title: WT_preNeu_R3

city: London

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Obtained FASTQ files were aligned and QC using the nf-core/rnaseq pipeline version 3.8.1,using '-profile crick --aligner star_rsem" as extra parameters.
Obtained counts were then uploaded and analyzed using Deseq2 on R.
Assembly: Ensembl GRCh38 release 95
Supplementary files format and content: gene counts per gene per sample

source_name: Human Neutrophils

extract_protocol:
RNA was isolated using RNAeasy microkit (Qiagen)
Libraries were prepared using KAPA Stranded with RiboErase RNA-seq kit (according to the manufacturer’s instructions). Briefly, 17–25 ng of starting RNA were subjected first to cytoplasmic and mitochondrial ribosomal RNA (rRNA) depletion by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides. Samples depleted of rRNA were then subjected to 94 °C for 6 min in the 2×Fragment, Prime, and Elute Buffer in order to obtain 200–300 bp fragments. cDNA synthesis was run in two steps following the manufacturer’s instructions. The ligation step consisted of a final volume of 110 μl of the adaptor ligation reaction mixture with 60 μl of input cDNA, 5μl of diluted adaptor, and 45 μl of ligation mix (50 μl of ligation buffer + 10 μl of DNA ligase). The Kapa Dual- Indexed Adaptors stock concentration was diluted to 1.5mM to get the best adaptor concentration for library construction. The ligation cycle was run according to the manufacturer’s instructions. To remove short fragments such as adaptor dimers, 2X AMPure XP bead clean-ups were done (0.63 SPRI and 0.7 SPRI).

value: Human Neutrophils


title: WT_preNeu_R4

status: Public on Jun 05 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: genotype

value: WT


title: WT_preNeu_R5


title: Triple Positive DLBCL 26

type: genomic

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

molecule: genomic DNA

source_name: Mesenteric mass

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: tissue

value: Triple Positive DLBCL

tag: gender

value: Female

tag: tissue preparation

value: FFPE


title: Liver LMRE 0-1

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

country: USA

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using Tuxedo pipeline tophat
Read counting for each gene and normalization to FPKM values  using Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (FPKM) of the standard RNAseq analysis are reported in the genes_fpkm.csv file

organism: Mus musculus

source_name: liver

extract_protocol: none provided by the submitter

tag: strain

value: LMRE


title: ZR751_DMSO_48hr_R3

city: San Diego

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

library_source: genomic

data_processing:
For ATAC-seq data analysis, paired-end sequencing reads for each sample were mapped to hg38 human reference genome with Bowtie2 (Langmead and Salzberg, 2012) using the following parameters: -t -X 2000 --no-mixed --no-discordant --trim-to 3:30. Sam files were converted into Bam with Samtools. Peak calling was performed with MACS2 (Zhang et al., 2008) using these parameters: callpeak -g hs --nolambda --nomodel --shift -100 --extsize 200 --bdg --SPMR -q 5e-2. Peaks overlap with ENCODE black list regions were removed from downstream analysis using Bedtools. Bedgraph files were converted to Bigwig using bedGraphToBigWig (Kent et al., 2010) and signal tracks were visualized with IGV (Robinson et al., 2011). To correct for ATAC-seq bias, we extracted genome wide signal at 100 bp resolution using DeepTools (Ramirez et al., 2014), and performed quantile normalization on the signal data using the R package preprocessCore (https://rdrr.io/bioc/preprocessCore/).
Assembly: hg38
Supplementary files format and content: BigWig files of normalized ATAC-seq signal; bed files of differential called peaks

growth_protocol: Cells were maintained based on ATCC recommendations

extract_protocol: qPCR was performed on the DNA library to decide the optimal cycle number for library amplification. The library was then purified with Ampure XP beads (A63880, Beckman Coulter), quantified using Qubit (Qubit dsDNA HS Assay Kit, Q32851, Thermo Fisher Scientific) and checked for size distribution using 4200 TapeStation (High Sensitivity D1000 ScreenTape, 5067-5584, Agilent Technologies). Sequencing was performed with Illumina HiSeq4000 (50 bp PE, Nextera v2 libraries).

treatment_protocol: T47D, ZR751 and MCF7 cells were treated in triplicate with DMSO control or 30nM CTx-648/PF-9363 for 2 or 5 days and processed with the transposition assay. Briefly, 50,000 nuclei from each sample were used in each reaction with 20 µl of transposition mix and incubated at 37oC for 60 minutes.

tag: cell line

value: Breast cancer cells

tag: treatment

value: DMSO

tag: time

value: 48 hr


title: ZR751_DMSO_48hr_R2


title: WT_preNeu_R2


title: WT_MatNeu_R6


title: T-cell lymphoblastic lymphoma 10

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL10

source_name: Pleural effussion

value: T-cell lymphoblastic lymphoma

value: Male


title: Liver LMRE 4-6


title: Triple Positive DLBCL 25

source_name: LN


title: WT_MatNeu_R5


title: Liver WT Dub 20-3


title: Liver LMRE 4-1


title: Triple Positive DLBCL 16

source_name: Inguinal LN


title: ZR751_DMSO_48hr_R1


title: Liver WT Dub 20-2


title: T47D_KAT6 inhibitor_48hr_R3

value: KAT6 inhibitor


title: Liver WT Dub 20-1


title: T47D_KAT6 inhibitor_48hr_R1


title: WT_ImmNeu_R5


title: WT_MatNeu_R2


title: WT_MatNeu_R1


title: Triple Positive DLBCL 2

source_name: Teste


title: WT_ImmNeu_R4


title: T47D_KAT6 inhibitor_48hr_R2


title: Smarce1-AID_IAA_mit_aid23_rep2

city: Memphis

first: Xiaolong

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

description:
nascent RNA
Smarce1-AID_IAA_mit_aid23_2425119

data_processing:
Illumina Casava1.7 software used for basecalling.
Total stranded RNA sequencing data were mapped to mouse genome assemblymm10 using an internalAutoMapperpipeline. Briefly, the raw reads were trimmed with trimgalore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a.
Then the read counts were computed usingRSEM(V1.3.0) based on GENCODE vM23.
RPM (Reads Per Million) was applied to normalize read counts in bigwig tracks
Assembly: mm10
Supplementary files format and content: read counts from RSEM

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
Click-iT® Nascent RNA Capture Kit (https://www.thermofisher.com/order/catalog/product/C10365)
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off. For mitotic release, mitotic cells were washed out three times by fresh mESC culture medium to remove residual nocodazole and then cultured in mESC medium for the indicated time.

value: mouse embryonic stem cells

value: nocodazole treatment for 6 hours


title: Smarce1-AID_IAA_mit_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_mit_aid23_2425073


title: T47D_DMSO_48hr_R2


title: Smarce1-AID_IAA_mit_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_mit_aid06_2425112


title: Liver WT Dub 12-3


title: T47D_DMSO_48hr_R3


title: T47D_DMSO_48hr_R1


title: Liver WT Dub 16-1


title: WT_ImmNeu_R1


title: Triple Positive DLBCL 5

source_name: Submandicular gland


title: Smarce1-AID_IAA_mit_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_mit_aid06_2425066


title: flag-hct116-orc1-oe-up-rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

description:
On the iCLIP gel isolation cut upper band than expected ORC1 molecular weight, with Low RNase treatment Replicate 3
Flag_HCT116_ORC1_up_merge_grouped_cdna.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_norm.bigWig

data_processing:
Library strategy: iCLIP-seq
iCLIP sequencing reads were analysed on the iMaps server (https://imaps.genias.com/) using the iCount software (https://github.com/tomazc/iCount 18).
Briefly, experimental barcodes were removed and sequencing reads aligned with STAR 9 to human genome build GRCh38 primary assembly GENCODE version 27, allowing two mismatches and ten secondary alignments.
Unique Molecular Identifiers (UMIs), were used to distinguish and remove PCR duplicates. To determine protein-RNA contact sites, the sequencing read preceding nucleotide was allocated as the crosslink site event.
Significant contact sites were then identified, using the iCount peak function, based on false discovery rate (FDR) <0.05 comparing specific sites within a window of three nucleotides with randomised data (100 permutations) and within co-transcribed regions (https://github.com/tomazc/iCount/blob/master/iCount/analysis/peaks.py). The significant crosslink signal was normalised by CPM. For individual samples we also used Paraclu peak caller.
Assignment of crosslink sites to coding transcripts, non-coding or biotype features, was done by following segmentation hierarchy rules (https://github.com/tomazc/iCount/blob/master/iCount/genomes/segment.py).
Then, replicates were merged and summary of cDNA counts within genes and genic regions were generated with iCount summary function, normalising the counts by the length of the corresponding region.
Genome_build: GRCh38 primary assembly GENCODE version 27
Supplementary_files_format_and_content: Crosslink bed, group bed, peaks bed, group peaks bed, normalised bigwig.
Supplementary_files_format_and_content: flag-hct116-notf-down_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-notf-up_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep3_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep1_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep1_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep3_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-notf-down_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-notf-up_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep3_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep1_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep1_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep3_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna_norm.bigWig: normalised bigwig

source_name: Colorectal Cancer

growth_protocol: HCT116 cells were grown in RPMI medium at 37ºC.

extract_protocol:
The iCLIP protocol was followed to isolate RNA bound to ORC1-3xFlag and amplify a cDNA library as described in Mas et al. 2021.
Adapter ligation was performed after immunoprecipitation and samples for each condition were barcoded during RT, using RT primers with specific barcodes. Random nucleotides (UMIs) were also incorporated into cDNAs to distinguish between PCR duplication of cDNA products.

treatment_protocol: 48 hours transfection of pcDNA3.1-ORC1-3xFLAG.

