title: scRepliseq_HAP1_RIF1KO_part2

description:
single cell Repli-seq
HAP1_RIF1KO_single_cell_Repli-seq_binarised_array.txt.gz

growth_protocol: HAP1 cells were grown in IMDM plus 10% FBS and 1% Pen/Strep and passaged by trypsinization according to manufacturer's instructions.

extract_protocol:
single cells were sorted from five evenly spaced windows throughout S phase directly into individual wells of a 96 well plate containing single cell lysis buffer and lysed at 50°C for 1 hour followed by 4 minutes at 99°C
Whole genome amplification (WGA) was performed as previously described (PMID: 22555242) and unique barcodes were added to each individual WGA product followed by purification and pooling for NEBNext Ultra DNA Library preparation.

value: human haploid CML cell line

value: RIF1 KO


title: PVG_OM_treated_Control_Saline_0_lung_rep3

status: Public on Apr 26 2021

type: SRA

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

description:
genecounts_lung.csv
RL69_HGMMWDMXX_GCCACAGG.CATGCCAT_L002_R1.fastq.gz

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.3.0 and Real Time Analysis (RTA) vv3.3.3, running on the instrument computer. RTA performs  real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Read libraries were mapped to the rat genome (rn6) using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: rn6
Supplementary_files_format_and_content: genecounts_lung.csv and genecounts_bonemarrow.csv files contain a matrix of raw gene counts (unfiltered and un-normalised data)

molecule: total RNA

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Single-cell suspensions of bone marrow and lung tissue were resuspended in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80°C. Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (Qiagen Gmbh, Hilden, Germany). Total RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit, Illumina Inc, San Diego, CA. Sequencing was performed by the Australian Genome Research Facility (Illumina HiSeq2500, 50bp single-end reads, v4 chemistry).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: PVG

tag: treatment group

tag: experimental group

value: days post infection (dpi):0

tag: Sex

value: male

tag: rna integrity number


title: PVG_Untreated_Virus_OVA_9_lung_rep3

description:
genecounts_lung.csv
RL68_HGMMWDMXX_CCTTCACC.GACGCTCC_L002_R1.fastq.gz

value: Untreated

value: days post infection (dpi):9


title: PVG_OM_treated_Virus_OVA_2_lung_rep3

description:
genecounts_lung.csv
RL71_HGMMWDMXX_ACTCGTGT.ATTGGAAC_L002_R1.fastq.gz

value: days post infection (dpi):2


title: scRepliseq_HAP1_WT_part2

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Department of Biological Science

country: USA

institute: Florida State University

description:
single cell Repli-seq
HAP1_WT_single_cell_Repli-seq_binarised_array.txt.gz

library_source: genomic

data_processing:
Repli-Seq experiments that are marked E and L were analysed according to (Marchal et al., 2018 PMID: 29599440). High-resolution Repli-Seq analysis was performed according to (Zhao et al., 2020 PMID: 32209126). Single-cell repli-seq reads were split according to the barcode list provided in the accompanying manuscript using awk. The subsequent analyses and construction of binarised arrays were performed according to (Dileep et al., 2018, PMID: 29382831). The Hi-C experiments were aligned and deduplicated using HiCUP (https://www.bioinformatics.babraham.ac.uk/projects/hicup/). The subsequent bam files were converted to pair text files using 4DN DCIC utility bam2pairs. Pairs were loaded into cooler at various bin sizes for downstream analyses. ChIP-seq reads were aligned using bowtie-2 to hg38 and PCR duplicates were removed using samtools markdup. Peak calling and fold enrichment over input were calculated using MACS2. In the cases where drosophila spike-in was used the datasets to be compared against each other (e.g. WT vs KO) were normalised according to (Orlando et al 2014, Cell Reports, PMID: 25437568).RNA-seq reads were aligned using STAR. The gene annotation for genome build GRCh38.p10 used for alignment was downloaded from Ensembl. Single cell RNA-seq was aligned to GRCh38 using 10X Genomics spaceranger v1.0.0. The gene count matrix output was used as input for Seurat v 4.0 for further downstream analyses.
Genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cells

tag: cell type

tag: genotype

value: Wild type

tag: chip antibody


title: PVG_OM_treated_Virus_OVA_9_lung_rep2

description:
genecounts_lung.csv
RL64_HGMMWDMXX_CCATTCGA.GTTGTCCG_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_2_lung_rep2

description:
genecounts_lung.csv
RL63_HGMMWDMXX_TTGCCTAG.ACCACTTA_L002_R1.fastq.gz


title: scRNAseq_HAP1_WT

description:
single cell RNA-seq
scRNAseq_tsne.txt

extract_protocol:
cells were harvested with 0.05% trypsin-0.442 nM EDTA and H9 hESCs were harvested with Gentle Cell Dissociation Reagent (StemCell Technologies 07174).   Single cell suspension was adjusted to 1000 cells/ uL for generating single cell RNA-seq libraries using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per manufacturer’s instruction.
single cell RNA-seq libraries were constructed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per manufacturer’s instruction


title: scRNAseq_H9_RIF1KO

description:
single cell RNA-seq
scRNAseq_tsne.txt

source_name: H9 hESCs

growth_protocol: H9 hESCs were grown in feeder free conditions on Geltrex matrix (Thermo Fisher A14133) coated dishes in StemPro (Thermo Fisher A100701) media according to manufacturer's specifications. hESCs were passaged with ReLeSR (StemCell Technologies 05872) according to manufacturer’s specifications.

value: human embryonic stem cell line


title: scRepliseq_HAP1_WT_part1


title: PVG_OM_treated_Control_Saline_0_lung_rep2

description:
genecounts_lung.csv
RL61_HGMMWDMXX_CGGAACTG.CACTACGA_L002_R1.fastq.gz


title: scRNAseq_HAP1_RIF1KO

description:
single cell RNA-seq
scRNAseq_tsne.txt


title: scRNAseq_HCT_RIF1KO

description:
single cell RNA-seq
scRNAseq_tsne.txt

source_name: HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy’s 5A media plus 10% FBS and 1% Pen/Strep and passaged by trypsinization.

value: human colorectal cancer cell line


title: PVG_OM_treated_Virus_Saline_1_lung_rep2

description:
genecounts_lung.csv
RL62_HGMMWDMXX_TAAGGTCA.TGTCGTAG_L002_R1.fastq.gz

value: days post infection (dpi):1


title: PVG_Untreated_Virus_Saline_1_lung_rep2

description:
genecounts_lung.csv
RL58_HGMMWDMXX_CATAATAC.TTCTAACG_L002_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_lung_rep2

description:
genecounts_lung.csv
RL57_HGMMWDMXX_TGCGGCGT.CCTCGGTA_L002_R1.fastq.gz


title: scRNAseq_H9_WT

description:
single cell RNA-seq
scRNAseq_tsne.txt


title: E_fraction_HCT_RIF1KO_H3K9me3KD_Repliseq

description:
Repli-seq
HCT_RIF1KO_H3K9me3KD_KDsiRNA_log2EL_RT.bigwig

extract_protocol:
gDNA was isolated with SDS-PK buffer containing 0.2 mg/ml proteinase K for 2 hours at 56C followed by purification with 800 µl of Genomic Lysis Buffer from the Zymo Quick-DNA Microprep Kit according to manufacturers instructions
DNA from was made into repli-seq library described in (PMID: 29599440)

treatment_protocol: Cells were transfected with siRNAs against SUV39H1/2 and SETDB1 and allowed to recover for 72hrs before a second transfection with the same siRNAs and 48hrs recovery. Cells were then labeled with 100uM BrdU for 2 hours before fixation.

value: RIF1 KO H3K9me3 KD


title: PVG_Untreated_Virus_OVA_9_lung_rep2

description:
genecounts_lung.csv
RL60_HGMMWDMXX_AGCTCGCT.GCAGAATC_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_OVA_9_lung_rep1

description:
genecounts_lung.csv
RL56_HGMMWDMXX_GAATGAGA.GAGGCATT_L002_R1.fastq.gz


title: L_fraction_HCT_RIF1AID_KD_Firstcellcycle_Repliseq

description:
Repli-seq
HCT_RIF1AID_plus_AUX_1st_cell_cycle_sync_log2EL_RT.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and auxin was added to degrade RIF1 then cells were released into the cell cycle for 10, 14, 18, and 22 hours and treated with 100uM BrdU two hours before fixation. Equal numbers of cells from each time point were pooled together for retroactive synchronization by FACS sorting according to DNA content

value: RIF1 KD


title: E_fraction_HCT_RIF1AID_KD_Firstcellcycle_Repliseq


title: PVG_Untreated_Virus_OVA_2_lung_rep2

description:
genecounts_lung.csv
RL59_HGMMWDMXX_GATCTATC.ATGAGGCT_L002_R1.fastq.gz


title: scRNAseq_HCT_WT

description:
single cell RNA-seq
scRNAseq_tsne.txt


title: scRepliseq_HAP1_RIF1KO_part1


title: E_fraction_HCT_RIF1AID_control_Firstcellcycle_Repliseq

description:
Repli-seq
HCT_RIF1AID_ctl_1st_cell_cycle_sync_log2EL_RT.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and released into the cell cycle for 10, 14, 18, and 22 hours and treated with 100uM BrdU two hours before fixation. Equal numbers of cells from each time point were pooled together for retroactive synchronization by FACS sorting according to DNA content

value: control


title: L_fraction_HCT_RIF1KO_H3K9me3KD_Repliseq


title: PVG_Untreated_Virus_Saline_1_lung_rep3

description:
genecounts_lung.csv
RL66_HGMMWDMXX_GTGTCGGA.GCTTGCGC_L002_R1.fastq.gz


title: PVG_Untreated_Control_Saline_0_lung_rep3

description:
genecounts_lung.csv
RL65_HGMMWDMXX_ACACTAAG.ATCCATAT_L002_R1.fastq.gz


title: L_fraction_HCT_RIF1AID_96hr_degrade_Repliseq

description:
Repli-seq
HCT116_RIF1AID_KD_4cellcycles_log2EL_RT.bigwig

treatment_protocol: Cells were treated with auxin to degrade RIF1 for 96 hours


title: PVG_OM_treated_Control_Saline_0_lung_rep1

description:
genecounts_lung.csv
RL53_HGMMWDMXX_CAACAATG.CTTCACGG_L002_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_9_lung_rep1

description:
genecounts_lung.csv
RL52_HGMMWDMXX_GGTGAACC.GCGTTGGA_L002_R1.fastq.gz


title: PVG_Untreated_Virus_OVA_2_lung_rep1

description:
genecounts_lung.csv
RL51_HGMMWDMXX_AACAGGTT.ATACCAAG_L002_R1.fastq.gz


title: L_fraction_HCT_RIF1AID_48hr_degrade_Repliseq

description:
Repli-seq
HCT116_RIF1AID_KD_2cellcycles_log2EL_RT.bigwig

treatment_protocol: Cells were treated with auxin to degrade RIF1 for 48 hours


title: E_fraction_HCT_RIF1AID_48hr_degrade_Repliseq


title: E_fraction_HCT_RIF1AID_96hr_degrade_Repliseq


title: L_fraction_HCT_RIF1AID_24hr_degrade_Repliseq

description:
Repli-seq
HCT116_RIF1AID_KD_1cellcycle_log2EL_RT.bigwig

treatment_protocol: Cells were treated with auxin to degrade RIF1 for 24 hours


title: BN_OM_treated_Virus_OVA_9_lung_rep6

description:
genecounts_lung.csv
RL48_HGMMWDMXX_ACCTTGGC.GGCCTCAT_L002_R1.fastq.gz

value: BN


title: PVG_OM_treated_Virus_OVA_2_lung_rep1

description:
genecounts_lung.csv
RL55_HGMMWDMXX_AGGCAGAG.AGAATGCC_L002_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_lung_rep6

description:
genecounts_lung.csv
RL47_HGMMWDMXX_GTTCCAAT.AATTCTGC_L002_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_lung_rep6

description:
genecounts_lung.csv
RL46_HGMMWDMXX_GCAATGCA.GGAACGTT_L002_R1.fastq.gz


title: E_fraction_HCT_RIF1AID_untreated_Repliseq

description:
Repli-seq
HCT116_RIF1AID_Ctl_log2EL_RT.bigwig


title: L_fraction_HCT_RIF1AID_control_Firstcellcycle_Repliseq


title: HCT_RIF1AID_96hr_degrade_r2_RNAseq

description:
RNA-seq
HCT116_Ctl_vs_4cellcycles_RIF1KD_DESeq2_output.txt

extract_protocol:
Total RNA was prepared with Direct-zol RNA Miniprep Kit (Zymo Research) according to manufacturer's instrctions
Libraries were prepared with NEBNEXT rRNA Depletion kit (human/mouse/rat) (New England Biolabs E6310) and NEBNEXT Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs E7760) according to manufacturer’s instructions.


