title: C9ORF72-ALS/FTD-neuroprotected fly expressing 36 G4C2 repeats and the disrupted SRSF1 allele. Biological replicate 2

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

hyb_protocol: The cRNA molecules produced incorporated biotin labelled ribonucleotides, which acted as a target for the subsequent detection of hybridization, using fluorescently labelled streptavidin. 12.5 μg of cRNA molecules were heat fragmented and applied to the GeneChips in a hybridization solution according to the Affymetrix protocol. Hybridization took place overnight in a rotating hybridization oven at 60 rpm, 45°C for 16 hours.

scan_protocol: After washing and development of the fluorescent signal, the GeneChip arrays were scanned using GC30007 scanner.

data_processing: The data was processed using the Affymetrix expression Console, adopting PLIER as method for quantification.

label: biotin

source_name: heads

label_protocol: 200 ng of total RNA was converted into cDNA using an oligo(dT) which also carries the binding site for T7 RNA polymerase. Following first strand synthesis, residual RNA was degraded by addition of RNaseH and a double stranded cDNA molecule was generated using DNA Polymerase I and DNA ligase. These cDNA molecules were used as a substrate for the T7 RNA polymerase to produce multiple copies of antisense RNA using an IVT labelling system.

growth_protocol: Flies were raised under standard conditions in a humidified, temperature-controlled incubator with a 12 h:12 h light:dark cycle at 25 °C, on food consisting of agar, cornmeal, molasses, propionic acid and yeast. The following strains were obtained from the Bloomington Drosophila Stock Center (RRIDs indicated): UAS-Luciferase RNAi (BDSC_31603), D42-GAL4 (BDSC_8816), nSyb-GAL4 (BDSC_51635), SKMi10378 (BDSC_55475), SKMi09020 (BDSC_51246). The following strains were obtained from the Vienna Drosophila Resource Center: UAS-SF2-RNAi (VDRC v27776). UAS-G4C2x3 and UAS-G4C2x36 lines were a gift from Adrian M. Issacs (Department of Neurodegenerative Disease, UCL Institute of Neurology, London). Unless otherwise stated, all experiments were conducted using male flies.

extract_protocol: Total RNA was extracted from Drosophila heads which had been ground to a powder under liquid nitrogen. Drosophila and iNeuron total extracts were added to PureZOL™ to extract the RNA. All PureZol™ extracted RNA samples were treated with DNaseI and quantified using a Nanodrop (NanoDrop Technologies). Fractionated extracts were subjected to RNA extraction using Direct-zol™ RNA microprep kits following the manufacturer’s protocol, including the recommended in-column DNase I treatment and quantified using a Nanodrop. RNA quality was then assessed using a eukaryote total RNA Nano 6000 Kit prior to high depth RNA sequencing or microarray analysis.

treatment_protocol: Transgene expression was induced using the tissue specific D42-GAL4 or nSyb-GAL4 driver.

tag: line

value: G4C2x36 + <delta>SRSF1

value: Heads

value: Male


title: F_2_q

status: Public on Jul 21 2021

type: SRA

city: Stockholm

first: Szabolcs

last: Éliás

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institute

library_source: genomic

data_processing:
Base-calling was performed using Illumina HiSeq Control/Real Time Analysis software.
Base-call files were demultiplexed and converted to fastq files using bcl2fastq version 2.17.1.14.
Fastq files were adapter-trimmed using scythe version 0.991 and quality-trimmed using sickle version 1.33.
Trimmed fastq files were aligned to the human genome version hg38 using bowtie version 2.3.0 with the ‘--very-sensitive’ setting.
Bam files were sorted, indexed and filtered using samtools version 0.1.19 to remove duplicates, alignments with a mapping score below 10, and alignments not mapped to chromosomes 1-22, X or Y.
Peak-calling was performed using the ‘findPeaks’ script from the Homer suite version 4.9.1 with the '-style factor' setting.
A consensus peak-set containing genomic regions with reproducible accessibility was generated as described in the accompanying publication.
Reads in the genomic regions defined by the consensus peak-set were counted for each sample using the featureCounts version 1.5.2 with the settings ‘-s 0 –minOverlap 1 --fracOverlap 0.5’.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file containing read counts at reproducibly accessible genomic regions (consensus peaks)

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Blood

growth_protocol: Primary cells from human peripheral blood.

extract_protocol:
Nuclear isolation was carried out according to Buenrostro et al. 2013 (PMID: 24097267).
Library construction including tagmentation and PCR amplification was performed according to Buenrostro et al. 2013 (PMID: 24097267) followed by additional gel size selection of DNA in the size range of 150-230 base pairs.

treatment_protocol: Peripheral blood mononuclear cell (PBMC) isolation by Ficoll gradient, followed by magnetic activated cell sorting (MACS) of given CD4 T cell sub-populations as follows. Naive, total (bulk) and memory CD4 T cells were isolated in parallel by negative magnetic isolation according to the manufacturer's protocol (Miltenyi Biotec). From an aliquot of total CD4 T cells, GM-CSF producing and GM-CSF negative cells were subsequently isolated without restimulation using the GM-CSF Secretion Assay - Cell Enrichment and Detection Kit (PE), human (Miltenyi Biotec), according to the manufacturer’s instructions. For each isolated cell type and donor, three technical replicates (denoted “p”, “q”, “r”; except donor A, two technical replicates) with 50000 cells each were further processed.

tag: tissue

value: Peripheral Blood

tag: cell type

value: GM-CSF positive CD4 T cells

tag: donor

value: F

tag: gender

value: male


title: HCC3_Urea_C5_146

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Plate2_IndexB
HCC3_Urea_C5_146_S146

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Genome_build: Biospyder S1500 Gene Set
Supplementary_files_format_and_content: count_table.csv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

molecule: total RNA

source_name: Human Hepatoma HepaRG™ Cell Line

growth_protocol: Terminally differentiated human HepaRG™ cells, derived from a hepatocellular carcinoma, were seeded at approximately 4.0-5.0 x 10^4 viable cells per well in a collagen-coated 96-well CometChip® in William's E medium with TRL's Thawing and Plating Supplment. Cells were incubated for seven days following seeding to allow the cells to regain peak metabolic function.

extract_protocol:
RNA was not extracted from control and treated HepaRG™ cells, as TempO-Seq libraries were constructed directly from cell lysates according tp the TempO-Seq® Assay User Guide (Version 2.1, September 6, 2017).
Four hours following the last treatment, the media was aspirated from control (C0) and treated HepaRG™ cells (C1-C5). The cells were then washed with sterile PBS. Following aspiration of the PBS wash, 1X TempO-Seq lysis buffer was added to lyse the cells for 10 minutes at room temperature on a rocking plate. Lysed cells were then frozen at -80 degrees Celsius until library construction. The TempO-Seq® Assay User Guide (Version 2.1, September 6, 2017) was used to build the TempO-Seq libraries for panels with less than 5,000 probes using the TempO-Seq Reagent Kit with HumanTox+Surrogate Panel DO Kit in a 96-well format). Index Set A was used for plate 1, Index Set B for plate 2 and Index Set C for plate 3 (288 samples in total). Following amplification, libraries were pooled and purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit with modifications outlined in the TempO-Seq® User Guide. Pooled, purified libraires were quantified using the KAPA Biosystems qPCR library quantification kit and diluted to 4 nM for denaturation and dilution for sequencing.
Human TempO-Seq® Tox+ Surrogate (S1500+) kits - Index Sets A (plate 1), B (plate 2) & C (plate 3); sequenced using an Illumina NextSeq500.

treatment_protocol: Cells were then exposed in culture medium containing TRL's Pre-Induction/Tox Supplement to five concentrations of each DDI or non-DDI chemical plus matched vehicle controls daily for three days in a repeated exposure design (exposures at 0 hr, 24 hr, and 48 hr). Four hours following the last treatment (52 hr total time), one plate of cells was used for cell viability (n = 2 per treatment group alongside matched solvent controls) and CometChip® analysis and the second plate was used to generate cell lysates for gene expression analysis (n = 4 per treatment group per assay for CometChip® and TempO-Seq). The media was aspirated from exposed cells and they were washed with PBS, prior to adding 100 µl of TrypLE™ (for cell viability and CometChip® assays; ThermoFisher Scientific, Waltham, MA, USA) or 1X TempO-Seq Lysis Buffer in PBS (for TempO-Seq assay; BioSpyder Technologies, Carlsbad, CA, USA) to each well to lyse cells for 10 minutes at room temperature. Cell lysates were then frozen and stored at -80°C for subsequent TempO-Seq S1500+ transcriptome profiling. Samples used for the analysis of cell viability and DNA damage using CometChip® were neutralized with the addition of 100 µl of culture medium to each well and were processed as per manufacturer's User Guides.

tag: cell line

value: Human Hepatoma HepaRG Cell Line

tag: treatment

value: Urea

tag: concentration

tag: index

value: ATCGCGACT

value: GCAGATGCA

tag: molecule source

value: Cell lysate (total RNA)


title: C9ORF72-ALS/FTD fly expressing 36 G4C2 repeats and the RNAi control. Biological replicate 2

type: RNA

country: United Kingdom

organism: Drosophila melanogaster

value: G4C2x36 + C-RNAi


title: C9ORF72-ALS/FTD fly expressing 36 G4C2 repeats and the RNAi control. Biological replicate 3


title: Control fly expressing 3 G4C2 repeats and a luciferase-RNAi control. Biological replicate 2

value: G4C2x3 + C-RNAi


title: F_1_r

value: Naive CD4 T cells


title: C9ORF72-ALS/FTD fly expressing 36 G4C2 repeats and the RNAi control. Biological replicate 1


title: F_2_p


title: C9ORF72-ALS/FTD-neuroprotected fly expressing 36 G4C2 repeats and the disrupted SRSF1 allele. Biological replicate 1


title: F_1_q


title: Control fly expressing 3 G4C2 repeats and a luciferase-RNAi control. Biological replicate 3


title: HCC3_PG_C0_144

description:
Plate2_IndexB
HCC3_PG_C0_144_S144

value: Propyl Gallate (PG)

value: 0 µM

value: TAGCTCTTC

value: TTGACGCTA


title: C9ORF72-ALS/FTD-neuroprotected fly expressing 36 G4C2 repeats and the disrupted SRSF1 allele. Biological replicate 3

value: G4C2x36 + <delta>SRSF1

value: Heads

value: Male


title: Control fly expressing 3 G4C2 repeats and a luciferase-RNAi control. Biological replicate 1


title: HCC3_PG_C0_143

description:
Plate2_IndexB
HCC3_PG_C0_143_S143

value: GGTCTAGCT


title: F_1_p

value: Peripheral Blood

value: F

value: male


title: HCC3_Urea_C5_145

description:
Plate2_IndexB
HCC3_Urea_C5_145_S145

value: Human Hepatoma HepaRG Cell Line

value: Urea

value: ATCGCGACT

value: TATGCTATG


title: HCC3_PG_C0_142

description:
Plate2_IndexB
HCC3_PG_C0_142_S142

value: ATACCGGCA

value: Cell lysate (total RNA)


title: HCC3_Urea_C5_148

description:
Plate2_IndexB
HCC3_Urea_C5_148_S148

value: ATACGCAGC


title: E_5_r

value: Memory CD4 T cells

value: E


title: HCC3_CP_C0_137

description:
Plate2_IndexB
HCC3_CP_C0_137_S137

value: Cyclophosphamide (CP)

value: 0 µM

value: TAGCTCTTC


title: HCC3_PG_C1_136

description:
Plate2_IndexB
HCC3_PG_C1_136_S136

value: Propyl Gallate (PG)

value: TCCTTCGTG

value: TTGACGCTA


title: E_5_q

value: Peripheral Blood


title: HCC3_CP_C0_138

description:
Plate2_IndexB
HCC3_CP_C0_138_S138

value: GCAGATGCA


title: E_4_p

value: Bulk CD4 T cells

value: male


title: E_4_r


title: HCC3_CP_C0_140

description:
Plate2_IndexB
HCC3_CP_C0_140_S140

value: Human Hepatoma HepaRG Cell Line


title: E_5_p


title: HCC3_PG_C0_141

description:
Plate2_IndexB
HCC3_PG_C0_141_S141

value: GCACCTATT


title: E_3_q

value: GM-CSF negative CD4 T cells


title: E_4_q


title: HCC3_PG_C1_135

description:
Plate2_IndexB
HCC3_PG_C1_135_S135

value: GGTCTAGCT

value: Cell lysate (total RNA)