value: Transfected with pcDNA3.1-ORC1-3xFLAG

tag: antibody

value: FLAG antibody (M2, F1804, Sigma)

tag: replicate


title: Smarce1-AID_IAA_90min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_90_aid23_2425104

value: cells were released from mitosis for 90 min


title: Liver WT Dub 12-2


title: TET2_preNeu_R5

value: Human Neutrophils


title: Liver WT Dub 16-3

value: WT


title: Liver WT Dub 16-2


title: TET2_preNeu_R4


title: Liver WT Dub 8-3


title: TET2_preNeu_R3


title: WT_ImmNeu_R3


title: Liver WT Dub 8-2


title: Smarce1-AID_IAA_90min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_90_aid06_2425096


title: Smarce1-AID_IAA_90min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_90_aid23_2425088


title: flag-hct116-orc1-oe-up-rep2

description:
On the iCLIP gel isolation cut upper band than expected ORC1 molecular weight, with Low RNase treatment Replicate 2
Flag_HCT116_ORC1_up_merge_grouped_cdna.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_norm.bigWig


title: flag-hct116-orc1-oe-up-rep1

description:
On the iCLIP gel isolation cut upper band than expected ORC1 molecular weight, with Low RNase treatment Replicate 1
Flag_HCT116_ORC1_up_merge_grouped_cdna.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1_up_merge_grouped_cdna_norm.bigWig


title: Liver WT Dub 8-1


title: flag-hct116-orc1-oe-highrnase-up-rep2

description:
On the iCLIP gel isolation cut upper band than expected ORC1 molecular weight, with High RNase treatment Replicate 2
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna.bed
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_norm.bigWig


title: TET2_MatNeu_R5


title: flag-hct116-orc1-oe-highrnase-up-rep1

description:
On the iCLIP gel isolation cut upper band than expected ORC1 molecular weight, with High RNase treatment Replicate 1
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna.bed
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_norm.bigWig


title: Smarce1-AID_IAA_90min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_90_aid06_2425080


title: TET2_preNeu_R2


title: Liver WT Dub 4-3


title: Smarce1-AID_IAA_60min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_60_aid23_2425121

value: cells were released from mitosis for 60 min


title: TET2_MatNeu_R4


title: flag-hct116-orc1-oe-down-rep3

description:
On the iCLIP gel isolation cut lower band than expected ORC1 molecular weight, with Low RNase treatment Replicate 2
Flag_HCT116_ORC1_down_merge_grouped_cdna.bed
Flag_HCT116_ORC1_down_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1_down_merge_grouped_cdna_norm.bigWig


title: Smarce1-AID_IAA_60min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_60_aid23_2425075


title: Liver WT Dub 12-1


title: TET2_MatNeu_R2


title: Liver WT Dub 4-2


title: TET2_MatNeu_R1


title: Liver WT Dub 4-4


title: TET2_ImmNeu_R5


title: flag-hct116-notf-down

description:
Not transfected control, gel isolation cut lower band than expected ORC1 molecular weight
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna.bed
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_peaks.bed
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_norm.bigWig

value: Untreated


title: Smarce1-AID_IAA_30min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_30_aid23_2425074

value: cells were released from mitosis for 30 min


title: Smarce1-AID_IAA_30min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_30_aid23_2425120


title: Liver WT Dub 0-1


title: TET2_ImmNeu_R2


title: Muscle LMRE 20-3

source_name: muscle

value: LMRE


title: ZR751-DMSO-Pol2-rep2

data_processing:
Paired-end sequencing fastq files were mapped to human hg38 genome using Bowtie2 (Langmead and Salzberg, 2012). Sam files were converted into bam files and sorted by Samtools (Li et al., 2009). For spike-in normalization of ChIP-seq signal, E Coli spike-in reads were mapped to MG1655 genome using Bowtie2, and scaling factors (SF) were calculated as 1 / (MG1655 reads X 100 / total reads), and each bam file was normalized and converted into bigwig files based on the corresponding scaling factor using DeepTools bamCoverage (Ramirez et al., 2014) with these parameters: --scaleFactor SF --effectiveGenomeSize 2913022398 --normalizeUsing RPKM –ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: BigWig files of ChIP-seq or CUT&RUN signal after spike-in normalization
Library strategy: CUT&RUN

extract_protocol:
ChIPseq was performed as previously described (Zhou et al., 2022). Briefly, Dynabeads Protein G (Invitrogen, Cat. 10003D) were resuspended in PBS+0.5% BSA and incubated with 30 μg of antibodies recognizing Pol2 (CST, cat. 14958S) or Pol2 S2P (Abcam, ab5095) for 8h at 4°C. 3x 107 ZR75-1 cells treated with DMSO or PF-9363 for 24h, were crosslinked for 30min at RT in PBS with 1.5mM ethylene glycol-bis (succinic acid N-hydroxysuccinimide ester) (EGS) (Thermo Fisher, Cat. 21565) followed by 15min with 1% formaldehyde (Thermo Scientific, Cat. 28908) and quenched with 0.2M glycine. Crosslinked cells were washed 2x with PBS, lysed and sonicated on Covaris M220 with PIP 75, DF 10, CPB 200 for total of 8min. Chromatin lysates were cleared by centrifugation and Triton X-100 was added to a final concentration of 1%. Lysates were incubated overnight at 4°C with Protein G Dynabeads conjugated to antibodies against Pol2 or Pol2 S2P. Beads were washed with low salt wash buffer, high salt wash buffer, LiCl buffer and TE with 50mM NaCl and DNA-protein complexes were eluted twice for 30 min at 65 °C with shaking. Buffers in all steps above were supplemented with protease inhibitors (Roche, Cat. 11697498001). Input sample was prepared by the same approach without immunoprecipitation. RNase (Thermo Scientific, Cat. FEREN0531) and proteinase K (Invitrogen, Cat. 25530049) treatments were performed at 37 °C for 1h and 55 °C for 2h, respectively, and samples were de-crosslinked overnight at 65 °C. DNA was purified using Qiagen QiaQuick PCR purification kit (Qiagen, Cat. 28106) and quantified with Qubit (Invitrogen, Cat. Q32854).
Cut&Run was performed using CUTANA™ ChIC/CUT&RUN kit (EpiCypher, Cat. 14-1048) per manufacturer recommendations. Briefly, ZR-75-1 cells or MCF7 cells were fixed with 0.1% formaldehyde (Fisher Scientific, Cat. F79-500) for 1min and fixation was quenched with 125mM glycine (Fisher Scientific, cat. AAJ1640736). Fixed cells were washed with PBS (Gibco, Cat. 10010-031) and nuclei were isolated with nuclear extraction buffer (20mM HEPES, pH7.9, 10mM KaCl, 0.1% Triton X-100, 20% glycerol, 1mM MnCl2) and inspected under the microscope to confirm efficiency of nuclei extraction and their integrity. 5x105 nuclei were washed with wash buffer and immobilized to Concavalin-A beads, resuspended in 50 µl antibody buffer and incubated with 0.5 µg of the following antibodies: IgG (EpiCypher, Cat.13-0042k), H3K4me3 (EpiCypher, Cat.13-0041k), H3K9ac (EpiCypher, Cat.13-0033), H3K27ac (EpiCypher, Cat. 13-0045), H3K27me3 (Thermo-Fisher, MA5-11198) or H3K23ac (CST, Cat.14932S or Abcam, ab177275) overnight at 4°C. Beads were washed with Cell Permeabilization buffer and incubated with pAG-MNase for 10min at RT. After activation by CaCl2 beads were incubated for 2h at 4°C, Stop buffer was added together with 0.5ng of E. coli Spike-in DNA and incubated at 37°C for 10min to release Cut&Run fragments from the insoluble nuclear chromatin. DNA was then decrosslinked overnight at 55°C and purified using DNA Cleanup Columns from the kit. Wash buffer, Cell Permeabilization buffer and Antibody buffer were supplemented with 0.05% SDS (Invitrogen, Cat. 15553027) and 1%Triton X-100 (Sigma, Cat. 93443-500ML).
Libraries were prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, Cat. E7645S). Two replicates were performed for each condition. Libraries were indexed with NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1, NEB, Cat. E7600S) and validated for quality and size distribution using a TapeStation 4200 (Agilent). Paired-end sequencing (150 bp+150 bp) was performed on Ilumina sequencer.

treatment_protocol: ZR751 cells were treated in duplicate with DMSO control or 30 nM CTx-648/PF-9363 for 24 hours before performing ChIP-seq or CUT&RUN procedures

value: Breast cancer cells

value: 24 hr


title: TET2_ImmNeu_R1


title: ZR751-input

value: DMSO


title: Smarce1-AID_IAA_30min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_30_aid06_2425067


title: T47D-FAR (fulvestrant + abemaciclib resistant), rep2

city: Naples

first: Luigi

last: Formisano

address: Via Sergio Pansini, 5

department: Department of Clinical Medicine and Surgery

country: Italy

institute: University of Naples "Federico II"

data_processing:
Reads quality control was perfomed using FastQC
Sequence reads were trimmed to remove possible adaptor sequence/low-quality nucleotides using Trimmomatatic v.0.36
Trimmed sequence reads were mapped to GrCM38/mm10 using the STAR aligner v.2.5.2b
Read count extraction and normalization were performed using featureCounts from the Subread package v.1.5.2
Hit counts comparing between groups with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample

growth_protocol: MCF7, T47D, MCF7-FAR, and T47D-FAR were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Library preparation, Illumina, RNA with PolyA selection, following manufacturer's protocols.

treatment_protocol: Cells were treated with 1μM fulvestrant and 0,25μM abemaciclib for 18 hours in DMEM 10% FBS

value: epithelial cell

tag: disease state

value: ER+ breast cancer

value: 1 μM fulvestrant + 0,25 μM abemaciclib

value: 18 hours

tag: phenotype

value: FAR


title: ZR751-DMSO-Pol2-rep1


title: ZR751-DMSO-Pol2-S2P-rep2


title: Muscle LMRE 20-1


title: Liver WT Dub 0-3


title: T47D-FAR (fulvestrant + abemaciclib resistant), rep3


title: ZR751-DMSO-Pol2-S2P-rep1


title: Smarce1-AID_IAA_60min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_60_aid06_2425068

value: mouse embryonic stem cells


title: Muscle LMRE 16-3


title: TET2_ImmNeu_R4


title: Liver WT Dub 0-2


title: Smarce1-AID_IAA_240min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_240_aid23_2425091

value: cells were released from mitosis for 240 min


title: Smarce1-AID_IAA_30min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_30_aid06_2425113


title: T47D-FAR (fulvestrant + abemaciclib resistant), rep1


title: Smarce1-AID_IAA_240min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_240_aid06_2425099


title: T47D cells, rep3

value: control


title: Smarce1-AID_IAA_240min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_240_aid23_2425107


title: Muscle LMRE 16-2


title: Muscle LMRE 16-1


title: T47D cells, rep2


title: ZR751-9363-Pol2-rep1


title: ZR751-9363-Pol2-S2P-rep2


title: T47D cells, rep1


title: Muscle LMRE 12-5


title: Smarce1-AID_IAA_180min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_180_aid23_2425090

value: cells were released from mitosis for 180 min


title: Smarce1-AID_IAA_240min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_240_aid06_2425083


title: Smarce1-AID_IAA_180min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_180_aid06_2425098


title: MCF7-FAR (fulvestrant + abemaciclib resistant), rep3

value: WT


title: ZR751-DMSO-H3K23ac-ab177275-rep2

data_processing:
Paired-end sequencing fastq files were mapped to human hg38 genome using Bowtie2 (Langmead and Salzberg, 2012). Sam files were converted into bam files and sorted by Samtools (Li et al., 2009). For spike-in normalization of ChIP-seq signal, E Coli spike-in reads were mapped to MG1655 genome using Bowtie2, and scaling factors (SF) were calculated as 1 / (MG1655 reads X 100 / total reads), and each bam file was normalized and converted into bigwig files based on the corresponding scaling factor using DeepTools bamCoverage (Ramirez et al., 2014) with these parameters: --scaleFactor SF --effectiveGenomeSize 2913022398 --normalizeUsing RPKM –ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: BigWig files of ChIP-seq or CUT&RUN signal after spike-in normalization


