DMSplus_Rep1_primer3_withTP
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR with the MS2 (TP) protein co- expressed


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 2, Amplicon 3

description:
Library name: no-TH_DMSminus_Rep2_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 2, Amplicon 1

description:
Library name: no-TH_DMSplus_Rep2_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 2, Amplicon 2

description:
Library name: no-TH_DMSminus_Rep2_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 2, Amplicon 2

description:
Library name: no-TH_DMSplus_Rep2_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 2, Amplicon 1

description:
Library name: no-TH_DMSminus_Rep2_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with no MS2 stem loop (TH)


title: sEVs from old-passage 5 ASCs

city: Tokyo

first: Toshiya

last: Tsubaki

address: 7-3-1 Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Sample 4

library_source: other

data_processing:
The raw data were mapped to a reference genome (GCF_000001405.38_GRCh38.p12) using Bowtie2 (ver. 2.2.9) after adapter sequences were removed using SOAPnuke (ver. 1.5.6). Expression values were calculated using the following formula: Expression = (the number of UMI reads that are mapped to the small RNA * 1,000,000) / the UMI number of total clean reads in the sample.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-delimited text file includes rae read counts for each Sample

molecule: other

source_name: small extracellular vesicles

growth_protocol: ASCs were cultured in MSC NutriStem® XF Basal Medium (NutriStem, Sartorius Stedim Biotech, Lower Saxony, Germany) supplemented with 2% fetal bovine serum (FBS) and 0.1% penicillin-streptomycin at 37°C in an incubator with humidified 5% CO2.

extract_protocol:
The precipitated sEVs (sEV extraction) were lysed with TRI reagent (Molecular Research Center, Inc., Cincinnati, OH, USA), and RNA was extracted using the Direct-zol RNA kit.
Outsourced to BGI Japan Co., Ltd.

treatment_protocol: ASCs were seeded into 15-cm dishes and cultured to 80% confluence. The medium was then replaced with sEV collection medium (NutriStem:DMEM = 1:1). After 48 h, the culture supernatant was collected. The supernatant was centrifuged at 2000 g for 10 min to remove cell debris and filtered using a 0.22 µm filter (Thermo Fisher Scientific, Massachusetts, USA). The filtered supernatant was ultrafiltered using Vivaspin®20 Membrane: 100,000 MWCO PES (Sartorius Stedim Biotech, Lower Saxony, Germany). Exosomes were purified from the ultrafiltered supernatant using Exoquick TC (System Biosciences, Palo Alto, CA, USA).

value: small extracellular vesicles

value: mesenchymal stem cells


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 1, Amplicon 3

description:
Library name: no-TH_DMSminus_Rep1_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with no MS2 stem loop (TH)


title: sEVs from young-passage 5 ASCs

description: Sample 1


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 1, Amplicon 2

description:
Library name: no-TH_DMSplus_Rep1_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 1, Amplicon 1

description:
Library name: no-TH_DMSplus_Rep1_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 1, Amplicon 2

description:
Library name: no-TH_DMSminus_Rep1_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with no MS2 stem loop (no-TH), control, Replicate 1, Amplicon 1

description:
Library name: no-TH_DMSminus_Rep1_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 1, Amplicon 1, with TP expressed

description:
Library name: CDS1_DMSplus_Rep1_primer1_withTP
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1) with the MS2 (TP) protein co-expressed


title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 2, Amplicons 1-3

description:
Library name: 3UTR_DMSminus_Rep2_all-primers
non-treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the 3UTR


title: AdultBrain_gDNA

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: SABER x her4.3:switchCas9 double transgenic adult fish that were subject to Notch recording in early development

library_source: genomic

data_processing:
genomic DNA GESTALT and scGESTALT libraries were processed using the McKenna lab’s SingleCellLineage package from Github
Assembly: GRCz11
Supplementary files format and content: .stats.txt files contain edited barcodes from gDNA sequencing
Library strategy: DNA SABER

molecule: genomic DNA

organism: Danio rerio

source_name: zebrafish brain

growth_protocol: This work was performed under protocol numbers 807110 and 807259, which were approved by the University of Pennsylvania’s Office of Animal Welfare of Institutional Animal Care and Use Committee (IACUC). All zebrafish work in this study follows the University of Pennsylvania Institutional Animal Care and Use Committee regulations.

extract_protocol:
gDNA from juvenile and adult tissues were prepared using E.Z.N.A. Tissue DNA kit according to the manufacturer’s protocol.
Samples were UMI tagged and PCR amplified using primers flanking the barcode as described in McKenna et al., Science, 2016. Sequencing adapters, sample indexes and flow cell adapters were incorporated by PCR.

value: zebrafish brain

tag: developmental stage

value: 1 year, Adult

tag: genotype

value: WT/TLAB


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 1, Amplicon 1, with TP expressed

description:
Library name: CDS1_DMSminus_Rep1_primer1_withTP
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1) with the MS2 (TP) protein co-expressed


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 2, Amplicon 3

description:
Library name: no-TH_DMSplus_Rep2_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with no MS2 stem loop (TH)


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 1, Amplicon 3

description:
Library name: 3UTR_DMSplus_Rep1_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR


title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 1, Amplicon 3

description:
Library name: 3UTR_DMSminus_Rep1_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 3UTR


title: AdultSkin_gDNA

source_name: zebrafish skin

value: zebrafish skin


title: AdultEye_gDNA

source_name: zebrafish eye

value: zebrafish eye


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 1, Amplicon 2

description:
Library name: 3UTR_DMSplus_Rep1_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the 3UTR


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 1, Amplicon 1

description:
Library name: 3UTR_DMSplus_Rep1_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the 3UTR


title: AdultJaw_gDNA

source_name: zebrafish jaw

value: zebrafish jaw


title: AdultFin_gDNA

source_name: zebrafish fin

value: zebrafish fin


title: NanoLuc mRNA with no MS2 stem loop (no-TH), DMS treatment, Replicate 1, Amplicon 3

description:
Library name: no-TH_DMSplus_Rep1_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with no MS2 stem loop (TH)


title: JuvenileBrain_gDNA

description: SABER x her4.3:switchCas9 double transgenic juvenile fish that were subject to Notch recording in early development

value: 21-23 dpf, Juvenile


title: JuvenileJawFin_gDNA

source_name: zebrafish jaw & fin

value: zebrafish jaw & fin


title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 1, Amplicon 2

description:
Library name: 3UTR_DMSminus_Rep1_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the 3UTR


title: NanoLuc mRNA with MS2 stem loop in CDS(2), DMS treatment, Replicate 2, Amplicons 1-3

description:
Library name: CDS2_DMSplus_Rep2_all-primers
treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the CDS(2)


title: NanoLuc mRNA with MS2 stem loop in CDS(2), control, Replicate 2, Amplicons 1-3

description:
Library name: CDS2_DMSminus_Rep2_all-primers
non-treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the CDS(2)


title: NanoLuc mRNA with MS2 stem loop in CDS(2), DMS treatment, Replicate 1, Amplicon 3

description:
Library name: CDS2_DMSplus_Rep1_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the CDS(2)


title: Buffy coat from patient without PNPs ET03919 at time of colonoscopy

type: genomic

city: Miami

first: Shria

last: Kumar

state: FL

address: 1120 NW 14th St

department: Gastroenterology

institute: University of Miami

description:
ET03919
genomic DNA extracted from peripheral leukocytes

hyb_protocol: Extracted DNA underwent bisulfite conversion using Zymo EZ DNA methylation according to standard protocol

scan_protocol: Scanned on the iScanTM

data_processing: Raw methylation signal intensities were retrieved using the function read.metharray.exp of the minfi v1.40.0 R package, followed by linear dye bias correction and noob background correction to account for technical variation in background fluorescence signal.  The β-value was calculated from the intensity of the methylated and unmethylated sites, as the ratio of fluorescent signals.

label: Cy3 and Cy5

source_name: Buffy Coat

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from buffy coat samples using Zymo Research High Molecular Weight DNA Extraction Kit

value: Buffy Coat


title: JuvenileEye_gDNA


title: NanoLuc mRNA with MS2 stem loop in CDS(2), control, Replicate 1, Amplicon 2

description:
Library name: CDS2_DMSminus_Rep1_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the CDS(2)


title: Buffy coat from patient without PNPs ET03916 at time of colonoscopy

description:
ET03916
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in CDS(2), DMS treatment, Replicate 1, Amplicon 1

description:
Library name: CDS2_DMSplus_Rep1_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(2)


title: NanoLuc mRNA with MS2 stem loop in CDS(2), control, Replicate 1, Amplicon 1

description:
Library name: CDS2_DMSminus_Rep1_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(2)


title: AdultSkull_gDNA

description: SABER x her4.3:switchCas9 double transgenic adult fish that were subject to Notch recording in early development

source_name: zebrafish skull

value: zebrafish skull


title: Buffy coat from patient with PNPs ET03917 at time of colonoscopy

description:
ET03917
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039155 at time of colonoscopy

description:
ET039155
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 3UTR, control, Replicate 1, Amplicon 1

description:
Library name: 3UTR_DMSminus_Rep1_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the 3UTR