title: HCC3_PG_C1_134

description:
Plate2_IndexB
HCC3_PG_C1_134_S134

value: ATACCGGCA


title: HCC3_PG_C1_133

description:
Plate2_IndexB
HCC3_PG_C1_133_S133


title: E_2_r

value: GM-CSF positive CD4 T cells

value: E


title: HCC3_CP_C1_132

description:
Plate2_IndexB
HCC3_CP_C1_132_S132

value: Cyclophosphamide (CP)

value: ATACGCAGC


title: E_3_p


title: E_3_r


title: E_1_r

value: Naive CD4 T cells


title: E_2_q


title: E_2_p


title: HCC3_CP_C1_131

description:
Plate2_IndexB
HCC3_CP_C1_131_S131

value: TCCTTCGTG

value: AAGTAGGCT


title: E_1_q

value: Peripheral Blood


title: HCC3_CP_C1_130

description:
Plate2_IndexB
HCC3_CP_C1_130_S130

value: GCAGATGCA


title: E_1_p


title: HCC3_CP_C0_139

description:
Plate2_IndexB
HCC3_CP_C0_139_S139

value: 0 µM

value: TAGCTCTTC


title: HCC3_PG_C2_128

description:
Plate2_IndexB
HCC3_PG_C2_128_S128

value: Human Hepatoma HepaRG Cell Line

value: Propyl Gallate (PG)

value: GCATGGACC

value: TTGACGCTA


title: D_5_r

value: Memory CD4 T cells

value: D

value: male


title: HCC3_PG_C2_125

description:
Plate2_IndexB
HCC3_PG_C2_125_S125

value: GCACCTATT

value: Cell lysate (total RNA)


title: HCC3_PG_C2_127

description:
Plate2_IndexB
HCC3_PG_C2_127_S127

value: GGTCTAGCT


title: HCC3_PG_C2_126

description:
Plate2_IndexB
HCC3_PG_C2_126_S126

value: ATACCGGCA


title: D_4_r

value: Bulk CD4 T cells


title: D_5_p


title: D_4_q


title: HCC3_CP_C2_124

description:
Plate2_IndexB
HCC3_CP_C2_124_S124

value: Cyclophosphamide (CP)

value: ATACGCAGC


title: HCC3_CP_C2_122

description:
Plate2_IndexB
HCC3_CP_C2_122_S122

value: GCAGATGCA


title: HCC3_CP_C1_129

description:
Plate2_IndexB
HCC3_CP_C1_129_S129

value: TCCTTCGTG

value: TATGCTATG


title: HCC3_CP_C2_121

description:
Plate2_IndexB
HCC3_CP_C2_121_S121

value: Human Hepatoma HepaRG Cell Line


title: D_4_p

value: Peripheral Blood


title: D_3_r

value: GM-CSF negative CD4 T cells


title: HF_variant_offtarget_pDNA

city: Cambridge

first: John

middle: G

last: Doench

state: MA

address: 75 Ames St.

department: Genetic Perturbation Platform

country: USA

institute: Broad Institute

description:
Plasmid DNA for HF variant off-target library
processed data in: Supplementary_Data2_v2.xlsx

data_processing:
Library strategy: DNA-seq
Raw read counts were retrieved from sequencing data using PoolQ Version 3
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Excel spreadsheets with guide-level read counts and library annotations

organism: unidentified plasmid

source_name: not applicable

growth_protocol: Cells were cultured for 21 days. Every 2-3 cells were passaged and library representation was maintained >1000x.

extract_protocol:
Cells were lysed and genomic DNA was extracted using? Genomic DNA was PCR amplified using barcoded primers, then pooled and SPRI purified before submission for sequencing.
Oligonucleotide pools were synthesized by CustomArray. BsmBI recognition sites were appended to each sgRNA sequence  for cloning into the sgRNA expression plasmids, as well as primer sites to allow differential amplification of subsets from the same synthesis pool. The resulting amplicons were PCR-purified (Qiagen) and cloned into the library vector via Golden Gate cloning with Esp3I (Fisher Scientific) and T7 ligase (Epizyme)

treatment_protocol: If cells received drug treatment, drug was added to the cell culture media at each passage from D7 until D21.

value: not applicable

tag: description


title: HCC3_PG_C3_120

description:
Plate2_IndexB
HCC3_PG_C3_120_S120

value: Propyl Gallate (PG)

value: GGAATGCAT

value: TTGACGCTA


title: D_3_q

value: D

value: male


title: Cas9NG_CBE_BRCA1_tiling_pDNA

description:
Plasmid DNA for CBE BRCA1 tiling library with Cas9-NG
processed data in: Supplementary_Data5_v2.xlsx


title: Cas9NG_ABE8e_BCL2_tiling_pDNA

description:
Plasmid DNA for ABE8e BCL2 tiling library with Cas9-NG
processed data in: Supplementary_Data7_v2.xlsx


title: HCC3_PG_C3_119

description:
Plate2_IndexB
HCC3_PG_C3_119_S119

value: GGTCTAGCT

value: Cell lysate (total RNA)


title: D_3_p


title: SpG_ABE8e_BRCA1_tilingpDNA

description:
Plasmid DNA for ABE8e BRCA1 tiling library with SpG
processed data in: Supplementary_Data6_v2.xlsx


title: PAM_flexible_variant_offtarget_pDNA

description:
Plasmid DNA for PAM-flexible variant off-target library
processed data in: Supplementary_Data3_v3.xlsx


title: Cas9NG_CBE_BCL2_tiling_pDNA

description:
Plasmid DNA for CBE BCL2 tiling library with Cas9-NG
processed data in: Supplementary_Data7_v2.xlsx


title: HCC3_CP_C2_123

description:
Plate2_IndexB
HCC3_CP_C2_123_S123

value: GCATGGACC

value: AAGTAGGCT


title: D_5_q

value: Memory CD4 T cells


title: Cas9NG_ABE8e_BRCA1_tiling_pDNA

description:
Plasmid DNA for ABE8e BRCA1 tiling library
processed data in: Supplementary_Data6_v2.xlsx


title: WTCas9_ABE_BRCA1_tiling_pDNA

description:
Plasmid DNA for ABE8e BRCA1 tiling library with WTCas9-ABE8e
processed data in: Supplementary_Data6_v2.xlsx


title: LIF/FBS Dax1 KO Rep1

city: chongqing

first: wang

last: jiaqi

state: chongqing

address: Gaotanyan Main Street, Shapingba District

country: China

institute: army medical school

description: Dax1-Knochout ESCs cultured in LIF/serum culture

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by DESeq2 method. Finally, the count reads value of each gene was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: raw reads counts

organism: Mus musculus

source_name: mESC_LIF/FBS Dax1 KO

growth_protocol: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the indicated medium. LIF/serum culture: DMEM supplemented with 15% FBS, 2mM GlutaMAX, 1% MEM non-essential amino acids, 0.1mM β-mercaptoethanol (all from Invitrogen) and 10 ng/ml LIF (Millipore). 2i/LIF culture: N2B27 medium was supplemented with 1 μM PD0325901, 3 μM CHIR99021(Selleck) and 10 ng/ml LIF26. 293FT cells were maintained in DMEM supplemented with 10% FBS, 2mM GlutaMAX and 1% MEM non-essential amino acids.

extract_protocol:
Total RNA was extracted using TRIzol Reagent(Invitrogen,Cat:15596026) and a miRNeasy Micro Kit (QIAGEN,Cat:217084) according the manufacturer's manual. The RNA quality were measured using Agilent 4200 TapeStation.
RNA samples were send to Genminix Informatic Ltd. (Shanghai, China) for mRNA sequencing on Illumina Hiseq platform (Illumina, San Diego, California, USA) with 6Gbps.

value: mESC

tag: passage

value: passage 3

tag: genotype/variation

value: Dax1-knockout (KO)


title: LIF/FBS Dax1 KO Rep2


title: HCC3_PG_C3_118

description:
Plate2_IndexB
HCC3_PG_C3_118_S118

value: Human Hepatoma HepaRG Cell Line

value: ATACCGGCA


title: D_2_r

value: Peripheral Blood

value: GM-CSF positive CD4 T cells


title: D_2_q


title: SpG_CBE_BRCA1_tiling_pDNA

description:
Plasmid DNA for CBE BRCA1 tiling library with SpG
processed data in: Supplementary_Data5_v2.xlsx

value: not applicable


title: LIF/FBS Control Rep1

description: Control ESCs cultured in LIF/serum culture

source_name: mESC_LIF/FBS Control

value: control


title: 2i/LIF Dax1 KO Rep2

description: Dax1-Knochout ESCs cultured in 2i/LIF culture

source_name: mESC_2i/LIF Dax1 KO


title: D_2_p


title: HCC3_CP_C3_116

description:
Plate2_IndexB
HCC3_CP_C3_116_S116

value: Cyclophosphamide (CP)

value: GGAATGCAT

value: ATACGCAGC


title: HCC3_CP_C3_115

description:
Plate2_IndexB
HCC3_CP_C3_115_S115


title: 2i/LIF Control Rep2

description: Control ESCs cultured in 2i/LIF culture

source_name: mESC_2i/LIF Control


title: D_1_r

value: Naive CD4 T cells

value: D

value: male


title: 2i/LIF Control Rep1

description: Control ESCs cultured in 2i/LIF culture


title: D_1_q


title: 2i/LIF Dax1 KO Rep1


title: HCC3_CP_C3_114

description:
Plate2_IndexB
HCC3_CP_C3_114_S114

value: GCAGATGCA

value: Cell lysate (total RNA)


title: HCC3_CP_C3_113

description:
Plate2_IndexB
HCC3_CP_C3_113_S113

value: TATGCTATG


title: HCC3_PG_C3_117

description:
Plate2_IndexB
HCC3_PG_C3_117_S117

value: Propyl Gallate (PG)

value: GCACCTATT


title: LIF/FBS Control Rep2

value: mESC

value: passage 3


title: D_1_p

value: Peripheral Blood


title: HCC3_PG_C4_111

description:
Plate2_IndexB
HCC3_PG_C4_111_S111

value: Human Hepatoma HepaRG Cell Line

value: GTGATCTGA

value: GGTCTAGCT


title: C_5_r

value: Memory CD4 T cells

value: C


title: HCC3_PG_C4_112

description:
Plate2_IndexB
HCC3_PG_C4_112_S112

value: TTGACGCTA


title: HCC3_PG_C4_110

description:
Plate2_IndexB
HCC3_PG_C4_110_S110

value: ATACCGGCA


title: C_5_p


title: HCC3_PG_C4_109

description:
Plate2_IndexB
HCC3_PG_C4_109_S109


title: C_4_r

value: Bulk CD4 T cells


title: HCC3_CP_C4_108

description:
Plate2_IndexB
HCC3_CP_C4_108_S108

value: Cyclophosphamide (CP)

value: ATACGCAGC


title: C_5_q

value: male


title: C_4_q


title: C_4_p


title: HCC3_CP_C4_107

description:
Plate2_IndexB
HCC3_CP_C4_107_S107

value: AAGTAGGCT

value: Cell lysate (total RNA)


title: Scc1-PK9 4 hours of 2% galactose (DSB site is uncleavable) + nocodazole  [HB45]

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: Chip-seq (IP)

data_processing:
alignement Bowtie2 was used for two rounds of alignments, first on C. glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively maped on S. cerevisiae (an vice-versa for C. glabrata).
The obtained SAM file was filtered and converted into a BAM file using Samtools view (parameters -q 5 -F 4).
calibration ChIP-seq profiles were then normalised by the number of million sequences and multiplied by ORi factor as in Hu et al . 2015 (WCE(Cg) x IP(Sc) / WCE(Sc) x IP(Cg), in which WCE(Cg) and IP(Cg) correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads) using bedtools genomecov.
bin 1kb Number of reads were then averaged within each 1kb bin, into a bed file.
Genome_build: W303genome710 and C_glabrata_CBS138_current_chromosomes
Supplementary_files_format_and_content: bed files containing Scc1 Chip-seq and WCE signal
Supplementary_files_format_and_content: peak calling Cohesin enrichment sites (bin: 1 kb) were determined from Scc1-PK9 (HB44) ChIP-seq profile 4 hours after DSB induction using MACS2 software in callpeak mode and broad option. Only the 500 most enriched sites were considered. The start of the cohesin enriched site was centered between the position detected by MACS2 and the end was arbitrarily fixed to 1 kb further.