title: PVG_Untreated_Control_Saline_0_lung_rep1

description:
genecounts_lung.csv
RL49_HGMMWDMXX_ATATCTCG.ATCTTAGT_L002_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_lung_rep6

description:
genecounts_lung.csv
RL45_HGMMWDMXX_ATGGCATG.AAGGTACC_L002_R1.fastq.gz


title: PVG_OM_treated_Virus_Saline_1_lung_rep1

description:
genecounts_lung.csv
RL54_HGMMWDMXX_TGGTGGCA.TCCTGTAA_L002_R1.fastq.gz


title: E_fraction_HCT_RIF1AID_24hr_degrade_Repliseq


title: L_fraction_HCT_RIF1AID_untreated_Repliseq


title: BN_Untreated_Virus_OVA_9_lung_rep6

description:
genecounts_lung.csv
RL44_HGMMWDMXX_GGAGCGTC.GTCCGTGC_L002_R1.fastq.gz


title: HCT_RIF1AID_48hr_degrade_r2_RNAseq

description:
RNA-seq
HCT116_Ctl_vs_2cellcycles_RIF1KD_DESeq2_output.txt


title: HCT_RIF1AID_48hr_degrade_r1_RNAseq


title: BN_Untreated_Virus_OVA_2_lung_rep6

description:
genecounts_lung.csv
RL43_HGMMWDMXX_AAGATACT.ACTTACAT_L002_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_lung_rep6

description:
genecounts_lung.csv
RL41_HGMMWDMXX_ATATGGAT.CTGTATTA_L002_R1.fastq.gz


title: HCT_RIF1AID_24hr_degrade_r2_RNAseq

description:
RNA-seq
HCT116_Ctl_vs_1cellcycle_RIF1KD_DESeq2_output.txt


title: HCT_RIF1AID_24hr_degrade_r1_RNAseq


title: BN_OM_treated_Virus_OVA_9_lung_rep5

description:
genecounts_lung.csv
RL40_HGMMWDMXX_CGGACAAC.TCCGGATT_L002_R1.fastq.gz


title: PVG_Untreated_Virus_Saline_1_lung_rep1

description:
genecounts_lung.csv
RL50_HGMMWDMXX_GCGCTCTA.GCTCCGAC_L002_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_lung_rep5

description:
genecounts_lung.csv
RL39_HGMMWDMXX_TAAGTGGT.CTTAAGCC_L002_R1.fastq.gz


title: HCT_RIF1AID_untreated_r2_RNAseq

description:
RNA-seq
HCT116_Ctl_vs_2cellcycles_RIF1KD_DESeq2_output.txt
HCT116_Ctl_vs_1cellcycle_RIF1KD_DESeq2_output.txt


title: BN_OM_treated_Virus_Saline_1_lung_rep5

description:
genecounts_lung.csv
RL38_HGMMWDMXX_CTACGACA.GAGTCCAA_L002_R1.fastq.gz


title: HCT_RIF1AID_untreated_r1_RNAseq


title: BN_OM_treated_Control_Saline_0_lung_rep5

description:
genecounts_lung.csv
RL37_HGMMWDMXX_TCGTAGTG.AGACTTGG_L002_R1.fastq.gz


title: HCT_RIF1AID_96hr_degrade_r1_RNAseq


title: H3K9me3_HCT_RIF1AID_96hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_4cellcycles_H3K9me3_dm_normed_tag_count.bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
After washing with high salt buffer, LiCl buffer, and TE, chromatin was eluted and reverse crosslinked. Purified DNA was ethanol precipitated followed by Illumina Truseq library preparation. Libraries for Illumina sequencing were constructed using the following standard protocol. Fragment ends were repaired using the NEBNext End Repair Module and adenosine was added at the 3’ ends of fragments using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), universal adaptors were ligated to the A-tailed DNA fragments at room temperature for 1 h with T4 DNA ligase (New England Biolabs) and amplified with Illumina barcoded primers using KAPA SYBR FAST qPCR Master Mix for 5~12 PCR cycles to obtain enough DNA for sequencing.

value: H3K9me3 Abcam (ab8898)


title: H3K27ac_HCT_RIF1AID_96hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_4cellcycles_H3K27ac_dm_normed_tag_count.bigwig

value: H3K27ac Abcam (ab4729)


title: BN_Untreated_Virus_OVA_9_lung_rep5

description:
genecounts_lung.csv
RL36_HGMMWDMXX_GATTCTGC.GACGAGAG_L002_R1.fastq.gz


title: BN_Untreated_Virus_Saline_1_lung_rep6

description:
genecounts_lung.csv
RL42_HGMMWDMXX_GCGCAAGC.TCACGCCG_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_lung_rep5

description:
genecounts_lung.csv
RL35_HGMMWDMXX_AGCCTCAT.AGTAGAGA_L002_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_lung_rep5

description:
genecounts_lung.csv
RL33_HGMMWDMXX_TACCGAGG.CCTGAACT_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_24hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_1cellcycle_H3K9me3_dm_normed_tag_count.bigwig


title: H3K27ac_HCT_RIF1AID_48hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_2cellcycles_H3K27ac_dm_normed_tag_count.bigwig


title: H3K9me3_HCT_RIF1AID_48hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_2cellcycles_H3K9me3_dm_normed_tag_count.bigwig


title: H3K27ac_HCT_RIF1AID_24hr_degrade_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_1cellcycle_H3K27ac_dm_normed_tag_count.bigwig


title: HCT_RIF1AID_96hr_degrade_HiC

description:
Hi-C
HCT116_RIFAID_Auxin_4_cellcycles_HiC_pairs.txt.gz

extract_protocol:
For cell lysis, 550 μl lysis buffer (500 μl 10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Ige cal CA630; 50 μl protease inhibitors (Sigma, St. Louis, MO ) were added to one batch of cells (~ 25 million cells). Cells were incubated on ice for at least 15 minutes. Next, cells were lysed with a Dounce homogenizer by moving the pestle A up and down 10 times, incubating on ice for one minute followed by 10 more strokes with the pestle. The suspension was spun down for 5 minutes at 5000 rpm at RT.
Cells were prepared and processed for Hi-C as previously described (PMID: 19815776)  using DpnII for digestion.


title: HCT_RIF1AID_48hr_degrade_HiC

description:
Hi-C
HCT116_RIFAID_Auxin_2_cellcycles_HiC_pairs.txt.gz


title: BN_OM_treated_Virus_OVA_2_lung_rep4

description:
genecounts_lung.csv
RL31_HGMMWDMXX_GGCATTCT.CTAGCTTG_L002_R1.fastq.gz


title: HCT_RIF1AID_24hr_degrade_HiC

description:
Hi-C
HCT116_RIFAID_Auxin_1_cellcycle_HiC_pairs.txt.gz


title: BN_OM_treated_Control_Saline_0_lung_rep4

description:
genecounts_lung.csv
RL29_HGMMWDMXX_CCGTGAAG.CAGTGGAT_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_lung_rep4

description:
genecounts_lung.csv
RL28_HGMMWDMXX_TCCAACGC.TTGGACTT_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_lung_rep4

description:
genecounts_lung.csv
RL27_HGMMWDMXX_CTTGGTAT.CCAAGTCC_L002_R1.fastq.gz


title: HCT_RIF1AID_untreated_HiC

description:
Hi-C
HCT116_RIFAID_Ctl_HiC_pairs.txt.gz


title: BN_Untreated_Virus_Saline_1_lung_rep4

description:
genecounts_lung.csv
RL26_HGMMWDMXX_GTCGGAGC.GGTTATAA_L002_R1.fastq.gz


title: BN_Untreated_Control_Saline_0_lung_rep4

description:
genecounts_lung.csv
RL25_HGMMWDMXX_ACTAAGAT.AACCGCGG_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_KD_LateS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_lateS_H3K9me3_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and auxin was used to KD RIF1 followed by synchronization in early S with thymidine block and release for 5.75 hours before fixation


title: H3K27ac_HCT_RIF1AID_KD_MidS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_midS_H3K27ac_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and auxin was used to KD RIF1 followed by synchronization in early S with thymidine block and release for 3.5 hours before fixation


title: H3K9me3_HCT_RIF1AID_KD_MidS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_midS_H3K9me3_dm6_normed_tag_count.bigwig


title: BN_Untreated_Virus_Saline_1_lung_rep5

description:
genecounts_lung.csv
RL34_HGMMWDMXX_CGTTAGAA.TTCAGGTC_L002_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_2_lung_rep3

description:
genecounts_lung.csv
RL23_HGMMWDMXX_GCAGAATT.ACCGGCCA_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_KD_EarlyS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_earlyS_H3K9me3_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and auxin was used to KD RIF1 followed by synchronization in early S with thymidine block before fixation


title: H3K27ac_HCT_RIF1AID_KD_EarlyS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_earlyS_H3K27ac_dm6_normed_tag_count.bigwig


title: BN_OM_treated_Virus_Saline_1_lung_rep3

description:
genecounts_lung.csv
RL22_HGMMWDMXX_AACGTTCC.GGAGTACT_L002_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_lung_rep4

description:
genecounts_lung.csv
RL32_HGMMWDMXX_AATGCCTC.TCGATCCA_L002_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_lung_rep3

description:
genecounts_lung.csv
RL21_HGMMWDMXX_GGTACCTT.AAGACGTC_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_lung_rep3

description:
genecounts_lung.csv
RL20_HGMMWDMXX_GCACGGAC.GTCTCGCA_L002_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_lung_rep4

description:
genecounts_lung.csv
RL30_HGMMWDMXX_TTACAGGA.TGACAAGC_L002_R1.fastq.gz


title: H3K27ac_HCT_RIF1AID_KD_G1_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_G1_H3K27ac_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin and auxin was used to KD RIF1 before fixation


title: BN_Untreated_Virus_OVA_2_lung_rep3

description:
genecounts_lung.csv
RL19_HGMMWDMXX_ATGTAAGT.ACTCTATG_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_KD_G1_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_G1_H3K9me3_dm6_normed_tag_count.bigwig


title: BN_Untreated_Control_Saline_0_lung_rep3

description:
genecounts_lung.csv
RL17_HGMMWDMXX_TAATACAG.ATATTCAC_L002_R1.fastq.gz


title: H3K27ac_HCT_RIF1AID_KD_LateS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_KD_lateS_H3K27ac_dm6_normed_tag_count.bigwig


title: H3K27ac_HCT_RIF1AID_control_LateS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_late_H3K27ac_G1_compensated_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin followed by sychronization in early S by thymidine and release for 5.75 hours block before fixation


title: H3K27ac_HCT_RIF1AID_control_MidS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_midS_H3K27ac_G1_compensated_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin followed by sychronization in early S by thymidine and release for 3.5 hours block before fixation


title: H3K9me3_HCT_RIF1AID_control_LateS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_ctl_lateS_H3K9me3_G1_compensated_dm6_normed_tag_count.bigwig


title: BN_OM_treated_Virus_OVA_9_lung_rep2

description:
genecounts_lung.csv
RL16_HGMMWDMXX_AATCCGGA.CTACAGTT_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_control_MidS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_midS_H3K9me3_G1_compensated_dm6_normed_tag_count.bigwig


title: H3K27ac_HCT_RIF1AID_control_EarlyS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_earlyS_H3K27ac_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin followed by sychronization in early S by thymidine block before fixation