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 2, Amplicons 1-3

description:
Library name: CDS1_DMSminus_Rep2_all-primers
non-treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the CDS(1)


title: Buffy coat from patient without PNPs ET039154 at time of colonoscopy

description:
ET039154
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039156 at time of colonoscopy

description:
ET039156
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039151 at time of colonoscopy

description:
ET039151
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 1, Amplicon 3

description:
Library name: CDS1_DMSplus_Rep1_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the CDS(1)


title: Buffy coat from patient without PNPs ET039152 at time of colonoscopy

description:
ET039152
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 1, Amplicon 3

description:
Library name: CDS1_DMSminus_Rep1_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the CDS(1)


title: NanoLuc mRNA with MS2 stem loop in CDS(2), control, Replicate 1, Amplicon 3

description:
Library name: CDS2_DMSminus_Rep1_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the CDS(2)


title: NanoLuc mRNA with MS2 stem loop in 3UTR, DMS treatment, Replicate 2, Amplicons 1-3

description:
Library name: 3UTR_DMSplus_Rep2_all-primers
treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the 3UTR


title: NanoLuc mRNA with MS2 stem loop in CDS(2), DMS treatment, Replicate 1, Amplicon 2

description:
Library name: CDS2_DMSplus_Rep1_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the CDS(2)


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 2, Amplicons 1-3

description:
Library name: CDS1_DMSplus_Rep2_all-primers
treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the CDS(1)


title: Buffy coat from patient without PNPs ET039150 at time of colonoscopy

description:
ET039150
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET03918 at time of colonoscopy

description:
ET03918
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039148 at time of colonoscopy

description:
ET039148
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 1, Amplicon 2

description:
Library name: CDS1_DMSminus_Rep1_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the CDS(1)


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 1, Amplicon 2

description:
Library name: CDS1_DMSplus_Rep1_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the CDS(1)


title: NanoLuc mRNA with MS2 stem loop in CDS(1), control, Replicate 1, Amplicon 1

description:
Library name: CDS1_DMSminus_Rep1_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1)


title: NanoLuc mRNA with MS2 stem loop in CDS(1), DMS treatment, Replicate 1, Amplicon 1

description:
Library name: CDS1_DMSplus_Rep1_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the CDS(1)


title: Buffy coat from patient without PNPs ET03915 at time of colonoscopy

description:
ET03915
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039147 at time of colonoscopy

description:
ET039147
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, DMS treatment, Replicate 2, Amplicons 1-3

description:
Library name: 5UTR_DMSplus_Rep2_all-primers
treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the 5'-UTR


title: Buffy coat from patient without PNPs ET039146 at time of colonoscopy

description:
ET039146
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039144 at time of colonoscopy

description:
ET039144
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, control, Replicate 1, Amplicon 3

description:
Library name: 5UTR_DMSminus_Rep1_primer3
non-treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 5'-UTR


title: Buffy coat from patient without PNPs ET039142 at time of colonoscopy

description:
ET039142
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, control, Replicate 2, Amplicons 1-3

description:
Library name: 5UTR_DMSminus_Rep2_all-primers
non-treated samples for NanoLuc mRNA (amplicon 1-3) with MS2 stem loop in the 5'-UTR


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, DMS treatment, Replicate 1, Amplicon 2

description:
Library name: 5UTR_DMSplus_Rep1_primer2
treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the 5'-UTR


title: Buffy coat from patient without PNPs ET039145 at time of colonoscopy

description:
ET039145
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, DMS treatment, Replicate 1, Amplicon 3

description:
Library name: 5UTR_DMSplus_Rep1_primer3
treated samples for NanoLuc mRNA (amplicon 3, last 450 nucleotides) with MS2 stem loop in the 5'-UTR


title: Buffy coat from patient without PNPs ET03914 at time of colonoscopy

description:
ET03914
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, control, Replicate 1, Amplicon 2

description:
Library name: 5UTR_DMSminus_Rep1_primer2
non-treated samples for NanoLuc mRNA (amplicon 2, middle 450 nucleotides) with MS2 stem loop in the 5'-UTR


title: Buffy coat from patient with PNPs ET039140 at time of colonoscopy

description:
ET039140
genomic DNA extracted from peripheral leukocytes


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, control, Replicate 1, Amplicon 1

description:
Library name: 5UTR_DMSminus_Rep1_primer1
non-treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the 5'-UTR


title: shoot_qlsu_nS_4

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: sequencing pool 1

data_processing:
In our sequencing strategy read R1 contains UMI, barcode and first nucleotide of oligo(dT). We trim read R1 to keep only UMI and barcode. Our oligo(dT) primers has two parts of UMI splited by barcode sequence - we move UMI sequences to be next to each other. For all of this we use single awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 from the pools was demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Seeds were dry sterilized, plated onto half-strength Hoagland’s medium containing 0.8% agar, and stratified at 8 °C for 2 days. The plates were placed vertically in a plant growth chamber with a photoperiod of 8 h of light and 16 h of darkness. Half-strength Hoagland medium containing 1 mM sulfate was treated as a sulfur-sufficient medium (normal sulfur); in sulfur-deficient medium, MgSO4 was replaced with equimolar MgCl2.

extract_protocol:
Total RNA was isolated separately from shoots and roots using TRI Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s protocol. Plant tissue was collected from at least 10 seedlings. The quality and concentration of RNA were evaluated via a NanoDrop ND-100 (Thermo Fisher Scientific, Waltham, MA, USA) spectrophotometer.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. Four pools were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence).

treatment_protocol: The plants were grown under normal sulfur conditions for 10 days and then transferred to either normal sulfur or sulfur deficiency conditions for another 5 days.

value: shoot

tag: ecotype

value: q-lsu-KO

value: normal sulfur


title: shoot_qlsu_nS_2

description: sequencing pool 1


title: Buffy coat from patient without PNPs ET039139 at time of colonoscopy

description:
ET039139
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039136 at time of colonoscopy

description:
ET039136
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039138 at time of colonoscopy

description:
ET039138
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039137 at time of colonoscopy

description:
ET039137
genomic DNA extracted from peripheral leukocytes


title: shoot_qlsu_nS_1

description: sequencing pool 1


title: shoot_qlsu_dS_4

description: sequencing pool 2

value: sulfur deficiency


title: Buffy coat from patient with PNPs ET039135 at time of colonoscopy

description:
ET039135
genomic DNA extracted from peripheral leukocytes


title: shoot_qlsu_dS_3

description: sequencing pool 2


title: Buffy coat from patient with PNPs ET039134 at time of colonoscopy

description:
ET039134
genomic DNA extracted from peripheral leukocytes


title: shoot_qlsu_nS_3

description: sequencing pool 1


title: Buffy coat from patient with PNPs ET039133 at time of colonoscopy

description:
ET039133
genomic DNA extracted from peripheral leukocytes


title: WT_input

status: Public on Dec 12 2024

city: Nanjing

first: Chen

last: Xu

address: 101 Longmian Avenue, Jiangning District

country: China

institute: Nanjing Medical University

data_processing:
Reads were aligned to the mouse reference genome mm10 with BOWTIE software (bowtie2 version 2.3.4.3), followed by the removal of those reads that with low mapping quality and duplicated through sample amplification or sequencing.
Peak calling was carried out by using MACS2 (version 2.1.2, with options'-mfold 5, 50-p 0.0001'), on ChIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0).
Assembly: mm10
Supplementary files format and content: bigWig files

organism: Mus musculus

source_name: Testis

extract_protocol:
Fresh testes were collected from wild-type and Nkapl KO mice at postnatal day 21, ground into powder in liquid N2, and crosslinked by 1% formaldehyde, followed by quenching with glycine solution. Chromatin was fragmented by sonication in ChIP SDS lysis buffer (50 mM Tris-HCl, pH=8; 10 mM EDTA, pH=8; 1% SDS) using the Covaris-S220 sonicator. Crosslinked chromatin was incubated with indicated antibodies in ChIP dilution buffer (50 mM HEPES, pH7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxycholate) with protease inhibitors overnight. Crosslinking was reversed overnight at 65°C, and DNA was extracted by using phenol/chloroform/isoamyl alcohol.
Precipitated DNA was amplified for deep-sequencing. For ChIP-seq, equal DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers.

