title: experimental_2

city: Kunming

first: Yunyi

last: Lan

state: Yunnan

address: NO.519,Kunzhou Road,Xishan District

department: Molecular Diagnostic Center

institute: The Third Affiliated Hospital of Kunming Medical University

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 benchwok(parameters-mismath cost:2 insertion cost:3 length fraction:0.8 similarity fraction:0.8)
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.
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

source_name: blood

growth_protocol: no growth

extract_protocol:
RNA was harvested using RNasy® Mini Kit(Qiagen). About 500ng 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.

treatment_protocol: the leukocytes were seperated from the whole blood and were used for RNA extraction directly

value: blood

value: leukocyte

value: WT

value: Gemcitabine resistance


title: AB13514

status: Public on Feb 06 2024

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_tumor_early_HISAT_annotated.txt
Supplementary files format and content: metadata_dln_late_annotated.txt
Supplementary files format and content: metadata_tumor_late_annotated.txt
Supplementary files format and content: metadata_q_SPID_BiSE.txt

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

tag: tissue

value: tumor

tag: cell type

tag: treatment


title: AB13513

description: metadata_tumor_early_HISAT_annotated.txt

value: TCRB+


title: experimental_3

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: genotype


title: HeLa - Chip2 Subpool2 RNA Rep 1 / Chip2 Subpool4 RNA Rep 1

city: Los Angeles

first: Xinshu

middle: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive South, Room 2000E

department: Integrative Biology and Physiology

country: USA

institute: UCLA

data_processing:
Read sequences and adaptors were extracted using UMItools (v 0.5.5). The library sequences were then aligned to the designed reference sequences using Botwtie2 (version 2.3.5), allowing up to 1 mismatch per alignment. We only retained perfectly mapped reads or reads with 1 mismatch at positions other than the designed SNPs. PCR duplicates were removed by retaining only one read with the same UMI that mapped to the same reference sequence. The UMIs were then counted in the DNA- and RNA-seq libraries, respectively. The counts were quantile-normalized across the 3 biological replicates.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain UMI counts for each Sample

source_name: Uterus; Cervix

growth_protocol: HEK293/HeLa cells were maintained in DMEM (Gibco, Cat# 11995065) with 10% FBS (Gibco, Cat# 26140079) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37 °C with 5% CO2 supply.

extract_protocol:
24 hours after electroporation, HEK293/HeLa cells were lysed using TRIzol (Thermo Fisher Scientific, Cat# 15596026). Each 500 μl TRIzol-lysed solution was mixed with 100 μl chloroform (Fisher Chemical, Cat# C298-500) to allow phase separation. The upper aqueous phase was transferred and mixed with equal volume ethanol (200 proof, Fisher BioReagents). The mixture was loaded to the column supplied by the Direct-zol RNA Miniprep Plus kit (Zymo Research, Cat# R2072) to isolate total RNA following the manufacturer’s protocol. PolyA selection was carried out to isolate mRNA from total RNA using Dynabeads™ Oligo(dT)25 (Thermo Fisher Scientific, Cat# 61002).
custom DNA-Seq and RNA-Seq
The UMI-containing libraries were generated from the plasmid library (DNA) before electroporation, as well as mRNA isolated after electroporation. The mRNA was reverse transcribed into cDNA using the SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific, Cat# 18090010) and a gene-specific reverse transcription (RT) primer (MPP3) that contains a 15-mer unique molecular identifier (UMI), which was synthesized as -NNNNNNNNNNNNNNN- (See Supplementary Protocol for primer sequences). After RT, mRNA was removed via RNase H treatment. Both cDNA and plasmid DNA underwent two rounds of PCR. The first-round (3 cycles) utilized custom primers (MPP2 & MPP3) to add UMIs to the cDNA or plasmid DNA samples. The low-cycle number was utilized to minimize PCR amplification bias. The first-round PCR products were cleaned up using the DNA Clean & Concentrator kit (Zymo Research, Cat# D4004). Next, a second-round PCR was performed using the purified first-round PCR products and primers (MPP2 & MPP4), which added sample indexes and Illumina sequencing adaptors (P5/7). To avoid over-amplification, a pilot reaction for the second-step PCR was performed using the PowerUp™ SYBR® Green Master Mix (Thermo Fisher Scientific, Cat# A25742) and ran on a qPCR thermal cycler. An amplification curve was obtained for each sample to determine the cycle number before the plateau. This cycle number (or a smaller value) was then used in the second-round PCR (See Supplementary Protocol). All PCR steps for sequencing library generation were performed using the Q5 polymerase (NEB, Cat# M0492L). PCR reactions for the same sample were pooled and purified using the DNA Clean & Concentrator kit (Zymo Research, Cat# D4004). Purified PCR products were resolved on a 2% agarose gel and the band at the expected library size (377bp) was cut out and purified using the Zymoclean™ Gel DNA Recovery Kit (Zymo Research, Cat# D4002). UMI-containing libraries made from DNA/RNA were mixed and sequenced using custom sequencing primers on Illumina Hiseq3000 PE150 or Novaseq SP PE150 with 15% PhiX spike-in.

treatment_protocol: HEK293/HeLa cells were transfected with MapUTR plasmid library via electroporation and incubated in growth media at 37 °C for 24 hours before extraction.

value: Uterus; Cervix

tag: cell line

value: HeLa

value: epithelial cell


title: AB13571


title: PDSChemMap_SWP_Bio3.Tech2

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and the coresponding modified genomes, and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt. For the polymerase tracks the tracks were further rescaled, normalised for the E coli reads in the library.
Assembly: hg38 , hg38_MutMYCG4, hg38_SwapKRASG4, hg38_MYCFlip_StrandSwap, mm10
Supplementary files format and content: bigWig
Library strategy: Chemmap

molecule: genomic DNA

growth_protocol:
Human embryonic kidney (HEK293T), cells were cultured in DMEM (Dulbecco's Modified Eagle Medium, Gibco, 41966-029) growth media supplemented with 10% fetal bovine serum (Gibco, A3840401) and 2 mM L-Glutamine (Gibco, 25030024). Cells were maintained at standard conditions (5% CO2, 37°C) on TC-treated 6-well plates (Corning, 3516) and regularly tested for mycoplasma contamination (RICS, CRUK-CI Core Facility). For passaging, cells were washed with DPBS pH 7.4 (Gibco, 14190094), detached with StemPro Accutase (Gibco, A11105-01) at 37°C for 5mins and resuspended in 10-fold excess of growth media. Wild type J1 (129/Sv/Jae) mouse embryonic stem cell (mESC) cultures were routinely maintained in DMEM high glucose (Sigma, D6546) containing 10% FBS (Gibco, 16141079), 1x GlutaMax-I (Gibco, 35050-038), 1x NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148 diluted to 50 mM in 50 µM EDTA/PBS solution), 1000 U/mL recombinant LIF (PeproTech, murine LIF, 250-02) and 1 µM PD (Sigma, PZ0162-5MG), 3 µM CHIR (Cambridge biosciences, HY-10182A-5MG). Cells were cultured under standard conditions at 37°C in water saturated, CO2 (5%) enriched atmosphere on 0.2% (w/v) gelatine-coated (Sigma, G9391) plates and regularly tested for mycoplasma contamination (RICS, CRUK CI core). Authentication of mESCs was performed by mouse STR analysis (RICS, CRUK CI core). For passaging cells were washed with PBS (Gibco, 14190094), detached with TrypLE (Gibco, 12604-013) at 37°C for 5 min and resuspended in 10-fold excess of mESC growth medium as described.
Human embryonic kidney (HEK293T), cells were cultured in DMEM (Dulbecco's Modified Eagle Medium, Gibco, 41966-029) growth media supplemented with 10% fetal bovine serum (Gibco, A3840401) and 2 mM L-Glutamine (Gibco, 25030024). Cells were maintained at standard conditions (5% CO2, 37°C) on TC-treated 6-well plates (Corning, 3516) and regularly tested for mycoplasma contamination (RICS, CRUK-CI Core Facility). For passaging, cells were washed with DPBS pH 7.4 (Gibco, 14190094), detached with StemPro Accutase (Gibco, A11105-01) at 37°C for 5mins and resuspended in 10-fold excess of growth media. Wild type J1 (129/Sv/Jae) mouse embryonic stem cell (mESC) cultures were routinely maintained in DMEM high glucose (Sigma, D6546) containing 10% FBS (Gibco, 16141079), 1x GlutaMax-I (Gibco, 35050-038), 1x NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148 diluted to 50 mM in 50 µM EDTA/PBS solution), 1000 U/mL recombinant LIF (PeproTech, murine LIF, 250-02) and 1 µM PD (Sigma, PZ0162-5MG), 3 µM CHIR (Cambridge biosciences, HY-10182A-5MG). Cells were cultured under standard conditions at 37°C in water saturated, CO2 (5%) enriched atmosphere on 0.2% (w/v) gelatine-coated (Sigma, G9391) plates and regularly tested for mycoplasma contamination (RICS, CRUK CI core). Authentication of mESCs was performed by mouse STR analysis (RICS, CRUK CI core). For passaging cells were washed with PBS (Gibco, 14190094), detached with TrypLE (Gibco, 12604-013) at 37°C for 5 min and resuspended in 10-fold excess of mESC growth medium as described.