title: BN_OM_treated_Virus_Saline_1_lung_rep2

description:
genecounts_lung.csv
RL14_HGMMWDMXX_TTGGACTC.GGAAGCAG_L002_R1.fastq.gz


title: H3K9me3_HCT_RIF1AID_control_EarlyS_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_earlyS_H3K9me3_dm6_normed_tag_count.bigwig


title: H3K27ac_HCT_RIF1AID_control_G1_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_G1_H3K27ac_dm6_normed_tag_count.bigwig

treatment_protocol: Cells were synchronized in G1 with lovastatin before fixation


title: BN_OM_treated_Virus_OVA_2_lung_rep2

description:
genecounts_lung.csv
RL15_HGMMWDMXX_GGCTTAAG.TCGTGACC_L002_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_lung_rep2

description:
genecounts_lung.csv
RL13_HGMMWDMXX_CCAAGTCT.AAGGATGA_L002_R1.fastq.gz


title: BN_OM_treated_Virus_OVA_9_lung_rep3

description:
genecounts_lung.csv
RL24_HGMMWDMXX_ATGAGGCC.GTTAATTG_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_9_lung_rep2

description:
genecounts_lung.csv
RL12_HGMMWDMXX_CTCTCGTC.TATAACCT_L002_R1.fastq.gz


title: BN_Untreated_Virus_OVA_2_lung_rep2

description:
genecounts_lung.csv
RL11_HGMMWDMXX_TCTCTACT.CGCGGTTC_L002_R1.fastq.gz


title: HCT_RIF1AID_KD_LateS_HiC

description:
Hi-C
HCT116_RIFAID_Aux_lateS_pairs.txt.gz


title: H3K9me3_HCT_RIF1AID_control_G1_ChIPseq

description:
ChIP-seq
HCT116_RIF1AID_Ctl_G1_H3K9me3_dm6_normed_tag_count.bigwig


title: BN_Untreated_Virus_Saline_1_lung_rep2

description:
genecounts_lung.csv
RL10_HGMMWDMXX_GACCTGAA.TTGGTGAG_L002_R1.fastq.gz


title: HCT_RIF1AID_KD_EarlyS_HiC

description:
Hi-C
HCT116_RIFAID_Aux_earlyS_pairs.txt.gz


title: BN_Untreated_Control_Saline_0_lung_rep2

description:
genecounts_lung.csv
RL09_HGMMWDMXX_AGTTCAGG.CCAACAGA_L002_R1.fastq.gz


title: HCT_RIF1AID_KD_G1_HiC

description:
Hi-C
HCT116_RIFAID_Aux_G1_pairs.txt.gz


title: BN_Untreated_Virus_Saline_1_lung_rep3

description:
genecounts_lung.csv
RL18_HGMMWDMXX_CGGCGTGA.GCGCCTGT_L002_R1.fastq.gz


title: HCT_RIF1AID_KD_MidS_HiC

description:
Hi-C
HCT116_RIFAID_Aux_midS_pairs.txt.gz


title: BN_OM_treated_Virus_OVA_2_lung_rep1

description:
genecounts_lung.csv
RL07_HGMMWDMXX_CAAGCTAG.ACATAGCG_L002_R1.fastq.gz


title: HCT_RIF1AID_control_LateS_HiC

description:
Hi-C
HCT116_RIFAID_Ctl_lateS_pairs.txt.gz


title: BN_OM_treated_Virus_OVA_9_lung_rep1

description:
genecounts_lung.csv
RL08_HGMMWDMXX_TGGATCGA.GTGCGATA_L002_R1.fastq.gz


title: BN_OM_treated_Virus_Saline_1_lung_rep1

description:
genecounts_lung.csv
RL06_HGMMWDMXX_GCTTGTCA.GAACATAC_L002_R1.fastq.gz


title: BN_OM_treated_Control_Saline_0_lung_rep1

description:
genecounts_lung.csv
RL05_HGMMWDMXX_ATCCACTG.AGGTGCGT_L002_R1.fastq.gz


title: HCT_RIF1AID_control_MidS_HiC

description:
Hi-C
HCT116_RIFAID_Ctl_midS_pairs.txt.gz


title: HCT_RIF1AID_control_G1_HiC

description:
Hi-C
HCT116_RIFAID_Ctl_G1_HiC_pairs.txt.gz


title: BN_Untreated_Virus_OVA_9_lung_rep1

description:
genecounts_lung.csv
RL04_HGMMWDMXX_AAGTCCAA.TATGAGTA_L002_R1.fastq.gz


title: HCT_RIF1AID_control_EarlyS_HiC

description:
Hi-C
HCT116_RIFAID_Ctl_earlyS_pairs.txt.gz


title: HCT_RIF1KO_r2_RNAseq

description:
RNA-seq
HCT116_WT_vs_KO_DESeq2_output.txt

value: RIF1 KO


title: BN_Untreated_Virus_OVA_2_lung_rep1

description:
genecounts_lung.csv
RL03_HGMMWDMXX_GGACTTGG.CGCAGACG_L002_R1.fastq.gz


title: HCT_RIF1KO_r1_RNAseq


title: BN_Untreated_Control_Saline_0_lung_rep1

description:
genecounts_lung.csv
RL01_HGMMWDMXX_CCGCGGTT.AGCGCTAG_L002_R1.fastq.gz


title: HCT_WT_r2_RNAseq


title: H9_RIF1KO_r2_RNAseq

description:
RNA-seq
H9_WT_vs_KO_DESeq2_output.txt


title: HCT_WT_r1_RNAseq


title: H9_RIF1KO_r1_RNAseq

description:
RNA-seq
H9_WT_vs_KO_DESeq2_output.txt


title: H9_WT_r2_RNAseq

description:
RNA-seq
H9_WT_vs_KO_DESeq2_output.txt


title: hechec2 28 rep3

city: Austin

first: Enamul

last: Huq

state: TX

address: Department of MBS, NHB 2.606, Stop A5000, 100 East 24th St.

institute: The University of Texas at Austin

description:
h12-6
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt

data_processing:
FastQC
Bowtie2
Tophat
Htseq
EdgeR
Genome_build: bowtie2 with TAIR10
Supplementary_files_format_and_content: total_count.txt: Tab-delimited text file with htseq counts.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings

growth_protocol: Total three genotypes; Col-0, hec1hec2, and pifQ plants were used for mRNA sequencing analysis.

extract_protocol:
Total RNA was isolated using Sigma plant total RNA kit (Sigma, Cat.# STRN250).
3'Tag-Seq method article was used to generate TagSeq library according to the manufacturer’s instruction. (doi: 10.1111/1755-0998.12529)

treatment_protocol: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days in dark to induce germination. After three days, seeds were further treated 5 days in 22℃ with white light (25 µmole/s2/m2). After 5 days, seedlings were treated with 24 hour of continuous white light (25 µmole/s2/m2) in either 22degC or 28degC.

tag: ecotype/background

tag: tissue

value: Seedlings

tag: treatment

value: 24hr in 28'C


title: HCT_RIF1KO_r2_HiC

description:
Hi-C
HCT116_RIF1KO_100k.cool
HCT116_RIF1KO_HiC_Rep1_pairs.txt.gz


title: pifQ 28 rep1

description:
pq-4
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt

value: pifQ


title: pifQ 28 rep3

description:
pq-6
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: hechec2 28 rep1

description:
h12-4
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: Col-0 28 rep2

description:
wt-5
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt

value: WT


title: Col-0 28 rep3

description:
wt-6
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: HCT_RIF1KO_r1_HiC


title: H9_RIF1KO_r2_HiC

description:
Hi-C
H9_RIF1KO_100k.cool
H9_RIF1KO_HiC_pairs.txt.gz


title: H9_WT_r1_RNAseq

description:
RNA-seq
H9_WT_vs_KO_DESeq2_output.txt


title: hechec2 28 rep2

description:
h12-5
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: pifQ 28 rep2

description:
pq-5
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: Col-0 28 rep1

description:
wt-4
Light grown 5-days seedlings+24hr in 28'C
3'Tag-RNA-seq
total_count.txt


title: pifQ 22 rep3

description:
pq-3
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt

value: 24hr in 22'C


title: BN_Untreated_Virus_Saline_1_lung_rep1

description:
genecounts_lung.csv
RL02_HGMMWDMXX_TTATAACC.GATATCGA_L002_R1.fastq.gz

value: Untreated

value: male


title: hec1hec2 22 rep3

description:
h12-3
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: Rad21_HCT_RIF1KO_r1_ChIPSeq

description:
ChIP-seq
HCT116_RIF1KO_Rad21_log2_FE_over_Input.bigwig

value: RAD21 Abcam (ab992)


title: pifQ 22 rep1

description:
pq-1
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: pifQ 22 rep2

description:
pq-2
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: H3K27ac_HCT_RIF1KO_r2_ChIPSeq

description:
ChIP-seq
HCT116_RIF1KO_H3K27ac_log2_FE_over_input.bw

value: human colorectal cancer cell line


title: H9_RIF1KO_r1_HiC

value: human embryonic stem cell line


title: H3K4me3_HCT_RIF1KO_r1_ChIPSeq

description:
ChIP-seq
HCT116_RIF1KO_H3K4me3_log2_FE_over_input.bigwig

value: H3K4me3 Abcam (ab8580)


title: hec1hec2 22 rep1

description:
h12-1
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: Col-0 22 rep3

description:
wt-3
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: H3K4me3_HCT_RIF1KO_r2_ChIPSeq


title: hec1hec2 22 rep2

description:
h12-2
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: H3K27me3_HCT_RIF1KO_r2_ChIPSeq

description:
ChIP-seq
HCT116_RIF1KO_H3K27me3_log2_FE_over_input.bigwig

value: H3K27me3 Millipore (07-449)


title: H3K27me3_HCT_RIF1KO_r1_ChIPSeq


title: RIF1_H9_WT_r2_CutnRun

description:
Cut&Run
H9_RIF1_CutnRun_log2_FE_over_Input.bigwig

extract_protocol:
Cells were washed and bound to Concanavalin-A-coated magnetic beads, and permeabilized in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete protein inhibitor tablet per 50 mL) containing 0.03% digitonin and 20 mM EDTA (Dig-wash). Antibody was added to a final concentration of 1:100 and incubated overnight at 4°C. Cells were washed with Dig-wash buffer and incubated with Protein-A-MNase (pA-MN) for 1 hour at 4°C. Cells were washed three times with Dig-wash buffer to remove unbound pA-MN before placing cells in an ice-cold block and activating cleavage with the addition of CaCl2 to 2mM final concentration. Cleavage was stopped by the addition of 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 μg/mL RNase A), and fragments were released by 30 min incubation at 37°C. Supernatant was recovered and DNA was purified with phenol:chloroform extraction and precipitation with ethanol, before being used as input for library preparation.
Sequencing libraries were prepared from DNA fragments as described in (PMID: 28079019) but without size-selection, following the KAPA DNA polymerase library preparation kit protocol

value: eGFP MBL (598)


title: RIF1_HCT_WT_r2_CutnRun

description:
Cut&Run
HCT116_RIF1_CutnRun_rep2_log2_FE_over_Input.bigwig


title: RIF1_H9_WT_r1_CutnRun


title: H3K9me3_HCT_RIF1KO_Dm_spikein_r2_ChIPSeq

description:
ChIP-seq
HCT116_RIF1KO_H3K9me3_dm_normed_tag_count.bigwig


title: Donor_4_YY1_RNA

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
Adapters were trimmed from fastq files using cutadapt version 2.10 with default settings keeping a minimum read length of 20 bp. Reads were mapped to the human genome GRCh38 keeping only uniquely mapping reads using STAR version 2.7.b with the following settings “--outFilterMultimapNmax 1”. UMIs were extracted from fastqs using umi_tools version 1.0.1 extract command with the following settings “--extract-method=regex --bc-pattern='(?P<umi_1>.{{6}})(?P<discard_1>.{{4}}).*'”. Reads were then deduplicated using umi_tools dedup command with default settings. Deduplicated reads overlapping genes were then counted using featureCounts version 2.0.1 with the following settings “-s 1” and using the Genocde version 35 basic transcriptome annotation.
Genome_build: hg38
Supplementary_files_format_and_content: UMI deduplicated RNA-Seq counts.