value: Testis

tag: time

value: postnatal day 21

tag: strain

value: Wild-type

tag: chip antibody


title: Buffy coat from patient without PNPs ET039141 at time of colonoscopy

description:
ET039141
genomic DNA extracted from peripheral leukocytes


title: shoot_qlsu_dS_2

description: sequencing pool 2


title: Buffy coat from patient with PNPs ET039132 at time of colonoscopy

description:
ET039132
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039130 at time of colonoscopy

description:
ET039130
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039131 at time of colonoscopy

description:
ET039131
genomic DNA extracted from peripheral leukocytes


title: shoot_qlsu_dS_1

description: sequencing pool 2


title: Buffy coat from patient without PNPs ET03913 at time of colonoscopy

description:
ET03913
genomic DNA extracted from peripheral leukocytes


title: shoot_Col0_nS_3

description: sequencing pool 1

value: wild type


title: shoot_Col0_nS_2

description: sequencing pool 1


title: shoot_Col0_nS_4

description: sequencing pool 1


title: NanoLuc mRNA with MS2 stem loop in 5'-UTR, DMS treatment, Replicate 1, Amplicon 1

description:
Library name: 5UTR_DMSplus_Rep1_primer1
treated samples for NanoLuc mRNA (amplicon 1, first 450 nucleotides) with MS2 stem loop in the 5'-UTR

value: Human Embrionic Kidney

value: adherent epithelial cell

value: dimethyl sulfate


title: Buffy coat from patient without PNPs ET039129 at time of colonoscopy

description:
ET039129
genomic DNA extracted from peripheral leukocytes


title: shoot_Col0_dS_4

description: sequencing pool 2


title: Buffy coat from patient without PNPs ET039128 at time of colonoscopy

description:
ET039128
genomic DNA extracted from peripheral leukocytes


title: shoot_Col0_nS_1

description: sequencing pool 1


title: Buffy coat from patient with PNPs ET039125 at time of colonoscopy

description:
ET039125
genomic DNA extracted from peripheral leukocytes


title: shoot_Col0_dS_2

description: sequencing pool 2


title: Buffy coat from patient without PNPs ET039123 at time of colonoscopy

description:
ET039123
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039122 at time of colonoscopy

description:
ET039122
genomic DNA extracted from peripheral leukocytes


title: shoot_Col0_dS_1

description: sequencing pool 2


title: shoot_Col0_dS_3

description: sequencing pool 2


title: Buffy coat from patient with PNPs ET039120 at time of colonoscopy

description:
ET039120
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_nS_3

description: sequencing pool 3

source_name: root

value: root


title: Buffy coat from patient without PNPs ET03912 at time of colonoscopy

description:
ET03912
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_nS_4

description: sequencing pool 3


title: Buffy coat from patient with PNPs ET039124 at time of colonoscopy

description:
ET039124
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_nS_1

description: sequencing pool 3


title: roots_qlsu_nS_2

description: sequencing pool 3


title: Buffy coat from patient without PNPs ET039117 at time of colonoscopy

description:
ET039117
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039118 at time of colonoscopy

description:
ET039118
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient without PNPs ET039119 at time of colonoscopy

description:
ET039119
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039116 at time of colonoscopy

description:
ET039116
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_dS_3

description: sequencing pool 4


title: roots_qlsu_dS_2

description: sequencing pool 4


title: roots_Col0_nS_4

description: sequencing pool 3


title: Buffy coat from patient without PNPs ET039114 at time of colonoscopy

description:
ET039114
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_dS_4

description: sequencing pool 4


title: Buffy coat from patient without PNPs  ET039115 at time of colonoscopy

description:
ET039115
genomic DNA extracted from peripheral leukocytes


title: roots_qlsu_dS_1

description: sequencing pool 4


title: Buffy coat from patient without PNPs ET039126 at time of colonoscopy

description:
ET039126
genomic DNA extracted from peripheral leukocytes


title: roots_Col0_nS_3

description: sequencing pool 3


title: Buffy coat from patient without PNPs ET039112 at time of colonoscopy

description:
ET039112
genomic DNA extracted from peripheral leukocytes


title: Buffy coat from patient with PNPs ET039113 at time of colonoscopy

description:
ET039113
genomic DNA extracted from peripheral leukocytes


title: roots_Col0_nS_2

description: sequencing pool 3


title: roots_Col0_nS_1

description: sequencing pool 3


title: Buffy coat from patient without PNPs ET039111 at time of colonoscopy

description:
ET039111
genomic DNA extracted from peripheral leukocytes


title: roots_Col0_dS_4

description: sequencing pool 4


title: Buffy coat from patient without PNPs ET03911 at time of colonoscopy

description:
ET03911
genomic DNA extracted from peripheral leukocytes


title: roots_Col0_dS_2

description: sequencing pool 4


title: roots_Col0_dS_3

description: sequencing pool 4


title: roots_Col0_dS_1

description: sequencing pool 4


title: 27596 Diagnosis RNA-seq

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

description:
27596
MR30

data_processing:
RNA-Seq reads were processed using STAR https://github.com/alexdobin/STAR.
read counts from featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: Leukemia cells

extract_protocol:
Total RNA was extracted using the standard protocol.
Libraries were constructed using the standard protocol.

tag: sample id

tag: time point

value: Diagnosis

value: Leukemia cells


title: Pontin TG heart tissue biol rep 2

city: Manchester

first: Delvac

last: Oceandy

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
Library name: Sample 2
Column name in raw counts gene_count.txt: TG2

data_processing:
The raw data were filtered and cleaned up to remove low-quality reads as well as sequences that contain adapters using fastp.
Clean data were mapped to reference genome (mouse GRCm39/mm39) using HISAT2
Gene counts were conducted using Feature Counts, to calculate the number or reads that map to each gene. Gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced
Analysis of differentially expressed genes was done using DESeq2. This software uses gene count/gene expression data to calculate a group mean and a global mean. It then calculates the deviations of the group mean from the global mean to determine if any changes in gene expression are significant.
Assembly: GRCm39/mm39
Supplementary files format and content: gene_count_all_samples.txt contains raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.

source_name: Heart

extract_protocol:
RNA was extracted using Trizol reagent as per manufacturer's instructions.
Library construction and sequencing were performed at Novogene

treatment_protocol: Mice were treated with angiotensin II for 14 days at a dose of 1.5 mg/kg BW/day using mini-osmotic pump

value: Heart

value: Transgenic

value: Angiotensin II infusion (1.5 mg/kg BW/day) for 14 days


title: Wild type heart tissue biol rep 3

description:
Library name: Sample 6
Column name in raw counts gene_count.txt: WT3

value: Wild type


title: Wild type heart tissue biol rep 2

description:
Library name: Sample 5
Column name in raw counts gene_count.txt: WT2


title: Pontin TG heart tissue biol rep 1

description:
Library name: Sample 1
Column name in raw counts gene_count.txt: TG1


title: Wild type heart tissue biol rep 1

description:
Library name: Sample 4
Column name in raw counts gene_count.txt: WT1


title: Pontin TG heart tissue biol rep 3

description:
Library name: Sample 3
Column name in raw counts gene_count.txt: TG3


title: RNAseq_PS_Amyb_KO_rep3

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
Raw sequence reads were trimmed and filtered using Trim Galore (https://github.com/FelixKrueger/TrimGalore)  v0.6.6.
Trimmed sequence reads were aligned to the mouse genome (GRCm38/mm10) using STAR version 2.5.3a with --outFilterMultimapNmax 1 options for unique alignments.
Aligned read counts for each gene were generated using featureCounts v2.0.1 based on the UCSC mouse refGene annotation and ERCC annotated sequences.
The TPM normalization were performed using StringTie v2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: testis

extract_protocol:
Testis were collected from P17 or 18 A-myb+/- and A-myb-/- mice and pachytene spermatocytes were isolated using fluorescence-activated cell sorting (FACS) with Vybrant DyeCycle Violet Stain (DCV). Sorting cells were used for RNA-seq libraries using Smart-Seq2 method. For each of the three independent biological replicates, approximately 10,000 cells were used. Prior to RNA extraction, the External RNA Controls Consortium (ERCC) RNA Spike-In Mix was added to the cell lysis. Total RNA was extracted using the RNeasy plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions. This mix was first diluted 3,000-fold with nuclease-free water, and then 1μL of this dilution was added to each suspension.
Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instruction.  Prepared RNA-seq libraries were sequenced on the Novaseq X Plus system (Illumina) with paired-ended 150-bp reads.