extract_protocol:
CUT&Tag and Chem-map were performed as previously described (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019),Yu, Z., et al. Nat Biotechnol (2023)).G4 mapping (BG4, SG4, SG4mut-R105A) and R-loop profiling were performed as 3-layer CUT&Tag on DynabeadsTMMyOneTMStreptavidinT1 (Thermo Fisher, cat#65601). SG4 and SG4mutR105A CUT&Tag was performed in extracted nuclei as previously described (Hui W.W.I., et al. Sci Rep (2021)). PDS Chem-map, G4 interactome CUT&Tag experiments (SP1, CNBP, MLL1, MLL4, SIN3A, SMARCA4, RNAPIIS5P, RNAPIIS2P) and histone marks (H3K4me1, H3K4me3, H3K27me) were performed as 2-layer CUT&Tag on ConcanavalinA (ConA)-coated magnetic beads (Bangs Laboratories, BP531).MyOneT1 beads were washed twice with PBS pH 6.8, resuspended in 1xPBS pH 6.8 supplemented with 0.01% Tween-20 and mixed with the biotin-conjugated ConA (Sigma-Aldrich, cat#C5275-5MG) solution at 2.3mg/mL at a 1:0.5 ratio. The mix was then incubated at 22°C at 400 rpm for 30min. Aliquots of 500,000 cells/100mL were added to 10mL of beads, washed twice with 100mL wash buffer and resuspended in 1% BSA Antibody Buffer. Primary antibodies were added (1:50), and the mix was incubated at 4°C overnight at 600 rpm. Cells were then washed twice with 100mL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH 7.5, 150 mM KCl, 0.5 mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and resuspended in 50mL dig-wash buffer. Secondary antibodies were added 1:50 to the samples and incubated at 25°C for 2h at 600 rpm (2-layer CUT&Tag). For G4-mapping samples, cells were washed three times with 500mL dig-wash buffer and resuspended in 50mL dig-wash buffer and 0.5mL of guinea-pig anti-rabbit antibody (Antibodies online, ABIN101961)was added and incubated with the cells at 25°C for 1h at 600 rpm (3-layer CUT&Tag). Cells were then washed three times with 100mL Dig-300 buffer (0.01% digitonin, 20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer at 25°C for 1h at 600rpm.Cells were then washed three times with 500 µL Dig-300 buffer and the Tn5 tagmentation was activated by incubating in 300mL Dig-300 buffer supplemented with 10 mM MgCl2at 37°C for 1h at 600 rpm. Cells were then washed twice with 500 µL TAPS buffer and resuspended in 0.5 mg/mL Proteinase K, 0.5% SDS in 10 mM Tris-HCl buffer pH 8.0 at 55°C for 1h at 800 rpm. Tagmented DNA was purified with DNA clean & concentrator columns (Zymo Research, D4013).
For Illumina library preparation, genomic DNA extracted by CUT&Tag was used. Libraries were generated as previously described with a universal i5 and a uniquely barcoded i7 primer(Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)). Libraries were visualized and quantified on a high-sensitivity D1000 tape on a Tape Station (AgilentTechnologies 2200)andwith the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S), following the manufacturer’s instructions.Libraries were sequenced on an Illumina NextSeq 500 (High Output Kit v2.5, 75 cycles) or NextSeq 2000 instrument(P2 or P3 reagents, 100 cycles). RNA-seq and library preparation Total RNA was extracted from 1.0x106 cells using the RNeasy Plus Mini Kit (Qiagen, cat#74134) as per manufacturer’s instructions. RNA quality was checked via TapeStation (Agilent Technologies 2200, RIN>9) and RNA concentration determined using a Qubit fluorometer (Thermo Fisher, Qubit 4). Libraries were generated from 700ng RNA using the NEBNext®Poly(A) mRNA Magnetic Isolation Module (NEB, cat#7490S) together with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. Libraries were sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles). For MNase 1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).

value: Human embryonic kidney

tag: chip antibody

value: btPDS, CHEMMAP


title: AB13512


title: HeLa - Chip2 Subpool1 RNA Rep 3 / Chip2 Subpool3 RNA Rep 1


title: PDSChemMap_SWP_Bio3.Tech1


title: HeLa - Chip2 Subpool1 RNA Rep 2


title: AB13511


title: sensitivity_4

value: Gemcitabine sensitivity


title: PDSChemMap_SWP_Bio2.Tech2


title: sensitivity_3


title: HeLa - Chip1 Subpool3 RNA Rep 3


title: HeLa - Chip2 Subpool2 RNA Rep 2 / Chip2 Subpool4 RNA Rep 2


title: AB13510


title: PDSChemMap_SWP_Bio2.Tech1


title: sensitivity_2


title: HeLa - Chip1 Subpool3 RNA Rep 2 / Chip3 Subpool1 RNA Rep 3


title: HeLa - Chip2 Subpool1 RNA Rep 1


title: sensitivity_1


title: PDSChemMap_SWP_Bio1.Tech1


title: sample5

value: No treatment


title: HeLa - Chip1 Subpool3 RNA Rep 1


title: AB13508

value: PBS


title: AB13507


title: PDSChemMap_MUT_Input

value: bt,CHEMMAP


title: AB13506


title: HeLa - Chip1 Subpool2 RNA Rep 2


title: HeLa - Chip1 Subpool2 RNA Rep 3


title: AB13505


title: experimental_1


title: PDSChemMap_MUT_Bio3.Tech2


title: HeLa - Chip1 Subpool2 RNA Rep 1


title: sample3


title: PDSChemMap_MUT_Bio3.Tech1


title: AB13509


title: sample2


title: AB13503


title: AB13504


title: HeLa - Chip1 Subpool1 RNA Rep 3


title: PDSChemMap_SWP_Bio1.Tech2


title: PDSChemMap_MUT_Bio2.Tech2


title: sample1


city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description:
Sarc016
Cancer-associated fibroblasts enriched from a pool of 4 mouse Undifferentiated Pleiomorphic Sarcoma p53-/-Ccne1+ tumors.

data_processing:
Cell Ranger software (10X Genomics, v6 and v7) was used to align, filter, and count reads.
The Seurat (v4) package for R was used to normalize reads and find variable features (SCTransform), perform dimensionality reduction (PCA, UMAP), cluster cells, and to filter for doublets and dead cells. Biological replicate identity (mouse ID) was demultiplexed based on oligo hashtag libraries.
Assembly: mm10
Supplementary files format and content: h5: Hierarchical data file
Supplementary files format and content: csv: original sample ID of each single-cell barcode corresponding to a high-quality cell, and associated cell metadata.

source_name: Undifferentiated Pleiomorphic Sarcoma tumor

growth_protocol: 200,000 mouse Undifferentiated Pleiomorphic Sarcoma cells bearing either p53-/-Ccne1+ or p53-/-Vgll3+ genetics were seeded onto a polyurethane scaffold (DSM Biomedical), which was then implanted subcutaneously into syngeneic Bl6 recipient mice. Tumors were grown for 3 weeks or until tumor size reached 1cm3.

extract_protocol:
Sarcoma tumors were digested into single-cell suspensions using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi) and filtered twice through 70um filters before ACK red blood cell lysis. Cells were washed in FBS-containing medium, stained with antibodies, and enriched by MACS or FACS.
Where applicable, each individual biological replicate (mouse tumors) was stained with a unique hashtag oligonucleotide antibody (Biolegend TotalSeq-A). Biolgeical replicates were then combined in equal proportions into a single pool of cells prior to capture.
For each library, 16,000 cells were loaded into one well of a 10X Genomics Chromium chip for NextGEM 3' v3.1 droplet sequencing, at a concentration between 600-1400 cells/uL, thus targeting capture of 10,000 cells per sample.
Each 10X NextGEM 3' v3.1 library was constructed according to manufacturer protocols and sequenced on the NovaSeq 6000, targeting 20,000 paired-end reads per cell for gene expression libraries, or 500 reads per cell for hashtag libraries.

tag: strain

tag: cell types_enriched_for

value: Cancer-associated fibroblast

tag: Sex

value: Female

tag: tumor genetics

tag: enrichment strategy

value: FACS Sorted Live, tumor-dsRed-, CD45-, CD31-, CD90+ cells

tag: hashtags


title: PDSChemMap_MUT_Bio2.Tech1


title: HbecWT4

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

description: CountsTableHBEC.txt

data_processing:
Align to mm10 with Rsubread
Quantification with FeatureCounts
Normalization and diffierential expression with DESeq2
Assembly: mm10, hg38
Supplementary files format and content: tab delimited file with raw counts for each sample

source_name: Brain

extract_protocol:
Rneasy Plus micro kit Qiagen
NEBNext Ultra II RNA Library Prep Kit

value: Brain

value: HBEC

value: Endothelial cell

value: wild-type


title: HeLa - Chip1 Subpool1 RNA Rep 2 / Chip2 Subpool3 RNA Rep 3


title: PDSChemMap_MUT_Bio1.Tech2


title: HeLa - Chip1 Subpool1 RNA Rep 1 / Chip2 Subpool3 RNA Rep 2


title: sample4

value: blood

value: leukocyte

value: WT


title: IRAK1 alternative allele A single cell clone 8-3-4

data_processing:
Reads were adaptor trimmed followed by read alignment using HISAT2 (v2.1.0). Uniquely mapped reads were used to calculate TPM values for each gene.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain TPM values for each sample.

source_name: kidney; Embryo

growth_protocol: Hek293T cells were maintained in DMEM (Gibco, Cat# 11995065) with 10% FBS (Gibco, Cat# 26140079) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37 °C with 5% CO2 supply.

extract_protocol:
Total RNA was extracted from HEK293T cells using TRIzol (Thermo Fisher Scientific, Cat# 15596026). Each 500 μl TRIzol-lysed solution was mixed with 100 μl chloroform (Fisher Chemical, Cat# C298-500) to allow phase separation. The upper aqueous phase was transferred and mixed with equal volume ethanol (200 proof, Fisher BioReagents). The mixture was loaded to the column supplied by the Direct-zol RNA Miniprep Plus kit (Zymo Research, Cat# R2072) to isolate total RNA following the manufacturer’s protocol.
Total RNA was used to generate RNA-Seq libraries using standard protocols at TCGB UCLA.

value: kidney; Embryo

value: epithelial cell


title: HbecWT3

description: CountsTableHBEC.txt


title: IRAK1 alternative allele A single cell clone 8-3-5


title: HbecWT2

description: CountsTableHBEC.txt


title: MNase_WT_60min_Bio2

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and the coresponding modified genomes, and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt. For the polymerase tracks the tracks were further rescaled, normalised for the E coli reads in the library.
Assembly: hg38 , hg38_MutMYCG4, hg38_SwapKRASG4, hg38_MYCFlip_StrandSwap, mm10
Supplementary files format and content: bigWig

extract_protocol:
1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4oC and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37oC for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37oC for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).
For Illumina library preparation, genomic DNA extracted by CUT&Tag was used. Libraries were generated as previously described with a universal i5 and a uniquely barcoded i7 primer(Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)). Libraries were visualized and quantified on a high-sensitivity D1000 tape on a Tape Station (AgilentTechnologies 2200)andwith the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S), following the manufacturer’s instructions.Libraries were sequenced on an Illumina NextSeq 500 (High Output Kit v2.5, 75 cycles) or NextSeq 2000 instrument(P2 or P3 reagents, 100 cycles). RNA-seq and library preparation Total RNA was extracted from 1.0x106 cells using the RNeasy Plus Mini Kit (Qiagen, cat#74134) as per manufacturer’s instructions. RNA quality was checked via TapeStation (Agilent Technologies 2200, RIN>9) and RNA concentration determined using a Qubit fluorometer (Thermo Fisher, Qubit 4). Libraries were generated from 700ng RNA using the NEBNext®Poly(A) mRNA Magnetic Isolation Module (NEB, cat#7490S) together with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. Libraries were sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles). For MNase 1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).