organism: Saccharomyces cerevisiae W303

extract_protocol:
Fixed cells were lysed, sonicated, and Immunoprecipitation was performed on clarified samples.
TruSeq Nano DNA Library Prep (Illumina, cat. FC-121-9010DOC)

tag: strain

tag: internal contol to calibrate chip-seq

value: Candida glabrata

value: 4 hours of 2percent galactose (DSB site is uncleavable) + nocodazole

tag: chip antibody

value: anti-Pk antibody (Abcam, cat. ab27671)


title: Scc1-PK9 DSB t4  [HB42]

description: Chip-seq (WCE)

value: 4 hours of DSB induction


title: Scc1-6HA DSB t4 + nocodazole replicate 1 [HB70]

description: Chip-seq (WCE)

value: 4 hours of DSB induction + nocodazole

value: anti-HA antibody (Merck, 12CA5)


title: Scc1-6HA pds5-AID DSB t4 + nocodazole replicate 1 [HB68]

description: Chip-seq (IP)


title: Scc1-6HA rad17 pds5-AID DSB t4 + nocodazole replicate 1 [HB67]

description: Chip-seq (IP)


title: Scc1-PK9 DSB t4 + nocodazole [HB46]

description: Chip-seq (IP)


title: Scc1-6HA rad17 DSB t4 + nocodazole replicate 1 [HB66]

description: Chip-seq (IP)


title: Scc1-6HA rad17 DSB t4 + nocodazole replicate 1 [HB71]

description: Chip-seq (WCE)


title: DSB t4 + nocodazole [HB69]

description: Chip-seq (IP)


title: Scc1-PK9 DSB t4  [HB44]

description: Chip-seq (IP)


title: SCC-13 cells, parentals (P)

type: genomic

city: Madrid

last: Mascaraque-Checa

state: Madrid (ES)

address: C/Darwin nº2

country: Spain

institute: Universidad Autónoma de Madrid

hyb_protocol: Hybridization and washing was done according to Agilent protocol (65ºC 24h, 20rpm in hyb chambers)

scan_protocol: Scanned on an Agilent G2565C scanner (3um and Cy5/Cy3 analysis). Images were quantified using Agilent Feature Extraction Software (version 10.7.1).

data_processing: Agilent Genomic Workbench using ADM-2 method (ADM=6) using at least 5 consecutive probes for aberration detection.

source_name: SCC-13 cells, parentals (P)

label_protocol: 500 ng were labeled using Agilent CGH enzymatic protocol 7.2 (Agilent Technologies)

growth_protocol: SCC-13 cells, controls and resistant cultures to PDT were cultured under conventional conditions in DMEM with 10% of FBS

extract_protocol: cell DNA was extracted using Dneasy Blood and tissue kit (QUIAGEN)

tag: cell line background

source_name: Promega control

value: Lymphocyte


title: Scc1-PK9 rad17 DSB t4 + nocodazole [HB51]

description: Chip-seq (WCE)


title: Scc1-PK9 rad17 DSB t4 + nocodazole [HB47]

description: Chip-seq (IP)


title: Scc1-PK9 4 hours of 2% galactose (DSB site is uncleavable) + nocodazole [HB43]

description: Chip-seq (WCE)


title: Scc1-PK9 DSB t4 + nocodazole [HB50]

description: Chip-seq (WCE)


title: Scc1-6HA DSB t4 + nocodazole replicate 1 [HB65]

description: Chip-seq (IP)


title: SCC-13 cells_10G generations (10G)

source_name: SCC-13 cells subjected to 10 sequential PDT treatments (10G)

tag: phenotype

value: resistant to PDT


title: SCC-13 cells_10GT generation of resistant cells (10GT)

source_name: SCC-13 cells subjeted to 10 sequential PDT treatments and inoculated in immunosupressed and the tumors were subcultured by explants to obtain a cell resistant population (10GT)


title: HCC3_CP_C4_106

description:
Plate2_IndexB
HCC3_CP_C4_106_S106

value: Human Hepatoma HepaRG Cell Line

value: GTGATCTGA

value: GCAGATGCA


title: C_3_r

tag: tissue

value: Peripheral Blood

value: GM-CSF negative CD4 T cells

value: C


title: G1 alpha-factor bloc DSB t4

description: Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format

data_processing:
Reads were aligned and the contact data processed using Hicstuff 9. Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome (GCA_002163515.1). The reference was deleted for the URA3 and LYS2 genes, which are either absent or partially duplicated in our strains, respectively. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in ref. 10. PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps were generated with the “view” function of Hicstuff and normalized using the iterative correction and eigenvector decomposition (ICE) procedure11. Bins were set at either 1 or 2 kb for single chromosomes, or 5 kb for multiple chromosomes, log10 transformed, and rendered.
Supplementary_files_format_and_content: cool

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. 2020. Quenching of formaldehyde with 300 mM glycine was performed at room temperature for 20 min. Most Hi-C experiments were performed with the Arima Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions, except those presented in Supplementary Fig. 3, performed as in Dauban et al. 2020 with a single DpnII restriction digestion.
TruSeq Nano DNA Library Prep (Illumina, cat. FC-121-9010DOC) or Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems (A38606024).

value: DSB 4 hr


title: rad51 DSB t4


title: sml1 DSB t4 + nocodazole - replicate 1


title: HCC3_CP_C4_105

description:
Plate2_IndexB
HCC3_CP_C4_105_S105

value: Cyclophosphamide (CP)

value: TATGCTATG


title: mec1 sml1 DSB t4 + nocodazole - replicate 1


title: C_3_q

tag: cell type

value: male


title: Tir1 Cdc45-AID DSB t4 + IAA  (induced while releasing from G1 block) replicate1

value: DSB 4 hr + IAA (after G1 release)


title: Tir1 Cdc45-AID DSB t4 + DMSO  (induced while releasing from G1 block) replicate1

value: DSB 4 hr + DMSO (after G1 release)


title: HCC3_ctrl_HBTR_104

description:
Plate2_IndexB
HCC3_ctrl_HBTR_104_S104

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

value: GCTGTAGTT

value: TTGACGCTA

value: Cell lysate (total RNA)


title: C_3_p

tag: donor


title: Tir1  Pds5-AID nocodazole block - DSB t4 replicate 1

value: DSB 4 hr + Nocodazole


title: mec3 DSB t4 + nocodazole


title: Scc1-Pk9 DSB t4


title: WT DSB  t4 nocodazole block replicate 1 [NextSeq 500]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB25_1_2_merged_1kb.cool


title: C_1_r

value: Naive CD4 T cells

tag: gender


title: Tir1  Pds5-AID rad17 nocodazole block - DSB t4 replicate 1


title: mec3 DSB t4 + nocodazole -same sample as HB37 for deeper sequencing


title: Tir1 no tag - DSB t4 + IAA (induced 1 hour before releasing from G1 block)

value: DSB 4 hr + IAA (after 1 hr before G1 release)


title: C_2_r

value: Peripheral Blood

value: GM-CSF positive CD4 T cells


title: HCC3_ctrl_HBTR_103

description:
Plate2_IndexB
HCC3_ctrl_HBTR_103_S103

tag: cell line

value: Human Hepatoma HepaRG Cell Line

value: GGTCTAGCT


title: C_2_q

value: C


title: cdc20 t4 (without DSB) replicate 2

tag: treatment

value: Galactose 2percent (no DSB is induced)


title: mre11 DSB  t4 nocodazole block [NextSeq 500]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB26_1_2_merged_1kb.cool


title: C_1_q

value: male


title: WT DSB  t4 nocodazole block replicate 2


title: C_2_p


title: HCC3_ctrl_HBTR_102

description:
Plate2_IndexB
HCC3_ctrl_HBTR_102_S102

tag: concentration

value: ATACCGGCA


title: HCC3_CP_C5_098

description:
Plate2_IndexB
HCC3_CP_C5_098_S98

value: Cyclophosphamide (CP)

tag: index

value: GCAGATGCA


title: HCC3_ctrl_neg_101

description:
Plate2_IndexB
HCC3_ctrl_neg_101_S101

value: No cells; Negative control

value: No cells; Negative control_0

value: GCACCTATT

tag: molecule source


title: HCC3_CP_C5_099

description:
Plate2_IndexB
HCC3_CP_C5_099_S99

value: GCTGTAGTT

value: AAGTAGGCT

value: Cell lysate (total RNA)


title: C_1_p

value: Naive CD4 T cells


title: exo1-D173A t4 XP1

value: DSB 4 hr


title: rad52 DSB t4 replicate2


title: B_5_r

value: Peripheral Blood

value: Memory CD4 T cells

value: B


title: rad17 DSB  t4 nocodazole block replicate 1 [NextSeq 500]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB27_1_2_merged_1kb.cool

value: DSB 4 hr + Nocodazole


title: HCC3_CP_C5_097

description:
Plate2_IndexB
HCC3_CP_C5_097_S97

value: Human Hepatoma HepaRG Cell Line

value: TATGCTATG


title: WT DSB on chrIV t4 replicate2


title: HCC3_CP_C5_100

description:
Plate2_IndexB
HCC3_CP_C5_100_S100

value: ATACGCAGC


title: HCC3_BaP_C0_096

description:
Plate1_IndexA
HCC3_BaP_C0_096_S96

value: Benzo(a)pyrene (BaP)

value: 0 µM

value: GTAGCTCCA

value: ATGCTCACA


title: rad52 DSB t4 replicate1


title: WT DSB on chrIV t4 replicate1


title: B_5_q

value: male


title: WT diploid heterozygous DSB t6

value: DSB 6 hr


title: cdc20 t4 (without DSB) replicate 1

value: Galactose 2percent (no DSB is induced)


title: WT diploid heterozygous DSB t4


title: HCC3_BaP_C0_094

description:
Plate1_IndexA
HCC3_BaP_C0_094_S94

value: CGTAACTTA

value: Cell lysate (total RNA)


title: B_5_p


title: WT diploid heterozygous DSB t2

value: DSB 2 hr


title: B_4_q

value: Peripheral Blood

value: Bulk CD4 T cells


title: HCC3_ENU_C0_092

description:
Plate1_IndexA
HCC3_ENU_C0_092_S92

value: 1-Ethyl-1-nitrosourea (ENU)

value: GCCGTTACA


title: B_4_p

value: B


title: WT diploid heterozygous DSB t0

value: No DSB


title: WT G1 arrest (no DSB)


title: HCC3_ENU_C0_091

description:
Plate1_IndexA
HCC3_ENU_C0_091_S91

value: Human Hepatoma HepaRG Cell Line

value: TCTAACCAT


title: B_4_r


title: Tir1 Cdc45-AID DSB t4 + IAA  (induced while releasing from G1 block) replicate2

value: DSB 4 hr + IAA (after G1 release)


title: Tir1 Cdc45-AID DSB t4 + DMSO  (induced while releasing from G1 block) replicate2

value: DSB 4 hr + DMSO (after G1 release)


title: WT DSB t4 (induced while releasing from G1 block) - replicate 1

value: DSB 4 hr (after G1 release)


title: HCC3_BaP_C0_093

description:
Plate1_IndexA
HCC3_BaP_C0_093_S93

value: Benzo(a)pyrene (BaP)

value: 0 µM

value: GTAGCTCCA

value: GATTGTGTT


title: B_3_r

value: GM-CSF negative CD4 T cells

value: male


title: Tir1 no tag - DSB t4 +IAA (+2 hrs)

value: DSB 4 hr + IAA (2 hours post DSB induction)


title: B_3_q

value: Peripheral Blood


title: Tir1 Pds5-AID - DSB t4 +DMSO

value: DSB 4 hr + DMSO


title: Tir1 Scc1-AID - DSB t4 +IAA (+2 hrs)


title: HCC3_ENU_C0_090

description:
Plate1_IndexA
HCC3_ENU_C0_090_S90

value: 1-Ethyl-1-nitrosourea (ENU)

