title: P8, snRNAseq

city: Miami

first: James

middle: S

last: Choi

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

description: 10X Genomics 3’ v3

data_processing:
Libraries were sequenced on NovaSeq SP 100 (200,000 reads/nucleus). Samples were each sequenced across two lanes. After sequencing, Illumina output was processed using CellRanger v3.0.2. Base call files for each sample were demultiplexed. A pre-mRNA reference was generated with cellranger mkref using the mm10 mouse genome. Each sample was aligned to the custom mm10 mouse reference genome using CellRanger. The two sequencing lanes/runs per sample were concatenated to generate the final count matrix.
To distinguish nuclei-containing droplets from empty droplets, we performed cell calling on the unfiltered UMI count matrices using a combination of barcode-ranking and the empty-droplet detection emptyDrops function as omplemented in the DropletUtils R package (Lun et al., 2019). First, nuclei were ranked according to total UMI count and visualized in a log-total UMI vs log-rank plot. A spline curve was fit to the data to identify “knee” and inflection points, and cells with total UMI count above the knee were considered nuclei-containing droplets. Next, we used the emptyDrops algorithm to further distinguish empty droplets from nuclei for nuclei with lower total UMI counts. To remove potential doublets, we applied the Python package Scrublet (Wolock et al., 2019) to each individual sample using default parameters. In brief, Scrublet simulates multiplets by sampling from the data and builds a nearest-neighbor-based classifier. Cells with high doublet scores were flagged and removed.   We performed further quality control based on metrics such as total UMI, number of unique genes detected, mitochondrial transcript content. Lower-bound thresholds for total UMI and unique gene detection rates were determined by computing three absolute median deviations below the median.
Assembly: mm10
Supplementary files format and content: Tab-separated value files, contains metadata from experiment design and analysis results
Supplementary files format and content: Matrix files, contains count matrix for all samples combined

source_name: Superior colliculus

extract_protocol:
Superior colliculus was microdissected from embryonic day 19 (E10), post-natal day 4 (P4), P8, or P21 C57BL/6J mice. Tissue was pooled from multiple animals and homogenized inRNAase-free lysis buffer (0.32 M sucrose, 3 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl,1 mM DTT, 0.1% Triton X-100 in DEPC-treated water) using glass dounce homogenizer on ice. The homogenate was loaded into a polycarbonate ultracentrifuge tube containing sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, 10 mM Tris-HCl in DEPC-treated water) in the bottom and centrifuged at 107,000 g for 2.5 hours at 4°C. Supernatant was aspirated, and the nuclei containing pellet was incubated in RNAse-free 1x PBS, 0.04% BSA, 0.2 U/µl RNAse Inhibitor on ice before resuspending the pellet. The nuclear suspension was filtered twice through a 30 µm cell strainer RNAase-free.
Single nucleus suspension was processed and sequenced using 10X Genomics 3’ v3 snRNA-seq platform with a target capture of 2000 nuclei per sample.

value: Superior colliculus

tag: strain

tag: development stage


title: P21, snRNAseq

status: Public on Apr 12 2023

type: SRA

country: USA

description: 10X Genomics 3’ v3

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06H]

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic

data_processing:
For the sci-RNA-seq3 transcriptome libraries, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. Reads were filtered based on RT and ligation index, by allowing <2 hamming distance from reference. Filtered reads were trimmed with TrimGalore (v0.6.6) with parameters: -a AAAAAAAA --three_prime_clip_R1 1. Reads were then aligned to the GRCh38 reference genome using STAR (v2.7.6a). PCR duplicates were collapsed using the RT index, ligation index, UMI sequence and end coordinate of reads. Reads were further demultiplexed based on the combination of the RT, ligation and PCR index and split into files for individual cells. To generate gene expression count matrices, reads were assigned to the exonic and intronic region of closest genes with HTseq (v.2.0.2). Reads with ambiguous assignments were discarded. Cells were further filtered based on total UMI (> 100) and mitochondrial reads percentage (<10%). Cells with the number of features detected between 10% and 90% percentile of all cells were kept and considered high-quality cells. The single cell analysis was performed using the Seurat (v4.0.0) package in R.
For capture libraries of the synHEK3 and shRNA constructs, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. A custom script was used to further demultiplex and filter the synHEK3 and shRNA libraries based on the combination of RT, ligation and PCR index (cell ID), by allowing <2 hamming distance from reference. For the synHEK3 library, reporter barcodes (<2 hamming distance to the reference barcode set), prime editing outcomes and read UMIs were extracted. For the shRNA library, shRNA sequences (<2 hamming distance to the reference barcode set) and read UMIs were extracted. UMIs <3 hamming distance were collapsed.   A series of pre-processing steps were applied to the data. 1) We matched cell IDs between the sci-RNA-seq3 transcriptome libraries and the capture libraries, and only kept high-quality cells (number of features between 10% and 90% percentile). 2) For the shRNA library, cells with <3 or >200 UMIs or >20 shRNA were removed. 3) For the synHEK3 library, cells with <4 UMIs were first removed. We counted UMIs for synHEK3 reporters belonging to the two clones and calculated a clone UMI/total UMI ratio. If the ratio was >80% for a specific clone, the cell is assigned to the corresponding clone. Cells with extremely high UMIs (cutoff between 100 and 250 UMIs, depending on library complexity and sequencing depth of the plate) were also removed for downstream analysis. 4) For a cell-synHEK3 barcode combination, if multiple insertion sequences were observed, sequences <3 hamming distance were collapsed. Cell-synHEK3 barcode pairs having conflicting editing outcomes were discarded. 5) A cell-synHEK3 barcode-editing outcome-shRNA matrix was generated for a common set of cells identified by the shRNA and synHEK3 libraries.
Assembly: GRCh38
Supplementary files format and content: cell_synHEK3_shRNA.csv.gz contains a cell-synHEK3-shRNA capture matrix

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL).

extract_protocol: We performed a modified version of sci-RNA-seq3 (Martin et al., 2022). In brief, K562 cells were lysed with 5 mL of a hypotonic, PBS-based lysis buffer containing DEPC. The resulting nuclei were fixed with 4 volume of ice-cold methanol. After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton buffer (SPBST), the nuclei were treated with T7 polymerase in an NTP mix buffer at 37oC for 30 min. Then nuclei were washed, sonicated briefly and counted. The nuclei were distributed to a 96-well plate for reverse transcription, with a cocktail of three indexed primers: oligo-dT, HEK3 and CS1 -- specific for the cellular transcriptome, and RNAs produced from the synHEK3 reporter and the shRNA constructs, respectively. After reverse transcription, nuclei were pooled, washed in SPBST and redistributed to 4 fresh plates for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to 4 final plates at two different concentrations (1300 cell per well for 2 plates and 2500 cell per well for 2 plates) for second strand synthesis and extraction. Nuclear lysates were split in half, with one half undergoing normal sci-RNA-seq3 transcriptome library preparation (tagmentation and PCR to add the third index) and the other half subjected to indexed enrichment PCR for both the synHEK3 and shRNA constructs. Products were pooled by PCR plate, size-selected and sequenced on an Illumina Nextseq 2000 or Nextseq 550.

treatment_protocol: Two monoclonal K562 PE2-Puro lines (clone 3 and clone 5) containing multiple randomly integrated chromatin sensors for prime editing (synHEK3) were transduced with Lenti-rtTA-P2A-Blast viruses and selected in 10 ug/mL Blasticidin for 7 days. Monoclonal lines were derived and further transduced with a DNA damage response gene-focused lentiviral shRNA library containing 304 hairpins targeting 76 genes. Cells were transdcued at either low MOI (<1) or high MOI (~10) and selected in 800 ug/mL Geneticin for 7 days. For preparing sci-RNA-seq3 libraries, at the RT step, the low MOI cells are placed in the first 6 columns of the 96-well plate, while the high MOI cells were placed in the 7-12 columns of the 96-well palte. Low MOI and High MOI transduced cells can be distiguished by RT indices.

tag: cell line

tag: cell type

value: lymphoblast

tag: treatment

value: lentiviral transduction of a DDR-focused shRNA library


title: 15_13160NMS198.CEL

type: RNA

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HU-133A-2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The raw CEL files were adjusted for GC content.
Probe sets summarized by median polish algorithm implemented in Partek software (www.partel.com)

label: biotin

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PBMC were purified using Ficoll hypaque gradient (Invitrogen, USA).

tag: patient diagnosis

value: multiple sclerosis

value: PBMC

tag: age(years)

tag: gender

value: female

tag: batch number


title: Sca1_AAV_NC

city: Hangzhou

first: Lingxia

last: Lyu

address: No.79 Qingchun Road

country: China

institute: Zhejiang university

description: 10x Genomics

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: veingraft

extract_protocol:
Veingrafts were harvested and digested. After full digestion, cell pellets were suspended in PBS and stained with a LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit (1:1000) and Hoechst 33342 (Invitrogen, H3570, 1:1000). After washing using PBS, cells were resuspended in PBS, after which single nucleated live cells (Hoechst+ & Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a BD FACS ARIA II Flow Cytometer (BD Biosciences). For CD45- cells, a CD45 antibody (Invitrogen, 14-0452-82, 1:2000) was additionally used. For RFP+ cells, FACS sorting was based on their autofluorescence. Samples were subjected to scRNA-seq.
A ChromiumTM Single Cell 3' Reagent Kit v2 or v3 chemistry (10x Genomics) was used and a standard protocol followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.