value: Human embryonic kidney


title: Tumor and immune cells from mouse Undifferented Pleomorphic Sarcoma p53-/-Ccne1+ and p53-/-Vgll3+ tumors (tech rep 2)

description:
Sarc011-rep2
Tumor and immune cells (Cd11b depleted) from mouse Undifferented Pleomorphic Sarcoma p53-/-Ccne1+ (n=4) and p53-/-Vgll3+ (n=4) tumors. (technical replicate 2)

value: Undifferentiated Pleiomorphic Sarcoma tumor

value: Tumor, T cells

value: MACS CD11b depletion, CD45 enrichment, Dead Cell Removal

value: p53-/-Ccne1+ tumors:TotalSeq-A hashtags 1-4. p53-/-Vgll3 tumors:TotalSeq-A hastags 5, 6, 11, 12.


title: Tumor cells enriched from mouse Undifferentiated Pleiomorphic Sarcoma tumors (p53-/-Ccne1+) (tech rep 2)

description:
Sarc004-rep2
Tumor cells enriched from mouse Undifferentiated Pleiomorphic Sarcoma tumors (p53-/-Ccne1+, n = 12), individually hashtagged (technical replicate 2)

value: Tumor, non-macrophage immune cells, cancer-associated fibroblast

value: MACS CD11b depletion, Dead Cell Removal

value: TotalSeq-A hashtags 1-12


title: IRAK1 reference allele G single cell clone 9-2


title: PDSChemMap_MUT_Bio1.Tech1

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and the coresponding modified genomes, and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt. For the polymerase tracks the tracks were further rescaled, normalised for the E coli reads in the library.
Assembly: hg38 , hg38_MutMYCG4, hg38_SwapKRASG4, hg38_MYCFlip_StrandSwap, mm10
Supplementary files format and content: bigWig
Library strategy: CYT&Tag

value: btPDS, CHEMMAP


title: Tumor cells enriched from mouse Undifferentiated Pleiomorphic Sarcoma tumors (p53-/-Ccne1+) (tech rep 1)

description:
Sarc004-rep1
Tumor cells enriched from mouse Undifferentiated Pleiomorphic Sarcoma tumors (p53-/-Ccne1+, n = 12), individually hashtagged (technical replicate 1)

value: Female


title: HCC827ASCL1, persister, rep2

city: New Haven

first: Bomiao

last: Hu

state: CT

address: 310 Cedar Street

institute: Yale University

description: HCCAP.merge.merge.RPKM.bw

data_processing:
Quality control of the reads with FastQC; trimming and adapter removal of the reads with Trimmomatic; alignment to human genome build 37 (GRCh37/hg19) reference genome with Bowtie2; marking and removal of duplicates with Picard. Samtools was used to manage SAM & BAM files.
Coverage of BAM files was obtained using deepTools bamCoverage. Kent tools from UCSC were used to generate the visualization of bigwig files, which were managed in Integrative Genomics Viewer (IGV).
The heatmaps of differentially accessible regions were made with deepTools. BAM files from replicates were merged using Samtools and the peaks were called using Macs2. Peaks were counted using featureCounts.
Annotation of peaks was performed with HOMER.
Assembly: hg19
Supplementary files format and content: bigWig files including peak information in each experimental group

growth_protocol: RPMI 1640 supplemented with 10% tet system-certified FBS, 1μg/ml doxycycline, 1mM sodium pyruvate, 10mM HEPES, 100U/ml penicillin and 100μg/ml streptomycin.

extract_protocol:
Cell nuclei were extracted with resuspension buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin, followed by tagmentation with transposase (illumina, 20034197). The tagmented DNA was purified with DNA cleanup kit (Zymo, D4014).
The tagmented DNA was amplified using NEBNext Master Mix (NEB, M0541S) to construct illumina sequencer-compatible libraries. ATAC-seq DNA libraries was purified with AMPure XP magnetic beads (Beckman Coulter, A63880) and quantified with KAPA Library Quantification Kit (KAPA, KK4854).

treatment_protocol: vehicle or 100nM osimertinib

value: human NSCLC cell line

tag: transfection

value: inducible ASCL1 transfected

value: osimertinib for 10 days


title: S87L_MEF_rep2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Adapter sequences (TruSeq universal and indexed adapters) were removed using Trimmomatic software (v0.39).
The adapter-trimmed reads were then aligned to the Mus musculus reference genome (GRCm38) using HISAT2 aligner (v2.2.1) with default options.
After filtering out duplicated reads using Picard tools (v2.25.5), the number of reads mapped to gene features (GTF file of GRCm38) were counted using HTSeq (v0.11.3).
Fragments per kilobase of transcript per million fragments mapped (FPKM) was estimated by dividing the mapped read counts by gene length and total number of reads mapped onto protein-coding genes.
Assembly: GRCm38
Supplementary files format and content: A tab-delimited text file including FPKM values for each sample

source_name: mouse fetal fibroblast

extract_protocol:
Total RNA was extracted from the spinal cord (SC) and mouse fetal fibroblast (MEF) of wild-type (WT) or Morc2a p.S87L heterozygote (S87L) mice (n=3 for WT-SC, S87L-SC, and WT-MEF; n=2 for S87L-MEF) using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA).
After quality assessment and RNA quantification, libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA).

value: mouse fetal fibroblast

value: Morc2a p.S87L heterozygote


title: IRAK1 reference allele G single cell clone 10

value: kidney; Embryo


title: Mnase_WT_40min


title: HCC827ASCL1, persister, rep1

description: HCCAP.merge.merge.RPKM.bw


title: S87L_MEF_rep1


title: Mnase.WT_20min


title: IRAK1 reference allele G single cell clone 9

value: epithelial cell


title: HCC827ASCL1, osimertinib, rep1

description: HCCAO.merge.merge.RPKM.bw

value: osimertinib for 3 days


title: FOSL2 alternative allele A single cell clone 7-1


title: HCC827ASCL1, osimertinib, rep2

description: HCCAO.merge.merge.RPKM.bw


title: WT_MEF_rep2

value: wild-type


title: MNase_MUT_60min_Bio2

value: Human embryonic kidney


title: MNase_MUT_60min_Bio1


title: HbecWT1

description: CountsTableHBEC.txt

value: Brain

value: HBEC

value: Endothelial cell


title: HCC827ASCL1, vehicle, rep2

description: HCCAV.merge.merge.RPKM.bw

value: vehicle treated


title: WT_MEF_rep1


title: HCC827ASCL1, vehicle, rep1

description: HCCAV.merge.merge.RPKM.bw


title: Tumor and immune cells from mouse Undifferented Pleomorphic Sarcoma p53-/-Ccne1+ and Vgll3+ tumors (tech rep 1)

description:
Sarc011-rep1
Tumor and immune cells (Cd11b depleted) from mouse Undifferented Pleomorphic Sarcoma p53-/-Ccne1+ (n=4) and Vgll3+ (n=4) tumors. (technical replicate 1)

value: Undifferentiated Pleiomorphic Sarcoma tumor

value: Tumor, T cells

value: p53-/-Ccne1+ and Vgll3+

value: MACS CD11b depletion, CD45 enrichment, Dead Cell Removal

value: p53-/-Ccne1+ tumors:TotalSeq-A hashtags 1-4. p53-/-Vgll3 tumors:TotalSeq-A hastags 5, 6, 11, 12.


title: FOSL2 reference allele G single cell clone 17


title: S87L_SC_rep3

source_name: spinal cord

value: spinal cord


title: Mnase.MUT_20min

extract_protocol:
1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).
For Illumina library preparation, genomic DNA extracted by CUT&Tag was used. Libraries were generated as previously described with a universal i5 and a uniquely barcoded i7 primer(Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)). Libraries were visualized and quantified on a high-sensitivity D1000 tape on a Tape Station (AgilentTechnologies 2200)andwith the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S), following the manufacturer’s instructions.Libraries were sequenced on an Illumina NextSeq 500 (High Output Kit v2.5, 75 cycles) or NextSeq 2000 instrument(P2 or P3 reagents, 100 cycles). RNA-seq and library preparation Total RNA was extracted from 1.0x106 cells using the RNeasy Plus Mini Kit (Qiagen, cat#74134) as per manufacturer’s instructions. RNA quality was checked via TapeStation (Agilent Technologies 2200, RIN>9) and RNA concentration determined using a Qubit fluorometer (Thermo Fisher, Qubit 4). Libraries were generated from 700ng RNA using the NEBNext®Poly(A) mRNA Magnetic Isolation Module (NEB, cat#7490S) together with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. Libraries were sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles). For MNase 1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).


title: HCC827EV, osimertinib, rep2

description: HCCEO.merge.merge.RPKM.bw

value: human NSCLC cell line

value: empty vector transfected


title: MNase_WT_60min_Bio1


title: FOSL2 reference allele G single cell clone 16

value: kidney; Embryo


title: Mnase_MUT_40min


title: MLL4_WT_Bio3

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and the coresponding modified genomes, and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt. For the polymerase tracks the tracks were further rescaled, normalised for the E coli reads in the library.
Assembly: hg38 , hg38_MutMYCG4, hg38_SwapKRASG4, hg38_MYCFlip_StrandSwap, mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: anti-KMT2D, ABE1867


title: WT_MEF_rep3

value: mouse fetal fibroblast


title: S87L_SC_rep2

value: Morc2a p.S87L heterozygote


title: HCC827EV, osimertinib, rep1

description: HCCEO.merge.merge.RPKM.bw

value: osimertinib for 3 days


title: MLL4_WT_Bio2

value: Human embryonic kidney


title: S87L_SC_rep1


title: MFN2 alternative allele T single cell clone 37-9

value: epithelial cell


title: FOSL2 alternative allele A single cell clone 20


title: MLL4_WT_Bio1


title: HCC827EV, vehicle, rep2

description: HCCEV.merge.merge.RPKM.bw


title: HCC827EV, vehicle, rep1

description: HCCEV.merge.merge.RPKM.bw


title: WT_SC_rep3

value: wild-type


title: MFN2 alternative allele T single cell clone 37-6


title: FOSL2 alternative allele A single cell clone 4


title: MLL4_SWP_Bio3


title: WT_SC_rep2


title: MFN2 alternative allele T single cell clone 51


title: PC9ASCL1, osimertinib, rep2

value: inducible ASCL1 transfected


title: WT_SC_rep1


title: PC9ASCL1, osimertinib, rep1


title: MLL4_SWP_Bio2


title: MLL4_SWP_Bio1


title: MFN2 reference allele G single cell clone 4


title: MLL4_MUT_Bio3


title: MFN2 reference allele G single cell clone 6


title: FOSL2 reference allele G single cell clone 3


title: MLL4_MUT_Bio2


title: BMCC, Nbeal2 -/-, IL-33 treatment, rep 3 [NB3_33]