source_name: CD4+CD25- T cells

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
Cells were lysed with Zymo QuickRNA lysis buffer and isolated with the Zymo QuickRNA micro kit (Zymo, Cat #R1050) using the manufacturer's protocol. RNA samples were treated with 1.5 ul of Turbo DNase (Invitrogen, Cat # AM2238) and then cleaned up using the Zymo RNA-5 Clean and Concentrator (Zymo, Cat #R1016). Isolated RNA integrity and concentration was checked using Agilent RNA Screen Tapes (Agilent, Cat #5067-5576)
RNA was submitted to the UC Davis DNA Technologies and Expression Analysis Core to generate 3’ Tag-Seq libraries with unique molecular indices (UMIs). Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer (Lexogen). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. Samples were sequenced on a HiSeq 4000 sequencer (Illumina, San Diego, CA).

treatment_protocol: CD4+CD25- T cells were isolated from 3 donors using consented Luekopaks (STEMCELL). Guide RNAs against 24 targets or 8 AAVS1 controls were assembled into Cas9 ribonucleoproteins and electroporated into the cells. Five days after electroporation cells were collected.

value: CD4+CD25- T cells


title: Donor_4_RELA_RNA


title: Donor_4_TNFAIP3_RNA


title: Donor_4_STAT5A_RNA


title: H3K27ac_H9_RIF1KO_r2_ChIPSeq

description:
ChIP-seq
H9_RIF1KO_H3K27ac_FE.bw


title: RIF1_HCT_WT_r1_CutnRun

description:
Cut&Run
HCT116_RIF1_CutnRun_log2_FE_over_Input.bigwig


title: Donor_4_ZNF217_RNA


title: Donor_4_STAT5B_RNA


title: H3K27me3_H9_RIF1KO_r2_ChIPSeq

description:
ChIP-seq
H9_KO_H3K27me3_FE.bigwig


title: H3K4me3_H9_RIF1KO_r1_ChIPSeq

description:
ChIP-seq
H9_KO_H3K4me3_FE.bigwig


title: H3K27me3_H9_RIF1KO_r1_ChIPSeq

description:
ChIP-seq
H9_KO_H3K27me3_FE.bigwig


title: Donor_4_MED12_RNA


title: Donor_4_PTEN_RNA


title: H3K4me3_H9_RIF1KO_r2_ChIPSeq

description:
ChIP-seq
H9_KO_H3K4me3_FE.bigwig


title: Donor_4_MYB_RNA


title: H3K9me3_H9_RIF1KO_Dm_spikein_r2_ChIPSeq

description:
ChIP-seq
H9_RIF1KO_H3K9me3_dm_normed_tag_count.bigwig

value: H3K9me3 Abcam (ab8898)


title: H3K9me3_H9_RIF1KO_Dm_spikein_r1_ChIPSeq


title: Donor_4_MBD2_RNA


title: S16_fraction_HCT_RIF1KO_Highres_Repli-seq

description:
Repli-seq
HCT116_RIF1KO_Rep1_highres_Repliseq_hg38.mat.gz

extract_protocol:
gDNA was isolated with SDS-PK buffer containing 0.2 mg/ml proteinase K for 2 hours at 56C followed by purification with 800 µl of Genomic Lysis Buffer from the Zymo Quick-DNA Microprep Kit according to manufacturers instructions
DNA from G1 fraction was made into whole-genome sequencing library to normalize any bias during library preparation, sequencing and sequence read mapping. DNA from S1-S16 fractions were made into repli-seq library basically as described in (PMID: 29599440) but from 80K sorted cells instead of 20K sorted cells.

treatment_protocol: When the cell reached approximately 70% confluent, asynchronously growing cells were pulse-labeled with 400uM BrdU for 30 minutes, harvested and ethanol fixed, then retroactively synchronized by FACS sorting according to the DNA content.


title: Col-0 22 rep2

description:
wt-2
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: Donor_4_KMT2A_RNA


title: Col-0 22 rep1

description:
wt-1
Light grown 5-days seedlings+24hr in 22'C
3'Tag-RNA-seq
total_count.txt


title: Donor_4_JAK3_RNA


title: H3K27ac_H9_RIF1KO_Dm_spikein_r1_ChIPSeq

description:
ChIP-seq
H9_RIF1KO_H3K27ac_FE.bw

value: H3K27ac Abcam (ab4729)


title: Donor_4_IRF4_RNA


title: S14_fraction_HCT_RIF1KO_Highres_Repli-seq

value: RIF1 KO


title: S15_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S13_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_IRF2_RNA


title: Donor_4_IRF1_RNA


title: S12_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S11_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_GATA3_RNA


title: Donor_4_HIVEP2_RNA


title: S10_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S7_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_FOXP1_RNA


title: Donor_4_ETS1_RNA


title: S8_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S9_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_FOXK1_RNA


title: Donor_4_KLF2_RNA


title: S6_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_ATXN7L3_RNA


title: Donor_4_AAVS1_8_RNA


title: Donor_4_CBFB_RNA


title: Donor_4_AAVS1_7_RNA


title: S5_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S4_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S3_fraction_HCT_RIF1KO_Highres_Repli-seq


title: S2_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_IL2RA_RNA


title: Donor_4_AAVS1_5_RNA


title: Donor_4_AAVS1_6_RNA


title: S1_fraction_HCT_RIF1KO_Highres_Repli-seq


title: G1_fraction_HCT_RIF1KO_Highres_Repli-seq


title: Donor_4_AAVS1_4_RNA


title: Donor_4_AAVS1_3_RNA


title: S15_fraction_H9_RIF1KO_Highres_Repli-seq

description:
Repli-seq
H9_RIF1KO_Rep1_highres_Repliseq_hg38.mat.gz

treatment_protocol: When the cell reached approximately 70% confluent, asynchronously growing cells were pulse-labeled with 100uM BrdU for 30 minutes, harvested and ethanol fixed, then retroactively synchronized by FACS sorting according to the DNA content.


title: S16_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_4_AAVS1_2_RNA


title: Donor_4_AAVS1_1_RNA


title: Donor_3_ZNF217_RNA


title: S14_fraction_H9_RIF1KO_Highres_Repli-seq


title: S12_fraction_H9_RIF1KO_Highres_Repli-seq


title: S9_fraction_H9_RIF1KO_Highres_Repli-seq


title: S11_fraction_H9_RIF1KO_Highres_Repli-seq


title: S10_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_STAT5B_RNA


title: Donor_3_YY1_RNA


title: S7_fraction_H9_RIF1KO_Highres_Repli-seq


title: S8_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_TNFAIP3_RNA


title: Donor_3_PTEN_RNA


title: Donor_3_RELA_RNA


title: Donor_3_MYB_RNA


title: Donor_3_STAT5A_RNA


title: S6_fraction_H9_RIF1KO_Highres_Repli-seq


title: S5_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_MED12_RNA


title: S4_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_MBD2_RNA


title: Donor_3_KMT2A_RNA


title: S13_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_KLF2_RNA


title: Donor_3_JAK3_RNA


title: S2_fraction_H9_RIF1KO_Highres_Repli-seq


title: L_fraction_HAP1_RIF1KO_r1_RepliSeq

description:
Repli-seq
HAP_RIF1KO_log2EL_RT.bigwig

treatment_protocol: When the cell reached approximately 70% confluent, asynchronously growing cells were pulse-labeled with 100uM BrdU for 2 hours, harvested and ethanol fixed, then retroactively synchronized by FACS sorting according to the DNA content.

value: human haploid CML cell line


title: S1_fraction_H9_RIF1KO_Highres_Repli-seq


title: G1_fraction_H9_RIF1KO_Highres_Repli-seq


title: Donor_3_HIVEP2_RNA


title: E_fraction_HAP1_WT_r1_RepliSeq

description:
Repli-seq
HAP_WT_log2EL_RT.bigwig

value: Wild type


title: Donor_3_IRF1_RNA


title: Donor_3_IRF2_RNA


title: S3_fraction_H9_RIF1KO_Highres_Repli-seq


title: L_fraction_HCT_RIF1KO_r2_RepliSeq

description:
Repli-seq
HCT116_KO_log2EL_RT.bigwig


title: L_fraction_H9_RIF1KO_r2_RepliSeq

description:
Repli-seq
H9_RIF1KO_log2EL_RT.bigwig


title: E_fraction_H9_RIF1KO_r2_RepliSeq

description:
Repli-seq
H9_RIF1KO_log2EL_RT.bigwig


title: E_fraction_HCT_RIF1KO_r1_RepliSeq

description:
Repli-seq
HCT116_KO_log2EL_RT.bigwig


title: Donor_3_ATXN7L3_RNA


title: Donor_3_CBFB_RNA


title: L_fraction_H9_RIF1KO_r1_RepliSeq

description:
Repli-seq
H9_RIF1KO_log2EL_RT.bigwig


title: E_fraction_HCT_RIF1KO_r2_RepliSeq

description:
Repli-seq
HCT116_KO_log2EL_RT.bigwig


title: L_fraction_HCT_RIF1KO_r1_RepliSeq

description:
Repli-seq
HCT116_KO_log2EL_RT.bigwig


title: L_fraction_HAP1_WT_r1_RepliSeq

description:
Repli-seq
HAP_WT_log2EL_RT.bigwig


title: Donor_3_GATA3_RNA


title: Donor_3_FOXK1_RNA


title: Donor_3_AAVS1_8_RNA


title: E_fraction_HAP1_RIF1KO_r1_RepliSeq

description:
Repli-seq
HAP_RIF1KO_log2EL_RT.bigwig


title: Donor_3_AAVS1_7_RNA


title: Donor_3_IRF4_RNA


title: Donor_3_FOXP1_RNA


title: Donor_3_AAVS1_4_RNA


title: Hypoxia SETX- Rep 3

city: Oxford

first: Ester

last: Hammond

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

data_processing:
trimmomatic-0.32
tophat v2.0.13
Cuffdiff-2.2.1
Picard 1.124
Product 3.3
Genome_build: GRCh38 release 82
Supplementary_files_format_and_content: cuffdiff output files

source_name: RKO

growth_protocol: DMEM supplemented with 10% FBS and cultured in humidified incubators at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using TRI reagent (Sigma) and treated with DNase I (NEB).
The samples were urified using the RNeasy MinElute Clean-up kit (Qiagen) and purity confirmed using a Bioanalyzer. The mRNA fraction was selected for reverse transcription to cDNA. The cDNA generated was endrepaired, A-tailed and adapter-ligated.
cDNA libraries were size selected, multiplexed, tested for quality and subjected to paired end sequencing in one lane of a flow cell.