title: MCF7-FAR (fulvestrant + abemaciclib resistant), rep2


title: ZR751-DMSO-H3K23ac-ab177275-rep1


title: ZR751-9363-Pol2-S2P-rep1


title: Muscle LMRE 12-3


title: Muscle LMRE 12-2


title: ZR751-9363-Pol2-rep2


title: Smarce1-AID_IAA_180min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_180_aid06_2425082


title: Muscle LMRE 8-3


title: Smarce1-AID_IAA_180min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_180_aid23_2425106


title: Smarce1-AID_IAA_120min_aid23_rep2

description:
nascent RNA
Smarce1-AID_IAA_120_aid23_2425105

value: cells were released from mitosis for 120 min


title: MCF7 cells, rep3


title: ZR751-9363-H3K23ac-ab177275-rep2


title: MCF7-FAR (fulvestrant + abemaciclib resistant), rep1


title: Muscle LMRE 8-2


title: ZR751-9363-H3K23ac-ab177275-rep1


title: Smarce1-AID_IAA_120min_aid23_rep1

description:
nascent RNA
Smarce1-AID_IAA_120_aid23_2425089


title: Muscle LMRE 8-1


title: Smarce1-AID_IAA_120min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_120_aid06_2425097


title: Muscle LMRE 4-6


title: ZR751_DMSO-IgG-rep2


title: MCF7 cells, rep1


title: Muscle LMRE 4-5


title: ZR751_PF9363-IgG-rep2


title: Etoposide.6h_Alpha_Amanitin.6h

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
The 96 RNA-seq samples in this submission were combined with 34 RNA-seq samples from our previous studies (GEO accession numbers GSE173221 and GSE190735). Quality filtered NGS reads from the 130 RNA-seq samples were trimmed with fastx toolkit (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/download.html) and aligned to the human genome (GRCh38/hg38) by Tophat2 (version 2.1.1). PCR duplicates were removed using Picard suite (version 2.0.1). The alignments were sorted and indexed by SAMtools (version 1.9) and used for RNA editing sites detection. REDItools, RED-ML and SPRINT were separately applied to detect RNA editing sites. REDItools (https://sourceforge.net/projects/reditools) was run with the parameters ‘-m 50 -u -T 6-0 -n 0.0’. RED-ML (https://github.com/BGIRED/RED-ML) and SPRINT (https://github.com/jumphone/SPRINT) were run using the default parameters. Putative ADAR editing sites were filtered against the common SNPs from dbSNP 151 and K562 in-house SNPs to remove sequence variants. The sites mapping to repeats as annotated by the RepeatMasker track of the UCSC Genome Browser were removed. The remaining sites were then filtered based on their mappability scores as defined by the “Mappability or Uniqueness of Reference Genome from ENCODE” track from the UCSC Genome Browser. Only the sites with a mappability score of 1 based on 100mer alignability and an average mappability score of > 0.5 calculate based on the 24mer alignability in the ± 150bp window around the sites were kept. The editing level for each site was determined as the ratio of the reads containing the A>G change out of the total number of reads mapping to the site. RNA editing candidates with the maximum editing level among the 130 samples of > 0.2 and found in at least 2 samples were kept and then further processed using in-house pipeline based on Sanger validation to generate a compendium of authentic ADAR sites.
Assembly: GRCh38/hg38
Supplementary files format and content: A tab-delimited text file that contains information on the 4,149 authentic ADAR editing sites detected in the K562 cell line. The information for each site includes: the genomic coordinates; strand; the analytical method(s) by which it was detected; location in a genomic element; the annotated or unannotated status of the site; and the editing level in each of the 130 samples (with the exception of the 46 sites detected by Sanger only). The coordinates are based on the UCSC BED files system: 0-based, half-open.

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated with TRNzol (TIANGEN, Beijing).
The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

value: human erythroleukemic cell line

value: Etoposide+Alpha Amanitin


title: Smarce1-AID_IAA_120min_aid06_rep1

description:
nascent RNA
Smarce1-AID_IAA_120_aid06_2425081


title: MCF7 cells, rep2


title: Smarce1-AID_dmso_mit_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_mit_aid23_2425116

value: nocodazole treatment for 6 hours


title: Muscle LMRE 4-1

value: LMRE


title: ZR751_PF9363-IgG-rep1

value: Breast cancer cells

value: 24 hr


title: DMSO.6h_Alpha_Amanitin.6h

value: DMSO+Alpha Amanitin


title: Muscle LMRE 0-4


title: Smarce1-AID_dmso_mit_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_mit_aid23_2425070


title: Etoposide.6h_Alpha_Amanitin.4h


title: ZR751_DMSO-IgG-rep1

value: DMSO


title: Smarce1-AID_dmso_mit_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_mit_aid06_2425109


title: Muscle LMRE 0-2


title: DMSO.6h_Alpha_Amanitin.4h


title: Smarce1-AID_dmso_mit_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_mit_aid06_2425063


title: ZR751_PF9363-K27me3-rep2


title: ZR751_PF9363-K27me3-rep1


title: ZR751_DMSO-K27me3-rep2


title: Smarce1-AID_dmso_90min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_90_aid23_2425100

value: cells were released from mitosis for 90 min


title: Muscle WT Dub 20-3


title: Smarce1-AID_dmso_90min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_90_aid23_2425084


title: ZR751_DMSO-K27me3-rep1


title: ZR751_PF9363-K27ac-rep2


title: DMSO.6h_Alpha_Amanitin.2h


title: Muscle LMRE 20-2


title: flag-hct116-notf-up

description:
Not transfected control, gel isolation cut upper band than expected ORC1 molecular weight
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna.bed
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_peaks.bed
Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_norm.bigWig

value: Untreated

value: FLAG antibody (M2, F1804, Sigma)


title: Muscle WT Dub 20-1


title: Smarce1-AID_dmso_90min_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_90_aid06_2425092

value: mouse embryonic stem cells


title: Smarce1-AID_dmso_90min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_90_aid06_2425076


title: Alpha_Amanitin.6h

value: Alpha Amanitin


title: Muscle WT Dub 16-3


title: ZR751_PF9363-K27ac-rep1


title: ZR751_DMSO-K27ac-rep2


title: Muscle LMRE 0-1


title: Etoposide.6h_Alpha_Amanitin.2h


title: Muscle WT Dub 16-2


title: Alpha_Amanitin.2h


title: Muscle WT Dub 16-1


title: Smarce1-AID_dmso_60min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_60_aid23_2425072

value: cells were released from mitosis for 60 min


title: ZR751_DMSO-K27ac-rep1


title: Etoposide.6h_Alpha_Amanitin.0h


title: ZR751_PF9363-K9ac-rep2


title: Smarce1-AID_dmso_60min_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_60_aid06_2425111


title: DMSO.2h.rep2


title: Etoposide.6h_wash.6h

value: Etoposide-wash


title: Smarce1-AID_dmso_60min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_60_aid06_2425065


title: Muscle WT Dub 12-2

value: WT


title: ZR751_PF9363-K9ac-rep1


title: DMSO.6h_Alpha_Amanitin.0h


title: Smarce1-AID_dmso_60min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_60_aid23_2425118


title: DMSO.6h_wash.6h

value: DMSO-wash


title: Smarce1-AID_dmso_30min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_30_aid23_2425117

value: cells were released from mitosis for 30 min


title: ZR751_DMSO-K9ac-rep1


title: ZR751_DMSO-K9ac-rep2


title: Muscle WT Dub 8-3


title: SN-38.6h_wash.6h

value: human erythroleukemic cell line


title: Etoposide.6h_wash.2h


title: Muscle WT Dub 8-2


title: ZR751_PF9363-K4me3-rep2


title: SN-38.6h_wash.2h


title: Smarce1-AID_dmso_30min_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_30_aid06_2425110


title: Muscle WT Dub 20-2


title: Muscle WT Dub 12-3


title: ZR751_PF9363-K4me3-rep1


title: Smarce1-AID_dmso_30min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_30_aid23_2425071


title: Smarce1-AID_dmso_240min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_240_aid23_2425103

value: cells were released from mitosis for 240 min


title: Muscle WT Dub 4-4


title: Muscle WT Dub 8-1


title: DMSO.6h_wash.2h


title: Muscle WT Dub 4-3


title: ZR751_DMSO-K4me3-rep1


title: Muscle WT Dub 12-1


title: SN-38.6h_wash.0h


title: Etoposide.6h_wash.0h


title: Smarce1-AID_dmso_240min_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_240_aid06_2425095


title: DMSO.6h_wash.0h


title: Smarce1-AID_dmso_240min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_240_aid06_2425079


title: SOW004_MCF7_8hDMSO_2

data_processing:
Assembly: hg38
BigWig files of BrU-seq signal in plus and minus strand; csv files for RPKM expression and differential expression calling
Library strategy: BrU-Seq

extract_protocol: In brief, bromouridine was added into live cell culture at treatment end points to a final concentration of 2 mM and incubated at 37 degree for 30 minutes. Total RNA was extracted with Trizol reagent (Invitrogen #15596-018) and BrU-RNA isolation, library preparation, sequencing and data analysis were performed as described previously (Paulsen et al., 2014).

treatment_protocol: T47D, ZR751 and MCF7 cells were treated in triplicate with DMSO control or 30 nM CTx-648/PF-9363 for 4, 8 or 24 hours before performing BrU-seq procedures (Paulsen et al., 2014)

value: 8 hr


title: Muscle WT Dub 0-3


title: Muscle WT Dub 4-2


title: SOW004_MCF7_8hDMSO_3

value: Breast cancer cells


title: ZR751_DMSO-K4me3-rep2

value: 24 hr


title: DMSO.6h.rep4


title: Smarce1-AID_dmso_30min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_30_aid06_2425064


title: Smarce1-AID_dmso_180min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_180_aid23_2425102

value: cells were released from mitosis for 180 min


title: Muscle WT Dub 0-2


title: SOW004_MCF7_8hDMSO_1

value: DMSO


title: Smarce1-AID_dmso_180min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_180_aid23_2425086


title: SOW004_MCF7_8h9363_3

value: KAT6 inhibitor


title: Actinomycin_D.6h


title: DMSO.2h.rep1


title: Muscle WT Dub 0-1


title: Smarce1-AID_dmso_240min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_240_aid23_2425087


title: Smarce1-AID_dmso_180min_aid06_rep2

description:
nascent RNA
Smarce1-AID_dmso_180_aid06_2425094


title: SOW004_MCF7_8h9363_2


title: Actinomycin_D.2h


title: ATACseq_Dpf2D/D LK rep3

city: Miami

first: Gloria

last: Mas Martin

state: Florida

address: 1501 NW 10th Avenue

institute: University of Miami

description: ATACseq

data_processing:
ATAC-Seq chromatin accessible regions were determined using ENCODE pipeline standards (https://github.com/ENCODE-DCC/atac-seq-pipeline; git commit 2b693ab). Briefly, sequencing indices were trimmed from merged fastq files using cutadapt (v1.9.1) and then aligned to mm10 using bowtie2 (v2.2.6).  After de-duplication, reads were tn5 shifted, replicate peaks were called, and fold enrichment signal files were generated using macs2 (v2.1.0). Final peaks were determined using IDR (v2.0.4) of true replicates.
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For ATACseq, ChIPseq and Cut&Run samples, the processed data files are in bigwig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

source_name: bone marrow sorted LK cells

extract_protocol:
Approximately 200,000 sorted Lin- cKit+ cells were processed following the OMIM-ATAC-seq protocol (Corces MR et al., Nature Methods 2017). Libraries were sequenced on a NextSeq (75bp, paired end reads) to obtain more than 40 million reads/sample.
ATACseq libraries were generated as previously described (Corces et al., Nature Methods 2017) using Tn5 transposase and 6 PCR cycles for final amplification.