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
Mapping of reads was done using Top Hat (v2.1, parameters: --no-convert-bam--no-coverage-search -x 1 -g 1)
All reads mapped to an Ensembl gene were counted using FeatureCounts v1.6.5 (parameters: -s 2).
Assembly: GRCm38.100
Supplementary files format and content: excel file containing reads counts, RPMs and RPKMs per gene over all samples

source_name: Bone Marrow Mononuclear Cells (BMMCs)

extract_protocol:
Total RNA from wt or Nbeal2-/- BMMCs was isolated by using Qiazol reagent (Qiagen).
Libraries were prepared from 500 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) following the manufacturer's instructions (New England Biolabs).

tag: strain background

value: Bone Marrow Mononuclear Cells (BMMCs)

value: IL-33 treatment


title: BMCC, Nbeal2 -/-, IL-33 treatment, rep 4 [NB4_33]


title: MLL4_MUT_Bio1


title: PC9EV, osimertinib, rep2


title: BMCC, Nbeal2 -/-, no treatment, rep 3 [NB3_wo33]

value: no treatment


title: PC9EV, osimertinib, rep1


title: WES - Pt20_PT

city: Guangzhou

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University First Affiliated Hospital

data_processing:
The adaptor sequence was removed, then reads with high quality were gapped aligned to the NCBI human reference genome (hg38) using BWA by default parameters.
Copy number calling was conducted following the pipeline of CNVkit.
Assembly: hg38
Supplementary files format and content: Copy number segmented format file (CNVkit output file)
Library strategy: Whole-exome sequencing

source_name: tumor (primary tumor of colorectal cancer)

extract_protocol:
Total DNA was extracted from the snap frozen tissues using QIAGEN DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).
The qualified genomic DNA of tissue samples was fragmented to 200-300 bp by Covaris technology with resultant library, and then adapters were ligated to both ends of the fragments. Extracted DNA was amplified by ligation-mediated PCR (LM-PCR), then purified and hybridized to the Agilent human exome array for enrichment. The library was sequenced on the Illumina NovaSeq 6000 platform.


title: WES - Pt20_LM

source_name: tumor (liver metastasis of colorectal cancer)


title: BMCC, Nbeal2 -/-, IL-33 treatment, rep 2 [NB2_33]


title: PC9EV, vehicle, rep2

value: vehicle treated


title: MLL1_WT_Bio3

value: anti-KMT2A EMC Millipore, 05-765


title: MLL1_WT_Bio2


title: WES - Pt19_LM

value: tumor (liver metastasis of colorectal cancer)


title: PC9EV, vehicle, rep1

value: human NSCLC cell line


title: BMCC, Nbeal2 -/-, no treatment, rep 2 [NB2_wo33]


title: WES - Pt19_PT

value: tumor (primary tumor of colorectal cancer)


title: WES - Pt18_PT


title: YU-006 PDX, residual

description: 10X Genomics

data_processing:
The single-cell sequencing raw data were processed and mapped to a human-mouse hybrid genome to distinguish between human and mouse cells.
Gene expression matrix for human cells is generated by Cell Ranger pipeline and analyzed using Seurat package.
Genes whose expression is identified in at least three cells will be considered as features and cells with number of feature genes greater than 200 but smaller than 7000 and percentage of mitochondria reads less than 50% were included in the following analyses.
The single-cell expression data were normalized by SCTransform embedded in Seurat and then underwent linear dimensional reduction through PCA. The first 100 principal components were used to cluster cells, with a resolution of 0.4.
The clustering results were visualized in UMAP plot.
Assembly: hg38
Supplementary files format and content: matrix files

source_name: Patient-derived xenograft

growth_protocol: Dissociated PDX tissues were implanted subcutaneously into NSG mice. Treatment was started as the tumors grew to appropriate size.

extract_protocol:
Subcutaneous PDX tumors were resected from mice and processed with tumor dissociation kit (Miltenyi Biotech, 130-095-929). The single-cell suspension was stained with human EpCAM antibody (BioLegend, 324209, 1:100) and LIVE/DEAD cell stain (invitrogen, L34971, 1:250), and subjected to FACS to isolate live tumor cells.
The sorted cells were re-suspended in FACS buffer and loaded on the Single Cell A Chip together with RT Master Mix and barcoded gel beads to form nanoliter-scale Gel Beads in Emulsions (GEMs) through Chromium Controller. The single-cell cDNA libraries were constructed using 3’ library prep kit v3 (10X genomics).

treatment_protocol: Mice were treated with with osimertinib at 25mg/kg for five consecutive days each week. The treatment lasted for 6 weeks before drug tolerant residual tumor was excised.

value: Patient-derived xenograft

value: Tumor cells

value: Osimertinib for 6 weeks


title: BMCC, Nbeal2 -/-, IL-33 treatment, rep 1 [NB1_33]


title: PC9ASCL1, vehicle, rep1


title: PC9ASCL1, vehicle, rep2


title: MLL1_SWP_Bio3


title: MLL1_WT_Bio1


title: BMCC, Nbeal2 -/-, no treatment, rep 4 [NB4_wo33]


title: MFN2 reference allele G single cell clone 2

value: kidney; Embryo


title: MLL1_SWP_Bio2


title: WES - Pt17_PT


title: BMCC, WT, IL-33 treatment, rep 4 [WT4_33]

value: WT


title: YU-006 PDX, untreated

description: 10X Genomics

value: Untreated


title: YU-003 PDX, residual

description: 10X Genomics


title: BMCC, Nbeal2 -/-, no treatment, rep 1 [NB1_wo33]


title: WES - Pt17_LM


title: MLL1_SWP_Bio1

value: Human embryonic kidney


title: WES - Pt16_LM


title: YU-003 PDX, untreated

description: 10X Genomics


title: BMCC, WT, IL-33 treatment, rep 3 [WT3_33]


title: MLL1_MUT_Bio3


title: BMCC, WT, no treatment, rep 4 [WT4_wo33]


title: BEND3WT4

value: Brain

value: Endothelial cell

value: wild-type


title: WES - Pt15_LM


title: BMCC, WT, no treatment, rep 3 [WT3_wo33]

value: Bone Marrow Mononuclear Cells (BMMCs)


title: BEND3WT3


title: BMCC, WT, IL-33 treatment, rep 2 [WT2_33]

value: IL-33 treatment


title: WES - Pt15_PT


title: BEND3WT2


title: MLL1_MUT_Bio2


title: H3K4me3_WT_Bio3

value: anti-H3K4me3, Abcam, ab8580


title: WES - Pt13_PT


title: H3K4me3_WT_Bio2


title: BMCC, WT, IL-33 treatment, rep 1 [WT1_33]


title: NIH-3T3 cells, 800 µM 4sU, TUC-seq, rep B

city: Würzburg

first: Kevin

last: Berg

address: Versbacher Str. 7

institute: University of Würzburg

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt, reads with length < 18 were removed
Trimmed sequence reads were mapped to rRNA (U13369.1) and Mycoplasma database using bowtie2 (v. 2.3.0). Mapped reads were filtered out
Trimmed and filtered sequence reads were mapped to the mouse genome (ensembl 102) using STAR v. 2.7.10b (parameters: --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH –outSAMunmapped Within)
Subsequent analyses were conducted in R.
Assembly: mus musculus (ensembl 90)
Supplementary files format and content: Tab-separated values files

growth_protocol: NIH-3T3 cells were grown in DMEM supplemented with 100 IU/mL Penicillin and, 100 g/mL Streptomycin and supplemented with 10% NCS at 37°C, 5% CO2

extract_protocol:
Cells were harvested using TRI reagent (Sigma) and RNA isolation was conducted using the Zymo DirectZol RNA-microprep kit (R2062) as described by the manufacturer and re-suspended in 1X PBS buffer
SLAM-seq was conducted using IAA to mediate U>C conversions at 50oC/20 minutes. The reaction was quenched using excess DTT. RNA was then purified using RNeasy Mini elute kit (Qiagen). TUC chemistry was performed by incubation with OsO4/NH4C for 1h at 40°C. RNA was purified by precipitation.
Nucleotide conversion  RNA-seq (SLAM-/TUC-seq)

treatment_protocol: Cells were treated with 800 µM Uridine or 800 µM 4sU for 2 hours.

value: fibroblast cells

value: 800 uM 4sU

tag: protocol

value: TUC-seq


title: BMCC, WT, no treatment, rep 2 [WT2_wo33]

value: no treatment


title: WES - Pt11_LM

value: tumor (liver metastasis of colorectal cancer)


title: BMCC, WT, no treatment, rep 1 [WT1_wo33]


title: BEND3WT1


title: WES - Pt11_PT

value: tumor (primary tumor of colorectal cancer)


title: H3K4me3_WT_Bio1


title: WES - Pt10_LM


title: H3K4me3_SWP_Bio3


title: NIH-3T3 cells, 800 µM 4sU, SLAM-seq, rep B

value: SLAM-seq


title: WNK1 deficient and littermate controls

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GRCm38 - M. musculus
Supplementary_files_format_and_content: .tsv file with counts

extract_protocol:
Single cells were sort purified and loaded into droplets using 10X Chromium
mRNA library was prepared using the Illumina TruSeq platform

treatment_protocol: MPP3s were isolated from CSF1R-Cre x WNK1 flox mice or littermate controls

tag: origin

value: FACS sort purified

tag: mixed sample

value: Hashtagged Kos and WTs

value: Lin- cKit+ Sca-1+ Flt3- CD48+ CD150-


title: NIH-3T3 cells, 800 µM 4sU, TUC-seq, rep A

value: WT


title: WES - Pt10_PT

tag: tissue


title: MLL1_MUT_Bio1

tag: cell type

value: Human embryonic kidney

value: anti-KMT2A EMC Millipore, 05-765


title: NIH-3T3 cells, 800 µM 4sU, SLAM-seq, rep A

tag: treatment


title: H3K4me3_SWP_Bio2


title: H3K4me3_SWP_Bio1


title: NIH-3T3 cells, 800 µM 4sU, rep B

tag: genotype


title: H3K4me3_MUT_Bio3

tag: cell line


title: WES - Pt08_PT1


title: NIH-3T3 cells, 800 µM 4sU, rep A


title: WES - Pt08_LM


title: WES - Pt07_LM


title: H3K4me3_MUT_Bio2

tag: chip antibody


title: WES - Pt07_PT


title: H3K4me1_WT_Bio3

value: anti-H3K4me1, Abcam, ab8895


title: NIH-3T3 cells, 800 µM Uridine, rep B

value: 800 uM Uridine


title: NIH-3T3 cells, 800 µM Uridine, rep A


title: H3K4me3_MUT_Bio1


title: H3K4me1_WT_Bio2


title: NIH-3T3 cells, no treatment, rep A


title: WES - Pt06_LM1


title: NIH-3T3 cells, no treatment, rep B


title: H3K4me1_WT_Bio1


title: WES - Pt08_PT2


title: Lig_48h_1

type: RNA

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Ciona intestinalis custom-designed array (CINT06a520380F - GPL15657) according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files imported into Affymetrix Expression Console software and processed with the custom annotation file and RMA.