value: veingraft

value: Goblet cells

value: all cells

tag: genotype

value: Sca1 creER;R26-tdtomato

value: AAV-NC


title: WT7 (timecourse) - day1

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
antNPCs_F1Tm1_2_counts.csv
antNPCs_F1Tm1_2_TPM.csv

data_processing:
Adapters, polyA/T tails, and bad quality reads (Phred score > 20) were trimmed using Trim Galore! (v0.6.4_dev) with default parameters. Reads were aligned to the transcriptome and quantified using Salmon (v0.14.1) (Patro et al., 2017) with default parameters using GENCODE release 23 of the mouse reference transcriptome sequences and the comprehensive gene annotation. Subsequently, the counts were imported into R (v4.0.2) using tximport (v1.18.0). Differentially expressed genes were defined using DEseq2 (v1.30.0) (Love et al., 2014) and log fold changes corrected using “ashr” method (FDR adjusted p.val < 0.05 & |log2(fold change)| > 1.5) (Stephens, 2017). Temporal differentially expressed genes were determined using xxx with default settings. GO term enrichment was performed using Cluster Profiler (3.18.1), while transcription factor enrichment was calculated using TRRUST website (https://www.grnpedia.org/trrust/) (Han et al., 2018). Lineage marker gene sets were determined by stratifying cell types of the mouse gastrulation reference dataset (Pijuan-Sala et al., 2019) per lineage and calculate markers function of Seurat (Hao et al., 2021). Single cell deconvolution was done with R package SCDC (v1.1.3) (Dong et al., 2021), using the two mixed gastrulation samples from the mouse gastrulation reference dataset as reference. TPM values were calculated using tximport.
Assembly: mm10
Supplementary files format and content: tab separated file with raw counts per sample
Supplementary files format and content: tab separated file with TPM normalized counts per sample

source_name: mESC B6129S6F1 Tet1<tm1Koh>

growth_protocol: Anterior neural progenitor differentiation was performed as previously described (Cruz-Molina et al., 2017; Gouti et al., 2014; Luo et al., 2020). Feeder depleted serum cultured ESCs were plated on gelatin coated plates at 10,000 cells/cm2 (90,000 cells per well in a 6-well plate) in advanced N2B27 defined media compromising a 1:1 mix of 1:1 DMEM/F12 (Invitrogen, 12634-010, Invitrogen) and Neurobasal medium (Invitrogen, 10888-022) supplemented with 0.5x B27 without vitamin A (Invitrogen, 12587-010), 0.5x N2 (Invitrogen, 17502-048), 2 mM L-glutamine (Invitrogen, 25030-024), 40 mg/ml BSA fraction V (Invitrogen, 15260037), 0.1 mM 2-mercaptoethanol (Invitrogen, 31350-010) and 100:100 units:µg/ml penicillin:streptomycin (Sigma-Aldrich, P4333; or Gibco, 15140122). Cells were supplemented with 10 ng/ml bFGF (Cat#100-18C, Peprotech) from day 0 until day 3. At day 3 the medium was changed to medium without bFGF. In some experiments, 5 µM of the Wnt inhibitor XAV939 (Sigma-Aldrich, X3004), 2.5 µM of the TGF-β receptor inhibitor SB431542 (Sigma-Aldrich, S4317), 0.1 µM BMP inhibitor LDN193189 (Sigma-Aldrich, SML0559), 0.3 µM or 3 μM GSK3 β inhibitor CHIR99021 (Axon Medchem BV,1408), 5 or 25 ng/ml of Activin A (Peprotechm 120-14E), or equivalent amount of DMSO (vehicle control) were added from day 2 until day 5. The medium was changed every day during differentiation, except on day 1. At day 4, 1.5x amount of medium was added. The experimental end-point is day 5.

extract_protocol:
Total RNA was extracted from cells using Trizol using the manufacturer’s instructions.
RNA sequencing (RNAseq) libraries were prepared from 4 µg of total RNA using the KAPA stranded mRNA-seq kit (Roche, KK8421) according to manufacturer’s specifications. 100 nM KAPA-single index adapters (Roche, KK8700) were added to A-tailed cDNA, and libraries were amplified for 10 cycles. Finally, 1x library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter, A63881). Library fragment size was assessed using Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). Each library was diluted to 4 nM and pooled for sequencing on an Illumina Hiseq4000, aiming at 15-20 million SE50 reads per sample (19 million reads on average).
SE50

value: mESC B6129S6F1 Tet1<tm1Koh>

value: mESC

value: WT


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06D]

description: sci-RNA-seq3 library


title: 15_13058NMS198.CEL

value: male


title: KO15 (timecourse) - day 4

value: Tet1 KO

value: day 4


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06G]

description: sci-RNA-seq3 library


title: E19, snRNAseq

description: 10X Genomics 3’ v3

value: Superior colliculus


title: WT7 (timecourse) - day3


title: KO15 (timecourse) - day 3

value: day 3


title: KO15 (timecourse) - day 2

value: day 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06A]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: Con_Veh_3

city: CHARLOTTESVILLE

first: Charles

last: Farber

state: VA

address: P.O. Box 800793, School of Medicine

institute: University of Virginia

data_processing:
Alignment with HISAT2
Assembly with StringTie
Assembly: mm10
Supplementary files format and content: Gene count matrix to input in DEseq2

source_name: primary calvarial osteoblast

extract_protocol:
QIAGEN RNeasy Kit
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc

value: primary calvarial osteoblast

value: adipogenic differentiation for 7 days and treated with Vehicle for 24 hours


title: Con_Veh_4


title: Con_Veh_2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05H]

description: sci-RNA-seq3 library


title: KO15 (timecourse) - day 1

value: day 1


title: 15_12950NMS198.CEL

value: multiple sclerosis

value: PBMC

value: female


title: 15_13053NMS198.CEL


title: 15_12871NMS198.CEL


title: KO1 (timecourse) - day 5

value: mESC B6129S6F1 Tet1<tm1Koh>

value: day 5


title: P4, snRNAseq

description: 10X Genomics 3’ v3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-06C]

description: sci-RNA-seq3 library


title: 15_11135RRMS198.CEL


title: 15_10818RRMS198.CEL


title: Con_PTH_4

value: adipogenic differentiation for 7 days and treated with PTH for 24 hours


title: KO1 (timecourse) - day 4

value: mESC


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05G]

description: sci-RNA-seq3 library


title: Con_PTH_3


title: KO1 (timecourse) - day 3

value: Tet1 KO


title: Con_Veh_1


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05D]

description: sci-RNA-seq3 library


title: 15_10204NMS198.CEL


title: KO1 (timecourse) - day 2


title: 14_9895NMS193.CEL


title: KO1 (timecourse) - day 1


title: Con_PTH_2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05C]

description: sci-RNA-seq3 library


title: 14_4918NMS193.CEL


title: WT34 - day 5

description:
antNPCs_F1Tm1_counts.csv
antNPCs_F1Tm1_TPM.csv

value: WT


title: WT34 - day 3


title: 14_8555RRMS193.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04G]

description: sci-RNA-seq3 library


title: WT7 - day 5


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04H]

description: sci-RNA-seq3 library


title: WT34 - day 0 (mESC)

value: day 0 (mESC)


title: PRDM6_CHIP_1

city: Chapel Hill

first: meng

last: zou

state: NC

address: 1521 E Franklin St, Apt C300

institute: UNC-CH

library_source: genomic

data_processing:
Reads with >50% low quality base (<20) and with greater than 15% uncalled bases (N) were removed.
Adapters were trimmed and resulting reads <18 bases were removed.
The remaining sequences were aligned to the mm10 reference genome using BWA (44) requiring a mapping quality of at least 13.
Initial peaks were called using MACS2 using matching input controls (p<0.001). Consistently called peaks across replicates were determined using the IDR method ranking peaks by p-value
Assembly: mm10
Supplementary files format and content: PRDM6_idr_peaks.sorted.narrowPeak
Supplementary files format and content: PRDM6_Peak__annotations

molecule: genomic DNA

source_name: Outflow tract smooth muscle cells

growth_protocol: DMEM:F12, 10% fetal bovine serum, 0.5% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After nuclei pellet and micrococcal nuclease digestion (0.5ul/IP), lysate was then sonicated as the cross-linked chromatin preparation with a final DNA length of ~150-900bp, following the instructions of Cell Signaling SimpleChIP Enzymatic Chromatin IP Kit
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library Prep Kit

treatment_protocol: Cells were infected with Lentivirus to overexpress FLAG-tagged PRDM6

value: Outflow tract smooth muscle cells

tag: chip antibody


title: 14_11431NMS193.CEL


title: 14_11532NMS193.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04F]

description: sci-RNA-seq3 library


title: Input_1


title: WT7 - day 0 (mESC)


title: 14_11362NMS193.CEL


title: Con_PTH_1


title: PRDM6_WT_AO_biolrep5

department: Pathology

data_processing:
Sequences were filtered using fastq_quality_filter (FASTX-Toolkit (RRID:SCR_005534)) requiring at least 90 percent of bases (-p 90) to have a minimum quality score of 20 (-q 20).
Adapter sequences were removed using tagdust  at false discovery rate (-f) of 0.001.
Sequences were aligned to the mm10 mouse reference genome and GENCODE version 20 gene annotation with STAR using default parameters, with an average of almost 95% of reads aligned.
Expression was quantified with rsem  using default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Ascending Aorta

extract_protocol:
Total RNA from each sample was isolated using the RNeasy UCP Micro kit (Qiagen) per   manufacturer’s instructions. Total RNA amounts in DA samples varied from 20~59 ng and in ascending aorta   samples from 94~210 ng.  manufacturer’s instructions. Total RNA amounts in DA samples varied from 20~59 ng and in ascending aorta   samples from 94~210 ng
 RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.
Low-input RNAseq

value: Ascending Aorta


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-05F]

description: sci-RNA-seq3 library

value: lymphoblast


title: KO15 - day 5


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04E]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: PRDM6_WT_AO_biolrep4


title: PRDM6_WT_AO_biolrep6


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04D]