value: bone marrow

tag: age

value: post natal day 28


title: Untreated.R3

value: Untreated


title: ATACseq_Dpf2D/D LK rep2

description: ATACseq


title: Smarce1-AID_dmso_180min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_180_aid06_2425078

value: mouse embryonic stem cells


title: SOW004_MCF7_4hDMSO_3

value: 4 hr


title: Cyclophosphamide.6h_Actinomycin_D.6h


title: ATACseq_Dpf2D/D LK rep1

description: ATACseq


title: SOW004_MCF7_4hDMSO_2


title: Smarce1-AID_dmso_120min_aid23_rep1

description:
nascent RNA
Smarce1-AID_dmso_120_aid23_2425085

value: cells were released from mitosis for 120 min


title: ATACseq_Dpf2f/f LK rep4

description: ATACseq


title: Etoposide.6h_Actinomycin_D.6h


title: SOW004_MCF7_4hDMSO_1

value: WT


title: ATACseq_Dpf2f/f LK rep3

description: ATACseq


title: SOW004_MCF7_4h9363_3


title: ATACseq_Dpf2f/f LK rep2

description: ATACseq


title: Smarce1-AID_asyn_aid23_rep2

description:
nascent RNA
Smarce1-AID_asyn_aid23_2425115

value: untreated


title: Talazoparib.6h_Actinomycin_D.6h


title: SOW004_MCF7_8h9363_1


title: SOW004_MCF7_4h9363_2


title: RNAseq_Dpf2D/D LK rep5

description: RNAseq

data_processing:
Reads were aligned to the mm10 transcriptome and ERCC spike-in indexes using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations. Differentially expressed genes were determined by DESeq2 (v1.18.1, Wald Test, p-adj < 0.05) after gene counts were corrected based on ERCC variances using RUVseq (v1.12.0).
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For RNAseq samples, the processed data files are in .txt format and contain the expected gene and transcript counts

extract_protocol:
total RNA was obtained using the RNEasy Plus micro kit (Qiagen, 74034). Ribosomal RNA vas removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310) following manufacturer’s protocols, and RNA-Seq libraries were prepared using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies). RNA-Seq libraries were sequenced on an Illumina NextSeq 500 High-Output kit platform (paired-end, 75 bp reads) to obtain ~40 M reads/sample.
RNAseq libraries were prepared for sequencing using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies).


title: Etoposide.6h_Actinomycin_D.4h


title: Smarce1-AID_dmso_120min_aid23_rep2

description:
nascent RNA
Smarce1-AID_dmso_120_aid23_2425101


title: SOW004_MCF7_4h9363_1


title: Smarce1-AID_asyn_aid06_rep2

description:
nascent RNA
Smarce1-AID_asyn_aid06_2425108


title: SOW004_MCF7_24hDMSO_3


title: RNAseq_Dpf2D/D LK rep4

description: RNAseq


title: DMSO.6h_Actinomycin_D.4h


title: Cyclophosphamide.6h_Actinomycin_D.2h


title: Smarce1-AID_asyn_aid06_rep1

description:
nascent RNA
Smarce1-AID_asyn_aid06_2425062


title: SOW004_MCF7_24hDMSO_2


title: RNAseq_Dpf2D/D LK rep3

description: RNAseq


title: RNAseq_Dpf2D/D LK rep1

description: RNAseq


title: SOW004_MCF7_24h9363_3


title: RNAseq_Dpf2f/f LK rep3

description: RNAseq


title: SOW004_MCF7_24h9363_2


title: 4716-11, sgPpia#3.2, Restored

city: Philadelphia

first: Jonuelle

last: Acosta

state: PA

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.Fastq file generation was conducted by Azenta Life Sciences.
Fastq files for each sample were aligned against the mouse genome mm10 (GRCm39) using HISAT2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing TPMs in all samples

extract_protocol:
RNA was isolated from cell lines using the Rneasy Mini Kit (Qiagen) per manufacturer's instructions.
RNA sequencing libraries were prepared by Azenta Life Sciences using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions

value: Small cell lung cancer

value: Type D

value: sgPpia#3.2 + 4-OHT


title: ATACseq_Dpf2f/f LK rep1

description: ATACseq


title: DMSO.6h_Actinomycin_D.6h

value: human erythroleukemic cell line


title: SN-38.6h_Actinomycin_D.2h


title: 4716-11, sgPpia#4.1, Control

value: sgPpia#4.1 + Vehicle


title: Etoposide.6h_Actinomycin_D.2h


title: Talazoparib.6h_Actinomycin_D.2h


title: 4716-11, sgPpia#3.2, Control

value: sgPpia#3.2 + Vehicle


title: DMSO.6h_Actinomycin_D.2h


title: 4716-11, sgBgal, Restored

value: sgBgal + 4-OHT


title: RNAseq_Dpf2f/f LK rep2

description: RNAseq


title: SOW004_MCF7_24hDMSO_1

value: Breast cancer cells

value: DMSO

value: 24 hr


title: RNAseq_Dpf2f/f LK rep1

description: RNAseq

value: bone marrow

value: post natal day 28


title: Etoposide.6h_Actinomycin_D.1h


title: 4716-11, sgBgal, Control

value: sgBgal + Vehicle


title: AGNHW

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Adult

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample .

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

treatment_protocol: Mice were randomly divided into the groups of sham, middle cerebral artery occlusion (Vehicle) model, and AGNHW (3 mg/g/d)

value: Brain

value: Yes


title: SOW004_MCF7_24h9363_1

value: WT

value: KAT6 inhibitor


title: SOW004_ZR751_8hDMSO_3

value: 8 hr


title: SOW004_ZR751_8hDMSO_2


title: Vehicle

description: Adult

value: No


title: SOW004_ZR751_8hDMSO_1


title: DMSO.6h_Actinomycin_D.1h


title: 4711-18, sgPpia#4.1, Restored

value: Small cell lung cancer

value: Type D

value: sgPpia#4.1 + 4-OHT


title: SOW004_ZR751_8h9363_3


title: Cyclophosphamide.6h_Actinomycin_D.0h

value: human erythroleukemic cell line


title: 4711-18, sgPpia#4.1, Control

value: sgPpia#4.1 + Vehicle


title: Sham

description: Adult


title: ThPOK-/- modified GMP Cell_41

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_41

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes. MultiPath-PSI workflow in AltAnalyze was used to quantify exon-exon and exon-intron junction expression from STAR aligned BAM files (mm10 genome/transcriptome reference), requiring detection of splicing in at least 20% of the single-cell libraries of each cellHarmony assigned cell populations (dPSI > 0.1, eBayes t-test p<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Mm-ThPOK-RSEM-TPM-log2.txt: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: ThPOK-WT_MultiPath-PSI.txt.zip: Alternative Splicing quantification and annotations text file from MultiPath-PSI (AltAnalyze) (archival and ThPOK Fluidigm)
Supplementary_files_format_and_content: groups.ThPOK-WT_MultiPath-PSI: Group annotations assigned by cellHarmony (text file) (archival and ThPOK Fluidigm) (text file)

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting, then cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

value: ThPOK-/-

value: Bone marrow derived GMP


title: Etoposide.6h_Actinomycin_D.0h


title: SN-38.6h_Actinomycin_D.0h


title: ThPOK-/- modified GMP Cell_40

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_40


title: SOW004_ZR751_8h9363_1

value: Breast cancer cells


title: 4711-18, sgPpia#3.2, Control

value: sgPpia#3.2 + Vehicle


title: SOW004_ZR751_8h9363_2


title: 4711-18, sgPpia#3.2, Restored

value: sgPpia#3.2 + 4-OHT


title: Talazoparib.6h_Actinomycin_D.0h


title: ThPOK-/- modified GMP Cell_55

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_55


title: SOW004_ZR751_4hDMSO_3

value: DMSO

value: 4 hr


title: ThPOK-/- modified GMP Cell_69

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_69


title: 4711-18, sgBgal, Restored

value: sgBgal + 4-OHT


title: 4711-18, sgBgal, Control

value: sgBgal + Vehicle


title: ThPOK-/- modified GMP Cell_62

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_62


title: SOW004_ZR751_4hDMSO_2

value: WT


title: ThPOK-/- modified GMP Cell_76

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_76


title: DMSO.36h


title: ThPOK-/- modified GMP Cell_83

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_83


title: 4711-1, sgPpia#4.1, Control


title: 4711-1, sgPpia#4.1, Restored


title: DMSO.48h


title: SOW004_ZR751_4hDMSO_1


title: 4711-1, sgPpia#3.2, Restored


title: SOW004_ZR751_4h9363_3

value: KAT6 inhibitor


title: ThPOK-/- modified GMP Cell_90

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_90


title: 4711-1, sgPpia#3.2, Control


title: DMSO.12h


title: ThPOK-/- modified GMP Cell_89

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_89


title: SOW004_ZR751_4h9363_2


title: SOW004_ZR751_4h9363_1


title: DMSO.24h


title: DMSO.6h.rep3


title: DMSO.6h_Actinomycin_D.0h


title: ThPOK-/- modified GMP Cell_32

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_32


title: SOW004_ZR751_24hDMSO_3

value: 24 hr


title: Romidepsin.48h

value: Romidepsin


title: 4711-1, sgBgal, Restored

value: Small cell lung cancer

value: Type D


title: Romidepsin.36h

value: human erythroleukemic cell line


title: SOW004_ZR751_24hDMSO_2


title: 4711-1, sgBgal, Control


title: ThPOK-/- modified GMP Cell_39

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_39


title: SOW004_ZR751_24hDMSO_1


title: ThPOK-/- modified GMP Cell_54

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_54


title: Romidepsin.24h


title: ThPOK-/- modified GMP Cell_61

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_61


title: SOW004_ZR751_24h9363_3


title: Romidepsin.12h


title: ThPOK-/- modified GMP Cell_68

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_68


title: Romidepsin.6h.rep2


title: RatIgG control

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
All preprocessing was done with the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: CellRanger filtered read counts in MatrixMarket format, features and barcodes in tab delimited format.