value: TAACGCGTC

value: Cell lysate (total RNA)


title: Tir1 Scc1-AID - DSB t4 +IAA

value: DSB 4 hr + IAA


title: HCC3_ENU_C0_089

description:
Plate1_IndexA
HCC3_ENU_C0_089_S89

value: Human Hepatoma HepaRG Cell Line

value: ACGACTTGG


title: HCC3_BaP_C0_095

description:
Plate1_IndexA
HCC3_BaP_C0_095_S95

value: AGACACAAT


title: Tir1 Scc1-AID - DSB t4 +DMSO


title: B_3_p

value: B


title: Tir1 no tag - DSB t4 +IAA


title: B_2_r

value: GM-CSF positive CD4 T cells


title: Tir1 no tag - DSB t4 +DMSO


title: B_2_q


title: WT DSB t0 replicate2 - DpnII digestion only

description: Hi-C matrix filtered and PCR duplicate-free binned at 2 kb in cooler format

value: No DSB


title: HCC3_BaP_C1_087

description:
Plate1_IndexA
HCC3_BaP_C1_087_S87

value: Benzo(a)pyrene (BaP)

value: TCAGCTAAT


title: HCC3_BaP_C1_086

description:
Plate1_IndexA
HCC3_BaP_C1_086_S86

value: CGTAACTTA


title: WT DSB t4 (induced while releasing from G1 block)

value: DSB 4 hr (after G1 release)


title: HCC3_BaP_C1_088

description:
Plate1_IndexA
HCC3_BaP_C1_088_S88

value: ATGCTCACA


title: B_2_p

value: Peripheral Blood

value: male


title: HCC3_BaP_C1_085

description:
Plate1_IndexA
HCC3_BaP_C1_085_S85

value: GATTGTGTT


title: exo1 DSB t4 replicate1

value: DSB 4 hr


title: WT no donor DSB t4 replicate3


title: B_1_r

value: Naive CD4 T cells


title: WT DSB t2 replicate2

value: DSB 2 hr


title: HCC3_ENU_C1_084

description:
Plate1_IndexA
HCC3_ENU_C1_084_S84

value: Human Hepatoma HepaRG Cell Line

value: 1-Ethyl-1-nitrosourea (ENU)

value: GCCGTTACA

value: Cell lysate (total RNA)


title: WT no donor DSB t6 replicate2 - DpnII digestion only

value: DSB 6 hr


title: HCC3_ENU_C1_083

description:
Plate1_IndexA
HCC3_ENU_C1_083_S83

value: TCTAACCAT


title: B_1_p

value: B


title: WT no donor DSB t4 replicate2 - DpnII digestion only


title: WT no donor DSB t2 replicate2 - DpnII digestion only


title: A_4_q

value: Bulk CD4 T cells

value: A


title: WT no donor DSB t4 replicate1 - DpnII digestion only


title: WT DSB t0 replicate2

value: No DSB


title: exo1sgs1 DSB t4


title: A_4_p


title: HCC3_ENU_C1_082

description:
Plate1_IndexA
HCC3_ENU_C1_082_S82

value: TCAGCTAAT

value: TAACGCGTC


title: WT no donor DSB t0 replicate1 - DpnII digestion only


title: WT DSB t4 replicate1 - DpnII digestion only


title: WT DSB t2 replicate1 - DpnII digestion only


title: HCC3_BaP_C2_080

description:
Plate1_IndexA
HCC3_BaP_C2_080_S80

value: Benzo(a)pyrene (BaP)

value: TGCTTATTC

value: ATGCTCACA


title: WT DSB t4 replicate2

value: DSB 4 hr


title: A_3_q

value: Peripheral Blood

value: GM-CSF negative CD4 T cells

value: male


title: WT DSB t0 replicate1 - DpnII digestion only


title: WT no HO cut site - t4


title: A_3_p


title: HCC3_BaP_C2_079

description:
Plate1_IndexA
HCC3_BaP_C2_079_S79

value: Human Hepatoma HepaRG Cell Line

value: AGACACAAT


title: Scc1-6HA 4 hours of 2% galactose (DSB site is uncleavable) + nocodazole [HB88]

description: Chip-seq (WCE)

value: Candida glabrata

value: 4 hours of DSB induction + nocodazole

value: anti-HA antibody (Merck, 12CA5)


title: B_1_q

value: Naive CD4 T cells

value: B


title: HCC3_BaP_C2_078

description:
Plate1_IndexA
HCC3_BaP_C2_078_S78

value: CGTAACTTA

value: Cell lysate (total RNA)


title: HCC3_BaP_C2_077

description:
Plate1_IndexA
HCC3_BaP_C2_077_S77

value: GATTGTGTT


title: Scc1-6HA rad17 pds5-AID DSB t4 + nocodazole replicate 2 [HB86]

description: Chip-seq (WCE)


title: Scc1-6HA rad17 DSB t4 + nocodazole replicate 2 [HB85]

description: Chip-seq (WCE)


title: A_2_q

value: GM-CSF positive CD4 T cells

value: A


title: A_1_q


title: HCC3_ENU_C1_081

description:
Plate1_IndexA
HCC3_ENU_C1_081_S81

value: 1-Ethyl-1-nitrosourea (ENU)

value: TCAGCTAAT

value: ACGACTTGG


title: Scc1-6HA DSB t4 + nocodazole replicate 2 [HB84]

description: Chip-seq (WCE)


title: HCC3_ENU_C2_076

description:
Plate1_IndexA
HCC3_ENU_C2_076_S76

value: TGCTTATTC

value: GCCGTTACA


title: WT no donor DSB t2 replicate1 - DpnII digestion only

value: DSB 2 hr


title: Scc1-6HA 4 hours of 2% galactose (DSB site is uncleavable) + nocodazole [HB83]

description: Chip-seq (IP)


title: HCC3_ENU_C2_075

description:
Plate1_IndexA
HCC3_ENU_C2_075_S75

value: Human Hepatoma HepaRG Cell Line

value: TCTAACCAT


title: Scc1-6HA rad17 pds5-AID DSB t4 + nocodazole replicate 2 [HB81]

description: Chip-seq (IP)

value: Candida glabrata

value: 4 hours of DSB induction + nocodazole


title: A_1_p

value: Peripheral Blood

value: Naive CD4 T cells

value: male


title: sgs1 DSB t4

value: DSB 4 hr


title: Scc1-6HA rad17 DSB t4 + nocodazole replicate 2 [HB80]

description: Chip-seq (IP)

value: anti-HA antibody (Merck, 12CA5)


title: Scc1-6HA DSB t4 + nocodazole replicate 2 [HB79]

description: Chip-seq (IP)


title: DSB t4 + nocodazole [HB74]

description: Chip-seq (WCE)


title: Scc1-6HA pds5-AID DSB t4 + nocodazole replicate 2 [HB82]

description: Chip-seq (IP)


title: Scc1-6HA pds5-AID DSB t4 + nocodazole replicate 1 [HB73]

description: Chip-seq (WCE)


title: NOP56_CLASH_6

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Library strategy: CLASH/FLASH
Demultiplexing, adapter trimming and PCR collapsing of raw reads was performed using the hyb pipeline (https://github.com/gkudla/hyb), using the command hyb demultiplex preprocess check in=[RAW FASTQ FILE] code=[BARCODES FILE]
The preprocessed files were aligned to a human unspliced genes database, using the command blastall -p blastn -d "[DATABASE]" -i "[PRE-PROCESSED READS]" -o "[ALIGNED READS]" -m 8 -W 11 -e 0.1 -a 1
Unique hybrids were obtained from aligned files using the hyb pipeline, with a modification to prefer snoRNA hybrids rather than miRNA hybrids. Hybrid sequences that could be mapped against the complete human genome (Ensembl Homo sapiens hg38 assembly, release 77) using novoalign 2.07 were filtered out.
Genome_build: Unspliced genes taken from Ensembl Homo sapiens hg38 assembly, release 77 with snoRNA co-ordinates from https://pubmed.ncbi.nlm.nih.gov/27174936/, extended by 20bps on each side and masked out in mRNAs, and tRNAs taken from http://gtrnadb.ucsc.edu/.
Supplementary_files_format_and_content: Unique hybrids are provided in hyb and viennad formats, as specified in https://pubmed.ncbi.nlm.nih.gov/24211736/.

source_name: HEK293 cells

growth_protocol: DMEM 10% FBS

extract_protocol:
Flag-tagged proteins were bound to M2 Sepharose beads and briefly crosslinked with formaldehyde (in case of FLASH) or after washes denatured in 6 M guanidine and bound to nickel resin. Subsequent linker ligation reactions were performed at 16 °C, largely preserving RNA stem structures and allowing formation of chimeras.
RNA-protein complexes we resolved on a NuPage gel, RNA was isolated, cDNA library was amplified and sent for sequencing.

treatment_protocol: Intact HEK cells expressing His6-Pressision Protease-cleavage site-Flag–tagged snoRNP proteins were UV-irradiated.

tag: bait protein

tag: library strategy

value: CLASH


title: NOP56_FLASH_1

value: FLASH


title: Scc1-6HA rad17 pds5-AID DSB t4 + nocodazole replicate 1 [HB72]

description: Chip-seq (WCE)


title: NOP56_CLASH_7


title: HCC3_ENU_C2_073

description:
Plate1_IndexA
HCC3_ENU_C2_073_S73

value: 1-Ethyl-1-nitrosourea (ENU)

value: Cell lysate (total RNA)


title: Scc1-6HA pds5-AID DSB t4 + nocodazole replicate 2 [HB87]

description: Chip-seq (WCE)


title: HCC3_ENU_C2_074

description:
Plate1_IndexA
HCC3_ENU_C2_074_S74

value: TAACGCGTC


title: HCC3_BaP_C3_071

description:
Plate1_IndexA
HCC3_BaP_C3_071_S71

value: Benzo(a)pyrene (BaP)

value: GCGATAGTG

value: AGACACAAT


title: NOP56_CLASH_5


title: HCC3_BaP_C3_072

description:
Plate1_IndexA
HCC3_BaP_C3_072_S72

value: Human Hepatoma HepaRG Cell Line

value: ATGCTCACA


title: A_2_p

value: GM-CSF positive CD4 T cells

value: A


title: HCC3_BaP_C3_070

description:
Plate1_IndexA
HCC3_BaP_C3_070_S70

value: CGTAACTTA


title: HCC3_BaP_C3_069

description:
Plate1_IndexA
HCC3_BaP_C3_069_S69

value: GATTGTGTT


title: NOP56_CLASH_4


title: NOP56_CLASH_3


title: HCC3_ENU_C3_068

description:
Plate1_IndexA
HCC3_ENU_C3_068_S68

value: GCCGTTACA


title: HCC3_ENU_C3_067

description:
Plate1_IndexA
HCC3_ENU_C3_067_S67

value: TCTAACCAT


title: NOP56_CLASH_2


title: NOP56_CLASH_1


title: Fibrillarin_FLASH_2

value: Fibrillarin


title: LD_99_PT

city: Gdansk

first: Anna

middle: J.

last: Zaczek

address: Debinki 1

country: Poland

institute: Medical University of Gdansk

hyb_protocol: Extracted RNA (4 µl) was pre-amplified using the nCounter Low RNA Input Kit (NanoString Technologies) with the dedicated Primer Pool covering the sequences of 730 immune-related genes included in the nCounter PanCancer Immune Profiling Panel (NanoString Technologies). Pre-amplified samples were analyzed according to the manufacturer’s procedures for hybridization, detection, and scanning.

data_processing: PT and LNM samples were normalized together. Background level was estimated by thresholding over the mean plus 2 standard deviations of  negative control counts. Subsequently, data were normalized according to the global mean of the counts of positive controls and 4 most stably expressed housekeeping genes - ABCF1, EDC3, HDAC3, and CNOT4 (selected using NormFinder). The negative and positive control probes were included in the assay.

label: NanoString

source_name: primary breast cancer

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue samples - primary tumors and lymph node metastasis fragments (four 10 µm-thick, unstained FFPE sections per tissue), using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration and purity were determined using NanoDrop 1000 spectrophotometer (Thermo Scientific). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 Pico Kit (Agilent Technologies).