description: sci-RNA-seq3 library


title: PRDM6_CHIP_2


title: KO15 - day 3

value: day 3


title: 14_10295NMS193.CEL


title: 14_10975RRMS193.CEL


title: Input_2


title: 14_10165NMS193.CEL


title: 14_427NMS193.CEL


title: KO15 - day 0 (mESC)


title: WT7 - day 3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04C]

description: sci-RNA-seq3 library


title: PRDM6_WT_AO_biolrep1


title: PRDM6_WT_AO_biolrep2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-04B]

description: sci-RNA-seq3 library


title: 13_9928BASL180.CEL


title: KO1 - day 3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03H]

description: sci-RNA-seq3 library


title: PRDM6_WT_DA_biolrep7

source_name: Ductus Arteriosus

value: Ductus Arteriosus


title: KO1 - day 0 (mESC)


title: PRDM6_WT_DA_biolrep6


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03F]

description: sci-RNA-seq3 library


title: PRDM6_WT_DA_biolrep5


title: 13_9974BASL180.CEL


title: G46

city: Bronx

first: Wenge

state: NY

address: 1300 Morris Park Avenue

department: Medicine

institute: Albert Einstein College of Medicine

description: Ppargc1a -/-

data_processing:
Cell Ranger pipeline v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format

source_name: Intestinal epithelial cells

growth_protocol: Ppargc1aF/+, Lgr5GFP-creERT, ROSA26TOM or Ppargc1aF/F, Lgr5GFP-creERT, ROSA26TOM mice grow under standard condition

extract_protocol: not provided

treatment_protocol: After weaning, mice were fed with AIN for 3 months and subject to scRNAseq examination. For deletion of Ppargc1a gene, tamoxifen was given i.p. at 75 mg/kg. After 3 days of tamoxifen injection, mice were sacrificed for scRNAseq preperation.

value: Ppargc1aF/F, Lgr5GFP-creERT, ROSA26TOM

value: Intestinal epithelial cells

tag: cell markers

value: Epcam +, Cd45 -


title: 13_9829BASL180.CEL

value: multiple sclerosis

value: PBMC

value: female


title: PRDM6_WT_AO_biolrep3


title: G37

description: Ppargc1a -/-


title: PRDM6_WT_DA_biolrep4


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03E]

description: sci-RNA-seq3 library


title: 13_10288BASL180.CEL


title: 13_9876BASL180.CEL


title: PRDM6_WT_DA_biolrep3


title: KO1 - day 5

value: mESC B6129S6F1 Tet1<tm1Koh>

value: day 5


title: 13_10035BASL180.CEL

value: male


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03D]

description: sci-RNA-seq3 library


title: G33

description: Ppargc1a -/-


title: 13_10237BASL180.CEL


title: 13_10215BASL180.CEL


title: G47

description: Ppargc1a +/-

value: Ppargc1aF/+, Lgr5GFP-creERT, ROSA26TOM


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03C]

description: sci-RNA-seq3 library


title: PRDM6_WT_DA_biolrep2


title: G34

description: Ppargc1a +/-


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03B]

description: sci-RNA-seq3 library


title: 13_10034BASL180.CEL


title: PRDM6_WT_DA_biolrep1


title: G32

description: Ppargc1a +/-


title: PRDM6_KO_AO_biolrep5


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-03A]

description: sci-RNA-seq3 library


title: 12_9749BASL178.CEL


title: k67

data_processing:
Cell Ranger pipeline v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tar archive of Cell Ranger output: barcodes, features, matrix

source_name: intestinal epithelial cells

growth_protocol: After weaning, mice were fed with AIN or NWD1 for 3 months.

extract_protocol:
our FACS protocol has been described in detail in Li et al, (2019) Carcinogenesis 40:937
Our single cell RNAseq (scRNAseq) libraries were made according to the manufacturer’s protocol for Chromium Next GEM (gel beads in emulsion) single cell 3’ kit (10X Genomics)

treatment_protocol: Dedifferention of Bmi1 cells was induced by 100 ul inraperitoneal injection of 1 mg freshly prepared tamoxifen(TAM) in corn oil. The animals were sacrified 3 days (short term, ST) or 70 days (long term, LT) after TAM injection.

value: intestinal epithelial cells

tag: cell isolation markers

value: Epcam +, Cd45 - , Tomato +


title: PRDM6_KO_AO_biolrep4

value: Ascending Aorta


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02H]

description: sci-RNA-seq3 library

value: lymphoblast


title: k16


title: 12_9753BASL178.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02G]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: k19


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02F]

description: sci-RNA-seq3 library


title: PRDM6_KO_AO_biolrep3


title: k17


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02E]

description: sci-RNA-seq3 library


title: PRDM6_KO_AO_biolrep1


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02D]

description: sci-RNA-seq3 library


title: 12_9411BASL178.CEL


title: k21


title: PRDM6_KO_DA_biolrep7


title: J40


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02C]

description: sci-RNA-seq3 library


title: 12_9228BASL178.CEL


title: k20


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02B]

description: sci-RNA-seq3 library


title: PRDM6_KO_DA_biolrep5


title: PRDM6_KO_DA_biolrep4


title: PRDM6_KO_AO_biolrep2


title: I36

data_processing:
sequences were trimed and aligned to mm9 refseq using STAR (v.2.4.2a), annotated using gencode ENSEMBL transcript annotations (vM1)
The number of reads aligned to each defined gene was quantified using HTSeq-count (v0.6.1)
Transcripts per million (TPM) was used as the expression quantification method.
Genome_build: mm9
Supplementary_files_format_and_content: TPM

source_name: intestinal stem cells

growth_protocol: Lgr5EGFPcreERT2 mice grown under standard conditions

extract_protocol:
high quality RNA (1-10ng, RIN >=9) were extracted from FACS purified ISCs (Ref: Li et al, (2019) Carcinogenesis 40:937)
RNAs were converted to cDNAs using SMARt-Seq v4 ultra low input RNA kit (Takara), RNAseq libraries were constructed using Nextera XT kit (Illumina). Ref: Li et al, (2019) Carcinogenesis 40:937

treatment_protocol: After weaning, Lgr5EGFPcreERT2 mice were fed with AIN or NWD1 for 3 or 12 months and subjected to RNAseq examination. For Crossover experiments, after 3 months feeding of NWD1, the diet was switched to AIN, and mice were examined in 6 months or 12 months.

value: CO, 12 months

value: ISCs

tag: cell marker

value: Lgr5 (the definitive stem cell marker of ISCs)


title: J30


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01H]

description: sci-RNA-seq3 library


title: 12_105691Y178.CEL


title: PRDM6_KO_DA_biolrep2

value: Ductus Arteriosus


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-02A]

description: sci-RNA-seq3 library


title: I34


title: 12_104281Y178.CEL


title: 12_9340BASL178.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01G]

description: sci-RNA-seq3 library


title: 12_105501Y178.CEL


title: 12_104341Y178.CEL


title: I31


title: PRDM6_KO_DA_biolrep6


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01F]

description: sci-RNA-seq3 library


title: PRDM6_KO_DA_biolrep1


title: I26


title: 12_103981Y178.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01E]

description: sci-RNA-seq3 library


title: 11_9085BASL177.CEL


title: 11_9244BASL177.CEL


title: I22


title: Astro-01Gy-24h-n4

city: Koeln

first: Christine

middle: Elisabeth

last: Hellweg

state: Nordrhein-Westfalen

address: Linder Hoehe

department: r, IInstitute of Aerospace Medicine

country: Germany

institute: German Aerospace Center

data_processing:
trimming by GENEWIZ
mapping by GENEWIZ
differential gene expression by GENEWIZ
Assembly: mm10
Supplementary files format and content: tab-delimited text files include GeneID,  Chr, Start, End, Strand, Length for each Sample

source_name: brain cortex

growth_protocol: Primary murine astrocytes were seeded in cell culture dishes (6 cm) at a density of 2 x 10e4 cells/cm2.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen). At least 3 µg total RNA per sample (4 biological repeats per condition) were sent on dry ice to GENEWIZ (Leipzig, Germany) for mRNA sequencing in the same run after Poly(A) selection using the Illumina NovaSeq6000 platform (configuration: 2x150 bp, 350M read pairs)
RNA libraries for RNA-seq were prepared by GENEWIZ.

treatment_protocol: Three days after seeding, cells were irradiated with 0, 0.1 and 2 Gy of X-rays (200 kV, X-ray source RS225, Gulmay Medical, now: X-Strahl, Surrey, UK) at a dose rate of 1 Gy/min and room temperature, at DLR, Cologne

value: brain cortex

value: primary astrocytes

value: wild type

value: X-rays exposure (0.1 Gy), Replicate 4

tag: time


title: Astro-2Gy-24h-n4

value: X-rays exposure (2 Gy), Replicate 4


title: 11_8900BASL177.CEL

value: multiple sclerosis

value: PBMC

value: female


title: 11_8633BASL177.CEL

value: male


title: 12_103741Y178.CEL


title: Astro-0Gy-24h-n4

value: X-rays exposure (0 Gy), Replicate 4


title: Astro-2Gy-24h-n3

value: X-rays exposure (2 Gy), Replicate 3


title: I38

value: CO, 6 months


title: I40


title: Astro-01Gy-24h-n3

value: X-rays exposure (0.1 Gy), Replicate 3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01A]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: 11_8503BASL177.CEL


title: I44

value: ISCs

value: Lgr5 (the definitive stem cell marker of ISCs)


title: I41


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12H]

description: sci-RNA-seq3 library


title: 11_8615BASL177.CEL


title: Astro-2Gy-24h-n2

value: brain cortex

value: X-rays exposure (2 Gy), Replicate 2


title: Astro-0Gy-24h-n3

value: primary astrocytes

value: wild type

value: X-rays exposure (0 Gy), Replicate 3


title: 11_8485BASL177.CEL

value: multiple sclerosis


title: I37


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12G]