value: testis

tag: strain background

value: pachytene spermatocytes


title: 22259 Diagnosis RNA-seq

description:
22259
MR25


title: RNAseq_PS_Amyb_KO_rep1


title: RNAseq_PS_Amyb_KO_rep2


title: CUL-297 Diagnosis RNA-seq

description:
CUL-297
MR21


title: RNAseq_PS_Amyb_Ctrl_rep3

value: WT


title: CUL-249 Diagnosis RNA-seq

description:
CUL-249
MR20


title: 13684 Diagnosis RNA-seq

description:
13684
MR24


title: CUL-76 Diagnosis RNA-seq

description:
CUL-76
MR19


title: PATVDU Relapse RNA-seq

description:
PATVDU-R
PATVDU-R

value: PATVDU

value: Relapse


title: RNAseq_PS_Amyb_Ctrl_rep2


title: PATDDT Diagnosis RNA-seq

description:
PATDDT-D
PATDDT-D

value: PATDDT


title: PATDDT Relapse RNA-seq

description:
PATDDT-R
ptddt-r


title: RNAseq_PS_Amyb_Ctrl_rep1


title: PASVYP Relapse RNA-seq

description:
PASVYP-R
PASVYP-R-Resub

value: PASVYP


title: HTH

city: shanghai

last: kaiwen

state: Shanghai

address: shanghai jiaotong university

institute: shanghai jiaotong university

description: Library name: sample2

library_source: transcriptomic single cell

data_processing:
The CellRanger (v 5.0.1) was used to align the clean reads with mm10. The Seura 79 (v 5.1.0) pipeline was integrated into analysis and visualization, including clustering, dimension reduction, and cell type identification. Cell types were annotated based on the expression of known markers shown in Figure S3-E. The genes expressed in less than three cells were removed. The cells that expressed less than 200 genes were not included in the analysis. The harmony was used to remove the batch effects between samples. The dimension reduction of umap was calculated based on 40 harmony components. The significantly up-regulated genes in the specific sample and/or subpopulation were identified by FindMarkers and FindAllMarkers. The clusterProfiler was used to annotate the top markers of each subpopulation with the KEGG database. The macrophage gene score was evaluated with AddModuleScore. The ggplot2 was used to display the expression patterns of gene modules.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
To control the final number of cells captured, approximately 30,000 cells per sample were loaded onto 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol
Library was performed according to the manufacter's instructions (single cell 3’v3protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loadedtogether with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEMwas retrotranscripted to cDNA, which contains an llumina R1 primer sequence, UniqueMolecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was thencleaned up with Silane DynaBeads, amplified by PCR and the apropiated sizedfragments were selected with SPRlselect reagent for subsequent library construction.During the library construction llumina R2 primer sequence, paired-end constructs withP5 and P7 sequences and a sample index were added.

value: tumor


title: VEC

description: Library name: sample1


title: PASVYP Diagnosis RNA-seq

description:
PASVYP-D
PASVYP-D-Resub


title: 20165 Diagnosis RNA-seq

description:
20165
MR27


title: PASRPK Relapse RNA-seq

description:
PASRPK-R
PASRPK-R

value: PASRPK


title: PASRPK Diagnosis RNA-seq

description:
PASRPK-D
pasrpk-d


title: Ovary, Control 6mo, rep4

city: Oklahoma City

first: Michael

last: Stout

state: Oklahoma

address: 825 NE 13th St.

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description:
Library name: Young16
column name in CANA_gene_count.csv: Young16

data_processing:
RNA-Seq analysis was conducted in Partek Flow software (Version 11.0, Illumina).
Assembly: mm39
Supplementary files format and content: comma-delimited excel file includes raw counts for each sample

source_name: Ovary

extract_protocol:
Whole ovary RNA was extracted from one of the ovaries from each mouse from Con-12mo and Cana-12mo groups by the Trizol method.
cDNA Libraries were constructed from 40 ng total RNA using the NEB Ultra II Directional Library preparation kit (#NEBE7760L, New England Biolabs) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L, New England Biolabs), as previously described . Library sizing was performed with HSD1000 ScreenTape (#5067-5584, Agilent Technologies) and quantified by Qubit dsDNA HS Assay Kit (#Q32851, ThermoFisher Scientific) on a Qubit 4 Fluorometer (#Q33226, ThermoFisher Scientific). The sequence depth obtained was ~20,000 reads. The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system

treatment_protocol: At 6 months of age, mice were randomly assigned to one of three groups: [1] 6-month-old control mice, [2] 12-month-old control mice, or [3] 12-month-old mice that were treated with Cana from 6 to 12 months of age.

value: Ovary


title: Ovary, Control 6mo, rep5

description:
Library name: Young17
column name in CANA_gene_count.csv: Young17


title: PASJFJ Relapse RNA-seq

description:
PASJFJ-R
pasjfj-r

value: PASJFJ


title: Ovary, Control 6mo, rep2

description:
Library name: Young14
column name in CANA_gene_count.csv: Young14


title: PASJFJ Diagnosis RNA-seq

description:
PASJFJ-D
PASJFJ-D

value: Diagnosis


title: PARYMD Diagnosis RNA-seq

description:
PARYMDD
PARYMD-D-Resub

value: PARYMD

value: Leukemia cells


title: Ovary, Control 6mo, rep1

description:
Library name: Young13
column name in CANA_gene_count.csv: Young13


title: PARVUE Diagnosis RNA-seq

description:
PARVUE-D
PARVUE-D-2

value: PARVUE


title: Ovary, Control 6mo, rep3

description:
Library name: Young15
column name in CANA_gene_count.csv: Young15


title: Ovary, Control 12mo, rep2

description:
Library name: Control9
column name in CANA_gene_count.csv: Control9


title: Ovary, Control 12mo, rep3

description:
Library name: Control10
column name in CANA_gene_count.csv: Control10


title: PARPCK Relapse RNA-seq

description:
PARPCK-R
AK036

value: PARPCK


title: Ovary, Control 12mo, rep4

description:
Library name: Control11
column name in CANA_gene_count.csv: Control11


title: PARVUE Relapse RNA-seq

description:
PARVUE-R
PARVUE-R-2


title: PARMJA Relapse RNA-seq

description:
PARMJA-R
AK034

value: PARMJA


title: PARPCK Diagnosis RNA-seq

description:
PARPCK-D
AK035


title: Ovary, Control 12mo, rep1

description:
Library name: Control7
column name in CANA_gene_count.csv: Control7


title: Ovary, Cana treated, rep4

description:
Library name: Cana4
column name in CANA_gene_count.csv: Cana4


title: PARGIR Diagnosis RNA-seq

description:
PARGIRD
pargir-d

value: PARGIR


title: PARGIR Relapse RNA-seq

description:
PARGIRR
PARGIR-R-2


title: PARMJA Diagnosis RNA-seq

description:
PARMJA-D
AK033


title: Ovary, Cana treated, rep2

description:
Library name: Cana2
column name in CANA_gene_count.csv: Cana2


title: Ovary, Cana treated, rep3

description:
Library name: Cana3
column name in CANA_gene_count.csv: Cana3


title: Ovary, Control 12mo, rep5

description:
Library name: Control12
column name in CANA_gene_count.csv: Control12


title: 6953 Relapse RNA-seq

description:
6953rel
6953-rel


title: Ovary, Cana treated, rep1

description:
Library name: Cana1
column name in CANA_gene_count.csv: Cana1


title: 7300 Relapse RNA-seq

description:
7300rel
AK016


title: EOP+EP+DMF-4

city: Xiamen

first: Xing

address: 422, Siming South Road

institute: Xiamen University

description:
Library name: sample43
expression matrix (txt) and original file (fastq)

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/linl-linl/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

source_name: Ascites

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.

treatment_protocol: The cellular contents of SW480 cells were extracted initially prior to the ARV771 treatment, designated as the sample at 0 h. Immediately thereafter 250 nM ARV771 was added to the culture medium, and the cells were extracted at 1 h and 4 h.

value: Ascites

value: Macrophage


title: 6787 Diagnosis RNA-seq

description:
6787dx
AK001


title: 7300 Diagnosis RNA-seq

description:
7300dx
AK015


title: EOP+EP+DMF-7

description:
Library name: sample46
expression matrix (txt) and original file (fastq)

value: WT


title: EOP+EP+DMF-6

description:
Library name: sample45
expression matrix (txt) and original file (fastq)


title: 6787 Relapse RNA-seq

description:
6787rel
AK002

value: Relapse


title: EOP+EP+DMF-3

description:
Library name: sample42
expression matrix (txt) and original file (fastq)


title: EOP+EP+DMF-1

description:
Library name: sample40
expression matrix (txt) and original file (fastq)


title: CD8 ATAC-seq 1

data_processing:
ATAC-seq reads were processed using proatac package https://github.com/buenrostrolab/proatac.
summits files were generated using macs2.
Genome_build: hg19
Supplementary_files_format_and_content: summits files

source_name: Normal T cells

extract_protocol:
ATAC-seq samples were extracted as described in Buenrostro et al., Curr Protoc Mol Biol, 2016.
Libraries were constructed using the standard protocol.