tag: grade

tag: histology

value: ductal

value: positive

tag: t

tag: nodes

value: involved

tag: m


title: HCC3_ENU_C3_065

description:
Plate1_IndexA
HCC3_ENU_C3_065_S65

value: 1-Ethyl-1-nitrosourea (ENU)

value: ACGACTTGG

value: Cell lysate (total RNA)


title: LD_111_PT

scan_protocol: Extracted RNA (4 µl) was pre-amplified using the nCounter Low RNA Input Kit (NanoString Technologies) with the dedicated Primer Pool covering the sequences of 730 immune-related genes included in the nCounter PanCancer Immune Profiling Panel (NanoString Technologies). Pre-amplified samples were analyzed according to the manufacturer’s procedures for hybridization, detection, and scanning.


title: LD_125_PT

label_protocol: Extracted RNA (4 µl) was pre-amplified using the nCounter Low RNA Input Kit (NanoString Technologies) with the dedicated Primer Pool covering the sequences of 730 immune-related genes included in the nCounter PanCancer Immune Profiling Panel (NanoString Technologies). Pre-amplified samples were analyzed according to the manufacturer’s procedures for hybridization, detection, and scanning.

value: negative

value: univolved


title: HCC3_ENU_C3_066

description:
Plate1_IndexA
HCC3_ENU_C3_066_S66

value: Human Hepatoma HepaRG Cell Line

value: GCGATAGTG

value: TAACGCGTC


title: LD_109_PT


title: LD_116_PT


title: HCC3_BaP_C4_064

description:
Plate1_IndexA
HCC3_BaP_C4_064_S64

value: Benzo(a)pyrene (BaP)

value: TTCCGCACC

value: ATGCTCACA


title: LD_110_PT


title: LD_104_PT


title: Fibrillarin_CLASH_8

value: CLASH


title: LD_100_PT


title: LD_103_PT


title: LD_101_PT


title: LD_47_LNM

source_name: lymph node metastasis


title: LD_126_PT


title: LD_65_LNM


title: LD_132_PT


title: HCC3_BaP_C4_063

description:
Plate1_IndexA
HCC3_BaP_C4_063_S63

value: AGACACAAT


title: Fibrillarin_CLASH_7

value: Fibrillarin


title: HCC3_BaP_C4_062

description:
Plate1_IndexA
HCC3_BaP_C4_062_S62

value: CGTAACTTA


title: Fibrillarin_FLASH_1

value: FLASH


title: LD_24_LNM

value: ductal

value: positive

value: involved


title: LD_21_LNM


title: Fibrillarin_CLASH_6


title: LD_132_LNM


title: LD_31_LNM


title: Fibrillarin_CLASH_5


title: HCC3_BaP_C4_061

description:
Plate1_IndexA
HCC3_BaP_C4_061_S61

value: GATTGTGTT

value: Cell lysate (total RNA)


title: HCC3_ENU_C4_059

description:
Plate1_IndexA
HCC3_ENU_C4_059_S59

value: 1-Ethyl-1-nitrosourea (ENU)

value: TCTAACCAT


title: LD_12_LNM

value: negative


title: HCC3_ENU_C4_060

description:
Plate1_IndexA
HCC3_ENU_C4_060_S60

value: Human Hepatoma HepaRG Cell Line

value: GCCGTTACA


title: LD_28_LNM


title: LD_116_LNM


title: Fibrillarin_CLASH_1


title: LD_103_LNM


title: LD_111_LNM


title: Fibrillarin_CLASH_4


title: Fibrillarin_CLASH_3


title: LD_36_PT

value: univolved


title: LD_33_PT


title: LD_47_PT


title: LD_40_PT


title: Fibrillarin_CLASH_2


title: HCC3_ENU_C4_057

description:
Plate1_IndexA
HCC3_ENU_C4_057_S57

value: TTCCGCACC

value: ACGACTTGG


title: LD_31_PT


title: LD_28_PT


title: HCC3_ENU_C4_058

description:
Plate1_IndexA
HCC3_ENU_C4_058_S58

value: TAACGCGTC


title: LD_30_PT


title: HCC3_BaP_C5_056

description:
Plate1_IndexA
HCC3_BaP_C5_056_S56

value: Benzo(a)pyrene (BaP)

value: 15 µM

value: ATCGCGACT

value: ATGCTCACA


title: LD_21_PT

value: ductal

value: positive


title: LD_24_PT

value: involved


title: HCC3_BaP_C5_055

description:
Plate1_IndexA
HCC3_BaP_C5_055_S55

value: AGACACAAT

value: Cell lysate (total RNA)


title: Mouse kidney scRNA-seq_IRI_long_14d_sample2

city: Berlin

first: Michael

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

country: Germany

institute: Charité - Universitätsmedizin Berlin

description:
EXPORT_clusters.txt
EXPORT_counts.rds
EXPORT_pheno.txt
EXPORT_umap.txt
EXPORTinhib_clusters.txt
EXPORTinhib_counts.rds
EXPORTinhib_pheno.txt
EXPORTinhib_umap.txt

data_processing:
STEP1 (Alignment & Quality Control): Raw fastq files were aligned to the mm10 (Ensembl GRCm38.93) reference genome and quantified using CellRanger. Seurat was used for data quality control, preprocessing, and dimensional reduction analysis. After gene-cell data matrix generation of n=12 IRI samples and n=6 control samples, all 18 matrices were merged and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >50 were excluded. Remaining barcodes of high-quality cells were exported.
STEP2 (Batch integration): 10X filtered output matrices of all 18 batches were merged and subset to the barcodes of cells above and subjected to batch integration using LIGER (Linked Inference of Genomic Experimental Relationships) package.34 In short, LIGER identifies shared and dataset-specific factors through integrative non-negative matrix factorization (iNMF). After normalization by number of unique molecular identifiers (UMIs), gene expression was scaled but not centered because NMF requires non-negative values. Function optimizeALS was used with kappa=20 and lambda=5, followed by quantile normalization using function quantile_norm as well as joint clustering with louvainCluster with a resolution of 0.25. For dimensionality reduction, dimensions 1:ncol(object@H.norm), perplexity=30 and theta=0.5 were used as per default settings for visualization in UMAP space. Function ligerToSeurat was used to export the results back to Seurat.
STEP3 (Ambient RNA quantification): As in droplet based scRNA-seq experiments there is always a certain amount of background mRNAs present that get distributed into droplets and sequenced along with cells. In order to quantify the net effect of ambient RNA contamination, we used R package SoupX.55 Function autoEstCount was used to estimate the contamination fraction in P0 and adult batches separately. We visualized the change in expression due to soup correction in UMAP space. Function adjustCounts was used to correct the count expression matrices for downstream processing. We then used the corrected matrices and reran the whole Seurat pipeline with the same parameters. The average expression of genes per cluster were used for Pearson correlation coefficient analysis to compare between matrices with and without ambient RNA correction. As results with and without ambient RNA were similar, results without ambient RNA correction are shown throughout the manuscript.
STEP4 (Removal of doublet-like cells): Doublet-like cells were identified using package DoubletFinder.56 Assuming no ground truth in order to facilitate an unbiased approach, pK was identified using paramSweep_v3 function with PCs=1:10. Homotypic doublet proportion was estimated with function modelHomotypic using above clustering information after LIGER integration as annotations. Finally, function doubletFinder_v3 was run with pN=0.25, pK and nExp as identified by the functions above. After excluding 9,394 cells that were identified to likely be doublets, 113,579 singlet cells remained.
Genome_build: mm10
Supplementary_files_format_and_content: rds

molecule: polyA RNA

source_name: Kidney

extract_protocol:
Euthanized mice were perfused with chilled 1x PBS via the left ventricle. Kidneys were harvested, minced into approximately 1 mm3 cubes and digested using Multi Tissue dissociation kit (Miltenyi, 130-110-201). The tissue was homogenized using 21G and 26.5G syringes. Up to 0.25 g of the tissue was digested with 50 µl of Enzyme D, 25 µl of Enzyme R and 6.75 µl of Enzyme A in 1 ml of RPMI and incubated for 30 min at 37 °C. Reaction was deactivated by 10% FBS. The solution was then passed through a 40 µm cell strainer. After centrifugation at 400 g for 5 min, cell pellet was incubated with 1 ml of RBC lysis buffer on ice for 3 min. Cell number and viability were analyzed using Countess AutoCounter (Invitrogen, C10227). This method generated single-cell suspensions with >80% viability.
Libraries were generated using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, PN-1000092) and Chromium i7 Multiplex Kit (10X Genomics, PN-120262) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Quantification analysis was performed by Illumina Library Quantification Kit (KAPA Biosystems, KK4824).

treatment_protocol: 10-12 weeks old mice were anesthetized with isoflurane and placed on an automatic closed loop temperature control system (Homeothermic Monitoring System, Harvard Apparatus, Holliston, CA). Core body temperature as measured via rectal probe was maintained at 36.8-37.2 °C throughout the procedure. Kidneys were exposed via dorsal incision. Renal pedicles of both kidneys were exposed and bilateral clamping was performed with arterial clips to induce bilateral renal ischemia, which was visually confirmed by color change. 6 animals were subjected to moderate renal ischemia (23 min), whereas another 6 mice were subjected to severe injury (30 min). Buprenorphine SR (0.1 mg/kg s.c.) was administered after release of arterial clips and before weaning of anesthesia. Animals were sacrificed and blood and kidneys were sampled 1, 3, and 14 days post-ischemia, respectively.    In a second set of experiments, mice were treated with intraperitoneal injection of inhibitors or vehicle 30 min before as well as every 24 hours for 14 days after long IRI (30 min). In a sham group, renal pedicles were not clamped after bilateral visualization and anesthesia was maintained for the identical time. Inhibitors VX-765 (100 mg/kg) and liproxstatin (10 mg/kg) were dissolved in DMSO and formulated in sesame oil to final concentrations of 16.67 and 1.67 mg/ml, respectively. The vehicle group received equal amounts of DMSO.

value: IRI long

tag: time post-ischemia


title: Mouse kidney scRNA-seq_IRI_long_14+VX765

value: IRI long+VX765


title: HCC3_BaP_C5_054

description:
Plate1_IndexA
HCC3_BaP_C5_054_S54

value: Human Hepatoma HepaRG Cell Line

value: CGTAACTTA


title: HCC3_BaP_C5_053

description:
Plate1_IndexA
HCC3_BaP_C5_053_S53

value: GATTGTGTT


title: LD_19_PT

value: negative

value: univolved


title: LD_12_PT


title: Mouse kidney scRNA-seq_IRI_long_14d_sample1


title: Mouse kidney scRNA-seq_IRI_long_3d_sample2


title: HCC3_ctrl_HBTR_052

description:
Plate1_IndexA
HCC3_ctrl_HBTR_052_S52

value: No cells; Brain +ve control

value: No cells; Brain +ve control_0

value: GCCGTTACA


title: LD_94_PT


title: LD_95_PT


title: LD_98_PT

value: other


title: LD_89_PT


title: LD_73_PT


title: HCC3_ctrl_UHRR_051

description:
Plate1_IndexA
HCC3_ctrl_UHRR_051_S51

value: No cells; Universal human +ve control

value: No cells; Universal human +ve control_0

value: ATCGCGACT

value: TCTAACCAT


title: Mouse kidney scRNA-seq_IRI_long_3d_sample1


title: HCC3_ctrl_neg_050

description:
Plate1_IndexA
HCC3_ctrl_neg_050_S50

value: No cells; Negative control

value: No cells; Negative control_0

value: TAACGCGTC


title: Mouse kidney scRNA-seq_IRI_long_14d+Liproxstatin

value: IRI long+Liproxstatin


title: LD_65_PT

value: ductal

value: positive

value: involved


title: LD_63_PT

value: negative


title: HCC3_ctrl_neg_049

description:
Plate1_IndexA
HCC3_ctrl_neg_049_S49

value: Human Hepatoma HepaRG Cell Line

value: ACGACTTGG

value: Cell lysate (total RNA)


title: Mouse kidney scRNA-seq_IRI_long_1d_sample2

value: IRI long


title: HCC3_MMS_C0_048

description:
Plate1_IndexA
HCC3_MMS_C0_048_S48

value: Methyl methanesulfonate (MMS)

value: 0 µM

value: TAGCTCTTC

value: ATGCTCACA


title: PA14_ctrl_1

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

data_processing:
Raw reads were trimmed using CLC Genomics Workbench software (Qiagen).
Trimmed reads were aligned to the Pseudomonas earuginosa PA14 reference genome using CLC Genomics Workbench.
Reads that did not align to Pseudomonas earuginosa were aligned to the human reference genome using CLC Genomics Workbench.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with counts for reads that aligned with the human reference