label: biotin

organism: Ciona intestinalis

source_name: Heart, ligated, 48h

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: Ciona intestinalis adults (7-12 cm) were obtained by M-REP (San Diego, CA).  The animals were maintained in a 65-gallon saltwater tank equipped with appropriate water circulation and filtration system.

extract_protocol: Total RNA was isolated by RNeasy Mini Kit (Qiagen) from injured and control hearts at 24h or 48h following treatment.

treatment_protocol: Samples were prepared from control hearts (exposed but not ligated) or injured hearts (ligated or cryo injury) at 24h or 48h following treatment with two biological replicates per sample type. To set up ligations, hearts were exposed via a 3 cm incision in the animal’s tunic. Surgical silk (4 cm pieces of 000 gauge (Ethicon, NJ)) was tied around the exposed heart apex.  Animals were placed in separate baskets for a 24- or 48-hour recovery period.  At the end of each of these periods, hearts that were still visibly beating were processed for analysis. A minimum of 4 hearts per group was done for each experiment.

value: heart

tag: injury

value: ligated

tag: time point


title: Cry_48h_2

source_name: Heart, cryo injury, 48h

value: cryo


title: Cry_48h_1


title: sRNA-Yak-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
The raw data in fastq format was removed by Trimmomatic software to remove adapters, remove poly-N reads and low-quality reads, and obtain clean reads. Clean reads were aligned to the cattle genome using HISAT2 (version 2.0.5) (version: Bos_taurus.UMD3.1). The mapped reads of each sample were assembled by StringTie (v1.3.4) in a reference-based approach. Cufflinks was used to calculated FPKM (Fragments Per Kilobase of exon Model per million mapped fragments) values of transcripts.
The raw data in fastq format is used to remove joints and low-quality reads by custom perl and python scripts. Bowtie was used to map small RNAs with a length range of 18-35 nt to the reference genome. Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself. The signature hairpin structure of miRNA precursors can be used to predict new miRNAs, and integrate miREvo and mirdeep2 miRNA prediction software to analyze new miRNAs. miRNA expression levels were estimated by TPM through the criteria。The predicted miRNA target genes were the intersection results of miRanda, PITA and RNAhybrid.
Assembly: Bos_taurus.UMD3.1
Supplementary files format and content: Excle include FPKM/TPM values for each Sample...

organism: Bos grunniens

source_name: testis

growth_protocol: Four-year-old cattle, yaks and cattle-yaks ( three each ) were selected from the same cooperative in Gannan Tibetan Autonomous Prefecture for castration.

extract_protocol:
Total RNA was extracted from each testicular sample using TRIzol reagent. RNA quality was assessed using Nanodrop-2000 and 1% agarose gel electrophoresis.
RNA-seq：A total amount of 5μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit (Epicentre, USA). Second, the sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Third, the library quality was assessed on the Agilent Bioanalyzer 2100 system. At last, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. And sequencing the library on the Illumina Hiseq 2500 platform and and 125bp.paired -end reads were generated.      miRNA-seq：A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA high sensitivity chips. After clustering the samples, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50 bp single-end reads were generated.

treatment_protocol: The testicular tissue was washed with PBS and quickly placed in a freezer tube, immediately stored in liquid nitrogen.

value: testis

value: Four years old


title: Con_48h_2

source_name: Heart, exposed but unligated, 48h

value: not injured


title: Lig_48h_2


title: Con_48h_1


title: H3K4me1_SWP_Bio3


title: WES - Pt06_PT


title: sRNA-Yak-2


title: WES - Pt05_LM2

value: tumor (liver metastasis of colorectal cancer)


title: H3K4me1_SWP_Bio2


title: Lig_24h_2

source_name: Heart, ligated, 24h


title: sRNA-Yak-1


title: WES - Pt06_LM2


title: WES - Pt05_PT

value: tumor (primary tumor of colorectal cancer)


title: H3K4me1_SWP_Bio1


title: H3K4me1_MUT_Bio3


title: Cry_24h_2

source_name: Heart, cryo injury, 24h


title: WES - Pt04_PT


title: Yak-2


title: H3K4me1_MUT_Bio2


title: HEK293 - Chip3 Subpool1 RNA Rep 3

data_processing:
Read sequences and adaptors were extracted using UMItools (v 0.5.5). The library sequences were then aligned to the designed reference sequences using Botwtie2 (version 2.3.5), allowing up to 1 mismatch per alignment. We only retained perfectly mapped reads or reads with 1 mismatch at positions other than the designed SNPs. PCR duplicates were removed by retaining only one read with the same UMI that mapped to the same reference sequence. The UMIs were then counted in the DNA- and RNA-seq libraries, respectively. The counts were quantile-normalized across the 3 biological replicates.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain UMI counts for each Sample

value: kidney; Embryo

value: epithelial cell


title: Lig_24h_1


title: Cry_24h_1


title: Con_24h_2

source_name: Heart, exposed but unligated, 24h


title: Yak-1


title: WES - Pt02_LM


title: WES - Pt03_PT


title: Con_24h_1


title: LTS3_LTS

city: Xuzhou

first: Jiahao

last: Zhu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GT4SP_v3
Supplementary files format and content: excel files include count values for each sample

organism: Ipomoea batatas

source_name: root

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

value: 4 C


title: HEK293 - Chip3 Subpool1 RNA Rep 1

extract_protocol:
24 hours after electroporation, HEK293/HeLa cells were lysed using TRIzol (Thermo Fisher Scientific, Cat# 15596026). Each 500 μl TRIzol-lysed solution was mixed with 100 μl chloroform (Fisher Chemical, Cat# C298-500) to allow phase separation. The upper aqueous phase was transferred and mixed with equal volume ethanol (200 proof, Fisher BioReagents). The mixture was loaded to the column supplied by the Direct-zol RNA Miniprep Plus kit (Zymo Research, Cat# R2072) to isolate total RNA following the manufacturer’s protocol. PolyA selection was carried out to isolate mRNA from total RNA using Dynabeads™ Oligo(dT)25 (Thermo Fisher Scientific, Cat# 61002).
custom DNA-Seq and RNA-Seq
The UMI-containing libraries were generated from the plasmid library (DNA) before electroporation, as well as mRNA isolated after electroporation. The mRNA was reverse transcribed into cDNA using the SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific, Cat# 18090010) and a gene-specific reverse transcription (RT) primer (MPP3) that contains a 15-mer unique molecular identifier (UMI), which was synthesized as -NNNNNNNNNNNNNNN- (See Supplementary Protocol for primer sequences). After RT, mRNA was removed via RNase H treatment. Both cDNA and plasmid DNA underwent two rounds of PCR. The first-round (3 cycles) utilized custom primers (MPP2 & MPP3) to add UMIs to the cDNA or plasmid DNA samples. The low-cycle number was utilized to minimize PCR amplification bias. The first-round PCR products were cleaned up using the DNA Clean & Concentrator kit (Zymo Research, Cat# D4004). Next, a second-round PCR was performed using the purified first-round PCR products and primers (MPP2 & MPP4), which added sample indexes and Illumina sequencing adaptors (P5/7). To avoid over-amplification, a pilot reaction for the second-step PCR was performed using the PowerUp™ SYBR® Green Master Mix (Thermo Fisher Scientific, Cat# A25742) and ran on a qPCR thermal cycler. An amplification curve was obtained for each sample to determine the cycle number before the plateau. This cycle number (or a smaller value) was then used in the second-round PCR (See Supplementary Protocol). All PCR steps for sequencing library generation were performed using the Q5 polymerase (NEB, Cat# M0492L). PCR reactions for the same sample were pooled and purified using the DNA Clean & Concentrator kit (Zymo Research, Cat# D4004). Purified PCR products were resolved on a 2% agarose gel and the band at the expected library size (377bp) was cut out and purified using the Zymoclean™ Gel DNA Recovery Kit (Zymo Research, Cat# D4002). UMI-containing libraries made from DNA/RNA were mixed and sequenced using custom sequencing primers on Illumina Hiseq3000 PE150 or Novaseq SP PE150 with 15% PhiX spike-in.