value: Normal T cells

tag: cell subtype


title: CD8 ATAC-seq 2


title: CD4-Positive ATAC-seq 2


title: CD4-Positive ATAC-seq 1


title: EOP+EP+DMF-2

description:
Library name: sample41
expression matrix (txt) and original file (fastq)


title: EOP+EP-6

description:
Library name: sample38
expression matrix (txt) and original file (fastq)


title: DP-CD3-Positive ATAC-seq 2


title: EOP+EP-7

description:
Library name: sample39
expression matrix (txt) and original file (fastq)


title: Ovary, Cana treated, rep5

description:
Library name: Cana6
column name in CANA_gene_count.csv: Cana6


title: Buffy coat from patient without PNPs ET039153 at time of colonoscopy

description:
ET039153
genomic DNA extracted from peripheral leukocytes

value: Buffy Coat


title: EOP+EP-5

description:
Library name: sample37
expression matrix (txt) and original file (fastq)


title: DP-CD3-Positive ATAC-seq 1


title: EOP+EP-4

description:
Library name: sample36
expression matrix (txt) and original file (fastq)


title: EOP+EP-3

description:
Library name: sample35
expression matrix (txt) and original file (fastq)


title: 6953 Diagnosis RNA-seq

description:
6953dx
6953-dx


title: DP-CD3-Negative ATAC-seq 1


title: EOP+EP-2

description:
Library name: sample34
expression matrix (txt) and original file (fastq)


title: EOP+EP+DMF-5

description:
Library name: sample44
expression matrix (txt) and original file (fastq)


title: ISP ATAC-seq 2

value: ISP


title: ISP ATAC-seq 1


title: EOP+EP-1

description:
Library name: sample33
expression matrix (txt) and original file (fastq)


title: EOP-EP-7

description:
Library name: sample32
expression matrix (txt) and original file (fastq)


title: EOP-EP-4

description:
Library name: sample29
expression matrix (txt) and original file (fastq)


title: CD34-Cd1a-Negative ATAC-seq 2


title: EOP-EP-2

description:
Library name: sample27
expression matrix (txt) and original file (fastq)


title: EOP-EP-3

description:
Library name: sample28
expression matrix (txt) and original file (fastq)


title: CD34-Cd1a-Positive ATAC-seq 2


title: CD34-Cd1a-Positive ATAC-seq 1


title: EOP-EP-6

description:
Library name: sample31
expression matrix (txt) and original file (fastq)


title: 22259 Diagnosis ATAC-seq


title: 20165 Diagnosis ATAC-seq


title: 27596 Diagnosis ATAC-seq


title: EOP-EP-1

description:
Library name: sample26
expression matrix (txt) and original file (fastq)


title: Ncr1creIrf4floxflox NK cells

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

description: Library name: Ncr1creIrf4floxflox_NK cells, ATAC

data_processing:
Reads were trimmed, aligned to mm10 using Bowtie2, and duplicates removed.
Peaks called with MACS2.
Signal tracks generated with deepTools.
Assembly: mm10
Supplementary files format and content: Signal tracks in BigWig format.

source_name: spleen

extract_protocol:
Nuclei were isolated using a lysis buffer, followed by tagmentation with Tn5 transposase, DNA purification, and quantification.
Libraries were prepared using the Illumina Nextera DNA Library Prep Kit, size-selected with AMPure beads, and sequenced on NovaSeq 6000.

value: spleen

value: primary NKP cells

value: NK cell


title: Irf4floxflox NK cells

description: Library name: Irf4floxflox_NK cells, ATAC


title: Irf4ko NK cells

description: Library name: Irf4ko_NK cells, ATAC


title: CUL-297 Diagnosis ATAC-seq

value: Diagnosis


title: CUL-249 Diagnosis ATAC-seq


title: WT_lyHSC_2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Assembly: mm10
Supplementary files format and content: text file

source_name: Bone marrow

extract_protocol:
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Hematopoietic stem cell

value: control

tag: batch


title: WT NK cells

description: Library name: WT_NK cells, ATAC


title: PATVDU Relapse ATAC-seq

description: PATVDU-R.proatac

value: Leukemia cells


title: WT_lyHSC_1


title: PATVDU Diagnosis ATAC-seq

description: PATVDU-D.proatac


title: WT_myHSC_4


title: PATENL Relapse ATAC-seq

description: PATENL-R.proatac


title: WT_myHSC_3


title: EOP-EP-5

description:
Library name: sample30
expression matrix (txt) and original file (fastq)


title: DP-CD3-Negative ATAC-seq 2


title: CD34-Cd1a-Negative ATAC-seq 1


title: 13684 Diagnosis ATAC-seq


title: PATENL Diagnosis ATAC-seq

description: PATENL-D.proatac


title: Sema4aKO_myHSC_4


title: WT_myHSC_2


title: PASVYP Relapse ATAC-seq

description: PASVYP-R.proatac


title: PATDDT Relapse ATAC-seq

description: PATDDT-R.proatac


title: Sema4aKO_myHSC_1


title: PASRPK Relapse ATAC-seq

description: PASRPK-R.proatac


title: PASRPK Diagnosis ATAC-seq

description: PASRPK-D.proatac


title: WT_myHSC_1


title: PASVYP Diagnosis ATAC-seq

description: PASVYP-D.proatac


title: CUL-76 Diagnosis ATAC-seq


title: PASJFJ Relapse ATAC-seq

description: PASJFJ-R.proatac


title: Sema4aKO_myHSC_3


title: PASJFJ Diagnosis ATAC-seq

description: PASJFJ-D.proatac


title: Sema4aKO_myHSC_2


title: PARYMD Diagnosis ATAC-seq

description: PARYMDD.proatac


title: PHDi-ISM012-042_day2_rep5

city: Shanghai

first: Chenxi

address: JinKe Road

institute: Insilico Medicine

data_processing:
The raw sequencing data obtained were processed using the DRAGEN (v 4.0.3) pipeline [https://support-docs.illumina.com/APP/AppGermline-v403/Content/APP/AppGermline.htm], which aligned the reads against the NCBIrefseq mouse genome (mm10) to generate count data.
Assembly: mm10
Supplementary files format and content: csv file includes TPM values for each sample

source_name: colon

extract_protocol:
Samples were homogenized with a Qiagen TissueLyser LT in TRI Reagent, and the total RNA was purified using the RNeasy Mini Kit (Qiagen).
RNA was converted into cDNA using FastKing RT Kit (TIANGEN) according to the manufacturer’s instructions.