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa strain PA14 were grown in Luria broth. Primary human airway epithelial cells from 3 donors were obtained from Dr. Scott Randell (University of North Carolina, Chapel Hill, NC) and cultured in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. # LM-0007) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. # LS-1047) as well as 10,000 U/ml Penicillin and 10,000 μg/ml Streptomycin (Sigma-Aldrich, Cat. # P4333). EVs were purified from cell culture supernatants (passages 4-8) using the ExoQuick-TC EV isolation kit (System Biosciences, Palo Alto, CA, Cat. # EXOTC50A-1).

extract_protocol:
Total RNA was isolated with the miRNeasy Mini Kit (Qiagen, Germantown, MD, Cat. # 217004), including the on-column DNA digestion.
Sequencing libraries were prepared with the QIAseq smRNA kit (Qiagen).
75-bp single-end reads were generated using an Illumina MiniSeq.

treatment_protocol: P. aeruginosa (1.5E+07 CFU) were exposed to PBS vehicle control or EVs (5E+09 EV/ml) for 6 h. To avoid possible carry-over of EVs (and miRNA) attached to the outside of the bacteria, the bacteria were washed with PBS and the bacterial outer membrane was lysed with EDTA to release periplasmic contents and factors associated with the bacterial outer membrane and periplasm (77-79). The cells were then washed again in PBS, and cytoplasmic RNA was harvested after lysis of bacterial cell wall and inner membrane.

value: PBS vehicle control


title: LD_54_PT

value: univolved


title: LD_61_PT

value: other


title: Mouse kidney scRNA-seq_IRI_short_14d_sample2

value: IRI short


title: Mouse kidney scRNA-seq_IRI_long_1d_sample1


title: Mouse kidney scRNA-seq_IRI_short_14d_sample1


title: LD_52_PT


title: LD_48_PT


title: HCC3_MMS_C0_047

description:
Plate1_IndexA
HCC3_MMS_C0_047_S47

value: AGACACAAT


title: HCC3_MMS_C0_046

description:
Plate1_IndexA
HCC3_MMS_C0_046_S46

value: CGTAACTTA


title: Mouse kidney scRNA-seq_IRI_short_3d_sample2


title: HCC3_MMS_C0_045

description:
Plate1_IndexA
HCC3_MMS_C0_045_S45

value: GATTGTGTT


title: LD_64_PT

value: ductal

value: positive

value: involved


title: SALL4_2

city: Singapore

first: Daniel

last: Tenen

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg38 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: rawcounts
Supplementary_files_format_and_content: diffexpgene_SALL4OE

growth_protocol: H1299-GFP/SALL4 cells were cultured with RPMI1640 supplied with 10% FBS.

extract_protocol:
RNeasy Micro Kit (Qiagen, Hilden, Germany) were used for RNA extraction according to manufacturers' protocol.
Libraries were prepared using Qiagen Fast Select rRNA removal reagents followed by Kapa RNA Hyper Prep reagent kits from 200ng of purified total RNA according to manufacturers' protocols.

treatment_protocol: No treatment

tag: genotype

value: SALL4 OE


title: SALL4_1


title: Mouse kidney scRNA-seq_IRI_short_3d_sample1


title: PA14_ctrl_2


title: PA14_EV_55J

value: airway epithelial cell EVs donor 55J


title: PA14_ctrl_3


title: PA14_EV_42I

value: airway epithelial cell EVs donor 42I


title: PA14_EV_25J

value: airway epithelial cell EVs donor 25J


title: GFP_1

value: Control


title: HCC3_ZDV_C0_044

description:
Plate1_IndexA
HCC3_ZDV_C0_044_S44

value: Human Hepatoma HepaRG Cell Line

value: Zidovudine (ZDV)

value: 0 µM

value: TAGCTCTTC

value: GCCGTTACA

value: Cell lysate (total RNA)


title: Mouse kidney scRNA-seq_IRI_short_1d_sample2

value: IRI short


title: Mouse kidney scRNA-seq_IRI_short_1d_sample1


title: HCC3_ZDV_C0_042

description:
Plate1_IndexA
HCC3_ZDV_C0_042_S42

value: TAACGCGTC


title: HCC3_ZDV_C0_041

description:
Plate1_IndexA
HCC3_ZDV_C0_041_S41

value: ACGACTTGG


title: Mouse kidney scRNA-seq_Control 6


title: Mouse kidney scRNA-seq_Control 5


title: Mouse kidney scRNA-seq_Control 4


title: HCC3_MMS_C1_039

description:
Plate1_IndexA
HCC3_MMS_C1_039_S39

value: Methyl methanesulfonate (MMS)

value: TCCTTCGTG

value: AGACACAAT


title: Mouse kidney scRNA-seq_Control 3


title: Mouse kidney scRNA-seq_Control 2


title: Mouse kidney scRNA-seq_Control 1


title: GFP_2


title: HCC3_ZDV_C1_035

description:
Plate1_IndexA
HCC3_ZDV_C1_035_S35

value: TCTAACCAT


title: HCC3_ZDV_C1_036

description:
Plate1_IndexA
HCC3_ZDV_C1_036_S36


title: 33.HCT116.KO.siHERVH#2.rep1

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

data_processing:
CASAVA1.4
Raw reads were first cleaned using trim_galore v0.6.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) : trim_galore –paired ${sample}_1.fq.gz ${sample}_2.fq.gz --gzip -o trim
The reads from each RNA-seq sample were then mapped to hg38 genome assembly downloaded from UCSC, using STAR v2.5.3a. The key alignment parameters were as follows: “--outFilterMismatchNoverLmax 0.04 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 500 --outMultimapperOrder Random --outSAMmultNmax 1”; the parameters “--outFilterMultimapNmax 500”  and “--outMultimappedOrder Random” ensured that multiple aligned reads were included but only one position was assigned randomly.
Genes expression was quantified using featureCounts v1.6.583 of subread-1.6.5 package based on hg38 RefSeq genes annotation file. Repeats expression was quantified using featureCounts v1.6.5 (“featureCounts --M --fraction”) based on repeats annotation files downloaded from https://genome.ucsc.edu/cgi-bin/hgTables.
To quantify the transcripts abundance, we used the function “fpm” in R package DEseq2 to calculate CPM (Counts Per Million mapped fragments) for each gene in all the samples, and then we transformed the CPM to Log2 scale (CPM+1 was used to avoid Log2 0).
Genome_build: hg38

growth_protocol: HCT116 cells were cultured in RPMI 1640 medium containing 10% FBS and incubated at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
The RNA of the treated cells was extracted by TRIzol (Life Technologies, 87804) according to the manufacturer’s protocol.
Total RNA was made into libraries for sequencing using the mRNA-Seq Sample Preparation Kit (Illumina) and sequenced on an Illumina Hiseq platform (Novagene, Tianjin, China), which includes that mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: For shRNA, shRNA oligos were synthesized by Tsingke (Tsingke Biotechnology Co., Ltd.) and cloned into pLKO.1 TRC Cloning vector. The shRNA and packaging vectors (pMD2.G and psPAX2) were transiently co-transfected into 293T cells by polyethylenimine (Sigma, P3143), and the resulted lentivirus particles were harvested and precipitated by PEG8000. The target cells were treated with lentivirus particles and 8 µg/mL polybrene for 24 hours, and the efficacy of shRNA interference   was determined by qPCR. The siRNA oligos were synthesized by GenePharma (Shanghai GenePharma Co., Ltd.). Cells were transfected with the indicated siRNA by Lipofectamine 2000. After 48 hours, the cells were harvested and the efficiency of silencing was verified by qPCR.

tag: tissue

value: colorectal carcinoma cell line

tag: sequencing time

value: KD HERVH


title: HCC3_ZDV_C1_034

description:
Plate1_IndexA
HCC3_ZDV_C1_034_S34


title: 31.HCT116.KO.siHERVH#1.rep1


title: HCC3_ZDV_C1_033

description:
Plate1_IndexA
HCC3_ZDV_C1_033_S33


title: 32.HCT116.KO.siHERVH#1.rep2


title: HCC3_MMS_C2_031

description:
Plate1_IndexA
HCC3_MMS_C2_031_S31

value: GCATGGACC


title: HCC3_MMS_C2_032

description:
Plate1_IndexA
HCC3_MMS_C2_032_S32

value: ATGCTCACA


title: 30.HCT116.KO.siBRD4.rep2

value: KD BRD4


title: HCC3_ZDV_C0_043

description:
Plate1_IndexA
HCC3_ZDV_C0_043_S43

value: Human Hepatoma HepaRG Cell Line

value: Zidovudine (ZDV)


title: HCC3_MMS_C2_029

description:
Plate1_IndexA
HCC3_MMS_C2_029_S29

value: GATTGTGTT


title: 29.HCT116.KO.siBRD4.rep1


title: 27.HCT116.KO.siNT.rep1

value: KD NT

value: siNT


title: 26.HCT116.KO.siYY1.rep2

value: KD YY1


title: HCC3_ZDV_C2_027

description:
Plate1_IndexA
HCC3_ZDV_C2_027_S27

value: Cell lysate (total RNA)


title: HCC3_ZDV_C2_028

description:
Plate1_IndexA
HCC3_ZDV_C2_028_S28

value: GCCGTTACA


title: HCC3_MMS_C1_040

description:
Plate1_IndexA
HCC3_MMS_C1_040_S40

value: Methyl methanesulfonate (MMS)


title: HCC3_ZDV_C2_026

description:
Plate1_IndexA
HCC3_ZDV_C2_026_S26

value: TAACGCGTC


title: HCC3_MMS_C1_038

description:
Plate1_IndexA
HCC3_MMS_C1_038_S38

value: TCCTTCGTG

value: CGTAACTTA


title: 25.HCT116.KO.siYY1.rep1

value: colorectal carcinoma cell line


title: 24.HCT116.KO.siSP1.rep2

value: KD SP1


title: HCC3_MMS_C1_037

description:
Plate1_IndexA
HCC3_MMS_C1_037_S37


title: HCC3_ZDV_C2_025

description:
Plate1_IndexA
HCC3_ZDV_C2_025_S25

value: GCATGGACC

value: ACGACTTGG


title: 34.HCT116.KO.siHERVH#2.rep2

value: KD HERVH


title: 23.HCT116.KO.siSP1.rep1


title: HCC3_MMS_C3_024

description:
Plate1_IndexA
HCC3_MMS_C3_024_S24

value: Human Hepatoma HepaRG Cell Line

value: GGAATGCAT

value: ATGCTCACA


title: 22.HCT116.KO.siNT.rep2

value: KD NT


title: 21.HCT116.KO.siNT.rep1

value: siNT


title: HCC3_MMS_C3_023

description:
Plate1_IndexA
HCC3_MMS_C3_023_S23

value: AGACACAAT


title: HCC3_MMS_C3_022

description:
Plate1_IndexA
HCC3_MMS_C3_022_S22

value: Cell lysate (total RNA)


title: HCC3_MMS_C2_030

description:
Plate1_IndexA
HCC3_MMS_C2_030_S30


title: 28.HCT116.KO.siNT.rep2


title: HCC3_ZDV_C3_020

description:
Plate1_IndexA
HCC3_ZDV_C3_020_S20

value: Zidovudine (ZDV)

value: GCCGTTACA


title: 17.HCT116.KO.siMED1.rep1

value: KD MED1


title: 19.HCT116.KO.siMED6.rep1

value: KD MED6


title: 18.HCT116.KO.siMED1.rep2


title: HCC3_ZDV_C3_019

description:
Plate1_IndexA
HCC3_ZDV_C3_019_S19

value: TCTAACCAT


title: 20.HCT116.KO.siMED6.rep2

value: colorectal carcinoma cell line


title: HCC3_MMS_C3_021

description:
Plate1_IndexA
HCC3_MMS_C3_021_S21

value: Methyl methanesulfonate (MMS)