title: LTS2_LTS


title: H3K27me3_WT_Bio3

extract_protocol:
CUT&Tag and Chem-map were performed as previously described (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019),Yu, Z., et al. Nat Biotechnol (2023)).G4 mapping (BG4, SG4, SG4mut-R105A) and R-loop profiling were performed as 3-layer CUT&Tag on DynabeadsTMMyOneTMStreptavidinT1 (Thermo Fisher, cat#65601). SG4 and SG4mutR105A CUT&Tag was performed in extracted nuclei as previously described (Hui W.W.I., et al. Sci Rep (2021)). PDS Chem-map, G4 interactome CUT&Tag experiments (SP1, CNBP, MLL1, MLL4, SIN3A, SMARCA4, RNAPIIS5P, RNAPIIS2P) and histone marks (H3K4me1, H3K4me3, H3K27me) were performed as 2-layer CUT&Tag on ConcanavalinA (ConA)-coated magnetic beads (Bangs Laboratories, BP531).MyOneT1 beads were washed twice with PBS pH 6.8, resuspended in 1xPBS pH 6.8 supplemented with 0.01% Tween-20 and mixed with the biotin-conjugated ConA (Sigma-Aldrich, cat#C5275-5MG) solution at 2.3mg/mL at a 1:0.5 ratio. The mix was then incubated at 22°C at 400 rpm for 30min. Aliquots of 500,000 cells/100mL were added to 10mL of beads, washed twice with 100mL wash buffer and resuspended in 1% BSA Antibody Buffer. Primary antibodies were added (1:50), and the mix was incubated at 4°C overnight at 600 rpm. Cells were then washed twice with 100mL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH 7.5, 150 mM KCl, 0.5 mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and resuspended in 50mL dig-wash buffer. Secondary antibodies were added 1:50 to the samples and incubated at 25°C for 2h at 600 rpm (2-layer CUT&Tag). For G4-mapping samples, cells were washed three times with 500mL dig-wash buffer and resuspended in 50mL dig-wash buffer and 0.5mL of guinea-pig anti-rabbit antibody (Antibodies online, ABIN101961)was added and incubated with the cells at 25°C for 1h at 600 rpm (3-layer CUT&Tag). Cells were then washed three times with 100mL Dig-300 buffer (0.01% digitonin, 20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer at 25°C for 1h at 600rpm.Cells were then washed three times with 500 µL Dig-300 buffer and the Tn5 tagmentation was activated by incubating in 300mL Dig-300 buffer supplemented with 10 mM MgCl2at 37°C for 1h at 600 rpm. Cells were then washed twice with 500 µL TAPS buffer and resuspended in 0.5 mg/mL Proteinase K, 0.5% SDS in 10 mM Tris-HCl buffer pH 8.0 at 55°C for 1h at 800 rpm. Tagmented DNA was purified with DNA clean & concentrator columns (Zymo Research, D4013).
For Illumina library preparation, genomic DNA extracted by CUT&Tag was used. Libraries were generated as previously described with a universal i5 and a uniquely barcoded i7 primer(Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)). Libraries were visualized and quantified on a high-sensitivity D1000 tape on a Tape Station (AgilentTechnologies 2200)andwith the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S), following the manufacturer’s instructions.Libraries were sequenced on an Illumina NextSeq 500 (High Output Kit v2.5, 75 cycles) or NextSeq 2000 instrument(P2 or P3 reagents, 100 cycles). RNA-seq and library preparation Total RNA was extracted from 1.0x106 cells using the RNeasy Plus Mini Kit (Qiagen, cat#74134) as per manufacturer’s instructions. RNA quality was checked via TapeStation (Agilent Technologies 2200, RIN>9) and RNA concentration determined using a Qubit fluorometer (Thermo Fisher, Qubit 4). Libraries were generated from 700ng RNA using the NEBNext®Poly(A) mRNA Magnetic Isolation Module (NEB, cat#7490S) together with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. Libraries were sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles). For MNase 1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).

value: anti-H3K27me3. Cell signaling, 9733


title: WES - Pt02_PT


title: Yak-3


title: HEK293 - Chip2 Subpool4 RNA Rep 3


title: WES - Pt05_LM1


title: H3K27me3_WT_Bio2

value: Human embryonic kidney


title: HEK293 - Chip2 Subpool4 RNA Rep 2


title: H3K27me3_WT_Bio1


title: LTS1_LTS


title: CK3_CK

value: untreated


title: H3K27me3_MUT_Bio3


title: WES - Pt01_PT


title: CK2_CK


title: RNA-Seq - Pt20PT

data_processing:
The quality control of RNA-Seq raw data was performed by FastQC.
Qualified reads were obtained after removing raw reads with adapters or of low quality. We applied HISAT2 and RSeQC pipeline to quantify gene expression level, with GRCh38 as the reference genome.
Assembly: hg38
Supplementary files format and content: Comma-separated values file includes raw count for each Sample

extract_protocol:
Total RNA was extracted from tumor tissues using Qiagen kits.
Samples were collected and RNA libraries were prepared using the TruSeq stranded kit, sequenced on the Illumina NovaSeq 6000 platform


title: HEK293 - Chip2 Subpool4 RNA Rep 1


title: H3K4me1_MUT_Bio1

value: anti-H3K4me1, Abcam, ab8895


title: HEK293 - Chip3 Subpool1 RNA Rep 2


title: RNA-Seq - Pt20LM


title: CK1_CK


title: HEK293 - Chip2 Subpool3 RNA Rep 3


title: H3K27me3_MUT_Bio1


title: HEK293 - Chip2 Subpool3 RNA Rep 2


title: ATS3_ATS


title: RNA-Seq - Pt19LM


title: WES - Pt01_LM


title: ATS2_ATS


title: HEK293 - Chip2 Subpool3 RNA Rep 1


title: CNBP_WT_Bio2

value: anti-CNBP, Protein Tech, 67109-Ig


title: CNBP_WT_Bio3


title: RNA-Seq - Pt18PT


title: RNA-Seq - Pt17PT


title: sRNA-Dzo-3

organism: Bos grunniens x Bos taurus


title: HEK293 - Chip2 Subpool2 RNA Rep 2


title: HEK293 - Chip2 Subpool2 RNA Rep 1


title: CNBP_SWP_Bio3


title: ATS1_ATS


title: sRNA-Dzo-2


title: CNBP_WT_Bio1


title: sRNA-Dzo-1


title: RNA-Seq - Pt16LM


title: HEK293 - Chip2 Subpool1 RNA Rep 3


title: H3K27me3_MUT_Bio2


title: RNA-Seq - Pt19PT


title: CNBP_SWP_Bio1


title: Dzo-3


title: CNBP_SWP_Bio2


title: HEK293 - Chip2 Subpool1 RNA Rep 2


title: HEK293 - Chip2 Subpool1 RNA Rep 1


title: CNBP_MUT_Bio3


title: Dzo-2


title: RNA-Seq - Pt15LM


title: HEK293 - Chip2 Subpool2 RNA Rep 3


title: CNBP_MUT_Bio2


title: RNA-Seq - Pt15PT


title: HEK293 - Chip1 Subpool3 RNA Rep 3


title: RNA-Seq - Pt13PT


title: CNBP_MUT_Bio1


title: HEK293 - Chip1 Subpool3 RNA Rep 2


title: RNA-Seq - Pt11PT


title: D5 inshore, treatment, 31 days

city: Miammi

first: Catalina

last: Aguilar

state: Florida

address: 4600 Rickenbacker Causeway

department: Rosenstiel School of Marine, Atmospheric & Earth Science

institute: University of Miami

data_processing:
Adapters and low-quality reads were removed in Trimmomatic v0.36 (phred33, quality score > 20, 4 bp sliding window; Bolger, Lohse, and Usadel 2014)
The reads were used for de novo assembly in Trinity v2.5.1  (https://github.com/trinityrnaseq/trinityrnaseq/wiki, Grabherr et al., 2011).
After the assembly, a Trinity script (get_longest_isoform_seq_per_trinity_gene.pl) was used to select the longest isoform per gene.
The metatranscriptome was filtered by performing BLASTx (e-value < 1e−5) searches against two coral proteomes, and BLASTn (e-value < 1e−5) searches against four Symbiodiniaceae genomes (as of June, 2018) (coral: Acropora digifitera and Orbicella faveolata. Symbiodiniaceae: Symbiodinium microadriaticum; Breviolum minutum; Cladocopium goreaui; Durusdinium trenchii).
Trinity scripts (Grabherr et al., 2011) were used to map the reads back to both transcriptomes using the alignment-based abundance estimation method RSEM (RNA-Seq by Expectation-Maximization) and to build an expression matrix from the transcript abundance files.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Orbicella faveolata

source_name: coral tissue

extract_protocol:
Total RNA was extracted using the total RNAqueous kit (AM1912, Life Technologies), according to the manufacturer’s instructions
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit following the manufacturer’s protocol at the Duke Center for Genomic and Computational Biology

treatment_protocol: Following acclimation, temperatures were gradually increased at different rates over an additional seven days to reach one of three elevated temperatures (31C, 32C, 33C), or control (30C).