value: colon


title: PHDi-ISM012-042_day2_rep6


title: PHDi-ISM012-042_day2_rep4


title: PHDi-ISM012-042_day2_rep2


title: PHDi-ISM012-042_day2_rep1


title: PARVUE Diagnosis ATAC-seq

description: PARVUE-D.proatac


title: colon_Vehicle_day2_rep6

value: Vehicle


title: PATDDT Diagnosis ATAC-seq

description: PATDDT-D.proatac


title: PARPCK Relapse ATAC-seq

description: PARPCK-R.proatac


title: colon_Vehicle_day2_rep5


title: PARPCK Diagnosis ATAC-seq

description: PARPCK-D.proatac


title: PARMJA Relapse ATAC-seq

description: PARMJA-R.proatac


title: colon_Vehicle_day2_rep4


title: colon_Vehicle_day2_rep3


title: colon_Vehicle_day2_rep2


title: PARMJA Diagnosis ATAC-seq

description: PARMJA-D.proatac


title: PHDi-ISM012-042_day2_rep3


title: colon_sham_day2_rep6

value: sham


title: 6953 Relapse ATAC-seq


title: PARGIR Diagnosis ATAC-seq

description: PARGIRD.proatac


title: colon_sham_day2_rep4


title: 6953 Diagnosis ATAC-seq


title: PARVUE Relapse ATAC-seq

description: PARVUE-R.proatac


title: colon_sham_day2_rep3


title: PARYMD Relapse ATAC-seq

description: PARYMDR.proatac


title: 6787 Diagnosis ATAC-seq


title: colon_sham_day2_rep1


title: colon_sham_day2_rep5


title: PARGIR Relapse ATAC-seq

description: PARGIRR.proatac


title: 7300 Relapse ATAC-seq


title: KO2-1

city: Cincinnati

first: Fukun

last: Guo

state: OH

address: 3333 Burnet Avenue

institute: Children's Hospital Medical Center

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments.  The programs used in these steps were FastQC v0.11.7 (Andrews), Trim Galore! v0.4.2 (Krueger) and cutadapt v1.9.1 (Martin, 2011). The trimmed reads were aligned to reference mouse genome version mm10 with the program STAR v2.6.1e (Dobin et al., 2013). Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8 (Tarasov et al., 2015). Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database (O'Leary et al., 2016). Read counting was done with the program featureCounts v1.6.2 from the Rsubread package (Liao et al., 2019). Raw counts were normalized as transcripts per million (TPM). The list of differentially expressed genes and log2 fold changes are further used for Gene Set Enrichment Analysis. GSEAPreranked tool within GSEA v3.0.0 (Mootha et al., 2003; Subramanian et al., 2005) was applied with MH gene set from the Molecular Signatures Database (MSigDB) (Castanza et al., 2023; Liberzon et al., 2011). Heatmap was generated using base graphics in R.
ATAC-seq and CHIP-seq raw reads in FASTQ files were assessed for quality control using FastQC v0.11.9 (Andrews). Trimming of raw reads was performed using TrimGalore! V0.6.7 (Krueger) and cutadapt v3.5 (Martin, 2011). The trimmed reads were aligned to mouse reference genome mm39 with HISAT2 v2.2.1-3n-0.0.2. (Kim et al., 2015). Duplicate reads were removed using sambamba v0.8.2 (Tarasov et al., 2015). Peaks were called using Macs2 v2.2.7.1 (Zhang et al., 2008) and aggregated on each duplicate samples by combining overlapping peaks with bedtools v1.16.1 (Quinlan and Hall, 2010). A minimum of 50% overlap was considered. Peaks showing only in one replicate were removed. A final list of peaks was derived by taking the union of all aggregated peak lists. Reads under the final list of peaks were counted using featureCounts v1.5.3 (Liao et al., 2014) on each BAM file. Heatmaps and peak profiles were generated using deeptools v3.5.5 (computeMatrix, plotHeatmap and plotProfile) (Ramirez et al., 2016). CHIP peaks were further overlapped with CHD8-/- ATAC peaks. The overlapping CHD8-/- ATAC peaks were split up into three classes, up, down and same, according to their log2FC between WT and CHD8-/- ATAC. 'Regions' 1.5Kb around center of the described CHD8-/- ATAC peaks were then employed to generate heatmaps and profiles using deeptools. These regions defined by the overlapped CHD8-/- ATAC peaks were used to pair WT and CHD8-/- regions and plotted side-by-side in heatmaps. In parallel, CHD8-/- ATAC peaks non-overlapping with CHIP peaks were processed similarly to CHD8-/- ATAC peaks overlapping with CHIP peaks.  Two methods were used for gene set enrichments:1) GSEA (Gene Set Enrichment Analysis) (Subramanian et al., 2005) when using a ranked list. The list of genes is ranked by the log2FC values. 2) Enrichr (Chen et al., 2013; Kuleshov et al., 2016; Xie et al., 2021). Out of the complete Enrichr output, only the Hallmark gene set was used, with the 10 most enriched gene sets. Venn diagrams and bar graphs were generated using the R environment and the ggplot2 package (Wickham, 2016).
Assembly: mm9
Supplementary files format and content: txt: matrix.tpm-1
Supplementary files format and content: txt: chip_tpm_matrix / atac_tpm_matrix

extract_protocol:
The splenocytes were prepared freshly from CHD8-/- mice and their WT littermates. Natural regulatory T cells (nTregs) were isolated from spleens with a CD4+CD25+ Regulatory T Cell Isolation kit by AutoMACS Pro (Miltenyi Biotec, Auburn, CA). The purity of isolated Tregs was checked by FACS. Where indicated, splenocyte were stimulated with PMA (25 ng/ml) plus ionomycin (500 ng/ml) (Sigma, St Louis, MO) for 5 h with GolgiStop (BD Bioscience, San Jose, CA) in the last 2 h for intracellular cytokine staining.
RNA seq: Splenic CD4+ T cells were isolated from WT and CHD8-/- mice by AutoMACS Pro. YFP+ cells were then sorted by FACS and analyzed for gene expression profiles by RNA-Seq. The Next Generation Sequencing technology (10X Genomics Next GEM 3v3.1 Assay) was performed by the Single Cell Genomics Core, Cincinnati Children's Hospital Medical Center. RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit and sequenced using a HiSeq 2500 sequencer. Chip seq:Half million Tregs were used for ChIP-seq that was performed according to a previously described protocol with slight modifications (Boyer et al., 2005; Rada-Iglesias et al., 2011). In brief, Tregs were crosslinked with 1% formaldehyde at room temperature for 15 min with rotation, and then quenched with 125 mM glycine. Isolation of nuclei, extraction of chromatin and shearing with sonication were carried out as previously described (Cotney et al., 2013) using the Magna ChIP A/G kit (Millipore Sigma, Catalog#17-10085). Chromatin was immunoprecipitated by incubating soluble chromatin with 1.5 μg of CHD8 antibody (Bethyl Laboratories, # A301-224) or 1.5 μg of IgG antibody (Abcam, ab37355) at 4°C overnight. Magna ChIP® Protein A+G Magnetic Beads (Millipore Sigma, Catalog#16-663) were added next day and incubated for 2 hrs. CHD8-bound beads were washed in Low salt wash buffer, High salt wash buffer, LiCl wash buffer and TE buffer subsequentially. Harvested chromatin was then eluted from the beads, crosslinks were reversed and DNA was purified as previously described (Cotney et al., 2013), in which MinElute PCR Purification Kit (QIAGEN # 28204) was used for DNA purification. Libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (#E7645). Barcoded libraries were sequenced using a Novaseq 6000 sequencer at the DNA core of Cincinnati Children’s Hospital Medical Center. ATAC seq:ATAC-seq was carried out as described by Buenrostro et al (Buenrostro et al., 2015). Briefly, ~50,000 sorted WT and CHD8-/- CD4+YFP+ Tregs were centrifuged at 500 x g for 20 minutes at 4 °C. Cells were lysed in ice cold lysis buffers (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40), centrifuged at 500xg at 40C for isolation of nuclei. Transposase reaction was performed by incubating the isolated nuclei with Tn5 transposase from the Nextera DNA Library Preparation Kit (Illumina) for 30 minutes at 37 °C. Transposed DNA was purified using QIAGEN mini elute DNA purification kit per manufacturer’s instructions. PCR amplification and barcoding were done using forward (i5 Forward) and reverse (i7 Reverse) primers with specific index, NEB 2 x PCR Mix (New England Biolabs), and tagmented DNA. PCR conditions were as following: 72°C for 5 minutes, 98°C for 30 seconds, 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. After the first PCR, DNA size was selected with 0.5 x volume SPRI beads (Agencourt AMPure, Beckman Coulter), and cleaned up with 1.5 x SPRI beads. The second PCR (98°C for 30 seconds, followed by 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute) was performed with same forward and reverse primers. Libraries were purified with 1.5 x SPRI beads, and concentration and ATAC DNA profiles were analyzed with the Bioanalyzer DNA High Sensitivity Kit (Agilent). Libraries were sequenced on Novaseq 6000 (Illumina), and with an average of 25 million paired-end reads per sample.
RNA seq: The Next Generation Sequencing technology (10X Genomics Next GEM 3v3.1 Assay) was performed by the Single Cell Genomics Core, Cincinnati Children's Hospital Medical Center. RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit and sequenced using a HiSeq 2500 sequencer. CHIP-seq:Barcoded libraries were sequenced using a Novaseq 6000 sequencer at the DNA core of Cincinnati Children’s Hospital Medical Center. ATAC-seq: Libraries were sequenced on Novaseq 6000 (Illumina), and with an average of 25 million paired-end reads per sample.

value: Treg cells

value: Poly IC injection


title: WT-3


title: cv. Fielder, 3rd, 4th, 5th leaves,  day 11 of Fe deficiency, rep 3

city: Parkville

first: Oscar

last: Fung

state: VIC

address: BioSciences 3

department: School of BioSciences

country: Australia

institute: The University of Melbourne

description:
Library name: 112_11_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X112_11_L

data_processing:
Analysis of RNA-sequencing data was performed in Galaxy Australia (v1.0.0). Paired-end files from each sample and lane were concatenated (Galaxy v1.0.0) to generate single files for each read pair (R1 and R2). Quality checks were performed using FastQC (v0.74+galaxy1) and summarised with MultiQC (v1.11+galaxy1). Adapter trimming and low-quality base removal were done with Trim Galore (v0.6.7+galaxy0), applying a Phred score threshold of 10 and discarding reads under 30 base pairs (bp). Post-trimming quality was reassessed with FastQC. Reads were aligned to the “161010_Chinese_Spring_v1.0_pseudomolecules.fasta” reference genome (https://urgi.versailles.inra.fr/) using HISAT2 (v2.2.1+galaxy1), with paired-end and reverse strand (RF) options. Transcripts were assembled with StringTie (v2.2.3+galaxy0) using the HISAT2 BAM output and the reference high confidence GTF file (IWGSC_v1.1_HC_20170706.gtf) and also the low confidence GTF file (IWGSC_v1.1_LC_20170706.gtf) to capture all low confidence TaNAS genes (https://urgi.versailles.inra.fr/). Gene counts were quantified with FeatureCounts (v2.0.3+galaxy2).
Assembly: Reads were aligned to the “161010_Chinese_Spring_v1.0_pseudomolecules.fasta” reference genome (https://urgi.versailles.inra.fr/) using HISAT2 (v2.2.1+galaxy1).  Transcripts were assembled with StringTie (v2.2.3+galaxy0) using the reference high confidence GTF file (IWGSC_v1.1_HC_20170706.gtf) and also the low confidence GTF file (IWGSC_v1.1_LC_20170706.gtf) (https://urgi.versailles.inra.fr/).
Supplementary files format and content: Raw gene counts in tabular format were calculated using FeatureCounts combined into a single CSV using Rstudio.