value: GATTGTGTT


title: 16.HCT116.KO.siMED12.rep2

value: KD MED12


title: HCC3_ZDV_C3_018

description:
Plate1_IndexA
HCC3_ZDV_C3_018_S18

value: TAACGCGTC


title: HCC3_MMS_C4_015

description:
Plate1_IndexA
HCC3_MMS_C4_015_S15

value: Human Hepatoma HepaRG Cell Line

value: GTGATCTGA


title: HCC3_ZDV_C3_017

description:
Plate1_IndexA
HCC3_ZDV_C3_017_S17

value: GGAATGCAT

value: ACGACTTGG


title: HCC3_MMS_C4_016

description:
Plate1_IndexA
HCC3_MMS_C4_016_S16

value: ATGCTCACA


title: HCC3_MMS_C4_014

description:
Plate1_IndexA
HCC3_MMS_C4_014_S14

value: CGTAACTTA


title: 15.HCT116.KO.siMED12.rep1


title: 14.HCT116.KO.siCEBPB.rep2

value: KD CEBPB

value: siCEBPB


title: HCC3_MMS_C4_013

description:
Plate1_IndexA
HCC3_MMS_C4_013_S13

value: Cell lysate (total RNA)


title: 11.HCT116.KO.siCDK8.rep1

value: KD CDK8


title: 13.HCT116.KO.siCEBPB.rep1


title: HCC3_ZDV_C4_012

description:
Plate1_IndexA
HCC3_ZDV_C4_012_S12

value: Zidovudine (ZDV)

value: GCCGTTACA


title: 12.HCT116.KO.siCDK8.rep2

value: colorectal carcinoma cell line


title: 10.HCT116.KO.siBRD4.rep2

value: KD BRD4


title: 9.HCT116.KO.siBRD4.rep1


title: HCC3_ZDV_C4_010

description:
Plate1_IndexA
HCC3_ZDV_C4_010_S10


title: 8.HCT116.KO.shHERVH#1.rep2

value: KD HERVH


title: 7.HCT116.KO.shHERVH#1.rep1


title: HCC3_ZDV_C4_009

description:
Plate1_IndexA
HCC3_ZDV_C4_009_S9


title: HCC3_MMS_C5_008

description:
Plate1_IndexA
HCC3_MMS_C5_008_S8

value: Methyl methanesulfonate (MMS)

value: GCTGTAGTT


title: HCC3_MMS_C5_007

description:
Plate1_IndexA
HCC3_MMS_C5_007_S7

value: Human Hepatoma HepaRG Cell Line

value: AGACACAAT


title: HCC3_ZDV_C4_011

description:
Plate1_IndexA
HCC3_ZDV_C4_011_S11

value: GTGATCTGA

value: TCTAACCAT


title: 3.HCT116.WT.shHERVH#1.rep1


title: 5.HCT116.KO.shGFP.rep1

value: KD GFP

value: shGFP


title: 4.HCT116.WT.shHERVH#1.rep2


title: 2.HCT116.WT.shGFP.rep2


title: HCC3_ZDV_C5_003

description:
Plate1_IndexA
HCC3_ZDV_C5_003_S3


title: HCC3_MMS_C5_005

description:
Plate1_IndexA
HCC3_MMS_C5_005_S5

value: GATTGTGTT


title: HCC3_ZDV_C5_004

description:
Plate1_IndexA
HCC3_ZDV_C5_004_S4


title: 1.HCT116.WT.shGFP.rep1


title: HCC3_ZDV_C5_001

description:
Plate1_IndexA
HCC3_ZDV_C5_001_S1

value: ACGACTTGG


title: HCC3_ZDV_C5_002

description:
Plate1_IndexA
HCC3_ZDV_C5_002_S2

value: TAACGCGTC

value: Cell lysate (total RNA)


title: Patient 1, pre treatment

city: York

first: Paul

last: Kaye

address: Wentworth way

institute: University of York

description: Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

data_processing:
cutadapt v1.8.3 to remove illumina universal adaptors
sickle v 1.33 was used to trim bases with a quality less than Q20
STAR version 2.5.1b was used to align to reference GRCh38.84
Reads were counted using the union algorithm in HTseq count
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Gene counts

source_name: Whole Blood

extract_protocol:
Total RNA was extracted from formalin fixed paraffin embedded samples using RNAeasy FFPE kit
Paired end illumina RNA sequencing libraries were generated using polyA enrichment followed by using the NEB next RNA kit

value: Whole Blood

tag: subject

value: Patient 1

tag: disease state

value: cutaneous leishmaniasis

tag: timepoint

value: pre treatment


title: Patient 4, on treatment

value: Patient 4

value: on treatment


title: Patient 7, pre treatment

value: Patient 7


title: Patient 8, on treatment

value: Patient 8


title: Patient 5, on treatment

value: Patient 5


title: Patient 5, pre treatment


title: Patient 7, on treatment


title: Patient 6, pre treatment

value: Patient 6


title: Patient 1, on treatment


title: Patient 8, pre treatment


title: Patient 6, on treatment


title: SpG_CBE_BRCA1_tiling_Meljuso_Dropout_RepB

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

source_name: melanoma cell line

value: Skin

tag: cell line

value: MELJUSO

tag: treatment

value: untreated

tag: description

value: Dropout screen with CBE BRCA1 tiling library using SpG in Meljuso cells, replicate B


title: 6.HCT116.KO.shGFP.rep2

value: colorectal carcinoma cell line

value: KD GFP

value: shGFP


title: SpG_CBE_BRCA1_tiling_Meljuso_Dropout_RepA

value: Dropout screen with CBE BRCA1 tiling library using SpG in Meljuso cells, replicate A


title: 34 QKO [TRA00038986]

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file contains read counts.

extract_protocol:
RNA was extracted from a mixture of powdered Quad and gastrocnemius muscles using Trizol reagent (Invitrogen).
Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen).

tag: strain background

value: mixed

value: KO

value: QKO

value: Muscle


title: HCC3_MMS_C5_006

description:
Plate1_IndexA
HCC3_MMS_C5_006_S6

source_name: Human Hepatoma HepaRG™ Cell Line

value: Human Hepatoma HepaRG Cell Line

value: Methyl methanesulfonate (MMS)

tag: concentration

tag: index

value: GCTGTAGTT

value: CGTAACTTA

tag: molecule source

value: Cell lysate (total RNA)


title: 33 MIGIRKO [TRA00038985]

value: MIGIRKO


title: 32 IRIGFRlox [TRA00038984]

value: Lox

value: IRIGFRlox


title: SpG_CBE_BRCA1_tiling_Meljuso_Cisplatin_RepB

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Cisplatin for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

value: Skin

value: MELJUSO

value: 1uM Cisplatin

value: Cisplatin screen with CBE BRCA1 tiling library using SpG in Meljuso cells, replicate B


title: SpG_CBE_BRCA1_tiling_Meljuso_Cisplatin_RepA

value: Cisplatin screen with CBE BRCA1 tiling library using SpG in Meljuso cells, replicate A


title: 30 IGFRlox [TRA00038982]

value: mixed

value: IGFRlox


title: 31 MIRKO [TRA00038983]

value: KO

value: MIRKO


title: SpG_CBE_BRCA1_tiling_HAP1_Dropout_RepB

description:
HAP1 cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

source_name: CML cell line

value: Blood

value: untreated

value: Dropout screen with CBE BRCA1 tiling library using SpG in HAP1 cells, replicate B


title: Patient 4, pre treatment

value: Whole Blood

value: Patient 4

value: cutaneous leishmaniasis

value: pre treatment


title: SpG_CBE_BRCA1_tiling_HAP1_Dropout_RepA

value: Dropout screen with CBE BRCA1 tiling library using SpG in HAP1 cells, replicate A


title: 28 MIGIRKO [TRA00038947]

value: MIGIRKO

value: Muscle


title: 29 QKO [TRA00038948]

value: QKO


title: T1AM09

type: protein

city: Bronx

first: Jacqueline

last: Achkar

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

description: IgG

hyb_protocol: Arrays were blocked with 3% BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected by goat anti-human biotin-labeled IgG (Jackson Immunoresearch), followed by a Streptavidin probe tagged with SureLight®P3 Cy5 (Cayman Chemicals). Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The GenePix 4000 Microarray scanner system (Molecular Devices, CA) was used for scanning.

data_processing: We analyzed images using GenePix Pro 7.3.0.0 to measure median pixel intensity (MPI) and neighboring background pixel intensity (BPI) of individual spots. The median fluorescence intensity (MFI), representing AM-epitope specific mAb reactivity, was calculated using the MPI minus the BPI and averaged from the triplicate spots.

molecule: protein

source_name: monoclonal antibody

label_protocol: SureLight®P3 Cy5

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:50

tag: antibody


title: 26 MIGF1RKO [TRA00038945]


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Cisplatin_RepC

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing WTCas9-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Cisplatin for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: Skin

value: MELJUSO

value: 1uM Cisplatin

value: Cisplatin screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate C


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Dropout_RepC

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing WTCas9-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate C


title: Root_72h-rep2

city: Guang Zhou

first: Yan

last: Lin

state: Guang Dong

address: 广州市石榴岗路10号

department: Institute of Nanfan ＆Seed Industry

institute: Guangdong Academy of Sciences

description:
rpkm.txt
Sample D32

data_processing:
Remove the adaptor-polluted reads (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out)
Remove the low-quality reads (Reads with the number of low quality bases(phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low -quality reads).
Remove reads with number of N  bases accounting for more than 5 %.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads ) was then calculated to estimate the expression level of genes in each sample
Screening DEGs using NOISeq.
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample .

organism: Stylosanthes guianensis

source_name: Root

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent for the purification of total RNA from the plant tissue
BGI RNA-Seq kit

tag: time

value: 72h after germination

value: Root


title: Root_72h-rep3

description:
rpkm.txt
Sample D33


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Cisplatin_RepA

value: Cisplatin screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate A


title: Root_72h-rep1

description:
rpkm.txt
Sample D31


title: 24 IGFRlox [TRA00038943]

value: mixed

value: Lox

value: IGFRlox


title: Root_48h-rep3

description:
rpkm.txt
Sample D23

value: 48h after germination


title: Root_48h-rep2

description:
rpkm.txt
Sample D22


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Cisplatin_RepB

value: Cisplatin screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate B


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Dropout_RepA

value: untreated

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate A


title: L1AM04

description: IgG


title: CS-35

description: IgG


title: WTCas9_ABE_BRCA1_tiling_MELJUSO_Dropout_RepB

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in Meljuso cells, replicate B


title: WTCas9_ABE_BRCA1_tiling_HAP1_Dropout_RepC

description:
HAP1 cells were transduced with the BRCA1 tiling library cloned into a vector containing WTCas9-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: Blood