value: coral tissue

value: not applicable

tag: time


title: BG4_WT_Input


title: RNA-Seq - Pt11LM


title: RNA-Seq - Pt17LM


title: D4 inshore, treatment, 31 days


title: BG4_WT_Bio3.Tech2


title: RNA-Seq - Pt10PT


title: D3 inshore, treatment, 31 days


title: BG4_WT_Bio3.Tech1


title: C5 offshore, treatment, 31 days


title: HEK293 - Chip1 Subpool2 RNA Rep 3


title: RNA-Seq - Pt10LM


title: BG4_WT_Bio2.Tech2


title: RNA-Seq - Pt08PT2


title: HEK293 - Chip1 Subpool2 RNA Rep 2


title: RNA-Seq - Pt08PT1


title: BG4_WT_Bio2.Tech1


title: HEK293 - Chip1 Subpool1 RNA Rep 3


title: HEK293 - Chip1 Subpool2 RNA Rep 1


title: HEK293 - Chip1 Subpool1 RNA Rep 2


title: BLY5 inshore, treatment, 31 days


title: RNA-Seq - Pt08LM


title: Dzo-1


title: BG4_WT_Bio1.Tech2


title: HEK293 - Chip1 Subpool1 RNA Rep 1


title: BG4_WT_Bio1.Tech1


title: B3 inshore, treatment, 31 days


title: HEK293 - Chip1 Subpool3 RNA Rep 1


title: RNA-Seq - Pt07PT


title: BG4_SWP_Input2


title: Chip3 Subpool1 Pre-transfection DNA Rep 3

library_source: other

molecule: other

tag: molecule subtype

value: Pre-transfection plasmid DNA


title: RNA-Seq - Pt07LM


title: B2 inshore, treatment, 31 days


title: BG4_SWP_Input


title: Chip3 Subpool1 Pre-transfection DNA Rep 2


title: A5 inshore, treatment, 31 days


title: RNA-Seq - Pt06PT


title: C4 offshore, treatment, 31 days


title: RNA-Seq - Pt06LM2


title: C2 offshore, treatment, 31 days


title: BG4_SWP_Bio3.Tech2


title: Chip3 Subpool1 Pre-transfection DNA Rep 1


title: Chip2 Subpool4 Pre-transfection DNA Rep 3


title: A2 inshore, treatment, 31 days


title: RNA-Seq - Pt05PT


title: BG4_SWP_Bio3.Tech1


title: RNA-Seq - Pt06LM1


title: D6 inshore, control, 31 days


title: BG4_SWP_Bio2.Tech2


title: Chip2 Subpool4 Pre-transfection DNA Rep 2


title: Chip2 Subpool4 Pre-transfection DNA Rep 1


title: RNA-Seq - Pt05LM1


title: D5 inshore, control, 31 days


title: BG4_SWP_Bio2.Tech1


title: Chip2 Subpool3 Pre-transfection DNA Rep 3


title: Chip2 Subpool3 Pre-transfection DNA Rep 2


title: BG4_SWP_Bio1.Tech1


title: BG4_MUT_Input


title: RNA-Seq - Pt02PT


title: D4 inshore, control, 31 days


title: Chip2 Subpool3 Pre-transfection DNA Rep 1


title: RNA-Seq - Pt02LM


title: C4 offshore, control, 31 days


title: Chip2 Subpool2 Pre-transfection DNA Rep 3


title: RNA-Seq - Pt01PT


title: BG4_MUT_Bio3.Tech2


title: BG4_MUT_Bio3.Tech1


title: Chip2 Subpool2 Pre-transfection DNA Rep 2


title: C2 offshore, control, 31 days


title: RNA-Seq - Pt05LM2


title: BLY5 inshore, control, 31 days


title: BG4_MUT_Bio2.Tech2


title: RNA-Seq - Pt01LM


title: Chip2 Subpool1 Pre-transfection DNA Rep 3


title: BG4_MUT_Bio2.Tech1


title: Chip2 Subpool2 Pre-transfection DNA Rep 1


title: BG4_SWP_Bio1.Tech2


title: C5 offshore, control, 31 days


title: B3 inshore, control, 31 days


title: B2 inshore, control, 31 days


title: Non responder-P8

first: Yexing

last: Huang

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
The bcl2Fastq software (version 2.1.7), with default parameter, converts basecalls from Illumina High Throughput Sequencing (HTS) machines to fastQ files containing sequence information ready for further analysis.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default parameter (version 0.23.4)
Trimmed sequence reads were mapped to hg38 using STAR software with default parameter(version 2.7.10b)
Read count extraction using featureCounts (version 2.0.6) in pair-end mode
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
In brief, RNA was extracted using TRIZOL/Chlorophorm/Phenol method.
The Illumina RNA Library Prep kit (NEBNext® UltraTM) was used. The libraries were tagged with unique adapter indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qRT-PCR, pooled at equimolar ratios, diluted, denatured, and loaded onto an Illumina novaseq 6000

value: Liver

value: intrahepatic cholangiocarcinoma

value: FOLFOX-HAIC+Lenvatinib+PD-1 blockade

tag: group

value: Non responder


title: Non responder-P9


title: A5 inshore, control, 31 days


title: BG4_MUT_Bio1.Tech1


title: Chip2 Subpool1 Pre-transfection DNA Rep 2


title: Non responder-P6


title: A4 inshore, control, 31 days


title: Chip2 Subpool1 Pre-transfection DNA Rep 1


title: A2 inshore, control, 31 days


title: HCT116 cells, 400 µM

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt, reads with length < 18 were removed
Trimmed sequence reads were mapped to rRNA (U13369.1) and Mycoplasma database using bowtie2 (v. 2.3.0). Mapped reads were filtered out
Trimmed and filtered sequence reads were mapped to the human genome (ensembl 90) using STAR v. 2.7.10b (parameters: --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH –outSAMunmapped Within)
Subsequent analyses were conducted in R.
Assembly: homo sapiens (ensembl 90)
Supplementary files format and content: Tab-separated values files
Library strategy: SLAM-seq

growth_protocol: Human U2OS, HFF-TerT and HCT 116 cells were cultured in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C, 5% CO2

extract_protocol:
Cells subject to 4sU-labeling were harvested using TRI reagent (Sigma) and RNA isolation was conducted using the Zymo DirectZol RNA-microprep kit (R2062) as described by the manufacturer and re-suspended in 1X PBS buffer
SLAM-seq was conducted using IAA to mediate U>C conversions at 50oC/20 minutes. The reaction was quenched using excess DTT. RNA was then purified using RNeasy Mini elute kit (Qiagen)

treatment_protocol: Cells were treated with 0, 100, 200, 400 or 800 µM 4sU for 1h.

value: colon carcinoma cells

value: WT

value: 400 microM 4sU

value: 2 hours


title: Non responder-P5


title: Chip1 Subpool3 Pre-transfection DNA Rep 3


title: D6 inshore, treatment, 5 days


title: Non responder-P4


title: HCT116 cells, 200 µM

value: 200 microM 4sU


title: Chip1 Subpool3 Pre-transfection DNA Rep 2


title: D5 inshore, treatment, 5 days


title: Chip1 Subpool3 Pre-transfection DNA Rep 1


title: HCT116 cells, 100 µM

value: 100 microM 4sU


title: D3 inshore, treatment, 5 days


title: HCT116 cells, no4sU


title: Non responder-P2


title: BG4_MUT_Bio1.Tech2

value: Human embryonic kidney


title: Non responder-P7


title: Non responder-P1


title: HFF-TerT cells, 800 µM

source_name: HFF-TerT

value: HFF-TerT

value: fibroblast cells

value: 800 microM 4sU


title: Non responder-P3


title: Chip1 Subpool2 Pre-transfection DNA Rep 1


title: C2 offshore, treatment, 5 days

value: coral tissue


title: HCT116 cells, 800 µM


title: C5 offshore, treatment, 5 days

value: not applicable


title: Chip1 Subpool1 Pre-transfection DNA Rep 3

value: Pre-transfection plasmid DNA


title: Responder-P9

value: Liver

value: Responder


title: HFF-TerT cells, 400 µM


title: C1 offshore, treatment, 5 days


title: Responder-P8

value: intrahepatic cholangiocarcinoma

value: FOLFOX-HAIC+Lenvatinib+PD-1 blockade


title: HFF-TerT cells, 200 µM


title: HFF-TerT cells, 100 µM


title: Chip1 Subpool1 Pre-transfection DNA Rep 1


title: Chip1 Subpool1 Pre-transfection DNA Rep 2


title: A4 inshore, treatment, 31 days


title: Chip1 Subpool2 Pre-transfection DNA Rep 3


title: BLY5 inshore, treatment, 5 days


title: Responder-P7


title: Responder-P6


title: Responder-P5


title: HFF-TerT cells, no4sU


title: A6 inshore, treatment, 5 days


title: U2OS cells, 800 µM

value: osteosarcoma cells


title: B4 inshore, treatment, 5 days


title: Chip1 Subpool2 Pre-transfection DNA Rep 2


title: A4 inshore, treatment, 5 days


title: U2OS cells, 200 µM

value: WT


title: U2OS cells, 400 µM

value: 400 microM 4sU


title: Responder-P4


title: A3 inshore, treatment, 5 days


title: day 12 rep 1

city: St. Louis

first: Matthew

last: Mosley

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis School of Medicine

data_processing:
Clean reads were obtained by filtereing reads containing adapters, poly-N reads, and low quality reads.
Fastq files were aligned to the reference genome using STAR version 2.7.3a.
Gene counts were determined using the featureCounts function in the R package Rsubread.
Assembly: Caenorhabditis elegans WBcel235.94
Supplementary files format and content: Gene counts for each sample in tab-delimitted text format.

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
Animals were wahsed off plates with M9 buffer and allowed to settle by gravity. Samples were lysed by addition of TRIzol (ThermoFisher) with repeated flash-freeze/thaw cycles in liquid nitrogen. Total RNA was obtained by phenol chloroform extraction and purified according to the RNeasy Micro kit protocl (Qiagen), including on-column DNase treatment.
mRNA was enriched using oligo(dT) beads, and the Ribo-Zero kit (Illumina) was used to remove rRNA. First, mRNA was fragmented randomly by adding fragmentation buffer, then cDNA was synthesized by using mRNA template and random hexamers primer, after which a second-strand synthesis buffer (Illumina) , dNTPs, RNase H, and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Whole body

value: day 12


title: day 11 rep 1

value: day 11


title: day 12 rep 2


title: U2OS cells, 100 µM

value: 100 microM 4sU

value: 2 hours


title: Responder-P2


title: BLY6 inshore, treatment, 5 days


title: D6 inshore, control, 5 days


title: U2OS cells, no4sU


title: Responder-P1


title: day 10 rep 3

value: day 10


title: D5 inshore, control, 5 days


title: day 10 rep 2


title: D3 inshore, control, 5 days


title: C5 offshore, control, 5 days


title: day 10 rep 1


title: day 11 rep 3


title: day 11 rep 2


title: Responder-P3


title: C1 offshore, control, 5 days


title: C2 offshore, control, 5 days


title: day 9 rep 3

value: day 9


title: DMPK Bisulfite Massive Parallel Sequencing in untransfected DM1 hESC

city: jerusalem

first: Rachel

last: Eiges

address: Shmu'el Bait St 12, Jerusalem, 9103102

institute: Shaare Zedek medical center

data_processing:
Raw sequence reads were mapped to the human genome (build GRCh37) using Bismark. Methylation calls were extracted after duplicate sequences were removed. Data visualization and analysis were performed using Bismark2Summary. CpG methylation was calculated as the average methylation at each CpG position, and non‐CpG methylation was extracted from the Bismark reports.
Genome_build: hg19
Supplementary_files_format_and_content: Raw data for the bisulfite footprinting analysis is provided as fastq files and the processed data files are provided as Text files.

growth_protocol: HESCs were grown in feeder-free culture conditions using defined Essential 8 medium combined with Vitronectin (Gibco) coated surfaces.

extract_protocol:
DNA extracted under native conditions
Genomic DNA (2 mg) was modified by bisulfite treatment (EZ DNA methylation kit, Zymo Research) and amplified by FastStart DNA polymerase (Roche). PCR was carried out using 5’ primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTGGTTGTGGGTTAGTGTT 3’ primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCCAACAACCTACAACTATTAT (DMPK specific sequences are marked with underlines; adaptors for library preparation are at the 5’ end of each primer).These amplified products were quality controlled, for size using the D1000 ScreenTape kit (catalog #5067‐5582; Agilent Technologies), and for concentration using the Qubit® DNA HS Assay kit (catalog #32854; Invitrogen). Subsequently, the PCR products were bead purified with Agencourt Ampure XP beads (Beckman Coulter) according to the manufacturer’s protocol. Next, amplicons were subjected to a second PrimMax Takara PCR reaction (1st purified PCR DNA (7.5 μl), 2.5 μl N7XX primer (nextera barcode 1), 2.5 ul S5XX primer (nextera barcode 2), 12.5 μl 2X Primstar ReadyMix). PCR program: 98°C for 1 minute followed by 8 cycles of: 98°C for 10 seconds, 55°C for 10 seconds, 72°C for 30 seconds, then 72°C for 5 minutes and finally held at 10°C. The 2nd PCR was bead purified, quality controlled using the D1000 ScreenTape kit and the Qubit®DNA HS Assay kit, and all resultant libraries were normalized and pooled at 10nM concentration.Denaturation and dilution of the sequencing pool was performed according to standardIllumina protocol. Ultimately, 1.5 pM of pool (combined with 40% spiked‐in) was loaded onto a NextSeq 500 Mid‐Output Kit (150 cycles) cartridge (catalog #FC‐102‐1001; Illumina, San Diego, CA) for high throughput sequencing on a NextSeq 500 instrument (Illumina), with 150 cycle, single‐read run conditions.
NextSeq