source_name: Large Intestine

extract_protocol:
FcR Blocking Reagent (murine, Miltenyi) was used to inhibit unspecific antibody binding. Using fluorescence activated cell sorting (FACS) on a MoFlo Astrios EQ (Beckman Coulter), viable CD45+ LPMCs were separated.
Cells were further prepared for single cell sequencing according to the instructions for the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 from 10x Genomics (Pleasanton).
The libraries were shipped to GeneWiz (South Plainfield) for sequencing. All samples were sequenced together in one Illumina® NovaSeq™ 6000 lane.

treatment_protocol: LPMCs from C57/BL6J mice with acute DSS-colitis treated with DATK32, MECA367 or rat IgG were stained for viability (Fixable Viability Dye eFluor™ 780, Invitrogen) and CD45 (clone 30-F11, Biolegend).

value: Large Intestine

value: LPMC

value: RatIgG


title: Treated with ontamalimab surrogate DATK32

description: 10x Genomics


title: Treated with vedolizumab surrogate MECA367

description: 10x Genomics


title: ChP, SpecificPathogenFreeReconstituted, rep5

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

description:
Sequencing batch 2
510_C_R5_CP_S10

data_processing:
Illumina software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a, converted to BAM-files with Samtools v1.9 and finally counted with HTSeqCount v0.11.2
Limma v3.42.2 was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample

source_name: Choroid Plexus

extract_protocol:
The choroid plexus tissues were collected from the lateral ventricles and snap-frozen immediately before storing at -80°C. Total RNA from choroid plexus was extracted using Aurum total RNA kit (Bio-Rad).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For substantial depletion of the microbiota, SPF mice were provided drinking water containing 0.2 mg/ml ciprofloxacin (Sigma-Aldrich), 1 mg/ml ampicillin (Sigma-Aldrich), 1 mg/ml metronidazole (Sigma-Aldrich), and 0.5 mg/ml vancomycin (Duchefa Biochemie) for 2 weeks ad libitum. Antibiotics were renewed every other day. For recolonization, mice received fecal matter from the SPF mice through two gavages at day 0 and day 2 (once a day) and then were left for 2 weeks before being sacrificed.

value: Choroid Plexus

tag: condition

value: SPFR


title: ThPOK-/- modified GMP Cell_75

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_75

value: ThPOK-/-

value: Bone marrow derived GMP


title: ChP, SpecificPathogenFreeReconstituted, rep4

description:
Sequencing batch 2
509_C_R4_CP_S9


title: ThPOK-/- modified GMP Cell_82

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_82


title: Etoposide.48h

value: Etoposide


title: Etoposide.36h


title: SOW004_T47D_8hDMSO_3

value: Breast cancer cells

value: DMSO

value: 8 hr


title: 4716-11, sgPpia#4.1, Restored

value: sgPpia#4.1 + 4-OHT


title: ChP, SpecificPathogenFreeReconstituted, rep2

description:
Sequencing batch 2
507_C_R2_CP_S7


title: ChP, SpecificPathogenFreeReconstituted, rep3

description:
Sequencing batch 2
508_C_R3_CP_S8


title: SOW004_ZR751_24h9363_2

value: WT

value: KAT6 inhibitor

value: 24 hr


title: SOW004_ZR751_24h9363_1


title: Etoposide.12h


title: ThPOK-/- modified GMP Cell_81

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_81


title: Etoposide.24h


title: ChP, SpecificPathogenFreeReconstituted, rep1

description:
Sequencing batch 2
506_C_R1_CP_S6


title: Smarce1-AID_asyn_aid23_rep1

description:
nascent RNA
Smarce1-AID_asyn_aid23_2425069

value: mouse embryonic stem cells

value: untreated


title: ThPOK-/- modified GMP Cell_24

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_24


title: Etoposide.6h.rep2

value: human erythroleukemic cell line


title: ChP, GermFreeReconstituted, rep4

description:
Sequencing batch 2
505_GF_R5_CP_S5

value: GFR


title: ThPOK-/- modified GMP Cell_38

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_38


title: Imatinib.48h

value: Imatinib


title: ThPOK-/- modified GMP Cell_53

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_53


title: SOW004_T47D_8hDMSO_2


title: ChP, GermFreeReconstituted, rep3

description:
Sequencing batch 2
504_GF_R4_CP_S4

value: Choroid Plexus


title: Imatinib.36h


title: SOW004_T47D_8hDMSO_1


title: ChP, GermFreeReconstituted, rep2

description:
Sequencing batch 2
503_GF_R3_CP_S3


title: Imatinib.24h


title: SOW004_T47D_4hDMSO_3

value: 4 hr


title: ThPOK-/- modified GMP Cell_31

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_31

value: ThPOK-/-


title: SOW004_T47D_8h9363_1


title: SOW004_T47D_8h9363_3


title: SOW004_T47D_8h9363_2


title: ThPOK-/- modified GMP Cell_60

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_60

value: Bone marrow derived GMP


title: SOW004_T47D_4hDMSO_2


title: Imatinib.12h


title: Imatinib.6h.rep2


title: SOW004_T47D_4h9363_3


title: ThPOK-/- modified GMP Cell_67

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_67


title: SOW004_T47D_4hDMSO_1


title: ThPOK-/- modified GMP Cell_74

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_74


title: ChP, AntibioticsTreatedReconstituted, rep5

description:
Sequencing batch 1
324_AB88_5_CP_S21

value: ABR


title: ChP, GermFreeReconstituted, rep1

description:
Sequencing batch 2
502_GF_R2_CP_S2


title: ThPOK-/- modified GMP Cell_73

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_73


title: ChP, AntibioticsTreatedReconstituted, rep4

description:
Sequencing batch 1
323_AB88_4_CP_S20


title: MRE11A.Doxycycline.8d

value: Doxycycline

value: 8 days


title: ChP, AntibioticsTreatedReconstituted, rep3

description:
Sequencing batch 1
322_AB88_3_CP_S19


title: SOW004_T47D_4h9363_2

value: Breast cancer cells


title: ThPOK-/- modified GMP Cell_16

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_16


title: MRE11A.Doxycycline.5d

value: 5 days


title: ChP, AntibioticsTreatedReconstituted, rep2

description:
Sequencing batch 1
321_AB88_2_CP_S18


title: SOW004_T47D_4h9363_1

value: WT


title: SOW004_T47D_24hDMSO_3

value: DMSO


title: MRE11A.Water.8d

value: water


title: ChP, AntibioticsTreatedReconstituted, rep1

description:
Sequencing batch 1
320_AB88_1_CP_S17


title: ThPOK-/- modified GMP Cell_23

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_23


title: ThPOK-/- modified GMP Cell_30

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_30


title: LIG3.Doxycycline.8d


title: SOW004_T47D_24hDMSO_2

value: 24 hr


title: ThPOK-/- modified GMP Cell_52

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_52


title: MRE11A.Water.5d


title: ChP, AntibioticsTreated, rep4

description:
Sequencing batch 1
318_AB46_4_CP_S15

value: AB


title: ChP, AntibioticsTreated, rep5

description:
Sequencing batch 1
319_AB46_5_CP_S16


title: ThPOK-/- modified GMP Cell_37

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_37


title: LIG3.Water.8d

value: human erythroleukemic cell line


title: ChP, AntibioticsTreated, rep3

description:
Sequencing batch 1
317_AB46_3_CP_S14


title: SOW004_T47D_24hDMSO_1


title: CSB.Doxycycline.2d

value: 2 days


title: SOW004_T47D_24h9363_3

value: KAT6 inhibitor


title: SOW004_T47D_24h9363_2


title: ThPOK-/- modified GMP Cell_66

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_66


title: ChP, AntibioticsTreated, rep2

description:
Sequencing batch 1
316_AB46_2_CP_S13

value: Choroid Plexus


title: ThPOK-/- modified GMP Cell_65

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_65


title: ChP, AntibioticsTreated, rep1

description:
Sequencing batch 1
315_AB46_1_CP_S12


title: SOW004_T47D_24h9363_1


title: LINE.Doxycycline.2d


title: ChP, SpecificPathogenFree, rep6

description:
Sequencing batch 1
313_C8_CP_S11

value: SPF


title: ThPOK-/- modified GMP Cell_8

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_8

value: ThPOK-/-


title: LINE.Water.2d


title: ThPOK-/- modified GMP Cell_15

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_15

value: Bone marrow derived GMP


title: ChP, SpecificPathogenFree, rep4

description:
Sequencing batch 1
311_C6_CP_S9


title: ChP, SpecificPathogenFree, rep5

description:
Sequencing batch 1
312_C7_CP_S10


title: CAMA1_KAT6 inhibitor_120hr_R2

data_processing:
Bulk RNA sequencing reads were mapped against the Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium (http://ftp.ensembl.org/, build 38, R100) and alignment files converted into BAM format using the R package Rsubread (ver 2.6.4) (Liao et al., 2019). Aligned reads were then counted and assigned to features of the corresponding gene annotation file (ensemble R100) using featureCounts from Rsubread. Read counts data were converted to log2 counts per million (logCPM) and were normalised using the trimmed mean of M-values (TMM) method (Robinson and Oshlack, 2010) using all genes in the panel.
Differential expression (DE) and pathway enrichment analysis were carried out using R/Bioconductor packages edgeR (v3.30.3) (McCarthy et al., 2012; Robinson et al., 2010) and limma (v3.44.3) (Ritchie et al., 2015). DE analysis was modelled using linear models and empirical Bayes moderated t-statistic which is more robust than a t-statistic from a classic t-test.
Assembly: hg38
Supplementary files format and content: Gene expression qunatification in TPM

extract_protocol: Cells were treated in triplicate with DMSO control or 30 nM PF-9363 for 2 or 5 days and resuspended in RNALater (Ambion #AM-7020) for RNA extraction. At this dose KAT6 biomarker, H3K23Ac is strongly inhibited while having minimal effects on KAT7 biomarker, H3K14Ac (Figure S12). RNA quality was ensured with >8 RIN value using Agilent 2100 Bioanalyzer. cDNA library was generated with TruSeq Stranded mRNA Library Prep kit (Illumina #20020595) and sequenced with Illumina HiSeq X Ten Platform with 150 bp paired-end reads with > 30 million clusters per sample.