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in HAP1 cells, replicate C


title: 27 Qlox [TRA00038946]

value: Qlox

value: Muscle


title: Root_48h-rep1

description:
rpkm.txt
Sample D21


title: WTCas9_ABE_BRCA1_tiling_HAP1_Dropout_RepB

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in HAP1 cells, replicate B


title: 22 MIGIRKO [TRA00038926]

value: KO

value: MIGIRKO


title: 20 MIGF1RKO [TRA00038924]


title: 23 QKO [TRA00038927]

value: QKO


title: Root_24h-rep2

description:
rpkm.txt
Sample D12

value: 24h after germination

value: Root


title: WTCas9_ABE_BRCA1_tiling_HAP1_Dropout_RepA

value: Dropout screen with ABE8e BRCA1 tiling library using WTCas9 in HAP1 cells, replicate A


title: Root_24h-rep1

description:
rpkm.txt
Sample D11


title: 25 MIRKO [TRA00038944]

value: mixed

value: MIRKO


title: SpG_ABE8e_BRCA1_tiling_MELJUSO_Dropout_RepB

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: Skin

value: MELJUSO

value: Dropout screen with ABE8e BRCA1 tiling library using SpG in Meljuso cells, replicate B


title: 18 IGFRlox [TRA00038922]

value: Lox

value: IGFRlox


title: HCT116 Glucose free medium

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

description: Glucose deprivation for 24 hours

data_processing:
Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
log2Fc method is used in calculated differential expressed genes
Genome_build: hg19

source_name: Glucose deprivation

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

treatment_protocol: HCT116 cell were cultured with indicated medium for 24 hours

tag: cell type

value: colon cancer cell line

value: colon

value: wild type


title: 5 samples: tag

city: KYOTO

first: LIU

last: YAJING

address: 53 KAWAHARA-CHO,SHOGOIN,SAKYO-KU

department: STEM CELL DIFFERENTIATION

country: Japan

institute: CIRA

description: single cell RNA-Seq data

data_processing:
For mouse data, after adapter removal by using Cutadapt-2.10, gene-expression libraries were aligned to the mm10 reference transcriptome by using Bowtie2-2.3.4.1, and count matrices were generated using home-built shell scripts and the modified python script of BD Rhapsody workflow. Valid cell barcodes were identified as cell barcodes above inflection threshold of knee-plot of total read counts of each cell barcode identified by DropletUtils package (Griffiths JA et al. Nat. Commun. 2018). Each sample origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. Data were log-transformed [log(TPM + 1)] for all downstream analyses, most of which were performed using the R software package Seurat v2.3.4 (http://satijalab.org/seurat)
For each cell, three quality control metrics were calculated: (1) the total detected number of genes; (2) the proportion of ribosome encoded transcripts; and (3) the proportion of mitochondrially encoded transcripts. Cells were excluded from downstream analysis if fewer than 200 genes were detected.  There was an expression matrix of 7,613 cells by 22,833 genes. Each gene expression measurement was normalized by total expression within the corresponding cell and multiplied by a scaling factor of 1,000,000. Highly-variable genes identified by Seurat package were used for principal components analysis. Principal components were determined to be significant (P < 0.05) using the jackstraw method and FIt-SNE (https://www.nature.com/articles/s41592-018-0308-4) was performed on these key principal components. Unsupervised clustering was performed using a shared nearest neighbor modularity optimization-based algorithm
Genome_build: mm10
Supplementary_files_format_and_content: .txt

source_name: epiblast

growth_protocol: Primed mEpiSCs are culutred on MEF in FGF2 and Actinvin A before one day of reversion. We treated cells with  AICAR+LIF . After 8 or 16 days, single cells were colltected. We also colloected single cell of naive mESCs, primed mEpiSCs and reverted cells cultured in 2iL after 10 pasaages.

extract_protocol:
Cells were determined by FlowCount beads (Beckman Coulter) using combination of Biotin-CD9 and Biotin-CD63 (Biolegend) conjunction with TotalSeq™-A095(1-5) PE Streptavidin, respectively
For scRNA-seq, cDNA libraries and hashtag libraries were prepared combined by an BD Rhapsody system and an optimized process similar to the magnetic bead-based bulk RNA-seq method (Shichino et al. JCI insight 2019). Sequencing libraries were generated by using NEBNext UltraII FS library prep kit (New England Biolabs), and QC of cDNA/Hashtag libraries was performed by MultiNA (Shimazu) and qPCR library quantification assay (KAPA).
BD Rhapsody WTA

tag: strain


title: SpG_ABE8e_BRCA1_tiling_MELJUSO_Dropout_RepA

data_processing:
Library strategy: DNA-seq
Raw read counts were retrieved from sequencing data using PoolQ Version 3
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Excel spreadsheets with guide-level read counts and library annotations

extract_protocol:
Cells were lysed and genomic DNA was extracted using? Genomic DNA was PCR amplified using barcoded primers, then pooled and SPRI purified before submission for sequencing.
Oligonucleotide pools were synthesized by CustomArray. BsmBI recognition sites were appended to each sgRNA sequence  for cloning into the sgRNA expression plasmids, as well as primer sites to allow differential amplification of subsets from the same synthesis pool. The resulting amplicons were PCR-purified (Qiagen) and cloned into the library vector via Golden Gate cloning with Esp3I (Fisher Scientific) and T7 ligase (Epizyme)

value: untreated

value: Dropout screen with ABE8e BRCA1 tiling library using SpG in Meljuso cells, replicate A


title: 17 QKO [TRA00038895]

tag: genotype

value: KO

value: Muscle


title: HCT116 normal medium

description: no treatment

source_name: CTRL

tag: tissue


title: SpG_ABE8e_BRCA1_tiling_MELJUSO_1uMCisplatin_RepB

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Cisplatin for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: 1uM Cisplatin

value: Cisplatin screen with ABE8e BRCA1 tiling library using SpG in Meljuso cells, replicate B


title: 15 QKO [TRA00038893]

value: QKO


title: 21 Qlox [TRA00038925]

value: mixed

value: Qlox


title: SpG_ABE8e_BRCA1_tiling_HAP1_Dropout_RepB

description:
HAP1 cells were transduced with the BRCA1 tiling library cloned into a vector containing SpG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: Blood

value: Dropout screen with ABE8e BRCA1 tiling library using SpG in HAP1 cells, replicate B


title: 13 IRlox [TRA00038890]

value: IRlox


title: Root_24h-rep3

description:
rpkm.txt
Sample D13

value: 24h after germination

value: Root


title: SpG_ABE8e_BRCA1_tiling_MELJUSO_1uMCisplatin_RepA

value: Skin

value: MELJUSO

value: Cisplatin screen with ABE8e BRCA1 tiling library using SpG in Meljuso cells, replicate A


title: 16 MIGIRKO [TRA00038894]

value: MIGIRKO


title: 5 samples: cDNA

description: single cell RNA-Seq data


title: 14 MIGF1RKO [TRA00038892]


title: 12 QKO [TRA00038435]


title: SpG_ABE8e_BRCA1_tiling_HAP1_Dropout_RepA

value: untreated

value: Dropout screen with ABE8e BRCA1 tiling library using SpG in HAP1 cells, replicate A


title: PAM_flexible_variant_offtarget_SpG_A375_Dropout_RepB

description:
A375 cells were transduced with the PAM-flexible variant off-target library cloned into a vector containing SpG and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data3_v3.xlsx

value: Dropout screen with PAM-flexible variant off-target library using SpG in A375 cells, replicate B


title: 2-1211707: WTCAR2 WGBS

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: CD8 T cells

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

value: WT CAR T


title: 11 MIGIRKO [TRA00038434]

value: KO

value: Muscle


title: 2-1211708: WTCAR3 WGBS


title: 2-1211710: Regnase1KOCAR2 WGBS

value: Regnase-1-deficient CAR T


title: PAM_flexible_variant_offtarget_SpG_A375_Dropout_RepA

city: Cambridge

last: Doench

address: 75 Ames St.

institute: Broad Institute

value: Dropout screen with PAM-flexible variant off-target library using SpG in A375 cells, replicate A


title: 19 MIRKO [TRA00038923]

value: mixed

value: MIRKO


title: 2-1211711: Regnase1KOCAR3 WGBS


title: PAM_flexible_variant_offtarget_Cas9NG_Dropout_RepB

description:
A375 cells were transduced with the PAM-flexible variant off-target library cloned into a vector containing Cas9-NG and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data3_v3.xlsx

value: Dropout screen with PAM-flexible variant off-target library using Cas9-NG in A375 cells, replicate B


title: 10 IRIGFRlox [TRA00038433]

value: Lox

value: IRIGFRlox


title: 2-1211709: Regnase1KOCAR1 WGBS


title: PAM_flexible_variant_offtarget_Cas9NG_Dropout_RepA

value: Skin

value: Dropout screen with PAM-flexible variant off-target library using Cas9-NG in A375 cells, replicate A


title: 9 MIGF1RKO [TRA00038432]


title: Cas9NG_ABE8e_BRCA1_tiling_MELJUSO_Dropout_RepB

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: MELJUSO

value: Dropout screen with ABE8e BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate B


title: Cas9NG_ABE8e_BRCA1_tiling_MELJUSO_Dropout_RepA

value: untreated

value: Dropout screen with ABE8e BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate A


title: 6 QKO [TRA00038418]

value: QKO


title: 7 IRlox [TRA00038430]

value: IRlox


title: Cas9NG_ABE8e_BRCA1_tiling_MELJUSO_Cisplatin_RepA

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Cisplatin for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

value: 1uM Cisplatin

value: Cisplatin screen with ABE8e BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate A


title: 3 MIGF1RKO [TRA00038415]

value: KO

value: Muscle


title: 8 MIRKO [TRA00038431]

value: mixed


title: Cas9NG_ABE8e_BRCA1_tiling_MELJUSO_Cisplatin_RepB

value: Cisplatin screen with ABE8e BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate B


title: Colon26 tumors, CD45+ cells, treated (cDNA library)

first: Alex Chang-Yu

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

description:
hashtag index A0301 = Control_1
hashtag index A0302 = Control_2
hashtag index A0303 = Control_3
hashtag index A0304 = minP1_1
hashtag index A0305 = minP1_2
hashtag index A0306 = minP1_3
hashtag index A0307 = minP1_4
hashtag index A0308 = PDL1_1
hashtag index A0309 = PDL1_2
hashtag index A0310 = PDL1_3
hashtag index A0311 = minP1_PDL1_1
hashtag index A0312 = minP1_PDL1_2
hashtag index A0313 = minP1_PDL1_3
hashtag index A0314 = minP1_PDL1_4

data_processing:
For mouse data, after adapter removal by using Cutadapt-2.10, gene-expression libraries were aligned to the mm10 reference transcriptome by using Bowtie2-2.3.4.1, and count matrices were generated using home-built shell scripts and the modified python script of BD Rhapsody workflow. Valid cell barcodes were identified as cell barcodes above inflection threshold of knee-plot of total read counts of each cell barcode identified by DropletUtils package (Griffiths JA et al. Nat. Commun. 2018). Each sample origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. Data were log-transformed [log(TPM + 1)] for all downstream analyses, most of which were performed using the R software package Seurat v2.3.4 (http://satijalab.org/seurat) to analyze immune cell populations.
For each cell, three quality control metrics were calculated: (1) the total detected number of genes; (2) the proportion of ribosome encoded transcripts; and (3) the proportion of mitochondrially encoded transcripts. Cells were excluded from downstream analysis if fewer than 200 genes were detected.  There was an expression matrix of 7,613 cells by 22,833 genes. Each gene expression measurement was normalized by total expression within the corresponding cell and multiplied by a scaling factor of 1,000,000. Highly-variable genes identified by Seurat package were used for principal components analysis. Principal components were determined to be significant (P < 0.05) using the jackstraw method and FIt-SNE (https://www.nature.com/articles/s41592-018-0308-4) was performed on these key principal components. Unsupervised clustering was performed using a shared nearest neighbor modularity optimization-based algorithm
Genome_build: mm10
Supplementary_files_format_and_content: ProcessedData_Final_Matrix.txt.gz (Column names were named as "Hashtag_ID"_"Cell barcode", and row names were gene symbols).

source_name: intestinal CD45+ cells

extract_protocol:
Tumor were cut into small pieces with a razor blade and digested enzymatically using 0.25% Liberase TM (Merck) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Tumor cell and dead cell were removed by 40% Percoll (GE Healthcare, Buckinghamshire, UK) density separation.
For scRNA-seq, cDNA libraries and hashtag libraries were prepared combined by an BD Rhapsody system and an optimized process similar to our magnetic bead-based bulk RNA-seq method (Shichino et al. JCI insight 2019). Sequencing libraries were generated by using NEBNext UltraII FS library prep kit (New England Biolabs), and QC of cDNA/Hashtag libraries was performed by MultiNA (Shimazu) and qPCR library quantification assay (KAPA).
BD Rhapsody WTA

treatment_protocol: Colon26 (2 x 10^5 cells/mouse) were subcutaneously inoculated into the right flank of BALB/c mice. The HMGN1 immunostimulatory peptide (minP1, at a dose of 0.08 microgram per mouse per injection, unless otherwise noted) was administered intraperitoneally on day 9 after tumor inoculation. Anti-PD-L1 antibody (clone 10F.9G2; BioXcell, USA) was injected intraperitoneally on days 4 and 8 after tumor inoculation (at a dose of 200 micrograms per mouse per injection). On day 10, the CD45+ cells of tumor tissue from each implanted mouse were used as a single-cell RNA sequencing sample.

value: BALB/c

value: Colon26 tumor

value: intestinal CD45+ cells

tag: model

value: subcutaneous tumor model

value: wild type

value: mixed sample (non-demultiplexed) representing Control, minP1, PDL1, minP1_PDL1


title: Colon26 tumors, CD45+ cells, treated (hashtag library)