treatment_protocol: Bactron II and BactronEZ anaerobic chambers (Shel Lab) were used for <0.1% O2 and 6 hours

value: colon

tag: condition

value: Hypoxia SETX-


title: Hypoxia SETX- Rep 1


title: Donor_3_AAVS1_3_RNA


title: Hypoxia SETX- Rep 2


title: Normoxia SETX- Rep 3

value: Normoxia SETX-


title: Donor_3_IL2RA_RNA


title: Normoxia SETX- Rep 2


title: Hypoxia SETX+ Rep 1

description:
HYPO_vs_NORM_S1.txt
HYPO_SETX-_vs_SETX+_S1.txt

value: Hypoxia SETX+


title: Donor_1_ZNF217_RNA


title: Donor_3_AAVS1_2_RNA


title: E_fraction_H9_RIF1KO_r1_RepliSeq

description:
Repli-seq
H9_RIF1KO_log2EL_RT.bigwig


title: Normoxia SETX+ Rep 2

description:
HYPO_vs_NORM_S2.txt
NORM_SETX-_vs_SETX+_S2.txt

value: Normoxia SETX+


title: Donor_3_AAVS1_1_RNA


title: Donor_1_YY1_RNA


title: Hypoxia SETX+ Rep 3

description:
HYPO_vs_NORM_S3.txt
HYPO_SETX-_vs_SETX+_S3.txt


title: Hypoxia SETX+ Rep 2

description:
HYPO_vs_NORM_S2.txt
HYPO_SETX-_vs_SETX+_S2.txt


title: Donor_1_STAT5B_RNA


title: Normoxia SETX- Rep 1


title: Donor_1_STAT5A_RNA


title: Donor_1_TNFAIP3_RNA


title: Donor_3_AAVS1_6_RNA


title: Normoxia SETX+ Rep 1

description:
HYPO_vs_NORM_S1.txt
NORM_SETX-_vs_SETX+_S1.txt


title: Donor_1_RELA_RNA


title: M34LA

city: Washington

first: Igor

last: Efimov

state: DC

address: 800 22nd St NW

department: Biomedical Engineering

institute: The George Washington University

data_processing:
The raw reads were aligned to the reference genome hg38 using STAR (v2.5).
FeatureCounts was used to count the read numbers mapped of each gene.
Differential expression analysis was carried out using DESeq2. Differentially expressed genes (DEGs) were identified with the significance criterion padj<0.05.
Genome_build: hg38

source_name: Cardiac tissue

extract_protocol:
Tissues were removed, rinsed of blood, and submerged in RNAlater for >24 hours. RNA was purfied and extracted using Qiagen's RNeasy Fibrous Tissue Mini Kit. Illumina Platform PE150 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: Left atrial tissue

tag: age (days)

tag: gender

value: Male


title: Donor_1_PTEN_RNA


title: M26LA


title: Donor_3_AAVS1_5_RNA


title: Donor_1_MYB_RNA


title: F36LA

value: Female


title: Donor_1_MED12_RNA


title: Normoxia SETX+ Rep 3

description:
HYPO_vs_NORM_S3.txt
NORM_SETX-_vs_SETX+_S3.txt


title: Donor_1_MBD2_RNA


title: M34RA

value: Right atrial tissue


title: F36RA


title: F35RA


title: Donor_1_JAK3_RNA


title: Donor_1_KLF2_RNA


title: HSB_0807

value: Inferior sinoatrial node


title: Donor_1_KMT2A_RNA


title: Donor_1_IL2RA_RNA


title: HSB_1003


title: HSB_0920


title: HST_1003

value: Superior sinoatrial node


title: Donor_1_IRF1_RNA

value: CD4+CD25- T cells


title: Donor_1_HIVEP2_RNA


title: Donor_1_IRF4_RNA


title: HST_0920


title: HST_0807


title: Donor_1_GATA3_RNA


title: Donor_1_FOXP1_RNA


title: Donor_1_FOXK1_RNA


title: Donor_1_ETS1_RNA


title: Donor_1_CBFB_RNA


title: F26RA


title: Donor_1_IRF2_RNA


title: Donor_1_ATXN7L3_RNA


title: Donor_1_AAVS1_8_RNA


title: Donor_1_AAVS1_6_RNA


title: Donor_1_AAVS1_7_RNA


title: Donor_1_AAVS1_5_RNA


title: Donor_1_AAVS1_3_RNA


title: Donor_1_AAVS1_2_RNA


title: CRISPR_plasmid

data_processing:
Library strategy: CRISPR sequencing
A table of individual guide abundance in each sample was generated using the count command in MAGeCK version 0.5.8
Genome_build: None
Supplementary_files_format_and_content: Count of guide RNAs.
Supplementary_files_format_and_content: raw counts

extract_protocol:
After sorting, cells were washed with PBS, counted, pelleted, and resuspending at up to 5E6 cells per 400 µl of lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA). The remaining protocol reflects additives/procedures performed per each 400 µl of sample. 16µl of NaCl (5M) was added, and the sample was incubated on a heat block overnight at 66°C. The next morning, 8µl of RNAse A (10mg/ml, resuspended in ddH2O) (Zymo, Cat #E1008) was added, and the sample was vortexed briefly, and incubated at 37°C for 1 hour. Next, 8µl of Proteinase K (20mg/ml) (Zymo, Cat #D3001) was added, the sample was vortexed briefly, and incubated at 55°C for 1 hour. A phase lock tube (Quantabio, Cat #2302820) was prepared for each sample by spinning down the gel to the bottom of the tube at 20,000g for 1 minute and then 400µl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1) was added to each tube. 400µl of the sample was then added to the phase lock tube and the tube was shaken vigorously. The sample was centrifuged at maximum speed at room temperature for 5 minutes. The aqueous phase was transferred to a low-binding eppendorf tube (Eppendorf, Cat #022431021) and then 40µl of Sodium Acetate (3M), 1µl GlycoBlue (Invitrogen, Cat # AM9515), and 600µl of room temperature isopropanol was added. The sample was then vortexed and stored at -80°C for 30 minutes or until the sample had frozen solid. Next the sample was centrifuged at maximum speed at 4°C for 30 minutes, the pellet was washed with fresh 70% room temperature Ethanol, and allowed to air dry for 15 minutes. Pellets were then resuspended in Zymo DNA elution buffer (Zymo, Cat No: D3004-4-10), and placed on the heat block at 65°C for 1 hour to completely dissolve the genomic DNA.
sgRNA was amplified and barcoded from the genomic DNA according to the protocol by Joung et al. (Joung et al. 2017). Up to 2.5 µg of genomic DNA were added to each 50 µL reaction, which included 25 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), 1.25 µL of the 10 µM forward primer and 1.25 µL of the 10 µM reverse primer, and H2O to 50 uL. The following PCR cycling conditions were used: 98°C for 3 minutes, followed by 23 cycles at 98°C for 10 seconds, 63°C for 10 seconds, and 72°C for 25 seconds, and ending with 2 minutes at 72°C. Samples were then cleaned and concentrated in Zymo Spin-V columns (Zymo, Cat #C1016-50) following Joung et al., and eluted in 150 uL of Zymo DNA elution buffer. Up to 2 µg of each library were loaded on a 2% agarose gel, and the band at ~250 base pairs was extracted using the Zymoclean Gel DNA recovery kit (Zymo, Cat #D4008). The concentration of each sample was then measured using the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific, Cat #Q32854). Samples were then sequenced on an Illumina HiSeq 4000 using 10-30% PhiX (Illumina, Cat #15017872), and a custom sequencing primer.

treatment_protocol: CD4+CD25- T cells were infected with lentivirus containing a 6000 guide RNA CRISPR library. Cas9 ribonucleoprotein complex was electroporated. 6 days after electroporation, FACS was performed to isolate CD25, IL-2, or CTLA4 high and low expressing cells.


title: day 2 Th17 cells WT replicate 2

type: RNA

city: Illkirch

first: Celine

last: Charvet

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse Gene 2.0 ST arrays (Affymetrix) interrogating 35240 RefSeq transcripts and ~ 2000 LncRNAs represented by approximately 27 probes spread across the full length of the transcript.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

organism: Mus musculus

source_name: Splenic naive CD4 T cells after 2 days of culture in Th17 conditions

label_protocol: Biotinylated double strand cDNA targets were prepared from 12.8 to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro  kit

value: WT

value: male


title: day 2 Th17 cells WT replicate 3

value: CD4 T cells after 2 days of culture in Th17 conditions


title: CRISPR_Donor3_IL2_high


title: CRISPR_Donor3_IL2_low


title: day 1 Th17 cells WT replicate 3

source_name: Splenic naive CD4 T cells after 1 day of culture in Th17 conditions


title: Donor_1_AAVS1_4_RNA


title: day 2 Th17 cells WT replicate 1


title: day 2 Th17 cells mutant replicate 1

value: ikaros mutant


title: day 1 Th17 cells WT replicate 2

value: CD4 T cells after 1 day of culture in Th17 conditions


title: day 1 Th17 cells mutant replicate 1


title: day 1 Th17  cells mutant replicate 3

value: female and male


title: day 1 Th17 cells WT replicate 1


title: CRISPR_Donor3_CTLA4_low


title: CRISPR_Donor3_GFP


title: CRISPR_Donor3_CTLA4_high


title: day 2 Th17 cells mutant replicate 2

value: female


title: Donor_1_AAVS1_1_RNA


title: day 0 naive CD4 T cells WT replicate 1

source_name: sorted splenic naive CD4 T cells (CD4+CD8-CD44loTCRgd-NK1.1-CD25-) d0

value: naive CD4 T cells


title: day 0 naive CD4 T cells WT replicate 2


title: CRISPR_Donor3_CD25_low


title: C6/5

city: New York

first: Sander

last: Houten

state: NY

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.4.0 g1)
gene-level read quantification via featureCounts v1.4.4
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing read count per gene

molecule: polyA RNA

source_name: heart

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture) and samples were run on an Illumina HiSeq 2500 sequencer to yield a total read depth of approximately 52 million 100 nucleotide single-end reads per sample

value: WT/WT

tag: diet

value: chow


title: day 0 naive CD4 T cells WT replicate 3


title: C6/4


title: CRISPR_Donor3_CD25_high


title: day 1 Th17 cells mutant replicate 2


title: day 0 naive CD4 T cells mutant replicate 2


title: day 0 naive CD4 T cells mutant replicate 1


title: C4/8


title: CRISPR_Donor2_IL2_low


title: C3/10


title: day 2 Th17  cells mutant replicate 3


title: CRISPR_Donor2_GFP


title: C3/7


title: CRISPR_Donor2_IL2_high


title: CRISPR_Donor2_CTLA4_high


title: CRISPR_Donor2_CTLA4_low


title: CRISPR_Donor2_CD25_high


title: C3/9


title: CRISPR_Donor2_CD25_low


title: C4/9

description: Potential outlier


title: day 0 naive CD4 T cells mutant replicate 3


title: C4/6


title: C3/8


title: C2/6

description: Potential outlier


title: CRISPR_Donor1_GFP


title: C2/7

description: Potential outlier


title: MEFs reprogramming - OE day 12 - T7-TIA1 rep 2

city: Barcelona

first: Claudia

last: Vivori

address: Carrer Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
[For gene counts]  Reads alignment to mm10 genome performed with STAR v2.7.1a, with the following parameters: --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 6 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode GeneCounts
[For gene counts]  Filtering of for minimum expression was performed with edgeR v3.16.5. We required minimum 1 cpm per sample and 5 cpm in at least in 33% of samples (8 for KDs dataset and 2 for OE dataset).
[For alternative splicing (AS) events]  Reads alignment and alternative splicing analysis performed with vast-tools v2.2.2.
Genome_build: mm10
Supplementary_files_format_and_content: FilteredGeneCpm_KD.txt and FilteredGeneCpm_OE.txt:  text files with filtered gene counts.  INCLUSION_LEVELS_FULL-Mm218.tab:  text file with mapped AS events.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Primary reprogrammable MEFs were cultured on gelatin-coated plates in MEF medium, for a maximum of 2 passages before inducing reprogramming. Reprogramming day 00: infection was performed by substituting the medium with the filtered retroviral or lentiviral supernatant, prepared in reprogramming medium and supplemented with LIF and doxycycline to induce reprogramming concomitantly (two subsequent infections 12 hours apart). Reprogramming day 02: cells were trypsinized and FACS-sorted for GFP expression by flow cytometry. Sorted MEFs were seeded on irradiated feeders on gelatin-coated plates. Medium was substituted every 2 days starting from day 4. Reprogramming day 12: cells were harvested with trypsin 0.25%.