treatment_protocol: Approximately Two million cells in triplicate were harvested, rinsed with PBS and stored in RNAlater RNA stabilization solution


title: Cas9.Doxycycline.2d


title: ThPOK-/- modified GMP Cell_59

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_59


title: ChP, SpecificPathogenFree, rep3

description:
Sequencing batch 1
309_C4_CP_S8


title: CAMA1_DMSO_120hr_R3


title: ThPOK-/- modified GMP Cell_22

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_22


title: Cas9.Water.2d


title: ThPOK-/- modified GMP Cell_29

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_29


title: CAMA1_DMSO_120hr_R2


title: CAMA1_KAT6 inhibitor_120hr_R3


title: CAMA1_DMSO_120hr_R1


title: AsiSI.Water.13d

value: AsiSI-overexpression

value: 13 days


title: ChP, SpecificPathogenFree, rep1

description:
Sequencing batch 1
307_C2_CP_S6


title: CSB.Water.2d


title: CAMA1_KAT6 inhibitor_120hr_R1


title: ThPOK-/- modified GMP Cell_51

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_51


title: ThPOK-/- modified GMP Cell_36

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_36


title: AsiSI.Doxycycline.4d

value: Doxycycline

value: 4 days


title: ChP, SpecificPathogenFree, rep2

description:
Sequencing batch 1
308_C3_CP_S7


title: CAMA1_KAT6 inhibitor_48hr_R3

value: Breast cancer cells

value: 48 hr


title: ChP, GermFree, rep5

description:
Sequencing batch 1
305_GF2_5_CP_S5

value: GF


title: AsiSI.Water.4d

value: water


title: ChP, GermFree, rep4

description:
Sequencing batch 1
304_GF2_4_CP_S4


title: CAMA1_KAT6 inhibitor_48hr_R2

value: WT


title: ThPOK-/- modified GMP Cell_57

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_57


title: ChP, GermFree, rep3

description:
Sequencing batch 1
303_GF2_3_CP_S3


title: AsiSI.Doxycycline.13d


title: AZ-20_KU-60019_NU7441.3h_ Mirin.6h


title: AZ-20_KU-60019_NU7441.3h_Etoposide.6h


title: CAMA1_DMSO_48hr_R3

value: DMSO


title: ChP, GermFree, rep2

description:
Sequencing batch 1
302_GF2_2_CP_S2


title: ThPOK-/- modified GMP Cell_7

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_7


title: CAMA1_DMSO_48hr_R2


title: AZ-20_KU-60019_NU7441.3h_SN-38.6h

value: human erythroleukemic cell line


title: DMSO.3h_Etoposide.6h

value: DMSO+Etoposide


title: ThPOK-/- modified GMP Cell_14

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_14


title: ThPOK-/- modified GMP Cell_58

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_58


title: CAMA1_DMSO_48hr_R1


title: ThPOK-/- modified GMP Cell_48

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_48


title: CAMA1_KAT6 inhibitor_48hr_R1

value: KAT6 inhibitor


title: ThPOK-/- modified GMP Cell_21

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_21


title: HCC1954_KAT6 inhibitor_120hr_R3


title: HCC1954_KAT6 inhibitor_120hr_R2


title: DMSO.3h_Mirin.6h

value: DMSO+ Mirin


title: dBet6_r2

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Sequencing reads were trimmed using cutadapt and aligned to the mouse genome using STAR
Gene count matrix was obtained from the aligned 3’ reads using featureCounts
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: SHH-GFP

growth_protocol: SHH-GFP cells were grown to confluency, serum-starved overnight and then treated with DMSO alone or DMSO, 10 mM HPI-1, 1 mM HPP-9 or 1 mM dBet6 for 8 hours (and 24h exclusively for the HPP-9 sample) in the presence of ShhN in starvation medium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Collibri 3’ mRNA kit for Illumina sequencing (Invitrogen)

treatment_protocol: DMSO alone or DMSO, 10uM HPI-1, 1 uM HPP-9 or 1 uM dBet6 for 8 hours (and 24h exclusively for the HPP-9 sample).

value: SHH-GFP

value: dBet6 +Shh


title: HPP9-24h_r2

value: HPP9 (24h) +Shh


title: DMSO.3h_DMSO.6h

value: DMSO+DMSO


title: ThPOK-/- modified GMP Cell_35

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_35

value: ThPOK-/-

value: Bone marrow derived GMP


title: HPP9_r2

value: HPP9 +Shh


title: ThPOK-/- modified GMP Cell_28

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_28


title: HPI1_r2

value: HPI1 +Shh


title: HCC1954_KAT6 inhibitor_120hr_R1

value: Breast cancer cells


title: ThPOK-/- modified GMP Cell_50

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_50


title: Smarce1-AID_IAA_60min_aid06_rep2

description:
nascent RNA
Smarce1-AID_IAA_60_aid06_2425114

value: mouse embryonic stem cells

value: cells were released from mitosis for 60 min


title: ChP, GermFree, rep1

description:
Sequencing batch 1
301_GF2_1_CP_S1

value: Choroid Plexus

value: GF


title: AZ-20_KU-60019_NU7441.3h_Talazoparib.3h

value: human erythroleukemic cell line


title: HCC1954_DMSO_120hr_R3

value: WT

value: DMSO


title: DMSO.3h_SN-38.6h


title: DMSOShh_r2

value: DMSO +Shh


title: ThPOK-/- modified GMP Cell_49

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_49


title: ThPOK-/- modified GMP Cell_96

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_96


title: DMSO.3h_Talazoparib.3h

value: DMSO+Talazoparib


title: HPP9-24h_r1

value: SHH-GFP


title: DMSO_r2


title: HCC1954_DMSO_120hr_R2


title: DMSO.3h_DMSO.3h


title: HCC1954_DMSO_120hr_R1


title: dBet6_r1

value: dBet6 +Shh


title: HCC1954_KAT6 inhibitor_48hr_R2

value: KAT6 inhibitor

value: 48 hr


title: Romidepsin.3h

value: Romidepsin


title: HCC1954_KAT6 inhibitor_48hr_R3


title: ThPOK-/- modified GMP Cell_6

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_6

value: ThPOK-/-

value: Bone marrow derived GMP


title: ThPOK-/- modified GMP Cell_13

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_13


title: ThPOK-/- modified GMP Cell_47

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_47


title: Torin1.6h


title: HCC1954_KAT6 inhibitor_48hr_R1

value: Breast cancer cells


title: HPP9_r1

value: HPP9 +Shh


title: ThPOK-/- modified GMP Cell_20

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_20


title: HCC1954_DMSO_48hr_R3


title: HPI1_r1

value: HPI1 +Shh


title: Rapamycin.6h

value: Rapamycin


title: DMSOShh_r1


title: Torin1.3h


title: ThPOK-/- modified GMP Cell_27

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_27


title: HCC1954_DMSO_48hr_R2


title: Romidepsin.6h.rep1


title: ThPOK-/- modified GMP Cell_34

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_34


title: DMSO_r1


title: HCC1954_DMSO_48hr_R1


title: ThPOK-/- modified GMP Cell_33

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_33


title: HCC1187_KAT6 inhibitor_120hr_R3


title: ThPOK-/- modified GMP Cell_88

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_88


title: DEX_PCP_3

last: Song

address: 8 Gongren Tiyuchang Nanlua, Chaoyang District

department: Medical Research Center

institute: Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Mice were sacrificed under anesthetization at specific time points. Lung tissues were collected, minced and then digested using the Lung Dissociation Kit (Miltenyi Biotech) in combination with the gentleMACS™ Dissociators (Miltenyi Biotech) in accordance with the instruction manual. After incubation at 37°C for 30 min with shaking, cell suspensions were filtered with 70 μm cell strainers and centrifuged at 300 g for 5 min. Then the resulting pellet was lysed with RBC lysing buffer (BD) to remove erythrocytes followed by centrifugation and cell numbers as well as viability determination.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cell suspensions were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3‘ Library and Gel Bead Kit V3 and Chromium Single Cell A Chip Kit according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. After reverse transcription , single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads. cDNA was generated and amplified, and quality was assessed using the Agilent 4200. Finally sequencing was performed on an Illumina Novaseq 6000.

value: Lung

value: Lung cells

value: 6-8 weeks old

tag: group


title: DEX_PCP_1

description: 10x Genomics


title: DEX_PCP_2

description: 10x Genomics


title: HCC1187_KAT6 inhibitor_120hr_R1

value: WT


title: HCC1187_KAT6 inhibitor_120hr_R2


title: LUMC04i10 Day 110

city: Leiden

first: Wouter

middle: H

last: van der Valk

address: Albinusdreef 2

department: Department of Otorhinolaryngology and Head & Neck Surgery

country: Netherlands

institute: Leiden University Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PSC-derived inner ear organoids

growth_protocol: Experiments were performed with eight apparently healthy PSC lines. The WA01 human embryonic stem cell line (male, passages 47-52) was purchased from WiCell Research Institute. The two commercially available hiPSC lines that were used are from the same parental male background line (GM25256 from the Coriell Institute): AICS-0074 with the SRY-Box Transcription Factor 2-mEGFP (SOX2-GFP) reporter (hereafter WTC-SOX2, passages 34-46) acquired from the Allen Institute and WTC-GCaMP with a version of the genetically engineered calcium indicator (passages 36-44) provided by Bruce Conklin at the Gladstone Institutes/UCSF (Huebsch et al., 2015). We used additional hiPSC lines that were generated in-house. Generated by the Human iPSC Hotel (Leiden University Medical Center) LUMC0004iCtrl10 (hereafter LUMC04i10, male, passages 15-36) (Dambrot et al., 2014), LUMC044iCtrl44 (hereafter LUMC44i44, female, passages 20-43) (Chen et al., 2017), or generated by the Human Neuron Core (Boston Children’s Hospital) SAH0047-02 (female, passages 23-25) (Ebrahimi-Fakhari et al., 2016), GON0515-03 (male, passages 22-24) (Shlevkov et al., 2019), GON0926-02 (female, passages 19-21). The cell lines tested negative for mycoplasma prior to experimentation. Cells were cultured on 6-well plates coated with vitronectin recombinant human protein (A14700, Gibco, concentration 0.5 µg/cm) and maintained in Essential 8 Flex medium (A2858501, Gibco) with Normocin (ant-nr-1, Invivogen, concentration 100 µg/ml), hereafter E8 medium. The E8 medium was replenished every other day or every day depending on cell confluency. At approximately 80% confluence (every 4-5 days on average), WTC-SOX2 cells were passaged as single cells using Stempro Accutase Cell Dissociation Reagent (hereafter Accutase; A1110501, Gibco) using 10 µM Y27632 (04-0012-02, Stemgent). The Y27632 was removed within 24 hours after passaging by a medium replenishment. All other lines were passaged at approximately 80% confluency (every 4-5 days on average) as tiny cluster (3-5 cells on average) using 0.5 mM EDTA (15575020, Gibco, concentration 10 mM).