description: sci-RNA-seq3 library


title: Astro-01Gy-24h-n2

value: X-rays exposure (0.1 Gy), Replicate 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12F]

description: sci-RNA-seq3 library


title: Astro-0Gy-24h-n2

value: X-rays exposure (0 Gy), Replicate 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12E]

description: sci-RNA-seq3 library


title: 11_8240BASL177.CEL

value: PBMC

value: male


title: 10_9183BASL175.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01B]

description: sci-RNA-seq3 library


title: I45

value: NWD1, 12 months


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_2_P1-01C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12D]

description: sci-RNA-seq3 library


title: H71


title: Astro-2Gy-24h-n1

value: X-rays exposure (2 Gy), Replicate 1


title: 10_9174BASL175.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12C]

description: sci-RNA-seq3 library


title: L7

value: NWD1, 3 months


title: L15


title: Astro-0Gy-24h-n1

value: X-rays exposure (0 Gy), Replicate 1


title: 10_9150BASL175.CEL

value: female


title: Astro-2Gy-6h-n4

value: X-rays exposure (2 Gy), Replicate 4

value: 6 h


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12B]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: 10_9005BASL175.CEL


title: L6

value: ISCs

value: Lgr5 (the definitive stem cell marker of ISCs)


title: 10_103351Y175.CEL


title: I20


title: L4


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11H]

description: sci-RNA-seq3 library


title: 11_8362BASL177.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11G]

description: sci-RNA-seq3 library


title: Astro-2Gy-6h-n3

value: brain cortex

value: primary astrocytes

value: wild type

value: X-rays exposure (2 Gy), Replicate 3


title: Astro-0Gy-6h-n4

value: X-rays exposure (0 Gy), Replicate 4


title: Astro-01Gy-6h-n4

value: X-rays exposure (0.1 Gy), Replicate 4


title: L2


title: 10_103231Y175.CEL

value: multiple sclerosis

value: PBMC

value: male


title: Astro-01Gy-24h-n1

value: X-rays exposure (0.1 Gy), Replicate 1


title: H68

value: AIN, 12 months


title: 10_103221Y175.CEL

value: female


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11F]

description: sci-RNA-seq3 library


title: I23


title: Astro-01Gy-6h-n3

value: X-rays exposure (0.1 Gy), Replicate 3

value: 6 h


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-12A]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: I14

value: ISCs

value: Lgr5 (the definitive stem cell marker of ISCs)


title: Astro-2Gy-6h-n2

value: brain cortex

value: primary astrocytes

value: X-rays exposure (2 Gy), Replicate 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11D]

description: sci-RNA-seq3 library


title: I9


title: 9_8675BASL172.CEL


title: 10_102911Y175.CEL


title: 9_8674BASL172.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11C]

description: sci-RNA-seq3 library


title: Astro-01Gy-6h-n2

value: wild type

value: X-rays exposure (0.1 Gy), Replicate 2


title: 9_8667BASL172.CEL

value: multiple sclerosis


title: L1

value: AIN, 3 months


title: 9_8669BASL172.CEL

value: PBMC


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11B]

description: sci-RNA-seq3 library


title: Astro-0Gy-6h-n2

value: X-rays exposure (0 Gy), Replicate 2


title: Astro-2Gy-6h-n1

value: X-rays exposure (2 Gy), Replicate 1


title: J15


title: J17


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11A]

description: sci-RNA-seq3 library


title: 9_8660BASL172.CEL

value: male


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10H]

description: sci-RNA-seq3 library


title: Astro-01Gy-6h-n1

value: X-rays exposure (0.1 Gy), Replicate 1


title: Astro-0Gy-6h-n3

value: X-rays exposure (0 Gy), Replicate 3

value: 6 h


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-11E]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: 9_8656BASL172.CEL

value: female


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10G]

description: sci-RNA-seq3 library


title: 8_9227SP163.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10F]

description: sci-RNA-seq3 library


title: Astro-0Gy-6h-n1

value: brain cortex

value: X-rays exposure (0 Gy), Replicate 1


title: 9_8652BASL172.CEL


title: acd6-3flk-5 rep3

city: Baltimore

first: HUA

last: LU

state: MD

address: 1000 Hilltop Circle

department: Biology

institute: University of Maryland Baltimore County

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Quantification: Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis: A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology (GO) annotates genes to biological processes, molecular functions, and cellular components in a directed acyclic graph structure, and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotates genes to pathway.
Genome_build: Reference genome (TAIR10) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Supplementary_files_format_and_content: excel with RPKM values for each gene.

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Plants were grown in growth chambers with a light intensity at 180 µmol m−2 s−1, 60% humidity and 22°C either in 12 h light/12 h dark (LD) cycle.

extract_protocol:
Total RNA extraction with TRIzol solution
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: whole plants

tag: age

value: 25 day old

value: mutant


title: 10x - CM69 - day5

description:
10xGenomics
antNPC.MNN.KOvsCMvsWT.rds

data_processing:
Reads were processed and aligned using Cell Ranger (v3.0.2) against mm10. Count matrix was imported in Seurat (v4.0.1) (Hao et al., 2021). Cells were selected which have 2000 to 8000 detected features per cell and a mitochondrial content between 1 and 10% as good quality cells. The cells are normalized per sample using the NormalizeData function in Seurat, using the “LogNormalize” method and a scaling factor of a 1000. The samples are integrated using the “fastMNN” method. The first 50 dimensions from the MNN reduction was used to determine the UMAP reduction and find clusters. These clusters were used in the “findAllMarkers” function to find genes that are differentially expressed between clusters. SingleR (v1.4.1) was used to annotate cell types using the mouse gastrulation dataset reference (Aran et al., 2019; Pijuan-Sala et al., 2019). pySCENIC (v 0.11.2) was used to determine regulon activity per cell using normalized count matrix (Kumar et al., 2021). The Seurat function “findAllMarkers” with the “wilcox” test was used to determine differential regulon activity.
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes files
Supplementary files format and content: Tab-separated feature files
Supplementary files format and content: Tab-separated matrix files
Supplementary files format and content: .rds file containing seurat object per sample
Supplementary files format and content: .rds file containing integrated seurat object day 3 + day 5 KOvsWT
Supplementary files format and content: .rds file containing integrated seurat object day 5 KOvsWT with different treatments
Supplementary files format and content: .rds file containing integrated seurat object day 5 KOvsCMvsWT with different treatments

source_name: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

extract_protocol:
For library preparations, cells were washed with PBS and incubated for 5 minutes with TrypLE, which was subsequently quenched with advanced DMEM/F12. Single cells were washed 3x with 0.4% BSA in PBS. Cells were counted using the LUNA counter and an AO/PI fluorescent stain.
Cells were loaded to target 5000 following the 10xGenomics protocol for single cell 3’ prime reagent kit v3.1 (single indexes). Quality control was performed and pooled according to instructions and sequenced following the 10xGenomics guidelines at 28-8-0-91 on a NovaSeq 6000 Instrument. First a shallow sequencing run was performed to perform quality control on the libraries and estimate the number of captured cells, followed by a deeper sequencing run to reach a mean of 20,000 reads per cell. In total we captured 54708 high quality cells after filtering, with on average 5471 cells per sample.

value: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

value: mESC

value: Tet1 MUT

value: day 5


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10E]

description: sci-RNA-seq3 library


title: 10x - WT70 - day5

description:
10xGenomics
antNPC.MNN.KOvsCMvsWT.rds

value: mESC B6129S6F1 Tet1<tm1Koh>

value: WT


title: acd6-3 rep3

tag: strain


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10D]

description: sci-RNA-seq3 library


title: 8_8620SP163.CEL

value: multiple sclerosis

value: PBMC

value: male


title: flk-5 rep3


title: 8_8612SP163.CEL


title: 10x - KO1 - day5 + SB

description:
10xGenomics
antNPC.MNN.treatment.rds

value: Tet1 KO

value: day 5 + SB


title: 10x - WT7 - day5 + SB

description:
10xGenomics
antNPC.MNN.treatment.rds


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10C]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10B]

description: sci-RNA-seq3 library


title: J11

value: AIN, 3 months

value: ISCs

value: Lgr5 (the definitive stem cell marker of ISCs)


title: Col-0 rep3

value: whole plants

value: 25 day old

value: mutant


title: flk-3 rep3


title: acd6-1flk-1 rep2


title: 10x - WT7 - day5 + XAV

description:
10xGenomics
antNPC.MNN.treatment.rds

value: mESC

value: day 5 + XAV


title: 8_8591SP163.CEL

value: female


title: acd6-3flk-3 rep3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-10A]

description: sci-RNA-seq3 library


title: 8_8611SP163.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09H]

description: sci-RNA-seq3 library


title: 10x - KO1 - day5

description:
10xGenomics
antNPC.MNN.KOvsWT.rds
antNPC.MNN.treatment.rds
antNPC.MNN.KOvsCMvsWT.rds

value: mESC B6129S6F1 Tet1<tm1Koh>

value: day 5


title: acd6-1 rep2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09G]

description: sci-RNA-seq3 library


title: 8_8164RR163.CEL

value: multiple sclerosis

value: PBMC


title: flk-5 rep2


title: 8_8617SP163.CEL

value: male


title: 10x - WT7 - day5

value: WT


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09F]

description: sci-RNA-seq3 library

value: lymphoblast


title: 8_2867SP163.CEL


title: flk-1 rep2


title: 10x - KO1 - day3

description:
10xGenomics
antNPC.MNN.KOvsWT.rds

value: Tet1 KO

value: day 3


title: 7_9229SP162.CEL


title: 7_9239SP162.CEL


title: 10x - KO1 - day5 + XAV

description:
10xGenomics
antNPC.MNN.treatment.rds


title: Col-0 rep2


title: 7_8509RR162.CEL


title: 10x - WT7 - day3

description:
10xGenomics
antNPC.MNN.KOvsWT.rds


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09D]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: oxBS - WT72 - day 2