extract_protocol:
RNA extraction and DNAse treatment was performed using RNeasy Mini kit (Qiagen), following the manufacturers’ instructions.
Stranded RNA libraries were prepared for sequencing using standard Illumina protocols

value: Collagen-OKSM, M2rtta+

value: Embryo

value: Fibroblasts

tag: time

value: Day 12 of doxycycline treatment

tag: type of infection (day0)

value: Retroviral

tag: infected with (day0)

value: T7-TIA1 cDNA


title: CRISPR_Donor1_CD25_low

value: CD4+CD25- T cells


title: C4/7

tag: strain


title: Donor_3_ETS1_RNA


title: CRISPR_Donor1_CD25_high


title: MEFs reprogramming - OE day 12 - Empty rep 2

value: Empty vector


title: LV_1002

data_processing:
The raw reads were filtered by removing reads containing adapters, reads containing N > 0.1% (N represents base that could not be determined), and low-quality reads.
The reads were aligned to the reference genome by HISAT2.
Expression values were calculated using HTSeq v0.6.1.
Differential expression analysis was carried out using DESeq2. Differentially expressed genes (DEGs) were identified with the significance criterion padj<0.05.
Genome_build: Rattus norvegicus release 98

value: Left ventricle

value: Sprague Dawley

value: Male


title: MDS2

city: Paris

first: Olivier

last: Kosmider

state: Ile de france

address: 22 rue Méchain

department: Reproduction and cancer

institute: Institut Cochin

data_processing:
Cell Ranger software  (Version 2.0.2) was used to process the raw data from Illumina sequencing and generate the gene-cell expression matrices. The reads were aligned on the GRCh38 reference genome by STAR with the ENSEMBL annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Bone marrow CD34+ HSPC

extract_protocol:
The bone marrow samples from SF3B1 mutated MDS were harvested by bone marrow aspiration. The bone marrow samples from healthy donors were harvested from femoral head after patients underwent hip surgery. Following the sample, the mononuclear cells were isolated on a Ficoll gradient. Once isolated, mononuclear bone marrow cells were counted and resuspended in an adequate solution (IMDM, SVF 40%, DMSO 15%) and frozen in liquid nitrogen at a concentration of 20 to 30 million cells per mL. Bone marrow mononuclear cells were thawed, and dead cells were eliminated by immunomagnetic negative sorting (MACS MicroBead technology from Miltenyi Biotec ™). A second CD34 positive immunomagnetic sorting was performed to isolate stem and progenitor cells. Cells were then washed with PBS containing 0.04% of BSA. Cell concentration and viability were determined microscopically with a Malassez counting chamber cell after staining with trypan blue.
Libraries were prepared with the chromium system of 10x genomics, with the Chromium Single Cell 3 ’V2 kit according to the manufacturer's protocol (www.10xgenomics.com). The four samples (Ctrl1, Ctrl3, MDS2 and MDS4) were processed on the same chromium chip. The number of cells targeted per sample was 5000 cells. The libraries were sequenced by the Integragen company on an Illumina HiSeq4000 sequencer with a target depth of 50,000 reads per cell.

value: Bone marrow CD34+ HSPC

tag: targeted mutations

value: SF3B1 K700E, TET2 Q769X


title: Ctrl3


title: MEFs reprogramming - OE day 12 - Empty rep 1


title: MEFs reprogramming - OE day 00 - NI rep 2

value: Non-infected


title: LV_1001


title: LA_0920

value: Left atrial tissue


title: LA_0921


title: MEFs reprogramming - KD day 12 - shUL1#2 rep 2

value: Day 00 of doxycycline treatment

value: Lentiviral

value: shRNA UL1 #2


title: LA_1002


title: MEFs reprogramming - KD day 12 - shUL1#2 rep 1

value: Collagen-OKSM, M2rtta+

value: Embryo


title: LA_1001


title: MEFs reprogramming - KD day 12 - shUL1#1 rep 1

value: Fibroblasts

value: Day 12 of doxycycline treatment

value: shRNA UL1 #1


title: MDS4

value: SF3B1 K666R


title: F26LA

value: Female


title: MEFs reprogramming - KD day 12 - shUL1#1 rep 2


title: C2/3

description: Potential outlier

tag: Sex

value: male

value: chow


title: RA_1002

value: Right atrial tissue

value: Sprague Dawley

value: Male


title: MEFs reprogramming - OE day 12 - T7-TIA1 rep 1

tag: cell type

value: Retroviral

value: T7-TIA1 cDNA


title: MEFs reprogramming - KD day 12 - shCPSF3#2 rep 2

tag: genotype

value: shRNA CPSF3 #2


title: RA_1001


title: RA_0920


title: RA_0921


title: MEFs reprogramming - KD day 12 - shCPSF3#1 rep 2

value: Lentiviral

value: shRNA CPSF3 #1


title: MEFs reprogramming - KD day 12 - shCPSF3#2 rep 1

value: Collagen-OKSM, M2rtta+


title: MEFs reprogramming - KD day 12 - shCPSF3#1 rep 1

value: Embryo


title: Ctrl1

value: Bone marrow CD34+ HSPC


title: SB_1002

value: Inferior sinoatrial node


title: MEFs reprogramming - KD day 12 - shSCR rep 2

value: Fibroblasts

value: Day 12 of doxycycline treatment

value: shRNA scrambled control


title: MEFs reprogramming - OE day 00 - NI rep 1

value: Non-infected


title: SB_0920


title: MEFs reprogramming - KD day 12 - shSCR rep 1


title: ST_1001

value: Superior sinoatrial node


title: SB_0921


title: ST_1002


title: QUAD_11

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Demultiplexed fastq files were generated with CASAVA software (Illumina).
Illumina adapter contaminations were removed from reads using Cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM.
Counts were normalized using Voom and TMM, from R packages Limma and EdgeR, respectively.
Genome_build: GRCm38 assembly, Ensembl genebuild 91.
Supplementary_files_format_and_content: NormCounts.txt fiile contains ENSEMBL gene Ids and normalized counts per million for each sample.

source_name: Quadriceps muscle

growth_protocol: RNA-Seq experiments were conducted with 18 month-old male mice.

extract_protocol:
Nine months after treatment, quadriceps muscle samples were extracted and homogenized in Trizol. Total RNA was then column purified by PureLinkTM RNA Mini Kit (Invitrogen, 12183018A).
cDNA libraries were prepared for sequencing using NEBNext Ultra RNA Library preparation kit (New England Biolabs).
Libraries were sequenced (single-end mode and length 61 bp) on the Illumina HiSeq2500 system.

treatment_protocol: Nine month-old mice were treated by intravenous injection in the tail of either PBS or vector AAV8-sp7-delta8-hGAAco, to provide for transgenic expression of secGAA.

value: GAA KO

value: secGAA

tag: age

value: 18 month


title: QUAD_13

value: Male


title: QUAD_8

value: PBS


title: SB_1001

value: Sprague Dawley


title: ST_0920


title: QUAD_12


title: QUAD_4

value: WT


title: MEFs reprogramming - KD day 00 - NI rep 1

value: Day 00 of doxycycline treatment


title: QUAD_3


title: ST_0921


title: QUAD_7


title: MEFs reprogramming - KD day 00 - NI rep 2

value: Collagen-OKSM, M2rtta+


title: QUAD_2


title: Sample-18: p hAFS-EVs_normoxia-Donor6

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
Base calling was performed with default Illumina NextSeq500 workflow
Reads are first processed by trimming off the 3’ adapter and low-quality bases using cutadapt (cutadapt.readthedocs.io/en/stable/guide.html). Reads with no adapter sequence are tallied (no_adapter_reads).Following trimming, the insert sequences and UMI sequences are identified. Reads with less than 16 bp insert sequences (too_short_reads) or less than 10 bp UMI sequences (UMI_defective_reads) are discarded.
To annotate the insert sequences, a unique sequence set is made for all readsets/samples in a submitted job. Following this, reads were alligned miRBase mature, using bowtie (bowtiebio.sourceforge.net/index.shtml). miRBase V21 is used for miRNA, and piRNABank is used for piRNA.
For each sample in a submitted job, all reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are aggregated to count unique molecules. Only UMI counts are presented in the output CSV file
Genome_build: miRBase 21 - Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: hAFs_EV_miRNA_Profile_UMIcounts.csv presents UMI counts for each miRNA in miRBase21  in each sample
Supplementary_files_format_and_content: hAFs_EV_RNA_Type_Reads.csv presents the total reads distribution over RNA types in each sample

source_name: p hAFS-EVs_normoxia-Donor6

growth_protocol: Human amniotic fluid stem cells (hAFS) were isolated from leftover samples of amniotic fluid (AF) collected by routine prenatal screening via II trimester amniocentesis (fetal hAFS, f-hAFS), or as clinical waste during scheduled cesarean-section delivery during III trimester (perinatal hAFS, p-hAFS). Informed written consent was obtained from all donors according to local ethical committee authorization (protocol P.R. 428REG2015). Fetal and perinatal hAFS were isolated by immunomagnetic sorting for c-KIT expression (CD117 MicroBead Kit, Miltenyi Bio-technology) from adherent AF mesenchymal stromal cells. c-KIT+ hAFS were cultured in Minimal Essential Medium (MEM)-alpha with 15% FBS (Gibco - Thermo Fisher Scientific), 18% Chang B and 2% Chang C Medium (Irvine Scientific) with 1% L-glutamine and 1% penicillin/streptomycin (Gibco - Thermo Fisher Scientific), in an incubator at 37°C with 5% CO2 and 20% O2 atmosphere and cultured up to 5 passages in vitro before being used to isolate their secretome. f-hAFS and p-hAFS were cultured in normoxic or hypoxic conditions for 24h in serum-free medium

extract_protocol:
hAFS-EVs were isolated by serial ultracentrifugation from concentrated hAFS-CM. Briefly, hAFS-CM was collected and centrifuged at 4°C at 300×g for 10’, 2000×g for 20’ to remove cell debris. Surnatant was then processed at 10,000×g for 40’. Pellet was then discarded and surnatant further processed by ultracentrifugation in an Optima L-90K (Beckmann Coulter, Brea, California) at 100,000×g for 120’ using Beckman Coulter's swinging-bucket SW55Ti centrifuge rotors. The pellet containing heterogenous hAFS-EVs was washed in PBS by a final step at 100,000×g for 120’ and then re-suspended in 0,22 µm filtered PBS. hAFS-CM and hAFS-EV protein concentration were measured using the BiCinchoninic Acid (BCA) assay (Thermo Fisher Scientiﬁc, Wal-tham, Massachusetts). EVs isolated from hAFs were suspended in 700 µL of Qiazol reagent (Qiagen,). EV RNA was extracted with the miRNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. miRNA content was assessed by performing the Qubit microRNA Assay Kit and RNA quality and sizes were checked with Agilent 2100 Bioanalyzer using the Agilent Small RNA chip according to manufacturer’s protocol. Each sequencing library was constructed from 9.2ng of isolated miRNA.
Small RNA libraries were prepared and amplified using QIAseq miRNA Library kit (Qiagen), following manufacturer's instructions. Libraries were pooled after quality check and quantification by TapeStation (Agilent Technologies) using Agilent High Sensitivity D1000 ScreenTape. Pooled libraries were quantified by real-time qPCR following “Sequencing Library qPCR Quantification” Guide (Illumina Inc.) and sequenced by Illumina NextSeq platform using the 75 cycles high output kit (Illumina Inc.).

value: Human amniotic fluid stem cells (hAFS)

tag: preconditioning of ev releasing cells

value: normoxia

tag: gestational stage

value: Perinatal

tag: subject


title: Sample-17: p hAFS-EVs_hypoxia-Donor5

source_name: p hAFS-EVs_hypoxia-Donor5

value: hypoxia


title: dCAPH2_clone218_RNAseq_rep3

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Hap1 dCAPH2-18 RNA-seq replicate 3

data_processing:
Reads were processed with fastp 0.12.2 to remove potential adapter sequences and low-quality reads
Reads were aligned to GRCh38 v15 and counted in Gencode genes v24 with STAR 2.5.4a
Differential analysis was performed with DESeq2 1.18.1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of rnaseq reads, reads per million normalized. The count table used for all analyses is also provided.

source_name: Hap1 cells

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Gibco) supplemented with 10% FBS (Sigma Aldrich), 1% Penicillin-Streptomycin (Gibco) and 1% L-Glutamine (Gibco). Cells were cultured at 37 degrees with 5% CO2.

extract_protocol:
Total RNA was extracted using RLT buffer supplemented with B-mercaptoethanol (Qiagen).
Strand-specific libraries were created as described in Haarhuis et al (2017), using the TruSeq PolyA Stranded mRNA preparation kit.

treatment_protocol: CAP-H2 knockout cells were obtained as described in (Elbatsh et al. 2019).

tag: cell line


title: ATCC17616_WT, biological rep1

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description: Mucoid wild-type environmental strain