value: hESCs

tag: sample type

value: DM1 hESC


title: DMPK Bisulfite Massive Parallel Sequencing in eidted DM1 hESC #29

treatment_protocol: Genomic DNA (2 mg) was modified by bisulfite treatment (EZ DNA methylation kit, Zymo  Research) and amplified by FastStart DNA polymerase (Roche)


title: day 9 rep 2


title: mESCs_J1_input

growth_protocol:
Wild-type J1 (129/Sv/Jae) mouse embryonic stem cell (mESC) cultures were routinely maintained in high-glucose DMEM (Sigma, D6546) containing 10% FBS (Gibco, 16141079), 1X GlutaMax-I (Gibco, 35050-038), 1X NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148 diluted to 50mM in 50µM EDTA/PBS solution), 1000U/mL recombinant LIF (PeproTech, murine LIF, 250-02), 1µMPD (Sigma, PZ0162-5MG) and 3µMCHIR (Cambridge biosciences, HY-10182A-5MG). Cells were cultured under standard conditions at 37°C in water-saturated, CO2-enriched (5%) atmosphere on 0.2% (w/v) gelatine-coated (Sigma, G9391) platesand regularly tested for mycoplasma contamination (RICS, CRUKCI core). Authentication of mESCs was performed by mouse STR analysis (RICS, CRUKCI core).For sub-culturing, cells were washed with PBS (Gibco, 14190094), detached with TrypLE (Gibco, 12604-013) at 37°C for 5min and resuspended in 10-fold excess of mESC growth medium.
Human embryonic kidney (HEK293T), cells were cultured in DMEM (Dulbecco's Modified Eagle Medium, Gibco, 41966-029) growth media supplemented with 10% fetal bovine serum (Gibco, A3840401) and 2 mM L-Glutamine (Gibco, 25030024). Cells were maintained at standard conditions (5% CO2, 37°C) on TC-treated 6-well plates (Corning, 3516) and regularly tested for mycoplasma contamination (RICS, CRUK-CI Core Facility). For passaging, cells were washed with DPBS pH 7.4 (Gibco, 14190094), detached with StemPro Accutase (Gibco, A11105-01) at 37°C for 5mins and resuspended in 10-fold excess of growth media. Wild type J1 (129/Sv/Jae) mouse embryonic stem cell (mESC) cultures were routinely maintained in DMEM high glucose (Sigma, D6546) containing 10% FBS (Gibco, 16141079), 1x GlutaMax-I (Gibco, 35050-038), 1x NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148 diluted to 50 mM in 50 µM EDTA/PBS solution), 1000 U/mL recombinant LIF (PeproTech, murine LIF, 250-02) and 1 µM PD (Sigma, PZ0162-5MG), 3 µM CHIR (Cambridge biosciences, HY-10182A-5MG). Cells were cultured under standard conditions at 37°C in water saturated, CO2 (5%) enriched atmosphere on 0.2% (w/v) gelatine-coated (Sigma, G9391) plates and regularly tested for mycoplasma contamination (RICS, CRUK CI core). Authentication of mESCs was performed by mouse STR analysis (RICS, CRUK CI core). For passaging cells were washed with PBS (Gibco, 14190094), detached with TrypLE (Gibco, 12604-013) at 37°C for 5 min and resuspended in 10-fold excess of mESC growth medium as described.

extract_protocol:
CUT&Tag was performed as previously described (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)).G4 mapping (BG4) was performed as 2-layer CUT&Tag on ConcanavalinA (ConA)-coated magnetic beads (Bangs Laboratories, BP531). Aliquots of 200,000 cells/100mL were added to 10mL of beads, washed twice with 100mL wash buffer and resuspended in 1% BSA Antibody Buffer. Primary antibodies were added (1:50), and the mix was incubated at 4°C overnight at 600 rpm. Cells were then washed twice with 100mL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH 7.5, 150 mM KCl, 0.5 mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and resuspended in 50mL dig-wash buffer. Secondary antibodies were added 1:50 to the samples and incubated at 25°C for 2h at 600 rpm (2-layer CUT&Tag). Cells were then washed three times with 100mL Dig-300 buffer (0.01% digitonin, 20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer at 25°C for 1h at 600rpm.Cells were then washed three times with 500 µL Dig-300 buffer and the Tn5 tagmentation was activated by incubating in 300mL Dig-300 buffer supplemented with 10 mM MgCl2at 37°C for 1h at 600 rpm. Cells were then washed twice with 500 µL TAPS buffer and resuspended in 0.5 mg/mL Proteinase K, 0.5% SDS in 10 mM Tris-HCl buffer pH 8.0 at 55°C for 1h at 800 rpm. Tagmented DNA was purified with DNA clean & concentrator columns (Zymo Research, D4013).
For Illumina library preparation, genomic DNA extracted by CUT&Tag was used. Libraries were generated as previously described with a universal i5 and a uniquely barcoded i7 primer(Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. Nat Commun 10, 1930 (2019)). Libraries were visualized and quantified on a high-sensitivity D1000 tape on a Tape Station (AgilentTechnologies 2200)andwith the NEBNext®Library Quant Kit for Illumina (NEB, cat#7630S), following the manufacturer’s instructions.Libraries were sequenced on an Illumina NextSeq 500 (High Output Kit v2.5, 75 cycles) or NextSeq 2000 instrument(P2 or P3 reagents, 100 cycles). RNA-seq and library preparation Total RNA was extracted from 1.0x106 cells using the RNeasy Plus Mini Kit (Qiagen, cat#74134) as per manufacturer’s instructions. RNA quality was checked via TapeStation (Agilent Technologies 2200, RIN>9) and RNA concentration determined using a Qubit fluorometer (Thermo Fisher, Qubit 4). Libraries were generated from 700ng RNA using the NEBNext®Poly(A) mRNA Magnetic Isolation Module (NEB, cat#7490S) together with the NEBNext®UltraTMII Directional RNA Library Prep Kit for Illumina (NEB, cat#7760S) as per manufacturer’s instructions. Libraries were sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles). For MNase 1.0 x 106 cells were washed in ice-cold PBS and incubated in 1mL lysis buffer (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT, 0.1% NP-40) for 10 mins on ice. Cells were then centrifuged at 1,000 x g for 5 mins at 4 °C and resuspended in lysis buffer without NP-40 (10 mM Tris-HCl pH 8.0, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2, 1 mM DTT). Cells were then incubated at 37 °C for 5 mins supplemented with 2 mM CaCl2 and digested with 10 U MNase at 37 °C for 60 mins. The digestion was stopped with a final concentration of 40 mM EDTA, 0.5% SDS. DNA was incubated with RNase A (Thermo Scientific, cat #EN0531) for 1 h at 37oC. DNA was purified using Phenol-chloroform-isoamyl alcohol (PCl, Thermo Scientific, cat #15593049). Libraries were generated with the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, cat #7760S) as per manufacturer’s instructions. A bead-based size selection of 200 bp was performed to isolate mononucleosomal fragments. Libraries were then quantified with the NEBNext® Library Quant Kit for Illumina (NEB, cat #7630S) and sequenced on a NextSeq 500 system (High Output Kit v2.5, 75 cycles).

value: mouse embryonic stem cells


title: DMPK Bisulfite Massive Parallel Sequencing in eidted DM1 hESC #9

value: edited-DM1 hESC


title: NIH-3T3 cells, 120 min, replicate A

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt, reads with length < 18 were removed
Trimmed sequence reads were mapped to rRNA (U13369.1) and Mycoplasma database using bowtie2 (v. 2.3.0). Mapped reads were filtered out
Trimmed and filtered sequence reads were mapped to the mouse genome (ensembl 102) using STAR v. 2.7.10b (parameters: --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH –outSAMunmapped Within)
Subsequent analyses were conducted in R.
Assembly: mus musculus (ensembl 102)
Supplementary files format and content: Tab-separated values files
Library strategy: SLAM-seq

treatment_protocol: Cells were treated with 800 µM 4sU for 15, 30, 60, 90 and 120 minutes.

value: fibroblast cells

value: 800 microM 4sU

value: 120 min


title: day 8 rep 2

value: day 8


title: B4 inshore, control, 5 days

value: coral tissue

value: not applicable


title: NIH-3T3 cells, 120 min, replicate B

value: WT


title: BLY5 inshore, control, 5 days


title: BLY6 inshore, control, 5 days


title: A6 inshore, control, 5 days


title: NIH-3T3 cells, 90 min, replicate A

value: 90 min


title: day 8 rep 1

value: Whole body


title: NIH-3T3 cells, 90 min, replicate B


title: day 7 rep 3

value: day 7


title: NIH-3T3 cells, 60 min, replicate B

value: 60 min


title: day 7 rep 2


title: A3 inshore, control, 5 days


title: mESCs_J1_BG4

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and the coresponding modified genomes, and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt. For the polymerase tracks the tracks were further rescaled, normalised for the E coli reads in the library.
Assembly: hg38 , hg38_MutMYCG4, hg38_SwapKRASG4, hg38_MYCFlip_StrandSwap, mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag


title: NIH-3T3 cells, 60 min, replicate A


title: day 6 rep 3

value: day 6


title: day 9 rep 1

value: day 9


title: day 7 rep 1


title: A4 inshore, control, 5 days


title: Non-migrant eye, 57dpf, 3

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

data_processing:
Good-quality raw reads were aligned against the turbot genome assembly (ASM318616v1) using STAR v2.7.0e alignment software
Reads were assigned to unique genes with HTseq software v0.10.0
Assembly: ASM318616v1
Supplementary files format and content: text file including raw counts for each sample

organism: Scophthalmus maximus

source_name: Non-migrant eye

extract_protocol:
Total RNA was extracted from the tissues and purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s intructions.
BGISEQ-500 stranded mRNA library

value: Non-migrant eye

tag: age


title: NIH-3T3 cells, 30 min, replicate A

value: 30 min


title: day 6 rep 1


title: Non-migrant eye, 57dpf, 2


title: NIH-3T3 cells, 15 min, replicate B

value: 15 min


title: day 5 rep 3

value: day 5


title: Non-migrant eye, 57dpf, 1


title: day 6 rep 2


title: NIH-3T3 cells, 15 min, replicate A

value: fibroblast cells


title: NIH-3T3 cells, 30 min, replicate B

value: 800 microM 4sU