description:
oxBS_d2_WT.deduplicated.sorted.meth
WT_d2_oxBS.bw
d2_WT.5mC.bw
d2_WT.5hmC.bw
oxBS_d2.overlap.hyperDMR.bed
oxBS_d2.overlap.hyperDMR.CpGi.bed
oxBS_d2.overlap.hyperDMR.inter.bed
oxBS_d2_KOvsWT.hypoDMR.filt.bed

data_processing:
Using Cutadapt (v3.7), reads were first trimmed based on quality (PHRED < 20) . Custom adapters were removed in paired end mode (“-a AGATCGGAAGAGC -A AAATCAAAAAAAC”) and only reads with al minimum length of 15 bp were kept. Using Bismark (v0.23.1), the trimmed reads were aligned to GENCODE mm10 GRCm38.p6 with a maximal insert size of 500 bp , followed by deduplication and methylation extraction. Using a custom script the CpG counts were merged to one strand and made in to a file format which can be used in methPipe software (Song et al., 2013). For DMR analysis methylation calls for replicates were merged together. On average we detected 19047561 CpGs with a coverage > 5x in merged replicates. To find differentially methylated regions (DMRs), first lowly methylated regions were determined for each sample using the hmr program which uses a hidden Markov model approach, and a differential methylation score for each CpG between samples was calculated using the methdiff program. Using the dmr program, hypo methylated regions and differential CpGs were combined to form DMRs with minimally 2 differential CpGs per DMR. DMRs were annotated using AnnotatR (v1.16.0) and ChIPseeker (v1.26.2) packages in R (v4.0.5) using UCSC gene feature and CpG island (CpGi) locations. A DMR was considered to be a “CpG island associated DMR” if the DMR was within 4 kb (CpGi shore + shelf) of a CpGi. DMR subsets were made using bedtools intersect (v2.30.0). Genes were associated with DMRs using the rGREAT (v1.22.0) package. A DMR was considered to be associated with a bivalent domain (which contains both a H3K27me3 and H3K4me3 peak in mouse ESCs) if it was within 3 kb. A gene was considered to be associated with a DMR if the transcription start site was within 10 kb. GO term enrichment was performed using Cluster Profiler (v3.18.1). 5hmC rate was calculated by subtracting oxBS methylation rate (true 5mC) from regular BS methylation rate (5mC + 5hmC) for CpGs which in both datasets had at least a coverage of 5x, while for 5mC CpGs with a 5x coverage in oxBS dataset were used. Profile plots were made using DeepTools (v3.4.3).
Assembly: mm10
Supplementary files format and content: .meth files of individual samples
Supplementary files format and content: .meth files of pooled samples, used to define DMRs
Supplementary files format and content: bigwig files of CpG methylation of individual samples
Supplementary files format and content: bigwig files of CpG methylation of pooled samples
Supplementary files format and content: bigwig files with true 5mC
Supplementary files format and content: bigwig files with 5hmC
Supplementary files format and content: bed file with hyperDMRs (not split)
Supplementary files format and content: bed file with hyperDMRs associated with CpGi
Supplementary files format and content: bed file with hyperDMRs not associated with CpGi
Supplementary files format and content: bed file with hypoDMRs

extract_protocol:
Genomic DNA was extracted from minimally 106 cells using the Purelink genomic DNA Mini Kit (Invitrogen, K182001), according to the manufacturer’s instructions. The quality of the gDNA was assessed using Nanodrop and absence of RNA contamination was checked by running the samples on a 0.8% agarose gel stained with SYBER Safe. Per sample, 1.5 µg of gDNA in a total volume of 50 µl was sheared using COVARIS M220 for 2 x 60 seconds with at an intensity of 5 at 7 °C followed by a 1.8x clean-up using AMPure XP beads (Beckman Coulter, A63881) to concentrate fragmented DNA. Fragmentation was assessed Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854).
Libraries were made and (oxidative) bisulfite converted using the Ultralow Methyl-Seq kit (Tecan/Nugen), according to the manufacturer’s instructions. For BS and oxBS, libraries were made in parallel starting from the same fragmented gDNA., with the only difference being that the For each library, 300 ng of fragmented gDNA was used as input and fragments were end repaired and ligated to single-indexed sequencing adapters provided in the kit, followed by final repair. Before oxidation and bisulfite conversion, libraries were purified and washed 3x with 80% acetonitrile to get rid of any residual ethanol, followed by incubation at 37 ºC for 5 minutes with denaturing buffer provided with the kit to denature the DNA. oxBS libraries were oxidized by addition of TrueMethyl oxidation solution while BS libraries were mock treated using ultra-pure water during an incubation at 40 ºC for 10 minutes. For each library, the optimal amplification was optimized using qPCR; 1/6th of the libraries was added to amplification master mix containing SYBR Green and run on a Applied Biosystems StepOnePlus Real-Time PCR system  for 30 cycles. Relative log-fluorescence vs amplification cycle was plotted out to manually determine the appropriate amplification cycles. The number of cycles was selected within the middle to late exponential phase of amplification. The BS libraries were amplified between 7 to 12 cycles, while oxBS libraries were amplified between 10 to 15 cycles. Following amplification, bisulfite converted libraries were purified finally with a 1x cleanup using AMPure XP beads. The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). The libraries were first sequenced shallow to estimate library quality, bisulfite conversion efficiency, and duplicate rate, followed by multiple deep sequencing PE150 runs to obtain an average coverage of 5x per library. For sequencing the custom sequencing primer MetSeq Primer 1 was used, as per manufacturer specification.
oxWGBS
PE150

value: day 2

tag: molecule type

value: oxBS DNA


title: acd6-1flk-1 rep1

tag: tissue

value: whole plants

value: 25 day old


title: acd6-1flk-5 rep1

value: mutant


title: oxBS - WT70 - day 2


title: 7_8500RR162.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09B]

description: sci-RNA-seq3 library

tag: cell line


title: oxBS - WT34 - day 5 + XAV

description:
oxBS_d5_XAV_WT.deduplicated.sorted.meth
WT_d5_X_oxBS.bw
oxBS_d5_XAV_KOvsWT.hyperDMR.filt.bed
oxBS.d5_XAV.KOvsWT.hyperDMR.CpGi.bed
oxBS.d5_XAV.KOvsWT.hyperDMR.inter.bed

tag: cell type

value: day 5 + XAV


title: flk-5 rep1


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09A]

description: sci-RNA-seq3 library

tag: treatment


title: acd6-1 rep1


title: 7_8477RR162.CEL

tag: patient diagnosis

value: female


title: 6_9521MS161.CEL

tag: age(years)


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08G]

description: sci-RNA-seq3 library


title: flk-1 rep1

value: wild type


title: Col-0 rep1


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09E]

description: sci-RNA-seq3 library


title: 6_9484MS161.CEL

tag: gender


title: 6_9513NMS161.CEL

tag: batch number


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-09C]

description: sci-RNA-seq3 library


title: oxBS - KO15 - day 5 + XAV

description:
oxBS_d5_XAV_KO.deduplicated.sorted.meth
KO_d5_X_oxBS.bw
oxBS_d5_XAV_KOvsWT.hyperDMR.filt.bed
oxBS.d5_XAV.KOvsWT.hyperDMR.CpGi.bed
oxBS.d5_XAV.KOvsWT.hyperDMR.inter.bed

value: mESC B6129S6F1 Tet1<tm1Koh>

tag: genotype

value: KO


title: oxBS - WT7 - day 5 + XAV


title: Rat lung tissue-BLM-2

city: shanghai

first: Xiucheng

last: Liu

address: zhengmin road 557

institute: Shanghai pulmonary hospital

data_processing:
Firstly, we calculated a spearman coefficient for single cell and then performed correlation analysis on highly variable genes among cell types in the reference data set. Multiple correlation coefficients were made per cell type according to the named annotations of the reference data set and aggregated to provide a single value per cell type per single cell. Secondly, the least relevant cell types (or values more than 0.05 below the top value) were successively removed, and this action was repeated until annotation of the target cells was achieved.
The Wilcoxon rank sum test was performed to determine genes differentially expressed between clusters. Differentially expressed genes were scored by group one vs. the remainder. Genes that were specifically and highly expressed (logFC > 0.25) and expressed in at least 20% of cells were considered to be ideal marker genes for each cluster.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: lung tissue

extract_protocol:
Rat lungs were harvested and 3 mm3 lung tissues were taken for digestion to generate single-cell suspensions.
Sequencing libraries were quantified using a high sensitivity DNA chip on a Bioanalyzer 2100 and the qubit high sensitivity DNA assay. The libraries were sequenced on NovaSeq6000 (Illumina) using 2 × 150 chemistry.

treatment_protocol: After adequate anesthesia, BLMwas administered by oral tracheal intubation via a 16-gauge catheter. One dose of BLM (5 mg/kg, the BLM-treated group) or an equal volume of saline was administered via the catheter. The rats were rotated immediately after instillation to ensure thorough drug distribution in the lungs. All rats were killed by cervical dislocation and lungs were harvested 28 days after intratracheal BLM or saline treatment. Rat lungs were harvested and 3 mm3 lung tissues were taken for digestion to generate single-cell suspensions.Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a microwell. Whole transcriptome libraries were prepared using the BD Rhapsody system (BD Bio_x0002_sciences).

value: Lung

value: bleomycin


title: oxBS - KO1 - day 2

description:
oxBS_d2_KO.deduplicated.sorted.meth
KO_d2_oxBS.bw
d2_KO.5mC.bw
d2_KO.5hmC.bw
oxBS_d2.overlap.hyperDMR.bed
oxBS_d2.overlap.hyperDMR.CpGi.bed
oxBS_d2.overlap.hyperDMR.inter.bed
oxBS_d2_KOvsWT.hypoDMR.filt.bed