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software. Subsequent analysis was carried out with DNA-Chip Analyzer 2008. First a digital mask was applied, leaving for analysis only the 9610 probe sets on the array representing Burkholderia multivorans ATCC 17616 transcripts. Then the 6 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Burkholderia multivorans

source_name: ATCC 17616 wild-type with 10 h growth in SM medium

label_protocol: RNA was processed for use on Affymetrix custom dual species Burkholderia arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: Bacterial strains were grown in 100 ml salts-mannitol (SM) medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 10 h

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAprotect bacteria reagent (Qiagen).

tag: isolate

value: ATCC 17616 mucoid


title: ATCC17616_WT, biological rep3

description: Mucoid wild-type environmental strain


title: BN_Untreated_Virus_Saline_1_bone_marrow_rep1

description:
genecounts_bonemarrow.csv
RB02_HGMMWDMXX_TTATAACC.GATATCGA_L001_R1.fastq.gz

source_name: bone marrow

extract_protocol:
Single-cell suspensions of bone marrow and lung tissue were resuspended in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80°C. Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (Qiagen Gmbh, Hilden, Germany). Total RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit, Illumina Inc, San Diego, CA. Sequencing was performed by the Australian Genome Research Facility (Illumina HiSeq2500, 50bp single-end reads, v4 chemistry).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BN

tag: treatment group

value: Untreated

tag: experimental group

value: days post infection (dpi):1

value: male

tag: rna integrity number


title: QUAD_9

value: GAA KO

tag: treatment

tag: gender


title: dCAPH2_clone211_RNAseq_rep3

description: Hap1 dCAPH2-11 RNA-seq replicate 3


title: ATCC17616_WT, biological rep2

description: Mucoid wild-type environmental strain


title: 17616nmv, biological rep1

description: Evolved nonmucoid variant

source_name: ATCC 17616 variant with 10 h growth in SM medium

value: ATCC 17616 nonmucoid


title: 17616nmv, biological rep2

description: Evolved nonmucoid variant


title: dCAPH2_clone218_RNAseq_rep2

description: Hap1 dCAPH2-18 RNA-seq replicate 2


title: WT_RNAseq_rep2

description: Hap1 wildtype RNA-seq replicate 2


title: WT_RNAseq_rep1

description: Hap1 wildtype RNA-seq replicate 1


title: Sample-12: p hAFS-EVs_hypoxia-Donor6

source_name: p hAFS-EVs_hypoxia-Donor6


title: Sample-16: p hAFS-EVs_hypoxia-Donor4

source_name: p hAFS-EVs_hypoxia-Donor4


title: 17616nmv, biological rep3

description: Evolved nonmucoid variant


title: dCAPH2_clone218_RNAseq_rep1

description: Hap1 dCAPH2-18 RNA-seq replicate 1


title: Sample-13: f hAFS-EVs_normoxia-Donor1

source_name: f hAFS-EVs_normoxia-Donor1

value: Fetal


title: dCAPH2_clone211_RNAseq_rep1

description: Hap1 dCAPH2-11 RNA-seq replicate 1


title: Sample-09: p hAFS-EVs_normoxia-Donor5

source_name: p hAFS-EVs_normoxia-Donor5


title: Sample-08: p hAFS-EVs_hypoxia-Donor4


title: Sample-15: p hAFS-EVs_normoxia-Donor4

source_name: p hAFS-EVs_normoxia-Donor4


title: WT_RNAseq_rep3

description: Hap1 wildtype RNA-seq replicate 3


title: Sample-07: p hAFS-EVs_normoxia-Donor4


title: Sample-10: p hAFS-EVs_hypoxia-Donor5


title: dCAPH2_clone218_Dam-only_rep1

description: Hap1 dCAPH2-18 Dam-control replicate 2

data_processing:
Library strategy: DamID-seq
The full protocol is described in Leemans, 2019.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17.
Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins

extract_protocol:
Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, with the addition of a dephosphase step to prevent amplification of apoptotic fragments. 500 ng of genomic DNA was first dephosphorylated with rSAP (NEB), before digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. Following DpnII digestion of intact GATC sequences, DNA fragments were amplified with 22-26 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 9-12 PCR cycles with illumina index adapters.

treatment_protocol: CAP-H2 knockout cells were obtained as described in (Elbatsh et al. 2019). 200.000 cells were plated in a 6-well plate in 2mL full medium, supplemented with 8 μg/mL polybrene to enhance viral transduction efficiency. Cells were transduced with either Dam-only lentivirus or Dam-LMNB1lentivirus. The following day, medium was refreshed. Three days after transduction, cells were harvested and genomic DNA was isolated.


title: dCAPH2_clone218_Dam-only_rep3

description: Hap1 dCAPH2-18 Dam-control replicate 4


title: dCAPH2_clone211_RNAseq_rep2

description: Hap1 dCAPH2-11 RNA-seq replicate 2


title: dCAPH2_clone218_Dam-only_rep2

description: Hap1 dCAPH2-18 Dam-control replicate 3


title: Sample-05: f hAFS-EVs_normoxia-Donor3

source_name: f hAFS-EVs_normoxia-Donor3


title: Sample-04: f hAFS-EVs_hypoxia-Donor2

source_name: f hAFS-EVs_hypoxia-Donor2


title: Sample-03: f hAFS-EVs_normoxia-Donor2

source_name: f hAFS-EVs_normoxia-Donor2


title: dCAPH2_clone211_Dam-only_rep2

description: Hap1 dCAPH2-11 Dam-control replicate 4


title: Sample-06: f hAFS-EVs_hypoxia-Donor3

source_name: f hAFS-EVs_hypoxia-Donor3


title: dCAPH2_clone211_Dam-only_rep1

description: Hap1 dCAPH2-11 Dam-control replicate 1


title: WT_Dam-only_rep4

description: Hap1 wildtype Dam-control replicate 4


title: WT_Dam-only_rep3

description: Hap1 wildtype Dam-control replicate 3


title: Sample-02: f hAFS-EVs_hypoxia-Donor1

source_name: f hAFS-EVs_hypoxia-Donor1


title: Sample-14: f hAFS-EVs_hypoxia-Donor2


title: Sample-11: p hAFS-EVs_normoxia-Donor6


title: WT_Dam-only_rep1

description: Hap1 wildtype Dam-control replicate 1


title: WT_Dam-only_rep2

description: Hap1 wildtype Dam-control replicate 2


title: Sample-01: f hAFS-EVs_normoxia-Donor1


title: Day 35S rep3

data_processing:
Illumina base-calling software: Real-Time Analysis (RTA) called RTA v2
TrimGalore v0.4.4  (-q 20 --stringency 1 --fastqc --length 10)
STAR v2.7.0 (--outFilterScoreMin 10 --outFilterMultimapNmax 1)
FeatureCounts/Rsubread v2.2.6  (GTF file from Human (GRCh38) Ensembl v90;  isGTFAnnotationFile = TRUE, strandSpecific = 1)
Genome_build: hg38

source_name: iPSC-derived cerebellar organoids

extract_protocol:
Aggregates were dissociated with accutase at 37ºC for 7 min. After enzymatic neutralization, the cell pellet was washed with phosphate buffered saline (PBS, 0.1M) and then stored at -80ºC. Total RNA was extracted from samples using High Pure RNA Isolation Kit (Roche, Cat. 11828665001), according to the manufacturer instructions.
RNA libraries were prepared for deep sequencing, starting with 500 ng of Total RNA and following Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina using standard protocols.
3'Tag RNA-seq

value: iPSC-derived cerebellar organoids

tag: protocol

value: Static

tag: differentiation day

value: Day 35


title: Day 35S rep1


title: Day 35S rep2


title: dCAPH2_clone218_Dam-Lamin_rep3

description: Hap1 dCAPH2-18 Dam-LMNB1 replicate 4


title: dCAPH2_clone218_Dam-Lamin_rep2

description: Hap1 dCAPH2-18 Dam-LMNB1 replicate 3


title: Day 35D rep2

value: Dynamic


title: Day 35D rep1


title: Day 14S rep3

value: Day 14


title: dCAPH2_clone211_Dam-Lamin_rep2

description: Hap1 dCAPH2-11 Dam-LMNB1 replicate 4


title: dCAPH2_clone218_Dam-Lamin_rep1

description: Hap1 dCAPH2-18 Dam-LMNB1 replicate 2


title: WT_Dam-Lamin_rep4

description: Hap1 wildtype Dam-LMNB1 replicate 4


title: WT_Dam-Lamin_rep3

description: Hap1 wildtype Dam-LMNB1 replicate 3


title: Day 14S rep2


title: dCAPH2_clone211_Dam-Lamin_rep1

description: Hap1 dCAPH2-11 Dam-LMNB1 replicate 1


title: Day 14S rep1


title: Day 14D rep3


title: Day 14D rep2


title: PAG175_Inf Malaria Symptomatic stage mRNA Year2 Sample

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analyses
Genome_build: hg38

source_name: Blood

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

tag: visit

value: Malaria Symptomatic stage


title: Day 14D rep1


title: PAG175_NonInf Malaria Before Infection mRNA Year2 Sample

value: Malaria Before Infection


title: WT_Dam-Lamin_rep2

description: Hap1 wildtype Dam-LMNB1 replicate 2


title: WT_Dam-Lamin_rep1

description: Hap1 wildtype Dam-LMNB1 replicate 1


title: PAG174_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: Day 0 rep2

source_name: human induced pluripotent stem cells (iPSCs)

value: Control

value: Day 0


title: Day 0 rep3

value: human induced pluripotent stem cells (iPSCs)


title: PAG174_NonInf Malaria Before Infection mRNA Year2 Sample


title: Day 35D rep3


title: PAG172_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: Day 0 rep1


title: PAG172_NonInf Malaria Before Infection mRNA Year2 Sample


title: 158-NPF2

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.1
Genome_build: GRCh38 (Ensembl 97)
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

extract_protocol: 10X Genomics Single cell 3' gene expression V2

tag: donor  id

tag: condition

value: Crigler Najjar

tag: Sex

value: Female

tag: tissue

value: Liver

tag: fraction

value: non-parenchymal

tag: cell viability


title: 158-NPF1

tag: age


title: PAG171_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG171_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG170_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG165_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: 158-PF

value: parenchymal


title: PAG170_NonInf Malaria Before Infection mRNA Year2 Sample


title: 156-NPF2

value: Healthy

value: Male


title: PAG161_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: 156-NPF1


title: 156-PF2


title: PAG165_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG161_NonInf Malaria Before Infection mRNA Year2 Sample


title: C42-shRB E2F1 ChIP-seq DHT

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
Alignment to hg19 genome
peak calling with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: BED file

source_name: C4-2 cell line

growth_protocol: LNCaP and C4-2 cells (shCon and shRB) were cultured in hormone proficient media

extract_protocol:
ChIP was performed as previously described (McNair et al 2018)
Library prep was performed as previously described (McNair et al 2018)

treatment_protocol: LNCaP and C4-2 cells (shCon and shRB) were moved to hormone deficient media for 72 hours followed by treatment with 10 nm DHT for 3 hours prior to harvest

tag: cell line

value: C4-2 cell line

tag: knockdown

value: shRB

value: 72 hrs CDT, 3 hrs 10 nM DHT

tag: chip antibody


title: LNCaP-shRB E2F1 ChIP-seq DHT

source_name: LNCaP cell line

value: LNCaP cell line


title: LNCaP-shCon E2F1 ChIP-seq DHT

value: shCon


title: C42_shRb_16hr_3

description:
C42_shRB_DHT_16hr_3
processed data file: C42_CountTable_16hr_FeatureCounts.txt

data_processing:
Alignment to hg19 with STAR
Generate count table using featureCounts
Differential expression using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: count matrix

extract_protocol:
RNA seq was performed as previously described (McNair et al 2018)
RNA seq libraries were constructed as previously described (McNair et al 2018)

treatment_protocol: LNCaP and C4-2 cells (shCon and shRB) were moved to hormone deficient media for 72 hours followed by treatment with 10 nM DHT for 16 hours prior to harvest