organism: Triticum aestivum

source_name: 3rd, 4th, 5th leaves

growth_protocol: Grain harvested from cv. Fielder plants were stratified at 4°C for two days and then surface sterilised with VitaVax 200FF (Hewitt & Whitty, Geelong, Victoria, Australia) and placed on sterile moist filter paper at 20°C for two days. Germinated seedlings were transferred to hydroponic boxes containing a nutrient replete solution: 2 mM NH4NO3, 5 mM KNO3, 2 mM Ca(NO3)2·4H2O, 2mM MgSO4·7H2O, 0.1 mM KH2PO4, 10 µM H3BO3, 5 µM MnCl2·4H2O, 5 µM ZnSO4·7H2O, 0.5 µM CuSO4·5H2O, 0.1 µM Na2MoO4·2H2O, and 50 µM NaFe3+EDTA. Following 12 days of nutrient replete growth, the solution was replaced with an Fe deficient solution (0 µM NaFe3+EDTA) and grown for a further 11 days. The nutrient solution was replaced every four days. Leaf tissues were harvested at days 0, 1, 7 and 11 of Fe deficiency and root tissues were harvested at day 11 of Fe deficiency. All tissues were immediately snap frozen in liquid nitrogen following sampling.

extract_protocol:
Approximately 50 mg of tissue in TRI Reagent® (Merck, Darmstadt, Germany) was homogenised with stainless steel beads and a TissueLyser II (Qiagen, Hilden, Germany). The Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, California, USA) was used to extract RNA according to the manufacturer’s instructions.
Quality control and RNA-sequencing was performed by the Australian Genome Research Facility (AGRF, Melbourne, Victoria, Australia). Briefly, sample quality was assessed using the Agilent 4200 TapeStation and Agilent RNA ScreenTape (Agilent Technologies, Santa Clara, California, USA) and reagents according to the manufacturer’s instructions. Sample concentrations were measured using the QuantiFluor RNA Kit (Promega, Madison, Wisconsin, USA). Library preparation was performed using the Illumina Stranded mRNA library preparation workflow and sequencing was completed with the Illumina NovaSeq X Plus with 150 paired end reads and one lane of a 10B-300 flow cell according to the manufacturer’s instructions (Illumina, San Diego, California, USA).

treatment_protocol: Iron (Fe) sufficient solution contained 50 µM NaFe3+EDTA (12 days of growth) and the Fe deficient solution contained 0 µM NaFe3+EDTA (11 days of growth).

value: 3rd, 4th, 5th leaves

value: WT

value: Day 11 of Fe deficiency


title: cv. Fielder, roots, day 11 of Fe deficiency, rep 3

description:
Library name: 112_11_R
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X112_11_R

source_name: roots

value: roots


title: cv. Fielder, 3rd leaf,  day 7 of Fe deficiency, rep 3

description:
Library name: 112_7_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X112_7_L

source_name: 3rd leaf

value: 3rd leaf

value: Day 7 of Fe deficiency


title: colon_Vehicle_day2_rep1


title: 7300 Diagnosis ATAC-seq


title: 6787 Relapse ATAC-seq

value: Relapse


title: colon_sham_day2_rep2


title: WT-1

value: spleen


title: KO2-3


title: KO1-3


title: cv. Fielder, 1st leaf,  day 0 of Fe deficiency, rep 3

description:
Library name: 112_0_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X112_0_L

source_name: 1st leaf

value: 1st leaf

value: Day 0 of Fe deficiency


title: KO1-1


title: cv. Fielder, 3rd leaf,  day 7 of Fe deficiency, rep 2

description:
Library name: 106_7_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X106_7_L


title: 2G-IgG-3


title: 1G-IgG-1


title: cv. Fielder, roots, day 11 of Fe deficiency, rep 2

description:
Library name: 106_11_R
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X106_11_R


title: cv. Fielder, 1st leaf,  day 0 of Fe deficiency, rep 2

description:
Library name: 106_0_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X106_0_L


title: 2G-CHD8-3


title: 1G-IgG-3


title: cv. Fielder, 3rd leaf,  day 7 of Fe deficiency, rep 1

description:
Library name: 105_7_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X105_7_L


title: cv. Fielder, 1st leaf,  day 1 of Fe deficiency, rep 1

description:
Library name: 105_1_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X105_1_L

value: Day 1 of Fe deficiency


title: 1G-CHD8-1


title: cv. Fielder, 1st leaf,  day 0 of Fe deficiency, rep 1

description:
Library name: 105_0_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X105_0_L


title: cv. Fielder, roots, day 11 of Fe deficiency, rep 1

description:
Library name: 105_11_R
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X105_11_R


title: Guo-W2-18870


title: Guo-W1-18869


title: Guo-K1-18871


title: 4x_20_5FU

data_processing:
Raw sequencing fragments were trimmed using TrimGalore (0.4.3)
Alignment to the mouse reference genome (build mm10) was performed using Bismark (v0.23.1)
Differentially methylated sites were generated using methylKit (v1.22.0)
Assembly: mm10
Supplementary files format and content: DNA methylation level, text format
Library strategy: DNA-seq

source_name: blood

extract_protocol:
Qiagen DNA extraction kit
Reduced representation bisulfite sequencing(RRBS)

value: blood

value: HSC


title: Guo-K2-18872


title: 2G-CHD8-1


title: cv. Fielder, 1st leaf,  day 1 of Fe deficiency, rep 3

description:
Library name: 112_1_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X112_1_L


title: 2G-IgG-1


title: cv. Fielder, 3rd, 4th, 5th leaves,  day 11 of Fe deficiency, rep 2

description:
Library name: 106_11_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X106_11_L


title: cv. Fielder, 3rd, 4th, 5th leaves,  day 11 of Fe deficiency, rep 1

description:
Library name: 105_11_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X105_11_L


title: 1G-CHD8-3


title: expt2 bcd osk tsl RNA Pol 2 pSer5 ChIP replicate 4

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description: Library name: bcdosktsl_pSer5_rep4

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates
Duplicate-marked mapped reads were imported into R, discarding duplicates, and keeping only reads with map-quality scores of 10 or greater. Wiggle files were generated by calculating the average number of mapped reads within 10 bp windows, and normalizing to millions of reads in the overall sample.
Assembly: Drosophila dm6
Supplementary files format and content: bigWig files for samples (merged replicates) are provided showing counts per million (CPM) normalized average coverage in 10 bp windows across the canonical dm6 chromosome assemblies. Weird scaffolds were excluded.

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
Following ChIP fixation (15 minutes formaldehyde + PBS-triton-X-100 + Heptane) embryos were sorted by stage. For experiment 1, embryos were selected for nuclear cycle 13 morphology, and HU-treated embryos were further scored for the apparent presence of foci of GFP-tagged replication protein A 70. For experiment 2, embryos were sorted simply by cellular blastoderm stage (stage 5) morphology.
ChIP was performed by initially sonicating chromatin and incubating overnight with a primary antibody. Antibody-DNA complexes were pulled down using protein G dynabeads. Before washing, antibody-DNA complexes were subjected to tagmentation with Illumina Tn5 transposase for 40 minutes at 37°C. Transposed samples were then washed in low and high salt solutions (2x 5' each) followed by one wash in TE buffer. Crosslinks were reversed for 4 hours at 65°C with moderate shaking in the presence of 5 µg/ml ProteinaseK. DNA was cleaned up using a Qiagen MinElute Reaction Clean-Up Kit, and PCR was performed using sets of unique-dual-indexed Nextera PCR primers. Libraries were amplified within the linear range of PCR prior to Ampure clean up. Libraries were pooled as necessary and sent to Admera Health for sequencing on a NovaSeq X platform (paired-end 150 bp reads). Admera returned barcode-split, compressed fastq files for reads 1 and 2.

treatment_protocol: For both experiments, embryos were dechorionated prior to further processing. For the replication inhibition experiment, embryos were further permeabilized by a 2-minute exposure to CitraSolv followed by extensive washing in water. To inhibit DNA replication, permeabilized embryos were incubated in a solution of 100 mM hydroxyurea in 1x PBS for 40 minutes prior to fixation for ChIP. Control embryos were incubated for 40 minutes in 1x PBS. For the second experiment, no additional treatments were performed after dechorionation, and embryos were directly fixed for ChIP.