extract_protocol:
Aggregate dissociation to single cells for scRNAseq    Vibratomed sections or randomly selected aggregates were pooled at specified time points. Three to four number of aggregates were placed in warm TrypLE (12605036, Gibco) and incubated in a 37°C incubator under 5% CO2 on an orbital shaker set to 65 rpm. The mixture was triturated with a pipette using wide bore p1000 tips every 10 minutes. Dissociation to single cells was complete after 60 minutes and confirmed by bright-field visualization using a Nikon TS2R. TrypLE activity was stopped by adding cold 3% bovine serum albumin (BSA; A7030, Sigma‐Aldrich) in PBS. To remove residual cell aggregates and debris, the suspension was filtered with a 40 μm Flowmi cell strainer (H13680-0040, Bel-Art). After washing three times with 3% BSA in PBS, cells were resuspended in cold 3% BSA in PBS and filtered again with a 40 μm Flowmi cell strainer. Cell viability was determined by using Trypan Blue (15250061, Gibco) and an automated cell counter (Countess II, Thermo Fisher). Cell suspensions were diluted with cold 3% BSA in PBS to reach a final concentration of 1,000 cells/μL.     Aggregate dissociation to single nuclei for snRNAseq  2-4 randomly selected aggregates were processed at specified time points. Aggregates were pooled, washed once with ice-cold PBS, and resuspended in lysis buffer that contained 10 mM Tris-HCl (T2194, Millipore-Sigma), 10 mM NaCl (59222C, Millipore-Sigma), 3 mM MgCl2 (M1028, Millipore-Sigma), 0.1% Nonidet P40 Substitute (74385, Millipore-Sigma) in DEPC-treated water (750024, Invitrogen). The suspension was transferred to a Dounce tissue grinder (885300-0002, Kimble) and ground every 5 min. After 20 min, dissociation to single nuclei was confirmed by bright-field visualization (EVOS M5000, Thermo Scientific). After trituration using p1000 and p200 tips, the suspension was filtered through a 70 μm MACS SmartStrainer (130-098-462, Miltenyi Biotec), centrifuged at 500xg for 5 min at 4°C and resuspended in 1% BSA in PBS (AM2616, Invitrogen) containing 200 U/μL RNase inhibitor (3335402001, Millipore-Sigma). After filtration using a 40 μm Flowmi cell strainer and centrifugation at 500g for 5 minutes at 4°C, the nuclei suspension was resuspended to a final concentration of 1,000 cells/μL.  For one experiment of D110 aggregates generated using the LUMC04i10 hiPSC line, we performed nuclear hashtagging of two separate aggregates using single nuclei hashing antibodies (MAb414, Merck). To this end, the nuclei suspension was blocked using Fc Blocking reagent (422302, Biolegend) for 5 min on ice followed by incubation with the hashing antibody (1 µg per 100 µl) for 10 min on ice. Subsequently, nuclei were washed three times using 1% BSA in PBS containing 200 U/μL RNase inhibitor, pooled together 1:1, and resuspended to a final concentration of 1,000 cells/μL.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and the NexSeq500 or NovaSeq 6000 sequencer (Illumina, Inc). Approximately 17,000 cells or nuclei (targeting for 10,000 cells) per sample were added to a single cell master mix, following the Chromium Single Cell 3’ Reagent Kits v2 and v3.1 User Guide (10x Genomics, Inc). Along with the single-cell gel beads and partitioning oil in separate wells of a Single Cell A Chip or Chromium Next GEM Chip G Single Cell (10x Genomics), the single cell reaction mixture was loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer. The resulting library was sequenced in a custom program for 26b plus 98b paired-end sequencing on an Illumina NextSeq500 or 28b plus 91b paired-end on Illumina NovaSeq 6000 to a read depth of >30,000 reads per cell. FASTQ files were generated using Cell Ranger mkfastq (10x Genomics).

treatment_protocol: Inner ear organoid induction followed the protocol recently published with minor alterations (Koehler et al., 2017; Steinhart et al., 2021). In brief, colonies of human pluripotent stem cells were detached and dissociated using Accutase and collected as a single cell suspension in E8 medium containing 20 µM Y27632. 3,500 cells in 100 µl suspension were distributed per well into 96-well U-bottom plates with a super low cell attachment surface (174925, Thermo Scientific). After centrifugation at 110xg for 6 min to aid aggregation, the cell aggregates were incubated in 37°C incubator under 5% CO2 for 48 h. After 24 h incubation, 100 µl of fresh E8 medium was added per well to dilute out Y27632.   To start differentiation, that is differentiation day 0 (D0), all cell aggregates were collected and individually transferred to a new 96-well U bottom plate with a super low cell attachment surface in 100 µl of E6 medium (A1516401, Gibco) with Normocin (concentration 100 µg/ml), hereafter E6 medium, containing 2% Matrigel Growth Factor Reduced (hereafter Matrigel; 354230, Corning), 10 µM SB431542 (04-0010-05, Stemgent), 4 ng/ml basic FGF (hereafter FGFb; 100-18B, PeproTech) and 0-40 ng/ml BMP-4 (listed in the Key Resources Table). On D3, 25 µl of E6 per well was added in with an end-concentration of 200 ng/ml LDN (04-0074-02, Stemgent) and 50 µg/ml FGFb, making the total volume 125 µl per well. This treatment induces cranial neural crest formation. On D6, the total volume is increased to 200 µl by adding 75 µl of fresh E6 medium. On D8, 100 µl of the medium was changed for E6 containing 6 µM CHIR99021 (hereafter CHIR; 04-0004-02, Stemgent) to induce otic placode formation. On D10, 100 µl of the medium was changed for fresh E6 containing 3 µM CHIR.   On D12, the aggregates were transferred to Organoid Maturation Medium (OMM) containing 1% Matrigel and 3 µM CHIR in a 24-well plate with a super low cell attachment surface (174930, Thermo Scientific) on an in-incubator orbital shaker. OMM is a 1:1 mixture of Advanced DMEM:F12 (12634010, Gibco) and Neurobasal Medium (21103049, Gibco), supplemented with 0.5x B27 without Vitamin A (12587010, Gibco), 0.5x N2 Supplement (17502048, Gibco), 1x Glutamax (35050061, Gibco), 0.1 mM ß-Mercaptoethanol (21985023, Gibco), and Normocin. On D15, a half medium change was performed with OMM containing 1% Matrigel and 3 µM CHIR. On D18, a half medium change with OMM was performed, diluting out the Matrigel and CHIR. On D21, a full medium change with OMM was performed. Half of the spent medium was replenished every three days, with a full medium change every nine days. The volume was gradually increased starting from 500 µl at D12, to 1 ml on approximately D45, to 1.5 ml on approximately D60 and later.

value: PSC-derived inner ear organoids

value: hiPSC

value: Healthy


title: LUMC04i10 and WA01 D75

description: 10x Genomics

value: WA01 and LUMC0004iCtrl10

value: ESC/hiPSC

value: Inner ear organoid induction followed the protocol recently published with minor alterations (Koehler et al., 2017; Steinhart et al., 2021). In brief, colonies of human pluripotent stem cells were detached and dissociated using Accutase and collected as a single cell suspension in E8 medium containing 20 µM Y27632. 3,500 cells in 100 µl suspension were distributed per well into 96-well U-bottom plates with a super low cell attachment surface (174925, Thermo Scientific). After centrifugation at 110xg for 6 min to aid aggregation, the cell aggregates were incubated in 37°C incubator under 5% CO2 for 48 h. After 24 h incubation, 100 µl of fresh E8 medium was added per well to dilute out Y27632.   To start differentiation, that is differentiation day 0 (D0), all cell aggregates were collected and individually transferred to a new 96-well U bottom plate with a super low cell attachment surface in 100 µl of E6 medium (A1516401, Gibco) with Normocin (concentration 100 µg/ml), hereafter E6 medium, containing 2% Matrigel Growth Factor Reduced (hereafter Matrigel; 354230, Corning), 10 µM SB431542 (04-0010-05, Stemgent), 4 ng/ml basic FGF (hereafter FGFb; 100-18B, PeproTech) and 0-40 ng/ml BMP-4 (listed in the Key Resources Table). On D3, 25 µl of E6 per well was added in with an end-concentration of 200 ng/ml LDN (04-0074-02, Stemgent) and 50 µg/ml FGFb, making the total volume 125 µl per well. This treatment induces cranial neural crest formation. On D6, the total volume is increased to 200 µl by adding 75 µl of fresh E6 medium. On D8, 100 µl of the medium was changed for E6 containing 6 µM CHIR99021 (hereafter CHIR; 04-0004-02, Stemgent) to induce otic placode formation. On D10, 100 µl of the medium was changed for fresh E6 containing 3 µM CHIR.   On D12, the aggregates were transferred to Organoid Maturation Medium (OMM) containing 1% Matrigel and 3 µM CHIR in a 24-well plate with a super low cell attachment surface (174930, Thermo Scientific) on an in-incubator orbital shaker. OMM is a 1:1 mixture of Advanced DMEM:F12 (12634010, Gibco) and Neurobasal Medium (21103049, Gibco), supplemented with 0.5x B27 without Vitamin A (12587010, Gibco), 0.5x N2 Supplement (17502048, Gibco), 1x Glutamax (35050061, Gibco), 0.1 mM ß-Mercaptoethanol (21985023, Gibco), and Normocin. On D15, a half medium change was performed with OMM containing 1% Matrigel and 3 µM CHIR. On D18, a half medium change with OMM was performed, diluting out the Matrigel and CHIR. On D21, a full medium change with OMM was performed. Half of the spent medium was replenished every three days, with a full medium change every nine days. The volume was gradually increased starting from 500 µl at D12, to 1 ml on approximately D45, to 1.5 ml on approximately D60 and later.