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08F]

description: sci-RNA-seq3 library


title: 7_8480SP162.CEL

value: multiple sclerosis

value: PBMC


title: 6_9213MS161.CEL

value: male


title: 6_9240MS161.CEL


title: Rat lung tissue-BLM-1


title: 6_8641NMS161.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08C]

description: sci-RNA-seq3 library

value: lymphoblast


title: oxBS - KO15 - day 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08H]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: oxBS - CM59 - day 2

description:
oxBS_d2_CM.deduplicated.sorted.meth
CM_d2_oxBS.bw
d2_CM.5mC.bw
d2_CM.5hmC.bw
oxBS_d2.overlap.hyperDMR.bed
oxBS_d2.overlap.hyperDMR.CpGi.bed
oxBS_d2.overlap.hyperDMR.inter.bed

value: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

value: MUT

value: day 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08B]

description: sci-RNA-seq3 library


title: Rat lung tissue-BLM-3


title: Rat lung tissue-Control-2

value: saline


title: Rat lung tissue-Control-3


title: BS - WT72 - day 2

description:
BS_d2_WT.deduplicated.sorted.meth
WT_d2_BS.bw
d2_WT.5mC.bw
d2_WT.5hmC.bw

value: WT

value: BS DNA


title: 5_8668NMS157.CEL

value: female


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08A]

description: sci-RNA-seq3 library


title: oxBS - CM69 - day 2

value: oxBS DNA


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07H]

description: sci-RNA-seq3 library


title: BS - WT70 - day 2

value: mESC B6129S6F1 Tet1<tm1Koh>


title: 5_8173RR157.CEL


title: Rat lung tissue-Control-1


title: 5_8071RR157.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08E]

description: sci-RNA-seq3 library


title: BS - KO15 - day 2

description:
BS_d2_KO.deduplicated.sorted.meth
KO_d2_BS.bw
d2_KO.5mC.bw
d2_KO.5hmC.bw

value: KO


title: BS - CM69 - day 2

description:
BS_d2_CM.deduplicated.sorted.meth
CM_d2_BS.bw
d2_CM.5mC.bw
d2_CM.5hmC.bw


title: 5_582CIS157.CEL


title: 5_600CIS157.CEL


title: NHF1_UVC80J

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Base calling by Rapid Genomics
Fastq files were separated into individual libraries using custom barcodes/indices. The resulting fastq files were uploaded as the raw sequencing data for each experiment.
Fastq files were aligned to the human genome (hg19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy; i.e., TT, TC, CT, CC) were retained in BED files using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools or custom perl scripts
Assembly: hg19
Supplementary files format and content: WIG files containing counts of CPD-capture-seq damage reads filtered for only dipyrimidine mapping sequences (dipy files).
Library strategy: CPD-capture-seq

source_name: NHF1 genomic DNA

growth_protocol: Telomerase-immortalized normal human fibroblast (NHF1) cells were grown in 10 cm plates to confluence in Dulbecco's  modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) at 37 C and 5% CO2. Primary melanocytes were grown to confluence using Melanocyte culture medium (LL-0027, Lifeline cell technology) at 37C and 5%CO2.

extract_protocol:
NHF1 or primary melanocyte genomic DNA was isolated with GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer’s manual. Cells used for naked DNA samples were cultured and DNA isolated as previously described, excluding the UV exposure. Following genomic DNA isolation, samples were pipetted onto a microscope cover slip in 10µL aliquots, and exposed to UV irradiation. The genomic DNA from NHF1 cells were exposed to either 80J/m2 UVC or 500J/m2 UVB and the DNA from primary melanocytes were exposed to 400J/m2 UVC or 2500J/m2 UVB. Library preparation then continued as described, resuming at sonication.
CPD-capture-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our recently published CPD-seq protocol (Methods in Molecular Biology 2020, 2175, 79-94). Briefly, sonicated DNA fragments were ligated to a double-stranded adaptor DNA F1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-GTP.  CPD lesions were cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to biotin labelled second adapter, S2.   The single stranded DNA was purified with streptavidin beads and final PCR was done for upto 6 cycles with F1 primer and different barcoded RAPID primers ( RAPID 1:TAGAACAC; RAPID 2: GAGCCAAT; RAPID3: CAGATCTG; RAPID 4:TGTGAAGA; RAPID 5:ACAGTGGT; RAPID 6:TGAACTGG; RAPID 7:TCTACGAC; RAPID 8:GCAATCCG; RAPID9:TCCGTCTT; RAPID 10:TCAGGAGG) to generate libraries for different  samples. The resulting DNA libraries were used for DNA sequencing. CPD-seq library fragments were captured for selected genomic regions (~4000 regions, including recurrent mutations in melanoma, ETS binding sites, etc.) by the company RAPID Genomics prior to sequencing.

treatment_protocol: The medium was removed from confluent NHF1 cells and  the cells were washed with PBS. The cells were layered with 2mL PBS and were exposed to 100J/m2 UVC or 500J/m2 UVB  light. Cells were then treated with trypsin to digest cell adhesions,neutralized with DMEM+10% FBS, and transferred to a 15mL conical tube and pelleted at 400xg for 4 minutes. Same for confluent primary melanocytes, except the doses were 500J/m2 UVC or 2,500 J/m2 UVB.

value: NHF1 genomic DNA

value: UVC irradiated 80 J/m2

tag: repair time


title: BS - KO1 - day 2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07E]

description: sci-RNA-seq3 library


title: NHF1_UVB500J

value: UVB irradiated 500 J/m2


title: NHF1_UVC0h

source_name: NHF1 cells

value: NHF1 cells

value: UVC irradiated 100 J/m2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07D]

description: sci-RNA-seq3 library

value: lymphoblast


title: 5_2115RR157.CEL

value: multiple sclerosis

value: PBMC

value: male


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07F]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: NHF1_UVB0hr


title: NHF1_NoUV


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07C]

description: sci-RNA-seq3 library


title: E4-C39

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

data_processing:
Sequencing was carried out on Paired End 100b reads of Illumina NovaSeq.Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.  Fastq were generated with bcl2fastq (2.17).
The reads were first trimmed for adapters and low-quality ends by the TrimGalore! Algorithm (-- t, -q, -e, -- length 20) available on the Galaxy web server (https://usegalaxy.org/). Reads were then aligned onto the mouse genome (mm10) by bowtie2 (-- fr, --no-mixed, --no-discordant, -- sensitive)
.bam files containing aligned reads were further processed by the featureCounts tool (-B, -C, -O) (Lio et al., 2013) to evaluate gene expression levels using the mus_musculus. GRCm38.98 Ensembl version of genes’ annotations was used.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files that includes  the number of reads aligned on Ensembl GRCm38.98 annotated genes.

source_name: carotid artery

extract_protocol:
RNA was isolated from carotid arteries through the phenol-chloroform method using TRIzol (Ambion) reagent. The resulting RNA quality was determined using a Fragment Analyzer Instrument and all samples had RNA integrity numbers above 7.4.
RNA sequencing libraries were prepared according to Illumina's protocols using the Illumina Illumina TruSeq Stranded mRNA kit (ref #20020595). Eleven cycles of PCR were applied to amplify the libraries. Library quality was assessed using a Fragment Analyzer Instrument and libraries were quantified by QPCR using the kit KAPA KK4824, on the QuantStudio 6 of Thermo Fisher Scientific. Sequencing was performed in paired-end (2x150 pb) on an Illumina NovaSeq sequencer at the Integragen company platform

value: Placebo

value: carotid artery

value: 9 weeks


title: E4-C38


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07B]

description: sci-RNA-seq3 library

data_processing:
For the sci-RNA-seq3 transcriptome libraries, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. Reads were filtered based on RT and ligation index, by allowing <2 hamming distance from reference. Filtered reads were trimmed with TrimGalore (v0.6.6) with parameters: -a AAAAAAAA --three_prime_clip_R1 1. Reads were then aligned to the GRCh38 reference genome using STAR (v2.7.6a). PCR duplicates were collapsed using the RT index, ligation index, UMI sequence and end coordinate of reads. Reads were further demultiplexed based on the combination of the RT, ligation and PCR index and split into files for individual cells. To generate gene expression count matrices, reads were assigned to the exonic and intronic region of closest genes with HTseq (v.2.0.2). Reads with ambiguous assignments were discarded. Cells were further filtered based on total UMI (> 100) and mitochondrial reads percentage (<10%). Cells with the number of features detected between 10% and 90% percentile of all cells were kept and considered high-quality cells. The single cell analysis was performed using the Seurat (v4.0.0) package in R.
For capture libraries of the synHEK3 and shRNA constructs, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. A custom script was used to further demultiplex and filter the synHEK3 and shRNA libraries based on the combination of RT, ligation and PCR index (cell ID), by allowing <2 hamming distance from reference. For the synHEK3 library, reporter barcodes (<2 hamming distance to the reference barcode set), prime editing outcomes and read UMIs were extracted. For the shRNA library, shRNA sequences (<2 hamming distance to the reference barcode set) and read UMIs were extracted. UMIs <3 hamming distance were collapsed.   A series of pre-processing steps were applied to the data. 1) We matched cell IDs between the sci-RNA-seq3 transcriptome libraries and the capture libraries, and only kept high-quality cells (number of features between 10% and 90% percentile). 2) For the shRNA library, cells with <3 or >200 UMIs or >20 shRNA were removed. 3) For the synHEK3 library, cells with <4 UMIs were first removed. We counted UMIs for synHEK3 reporters belonging to the two clones and calculated a clone UMI/total UMI ratio. If the ratio was >80% for a specific clone, the cell is assigned to the corresponding clone. Cells with extremely high UMIs (cutoff between 100 and 250 UMIs, depending on library complexity and sequencing depth of the plate) were also removed for downstream analysis. 4) For a cell-synHEK3 barcode combination, if multiple insertion sequences were observed, sequences <3 hamming distance were collapsed. Cell-synHEK3 barcode pairs having conflicting editing outcomes were discarded. 5) A cell-synHEK3 barcode-editing outcome-shRNA matrix was generated for a common set of cells identified by the shRNA and synHEK3 libraries.
Assembly: GRCh38
Supplementary files format and content: cell_synHEK3_shRNA.csv.gz contains a cell-synHEK3-shRNA capture matrix