value: embryo

value: bcd osk tsl


title: expt2 bcd osk tsl RNA Pol 2 pSer5 ChIP replicate 3

description: Library name: bcdosktsl_pSer5_rep3


title: expt2 bcd osk tsl RNA Pol 2 pSer5 ChIP replicate 1

description: Library name: bcdosktsl_pSer5_rep1


title: expt2 bcd osk tsl negative control ChIP replicate 2

description: Library name: bcdosktsl_negctrl_rep2


title: expt2 bcd osk tsl RNA Pol 2 pSer5 ChIP replicate 2

description: Library name: bcdosktsl_pSer5_rep2


title: expt2 bcd osk tsl negative control ChIP replicate 1

description: Library name: bcdosktsl_negctrl_rep1


title: expt2 wild type RNA Pol 2 pSer5 ChIP replicate 3

description: Library name: wildtype_pSer5_rep3

value: w


title: 2x_18_5FU


title: expt2 wild type RNA Pol 2 pSer5 ChIP replicate 2

description: Library name: wildtype_pSer5_rep2


title: cv. Fielder, 1st leaf,  day 1 of Fe deficiency, rep 2

description:
Library name: 106_1_L
The processed CSV contains raw counts from FeatureCounts for all samples using high confidence (HC) and low confidence (LC) gene annotations. Row: X106_1_L


title: 4x_05_5FU


title: 2x_17_5FU


title: 4x_19_5FU


title: 4x_06_5FU


title: expt2 wild type negative control ChIP replicate 3

description: Library name: wildtype_negctrl_rep3


title: expt1 hydroxyurea treatment RNA Pol 2 ChIP replicate 1

description: Library name: HU_pol2_rep1

value: w; RpA70-EGFP

value: hydroxyurea


title: expt2 wild type negative control ChIP replicate 1

description: Library name: wildtype_negctrl_rep1


title: 2x_03_5FU


title: expt1 hydroxyurea treatment RNA Pol 2 ChIP replicate 2

description: Library name: HU_pol2_rep2


title: 2x_04_5FU


title: 10x_32_5FU


title: TEX_sgscramble_H3K27ac_rep2 (paired with sgKAT2A)

city: La Jolla

first: Shixin

last: Ma

address: 10010 N Torrey Pines Rd

department: IMPL-K

institute: SALK Institute for biological studies

data_processing:
Sequence reads were aligned to mm10 using bowtie2
Assembly: mm10
Supplementary files format and content: bigwig

source_name: sgscramble

extract_protocol:
DNA extraction following Cut&Tag protocol
Library preparation following Cut& Tag protocol

value: sgscramble

value: LCMV-clone 13


title: expt1 hydroxyurea treatment bicoid ChIP replicate 1

description: Library name: HU_bcd_rep1


title: TEX_sgKat2a_H3K27ac_rep1


title: 10x_33_5FU


title: expt1 hydroxyurea treatment negative control ChIP replicate 1

description: Library name: HU_negctrl_rep1


title: 2x_15_5FU


title: TEX_sgscramble_H3K27ac_rep1 (paired with sgKAT2A)


title: TEX_sgKat2a_H3K27ac_rep2


title: TEX_sgEp300_H3K27ac_rep1


title: 10x_11_5FU


title: 10x_31_5FU


title: expt2 wild type RNA Pol 2 pSer5 ChIP replicate 1

description: Library name: wildtype_pSer5_rep1


title: expt2 wild type negative control ChIP replicate 2

description: Library name: wildtype_negctrl_rep2


title: expt1 control treatment RNA Pol 2 ChIP replicate 2

description: Library name: control_pol2_rep2

value: control


title: expt1 hydroxyurea treatment bicoid ChIP replicate 2

description: Library name: HU_bcd_rep2


title: 10x_12_5FU


title: TEX_sgscramble_H3K27ac_rep2 (paired with sgEp300)


title: 2x_16_5FU


title: TEX_sgscramble_H3K27ac_rep1 (paired with sgEp300)


title: 0x_14_5FU


title: TEX_sgEp300_H3K27ac_rep2


title: TEX_sgAcss2_H4ac_rep2

value: Day 6

value: in vitro exhaustion culture


title: expt1 control treatment RNA Pol 2 ChIP replicate 1

description: Library name: control_pol2_rep1


title: TEX_sgAcss2_H4ac_rep1


title: expt1 control treatment bicoid ChIP replicate 1

description: Library name: control_bcd_rep1


title: TEX_sgAcss2_H3K9ac_rep1


title: TEX_sgAcss2_H3K9ac_rep2


title: TEX_sgAcss2_H3K27ac_rep2


title: expt1 control treatment bicoid ChIP replicate 2

description: Library name: control_bcd_rep2


title: expt1 control treatment negative control ChIP replicate 2

description: Library name: control_negctrl_rep2


title: TEX_sgAcss2_H3K27ac_rep1


title: expt1 control treatment negative control ChIP replicate 1

description: Library name: control_negctrl_rep1


title: TIL_ACSS2NLS_rep2

data_processing:
Sequence reads were aligned to mm10 using STAR v2.5.3a (parameters- default)
RNA expression was quantified using homer
Assembly: mm10
Supplementary files format and content: fpkm value, txt file

extract_protocol:
RNA was harvested using Rneasy Plus Micro kit (Qiagen) and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA kit following manufacturer's protocols.

value: Day 21

value: B16-GP33 tumor


title: TIL_EV_rep2

value: EV


title: Cre_4week_4

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data (by Novogene)
clean reads were mapped to the reference genome GRCm38 using HISAT2 (by Novogene)
HTSeq was used to count the read numbers mapped to each gene (by Novogene)
Assembly: mm38
Supplementary files format and content: Comma-separated text file containing raw count values for each sample

source_name: pancreas

growth_protocol: Pancreatic fibroblasts were isolated from KPC and CRE mice of age 4,6,8,10 12 weeks by Nycodenz density gradient method. Fibroblast were further cultured in DMEM media supplemented with 15% FBS, 1% penicillin-streptomycin, and 1% Amphotericin B at 37°C .

extract_protocol:
Total RNA isolation from fibroblast was performed using the Direct-zol RNA Microprep Kit (Zymo Research)
RNA samples were analyzed together with Novogene Co Ltd. (Cambridge, UK). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) by Novogene.

value: pancreas

value: murine pancreatic stellate cells

value: week 4


title: S-19_4h

description:
Library name: sample154
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line

value: WT

value: ARV771 treatment


title: TIL_ACSS2NLS_H4ac_rep2

data_processing:
Sequence reads were aligned to mm10 using bowtie2
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Cut&Run


title: Cre_4week_2


title: S-19_1h

description:
Library name: sample153
expression matrix (txt) and original file (fastq)


title: TIL_ACSS2NLS_H4ac_rep1


title: Cre_4week_3


title: TIL_EV_H4ac_rep2


title: S-19_0h

description:
Library name: sample152
expression matrix (txt) and original file (fastq)


title: 0x_13_5FU

value: blood

value: HSC


title: TIL_ACSS2NLS_rep1


title: TIL_EV_rep1


title: TIL_ACSS2NLS_H3K9ac_rep2


title: 0x_02_5FU


title: Cre_4week_1


title: TIL_EV_H4ac_rep1


title: 0x_01_5FU


title: S-18_1h

description:
Library name: sample150
expression matrix (txt) and original file (fastq)


title: S-18_4h

description:
Library name: sample151
expression matrix (txt) and original file (fastq)


title: Cre_6week_4

value: week 6


title: TIL_ACSS2NLS_H3K9ac_rep1


title: TIL_EV_H3K9ac_rep2


title: Cre_6week_3


title: TIL_ACSS2NLS_H3K27ac_rep2


title: S-18_0h

description:
Library name: sample149
expression matrix (txt) and original file (fastq)


title: Cre_6week_2


title: TIL_EV_H3K27ac_rep1


title: S-17_4h

description:
Library name: sample148
expression matrix (txt) and original file (fastq)


title: TIL_EV_H3K27ac_rep2


title: TIL_ACSS2NLS_H3K27ac_rep1


title: Resistant_3

city: Wuhan

first: Zhiwen

last: FU

state: Hubei

address: 1277 Jianghan District, Wuhan, China

institute: Wuhan Union Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: colorectal carcinoma cell


title: S-17_0h

description:
Library name: sample146
expression matrix (txt) and original file (fastq)


title: Cre_8week_3

value: week 8


title: TEX_sgAcly_H4ac_rep2

value: sgAcly

value: Day 6


title: S-17_1h

description:
Library name: sample147
expression matrix (txt) and original file (fastq)


title: TEX_sgAcly_H4ac_rep1

value: in vitro exhaustion culture


title: Resistant_2


title: Cre_8week_4


title: Resistant_1


title: Cre_8week_2


title: TIL_EV_H3K9ac_rep1

value: Day 21

value: B16-GP33 tumor


title: S-16_4h

description:
Library name: sample145
expression matrix (txt) and original file (fastq)


title: TEX_sgscramble_H4ac_rep2

value: sgscramble