title: ThPOK-/- modified GMP Cell_46

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_46


title: DEX_2

description: 10x Genomics

value: DEX


title: DEX_3

description: 10x Genomics


title: Rapamycin.3h

value: human erythroleukemic cell line


title: WTC-SOX2 Day 100 2

description: 10x Genomics


title: HCC1187_DMSO_120hr_R2

value: DMSO


title: ThPOK-/- modified GMP Cell_5

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_5

value: ThPOK-/-

value: Bone marrow derived GMP


title: WTC-GCaMP Day 75

description: 10x Genomics

value: WTC-GCaMP


title: DEX_1

description: 10x Genomics


title: ThPOK-/- modified GMP Cell_12

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_12


title: LUMC04i10 and WA01 D110

description: 10x Genomics


title: WTC-SOX2 Day 100

description: 10x Genomics


title: HCC1187_DMSO_120hr_R1

value: Breast cancer cells


title: ThPOK-/- modified GMP Cell_95

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_95


title: HCC1187_DMSO_120hr_R3


title: WT_PCP_3

description: 10x Genomics

value: Lung


title: flag-hct116-orc1-oe-down-rep2

description:
On the iCLIP gel isolation cut lower band than expected ORC1 molecular weight, with Low RNase treatment Replicate 1
Flag_HCT116_ORC1_down_merge_grouped_cdna.bed
Flag_HCT116_ORC1_down_merge_grouped_cdna_peaks.bed
Flag_HCT116_ORC1_down_merge_grouped_cdna_norm.bigWig

data_processing:
Library strategy: iCLIP-seq
iCLIP sequencing reads were analysed on the iMaps server (https://imaps.genias.com/) using the iCount software (https://github.com/tomazc/iCount 18).
Briefly, experimental barcodes were removed and sequencing reads aligned with STAR 9 to human genome build GRCh38 primary assembly GENCODE version 27, allowing two mismatches and ten secondary alignments.
Unique Molecular Identifiers (UMIs), were used to distinguish and remove PCR duplicates. To determine protein-RNA contact sites, the sequencing read preceding nucleotide was allocated as the crosslink site event.
Significant contact sites were then identified, using the iCount peak function, based on false discovery rate (FDR) <0.05 comparing specific sites within a window of three nucleotides with randomised data (100 permutations) and within co-transcribed regions (https://github.com/tomazc/iCount/blob/master/iCount/analysis/peaks.py). The significant crosslink signal was normalised by CPM. For individual samples we also used Paraclu peak caller.
Assignment of crosslink sites to coding transcripts, non-coding or biotype features, was done by following segmentation hierarchy rules (https://github.com/tomazc/iCount/blob/master/iCount/genomes/segment.py).
Then, replicates were merged and summary of cDNA counts within genes and genic regions were generated with iCount summary function, normalising the counts by the length of the corresponding region.
Genome_build: GRCh38 primary assembly GENCODE version 27
Supplementary_files_format_and_content: Crosslink bed, group bed, peaks bed, group peaks bed, normalised bigwig.
Supplementary_files_format_and_content: flag-hct116-notf-down_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-notf-up_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep3_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep1_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep1_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep2_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep3_trimmed_single.bed: crosslink bed
Supplementary_files_format_and_content: flag-hct116-notf-down_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-notf-up_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-down-rep3_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep1_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-highrnase-up-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep1_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep2_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: flag-hct116-orc1-oe-up-rep3_trimmed_single_peaks.bed: peaks bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna.bed: group bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna_peaks.bed: group peaks bed
Supplementary_files_format_and_content: Flag_HCT116_NoTF_Up_Down_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1_down_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1-OE_HighRNase_Up_merge_grouped_cdna_norm.bigWig: normalised bigwig
Supplementary_files_format_and_content: Flag_HCT116_ORC1_up_merge_grouped_cdna_norm.bigWig: normalised bigwig

value: Transfected with pcDNA3.1-ORC1-3xFLAG

value: FLAG antibody (M2, F1804, Sigma)


title: WTC-SOX2 Day 75

description: 10x Genomics


title: ThPOK-/- modified GMP Cell_19

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_19


title: ThPOK-/- modified GMP Cell_25

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_25


title: WT_PCP_1

description: 10x Genomics

value: Lung cells

value: 6-8 weeks old


title: ThPOK-/- modified GMP Cell_26

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_26


title: HCC1187_KAT6 inhibitor_48hr_R2

value: WT

value: KAT6 inhibitor

value: 48 hr


title: WT_PCP_2

description: 10x Genomics


title: HCC1187_KAT6 inhibitor_48hr_R3


title: Vestibular adult

description: 10x Genomics

source_name: Utricle and crista ampullaris

growth_protocol: Collection of human embryonic and inner ear tissue was performed according to the Dutch legislation (Fetal Tissue Act, 2001) and the WMA Declaration of Helsinki guidelines. For this project, we obtained approval from the Medical Research Ethics Committee of Leiden University Medical Center (protocol registration number B19.070) as well as written informed consent of the donor following the Guidelines on the Provision of Fetal Tissue set by the Dutch Ministry of Health, Welfare, and Sport (revised version, 2018). The inner tissue was collected after elective termination of pregnancy by vacuum aspiration. Embryonic or fetal age was determined by obstetric ultrasonography prior to termination, with a standard error of 2 days.  Adult vestibular tissue was collected during translabyrinthine vestibular schwannoma surgery. This project was also approved by the Medical Research Ethics Committee of Leiden University Medical Center (protocol registration number B18.028) and tissue was obtained after written informed consent of the donor.

extract_protocol:
Human fetal inner ear tissue was stored in RNAlater (AM7020, Invitrogen) at 4°C and processed to a single nuclei suspension within 16 h after collection. Human adult tissue was processed within 2 h after collection. After collection of the inner ear tissue, the tissue was evaluated using a dissection microscope (M205C, Leica). The otic capsule of the W9.2 fetal inner ear was removed. The tissue was washed once with ice-cold PBS, and resuspended in lysis buffer that contained 10 mM Tris-HCl (T2194, Millipore-Sigma), 10 mM NaCl (59222C, Millipore-Sigma), 3 mM MgCl2 (M1028, Millipore-Sigma), 0.005% Nonidet P40 Substitute (74385, Millipore-Sigma) in DEPC-treated water (750024, Invitrogen). The suspension was transferred to a Dounce tissue grinder (885300-0002, Kimble) and ground every 5 min. After 20 min, dissociation to single nuclei was confirmed by bright-field visualization (EVOS M5000, Thermo Scientific). After trituration using p1000 and p200 tips, the suspension was filtered through a 70 μm MACS SmartStrainer (130-098-462, Miltenyi Biotec), centrifuged at 500xg for 5 min at 4°C and resuspended in 1% BSA in PBS (AM2616, Invitrogen) containing 200 U/μL RNase inhibitor (3335402001, Millipore-Sigma). After filtration using a 40 μm Flowmi cell strainer, as well as filtratration through a 20 μm and 10 μm Pluristrainer (43-10020-40 and 43-10010-40, PluriSelect), the nuclei suspension was resuspended to a final concentration of 1,000 cells/μL.
Single nucleus gene expression libraries were generated on the 10x Genomics Chromium platform using the Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to the manufacturer’s protocol.  Gene expression was sequenced on a NovaSeq 6000 S4 flow cell using v1 chemistry (Illumina) and FASTQ files were generated using Cell Ranger mkfastq (10x Genomics).

value: Utricle and crista ampullaris


title: HCC1187_KAT6 inhibitor_48hr_R1


title: Inner ear fetal age W9.2

description: 10x Genomics

source_name: Whole inner ear, only membranous labyrinth


title: ThPOK-/- modified GMP Cell_80

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_80


title: HCC1187_DMSO_48hr_R3


title: CON_2

description: 10x Genomics

value: CON


title: CON_3

description: 10x Genomics


title: ThPOK-/- modified GMP Cell_87

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_87


title: Inner ear fetal age W7.5

description: 10x Genomics

source_name: Whole inner ear containing otic capsule

value: Whole inner ear containing otic capsule


title: ThPOK-/- modified GMP Cell_94

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_94


title: Galdos_Seq_Run3

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

address: 265 Campus Dr.

department: Cardiovascular Institute

institute: Stanford University

description:
Human induced pluripotent stem cells were differentiated using biphasic WNT protocol for cardiomyocyte differentiation. Samples were frozen at each day of differentiation for both WTC and SCVI-111 cell lines. Samples were thawed to conduct scRNA-seq run using sample multiplexing (CellPlex) protocol.
Sample hashtags sequences are available in the file scRNA-seq-Run_Sample_Descriptions.xlsx on the series record.

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
Droplet Based Sequencing: Data generated using the 10X Genomics 3' scRNA-seq v3.1 kit  were processed using CellRanger v6.0.0 (10X Genomics) count function. Default parameters were used for alignment. The reference genomes used were refdata-gex-GRCh38-2020-A  for Human sequence alignment. References were obtained from the 10X Genomics website.
Chemically modified oligos hashtag sequences were used for demultiplexing samples for each single cell run using the hashtag oligo demultiplexing pipeline published by the developers of the Seurat package.
Assembly: GRCh38 (for Human)
Supplementary files format and content: H5 Format filtered and raw counts matrices

molecule: polyA RNA

source_name: hiPSC-derived Cardiac Differentiation

extract_protocol:
Droplet based extraction: HiPSC-derived cardiac differentiation cells were dissociated into single cell suspensions. Individual samples per timepoint and cell line were labeled using chemically modified lipid oligos using the 10X Genomics CellPlex kit. Single cells  were subsequently captured and lysed using 10X Genomics Chromium Next GEM Single Cell 3' v3.1 Kit with CellPlex. mRNA was reverse transcribed to cDNA, and cDNA pre-amplification was conducted following manufacturer's protocol.
Droplet based library construction: Libraries for samples processed using 10X Genomics Single Cell 3' v3.1 with CellPlex kit were prepared from pre-amplified cDNA and CellPlex libraries according to manufactrer's protocol. Gene expression libraries were generated for all 10X samples, and CellPlex multiplexing libraries were generated for each individual single cell run. Individual library index primers were used for multiplexing libraries on flow cell during sequencing.

value: hiPSC-derived cardiomyocytes

tag: developmental stage

value: multiplexed sample:Days 13, 15, 30

value: multiplexed sample:WTC and SCVI-111


title: CON_1

description: 10x Genomics

tag: cell type


title: HCC1187_DMSO_48hr_R1

tag: genotype

value: DMSO


title: Galdos_Seq_Run2

value: multiplexed sample:Days 0, 7, 11


title: HCC1187_DMSO_48hr_R2

value: Breast cancer cells


title: SARS2 infected, PEG24 pretreated, 1

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

data_processing:
pseudoalignment with kallisto v0.44
DESeq2, in R
Assembly: mmGRCm38
Supplementary files format and content: geo_counts.tsv = flat file of raw per gene counts from kallisto, per sample

source_name: lung

extract_protocol:
NucleoSpin RNA Kit (Macherey-Nagel), manufacturer's protocol
Truseq stranded total mRNA (Illumina), manufacturer's protocol

tag: tissue

value: lung

tag: virus infection

value: treated

tag: treatment timing

value: Pre-Infection

tag: peptide


title: ThPOK-/- modified GMP Cell_45

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_45

tag: strain

value: ThPOK-/-

value: Bone marrow derived GMP


title: Galdos_Seq_Run1

value: multiplexed sample:Days 1,2,3,4,5,6

tag: cell line


title: YMB1_KAT6 inhibitor_120hr_R3

value: WT

tag: treatment

value: KAT6 inhibitor

tag: time


title: YMB1_KAT6 inhibitor_120hr_R2


title: ThPOK-/- modified GMP Cell_11

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_11


title: ThPOK-/- modified GMP Cell_4

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_4


title: SARS2 infected, dimer pretreated, 1

value: Dimer


title: RNAseq_SKNO1_DOX_Rep3

description: RNAseq

source_name: SKNO1 AML cell line (DSMZ no.: ACC 690)

value: bone marrow

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)

value: SKNO1 acute myeloid leukemia

value: 7 days with 1ug/ml Doxycycline


title: SARS2 infected, dimer pretreated, 2