extract_protocol: We performed a modified version of sci-RNA-seq3 (Martin et al., 2022). In brief, K562 cells were lysed with 5 mL of a hypotonic, PBS-based lysis buffer containing DEPC. The resulting nuclei were fixed with 4 volume of ice-cold methanol. After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton buffer (SPBST), the nuclei were treated with T7 polymerase in an NTP mix buffer at 37oC for 30 min. Then nuclei were washed, sonicated briefly and counted. The nuclei were distributed to a 96-well plate for reverse transcription, with a cocktail of three indexed primers: oligo-dT, HEK3 and CS1 -- specific for the cellular transcriptome, and RNAs produced from the synHEK3 reporter and the shRNA constructs, respectively. After reverse transcription, nuclei were pooled, washed in SPBST and redistributed to 4 fresh plates for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to 4 final plates at two different concentrations (1300 cell per well for 2 plates and 2500 cell per well for 2 plates) for second strand synthesis and extraction. Nuclear lysates were split in half, with one half undergoing normal sci-RNA-seq3 transcriptome library preparation (tagmentation and PCR to add the third index) and the other half subjected to indexed enrichment PCR for both the synHEK3 and shRNA constructs. Products were pooled by PCR plate, size-selected and sequenced on an Illumina Nextseq 2000 or Nextseq 550.


title: MELA_UVC400J

source_name: primary melanocyte genomic DNA

value: primary melanocyte genomic DNA

value: UVC irradiated 400 J/m2


title: E4-C36


title: MELA_UVC0hr

source_name: primary melanocyte cells

value: primary melanocyte cells

value: UVC irradiated 500 J/m2


title: E4-C20


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06H]

description: sci-RNA-seq3 library


title: 4_2472STBMS153.CEL

data_processing:
The raw CEL files were adjusted for GC content.
Probe sets summarized by median polish algorithm implemented in Partek software (www.partel.com)

source_name: PBMC

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: E4-C19


title: 4_3231SWBMS153.CEL


title: MELA_UVB2500J

value: UVB irradiated 2500 J/m2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06G]

description: sci-RNA-seq3 library


title: MELA_UVB0hr


title: 4_4213SWBMS153.CEL

value: female


title: K562-H3K27ac-20-T1

city: ROCHESTER

first: JEONG-HEON

last: LEE

state: Minnesota

address: 200 1ST STREET S.W.

department: Epigenomics program/CIM

institute: MAYO CLINIC

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg38) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10).
Assembly: hg38
Supplementary files format and content: NARROWPEAK File (exept for Input sample)

growth_protocol: K562 cells were purchased from ATCC and grown in IMDM (Iscove's Modified Dulbecco's Media) at 37°C and 5% CO2. The media contained 10% calf bovine serum and 1% Penicillin/Streptomycin.

extract_protocol:
Chromatin input was prepared from fixed K562 cells and incubated with H3K27ac antibody. DNA was isolated from the enriched chromatin-DNA complexes.
ChIP-seq: Libraries were prepared according to ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. . Briefly,In the first step, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by AMpure reagents. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

value: Human erythroleukemia

tag: chip antibody


title: A7

description: mRNAs

growth_protocol: After weaning, C57Bl/6 mice were fed with AIN diet for 3 months

extract_protocol:
The protocol to isolate intestinal epithelial cells for FACS isolation of Epcam+Cd45- single epithelial cells is similar to the protocol described in Li et al, (2019) Carcinogenesis 40:937
Our single cell RNAseq (scRNAseq) libraries were made according to the manufacturer’s protocol for Chromium Next GEM (gel beads in emulsion) single cell 3’ kit (10X Genomics)

treatment_protocol: For 3 mice in the first (control) group, they were fed with AIN. For 3 mice in the second (switch) group, they were fed 4 days of NWD1. For 3 mice in the third (switch-back) group, they were fed with 4 days of NWD1, followeed by 4 days of AIN.  All mice were sacrificed immediately after their feeding paradigm.

tag: diet

value: after 3 months of AIN feeding, 4 days NWD1

value: Intestinal epithelial cells

tag: cell markers

value: Epcam +, Cd45 -


title: 4_158SWBMS153.CEL

value: multiple sclerosis


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06F]

description: sci-RNA-seq3 library

value: lymphoblast


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06E]

description: sci-RNA-seq3 library


title: BS - CM59 - day 2

value: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

value: MUT

value: day 2

value: BS DNA


title: B32

description: mRNAs

value: after 3 months of AIN feeding, 4 days NWD1, switchback to AIN for 4 days


title: 4_2260SWBMS153.CEL

value: PBMC


title: 4_229SWBMS153.CEL

value: male


title: K562-H3K27ac-5-T1


title: MELA_NoUV

value: primary melanocyte cells


title: A41

description: mRNAs


title: K562-H3K27ac-10-T1b


title: E4-C16

value: Placebo

value: carotid artery

value: 9 weeks


title: 4_1188SWBMS153.CEL

value: female


title: 4_1359SWBMS153.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06D]

description: sci-RNA-seq3 library

value: lentiviral transduction of a DDR-focused shRNA library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06B]

description: sci-RNA-seq3 library


title: 4_1142SWBMS153.CEL


title: A43

description: mRNAs

value: Intestinal epithelial cells


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-07A]

description: sci-RNA-seq3 library


title: 4_1320SWBMS153.CEL


title: K562-H3K27ac-1.25-T1

value: Human erythroleukemia


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06C]

description: sci-RNA-seq3 library


title: 3_734STBMS152.CEL

value: multiple sclerosis


title: K562-H3K27ac-2.5-T1


title: A20

description: mRNAs

value: after 3 months of AIN feeding, 4 days NWD1

value: Epcam +, Cd45 -


title: K562-H3K27ac-0.62-T1


title: A40

description: mRNAs


title: 5_1729CIS157.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-06A]

description: sci-RNA-seq3 library

value: lymphoblast


title: A14

description: mRNAs

value: AIN all time


title: 3_63STBMS152.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05G]

description: sci-RNA-seq3 library


title: 3_443STBMS152.CEL


title: 3_3122STBMS152.CEL


title: A11

description: mRNAs


title: A10

description: mRNAs


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05E]

description: sci-RNA-seq3 library


title: K562-H3K27ac-10-T1a


title: spinal_dura_EAE14

city: Helsinki

first: Zhilin

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: EAE mice at 14 dpi

data_processing:
The Cell Ranger v 6.0 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10.
We used the Seurat R package (v4.0.4) for QC, filtering and analysis of the filtered data (Hao et al. Cell 2021).
Cells were filtered based on nfeature_RNA, nCount_RNA, and the percentage of mitochondrial genes.
Genome_build: mm10

source_name: spinal dura

extract_protocol:
Mice were perfused with ice-cold PBS and the brain, SC, cranial dura, and spinal dura were dissected. For the cranial and spinal dura, after enzymatic digestion with Collagenase VIII and DNaseI and mechanical dissociation, cells were  pre-incubated with mouse Fc Blocker (clone 2.4G2, BD Pharmingen), and then stained with CD45-FITC (clone 30-F11, BioLegend), CD31-APC (clone MEC13.3, BD Pharmingen), and DAPI. For the brain and SC, after enzymatic digestion, mechanical dissociation and myelin debris removal, cells were pre-incubated with mouse Fc Blocker, and then stained with CD45-FITC, CD31-APC, and DAPI. Approximately 1:1~3:1 of viable DAPI-CD45+ immune cells and DAPI-CD31+ endothelial cells were sorted with BD Influx Cell Sorter (BD Biosciences) into PBS supplemented with 0.04% BSA.
Libraries were prepared according to 10XGenomics's instructions.
Sample libraries were sequenced on the Illumina NovaSeq 6000 system.

treatment_protocol: Naïve mice were left untreated. Wild-type mice were induced with EAE by active immunization with MOG35-55.

value: spinal dura

tag: eae disease stage

value: EAE peak


title: 3_2742STBMS152.CEL

value: PBMC


title: K562-H3K27ac-5-T2


title: spinal_dura_EAE10

description: EAE mice at 10 dpi

value: EAE onset


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05C]

description: sci-RNA-seq3 library


title: 3_2244STBMS152.CEL


title: 3_2256STBMS152.CEL


title: K562-H3K27ac-0.31-T1


title: 3_2037STBMS152.CEL


title: K562-H3K27ac-2.5-T4


title: spinal_dura_naive

description: naïve mice

value: naive


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05B]

description: sci-RNA-seq3 library


title: K562-Input2


title: cranial_dura_EAE14

description: EAE mice at 14 dpi

source_name: cranial dura

value: cranial dura


title: K562-H3K27ac-1.25-T8


title: cranial_dura_EAE10

description: EAE mice at 10 dpi


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-05D]

description: sci-RNA-seq3 library


title: K562-H3K27ac-0.62-T16


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04H]

description: sci-RNA-seq3 library


title: cranial_dura_naive

description: naïve mice


title: K562-H3K27ac-0.31-T32


title: K562-H3K27ac-20-T0.5


title: 3_1969STBMS152.CEL


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04G]

description: sci-RNA-seq3 library


title: K562-Input1


title: SC_EAE14

description: EAE mice at 14 dpi

source_name: spinal cord

value: spinal cord


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-08D]