value: 72 hrs CDT, 16 hrs 10 nM DHT


title: C42_shRb_16hr_1

description:
C42_shRB_DHT_16hr_1
processed data file: C42_CountTable_16hr_FeatureCounts.txt


title: 158-WF

value: whole


title: C42_shRb_16hr_2

description:
C42_shRB_DHT_16hr_2
processed data file: C42_CountTable_16hr_FeatureCounts.txt


title: C42_shCON_16hr_3

description:
C42_shCON_DHT_16hr_3
processed data file: C42_CountTable_16hr_FeatureCounts.txt


title: C42_shCON_16hr_2

description:
C42_shCON_DHT_16hr_2
processed data file: C42_CountTable_16hr_FeatureCounts.txt


title: PAG153_Inf Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: PAG157_NonInf Malaria Before Infection mRNA Year2 Sample

value: Malaria Before Infection


title: PAG158_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: PAG157_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG151_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG151_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: PAG148_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG153_NonInf Malaria Before Infection mRNA Year2 Sample


title: LN_shRb_16hr_3

description:
LN_shRB_DHT_16hr_3
processed data file: LN_CountTable_16hr_FeatureCounts.txt


title: PAG158_NonInf Malaria Before Infection mRNA Year2 Sample


title: C42_shCON_16hr_1

description:
C42_shCON_DHT_16hr_1
processed data file: C42_CountTable_16hr_FeatureCounts.txt


title: PAG145_NonInf Malaria Before Infection mRNA Year2 Sample


title: LN_shCON_16hr_3

description:
LN_shCON_DHT_16hr_3
processed data file: LN_CountTable_16hr_FeatureCounts.txt


title: PAG145_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG144_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: LN_shRb_16hr_1

description:
LN_shRB_DHT_16hr_1
processed data file: LN_CountTable_16hr_FeatureCounts.txt


title: C42-shCon E2F1 ChIP-seq DHT


title: PAG144_NonInf Malaria Before Infection mRNA Year2 Sample


title: 156-PF1


title: LN_shCON_16hr_2

description:
LN_shCON_DHT_16hr_2
processed data file: LN_CountTable_16hr_FeatureCounts.txt


title: LN_shCON_16hr_1

description:
LN_shCON_DHT_16hr_1
processed data file: LN_CountTable_16hr_FeatureCounts.txt


title: PAG143_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: PAG143_NonInf Malaria Before Infection mRNA Year2 Sample


title: SP49-Sen [input]

city: Tampa

first: Jianguo

last: Tao

state: Florida

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: 20180917_SP49-sen2_Input_H3K27ac_PP6074_S2

data_processing:
Bamliquidator was used to calculate read density which can be found at http://github.com/BradnerLab/pipeline/wiki/bamliquidator
ROSE2, was used to identify enhancers and can be found at https://github.com/BradnerLab/pipeline/(ROSE2_main.py)
All datasets were aligned using Bowtie2 (version 2.2.1). All default parameters, except for –N 1 (reads that mapped uniquely to the genome with one or fewer mismatches) were used to align to human genome build NCBI37/HG19.
The MACS version 1.4.1 (Model based analysis of ChIP-Seq) 67 peak finding algorithm was used to identify regions of ChIP-Seq enrichment over background. A p value threshold of enrichment of 1e-9 was used for all datasets.
Atibody used for CHIP is anti-H3K27ac (ABCAM ab4729) Lot:GR299725-1
Genome_build: hg19
Supplementary_files_format_and_content: bed file

growth_protocol: Jeko-1 and  SP49 parental ibrutinib sensitive cells were grown in RPMI-1640 medium with 10% FBS.

extract_protocol:
ChIP-seq was performed according to established protocols, with minor modifications. 50 million cells were used for ChIP-seq of H3K27ac. DNA was isolated with phenol chloroform extraction and ethanol precipitation
Libraries for Illumina sequencing were prepared using ThruPLEX DNA-seq Kit (Rubicon) using 50 ng of DNA or less and amplifying according to manufacturer instructions. Amplified libraries were size-selected first using AMPure beads (Agencourt AMPure XP) and subsequently, using a 2% gel cassette in the Pippin Prep (SAGE Sciences) to capture fragments of 200-700 bp. Libraries were quantified by qPCR using the KAPA Biosystems library quantification kit, multiplexed with equimolar DNA content, and sequenced on an Illumina NextSeq 500 (single end 75 bp reads).

tag: cell type

value: Mantle cell lympohoma

tag: group

tag: ibrutnib sensitivity

value: Sensitive


title: SP49-Sen [ChIP-seq]


title: PAG148_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG136_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: LN_shRb_16hr_2

description:
LN_shRB_DHT_16hr_2
processed data file: LN_CountTable_16hr_FeatureCounts.txt

tag: treatment


title: PAG136_NonInf Malaria Before Infection mRNA Year2 Sample


title: SP49-IR [ChIP-seq]

value: resistant


title: Jeko-1-Sen [input]

description: 20180917_Jeko-sen2_Input_H3K27ac_PP6074_S6


title: SP49-IR [input]

description: 20180917_SP49-IR2_Input_H3K27ac_PP6074_S4


title: PAG123_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Pulldown Med15 LibA input

city: Stanford

first: Adrian

middle: L

last: Sanborn

address: 299 Campus Drive West

institute: Stanford University

description: cDNA of mRNA-tagged protein

data_processing:
UMI deduplication using umi_tools 1.0.0
cutadapt 1.18 was used to discard reads without matching paired-end sublibrary sequencing primers and trim the primers in reads with matching primers
bwa-mem 0.7.17-r1188 was used to perform a first-pass alignment of reads to the DNA fragment library
Imperfectly mapped read pairs (i.e., those without paired read SAM flags of 99 and 147) were re-mapped to the library sequence with minimal edit distance
Supplementary_files_format_and_content: Excel file containing counts of reads aligned to each protein fragment

organism: synthetic construct

source_name: Med15 LibA input

extract_protocol:
N/A
The cDNA region encoding the variable protein fragment was PCR-amplified for 11-20 cycles  using Phusion polymerase with PCR primers that added flanking sequences corresponding to the standard Illumina sequencing primers. After a column cleanup, a second PCR was performed with primers that added sample-specific barcodes and the P5 and P7 sequences for Illumina sequencing.
OTHER:sequncing of designed oligo library

treatment_protocol: In vitro expressed protein library input was incubated with the bait-coated beads in binding buffer with salmon sperm DNA and BSA at 100 µL total volume for 8 min with mixing. Afterward, the beads were separated on a magnet, briefly washed once with cold binding buffer, and then immediately separated on a magnet again. cDNA from bound fragments was eluted by suspending the beads in 10 mM Tris pH 8.0 with proteinase K (NEB) and incubated for 30 min at room temperature. Proteinase K was heat inactivated at 95C for 10 min, beads were separated on a magnet, and the eluate was collected.

tag: pulldown


title: Pulldown TFIID LibA input

description: cDNA of mRNA-tagged protein

source_name: TFIID LibA input

value: TFIID


title: Pulldown Med15 LibAB replicate3

description: cDNA of mRNA-tagged protein

source_name: Med15 LibAB replicate3


title: PAG122_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Pulldown Med15/TFIID LibB input

description: cDNA of mRNA-tagged protein

source_name: Med15/TFIID LibB input


title: Small Hepatocytes

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

country: Japan

institute: Sapporo Medical University School of Medicine

description:
Purified by FACS as CD31(-)CD45(-)EpCAM(-)ICAM-1(+) cells
group 1 vs. group 2 GE

data_processing:
RNA-Seq data were analyzed using CLC Genomics Workbench (Qiagen Bioinformatics) to identify the differentially expressed genes.
The raw transcriptome data was trimmed with quality scores limit set to 0.01, ambiguous limit set to 2.
Trimmed reads of cDNA libraries were then aligned to the Mus musculus genome downloaded from NCBI database (mm10) with the following parameters: (1) maximum number of allowed mismatches was 2; (2) minimum length fraction was set at 0.8; (3) minimum similarity fraction was set at 0.8; and (4) maximum number of hits per read was 10.
Gene expression values were reported as RPKM (Reads Per Kilobase of exon per Million mapped reads) using the CLC transcriptomic analysis module.
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads

source_name: Liver

growth_protocol: Cells were isolated freshly isolated by the liver by collagenase perfusion

extract_protocol:
Total RNA were extracted from by using RNeasy Mini kit (Qiagen).
Poly(A) RNAs were purified and cDNA libraries were constructed by using Ion Total RNA-Seq Kit v2 (ThermoFisher). RNA sequence was performed on an Ion Proton system (ThermoFisher).

treatment_protocol: Hepatocytes and small hepatocytes that was isolated as CD31(-)CD45(-)ICAM-1(+)EpCAM(-) cells were isolated from the same mice.

tag: strain

value: Small hepatocytes, intrindic hepatocyte progenitors, isolated from mouse


title: Pulldown Med15 LibAB replicate2

description: cDNA of mRNA-tagged protein

source_name: Med15 LibAB replicate2


title: Jeko-1-IR [input]

description: 20180917_Jeko-IR2_Input_H3K27ac_PP6074_S8


title: Pulldown TFIID LibAB replicate1

description: cDNA of mRNA-tagged protein

source_name: TFIID LibAB replicate1


title: RNAseq of c-exNDI treated 93T449 liposarcoma cell line rep3

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

description: 93T449 cell line was established from a well-differentiated liposarcoma from the retroperitoneum of a 68 year old female.

data_processing:
Single end RNA-seq reads were mapped to the human genome (hg38) using STAR (Dobin et al., 2013). Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Genome_build: hg38
Supplementary_files_format_and_content: NT_93T449_RNAseq_rep1_rsem.genes.results, NT_93T449_RNAseq_rep2_rsem.genes.results, NT_93T449_RNAseq_rep3_rsem.genes.results, Pham_93T449_RNAseq_rep1_rsem.genes.results, Pham_93T449_RNAseq_rep2_rsem.genes.results, Pham_93T449_RNAseq_rep3_rsem.genes.results. These Files were generated with RSEM

growth_protocol: 93T449 cells were routinely subcultured with a 1:2 to 1:4 ratio using Trypsin-EDTA solution and typically kept into a T75 flask of uncoated plastic in RPMI 1640 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10 % heat inactivated FBS.

extract_protocol:
Total RNA was extracted with TRI Reagent® (Sigma Aldrich #93289) and RNA clean and concentrator kit (Zymo research #R1017), including the on-column DNAse step. Ribo-depletion with Ribozero goldkit (Illumina #MRZG126)
NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)

treatment_protocol: The G4-ligand c-exNDI was administered directly to the cell culture 24 h after cells seeding. Being the compound solubilized in DMSO, an equivalent amount of DMSO was administered to the non-treated control sample. c-exNDI is a core-extended napthalene diimide merged to a dihydrobenzophenazine polynuclear heterocycle to improve its solubility and interaction with G4 structures. The synthesis and structure of the coumpound were previously published in Perrone et al. J Med Chem. 2015.

tag: genotype


title: RNAseq of c-exNDI treated 93T449 liposarcoma cell line rep2


title: Jeko-1-IR [ChIP-seq]


title: RNAseq of c-exNDI treated 93T449 liposarcoma cell line rep1


title: Mature Hepatocytes

description:
Dead cells were eliminated by percoll gradient centrifugation
group 1 vs. group 2 GE

value: Mature hepatocytes freshly isolated from mouse


title: PAG118_NonInf Malaria Before Infection mRNA Year2 Sample

tag: visit


title: RNAseq of 93T449 liposarcoma cell line rep3


title: PAG102_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: RNAseq of 93T449 liposarcoma cell line rep2


title: PAG123_NonInf Malaria Before Infection mRNA Year2 Sample


title: Pulldown TFIID LibAB replicate2

description: cDNA of mRNA-tagged protein

source_name: TFIID LibAB replicate2


title: Pulldown Med15 LibAB replicate1

description: cDNA of mRNA-tagged protein

source_name: Med15 LibAB replicate1


title: RNAseq of 93T449 liposarcoma cell line rep1


title: Jeko-1-Sen [ChIP-seq]