description: sci-RNA-seq3 library


title: 3_1240STBMS152.CEL


title: 3_1234STBMS152.CEL

value: male


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04F]

description: sci-RNA-seq3 library


title: 2_7062ONCIS150.CEL

value: female


title: Blood, fat, rep9

city: Ioannina

first: Anastasios

last: Bounas

address: University Campus

department: Department of Biological Applications and Technology

country: Greece

institute: University of Ioannina

data_processing:
Raw reads were demultiplexed and adapters were masked with Illumina BCL Convert v3.9.31
Reads were trimmed with ERNE 2 and subjected to quality control using FastQC with a passing score threshold Q > 30
STAR was used with default parameters to map reads to the latest Zebra finch genome (GCF_008822105.2)
Read count extraction and quantification were performed using StringTie
Assembly: GCF_008822105.2
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Sylvia borin

source_name: whole blood

extract_protocol:
RNA was extracted using the Quick RNA whole-blood kit (Zymo Research, Orange, CA)
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) was used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

treatment_protocol: Blood was stored in DNA/RNA Shield buffer at -20oC

value: whole blood

value: blood cells

value: fat

tag: time

value: Day 5


title: SC_naive

description: naïve mice

tag: strain


title: Blood, fat, rep8


title: brain_EAE14

description: EAE mice at 14 dpi

source_name: brain

value: brain


title: 2_5592CIS150.CEL

value: multiple sclerosis


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04E]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: SC_EAE10

description: EAE mice at 10 dpi


title: 2_4374ONCIS150.CEL


title: 3_1409STBMS152.CEL


title: Blood, fat, rep7


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04D]

description: sci-RNA-seq3 library


title: brain_EAE10

description: EAE mice at 10 dpi


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04B]

description: sci-RNA-seq3 library


title: brain_naive

description: naïve mice


title: Blood, fat, rep10


title: 2_2498CIS150.CEL


title: Blood, fat, rep6


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03H]

description: sci-RNA-seq3 library


title: E13-5dKOWT2_S8

city: Ottawa

first: Dave

last: Picketts

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: OHRI

data_processing:
Pseudoalignment to mm10 transcriptome with Salmon (v1.4.0)
Differencial expression analysis by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Pseudoaligned and quantified - .sf

source_name: Cortical whole tissue

growth_protocol: Murine cortical tissue dissected at E13.5

extract_protocol:
RNA was extracted in Trizol and purified by PureLink RNA cleanup kit (Thermo Fisher, cat 12183020) with in-column DNaseI treatment
NEB mRNA stranded library preparation was carried out following Bioanalyser analysis of RNA

value: Smarca1 +/+; Cre -/-


title: Blood, fat, rep5


title: E13-5dKOWT3_S9


title: 2_1794CIS150.CEL


title: Blood, fat, rep4


title: 2_2065CIS150.CEL


title: oxBS - KO1 - day 5 + XAV

source_name: mESC B6129S6F1 Tet1<tm1Koh>

value: mESC B6129S6F1 Tet1<tm1Koh>

value: KO

value: day 5 + XAV

tag: molecule type

value: oxBS DNA


title: 2_1021CIS150.CEL

tag: tissue

value: PBMC


title: Blood, fat, rep3


title: E13-5dKODKO3_S6

value: Smarca1 -/-; Cre +/-


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03E]

description: sci-RNA-seq3 library

tag: cell line


title: E13-5dKODKO2_S5


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03F]

description: sci-RNA-seq3 library

tag: cell type


title: E13-5dKOWT1_S7


title: Blood, fat, rep1

tag: treatment


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04C]

description: sci-RNA-seq3 library


title: Blood, fat, rep2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03G]

description: sci-RNA-seq3 library


title: E13-5dKODKO1_S4


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03D]

description: sci-RNA-seq3 library


title: Blood, lean, rep10

value: lean

value: Day 1


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-04A]

description: sci-RNA-seq3 library


title: Blood, lean, rep9

value: whole blood


title: Blood, lean, rep8

value: blood cells


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03B]

description: sci-RNA-seq3 library


title: 1_6574RR145.CEL

tag: patient diagnosis

value: female


title: E13-5dKO2LKO2_S2

value: Smarca1 -/-; Cre -/-


title: 1_6555RR145.CEL

tag: age(years)

value: male


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-03A]

description: sci-RNA-seq3 library


title: 1_6573RR145.CEL

value: multiple sclerosis

tag: gender


title: 1_6696RR145.CEL

tag: batch number


title: 1_6553RR145.CEL


title: 1_7115RR145.CEL


title: 1_5730RR145.CEL


title: Macrophage PM_3

city: guangzhou

first: Xingyang

state: Guangdong

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

data_processing:
Fastp was used for fastq data cleaning.
STAR was used for fastq data alignment.
RSEM was used for RNA expressed calculation.
Genome_build: mm10
Supplementary_files_format_and_content: expected_count  TPM     FPKM

source_name: Macrophage

growth_protocol: The mouse macrophage cell line, RAW264.7 (National Collection of Authenticated Cell Cultures, TCM13, Shanghai, China) was used as a model of macrophage. The cells were maintained in high glucose DMEM (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1% Penicillin-Streptomycin solution (Gibco, USA), under 37℃ supplied with 5% CO2 and 95% air atmosphere.

extract_protocol:
Total RNA was extracted by using the Trizol kit (Invitrogen, Carlsbad, CA, United States), according to the manufacturer’s protocol.
The RNA concentration was determined using Qubit, and the RNA amount and purity of each sample was assessed with a NanoDrop spectrophotometer. RNA was isolated in 40 µl of DEPC water and stored at -80.

treatment_protocol: Macrophages (3000 cells/well) were cultured in 96-well plates in presence of 0, 75, 100, 125 or 150 μg/mL C2S extract groups and incubated the cells for 4, 24, 48, and 72 h. The cell vitality was evaluated using the cell counting kit-8 assay (CCK8, BestBio, China) as described previously3.

value: Macrophage

value: BALB/c

tag: treament


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02G]

city: Seattle

first: Xiaoyi

address: 3720 15th Ave NE

institute: University of Washington

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: 1_6464RR145.CEL

city: Ramat Gan

first: Michael

address: Tel Hashomer

institute: Sheba Medical Center


title: Macrophage PM_2


title: Blood, lean, rep6


title: E13-5dKO2LKO3_S3

tag: genotype


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02F]

description: sci-RNA-seq3 library


title: Blood, lean, rep4


title: Macrophage PM_1


title: Blood, lean, rep3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02E]

description: sci-RNA-seq3 library


title: Macrophage C2S_2


title: 1_3864RR145.CEL


title: Blood, lean, rep2


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02C]

description: sci-RNA-seq3 library


title: 1_3380RR145.CEL


title: E13-5dKO2LKO1_S1


title: Macrophage C2S_1


title: Blood, lean, rep7


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02B]

description: sci-RNA-seq3 library


title: Blood, lean, rep1


title: 1_3285RR145.CEL


title: IL15Δ/Δ, dam 2

city: London

first: Stephen

middle: J

last: Renaud

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

description: Gene expression data from placentas isolated from dams fed an iron-deficient diet

hyb_protocol: Samples were hybridized to the Clariom S GeneChip microarray (ThermoFisher) as per directions from the GeneChip WT Plus Reagent kit (ThermoFisher). Overnight hybridization to the Clariom S GeneChip took place at 45C for ~16 h.

scan_protocol: After washing and staining as per directions for the GeneChip WT Plus Reagent kit (ThermoFisher), images were captured using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrx GCOS software (ThermoFisher).

data_processing: The CEL file was uploaded to Transcriptome Analysis Console Sotware 4.0 (ThermoFisher) to analyze expression patterns of genes, pathways, and network interactions.

organism: Rattus

source_name: Gestational day 9.5 Imp. Site from Null

label_protocol: Sense strand cDNA was generated, fragmented, and labelled using the GeneChip WT Plus Reagent kit (ThermoFisher) as per directions.

growth_protocol: Dams were aged 6-8 weeks before mating with a WT male. Implantation sites were isolated on gestaional day 9.5

extract_protocol: Frozen placental tissue was homogenized in TRIzol, the aqueous phase removed following mixing in chloroform, mixed with 70% ethanol, and then placed onto an Rneasy column (Qiagen). Following on-column Dnase I digestion, RNA was purified. RNA from two placentas per dam was pooled.

treatment_protocol: Implantation sites were isolated on gestational day 9.5, frozen in liquid nitrogen, and maintained at -80C until RNA extraction.

value: Placenta

tag: developmental stage

value: Gestational day 9.5


title: Blood, lean, rep5


title: IL15Δ/Δ, dam 3


title: AML patient (UD10), methylation table, onset phase

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

data_processing:
DNA from each of three pairs of matched AMLs was sequenced on the GridION X5 instrument with a  run-time of 48h by using five or six individual R9.4 flow
The reads generated by each run were base-called using Guppy v2.0.2
The reads generated by each run were base-called using Guppy v2.0.2
The and quality assessment was performed with NanoR and PyPore
High-quality pass reads were then aligned against the human reference genome (hg19) with minimap2
Assembly: hg19
Supplementary files format and content: Processed data files contain genomic coordinates (Chr, start, end), CpG found in the segment, methyalted CpG found in the segment

source_name: bone marrow

extract_protocol:
Genomic DNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
Genomic DNA by ligation SQK-LSK109 (Oxford Nanopore Technologies, ONT)

tag: phase

value: onset

tag: disease state

value: AML

value: bone marrow


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02A]

description: sci-RNA-seq3 library


title: AML patient (UD10), methylation table, relapse phase

value: relapse


title: TAM-C33

value: Tamoxifen

value: carotid artery

tag: age

value: 9 weeks


title: TAM-C35


title: Macrophage C2S_3


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01G]

description: sci-RNA-seq3 library


title: AML patient (UD5), methylation table, relapse phase